% Encoding: UTF-8
@article{Belanger:2011a,
	Abstract = {The energy requirements of the brain are very high, and tight regulatory mechanisms operate to ensure adequate spatial and temporal delivery of energy substrates in register with neuronal activity. Astrocytes-a type of glial cell-have emerged as active players in brain energy delivery, production, utilization, and storage. Our understanding of neuroenergetics is rapidly evolving from a "neurocentric" view to a more integrated picture involving an intense cooperativity between astrocytes and neurons. This review focuses on the cellular aspects of brain energy metabolism, with a particular emphasis on the metabolic interactions between neurons and astrocytes.},
	Author = {B{\'e}langer, Mireille and Allaman, Igor and Magistretti, Pierre J},
	Date-Added = {2018-09-27 18:53:44 +0000},
	Date-Modified = {2018-09-27 18:53:44 +0000},
	Doi = {10.1016/j.cmet.2011.08.016},
	Journal = {Cell Metab},
	Journal-Full = {Cell metabolism},
	Mesh = {Astrocytes; Brain; Energy Metabolism; Glycogen; Lactic Acid; Models, Biological; Neurons; Oxidative Stress; Regional Blood Flow},
	Month = {Dec},
	Number = {6},
	Pages = {724-38},
	Pmid = {22152301},
	Pst = {ppublish},
	Title = {Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation},
	Volume = {14},
	Year = {2011},
	File = {papers/Bélanger_CellMetab2011a.pdf}}

@article{Joshi:2008,
	Abstract = {While progenitor-restricted factors broadly specify area identities in developing neocortex, the downstream regulatory elements involved in acquisition of those identities in postmitotic neurons are largely unknown. Here, we identify Bhlhb5, a transcription factor expressed in layers II-V, as a postmitotic regulator of area identity. Bhlhb5 is initially expressed in a high caudomedial to low rostrolateral gradient that transforms into a sharp border between sensory and rostral motor cortices. Bhlhb5 null mice exhibit aberrant expression of area-specific genes and structural organization in the somatosensory and caudal motor cortices. In somatosensory cortex, Bhlhb5 null mice display postsynaptic disorganization of vibrissal barrels. In caudal motor cortex, Bhlhb5 null mice exhibit anomalous differentiation of corticospinal motor neurons, accompanied by failure of corticospinal tract formation. Together, these results demonstrate Bhlhb5's function as an area-specific transcription factor that regulates the postmitotic acquisition of area identities and elucidate the genetic hierarchy between progenitors and postmitotic neurons driving neocortical arealization.},
	Author = {Joshi, Pushkar S and Molyneaux, Bradley J and Feng, Liang and Xie, Xiaoling and Macklis, Jeffrey D and Gan, Lin},
	Date-Added = {2018-09-18 20:50:58 +0000},
	Date-Modified = {2018-09-18 20:50:58 +0000},
	Doi = {10.1016/j.neuron.2008.08.006},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Basic Helix-Loop-Helix Transcription Factors; Body Patterning; Cell Differentiation; Cell Movement; Efferent Pathways; Mice; Mice, Knockout; Mice, Transgenic; Mitosis; Motor Cortex; Neocortex; Neurons; Pyramidal Tracts; Somatosensory Cortex; Stem Cells; Telencephalon; Transcriptional Activation},
	Month = {Oct},
	Number = {2},
	Pages = {258-72},
	Pmc = {PMC2643370},
	Pmid = {18957218},
	Pst = {ppublish},
	Title = {Bhlhb5 regulates the postmitotic acquisition of area identities in layers II-V of the developing neocortex},
	Volume = {60},
	Year = {2008},
	File = {papers/Joshi_Neuron2008.pdf}}

@article{Strange:2014,
	Abstract = {The precise functional role of the hippocampus remains a topic of much debate. The dominant view is that the dorsal (or posterior) hippocampus is implicated in memory and spatial navigation and the ventral (or anterior) hippocampus mediates anxiety-related behaviours. However, this 'dichotomy view' may need revision. Gene expression studies demonstrate multiple functional domains along the hippocampal long axis, which often exhibit sharply demarcated borders. By contrast, anatomical studies and electrophysiological recordings in rodents suggest that the long axis is organized along a gradient. Together, these observations suggest a model in which functional long-axis gradients are superimposed on discrete functional domains. This model provides a potential framework to explain and test the multiple functions ascribed to the hippocampus. },
	Author = {Strange, Bryan A and Witter, Menno P and Lein, Ed S and Moser, Edvard I},
	Date-Added = {2018-07-17 06:25:29 +0000},
	Date-Modified = {2018-07-17 06:25:29 +0000},
	Doi = {10.1038/nrn3785},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Gene Expression; Hippocampus; Humans},
	Month = {Oct},
	Number = {10},
	Pages = {655-69},
	Pmid = {25234264},
	Pst = {ppublish},
	Title = {Functional organization of the hippocampal longitudinal axis},
	Volume = {15},
	Year = {2014},
	File = {papers/Strange_NatRevNeurosci2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn3785}}

@article{Lisman:2017,
	Author = {Lisman, John and Buzs{\'a}ki, Gy{\"o}rgy and Eichenbaum, Howard and Nadel, Lynn and Ranganath, Charan and Redish, A David},
	Date-Added = {2018-07-17 06:24:52 +0000},
	Date-Modified = {2018-07-17 06:24:52 +0000},
	Doi = {10.1038/nn.4661},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Month = {10},
	Number = {11},
	Pages = {1434-1447},
	Pmc = {PMC5943637},
	Pmid = {29073641},
	Pst = {ppublish},
	Title = {Viewpoints: how the hippocampus contributes to memory, navigation and cognition},
	Volume = {20},
	Year = {2017},
	File = {papers/Lisman_NatNeurosci2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4661}}

@article{Cullen:2017,
	Abstract = {In this Perspective, we evaluate current progress in understanding how the brain encodes our sense of direction, within the context of parallel work focused on how early vestibular pathways encode self-motion. In particular, we discuss how these systems work together and provide evidence that they involve common mechanisms. We first consider the classic view of the head direction cell and results of recent experiments in rodents and primates indicating that inputs to these neurons encode multimodal information during self-motion, such as proprioceptive and motor efference copy signals, including gaze-related information. We also consider the paradox that, while the head-direction network is generally assumed to generate a fixed representation of perceived directional heading, this computation would need to be dynamically updated when the relationship between voluntary motor command and its sensory consequences changes. Such situations include navigation in virtual reality and head-restricted conditions, since the natural relationship between visual and extravisual cues is altered.},
	Author = {Cullen, Kathleen E and Taube, Jeffrey S},
	Date-Added = {2018-07-17 06:23:49 +0000},
	Date-Modified = {2018-07-17 06:23:49 +0000},
	Doi = {10.1038/nn.4658},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Month = {Oct},
	Number = {11},
	Pages = {1465-1473},
	Pmid = {29073639},
	Pst = {aheadofprint},
	Title = {Our sense of direction: progress, controversies and challenges},
	Volume = {20},
	Year = {2017},
	File = {papers/Cullen_NatNeurosci2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4658}}

@article{Moser:2017,
	Abstract = {Since the first place cell was recorded and the cognitive-map theory was subsequently formulated, investigation of spatial representation in the hippocampal formation has evolved in stages. Early studies sought to verify the spatial nature of place cell activity and determine its sensory origin. A new epoch started with the discovery of head direction cells and the realization of the importance of angular and linear movement-integration in generating spatial maps. A third epoch began when investigators turned their attention to the entorhinal cortex, which led to the discovery of grid cells and border cells. This review will show how ideas about integration of self-motion cues have shaped our understanding of spatial representation in hippocampal-entorhinal systems from the 1970s until today. It is now possible to investigate how specialized cell types of these systems work together, and spatial mapping may become one of the first cognitive functions to be understood in mechanistic detail.},
	Author = {Moser, Edvard I and Moser, May-Britt and McNaughton, Bruce L},
	Date-Added = {2018-07-17 06:23:15 +0000},
	Date-Modified = {2018-07-17 06:23:15 +0000},
	Doi = {10.1038/nn.4653},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Action Potentials; Animals; Brain Mapping; Grid Cells; Hippocampus; Humans; Photic Stimulation; Space Perception},
	Month = {Oct},
	Number = {11},
	Pages = {1448-1464},
	Pmid = {29073644},
	Pst = {ppublish},
	Title = {Spatial representation in the hippocampal formation: a history},
	Volume = {20},
	Year = {2017},
	File = {papers/Moser_NatNeurosci2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.4653}}

@article{Kim:2014,
	Abstract = {Larval zebrafish offer the potential for large-scale optical imaging of neural activity throughout the central nervous system; however, several barriers challenge their utility. First, ~panneuronal probe expression has to date only been demonstrated at early larval stages up to 7 days post-fertilization (dpf), precluding imaging at later time points when circuits are more mature. Second, nuclear exclusion of genetically-encoded calcium indicators (GECIs) limits the resolution of functional fluorescence signals collected during imaging. Here, we report the creation of transgenic zebrafish strains exhibiting robust, nuclearly targeted expression of GCaMP3 across the brain up to at least 14 dpf utilizing a previously described optimized Gal4-UAS system. We confirmed both nuclear targeting and functionality of the modified probe in vitro and measured its kinetics in response to action potentials (APs). We then demonstrated in vivo functionality of nuclear-localized GCaMP3 in transgenic zebrafish strains by identifying eye position-sensitive fluorescence fluctuations in caudal hindbrain neurons during spontaneous eye movements. Our methodological approach will facilitate studies of larval zebrafish circuitry by both improving resolution of functional Ca(2+) signals and by allowing brain-wide expression of improved GECIs, or potentially any probe, further into development. },
	Author = {Kim, Christina K and Miri, Andrew and Leung, Louis C and Berndt, Andre and Mourrain, Philippe and Tank, David W and Burdine, Rebecca D},
	Date-Added = {2018-07-16 22:03:08 +0000},
	Date-Modified = {2018-07-16 22:03:08 +0000},
	Doi = {10.3389/fncir.2014.00138},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {brain-wide expression; genetically encoded calcium indicators; in vivo calcium imaging; nuclear calcium signals; transgenic zebrafish},
	Mesh = {Action Potentials; Animals; Animals, Genetically Modified; Brain; Brain Mapping; Cell Nucleus; Cells, Cultured; Eye Movements; Fluorescence; HEK293 Cells; Humans; Nerve Tissue Proteins; Neural Pathways; Neurons; Nuclear Proteins; Rats; Transfection; Zebrafish; Zebrafish Proteins},
	Pages = {138},
	Pmc = {PMC4244806},
	Pmid = {25505384},
	Pst = {epublish},
	Title = {Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping},
	Volume = {8},
	Year = {2014},
	File = {papers/Kim_FrontNeuralCircuits2014.pdf}}

@article{Bonini:2016,
	Abstract = {Mirror neurons (MNs) are a fascinating class of cells originally discovered in the ventral premotor cortex (PMv) and, subsequently, in the inferior parietal lobule (IPL) of the macaque, which become active during both the execution and observation of actions. In this review, I will first highlight the mounting evidence indicating that mirroring others' actions engages a broad system of reciprocally connected cortical areas, which extends well beyond the classical IPL-PMv circuit and might even include subcortical regions such as the basal ganglia. Then, I will present the most recent findings supporting the idea that the observation of one's own actions, which might play a role in the ontogenetic origin and tuning of MNs, retains a particular relevance within the adult MN system. Finally, I will propose that both cortical and subcortical mechanisms do exist to decouple MN activity from the motor output, in order to render it exploitable for high-order perceptual, cognitive, and even social functions. The findings reviewed here provide an original framework for envisaging the main challenges and experimental directions of future neurophysiological and neuroanatomical studies of the monkey MN system.},
	Author = {Bonini, Luca},
	Date-Added = {2018-07-16 22:02:19 +0000},
	Date-Modified = {2018-07-16 22:02:19 +0000},
	Doi = {10.1177/1073858415626400},
	Journal = {Neuroscientist},
	Journal-Full = {The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry},
	Keywords = {action observation; basal ganglia; development; grasping; social cognition},
	Month = {Jan},
	Pmid = {26747293},
	Pst = {aheadofprint},
	Title = {The Extended Mirror Neuron Network: Anatomy, Origin, and Functions},
	Year = {2016},
	File = {papers/Bonini_Neuroscientist2016.pdf}}

@article{Shadrin:2015,
	Abstract = {Cardiac cell therapies involving bone marrow-derived human mesenchymal stem cells (hMSCs) have shown promising results, although their mechanisms of action are still poorly understood. Here, we investigated direct interactions between hMSCs and cardiomyocytes in vitro. Using a genetic Ca(2+) indicator gCaMP3 to efficiently label hMSCs in co-cultures with neonatal rat ventricular myocytes (NRVMs), we determined that 25-40% of hMSCs (from 4 independent donors) acquired periodic Ca(2+) transients and cardiac markers through spontaneous fusion with NRVMs. Sharp electrode and voltage-clamp recordings in fused cells showed action potential properties and Ca(2+) current amplitudes in between those of non-fused hMSCs and NRVMs. Time-lapse video-microscopy revealed the first direct evidence of active fusion between hMSCs and NRVMs within several hours of co-culture. Application of blebbistatin, nifedipine or verapamil caused complete and reversible inhibition of fusion, suggesting potential roles for actomyosin bridging and Ca(2+) channels in the fusion process. Immunostaining for Cx43, Ki67, and sarcomeric α-actinin showed that fused cells remain strongly coupled to surrounding NRVMs, but downregulate sarcomeric structures over time, acquiring a non-proliferative and non-contractile phenotype. Overall, these results describe the phenotype and mechanisms of hybrid cell formation via fusion of hMSCs and cardiomyocytes with potential implications for cardiac cell therapy. },
	Author = {Shadrin, Ilya Y and Yoon, Woohyun and Li, Liqing and Shepherd, Neal and Bursac, Nenad},
	Date-Added = {2018-07-16 22:01:58 +0000},
	Date-Modified = {2018-07-16 22:01:58 +0000},
	Doi = {10.1038/srep12043},
	Journal = {Sci Rep},
	Journal-Full = {Scientific reports},
	Mesh = {Actinin; Action Potentials; Animals; Caffeine; Calcium; Calcium Channels, L-Type; Cell Fusion; Cell Movement; Cells, Cultured; Coculture Techniques; Connexin 43; Humans; Ions; Mesenchymal Stromal Cells; Microscopy, Video; Myocytes, Cardiac; Myosin Type II; Rats; Rats, Sprague-Dawley; Real-Time Polymerase Chain Reaction; Time-Lapse Imaging; Troponin T},
	Month = {Jul},
	Pages = {12043},
	Pmc = {PMC4498233},
	Pmid = {26159124},
	Pst = {epublish},
	Title = {Rapid fusion between mesenchymal stem cells and cardiomyocytes yields electrically active, non-contractile hybrid cells},
	Volume = {5},
	Year = {2015},
	File = {papers/Shadrin_SciRep2015.pdf}}

@article{10.7554/eLife.28158,
	Abstract = {The internal brain dynamics that link sensation and action are arguably better studied during natural animal behaviors. Here, we report on a novel volume imaging and 3D tracking technique that monitors whole brain neural activity in freely swimming larval zebrafish (\textit{Danio rerio}). We demonstrated the capability of our system through functional imaging of neural activity during visually evoked and prey capture behaviors in larval zebrafish.},
	Article_Type = {journal},
	Author = {Cong, Lin and Wang, Zeguan and Chai, Yuming and Hang, Wei and Shang, Chunfeng and Yang, Wenbin and Bai, Lu and Du, Jiulin and Wang, Kai and Wen, Quan},
	Citation = {eLife 2017;6:e28158},
	Date-Added = {2018-07-16 22:01:38 +0000},
	Date-Modified = {2018-07-16 22:01:38 +0000},
	Doi = {10.7554/eLife.28158},
	Editor = {Calabrese, Ronald L},
	Issn = {2050-084X},
	Journal = {eLife},
	Keywords = {freely behaving larval zebrafish, whole brain Imaging, 3D tracking system, light field microscope, prey capture behavior},
	Month = {sep},
	Pages = {e28158},
	Pub_Date = {2017-09-20},
	Publisher = {eLife Sciences Publications, Ltd},
	Title = {Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (\textit{Danio rerio})},
	Url = {https://doi.org/10.7554/eLife.28158},
	Volume = 6,
	Year = 2017,
	File = {papers/Cong_eLife2017.pdf},
	Bdsk-Url-1 = {https://doi.org/10.7554/eLife.28158},
	Bdsk-Url-2 = {http://dx.doi.org/10.7554/eLife.28158}}

@article{Itzhaki:2016,
	Author = {Itzhaki, Ruth F and Lathe, Richard and Balin, Brian J and Ball, Melvyn J and Bearer, Elaine L and Braak, Heiko and Bullido, Maria J and Carter, Chris and Clerici, Mario and Cosby, S Louise and Del Tredici, Kelly and Field, Hugh and Fulop, Tamas and Grassi, Claudio and Griffin, W Sue T and Haas, J{\"u}rgen and Hudson, Alan P and Kamer, Angela R and Kell, Douglas B and Licastro, Federico and Letenneur, Luc and L{\"o}vheim, Hugo and Mancuso, Roberta and Miklossy, Judith and Otth, Carola and Palamara, Anna Teresa and Perry, George and Preston, Christopher and Pretorius, Etheresia and Strandberg, Timo and Tabet, Naji and Taylor-Robinson, Simon D and Whittum-Hudson, Judith A},
	Date-Added = {2018-07-16 21:29:57 +0000},
	Date-Modified = {2018-07-16 21:29:57 +0000},
	Doi = {10.3233/JAD-160152},
	Journal = {J Alzheimers Dis},
	Journal-Full = {Journal of Alzheimer's disease : JAD},
	Mesh = {Alzheimer Disease; Amyloid beta-Peptides; Animals; Brain; Communicable Diseases; Humans; Microbiota},
	Number = {4},
	Pages = {979-84},
	Pmc = {PMC5457904},
	Pmid = {26967229},
	Pst = {ppublish},
	Title = {Microbes and Alzheimer's Disease},
	Volume = {51},
	Year = {2016},
	File = {papers/Itzhaki_JAlzheimersDis2016.pdf}}

@article{10.7554/eLife.35261,
	Abstract = {Detection of salient objects in the visual scene is a vital aspect of an animal's interactions with its environment. Here, we show that neurons in the mouse superior colliculus (SC) encode visual saliency by detecting motion contrast between stimulus center and surround. Excitatory neurons in the most superficial lamina of the SC are contextually modulated, monotonically increasing their response from suppression by the same-direction surround to maximal potentiation by an oppositely-moving surround. The degree of this potentiation declines with depth in the SC. Inhibitory neurons are suppressed by any surround at all depths. These response modulations in both neuronal populations are much more prominent to direction contrast than to phase, temporal frequency, or static orientation contrast, suggesting feature-specific saliency encoding in the mouse SC. Together, our findings provide evidence supporting locally generated feature representations in the SC, and lay the foundations towards a mechanistic and evolutionary understanding of their emergence.},
	Article_Type = {journal},
	Author = {Barchini, Jad and Shi, Xuefeng and Chen, Hui and Cang, Jianhua},
	Citation = {eLife 2018;7:e35261},
	Date-Added = {2018-07-16 21:27:13 +0000},
	Date-Modified = {2018-07-16 21:27:13 +0000},
	Doi = {10.7554/eLife.35261},
	Editor = {Rieke, Fred},
	Issn = {2050-084X},
	Journal = {eLife},
	Month = {jul},
	Pages = {e35261},
	Pub_Date = {2018-07-02},
	Publisher = {eLife Sciences Publications, Ltd},
	Title = {Bidirectional encoding of motion contrast in the mouse superior colliculus},
	Url = {https://doi.org/10.7554/eLife.35261},
	Volume = 7,
	Year = 2018,
	File = {papers/Barchini_eLife2018.pdf},
	Bdsk-Url-1 = {https://doi.org/10.7554/eLife.35261},
	Bdsk-Url-2 = {http://dx.doi.org/10.7554/eLife.35261}}

@article{Tallinen:2016,
	Author = {Tallinen, Tuomas and Chung, Jun Young and Rousseau, Fran{\c c}ois and Girard, Nadine and Lef{\`e}vre, Julien and Mahadevan, L.},
	Date = {2016/02/01/online},
	Date-Added = {2018-04-05 23:47:18 +0000},
	Date-Modified = {2018-04-05 23:47:18 +0000},
	Day = {01},
	Journal = {Nature Physics},
	L3 = {10.1038/nphys3632; https://www.nature.com/articles/nphys3632#supplementary-information},
	Month = {02},
	Pages = {588 EP -},
	Publisher = {Nature Publishing Group SN -},
	Title = {On the growth and form of cortical convolutions},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nphys3632},
	Volume = {12},
	Year = {2016},
	File = {papers/Tallinen_NaturePhysics2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nphys3632}}

@article{Tallinen:2014,
	Abstract = {The exterior of the mammalian brain--the cerebral cortex--has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated as a soft solid lead to the formation of cusped sulci and smooth gyri similar to those in the brain. The resulting gyrification patterns are a function of relative cortical expansion and relative thickness (compared with brain size), and are consistent with observations of a wide range of brains, ranging from smooth to highly convoluted. Furthermore, this dependence on two simple geometric parameters that characterize the brain also allows us to qualitatively explain how variations in these parameters lead to anatomical anomalies in such situations as polymicrogyria, pachygyria, and lissencephalia.},
	Author = {Tallinen, Tuomas and Chung, Jun Young and Biggins, John S and Mahadevan, L},
	Date-Added = {2018-04-05 22:32:15 +0000},
	Date-Modified = {2018-04-05 22:32:15 +0000},
	Doi = {10.1073/pnas.1406015111},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {brain morphogenesis; elastic instability},
	Mesh = {Cell Proliferation; Cerebral Cortex; Compressive Strength; Dimethylpolysiloxanes; Elasticity; Gels; Humans; Models, Anatomic; Models, Neurological; Nerve Fibers, Myelinated; Neural Pathways; Neurons; Stress, Mechanical},
	Month = {Sep},
	Number = {35},
	Pages = {12667-72},
	Pmc = {PMC4156754},
	Pmid = {25136099},
	Pst = {ppublish},
	Title = {Gyrification from constrained cortical expansion},
	Volume = {111},
	Year = {2014},
	File = {papers/Tallinen_ProcNatlAcadSciUSA2014.pdf}}

@article{Treweek:2015,
	Abstract = {To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.},
	Author = {Treweek, Jennifer B and Chan, Ken Y and Flytzanis, Nicholas C and Yang, Bin and Deverman, Benjamin E and Greenbaum, Alon and Lignell, Antti and Xiao, Cheng and Cai, Long and Ladinsky, Mark S and Bjorkman, Pamela J and Fowlkes, Charless C and Gradinaru, Viviana},
	Date-Added = {2018-02-28 22:23:31 +0000},
	Date-Modified = {2018-02-28 22:23:31 +0000},
	Doi = {10.1038/nprot.2015.122},
	Journal = {Nat Protoc},
	Journal-Full = {Nature protocols},
	Mesh = {Animals; Detergents; Histocytochemistry; Lipids; Mice; Optical Imaging; Pathology; Rats; Specimen Handling; Staining and Labeling; Time Factors; Tissue Embedding; Tissue Fixation},
	Month = {Nov},
	Number = {11},
	Pages = {1860-1896},
	Pmc = {PMC4917295},
	Pmid = {26492141},
	Pst = {ppublish},
	Title = {Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping},
	Volume = {10},
	Year = {2015},
	File = {papers/Treweek_NatProtoc2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nprot.2015.122}}

@article{Treweek:2016,
	Abstract = {The scientific community has learned a great deal from imaging small and naturally transparent organisms such as nematodes and zebrafish. The consequences of genetic mutations on their organ development and survival can be visualized easily and with high-throughput at the organism-wide scale. In contrast, three-dimensional information is less accessible in mammalian subjects because the heterogeneity of light-scattering tissue elements renders their organs opaque. Likewise, genetically labeling desired circuits across mammalian bodies is prohibitively slow and costly via the transgenic route. Emerging breakthroughs in viral vector engineering, genome editing tools, and tissue clearing can render larger opaque organisms genetically tractable and transparent for whole-organ cell phenotyping, tract tracing and imaging at depth.},
	Author = {Treweek, Jennifer Brooke and Gradinaru, Viviana},
	Date-Added = {2018-02-28 22:23:19 +0000},
	Date-Modified = {2018-02-28 22:23:19 +0000},
	Doi = {10.1016/j.copbio.2016.03.012},
	Journal = {Curr Opin Biotechnol},
	Journal-Full = {Current opinion in biotechnology},
	Mesh = {Animals; Cell Physiological Phenomena; Cell Tracking; Drug Delivery Systems; Genetic Vectors; Humans; Imaging, Three-Dimensional; Phenotype; Single-Cell Analysis; Whole Body Imaging},
	Month = {Aug},
	Pages = {193-207},
	Pmc = {PMC4975678},
	Pmid = {27393829},
	Pst = {ppublish},
	Title = {Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors},
	Volume = {40},
	Year = {2016},
	File = {papers/Treweek_CurrOpinBiotechnol2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.copbio.2016.03.012}}

@article{Cho:2017,
	Abstract = {Ventral midbrain dopamine (DA) is unambiguously involved in motivation and behavioral arousal, yet the contributions of other DA populations to these processes are poorly understood. Here, we demonstrate that the dorsal raphe nucleus DA neurons are critical modulators of behavioral arousal and sleep-wake patterning. Using simultaneous fiber photometry and polysomnography, we observed time-delineated dorsal raphe nucleus dopaminergic (DRNDA) activity upon exposure to arousal-evoking salient cues, irrespective of their hedonic valence. We also observed broader fluctuations of DRNDAactivity across sleep-wake cycles with highest activity during wakefulness. Both endogenous DRNDAactivity and optogenetically driven DRNDAactivity were associated with waking from sleep, with DA signal strength predictive of wake duration. Conversely, chemogenetic inhibition opposed wakefulness and promoted NREM sleep, even in the face of salient stimuli. Therefore, the DRNDApopulation is a critical contributor to wake-promoting pathways and is capable of modulating sleep-wake states according to the outside environment, wherein the perception of salient stimuli prompts vigilance and arousal.},
	Author = {Cho, Jounhong Ryan and Treweek, Jennifer B and Robinson, J Elliott and Xiao, Cheng and Bremner, Lindsay R and Greenbaum, Alon and Gradinaru, Viviana},
	Date-Added = {2018-02-28 22:23:01 +0000},
	Date-Modified = {2018-02-28 22:23:01 +0000},
	Doi = {10.1016/j.neuron.2017.05.020},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {arousal; chemogenetics; dopamine; dorsal raphe nucleus; fiber photometry; in vivo optical imaging during behavior; optogenetics; salience; sleep-wake state; ventral periaqueductal gray},
	Mesh = {Animals; Arousal; Dopaminergic Neurons; Dorsal Raphe Nucleus; Electroencephalography; Electromyography; Hindlimb Suspension; Mice; Optical Imaging; Optogenetics; Photometry; Restraint, Physical; Sleep; Sleep, REM; Wakefulness},
	Month = {Jun},
	Number = {6},
	Pages = {1205-1219.e8},
	Pmid = {28602690},
	Pst = {ppublish},
	Title = {Dorsal Raphe Dopamine Neurons Modulate Arousal and Promote Wakefulness by Salient Stimuli},
	Volume = {94},
	Year = {2017},
	File = {papers/Cho_Neuron2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2017.05.020}}

@article{Owen:2018,
	Abstract = {Fast-spiking interneurons (FSIs) are a prominent class of forebrain GABAergic cells implicated in two seemingly independent network functions: gain control and network plasticity. Little is known, however, about how these roles interact. Here, we use a combination of cell-type-specific ablation, optogenetics, electrophysiology, imaging, and behavior to describe a unified mechanism by which striatal FSIs control burst firing, calcium influx, and synaptic plasticity in neighboring medium spiny projection neurons (MSNs). In vivo silencing of FSIs increased bursting, calcium transients, and AMPA/NMDA ratios in MSNs. In a motor sequence task, FSI silencing increased the frequency of calcium transients but reduced the specificity with which transients aligned to individual task events. Consistent with this, ablation of FSIs disrupted the acquisition of striatum-dependent egocentric learning strategies. Together, our data support a model in which feedforward inhibition from FSIs temporally restricts MSN bursting and calcium-dependent synaptic plasticity to facilitate striatum-dependent sequence learning.},
	Author = {Owen, Scott F and Berke, Joshua D and Kreitzer, Anatol C},
	Date-Added = {2018-02-28 22:20:45 +0000},
	Date-Modified = {2018-02-28 22:20:45 +0000},
	Doi = {10.1016/j.cell.2018.01.005},
	Journal = {Cell},
	Journal-Full = {Cell},
	Month = {Feb},
	Number = {4},
	Pages = {683-695.e15},
	Pmc = {PMC5810594},
	Pmid = {29425490},
	Pst = {ppublish},
	Title = {Fast-Spiking Interneurons Supply Feedforward Control of Bursting, Calcium, and Plasticity for Efficient Learning},
	Volume = {172},
	Year = {2018},
	File = {papers/Owen_Cell2018.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cell.2018.01.005}}

@article{Owen:2013,
	Abstract = {Neuromodulatory control by oxytocin is essential to a wide range of social, parental and stress-related behaviours. Autism spectrum disorders (ASD) are associated with deficiencies in oxytocin levels and with genetic alterations of the oxytocin receptor (OXTR). Thirty years ago, M{\"u}hlethaler et al. found that oxytocin increases the firing of inhibitory hippocampal neurons, but it remains unclear how elevated inhibition could account for the ability of oxytocin to improve information processing in the brain. Here we describe in mammalian hippocampus a simple yet powerful mechanism by which oxytocin enhances cortical information transfer while simultaneously lowering background activity, thus greatly improving the signal-to-noise ratio. Increased fast-spiking interneuron activity not only suppresses spontaneous pyramidal cell firing, but also enhances the fidelity of spike transmission and sharpens spike timing. Use-dependent depression at the fast-spiking interneuron-pyramidal cell synapse is both necessary and sufficient for the enhanced spike throughput. We show the generality of this novel circuit mechanism by activation of fast-spiking interneurons with cholecystokinin or channelrhodopsin-2. This provides insight into how a diffusely delivered neuromodulator can improve the performance of neural circuitry that requires synapse specificity and millisecond precision.},
	Author = {Owen, Scott F and Tuncdemir, Sebnem N and Bader, Patrick L and Tirko, Natasha N and Fishell, Gord and Tsien, Richard W},
	Date-Added = {2018-02-28 22:19:24 +0000},
	Date-Modified = {2018-02-28 22:19:24 +0000},
	Doi = {10.1038/nature12330},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Action Potentials; Animals; Brain; Cholecystokinin; Excitatory Postsynaptic Potentials; Feedback, Physiological; Glycine; Hippocampus; Interneurons; Mice; Neural Pathways; Oxytocin; Pyramidal Cells; Rats; Receptors, Oxytocin; Rhodopsin; Synapses; Synaptic Transmission; Threonine},
	Month = {Aug},
	Number = {7463},
	Pages = {458-62},
	Pmc = {PMC5283693},
	Pmid = {23913275},
	Pst = {ppublish},
	Title = {Oxytocin enhances hippocampal spike transmission by modulating fast-spiking interneurons},
	Volume = {500},
	Year = {2013},
	File = {papers/Owen_Nature2013.pdf}}

@article{De-Biase:2017,
	Abstract = {Microglia play critical roles in tissue homeostasis and can also modulate neuronal function and synaptic connectivity. In contrast to astrocytes and oligodendrocytes, which arise from multiple progenitor pools, microglia arise from yolk sac progenitors and are widely considered to be equivalent throughout the CNS. However, little is known about basic properties of deep brain microglia, such as those within the basal ganglia (BG). Here, we show that microglial anatomical features, lysosome content, membrane properties, and transcriptomes differ significantly across BG nuclei. Region-specific phenotypes of BG microglia emerged during the second postnatal week and were re-established following genetic or pharmacological microglial ablation and repopulation in the adult, indicating that local cues play an ongoing role in shaping microglial diversity. These findings demonstrate that microglia in the healthy brain exhibit a spectrum of distinct functional states and provide a critical foundation for defining microglial contributions to BG circuit function.},
	Author = {De Biase, Lindsay M and Schuebel, Kornel E and Fusfeld, Zachary H and Jair, Kamwing and Hawes, Isobel A and Cimbro, Raffaello and Zhang, Hai-Ying and Liu, Qing-Rong and Shen, Hui and Xi, Zheng-Xiong and Goldman, David and Bonci, Antonello},
	Date-Added = {2018-02-28 22:15:11 +0000},
	Date-Modified = {2018-02-28 22:15:11 +0000},
	Doi = {10.1016/j.neuron.2017.06.020},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {RNA sequencing; density; development; electrophysiology; heterogeneity; microglia; morphology; nucleus accumbens; substantia nigra; ventral tegmental area},
	Mesh = {Animals; Basal Ganglia; Cues; Mice, Transgenic; Microglia; Neurons; Phenotype},
	Month = {Jul},
	Number = {2},
	Pages = {341-356.e6},
	Pmc = {PMC5754189},
	Pmid = {28689984},
	Pst = {ppublish},
	Title = {Local Cues Establish and Maintain Region-Specific Phenotypes of Basal Ganglia Microglia},
	Volume = {95},
	Year = {2017},
	File = {papers/DeBiase_Neuron2017.pdf},
	Bdsk-File-2 = {papers/DeBiase_Neuron2017a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2017.06.020}}

@article{Sylwestrak:2016,
	Abstract = {In recently developed approaches for high-resolution imaging within intact tissue, molecular characterization over large volumes has been largely restricted to labeling of proteins. But volumetric nucleic acid labeling may represent a far greater scientific and clinical opportunity, enabling detection of not only diverse coding RNA variants but also non-coding RNAs. Moreover, scaling immunohistochemical detection to large tissue volumes has limitations due to high cost, limited renewability/availability, and restricted multiplexing capability of antibody labels. With the goal of versatile, high-content, and scalable molecular phenotyping of intact tissues, we developed a method using carbodiimide-based chemistry to stably retain RNAs in clarified tissue, coupled with amplification tools for multiplexed detection. The resulting technology enables robust measurement of activity-dependent transcriptional signatures, cell-identity markers, and diverse non-coding RNAs in rodent and human tissue volumes. The growing set of validated probes is deposited in an online resource for nucleating related developments from across the scientific community.},
	Author = {Sylwestrak, Emily Lauren and Rajasethupathy, Priyamvada and Wright, Matthew Arnot and Jaffe, Anna and Deisseroth, Karl},
	Date-Added = {2018-02-28 22:14:13 +0000},
	Date-Modified = {2018-02-28 22:14:13 +0000},
	Doi = {10.1016/j.cell.2016.01.038},
	Journal = {Cell},
	Journal-Full = {Cell},
	Mesh = {Adolescent; Animals; Brain Chemistry; Cyanates; Ethyldimethylaminopropyl Carbodiimide; Female; Humans; In Situ Hybridization; Male; Maleimides; Mice; Middle Aged; Nucleic Acid Amplification Techniques; Oligonucleotides; RNA; Succinimides; Transcriptome},
	Month = {Feb},
	Number = {4},
	Pages = {792-804},
	Pmc = {PMC4775740},
	Pmid = {26871636},
	Pst = {ppublish},
	Title = {Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution},
	Volume = {164},
	Year = {2016},
	File = {papers/Sylwestrak_Cell2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cell.2016.01.038}}

@article{Li:2009,
	Abstract = {Type 1 cannabinoid (CB1) receptors mediate widespread synaptic plasticity, but how this contributes to systems-level plasticity and development in vivo is unclear. We tested whether CB1 signaling is required for development and plasticity of the whisker map in rat somatosensory cortex. Treatment with the CB1 antagonist AM251 during an early critical period for layer (L) 2/3 development (beginning postnatal day [P] 12-16) disrupted whisker map development, leading to inappropriate whisker tuning in L2/3 column edges and a blurred map. Early AM251 treatment also prevented experience-dependent plasticity in L2/3, including deprivation-induced synapse weakening and weakening of deprived whisker responses. CB1 blockade after P25 did not disrupt map development or plasticity. AM251 had no acute effect on sensory-evoked spiking and only modestly affected field potentials, suggesting that plasticity effects were not secondary to gross activity changes. These findings implicate CB1-dependent plasticity in systems-level development and early postnatal plasticity of the whisker map.},
	Author = {Li, Lu and Bender, Kevin J and Drew, Patrick J and Jadhav, Shantanu P and Sylwestrak, Emily and Feldman, Daniel E},
	Date-Added = {2018-02-28 22:12:59 +0000},
	Date-Modified = {2018-02-28 22:12:59 +0000},
	Doi = {10.1016/j.neuron.2009.10.005},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Animals, Newborn; Brain Mapping; Critical Period (Psychology); Female; Male; Mice; Mice, Knockout; Neuronal Plasticity; Rats; Rats, Long-Evans; Receptor, Cannabinoid, CB1; Signal Transduction; Somatosensory Cortex; Vibrissae},
	Month = {Nov},
	Number = {4},
	Pages = {537-49},
	Pmc = {PMC2796273},
	Pmid = {19945395},
	Pst = {ppublish},
	Title = {Endocannabinoid signaling is required for development and critical period plasticity of the whisker map in somatosensory cortex},
	Volume = {64},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2009.10.005}}

@article{Kim:2015,
	Abstract = {Cortical layer 5 (L5) pyramidal neurons integrate inputs from many sources and distribute outputs to cortical and subcortical structures. Previous studies demonstrate two L5 pyramid types: cortico-cortical (CC) and cortico-subcortical (CS). We characterize connectivity and function of these cell types in mouse primary visual cortex and reveal a new subtype. Unlike previously described L5 CC and CS neurons, this new subtype does not project to striatum [cortico-cortical, non-striatal (CC-NS)] and has distinct morphology, physiology, and visual responses. Monosynaptic rabies tracing reveals that CC neurons preferentially receive input from higher visual areas, while CS neurons receive more input from structures implicated in top-down modulation of brain states. CS neurons are also more direction-selective and prefer faster stimuli than CC neurons. These differences suggest distinct roles as specialized output channels, with CS neurons integrating information and generating responses more relevant to movement control and CC neurons being more important in visual perception.},
	Author = {Kim, Euiseok J and Juavinett, Ashley L and Kyubwa, Espoir M and Jacobs, Matthew W and Callaway, Edward M},
	Date-Added = {2018-02-28 22:11:15 +0000},
	Date-Modified = {2018-02-28 22:11:15 +0000},
	Doi = {10.1016/j.neuron.2015.11.002},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Mice; Mice, Inbred C57BL; Mice, Transgenic; Nerve Net; Neurons; Pyramidal Cells; Visual Cortex},
	Month = {Dec},
	Number = {6},
	Pages = {1253-67},
	Pmc = {PMC4688126},
	Pmid = {26671462},
	Pst = {ppublish},
	Title = {Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function},
	Volume = {88},
	Year = {2015},
	File = {papers/Kim_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.11.002}}

@article{Sylwestrak:2012,
	Abstract = {Although synaptic transmission may be unidirectional, the establishment of synaptic connections with specific properties can involve bidirectional signaling. Pyramidal neurons in the hippocampus form functionally distinct synapses onto two types of interneurons. Excitatory synapses onto oriens-lacunosum moleculare (O-LM) interneurons are facilitating and have a low release probability, whereas synapses onto parvalbumin interneurons are depressing and have a high release probability. Here, we show that the extracellular leucine-rich repeat fibronectin containing 1 (Elfn1) protein is selectively expressed by O-LM interneurons and regulates presynaptic release probability to direct the formation of highly facilitating pyramidal-O-LM synapses. Thus, postsynaptic expression of Elfn1 in O-LM interneurons regulates presynaptic release probability, which confers target-specific synaptic properties to pyramidal cell axons.},
	Author = {Sylwestrak, Emily L and Ghosh, Anirvan},
	Date-Added = {2018-02-28 22:10:31 +0000},
	Date-Modified = {2018-02-28 22:10:31 +0000},
	Doi = {10.1126/science.1222482},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Axons; CA1 Region, Hippocampal; Cells, Cultured; Gene Knockdown Techniques; Green Fluorescent Proteins; HEK293 Cells; Humans; Interneurons; Mice; Nerve Tissue Proteins; RNA, Small Interfering; Rats; Rats, Inbred LEC; Synapses; Synaptic Transmission},
	Month = {Oct},
	Number = {6106},
	Pages = {536-40},
	Pmc = {PMC5297939},
	Pmid = {23042292},
	Pst = {ppublish},
	Title = {Elfn1 regulates target-specific release probability at CA1-interneuron synapses},
	Volume = {338},
	Year = {2012},
	File = {papers/Sylwestrak_Science2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1222482}}

@article{Beier:2017,
	Abstract = {Identification of neural circuit changes that contribute to behavioural plasticity has routinely been conducted on candidate circuits that were preselected on the basis of previous results. Here we present an unbiased method for identifying experience-triggered circuit-level changes in neuronal ensembles in mice. Using rabies virus monosynaptic tracing, we mapped cocaine-induced global changes in inputs onto neurons in the ventral tegmental area. Cocaine increased rabies-labelled inputs from the globus pallidus externus (GPe), a basal ganglia nucleus not previously known to participate in behavioural plasticity triggered by drugs of abuse. We demonstrated that cocaine increased GPe neuron activity, which accounted for the increase in GPe labelling. Inhibition of GPe activity revealed that it contributes to two forms of cocaine-triggered behavioural plasticity, at least in part by disinhibiting dopamine neurons in the ventral tegmental area. These results suggest that rabies-based unbiased screening of changes in input populations can identify previously unappreciated circuit elements that critically support behavioural adaptations.},
	Author = {Beier, Kevin T and Kim, Christina K and Hoerbelt, Paul and Hung, Lin Wai and Heifets, Boris D and DeLoach, Katherine E and Mosca, Timothy J and Neuner, Sophie and Deisseroth, Karl and Luo, Liqun and Malenka, Robert C},
	Date-Added = {2018-02-28 22:08:40 +0000},
	Date-Modified = {2018-02-28 22:08:40 +0000},
	Doi = {10.1038/nature23888},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Basal Ganglia; Cocaine; Dopaminergic Neurons; Female; Globus Pallidus; Male; Mice; Mice, Inbred C57BL; Neuronal Plasticity; Rabies virus; Staining and Labeling; Ventral Tegmental Area},
	Month = {09},
	Number = {7672},
	Pages = {345-350},
	Pmid = {28902833},
	Pst = {ppublish},
	Title = {Rabies screen reveals GPe control of cocaine-triggered plasticity},
	Volume = {549},
	Year = {2017},
	File = {papers/Beier_Nature2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature23888}}

@article{De-Biase:2010,
	Abstract = {The mammalian CNS contains an abundant, widely distributed population of glial cells that serve as oligodendrocyte progenitors. It has been reported that these NG2-immunoreactive cells (NG2(+) cells) form synapses and generate action potentials, suggesting that neural-evoked excitation of these progenitors may regulate oligodendrogenesis. However, recent studies also suggest that NG2(+) cells are comprised of functionally distinct groups that differ in their ability to respond to neuronal activity, undergo differentiation, and experience injury following ischemia. To better define the physiological properties of NG2(+) cells, we used transgenic mice that allowed an unbiased sampling of this population and unambiguous identification of cells in discrete states of differentiation. Using acute brain slices prepared from developing and mature mice, we found that NG2(+) cells in diverse brain regions share a core set of physiological properties, including expression of voltage-gated Na(+) (NaV) channels and ionotropic glutamate receptors, and formation of synapses with glutamatergic neurons. Although small amplitude Na(+) spikes could be elicited in some NG2(+) cells during the first postnatal week, they were not capable of generating action potentials. Transition of these progenitors to the premyelinating stage was accompanied by the rapid removal of synaptic input, as well as downregulation of AMPA and NMDA receptors and NaV channels. Thus, prior reports of physiological heterogeneity among NG2(+) cells may reflect analysis of cells in later stages of maturation. These results suggest that NG2(+) cells are uniquely positioned within the oligodendrocyte lineage to monitor the firing patterns of surrounding neurons.},
	Author = {De Biase, Lindsay M and Nishiyama, Akiko and Bergles, Dwight E},
	Date-Added = {2018-02-28 22:03:44 +0000},
	Date-Modified = {2018-02-28 22:03:44 +0000},
	Doi = {10.1523/JNEUROSCI.6000-09.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Cell Communication; Cell Lineage; Chondroitin Sulfate Proteoglycans; Gene Expression Profiling; Membrane Proteins; Mice; Mice, Transgenic; Oligodendroglia; Synapses},
	Month = {Mar},
	Number = {10},
	Pages = {3600-11},
	Pmc = {PMC2838193},
	Pmid = {20219994},
	Pst = {ppublish},
	Title = {Excitability and synaptic communication within the oligodendrocyte lineage},
	Volume = {30},
	Year = {2010},
	File = {papers/DeBiase_JNeurosci2010.pdf}}

@article{Brown:2001a,
	Abstract = {'Independent component analysis' is a technique of data transformation that finds independent sources of activity in recorded mixtures of sources. It can be used to recover fluctuations of membrane potential from individual neurons in multiple-detector optical recordings. There are some examples in which more than 100 neurons can be separated simultaneously. Independent component analysis automatically separates overlapping action potentials, recovers action potentials of different sizes from the same neuron, removes artifacts and finds the position of each neuron on the detector array. One limitation is that the number of sources--neurons and artifacts--must be equal to or less than the number of simultaneous recordings. Independent component analysis also has many other applications in neuroscience including, removal of artifacts from EEG data, identification of spatially independent brain regions in fMRI recordings and determination of population codes in multi-unit recordings.},
	Author = {Brown, G D and Yamada, S and Sejnowski, T J},
	Date-Added = {2018-02-28 22:03:12 +0000},
	Date-Modified = {2018-02-28 22:03:12 +0000},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Mesh = {Action Potentials; Algorithms; Animals; Brain; Electroencephalography; Humans; Linear Models; Membrane Potentials; Models, Neurological; Neurons},
	Month = {Jan},
	Number = {1},
	Pages = {54-63},
	Pmid = {11163888},
	Pst = {ppublish},
	Title = {Independent component analysis at the neural cocktail party},
	Volume = {24},
	Year = {2001},
	File = {papers/Brown_TrendsNeurosci2001a.pdf}}

@article{Beier:2013,
	Abstract = {The use of neurotropic viruses as transsynaptic tracers was first described in the 1960s, but only recently have such viruses gained popularity as a method for labeling neural circuits. The development of retrograde monosynaptic tracing vectors has enabled visualization of the presynaptic sources onto defined sets of postsynaptic neurons. Here, we describe the first application of a novel viral tracer, based on vesicular stomatitis virus (VSV), which directs retrograde transsynaptic viral spread between defined cell types. We use this virus in the mouse retina to show connectivity between starburst amacrine cells (SACs) and their known synaptic partners, direction-selective retinal ganglion cells, as well as to discover previously unknown connectivity between SACs and other retinal ganglion cell types. These novel connections were confirmed using physiological recordings. VSV transsynaptic tracing enables cell type-specific dissection of neural circuitry and can reveal synaptic relationships among neurons that are otherwise obscured due to the complexity and density of neuropil.},
	Author = {Beier, Kevin T and Borghuis, Bart G and El-Danaf, Rana N and Huberman, Andrew D and Demb, Jonathan B and Cepko, Constance L},
	Date-Added = {2018-02-28 22:03:01 +0000},
	Date-Modified = {2018-02-28 22:03:01 +0000},
	Doi = {10.1523/JNEUROSCI.0245-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Mice; Nerve Net; Neuronal Tract-Tracers; Neurons; Retina; Synapses; Vesiculovirus},
	Month = {Jan},
	Number = {1},
	Pages = {35-51},
	Pmc = {PMC3711516},
	Pmid = {23283320},
	Pst = {ppublish},
	Title = {Transsynaptic tracing with vesicular stomatitis virus reveals novel retinal circuitry},
	Volume = {33},
	Year = {2013},
	File = {papers/Beier_JNeurosci2013.pdf}}

@article{Sher:2013,
	Abstract = {CNS neurons change their connectivity to accommodate a changing environment, form memories, or respond to injury. Plasticity in the adult mammalian retina after injury or disease was thought to be limited to restructuring resulting in abnormal retinal anatomy and function. Here we report that neurons in the mammalian retina change their connectivity and restore normal retinal anatomy and function after injury. Patches of photoreceptors in the rabbit retina were destroyed by selective laser photocoagulation, leaving retinal inner neurons (bipolar, amacrine, horizontal, ganglion cells) intact. Photoreceptors located outside of the damaged zone migrated to make new functional connections with deafferented bipolar cells located inside the lesion. The new connections restored ON and OFF responses in deafferented ganglion cells. This finding extends the previously perceived limits of restorative plasticity in the adult retina and allows for new approaches to retinal laser therapy free of current detrimental side effects such as scotomata and scarring.},
	Author = {Sher, Alexander and Jones, Bryan W and Huie, Philip and Paulus, Yannis M and Lavinsky, Daniel and Leung, Loh-Shan S and Nomoto, Hiroyuki and Beier, Corinne and Marc, Robert E and Palanker, Daniel},
	Date-Added = {2018-02-28 22:02:52 +0000},
	Date-Modified = {2018-02-28 22:02:52 +0000},
	Doi = {10.1523/JNEUROSCI.1044-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Disease Models, Animal; Electric Stimulation; Glutamic Acid; In Vitro Techniques; Lasers; Light Coagulation; Male; Patch-Clamp Techniques; Photic Stimulation; Photoreceptor Cells; Rabbits; Recovery of Function; Retina; Retinal Diseases; Retinal Ganglion Cells; Synapses; Time Factors; Tomography, X-Ray Computed; Vision, Ocular; Visual Pathways; gamma-Aminobutyric Acid},
	Month = {Apr},
	Number = {16},
	Pages = {6800-8},
	Pmc = {PMC3865506},
	Pmid = {23595739},
	Pst = {ppublish},
	Title = {Restoration of retinal structure and function after selective photocoagulation},
	Volume = {33},
	Year = {2013},
	File = {papers/Sher_JNeurosci2013.pdf}}

@article{Behrens:2014,
	Abstract = {Bitter taste perception in vertebrates relies on a variable number of bitter taste receptor (Tas2r) genes, ranging from only three functional genes in chicken to as many as approximately 50 in frogs. Humans possess a medium-sized Tas2r repertoire encoding three broadly and several narrowly tuned receptors plus receptors with intermediate tuning properties. Such tuning information is not available for bitter taste receptors of other vertebrate species. In particular it is not known, whether a small Tas2r repertoire may be compensated for by broad tuning of these receptors, and on the other side, whether a large repertoire might entail a preponderance of narrowly tuned receptors. To elucidate this question, we cloned all three chicken Tas2rs, the two turkey Tas2rs, three zebra finch Tas2rs, and six Tas2rs of the Western clawed frog representative of major branches of the phylogenetic tree, and screened them with 46 different bitter compounds. All chicken and turkey Tas2rs were broadly tuned, the zebra finch Tas2rs were narrowly tuned, and frog Tas2rs ranged from broadly to narrowly tuned receptors. We conclude that a low number of functional Tas2r genes does not imply a reduced importance of bitter taste per se, as it can be compensated by large tuning width. A high number of functional Tas2r genes appears to allow the evolution of specialized receptors, possibly for toxins with species-specific relevance. In sum, we show that variability in tuning breadth, overlapping agonist profiles, and staggered effective agonist concentration ranges are shared features of human and other vertebrate Tas2rs.},
	Author = {Behrens, Maik and Korsching, Sigrun I and Meyerhof, Wolfgang},
	Date-Added = {2018-02-26 23:45:41 +0000},
	Date-Modified = {2018-02-26 23:45:41 +0000},
	Doi = {10.1093/molbev/msu254},
	Journal = {Mol Biol Evol},
	Journal-Full = {Molecular biology and evolution},
	Keywords = {G protein-coupled receptor; bitter taste receptor; evolution; heterologous expression},
	Mesh = {Amphibian Proteins; Animals; Anura; Avian Proteins; Birds; Evolution, Molecular; HEK293 Cells; Humans; Noscapine; Phylogeny; Quaternary Ammonium Compounds; Receptors, Cell Surface; Signal Transduction; Taste Buds},
	Month = {Dec},
	Number = {12},
	Pages = {3216-27},
	Pmid = {25180257},
	Pst = {ppublish},
	Title = {Tuning properties of avian and frog bitter taste receptors dynamically fit gene repertoire sizes},
	Volume = {31},
	Year = {2014},
	File = {papers/Behrens_MolBiolEvol2014.pdf}}

@article{Oike:2007,
	Abstract = {Recent progress in the molecular biology of taste reception has revealed that in mammals, the heteromeric receptors T1R1/3 and T1R2/3 respond to amino acids and sweeteners, respectively, whereas T2Rs are receptors for bitter tastants. Similar taste receptors have also been characterized in fish, but their ligands have not been identified yet. In the present study, we conducted a series of experiments to identify the fish taste receptor ligands. Facial nerve recordings in zebrafish (Danio rerio) demonstrated that the fish perceived amino acids and even denatonium, which is a representative of aversive bitter compounds for mammals and Drosophila. Calcium imaging analysis of T1Rs in zebrafish and medaka fish (Oryzias latipes) using an HEK293T heterologous expression system revealed that both T1R1/3 and a series of T1R2/3 responded to amino acids but not to sugars. A triple-labeling, in situ hybridization analysis demonstrated that cells expressing T1R1/3 and T1R2/3s exist in PLCbeta2-expressing taste bud cells of medaka fish. Functional analysis using T2Rs showed that zfT2R5 and mfT2R1 responded to denatonium. Behavior observations confirmed that zebrafish prefer amino acids and avoid denatonium. These results suggest that, although there may be some fish-specific way of discriminating ligands, vertebrates could have a conserved gustatory mechanism by which T1Rs and T2Rs respond to attractive and aversive tastants, respectively.},
	Author = {Oike, Hideaki and Nagai, Toshitada and Furuyama, Akira and Okada, Shinji and Aihara, Yoshiko and Ishimaru, Yoshiro and Marui, Takayuki and Matsumoto, Ichiro and Misaka, Takumi and Abe, Keiko},
	Date-Added = {2018-02-26 23:27:48 +0000},
	Date-Modified = {2018-02-26 23:27:48 +0000},
	Doi = {10.1523/JNEUROSCI.0651-07.2007},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Amino Acids; Animals; Cell Line; Dose-Response Relationship, Drug; Humans; Ligands; Oryzias; Quaternary Ammonium Compounds; Receptors, G-Protein-Coupled; Taste Buds; Zebrafish},
	Month = {May},
	Number = {21},
	Pages = {5584-92},
	Pmid = {17522303},
	Pst = {ppublish},
	Title = {Characterization of ligands for fish taste receptors},
	Volume = {27},
	Year = {2007},
	File = {papers/Oike_JNeurosci2007.pdf}}

@article{Yu:2016,
	Abstract = {We rely on movement to explore the environment, for example, by palpating an object. In somatosensory cortex, activity related to movement of digits or whiskers is suppressed, which could facilitate detection of touch. Movement-related suppression is generally assumed to involve corollary discharges. Here we uncovered a thalamocortical mechanism in which cortical fast-spiking interneurons, driven by sensory input, suppress movement-related activity in layer 4 (L4) excitatory neurons. In mice locating objects with their whiskers, neurons in the ventral posteromedial nucleus (VPM) fired in response to touch and whisker movement. Cortical L4 fast-spiking interneurons inherited these responses from VPM. In contrast, L4 excitatory neurons responded mainly to touch. Optogenetic experiments revealed that fast-spiking interneurons reduced movement-related spiking in excitatory neurons, enhancing selectivity for touch-related information during active tactile sensation. These observations suggest a fundamental computation performed by the thalamocortical circuit to accentuate salient tactile information.},
	Author = {Yu, Jianing and Gutnisky, Diego A and Hires, S Andrew and Svoboda, Karel},
	Date-Added = {2018-02-21 22:24:12 +0000},
	Date-Modified = {2018-02-21 22:24:12 +0000},
	Doi = {10.1038/nn.4412},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Action Potentials; Animals; Behavior, Animal; Electric Stimulation; Interneurons; Mice; Movement; Neural Pathways; Patch-Clamp Techniques; Physical Stimulation; Somatosensory Cortex; Thalamus; Touch; Vibrissae},
	Month = {Dec},
	Number = {12},
	Pages = {1647-1657},
	Pmid = {27749825},
	Pst = {ppublish},
	Title = {Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation},
	Volume = {19},
	Year = {2016},
	File = {papers/Yu_NatNeurosci2016.pdf}}

@article{Hartwick:2007,
	Abstract = {A small number (<2%) of mammalian retinal ganglion cells express the photopigment melanopsin and are intrinsically photosensitive (ipRGCs). Light depolarizes ipRGCs and increases intracellular calcium levels ([Ca2+]i) but the signaling cascades underlying these responses have yet to be elucidated. To facilitate physiological studies on these rare photoreceptors, highly enriched ipRGC cultures from neonatal rats were generated using anti-melanopsin-mediated plate adhesion (immunopanning). This novel approach enabled experiments on isolated ipRGCs, eliminating the potential confounding influence of rod/cone-driven input. Light induced a rise in [Ca2+]i (monitored using fura-2 imaging) in the immunopanned ipRGCs and the source of this Ca2+ signal was investigated. The Ca2+ responses were inhibited by 2-aminoethoxydiphenyl borate, SKF-96365 (1-2-(4-methoxyphenyl)-2-[3-(4-methoxyphenyl)propoxy]ethyl-1H-imidazole), flufenamic acid, lanthanum, and gadolinium, consistent with the involvement of canonical transient receptor potential (TRP) channels in ipRGC phototransduction. However, the contribution of direct Ca2+ flux through a putative TRP channel to ipRGC [Ca2+]i was relatively small, as most (approximately 90%) of the light-induced Ca2+ responses could be blocked by preventing action potential firing with tetrodotoxin. The L-type voltage-gated Ca2+ channel (VGCC) blockers verapamil and (+)-cis-diltiazem significantly reduced the light-evoked Ca2+ responses, while the internal Ca2+ stores depleting agent thapsigargin had negligible effect. These results indicate that Ca2+ influx through VGCCs, activated after action potential firing, was the primary source for light-evoked elevations in ipRGC [Ca2+]i. Furthermore, concurrent Ca2+ imaging and cell-attached electrophysiological recordings demonstrated that the Ca2+ responses were highly correlated to spike frequency, thereby establishing a direct link between action potential firing and somatic [Ca2+]i in light-stimulated ipRGCs.},
	Author = {Hartwick, Andrew T E and Bramley, Jayne R and Yu, Jianing and Stevens, Kelly T and Allen, Charles N and Baldridge, William H and Sollars, Patricia J and Pickard, Gary E},
	Date-Added = {2018-02-21 21:54:31 +0000},
	Date-Modified = {2018-02-21 21:54:31 +0000},
	Doi = {10.1523/JNEUROSCI.3626-07.2007},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Calcium Signaling; Photic Stimulation; Rats; Rats, Long-Evans; Retinal Ganglion Cells; Rod Opsins},
	Month = {Dec},
	Number = {49},
	Pages = {13468-80},
	Pmid = {18057205},
	Pst = {ppublish},
	Title = {Light-evoked calcium responses of isolated melanopsin-expressing retinal ganglion cells},
	Volume = {27},
	Year = {2007},
	File = {papers/Hartwick_JNeurosci2007.pdf}}

@article{Goyal:2014,
	Abstract = {Aerobic glycolysis (AG; i.e., nonoxidative metabolism of glucose despite the presence of abundant oxygen) accounts for 10%-12% of glucose used by the adult human brain. AG varies regionally in the resting state. Brain AG may support synaptic growth and remodeling; however, data supporting this hypothesis are sparse. Here, we report on investigations on the role of AG in the human brain. Meta-analysis of prior brain glucose and oxygen metabolism studies demonstrates that AG increases during childhood, precisely when synaptic growth rates are highest. In resting adult humans, AG correlates with the persistence of gene expression typical of infancy (transcriptional neoteny). In brain regions with the highest AG, we find increased gene expression related to synapse formation and growth. In contrast, regions high in oxidative glucose metabolism express genes related to mitochondria and synaptic transmission. Our results suggest that brain AG supports developmental processes, particularly those required for synapse formation and growth.},
	Author = {Goyal, Manu S and Hawrylycz, Michael and Miller, Jeremy A and Snyder, Abraham Z and Raichle, Marcus E},
	Date-Added = {2018-02-14 00:26:30 +0000},
	Date-Modified = {2018-02-14 00:26:36 +0000},
	Doi = {10.1016/j.cmet.2013.11.020},
	Journal = {Cell Metab},
	Journal-Full = {Cell metabolism},
	Keywords = {Energy Metabolism},
	Mesh = {Adult; Aerobiosis; Brain; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Ontology; Glucose; Glycolysis; Humans; Oxygen Consumption; Synapses; Transcription, Genetic},
	Month = {Jan},
	Number = {1},
	Pages = {49-57},
	Pmc = {PMC4389678},
	Pmid = {24411938},
	Pst = {ppublish},
	Title = {Aerobic glycolysis in the human brain is associated with development and neotenous gene expression},
	Volume = {19},
	Year = {2014},
	File = {papers/Goyal_CellMetab2014.pdf},
	Bdsk-File-2 = {papers/Goyal_CellMetab2014a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cmet.2013.11.020}}

@article{Magistretti:2015,
	Abstract = {The energy demands of the brain are high: they account for at least 20% of the body's energy consumption. Evolutionary studies indicate that the emergence of higher cognitive functions in humans is associated with an increased glucose utilization and expression of energy metabolism genes. Functional brain imaging techniques such as fMRI and PET, which are widely used in human neuroscience studies, detect signals that monitor energy delivery and use in register with neuronal activity. Recent technological advances in metabolic studies with cellular resolution have afforded decisive insights into the understanding of the cellular and molecular bases of the coupling between neuronal activity and energy metabolism and point at a key role of neuron-astrocyte metabolic interactions. This article reviews some of the most salient features emerging from recent studies and aims at providing an integration of brain energy metabolism across resolution scales.},
	Author = {Magistretti, Pierre J and Allaman, Igor},
	Date-Added = {2018-02-14 00:25:38 +0000},
	Date-Modified = {2018-02-14 00:25:45 +0000},
	Doi = {10.1016/j.neuron.2015.03.035},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Energy Metabolism},
	Mesh = {Animals; Astrocytes; Brain; Energy Metabolism; Glucose; Humans; Magnetic Resonance Imaging; Neurons},
	Month = {May},
	Number = {4},
	Pages = {883-901},
	Pmid = {25996133},
	Pst = {ppublish},
	Title = {A cellular perspective on brain energy metabolism and functional imaging},
	Volume = {86},
	Year = {2015},
	File = {papers/Magistretti_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.03.035}}

@article{Erecinska:2004,
	Abstract = {Production of energy for the maintenance of ionic disequilibria necessary for generation and transmission of nerve impulses is one of the primary functions of the brain. This review attempts to link the plethora of information on the maturation of the central nervous system with the ontogeny of ATP metabolism, placing special emphasis on variations that occur during development in different brain regions and across the mammalian species. It correlates morphological events and markers with biochemical changes in activities of enzymes and pathways that participate in the production of ATP. The paper also evaluates alterations in energy levels as a function of age and, based on the tenet that ATP synthesis and utilization cannot be considered in isolation, investigates maturational profiles of the key processes that utilize energy. Finally, an attempt is made to assess the relevance of currently available animal models to improvement of our understanding of the etiopathology of various disease states in the human infant. This is deemed essential for the development and testing of novel strategies for prevention and treatment of several severe neurological deficits.},
	Author = {Erecinska, Maria and Cherian, Shobha and Silver, Ian A},
	Date-Added = {2018-02-14 00:24:25 +0000},
	Date-Modified = {2018-02-14 00:24:46 +0000},
	Doi = {10.1016/j.pneurobio.2004.06.003},
	Journal = {Prog Neurobiol},
	Journal-Full = {Progress in neurobiology},
	Keywords = {Energy Metabolism},
	Mesh = {Adenosine Triphosphate; Animals; Blood Vessels; Body Water; Brain; Brain Chemistry; Cholesterol; DNA; Energy Metabolism; Extracellular Space; Humans; Ion Channels; Kinetics; Mitochondria; Nerve Tissue Proteins; Neurons},
	Month = {Aug},
	Number = {6},
	Pages = {397-445},
	Pmid = {15313334},
	Pst = {ppublish},
	Title = {Energy metabolism in mammalian brain during development},
	Volume = {73},
	Year = {2004},
	File = {papers/Erecinska_ProgNeurobiol2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.pneurobio.2004.06.003}}

@article{Lee:2017,
	Abstract = {In mammals, taste buds typically contain 50-100 tightly packed taste-receptor cells (TRCs), representing all five basic qualities: sweet, sour, bitter, salty and umami. Notably, mature taste cells have life spans of only 5-20 days and, consequently, are constantly replenished by differentiation of taste stem cells. Given the importance of establishing and maintaining appropriate connectivity between TRCs and their partner ganglion neurons (that is, ensuring that a labelled line from sweet TRCs connects to sweet neurons, bitter TRCs to bitter neurons, sour to sour, and so on), we examined how new connections are specified to retain fidelity of signal transmission. Here we show that bitter and sweet TRCs provide instructive signals to bitter and sweet target neurons via different guidance molecules (SEMA3A and SEMA7A). We demonstrate that targeted expression of SEMA3A or SEMA7A in different classes of TRCs produces peripheral taste systems with miswired sweet or bitter cells. Indeed, we engineered mice with bitter neurons that now responded to sweet tastants, sweet neurons that responded to bitter or sweet neurons responding to sour stimuli. Together, these results uncover the basic logic of the wiring of the taste system at the periphery, and illustrate how a labelled-line sensory circuit preserves signalling integrity despite rapid and stochastic turnover of receptor cells.},
	Author = {Lee, Hojoon and Macpherson, Lindsey J and Parada, Camilo A and Zuker, Charles S and Ryba, Nicholas J P},
	Date-Added = {2018-02-13 23:59:58 +0000},
	Date-Modified = {2018-02-13 23:59:58 +0000},
	Doi = {10.1038/nature23299},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Antigens, CD; Ganglia; Mice; Neurons; Semaphorin-3A; Semaphorins; Stem Cells; Sweetening Agents; Taste; Taste Buds},
	Month = {08},
	Number = {7667},
	Pages = {330-333},
	Pmc = {PMC5805144},
	Pmid = {28792937},
	Pst = {ppublish},
	Title = {Rewiring the taste system},
	Volume = {548},
	Year = {2017},
	File = {papers/Lee_Nature2017.pdf},
	Bdsk-File-2 = {papers/Lee_Nature2017a.pdf}}

@book{Kennedy:2016,
	Annote = {LDR    00863nam  22002535i 4500
001    18959929
005    20160203092018.0
008    160203s2016    nyu           000 0 eng  
906    $a0$bibc$corignew$d2$eepcn$f20$gy-gencatlg
925 0  $aacquire$b1 shelf copy$xpolicy default
955    $apc17 2016-02-03
010    $a  2016932376
020    $a9783319277769 (alk. paper)
040    $aDLC$beng$erda$cDLC
042    $apcc
100 1  $aKennedy, Henry.
245 10 $aMicro-, meso- and macro-connectomics of the brain /$cHenry Kennedy.
263    $a1602
264  1 $aNew York, NY :$bSpringer Berlin Heidelberg,$c2016.
300    $apages cm
336    $atext$btxt$2rdacontent
337    $aunmediated$bn$2rdamedia
338    $avolume$bnc$2rdacarrier
963    $aRahila Nahid K; phone: (44) 43950500; email: N.Rahila@spi-global.com; bc: reinhold.joest@springer.com
},
	Author = {Kennedy, Henry},
	Date-Added = {2018-02-13 23:56:07 +0000},
	Date-Modified = {2018-02-13 23:58:08 +0000},
	Isbn = {9783319277769 (alk. paper)},
	Library-Id = {2016932376},
	Title = {Micro-, meso- and macro-connectomics of the brain},
	File = {papers/Bookshelf_NBK435763.pdf}}

@article{Mergenthaler:2013,
	Abstract = {The mammalian brain depends upon glucose as its main source of energy, and tight regulation of glucose metabolism is critical for brain physiology. Consistent with its critical role for physiological brain function, disruption of normal glucose metabolism as well as its interdependence with cell death pathways forms the pathophysiological basis for many brain disorders. Here, we review recent advances in understanding how glucose metabolism sustains basic brain physiology. We synthesize these findings to form a comprehensive picture of the cooperation required between different systems and cell types, and the specific breakdowns in this cooperation that lead to disease.},
	Author = {Mergenthaler, Philipp and Lindauer, Ute and Dienel, Gerald A and Meisel, Andreas},
	Date-Added = {2018-01-25 01:38:17 +0000},
	Date-Modified = {2018-01-25 01:38:17 +0000},
	Doi = {10.1016/j.tins.2013.07.001},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {apoptosis; brain-body axis; glucose metabolism; metabolic brain disease; metabolic coupling},
	Mesh = {Animals; Brain; Energy Metabolism; Glucose; Humans},
	Month = {Oct},
	Number = {10},
	Pages = {587-97},
	Pmc = {PMC3900881},
	Pmid = {23968694},
	Pst = {ppublish},
	Title = {Sugar for the brain: the role of glucose in physiological and pathological brain function},
	Volume = {36},
	Year = {2013},
	File = {papers/Mergenthaler_TrendsNeurosci2013.pdf}}

@article{Gordon:2008,
	Abstract = {Calcium signalling in astrocytes couples changes in neural activity to alterations in cerebral blood flow by eliciting vasoconstriction or vasodilation of arterioles. However, the mechanism for how these opposite astrocyte influences provide appropriate changes in vessel tone within an environment that has dynamic metabolic requirements remains unclear. Here we show that the ability of astrocytes to induce vasodilations over vasoconstrictions relies on the metabolic state of the rat brain tissue. When oxygen availability is lowered and astrocyte calcium concentration is elevated, astrocyte glycolysis and lactate release are maximized. External lactate attenuates transporter-mediated uptake from the extracellular space of prostaglandin E(2), leading to accumulation and subsequent vasodilation. In conditions of low oxygen concentration extracellular adenosine also increases, which blocks astrocyte-mediated constriction, facilitating dilation. These data reveal the role of metabolic substrates in regulating brain blood flow and provide a mechanism for differential astrocyte control over cerebrovascular diameter during different states of brain activation.},
	Author = {Gordon, Grant R J and Choi, Hyun B and Rungta, Ravi L and Ellis-Davies, Graham C R and MacVicar, Brian A},
	Date-Added = {2018-01-25 01:34:21 +0000},
	Date-Modified = {2018-01-25 01:34:21 +0000},
	Doi = {10.1038/nature07525},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Adenosine; Animals; Arterioles; Astrocytes; Brain; Dinoprostone; Glycolysis; Lactic Acid; Male; Organic Anion Transporters; Oxygen; Pressure; Prostaglandin-Endoperoxide Synthases; Rats; Rats, Sprague-Dawley; Vasoconstriction; Vasodilation; Vasodilator Agents},
	Month = {Dec},
	Number = {7223},
	Pages = {745-9},
	Pmc = {PMC4097022},
	Pmid = {18971930},
	Pst = {ppublish},
	Title = {Brain metabolism dictates the polarity of astrocyte control over arterioles},
	Volume = {456},
	Year = {2008},
	File = {papers/Gordon_Nature2008.pdf},
	Bdsk-File-2 = {papers/Gordon_Nature2008a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature07525}}

@article{Pouchelon:2012,
	Abstract = {The topographical mapping of input is a fundamental organizing principle of sensory pathways. In the somatosensory system, a precise topographical representation of the face is first generated in the brainstem and then faithfully replicated in the thalamus and cortex. Although our knowledge of the distinct polysynaptic pathways that link cutaneous mechanoreceptors of the face with neocortical neurons has recently expanded, the molecular mechanisms controlling their neuron-type-specific assembly during development remain poorly understood. The increasing availability of genetic tools that enable manipulation of these developing circuits with cellular resolution now opens new perspectives in our understanding of the molecular mechanisms through which input from the periphery is converted into patterned central pathways.},
	Annote = {somatosensory pathways only review. No information on visual system developmental innervation.

- E12.5 Trigeminal axons innervate whisker follicle
- E14.5 trigeminal collaterals reach PrV (principal nucleus of brainstem trigeminal complex)
- E15.5 PrV axons reach VP (ventral posterior medial nucleus of thalamus)
- E18 VP axons reach cortical subplate
- P0 PrV axons branch into VP
- P3 VP axons branch into L4 of S1 neocortex
},
	Author = {Pouchelon, Gabrielle and Frangeul, Laura and Rijli, Filippo M and Jabaudon, Denis},
	Date-Added = {2018-01-25 01:03:08 +0000},
	Date-Modified = {2018-01-25 01:18:14 +0000},
	Doi = {10.1111/j.1460-9568.2012.08059.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Mesh = {Afferent Pathways; Animals; Brain Mapping; Humans; Models, Neurological; Neurons; Somatosensory Cortex; Thalamus; Vibrissae},
	Month = {May},
	Number = {10},
	Pages = {1533-9},
	Pmid = {22606999},
	Pst = {ppublish},
	Title = {Patterning of pre-thalamic somatosensory pathways},
	Volume = {35},
	Year = {2012},
	File = {papers/Pouchelon_EurJNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1460-9568.2012.08059.x}}

@article{Jabaudon:2012,
	Abstract = {Neurons in layer IV of the rodent whisker somatosensory cortex are tangentially organized in periodic clusters called barrels, each of which is innervated by thalamocortical axons transmitting sensory information from a single principal whisker, together forming a somatotopic map of the whisker pad. Proper thalamocortical innervation is critical for barrel formation during development, but the molecular mechanisms controlling layer IV neuron clustering are unknown. Here, we investigate the role in this mapping of the nuclear orphan receptor RORβ, which is expressed in neurons in layer IV during corticogenesis. We find that RORβ protein expression specifically increases in the whisker barrel cortex during barrel formation and that in vivo overexpression of RORβ is sufficient to induce periodic barrel-like clustering of cortical neurons. Remarkably, this clustering can be induced as early as E18, prior to innervation by thalamocortical afferents and whisker derived-input. At later developmental stages, these ectopic neuronal clusters are specifically innervated by thalamocortical axons, demonstrated by anterograde labeling from the thalamus and by expression of thalamocortical-specific synaptic markers. Together, these data indicate that RORβ expression levels control cytoarchitectural patterning of neocortical neurons during development, a critical process for the topographical mapping of whisker input onto the cortical surface.},
	Author = {Jabaudon, Denis and Shnider, Sara J and Tischfield, David J and Galazo, Maria J and Macklis, Jeffrey D},
	Date-Added = {2018-01-25 00:22:07 +0000},
	Date-Modified = {2018-01-25 00:22:07 +0000},
	Doi = {10.1093/cercor/bhr182},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Body Patterning; Fluorescent Antibody Technique; Mice; Mice, Transgenic; Microscopy, Confocal; Neocortex; Neurogenesis; Neurons; Nuclear Receptor Subfamily 1, Group F, Member 2; Somatosensory Cortex; Vibrissae},
	Month = {May},
	Number = {5},
	Pages = {996-1006},
	Pmc = {PMC3328343},
	Pmid = {21799210},
	Pst = {ppublish},
	Title = {RORβ induces barrel-like neuronal clusters in the developing neocortex},
	Volume = {22},
	Year = {2012},
	File = {papers/Jabaudon_CerebCortex2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhr182}}

@article{Bressler:1996,
	Abstract = {The primary visual cortex (V1) is part of a highly interconnected network of cortical areas, hierarchically organized but operating concurrently across hierarchical levels. The high degree of reciprocal interconnection among visual cortical areas provides a framework for their interaction during the performance of visual scene analysis. The functional interdependency of visual cortical areas which develops during scene analysis can be investigated by techniques which measure interareal correlated activity. Evidence from monkeys performing a visual pattern discrimination suggests that synchronization of aperiodic activity from neuronal ensembles in cortical areas at different hierarchical levels is a relevant aspect of visual function. The near-periodic nature of the synchronized response to moving light bars in earlier studies may have been a result of the type of stimulus used. Various models of visual cortex are discussed in which interareal synchronization plays a functional role.},
	Author = {Bressler, S L},
	Date-Added = {2018-01-25 00:05:15 +0000},
	Date-Modified = {2018-01-25 00:07:08 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Keywords = {functional connectivity; oscillations; synchrony; Neocortex; isocortex; cerebral; areas},
	Mesh = {Animals; Cats; Feedback; Haplorhini; Humans; Models, Neurological; Neurophysiology; Time Factors; Visual Cortex; Visual Pathways},
	Month = {Apr},
	Number = {1-2},
	Pages = {37-49},
	Pmid = {8734042},
	Pst = {ppublish},
	Title = {Interareal synchronization in the visual cortex},
	Volume = {76},
	Year = {1996},
	File = {papers/Bressler_BehavBrainRes1996.pdf}}

@article{Rumberger:2001,
	Abstract = {We have qualitatively and quantitatively analysed the anatomical connections within and between rat primary visual cortex (V1) and the rim region surrounding area V1, using both ortho- and retrograde anatomical tracers (biotinylated dextran amine, biocytin, cholera toxin b subunit). From the analysis of the projection patterns, and with the assumption that single points in the rat visual cortex, as in other species, have projection fields made up of multiple patches of terminals, we have concluded that just two V1 recipient areas occupy the entire rim region: an anterolateral area, probably homologous with V2 in other mammals, previously named Oc2L, and a medial area, corresponding to Oc2M. A non-reciprocal projection from the anterolateral area to the medial area was identified. Small injections (300-600microm uptake zone diameter) of the anatomical tracers in area V1, or in the rim region, label orthograde intra-areal connections from each injection site to offset small patches. This is found in all regions of the rim and within at least the relatively expanded central dorsal field representation of V1. From the extent of these projections in V1 and the two rim regions, we have estimated that the neurons at the injection site send diverging laterally spreading projections to other neurons whose receptive fields share any part of the area included in the pooled receptive fields of the neurons at the injection site. Orthogradely labelled inter-areal feedforward projections from V1 to either rim region are estimated to diverge in their projections to neurons that share any part of the area of the pooled receptive fields of the V1 intra-areal connectional field of the same injection. The orthogradely labelled feedback projections to V1, from injection sites in either rim region, reach V1 neurons whose pooled receptive fields match those of the neurons in the rim injection site, i.e. with no divergence. Despite patchy anatomical connectional fields, our estimates indicate that visual space is represented continuously in the receptive fields of neurons postsynaptic to each intra- or inter-areal field of orthograde label. We suggest that, despite the absence of regularly mapped functions in rat V1 (e.g. regularly arranged orientation specificity), which in other species (e.g. primates and cats) relate to the patchy connectional patterns, the rat visual cortex intra- and inter-areal anatomical connections follow similar patterns and scaling factors to those in other species.},
	Author = {Rumberger, A and Tyler, C J and Lund, J S},
	Date-Added = {2018-01-25 00:04:07 +0000},
	Date-Modified = {2018-01-25 00:04:07 +0000},
	Journal = {Neuroscience},
	Journal-Full = {Neuroscience},
	Mesh = {Animals; Biotin; Brain Mapping; Corpus Callosum; Dextrans; Female; Fluorescent Dyes; Lysine; Neural Pathways; Neurons; Rats; Rats, Long-Evans; Visual Cortex; Visual Perception},
	Number = {1},
	Pages = {35-52},
	Pmid = {11226668},
	Pst = {ppublish},
	Title = {Intra- and inter-areal connections between the primary visual cortex V1 and the area immediately surrounding V1 in the rat},
	Volume = {102},
	Year = {2001},
	File = {papers/Rumberger_Neuroscience2001.pdf}}

@article{Yamashita:2013,
	Abstract = {Primary sensory cortex discriminates incoming sensory information and generates multiple processing streams toward other cortical areas. However, the underlying cellular mechanisms remain unknown. Here, by making whole-cell recordings in primary somatosensory barrel cortex (S1) of behaving mice, we show that S1 neurons projecting to primary motor cortex (M1) and those projecting to secondary somatosensory cortex (S2) have distinct intrinsic membrane properties and exhibit markedly different membrane potential dynamics during behavior. Passive tactile stimulation evoked faster and larger postsynaptic potentials (PSPs) in M1-projecting neurons, rapidly driving phasic action potential firing, well-suited for stimulus detection. Repetitive active touch evoked strongly depressing PSPs and only transient firing in M1-projecting neurons. In contrast, PSP summation allowed S2-projecting neurons to robustly signal sensory information accumulated during repetitive touch, useful for encoding object features. Thus, target-specific transformation of sensory-evoked synaptic potentials by S1 projection neurons generates functionally distinct output signals for sensorimotor coordination and sensory perception.},
	Author = {Yamashita, Takayuki and Pala, Aur{\'e}lie and Pedrido, Leticia and Kremer, Yves and Welker, Egbert and Petersen, Carl C H},
	Date-Added = {2018-01-25 00:02:40 +0000},
	Date-Modified = {2018-01-25 00:02:40 +0000},
	Doi = {10.1016/j.neuron.2013.10.059},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Afferent Pathways; Animals; Male; Mice; Motor Cortex; Neural Pathways; Neurons; Physical Stimulation; Somatosensory Cortex; Synaptic Potentials; Touch Perception},
	Month = {Dec},
	Number = {6},
	Pages = {1477-90},
	Pmid = {24360548},
	Pst = {ppublish},
	Title = {Membrane potential dynamics of neocortical projection neurons driving target-specific signals},
	Volume = {80},
	Year = {2013},
	File = {papers/Yamashita_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.10.059}}

@article{Petersen:2013,
	Abstract = {Computations in neocortical circuits are predominantly driven by synaptic integration of excitatory glutamatergic and inhibitory GABAergic inputs. New optical, electrophysiological, and genetic methods allow detailed in vivo investigation of the superficial neocortical layers 2 and 3 (L2/3). Here, we review current knowledge of mouse L2/3 sensory cortex, focusing on somatosensory barrel cortex with comparisons to visual and auditory cortex. Broadly tuned, dense subthreshold synaptic input accompanied by sparse action potential (AP) firing in excitatory neurons provides a simple and reliable neural code useful for associative learning. Sparse AP firing is enforced by strong inhibition from genetically defined classes of GABAergic neurons. Subnetworks of strongly and specifically connected excitatory neurons may drive L2/3 network function, with potential contributions from dendritic spikes evoked by spatiotemporally clustered synaptic input. These functional properties of L2/3 are under profound regulation by brain state and behavior, providing interesting avenues for future mechanistic investigations into context-specific processing of sensory information.},
	Author = {Petersen, Carl C H and Crochet, Sylvain},
	Date-Added = {2018-01-25 00:02:39 +0000},
	Date-Modified = {2018-01-25 00:02:39 +0000},
	Doi = {10.1016/j.neuron.2013.03.020},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Afferent Pathways; Animals; Mice; Neocortex; Nerve Net; Neurons; Sensation; Synaptic Transmission},
	Month = {Apr},
	Number = {1},
	Pages = {28-48},
	Pmid = {23583106},
	Pst = {ppublish},
	Title = {Synaptic computation and sensory processing in neocortical layer 2/3},
	Volume = {78},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.03.020}}

@article{Bavelier:2002,
	Abstract = {Animal studies have shown that sensory deprivation in one modality can have striking effects on the development of the remaining modalities. Although recent studies of deaf and blind humans have also provided convincing behavioural, electrophysiological and neuroimaging evidence of increased capabilities and altered organization of spared modalities, there is still much debate about the identity of the brain systems that are changed and the mechanisms that mediate these changes. Plastic changes across brain systems and related behaviours vary as a function of the timing and the nature of changes in experience. This specificity must be understood in the context of differences in the maturation rates and timing of the associated critical periods, differences in patterns of transiently existing connections, and differences in molecular factors across brain systems.},
	Author = {Bavelier, Daphne and Neville, Helen J},
	Date-Added = {2018-01-25 00:00:21 +0000},
	Date-Modified = {2018-01-25 00:00:21 +0000},
	Doi = {10.1038/nrn848},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Brain; Cell Differentiation; Humans; Neural Pathways; Neuronal Plasticity; Neurons; Sensation; Sensory Deprivation; Synapses},
	Month = {Jun},
	Number = {6},
	Pages = {443-52},
	Pmid = {12042879},
	Pst = {ppublish},
	Title = {Cross-modal plasticity: where and how?},
	Volume = {3},
	Year = {2002},
	File = {papers/Bavelier_NatRevNeurosci2002.pdf}}

@article{Tagge:2018,
	Abstract = {The mechanisms underpinning concussion, traumatic brain injury, and chronic traumatic encephalopathy, and the relationships between these disorders, are poorly understood. We examined post-mortem brains from teenage athletes in the acute-subacute period after mild closed-head impact injury and found astrocytosis, myelinated axonopathy, microvascular injury, perivascular neuroinflammation, and phosphorylated tau protein pathology. To investigate causal mechanisms, we developed a mouse model of lateral closed-head impact injury that uses momentum transfer to induce traumatic head acceleration. Unanaesthetized mice subjected to unilateral impact exhibited abrupt onset, transient course, and rapid resolution of a concussion-like syndrome characterized by altered arousal, contralateral hemiparesis, truncal ataxia, locomotor and balance impairments, and neurobehavioural deficits. Experimental impact injury was associated with axonopathy, blood-brain barrier disruption, astrocytosis, microgliosis (with activation of triggering receptor expressed on myeloid cells, TREM2), monocyte infiltration, and phosphorylated tauopathy in cerebral cortex ipsilateral and subjacent to impact. Phosphorylated tauopathy was detected in ipsilateral axons by 24 h, bilateral axons and soma by 2 weeks, and distant cortex bilaterally at 5.5 months post-injury. Impact pathologies co-localized with serum albumin extravasation in the brain that was diagnostically detectable in living mice by dynamic contrast-enhanced MRI. These pathologies were also accompanied by early, persistent, and bilateral impairment in axonal conduction velocity in the hippocampus and defective long-term potentiation of synaptic neurotransmission in the medial prefrontal cortex, brain regions distant from acute brain injury. Surprisingly, acute neurobehavioural deficits at the time of injury did not correlate with blood-brain barrier disruption, microgliosis, neuroinflammation, phosphorylated tauopathy, or electrophysiological dysfunction. Furthermore, concussion-like deficits were observed after impact injury, but not after blast exposure under experimental conditions matched for head kinematics. Computational modelling showed that impact injury generated focal point loading on the head and seven-fold greater peak shear stress in the brain compared to blast exposure. Moreover, intracerebral shear stress peaked before onset of gross head motion. By comparison, blast induced distributed force loading on the head and diffuse, lower magnitude shear stress in the brain. We conclude that force loading mechanics at the time of injury shape acute neurobehavioural responses, structural brain damage, and neuropathological sequelae triggered by neurotrauma. These results indicate that closed-head impact injuries, independent of concussive signs, can induce traumatic brain injury as well as early pathologies and functional sequelae associated with chronic traumatic encephalopathy. These results also shed light on the origins of concussion and relationship to traumatic brain injury and its aftermath.awx350media15713427811001.},
	Author = {Tagge, Chad A and Fisher, Andrew M and Minaeva, Olga V and Gaudreau-Balderrama, Amanda and Moncaster, Juliet A and Zhang, Xiao-Lei and Wojnarowicz, Mark W and Casey, Noel and Lu, Haiyan and Kokiko-Cochran, Olga N and Saman, Sudad and Ericsson, Maria and Onos, Kristen D and Veksler, Ronel and Senatorov, Jr, Vladimir V and Kondo, Asami and Zhou, Xiao Z and Miry, Omid and Vose, Linnea R and Gopaul, Katisha R and Upreti, Chirag and Nowinski, Christopher J and Cantu, Robert C and Alvarez, Victor E and Hildebrandt, Audrey M and Franz, Erich S and Konrad, Janusz and Hamilton, James A and Hua, Ning and Tripodis, Yorghos and Anderson, Andrew T and Howell, Gareth R and Kaufer, Daniela and Hall, Garth F and Lu, Kun P and Ransohoff, Richard M and Cleveland, Robin O and Kowall, Neil W and Stein, Thor D and Lamb, Bruce T and Huber, Bertrand R and Moss, William C and Friedman, Alon and Stanton, Patric K and McKee, Ann C and Goldstein, Lee E},
	Date-Added = {2018-01-24 23:58:35 +0000},
	Date-Modified = {2018-01-24 23:58:35 +0000},
	Doi = {10.1093/brain/awx350},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {TREM2; chronic traumatic encephalopathy; concussion; tau protein; traumatic brain injury},
	Month = {Jan},
	Pmid = {29360998},
	Pst = {aheadofprint},
	Title = {Concussion, microvascular injury, and early tauopathy in young athletes after impact head injury and an impact concussion mouse model},
	Year = {2018},
	File = {papers/Tagge_Brain2018.pdf}}

@article{Li:2002d,
	Abstract = {We examined whether Gbx2 is required after embryonic day 9 (E9) to repress Otx2 in the cerebellar anlage and position the midbrain/hindbrain organizer. In contrast to Gbx2 null mutants, mice lacking Gbx2 in rhombomere 1 (r1) after E9 (Gbx2-CKO) are viable and develop a cerebellum. A Gbx2-independent pathway can repress Otx2 in r1 after E9. Mid/hindbrain organizer gene expression, however, continues to be dependent on Gbx2. We found that Fgf8 expression normally correlates with the isthmus where cells undergo low proliferation and that in Gbx2-CKO mutants this domain is expanded. We propose that Fgf8 permits lateral cerebellar development through repression of Otx2 and also suppresses medial cerebellar growth in Gbx2-CKO embryos. Our work has uncovered distinct requirements for Gbx2 during cerebellum formation and provided a model for how a transcription factor can play multiple roles during development.},
	Author = {Li, James Y H and Lao, Zhimin and Joyner, Alexandra L},
	Date-Added = {2018-01-24 23:14:27 +0000},
	Date-Modified = {2018-01-24 23:14:27 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Body Patterning; Cell Differentiation; Cerebellum; Female; Fetus; Gene Expression Regulation, Developmental; Homeodomain Proteins; Mesencephalon; Mice; Mice, Knockout; Nerve Tissue Proteins; Otx Transcription Factors; Proto-Oncogene Proteins; Rhombencephalon; Trans-Activators; Wnt Proteins; Zebrafish Proteins},
	Month = {Sep},
	Number = {1},
	Pages = {31-43},
	Pmid = {12367504},
	Pst = {ppublish},
	Title = {Changing requirements for Gbx2 in development of the cerebellum and maintenance of the mid/hindbrain organizer},
	Volume = {36},
	Year = {2002},
	File = {papers/Li_Neuron2002.pdf}}

@article{Cuoco:2017,
	Abstract = {C57BL/6 mice exhibit spontaneous cerebellar malformations consisting of heterotopic neurons and glia in the molecular layer of the posterior vermis, indicative of neuronal migration defect during cerebellar development. Recognizing that many genetically engineered (GE) mouse lines are produced from C57BL/6 ES cells or backcrossed to this strain, we performed histological analyses and found that cerebellar heterotopia were a common feature present in the majority of GE lines on this background. Furthermore, we identify GE mouse lines that will be valuable in the study of cerebellar malformations including diverse driver, reporter, and optogenetic lines. Finally, we discuss the implications that these data have on the use of C57BL/6 mice and GE mice on this background in studies of cerebellar development or as models of disease.},
	Author = {Cuoco, Joshua A and Esposito, Anthony W and Moriarty, Shannon and Tang, Ying and Seth, Sonika and Toia, Alyssa R and Kampton, Elias B and Mayr, Yevgeniy and Khan, Mussarah and Khan, Mohammad B and Mullen, Brian R and Ackman, James B and Siddiqi, Faez and Wolfe, John H and Savinova, Olga V and Ramos, Raddy L},
	Date-Added = {2018-01-19 23:05:48 +0000},
	Date-Modified = {2018-01-19 23:05:48 +0000},
	Doi = {10.1007/s12311-017-0892-3},
	Journal = {Cerebellum},
	Journal-Full = {Cerebellum (London, England)},
	Keywords = {C57BL/6; Cerebellar development; Knock-out mice; Transgenic mice},
	Month = {Oct},
	Pmid = {29043563},
	Pst = {aheadofprint},
	Title = {Malformation of the Posterior Cerebellar Vermis Is a Common Neuroanatomical Phenotype of Genetically Engineered Mice on the C57BL/6 Background},
	Year = {2017},
	File = {papers/Cuoco_Cerebellum2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s12311-017-0892-3}}

@article{Murabe:1983,
	Abstract = {Immunohistochemical studies with the use of the peroxidase-antiperoxidase (PAP) method revealed that "amoeboid microglial cells", in the brains of neonatal rats and "brain macrophages" in lesioned brains of adult rats react positively to an antiserum raised against macrophages. In brains of neonatal rats, "amoeboid microglial cells" stained by means of the PAP-method were observed in the corpus callosum, internal capsule, dorso-lateral region of the thalamus, subventricular zone of the lateral ventricle, and the subependymal layer of the ventricular system. These cellular elements were not detected in brains of rats aged 21 days or older. Resting microglial cells displaying a typical ramified structure were not specifically stained. Cells reacting positively to the macrophage antiserum appeared (i) in the cerebral cortex of adult rats following placement of a stab wound, or (ii) in the hippocampal formation after kainic acid-induced lesions; in the damaged areas immunoreactive cells exhibited the typical features of "brain macrophages". "Brain macrophages" and "amoeboid microglial cells" are considered to belong to the class of exudate macrophages derived from blood monocytes. Thus, elements of hematogenous origin do exist in the intact brain parenchyma of neonatal rats and in lesioned brains of adult rats. The relationship between brain macrophages and resting microglial cells is discussed.},
	Author = {Murabe, Y and Sano, Y},
	Date-Added = {2018-01-18 00:40:34 +0000},
	Date-Modified = {2018-01-18 00:40:34 +0000},
	Journal = {Cell Tissue Res},
	Journal-Full = {Cell and tissue research},
	Mesh = {Animals; Animals, Newborn; Brain; Immunoenzyme Techniques; Macrophages; Neuroglia; Rats},
	Number = {1},
	Pages = {85-95},
	Pmid = {6339067},
	Pst = {ppublish},
	Title = {Morphological studies on neuroglia. VII. Distribution of "brain macrophages" in brains of neonatal and adult rats, as determined by means of immunohistochemistry},
	Volume = {229},
	Year = {1983}}

@article{Reep:1988,
	Abstract = {The cerebral isocortex is usually considered to be a 6-layered structure. Our anatomical findings suggest that layer VII be recognized as a distinct entity in rodent isocortex. This conclusion is based on cytoarchitectural, fiberarchitectural, connectional and developmental data.},
	Author = {Reep, R L and Goodwin, G S},
	Date-Added = {2018-01-18 00:39:05 +0000},
	Date-Modified = {2018-01-18 00:39:05 +0000},
	Journal = {Neurosci Lett},
	Journal-Full = {Neuroscience letters},
	Mesh = {Animals; Cerebral Cortex; Fluorescent Dyes; Leucine; Rats; Somatosensory Cortex; Stilbamidines; Visual Cortex},
	Month = {Jul},
	Number = {1-2},
	Pages = {15-20},
	Pmid = {3412636},
	Pst = {ppublish},
	Title = {Layer VII of rodent cerebral cortex},
	Volume = {90},
	Year = {1988},
	File = {papers/Reep_NeurosciLett1988.pdf}}

@article{Selverston:1998,
	Abstract = {The lobster stomatogastric ganglion contains 30 neurons and when modulated can produce two distinct rhythmic motor patterns--the gastric mill and the pyloric. The complete neural circuitry underlying both patterns is well known. Without modulatory input no patterns are produced, and the neurons fire tonically or are silent. When neuromodulators are released into the ganglion from specific neurons or are delivered as hormones, the properties of the neurons and synapses change dramatically and modulator-specific gastric mill and pyloric patterns are produced. In general the rhythmicity derives from the induced burstiness of the neurons, and the pattern from the strengths of the electrical and chemical synapses. The organized activity can be traced to a marked reduction of chaotic activity in individual neurons when they shift from the unmodulated to the modulated state.},
	Author = {Selverston, A and Elson, R and Rabinovich, M and Huerta, R and Abarbanel, H},
	Date-Added = {2018-01-17 00:03:58 +0000},
	Date-Modified = {2018-01-17 00:03:58 +0000},
	Journal = {Ann N Y Acad Sci},
	Journal-Full = {Annals of the New York Academy of Sciences},
	Mesh = {Animals; Ganglia, Invertebrate; Motor Neurons; Nephropidae; Nervous System Physiological Phenomena; Periodicity; Stomach},
	Month = {Nov},
	Pages = {35-50},
	Pmid = {9928300},
	Pst = {ppublish},
	Title = {Basic principles for generating motor output in the stomatogastric ganglion},
	Volume = {860},
	Year = {1998},
	File = {papers/Selverston_AnnNYAcadSci1998.pdf}}

@article{Bliss:1973a,
	Abstract = {1. Potential changes evoked by stimulation of the perforant path have been recorded in the dentate area of the hippocampal formation in chronically prepared unanaesthetized rabbits.2. Components attributed to excitatory synaptic current flow and to action potentials in the granule cell population were distinguishable, with characteristics largely the same as in anaesthetized rabbits.3. Stimulation at 15/sec for several seconds usually led to the granule cells being more effectively activated by the individual stimuli of the train (;frequency potentiation'). Single stimuli then commonly produced multiple discharges in the granule cell population.4. After single periods of stimulation at 15/sec for 15-20 sec there was on 26% of the occasions (41% of those on which there was good frequency potentiation) a long-lasting potentiation of the responses to subsequent stimuli, lasting from 1 hr to 3 days.5. After a further 20% of the periods of repetitive stimulation there was a shorter lasting potentiation, and after 8% there was a short lasting depression.6. The potentiation, when present, was characterized by some or all of the following changes: increases in the amplitudes of the synaptic wave and population spike, reduction in the latency of the population spike, and reductions in the variability of the characteristics of the population spike.7. During the long-lasting potentiation there was an increase in the excitability of the post-synaptic cells and, on some but not all occasions, an increase in the extracellular current flow produced directly by synaptic action.},
	Author = {Bliss, T V and Gardner-Medwin, A R},
	Date-Added = {2018-01-17 00:01:47 +0000},
	Date-Modified = {2018-01-17 00:01:47 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Action Potentials; Animals; Electric Stimulation; Electrodes, Implanted; Electrophysiology; Evoked Potentials; Hippocampus; Microelectrodes; Neurons; Online Systems; Rabbits; Synapses; Time Factors},
	Month = {Jul},
	Number = {2},
	Pages = {357-74},
	Pmc = {PMC1350459},
	Pmid = {4727085},
	Pst = {ppublish},
	Title = {Long-lasting potentiation of synaptic transmission in the dentate area of the unanaestetized rabbit following stimulation of the perforant path},
	Volume = {232},
	Year = {1973}}

@article{Bliss:1973,
	Abstract = {1. The after-effects of repetitive stimulation of the perforant path fibres to the dentate area of the hippocampal formation have been examined with extracellular micro-electrodes in rabbits anaesthetized with urethane.2. In fifteen out of eighteen rabbits the population response recorded from granule cells in the dentate area to single perforant path volleys was potentiated for periods ranging from 30 min to 10 hr after one or more conditioning trains at 10-20/sec for 10-15 sec, or 100/sec for 3-4 sec.3. The population response was analysed in terms of three parameters: the amplitude of the population excitatory post-synaptic potential (e.p.s.p.), signalling the depolarization of the granule cells, and the amplitude and latency of the population spike, signalling the discharge of the granule cells.4. All three parameters were potentiated in 29% of the experiments; in other experiments in which long term changes occurred, potentiation was confined to one or two of the three parameters. A reduction in the latency of the population spike was the commonest sign of potentiation, occurring in 57% of all experiments. The amplitude of the population e.p.s.p. was increased in 43%, and of the population spike in 40%, of all experiments.5. During conditioning at 10-20/sec there was massive potentiation of the population spike (;frequency potentiation'). The spike was suppressed during stimulation at 100/sec. Both frequencies produced long-term potentiation.6. The results suggest that two independent mechanisms are responsible for long-lasting potentiation: (a) an increase in the efficiency of synaptic transmission at the perforant path synapses; (b) an increase in the excitability of the granule cell population.},
	Author = {Bliss, T V and Lomo, T},
	Date-Added = {2018-01-17 00:01:45 +0000},
	Date-Modified = {2018-01-17 00:01:45 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Action Potentials; Anesthesia, Intravenous; Animals; Electric Stimulation; Electrophysiology; Evoked Potentials; Female; Hippocampus; Male; Microelectrodes; Neurons; Rabbits; Synapses; Time Factors},
	Month = {Jul},
	Number = {2},
	Pages = {331-56},
	Pmc = {PMC1350458},
	Pmid = {4727084},
	Pst = {ppublish},
	Title = {Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path},
	Volume = {232},
	Year = {1973},
	File = {papers/Bliss_JPhysiol1973.pdf}}

@article{Brown:1914,
	Author = {Brown, T G},
	Date-Added = {2018-01-16 23:59:23 +0000},
	Date-Modified = {2018-01-16 23:59:23 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Month = {Mar},
	Number = {1},
	Pages = {18-46},
	Pmc = {PMC1420503},
	Pmid = {16993247},
	Pst = {ppublish},
	Title = {On the nature of the fundamental activity of the nervous centres; together with an analysis of the conditioning of rhythmic activity in progression, and a theory of the evolution of function in the nervous system},
	Volume = {48},
	Year = {1914},
	File = {papers/Brown_JPhysiol1914.pdf}}

@article{Sherrington:1913,
	Abstract = {IN a previous paper' an attempt was made to determine factors at work in the reflex act of stepping, that is to say in the stepping performed by a purely reflex preparation, either decerebrate or purely spinal. The present experiments are in contribution toward the same problem.
Method. In the present experiments the mode of evoking the rhythmic reflex has been that recently found by T. Graham Browns, A. Forbes3, and myself4; and the reflex preparation employed has consisted of an isolated pair of symmetrical extensor muscles5, i.e. the main extensor muscle of each knee, right and left, in the decerebrate mammal (cat).},
	Author = {Sherrington, C S},
	Date-Added = {2018-01-16 23:56:57 +0000},
	Date-Modified = {2018-01-16 23:57:30 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Month = {Nov},
	Number = {3},
	Pages = {196-214},
	Pmc = {PMC1420464},
	Pmid = {16993214},
	Pst = {ppublish},
	Title = {Further observations on the production of reflex stepping by combination of reflex excitation with reflex inhibition},
	Volume = {47},
	Year = {1913},
	File = {papers/Sherrington_JPhysiol1913.pdf}}

@article{Drew:2008,
	Abstract = {Spontaneous ultra-slow oscillations in brain signals are ubiquitous, although their source and function remain unknown. A new study now reports that this activity is correlated between functionally related areas across hemispheres in humans.},
	Author = {Drew, Patrick J and Duyn, Jeff H and Golanov, Eugene and Kleinfeld, David},
	Date-Added = {2018-01-16 23:49:59 +0000},
	Date-Modified = {2018-01-16 23:50:39 +0000},
	Doi = {10.1038/nn0908-991},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {teaching; facts; oscillations; synchrony; EEG; LFP; neurophysiology},
	Mesh = {Biological Clocks; Brain; Electroencephalography; Functional Laterality; Humans; Magnetic Resonance Imaging; Models, Neurological},
	Month = {Sep},
	Number = {9},
	Pages = {991-3},
	Pmid = {18725901},
	Pst = {ppublish},
	Title = {Finding coherence in spontaneous oscillations},
	Volume = {11},
	Year = {2008},
	File = {papers/Drew_NatNeurosci2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn0908-991}}

@article{Ramsden:2015,
	Abstract = {Neural circuits in the medial entorhinal cortex (MEC) encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.},
	Author = {Ramsden, Helen L and S{\"u}rmeli, G{\"u}l{\c s}en and McDonagh, Steven G and Nolan, Matthew F},
	Date-Added = {2018-01-16 23:48:30 +0000},
	Date-Modified = {2018-01-16 23:48:57 +0000},
	Doi = {10.1371/journal.pcbi.1004032},
	Journal = {PLoS Comput Biol},
	Journal-Full = {PLoS computational biology},
	Keywords = {method; technique; connectivity; computational biology},
	Mesh = {Animals; Entorhinal Cortex; Gene Expression Profiling; Image Processing, Computer-Assisted; Male; Mice; Mice, Inbred C57BL; Molecular Imaging; Organ Specificity},
	Month = {Jan},
	Number = {1},
	Pages = {e1004032},
	Pmc = {PMC4304787},
	Pmid = {25615592},
	Pst = {epublish},
	Title = {Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression},
	Volume = {11},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1004032}}

@article{Richardet:2015,
	Abstract = {MOTIVATION: In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles. One challenge for modern neuroinformatics is finding methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and the integration of such data into computational models. A key example of this is metascale brain connectivity, where results are not reported in a normalized repository. Instead, these experimental results are published in natural language, scattered among individual scientific publications. This lack of normalization and centralization hinders the large-scale integration of brain connectivity results. In this article, we present text-mining models to extract and aggregate brain connectivity results from 13.2 million PubMed abstracts and 630 216 full-text publications related to neuroscience. The brain regions are identified with three different named entity recognizers (NERs) and then normalized against two atlases: the Allen Brain Atlas (ABA) and the atlas from the Brain Architecture Management System (BAMS). We then use three different extractors to assess inter-region connectivity.
RESULTS: NERs and connectivity extractors are evaluated against a manually annotated corpus. The complete in litero extraction models are also evaluated against in vivo connectivity data from ABA with an estimated precision of 78%. The resulting database contains over 4 million brain region mentions and over 100 000 (ABA) and 122 000 (BAMS) potential brain region connections. This database drastically accelerates connectivity literature review, by providing a centralized repository of connectivity data to neuroscientists.},
	Author = {Richardet, Renaud and Chappelier, Jean-C{\'e}dric and Telefont, Martin and Hill, Sean},
	Date-Added = {2018-01-16 23:48:28 +0000},
	Date-Modified = {2018-01-16 23:48:57 +0000},
	Doi = {10.1093/bioinformatics/btv025},
	Journal = {Bioinformatics},
	Journal-Full = {Bioinformatics (Oxford, England)},
	Keywords = {method; technique; connectivity; computational biology},
	Mesh = {Animals; Artificial Intelligence; Atlases as Topic; Brain; Brain Mapping; Data Mining; Databases, Factual; Mice; Neuroanatomy; Periodicals as Topic; Software; Terminology as Topic},
	Month = {May},
	Number = {10},
	Pages = {1640-7},
	Pmc = {PMC4426844},
	Pmid = {25609795},
	Pst = {ppublish},
	Title = {Large-scale extraction of brain connectivity from the neuroscientific literature},
	Volume = {31},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btv025}}

@article{Kuan:2015,
	Abstract = {The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.},
	Author = {Kuan, Leonard and Li, Yang and Lau, Chris and Feng, David and Bernard, Amy and Sunkin, Susan M and Zeng, Hongkui and Dang, Chinh and Hawrylycz, Michael and Ng, Lydia},
	Date-Added = {2018-01-16 23:48:26 +0000},
	Date-Modified = {2018-01-16 23:48:57 +0000},
	Doi = {10.1016/j.ymeth.2014.12.013},
	Journal = {Methods},
	Journal-Full = {Methods (San Diego, Calif.)},
	Keywords = {Digital atlas; Image registration; Mouse connectivity atlas; Neuronal projection; Signal detection; method; technique; connectivity; computational biology},
	Mesh = {Animals; Atlases as Topic; Brain; Brain Mapping; Humans; Informatics; Mice; Mice, Inbred C57BL},
	Month = {Feb},
	Pages = {4-17},
	Pmid = {25536338},
	Pst = {ppublish},
	Title = {Neuroinformatics of the Allen Mouse Brain Connectivity Atlas},
	Volume = {73},
	Year = {2015},
	File = {papers/Kuan_Methods2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.ymeth.2014.12.013}}

@article{Ermentrout:2001,
	Abstract = {The theory of coupled phase oscillators provides a framework to understand the emergent properties of networks of neuronal oscillators. When the architecture of the network is dominated by short-range connections, the pattern of electrical output is predicted to correspond to traveling plane and rotating waves, in addition to synchronized output. We argue that this theory provides the foundation for understanding the traveling electrical waves that are observed across olfactory, visual, and visuomotor areas of cortex in a variety of species. The waves are typically present during periods outside of stimulation, while synchronous activity typically dominates in the presence of a strong stimulus. We suggest that the continuum of phase shifts during epochs with traveling waves provides a means to scan the incoming sensory stream for novel features. Experiments to test our theoretical approach are presented.},
	Author = {Ermentrout, G B and Kleinfeld, D},
	Date-Added = {2018-01-16 23:44:29 +0000},
	Date-Modified = {2018-01-16 23:44:29 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Biological Clocks; Cerebral Cortex; Humans; Models, Neurological; Nerve Net; Neural Networks (Computer); Synaptic Transmission},
	Month = {Jan},
	Number = {1},
	Pages = {33-44},
	Pmid = {11182079},
	Pst = {ppublish},
	Title = {Traveling electrical waves in cortex: insights from phase dynamics and speculation on a computational role},
	Volume = {29},
	Year = {2001},
	File = {papers/Ermentrout_Neuron2001.pdf}}

@article{Smith:2010a,
	Abstract = {BACKGROUND: Shortly after eye opening, initially disorganized visual cortex circuitry is rapidly refined to form smooth retinotopic maps. This process asymptotes long before adulthood, but it is unknown whether further refinement is possible. Prior work from our lab has shown that the retinotopic map of the non-dominant ipsilateral eye develops faster when the dominant contralateral eye is removed. We examined whether input from the contralateral eye might also limit the ultimate refinement of the ipsilateral eye retinotopic map in adults. In addition, we examined whether the increased refinement involved the recruitment of adjacent cortical area.
METHODOLOGY/PRINCIPAL FINDINGS: By surgically implanting a chronic optical window over visual cortex in mice, we repeatedly measured the degree of retinotopic map refinement using quantitative intrinsic signal optical imaging over four weeks. We removed the contralateral eye and observed that the retinotopic map for the ipsilateral eye was further refined and the maximum magnitude of response increased. However, these changes were not accompanied by an increase in the area of responsive cortex.
CONCLUSIONS/SIGNIFICANCE: Since the retinotopic map was functionally refined to a greater degree without taking over adjacent cortical area, we conclude that input from the contralateral eye limits the normal refinement of visual cortical circuitry in mice. These findings suggest that the refinement capacity of cortical circuitry is normally saturated.},
	Author = {Smith, Spencer L and Trachtenberg, Joshua T},
	Date-Added = {2018-01-16 23:41:35 +0000},
	Date-Modified = {2018-01-16 23:41:35 +0000},
	Doi = {10.1371/journal.pone.0009925},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Animals; Eye; Functional Laterality; Mice; Mice, Inbred C57BL; Neuronal Plasticity; Photic Stimulation; Retina; Sensory Deprivation; Vision, Ocular; Visual Cortex; Visual Pathways},
	Month = {Mar},
	Number = {3},
	Pages = {e9925},
	Pmc = {PMC2848025},
	Pmid = {20369001},
	Pst = {epublish},
	Title = {The refinement of ipsilateral eye retinotopic maps is increased by removing the dominant contralateral eye in adult mice},
	Volume = {5},
	Year = {2010},
	File = {papers/Smith_PLoSOne2010.pdf}}

@article{Faguet:2009,
	Abstract = {In the cerebral cortex, neuronal circuits are first laid down by intrinsic mechanisms and then refined by experience. In the canonical model, this refinement is driven by activity-dependent competition between inputs for some limited cortical resource. Here we examine this idea in the mouse visual cortex at the peak of the critical period for experience-dependent plasticity. By imaging intrinsic optical responses, we mapped the strength and size of each eye's cortical representation in normal mice, mice that had been deprived of patterned vision uni- or bilaterally, and in mice in which the contralateral eye had been removed. We find that for both eyes, a period of visual deprivation results in a loss of cortical responsiveness to stimulation through the deprived eye. In addition, the ipsilateral eye pathway is affected by the quality of vision through the opposite eye. Our findings indicate that although both contra- and ipsilateral eye pathways require visual experience for their maintenance, ipsilateral eye projections bear an additional, unique sensitivity to binocular interactions.},
	Author = {Faguet, Joshua and Maranhao, Bruno and Smith, Spencer L and Trachtenberg, Joshua T},
	Date-Added = {2018-01-16 23:40:47 +0000},
	Date-Modified = {2018-01-16 23:40:47 +0000},
	Doi = {10.1152/jn.90893.2008},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Mesh = {Animals; Brain Mapping; Cholera Toxin; Diagnostic Imaging; Eye; Fourier Analysis; Functional Laterality; Mice; Mice, Inbred C57BL; Neuronal Plasticity; Orientation; Photic Stimulation; Sensory Deprivation; Sensory Thresholds; Space Perception; Time Factors; Visual Cortex; Visual Pathways},
	Month = {Feb},
	Number = {2},
	Pages = {855-61},
	Pmc = {PMC2657065},
	Pmid = {19052109},
	Pst = {ppublish},
	Title = {Ipsilateral eye cortical maps are uniquely sensitive to binocular plasticity},
	Volume = {101},
	Year = {2009},
	File = {papers/Faguet_JNeurophysiol2009.pdf}}

@article{Kramer:2013,
	Abstract = {The optical neuroscience revolution is transforming how we study neural circuits. By providing a precise way to manipulate endogenous neuronal signaling proteins, it also has the potential to transform our understanding of molecular neuroscience. Recent advances in chemical biology have produced light-sensitive compounds that photoregulate a wide variety of proteins underlying signaling between and within neurons. Chemical tools for optopharmacology include caged agonists and antagonists and reversibly photoswitchable ligands. These reagents act on voltage-gated ion channels and neurotransmitter receptors, enabling control of neuronal signaling with a high degree of spatial and temporal precision. By covalently attaching photoswitch molecules to genetically tagged proteins, the newly emerging methodology of optogenetic pharmacology allows biochemically precise control in targeted subsets of neurons. Now that the tools for manipulating endogenous neuronal signaling proteins are available, they can be implemented in vivo to enhance our understanding of the molecular bases of brain function and dysfunctions.},
	Author = {Kramer, Richard H and Mourot, Alexandre and Adesnik, Hillel},
	Date-Added = {2018-01-16 23:37:48 +0000},
	Date-Modified = {2018-01-16 23:38:11 +0000},
	Doi = {10.1038/nn.3424},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {technique; method; optogenetics; activity manipulation},
	Mesh = {Animals; Humans; Ion Channels; Ligands; Neurons; Optogenetics; Photic Stimulation; Receptors, Neurotransmitter; Signal Transduction},
	Month = {Jul},
	Number = {7},
	Pages = {816-23},
	Pmc = {PMC4963006},
	Pmid = {23799474},
	Pst = {ppublish},
	Title = {Optogenetic pharmacology for control of native neuronal signaling proteins},
	Volume = {16},
	Year = {2013},
	File = {papers/Kramer_NatNeurosci2013.pdf}}

@article{Czajkowski:2014,
	Abstract = {The retrosplenial cortex (RSC) is part of a network of interconnected cortical, hippocampal, and thalamic structures harboring spatially modulated neurons. The RSC contains head direction cells and connects to the parahippocampal region and anterior thalamus. Manipulations of the RSC can affect spatial and contextual tasks. A considerable amount of evidence implicates the role of the RSC in spatial navigation, but it is unclear whether this structure actually encodes or stores spatial information. We used a transgenic mouse in which the expression of green fluorescent protein was under the control of the immediate early gene c-fos promoter as well as time-lapse two-photon in vivo imaging to monitor neuronal activation triggered by spatial learning in the Morris water maze. We uncovered a repetitive pattern of cell activation in the RSC consistent with the hypothesis that during spatial learning an experience-dependent memory trace is formed in this structure. In support of this hypothesis, we also report three other observations. First, temporary RSC inactivation disrupts performance in a spatial learning task. Second, we show that overexpressing the transcription factor CREB in the RSC with a viral vector, a manipulation known to enhance memory consolidation in other circuits, results in spatial memory enhancements. Third, silencing the viral CREB-expressing neurons with the allatostatin system occludes the spatial memory enhancement. Taken together, these results indicate that the retrosplenial cortex engages in the formation and storage of memory traces for spatial information.},
	Author = {Czajkowski, Rafa{\l} and Jayaprakash, Balaji and Wiltgen, Brian and Rogerson, Thomas and Guzman-Karlsson, Mikael C and Barth, Alison L and Trachtenberg, Joshua T and Silva, Alcino J},
	Date-Added = {2018-01-16 23:37:16 +0000},
	Date-Modified = {2018-01-16 23:37:16 +0000},
	Doi = {10.1073/pnas.1313222111},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Cyclic AMP Response Element-Binding Protein; Green Fluorescent Proteins; Gyrus Cinguli; Hippocampus; Maze Learning; Memory; Mice; Mice, 129 Strain; Mice, Inbred C57BL; Mice, Transgenic; Microscopy, Confocal; Microscopy, Fluorescence, Multiphoton; Neurons; Promoter Regions, Genetic; Proto-Oncogene Proteins c-fos; Space Perception},
	Month = {Jun},
	Number = {23},
	Pages = {8661-6},
	Pmc = {PMC4060653},
	Pmid = {24912150},
	Pst = {ppublish},
	Title = {Encoding and storage of spatial information in the retrosplenial cortex},
	Volume = {111},
	Year = {2014},
	File = {papers/Czajkowski_ProcNatlAcadSciUSA2014.pdf}}

@article{Quirin:2014,
	Abstract = {We introduce a scanless optical method to image neuronal activity in three dimensions simultaneously. Using a spatial light modulator and a custom-designed phase mask, we illuminate and collect light simultaneously from different focal planes and perform calcium imaging of neuronal activity in vitro and in vivo. This method, combining structured illumination with volume projection imaging, could be used as a technological platform for brain activity mapping.},
	Author = {Quirin, Sean and Jackson, Jesse and Peterka, Darcy S and Yuste, Rafael},
	Date-Added = {2018-01-16 23:36:18 +0000},
	Date-Modified = {2018-01-16 23:36:30 +0000},
	Doi = {10.3389/fncir.2014.00029},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {brain activity map; calcium imaging; spatial-light-modulator; three-dimensional imaging; volume imaging; technique; method},
	Mesh = {Animals; Hippocampus; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Mice; Mice, Inbred C57BL; Neurons; Zebrafish},
	Pages = {29},
	Pmc = {PMC3982072},
	Pmid = {24772066},
	Pst = {epublish},
	Title = {Simultaneous imaging of neural activity in three dimensions},
	Volume = {8},
	Year = {2014},
	File = {papers/Quirin_FrontNeuralCircuits2014.pdf}}

@article{Freeman:2014,
	Abstract = {Understanding brain function requires monitoring and interpreting the activity of large networks of neurons during behavior. Advances in recording technology are greatly increasing the size and complexity of neural data. Analyzing such data will pose a fundamental bottleneck for neuroscience. We present a library of analytical tools called Thunder built on the open-source Apache Spark platform for large-scale distributed computing. The library implements a variety of univariate and multivariate analyses with a modular, extendable structure well-suited to interactive exploration and analysis development. We demonstrate how these analyses find structure in large-scale neural data, including whole-brain light-sheet imaging data from fictively behaving larval zebrafish, and two-photon imaging data from behaving mouse. The analyses relate neuronal responses to sensory input and behavior, run in minutes or less and can be used on a private cluster or in the cloud. Our open-source framework thus holds promise for turning brain activity mapping efforts into biological insights.},
	Author = {Freeman, Jeremy and Vladimirov, Nikita and Kawashima, Takashi and Mu, Yu and Sofroniew, Nicholas J and Bennett, Davis V and Rosen, Joshua and Yang, Chao-Tsung and Looger, Loren L and Ahrens, Misha B},
	Date-Added = {2018-01-16 23:33:51 +0000},
	Date-Modified = {2018-01-16 23:34:15 +0000},
	Doi = {10.1038/nmeth.3041},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Keywords = {technique; method; Computational Biology},
	Mesh = {Action Potentials; Animals; Brain; Brain Mapping; Computer Simulation; Computing Methodologies; Data Interpretation, Statistical; Database Management Systems; Databases, Factual; Humans; Information Storage and Retrieval; Models, Neurological; Nerve Net; Neurons; Programming Languages; Software},
	Month = {Sep},
	Number = {9},
	Pages = {941-50},
	Pmid = {25068736},
	Pst = {ppublish},
	Title = {Mapping brain activity at scale with cluster computing},
	Volume = {11},
	Year = {2014},
	File = {papers/Freeman_NatMethods2014.pdf}}

@article{Mez:2017,
	Abstract = {Importance: Players of American football may be at increased risk of long-term neurological conditions, particularly chronic traumatic encephalopathy (CTE).
Objective: To determine the neuropathological and clinical features of deceased football players with CTE.
Design, Setting, and Participants: Case series of 202 football players whose brains were donated for research. Neuropathological evaluations and retrospective telephone clinical assessments (including head trauma history) with informants were performed blinded. Online questionnaires ascertained athletic and military history.
Exposures: Participation in American football at any level of play.
Main Outcomes and Measures: Neuropathological diagnoses of neurodegenerative diseases, including CTE, based on defined diagnostic criteria; CTE neuropathological severity (stages I to IV or dichotomized into mild [stages I and II] and severe [stages III and IV]); informant-reported athletic history and, for players who died in 2014 or later, clinical presentation, including behavior, mood, and cognitive symptoms and dementia.
Results: Among 202 deceased former football players (median age at death, 66 years [interquartile range, 47-76 years]), CTE was neuropathologically diagnosed in 177 players (87%; median age at death, 67 years [interquartile range, 52-77 years]; mean years of football participation, 15.1 [SD, 5.2]), including 0 of 2 pre-high school, 3 of 14 high school (21%), 48 of 53 college (91%), 9 of 14 semiprofessional (64%), 7 of 8 Canadian Football League (88%), and 110 of 111 National Football League (99%) players. Neuropathological severity of CTE was distributed across the highest level of play, with all 3 former high school players having mild pathology and the majority of former college (27 [56%]), semiprofessional (5 [56%]), and professional (101 [86%]) players having severe pathology. Among 27 participants with mild CTE pathology, 26 (96%) had behavioral or mood symptoms or both, 23 (85%) had cognitive symptoms, and 9 (33%) had signs of dementia. Among 84 participants with severe CTE pathology, 75 (89%) had behavioral or mood symptoms or both, 80 (95%) had cognitive symptoms, and 71 (85%) had signs of dementia.
Conclusions and Relevance: In a convenience sample of deceased football players who donated their brains for research, a high proportion had neuropathological evidence of CTE, suggesting that CTE may be related to prior participation in football.},
	Author = {Mez, Jesse and Daneshvar, Daniel H and Kiernan, Patrick T and Abdolmohammadi, Bobak and Alvarez, Victor E and Huber, Bertrand R and Alosco, Michael L and Solomon, Todd M and Nowinski, Christopher J and McHale, Lisa and Cormier, Kerry A and Kubilus, Caroline A and Martin, Brett M and Murphy, Lauren and Baugh, Christine M and Montenigro, Phillip H and Chaisson, Christine E and Tripodis, Yorghos and Kowall, Neil W and Weuve, Jennifer and McClean, Michael D and Cantu, Robert C and Goldstein, Lee E and Katz, Douglas I and Stern, Robert A and Stein, Thor D and McKee, Ann C},
	Date-Added = {2018-01-16 23:13:03 +0000},
	Date-Modified = {2018-01-16 23:13:03 +0000},
	Doi = {10.1001/jama.2017.8334},
	Journal = {JAMA},
	Journal-Full = {JAMA},
	Mesh = {Adult; Aged; Athletes; Athletic Injuries; Brain; Brain Concussion; Cause of Death; Chronic Traumatic Encephalopathy; Cognition Disorders; Football; Humans; Male; Mental Disorders; Middle Aged; Severity of Illness Index; Substance-Related Disorders; United States; tau Proteins},
	Month = {07},
	Number = {4},
	Pages = {360-370},
	Pmid = {28742910},
	Pst = {ppublish},
	Title = {Clinicopathological Evaluation of Chronic Traumatic Encephalopathy in Players of American Football},
	Volume = {318},
	Year = {2017},
	File = {papers/Mez_JAMA2017.pdf}}

@article{McKee:2014,
	Abstract = {The benefits of regular exercise, physical fitness and sports participation on cardiovascular and brain health are undeniable. Physical activity reduces the risk for cardiovascular disease, type 2 diabetes, hypertension, obesity, and stroke, and produces beneficial effects on cholesterol levels, antioxidant systems, inflammation, and vascular function. Exercise also enhances psychological health, reduces age-related loss of brain volume, improves cognition, reduces the risk of developing dementia, and impedes neurodegeneration. Nonetheless, the play of sports is associated with risks, including a risk for mild TBI (mTBI) and, rarely, catastrophic traumatic injury and death. There is also growing awareness that repetitive mTBIs, such as concussion and subconcussion, can occasionally produce persistent cognitive, behavioral, and psychiatric problems as well as lead to the development of a neurodegeneration, chronic traumatic encephalopathy (CTE). In this review, we summarize the beneficial aspects of sports participation on psychological, emotional, physical and cognitive health, and specifically analyze some of the less common adverse neuropathological outcomes, including concussion, second-impact syndrome, juvenile head trauma syndrome, catastrophic sudden death, and CTE. CTE is a latent neurodegeneration clinically associated with behavioral changes, executive dysfunction and cognitive impairments, and pathologically characterized by frontal and temporal lobe atrophy, neuronal and axonal loss, and abnormal deposits of paired helical filament (PHF)-tau and 43 kDa TAR deoxyribonucleic acid (DNA)-binding protein (TDP-43). CTE often occurs as a sole diagnosis, but may be associated with other neurodegenerative disorders, including motor neuron disease (CTE-MND). Although the incidence and prevalence of CTE are not known, CTE has been reported most frequently in American football players and boxers. Other sports associated with CTE include ice hockey, professional wrestling, soccer, rugby, and baseball.},
	Author = {McKee, Ann C and Daneshvar, Daniel H and Alvarez, Victor E and Stein, Thor D},
	Date-Added = {2018-01-16 23:12:43 +0000},
	Date-Modified = {2018-01-16 23:12:43 +0000},
	Doi = {10.1007/s00401-013-1230-6},
	Journal = {Acta Neuropathol},
	Journal-Full = {Acta neuropathologica},
	Mesh = {Animals; Athletic Injuries; Brain; Brain Injuries; Cognition; Humans; Sports},
	Month = {Jan},
	Number = {1},
	Pages = {29-51},
	Pmc = {PMC4255282},
	Pmid = {24366527},
	Pst = {ppublish},
	Title = {The neuropathology of sport},
	Volume = {127},
	Year = {2014},
	File = {papers/McKee_ActaNeuropathol2014.pdf}}

@article{Viswanathan:2012,
	Abstract = {Subplate neurons (SPNs) are a population of neurons in the mammalian cerebral cortex that exist predominantly in the prenatal and early postnatal period. Loss of SPNs prevents the functional maturation of the cerebral cortex. SPNs receive subcortical input from the thalamus and relay this information to the developing cortical plate and thereby can influence cortical activity in a feedforward manner. Little is known about potential feedback projections from the cortical plate to SPNs. Thus, we investigated the spatial distribution of intracortical synaptic inputs to SPNs in vitro in mouse auditory cortex by photostimulation. We find that SPNs fell into two broad classes based on their distinct spatial patterns of synaptic inputs. The first class of SPNs receives inputs from only deep cortical layers, while the second class of SPNs receives inputs from deep as well as superficial layers including layer 4. We find that superficial cortical inputs to SPNs emerge in the second postnatal week and that SPNs that receive superficial cortical input are located more superficially than those that do not. Our data thus suggest that distinct circuits are present in the subplate and that, while SPNs participate in an early feedforward circuit, they are also involved in a feedback circuit at older ages. Together, our results show that SPNs are tightly integrated into the developing thalamocortical and intracortical circuit. The feedback projections from the cortical plate might enable SPNs to amplify thalamic inputs to SPNs.},
	Author = {Viswanathan, Sarada and Bandyopadhyay, Sharba and Kao, Joseph P Y and Kanold, Patrick O},
	Date-Added = {2018-01-16 23:08:52 +0000},
	Date-Modified = {2018-01-16 23:08:52 +0000},
	Doi = {10.1523/JNEUROSCI.4748-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Cerebral Cortex; Female; Male; Mice; Mice, Inbred C57BL; Nerve Net; Neural Pathways; Photic Stimulation; Thalamus},
	Month = {Feb},
	Number = {5},
	Pages = {1589-601},
	Pmc = {PMC3517995},
	Pmid = {22302801},
	Pst = {ppublish},
	Title = {Changing microcircuits in the subplate of the developing cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Viswanathan_JNeurosci2012.pdf}}

@article{Petit:2014,
	Abstract = {OBJECTIVE: Subcortical band heterotopia (SBH) is a cortical malformation formed when neocortical neurons prematurely stop their migration in the white matter, forming a heterotopic band below the normotopic cortex, and is generally associated with intractable epilepsy. Although it is clear that the band heterotopia and the overlying cortex both contribute to creating an abnormal circuit prone to generate epileptic discharges, it is less understood which part of this circuitry is the most critical. Here, we sought to identify the origin of epileptiform activity in a targeted genetic model of SBH in rats.
METHODS: Rats with SBH (Dcx-KD rats) were generated by knocking down the Dcx gene using shRNA vectors transfected into neocortical progenitors of rat embryos. Origin, spatial extent, and laminar profile of bicuculline-induced interictal-like activity on neocortical slices were analyzed by using extracellular recordings from 60-channel microelectrode arrays. Susceptibility to pentylenetetrazole-induced seizures was assessed by electrocorticography in head-restrained nonanesthetized rats.
RESULTS: We show that the band heterotopia does not constitute a primary origin for interictal-like epileptiform activity in vitro and is dispensable for generating induced seizures in vivo. Furthermore, we report that most interictal-like discharges originating in the overlying cortex secondarily propagate to the band heterotopia. Importantly, we found that in vivo suppression of neuronal excitability in SBH does not alter the higher propensity of Dcx-KD rats to display seizures.
INTERPRETATION: These results suggest a major role of the normotopic cortex over the band heterotopia in generating interictal epileptiform activity and seizures in brains with SBH.},
	Author = {Petit, Ludovic Franck and Jalabert, Marion and Buhler, Emmanuelle and Malvache, Arnaud and Peret, Ang{\'e}lique and Chauvin, Yoann and Watrin, Fran{\c c}oise and Represa, Alfonso and Manent, Jean-Bernard},
	Date-Added = {2018-01-16 23:03:36 +0000},
	Date-Modified = {2018-01-16 23:03:36 +0000},
	Doi = {10.1002/ana.24237},
	Journal = {Ann Neurol},
	Journal-Full = {Annals of neurology},
	Mesh = {Animals; Bicuculline; Cerebral Cortex; Classical Lissencephalies and Subcortical Band Heterotopias; Convulsants; Disease Models, Animal; Electroencephalography; Electrophysiological Phenomena; Epilepsy; Gene Knockdown Techniques; Microtubule-Associated Proteins; Neocortex; Nerve Net; Neuropeptides; Pentylenetetrazole; Rats; Rats, Transgenic; Seizures; Somatosensory Cortex},
	Month = {Sep},
	Number = {3},
	Pages = {428-42},
	Pmid = {25074818},
	Pst = {ppublish},
	Title = {Normotopic cortex is the major contributor to epilepsy in experimental double cortex},
	Volume = {76},
	Year = {2014},
	File = {papers/Petit_AnnNeurol2014.pdf}}

@article{Herculano-Houzel:2014,
	Abstract = {It is a widespread notion that the proportion of glial to neuronal cells in the brain increases with brain size, to the point that glial cells represent "about 90% of all cells in the human brain." This notion, however, is wrong on both counts: neither does the glia/neuron ratio increase uniformly with brain size, nor do glial cells represent the majority of cells in the human brain. This review examines the origin of interest in the glia/neuron ratio; the original evidence that led to the notion that it increases with brain size; the extent to which this concept can be applied to white matter and whole brains and the recent supporting evidence that the glia/neuron ratio does not increase with brain size, but rather, and in surprisingly uniform fashion, with decreasing neuronal density due to increasing average neuronal cell size, across brain structures and species. Variations in the glia/neuron ratio are proposed to be related not to the supposed larger metabolic cost of larger neurons (given that this cost is not found to vary with neuronal density), but simply to the large variation in neuronal sizes across brain structures and species in the face of less overall variation in glial cell sizes, with interesting implications for brain physiology. The emerging evidence that the glia/neuron ratio varies uniformly across the different brain structures of mammalian species that diverged as early as 90 million years ago in evolution highlights how fundamental for brain function must be the interaction between glial cells and neurons.},
	Author = {Herculano-Houzel, Suzana},
	Date-Added = {2018-01-16 23:02:14 +0000},
	Date-Modified = {2018-01-16 23:02:43 +0000},
	Doi = {10.1002/glia.22683},
	Journal = {Glia},
	Journal-Full = {Glia},
	Keywords = {brain metabolism; brain size; cell size; teaching; facts},
	Mesh = {Animals; Biological Evolution; Brain; Cell Size; Humans; Neuroglia; Neurons; Organ Size; White Matter},
	Month = {Sep},
	Number = {9},
	Pages = {1377-91},
	Pmid = {24807023},
	Pst = {ppublish},
	Title = {The glia/neuron ratio: how it varies uniformly across brain structures and species and what that means for brain physiology and evolution},
	Volume = {62},
	Year = {2014},
	File = {papers/Herculano-Houzel_Glia2014.pdf}}

@article{Mori:2013,
	Abstract = {The orbitofrontal cortex receives multi-modality sensory inputs, including olfactory input, and is thought to be involved in conscious perception of the olfactory image of objects. Generation of olfactory consciousness may require neuronal circuit mechanisms for the "binding" of distributed neuronal activities, with each constituent neuron representing a specific component of an olfactory percept. The shortest neuronal pathway for odor signals to reach the orbitofrontal cortex is olfactory sensory neuron-olfactory bulb-olfactory cortex-orbitofrontal cortex, but other pathways exist, including transthalamic pathways. Here, we review studies on the structural organization and functional properties of the shortest pathway, and propose a model of neuronal circuit mechanisms underlying the temporal bindings of distributed neuronal activities in the olfactory cortex. We describe a hypothesis that suggests functional roles of gamma oscillations in the bindings. This hypothesis proposes that two types of projection neurons in the olfactory bulb, tufted cells and mitral cells, play distinct functional roles in bindings at neuronal circuits in the olfactory cortex: tufted cells provide specificity-projecting circuits which send odor information with early-onset fast gamma synchronization, while mitral cells give rise to dispersedly-projecting feed-forward binding circuits which transmit the response synchronization timing with later-onset slow gamma synchronization. This hypothesis also suggests a sequence of bindings in the olfactory cortex: a small-scale binding by the early-phase fast gamma synchrony of tufted cell inputs followed by a larger-scale binding due to the later-onset slow gamma synchrony of mitral cell inputs. We discuss that behavioral state, including wakefulness and sleep, regulates gamma oscillation couplings across the olfactory bulb, olfactory cortex, and orbitofrontal cortex.},
	Author = {Mori, Kensaku and Manabe, Hiroyuki and Narikiyo, Kimiya and Onisawa, Naomi},
	Date-Added = {2018-01-16 23:01:59 +0000},
	Date-Modified = {2018-01-16 23:01:59 +0000},
	Doi = {10.3389/fpsyg.2013.00743},
	Journal = {Front Psychol},
	Journal-Full = {Frontiers in psychology},
	Keywords = {gamma synchronization; olfactory bulb; olfactory consciousness; olfactory cortex; orbitofrontal cortex; tufted and mitral cells},
	Pages = {743},
	Pmc = {PMC3797617},
	Pmid = {24137148},
	Pst = {epublish},
	Title = {Olfactory consciousness and gamma oscillation couplings across the olfactory bulb, olfactory cortex, and orbitofrontal cortex},
	Volume = {4},
	Year = {2013},
	File = {papers/Mori_FrontPsychol2013.pdf}}

@article{Goard:2016,
	Abstract = {Mapping specific sensory features to future motor actions is a crucial capability of mammalian nervous systems. We investigated the role of visual (V1), posterior parietal (PPC), and frontal motor (fMC) cortices for sensorimotor mapping in mice during performance of a memory-guided visual discrimination task. Large-scale calcium imaging revealed that V1, PPC, and fMC neurons exhibited heterogeneous responses spanning all task epochs (stimulus, delay, response). Population analyses demonstrated unique encoding of stimulus identity and behavioral choice information across regions, with V1 encoding stimulus, fMC encoding choice even early in the trial, and PPC multiplexing the two variables. Optogenetic inhibition during behavior revealed that all regions were necessary during the stimulus epoch, but only fMC was required during the delay and response epochs. Stimulus identity can thus be rapidly transformed into behavioral choice, requiring V1, PPC, and fMC during the transformation period, but only fMC for maintaining the choice in memory prior to execution.},
	Author = {Goard, Michael J and Pho, Gerald N and Woodson, Jonathan and Sur, Mriganka},
	Date-Added = {2018-01-16 23:01:32 +0000},
	Date-Modified = {2018-01-16 23:01:32 +0000},
	Doi = {10.7554/eLife.13764},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {decision making; mouse; multiphoton microscopy; neuroscience; optogenetics; short-term memory},
	Mesh = {Animals; Brain Mapping; Choice Behavior; Functional Neuroimaging; Memory; Mice; Optogenetics; Parietal Lobe; Sensorimotor Cortex; Visual Cortex; Visual Perception},
	Month = {08},
	Pmc = {PMC4974053},
	Pmid = {27490481},
	Pst = {epublish},
	Title = {Distinct roles of visual, parietal, and frontal motor cortices in memory-guided sensorimotor decisions},
	Volume = {5},
	Year = {2016},
	File = {papers/Goard_Elife2016.pdf}}

@article{Guo:2015,
	Abstract = {Mammalian cerebral cortex is accepted as being critical for voluntary motor control, but what functions depend on cortex is still unclear. Here we used rapid, reversible optogenetic inhibition to test the role of cortex during a head-fixed task in which mice reach, grab, and eat a food pellet. Sudden cortical inhibition blocked initiation or froze execution of this skilled prehension behavior, but left untrained forelimb movements unaffected. Unexpectedly, kinematically normal prehension occurred immediately after cortical inhibition, even during rest periods lacking cue and pellet. This 'rebound' prehension was only evoked in trained and food-deprived animals, suggesting that a motivation-gated motor engram sufficient to evoke prehension is activated at inhibition's end. These results demonstrate the necessity and sufficiency of cortical activity for enacting a learned skill.},
	Author = {Guo, Jian-Zhong and Graves, Austin R and Guo, Wendy W and Zheng, Jihong and Lee, Allen and Rodr{\'\i}guez-Gonz{\'a}lez, Juan and Li, Nuo and Macklin, John J and Phillips, James W and Mensh, Brett D and Branson, Kristin and Hantman, Adam W},
	Date-Added = {2018-01-16 23:00:56 +0000},
	Date-Modified = {2018-01-16 23:01:17 +0000},
	Doi = {10.7554/eLife.10774},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {cortex; motor control; mouse; neuroscience; optogenetics; behavior; method; technique},
	Mesh = {Animals; Cerebral Cortex; Feeding Behavior; Locomotion; Mice; Optogenetics},
	Month = {Dec},
	Pages = {e10774},
	Pmc = {PMC4749564},
	Pmid = {26633811},
	Pst = {epublish},
	Title = {Cortex commands the performance of skilled movement},
	Volume = {4},
	Year = {2015},
	File = {papers/Guo_Elife2015.pdf}}

@article{Crair:2016,
	Abstract = {Although much is known about the regenerative capacity of retinal ganglion cells, very significant barriers remain in our ability to restore visual function following traumatic injury or disease-induced degeneration. Here we summarize our current understanding of the factors regulating axon guidance and target engagement in regenerating axons, and review the state of the field of neural regeneration, focusing on the visual system and highlighting studies using other model systems that can inform analysis of visual system regeneration. This overview is motivated by a Society for Neuroscience Satellite meeting, "Reconnecting Neurons in the Visual System," held in October 2015 sponsored by the National Eye Institute as part of their "Audacious Goals Initiative" and co-organized by Carol Mason (Columbia University) and Michael Crair (Yale University). The collective wisdom of the conference participants pointed to important gaps in our knowledge and barriers to progress in promoting the restoration of visual system function. This article is thus a summary of our existing understanding of visual system regeneration and provides a blueprint for future progress in the field.},
	Author = {Crair, Michael C and Mason, Carol A},
	Date-Added = {2018-01-16 22:59:41 +0000},
	Date-Modified = {2018-01-16 22:59:41 +0000},
	Doi = {10.1523/JNEUROSCI.1711-16.2016},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {axon; axon guidance; axon regeneration; eye; lateral geniculate nucleus; optic nerve; regeneration; retina; retinal ganglion cells; superior colliculus; traumatic brain injury; vision; visual cortex},
	Mesh = {Animals; Axons; Brain; Humans; Ocular Physiological Phenomena; Optic Nerve; Retinal Ganglion Cells; Visual Pathways},
	Month = {Oct},
	Number = {42},
	Pages = {10707-10722},
	Pmc = {PMC5083002},
	Pmid = {27798125},
	Pst = {ppublish},
	Title = {Reconnecting Eye to Brain},
	Volume = {36},
	Year = {2016},
	File = {papers/Crair_JNeurosci2016.pdf}}

@article{Seybold:2015,
	Abstract = {Cortical function is regulated by a strikingly diverse array of local-circuit inhibitory neurons. We evaluated how optogenetically activating somatostatin- and parvalbumin-positive interneurons subtractively or divisively suppressed auditory cortical cells' responses to tones. In both awake and anesthetized animals, we found that activating either family of interneurons produced mixtures of divisive and subtractive effects and that simultaneously recorded neurons were often suppressed in qualitatively different ways. A simple network model shows that threshold nonlinearities can interact with network activity to transform subtractive inhibition of neurons into divisive inhibition of networks, or vice versa. Varying threshold and the strength of suppression of a model neuron could determine whether the effect of inhibition appeared divisive, subtractive, or both. We conclude that the characteristics of response inhibition specific to a single interneuron type can be "masked" by the network configuration and cellular properties of the network in which they are embedded.},
	Author = {Seybold, Bryan A and Phillips, Elizabeth A K and Schreiner, Christoph E and Hasenstaub, Andrea R},
	Date-Added = {2018-01-16 22:58:49 +0000},
	Date-Modified = {2018-01-16 22:58:49 +0000},
	Doi = {10.1016/j.neuron.2015.09.013},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Auditory Cortex; Interneurons; Mice; Mice, Transgenic; Nerve Net; Neural Inhibition; Optogenetics},
	Month = {Sep},
	Number = {6},
	Pages = {1181-1192},
	Pmc = {PMC4635400},
	Pmid = {26402602},
	Pst = {ppublish},
	Title = {Inhibitory Actions Unified by Network Integration},
	Volume = {87},
	Year = {2015},
	File = {papers/Seybold_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.09.013}}

@article{Ledochowitsch:2015,
	Abstract = {BACKGROUND: To dissect the intricate workings of neural circuits, it is essential to gain precise control over subsets of neurons while retaining the ability to monitor larger-scale circuit dynamics. This requires the ability to both evoke and record neural activity simultaneously with high spatial and temporal resolution.
NEW METHOD: In this paper we present approaches that address this need by combining micro-electrocorticography (μECoG) with optogenetics in ways that avoid photovoltaic artifacts.
RESULTS: We demonstrate that variations of this approach are broadly applicable across three commonly studied mammalian species - mouse, rat, and macaque monkey - and that the recorded μECoG signal shows complex spectral and spatio-temporal patterns in response to optical stimulation.
COMPARISON WITH EXISTING METHODS: While optogenetics provides the ability to excite or inhibit neural subpopulations in a targeted fashion, large-scale recording of resulting neural activity remains challenging. Recent advances in optical physiology, such as genetically encoded Ca(2+) indicators, are promising but currently do not allow simultaneous recordings from extended cortical areas due to limitations in optical imaging hardware.
CONCLUSIONS: We demonstrate techniques for the large-scale simultaneous interrogation of cortical circuits in three commonly used mammalian species.},
	Author = {Ledochowitsch, P and Yazdan-Shahmorad, A and Bouchard, K E and Diaz-Botia, C and Hanson, T L and He, J-W and Seybold, B A and Olivero, E and Phillips, E A K and Blanche, T J and Schreiner, C E and Hasenstaub, A and Chang, E F and Sabes, P N and Maharbiz, M M},
	Date-Added = {2018-01-16 22:56:30 +0000},
	Date-Modified = {2018-01-16 22:56:50 +0000},
	Doi = {10.1016/j.jneumeth.2015.07.028},
	Journal = {J Neurosci Methods},
	Journal-Full = {Journal of neuroscience methods},
	Keywords = {Auditory; Cranial window; ECoG; Epidural; Mouse; NHP; Optogenetics; Parvalbumin; Rat; technique},
	Mesh = {Animals; Artifacts; Auditory Perception; Cerebral Cortex; Computer-Aided Design; Electric Impedance; Electrocorticography; Electrodes, Implanted; Equipment Design; Evoked Potentials; Macaca mulatta; Male; Mice, Transgenic; Neural Inhibition; Neurons; Optogenetics; Photic Stimulation; Rats, Long-Evans; Tin Compounds},
	Month = {Dec},
	Pages = {220-31},
	Pmid = {26296286},
	Pst = {ppublish},
	Title = {Strategies for optical control and simultaneous electrical readout of extended cortical circuits},
	Volume = {256},
	Year = {2015},
	File = {papers/Ledochowitsch_JNeurosciMethods2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jneumeth.2015.07.028}}

@article{Ryan:2017,
	Abstract = {Many states have recently made significant changes to their legislation making recreational and/or medical marijuana use by adults legal. Although these laws, for the most part, have not targeted the adolescent population, they have created an environment in which marijuana increasingly is seen as acceptable, safe, and therapeutic. This clinical report offers guidance to the practicing pediatrician based on existing evidence and expert opinion/consensus of the American Academy of Pediatrics regarding anticipatory guidance and counseling to teenagers and their parents about marijuana and its use. The recently published technical report provides the detailed evidence and references regarding the research on which the information in this clinical report is based.},
	Author = {Ryan, Sheryl A and Ammerman, Seth D and {COMMITTEE ON SUBSTANCE USE AND PREVENTION}},
	Date-Added = {2018-01-16 22:55:01 +0000},
	Date-Modified = {2018-01-16 22:55:01 +0000},
	Doi = {10.1542/peds.2016-4069},
	Journal = {Pediatrics},
	Journal-Full = {Pediatrics},
	Mesh = {Adolescent; Counseling; Humans; Marijuana Abuse; Marijuana Smoking; Parents; Pediatricians; Physician's Role},
	Month = {Mar},
	Number = {3},
	Pmid = {28242859},
	Pst = {ppublish},
	Title = {Counseling Parents and Teens About Marijuana Use in the Era of Legalization of Marijuana},
	Volume = {139},
	Year = {2017},
	File = {papers/Ryan_Pediatrics2017.pdf}}

@article{Tohmi:2009,
	Abstract = {Endogenous fluorescence signals derived from mitochondria reflect activity-dependent changes in brain metabolism and may be exploited in functional brain imaging. Endogenous flavoprotein fluorescence imaging in mice is especially important because many genetically manipulated strains of mice are available and the transparent skull of mice allows transcranial fluorescence imaging of cortical activities. In the primary sensory areas of mice, cortical activities and experience-dependent plasticity have been investigated using transcranial fluorescence imaging. Furthermore, differential imaging, based on stimulus specificity of cortical areas, distinguished activities in higher visual areas around the primary visual cortex from those in primary visual cortex. The combination of transcranial fluorescence imaging with the suppression of cortical activities using photobleaching of flavoproteins is expected to aid in elucidating the roles of sensory cortices including higher areas in mice.},
	Author = {Tohmi, Manavu and Takahashi, Kuniyuki and Kubota, Yamato and Hishida, Ryuichi and Shibuki, Katsuei},
	Date-Added = {2018-01-16 22:53:43 +0000},
	Date-Modified = {2018-01-16 22:54:17 +0000},
	Doi = {10.1111/j.1471-4159.2009.05926.x},
	Journal = {J Neurochem},
	Journal-Full = {Journal of neurochemistry},
	Keywords = {optical physiology; imaging; intrinsic signal; function; map},
	Mesh = {Animals; Cerebral Cortex; Flavoproteins; Mice; Neuronal Plasticity; Photobleaching; Spectrometry, Fluorescence},
	Month = {May},
	Pages = {3-9},
	Pmid = {19393002},
	Pst = {ppublish},
	Title = {Transcranial flavoprotein fluorescence imaging of mouse cortical activity and plasticity},
	Volume = {109 Suppl 1},
	Year = {2009},
	File = {papers/Tohmi_JNeurochem2009.pdf}}

@article{Kondo:2016,
	Abstract = {A minicolumn is the smallest anatomical module in the cortical architecture, but it is still in debate whether it serves as functional units for cortical processing. In the rodent primary visual cortex (V1), neurons with different preferred orientations are mixed horizontally in a salt and pepper manner, but vertical functional organization was not examined. In this study, we found that neurons with similar orientation preference are weakly but significantly clustered vertically in a short length and horizontally in the scale of a minicolumn. Interestingly, the vertical clustering is found only in a part of minicolumns, and others are composed of neurons with a variety of orientation preferences. Thus, the mouse V1 is a mixture of vertical clusters of neurons with various degrees of orientation similarity, which may be the compromise between the brain size and keeping the vertical clusters of similarly tuned neurons at least in a subset of clusters.},
	Author = {Kondo, Satoru and Yoshida, Takashi and Ohki, Kenichi},
	Date-Added = {2018-01-16 22:52:09 +0000},
	Date-Modified = {2018-01-16 22:52:09 +0000},
	Doi = {10.1038/ncomms13210},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Month = {Oct},
	Pages = {13210},
	Pmc = {PMC5078743},
	Pmid = {27767032},
	Pst = {epublish},
	Title = {Mixed functional microarchitectures for orientation selectivity in the mouse primary visual cortex},
	Volume = {7},
	Year = {2016},
	File = {papers/Kondo_NatCommun2016.pdf}}

@article{Kirmse:2015,
	Abstract = {A large body of evidence from in vitro studies suggests that GABA is depolarizing during early postnatal development. However, the mode of GABA action in the intact developing brain is unknown. Here we examine the in vivo effects of GABA in cells of the upper cortical plate using a combination of electrophysiological and Ca(2+)-imaging techniques. We report that at postnatal days (P) 3-4, GABA depolarizes the majority of immature neurons in the occipital cortex of anaesthetized mice. At the same time, GABA does not efficiently activate voltage-gated Ca(2+) channels and fails to induce action potential firing. Blocking GABA(A) receptors disinhibits spontaneous network activity, whereas allosteric activation of GABA(A) receptors has the opposite effect. In summary, our data provide evidence that in vivo GABA acts as a depolarizing neurotransmitter imposing an inhibitory control on network activity in the neonatal (P3-4) neocortex.},
	Author = {Kirmse, Knut and Kummer, Michael and Kovalchuk, Yury and Witte, Otto W and Garaschuk, Olga and Holthoff, Knut},
	Date-Added = {2018-01-16 22:50:06 +0000},
	Date-Modified = {2018-01-16 22:50:06 +0000},
	Doi = {10.1038/ncomms8750},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Mesh = {Action Potentials; Animals; Animals, Newborn; GABA Agents; Mice; Neocortex; Nerve Net; Neural Inhibition; Neurons; Occipital Lobe; Patch-Clamp Techniques; Receptors, GABA-A; Synaptic Transmission; gamma-Aminobutyric Acid},
	Month = {Jul},
	Pages = {7750},
	Pmid = {26177896},
	Pst = {epublish},
	Title = {GABA depolarizes immature neurons and inhibits network activity in the neonatal neocortex in vivo},
	Volume = {6},
	Year = {2015},
	File = {papers/Kirmse_NatCommun2015.pdf}}

@article{Minocha:2015,
	Abstract = {Guidepost cells present at and surrounding the midline provide guidance cues that orient the growing axons through commissures. Here we show that the transcription factor Nkx2.1 known to control the specification of GABAergic interneurons also regulates the differentiation of astroglia and polydendrocytes within the mouse anterior commissure (AC). Nkx2.1-positive glia were found to originate from three germinal regions of the ventral telencephalon. Nkx2.1-derived glia were observed in and around the AC region by E14.5. Thereafter, a selective cell ablation strategy showed a synergistic role of Nkx2.1-derived cells, both GABAergic interneurons and astroglia, towards the proper formation of the AC. Finally, our results reveal that the Nkx2.1-regulated cells mediate AC axon guidance through the expression of the repellent cue, Slit2. These results bring forth interesting insights about the spatial and temporal origin of midline telencephalic glia, and highlight the importance of neurons and astroglia towards the formation of midline commissures.},
	Author = {Minocha, Shilpi and Valloton, Delphine and Ypsilanti, Athena R and Fiumelli, Hubert and Allen, Elizabeth A and Yanagawa, Yuchio and Marin, Oscar and Ch{\'e}dotal, Alain and Hornung, Jean-Pierre and Lebrand, C{\'e}cile},
	Date-Added = {2018-01-16 22:49:01 +0000},
	Date-Modified = {2018-01-16 22:49:01 +0000},
	Doi = {10.1038/ncomms7887},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Mesh = {Animals; Anterior Cerebellar Commissure; Astrocytes; Axons; Cell Movement; Electroporation; Embryo, Mammalian; GABAergic Neurons; Gene Expression Regulation, Developmental; Immunohistochemistry; In Vitro Techniques; Intercellular Signaling Peptides and Proteins; Interneurons; Mice; Nerve Tissue Proteins; Neuroglia; Neurons; Nuclear Proteins; Telencephalon; Thyroid Nuclear Factor 1; Transcription Factors},
	Month = {Apr},
	Pages = {6887},
	Pmc = {PMC4423212},
	Pmid = {25904499},
	Pst = {epublish},
	Title = {Nkx2.1-derived astrocytes and neurons together with Slit2 are indispensable for anterior commissure formation},
	Volume = {6},
	Year = {2015},
	File = {papers/Minocha_NatCommun2015.pdf}}

@article{Srivatsa:2014,
	Abstract = {The pyramidal neurons of the mammalian neocortex form two major types of long-range connections-corticocortical and cortico-subcortical. The transcription factors Satb2 and Ctip2 are critical regulators of neuronal cell fate that control interhemispheric versus corticofugal connections respectively. Here, we investigate the axon guidance molecules downstream of Satb2 and Ctip2 that establish these connections. We show that the expression of two Netrin1 receptors- DCC and Unc5C is under direct negative regulation by Satb2 and Ctip2, respectively. Further, we show that the Netrin1-Unc5C/DCC interaction is involved in controlling the interhemispherical projection in a subset of early born, deep layer callosal neurons.},
	Author = {Srivatsa, Swathi and Parthasarathy, Srinivas and Britanova, Olga and Bormuth, Ingo and Donahoo, Amber-Lee and Ackerman, Susan L and Richards, Linda J and Tarabykin, Victor},
	Date-Added = {2018-01-16 22:48:47 +0000},
	Date-Modified = {2018-01-16 22:48:47 +0000},
	Doi = {10.1038/ncomms4708},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Mesh = {Animals; Chromatin Immunoprecipitation; Corpus Callosum; DCC Receptor; DNA Primers; Electroporation; Gene Expression Regulation, Developmental; In Situ Hybridization; Luciferases; Mice; Morphogenesis; Netrin Receptors; Plasmids; Receptors, Cell Surface; Receptors, Nerve Growth Factor; Tumor Suppressor Proteins},
	Month = {Apr},
	Pages = {3708},
	Pmc = {PMC3997811},
	Pmid = {24739528},
	Pst = {epublish},
	Title = {Unc5C and DCC act downstream of Ctip2 and Satb2 and contribute to corpus callosum formation},
	Volume = {5},
	Year = {2014},
	File = {papers/Srivatsa_NatCommun2014.pdf}}

@article{Hazrati:2013,
	Abstract = {BACKGROUND: Chronic traumatic encephalopathy (CTE) is the term coined for the neurodegenerative disease often suspected in athletes with histories of repeated concussion and progressive dementia. Histologically, CTE is defined as a tauopathy with a distribution of tau-positive neurofibrillary tangles (NFTs) that is distinct from other tauopathies, and usually shows an absence of beta-amyloid deposits, in contrast to Alzheimer's disease (AD). Although the connection between repeated concussions and CTE-type neurodegeneration has been recently proposed, this causal relationship has not yet been firmly established. Also, the prevalence of CTE among athletes with multiple concussions is unknown.
METHODS: We performed a consecutive case series brain autopsy study on six retired professional football players from the Canadian Football League (CFL) with histories of multiple concussions and significant neurological decline.
RESULTS: All participants had progressive neurocognitive decline prior to death; however, only 3 cases had post-mortem neuropathological findings consistent with CTE. The other 3 participants had pathological diagnoses of AD, amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD). Moreover, the CTE cases showed co-morbid pathology of cancer, vascular disease, and AD.
DISCUSSION: Our case studies highlight that not all athletes with history of repeated concussions and neurological symptomology present neuropathological changes of CTE. These preliminary findings support the need for further research into the link between concussion and CTE as well as the need to expand the research to other possible causes of taupathy in athletes. They point to a critical need for prospective studies with good sampling methods to allow us to understand the relationship between multiple concussions and the development of CTE.},
	Author = {Hazrati, Lili-Naz and Tartaglia, Maria C and Diamandis, Phedias and Davis, Karen D and Green, Robin E and Wennberg, Richard and Wong, Janice C and Ezerins, Leo and Tator, Charles H},
	Date-Added = {2018-01-16 22:47:35 +0000},
	Date-Modified = {2018-01-16 22:47:35 +0000},
	Doi = {10.3389/fnhum.2013.00222},
	Journal = {Front Hum Neurosci},
	Journal-Full = {Frontiers in human neuroscience},
	Keywords = {chronic traumatic encephalopathy; dementia; neurodegenerative disease; professional athletes; repetitive brain injury},
	Pages = {222},
	Pmc = {PMC3662898},
	Pmid = {23745112},
	Pst = {epublish},
	Title = {Absence of chronic traumatic encephalopathy in retired football players with multiple concussions and neurological symptomatology},
	Volume = {7},
	Year = {2013},
	File = {papers/Hazrati_FrontHumNeurosci2013.pdf}}

@article{Zhuang:2017,
	Abstract = {Visual perception and behavior are mediated by cortical areas that have been distinguished using architectonic and retinotopic criteria. We employed fluorescence imaging and GCaMP6 reporter mice to generate retinotopic maps, revealing additional regions of retinotopic organization that extend into barrel and retrosplenial cortices. Aligning retinotopic maps to architectonic borders, we found a mismatch in border location, indicating that architectonic borders are not aligned with the retinotopic transition at the vertical meridian. We also assessed the representation of visual space within each region, finding that four visual areas bordering V1 (LM, P, PM and RL) display complementary representations, with overlap primarily at the central hemifield. Our results extend our understanding of the organization of mouse cortex to include up to 16 distinct retinotopically organized regions.},
	Author = {Zhuang, Jun and Ng, Lydia and Williams, Derric and Valley, Matthew and Li, Yang and Garrett, Marina and Waters, Jack},
	Date-Added = {2018-01-16 22:40:48 +0000},
	Date-Modified = {2018-01-16 22:40:48 +0000},
	Doi = {10.7554/eLife.18372},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {cortex; mouse; neuroscience; topographic map; visual map},
	Month = {Jan},
	Pmc = {PMC5218535},
	Pmid = {28059700},
	Pst = {epublish},
	Title = {An extended retinotopic map of mouse cortex},
	Volume = {6},
	Year = {2017},
	File = {papers/Zhuang_Elife2017.pdf}}

@article{Sulak:2016,
	Abstract = {A major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. There is no correlation, however, between body size and cancer risk. This lack of correlation is often referred to as 'Peto's Paradox'. Here, we show that the elephant genome encodes 20 copies of the tumor suppressor gene TP53 and that the increase in TP53 copy number occurred coincident with the evolution of large body sizes, the evolution of extreme sensitivity to genotoxic stress, and a hyperactive TP53 signaling pathway in the elephant (Proboscidean) lineage. Furthermore, we show that several of the TP53 retrogenes (TP53RTGs) are transcribed and likely translated. While TP53RTGs do not appear to directly function as transcription factors, they do contribute to the enhanced sensitivity of elephant cells to DNA damage and the induction of apoptosis by regulating activity of the TP53 signaling pathway. These results suggest that an increase in the copy number of TP53 may have played a direct role in the evolution of very large body sizes and the resolution of Peto's paradox in Proboscideans.},
	Author = {Sulak, Michael and Fong, Lindsey and Mika, Katelyn and Chigurupati, Sravanthi and Yon, Lisa and Mongan, Nigel P and Emes, Richard D and Lynch, Vincent J},
	Date-Added = {2018-01-16 22:40:23 +0000},
	Date-Modified = {2018-01-16 22:40:23 +0000},
	Doi = {10.7554/eLife.11994},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {African elephant; Asian elephant; aardvark; armadillo; cell biology; evolutionary biology; genomics; hyrax},
	Mesh = {Animals; Apoptosis; Body Size; DNA Repair; Elephants; Evolution, Molecular; Gene Dosage; Gene Expression Profiling; Genes, p53; Protein Biosynthesis; Signal Transduction; Transcription, Genetic},
	Month = {09},
	Pmc = {PMC5061548},
	Pmid = {27642012},
	Pst = {epublish},
	Title = {TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants},
	Volume = {5},
	Year = {2016},
	File = {papers/Sulak_Elife2016.pdf}}

@article{Iverson:2004,
	Abstract = {PRIMARY OBJECTIVE: To examine the possibility that athletes with multiple concussions show cumulative effects of injury.
METHODS AND PROCEDURES: Amateur athletes with a history of three or more concussions were carefully matched (gender, age, education and sport) with athletes with no prior concussions. All completed a computerized neuropsychological test battery at preseason (ImPACT) and then within 5 days of sustaining a concussion (mean = 1.7 days).
MAIN OUTCOMES AND RESULTS: There were differences between groups in symptom reporting and memory performance. At baseline (i.e. preseason), athletes with multiple concussions reported more symptoms than athletes with no history of concussion. At approximately 2 days post-injury, athletes with multiple concussions scored significantly lower on memory testing than athletes with a single concussion. Athletes with multiple concussions were 7.7 times more likely to demonstrate a major drop in memory perfomance than athletes with no previous concussions.
CONCLUSIONS: This study provides preliminary evidence to suggest that athletes with multiple concussions might have cumulative effects.},
	Author = {Iverson, Grant L and Gaetz, Michael and Lovell, Mark R and Collins, Michael W},
	Date-Added = {2018-01-16 22:39:33 +0000},
	Date-Modified = {2018-01-16 22:39:33 +0000},
	Doi = {10.1080/02699050310001617352},
	Journal = {Brain Inj},
	Journal-Full = {Brain injury},
	Mesh = {Adolescent; Amnesia; Analysis of Variance; Athletic Injuries; Brain Concussion; Cumulative Trauma Disorders; Humans; Male; Memory; Neuropsychological Tests; Post-Concussion Syndrome; Psychomotor Performance; Reaction Time},
	Month = {May},
	Number = {5},
	Pages = {433-43},
	Pmid = {15195792},
	Pst = {ppublish},
	Title = {Cumulative effects of concussion in amateur athletes},
	Volume = {18},
	Year = {2004},
	File = {papers/Iverson_BrainInj2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1080/02699050310001617352}}

@article{Bogaert:2018,
	Abstract = {We conducted a direct test of an immunological explanation of the finding that gay men have a greater number of older brothers than do heterosexual men. This explanation posits that some mothers develop antibodies against a Y-linked protein important in male brain development, and that this effect becomes increasingly likely with each male gestation, altering brain structures underlying sexual orientation in their later-born sons. Immune assays targeting two Y-linked proteins important in brain development-protocadherin 11 Y-linked (PCDH11Y) and neuroligin 4 Y-linked (NLGN4Y; isoforms 1 and 2)-were developed. Plasma from mothers of sons, about half of whom had a gay son, along with additional controls (women with no sons, men) was analyzed for male protein-specific antibodies. Results indicated women had significantly higher anti-NLGN4Y levels than men. In addition, after statistically controlling for number of pregnancies, mothers of gay sons, particularly those with older brothers, had significantly higher anti-NLGN4Y levels than did the control samples of women, including mothers of heterosexual sons. The results suggest an association between a maternal immune response to NLGN4Y and subsequent sexual orientation in male offspring.},
	Author = {Bogaert, Anthony F and Skorska, Malvina N and Wang, Chao and Gabrie, Jos{\'e} and MacNeil, Adam J and Hoffarth, Mark R and VanderLaan, Doug P and Zucker, Kenneth J and Blanchard, Ray},
	Date-Added = {2018-01-16 22:37:59 +0000},
	Date-Modified = {2018-01-16 22:37:59 +0000},
	Doi = {10.1073/pnas.1705895114},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {NLGN4Y; fraternal birth order; homosexuality; maternal immune hypothesis; sexual orientation},
	Month = {Jan},
	Number = {2},
	Pages = {302-306},
	Pmid = {29229842},
	Pst = {ppublish},
	Title = {Male homosexuality and maternal immune responsivity to the Y-linked protein NLGN4Y},
	Volume = {115},
	Year = {2018},
	File = {papers/Bogaert_ProcNatlAcadSciUSA2018.pdf}}

@article{Helfrich:2018,
	Abstract = {The coupled interaction between slow-wave oscillations and sleep spindles during non-rapid-eye-movement (NREM) sleep has been proposed to support memory consolidation. However, little evidence in humans supports this theory. Moreover, whether such dynamic coupling is impaired as a consequence of brain aging in later life, contributing to cognitive and memory decline, is unknown. Combining electroencephalography (EEG), structural MRI, and sleep-dependent memory assessment, we addressed these questions in cognitively normal young and older adults. Directional cross-frequency coupling analyses demonstrated that the slow wave governs a precise temporal coordination of sleep spindles, the quality of which predicts overnight memory retention. Moreover, selective atrophy within the medial frontal cortex in older adults predicted a temporal dispersion of this slow wave-spindle coupling, impairing overnight memory consolidation and leading to forgetting. Prefrontal-dependent deficits in the spatiotemporal coordination of NREM sleep oscillations therefore represent one pathway explaining age-related memory decline.},
	Author = {Helfrich, Randolph F and Mander, Bryce A and Jagust, William J and Knight, Robert T and Walker, Matthew P},
	Date-Added = {2018-01-16 22:37:20 +0000},
	Date-Modified = {2018-01-16 22:37:40 +0000},
	Doi = {10.1016/j.neuron.2017.11.020},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {age-related memory decline; aging; atrophy; directional cross-frequency coupling; hierarchical nesting; hippocampus-dependent memory consolidation; overnight forgetting; prefrontal cortex; sleep spindles; slow oscillation; oscillations; synchrony},
	Month = {Jan},
	Number = {1},
	Pages = {221-230.e4},
	Pmc = {PMC5754239},
	Pmid = {29249289},
	Pst = {ppublish},
	Title = {Old Brains Come Uncoupled in Sleep: Slow Wave-Spindle Synchrony, Brain Atrophy, and Forgetting},
	Volume = {97},
	Year = {2018},
	File = {papers/Helfrich_Neuron2018.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2017.11.020}}

@article{Peixoto:2016,
	Abstract = {Some autistic individuals exhibit abnormal development of the caudate nucleus and associative cortical areas, suggesting potential dysfunction of cortico-basal ganglia (BG) circuits. Using optogenetic and electrophysiological approaches in mice, we identified a narrow postnatal period that is characterized by extensive glutamatergic synaptogenesis in striatal spiny projection neurons (SPNs) and a concomitant increase in corticostriatal circuit activity. SPNs during early development have high intrinsic excitability and respond strongly to cortical afferents despite sparse excitatory inputs. As a result, striatum and corticostriatal connectivity are highly sensitive to acute and chronic changes in cortical activity, suggesting that early imbalances in cortical function alter BG development. Indeed, a mouse model of autism with deletions in Shank3 (Shank3B(-/-)) shows early cortical hyperactivity, which triggers increased SPN excitatory synapse and corticostriatal hyperconnectivity. These results indicate that there is a tight functional coupling between cortex and striatum during early postnatal development and suggest a potential common circuit dysfunction that is caused by cortical hyperactivity.},
	Author = {Peixoto, Rui T and Wang, Wengang and Croney, Donyell M and Kozorovitskiy, Yevgenia and Sabatini, Bernardo L},
	Date-Added = {2018-01-16 22:36:20 +0000},
	Date-Modified = {2018-01-16 22:36:20 +0000},
	Doi = {10.1038/nn.4260},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Action Potentials; Animals; Autistic Disorder; Cerebral Cortex; Corpus Striatum; Disease Models, Animal; Female; Male; Mice; Mice, Knockout; Mice, Transgenic; Nerve Tissue Proteins; Neural Pathways; Neurons; Synapses},
	Month = {05},
	Number = {5},
	Pages = {716-724},
	Pmc = {PMC4846490},
	Pmid = {26928064},
	Pst = {ppublish},
	Title = {Early hyperactivity and precocious maturation of corticostriatal circuits in Shank3B(-/-) mice},
	Volume = {19},
	Year = {2016},
	File = {papers/Peixoto_NatNeurosci2016.pdf}}

@article{Hikosaka:2010,
	Abstract = {Surviving in a world with hidden rewards and dangers requires choosing the appropriate behaviours. Recent discoveries indicate that the habenula plays a prominent part in such behavioural choice through its effects on neuromodulator systems, in particular the dopamine and serotonin systems. By inhibiting dopamine-releasing neurons, habenula activation leads to the suppression of motor behaviour when an animal fails to obtain a reward or anticipates an aversive outcome. Moreover, the habenula is involved in behavioural responses to pain, stress, anxiety, sleep and reward, and its dysfunction is associated with depression, schizophrenia and drug-induced psychosis. As a highly conserved structure in the brain, the habenula provides a fundamental mechanism for both survival and decision-making.},
	Author = {Hikosaka, Okihide},
	Date-Added = {2018-01-16 22:35:23 +0000},
	Date-Modified = {2018-01-16 22:35:23 +0000},
	Doi = {10.1038/nrn2866},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Avoidance Learning; Decision Making; Habenula; Humans; Mental Disorders; Stress, Psychological},
	Month = {Jul},
	Number = {7},
	Pages = {503-13},
	Pmc = {PMC3447364},
	Pmid = {20559337},
	Pst = {ppublish},
	Title = {The habenula: from stress evasion to value-based decision-making},
	Volume = {11},
	Year = {2010},
	File = {papers/Hikosaka_NatRevNeurosci2010.pdf}}

@article{Zakharenko:1999a,
	Abstract = {In mature neurons, synaptic vesicles continuously recycle within the presynaptic nerve terminal. In developing axons which are free of contact with a postsynaptic target, constitutive membrane recycling is not localized to the nerve terminal; instead, plasma membrane components undergo cycles of exoendocytosis throughout the whole axonal surface (Matteoli et al., 1992; Kraszewski et al., 1995). Moreover, in growing Xenopus spinal cord neurons in culture, acetylcholine (ACh) is spontaneously secreted in the quantal fashion along the axonal shaft (Evers et al., 1989; Antonov et al., 1998). Here we demonstrate that in Xenopus neurons ACh secretion is mediated by vesicles which recycle locally within the axon. Similar to neurotransmitter release at the presynaptic nerve terminal, ACh secretion along the axon could be elicited by the action potential or by hypertonic solutions. We found that the parameters of neurotransmitter secretion at the nerve terminal and at the middle axon were strikingly similar. These results lead us to conclude that, as in the case of the presynaptic nerve terminal, synaptic vesicles involved in neurotransmitter release along the axon contain a complement of proteins for vesicle docking and Ca2+-dependent fusion. Taken together, our results support the idea that, in developing axons, the rudimentary machinery for quantal neurotransmitter secretion is distributed throughout the whole axonal surface. Maturation of this machinery in the process of synaptic development would improve the fidelity of synaptic transmission during high-frequency stimulation of the presynaptic cell.},
	Author = {Zakharenko, S and Chang, S and O'Donoghue, M and Popov, S V},
	Date-Added = {2018-01-16 22:35:04 +0000},
	Date-Modified = {2018-01-16 22:35:04 +0000},
	Journal = {J Cell Biol},
	Journal-Full = {The Journal of cell biology},
	Mesh = {ADP-Ribosylation Factors; Acetylcholine; Adaptor Protein Complex alpha Subunits; Adaptor Proteins, Vesicular Transport; Animals; Axons; Calcium; Cells, Cultured; Dynamins; Exocytosis; GTP Phosphohydrolases; GTP-Binding Proteins; Membrane Proteins; Nerve Endings; Nerve Tissue Proteins; Neurites; Neuronal Plasticity; Neurons; Neurotransmitter Agents; Presynaptic Terminals; Spider Venoms; Synaptic Vesicles; Xenopus},
	Month = {Feb},
	Number = {3},
	Pages = {507-18},
	Pmc = {PMC2132923},
	Pmid = {9971745},
	Pst = {ppublish},
	Title = {Neurotransmitter secretion along growing nerve processes: comparison with synaptic vesicle exocytosis},
	Volume = {144},
	Year = {1999}}

@article{Larsen:2006,
	Abstract = {In the developing neocortex, pyramidal neurons use molecular cues to form axonal arbors selectively in the correct layers. Despite the utility of mice for molecular and genetic studies, little work has been done on the development of layer-specific axonal arborizations of pyramidal neurons in mice. We intracellularly labeled and reconstructed the axons of layer 2/3 and layer 5 pyramidal neurons in slices of primary somatosensory cortex from C57Bl6 mice on postnatal days 7-21. For all neurons studied, the development of the axonal arborizations in mice follows a pattern similar to that seen in other species; laminar specificity of the earliest axonal branches is similar to that of mature animals. At P7, pyramidal neurons are very simple, having only a main descending axon and few primary branches. Between P7 and P10, there is a large increase in the total number of axonal branches, and axons continue to increase in complexity and total length from P10 to P21. Unlike observations in ferrets, cats, and monkeys, two types of layer 2/3 pyramidal neurons are present in both mature and developing mice; cells in superficial layer 2/3 lack axonal arbors in layer 4, and cells close to the layer 4 border have substantial axonal arbors within layer 4. We also describe axonal and dendritic arborization patterns of three pyramidal cell types in layer 5. The axons of tall-tufted layer 5 pyramidal neurons arborize almost exclusively within deep layers while tall-simple, and short layer 5 pyramidal neurons also project axons to superficial layers.},
	Author = {Larsen, DeLaine D and Callaway, Edward M},
	Date-Added = {2018-01-16 22:34:30 +0000},
	Date-Modified = {2018-01-16 22:34:30 +0000},
	Doi = {10.1002/cne.20754},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Axons; Dendrites; Imaging, Three-Dimensional; Mice; Mice, Inbred C57BL; Neurons; Pyramidal Cells; Somatosensory Cortex},
	Month = {Jan},
	Number = {3},
	Pages = {398-414},
	Pmc = {PMC4651208},
	Pmid = {16320250},
	Pst = {ppublish},
	Title = {Development of layer-specific axonal arborizations in mouse primary somatosensory cortex},
	Volume = {494},
	Year = {2006},
	File = {papers/Larsen_JCompNeurol2006.pdf}}

@article{Zakharenko:1999,
	Abstract = {In mature neurons, synaptic vesicles continuously recycle within the presynaptic nerve terminal. In developing axons which are free of contact with a postsynaptic target, constitutive membrane recycling is not localized to the nerve terminal; instead, plasma membrane components undergo cycles of exoendocytosis throughout the whole axonal surface (Matteoli et al., 1992; Kraszewski et al., 1995). Moreover, in growing Xenopus spinal cord neurons in culture, acetylcholine (ACh) is spontaneously secreted in the quantal fashion along the axonal shaft (Evers et al., 1989; Antonov et al., 1998). Here we demonstrate that in Xenopus neurons ACh secretion is mediated by vesicles which recycle locally within the axon. Similar to neurotransmitter release at the presynaptic nerve terminal, ACh secretion along the axon could be elicited by the action potential or by hypertonic solutions. We found that the parameters of neurotransmitter secretion at the nerve terminal and at the middle axon were strikingly similar. These results lead us to conclude that, as in the case of the presynaptic nerve terminal, synaptic vesicles involved in neurotransmitter release along the axon contain a complement of proteins for vesicle docking and Ca2+-dependent fusion. Taken together, our results support the idea that, in developing axons, the rudimentary machinery for quantal neurotransmitter secretion is distributed throughout the whole axonal surface. Maturation of this machinery in the process of synaptic development would improve the fidelity of synaptic transmission during high-frequency stimulation of the presynaptic cell.},
	Author = {Zakharenko, S and Chang, S and O'Donoghue, M and Popov, S V},
	Date-Added = {2018-01-16 22:34:02 +0000},
	Date-Modified = {2018-01-16 22:34:02 +0000},
	Journal = {J Cell Biol},
	Journal-Full = {The Journal of cell biology},
	Mesh = {ADP-Ribosylation Factors; Acetylcholine; Adaptor Protein Complex alpha Subunits; Adaptor Proteins, Vesicular Transport; Animals; Axons; Calcium; Cells, Cultured; Dynamins; Exocytosis; GTP Phosphohydrolases; GTP-Binding Proteins; Membrane Proteins; Nerve Endings; Nerve Tissue Proteins; Neurites; Neuronal Plasticity; Neurons; Neurotransmitter Agents; Presynaptic Terminals; Spider Venoms; Synaptic Vesicles; Xenopus},
	Month = {Feb},
	Number = {3},
	Pages = {507-18},
	Pmc = {PMC2132923},
	Pmid = {9971745},
	Pst = {ppublish},
	Title = {Neurotransmitter secretion along growing nerve processes: comparison with synaptic vesicle exocytosis},
	Volume = {144},
	Year = {1999},
	File = {papers/Zakharenko_JCellBiol1999.pdf}}

@article{Assimacopoulos:2012,
	Abstract = {The concept of an "organizer" is basic to embryology. An organizer is a portion of the embryo producing signals that lead to the creation of a patterned mature structure from an embryonic primordium. Fibroblast growth factor 8 (FGF8) is a morphogen that disperses from a rostromedial source in the neocortical primordium (NP), forms a rostral-to-caudal (R/C) gradient, and regulates embryonic and neonatal R/C patterns of gene expression in neocortex. Whether FGF8 also has organizer activity that generates the postnatal neocortical area map is uncertain. To test this possibility, new sources of FGF8 were introduced into the mouse NP with in utero microelectroporation at embryonic day 10.5, close to the estimated peak of area patterning. Results differed depending on the position of ectopic FGF8. Ectopic FGF8 in the caudalmost NP could duplicate somatosensory cortex (S1) and primary visual cortex (V1). FGF8 delivered to the midlateral NP generated a sulcus separating rostral and caudal portions of the NP, in effect creating duplicate NPs. In the caudal NP, ectopic FGF8 induced a second, inclusive area map, containing frontal cortex, S1, V1, and primary auditory areas. Moreover, duplicate S1 showed plasticity to sensory deprivation, and duplicate V1 responded to visual stimuli. Our findings implicate FGF8 as an organizer signal, and its source in the rostromedial telencephalon as an organizer of the neocortical area map.},
	Author = {Assimacopoulos, Stavroula and Kao, Tina and Issa, Naoum P and Grove, Elizabeth A},
	Date-Added = {2018-01-16 22:33:13 +0000},
	Date-Modified = {2018-01-16 22:33:13 +0000},
	Doi = {10.1523/JNEUROSCI.0071-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Brain Mapping; Electroporation; Female; Fibroblast Growth Factor 8; Male; Mice; Mice, Inbred C57BL; Mice, Inbred ICR; Morphogenesis; Neocortex; Neuronal Plasticity; Photic Stimulation; Pregnancy; Sensory Deprivation; Visual Perception},
	Month = {May},
	Number = {21},
	Pages = {7191-201},
	Pmc = {PMC3466079},
	Pmid = {22623663},
	Pst = {ppublish},
	Title = {Fibroblast growth factor 8 organizes the neocortical area map and regulates sensory map topography},
	Volume = {32},
	Year = {2012},
	File = {papers/Assimacopoulos_JNeurosci2012.pdf}}

@article{Demarque:2002,
	Abstract = {GABA and glutamate receptors are expressed in immature "silent" CA1 pyramidal neurons prior to synapse formation, but their function is unknown. We now report the presence of tonic, spontaneous, and evoked currents in embryonic and neonatal CA1 neurons mediated primarily by the activation of GABA(A) receptors. These currents are mediated by a nonconventional release of transmitters, as they persist in the presence of calcium channel blockers or botulinium toxin and are observed in Munc18-1-deficient mice in which vesicular release is abolished. This paracrine communication is modulated by glutamate but not GABA transporters, which do not operate during this period of life. Thus, a Ca(2+)- and SNARE-independent release of transmitters underlies a paracrine mode of communication before synapse formation.},
	Author = {Demarque, Michael and Represa, Alfonso and Becq, H{\'e}l{\`e}ne and Khalilov, Ilgam and Ben-Ari, Yehezkel and Aniksztejn, Laurent},
	Date-Added = {2018-01-16 22:30:38 +0000},
	Date-Modified = {2018-01-16 22:32:50 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Excitatory Amino Acid Antagonists;Fetus;Cell Differentiation;Electric Stimulation;SNARE Proteins;Synapses;Paracrine Communication;Rats;Calcium Signaling;Animals;Glutamic Acid;Synaptic Transmission;21 Epilepsy;gamma-Aminobutyric Acid;Vesicular Transport Proteins;Pyramidal Cells;Calcium;Rats, Wistar;Hippocampus;Receptors, GABA-A;Mice, Knockout;21 Neurophysiology;Membrane Potentials;GABA Antagonists;Mice;24 Pubmed search results 2008;Membrane Proteins;Receptors, N-Methyl-D-Aspartate},
	Mesh = {Animals; Calcium; Calcium Signaling; Cell Differentiation; Electric Stimulation; Excitatory Amino Acid Antagonists; Fetus; GABA Antagonists; GABA-A Receptor Antagonists; Glutamic Acid; Hippocampus; Membrane Potentials; Membrane Proteins; Mice; Mice, Knockout; Paracrine Communication; Pyramidal Cells; Rats; Rats, Wistar; Receptors, GABA-A; Receptors, N-Methyl-D-Aspartate; SNARE Proteins; Synapses; Synaptic Transmission; Vesicular Transport Proteins; gamma-Aminobutyric Acid},
	Month = {Dec},
	Number = {6},
	Pages = {1051-61},
	Pmid = {12495621},
	Pst = {ppublish},
	Title = {Paracrine intercellular communication by a Ca2+- and SNARE-independent release of GABA and glutamate prior to synapse formation},
	Volume = {36},
	Year = {2002},
	File = {papers/Demarque_Neuron2002.pdf}}

@article{Clarkson:2016,
	Abstract = {Sex differences in brain neuroanatomy and neurophysiology underpin considerable physiological and behavioural differences between females and males. Sexual differentiation of the brain is regulated by testosterone secreted by the testes predominantly during embryogenesis in humans and the neonatal period in rodents. Despite huge advances in understanding how testosterone, and its metabolite oestradiol, sexually differentiate the brain, little is known about the mechanism that actually generates the male-specific neonatal testosterone surge. This review examines the evidence for the role of the hypothalamus, and particularly the gonadotropin-releasing hormone (GnRH) neurons, in generating the neonatal testosterone surge in rodents and primates. Kisspeptin-GPR54 signalling is well established as a potent and critical regulator of GnRH neuron activity during puberty and adulthood, and we argue here for an equally important role at birth in driving the male-specific neonatal testosterone surge in rodents. The presence of a male-specific population of preoptic area kisspeptin neurons that appear transiently in the perinatal period provide one possible source of kisspeptin drive to neonatal GnRH neurons in the mouse.},
	Author = {Clarkson, Jenny and Herbison, Allan E},
	Date-Added = {2018-01-16 22:30:11 +0000},
	Date-Modified = {2018-01-16 22:30:11 +0000},
	Doi = {10.1098/rstb.2015.0115},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Keywords = {GPR54; GnRH; kisspeptin; sexual differentiation; testosterone},
	Mesh = {Animals; Animals, Newborn; Gene Expression Regulation, Developmental; Gonadotropin-Releasing Hormone; Hypothalamus; Male; Testosterone},
	Month = {Feb},
	Number = {1688},
	Pages = {20150115},
	Pmc = {PMC4785901},
	Pmid = {26833836},
	Pst = {ppublish},
	Title = {Hypothalamic control of the male neonatal testosterone surge},
	Volume = {371},
	Year = {2016},
	File = {papers/Clarkson_PhilosTransRSocLondBBiolSci2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rstb.2015.0115}}

@article{Turing:1952,
	Abstract = {It is suggested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis. Such a system, although it may originally be quite homogeneous, may later develop a pattern or structure due to an instability of the homogeneous equilibrium, which is triggered off by random disturbances. Such reaction-diffusion systems are considered in some detail in the case of an isolated ring of cells, a mathematically convenient, though biologically unusual system. The investigation is chiefly concerned with the onset of instability. It is found that there are six essentially different forms which this may take. In the most interesting form stationary waves appear on the ring. It is suggested that this might account, for instance, for the tentacle patterns on Hydra and for whorled leaves. A system of reactions and diffusion on a sphere is also considered. Such a system appears to account for gastrulation. Another reaction system in two dimensions gives rise to patterns reminiscent of dappling. It is also suggested that stationary waves in two dimensions could account for the phenomena of phyllotaxis. The purpose of this paper is to discuss a possible mechanism by which the genes of a zygote may determine the anatomical structure of the resulting organism. The theory does not make any new hypotheses; it merely suggests that certain well-known physical laws are sufficient to account for many of the facts. The full understanding of the paper requires a good knowledge of mathematics, some biology, and some elementary chemistry. Since readers cannot be expected to be experts in all of these subjects, a number of elementary facts are explained, which can be found in text-books, but whose omission would make the paper difficult reading.},
	Author = {A. M. Turing},
	Date-Added = {2018-01-16 22:20:28 +0000},
	Date-Modified = {2018-01-16 22:21:29 +0000},
	Issn = {00804622},
	Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
	Number = {641},
	Pages = {37-72},
	Publisher = {The Royal Society},
	Title = {The Chemical Basis of Morphogenesis},
	Url = {http://www.jstor.org/stable/92463},
	Volume = {237},
	Year = {1952},
	File = {papers/Turing_PhilosophicalTransactionsoftheRoyalSocietyofLondon.SeriesB,BiologicalSciences1952.pdf},
	Bdsk-Url-1 = {http://www.jstor.org/stable/92463}}

@article{Dalva:2007,
	Abstract = {Many cell adhesion molecules are localized at synaptic sites in neuronal axons and dendrites. These molecules bridge pre- and postsynaptic specializations but do far more than simply provide a mechanical link between cells. In this review, we will discuss the roles these proteins have during development and at mature synapses. Synaptic adhesion proteins participate in the formation, maturation, function and plasticity of synaptic connections. Together with conventional synaptic transmission mechanisms, these molecules are an important element in the trans-cellular communication mediated by synapses.},
	Author = {Dalva, Matthew B and McClelland, Andrew C and Kayser, Matthew S},
	Date-Added = {2018-01-16 22:15:29 +0000},
	Date-Modified = {2018-01-16 22:15:29 +0000},
	Doi = {10.1038/nrn2075},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Cell Adhesion Molecules; Models, Biological; Signal Transduction; Synapses},
	Month = {Mar},
	Number = {3},
	Pages = {206-20},
	Pmc = {PMC4756920},
	Pmid = {17299456},
	Pst = {ppublish},
	Title = {Cell adhesion molecules: signalling functions at the synapse},
	Volume = {8},
	Year = {2007},
	File = {papers/Dalva_NatRevNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2075}}

@article{Zuloaga:2014,
	Abstract = {Estrogen receptors regulate multiple brain functions, including stress, sexual, and memory-associated behaviors as well as controlling neuroendocrine and autonomic function. During development, estrogen signaling is involved in programming adult sex differences in physiology and behavior. Expression of estrogen receptor α changes across development in a region-specific fashion. By contrast, estrogen receptor β (ERβ) is expressed in many brain regions, yet few studies have explored sex and developmental differences in its expression, largely because of the absence of selective reagents for anatomical localization of the protein. This study utilized bacterial artificial chromosome transgenic mice expressing ERβ identified by enhanced green fluorescent protein (EGFP) to compare expression levels and distribution of ERβ in the male and female mouse forebrain on the day of birth (P0), on postnatal day 4 (P4), and on P21. By using qualitative analysis, we mapped the distribution of ERβ-EGFP and found developmental alterations in ERβ expression within the cortex, hippocampus, and hypothalamic regions including the arcuate, ventromedial, and paraventricular nuclei. We also report a sex difference in ERβ in the bed nucleus of the stria terminalis, with males showing greater expression at P4 and P21. Another sex difference was found in the anteroventral periventricular nucleus of P21, but not P0 or P4, mice, in which ERβ-EGFP-immunoreactive cells were densely clustered near the third ventricle in females but not males. These developmental changes and sex differences in ERβ indicate a mechanism through which estrogens might differentially affect brain functions or program adult physiology at select times during development.},
	Author = {Zuloaga, Damian G and Zuloaga, Kristen L and Hinds, Laura R and Carbone, David L and Handa, Robert J},
	Date-Added = {2018-01-16 22:14:36 +0000},
	Date-Modified = {2018-01-16 22:14:36 +0000},
	Doi = {10.1002/cne.23400},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {Esr2; age; development; estrogen receptor; estrogen receptor β; forebrain; sex difference},
	Mesh = {Age Factors; Animals; Chromosomes, Artificial, Bacterial; Estrogen Receptor beta; Female; Immunohistochemistry; Male; Mice; Mice, Transgenic; Prosencephalon; Sex Characteristics},
	Month = {Feb},
	Number = {2},
	Pages = {358-71},
	Pmc = {PMC4815281},
	Pmid = {23818057},
	Pst = {ppublish},
	Title = {Estrogen receptor β expression in the mouse forebrain: age and sex differences},
	Volume = {522},
	Year = {2014},
	File = {papers/Zuloaga_JCompNeurol2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.23400}}

@incollection{Puelles20153,
	Abstract = {Abstract Rodent brain gene patterns are readily comparable with counterparts in the human, avian, reptilian, amphibian, teleost, shark and agnathan species. This scenario provides substantial novel evidence for comparative neuroanatomy, both corroborating some earlier conclusions and calling for revision of other concepts. In recent years accumulated observations have shown that gene expression patterns frequently display reproducible boundaries; these tend to be aligned with the axial and dorsoventral dimensions of the neural tube and are topologically invariant during ontogenesis. Many early molecular patterns are remarkably resistant to evolutionary change. Accumulated comparative results over the last decade strongly indicate that there is a common pattern of differentially-specified neural regions among all vertebrates. This chapter studies the molecular approaches to understanding the structural and functional organization of the nervous system which promise new insights into modular brain domains conserved among various species. Fate-map analysis suggests that early differential molecular specification of progenitor regions and subregions in the neural plate and neural tube eventually correlates with specific prospective fates via patterned proliferation, neurogenesis and differentiation. },
	Address = {San Diego},
	Author = {Luis Puelles and Salvador Mart{\'\i}nez and Margaret Mart{\'\i}nez-De-La-Torre and John L.R. Rubenstein},
	Booktitle = {The Rat Nervous System (Fourth Edition)},
	Date-Added = {2018-01-16 22:12:46 +0000},
	Date-Modified = {2018-01-16 22:12:46 +0000},
	Doi = {https://doi.org/10.1016/B978-0-12-374245-2.00001-2},
	Edition = {Fourth Edition},
	Editor = {Paxinos, George},
	Isbn = {978-0-12-374245-2},
	Keywords = {Vertebrates},
	Pages = {3 - 24},
	Publisher = {Academic Press},
	Title = {Chapter 1 - Gene Maps and Related Histogenetic Domains in the Forebrain and Midbrain},
	Url = {https://www.sciencedirect.com/science/article/pii/B9780123742452000012},
	Year = {2015},
	File = {papers/Puelles_2015.pdf},
	Bdsk-Url-1 = {https://www.sciencedirect.com/science/article/pii/B9780123742452000012},
	Bdsk-Url-2 = {https://doi.org/10.1016/B978-0-12-374245-2.00001-2}}

@article{Schlaggar:2011,
	Abstract = {In this issue of Neuron, Chen and colleagues combine structural MRI and a twin-study design to investigate the influence of genetics on human cortical regionalization. Their results resonate with findings from animal studies and certain human syndromes of developmental cortical malformation.},
	Author = {Schlaggar, Bradley L},
	Date-Added = {2018-01-16 22:11:15 +0000},
	Date-Modified = {2018-01-16 22:11:15 +0000},
	Doi = {10.1016/j.neuron.2011.10.024},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Brain; Cerebral Cortex; Gene Expression Regulation, Developmental; Humans; Male; Twins},
	Month = {Nov},
	Number = {4},
	Pages = {499-501},
	Pmc = {PMC3226785},
	Pmid = {22099452},
	Pst = {ppublish},
	Title = {Mapping genetic influences on cortical regionalization},
	Volume = {72},
	Year = {2011},
	File = {papers/Schlaggar_Neuron2011.pdf}}

@article{Groten:2013,
	Abstract = {Although the contribution of Ca(2+) buffering systems can vary between neuronal types and cellular compartments, it is unknown whether distinct Ca(2+) sources within a neuron have different buffers. As individual Ca(2+) sources can have separate functions, we propose that each is handled by unique systems. Using Aplysia californica bag cell neurons, which initiate reproduction through an afterdischarge involving multiple Ca(2+)-dependent processes, we investigated the role of endoplasmic reticulum (ER) and mitochondrial sequestration, as well as extrusion via the plasma membrane Ca(2+)-ATPase (PMCA) and Na(+)/Ca(2+) exchanger, to the clearance of voltage-gated Ca(2+) influx, Ca(2+)-induced Ca(2+)-release (CICR), and store-operated Ca(2+) influx. Cultured bag cell neurons were filled with the Ca(2+) indicator, fura-PE3, to image Ca(2+) under whole-cell voltage clamp. A 5 Hz, 1 min train of depolarizing voltage steps elicited voltage-gated Ca(2+) influx followed by EGTA-sensitive CICR from the mitochondria. A compartment model of Ca(2+) indicated the effect of EGTA on CICR was due to buffering of released mitochondrial Ca(2+) rather than uptake competition. Removal of voltage-gated Ca(2+) influx was dominated by the mitochondria and PMCA, with no contribution from the Na(+)/Ca(2+) exchanger or sarcoplasmic/endoplasmic Ca(2+)-ATPase (SERCA). In contrast, CICR recovery was slowed by eliminating the Na(+)/Ca(2+) exchanger and PMCA. Last, store-operated influx, evoked by ER depletion, was removed by the SERCA and depended on the mitochondrial membrane potential. Our results demonstrate that distinct buffering systems are dedicated to particular Ca(2+) sources. In general, this may represent a means to differentially regulate Ca(2+)-dependent processes, and for Aplysia, influence how reproductive behavior is triggered.},
	Author = {Groten, Christopher J and Rebane, Jonathan T and Blohm, Gunnar and Magoski, Neil S},
	Date-Added = {2018-01-16 22:11:02 +0000},
	Date-Modified = {2018-01-16 22:11:02 +0000},
	Doi = {10.1523/JNEUROSCI.6384-11.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Aplysia; Calcium; Cells, Cultured; Egtazic Acid; Endoplasmic Reticulum; Membrane Potentials; Mitochondria; Molecular Imaging; Neuroendocrine Cells; Neurons; Plasma Membrane Calcium-Transporting ATPases; Sarcoplasmic Reticulum Calcium-Transporting ATPases; Sodium-Calcium Exchanger},
	Month = {Apr},
	Number = {15},
	Pages = {6476-91},
	Pmid = {23575846},
	Pst = {ppublish},
	Title = {Separate Ca2+ sources are buffered by distinct Ca2+ handling systems in aplysia neuroendocrine cells},
	Volume = {33},
	Year = {2013},
	File = {papers/Groten_JNeurosci2013.pdf}}

@article{Suarez:2014a,
	Abstract = {Axonal connections between the left and right sides of the brain are crucial for bilateral integration of lateralized sensory, motor, and associative functions. Throughout vertebrate species, forebrain commissures share a conserved developmental plan, a similar position relative to each other within the brain and similar patterns of connectivity. However, major events in the evolution of the vertebrate brain, such as the expansion of the telencephalon in tetrapods and the origin of the six-layered isocortex in mammals, resulted in the emergence and diversification of new commissural routes. These new interhemispheric connections include the pallial commissure, which appeared in the ancestors of tetrapods and connects the left and right sides of the medial pallium (hippocampus in mammals), and the corpus callosum, which is exclusive to eutherian (placental) mammals and connects both isocortical hemispheres. A comparative analysis of commissural systems in vertebrates reveals that the emergence of new commissural routes may have involved co-option of developmental mechanisms and anatomical substrates of preexistent commissural pathways. One of the embryonic regions of interest for studying these processes is the commissural plate, a portion of the early telencephalic midline that provides molecular specification and a cellular scaffold for the development of commissural axons. Further investigations into these embryonic processes in carefully selected species will provide insights not only into the mechanisms driving commissural evolution, but also regarding more general biological problems such as the role of developmental plasticity in evolutionary change.},
	Author = {Su{\'a}rez, Rodrigo and Gobius, Ilan and Richards, Linda J},
	Date-Added = {2018-01-16 22:08:37 +0000},
	Date-Modified = {2018-01-16 22:08:37 +0000},
	Doi = {10.3389/fnhum.2014.00497},
	Journal = {Front Hum Neurosci},
	Journal-Full = {Frontiers in human neuroscience},
	Keywords = {anterior commissure; axon guidance; commissural plate; comparative neuroanatomy; corpus callosum; hippocampal commissure},
	Pages = {497},
	Pmc = {PMC4094842},
	Pmid = {25071525},
	Pst = {epublish},
	Title = {Evolution and development of interhemispheric connections in the vertebrate forebrain},
	Volume = {8},
	Year = {2014},
	File = {papers/Suárez_FrontHumNeurosci2014.pdf}}

@article{Jones:2016,
	Abstract = {Though both clinicians and scientists have long recognized the influence of extracellular calcium on the function of muscle and nervous tissue, recent insights reveal that the mechanisms allowing changes in extracellular calcium to alter cellular excitability have been incompletely understood. For many years the effects of calcium on neuronal signaling were explained only in terms of calcium entry through voltage-gated calcium channels and biophysical charge screening. More recently however, it has been recognized that the calcium-sensing receptor is prevalent in the nervous system and regulates synaptic transmission and neuronal activity via multiple signaling pathways. Here we review the multiplicity of mechanisms by which changes in extracellular calcium alter neuronal signaling and propose that multiple mechanisms are required to describe the full range of experimental observations.},
	Author = {Jones, Brian L and Smith, Stephen M},
	Date-Added = {2018-01-16 22:08:12 +0000},
	Date-Modified = {2018-01-16 22:08:12 +0000},
	Doi = {10.3389/fphys.2016.00116},
	Journal = {Front Physiol},
	Journal-Full = {Frontiers in physiology},
	Keywords = {action potentials; calcium; calcium sensing receptor; excitability; ion channels; nervous system; synaptic transmission},
	Pages = {116},
	Pmc = {PMC4811949},
	Pmid = {27065884},
	Pst = {epublish},
	Title = {Calcium-Sensing Receptor: A Key Target for Extracellular Calcium Signaling in Neurons},
	Volume = {7},
	Year = {2016},
	File = {papers/Jones_FrontPhysiol2016.pdf}}

@article{Greig:2016,
	Abstract = {While transcriptional controls over the size and relative position of cortical areas have been identified, less is known about regulators that direct acquisition of area-specific characteristics. Here, we report that the transcription factor Ctip1 functions in primary sensory areas to repress motor and activate sensory programs of gene expression, enabling establishment of sharp molecular boundaries defining functional areas. In Ctip1 mutants, abnormal gene expression leads to aberrantly motorized corticocortical and corticofugal output connectivity. Ctip1 critically regulates differentiation of layer IV neurons, and selective loss of Ctip1 in cortex deprives thalamocortical axons of their receptive "sensory field" in layer IV, which normally provides a tangentially and radially defined compartment of dedicated synaptic territory. Therefore, although thalamocortical axons invade appropriate cortical regions, they are unable to organize into properly configured sensory maps. Together, these data identify Ctip1 as a critical control over sensory area development.},
	Author = {Greig, Luciano C and Woodworth, Mollie B and Greppi, Chlo{\'e} and Macklis, Jeffrey D},
	Date-Added = {2018-01-16 22:01:17 +0000},
	Date-Modified = {2018-01-16 22:01:17 +0000},
	Doi = {10.1016/j.neuron.2016.03.008},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axons; Carrier Proteins; Cell Differentiation; Gene Expression Regulation, Developmental; Mice; Mice, Knockout; Mutation; Neocortex; Neurons; Nuclear Proteins; Signal Transduction; Thalamus},
	Month = {04},
	Number = {2},
	Pages = {261-77},
	Pmc = {PMC4873772},
	Pmid = {27100196},
	Pst = {ppublish},
	Title = {Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex},
	Volume = {90},
	Year = {2016},
	File = {papers/Greig_Neuron2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2016.03.008}}

@article{Ypsilanti:2016,
	Abstract = {The development of the cortex is an elaborate process that integrates a plethora of finely tuned molecular processes ranging from carefully regulated gradients of transcription factors, dynamic changes in the chromatin landscape, or formation of protein complexes to elicit and regulate transcription. Combined with cellular processes such as cell type specification, proliferation, differentiation, and migration, all of these developmental processes result in the establishment of an adult mammalian cortex with its typical lamination and regional patterning. By examining in-depth the role of one transcription factor, Pax6, on the regulation of cortical development, its integration in the regulation of chromatin state, and its regulation by cis-regulatory elements, we aim to demonstrate the importance of integrating each level of regulation in our understanding of cortical development.},
	Author = {Ypsilanti, Ath{\'e}na R and Rubenstein, John L R},
	Date-Added = {2018-01-16 22:00:12 +0000},
	Date-Modified = {2018-01-16 22:00:12 +0000},
	Doi = {10.1002/cne.23866},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {Chromatin; Epigenetics; Pax6; Transcription; cortex; cortical development},
	Mesh = {Animals; Biological Evolution; Cerebral Cortex; Chromatin; Chromatin Assembly and Disassembly; Epigenesis, Genetic; Eye Proteins; Homeodomain Proteins; Humans; PAX6 Transcription Factor; Paired Box Transcription Factors; Repressor Proteins},
	Month = {Feb},
	Number = {3},
	Pages = {609-29},
	Pmc = {PMC4706819},
	Pmid = {26304102},
	Pst = {ppublish},
	Title = {Transcriptional and epigenetic mechanisms of early cortical development: An examination of how Pax6 coordinates cortical development},
	Volume = {524},
	Year = {2016},
	File = {papers/Ypsilanti_JCompNeurol2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.23866}}

@article{Furchtgott:2017,
	Abstract = {Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships.},
	Author = {Furchtgott, Leon A and Melton, Samuel and Menon, Vilas and Ramanathan, Sharad},
	Date-Added = {2018-01-16 21:58:50 +0000},
	Date-Modified = {2018-01-16 21:58:50 +0000},
	Doi = {10.7554/eLife.20488},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {Transcriptomics; computational biology; developmental biology; human; mouse; stem cells; systems biology},
	Month = {Mar},
	Pmc = {PMC5352226},
	Pmid = {28296636},
	Pst = {epublish},
	Title = {Discovering sparse transcription factor codes for cell states and state transitions during development},
	Volume = {6},
	Year = {2017},
	File = {papers/Furchtgott_Elife2017.pdf}}

@article{Homman-Ludiye:2014,
	Abstract = {The integration of the visual stimulus takes place at the level of the neocortex, organized in anatomically distinct and functionally unique areas. Primates, including humans, are heavily dependent on vision, with approximately 50% of their neocortical surface dedicated to visual processing and possess many more visual areas than any other mammal, making them the model of choice to study visual cortical arealisation. However, in order to identify the mechanisms responsible for patterning the developing neocortex, specifying area identity as well as elucidate events that have enabled the evolution of the complex primate visual cortex, it is essential to gain access to the cortical maps of alternative species. To this end, species including the mouse have driven the identification of cellular markers, which possess an area-specific expression profile, the development of new tools to label connections and technological advance in imaging techniques enabling monitoring of cortical activity in a behaving animal. In this review we present non-primate species that have contributed to elucidating the evolution and development of the visual cortex. We describe the current understanding of the mechanisms supporting the establishment of areal borders during development, mainly gained in the mouse thanks to the availability of genetically modified lines but also the limitations of the mouse model and the need for alternate species.},
	Author = {Homman-Ludiye, Jihane and Bourne, James A},
	Date-Added = {2018-01-16 21:57:26 +0000},
	Date-Modified = {2018-01-16 21:57:26 +0000},
	Doi = {10.3389/fncir.2014.00079},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {cell markers; cortical patterning; guidance molecules; neocortex},
	Mesh = {Animals; Biological Evolution; Brain Mapping; Nerve Tissue Proteins; Neurons; Visual Cortex; Visual Pathways},
	Pages = {79},
	Pmc = {PMC4081835},
	Pmid = {25071460},
	Pst = {epublish},
	Title = {Mapping arealisation of the visual cortex of non-primate species: lessons for development and evolution},
	Volume = {8},
	Year = {2014},
	File = {papers/Homman-Ludiye_FrontNeuralCircuits2014.pdf},
	Bdsk-File-2 = {papers/Homman-Ludiye_FrontNeuralCircuits2014.jpg}}

@article{Fenlon:2013,
	Author = {Fenlon, Laura R and Su{\'a}rez, Rodrigo},
	Date-Added = {2018-01-16 21:56:20 +0000},
	Date-Modified = {2018-01-16 21:56:20 +0000},
	Doi = {10.1523/JNEUROSCI.2859-13.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Gene Expression Regulation, Developmental; Neocortex; Thalamus},
	Month = {Aug},
	Number = {35},
	Pages = {13938-9},
	Pmid = {23986230},
	Pst = {ppublish},
	Title = {Thalamic afferents and neocortical arealization: an ongoing journey},
	Volume = {33},
	Year = {2013},
	File = {papers/Fenlon_JNeurosci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.2859-13.2013}}

@article{Pouchelon:2014,
	Abstract = {PURPOSE OF REVIEW: Neocortical and thalamic interactions are necessary for the execution of complex sensory-motor tasks and associated cognitive processes. Investigation of thalamocortical circuit development is therefore critical to understand developmental disorders involving abnormal cortical function. Here, we review recent advances in our understanding of thalamus-dependent cortical patterning and cortical neuron differentiation.
RECENT FINDINGS: Although the principles of cortical map patterning are increasingly understood, the extent to which thalamocortical inputs contribute to cortical neuron differentiation is still unclear. The recent development of genetic models allowing cell-type-specific dissection of cortical input pathways has shed light on some of the input-dependent and activity-dependent processes occurring during cortical development, which are discussed here.
SUMMARY: These recent studies have revealed interwoven links between thalamic and cortical neurons, in which cell intrinsic differentiation programs are tightly regulated by synaptic input during a prolonged period of development. Challenges in the years to come will be to identify the mechanisms underlying the reciprocal interactions between intrinsic and extrinsic differentiation programs, and their contribution to neurodevelopmental disorders and neuropsychiatric disorders at large.},
	Author = {Pouchelon, Gabrielle and Jabaudon, Denis},
	Date-Added = {2018-01-16 21:54:34 +0000},
	Date-Modified = {2018-01-16 21:54:34 +0000},
	Doi = {10.1097/WCO.0000000000000070},
	Journal = {Curr Opin Neurol},
	Journal-Full = {Current opinion in neurology},
	Mesh = {Animals; Brain Mapping; Humans; Neocortex; Nerve Net; Neural Pathways; Neurogenesis; Neurons; Thalamus},
	Month = {Apr},
	Number = {2},
	Pages = {142-8},
	Pmid = {24553463},
	Pst = {ppublish},
	Title = {Nurturing the cortex's thalamic nature},
	Volume = {27},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1097/WCO.0000000000000070}}

@article{Jabaudon:2017,
	Author = {Jabaudon, Denis},
	Date-Added = {2018-01-16 21:53:47 +0000},
	Date-Modified = {2018-01-16 21:53:47 +0000},
	Doi = {10.1038/ncomms16042},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Month = {Jul},
	Pages = {16042},
	Pmc = {PMC5500875},
	Pmid = {28671189},
	Pst = {epublish},
	Title = {Fate and freedom in developing neocortical circuits},
	Volume = {8},
	Year = {2017},
	File = {papers/Jabaudon_NatCommun2017.pdf}}

@article{Frangeul:2016,
	Abstract = {Modality-specific sensory inputs from individual sense organs are processed in parallel in distinct areas of the neocortex. For each sensory modality, input follows a cortico-thalamo-cortical loop in which a 'first-order' exteroceptive thalamic nucleus sends peripheral input to the primary sensory cortex, which projects back to a 'higher order' thalamic nucleus that targets a secondary sensory cortex. This conserved circuit motif raises the possibility that shared genetic programs exist across sensory modalities. Here we report that, despite their association with distinct sensory modalities, first-order nuclei in mice are genetically homologous across somatosensory, visual, and auditory pathways, as are higher order nuclei. We further reveal peripheral input-dependent control over the transcriptional identity and connectivity of first-order nuclei by showing that input ablation leads to induction of higher-order-type transcriptional programs and rewiring of higher-order-directed descending cortical input to deprived first-order nuclei. These findings uncover an input-dependent genetic logic for the design and plasticity of sensory pathways, in which conserved developmental programs lead to conserved circuit motifs across sensory modalities.},
	Author = {Frangeul, Laura and Pouchelon, Gabrielle and Telley, Ludovic and Lefort, Sandrine and Luscher, Christian and Jabaudon, Denis},
	Date-Added = {2018-01-16 21:49:52 +0000},
	Date-Modified = {2018-01-16 21:49:52 +0000},
	Doi = {10.1038/nature19770},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Afferent Pathways; Animals; Auditory Pathways; Female; Gene Expression Regulation, Developmental; Geniculate Bodies; Male; Mice; Mice, Inbred C57BL; Models, Genetic; Neuronal Plasticity; Somatosensory Cortex; Thalamic Nuclei; Transcription, Genetic; Visual Pathways},
	Month = {Oct},
	Number = {7623},
	Pages = {96-98},
	Pmid = {27669022},
	Pst = {ppublish},
	Title = {A cross-modal genetic framework for the development and plasticity of sensory pathways},
	Volume = {538},
	Year = {2016},
	File = {papers/Frangeul_Nature2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature19770}}

@article{Marques-Smith:2016,
	Abstract = {GABAergic activity is thought to influence developing neocortical sensory circuits. Yet the late postnatal maturation of local layer (L)4 circuits suggests alternate sources of GABAergic control in nascent thalamocortical networks. We show that a population of L5b, somatostatin (SST)-positive interneuron receives early thalamic synaptic input and, using laser-scanning photostimulation, identify an early transient circuit between these cells and L4 spiny stellates (SSNs) that disappears by the end of the L4 critical period. Sensory perturbation disrupts the transition to a local GABAergic circuit, suggesting a link between translaminar and local control of SSNs. Conditional silencing of SST+ interneurons or conversely biasing the circuit toward local inhibition by overexpression of neuregulin-1 type 1 results in an absence of early L5b GABAergic input in mutants and delayed thalamic innervation of SSNs. These data identify a role for L5b SST+ interneurons in the control of SSNs in the early postnatal neocortex.},
	Author = {Marques-Smith, Andre and Lyngholm, Daniel and Kaufmann, Anna-Kristin and Stacey, Jacqueline A and Hoerder-Suabedissen, Anna and Becker, Esther B E and Wilson, Michael C and Moln{\'a}r, Zolt{\'a}n and Butt, Simon J B},
	Date-Added = {2018-01-16 21:47:09 +0000},
	Date-Modified = {2018-01-16 21:48:58 +0000},
	Doi = {10.1016/j.neuron.2016.01.015},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {development; Circuits; activity-development; interneurons; Transient; Neocortex; isocortex},
	Mesh = {Animals; Electric Stimulation; Female; Interneurons; Male; Membrane Potentials; Mice; Mice, Transgenic; Neural Pathways; Neuregulin-1; Photic Stimulation; Somatosensory Cortex; Somatostatin; Thalamus; gamma-Aminobutyric Acid},
	Month = {Feb},
	Number = {3},
	Pages = {536-49},
	Pmc = {PMC4742537},
	Pmid = {26844833},
	Pst = {ppublish},
	Title = {A Transient Translaminar GABAergic Interneuron Circuit Connects Thalamocortical Recipient Layers in Neonatal Somatosensory Cortex},
	Volume = {89},
	Year = {2016},
	File = {papers/Marques-Smith_Neuron2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2016.01.015}}

@article{Ji:2015,
	Abstract = {Layer 1 (L1) of primary visual cortex (V1) is the target of projections from many brain regions outside of V1. We found that inputs to the non-columnar mouse V1 from the dorsal lateral geniculate nucleus and feedback projections from multiple higher cortical areas to L1 are patchy. The patches are matched to a pattern of M2 muscarinic acetylcholine receptor expression at fixed locations of mouse, rat, and monkey V1. Neurons in L2/3 aligned with M2-rich patches have high spatial acuity, whereas cells in M2-poor zones exhibited high temporal acuity. Together M2+ and M2- zones form constant-size domains that are repeated across V1. Domains map subregions of the receptive field, such that multiple copies are contained within the point image. The results suggest that the modular network in mouse V1 selects spatiotemporally distinct clusters of neurons within the point image for top-down control and differential routing of inputs to cortical streams.},
	Author = {Ji, Weiqing and G{\u a}m{\u a}nu{\c t}, R{\u a}zvan and Bista, Pawan and D'Souza, Rinaldo D and Wang, Quanxin and Burkhalter, Andreas},
	Date-Added = {2018-01-16 21:09:24 +0000},
	Date-Modified = {2018-01-16 21:09:24 +0000},
	Doi = {10.1016/j.neuron.2015.07.004},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Female; Haplorhini; Male; Mice; Mice, Inbred C57BL; Nerve Net; Photic Stimulation; Rats; Rats, Long-Evans; Visual Cortex; Visual Pathways},
	Month = {Aug},
	Number = {3},
	Pages = {632-43},
	Pmc = {PMC4529541},
	Pmid = {26247867},
	Pst = {ppublish},
	Title = {Modularity in the Organization of Mouse Primary Visual Cortex},
	Volume = {87},
	Year = {2015},
	File = {papers/Ji_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.07.004}}

@article{Chou:2013,
	Abstract = {Studies of area patterning of the neocortex have focused on primary areas, concluding that the primary visual area, V1, is specified by transcription factors (TFs) expressed by progenitors. Mechanisms that determine higher-order visual areas (V(HO)) and distinguish them from V1 are unknown. We demonstrated a requirement for thalamocortical axon (TCA) input by genetically deleting geniculocortical TCAs and showed that they drive differentiation of patterned gene expression that distinguishes V1 and V(HO). Our findings suggest a multistage process for area patterning: TFs expressed by progenitors specify an occipital visual cortical field that differentiates into V1 and V(HO); this latter phase requires geniculocortical TCA input to the nascent V1 that determines genetic distinctions between V1 and V(HO) for all layers and ultimately determines their area-specific functional properties.},
	Author = {Chou, Shen-Ju and Babot, Zoila and Leing{\"a}rtner, Axel and Studer, Michele and Nakagawa, Yasushi and O'Leary, Dennis D M},
	Date-Added = {2018-01-16 21:08:09 +0000},
	Date-Modified = {2018-01-16 21:08:09 +0000},
	Doi = {10.1126/science.1232806},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Axons; Gene Deletion; Gene Expression Regulation; Genetic Markers; Mice; Mice, Knockout; Neocortex; Neural Stem Cells; Thalamus; Transcription Factors; Visual Cortex; Visual Fields},
	Month = {Jun},
	Number = {6137},
	Pages = {1239-42},
	Pmc = {PMC3851411},
	Pmid = {23744949},
	Pst = {ppublish},
	Title = {Geniculocortical input drives genetic distinctions between primary and higher-order visual areas},
	Volume = {340},
	Year = {2013},
	File = {papers/Chou_Science2013.pdf},
	Bdsk-File-2 = {papers/Chou_Science2013a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1232806}}

@article{Bourane:2015,
	Abstract = {Sensory circuits in the dorsal spinal cord integrate and transmit multiple cutaneous sensory modalities including the sense of light touch. Here, we identify a population of excitatory interneurons (INs) in the dorsal horn that are important for transmitting innocuous light touch sensation. These neurons express the ROR alpha (RORα) nuclear orphan receptor and are selectively innervated by cutaneous low threshold mechanoreceptors (LTMs). Targeted removal of RORα INs in the dorsal spinal cord leads to a marked reduction in behavioral responsiveness to light touch without affecting responses to noxious and itch stimuli. RORα IN-deficient mice also display a selective deficit in corrective foot movements. This phenotype, together with our demonstration that the RORα INs are innervated by corticospinal and vestibulospinal projection neurons, argues that the RORα INs direct corrective reflex movements by integrating touch information with descending motor commands from the cortex and cerebellum.},
	Author = {Bourane, Steeve and Grossmann, Katja S and Britz, Olivier and Dalet, Antoine and Del Barrio, Marta Garcia and Stam, Floor J and Garcia-Campmany, Lidia and Koch, Stephanie and Goulding, Martyn},
	Date-Added = {2018-01-16 21:07:27 +0000},
	Date-Modified = {2018-01-16 21:07:27 +0000},
	Doi = {10.1016/j.cell.2015.01.011},
	Journal = {Cell},
	Journal-Full = {Cell},
	Mesh = {Animals; Interneurons; Mechanotransduction, Cellular; Mice; Motor Activity; Motor Neurons; Neural Pathways; Nuclear Receptor Subfamily 1, Group F, Member 1; Spinal Cord Dorsal Horn; Synapses; Touch},
	Month = {Jan},
	Number = {3},
	Pages = {503-15},
	Pmc = {PMC4431637},
	Pmid = {25635458},
	Pst = {ppublish},
	Title = {Identification of a spinal circuit for light touch and fine motor control},
	Volume = {160},
	Year = {2015},
	File = {papers/Bourane_Cell2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cell.2015.01.011}}

@article{Sun:2014,
	Abstract = {The size and extent of folding of the mammalian cerebral cortex are important factors that influence a species' cognitive abilities and sensorimotor skills. Studies in various animal models and in humans have provided insight into the mechanisms that regulate cortical growth and folding. Both protein-coding genes and microRNAs control cortical size, and recent progress in characterizing basal progenitor cells and the genes that regulate their proliferation has contributed to our understanding of cortical folding. Neurological disorders linked to disruptions in cortical growth and folding have been associated with novel neurogenetic mechanisms and aberrant signalling pathways, and these findings have changed concepts of brain evolution and may lead to new medical treatments for certain disorders.},
	Author = {Sun, Tao and Hevner, Robert F},
	Date-Added = {2018-01-16 21:04:52 +0000},
	Date-Modified = {2018-01-16 21:04:52 +0000},
	Doi = {10.1038/nrn3707},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Biological Evolution; Cerebral Cortex; Humans; Neural Stem Cells},
	Month = {Apr},
	Number = {4},
	Pages = {217-32},
	Pmc = {PMC4107216},
	Pmid = {24646670},
	Pst = {ppublish},
	Title = {Growth and folding of the mammalian cerebral cortex: from molecules to malformations},
	Volume = {15},
	Year = {2014},
	File = {papers/Sun_NatRevNeurosci2014.pdf}}

@article{Harris:2015,
	Abstract = {Similarities in neocortical circuit organization across areas and species suggest a common strategy to process diverse types of information, including sensation from diverse modalities, motor control and higher cognitive processes. Cortical neurons belong to a small number of main classes. The properties of these classes, including their local and long-range connectivity, developmental history, gene expression, intrinsic physiology and in vivo activity patterns, are remarkably similar across areas. Each class contains subclasses; for a rapidly growing number of these, conserved patterns of input and output connections are also becoming evident. The ensemble of circuit connections constitutes a basic circuit pattern that appears to be repeated across neocortical areas, with area- and species-specific modifications. Such 'serially homologous' organization may adapt individual neocortical regions to the type of information each must process.},
	Author = {Harris, Kenneth D and Shepherd, Gordon M G},
	Date-Added = {2018-01-16 21:04:43 +0000},
	Date-Modified = {2018-01-16 21:04:43 +0000},
	Doi = {10.1038/nn.3917},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Animals; Humans; Interneurons; Neocortex; Nerve Net},
	Month = {Feb},
	Number = {2},
	Pages = {170-81},
	Pmc = {PMC4889215},
	Pmid = {25622573},
	Pst = {ppublish},
	Title = {The neocortical circuit: themes and variations},
	Volume = {18},
	Year = {2015},
	File = {papers/Harris_NatNeurosci2015.pdf}}

@article{Alfano:2014,
	Abstract = {The mammalian neocortex is subdivided into cytoarchitectural areas with distinct connectivity, gene expression and neural functions. Areal identity is initially specified by rostrocaudal and mediolateral gene expression gradients in neuroepithelial and radial glial progenitors (the 'protomap'). On further differentiation, distinct sets of gene expression gradients arise in intermediate progenitors and postmitotic neurons, and are necessary to implement areal specification. However, it is still unknown whether postmitotic gene expression gradients can determine areal identity independently of protomap gradients. Here we show, by cell type-restricted genetic loss- and gain-of-function, that high levels of postmitotic COUP-TFI (Nr2f1) expression are necessary and sufficient for the development of sensory (caudal) areal identity. Our data indicate a crucial role for postmitotic patterning genes in areal specification and reveal an unexpected plasticity in this process, which may account for complex and evolutionarily novel structures characteristic of the mammalian neocortex.},
	Author = {Alfano, C and Magrinelli, E and Harb, K and Hevner, R F and Studer, M},
	Date-Added = {2018-01-16 21:04:33 +0000},
	Date-Modified = {2018-01-16 21:04:33 +0000},
	Doi = {10.1038/ncomms6632},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Mesh = {Animals; COUP Transcription Factor I; Female; Gene Expression Regulation, Developmental; Male; Mice; Mice, Knockout; Mitosis; Neocortex; Sensory Receptor Cells},
	Month = {Dec},
	Pages = {5632},
	Pmid = {25476200},
	Pst = {epublish},
	Title = {Postmitotic control of sensory area specification during neocortical development},
	Volume = {5},
	Year = {2014},
	File = {papers/Alfano_NatCommun2014.pdf}}

@article{Zembrzycki:2015,
	Abstract = {In mammals, the neocortical layout consists of few modality-specific primary sensory areas and a multitude of higher order ones. Abnormal layout of cortical areas may disrupt sensory function and behavior. Developmental genetic mechanisms specify primary areas, but mechanisms influencing higher order area properties are unknown. By exploiting gain-of and loss-of function mouse models of the transcription factor Emx2, we have generated bi-directional changes in primary visual cortex size in vivo and have used it as a model to show a novel and prominent function for genetic mechanisms regulating primary visual area size and also proportionally dictating the sizes of surrounding higher order visual areas. This finding redefines the role for intrinsic genetic mechanisms to concomitantly specify and scale primary and related higher order sensory areas in a linear fashion.},
	Author = {Zembrzycki, Andreas and Stocker, Adam M and Leing{\"a}rtner, Axel and Sahara, Setsuko and Chou, Shen-Ju and Kalatsky, Valery and May, Scott R and Stryker, Michael P and O'Leary, Dennis Dm},
	Date-Added = {2018-01-16 21:04:09 +0000},
	Date-Modified = {2018-01-16 21:04:09 +0000},
	Doi = {10.7554/eLife.11416},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {Emx2; brain evolution; developmental biology; extrastriate cortex; mouse; neocortical area patterning; neuroscience; sensory systems; stem cells; visual cortex},
	Mesh = {Animals; Gene Expression Regulation, Developmental; Homeodomain Proteins; Mice, Inbred C57BL; Mice, Transgenic; Transcription Factors; Vision, Ocular; Visual Cortex},
	Month = {Dec},
	Pmc = {PMC4739755},
	Pmid = {26705332},
	Pst = {epublish},
	Title = {Genetic mechanisms control the linear scaling between related cortical primary and higher order sensory areas},
	Volume = {4},
	Year = {2015},
	File = {papers/Zembrzycki_Elife2015.pdf}}

@article{Fenlon:2015b,
	Abstract = {BACKGROUND: Autism spectrum disorders (ASD) are a group of poorly understood behavioural disorders, which have increased in prevalence in the past two decades. Animal models offer the opportunity to understand the biological basis of these disorders. Studies comparing different mouse strains have identified the inbred BTBR T + tf/J (BTBR) strain as a mouse model of ASD based on its anti-social and repetitive behaviours. Adult BTBR mice have complete agenesis of the corpus callosum, reduced cortical thickness and changes in early neurogenesis. However, little is known about the development or ultimate organisation of cortical areas devoted to specific sensory and motor functions in these mice that may also contribute to their behavioural phenotype.
RESULTS: In this study, we performed diffusion tensor imaging and tractography, together with histological analyses to investigate the emergence of functional areas in the cerebral cortex and their connections in BTBR mice and age-matched C57Bl/6 control mice. We found evidence that neither the anterior commissure nor the hippocampal commissure compensate for the loss of callosal connections, indicating that no interhemispheric neocortical connectivity is present in BTBR mice. We also found that both the primary visual and somatosensory cortical areas are shifted medially in BTBR mice compared to controls and that cortical thickness is differentially altered in BTBR mice between cortical areas and throughout development.
CONCLUSIONS: We demonstrate that interhemispheric connectivity and cortical area formation are altered in an age- and region-specific manner in BTBR mice, which may contribute to the behavioural deficits previously observed in this strain. Some of these developmental patterns of change are also present in human ASD patients, and elucidating the aetiology driving cortical changes in BTBR mice may therefore help to increase our understanding of this disorder.},
	Author = {Fenlon, Laura R and Liu, Sha and Gobius, Ilan and Kurniawan, Nyoman D and Murphy, Skyle and Moldrich, Randal X and Richards, Linda J},
	Date-Added = {2018-01-16 21:03:53 +0000},
	Date-Modified = {2018-01-16 21:03:53 +0000},
	Doi = {10.1186/s13064-015-0033-y},
	Journal = {Neural Dev},
	Journal-Full = {Neural development},
	Mesh = {Agenesis of Corpus Callosum; Aging; Animals; Anterior Cerebellar Commissure; Autism Spectrum Disorder; Cerebral Cortex; Diffusion Tensor Imaging; Disease Models, Animal; Fornix, Brain; Mice; Mice, Inbred C57BL; Mice, Inbred Strains; Mice, Neurologic Mutants; Phenotype; Somatosensory Cortex; Visual Cortex},
	Month = {Apr},
	Pages = {10},
	Pmc = {PMC4412039},
	Pmid = {25879444},
	Pst = {epublish},
	Title = {Formation of functional areas in the cerebral cortex is disrupted in a mouse model of autism spectrum disorder},
	Volume = {10},
	Year = {2015},
	File = {papers/Fenlon_NeuralDev2015a.pdf}}

@article{Barber:2016,
	Abstract = {Tangential migration is a mode of cell movement, which in the developing cerebral cortex, is defined by displacement parallel to the ventricular surface and orthogonal to the radial glial fibers. This mode of long-range migration is a strategy by which distinct neuronal classes generated from spatially and molecularly distinct origins can integrate to form appropriate neural circuits within the cortical plate. While it was previously believed that only GABAergic cortical interneurons migrate tangentially from their origins in the subpallial ganglionic eminences to integrate in the cortical plate, it is now known that transient populations of glutamatergic neurons also adopt this mode of migration. These include Cajal-Retzius cells (CRs), subplate neurons (SPs), and cortical plate transient neurons (CPTs), which have crucial roles in orchestrating the radial and tangential development of the embryonic cerebral cortex in a noncell-autonomous manner. While CRs have been extensively studied, it is only in the last decade that the molecular mechanisms governing their tangential migration have begun to be elucidated. To date, the mechanisms of SPs and CPTs tangential migration remain unknown. We therefore review the known signaling pathways, which regulate parameters of CRs migration including their motility, contact-redistribution and adhesion to the pial surface, and discuss this in the context of how CR migration may regulate their signaling activity in a spatial and temporal manner. {\copyright} 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 847-881, 2016.},
	Author = {Barber, Melissa and Pierani, Alessandra},
	Date-Added = {2018-01-16 21:03:39 +0000},
	Date-Modified = {2018-01-16 21:03:39 +0000},
	Doi = {10.1002/dneu.22363},
	Journal = {Dev Neurobiol},
	Journal-Full = {Developmental neurobiology},
	Keywords = {Cajal-Retzius cells; cortical patterning; cortical plate transient neurons; glutamatergic neurons; subplate neurons; tangential migration},
	Mesh = {Animals; Cell Movement; Cerebral Cortex; Humans; Neurons},
	Month = {Aug},
	Number = {8},
	Pages = {847-81},
	Pmid = {26581033},
	Pst = {ppublish},
	Title = {Tangential migration of glutamatergic neurons and cortical patterning during development: Lessons from Cajal-Retzius cells},
	Volume = {76},
	Year = {2016},
	File = {papers/Barber_DevNeurobiol2016.pdf}}

@article{Vue:2013,
	Abstract = {The mammalian neocortex undergoes dramatic transformation during development, from a seemingly homogenous sheet of neuroepithelial cells into a complex structure that is tangentially divided into discrete areas. This process is thought to be controlled by a combination of intrinsic patterning mechanisms within the cortex and afferent axonal projections from the thalamus. However, roles of thalamic afferents in the formation of areas are still poorly understood. In this study, we show that genetically increasing or decreasing the size of the lateral geniculate nucleus of the mouse thalamus resulted in a corresponding change in the size of the primary visual area. Furthermore, elimination of most thalamocortical projections from the outset of their development resulted in altered areal gene expression patterns, particularly in the primary visual and somatosensory areas, where they lost sharp boundaries with adjacent areas. Together, these results demonstrate the critical roles of thalamic afferents in the establishment of neocortical areas.},
	Author = {Vue, Tou Yia and Lee, Melody and Tan, Yew Ei and Werkhoven, Zachary and Wang, Lynn and Nakagawa, Yasushi},
	Date-Added = {2018-01-16 21:03:03 +0000},
	Date-Modified = {2018-01-16 21:03:03 +0000},
	Doi = {10.1523/JNEUROSCI.5786-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Afferent Pathways; Animals; Animals, Newborn; Basic Helix-Loop-Helix Transcription Factors; Cell Count; Cell Size; Embryo, Mammalian; Gene Expression Regulation, Developmental; Hedgehog Proteins; Homeodomain Proteins; Mice; Mice, Transgenic; Mutation; Neocortex; Proteins; RNA, Messenger; RNA, Untranslated; Thalamus},
	Month = {May},
	Number = {19},
	Pages = {8442-53},
	Pmc = {PMC3732791},
	Pmid = {23658181},
	Pst = {ppublish},
	Title = {Thalamic control of neocortical area formation in mice},
	Volume = {33},
	Year = {2013},
	File = {papers/Vue_JNeurosci2013.pdf}}

@article{Cholfin:2007,
	Abstract = {The frontal cortex (FC) is the seat of higher cognition. The genetic mechanisms that control formation of the functionally distinct subdivisions of the FC are unknown. Using a set of gene expression markers that distinguish subdivisions of the newborn mouse FC, we show that loss of Fgf17 selectively reduces the size of the dorsal FC whereas ventral/orbital FC appears normal. These changes are complemented by a rostral shift of sensory cortical areas. Thus, Fgf17 functions similar to Fgf8 in patterning the overall neocortical map but has a more selective role in regulating the properties of the dorsal but not ventral FC.},
	Author = {Cholfin, Jeremy A and Rubenstein, John L R},
	Date-Added = {2017-12-12 01:42:38 +0000},
	Date-Modified = {2017-12-12 01:42:38 +0000},
	Doi = {10.1073/pnas.0702225104},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Biomarkers; Body Patterning; Fibroblast Growth Factor 8; Fibroblast Growth Factors; Frontal Lobe; Gene Expression Regulation, Developmental; Mice; Mice, Knockout; Mutation},
	Month = {May},
	Number = {18},
	Pages = {7652-7},
	Pmc = {PMC1863435},
	Pmid = {17442747},
	Pst = {ppublish},
	Title = {Patterning of frontal cortex subdivisions by Fgf17},
	Volume = {104},
	Year = {2007},
	File = {papers/Cholfin_ProcNatlAcadSciUSA2007.pdf}}

@article{Cederquist:2013,
	Abstract = {The mammalian neocortex is parcellated into anatomically and functionally distinct areas. The establishment of area-specific neuronal diversity and circuit connectivity enables distinct neocortical regions to control diverse and specialized functional outputs, yet underlying molecular controls remain largely unknown. Here, we identify a central role for the transcriptional regulator Lim-only 4 (Lmo4) in establishing the diversity of neuronal subtypes within rostral mouse motor cortex, where projection neurons have particularly diverse and multi-projection connectivity compared with caudal motor cortex. In rostral motor cortex, we report that both subcerebral projection neurons (SCPN), which send projections away from the cerebrum, and callosal projection neurons (CPN), which send projections to contralateral cortex, express Lmo4, whereas more caudal SCPN and CPN do not. Lmo4-expressing SCPN and CPN populations are comprised of multiple hodologically distinct subtypes. SCPN in rostral layer Va project largely to brainstem, whereas SCPN in layer Vb project largely to spinal cord, and a subset of both rostral SCPN and CPN sends second ipsilateral caudal (backward) projections in addition to primary projections. Without Lmo4 function, the molecular identity of neurons in rostral motor cortex is disrupted and more homogenous, rostral layer Va SCPN aberrantly project to the spinal cord, and many dual-projection SCPN and CPN fail to send a second backward projection. These molecular and hodological disruptions result in greater overall homogeneity of motor cortex output. Together, these results identify Lmo4 as a central developmental control over the diversity of motor cortex projection neuron subpopulations, establishing their area-specific identity and specialized connectivity.},
	Author = {Cederquist, Gustav Y and Azim, Eiman and Shnider, Sara J and Padmanabhan, Hari and Macklis, Jeffrey D},
	Date-Added = {2017-12-12 01:38:13 +0000},
	Date-Modified = {2017-12-12 01:38:13 +0000},
	Doi = {10.1523/JNEUROSCI.5140-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Adaptor Proteins, Signal Transducing; Animals; Brain Stem; Corpus Callosum; Female; Gene Expression Regulation; LIM Domain Proteins; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Motor Cortex; Neural Pathways; Neurons; Spinal Cord},
	Month = {Apr},
	Number = {15},
	Pages = {6321-32},
	Pmc = {PMC3698850},
	Pmid = {23575831},
	Pst = {ppublish},
	Title = {Lmo4 establishes rostral motor cortex projection neuron subtype diversity},
	Volume = {33},
	Year = {2013},
	File = {papers/Cederquist_JNeurosci2013.pdf}}

@article{Subramanian:2009,
	Abstract = {The early cortical primordium develops from a sheet of neuroepithelium that is flanked by distinct signaling centers. Of these, the hem and the antihem are positioned as longitudinal stripes, running rostro-caudally along the medial and lateral faces, respectively, of each telencepahlic hemisphere. In this review we examine the similarities and differences in how these two signaling centers arise, their roles in patterning adjacent tissues, and the cells and structures they contribute to. Since both the hem and the antihem have been identified across many vertebrate phyla, they appear to be part of an evolutionary conserved set of mechanisms that play fundamental roles in forebrain development.},
	Author = {Subramanian, Lakshmi and Remedios, Ryan and Shetty, Ashwin and Tole, Shubha},
	Date-Added = {2017-12-11 23:58:12 +0000},
	Date-Modified = {2017-12-11 23:58:12 +0000},
	Doi = {10.1016/j.semcdb.2009.04.001},
	Journal = {Semin Cell Dev Biol},
	Journal-Full = {Seminars in cell \& developmental biology},
	Mesh = {Animals; Biological Evolution; Homeodomain Proteins; Telencephalon; Transcription Factors; Wnt Proteins},
	Month = {Aug},
	Number = {6},
	Pages = {712-8},
	Pmc = {PMC2791850},
	Pmid = {19446478},
	Pst = {ppublish},
	Title = {Signals from the edges: the cortical hem and antihem in telencephalic development},
	Volume = {20},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.semcdb.2009.04.001}}

@article{Caronia-Brown:2014,
	Abstract = {The cortical hem, a source of Wingless-related (WNT) and bone morphogenetic protein (BMP) signaling in the dorsomedial telencephalon, is the embryonic organizer for the hippocampus. Whether the hem is a major regulator of cortical patterning outside the hippocampus has not been investigated. We examined regional organization across the entire cerebral cortex in mice genetically engineered to lack the hem. Indicating that the hem regulates dorsoventral patterning in the cortical hemisphere, the neocortex, particularly dorsomedial neocortex, was reduced in size in late-stage hem-ablated embryos, whereas cortex ventrolateral to the neocortex expanded dorsally. Unexpectedly, hem ablation also perturbed regional patterning along the rostrocaudal axis of neocortex. Rostral neocortical domains identified by characteristic gene expression were expanded, and caudal domains diminished. A similar shift occurs when fibroblast growth factor (FGF) 8 is increased at the rostral telencephalic organizer, yet the FGF8 source was unchanged in hem-ablated brains. Rather we found that hem WNT or BMP signals, or both, have opposite effects to those of FGF8 in regulating transcription factors that control the size and position of neocortical areas. When the hem is ablated a necessary balance is perturbed, and cerebral cortex is rostralized. Our findings reveal a much broader role for the hem in cortical development than previously recognized, and emphasize that two major signaling centers interact antagonistically to pattern cerebral cortex.},
	Author = {Caronia-Brown, Giuliana and Yoshida, Michio and Gulden, Forrest and Assimacopoulos, Stavroula and Grove, Elizabeth A},
	Date-Added = {2017-12-11 23:51:36 +0000},
	Date-Modified = {2017-12-11 23:51:36 +0000},
	Doi = {10.1242/dev.106914},
	Journal = {Development},
	Journal-Full = {Development (Cambridge, England)},
	Keywords = {Embryonic patterning; Fgf8; Mouse; Neocortex; Signaling center; Wnt3a},
	Mesh = {Animals; Body Patterning; Bone Morphogenetic Proteins; Cell Proliferation; Female; Fibroblast Growth Factor 8; Gene Deletion; Gene Expression Regulation, Developmental; Hippocampus; Mice; Neocortex; Organ Size; Organizers, Embryonic; Phenotype; Signal Transduction; Stem Cells; Wnt Proteins},
	Month = {Jul},
	Number = {14},
	Pages = {2855-65},
	Pmc = {PMC4197624},
	Pmid = {24948604},
	Pst = {ppublish},
	Title = {The cortical hem regulates the size and patterning of neocortex},
	Volume = {141},
	Year = {2014},
	File = {papers/Caronia-Brown_Development2014.pdf}}

@article{Puelles:2003,
	Abstract = {The prosomeric model attributes morphological meaning to gene expression patterns and other data in the forebrain. It divides this territory into the same transverse segments (prosomeres) and longitudinal zones in all vertebrates. The axis and longitudinal zones of this model are widely accepted but controversy subsists about the number of prosomeres and their nature as segments. We describe difficulties encountered in establishing continuity between prosomeric limits postulated in the hypothalamus and intra-telencephalic limits. Such difficulties throw doubt on the intersegmental nature of these limits. We sketch a simplified model, in which the secondary prosencephalon (telencephalon plus hypothalamus) is a complex protosegment not subdivided into prosomeres, which exhibits patterning singularities. By contrast, we continue to postulate that prosomeres p1-p3 (i.e. the pretectum, thalamus and prethalamus) are the caudal forebrain.},
	Author = {Puelles, Luis and Rubenstein, John L R},
	Date-Added = {2017-12-11 23:48:40 +0000},
	Date-Modified = {2017-12-11 23:48:40 +0000},
	Doi = {10.1016/S0166-2236(03)00234-0},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Mesh = {Animals; Gene Expression; Humans; Hypothalamus; Models, Neurological; Prosencephalon; Telencephalon},
	Month = {Sep},
	Number = {9},
	Pages = {469-76},
	Pmid = {12948657},
	Pst = {ppublish},
	Title = {Forebrain gene expression domains and the evolving prosomeric model},
	Volume = {26},
	Year = {2003},
	File = {papers/Puelles_TrendsNeurosci2003.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0166-2236(03)00234-0}}

@article{OLeary:2008,
	Abstract = {Arealization of the neocortex is controlled by a regulatory hierarchy beginning with morphogens secreted from patterning centers positioned at the perimeter of the dorsal telencephalon. These morphogens act in part to establish within cortical progenitors the differential expression of transcription factors that specify their area identity, which is inherited by their neuronal progeny, providing the genetic framework for area patterning. The two patterning centers most directly implicated in arealization are the commissural plate, which expresses fibroblast growth factors, and the cortical hem, which expresses bone morphogenetic proteins and vertebrate orthologs of Drosophila wingless, the Wnts. A third, albeit putative, patterning center is the antihem, identified by its expression of multiple signaling molecules. We describe recent findings on roles for these patterning centers in arealization. We also present the most recent evidence on functions of the four transcription factors, Emx2, COUP-TFI, Pax6, and Sp8, thus far implicated in arealization. We also describe screens for candidate target genes of these transcription factors, or other genes potentially involved in arealization. We conclude with an assessment of a forward genetics approach for identifying genes involved in determining area size based in part on quantitative trait locus mapping, and the implications for significant differences between individuals in area size on behavioral performance.},
	Author = {O'Leary, Dennis Dm and Sahara, Setsuko},
	Date-Added = {2017-12-11 22:37:47 +0000},
	Date-Modified = {2017-12-11 22:37:47 +0000},
	Doi = {10.1016/j.conb.2008.05.011},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Mesh = {Animals; Body Patterning; Gene Expression Regulation, Developmental; Genetic Variation; Intercellular Signaling Peptides and Proteins; Morphogenesis; Neocortex; Signal Transduction; Telencephalon; Transcription Factors},
	Month = {Feb},
	Number = {1},
	Pages = {90-100},
	Pmc = {PMC2677555},
	Pmid = {18524571},
	Pst = {ppublish},
	Title = {Genetic regulation of arealization of the neocortex},
	Volume = {18},
	Year = {2008},
	File = {papers/O'Leary_CurrOpinNeurobiol2008.pdf}}

@article{Hammock:2013,
	Abstract = {UNLABELLED: Oxytocin (OXT) has drawn increasing attention as a developmentally relevant neuropeptide given its role in the brain regulation of social behavior. It has been suggested that OXT plays an important role in the infant brain during caregiver attachment in nurturing familial contexts, but there is incomplete experimental evidence. Mouse models of OXT system genes have been particularly informative for the role of the OXT system in social behavior, however, the developing brain areas that could respond to ligand activation of the OXT receptor (OXTR) have yet to be identified in this species. Here we report new data revealing dynamic ligand-binding distribution of OXTR in the developing mouse brain. Using male and female C57BL/6J mice at postnatal days (P) 0, 7, 14, 21, 35, and 60 we quantified OXTR ligand binding in several brain areas which changed across development. Further, we describe OXTR ligand binding in select tissues of the near-term whole embryo at E18.5. Together, these data aid in the interpretation of findings in mouse models of the OXT system and generate new testable hypotheses for developmental roles for OXT in mammalian systems. We discuss our findings in the context of developmental disorders (including autism), attachment biology, and infant physiological regulation.
SUMMARY: Quantitative mapping of selective OXTR ligand binding during postnatal development in the mouse reveals an unexpected, transient expression in layers II/III throughout the mouse neocortex. OXTR are also identified in several tissues in the whole late embryo, including the adrenal glands, brown adipose tissue, and the oronasal cavity.},
	Author = {Hammock, Elizabeth A D and Levitt, Pat},
	Date-Added = {2017-12-09 14:28:14 +0000},
	Date-Modified = {2017-12-09 14:28:14 +0000},
	Doi = {10.3389/fnbeh.2013.00195},
	Journal = {Front Behav Neurosci},
	Journal-Full = {Frontiers in behavioral neuroscience},
	Keywords = {adrenal gland; autism; autoradiography; experience-dependent plasticity; kidney; neocortex; oronasal cavity; oxytocin},
	Pages = {195},
	Pmc = {PMC3858721},
	Pmid = {24376405},
	Pst = {epublish},
	Title = {Oxytocin receptor ligand binding in embryonic tissue and postnatal brain development of the C57BL/6J mouse},
	Volume = {7},
	Year = {2013},
	File = {papers/Hammock_FrontBehavNeurosci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fnbeh.2013.00195}}

@article{Ryden:1969,
	Abstract = {Using tritium-labelled oxytocin with a high specific activity, the halflife in the blood and the urinary excretion of intravenously injected oxytocin were followed in the female. The following groups of patients were studied: normally menstruating women during different phases of the menstrual cycle, women using a combination of gestagenic and oestrogenic hormones for oral contraception, and pregnant women in the first and second trimester. The pregnant women were admitted to the hospital for legal abortion in the 10th--20th week of gestation.

In the proliferative phase, t½ was 272 seconds (n = 14), in the secretory phase 221 seconds (n = 5), and in women using oral contraceptives 199 seconds (n = 10). In pregnant women during the first trimester, t½ was 178 seconds (n = 6). The corresponding value in women examined during the 14th--17th weeks and during the 18th--20th weeks of gestation was 295 seconds (n = 6) and 282 seconds (n = 6), respectively. T½ was also determined within 24 h of abortion in patients in the second trimester, where the abortion was induced by intra-amniotic instillation of 50% glucose. In all cases a decrease in t½ was found. The decrease was most marked in women during the 18th--20th weeks of gestation. Altogether 25--50% of the radioactivity injected was recovered in the urine from pregnant women within 3 h of the injection. Thin-layer chromatography of the urine did not reveal the presence of any intact oxytocin.

The results demonstrate that the disappearance of oxytocin from the blood seems to be influenced by the sex hormones. Thus, an oestrogendominated stage shows a lower disappearance rate, whereas gestagens produce the reverse effect. The pronounced decrease in t½ in pregnant women immediately after abortion might be due to a change to a more progesterone-dominated stage induced by the death of the foetus, or by an alteration in the affinity of oxytocin to the myometrium. },
	Author = {Ryd{\'e}n, G and Sj{\"o}holm, I},
	Date-Added = {2017-12-09 14:26:15 +0000},
	Date-Modified = {2017-12-09 14:27:00 +0000},
	Journal = {Acta Endocrinol (Copenh)},
	Journal-Full = {Acta endocrinologica},
	Mesh = {Abortion, Legal; Chromatography, Thin Layer; Contraceptives, Oral; Female; Gestational Age; Humans; Oxytocin; Pregnancy; Tritium},
	Month = {Jul},
	Number = {3},
	Pages = {425-31},
	Pmid = {5820054},
	Pst = {ppublish},
	Title = {Half-life of oxytocin in blood of pregnant and non-pregnant women},
	Volume = {61},
	Year = {1969}}

@article{Greenwood:2017,
	Abstract = {Oxytocin (OXT) is a pleiotropic regulator of physiology and behavior. An emerging body of evidence demonstrates a role for OXT in the transition to postnatal life of the infant. To identify potential sites of OXT action via the OXT receptor (OXTR) in the newborn mouse, we performed receptor autoradiography on 20 μm sagittal sections of whole postnatal day 0 male and female mice on a C57BL/6J background using the 125iodinated ornithine vasotocin analog ([125I]-OVTA) radioligand. A competitive binding assay on both wild-type (WT) and OXTR knockout (OXTR KO) tissue was used to assess the selectivity of [125I]-OVTA for neonatal OXTR. Radioactive ligand (0.05 nM [125I]-OVTA) was competed against concentrations of 0 nM, 10 nM, and 1000 nM excess unlabeled OXT. Autoradiographs demonstrated the high selectivity of the radioligand for infant peripheral OXTR. Specific ligand binding activity for OXTR was observed in the oronasal cavity, the eye, whisker pads, adrenal gland, and anogenital region in the neonatal OXTR WT mouse, but was absent in neonatal OXTR KO. Nonspecific binding was observed in areas with a high lipid content such as the scapular brown adipose tissue and the liver: in these regions, binding was present in both OXTR WT and KO mice, and could not be competed away with OXT in either WT or KO mice. Collectively, these data confirm novel OXT targets in the periphery of the neonate. These peripheral OXTR sites, coupled with the immaturity of the neonate's own OXT system, suggest a role for exogenous OXT in modulating peripheral physiology and development.},
	Author = {Greenwood, Maria A and Hammock, Elizabeth A D},
	Date-Added = {2017-12-09 04:27:42 +0000},
	Date-Modified = {2017-12-09 04:27:42 +0000},
	Doi = {10.1371/journal.pone.0172904},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Adipose Tissue, Brown; Adrenal Glands; Animals; Animals, Newborn; Binding Sites; Eye; Female; Liver; Male; Mice, Inbred C57BL; Organ Specificity; Oxytocin; Periodontium; Protein Binding; Receptors, Oxytocin; Tooth; Vibrissae},
	Number = {2},
	Pages = {e0172904},
	Pmc = {PMC5325587},
	Pmid = {28235051},
	Pst = {epublish},
	Title = {Oxytocin receptor binding sites in the periphery of the neonatal mouse},
	Volume = {12},
	Year = {2017},
	File = {papers/Greenwood_PLoSOne2017.pdf}}

@article{Khodagholy:2017,
	Abstract = {Consolidation of declarative memories requires hippocampal-neocortical communication. Although experimental evidence supports the role of sharp-wave ripples in transferring hippocampal information to the neocortex, the exact cortical destinations and the physiological mechanisms of such transfer are not known. We used a conducting polymer-based conformable microelectrode array (NeuroGrid) to record local field potentials and neural spiking across the dorsal cortical surface of the rat brain, combined with silicon probe recordings in the hippocampus, to identify candidate physiological patterns. Parietal, midline, and prefrontal, but not primary cortical areas, displayed localized ripple (100 to 150 hertz) oscillations during sleep, concurrent with hippocampal ripples. Coupling between hippocampal and neocortical ripples was strengthened during sleep following learning. These findings suggest that ripple-ripple coupling supports hippocampal-association cortical transfer of memory traces.},
	Author = {Khodagholy, Dion and Gelinas, Jennifer N and Buzs{\'a}ki, Gy{\"o}rgy},
	Date-Added = {2017-11-16 17:44:39 +0000},
	Date-Modified = {2017-11-16 17:44:39 +0000},
	Doi = {10.1126/science.aan6203},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Month = {10},
	Number = {6361},
	Pages = {369-372},
	Pmid = {29051381},
	Pst = {ppublish},
	Title = {Learning-enhanced coupling between ripple oscillations in association cortices and hippocampus},
	Volume = {358},
	Year = {2017},
	File = {papers/Khodagholy_Science2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.aan6203}}

@article{Cherry:2017,
	Abstract = {CCL11, a protein previously associated with age-associated cognitive decline, is observed to be increased in the brain and cerebrospinal fluid (CSF) in chronic traumatic encephalopathy (CTE) compared to Alzheimer's disease (AD). Using a cohort of 23 deceased American football players with neuropathologically verified CTE, 50 subjects with neuropathologically diagnosed AD, and 18 non-athlete controls, CCL11 was measured with ELISA in the dorsolateral frontal cortex (DLFC) and CSF. CCL11 levels were significantly increased in the DLFC in subjects with CTE (fold change = 1.234, p < 0.050) compared to non-athlete controls and AD subjects with out a history of head trauma. This increase was also seen to correlate with years of exposure to American football (β = 0.426, p = 0.048) independent of age (β = -0.046, p = 0.824). Preliminary analyses of a subset of subjects with available post-mortem CSF showed a trend for increased CCL11 among individuals with CTE (p = 0.069) mirroring the increase in the DLFC. Furthermore, an association between CSF CCL11 levels and the number of years exposed to football (β = 0.685, p = 0.040) was observed independent of age (β = -0.103, p = 0.716). Finally, a receiver operating characteristic (ROC) curve analysis demonstrated CSF CCL11 accurately distinguished CTE subjects from non-athlete controls and AD subjects (AUC = 0.839, 95% CI 0.62-1.058, p = 0.028). Overall, the current findings provide preliminary evidence that CCL11 may be a novel target for future CTE biomarker studies.},
	Author = {Cherry, Jonathan D and Stein, Thor D and Tripodis, Yorghos and Alvarez, Victor E and Huber, Bertrand R and Au, Rhoda and Kiernan, Patrick T and Daneshvar, Daniel H and Mez, Jesse and Solomon, Todd M and Alosco, Michael L and McKee, Ann C},
	Date-Added = {2017-11-14 21:44:33 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1371/journal.pone.0185541},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {concussion},
	Mesh = {Aged; Aged, 80 and over; Alzheimer Disease; Biomarkers; Brain; Chemokine CCL11; Chronic Traumatic Encephalopathy; Female; Football; Humans; Male; Middle Aged},
	Number = {9},
	Pages = {e0185541},
	Pmc = {PMC5614644},
	Pmid = {28950005},
	Pst = {epublish},
	Title = {CCL11 is increased in the CNS in chronic traumatic encephalopathy but not in Alzheimer's disease},
	Volume = {12},
	Year = {2017},
	File = {papers/Cherry_PLoSOne2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0185541}}

@article{Ojo:2016,
	Abstract = {Chronic traumatic encephalopathy (CTE) is a neurological and psychiatric condition marked by preferential perivascular foci of neurofibrillary and glial tangles (composed of hyperphosphorylated-tau proteins) in the depths of the sulci. Recent retrospective case series published over the last decade on athletes and military personnel have added considerably to our clinical and histopathological knowledge of CTE. This has marked a vital turning point in the traumatic brain injury (TBI) field, raising public awareness of the potential long-term effects of mild and moderate repetitive TBI, which has been recognized as one of the major risk factors associated with CTE. Although these human studies have been informative, their retrospective design carries certain inherent limitations that should be cautiously interpreted. In particular, the current overriding issue in the CTE literature remains confusing in regard to appropriate definitions of terminology, variability in individual pathologies and the potential case selection bias in autopsy based studies. There are currently no epidemiological or prospective studies on CTE. Controlled preclinical studies in animals therefore provide an alternative means for specifically interrogating aspects of CTE pathogenesis. In this article, we review the current literature and discuss difficulties and challenges of developing in-vivo TBI experimental paradigms to explore the link between repetitive head trauma and tau-dependent changes. We provide our current opinion list of recommended features to consider for successfully modeling CTE in animals to better understand the pathobiology and develop therapeutics and diagnostics, and critical factors, which might influence outcome. We finally discuss the possible directions of future experimental research in the repetitive TBI/CTE field.},
	Author = {Ojo, Joseph O and Mouzon, Benoit C and Crawford, Fiona},
	Date-Added = {2017-11-14 21:43:20 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1016/j.expneurol.2015.06.003},
	Journal = {Exp Neurol},
	Journal-Full = {Experimental neurology},
	Keywords = {Animal models; Astroglial tangles; CTE; Concussion; Neurobehaviour; Neurofibrillary tangles; Neuropathology; Repetitive TBI; Tau; Transgenic mice; concussion},
	Mesh = {Animals; Brain Injury, Chronic; Craniocerebral Trauma; Disease Models, Animal; Humans; Mice; Translational Medical Research; tau Proteins},
	Month = {Jan},
	Pages = {389-404},
	Pmid = {26054886},
	Pst = {ppublish},
	Title = {Repetitive head trauma, chronic traumatic encephalopathy and tau: Challenges in translating from mice to men},
	Volume = {275 Pt 3},
	Year = {2016},
	File = {papers/Ojo_ExpNeurol2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.expneurol.2015.06.003}}

@article{McKee:2013,
	Abstract = {Chronic traumatic encephalopathy is a progressive tauopathy that occurs as a consequence of repetitive mild traumatic brain injury. We analysed post-mortem brains obtained from a cohort of 85 subjects with histories of repetitive mild traumatic brain injury and found evidence of chronic traumatic encephalopathy in 68 subjects: all males, ranging in age from 17 to 98 years (mean 59.5 years), including 64 athletes, 21 military veterans (86% of whom were also athletes) and one individual who engaged in self-injurious head banging behaviour. Eighteen age- and gender-matched individuals without a history of repetitive mild traumatic brain injury served as control subjects. In chronic traumatic encephalopathy, the spectrum of hyperphosphorylated tau pathology ranged in severity from focal perivascular epicentres of neurofibrillary tangles in the frontal neocortex to severe tauopathy affecting widespread brain regions, including the medial temporal lobe, thereby allowing a progressive staging of pathology from stages I-IV. Multifocal axonal varicosities and axonal loss were found in deep cortex and subcortical white matter at all stages of chronic traumatic encephalopathy. TAR DNA-binding protein 43 immunoreactive inclusions and neurites were also found in 85% of cases, ranging from focal pathology in stages I-III to widespread inclusions and neurites in stage IV. Symptoms in stage I chronic traumatic encephalopathy included headache and loss of attention and concentration. Additional symptoms in stage II included depression, explosivity and short-term memory loss. In stage III, executive dysfunction and cognitive impairment were found, and in stage IV, dementia, word-finding difficulty and aggression were characteristic. Data on athletic exposure were available for 34 American football players; the stage of chronic traumatic encephalopathy correlated with increased duration of football play, survival after football and age at death. Chronic traumatic encephalopathy was the sole diagnosis in 43 cases (63%); eight were also diagnosed with motor neuron disease (12%), seven with Alzheimer's disease (11%), 11 with Lewy body disease (16%) and four with frontotemporal lobar degeneration (6%). There is an ordered and predictable progression of hyperphosphorylated tau abnormalities through the nervous system in chronic traumatic encephalopathy that occurs in conjunction with widespread axonal disruption and loss. The frequent association of chronic traumatic encephalopathy with other neurodegenerative disorders suggests that repetitive brain trauma and hyperphosphorylated tau protein deposition promote the accumulation of other abnormally aggregated proteins including TAR DNA-binding protein 43, amyloid beta protein and alpha-synuclein.},
	Author = {McKee, Ann C and Stern, Robert A and Nowinski, Christopher J and Stein, Thor D and Alvarez, Victor E and Daneshvar, Daniel H and Lee, Hyo-Soon and Wojtowicz, Sydney M and Hall, Garth and Baugh, Christine M and Riley, David O and Kubilus, Caroline A and Cormier, Kerry A and Jacobs, Matthew A and Martin, Brett R and Abraham, Carmela R and Ikezu, Tsuneya and Reichard, Robert Ross and Wolozin, Benjamin L and Budson, Andrew E and Goldstein, Lee E and Kowall, Neil W and Cantu, Robert C},
	Date-Added = {2017-11-14 21:41:39 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1093/brain/aws307},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {concussion},
	Mesh = {Adolescent; Adult; Aged; Aged, 80 and over; Athletes; Brain; Brain Injury, Chronic; Disease Progression; Football; Humans; Male; Middle Aged; Neurofibrillary Tangles; Tauopathies; Veterans; tau Proteins},
	Month = {Jan},
	Number = {Pt 1},
	Pages = {43-64},
	Pmc = {PMC3624697},
	Pmid = {23208308},
	Pst = {ppublish},
	Title = {The spectrum of disease in chronic traumatic encephalopathy},
	Volume = {136},
	Year = {2013},
	File = {papers/McKee_Brain2013.pdf}}

@article{Smith:2013a,
	Abstract = {Traumatic brain injury (TBI) has long been recognized to be a risk factor for dementia. This association has, however, only recently gained widespread attention through the increased awareness of 'chronic traumatic encephalopathy' (CTE) in athletes exposed to repetitive head injury. Originally termed 'dementia pugilistica' and linked to a career in boxing, descriptions of the neuropathological features of CTE include brain atrophy, cavum septum pellucidum, and amyloid-β, tau and TDP-43 pathologies, many of which might contribute to clinical syndromes of cognitive impairment. Similar chronic pathologies are also commonly found years after just a single moderate to severe TBI. However, little consensus currently exists on specific features of these post-TBI syndromes that might permit their confident clinical and/or pathological diagnosis. Moreover, the mechanisms contributing to neurodegeneration following TBI largely remain unknown. Here, we review the current literature and controversies in the study of chronic neuropathological changes after TBI.},
	Author = {Smith, Douglas H and Johnson, Victoria E and Stewart, William},
	Date-Added = {2017-11-14 21:40:36 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1038/nrneurol.2013.29},
	Journal = {Nat Rev Neurol},
	Journal-Full = {Nature reviews. Neurology},
	Keywords = {concussion},
	Mesh = {Aged; Athletic Injuries; Brain; Brain Injuries; Chronic Disease; Dementia; Disease Progression; Humans; Male; Neurofibrillary Tangles; Risk Factors; Young Adult},
	Month = {Apr},
	Number = {4},
	Pages = {211-21},
	Pmc = {PMC4513655},
	Pmid = {23458973},
	Pst = {ppublish},
	Title = {Chronic neuropathologies of single and repetitive TBI: substrates of dementia?},
	Volume = {9},
	Year = {2013},
	File = {papers/Smith_NatRevNeurol2013.pdf}}

@article{Hay:2016,
	Abstract = {Almost a century ago, the first clinical account of the punch-drunk syndrome emerged, describing chronic neurological and neuropsychiatric sequelae occurring in former boxers. Thereafter, throughout the twentieth century, further reports added to our understanding of the neuropathological consequences of a career in boxing, leading to descriptions of a distinct neurodegenerative pathology, termed dementia pugilistica. During the past decade, growing recognition of this pathology in autopsy studies of nonboxers who were exposed to repetitive, mild traumatic brain injury, or to a single, moderate or severe traumatic brain injury, has led to an awareness that it is exposure to traumatic brain injury that carries with it a risk of this neurodegenerative disease, not the sport or the circumstance in which the injury is sustained. Furthermore, the neuropathology of the neurodegeneration that occurs after traumatic brain injury, now termed chronic traumatic encephalopathy, is acknowledged as being a complex, mixed, but distinctive pathology, the detail of which is reviewed in this article.},
	Author = {Hay, Jennifer and Johnson, Victoria E and Smith, Douglas H and Stewart, William},
	Date-Added = {2017-11-14 21:39:50 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1146/annurev-pathol-012615-044116},
	Journal = {Annu Rev Pathol},
	Journal-Full = {Annual review of pathology},
	Keywords = {CTE; amyloid; axons; neurodegeneration; tau; traumatic brain injury; concussion},
	Mesh = {Animals; Brain Injuries, Traumatic; Chronic Traumatic Encephalopathy; Humans},
	Month = {May},
	Pages = {21-45},
	Pmc = {PMC5367053},
	Pmid = {26772317},
	Pst = {ppublish},
	Title = {Chronic Traumatic Encephalopathy: The Neuropathological Legacy of Traumatic Brain Injury},
	Volume = {11},
	Year = {2016},
	File = {papers/Hay_AnnuRevPathol2016.pdf}}

@article{Montenigro:2015,
	Abstract = {Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease that is most often identified in postmortem autopsies of individuals exposed to repetitive head impacts, such as boxers and football players. The neuropathology of CTE is characterized by the accumulation of hyperphosphorylated tau protein in a pattern that is unique from that of other neurodegenerative diseases, including Alzheimer's disease. The clinical features of CTE are often progressive, leading to dramatic changes in mood, behavior, and cognition, frequently resulting in debilitating dementia. In some cases, motor features, including parkinsonism, can also be present. In this review, the historical origins of CTE are revealed and an overview of the current state of knowledge of CTE is provided, including the neuropathology, clinical features, proposed clinical and pathological diagnostic criteria, potential in vivo biomarkers, known risk factors, and treatment options.},
	Author = {Montenigro, Philip H and Corp, Daniel T and Stein, Thor D and Cantu, Robert C and Stern, Robert A},
	Date-Added = {2017-11-14 21:39:33 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1146/annurev-clinpsy-032814-112814},
	Journal = {Annu Rev Clin Psychol},
	Journal-Full = {Annual review of clinical psychology},
	Keywords = {chronic traumatic encephalopathy; concussion; football; history; neurodegenerative disorders; traumatic brain injury; concussion},
	Mesh = {Biomarkers; Boxing; Brain; Brain Injury, Chronic; Football; History, 20th Century; History, 21st Century; Humans; Neuroimaging; Risk Factors},
	Pages = {309-30},
	Pmid = {25581233},
	Pst = {ppublish},
	Title = {Chronic traumatic encephalopathy: historical origins and current perspective},
	Volume = {11},
	Year = {2015},
	File = {papers/Montenigro_AnnuRevClinPsychol2015.pdf}}

@article{McKee:2016,
	Abstract = {Chronic traumatic encephalopathy (CTE) is a neurodegeneration characterized by the abnormal accumulation of hyperphosphorylated tau protein within the brain. Like many other neurodegenerative conditions, at present, CTE can only be definitively diagnosed by post-mortem examination of brain tissue. As the first part of a series of consensus panels funded by the NINDS/NIBIB to define the neuropathological criteria for CTE, preliminary neuropathological criteria were used by 7 neuropathologists to blindly evaluate 25 cases of various tauopathies, including CTE, Alzheimer's disease, progressive supranuclear palsy, argyrophilic grain disease, corticobasal degeneration, primary age-related tauopathy, and parkinsonism dementia complex of Guam. The results demonstrated that there was good agreement among the neuropathologists who reviewed the cases (Cohen's kappa, 0.67) and even better agreement between reviewers and the diagnosis of CTE (Cohen's kappa, 0.78). Based on these results, the panel defined the pathognomonic lesion of CTE as an accumulation of abnormal hyperphosphorylated tau (p-tau) in neurons and astroglia distributed around small blood vessels at the depths of cortical sulci and in an irregular pattern. The group also defined supportive but non-specific p-tau-immunoreactive features of CTE as: pretangles and NFTs affecting superficial layers (layers II-III) of cerebral cortex; pretangles, NFTs or extracellular tangles in CA2 and pretangles and proximal dendritic swellings in CA4 of the hippocampus; neuronal and astrocytic aggregates in subcortical nuclei; thorn-shaped astrocytes at the glial limitans of the subpial and periventricular regions; and large grain-like and dot-like structures. Supportive non-p-tau pathologies include TDP-43 immunoreactive neuronal cytoplasmic inclusions and dot-like structures in the hippocampus, anteromedial temporal cortex and amygdala. The panel also recommended a minimum blocking and staining scheme for pathological evaluation and made recommendations for future study. This study provides the first step towards the development of validated neuropathological criteria for CTE and will pave the way towards future clinical and mechanistic studies.},
	Author = {McKee, Ann C and Cairns, Nigel J and Dickson, Dennis W and Folkerth, Rebecca D and Keene, C Dirk and Litvan, Irene and Perl, Daniel P and Stein, Thor D and Vonsattel, Jean-Paul and Stewart, William and Tripodis, Yorghos and Crary, John F and Bieniek, Kevin F and Dams-O'Connor, Kristen and Alvarez, Victor E and Gordon, Wayne A and {TBI/CTE group}},
	Date-Added = {2017-11-14 21:38:47 +0000},
	Date-Modified = {2017-11-14 21:46:24 +0000},
	Doi = {10.1007/s00401-015-1515-z},
	Journal = {Acta Neuropathol},
	Journal-Full = {Acta neuropathologica},
	Keywords = {Brain trauma; Chronic traumatic encephalopathy; Neurodegenerative disorders; Tauopathy; Traumatic brain injury; concussion},
	Mesh = {Alzheimer Disease; Autopsy; Brain Injury, Chronic; Humans; National Institute of Biomedical Imaging and Bioengineering (U.S.); National Institute of Neurological Disorders and Stroke; Neurofibrillary Tangles; Neurons; Tauopathies; United States; tau Proteins},
	Month = {Jan},
	Number = {1},
	Pages = {75-86},
	Pmc = {PMC4698281},
	Pmid = {26667418},
	Pst = {ppublish},
	Title = {The first NINDS/NIBIB consensus meeting to define neuropathological criteria for the diagnosis of chronic traumatic encephalopathy},
	Volume = {131},
	Year = {2016},
	File = {papers/McKee_ActaNeuropathol2016.pdf}}

@article{Yagita:2005,
	Abstract = {We have generated 362 bp and 547 bp partial sequences for Rana pipiens ephrin-A2 and ephrin-A5 mRNA, respectively. Translation homologies for the comparable segments of cDNA of chicken, mouse and human are 90.8, 86.9 and 84.4% for the ephrin-A2 sequence and 85.7, 85.0 and 85.0% for the ephrin-A5 sequence. Digoxigenin-labeled riboprobes were prepared and applied by means of in situ hybridization to whole-mounts of the brains of mature adults and expression patterns in tadpoles were also explored. The RNA probes revealed similar posterior (high) to anterior (low) expression gradients in the adult tectum, demonstrating that both ephrin-As are expressed in the adult Ranid frog tectum. Only the ephrin-A2 probe was tested on tadpole brain, yielding an appropriately graded expression pattern similar to the adult.},
	Author = {Yagita, Yoshiki and Barjis, Isaac and Hecht, Michael and Bach, Helene and Feldheim, David A and Scalia, Frank},
	Date-Added = {2017-11-01 21:08:33 +0000},
	Date-Modified = {2017-11-01 21:08:33 +0000},
	Doi = {10.1016/j.devbrainres.2005.06.016},
	Journal = {Brain Res Dev Brain Res},
	Journal-Full = {Brain research. Developmental brain research},
	Mesh = {Animals; Chickens; Conserved Sequence; DNA, Complementary; Ephrin-A2; Ephrin-A5; Evolution, Molecular; Gene Expression Regulation, Developmental; Humans; Larva; Mice; Molecular Sequence Data; Nucleotides; RNA, Messenger; Rana pipiens; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Superior Colliculi},
	Month = {Sep},
	Number = {1},
	Pages = {72-7},
	Pmid = {16083970},
	Pst = {ppublish},
	Title = {Partial nucleotide sequences and expression patterns of frog (Rana pipiens) ephrin-A2 and ephrin-A5 mRNA},
	Volume = {159},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.devbrainres.2005.06.016}}

@article{Kramer:2004,
	Abstract = {This paper describes a simple method for the preparation and characterization of protein density gradients on solid supports. The method employs colloidal metal nanoparticles as protein carriers and optical tags and is capable of forming linear, exponential, 1D, 2D, and multiprotein gradients of varying slope without expensive or sophisticated surface patterning techniques. Surfaces patterned with proteins using the procedures described within are shown to support cell growth and are thus suitable for studies of protein-cell interactions.},
	Author = {Kr{\"a}mer, Stephan and Xie, Huan and Gaff, John and Williamson, John R and Tkachenko, Alexander G and Nouri, Navid and Feldheim, David A and Feldheim, Daniel L},
	Date-Added = {2017-11-01 21:08:22 +0000},
	Date-Modified = {2017-11-01 21:08:22 +0000},
	Doi = {10.1021/ja031674n},
	Journal = {J Am Chem Soc},
	Journal-Full = {Journal of the American Chemical Society},
	Mesh = {Animals; Axons; Cattle; Cell Division; Cells, Cultured; Chromatography, High Pressure Liquid; Gold Colloid; Hippocampus; Metals; Microscopy, Fluorescence; Nanotechnology; Neurons; Polylysine; Rats; Serum Albumin, Bovine; Spectrophotometry},
	Month = {May},
	Number = {17},
	Pages = {5388-95},
	Pmid = {15113210},
	Pst = {ppublish},
	Title = {Preparation of protein gradients through the controlled deposition of protein-nanoparticle conjugates onto functionalized surfaces},
	Volume = {126},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/ja031674n}}

@article{Jiao:2008,
	Abstract = {In the central nervous system (CNS) of adult mammals, neurogenesis occurs in only two restricted areas, the subgranular zone (SGZ) of the hippocampus and the subventricular zone (SVZ). Isolation of multipotent progenitor cells from other CNS regions suggests that their neurogenic potential is dictated by local environmental cues. Here, we report that astrocytes in areas outside of the SGZ and SVZ of adult mice express high levels of ephrin-A2 and -A3, which present an inhibitory niche, negatively regulating neural progenitor cell growth. Adult mice lacking both ephrin-A2 and -A3 display active ongoing neurogenesis throughout the CNS. These findings suggest that neural cell replacement therapies for neurodegeneration or injury in the adult CNS may be achieved by manipulating ephrin signaling pathways.},
	Author = {Jiao, Jian-Wei and Feldheim, David A and Chen, Dong Feng},
	Date-Added = {2017-11-01 21:08:18 +0000},
	Date-Modified = {2017-11-01 21:08:18 +0000},
	Doi = {10.1073/pnas.0708861105},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Astrocytes; Cell Differentiation; Central Nervous System; Ephrin-A2; Ephrin-A3; Ephrins; Mice; Mice, Transgenic; Neurons; Receptor, EphA7; Signal Transduction},
	Month = {Jun},
	Number = {25},
	Pages = {8778-83},
	Pmc = {PMC2438395},
	Pmid = {18562299},
	Pst = {ppublish},
	Title = {Ephrins as negative regulators of adult neurogenesis in diverse regions of the central nervous system},
	Volume = {105},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0708861105}}

@article{Triplett:2014,
	Abstract = {BACKGROUND: There are numerous functional types of retinal ganglion cells (RGCs), each participating in circuits that encode a specific aspect of the visual scene. This functional specificity is derived from distinct RGC morphologies and selective synapse formation with other retinal cell types; yet, how these properties are established during development remains unclear. Islet2 (Isl2) is a LIM-homeodomain transcription factor expressed in the developing retina, including approximately 40% of all RGCs, and has previously been implicated in the subtype specification of spinal motor neurons. Based on this, we hypothesized that Isl2+ RGCs represent a related subset that share a common function.
RESULTS: We morphologically and molecularly characterized Isl2+ RGCs using a transgenic mouse line that expresses GFP in the cell bodies, dendrites and axons of Isl2+ cells (Isl2-GFP). Isl2-GFP RGCs have distinct morphologies and dendritic stratification patterns within the inner plexiform layer and project to selective visual nuclei. Targeted filling of individual cells reveals that the majority of Isl2-GFP RGCs have dendrites that are monostratified in layer S3 of the IPL, suggesting they are not ON-OFF direction-selective ganglion cells. Molecular analysis shows that most alpha-RGCs, indicated by expression of SMI-32, are also Isl2-GFP RGCs. Isl2-GFP RGCs project to most retino-recipient nuclei during early development, but specifically innervate the dorsal lateral geniculate nucleus and superior colliculus (SC) at eye opening. Finally, we show that the segregation of Isl2+ and Isl2- RGC axons in the SC leads to the segregation of functional RGC types.
CONCLUSIONS: Taken together, these data suggest that Isl2+ RGCs comprise a distinct class and support a role for Isl2 as an important component of a transcription factor code specifying functional visual circuits. Furthermore, this study describes a novel genetically-labeled mouse line that will be a valuable resource in future investigations of the molecular mechanisms of visual circuit formation.},
	Author = {Triplett, Jason W and Wei, Wei and Gonzalez, Cristina and Sweeney, Neal T and Huberman, Andrew D and Feller, Marla B and Feldheim, David A},
	Date-Added = {2017-11-01 21:08:07 +0000},
	Date-Modified = {2017-11-01 21:08:07 +0000},
	Doi = {10.1186/1749-8104-9-2},
	Journal = {Neural Dev},
	Journal-Full = {Neural development},
	Mesh = {Animals; Axons; Dendrites; Geniculate Bodies; LIM-Homeodomain Proteins; Mice; Mice, Transgenic; Neural Pathways; Retinal Ganglion Cells; Superior Colliculi; Transcription Factors},
	Month = {Feb},
	Pages = {2},
	Pmc = {PMC3937143},
	Pmid = {24495295},
	Pst = {epublish},
	Title = {Dendritic and axonal targeting patterns of a genetically-specified class of retinal ganglion cells that participate in image-forming circuits},
	Volume = {9},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1749-8104-9-2}}

@article{Sweeney:2014,
	Abstract = {There are ∼20 types of retinal ganglion cells (RGCs) in mice, each of which has distinct molecular, morphological, and physiological characteristics. Each RGC type sends axon projections to specific brain areas that execute light-dependent behaviors. Here, we show that the T-box transcription factor Tbr2 is required for the development of several RGC types that participate in non-image-forming circuits. These types are molecularly distinct, project to non-image-forming targets, and include intrinsically photosensitive RGCs. Tbr2 mutant mice have reduced retinal projections to non-image-forming nuclei and an attenuated pupillary light reflex. These data demonstrate that Tbr2 acts to execute RGC type choice and/or survival in a set of RGCs that mediates light-induced subconscious behaviors.},
	Author = {Sweeney, Neal T and Tierney, Hannah and Feldheim, David A},
	Date-Added = {2017-11-01 21:08:01 +0000},
	Date-Modified = {2017-11-01 21:08:01 +0000},
	Doi = {10.1523/JNEUROSCI.0035-14.2014},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {TBR2; axon projections; retina; visual circuit},
	Mesh = {Age Factors; Animals; Animals, Newborn; Axons; Cadherins; Calbindin 2; Female; Gene Expression Regulation; Green Fluorescent Proteins; Male; Mice; Mice, Transgenic; Mutation; Pupil; Receptors, Dopamine D4; Reflex; Retinal Ganglion Cells; T-Box Domain Proteins; Visual Pathways},
	Month = {Apr},
	Number = {16},
	Pages = {5447-53},
	Pmc = {PMC3988404},
	Pmid = {24741035},
	Pst = {ppublish},
	Title = {Tbr2 is required to generate a neural circuit mediating the pupillary light reflex},
	Volume = {34},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0035-14.2014}}

@article{Sweeney:2015,
	Abstract = {In the retinocollicular projection, the axons from functionally distinct retinal ganglion cell (RGC) types form synapses in a stereotypical manner along the superficial to deep axis of the superior colliculus (SC). Each lamina contains an orderly topographic map of the visual scene but different laminae receive inputs from distinct sets of RGCs, and inputs to each lamina are aligned with the others to integrate parallel streams of visual information. To determine the relationship between laminar organization and topography of physiologically defined RGC types, we used genetic and anatomical axon tracing techniques in wild type and ephrin-A mutant mice. We find that adjacent RGCs of the same physiological type can send axons to both ectopic and normal topographic locations, supporting a penetrance model for ephrin-A independent mapping cues. While the overall laminar organization in the SC is unaffected in ephrin-A2/A5 double mutant mice, analysis of the laminar locations of ectopic terminations shows that the topographic maps of different RGC types are misaligned. These data lend support to the hypothesis that the retinocollicular projection is a superimposition of a number of individual two-dimensional topographic maps that originate from specific types of RGCs, require ephrin-A signaling, and form independently of the other maps.},
	Author = {Sweeney, Neal T and James, Kiely N and Sales, Emily C and Feldheim, David A},
	Date-Added = {2017-11-01 21:07:56 +0000},
	Date-Modified = {2017-11-01 21:07:56 +0000},
	Doi = {10.1002/dneu.22265},
	Journal = {Dev Neurobiol},
	Journal-Full = {Developmental neurobiology},
	Keywords = {ephrin-A; topographic mapping; visual system development},
	Mesh = {Amino Acids; Animals; Brain; Brain Mapping; Ephrins; Mice; Mice, Transgenic; Mutation; Retinal Ganglion Cells; Superior Colliculi; Visual Pathways},
	Month = {Jun},
	Number = {6},
	Pages = {584-93},
	Pmc = {PMC4437846},
	Pmid = {25649160},
	Pst = {ppublish},
	Title = {Ephrin-As are required for the topographic mapping but not laminar choice of physiologically distinct RGC types},
	Volume = {75},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/dneu.22265}}

@article{Owens:2015,
	Abstract = {Topographic maps in visual processing areas maintain the spatial order of the visual world. Molecular cues and neuronal activity both play critical roles in map formation, but their interaction remains unclear. Here, we demonstrate that when molecular- and activity-dependent cues are rendered nearly equal in force, they drive topographic mapping stochastically. The functional and anatomical representation of azimuth in the superior colliculus of heterozygous Islet2-EphA3 knockin (Isl2(EphA3/+)) mice is variable: maps may be single, duplicated, or a combination of the two. This heterogeneity is not due to genetic differences, since map organizations in individual mutant animals often differ between colliculi. Disruption of spontaneous waves of retinal activity resulted in uniform map organization in Isl2(EphA3/+) mice, demonstrating that correlated spontaneous activity is required for map heterogeneity. Computational modeling replicates this heterogeneity, revealing that molecular- and activity-dependent forces interact simultaneously and stochastically during topographic map formation.},
	Author = {Owens, Melinda T and Feldheim, David A and Stryker, Michael P and Triplett, Jason W},
	Date-Added = {2017-11-01 21:07:51 +0000},
	Date-Modified = {2017-11-01 21:07:51 +0000},
	Doi = {10.1016/j.neuron.2015.08.030},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Brain Mapping; Cues; Gene Knock-In Techniques; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neurons; Retinal Ganglion Cells; Stochastic Processes; Superior Colliculi; Visual Pathways},
	Month = {Sep},
	Number = {6},
	Pages = {1261-73},
	Pmc = {PMC4583656},
	Pmid = {26402608},
	Pst = {ppublish},
	Title = {Stochastic Interaction between Neural Activity and Molecular Cues in the Formation of Topographic Maps},
	Volume = {87},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.08.030}}

@article{Shanks:2016,
	Abstract = {UNLABELLED: Retinal ganglion cells (RGCs) relay information about the outside world to multiple subcortical targets within the brain. This information is either used to dictate reflexive behaviors or relayed to the visual cortex for further processing. Many subcortical visual nuclei also receive descending inputs from projection neurons in the visual cortex. Most areas receive inputs from layer 5 cortical neurons in the visual cortex but one exception is the dorsal lateral geniculate nucleus (dLGN), which receives layer 6 inputs and is also the only RGC target that sends direct projections to the cortex. Here we ask how visual system development and function changes in mice that develop without a cortex. We find that the development of a cortex is essential for RGC axons to terminate in the dLGN, but is not required for targeting RGC axons to other subcortical nuclei. RGC axons also fail to target to the dLGN in mice that specifically lack cortical layer 6 projections to the dLGN. Finally, we show that when mice develop without a cortex they can still perform a number of vision-dependent tasks.
SIGNIFICANCE STATEMENT: The dorsal lateral geniculate nucleus (dLGN) is a sensory thalamic relay area that receives feedforward inputs from retinal ganglion cells (RGCs) in the retina, and feed back inputs from layer 6 neurons in the visual cortex. In this study we examined genetically manipulated mice that develop without a cortex or without cortical layer 6 axonal projections, and find that RGC axons fail to project to the dLGN. Other RGC recipient areas, such as the superior colliculus and suprachiasmatic nucleus, are targeted normally. These results provide support for a new mechanism of target selection that may be specific to the thalamus, whereby descending cortical axons provide an activity that promotes feedforward targeting of RGC axons to the dLGN.},
	Author = {Shanks, James A and Ito, Shinya and Schaevitz, Laura and Yamada, Jena and Chen, Bin and Litke, Alan and Feldheim, David A},
	Date-Added = {2017-11-01 21:07:47 +0000},
	Date-Modified = {2017-11-01 21:07:47 +0000},
	Doi = {10.1523/JNEUROSCI.4599-15.2016},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {axon-targeting; cortex; dLGN; retina; target selection; visual system},
	Mesh = {Animals; Axon Guidance; Female; Geniculate Bodies; Male; Mice; Retinal Ganglion Cells; Visual Cortex},
	Month = {May},
	Number = {19},
	Pages = {5252-63},
	Pmc = {PMC4863061},
	Pmid = {27170123},
	Pst = {ppublish},
	Title = {Corticothalamic Axons Are Essential for Retinal Ganglion Cell Axon Targeting to the Mouse Dorsal Lateral Geniculate Nucleus},
	Volume = {36},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4599-15.2016}}

@article{Sweeney:2017,
	Abstract = {Retinal ganglion cells (RGCs) are tasked with transmitting all light information from the eye to the retinal recipient areas of the brain. RGCs can be classified into many different types by morphology, gene expression, axonal projections, and functional responses to different light stimuli. Ultimately, these classification systems should be unified into an all-encompassing taxonomy. Toward that end, we show here that nearly all RGCs express either Islet-2 (Isl2), Tbr2, or a combination of Satb1 and Satb2. We present gene expression data supporting the hypothesis that Satb1 and Satb2 are expressed in ON-OFF direction-selective (DS) RGCs, complementing our previous work demonstrating that RGCs that express Isl2 and Tbr2 are non-DS and non-image-forming, respectively. Expression of these transcription factors emerges at distinct embryonic ages and only in postmitotic cells. Finally, we demonstrate that these transcription factor-defined RGC classes are born throughout RGC genesis.},
	Author = {Sweeney, Neal T and James, Kiely N and Nistorica, Andreea and Lorig-Roach, Ryan M and Feldheim, David A},
	Date-Added = {2017-11-01 21:07:37 +0000},
	Date-Modified = {2017-11-01 21:07:37 +0000},
	Doi = {10.1002/cne.24172},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {RRID: AB_10615604; RRID: AB_11143446; RRID: AB_1608077; RRID: AB_2167511; RRID: AB_2301417; RRID: AB_2313614; RRID: AB_231491; RRID: AB_882455; cell fate; retinal ganglion cells; transcription factors},
	Month = {Jan},
	Pmid = {28078709},
	Pst = {aheadofprint},
	Title = {Expression of transcription factors divides retinal ganglion cells into distinct classes},
	Year = {2017},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.24172}}

@article{Ito:2017,
	Abstract = {The superior colliculus (SC) receives direct input from the retina and integrates it with information about sound, touch, and state of the animal that is relayed from other parts of the brain to initiate specific behavioral outcomes. The superficial SC layers (sSC) contain cells that respond to visual stimuli, whereas the deep SC layers (dSC) contain cells that also respond to auditory and somatosensory stimuli. Here, we used a large-scale silicon probe recording system to examine the visual response properties of SC cells of head-fixed and alert male mice. We found cells with diverse response properties including: (1) orientation/direction-selective (OS/DS) cells with a firing rate that is suppressed by drifting sinusoidal gratings (negative OS/DS cells); (2) suppressed-by-contrast cells; (3) cells with complex-like spatial summation nonlinearity; and (4) cells with Y-like spatial summation nonlinearity. We also found specific response properties that are enriched in different depths of the SC. The sSC is enriched with cells with small RFs, high evoked firing rates (FRs), and sustained temporal responses, whereas the dSC is enriched with the negative OS/DS cells and with cells with large RFs, low evoked FRs, and transient temporal responses. Locomotion modulates the activity of the SC cells both additively and multiplicatively and changes the preferred spatial frequency of some SC cells. These results provide the first description of the negative OS/DS cells and demonstrate that the SC segregates cells with different response properties and that the behavioral state of a mouse affects SC activity.SIGNIFICANCE STATEMENT The superior colliculus (SC) receives visual input from the retina in its superficial layers (sSC) and induces eye/head-orientating movements and innate defensive responses in its deeper layers (dSC). Despite their importance, very little is known about the visual response properties of dSC neurons. Using high-density electrode recordings and novel model-based analysis, we found several novel visual response properties of the SC cells, including encoding of a cell's preferred orientation or direction by suppression of the firing rate. The sSC and the dSC are enriched with cells with different visual response properties. Locomotion modulates the cells in the SC. These findings contribute to our understanding of how the SC processes visual inputs, a critical step in comprehending visually guided behaviors.},
	Author = {Ito, Shinya and Feldheim, David A and Litke, Alan M},
	Date-Added = {2017-11-01 21:07:32 +0000},
	Date-Modified = {2017-11-01 21:07:32 +0000},
	Doi = {10.1523/JNEUROSCI.3689-16.2017},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {mouse; silicon probe; superior colliculus; vision},
	Mesh = {Adaptation, Physiological; Animals; Gait; Locomotion; Male; Mice; Mice, Inbred C57BL; Nerve Net; Neuronal Plasticity; Spatial Navigation; Superior Colliculi; Visual Perception},
	Month = {Aug},
	Number = {35},
	Pages = {8428-8443},
	Pmc = {PMC5577856},
	Pmid = {28760858},
	Pst = {ppublish},
	Title = {Segregation of Visual Response Properties in the Mouse Superior Colliculus and Their Modulation during Locomotion},
	Volume = {37},
	Year = {2017},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.3689-16.2017}}

@article{Scalia:2009,
	Abstract = {Eph/ephrin-receptor/ligand A and B families play a variety of roles during CNS development, including patterning the retinotectal projection. However, the alignment of their expression gradients with developing retinotectal maps and gradients of cellular development is not well understood in species whose midbrain tecta undergo a protracted anterior to posterior development. By using anatomical tracing methods and (3)H-thymidine neuronography, we have mapped the retinotectal projection and the spatiotemporal progression of tectal cellular development onto Eph/ephrin expression patterns in the tectum of larval Rana pipiens, as studied by means of in situ affinity analysis with fusion proteins. EphA expression is maximal in anterior tectum (and temporal retina); ephrin-A expression is maximal at the posterior pole (and nasal retina). EphB expression is graded in the early larva, where it is maximal in the posterior tectum just anterior to the posterior pole (and in the ventral retina). Tectal EphB expression becomes uniform at later stages and remains so in the adult, although its retinal expression remains maximal ventrally. In the early larva, EphA, EphB, and ephrin-A protein gradients are parallel to each other and align with the temporonasal axis of the retinal projection. The early EphB expression maximum overlaps the boundary between the mantle layer of newly postmitotic cells and the posterior, epithelial region of cell proliferation, suggesting that the expression maximum is associated with the initial migrations of the postmitotic cells. Ephrin-B expression was detected in the olfactory bulb and dorsal retina at all ages, but not in the tectum.},
	Author = {Scalia, Frank and Currie, Julia R and Feldheim, David A},
	Date-Added = {2017-11-01 21:07:01 +0000},
	Date-Modified = {2017-11-01 21:07:01 +0000},
	Doi = {10.1002/cne.21968},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Ephrins; Larva; Prosencephalon; Rana pipiens; Receptors, Eph Family; Retina; Tectum Mesencephali; Visual Pathways},
	Month = {May},
	Number = {1},
	Pages = {30-48},
	Pmid = {19260054},
	Pst = {ppublish},
	Title = {Eph/ephrin gradients in the retinotectal system of Rana pipiens: developmental and adult expression patterns},
	Volume = {514},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.21968}}

@article{Feldheim:2010,
	Abstract = {Topographic maps are a two-dimensional representation of one neural structure within another and serve as the main strategy to organize sensory information. The retina's projection via axons of retinal ganglion cells to midbrain visual centers, the optic tectum/superior colliculus, is the leading model to elucidate mechanisms of topographic map formation. Each axis of the retina is mapped independently using different mechanisms and sets of axon guidance molecules expressed in gradients to achieve the goal of representing a point in the retina onto a point within the target. An axon's termination along the temporal-nasal mapping axis is determined by opposing gradients of EphAs and ephrin-As that act through their forward and reverse signaling, respectively, within the projecting axons, each of which inhibits interstitial branching, cooperating with a branch-promoting activity, to generate topographic specific branching along the shaft of the parent axons that overshoot their correct termination zone along the anterior-posterior axis of the target. The dorsal-ventral termination position is then determined using a gradient of ephrin-B that can act as a repellent or attractant depending on the ephrin-B concentration relative to EphB levels on the interstitial branches to guide them along the medial-lateral axis of the target to their correct termination zone, where they arborize. In both cases, axon-axon competition results in axon mapping based on relative rather than absolute levels of repellent or attractant activity. The map is subsequently refined through large-scale pruning driven in large part by patterned retinal activity.},
	Author = {Feldheim, David A and O'Leary, Dennis D M},
	Date-Added = {2017-11-01 21:06:54 +0000},
	Date-Modified = {2017-11-01 21:06:54 +0000},
	Doi = {10.1101/cshperspect.a001768},
	Journal = {Cold Spring Harb Perspect Biol},
	Journal-Full = {Cold Spring Harbor perspectives in biology},
	Mesh = {Animals; Brain; Brain Mapping; Ephrins; Humans; Receptors, Eph Family; Retina; Retinal Ganglion Cells; Signal Transduction; Visual Pathways},
	Month = {Nov},
	Number = {11},
	Pages = {a001768},
	Pmc = {PMC2964178},
	Pmid = {20880989},
	Pst = {ppublish},
	Title = {Visual map development: bidirectional signaling, bifunctional guidance molecules, and competition},
	Volume = {2},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1101/cshperspect.a001768}}

@article{Higenell:2012,
	Abstract = {The Eph family of receptor tyrosine kinases and their ligands the ephrins play an essential role in the targeting of retinal ganglion cell axons to topographically correct locations in the optic tectum during visual system development. The African claw-toed frog Xenopus laevis is a popular animal model for the study of retinotectal development because of its amenability to live imaging and electrophysiology. Its visual system undergoes protracted growth continuing beyond metamorphosis, yet little is known about ephrin and Eph expression patterns beyond stage 39 when retinal axons first arrive in the tectum. We used alkaline phosphatase fusion proteins of EphA3, ephrin-A5, EphB2, and ephrin-B1 as affinity probes to reveal the expression patterns of ephrin-As, EphAs, ephrin-Bs, and EphBs, respectively. Analysis of brains from stage 40 to adult frog revealed that ephrins and Eph receptors are expressed throughout development. As observed in other species, staining for ephrin-As displayed a high caudal to low rostral expression pattern across the tectum, roughly complementary to the expression of EphAs. In contrast with the prevailing model, EphBs were found to be expressed in the tectum in a high dorsal to low ventral gradient in young animals. In animals with induced binocular tectal innervation, ocular dominance bands of alternating input from the two eyes formed in the tectum; however, ephrin-A and EphA expression patterns were unmodulated and similar to those in normal frogs, confirming that the segregation of axons into eye-specific stripes is not the consequence of a respecification of molecular guidance cues in the tectum.},
	Author = {Higenell, Valerie and Han, Sang Myung and Feldheim, David A and Scalia, Frank and Ruthazer, Edward S},
	Date-Added = {2017-11-01 21:06:46 +0000},
	Date-Modified = {2017-11-01 21:06:46 +0000},
	Doi = {10.1002/dneu.20930},
	Journal = {Dev Neurobiol},
	Journal-Full = {Developmental neurobiology},
	Mesh = {Animals; Ephrins; Gene Expression Profiling; Neurogenesis; Receptor, EphA1; Retina; Superior Colliculi; Xenopus laevis},
	Month = {Apr},
	Number = {4},
	Pages = {547-63},
	Pmc = {PMC3395774},
	Pmid = {21656698},
	Pst = {ppublish},
	Title = {Expression patterns of Ephs and ephrins throughout retinotectal development in Xenopus laevis},
	Volume = {72},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/dneu.20930}}

@article{Osterhout:2011,
	Abstract = {Neural circuits consist of highly precise connections among specific types of neurons that serve a common functional goal. How neurons distinguish among different synaptic targets to form functionally precise circuits remains largely unknown. Here, we show that during development, the adhesion molecule cadherin-6 (Cdh6) is expressed by a subset of retinal ganglion cells (RGCs) and also by their targets in the brain. All of the Cdh6-expressing retinorecipient nuclei mediate non-image-forming visual functions. A screen of mice expressing GFP in specific subsets of RGCs revealed that Cdh3-RGCs which also express Cdh6 selectively innervate Cdh6-expressing retinorecipient targets. Moreover, in Cdh6-deficient mice, the axons of Cdh3-RGCs fail to properly innervate their targets and instead project to other visual nuclei. These findings provide functional evidence that classical cadherins promote mammalian CNS circuit development by ensuring that axons of specific cell types connect to their appropriate synaptic targets.},
	Author = {Osterhout, Jessica A and Josten, Nicko and Yamada, Jena and Pan, Feng and Wu, Shaw-wen and Nguyen, Phong L and Panagiotakos, Georgia and Inoue, Yukiko U and Egusa, Saki F and Volgyi, Bela and Inoue, Takayoshi and Bloomfield, Stewart A and Barres, Ben A and Berson, David M and Feldheim, David A and Huberman, Andrew D},
	Date-Added = {2017-11-01 21:06:29 +0000},
	Date-Modified = {2017-11-01 21:06:29 +0000},
	Doi = {10.1016/j.neuron.2011.07.006},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axons; Cadherins; Green Fluorescent Proteins; Mice; Mice, Knockout; Nerve Net; Retinal Ganglion Cells; Visual Cortex; Visual Pathways},
	Month = {Aug},
	Number = {4},
	Pages = {632-9},
	Pmc = {PMC3513360},
	Pmid = {21867880},
	Pst = {ppublish},
	Title = {Cadherin-6 mediates axon-target matching in a non-image-forming visual circuit},
	Volume = {71},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2011.07.006}}

@article{Triplett:2012a,
	Abstract = {The axonal connections between the retina and its midbrain target, the superior colliculus (SC), is mapped topographically, such that the spatial relationships of cell bodies in the retina are maintained when terminating in the SC. Topographic map development uses a Cartesian mapping system such that each axis of the retina is mapped independently. Along the nasal-temporal mapping axis, EphAs and ephrin-As, are graded molecular cues required for topographic mapping while the dorsal-ventral axis is mapped in part via EphB and ephrin-Bs. Because both Ephs and ephrins are cell surface molecules they can signal in the forward and reverse directions. Eph/ephrin signaling leads to changes in cytoskeletal dynamics that lead to actin depolymerization and endocytosis guiding axons via attraction and repulsion.},
	Author = {Triplett, Jason W and Feldheim, David A},
	Date-Added = {2017-11-01 21:06:20 +0000},
	Date-Modified = {2017-11-01 21:06:20 +0000},
	Doi = {10.1016/j.semcdb.2011.10.026},
	Journal = {Semin Cell Dev Biol},
	Journal-Full = {Seminars in cell \& developmental biology},
	Mesh = {Animals; Brain Mapping; Ephrins; Gene Expression; Humans; Receptors, Eph Family; Retinal Ganglion Cells; Signal Transduction; Superior Colliculi; Synapses; Visual Perception},
	Month = {Feb},
	Number = {1},
	Pages = {7-15},
	Pmc = {PMC3288406},
	Pmid = {22044886},
	Pst = {ppublish},
	Title = {Eph and ephrin signaling in the formation of topographic maps},
	Volume = {23},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.semcdb.2011.10.026}}

@article{Triplett:2011,
	Abstract = {Topographic maps are the primary means of relaying spatial information in the brain. Understanding the mechanisms by which they form has been a goal of experimental and theoretical neuroscientists for decades. The projection of the retina to the superior colliculus (SC)/tectum has been an important model used to show that graded molecular cues and patterned retinal activity are required for topographic map formation. Additionally, interaxon competition has been suggested to play a role in topographic map formation; however, this view has been recently challenged. Here we present experimental and computational evidence demonstrating that interaxon competition for target space is necessary to establish topography. To test this hypothesis experimentally, we determined the nature of the retinocollicular projection in Math5 (Atoh7) mutant mice, which have severely reduced numbers of retinal ganglion cell inputs into the SC. We find that in these mice, retinal axons project to the anteromedialj portion of the SC where repulsion from ephrin-A ligands is minimized and where their attraction to the midline is maximized. This observation is consistent with the chemoaffinity model that relies on axon-axon competition as a mapping mechanism. We conclude that chemical labels plus neural activity cannot alone specify the retinocollicular projection; instead axon-axon competition is necessary to create a map. Finally, we present a mathematical model for topographic mapping that incorporates molecular labels, neural activity, and axon competition.},
	Author = {Triplett, Jason W and Pfeiffenberger, Cory and Yamada, Jena and Stafford, Ben K and Sweeney, Neal T and Litke, Alan M and Sher, Alexander and Koulakov, Alexei A and Feldheim, David A},
	Date-Added = {2017-11-01 21:06:11 +0000},
	Date-Modified = {2017-11-01 21:06:11 +0000},
	Doi = {10.1073/pnas.1102834108},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Axons; Basic Helix-Loop-Helix Transcription Factors; Fluorescence; Humans; Mice; Mice, Mutant Strains; Models, Biological; Nerve Tissue Proteins; Retina; Space Perception; Statistics, Nonparametric; Superior Colliculi; Visual Pathways; Visual Perception},
	Month = {Nov},
	Number = {47},
	Pages = {19060-5},
	Pmc = {PMC3223436},
	Pmid = {22065784},
	Pst = {ppublish},
	Title = {Competition is a driving force in topographic mapping},
	Volume = {108},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1102834108}}

@article{Clandinin:2009,
	Abstract = {Visual system development utilizes global and local cues to assemble a topographic map of the visual world, arranging synaptic connections into columns and layers. Recent genetic studies have provided new insights into the mechanisms that underlie these processes. In flies, a precise temporal sequence of neural differentiation provides a global organizing cue; in vertebrates, gradients of ephrin-mediated signals, acting with neurotrophin co-receptors and neural activity, play crucial roles. In flies and mice, neural processes tile into precise arrays through homotypic, repulsive interactions, autocrine signals, and cell-intrinsic mechanisms. Laminar targeting specificity is achieved through temporally regulated cell-cell adhesion, as well as combinatorial expression of specific adhesion molecules. Future studies will define the interactions between these global and local cues.},
	Author = {Clandinin, Thomas R and Feldheim, David A},
	Date-Added = {2017-11-01 21:05:54 +0000},
	Date-Modified = {2017-11-01 21:05:54 +0000},
	Doi = {10.1016/j.conb.2009.04.011},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Mesh = {Animals; Brain; Neurons; Retina; Time Factors; Visual Pathways; Visual Perception},
	Month = {Apr},
	Number = {2},
	Pages = {174-80},
	Pmc = {PMC2726114},
	Pmid = {19481440},
	Pst = {ppublish},
	Title = {Making a visual map: mechanisms and molecules},
	Volume = {19},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.conb.2009.04.011}}

@article{Pfeiffenberger:2006,
	Abstract = {The development of topographic maps in the primary visual system is thought to rely on a combination of EphA/ephrin-A interactions and patterned neural activity. Here, we characterize the retinogeniculate and retinocollicular maps of mice mutant for ephrins-A2, -A3, and -A5 (the three ephrin-As expressed in the mouse visual system), mice mutant for the beta2 subunit of the nicotinic acetylcholine receptor (that lack early patterned retinal activity), and mice mutant for both ephrin-As and beta2. We also provide the first comprehensive anatomical description of the topographic connections between the retina and the dorsal lateral geniculate nucleus. We find that, although ephrin-A2/A3/A5 triple knock-out mice have severe mapping defects in both projections, they do not completely lack topography. Mice lacking beta2-dependent retinal activity have nearly normal topography but fail to refine axonal arbors. Mice mutant for both ephrin-As and beta2 have synergistic mapping defects that result in a near absence of map in the retinocollicular projection; however, the retinogeniculate projection is not as severely disrupted as the retinocollicular projection is in these mutants. These results show that ephrin-As and patterned retinal activity act together to establish topographic maps, and demonstrate that midbrain and forebrain connections have a differential requirement for ephrin-As and patterned retinal activity in topographic map development.},
	Author = {Pfeiffenberger, Cory and Yamada, Jena and Feldheim, David A},
	Date-Added = {2017-11-01 21:05:26 +0000},
	Date-Modified = {2017-11-01 21:05:26 +0000},
	Doi = {10.1523/JNEUROSCI.3595-06.2006},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Brain Mapping; Ephrin-A2; Ephrin-A5; Ephrins; Geniculate Bodies; Mice; Mice, Inbred C57BL; Mice, Knockout; Retina; Visual Pathways},
	Month = {Dec},
	Number = {50},
	Pages = {12873-84},
	Pmc = {PMC3664553},
	Pmid = {17167078},
	Pst = {ppublish},
	Title = {Ephrin-As and patterned retinal activity act together in the development of topographic maps in the primary visual system},
	Volume = {26},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.3595-06.2006}}

@article{Scalia:2005,
	Abstract = {Eph/ephrin expression was studied in Rana utricularia larvae and adults with in situ receptor and ligand affinity probes. From stages TK-II (early limb bud) to VI (early foot paddle larva), tectal EphB expression is highest in a band extending transversely across the posterior optic tectum and grades off anteriorly and posteriorly. The ephrin-A expression gradient is parallel to the EphB gradient rather than being orthogonal to it. However, its high point occupies the posterior pole, and it runs from high-posteriorly to low-anteriorly. Tectal EphA expression is high anteriorly and low posteriorly, while ephrin-Bs are expressed only in a thin line at the dorsal midline. At later stages and in adults, tectal EphB expression becomes uniform.},
	Author = {Scalia, Frank and Feldheim, David A},
	Date-Added = {2017-11-01 21:04:37 +0000},
	Date-Modified = {2017-11-01 21:04:37 +0000},
	Doi = {10.1016/j.devbrainres.2005.05.002},
	Journal = {Brain Res Dev Brain Res},
	Journal-Full = {Brain research. Developmental brain research},
	Mesh = {Animals; Body Patterning; Cell Line; Ephrins; Gene Expression Regulation, Developmental; Immunoprecipitation; Larva; Ligands; Mice; Protein Binding; Rana pipiens; Receptors, Eph Family; Superior Colliculi; Transfection; Visual Pathways},
	Month = {Aug},
	Number = {1-2},
	Pages = {102-6},
	Pmid = {16002151},
	Pst = {ppublish},
	Title = {Eph/ephrin A- and B-family expression patterns in the leopard frog (Rana utricularia)},
	Volume = {158},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.devbrainres.2005.05.002}}

@article{Ellsworth:2005,
	Abstract = {Sensory axons are targeted to modality-specific nuclei in the thalamus. Retinal ganglion cell axons project retinotopically to their principal thalamic target, the dorsal lateral geniculate nucleus (LGd), in a pattern likely dictated by the expression of molecular gradients in the LGd. Deafferenting the auditory thalamus induces retinal axons to innervate the medial geniculate nucleus (MGN). These retino-MGN projections also show retinotopic organization. Here we show that ephrin-A2 and -A5, which are expressed in similar gradients in the MGN and LGd, can be used to pattern novel retinal projections in the MGN. As in the LGd, retinal axons from each eye terminate in discrete eye-specific zones in the MGN of rewired wild-type and ephrin-A2/A5 knockout mice. However, ipsilateral eye axons, which arise from retinal regions of high EphA5 receptor expression and represent central visual field, terminate in markedly different ways in the two mice. In rewired wild-type mice, ipsilateral axons specifically avoid areas of high ephrin expression in the MGN. In rewired ephrin knockout mice, ipsilateral projections shift in location and spread more broadly, leading to an expanded representation of the ipsilateral eye in the MGN. Similarly, ipsilateral projections to the LGd in ephrin knockout mice are shifted and are more widespread than in the LGd of wild-type mice. In the MGN, as in the LGd, terminations from the two eyes show little overlap even in the knockout mice, suggesting that local interocular segregation occurs regardless of other patterning determinants. Our data demonstrate that graded topographic labels, such as the ephrins, can serve to shape multiple related aspects of afferent patterning, including topographic mapping and the extent and spread of eye-specific projections. Furthermore, when mapping labels and other cues are expressed in multiple target zones, novel projections are patterned according to rules that operate in their canonical targets.},
	Author = {Ellsworth, Charlene A and Lyckman, Alvin W and Feldheim, David A and Flanagan, John G and Sur, Mriganka},
	Date-Added = {2017-11-01 21:04:31 +0000},
	Date-Modified = {2017-11-01 21:04:31 +0000},
	Doi = {10.1002/cne.20602},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Animals, Newborn; Axons; Brain Mapping; Cholera Toxin; Ephrin-A2; Ephrin-A5; Eye; Functional Laterality; Gene Expression Regulation; Geniculate Bodies; Mice; Mice, Inbred C57BL; Mice, Knockout; Models, Neurological; Retina; Retinal Ganglion Cells; Superior Colliculi; Visual Pathways},
	Month = {Jul},
	Number = {2},
	Pages = {140-51},
	Pmid = {15924339},
	Pst = {ppublish},
	Title = {Ephrin-A2 and -A5 influence patterning of normal and novel retinal projections to the thalamus: conserved mapping mechanisms in visual and auditory thalamic targets},
	Volume = {488},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.20602}}

@article{Himanen:2004,
	Abstract = {The interactions between Eph receptor tyrosine kinases and their ephrin ligands regulate cell migration and axon pathfinding. The EphA receptors are generally thought to become activated by ephrin-A ligands, whereas the EphB receptors interact with ephrin-B ligands. Here we show that two of the most widely studied of these molecules, EphB2 and ephrin-A5, which have never been described to interact with each other, do in fact bind one another with high affinity. Exposure of EphB2-expressing cells to ephrin-A5 leads to receptor clustering, autophosphorylation and initiation of downstream signaling. Ephrin-A5 induces EphB2-mediated growth cone collapse and neurite retraction in a model system. We further show, using X-ray crystallography, that the ephrin-A5-EphB2 complex is a heterodimer and is architecturally distinct from the tetrameric EphB2-ephrin-B2 structure. The structural data reveal the molecular basis for EphB2-ephrin-A5 signaling and provide a framework for understanding the complexities of functional interactions and crosstalk between A- and B-subclass Eph receptors and ephrins.},
	Author = {Himanen, Juha-Pekka and Chumley, Michael J and Lackmann, Martin and Li, Chen and Barton, William A and Jeffrey, Phillip D and Vearing, Christopher and Geleick, Detlef and Feldheim, David A and Boyd, Andrew W and Henkemeyer, Mark and Nikolov, Dimitar B},
	Date-Added = {2017-11-01 21:04:20 +0000},
	Date-Modified = {2017-11-01 21:04:20 +0000},
	Doi = {10.1038/nn1237},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Alkaline Phosphatase; Animals; Animals, Newborn; Cell Line; Chromatography, Gel; Chromatography, Ion Exchange; Cricetinae; Cricetulus; Crystallography; Electrophoresis; Ephrin-A5; Ephrin-B2; Fluorescent Antibody Technique; Green Fluorescent Proteins; Humans; Infection; Luminescent Proteins; Mice; Neurites; Neuroblastoma; Phosphorylation; Protein Binding; Receptor, EphA3; Receptor, EphB2; Signal Transduction; Sindbis Virus; Spectrometry, Fluorescence; Surface Plasmon Resonance; Time Factors; Transfection; Video Recording},
	Month = {May},
	Number = {5},
	Pages = {501-9},
	Pmid = {15107857},
	Pst = {ppublish},
	Title = {Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling},
	Volume = {7},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn1237}}

@article{Feng:2000a,
	Abstract = {Motor axons form topographic maps on muscles: rostral motor pools innervate rostral muscles, and rostral portions of motor pools innervate rostral fibers within their targets. Here, we implicate A subfamily ephrins in this topographic mapping. First, developing muscles express all five of the ephrin-A genes. Second, rostrally and caudally derived motor axons differ in sensitivity to outgrowth inhibition by ephrin-A5. Third, the topographic map of motor axons on the gluteus muscle is degraded in transgenic mice that overexpress ephrin-A5 in muscles. Fourth, topographic mapping is impaired in muscles of mutant mice lacking ephrin-A2 plus ephrin-A5. Thus, ephrins mediate or modulate positionally selective synapse formation. In addition, the rostrocaudal position of at least one motor pool is altered in ephrin-A5 mutant mice, indicating that ephrins affect nerve-muscle matching by intraspinal as well as intramuscular mechanisms.},
	Author = {Feng, G and Laskowski, M B and Feldheim, D A and Wang, H and Lewis, R and Frisen, J and Flanagan, J G and Sanes, J R},
	Date-Added = {2017-11-01 21:03:24 +0000},
	Date-Modified = {2017-11-01 21:03:24 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axons; Cell Communication; Cells, Cultured; Ephrin-A2; Ephrin-A5; Fibroblasts; Gene Expression; Membrane Proteins; Mice; Mice, Inbred C57BL; Mice, Inbred CBA; Mice, Knockout; Motor Neurons; Muscle Fibers, Skeletal; Muscle, Skeletal; Neuromuscular Junction; Spinal Cord; Synapses; Transcription Factors},
	Month = {Feb},
	Number = {2},
	Pages = {295-306},
	Pmid = {10719886},
	Pst = {ppublish},
	Title = {Roles for ephrins in positionally selective synaptogenesis between motor neurons and muscle fibers},
	Volume = {25},
	Year = {2000}}

@article{Feldheim:2000,
	Abstract = {Ephrin-A2 and -A5 are thought to be anteroposterior mapping labels for the retinotectal/retinocollicular projection. Here, gene disruptions of both these ephrins are characterized. Focal retinal labeling reveals moderate map abnormalities when either gene is disrupted. Double heterozygotes also have a phenotype, showing an influence of absolute levels. In vitro assays indicate these ephrins are required for repellent activity in the target and also normal responsiveness in the retina. In double homozygotes, anteroposterior order is almost though not completely lost. Temporal or nasal retinal labelings reveal quantitatively similar but opposite shifts, with multiple terminations scattered widely over the target. These results indicate an axon competition mechanism for mapping, with a critical role for ephrins as anteroposterior topographic labels. Dorsoventral topography is also impaired, showing these ephrins are required in mapping both axes.},
	Author = {Feldheim, D A and Kim, Y I and Bergemann, A D and Fris{\'e}n, J and Barbacid, M and Flanagan, J G},
	Date-Added = {2017-11-01 21:03:20 +0000},
	Date-Modified = {2017-11-01 21:03:20 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axons; Biomarkers; Brain Mapping; Ephrin-A2; Ephrin-A3; Ephrin-A5; Gene Expression Regulation, Developmental; Membrane Proteins; Mice; Mice, Knockout; Phenotype; RNA, Messenger; Retina; Superior Colliculi; Transcription Factors; Visual Pathways},
	Month = {Mar},
	Number = {3},
	Pages = {563-74},
	Pmid = {10774725},
	Pst = {ppublish},
	Title = {Genetic analysis of ephrin-A2 and ephrin-A5 shows their requirement in multiple aspects of retinocollicular mapping},
	Volume = {25},
	Year = {2000}}

@article{Bach:2003,
	Abstract = {Many studies have demonstrated the involvement of the EphA family of receptor tyrosine kinases and their ligands, ephrin-A2 and -A5, in the development of the temporonasal axis of the retinotectal/collicular map, but the role of these molecules in optic nerve regeneration has not been well studied. Noting that the characteristic gradients of the EphA/ephrin-A family that are expressed topographically in the retina and tectum of embryonic chicks and mice tend to disappear after birth, we took as our starting point an analysis of EphA and ephrin-A expression in leopard frogs (Rana pipiens and utricularia), species capable of regenerating the retinotectal map as adults. For the EphA family to be involved in the regeneration, one would expect these topographic gradients to persist in the adult or, if downregulated after metamorphosis, to be reexpressed after optic nerve injury. Using EphA3 receptor and ephrin-A5 ligand alkaline phosphatase in situ affinity probes (RAP and LAP, respectively) in whole-mount applications, we report that reciprocally complementary gradients of RAP and LAP binding persist in the optic tract and optic tectum of postmetamorphic frogs, including mature adults. EphA expression in temporal retinal axons in the optic tract was significantly reduced after nerve section but returned during regeneration. However, ephrin-A expression in the tectal parenchyma was not significantly elevated by either eye removal, with degeneration of optic axons, or during regeneration of the retinotectal projection. Thus, the present study has demonstrated a persisting expression of EphA/ephrin-A family members in the retinal axons and tectal parenchyma that may help guide regenerating fibers, but we can offer no evidence for an upregulation of ephrin-A expression in conjunction with optic nerve injury.},
	Author = {Bach, Helene and Feldheim, David A and Flanagan, John G and Scalia, Frank},
	Date-Added = {2017-11-01 21:03:01 +0000},
	Date-Modified = {2017-11-01 21:03:01 +0000},
	Doi = {10.1002/cne.10941},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Affinity Labels; Alkaline Phosphatase; Animals; Ephrin-A5; Eye Enucleation; Geniculate Bodies; Nerve Regeneration; Optic Nerve; Rana pipiens; Receptors, Eph Family; Superior Colliculi; Visual Pathways},
	Month = {Dec},
	Number = {4},
	Pages = {549-65},
	Pmid = {14624488},
	Pst = {ppublish},
	Title = {Persistence of graded EphA/Ephrin-A expression in the adult frog visual system},
	Volume = {467},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.10941}}

@article{Feldheim:2004,
	Abstract = {EphA tyrosine kinases are thought to act as topographically specific receptors in the well-characterized projection map from the retina to the tectum. Here, we describe a loss-of-function analysis of EphA receptors in retinotectal mapping. Expressing patches of a cytoplasmically truncated EphA3 receptor in chick retina caused temporal axons to have reduced responsiveness to posterior tectal repellent activity in vitro and to shift more posteriorly within the map in vivo. A gene disruption of mouse EphA5, replacing the intracellular domain with beta-galactosidase, reduced in vitro responsiveness of temporal axons to posterior target membranes. It also caused map abnormalities in vivo, with temporal axons shifted posteriorly and nasal axons anteriorly, but with the entire target still filled by retinal axons. The anterior shift of nasal axons was not accompanied by increased responsiveness to tectal repellent activity, in contrast to the comparable anterior shift in ephrin-A knock-outs, helping to resolve a previous ambiguity in interpreting the ephrin gene knock-outs. The results show the functional requirement for endogenous EphA receptors in retinotectal mapping, show that the receptor intracellular domain is required for a forward signaling response to topographic cues, and provide new evidence for a role of axon competition in topographic mapping.},
	Author = {Feldheim, David A and Nakamoto, Masaru and Osterfield, Miriam and Gale, Nicholas W and DeChiara, Thomas M and Rohatgi, Rajat and Yancopoulos, George D and Flanagan, John G},
	Date-Added = {2017-11-01 21:02:59 +0000},
	Date-Modified = {2017-11-01 21:02:59 +0000},
	Doi = {10.1523/JNEUROSCI.0239-03.2004},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Axons; Chick Embryo; Gene Targeting; Genes, Reporter; Genetic Vectors; Mice; Mice, Mutant Strains; Receptor, EphA3; Receptor, EphA5; Receptors, Eph Family; Retinal Ganglion Cells; Sequence Deletion; Superior Colliculi; Visual Pathways},
	Month = {Mar},
	Number = {10},
	Pages = {2542-50},
	Pmid = {15014130},
	Pst = {ppublish},
	Title = {Loss-of-function analysis of EphA receptors in retinotectal mapping},
	Volume = {24},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0239-03.2004}}

@article{Stuart:1904,
	Author = {Stuart, T P},
	Date-Added = {2017-10-27 21:15:19 +0000},
	Date-Modified = {2017-10-27 21:15:19 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Month = {Mar},
	Number = {1},
	Pages = {38-48},
	Pmc = {PMC1465472},
	Pmid = {16992721},
	Pst = {ppublish},
	Title = {The function of the hyaloid canal and some other new points in the mechanism of the accommodation of the eye for distance},
	Volume = {31},
	Year = {1904},
	File = {papers/Stuart_JPhysiol1904.pdf}}

@article{Simpson:1988,
	Abstract = {1. To compare the spatial organization of the direction selectivity of neurons in the medial terminal nucleus (MTN) of the accessory optic system with that of neurons in the adjacent ventral tegmentum, extracellular single-unit recordings were made in the anesthetized rabbit. The ventral tegmental neurons were located in a region called the visual tegmental relay zone (VTRZ), which is defined by the ventral tegmental terminal field of contralaterally projecting MTN neurons. 2. Some of the present sample of MTN neurons (5 of 34) had monocular receptive fields composed of two parts distinguished by a marked difference in the orientation of their respective direction-selective tuning curves. For one part of the receptive field the preferred excitatory direction was "up," while for the other part it was "down." Such receptive fields for one eye were called bipartite, whereas the more usually encountered MTN receptive fields, which could be characterized by a single direction-selective tuning curve, were called uniform. 3. Of the 16 neurons recorded from the VTRZ, all but one were binocular. For these neurons, both uniform and bipartite receptive fields were found for each eye alone. The only monocular neuron encountered in the VTRZ had a contralateral, bipartite receptive field. 4. The spatial organization of the direction selectivity of bipartite receptive fields strongly suggests that they are suited to represent rotation of the visual field about a horizontal axis located in the vertical plane that divides the receptive field into two parts. 5. The boundary between the two parts of the bipartite receptive fields was found using handheld visual stimuli at one of two azimuthal locations, either close to 45 degrees or between 95 and 125 degrees (the 0 degree reference was rostral in the midsagittal plane). This particular structure of the bipartite receptive fields suggests that their preferred rotation axes have a close spatial relation to the best-response axes of the semicircular canals. 6. Seven VTRZ neurons were antidromically activated by electrical stimulation of the ipsilateral dorsal cap of the inferior olive. Since the receptive fields of VTRZ neurons have many of the structural features characteristic of the receptive fields of rostral dorsal cap neurons we conclude that the spatial organization of the receptive fields of dorsal cap neurons is, for the most part, synthesized prior to the inferior olive.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {Simpson, J I and Leonard, C S and Soodak, R E},
	Date-Added = {2017-10-27 18:52:35 +0000},
	Date-Modified = {2017-10-27 18:52:35 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Mesh = {Animals; Electric Stimulation; Neurons; Optic Chiasm; Photic Stimulation; Rabbits; Rotation; Vision, Ocular; Visual Perception},
	Month = {Dec},
	Number = {6},
	Pages = {2055-72},
	Pmid = {3236061},
	Pst = {ppublish},
	Title = {The accessory optic system of rabbit. II. Spatial organization of direction selectivity},
	Volume = {60},
	Year = {1988}}

@article{Collewijn:2000,
	Abstract = {To characterize vestibulo-ocular reflex (VOR) properties in the time window in which contributions by other systems are minimal, eye movements during the first 50-100 ms after the start of transient angular head accelerations ( approximately 1000 degrees /s(2)) imposed by a torque helmet were analyzed in normal human subjects. Orientations of the head and both eyes were recorded with magnetic search coils (resolution, approximately 1 min arc; 1000 samples/s). Typically, the first response to a head perturbation was an anti-compensatory eye movement with zero latency, peak-velocity of several degrees per second, and peak excursion of several tenths of a degree. This was interpreted as a passive mechanical response to linear acceleration of the orbital tissues caused by eccentric rotation of the eye. The response was modeled as a damped oscillation (approximately 13 Hz) of the orbital contents, approaching a constant eye deviation for a sustained linear acceleration. The subsequent compensatory eye movements showed (like the head movements) a linear increase in velocity, which allowed estimates of latency and gain with linear regressions. After appropriate accounting for the preceding passive eye movements, average VOR latency (for pooled eyes, directions, and subjects) was calculated as 8.6 ms. Paired comparisons between the two eyes revealed that the latency for the eye contralateral to the direction of head rotation was, on average, 1.3 ms shorter than for the ipsilateral eye. This highly significant average inter-ocular difference was attributed to the additional internuclear abducens neuron in the pathway to the ipsilateral eye. Average acceleration gain (ratio between slopes of eye and head velocities) over the first 40-50 ms was approximately 1.1. Instantaneous velocity gain, calculated as Veye(t)/Vhead(t-latency), showed a gradual build-up converging toward unity (often after a slight overshoot). Instantaneous acceleration gain also converged toward unity but showed a much steeper build-up and larger oscillations. This behavior of acceleration and velocity gain could be accounted for by modeling the eye movements as the sum of the passive response to the linear acceleration and the active rotational VOR. Due to the latency and the anticompensatory component, gaze stabilization was never complete. The influence of visual targets was limited. The initial VOR was identical with a distant target (continuously visible or interrupted) and in complete darkness. A near visual target caused VOR gain to rise to a higher level, but the time after which the difference between far and near targets emerged varied between individuals.},
	Author = {Collewijn, H and Smeets, J B},
	Date-Added = {2017-10-27 18:41:34 +0000},
	Date-Modified = {2017-10-27 18:41:34 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Mesh = {Abducens Nerve; Acceleration; Eye Movements; Head Movements; Head Protective Devices; Humans; Magnetics; Models, Neurological; Motion Perception; Photic Stimulation; Reaction Time; Reflex, Vestibulo-Ocular; Rotation; Torque},
	Month = {Jul},
	Number = {1},
	Pages = {376-89},
	Pmid = {10899212},
	Pst = {ppublish},
	Title = {Early components of the human vestibulo-ocular response to head rotation: latency and gain},
	Volume = {84},
	Year = {2000}}

@article{Szentagothai:1950,
	Author = {Szentagothai, J},
	Date-Added = {2017-10-27 18:27:53 +0000},
	Date-Modified = {2017-10-27 18:28:59 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {reflex, eye, vision, Vestibular Nuclei, Ocular},
	Mesh = {Humans; Nervous System Physiological Phenomena; Reflex; Reflex, Vestibulo-Ocular},
	Month = {Nov},
	Number = {6},
	Pages = {395-407},
	Pmid = {14784863},
	Pst = {ppublish},
	Title = {The elementary vestibulo-ocular reflex arc},
	Volume = {13},
	Year = {1950}}

@article{Collewijn:1977,
	Abstract = {1. Eye- and head movements were recorded in unrestrained, spontaneously behaving rabbits with a new technique, based upon phase detection of signals induced in implanted coils by a rotating magnetic field. 2. Movements of the eye in space were exclusively saccadic. In the intersaccadic intervals the eyes were stabilized in space, even during vigorous head movements. Most of this stability was maintained in darkness, except for the occurrence of slow drift. 3. Many saccades were initiated while the head was stationary. They were accompanied by a similar, but slower head rotation with approximately the same amplitude. The displacement of the eye in space was a pure step without appreciable under- or over-shoot. The deviation of the eye in the head was mostly transient. 4. Other saccades were started while the head was moving and were possibly fast phases of a vestibulo-ocular reflex. The time course of the eye movement in space was identical for all saccades, whether the head was moving prior to the saccade or not. Eye movements without any head movement were not observed. 5. Saccades were mostly large (average 20-6 +/- 12-4 degrees S.D.) and never smaller than 1 degree. The relations of maximal velocity and duration to amplitude were similar to those reported for man. 6. Visual pursuit of moving objects, when elicited, was only saccadic and never smooth. 7. It is concluded that the co-ordination and dynamics of the rabbit's head- and eye movements are similar to those of primates. In the absence of foveal specilization, the eye movements are restricted to a rather global redirection of the visual field, possibly in particular of the binocular area.},
	Author = {Collewijn, H},
	Date-Added = {2017-10-27 18:14:06 +0000},
	Date-Modified = {2017-10-27 18:14:06 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Animals; Behavior, Animal; Eye Movements; Head; Movement; Rabbits; Saccades; Time Factors; Vision, Ocular},
	Month = {Apr},
	Number = {2},
	Pages = {471-98},
	Pmc = {PMC1283576},
	Pmid = {857007},
	Pst = {ppublish},
	Title = {Eye- and head movements in freely moving rabbits},
	Volume = {266},
	Year = {1977}}

@article{Goldberg:1982,
	Abstract = {The eye movements produced by constant-speed rotations about an earth-horizontal axis (EHA) are similar in the alert squirrel monkey to those observed in other species. During EHA rotations, there are persistent eye movements, including a nonreversing nystagmus at lower rotation speeds and either a direction-reversing nystagmus or sinusoidal eye movements at higher rotation speeds. Horizontal eye movements are produced by "barbecue-spit" (yaw) rotations, vertical eye movements by "head-over-heels" (pitch) rotations. The responses can be viewed as composed of a bias component, reflected in the nonreversing nature of the nystagmus, and a cyclic component, reflected in the periodic modulation of slow-phase eye velocity as head position varies. Vestibular-nerve recordings in the barbiturate-anesthetized monkey indicate that neither semicircular-canal nor otolith afferents give rise to a directionally specific dc signal which can account for the bias component. Apparently the appropriate dc signal has to be constructed centrally from a sinusoidal or ac peripheral input. The otolith organs are a likely source of this peripheral input, although contributions from the semicircular canals and from somatosensory receptors must also be considered. Our results suggest that the directional information required to distinguish rotation direction, rather than being contained in the discharge of individual otolith afferents, is encoded across a population of afferents. Possible sources of such information are the phase differences in the sinusoidal responses of otolith afferents differing in their functional polarization vectors.},
	Author = {Goldberg, J M and Fern{\'a}ndez, C},
	Date-Added = {2017-10-27 18:07:26 +0000},
	Date-Modified = {2017-10-27 18:07:26 +0000},
	Journal = {Exp Brain Res},
	Journal-Full = {Experimental brain research},
	Mesh = {Acoustic Maculae; Animals; Cebidae; Eye Movements; Motion Perception; Neurons, Afferent; Rotation; Saimiri; Semicircular Canals; Vestibular Nerve},
	Number = {3},
	Pages = {393-402},
	Pmid = {6124447},
	Pst = {ppublish},
	Title = {Eye movements and vestibular-nerve responses produced in the squirrel monkey by rotations about an earth-horizontal axis},
	Volume = {46},
	Year = {1982}}

@article{McMullen:2004,
	Abstract = {Previous studies have suggested that abnormal visual experience early in life induces ocular motor abnormalities. The purpose of this study was to determine how visual deprivation alters the function and gene expression profile of the ocular motor system in mice. We measured the effect of dark rearing on eye movements, gene expression in the oculomotor nucleus, and contractility of isolated extraocular muscles. In vivo eye movement recordings showed decreased gains for optokinetic and vestibulo-ocular reflexes, confirming an effect of dark rearing on overall ocular motor function. Saccade peak velocities were preserved, however, arguing that the quantitative changes in these reflexes were not secondary to limitations in force generation. Using microarrays and quantitative PCR, we found that dark rearing shifted the oculomotor nucleus transcriptome to a state of delayed/arrested development. The expression of 132 genes was altered by dark rearing; these genes fit in various functional categories (signal transduction, transcription/translation control, metabolism, synaptic function, cytoskeleton), and some were known to be associated with neuronal development and plasticity. Extraocular muscle contractility was impaired by dark rearing to a greater extent than expected from the in vivo ocular motility studies: changes included decreased force and shortening speed and evidence of abnormal excitability. The results indicate that normal development of the mouse ocular motor system and its muscles requires visual experience. The transcriptional pattern of arrested development may indicate that vision is required to establish the adult pattern, but it also may represent the plastic response of oculomotor nuclei to abnormal extraocular muscles.},
	Author = {McMullen, Colleen A and Andrade, Francisco H and Stahl, John S},
	Date-Added = {2017-10-27 17:29:25 +0000},
	Date-Modified = {2017-10-27 17:29:25 +0000},
	Doi = {10.1523/JNEUROSCI.3234-03.2004},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Animals, Newborn; Darkness; Eye Movements; Gene Expression Profiling; Genomics; Mesencephalon; Mice; Mice, Inbred C57BL; Motor Neurons; Oculomotor Muscles; Sensory Deprivation},
	Month = {Jan},
	Number = {1},
	Pages = {161-9},
	Pmid = {14715949},
	Pst = {ppublish},
	Title = {Functional and genomic changes in the mouse ocular motor system in response to light deprivation from birth},
	Volume = {24},
	Year = {2004},
	File = {papers/McMullen_JNeurosci2004.pdf}}

@article{Hyvarinen:2000,
	Abstract = {A fundamental problem in neural network research, as well as in many other disciplines, is finding a suitable representation of multivariate data, i.e. random vectors. For reasons of computational and conceptual simplicity, the representation is often sought as a linear transformation of the original data. In other words, each component of the representation is a linear combination of the original variables. Well-known linear transformation methods include principal component analysis, factor analysis, and projection pursuit. Independent component analysis (ICA) is a recently developed method in which the goal is to find a linear representation of non-Gaussian data so that the components are statistically independent, or as independent as possible. Such a representation seems to capture the essential structure of the data in many applications, including feature extraction and signal separation. In this paper, we present the basic theory and applications of ICA, and our recent work on the subject.},
	Author = {Hyv{\"a}rinen, A and Oja, E},
	Date = {2000 May-Jun},
	Date-Added = {2017-10-26 21:29:59 +0000},
	Date-Modified = {2017-10-26 21:29:59 +0000},
	Journal = {Neural Netw},
	Journal-Full = {Neural networks : the official journal of the International Neural Network Society},
	Mesh = {Algorithms; Artifacts; Brain; Humans; Magnetoencephalography; Neural Networks (Computer); Normal Distribution},
	Number = {4-5},
	Pages = {411-30},
	Pmid = {10946390},
	Pst = {ppublish},
	Title = {Independent component analysis: algorithms and applications},
	Volume = {13},
	Year = {2000},
	File = {papers/Hyvärinen_NeuralNetw2000.pdf}}

@article{Chase:1945,
	Author = {Chase, H B},
	Date-Added = {2017-10-26 20:12:11 +0000},
	Date-Modified = {2017-10-26 20:13:46 +0000},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {BRAIN/anatomy and histology; EYES/abnormalities},
	Mesh = {Animals; Brain; Cranial Nerves; Eye Abnormalities; Mice},
	Month = {Oct},
	Pages = {121-39},
	Pmid = {21004976},
	Pst = {ppublish},
	Title = {Studies on an anophthalmic strain of mice; associated cranial nerves and brain centers},
	Volume = {83},
	Year = {1945},
	File = {papers/CHASE_JCompNeurol1945.pdf}}

@article{Vokoun:2010,
	Abstract = {The superior colliculus (SC) is a midbrain structure that plays a role in converting sensation into action. Most SC research focuses on either in vivo extracellular recordings from behaving monkeys or patch-clamp recordings from smaller mammals in vitro. However, the activity of neuronal circuits is necessary to generate behavior, and neither of these approaches measures the simultaneous activity of large populations of neurons that make up circuits. Here, we describe experiments in which we measured changes in membrane potential across the SC map using voltage imaging of the rat SC in vitro. Our results provide the first high temporal and spatial resolution images of activity within the SC. Electrical stimulation of the SC evoked a characteristic two-component optical response containing a short latency initial-spike and a longer latency after-depolarization. Single-pulse stimulation in the superficial SC evoked a pattern of intralaminar and interlaminar spread that was distinct from the spread evoked by the same stimulus applied to the intermediate SC. Intermediate layer stimulation produced a more extensive and more ventrally located activation of the superficial layers than did stimulation in the superficial SC. Together, these results indicate the recruitment of dissimilar subpopulations of circuitry depending on the layer stimulated. Field potential recordings, pharmacological manipulations, and timing analyses indicate that the patterns of activity were physiologically relevant and largely synaptically driven. Therefore, voltage imaging is a powerful technique for the study of spatiotemporal dynamics of electrical signaling across neuronal populations, providing insight into neural circuits that underlie behavior.},
	Author = {Vokoun, Corinne R and Jackson, Meyer B and Basso, Michele A},
	Date-Added = {2017-10-26 19:57:19 +0000},
	Date-Modified = {2017-10-26 19:57:19 +0000},
	Doi = {10.1523/JNEUROSCI.1387-10.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {2-Amino-5-phosphonovalerate; Action Potentials; Anesthetics, Local; Animals; Bicuculline; Biophysical Phenomena; Brain Mapping; Diagnostic Imaging; Electric Stimulation; Evoked Potentials; Excitatory Amino Acid Antagonists; GABA Antagonists; In Vitro Techniques; Neural Conduction; Neural Pathways; Quinoxalines; Rats; Rats, Sprague-Dawley; Reaction Time; Superior Colliculi; Synapses; Tetrodotoxin},
	Month = {Aug},
	Number = {32},
	Pages = {10667-82},
	Pmid = {20702698},
	Pst = {ppublish},
	Title = {Intralaminar and interlaminar activity within the rodent superior colliculus visualized with voltage imaging},
	Volume = {30},
	Year = {2010},
	File = {papers/Vokoun_JNeurosci2010.pdf}}

@article{Bosman:2011,
	Abstract = {The rodent whisker system is widely used as a model system for investigating sensorimotor integration, neural mechanisms of complex cognitive tasks, neural development, and robotics. The whisker pathways to the barrel cortex have received considerable attention. However, many subcortical structures are paramount to the whisker system. They contribute to important processes, like filtering out salient features, integration with other senses, and adaptation of the whisker system to the general behavioral state of the animal. We present here an overview of the brain regions and their connections involved in the whisker system. We do not only describe the anatomy and functional roles of the cerebral cortex, but also those of subcortical structures like the striatum, superior colliculus, cerebellum, pontomedullary reticular formation, zona incerta, and anterior pretectal nucleus as well as those of level setting systems like the cholinergic, histaminergic, serotonergic, and noradrenergic pathways. We conclude by discussing how these brain regions may affect each other and how they together may control the precise timing of whisker movements and coordinate whisker perception.},
	Author = {Bosman, Laurens W J and Houweling, Arthur R and Owens, Cullen B and Tanke, Nouk and Shevchouk, Olesya T and Rahmati, Negah and Teunissen, Wouter H T and Ju, Chiheng and Gong, Wei and Koekkoek, Sebastiaan K E and De Zeeuw, Chris I},
	Date-Added = {2017-10-25 19:57:33 +0000},
	Date-Modified = {2017-10-25 19:57:33 +0000},
	Doi = {10.3389/fnint.2011.00053},
	Journal = {Front Integr Neurosci},
	Journal-Full = {Frontiers in integrative neuroscience},
	Keywords = {anatomy; barrel cortex; basal ganglia; cerebellum; follicle--sinus complex; rhythmic movements; sensorimotor integration; vibrissa},
	Pages = {53},
	Pmc = {PMC3207327},
	Pmid = {22065951},
	Pst = {epublish},
	Title = {Anatomical pathways involved in generating and sensing rhythmic whisker movements},
	Volume = {5},
	Year = {2011},
	File = {papers/Bosman_FrontIntegrNeurosci2011.pdf}}

@article{Berzhanskaya:2017,
	Abstract = {Children with Fragile X syndrome (FXS) have deficits of attention and arousal. To begin to identify the neural causes of these deficits, we examined juvenile rats lacking the Fragile X mental retardation protein (FMR-KO) for disruption of cortical activity related to attention and arousal. Specifically, we examined the switching of visual cortex between activated and inactivated states that normally occurs during movement and quiet rest, respectively. In both wild-type and FMR-KO rats, during the third and fourth postnatal weeks cortical activity during periods of movement was dominated by an activated state with prominent 18-52 Hz activity. However, during quiet rest, when activity in wild-type rats became dominated by the inactivated state (3-9 Hz activity), FMR-KO rat cortex abnormally remained activated, resulting in increased high-frequency and reduced low-frequency power during rest. Firing rate correlations revealed reduced synchronization in FMR-KO rats, particularly between fast-spiking interneurons, that developmentally precede cortical state defects. Together our data suggest that disrupted inhibitory connectivity impairs the ability of visual cortex to regulate exit from the activated state in a behaviorally appropriate manner, potentially contributing to disrupted attention and sensory processing observed in children with FXS by making it more difficult to decrease cortical drive by unattended stimuli.},
	Author = {Berzhanskaya, Julia and Phillips, Marnie A and Gorin, Alexis and Lai, Chongxi and Shen, Jing and Colonnese, Matthew T},
	Date-Added = {2017-10-19 20:15:03 +0000},
	Date-Modified = {2017-10-19 20:15:03 +0000},
	Doi = {10.1093/cercor/bhv331},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {EEG; attention; autism; cortex; development},
	Month = {Feb},
	Number = {2},
	Pages = {1386-1400},
	Pmid = {26733529},
	Pst = {ppublish},
	Title = {Disrupted Cortical State Regulation in a Rat Model of Fragile X Syndrome},
	Volume = {27},
	Year = {2017},
	File = {papers/Berzhanskaya_CerebCortex2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhv331}}

@article{Murata:2016,
	Abstract = {Spontaneous retinal waves are critical for the development of receptive fields in visual thalamus (LGN) and cortex (VC). Despite a detailed understanding of the circuit specializations in retina that generate waves, whether central circuit specializations also exist to control their propagation through visual pathways of the brain is unknown. Here we identify a developmentally transient, corticothalamic amplification of retinal drive to thalamus as a mechanism for retinal wave transmission in the infant rat brain. During the period of retinal waves, corticothalamic connections excite LGN, rather than driving feedforward inhibition as observed in the adult. This creates an excitatory feedback loop that gates retinal wave transmission through the LGN. This cortical multiplication of retinal wave input ends just prior to eye-opening, as cortex begins to inhibit LGN. Our results show that the early retino-thalamo-cortical circuit uses developmentally specialized feedback amplification to ensure powerful, high-fidelity transmission of retinal activity despite immature connectivity.},
	Author = {Murata, Yasunobu and Colonnese, Matthew T},
	Date-Added = {2017-10-19 20:11:24 +0000},
	Date-Modified = {2017-10-19 20:11:24 +0000},
	Doi = {10.7554/eLife.18816},
	Journal = {Elife},
	Journal-Full = {eLife},
	Keywords = {EEG; activity depedent development; neuroscience; oscillations; plasticity; rat; retinal waves},
	Month = {Oct},
	Pmc = {PMC5059135},
	Pmid = {27725086},
	Pst = {epublish},
	Title = {An excitatory cortical feedback loop gates retinal wave transmission in rodent thalamus},
	Volume = {5},
	Year = {2016},
	File = {papers/Murata_Elife2016.pdf},
	Bdsk-File-2 = {papers/Murata_Elife2016a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.7554/eLife.18816}}

@article{Shen:2016,
	Abstract = {A comprehensive developmental timeline of activity in the mouse cortex in vivo is lacking. Understanding the activity changes that accompany synapse and circuit formation is important to understand the mechanisms by which activity molds circuits and would help to identify critical checkpoints for normal development. To identify key principles of cortical activity maturation, we systematically tracked spontaneous and sensory-evoked activity with extracellular recordings of primary visual cortex (V1) in nonanesthetized mice. During the first postnatal week (postnatal days P4-P7), V1 was not visually responsive and exhibited long (>10 s) periods of network silence. Activation consisted exclusively of "slow-activity transients," 2-10 s periods of 6-10 Hz "spindle-burst' oscillations; the response to spontaneous retinal waves. By tracking daily changes in this activity, two key components of spontaneous activity maturation were revealed: (1) spindle-burst frequency acceleration (eventually becoming the 20-50 Hz broadband activity caused by the asynchronous state) and (2) "filling-in" of silent periods with low-frequency (2-4 Hz) activity (beginning on P10 and complete by P13). These two changes are sufficient to create the adult-like pattern of continuous activity, alternation between fast-asynchronous and slow-synchronous activity, by eye opening. Visual responses emerged on P8 as evoked spindle-bursts and neuronal firing with a signal-to-noise ratio higher than adult. Both were eliminated by eye opening, leaving only the mature, short-latency response. These results identify the developmental origins of mature cortical activity and implicate the period before eye opening as a critical checkpoint. By providing a systematic description of electrical activity development, we establish the murine visual cortex as a model for the electroencephalographic development of fetal humans.
SIGNIFICANCE STATEMENT: Cortical activity is an important indicator of long-term health and survival in preterm infants and molds circuit formation, but gaps remain in our understanding of the origin and normal progression of this activity in the developing cortex. We aimed to rectify this by monitoring daily changes in cortical activity in the nonanesthetized mouse, an important preclinical model of disease and development. At ages approximately equivalent to normal human term birth, mouse cortex exhibits primarily network silence, with spontaneous "spindle bursts" as the only form of activity. In contrast, mature cortex is noisy, alternating between asynchronous/discontinuous and synchronous/continuous states. This work identifies the key processes that produce this maturation and provides a normative reference for murine-based studies of cortical circuit development.},
	Author = {Shen, Jing and Colonnese, Matthew T},
	Date-Added = {2017-10-19 20:04:18 +0000},
	Date-Modified = {2017-10-19 20:04:18 +0000},
	Doi = {10.1523/JNEUROSCI.1903-16.2016},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {EEG; mouse; spindle-burst; spontaneous activity},
	Mesh = {Action Potentials; Aging; Animals; Animals, Newborn; Biological Clocks; Mice; Mice, Inbred C57BL; Nerve Net; Neurogenesis; Visual Cortex; Visual Perception},
	Month = {Nov},
	Number = {48},
	Pages = {12259-12275},
	Pmc = {PMC5148222},
	Pmid = {27903733},
	Pst = {ppublish},
	Title = {Development of Activity in the Mouse Visual Cortex},
	Volume = {36},
	Year = {2016},
	File = {papers/Shen_JNeurosci2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.1903-16.2016}}

@article{Colonnese:2017,
	Abstract = {Synchronous firing among the elements of forming circuits is critical for stabilization of synapses. Understanding the nature of these local network interactions during development can inform models of circuit formation. Within cortex, spontaneous activity changes throughout development. Unlike the adult, early spontaneous activity occurs in discontinuous population bursts separated by long silent periods, suggesting a high degree of local synchrony. However, whether the micro-patterning of activity within early bursts is unique to this early age and specifically tuned for early development is poorly understood, particularly within the column. To study this we used single-shank multi-electrode array recordings of spontaneous activity in the visual cortex of non-anesthetized neonatal mice to quantify single-unit firing rates, and applied multiple measures of network interaction and synchrony throughout the period of map formation and immediately after eye-opening. We find that despite co-modulation of firing rates on a slow time scale (hundreds of ms), the number of coactive neurons, as well as pair-wise neural spike-rate correlations, are both lower before eye-opening. In fact, on post-natal days (P)6-9 correlated activity was lower than expected by chance, suggesting active decorrelation of activity during early bursts. Neurons in lateral geniculate nucleus developed in an opposite manner, becoming less correlated after eye-opening. Population coupling, a measure of integration in the local network, revealed a population of neurons with particularly strong local coupling present at P6-11, but also an adult-like diversity of coupling at all ages, suggesting that a neuron's identity as locally or distally coupled is determined early. The occurrence probabilities of unique neuronal "words" were largely similar at all ages suggesting that retinal waves drive adult-like patterns of co-activation. These findings suggest that the bursts of spontaneous activity during early visual development do not drive hyper-synchronous activity within columns. Rather, retinal waves provide windows of potential activation during which neurons are active but poorly correlated, adult-like patterns of correlation are achieved soon after eye-opening.},
	Author = {Colonnese, Matthew T and Shen, Jing and Murata, Yasunobu},
	Date-Added = {2017-10-19 20:02:41 +0000},
	Date-Modified = {2017-10-19 20:02:41 +0000},
	Doi = {10.3389/fncel.2017.00289},
	Journal = {Front Cell Neurosci},
	Journal-Full = {Frontiers in cellular neuroscience},
	Keywords = {development; oscillation; retinal wave; spindle-burst; spontaneous activity; synchronization; visual cortex},
	Pages = {289},
	Pmc = {PMC5611364},
	Pmid = {28979189},
	Pst = {epublish},
	Title = {Uncorrelated Neural Firing in Mouse Visual Cortex during Spontaneous Retinal Waves},
	Volume = {11},
	Year = {2017},
	File = {papers/Colonnese_FrontCellNeurosci2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fncel.2017.00289}}

@article{Berger:1997,
	Abstract = {To examine the involvement of supraspinal inputs in the maturation of motor activity patterns in the developing fetal lamb, we recorded spontaneous electromyographic activity from spinally innervated muscles at approximately 45, 65, and 95 days gestation (G45, G65, and G95; term = 147 days). At G45, fetal activity occurred in synchronized activity-inactivity cycles of approximately 2 min duration, with the activity phase lasting 22.2 +/- 4.8 s and the inactivity phase lasting 95.4 +/- 13.3 s (mean +/- standard error of the mean, n = 5). At G65 and G95, the organization of activity was clearly different from that at G45 in that it was no longer cyclic, nor was the discharge of different muscles synchronized. By contrast, after spinal cord transection at G62, synchronised cyclic activity occurred in muscles innervated by segmental levels below the transection, both at G65 and G95. At G65 the duration of the activity phase of the cycle was 53.5 +/- 6.0 s, while the inactivity phase lasted 171.6 +/- 22.1 s; these durations did not alter between G65 and G95. Since spinal cord transection leads to the motor behavior of the G65 fetus reverting to the cyclic pattern characteristic of the G45 fetus, we conclude that supraspinal inputs begin to modulate the output of the spinal pattern generators at some stage between G45 and G65. The observation that spinally transected fetuses generate identical behavior at G65 and G95, both in terms of its cyclic character and the duration of cycles, suggests that spinal circuits undergo little autonomous development over this period; that is, the altered behavior observed in the developing intact fetus reflects the influence of supraspinal inputs on the motor circuits of the spinal cord.},
	Author = {Berger, P J and Kyriakides, M A and Cooke, I R},
	Date-Added = {2017-10-09 20:59:20 +0000},
	Date-Modified = {2017-10-09 20:59:20 +0000},
	Journal = {J Neurobiol},
	Journal-Full = {Journal of neurobiology},
	Mesh = {Animals; Behavior, Animal; Diaphragm; Electromyography; Extremities; Female; Fetus; Motor Activity; Muscle Denervation; Muscle, Skeletal; Neurons, Efferent; Peripheral Nervous System; Pregnancy; Sheep; Spinal Cord},
	Month = {Sep},
	Number = {3},
	Pages = {276-88},
	Pmid = {9298765},
	Pst = {ppublish},
	Title = {Supraspinal influence on the development of motor behavior in the fetal lamb},
	Volume = {33},
	Year = {1997},
	File = {papers/Berger_JNeurobiol1997.pdf}}

@article{Zhang:2012,
	Abstract = {Self-avoidance is a mechanism by which dendrites from the same neuron repel one another in order to establish uniform coverage of the dendritic field. The importance of self-avoidance for the development of complex arborization patterns has been highlighted by studies of Drosophila sensory and mouse retinal neurons. However, it is unclear whether branch patterning in the mammalian central nervous system is also governed by this strategy. We reduced Satb2 expression in a population of layer II/III pyramidal neurons in vivo by RNA interference and found that the somas of Satb2-deficient neurons clumped together, and their dendrites failed to expand laterally but instead formed fascicles. Furthermore, experiments showed that reducing Satb2 caused the adhesion of not only neighboring Satb2-deficient neurons but also neighboring wild-type neurons. Our results indicate a cell autonomous and non-cell autonomous role for Satb2 in regulating the adhesive and/or repulsive properties of cerebral pyramidal neurons.},
	Author = {Zhang, Lei and Song, Ning-Ning and Chen, Jia-Yin and Huang, Ying and Li, He and Ding, Yu-Qiang},
	Date-Added = {2017-07-05 17:41:29 +0000},
	Date-Modified = {2017-07-05 17:41:29 +0000},
	Doi = {10.1093/cercor/bhr215},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Animals, Newborn; Cell Adhesion; Cell Communication; Cell Enlargement; Cells, Cultured; Dendrites; Matrix Attachment Region Binding Proteins; Mice; Pyramidal Cells; Transcription Factors},
	Month = {Jul},
	Number = {7},
	Pages = {1510-9},
	Pmid = {21885532},
	Pst = {ppublish},
	Title = {Satb2 is required for dendritic arborization and soma spacing in mouse cerebral cortex},
	Volume = {22},
	Year = {2012},
	File = {papers/Zhang_CerebCortex2012.pdf}}

@article{McCaig:2005,
	Abstract = {Direct-current (DC) electric fields are present in all developing and regenerating animal tissues, yet their existence and potential impact on tissue repair and development are largely ignored. This is primarily due to ignorance of the phenomenon by most researchers, some technically poor early studies of the effects of applied fields on cells, and widespread misunderstanding of the fundamental concepts that underlie bioelectricity. This review aims to resolve these issues by describing: 1) the historical context of bioelectricity, 2) the fundamental principles of physics and physiology responsible for DC electric fields within cells and tissues, 3) the cellular mechanisms for the effects of small electric fields on cell behavior, and 4) the clinical potential for electric field treatment of damaged tissues such as epithelia and the nervous system.},
	Author = {McCaig, Colin D and Rajnicek, Ann M and Song, Bing and Zhao, Min},
	Date-Added = {2017-07-05 17:39:21 +0000},
	Date-Modified = {2017-07-05 17:39:21 +0000},
	Doi = {10.1152/physrev.00020.2004},
	Journal = {Physiol Rev},
	Journal-Full = {Physiological reviews},
	Mesh = {Animals; Cell Physiological Phenomena; Central Nervous System; Electromagnetic Fields; Electrophysiology; Embryo, Mammalian; Female; Humans; Pregnancy},
	Month = {Jul},
	Number = {3},
	Pages = {943-78},
	Pmid = {15987799},
	Pst = {ppublish},
	Title = {Controlling cell behavior electrically: current views and future potential},
	Volume = {85},
	Year = {2005},
	File = {papers/McCaig_PhysiolRev2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/physrev.00020.2004}}

@article{Neafsey:1986,
	Abstract = {In conclusion, the rat primary motor cortex appears to be organized into irregularly shaped patches of cortex devoted to particular movements. The location of major subdivisions such as the forelimb or hindlimb areas is somatotopic and is consistent from animal to animal, but the internal organization of the pattern of movements represented within major subdivisions varies significantly between animals. The motor cortex includes both agranular primary motor cortex (AgL) and, in addition, a significant amount of the bordering granular somatic sensory cortex (Gr(SI)), as well as the rostral portion of the taste sensory insular or claustrocortex (Cl). The rat frontal cortex also contains a second, rostral motor representation of the forelimb, trunk and hindlimb, which is somatotopically organized and may be the rat's supplementary motor area. Both of these motor representations give rise to direct corticospinal projections, some of which may make monosynaptic connections with cervical enlargement motoneurons. Medial to the primary motor cortex, in cytoarchitectonic field AgM, is what appears to be part of the rat's frontal eye fields, a region which also includes the vibrissae motor representation. The somatic motor cortical output organization pattern in the rat is remarkably similar to that seen in the primate, whose primary, supplementary and frontal eye field cortical motor regions have been extensively studied.},
	Author = {Neafsey, E J and Bold, E L and Haas, G and Hurley-Gius, K M and Quirk, G and Sievert, C F and Terreberry, R R},
	Date-Added = {2017-06-13 17:30:19 +0000},
	Date-Modified = {2017-06-13 17:32:40 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {topographic map; microstimulation; rodent; rat; Somatosensory Cortex; Neocortex},
	Mesh = {Animals; Brain Mapping; Electric Stimulation; Forelimb; Hindlimb; Lip; Mandible; Motor Cortex; Rats; Somatosensory Cortex; Tongue; Vibrissae},
	Month = {Mar},
	Number = {1},
	Pages = {77-96},
	Pmid = {3708387},
	Pst = {ppublish},
	Title = {The organization of the rat motor cortex: a microstimulation mapping study},
	Volume = {396},
	Year = {1986},
	File = {papers/Neafsey_BrainRes1986.pdf}}

@article{Belluzzi:2003,
	Abstract = {The subventricular zone produces neuroblasts that migrate to the olfactory bulb (OB) and differentiate into interneurons throughout postnatal life (Altman and Das, 1966; Hinds, 1968; Altman, 1969; Kishi et al., 1990; Luskin, 1993; Lois and Alvarez-Buylla, 1994). Although such postnatally generated interneurons have been characterized morphologically, their physiological differentiation has not been thoroughly described. Combining retroviral-mediated labeling of newly generated neurons with patch-clamp electrophysiology, we demonstrated that soon after new cells enter the layers of the olfactory bulb, they display voltage-dependent currents typical of more mature neurons. We also show that these "newcomers" express functional GABA and glutamate receptor channels, respond synaptically to stimulation of the olfactory nerve, and may establish both axodendritic and dendrodendritic synaptic contacts within the olfactory bulb. These data provide a basic description of the physiology of newly generated cells in the OB and show that such new cells are functional neurons that synaptically integrate into olfactory bulb circuitry soon after their arrival.},
	Author = {Belluzzi, Ottorino and Benedusi, Mascia and Ackman, James and LoTurco, Joseph J},
	Date-Added = {2017-05-31 23:30:38 +0000},
	Date-Modified = {2017-05-31 23:32:18 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Potassium Channels/metabolism;Cell Differentiation;Electrophysiology/*methods;Animals;Stem Cells/cytology/physiology;Rats;Receptors, GABA/drug effects/metabolism;Interneurons/physiology/virology;Patch-Clamp Techniques;Female;Retroviridae/physiology;Rats, Wistar;Neurons/classification/*physiology/virology;Male;Olfactory Bulb/cytology/*physiology;01 Adult neurogenesis general;Luminescent Proteins/biosynthesis;Cell Lineage;Support, Non-U.S. Gov't;Support, U.S. Gov't, P.H.S.;Cell Movement/physiology;Receptors, Glutamate/drug effects/metabolism;Lateral Ventricles/cytology/physiology},
	Mesh = {Animals; Cell Differentiation; Cell Lineage; Cell Movement; Delayed Rectifier Potassium Channels; Electrophysiology; Female; Green Fluorescent Proteins; Interneurons; Lateral Ventricles; Luminescent Proteins; Male; Neurons; Olfactory Bulb; Patch-Clamp Techniques; Potassium Channels; Potassium Channels, Voltage-Gated; Rats; Rats, Wistar; Receptors, GABA; Receptors, Glutamate; Retroviridae; Stem Cells},
	Month = {Nov},
	Number = {32},
	Pages = {10411-8},
	Pmid = {14614100},
	Pst = {ppublish},
	Title = {Electrophysiological differentiation of new neurons in the olfactory bulb},
	Volume = {23},
	Year = {2003},
	File = {papers/Belluzzi_JNeurosci2003.pdf}}

@article{Bai:2003,
	Abstract = {Mutations in the doublecortin gene (DCX) in humans cause malformation of the cerebral neocortex. Paradoxically, genetic deletion of Dcx in mice does not cause neocortical malformation. We used electroporation of plasmids encoding short hairpin RNA to create interference (RNAi) of DCX protein in utero, and we show that DCX is required for radial migration in developing rat neocortex. RNAi of DCX causes both cell-autonomous and non-cell autonomous disruptions in radial migration, and creates two disruptions in neocortical development. First, many neurons prematurely stop migrating to form subcortical band heterotopias within the intermediate zone and then white matter. Second, many neurons migrate into inappropriate neocortical lamina within normotopic cortex. In utero RNAi can therefore be effectively used to study the specific cellular roles of DCX in neocortical development and to produce an animal model of double cortex syndrome.},
	Author = {Bai, Jilin and Ramos, Raddy L and Ackman, James B and Thomas, Ankur M and Lee, Richard V and LoTurco, Joseph J},
	Date-Added = {2017-05-31 23:29:27 +0000},
	Date-Modified = {2017-05-31 23:30:15 +0000},
	Doi = {10.1038/nn1153},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {Development;Female;Rats;Gene Deletion;Neuropeptides;Neocortex;RNA Interference;Rats, Wistar;Pregnancy;Animals, Newborn;Support, U.S. Gov't, P.H.S.;Animals;Cell Movement},
	Mesh = {Animals; Animals, Newborn; Cell Movement; Female; Gene Deletion; Microtubule-Associated Proteins; Neocortex; Neuropeptides; Pregnancy; RNA Interference; Rats; Rats, Wistar},
	Month = {Dec},
	Number = {12},
	Pages = {1277-83},
	Pmid = {14625554},
	Pst = {ppublish},
	Title = {RNAi reveals doublecortin is required for radial migration in rat neocortex},
	Volume = {6},
	Year = {2003},
	File = {papers/Bai_NatNeurosci2003.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn1153}}

@article{Pignatelli:2005,
	Author = {Pignatelli, Angela and Benedusi, Mascia and Ackman, James and Loturco, Joseph J and Belluzzi, Ottorino},
	Date-Added = {2017-05-31 23:28:19 +0000},
	Date-Modified = {2017-05-31 23:28:57 +0000},
	Doi = {10.1093/chemse/bjh143},
	Journal = {Chem Senses},
	Journal-Full = {Chemical senses},
	Keywords = {Adult neurogenesis general},
	Mesh = {Animals; Cell Movement; Chlorides; Green Fluorescent Proteins; Humans; Juxtaglomerular Apparatus; Kinetics; Mice; Models, Biological; Neurons; Olfactory Bulb},
	Month = {Jan},
	Pages = {i119-20},
	Pmid = {15738068},
	Pst = {ppublish},
	Title = {Functional properties of adult-born juxtaglomerular cells in the mammalian olfactory bulb},
	Volume = {30 Suppl 1},
	Year = {2005},
	File = {papers/Pignatelli_ChemSenses2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/chemse/bjh143}}

@article{Ackman:2006,
	Author = {Ackman, James B and LoTurco, Joseph J},
	Date-Added = {2017-05-31 23:27:12 +0000},
	Date-Modified = {2017-05-31 23:27:55 +0000},
	Doi = {10.1016/j.expneurol.2006.03.007},
	Journal = {Exp Neurol},
	Journal-Full = {Experimental neurology},
	Keywords = {01 Adult neurogenesis general;06 Adult neurogenesis injury induced;Hypoxia-Ischemia, Brain;Animals, Newborn;Animals;Humans;Cerebral Cortex;Neurons;review},
	Mesh = {Animals; Animals, Newborn; Cerebral Cortex; Humans; Hypoxia-Ischemia, Brain; Neurons},
	Month = {May},
	Number = {1},
	Pages = {5-9},
	Pmid = {16630614},
	Pst = {ppublish},
	Title = {The potential of endogenous neuronal replacement in developing cerebral cortex following hypoxic injury},
	Volume = {199},
	Year = {2006},
	File = {papers/Ackman_ExpNeurol2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.expneurol.2006.03.007}}

@article{Ackman:2006a,
	Abstract = {The neurogenic potential of the postnatal neocortex has not been tested previously with a combination of both retroviral and bromodeoxyuridine (BrdU) labeling. Here we report that injections of enhanced green fluorescent protein (eGFP) retrovirus into 134 postnatal rats resulted in GFP labeling of 642 pyramidal neurons in neocortex. GFP-labeled neocortical pyramidal neurons, however, unlike GFP-labeled glia, did not incorporate BrdU. Closer inspection of retrovirally labeled neurons revealed microglia fused to the apical dendrites of labeled pyramidal neurons. Retroviral infection of mixed cultures of cortical neurons and glia confirmed the presence of specific neuronal-microglial fusions. Microglia did not fuse to other glial cell types, and cultures not treated with retrovirus lacked microglial-neuronal fusion. Furthermore, activation of microglia by lipopolysaccharide greatly increased the virally induced fusion of microglia to neurons in culture. These results indicate a novel form of specific cell fusion between neuronal dendrites and microglia and further illustrate the need for caution when interpreting evidence for neuronogenesis in the postnatal brain.},
	Author = {Ackman, James B and Siddiqi, Faez and Walikonis, Randall S and LoTurco, Joseph J},
	Date-Added = {2017-05-31 23:25:47 +0000},
	Date-Modified = {2017-05-31 23:26:41 +0000},
	Doi = {10.1523/JNEUROSCI.3340-06.2006},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Cell Fusion;research support, n.i.h., extramural ;Cell Communication;Rats;Pyramidal Cells;Retroviridae;Neocortex;Rats, Wistar;11 Glia;Microglia;Cells, Cultured;Animals;Retroviridae Infections;Neurons},
	Mesh = {Animals; Cell Communication; Cell Fusion; Cells, Cultured; Microglia; Neocortex; Neurons; Pyramidal Cells; Rats; Rats, Wistar; Retroviridae; Retroviridae Infections},
	Month = {Nov},
	Number = {44},
	Pages = {11413-22},
	Pmid = {17079670},
	Pst = {ppublish},
	Title = {Fusion of microglia with pyramidal neurons after retroviral infection},
	Volume = {26},
	Year = {2006},
	File = {papers/Ackman_JNeurosci2006.pdf},
	Bdsk-File-2 = {papers/Ackman_JNeurosci2006a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.3340-06.2006}}

@article{Ackman:2007,
	Abstract = {The dentate gyrus is a site of continual neurogenesis in the postnatal mammalian brain. Here we investigated postnatal neurogenesis in the citron kinase (citron-K) null-mutant rat (flathead). The flathead rat has substantial deficits in embryonic neurogenesis that are due to failed cytokinesis and cell death. We report here the loss of citron-K function has an even severer effect on postnatal neurogenesis in the dentate gyrus. Analysis of phosphorylated histone H3 expression in postnatal neurogenic regions of the flathead mutant revealed a complete lack of mitotic cells in the dentate gyrus and a large reduction in the number of dividing cells in the flathead subventricular zone. Examination of 5-bromodeoxyuridine incorporation in the flathead rat revealed that the flathead rat had a 99% reduction in the number of newly generated cells in the dentate gyrus at postnatal day 10. In addition, doublecortin-positive cells were essentially absent from the postnatal flathead dentate gyrus which also lacked the vimentin- and nestin-positive radial glia scaffold that defines the neurogenic niche in the postnatal subgranular zone. Together these results indicate that postnatal neurogenesis in the dentate gyrus is eliminated by loss of citron-K function, and suggests that a citron-K-dependent progenitor lineage forms the postnatal neuronal progenitor population in the dentate gyrus.},
	Author = {Ackman, James B and Ramos, Raddy L and Sarkisian, Matthew R and Loturco, Joseph J},
	Date-Added = {2017-05-31 23:23:49 +0000},
	Date-Modified = {2017-05-31 23:25:01 +0000},
	Doi = {10.1159/000096216},
	Journal = {Dev Neurosci},
	Journal-Full = {Developmental neuroscience},
	Keywords = {research support, n.i.h., extramural;24 Pubmed search results 2008},
	Mesh = {Animals; Cell Count; Cell Cycle Proteins; Cell Differentiation; Cell Proliferation; Dentate Gyrus; Disease Models, Animal; Gene Expression Regulation, Developmental; Histones; Intracellular Signaling Peptides and Proteins; Mitosis; Nervous System Malformations; Neurons; Protein-Serine-Threonine Kinases; Rats; Rats, Mutant Strains; Stem Cells},
	Number = {1-2},
	Pages = {113-23},
	Pmc = {PMC2211714},
	Pmid = {17148954},
	Pst = {ppublish},
	Title = {Citron kinase is required for postnatal neurogenesis in the hippocampus},
	Volume = {29},
	Year = {2007},
	File = {papers/Ackman_DevNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1159/000096216}}

@article{Allene:2008,
	Abstract = {Developing cortical networks generate a variety of coherent activity patterns that participate in circuit refinement. Early network oscillations (ENOs) are the dominant network pattern in the rodent neocortex for a short period after birth. These large-scale calcium waves were shown to be largely driven by glutamatergic synapses albeit GABA is a major excitatory neurotransmitter in the cortex at such early stages, mediating synapse-driven giant depolarizing potentials (GDPs) in the hippocampus. Using functional multineuron calcium imaging together with single-cell and field potential recordings to clarify distinct network dynamics in rat cortical slices, we now report that the developing somatosensory cortex generates first ENOs then GDPs, both patterns coexisting for a restricted time period. These patterns markedly differ by their developmental profile, dynamics, and mechanisms: ENOs are generated before cortical GDPs (cGDPs) by the activation of glutamatergic synapses mostly through NMDARs; cENOs are low-frequency oscillations (approximately 0.01 Hz) displaying slow kinetics and gradually involving the entire network. At the end of the first postnatal week, GABA-driven cortical GDPs can be reliably monitored; cGDPs are recurrent oscillations (approximately 0.1 Hz) that repetitively synchronize localized neuronal assemblies. Contrary to cGDPs, cENOs were unexpectedly facilitated by short anoxic conditions suggesting a contribution of glutamate accumulation to their generation. In keeping with this, alterations of extracellular glutamate levels significantly affected cENOs, which are blocked by an enzymatic glutamate scavenger. Moreover, we show that a tonic glutamate current contributes to the neuronal membrane excitability when cENOs dominate network patterns. Therefore, cENOs and cGDPs are two separate aspects of neocortical network maturation that may be differentially engaged in physiological and pathological processes.},
	Author = {All{\`e}ne, Camille and Cattani, Adriano and Ackman, James B and Bonifazi, Paolo and Aniksztejn, Laurent and Ben-Ari, Yehezkel and Cossart, Rosa},
	Date-Added = {2017-05-31 23:21:58 +0000},
	Date-Modified = {2017-05-31 23:23:18 +0000},
	Doi = {10.1523/JNEUROSCI.3733-08.2008},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {21 Activity-development; 21 Cortical oscillations; 21 Neurophysiology 21 Activity-development; 21 Cortical oscillations; 21 Neurophysiology},
	Mesh = {Animals; Animals, Newborn; Biological Clocks; Calcium Signaling; Cortical Synchronization; Extracellular Fluid; Glutamic Acid; Hypoxia, Brain; Membrane Potentials; Nerve Net; Neurogenesis; Organ Culture Techniques; Rats; Rats, Wistar; Receptors, N-Methyl-D-Aspartate; Somatosensory Cortex; Synapses; Synaptic Potentials; Synaptic Transmission; gamma-Aminobutyric Acid},
	Month = {Nov},
	Number = {48},
	Pages = {12851-63},
	Pmid = {19036979},
	Pst = {ppublish},
	Title = {Sequential generation of two distinct synapse-driven network patterns in developing neocortex},
	Volume = {28},
	Year = {2008},
	File = {papers/Allène_JNeurosci2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.3733-08.2008}}

@article{Ackman:2009,
	Abstract = {In human patients, cortical dysplasia produced by Doublecortin (DCX) mutations lead to mental retardation and intractable infantile epilepsies, but the underlying mechanisms are not known. DCX(-/-) mice have been generated to investigate this issue. However, they display no neocortical abnormality, lessening their impact on the field. In contrast, in utero knockdown of DCX RNA produces a morphologically relevant cortical band heterotopia in rodents. On this preparation we have now compared the neuronal and network properties of ectopic, overlying, and control neurons in an effort to identify how ectopic neurons generate adverse patterns that will impact cortical activity. We combined dynamic calcium imaging and anatomical and electrophysiological techniques and report now that DCX(-/-)EGFP(+)-labeled ectopic neurons that fail to migrate develop extensive axonal subcortical projections and retain immature properties, and most of them display a delayed maturation of GABA-mediated signaling. Cortical neurons overlying the heterotopia, in contrast, exhibit a massive increase of ongoing glutamatergic synaptic currents reflecting a strong reactive plasticity. Neurons in both experimental fields are more frequently coactive in coherent synchronized oscillations than control cortical neurons. In addition, both fields displayed network-driven oscillations during evoked epileptiform burst. These results show that migration disorders produce major alterations not only in neurons that fail to migrate but also in their programmed target areas. We suggest that this duality play a major role in cortical dysfunction of DCX brains.},
	Author = {Ackman, James B and Aniksztejn, Laurent and Cr{\'e}pel, Val{\'e}rie and Becq, H{\'e}l{\`e}ne and Pellegrino, Christophe and Cardoso, Carlos and Ben-Ari, Yehezkel and Represa, Alfonso},
	Date-Added = {2017-05-31 23:19:57 +0000},
	Date-Modified = {2017-05-31 23:21:14 +0000},
	Doi = {10.1523/JNEUROSCI.4093-08.2009},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {21 Dysplasia-heterotopia; 21 Neurophysiology},
	Mesh = {Analysis of Variance; Animals; Animals, Genetically Modified; Animals, Newborn; Bicuculline; Cerebral Cortex; Disease Models, Animal; Electroporation; Excitatory Amino Acid Antagonists; Female; GABA Antagonists; Glutamate Decarboxylase; Glutamic Acid; Green Fluorescent Proteins; Humans; In Vitro Techniques; Malformations of Cortical Development; Membrane Potentials; Microtubule-Associated Proteins; Mutation; Nerve Net; Neurons; Neuropeptides; Pregnancy; Quinoxalines; RNA, Small Interfering; Rats; Rats, Wistar; Sodium Channel Blockers; Tetrodotoxin; Valine; gamma-Aminobutyric Acid},
	Month = {Jan},
	Number = {2},
	Pages = {313-27},
	Pmid = {19144832},
	Pst = {ppublish},
	Title = {Abnormal network activity in a targeted genetic model of human double cortex},
	Volume = {29},
	Year = {2009},
	File = {papers/Ackman_JNeurosci2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4093-08.2009}}

@article{Veinante:2003,
	Abstract = {In freely moving rats, whisking is associated with a slow modulation of neuronal excitability in the primary somatosensory cortex. Because it persists after the blockade of vibrissa input, it was suggested that the slow modulation might be mediated by motor-sensory corticocortical connections and perhaps result from the corollary discharges of corticofugal cells. In the present study, we identified motor cortical cells that project to the barrel field and reconstructed their axonal projections after juxtacellularly staining single cells with a biotinylated tracer. On the basis of the final destination of main axons, two groups of neurons contribute to motor-sensory projections: callosal cells (87.5%) and corticofugal cells (12.5%). Axon collaterals of callosal cells arborize in layers five to six of the granular and dysgranular zones and give off several branches that ascend between the barrels to ramify in the molecular layer. In contrast, the axon collaterals of corticofugal cells do not ramify in the infragranular layers but in layer 1. The origin of the majority of motor sensory projections from callosally projecting cells does not support the notion that the slow modulation results from the corollary discharges of corticofugal axons. It would rather originate from a separate population of cells, which could output the slow signal to the barrel field in parallel with the corticofugal commands to a brainstem pattern generator. As free whisking is characterized by bilateral concerted movements of the vibrissae, the transcallosal contribution of motor-sensory axons represents a substrate for synchronizing the slow modulation across both hemispheres.},
	Author = {Veinante, Pierre and Desch{\^e}nes, Martin},
	Date-Added = {2017-05-30 20:26:15 +0000},
	Date-Modified = {2017-05-30 20:26:15 +0000},
	Doi = {10.1002/cne.10769},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Axons; Biotin; Brain Mapping; Dextrans; Fluorescent Dyes; Motor Cortex; Neural Pathways; Neurons; Rats; Rats, Sprague-Dawley; Somatosensory Cortex; Vibrissae},
	Month = {Sep},
	Number = {1},
	Pages = {98-103},
	Pmid = {12866130},
	Pst = {ppublish},
	Title = {Single-cell study of motor cortex projections to the barrel field in rats},
	Volume = {464},
	Year = {2003},
	File = {papers/Veinante_JCompNeurol2003.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.10769}}

@article{Wilson:1987,
	Abstract = {The neurons of origin of the bilateral corticostriatal projection arising from the medial agranular cortical field in rats were identified by antidromic activation from contralateral neostriatal stimulation. The same cells were tested for antidromic activation from the contralateral neocortex and for orthodromic responses to stimulation of neocortex of the contralateral hemisphere or ipsilateral rostral thalamus. The neurons were then stained by intracellular injection of horseradish peroxidase. The laminar distribution of these neurons was compared to that of cortical cells stained retrogradely after injection of wheat germ agglutinin/HRP in the ipsilateral or contralateral neostriatum. The morphological features of physiologically identified corticostriatal neurons, their laminar organization, and their responses to stimulation were examined and compared with crossed corticocortical and brainstem-projecting cells. Crossed corticostriatal cells of the medial agranular cortical field were medium-sized pyramidal neurons found in the superficial part of layer V and in the deep part of layer III. Their basilar dendritic fields and initial intracortical axon collateral arborizations were coextensive with the layer defined by the distribution of corticostriatal neurons. The apical dendrites were thin and sparsely branched but consistently reached layer I, where they made a small arborization. These morphological features were shared by cortical neurons projecting to contralateral neocortex but not responding antidromically to stimulation of contralateral neostriatum, but they were not shared by brainstem-projecting cortical cells. Orthodromic responses to contralateral cortical stimulation consisted of brief excitatory postsynaptic potentials that were followed by powerful and longer-lasting inhibitory postsynaptic potentials. Corticostriatal cells also exhibited small excitatory postsynaptic potentials in response to thalamic stimulation. Many crossed corticostriatal neurons were also commissural corticocortical neurons. The results of reciprocal collision tests showed that this was due to the existence of two separate axonal branches, one projecting to contralateral neocortex and one to contralateral neostriatum. Intracellular staining of these neurons revealed ipsilateral axonal projections to the neostriatum and cortex.},
	Author = {Wilson, C J},
	Date-Added = {2017-05-30 20:05:48 +0000},
	Date-Modified = {2017-05-30 20:05:48 +0000},
	Doi = {10.1002/cne.902630408},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Cerebral Cortex; Corpus Striatum; Male; Neural Pathways; Neurons; Rats; Rats, Inbred Strains; Synapses; Synaptic Transmission},
	Month = {Sep},
	Number = {4},
	Pages = {567-80},
	Pmid = {2822779},
	Pst = {ppublish},
	Title = {Morphology and synaptic connections of crossed corticostriatal neurons in the rat},
	Volume = {263},
	Year = {1987},
	File = {papers/Wilson_JCompNeurol1987.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902630408}}

@article{Yorke:1975,
	Abstract = {Interhemispheric neocortical connections are widely distributed through the corpus callosum in the mouse. Callosal connections are present in all cytoarchitectonic fields except field 25. The distal extemity representations of SmI, and MsI the representation of the mystacial vibrissae in SmI, and the more peripheral field representation of VI are relatively acallosal. Dense projections lie in the midline or truncal representations of SmI, MsI, SmII, at the vertical meridian representations bordering field 17, and medial to the AI representation. The radial distribution of terminals is bimodal in most cytoarchitectonic fields. It is unimodal in the supracallosal segment of field 29b and fields 49 and 27, trimodal in fields 13 and 35. The cells of origin of callosal fibers appear to have the same topographic pattern of distribution as the callosal terminals, observing the same steep and gradual density gradients. No cells giving rise to callosal axons are identified in the acallosal regions of fields 2 and 17. Further, superficial focal lesions in cortical areas which receive callosal connections give rise only to homotopic contralateral degeneration. Acallosal areas of 17 and 2 give rise to no callosal connections. The cells of origin of callosal connections are located at all laminar levels of the cortex and include pyramidal and polymorphic cells but not the granule cells of layer IV.},
	Author = {Yorke, Jr, C H and Caviness, Jr, V S},
	Date-Added = {2017-05-30 19:53:12 +0000},
	Date-Modified = {2017-05-30 19:53:12 +0000},
	Doi = {10.1002/cne.901640206},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Corpus Callosum; Hybridization, Genetic; Mice; Mice, Inbred Strains; Neural Pathways; Peroxidases},
	Month = {Nov},
	Number = {2},
	Pages = {233-45},
	Pmid = {1184784},
	Pst = {ppublish},
	Title = {Interhemispheric neocortical connections of the corpus callosum in the normal mouse: a study based on anterograde and retrograde methods},
	Volume = {164},
	Year = {1975},
	File = {papers/Yorke_JCompNeurol1975.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901640206}}

@article{Mitchell:2005,
	Abstract = {Integration of sensory-motor information in premotor cortex of rodents occurs largely through callosal and frontal cortical association projections directed in a hierarchically organized manner. Although most anatomical studies in rodents have been performed in rats, mammalian genetic models have focused on mice, because of their successful manipulation on the genetic and cell biological levels. It is therefore important to establish the normal patterns of anatomical connectivity in mice, which potentially differ from those in rats. The goal of this study is to investigate the anatomical development of callosal and frontal premotor projection neurons (CPN and FPN, respectively) in mouse sensory-motor and premotor cortex and to investigate quantitatively the potential laminar differences between these neurons with simultaneous callosal and frontal projections during development. The retrograde tracers Fluoro-Gold and DiI were injected into sensory-motor and premotor cortices, respectively, C57Bl/6 mice at different developmental times (P2, P8, P21, adult). We found that, in contrast to the case in primate and cat, there is widespread overlap in populations of long-distance projection neurons in mice; many projection neurons have simultaneous projections to both contralateral somatosensory cortex and ipsilateral frontal cortex, and a considerable number of these dual projections persist into adulthood. In addition, there are significant laminar differences in the percentage of neurons with simultaneous callosal and frontal projections, and an isolated population of layer V FPN has bilateral projections to both premotor cortical hemispheres. Taken together, our results indicate that a large proportion of individual projection neurons maintains simultaneous callosal and frontal projections in adult mice, suggesting that these dual projections might serve the critical function of integrating motor coordination information with multimodal association areas.},
	Author = {Mitchell, Bartley D and Macklis, Jeffrey D},
	Date-Added = {2017-05-30 19:27:20 +0000},
	Date-Modified = {2017-05-30 19:28:22 +0000},
	Doi = {10.1002/cne.20428},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {Adult neurogenesis general;Research Support, Non-U.S. Gov't;17 Transplant Regeneration;Motor Skills;Motor Cortex;Prefrontal Cortex;Research Support, U.S. Gov't, P.H.S.;Neural Pathways;Mice, Inbred C57BL;Cell Count;Nerve Net;Animals;Somatosensory Cortex;Mice;Neurons;Corpus Callosum},
	Mesh = {Animals; Cell Count; Corpus Callosum; Mice; Mice, Inbred C57BL; Motor Cortex; Motor Skills; Nerve Net; Neural Pathways; Neurons; Prefrontal Cortex; Somatosensory Cortex},
	Month = {Jan},
	Number = {1},
	Pages = {17-32},
	Pmid = {15612019},
	Pst = {ppublish},
	Title = {Large-scale maintenance of dual projections by callosal and frontal cortical projection neurons in adult mice},
	Volume = {482},
	Year = {2005},
	File = {papers/Mitchell_JCompNeurol2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.20428}}

@article{Greig:2013,
	Abstract = {The sophisticated circuitry of the neocortex is assembled from a diverse repertoire of neuronal subtypes generated during development under precise molecular regulation. In recent years, several key controls over the specification and differentiation of neocortical projection neurons have been identified. This work provides substantial insight into the 'molecular logic' underlying cortical development and increasingly supports a model in which individual progenitor-stage and postmitotic regulators are embedded within highly interconnected networks that gate sequential developmental decisions. Here, we provide an integrative account of the molecular controls that direct the progressive development and delineation of subtype and area identity of neocortical projection neurons.},
	Author = {Greig, Luciano Custo and Woodworth, Mollie B and Galazo, Maria J and Padmanabhan, Hari and Macklis, Jeffrey D},
	Date-Added = {2017-05-30 18:55:33 +0000},
	Date-Modified = {2017-05-30 18:55:33 +0000},
	Doi = {10.1038/nrn3586},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Biological Evolution; Gene Expression Regulation, Developmental; Humans; Mitosis; Neocortex; Nerve Net; Neural Pathways; Neural Stem Cells; Neurons},
	Month = {Nov},
	Number = {11},
	Pages = {755-69},
	Pmc = {PMC3876965},
	Pmid = {24105342},
	Pst = {ppublish},
	Title = {Molecular logic of neocortical projection neuron specification, development and diversity},
	Volume = {14},
	Year = {2013},
	File = {papers/Greig_NatRevNeurosci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn3586}}

@article{Molyneaux:2007,
	Abstract = {In recent years, tremendous progress has been made in understanding the mechanisms underlying the specification of projection neurons within the mammalian neocortex. New experimental approaches have made it possible to identify progenitors and study the lineage relationships of different neocortical projection neurons. An expanding set of genes with layer and neuronal subtype specificity have been identified within the neocortex, and their function during projection neuron development is starting to be elucidated. Here, we assess recent data regarding the nature of neocortical progenitors, review the roles of individual genes in projection neuron specification and discuss the implications for progenitor plasticity.},
	Author = {Molyneaux, Bradley J and Arlotta, Paola and Menezes, Joao R L and Macklis, Jeffrey D},
	Date-Added = {2017-05-30 18:40:15 +0000},
	Date-Modified = {2017-05-30 18:40:15 +0000},
	Doi = {10.1038/nrn2151},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Cell Differentiation; Cell Lineage; Cerebral Cortex; Efferent Pathways; Gene Expression Regulation, Developmental; Genes, Homeobox; Humans; Neuronal Plasticity; Neurons; Stem Cells},
	Month = {Jun},
	Number = {6},
	Pages = {427-37},
	Pmid = {17514196},
	Pst = {ppublish},
	Title = {Neuronal subtype specification in the cerebral cortex},
	Volume = {8},
	Year = {2007},
	File = {papers/Molyneaux_NatRevNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2151}}

@article{Armentano:2007,
	Abstract = {We used cortex-specific deletion of the transcription factor gene COUP-TFI (also known as Nr2f1) in mice to demonstrate previously unknown fundamental roles for it in patterning mammalian neocortex into areas. The highest COUP-TFI expression is observed in the cortical progenitors and progeny in parietal and occipital cortex that form sensory areas, and the lowest expression was observed in frontal cortex that includes motor areas. Cortical deletion of COUP-TFI resulted in massive expansion of frontal areas, including motor, to occupy most of neocortex, paralleled by marked compression of sensory areas to caudal occipital cortex. These area patterning changes are preceded and paralleled by corresponding changes in molecular markers of area identity and altered axonal projections to maintain patterned area-specific input and output connections. We conclude that COUP-TFI is required for balancing patterning of neocortex into frontal/motor and sensory areas by acting in its expression domain to repress frontal/motor area identities and to specify sensory area identities.},
	Author = {Armentano, Maria and Chou, Shen-Ju and Tomassy, Giulio Srubek and Leing{\"a}rtner, Axel and O'Leary, Dennis D M and Studer, Mich{\`e}le},
	Date-Added = {2017-05-25 00:09:44 +0000},
	Date-Modified = {2017-05-25 00:09:44 +0000},
	Doi = {10.1038/nn1958},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Animals; Body Patterning; COUP Transcription Factor I; Embryo, Mammalian; Fibroblast Growth Factor 8; Gene Expression Regulation, Developmental; Homeodomain Proteins; Mice; Mice, Inbred C57BL; Mice, Transgenic; Motor Cortex; Neural Pathways; PAX2 Transcription Factor; Serotonin; Somatosensory Cortex; Transcription Factors},
	Month = {Oct},
	Number = {10},
	Pages = {1277-86},
	Pmid = {17828260},
	Pst = {ppublish},
	Title = {COUP-TFI regulates the balance of cortical patterning between frontal/motor and sensory areas},
	Volume = {10},
	Year = {2007},
	File = {papers/Armentano_NatNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn1958}}

@article{Yokoyama:2001,
	Abstract = {To investigate Eph-ephrin bidirectional signaling, a series of mutations were generated in the ephrin-B3 locus. The absence of both forward and reverse signaling resulted in mice with mirror movements as typified by a hopping locomotion. The corticospinal tract was defective as axons failed to respect the midline boundary of the spinal cord and bilaterally innervated both contralateral and ipsilateral motor neuron populations. A second mutation that expresses a truncated ephrin-B3 protein lacking its cytoplasmic domain did not lead to hopping, indicating that reverse signaling is not required for corticospinal innervation. Ephrin-B3 is concentrated at the spinal cord midline, while one of its receptors, EphA4, is expressed in postnatal corticospinal neurons as their fibers pathfind down the contralateral spinal cord. Our data indicate ephrin-B3 functions as a midline-anchored repellent to stimulate forward signaling in EphA4-expressing axons.},
	Author = {Yokoyama, N and Romero, M I and Cowan, C A and Galvan, P and Helmbacher, F and Charnay, P and Parada, L F and Henkemeyer, M},
	Date-Added = {2017-05-24 23:48:35 +0000},
	Date-Modified = {2017-05-24 23:48:35 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Alleles; Animals; Axons; Electric Stimulation; Ephrin-B3; Female; Fetal Proteins; Gait Disorders, Neurologic; Homozygote; Male; Membrane Proteins; Mice; Mice, Neurologic Mutants; Motor Cortex; Mutagenesis, Site-Directed; Pyramidal Tracts; Receptor Protein-Tyrosine Kinases; Receptor, EphA4; Signal Transduction; Spinal Cord},
	Month = {Jan},
	Number = {1},
	Pages = {85-97},
	Pmid = {11182083},
	Pst = {ppublish},
	Title = {Forward signaling mediated by ephrin-B3 prevents contralateral corticospinal axons from recrossing the spinal cord midline},
	Volume = {29},
	Year = {2001},
	File = {papers/Yokoyama_Neuron2001.pdf}}

@article{Dottori:1998,
	Abstract = {Members of the Eph family of tyrosine kinase receptors have been implicated in the regulation of developmental processes and, in particular, axon guidance in the developing nervous system. The function of the EphA4 (Sek1) receptor was explored through creation of a null mutant mouse. Mice with a null mutation in the EphA4 gene are viable and fertile but have a gross motor dysfunction, which is evidenced by a loss of coordination of limb movement and a resultant hopping, kangaroo-like gait. Consistent with the observed phenotype, anatomical studies and anterograde tracing experiments reveal major disruptions of the corticospinal tract within the medulla and spinal cord in the null mutant animals. These results demonstrate a critical role for EphA4 in establishing the corticospinal projection.},
	Author = {Dottori, M and Hartley, L and Galea, M and Paxinos, G and Polizzotto, M and Kilpatrick, T and Bartlett, P F and Murphy, M and K{\"o}ntgen, F and Boyd, A W},
	Date-Added = {2017-05-24 23:42:32 +0000},
	Date-Modified = {2017-05-24 23:42:32 +0000},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Base Sequence; Fetal Proteins; Gait; Gene Expression Regulation, Developmental; Genotype; Homozygote; Medulla Oblongata; Mice; Mice, Knockout; Molecular Sequence Data; Movement Disorders; Nerve Fibers; Nerve Tissue Proteins; Neural Pathways; Polymerase Chain Reaction; Receptor Protein-Tyrosine Kinases; Receptor, EphA4; Recombination, Genetic; Restriction Mapping; Spinal Cord; Stem Cells},
	Month = {Oct},
	Number = {22},
	Pages = {13248-53},
	Pmc = {PMC23772},
	Pmid = {9789074},
	Pst = {ppublish},
	Title = {EphA4 (Sek1) receptor tyrosine kinase is required for the development of the corticospinal tract},
	Volume = {95},
	Year = {1998},
	File = {papers/Dottori_ProcNatlAcadSciUSA1998.pdf}}

@article{Kullander:2001,
	Abstract = {The EphA4 receptor tyrosine kinase regulates the formation of the corticospinal tract (CST), a pathway controlling voluntary movements, and of the anterior commissure (AC), connecting the neocortical temporal lobes. To study EphA4 kinase signaling in these processes, we generated mice expressing mutant EphA4 receptors either lacking kinase activity or with severely downregulated kinase activity. We demonstrate that EphA4 is required for CST formation as a receptor for which it requires an active kinase domain. In contrast, the formation of the AC is rescued by kinase-dead EphA4, suggesting that in this structure EphA4 acts as a ligand for which its kinase activity is not required. Unexpectedly, the cytoplasmic sterile-alpha motif (SAM) domain is not required for EphA4 functions. Our findings establish both kinase-dependent and kinase-independent functions of EphA4 in the formation of major axon tracts.},
	Author = {Kullander, K and Mather, N K and Diella, F and Dottori, M and Boyd, A W and Klein, R},
	Date-Added = {2017-05-24 23:39:19 +0000},
	Date-Modified = {2017-05-24 23:39:19 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axons; Brain Stem; Ephrin-A4; Ephrin-B2; Fetal Proteins; In Situ Hybridization; Membrane Proteins; Mice; Mice, Knockout; Mice, Mutant Strains; Molecular Sequence Data; Motor Cortex; Organ Specificity; Prosencephalon; Protein Structure, Tertiary; Pyramidal Tracts; RNA, Messenger; Receptor Protein-Tyrosine Kinases; Receptor, EphA4; Signal Transduction; Temporal Lobe},
	Month = {Jan},
	Number = {1},
	Pages = {73-84},
	Pmid = {11182082},
	Pst = {ppublish},
	Title = {Kinase-dependent and kinase-independent functions of EphA4 receptors in major axon tract formation in vivo},
	Volume = {29},
	Year = {2001},
	File = {papers/Kullander_Neuron2001.pdf}}

@article{Leighton:2001,
	Abstract = {The search to understand the mechanisms regulating brain wiring has relied on biochemical purification approaches in vertebrates and genetic approaches in invertebrates to identify molecular cues and receptors for axon guidance. Here we describe a phenotype-based gene-trap screen in mice designed for the large-scale identification of genes controlling the formation of the trillions of connections in the mammalian brain. The method incorporates an axonal marker, which helps to identify cell-autonomous mechanisms in axon guidance, and has generated a resource of mouse lines with striking patterns of axonal labelling, which facilitates analysis of the normal wiring diagram of the brain. Studies of two of these mouse lines have identified an in vivo guidance function for a vertebrate transmembrane semaphorin, Sema6A, and have helped re-evaluate that of the Eph receptor EphA4.},
	Author = {Leighton, P A and Mitchell, K J and Goodrich, L V and Lu, X and Pinson, K and Scherz, P and Skarnes, W C and Tessier-Lavigne, M},
	Date-Added = {2017-05-24 22:51:25 +0000},
	Date-Modified = {2017-05-24 22:51:25 +0000},
	Doi = {10.1038/35065539},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Alkaline Phosphatase; Animals; Axons; Brain; Cell Adhesion Molecules, Neuronal; Cell Movement; Cells, Cultured; Female; Fetal Proteins; GPI-Linked Proteins; Genetic Techniques; Genetic Vectors; Humans; Isoenzymes; Male; Mice; Mice, Inbred C57BL; Mutation; Nerve Tissue Proteins; Neural Pathways; Neurons; Phenotype; Receptor Protein-Tyrosine Kinases; Receptor, EphA4; Ribosomes; Semaphorins; Sensory Receptor Cells; Thalamus},
	Month = {Mar},
	Number = {6825},
	Pages = {174-9},
	Pmid = {11242070},
	Pst = {ppublish},
	Title = {Defining brain wiring patterns and mechanisms through gene trapping in mice},
	Volume = {410},
	Year = {2001},
	File = {papers/Leighton_Nature2001.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/35065539}}

@article{Gallarda:2008,
	Abstract = {Execution of motor behaviors relies on circuitries effectively integrating immediate sensory feedback to efferent pathways controlling muscle activity. It remains unclear how, during neuromuscular circuit assembly, sensory and motor projections become incorporated into tightly coordinated, yet functionally separate pathways. We report that, within axial nerves, establishment of discrete afferent and efferent pathways depends on coordinate signaling between coextending sensory and motor projections. These heterotypic axon-axon interactions require motor axonal EphA3/EphA4 receptor tyrosine kinases activated by cognate sensory axonal ephrin-A ligands. Genetic elimination of trans-axonal ephrin-A --> EphA signaling in mice triggers drastic motor-sensory miswiring, culminating in functional efferents within proximal afferent pathways. Effective assembly of a key circuit underlying motor behaviors thus critically depends on trans-axonal signaling interactions resolving motor and sensory projections into discrete pathways.},
	Author = {Gallarda, Benjamin W and Bonanomi, Dario and M{\"u}ller, Daniel and Brown, Arthur and Alaynick, William A and Andrews, Shane E and Lemke, Greg and Pfaff, Samuel L and Marquardt, Till},
	Date-Added = {2017-05-24 22:50:00 +0000},
	Date-Modified = {2017-05-24 22:50:00 +0000},
	Doi = {10.1126/science.1153758},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Afferent Pathways; Animals; Axons; Cells, Cultured; Coculture Techniques; Efferent Pathways; Electrophysiology; Ephrins; Ganglia, Spinal; Growth Cones; Ligands; Mice; Mice, Transgenic; Motor Activity; Motor Neurons; Muscle, Skeletal; Mutation; Neurons, Afferent; Peripheral Nerves; Receptor, EphA3; Receptor, EphA4; Signal Transduction},
	Month = {Apr},
	Number = {5873},
	Pages = {233-6},
	Pmc = {PMC3158657},
	Pmid = {18403711},
	Pst = {ppublish},
	Title = {Segregation of axial motor and sensory pathways via heterotypic trans-axonal signaling},
	Volume = {320},
	Year = {2008},
	File = {papers/Gallarda_Science2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1153758}}

@article{Bedogni:2010,
	Abstract = {Areas and layers of the cerebral cortex are specified by genetic programs that are initiated in progenitor cells and then, implemented in postmitotic neurons. Here, we report that Tbr1, a transcription factor expressed in postmitotic projection neurons, exerts positive and negative control over both regional (areal) and laminar identity. Tbr1 null mice exhibited profound defects of frontal cortex and layer 6 differentiation, as indicated by down-regulation of gene-expression markers such as Bcl6 and Cdh9. Conversely, genes that implement caudal cortex and layer 5 identity, such as Bhlhb5 and Fezf2, were up-regulated in Tbr1 mutants. Tbr1 implements frontal identity in part by direct promoter binding and activation of Auts2, a frontal cortex gene implicated in autism. Tbr1 regulates laminar identity in part by downstream activation or maintenance of Sox5, an important transcription factor controlling neuronal migration and corticofugal axon projections. Similar to Sox5 mutants, Tbr1 mutants exhibit ectopic axon projections to the hypothalamus and cerebral peduncle. Together, our findings show that Tbr1 coordinately regulates regional and laminar identity of postmitotic cortical neurons.},
	Author = {Bedogni, Francesco and Hodge, Rebecca D and Elsen, Gina E and Nelson, Branden R and Daza, Ray A M and Beyer, Richard P and Bammler, Theo K and Rubenstein, John L R and Hevner, Robert F},
	Date-Added = {2017-05-24 20:46:48 +0000},
	Date-Modified = {2017-05-24 20:46:48 +0000},
	Doi = {10.1073/pnas.1002285107},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Biomarkers; DNA-Binding Proteins; Down-Regulation; Gene Expression Regulation, Developmental; Mice; Mitosis; Mutation; Neocortex; Neurons; Nuclear Proteins; Oligonucleotide Array Sequence Analysis; Organ Specificity; Protein Binding; Transcriptional Activation; Up-Regulation},
	Month = {Jul},
	Number = {29},
	Pages = {13129-34},
	Pmc = {PMC2919950},
	Pmid = {20615956},
	Pst = {ppublish},
	Title = {Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex},
	Volume = {107},
	Year = {2010},
	File = {papers/Bedogni_ProcNatlAcadSciUSA2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1002285107}}

@article{Kalil:2011,
	Abstract = {Precise wiring of cortical circuits during development depends upon axon extension, guidance, and branching to appropriate targets. Motile growth cones at axon tips navigate through the nervous system by responding to molecular cues, which modulate signaling pathways within axonal growth cones. Intracellular calcium signaling has emerged as a major transducer of guidance cues but exactly how calcium signaling pathways modify the actin and microtubule cytoskeleton to evoke growth cone behaviors and axon branching is still mysterious. Axons must often pause their extension in tracts while their branches extend into targets. Some evidence suggests a competition between growth of axons and branches but the mechanisms are poorly understood. Since it is difficult to study growing axons deep within the mammalian brain, much of what we know about signaling pathways and cytoskeletal dynamics of growth cones comes from tissue culture studies, in many cases, of non-mammalian species. Consequently it is not well understood how guidance cues relevant to mammalian neural development in vivo signal to the growth cone cytoskeleton during axon outgrowth and guidance. In this review we describe our recent work in dissociated cultures of developing rodent sensorimotor cortex in the context of the current literature on molecular guidance cues, calcium signaling pathways, and cytoskeletal dynamics that regulate growth cone behaviors. A major challenge is to relate findings in tissue culture to mechanisms of cortical development in vivo. Toward this goal, we describe our recent work in cortical slices, which preserve the complex cellular and molecular environment of the mammalian brain but allow direct visualization of growth cone behaviors and calcium signaling. Findings from this work suggest that mechanisms regulating axon growth and guidance in dissociated culture neurons also underlie development of cortical connectivity in vivo.},
	Author = {Kalil, Katherine and Li, Li and Hutchins, B Ian},
	Date-Added = {2017-05-23 05:43:57 +0000},
	Date-Modified = {2017-05-23 05:43:57 +0000},
	Doi = {10.3389/fnana.2011.00062},
	Journal = {Front Neuroanat},
	Journal-Full = {Frontiers in neuroanatomy},
	Keywords = {CaMKII; Wnt5a; axon branching; axon guidance; axon outgrowth; calcium signaling; corpus callosum; microtubules},
	Pages = {62},
	Pmc = {PMC3202218},
	Pmid = {22046148},
	Pst = {epublish},
	Title = {Signaling mechanisms in cortical axon growth, guidance, and branching},
	Volume = {5},
	Year = {2011},
	File = {papers/Kalil_FrontNeuroanat2011.pdf}}

@article{Paul:2007,
	Abstract = {Agenesis of the corpus callosum (AgCC), a failure to develop the large bundle of fibres that connect the cerebral hemispheres, occurs in 1:4000 individuals. Genetics, animal models and detailed structural neuroimaging are now providing insights into the developmental and molecular bases of AgCC. Studies using neuropsychological, electroencephalogram and functional MRI approaches are examining the resulting impairments in emotional and social functioning, and have begun to explore the functional neuroanatomy underlying impaired higher-order cognition. The study of AgCC could provide insight into the integrated cerebral functioning of healthy brains, and may offer a model for understanding certain psychiatric illnesses, such as schizophrenia and autism.},
	Author = {Paul, Lynn K and Brown, Warren S and Adolphs, Ralph and Tyszka, J Michael and Richards, Linda J and Mukherjee, Pratik and Sherr, Elliott H},
	Date-Added = {2017-05-23 02:33:29 +0000},
	Date-Modified = {2017-05-23 02:33:29 +0000},
	Doi = {10.1038/nrn2107},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Child Behavior; Child, Preschool; Corpus Callosum; Developmental Disabilities; Female; Humans; Infant; Infant, Newborn; Mental Disorders; Neuropsychological Tests; Pregnancy},
	Month = {Apr},
	Number = {4},
	Pages = {287-99},
	Pmid = {17375041},
	Pst = {ppublish},
	Title = {Agenesis of the corpus callosum: genetic, developmental and functional aspects of connectivity},
	Volume = {8},
	Year = {2007},
	File = {papers/Paul_NatRevNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2107}}

@article{Minshew:2007,
	Abstract = {This review covers a fraction of the new research developments in autism but establishes the basic elements of the new neurobiologic understanding of autism. Autism is a polygenetic developmental neurobiologic disorder with multiorgan system involvement, though it predominantly involves central nervous system dysfunction. The evidence supports autism as a disorder of the association cortex, both its neurons and their projections. In particular, it is a disorder of connectivity, which appears, from current evidence, to primarily involve intrahemispheric connectivity. The focus of connectivity studies thus far has been on white matter, but alterations in functional magnetic resonance imaging activation suggest that intracortical connectivity is also likely to be disturbed. Furthermore, the disorder has a broad impact on cognitive and neurologic functioning. Deficits in high-functioning individuals occur in processing that places high demands on integration of information and coordination of multiple neural systems. Intact or enhanced abilities share a dependence on low information-processing demands and local neural connections. This multidomain model with shared characteristics predicts an underlying pathophysiologic mechanism that impacts the brain broadly, according to a common neurobiologic principle. The multiorgan system involvement and diversity of central nervous system findings suggest an epigenetic mechanism.},
	Author = {Minshew, Nancy J and Williams, Diane L},
	Date-Added = {2017-05-23 02:28:39 +0000},
	Date-Modified = {2017-05-23 02:28:39 +0000},
	Doi = {10.1001/archneur.64.7.945},
	Journal = {Arch Neurol},
	Journal-Full = {Archives of neurology},
	Mesh = {Autistic Disorder; Cerebral Cortex; Child; Diagnostic Imaging; Genetic Predisposition to Disease; Humans; Models, Neurological; Nerve Fibers, Myelinated; Nervous System Malformations; Neural Pathways; Neurons},
	Month = {Jul},
	Number = {7},
	Pages = {945-50},
	Pmc = {PMC2597785},
	Pmid = {17620483},
	Pst = {ppublish},
	Title = {The new neurobiology of autism: cortex, connectivity, and neuronal organization},
	Volume = {64},
	Year = {2007},
	File = {papers/Minshew_ArchNeurol2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1001/archneur.64.7.945}}

@article{Fame:2011,
	Abstract = {Callosal projection neurons (CPN) are a diverse population of neocortical projection neurons that connect the two hemispheres of the cerebral cortex via the corpus callosum. They play key roles in high-level associative connectivity, and have been implicated in cognitive syndromes of high-level associative dysfunction, such as autism spectrum disorders. CPN evolved relatively recently compared to other cortical neuron populations, and have undergone disproportionately large expansion from mouse to human. While much is known about the anatomical trajectory of developing CPN axons, and progress has been made in identifying cellular and molecular controls over midline crossing, only recently have molecular-genetic controls been identified that specify CPN populations, and help define CPN subpopulations. In this review, we discuss the development, diversity and evolution of CPN.},
	Author = {Fame, Ryann M and MacDonald, Jessica L and Macklis, Jeffrey D},
	Date-Added = {2017-05-23 02:24:20 +0000},
	Date-Modified = {2017-05-23 02:24:20 +0000},
	Doi = {10.1016/j.tins.2010.10.002},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Mesh = {Animals; Cerebral Cortex; Corpus Callosum; Humans; Neurons},
	Month = {Jan},
	Number = {1},
	Pages = {41-50},
	Pmc = {PMC3053014},
	Pmid = {21129791},
	Pst = {ppublish},
	Title = {Development, specification, and diversity of callosal projection neurons},
	Volume = {34},
	Year = {2011},
	File = {papers/Fame_TrendsNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tins.2010.10.002}}

@article{Garcez:2007,
	Abstract = {The main alternative output routes of adult cortical axons are the internal capsule and the corpus callosum. How do callosal axons choose their trajectories? We hypothesized that bifurcation followed by elimination of one branch is a developmental strategy for accomplishing this aim. Using embryonic and postnatal mice, we labelled cortical projecting neurons and quantified their axonal bifurcations in correlation with the mediolateral position of their somata. Bifurcating axons were numerous in the younger brains but declined during further development. Most bifurcating axons pertained to neurons located in the dorsolateral cortex. Moreover, callosal neurons bifurcate more often than subcortically projecting cells. We then quantified bifurcations formed by dissociated green fluorescent cells plated onto cortical slices. Cells grown over dorsolateral cortex bifurcated more often than those grown over medial cortex, irrespective of their positional origin in the donor. Removal of intermediate targets from the slices prevented bifurcation. We concluded that transient bifurcation and elimination of the lateral branch is a strategy employed by developing callosal axons in search of their targets. As cell body position and intermediate targets determine axon behaviour, we suggest that bifurcations are regulated by cues expressed in the environment.},
	Author = {Garcez, Patricia P and Henrique, Narjara P and Furtado, Danilo A and Bolz, J{\"u}rgen and Lent, Roberto and Uziel, Daniela},
	Date-Added = {2017-05-23 00:57:18 +0000},
	Date-Modified = {2017-05-23 00:57:18 +0000},
	Doi = {10.1111/j.1460-9568.2007.05387.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Mesh = {Age Factors; Amino Acids; Animals; Animals, Newborn; Axons; Cells, Cultured; Coculture Techniques; Corpus Callosum; Embryo, Mammalian; Female; Functional Laterality; Green Fluorescent Proteins; Male; Mice; Neural Pathways; Neurons; Pregnancy},
	Month = {Mar},
	Number = {5},
	Pages = {1384-94},
	Pmid = {17425565},
	Pst = {ppublish},
	Title = {Axons of callosal neurons bifurcate transiently at the white matter before consolidating an interhemispheric projection},
	Volume = {25},
	Year = {2007},
	File = {papers/Garcez_EurJNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1460-9568.2007.05387.x}}

@article{Huang:2012,
	Abstract = {BACKGROUND: Adolescent alcohol abuse remains a serious public health concern, with nearly a third of high school seniors reporting heavy drinking in the previous month.
METHODS: Using the high ethanol-consuming C57BL/6J mouse strain, we examined the effects of ethanol (3.75 g/kg, IP, daily for 45 days) on body weight and brain region mass (cerebral cortex, cerebellum, corpus callosum) during peri-adolescence (postnatal day [P]25 to 70) or adulthood (P180 to 225) of both males and females.
RESULTS: In control peri-adolescent animals, body weight gain was greater in males compared with females. In the peri-adolescent exposure group, ethanol significantly reduced body weight gain to a similar extent in both male and female mice (82 and 84% of controls, respectively). In adult animals, body weight gain was much less than that of the peri-adolescent mice, with ethanol having a small but significant effect in males but not females. Between the control peri-adolescent and adult cohorts (measurements taken at P70 and 225, respectively), there were no significant differences in the mass of the cerebral cortex or the cerebellum from either male or female mice, although the rostro-caudal length of the corpus callosum increased slightly but significantly (6.1%) between these time points.
CONCLUSIONS: Ethanol treatment significantly reduced the mass of the cerebral cortex in peri-adolescent (-3.1%), but not adult, treated mice. By contrast, ethanol significantly reduced the length of the corpus callosum in adult (-5.4%), but not peri-adolescent, treated mice. Future studies at the histological level may yield additional details concerning ethanol and the peri-adolescent brain.},
	Author = {Huang, Chiming and Titus, Jennifer A and Bell, Richard L and Kapros, Tamas and Chen, Jie and Huang, Rosa},
	Date-Added = {2017-05-19 17:17:59 +0000},
	Date-Modified = {2017-05-19 17:17:59 +0000},
	Doi = {10.1111/j.1530-0277.2012.01759.x},
	Journal = {Alcohol Clin Exp Res},
	Journal-Full = {Alcoholism, clinical and experimental research},
	Mesh = {Age Factors; Alcoholism; Animals; Body Weight; Brain; Corpus Callosum; Disease Models, Animal; Ethanol; Female; Male; Mice; Mice, Inbred C57BL; Organ Size},
	Month = {Oct},
	Number = {10},
	Pages = {1728-37},
	Pmid = {22433022},
	Pst = {ppublish},
	Title = {A mouse model for adolescent alcohol abuse: stunted growth and effects in brain},
	Volume = {36},
	Year = {2012},
	File = {papers/Huang_AlcoholClinExpRes2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1530-0277.2012.01759.x}}

@article{Wit:2016,
	Abstract = {The molecular diversification of cell surface molecules has long been postulated to impart specific surface identities on neuronal cell types. The existence of unique cell surface identities would allow neurons to distinguish one another and connect with their appropriate target cells. Although progress has been made in identifying cell type-specific surface molecule repertoires and in characterizing their extracellular interactions, determining how this molecular diversity contributes to the precise wiring of neural circuitry has proven challenging. Here, we review the role of the cadherin, neurexin, immunoglobulin and leucine-rich repeat protein superfamilies in the specification of connectivity. The emerging evidence suggests that the concerted actions of these proteins may critically contribute to the assembly of neural circuits.},
	Author = {de Wit, Joris and Ghosh, Anirvan},
	Date-Added = {2017-05-19 00:57:07 +0000},
	Date-Modified = {2017-05-19 00:57:07 +0000},
	Doi = {10.1038/nrn.2015.3},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Brain; Cell Communication; Cell Membrane; Humans; Neurons; Proteins; Synapses},
	Month = {Jan},
	Number = {1},
	Pages = {22-35},
	Pmid = {26656254},
	Pst = {ppublish},
	Title = {Specification of synaptic connectivity by cell surface interactions},
	Volume = {17},
	Year = {2016},
	File = {papers/Wit_NatRevNeurosci2016.pdf}}

@article{Inoue:1998,
	Abstract = {Multiple subtypes of the cadherin homophilic cell-cell adhesion molecule are expressed differentially in developing and mature brains, each being expressed in restricted neuronal groups. Cadherin-6 (cad6) is one of such cadherins. Recent studies of cad6 mRNA expression in the postnatal mouse forebrain showed that it occurs in neurons constituting a specific subset of thalamocortical connections. Here we analyzed the localization of cad6 mRNA as well as its protein in the entire central nervous system and also in cranial ganglia of mice at late embryonic to postnatal stages. Our results showed that cad6 is expressed by a limited population of neurons or their precursors, which are synaptically connected to one another, throughout the perinatal stages, and that this expression delineates restricted neuronal circuits from the central to peripheral nervous systems, which include subpathways of the auditory, somatosensory, solitary, vestibular, and olivocerebellar systems. cad6 proteins were detected in these cad6 mRNA-positive neurons on the surface of their cell bodies or dendrites as well as in the cytoplasm. Confocal microscopic analysis revealed that the cad6 protein distribution overlapped that of synaptotagmin in synapse forming areas, suggesting that homotypic cad6 interactions are involved in synaptic connections between neurons expressing this protein. These findings support the idea that cadherin-mediated cell-cell adhesions take part in specific interneuronal connections.},
	Author = {Inoue, T and Tanaka, T and Suzuki, S C and Takeichi, M},
	Date-Added = {2017-05-19 00:54:36 +0000},
	Date-Modified = {2017-05-19 00:54:36 +0000},
	Doi = {10.1002/(SICI)1097-0177(199804)211:4<338::AID-AJA5>3.0.CO;2-I},
	Journal = {Dev Dyn},
	Journal-Full = {Developmental dynamics : an official publication of the American Association of Anatomists},
	Mesh = {Age Factors; Animals; Blotting, Northern; Blotting, Western; Brain; Cadherins; Immunohistochemistry; In Situ Hybridization; Interneurons; Mice; Mice, Inbred C57BL; Mice, Inbred ICR; Microtubule-Associated Proteins; Neurons; Synapses; Time Factors},
	Month = {Apr},
	Number = {4},
	Pages = {338-51},
	Pmid = {9566953},
	Pst = {ppublish},
	Title = {Cadherin-6 in the developing mouse brain: expression along restricted connection systems and synaptic localization suggest a potential role in neuronal circuitry},
	Volume = {211},
	Year = {1998},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1097-0177(199804)211:4%3C338::AID-AJA5%3E3.0.CO;2-I}}

@article{Nakagawa:1999,
	Abstract = {The differentiation of areas of the mammalian neocortex has been hypothesized to be controlled by intrinsic genetic programs and extrinsic influences such as those mediated by thalamocortical afferents (TCAs). To address the interplay between these intrinsic and extrinsic mechanisms in the process of arealization, we have analyzed the requirement of TCAs in establishing or maintaining graded or areal patterns of gene expression in the developing mouse neocortex. We describe the differential expression of Lhx2, SCIP, and Emx1, representatives of three different classes of transcription factors, and the type II classical cadherins Cad6, Cad8, and Cad11, which are expressed in graded or areal patterns, as well as layer-specific patterns, in the cortical plate. The differential expression of Lhx2, SCIP, Emx1, and Cad8 in the cortical plate is not evident until after TCAs reach the cortex, whereas Cad6 and Cad11 show subtle graded patterns of expression before the arrival of TCAs, which later become stronger. We find that these genes exhibit normal-appearing graded or areal expression patterns in Mash-1 mutant mice that fail to develop a TCA projection. These findings show that TCAs are not required for the establishment or maintenance of the graded and areal expression patterns of these genes and strongly suggest that their regulation is intrinsic to the developing neocortex.},
	Author = {Nakagawa, Y and Johnson, J E and O'Leary, D D},
	Date-Added = {2017-05-19 00:53:31 +0000},
	Date-Modified = {2017-05-19 00:53:31 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Animals, Newborn; Basic Helix-Loop-Helix Transcription Factors; Cadherins; Cerebral Cortex; DNA-Binding Proteins; Embryo, Mammalian; Gene Expression; Genes, Regulator; Homeodomain Proteins; LIM-Homeodomain Proteins; Mice; Mice, Inbred ICR; Mice, Neurologic Mutants; Neocortex; Neural Pathways; Octamer Transcription Factor-6; Thalamus; Time Factors; Transcription Factors},
	Month = {Dec},
	Number = {24},
	Pages = {10877-85},
	Pmid = {10594069},
	Pst = {ppublish},
	Title = {Graded and areal expression patterns of regulatory genes and cadherins in embryonic neocortex independent of thalamocortical input},
	Volume = {19},
	Year = {1999},
	File = {papers/Nakagawa_JNeurosci1999.pdf}}

@article{Suzuki:1997,
	Abstract = {A number of type-II classic cadherin cell-cell adhesion molecules are expressed in the brain. To investigate their roles in brain morphogenesis, we selected three type-II cadherins, cadherin-6 (cad6), -8 (cad8) and -11 (cad11), and mapped their expressions in the forebrain and other restricted regions of postnatal mouse brains. In the cerebral cortex, each cortical area previously defined was delineated by a specific combinatorial expression of these cadherins. The thalamus and other subcortical regions of the forebrain were also subdivided by differential expression of the three cadherins; e.g., the medial geniculate body expressed only cad6; the ventral posterior thalamic nucleus, cad6/cad11; and the anteroventral thalamic nucleus, cad6/cad8. Likewise, in the olivocerebellar system, each subdivision of the inferior olive expressed a unique set of the three cadherins, and the cerebellar cortex had parasagittal stripes of cad8/cad11 expressions. Close analysis of these cadherin expression patterns revealed that they are correlated with neuronal connection patterns. Examples of these correlations include that cad6 delineates the auditory projection system, cad6/cad8/ cad11 are expressed by part of the Papez circuit, and cad6/cad8 are expressed by subdivisions of the olivo-nuclear circuit. Together with the recent finding that the cadherin adhesion system is localized in synaptic junctions, our findings support the notion that cadherin-mediated cell-cell adhesion plays a role in selective interneuronal connections during neural network formation.},
	Author = {Suzuki, S C and Inoue, T and Kimura, Y and Tanaka, T and Takeichi, M},
	Date-Added = {2017-05-19 00:22:35 +0000},
	Date-Modified = {2017-05-19 00:22:35 +0000},
	Doi = {10.1006/mcne.1997.0626},
	Journal = {Mol Cell Neurosci},
	Journal-Full = {Molecular and cellular neurosciences},
	Mesh = {Animals; Animals, Newborn; Brain; Cadherins; Cell Differentiation; Cerebellum; Cerebral Cortex; Mice; Mice, Inbred ICR; Neurons; Olivary Nucleus; Thalamus},
	Number = {5-6},
	Pages = {433-47},
	Pmid = {9361280},
	Pst = {ppublish},
	Title = {Neuronal circuits are subdivided by differential expression of type-II classic cadherins in postnatal mouse brains},
	Volume = {9},
	Year = {1997},
	File = {papers/Suzuki_MolCellNeurosci1997.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1006/mcne.1997.0626}}

@article{Kim:2011a,
	Abstract = {Cadherins play a key role in the dynamics of cell-cell contact formation and remodeling of junctions and tissues. Cadherin-cadherin interactions are gated by extracellular Ca(2+), which serves to rigidify the cadherin extracellular domains and promote trans junctional interactions. Here we describe the direct visualization and quantification of spatiotemporal dynamics of N-cadherin interactions across intercellular junctions in living cells using a genetically encodable FRET reporter system. Direct measurements of transjunctional cadherin interactions revealed a sudden, but partial, loss of homophilic interactions (τ = 1.17 $\pm$ 0.06 s(-1)) upon chelation of extracellular Ca(2+). A cadherin mutant with reduced adhesive activity (W2A) exhibited a faster, more substantial loss of homophilic interactions (τ = 0.86 $\pm$ 0.02 s(-1)), suggesting two types of native cadherin interactions--one that is rapidly modulated by changes in extracellular Ca(2+) and another with relatively stable adhesive activity that is Ca(2+) independent. The Ca(2+)-sensitive dynamics of cadherin interactions were transmitted to the cell interior where β-catenin translocated to N-cadherin at the junction in both cells. These data indicate that cadherins can rapidly convey dynamic information about the extracellular environment to both cells that comprise a junction.},
	Author = {Kim, Sally A and Tai, Chin-Yin and Mok, Lee-Peng and Mosser, Eric A and Schuman, Erin M},
	Date-Added = {2017-05-19 00:12:46 +0000},
	Date-Modified = {2017-05-19 00:12:46 +0000},
	Doi = {10.1073/pnas.1019003108},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; COS Cells; Cadherins; Calcium; Cercopithecus aethiops; Fluorescence Resonance Energy Transfer; Green Fluorescent Proteins; HEK293 Cells; Humans; Intercellular Junctions; Kinetics; L Cells (Cell Line); Mice; Microscopy, Confocal; Protein Binding; Recombinant Fusion Proteins; Transfection; beta Catenin},
	Month = {Jun},
	Number = {24},
	Pages = {9857-62},
	Pmc = {PMC3116393},
	Pmid = {21613566},
	Pst = {ppublish},
	Title = {Calcium-dependent dynamics of cadherin interactions at cell-cell junctions},
	Volume = {108},
	Year = {2011},
	File = {papers/Kim_ProcNatlAcadSciUSA2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1019003108}}

@article{Tepass:2000,
	Abstract = {Cadherins not only maintain the structural integrity of cells and tissues but also control a wide array of cellular behaviours. They are instrumental for cell and tissue polarization, and they regulate cell movements such as cell sorting, cell migration and cell rearrangements. Cadherins may also contribute to neurite outgrowth and pathfinding, and to synaptic specificity and modulation in the central nervous system.},
	Author = {Tepass, U and Truong, K and Godt, D and Ikura, M and Peifer, M},
	Date-Added = {2017-05-19 00:02:41 +0000},
	Date-Modified = {2017-05-19 00:02:41 +0000},
	Doi = {10.1038/35040042},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Mesh = {Amino Acid Sequence; Animals; Cadherins; Cell Adhesion; Central Nervous System; Embryonic and Fetal Development; Humans; Molecular Sequence Data; Morphogenesis; Nervous System; Protein Structure, Secondary; Sequence Alignment; Sequence Homology, Amino Acid; Synapses},
	Month = {Nov},
	Number = {2},
	Pages = {91-100},
	Pmid = {11253370},
	Pst = {ppublish},
	Title = {Cadherins in embryonic and neural morphogenesis},
	Volume = {1},
	Year = {2000},
	File = {papers/Tepass_NatRevMolCellBiol2000.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/35040042}}

@article{Gumbiner:2005,
	Abstract = {Cadherin cell-adhesion proteins mediate many facets of tissue morphogenesis. The dynamic regulation of cadherins in response to various extracellular signals controls cell sorting, cell rearrangements and cell movements. Cadherins are regulated at the cell surface by an inside-out signalling mechanism that is analogous to the integrins in platelets and leukocytes. Signal-transduction pathways impinge on the catenins (cytoplasmic cadherin-associated proteins), which transduce changes across the membrane to alter the state of the cadherin adhesive bond.},
	Author = {Gumbiner, Barry M},
	Date-Added = {2017-05-18 23:34:43 +0000},
	Date-Modified = {2017-05-18 23:34:43 +0000},
	Doi = {10.1038/nrm1699},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Mesh = {Animals; Cadherins; Cell Adhesion; Cell Movement; Cytoskeletal Proteins; Intercellular Junctions; Morphogenesis; Signal Transduction},
	Month = {Aug},
	Number = {8},
	Pages = {622-34},
	Pmid = {16025097},
	Pst = {ppublish},
	Title = {Regulation of cadherin-mediated adhesion in morphogenesis},
	Volume = {6},
	Year = {2005},
	File = {papers/Gumbiner_NatRevMolCellBiol2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrm1699}}

@article{Gumbiner:1996,
	Abstract = {A variety of cell adhesion mechanisms underlie the way that cells are organized in tissues. Stable cell interactions are needed to maintain the structural integrity of tissues, and dynamic changes in cell adhesion participate in the morphogenesis of developing tissues. Stable interactions actually require active adhesion mechanisms that are very similar to those involved in tissue dynamics. Adhesion mechanisms are highly regulated during tissue morphogenesis and are intimately related to the processes of cell motility and cell migration. In particular, the cadherins and the integrins have been implicated in the control of cell movement. Cadherin mediated cell compaction and cellular rearrangements may be analogous to integrin-mediated cell spreading and motility on the ECM. Regulation of cell adhesion can occur at several levels, including affinity modulation, clustering, and coordinated interactions with the actin cytoskeleton. Structural studies have begun to provide a picture of how the binding properties of adhesion receptors themselves might be regulated. However, regulation of tissue morphogenesis requires complex interactions between the adhesion receptors, the cytoskeleton, and networks of signaling pathways. Signals generated locally by the adhesion receptors themselves are involved in the regulation of cell adhesion. These regulatory pathways are also influenced by extrinsic signals arising from the classic growth factor receptors. Furthermore, signals generated locally be adhesion junctions can interact with classic signal transduction pathways to help control cell growth and differentiation. This coupling between physical adhesion and developmental signaling provides a mechanism to tightly integrate physical aspects of tissue morphogenesis with cell growth and differentiation, a coordination that is essential to achieve the intricate patterns of cells in tissues.},
	Author = {Gumbiner, B M},
	Date-Added = {2017-05-18 23:34:08 +0000},
	Date-Modified = {2017-05-18 23:34:08 +0000},
	Journal = {Cell},
	Journal-Full = {Cell},
	Mesh = {Animals; Basement Membrane; Cadherins; Cell Adhesion; Cell Movement; Desmosomes; Extracellular Matrix; Humans; Integrins; Intercellular Junctions; Models, Biological; Morphogenesis; Signal Transduction},
	Month = {Feb},
	Number = {3},
	Pages = {345-57},
	Pmid = {8608588},
	Pst = {ppublish},
	Title = {Cell adhesion: the molecular basis of tissue architecture and morphogenesis},
	Volume = {84},
	Year = {1996},
	File = {papers/Gumbiner_Cell1996.pdf}}

@article{Wang:2009a,
	Abstract = {Research in cellular mechanotransduction often focuses on how extracellular physical forces are converted into chemical signals at the cell surface. However, mechanical forces that are exerted on surface-adhesion receptors, such as integrins and cadherins, are also channelled along cytoskeletal filaments and concentrated at distant sites in the cytoplasm and nucleus. Here, we explore the molecular mechanisms by which forces might act at a distance to induce mechanochemical conversion in the nucleus and alter gene activities.},
	Author = {Wang, Ning and Tytell, Jessica D and Ingber, Donald E},
	Date-Added = {2017-05-18 23:31:51 +0000},
	Date-Modified = {2017-05-18 23:31:51 +0000},
	Doi = {10.1038/nrm2594},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Mesh = {Animals; Cell Nucleus; Cytoplasm; Extracellular Matrix; Humans; Mechanotransduction, Cellular; Stress, Mechanical},
	Month = {Jan},
	Number = {1},
	Pages = {75-82},
	Pmid = {19197334},
	Pst = {ppublish},
	Title = {Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus},
	Volume = {10},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrm2594}}

@article{Takeichi:1988,
	Abstract = {Cadherins are a family of glycoproteins involved in the Ca2+-dependent cell-cell adhesion mechanism which is detected in most kinds of tissues. Inhibition of the cadherin activity with antibodies induces dissociation of cell layers, indicating a fundamental importance of these molecules in maintaining the multicellular structure. Cadherins are divided into subclasses, including E-, N- and P-cadherins. While all subclasses are similar in molecular weight, Ca2+- and protease-sensitivity, each subclass is characterized by a unique tissue distribution pattern and immunological specificity. Analysis of amino acid sequences deduced from cDNA encoding these molecules showed that they are integral membrane proteins of 723-748 amino acids long and share common sequences; similarity in the sequences between subclasses is in a range of 50-60% when compared within a single animal species. L cells, with very little endogenous cadherin activity, transfected with the cadherin cDNA acquired high cadherin-mediated aggregating activity. Their colony morphology was altered by the ectopic expression of cadherins from the dispersed type to the compact type, providing direct evidence for a key role of cadherins in cell-cell adhesion. It has been suggested that cadherins bind cells by their homophilic interactions at the extracellular domain and are associated with actin bundles at the cytoplasmic domain. It appears that each cadherin subclass has binding specificity and this molecular family is involved in selective cell-cell adhesion. In development, the expression of each cadherin subclass is spatiotemporally regulated and associated with a variety of morphogenetic events; e.g. the termination or initiation of expression of a cadherin subclass in a given cell collective is correlated with its segregation from or connection with other cell collectives. Antibodies to cadherins were shown to perturb the morphogenesis of some embryonic organs in vitro. These observations suggest that cadherins play a crucial role in construction of tissues and the whole animal body.},
	Author = {Takeichi, M},
	Date-Added = {2017-05-18 23:30:43 +0000},
	Date-Modified = {2017-05-18 23:30:43 +0000},
	Journal = {Development},
	Journal-Full = {Development (Cambridge, England)},
	Mesh = {Animals; Antigens, Surface; Calcium-Binding Proteins; Cell Adhesion; Cell Adhesion Molecules; Membrane Glycoproteins; Morphogenesis},
	Month = {Apr},
	Number = {4},
	Pages = {639-55},
	Pmid = {3048970},
	Pst = {ppublish},
	Title = {The cadherins: cell-cell adhesion molecules controlling animal morphogenesis},
	Volume = {102},
	Year = {1988}}

@article{Frisch:2001,
	Abstract = {Anoikis is defined as apoptosis that is induced by inadequate or inappropriate cell-matrix interactions. It is involved in a wide diversity of tissue-homeostatic, developmental and oncogenic processes. The central problem of anoikis is to understand how integrin-mediated cell adhesion signals control the apoptotic machinery. In particular, the initiation of the caspase cascade in anoikis remains to be explained.},
	Author = {Frisch, S M and Screaton, R A},
	Date-Added = {2017-05-18 23:27:58 +0000},
	Date-Modified = {2017-05-18 23:27:58 +0000},
	Journal = {Curr Opin Cell Biol},
	Journal-Full = {Current opinion in cell biology},
	Mesh = {Adaptor Proteins, Signal Transducing; Anoikis; Carrier Proteins; Cytoskeleton; Fas-Associated Death Domain Protein; Growth Substances; Humans; Integrins; MAP Kinase Signaling System; Models, Biological; Neoplasms; Phosphatidylinositol 3-Kinases; Protein-Serine-Threonine Kinases; Proto-Oncogene Proteins; Proto-Oncogene Proteins c-akt; Signal Transduction},
	Month = {Oct},
	Number = {5},
	Pages = {555-62},
	Pmid = {11544023},
	Pst = {ppublish},
	Title = {Anoikis mechanisms},
	Volume = {13},
	Year = {2001}}

@article{Nelson:2002,
	Abstract = {Contact inhibition of cell proliferation evokes a unique cellular program of growth arrest compared with stress, age, or other physical constraints. The last decade of research on genes activated by cell-cell contact has uncovered features of transmembrane signaling, cytoskeletal reorganization, and transcriptional control that initiate and maintain a quiescent phenotype. This review will focus on mechanisms controlling contact inhibition of cell proliferation, highlighting specific gene expression responses that are activated by cell-cell contact. Although a temporal framework for imposition of these mechanisms has not yet been well described, contact inhibition of cell proliferation clearly requires their coordinated function. Novel targets for intervention in proliferative disorders are emerging from these studies.},
	Author = {Nelson, Peter J and Daniel, Thomas O},
	Date-Added = {2017-05-18 23:25:29 +0000},
	Date-Modified = {2017-05-18 23:25:29 +0000},
	Doi = {10.1046/j.1523-1755.2002.0610s1099.x},
	Journal = {Kidney Int},
	Journal-Full = {Kidney international},
	Mesh = {Cell Communication; Cell Proliferation; Gene Expression; Molecular Biology; Receptors, Cell Surface},
	Month = {Jan},
	Number = {1 Suppl},
	Pages = {S99-105},
	Pmid = {11841621},
	Pst = {ppublish},
	Title = {Emerging targets: molecular mechanisms of cell contact-mediated growth control},
	Volume = {61},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1046/j.1523-1755.2002.0610s1099.x}}

@article{Radhakrishnan:2014,
	Abstract = {Cannabis is the most commonly used illicit drug worldwide, with ~5 million daily users worldwide. Emerging evidence supports a number of associations between cannabis and psychosis/psychotic disorders, including schizophrenia. These associations-based on case-studies, surveys, epidemiological studies, and experimental studies indicate that cannabinoids can produce acute, transient effects; acute, persistent effects; and delayed, persistent effects that recapitulate the psychopathology and psychophysiology seen in schizophrenia. Acute exposure to both cannabis and synthetic cannabinoids (Spice/K2) can produce a full range of transient psychotomimetic symptoms, cognitive deficits, and psychophysiological abnormalities that bear a striking resemblance to symptoms of schizophrenia. In individuals with an established psychotic disorder, cannabinoids can exacerbate symptoms, trigger relapse, and have negative consequences on the course of the illness. Several factors appear to moderate these associations, including family history, genetic factors, history of childhood abuse, and the age at onset of cannabis use. Exposure to cannabinoids in adolescence confers a higher risk for psychosis outcomes in later life and the risk is dose-related. Individuals with polymorphisms of COMT and AKT1 genes may be at increased risk for psychotic disorders in association with cannabinoids, as are individuals with a family history of psychotic disorders or a history of childhood trauma. The relationship between cannabis and schizophrenia fulfills many but not all of the standard criteria for causality, including temporality, biological gradient, biological plausibility, experimental evidence, consistency, and coherence. At the present time, the evidence indicates that cannabis may be a component cause in the emergence of psychosis, and this warrants serious consideration from the point of view of public health policy.},
	Author = {Radhakrishnan, Rajiv and Wilkinson, Samuel T and D'Souza, Deepak Cyril},
	Date-Added = {2017-05-18 21:05:51 +0000},
	Date-Modified = {2017-05-18 21:05:51 +0000},
	Doi = {10.3389/fpsyt.2014.00054},
	Journal = {Front Psychiatry},
	Journal-Full = {Frontiers in psychiatry},
	Keywords = {cannabis; psychophysiology; psychosis; schizophrenia; schizotypy; spice; synthetic cannabinoids},
	Pages = {54},
	Pmc = {PMC4033190},
	Pmid = {24904437},
	Pst = {epublish},
	Title = {Gone to Pot - A Review of the Association between Cannabis and Psychosis},
	Volume = {5},
	Year = {2014},
	File = {papers/Radhakrishnan_FrontPsychiatry2014.pdf}}

@article{Zaidel-Bar:2007,
	Abstract = {A detailed depiction of the 'integrin adhesome', consisting of a complex network of 156 components linked together and modified by 690 interactions is presented. Different views of the network reveal several functional 'subnets' that are involved in switching on or off many of the molecular interactions within the network, consequently affecting cell adhesion, migration and cytoskeletal organization. Examination of the adhesome network motifs reveals a relatively small number of key motifs, dominated by three-component complexes in which a scaffolding molecule recruits both a signalling molecule and its downstream target. We discuss the role of the different network modules in regulating the structural and signalling functions of cell-matrix adhesions.},
	Author = {Zaidel-Bar, Ronen and Itzkovitz, Shalev and Ma'ayan, Avi and Iyengar, Ravi and Geiger, Benjamin},
	Date-Added = {2017-05-18 20:33:31 +0000},
	Date-Modified = {2017-05-18 20:33:31 +0000},
	Doi = {10.1038/ncb0807-858},
	Journal = {Nat Cell Biol},
	Journal-Full = {Nature cell biology},
	Mesh = {Animals; Cell Adhesion; Cell-Matrix Junctions; Cytoskeleton; Databases, Factual; Integrins; Signal Transduction},
	Month = {Aug},
	Number = {8},
	Pages = {858-67},
	Pmc = {PMC2735470},
	Pmid = {17671451},
	Pst = {ppublish},
	Title = {Functional atlas of the integrin adhesome},
	Volume = {9},
	Year = {2007},
	File = {papers/Zaidel-Bar_NatCellBiol2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/ncb0807-858}}

@article{Fletcher:2010,
	Abstract = {The ability of a eukaryotic cell to resist deformation, to transport intracellular cargo and to change shape during movement depends on the cytoskeleton, an interconnected network of filamentous polymers and regulatory proteins. Recent work has demonstrated that both internal and external physical forces can act through the cytoskeleton to affect local mechanical properties and cellular behaviour. Attention is now focused on how cytoskeletal networks generate, transmit and respond to mechanical signals over both short and long timescales. An important insight emerging from this work is that long-lived cytoskeletal structures may act as epigenetic determinants of cell shape, function and fate.},
	Author = {Fletcher, Daniel A and Mullins, R Dyche},
	Date-Added = {2017-05-17 17:43:45 +0000},
	Date-Modified = {2017-05-17 17:43:45 +0000},
	Doi = {10.1038/nature08908},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Biomechanical Phenomena; Cell Physiological Phenomena; Cell Shape; Cytoskeleton; Epigenesis, Genetic; Humans},
	Month = {Jan},
	Number = {7280},
	Pages = {485-92},
	Pmc = {PMC2851742},
	Pmid = {20110992},
	Pst = {ppublish},
	Title = {Cell mechanics and the cytoskeleton},
	Volume = {463},
	Year = {2010},
	File = {papers/Fletcher_Nature2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature08908}}

@article{OBrien:1997,
	Abstract = {The effects of calcium (Ca) were assessed using video-enhanced differential interference contrast light microscopy on individual microtubules in vitro. Phosphocellulose-purified (PC) and microtubule associated protein (MAP)-containing preparations of porcine brain tubulin were assembled in a flow chamber onto sperm axoneme fragments and the pattern of growth and shortening of the microtubules was observed. Tubulin plus Ca was then added to the chamber and observation continued. Ca promoted the disassembly of microtubules by specifically promoting the catastrophe reaction in both PC- and MAP-containing microtubules, without an appreciable change in elongation rate. The effect on catastrophe frequency increased very rapidly above 0.5 mM free Ca, implying a possible cooperative effect. The rescue rate remained very high after Ca addition in MAP-containing microtubules, and the shortening rate was unchanged, while in phosphocellulose-purified microtubules, rescue appeared to be decreased by Ca addition and shortening rates increased 4 to 6-fold. These results illustrate that Ca can directly destabilize growing microtubule ends without changing the effective concentration of free tubulin, and that this effect can be seen even against the background of the profound differences in dynamics conferred by the microtubule-associated proteins. Considered within models of the GTP cap, the results imply that high Ca may act to increase the rate of GTP hydrolysis within the cap.},
	Author = {O'Brien, E T and Salmon, E D and Erickson, H P},
	Date-Added = {2017-05-17 17:42:40 +0000},
	Date-Modified = {2017-05-17 17:42:40 +0000},
	Doi = {10.1002/(SICI)1097-0169(1997)36:2<125::AID-CM3>3.0.CO;2-8},
	Journal = {Cell Motil Cytoskeleton},
	Journal-Full = {Cell motility and the cytoskeleton},
	Mesh = {Animals; Biopolymers; Calcium; In Vitro Techniques; Microtubule-Associated Proteins; Microtubules; Sea Urchins; Swine; Tubulin},
	Number = {2},
	Pages = {125-35},
	Pmid = {9015201},
	Pst = {ppublish},
	Title = {How calcium causes microtubule depolymerization},
	Volume = {36},
	Year = {1997},
	File = {papers/O'Brien_CellMotilCytoskeleton1997.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1097-0169(1997)36:2%3C125::AID-CM3%3E3.0.CO;2-8}}

@article{Mattila:2008,
	Abstract = {Filopodia are thin, actin-rich plasma-membrane protrusions that function as antennae for cells to probe their environment. Consequently, filopodia have an important role in cell migration, neurite outgrowth and wound healing and serve as precursors for dendritic spines in neurons. The initiation and elongation of filopodia depend on the precisely regulated polymerization, convergence and crosslinking of actin filaments. The increased understanding of the functions of various actin-associated proteins during the initiation and elongation of filopodia has provided new information on the mechanisms of filopodia formation in distinct cell types.},
	Author = {Mattila, Pieta K and Lappalainen, Pekka},
	Date-Added = {2017-05-17 17:41:42 +0000},
	Date-Modified = {2017-05-17 17:41:42 +0000},
	Doi = {10.1038/nrm2406},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Mesh = {Animals; Cell Movement; Humans; Pseudopodia},
	Month = {Jun},
	Number = {6},
	Pages = {446-54},
	Pmid = {18464790},
	Pst = {ppublish},
	Title = {Filopodia: molecular architecture and cellular functions},
	Volume = {9},
	Year = {2008},
	File = {papers/Mattila_NatRevMolCellBiol2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrm2406}}

@article{Angelucci:1996,
	Abstract = {We report an improved immunohistochemical protocol for revealing anterograde axonal transport of the subunit B of cholera toxin (CTB) which stains axons and terminals in great detail, so that single axons can be followed over long distances and their arbors reconstructed in their entirety. Our modifications enhance the quality of staining mainly by increasing the penetration of the primary antibody in the tissue. The protocol can be modified to allow combination in alternate sections with tetramethylbenzidine (TMB) histochemical staining of wheat germ agglutinin conjugated to horseradish peroxidase (WGA-HRP). Using the protocol, we tested the performance of CTB as an anterograde tracer under two experimental paradigms which render other anterograde tracers less sensitive or unreliable: (1) labeling the entire retinofugal projection to the brain after injections into the vitreal chamber of the eye, and (2) labeling developing projections in the cortex and thalamus of early postnatal mammals. Qualitative comparisons were made with other tracers (Phaseolus vulgaris leucoagglutinin, dextran rhodamine, biotinylated dextran, free WGA, or WGA-HRP) that were used to label these same projections. From these observations it is clear that CTB, visualized with our protocol, provides more sensitive anterograde labeling of retinofugal projections as well as of axonal connections in the neonatal forebrain.},
	Author = {Angelucci, A and Clasc{\'a}, F and Sur, M},
	Date-Added = {2017-05-16 19:00:22 +0000},
	Date-Modified = {2017-05-16 19:00:22 +0000},
	Journal = {J Neurosci Methods},
	Journal-Full = {Journal of neuroscience methods},
	Mesh = {Animals; Animals, Newborn; Axons; Benzidines; Biotin; Brain; Cholera Toxin; Chromogenic Compounds; Eye; Ferrets; Immunohistochemistry; Visual Pathways; Wheat Germ Agglutinin-Horseradish Peroxidase Conjugate},
	Month = {Mar},
	Number = {1},
	Pages = {101-12},
	Pmid = {8815303},
	Pst = {ppublish},
	Title = {Anterograde axonal tracing with the subunit B of cholera toxin: a highly sensitive immunohistochemical protocol for revealing fine axonal morphology in adult and neonatal brains},
	Volume = {65},
	Year = {1996},
	File = {papers/Angelucci_JNeurosciMethods1996.pdf}}

@article{Bilkei-Gorzo:2017,
	Abstract = {The balance between detrimental, pro-aging, often stochastic processes and counteracting homeostatic mechanisms largely determines the progression of aging. There is substantial evidence suggesting that the endocannabinoid system (ECS) is part of the latter system because it modulates the physiological processes underlying aging. The activity of the ECS declines during aging, as CB1 receptor expression and coupling to G proteins are reduced in the brain tissues of older animals and the levels of the major endocannabinoid 2-arachidonoylglycerol (2-AG) are lower. However, a direct link between endocannabinoid tone and aging symptoms has not been demonstrated. Here we show that a low dose of Δ(9)-tetrahydrocannabinol (THC) reversed the age-related decline in cognitive performance of mice aged 12 and 18 months. This behavioral effect was accompanied by enhanced expression of synaptic marker proteins and increased hippocampal spine density. THC treatment restored hippocampal gene transcription patterns such that the expression profiles of THC-treated mice aged 12 months closely resembled those of THC-free animals aged 2 months. The transcriptional effects of THC were critically dependent on glutamatergic CB1 receptors and histone acetylation, as their inhibition blocked the beneficial effects of THC. Thus, restoration of CB1 signaling in old individuals could be an effective strategy to treat age-related cognitive impairments.},
	Author = {Bilkei-Gorzo, Andras and Albayram, Onder and Draffehn, Astrid and Michel, Kerstin and Piyanova, Anastasia and Oppenheimer, Hannah and Dvir-Ginzberg, Mona and R{\'a}cz, Ildiko and Ulas, Thomas and Imbeault, Sophie and Bab, Itai and Schultze, Joachim L and Zimmer, Andreas},
	Date-Added = {2017-05-16 00:12:44 +0000},
	Date-Modified = {2017-05-16 00:12:44 +0000},
	Doi = {10.1038/nm.4311},
	Journal = {Nat Med},
	Journal-Full = {Nature medicine},
	Month = {May},
	Pmid = {28481360},
	Pst = {aheadofprint},
	Title = {A chronic low dose of Δ(9)-tetrahydrocannabinol (THC) restores cognitive function in old mice},
	Year = {2017},
	File = {papers/Bilkei-Gorzo_NatMed2017.pdf}}

@article{Hollenbeck:2005,
	Abstract = {Organelle transport is vital for the development and maintenance of axons, in which the distances between sites of organelle biogenesis, function, and recycling or degradation can be vast. Movement of mitochondria in axons can serve as a general model for how all organelles move: mitochondria are easy to identify, they move along both microtubule and actin tracks, they pause and change direction, and their transport is modulated in response to physiological signals. However, they can be distinguished from other axonal organelles by the complexity of their movement and their unique functions in aerobic metabolism, calcium homeostasis and cell death. Mitochondria are thus of special interest in relating defects in axonal transport to neuropathies and degenerative diseases of the nervous system. Studies of mitochondrial transport in axons are beginning to illuminate fundamental aspects of the distribution mechanism. They use motors of one or more kinesin families, along with cytoplasmic dynein, to translocate along microtubules, and bidirectional movement may be coordinated through interaction between dynein and kinesin-1. Translocation along actin filaments is probably driven by myosin V, but the protein(s) that mediate docking with actin filaments remain unknown. Signaling through the PI 3-kinase pathway has been implicated in regulation of mitochondrial movement and docking in the axon, and additional mitochondrial linker and regulatory proteins, such as Milton and Miro, have recently been described.},
	Author = {Hollenbeck, Peter J and Saxton, William M},
	Date-Added = {2017-05-16 00:06:30 +0000},
	Date-Modified = {2017-05-16 00:06:30 +0000},
	Doi = {10.1242/jcs.02745},
	Journal = {J Cell Sci},
	Journal-Full = {Journal of cell science},
	Mesh = {Animals; Axonal Transport; Dyneins; Humans; Kinesin; Mitochondria; Models, Biological; Myosins; Signal Transduction},
	Month = {Dec},
	Number = {Pt 23},
	Pages = {5411-9},
	Pmc = {PMC1533994},
	Pmid = {16306220},
	Pst = {ppublish},
	Title = {The axonal transport of mitochondria},
	Volume = {118},
	Year = {2005},
	File = {papers/Hollenbeck_JCellSci2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1242/jcs.02745}}

@article{Saxton:2012,
	Abstract = {Vigorous transport of cytoplasmic components along axons over substantial distances is crucial for the maintenance of neuron structure and function. The transport of mitochondria, which serves to distribute mitochondrial functions in a dynamic and non-uniform fashion, has attracted special interest in recent years following the discovery of functional connections among microtubules, motor proteins and mitochondria, and their influences on neurodegenerative diseases. Although the motor proteins that drive mitochondrial movement are now well characterized, the mechanisms by which anterograde and retrograde movement are coordinated with one another and with stationary axonal mitochondria are not yet understood. In this Commentary, we review why mitochondria move and how they move, focusing particularly on recent studies of transport regulation, which implicate control of motor activity by specific cell-signaling pathways, regulation of motor access to transport tracks and static microtubule-mitochondrion linkers. A detailed mechanism for modulating anterograde mitochondrial transport has been identified that involves Miro, a mitochondrial Ca(2+)-binding GTPase, which with associated proteins, can bind and control kinesin-1. Elements of the Miro complex also have important roles in mitochondrial fission-fusion dynamics, highlighting questions about the interdependence of biogenesis, transport, dynamics, maintenance and degradation.},
	Author = {Saxton, William M and Hollenbeck, Peter J},
	Date-Added = {2017-05-15 23:57:16 +0000},
	Date-Modified = {2017-05-15 23:57:16 +0000},
	Doi = {10.1242/jcs.053850},
	Journal = {J Cell Sci},
	Journal-Full = {Journal of cell science},
	Mesh = {Animals; Axonal Transport; Axons; Calcium; Drosophila melanogaster; Humans; Membrane Fusion; Microtubules; Mitochondria; Mitochondrial Proteins; Molecular Motor Proteins; Neurodegenerative Diseases; Protein Binding; Signal Transduction; rho GTP-Binding Proteins},
	Month = {May},
	Number = {Pt 9},
	Pages = {2095-104},
	Pmc = {PMC3656622},
	Pmid = {22619228},
	Pst = {ppublish},
	Title = {The axonal transport of mitochondria},
	Volume = {125},
	Year = {2012},
	File = {papers/Saxton_JCellSci2012.pdf}}

@article{Pilling:2006,
	Abstract = {To address questions about mechanisms of filament-based organelle transport, a system was developed to image and track mitochondria in an intact Drosophila nervous system. Mutant analyses suggest that the primary motors for mitochondrial movement in larval motor axons are kinesin-1 (anterograde) and cytoplasmic dynein (retrograde), and interestingly that kinesin-1 is critical for retrograde transport by dynein. During transport, there was little evidence that force production by the two opposing motors was competitive, suggesting a mechanism for alternate coordination. Tests of the possible coordination factor P150(Glued) suggested that it indeed influenced both motors on axonal mitochondria, but there was no evidence that its function was critical for the motor coordination mechanism. Observation of organelle-filled axonal swellings ("organelle jams" or "clogs") caused by kinesin and dynein mutations showed that mitochondria could move vigorously within and pass through them, indicating that they were not the simple steric transport blockades suggested previously. We speculate that axonal swellings may instead reflect sites of autophagocytosis of senescent mitochondria that are stranded in axons by retrograde transport failure; a protective process aimed at suppressing cell death signals and neurodegeneration.},
	Author = {Pilling, Aaron D and Horiuchi, Dai and Lively, Curtis M and Saxton, William M},
	Date-Added = {2017-05-15 23:38:27 +0000},
	Date-Modified = {2017-05-15 23:38:27 +0000},
	Doi = {10.1091/mbc.E05-06-0526},
	Journal = {Mol Biol Cell},
	Journal-Full = {Molecular biology of the cell},
	Mesh = {Animals; Axons; Biological Transport; Drosophila; Drosophila Proteins; Dynactin Complex; Dyneins; Kinesin; Microtubule-Associated Proteins; Mitochondria; Motor Neurons; Mutation; Nervous System},
	Month = {Apr},
	Number = {4},
	Pages = {2057-68},
	Pmc = {PMC1415296},
	Pmid = {16467387},
	Pst = {ppublish},
	Title = {Kinesin-1 and Dynein are the primary motors for fast transport of mitochondria in Drosophila motor axons},
	Volume = {17},
	Year = {2006},
	File = {papers/Pilling_MolBiolCell2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1091/mbc.E05-06-0526}}

@article{Macaskill:2009,
	Abstract = {Energy use, mainly to reverse ion movements in neurons, is a fundamental constraint on brain information processing. Trafficking of mitochondria to locations in neurons where there are large ion fluxes is essential for powering neural function. Mitochondrial trafficking is regulated by Ca2+ entry through ionotropic glutamate receptors, but the underlying mechanism is unknown. We show that the protein Miro1 links mitochondria to KIF5 motor proteins, allowing mitochondria to move along microtubules. This linkage is inhibited by micromolar levels of Ca2+ binding to Miro1. With the EF hand domains of Miro1 mutated to prevent Ca2+ binding, Miro1 could still facilitate mitochondrial motility, but mitochondrial stopping induced by glutamate or neuronal activity was blocked. Activating neuronal NMDA receptors with exogenous or synaptically released glutamate led to Miro1 positioning mitochondria at the postsynaptic side of synapses. Thus, Miro1 is a key determinant of how energy supply is matched to energy usage in neurons.},
	Author = {Macaskill, Andrew F and Rinholm, Johanne E and Twelvetrees, Alison E and Arancibia-Carcamo, I Lorena and Muir, James and Fransson, Asa and Aspenstrom, Pontus and Attwell, David and Kittler, Josef T},
	Date-Added = {2017-05-15 22:10:31 +0000},
	Date-Modified = {2017-05-15 22:10:31 +0000},
	Doi = {10.1016/j.neuron.2009.01.030},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Calcium Radioisotopes; Calcium Signaling; Cells, Cultured; Dendrites; Drosophila Proteins; Electrophysiology; Energy Metabolism; Glutathione Transferase; Immunoprecipitation; Kinesin; Mitochondria; Neurons; Rats; Receptors, Calcium-Sensing; Receptors, Glutamate; Synapses; rho GTP-Binding Proteins},
	Month = {Feb},
	Number = {4},
	Pages = {541-55},
	Pmc = {PMC2670979},
	Pmid = {19249275},
	Pst = {ppublish},
	Title = {Miro1 is a calcium sensor for glutamate receptor-dependent localization of mitochondria at synapses},
	Volume = {61},
	Year = {2009},
	File = {papers/Macaskill_Neuron2009.pdf},
	Bdsk-File-2 = {papers/Macaskill_Neuron2009a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2009.01.030}}

@article{Hirokawa:2009,
	Abstract = {Intracellular transport is fundamental for cellular function, survival and morphogenesis. Kinesin superfamily proteins (also known as KIFs) are important molecular motors that directionally transport various cargos, including membranous organelles, protein complexes and mRNAs. The mechanisms by which different kinesins recognize and bind to specific cargos, as well as how kinesins unload cargo and determine the direction of transport, have now been identified. Furthermore, recent molecular genetic experiments have uncovered important and unexpected roles for kinesins in the regulation of such physiological processes as higher brain function, tumour suppression and developmental patterning. These findings open exciting new areas of kinesin research.},
	Author = {Hirokawa, Nobutaka and Noda, Yasuko and Tanaka, Yosuke and Niwa, Shinsuke},
	Date-Added = {2017-05-15 22:06:46 +0000},
	Date-Modified = {2017-05-15 22:06:46 +0000},
	Doi = {10.1038/nrm2774},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Mesh = {Animals; Biological Transport; Dyneins; Humans; Kinesin; Models, Biological; Molecular Motor Proteins; Organelles; Phylogeny; Proteins; RNA, Messenger},
	Month = {Oct},
	Number = {10},
	Pages = {682-96},
	Pmid = {19773780},
	Pst = {ppublish},
	Title = {Kinesin superfamily motor proteins and intracellular transport},
	Volume = {10},
	Year = {2009},
	File = {papers/Hirokawa_NatRevMolCellBiol2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrm2774}}

@article{King:2012,
	Abstract = {Axonemal dyneins are AAA(+) enzymes that convert ATP hydrolysis to mechanical work. This leads to the sliding of doublet microtubules with respect to each other and ultimately the generation of ciliary/flagellar beating. However, in order for useful work to be generated, the action of individual dynein motors must be precisely controlled. In addition, cells modulate the motility of these organelles through a variety of second messenger systems and these signals too must be integrated by the dynein motors to yield an appropriate output. This review describes the current status of efforts to understand dynein control mechanisms and their connectivity focusing mainly on studies of the outer dynein arm from axonemes of the unicellular biflagellate green alga Chlamydomonas.},
	Author = {King, Stephen M},
	Date-Added = {2017-05-15 18:51:59 +0000},
	Date-Modified = {2017-05-15 18:51:59 +0000},
	Doi = {10.1016/j.jsb.2012.02.013},
	Journal = {J Struct Biol},
	Journal-Full = {Journal of structural biology},
	Mesh = {Axonemal Dyneins; Chlamydomonas; Dyneins},
	Month = {Aug},
	Number = {2},
	Pages = {222-8},
	Pmc = {PMC3378790},
	Pmid = {22406539},
	Pst = {ppublish},
	Title = {Integrated control of axonemal dynein AAA(+) motors},
	Volume = {179},
	Year = {2012},
	File = {papers/King_JStructBiol2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jsb.2012.02.013}}

@article{Humphries:2011,
	Abstract = {The endo-lysosomal pathway is essential for intracellular transport and the degradation of extracellular cargo. The relationship between three populations of endo-lysosomal vesicles--Rab7-positive, LAMP1-positive, and both Rab7- and LAMP1-postive--was probed with fluorescence microscopy and single particle tracking. Of specific interest was determining if these vesicles were intermediate or terminal vesicles in the transport of extracellular cargo. We find that the major organelle in the endo-lysosomal pathway, both in terms of population and cargo transport, is positive for Rab7 and LAMP1. Dextran, a fluid phase cargo, shifts from localization within all three populations of vesicles at 30 minutes and 1 hour to primarily LAMP1- and Rab7/LAMP1-vesicles at longer times. This demonstrates that LAMP1- and Rab7/LAMP1-vesicles are terminal vesicles in the endo-lysosomal pathway. We tested two possible mechanisms for this distribution of cargo, delivery to mannose 6-phosphate receptor (M6PR)-negative vesicles and the fusion dynamics of individual vesicles. We find no correlation with M6PR but do find that Rab7-vesicles undergo significantly fewer fusion events than LAMP1- or Rab7/LAMP1-vesicles suggesting that the distribution of fluid phase cargo is driven by vesicle dynamics.},
	Author = {Humphries, 4th, William H and Szymanski, Craig J and Payne, Christine K},
	Date-Added = {2017-05-11 21:39:29 +0000},
	Date-Modified = {2017-05-11 21:39:29 +0000},
	Doi = {10.1371/journal.pone.0026626},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Biological Transport; Cell Line; Dextrans; Endosomes; Humans; Lysosome-Associated Membrane Glycoproteins; Lysosomes; Microscopy, Confocal; rab GTP-Binding Proteins},
	Number = {10},
	Pages = {e26626},
	Pmc = {PMC3200357},
	Pmid = {22039519},
	Pst = {ppublish},
	Title = {Endo-lysosomal vesicles positive for Rab7 and LAMP1 are terminal vesicles for the transport of dextran},
	Volume = {6},
	Year = {2011},
	File = {papers/Humphries_PLoSOne2011.PDF}}

@article{Maday:2014,
	Abstract = {Axonal transport is essential for neuronal function, and many neurodevelopmental and neurodegenerative diseases result from mutations in the axonal transport machinery. Anterograde transport supplies distal axons with newly synthesized proteins and lipids, including synaptic components required to maintain presynaptic activity. Retrograde transport is required to maintain homeostasis by removing aging proteins and organelles from the distal axon for degradation and recycling of components. Retrograde axonal transport also plays a major role in neurotrophic and injury response signaling. This review provides an overview of axonal transport pathways and discusses their role in neuronal function.},
	Author = {Maday, Sandra and Twelvetrees, Alison E and Moughamian, Armen J and Holzbaur, Erika L F},
	Date-Added = {2017-05-11 20:56:20 +0000},
	Date-Modified = {2017-05-11 20:56:20 +0000},
	Doi = {10.1016/j.neuron.2014.10.019},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axonal Transport; Axons; Humans; Neurodegenerative Diseases; Neurons; Organelles; Signal Transduction},
	Month = {Oct},
	Number = {2},
	Pages = {292-309},
	Pmc = {PMC4269290},
	Pmid = {25374356},
	Pst = {ppublish},
	Title = {Axonal transport: cargo-specific mechanisms of motility and regulation},
	Volume = {84},
	Year = {2014},
	File = {papers/Maday_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.10.019}}

@article{Pan:2008,
	Abstract = {LIM-homeodomain (HD) and POU-HD transcription factors play crucial roles in neurogenesis. However, it remains largely unknown how they cooperate in this process and what downstream target genes they regulate. Here, we show that ISL1, a LIM-HD protein, is co-expressed with BRN3B, a POU-HD factor, in nascent post-mitotic retinal ganglion cells (RGCs). Similar to the Brn3b-null retinas, retina-specific deletion of Isl1 results in the apoptosis of a majority of RGCs and in RGC axon guidance defects. The Isl1 and Brn3b double null mice display more severe retinal abnormalities with a near complete loss of RGCs, indicating the synergistic functions of these two factors. Furthermore, we show that both Isl1 and Brn3b function downstream of Math5 to regulate the expression of a common set of RGC-specific genes. Whole-retina chromatin immunoprecipitation and in vitro transactivation assays reveal that ISL1 and BRN3B concurrently bind to and synergistically regulate the expression of a common set of RGC-specific genes. Thus, our results uncover a novel regulatory mechanism of BRN3B and ISL1 in RGC differentiation.},
	Author = {Pan, Ling and Deng, Min and Xie, Xiaoling and Gan, Lin},
	Date-Added = {2017-05-11 14:39:18 +0000},
	Date-Modified = {2017-05-11 14:39:18 +0000},
	Doi = {10.1242/dev.010751},
	Journal = {Development},
	Journal-Full = {Development (Cambridge, England)},
	Mesh = {Animals; Cell Differentiation; Chromatin Immunoprecipitation; Gene Expression Regulation, Developmental; Homeodomain Proteins; Immunohistochemistry; In Situ Hybridization; LIM-Homeodomain Proteins; Mice; Mice, Knockout; Mitosis; Promoter Regions, Genetic; Protein Binding; Retina; Retinal Ganglion Cells; Transcription Factor Brn-3B; Transcription Factors},
	Month = {Jun},
	Number = {11},
	Pages = {1981-90},
	Pmc = {PMC2758274},
	Pmid = {18434421},
	Pst = {ppublish},
	Title = {ISL1 and BRN3B co-regulate the differentiation of murine retinal ganglion cells},
	Volume = {135},
	Year = {2008},
	File = {papers/Pan_Development2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1242/dev.010751}}

@article{Yushkevich:2006,
	Abstract = {Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.},
	Author = {Yushkevich, Paul A and Piven, Joseph and Hazlett, Heather Cody and Smith, Rachel Gimpel and Ho, Sean and Gee, James C and Gerig, Guido},
	Date-Added = {2017-05-10 18:30:24 +0000},
	Date-Modified = {2017-05-10 18:30:24 +0000},
	Doi = {10.1016/j.neuroimage.2006.01.015},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Mesh = {Brain; Caudate Nucleus; Dominance, Cerebral; Humans; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Magnetic Resonance Imaging; Mathematical Computing; Software; Software Validation; User-Computer Interface},
	Month = {Jul},
	Number = {3},
	Pages = {1116-28},
	Pmid = {16545965},
	Pst = {ppublish},
	Title = {User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability},
	Volume = {31},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2006.01.015}}

@article{Rashid:2005,
	Abstract = {During development of the retinocollicular projection in mouse, retinal axons initially overshoot their future termination zones (TZs) in the superior colliculus (SC). The formation of TZs is initiated by interstitial branching at topographically appropriate positions. Ephrin-As are expressed in a decreasing posterior-to-anterior gradient in the SC, and they suppress branching posterior to future TZs. Here we investigate the role of an EphA7 gradient in the SC, which has the reverse orientation to the ephrin-A gradient. We find that in EphA7 mutant mice the retinocollicular map is disrupted, with nasal and temporal axons forming additional or extended TZs, respectively. In vitro, retinal axons are repelled from growing on EphA7-containing stripes. Our data support the idea that EphA7 is involved in suppressing branching anterior to future TZs. These findings suggest that opposing ephrin-A and EphA gradients are required for the proper development of the retinocollicular projection.},
	Author = {Rashid, Tahira and Upton, A Louise and Blentic, Aida and Ciossek, Thomas and Kn{\"o}ll, Bernd and Thompson, Ian D and Drescher, Uwe},
	Date-Added = {2017-05-09 18:36:46 +0000},
	Date-Modified = {2017-05-09 18:36:46 +0000},
	Doi = {10.1016/j.neuron.2005.05.030},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Axons; Brain Mapping; Ephrins; Histocytochemistry; In Situ Hybridization; Mice; Mice, Knockout; RNA; Receptor, EphA7; Retina; Superior Colliculi; Vision, Ocular; Visual Pathways},
	Month = {Jul},
	Number = {1},
	Pages = {57-69},
	Pmid = {15996548},
	Pst = {ppublish},
	Title = {Opposing gradients of ephrin-As and EphA7 in the superior colliculus are essential for topographic mapping in the mammalian visual system},
	Volume = {47},
	Year = {2005},
	File = {papers/Rashid_Neuron2005.pdf}}

@article{Drescher:1995,
	Abstract = {The results of previous in vitro experiments indicate that a glycosylphosphatidylinositol (GPI)-anchored protein may play an important role in the guidance of temporal retinal axons during the formation of the topographically ordered retinotectal projection. We have purified and cloned a GPI-anchored, 25 kDa glycoprotein that is a good candidate for a molecule involved in this process. During the time of innervation by retinal ganglion cells, this protein is gradedly expressed in the posterior part of the developing tectum. In two different in vitro assay systems, the recombinant protein induces growth cone collapse and repulsion of retinal ganglion cell axons. These phenomena are observed for axons of temporal as well as nasal origin, indicating that an additional activity may be necessary to confer the nasotemporal specificity observed in previous assays. We named the protein RAGS (for repulsive axon guidance signal). The sequence of RAGS shows significant homology to recently identified ligands for receptor tyrosine kinases of the Eph subfamily.},
	Author = {Drescher, U and Kremoser, C and Handwerker, C and L{\"o}schinger, J and Noda, M and Bonhoeffer, F},
	Date-Added = {2017-05-06 00:25:56 +0000},
	Date-Modified = {2017-05-06 00:25:56 +0000},
	Journal = {Cell},
	Journal-Full = {Cell},
	Mesh = {Amino Acid Sequence; Animals; Axons; Base Sequence; Cell Communication; Cell Division; Cells, Cultured; Chickens; Cloning, Molecular; DNA, Complementary; Ephrin-A2; Glycoproteins; Humans; Molecular Sequence Data; Proteins; Retinal Ganglion Cells; Sequence Alignment; Superior Colliculi},
	Month = {Aug},
	Number = {3},
	Pages = {359-70},
	Pmid = {7634326},
	Pst = {ppublish},
	Title = {In vitro guidance of retinal ganglion cell axons by RAGS, a 25 kDa tectal protein related to ligands for Eph receptor tyrosine kinases},
	Volume = {82},
	Year = {1995},
	File = {papers/Drescher_Cell1995.pdf}}

@article{Cheng:1995,
	Abstract = {Topographic maps with a defined spatial ordering of neuronal connections are a key feature of brain organization. Such maps are believed to develop in response to complementary position-specific labels in presynaptic and postsynaptic fields. However, the complementary labeling molecules are not known. In the well-studied visual map of retinal axons projecting to the tectum, the labels are hypothesized to be in gradients, without needing large numbers of cell-specific molecules. We recently cloned ELF-1 as a ligand for Eph family receptors. Here, RNA hybridization shows matching expression gradients for ELF-1 in the tectum and its receptor Mek4 in the retina. Binding activity detected with alkaline phosphatase fusions of ELF-1 and Mek4 also reveals gradients and provides direct evidence for molecular complementarity of gradients in reciprocal fields. ELF-1 and Mek4 may therefore play roles in retinotectal development and have properties predicted of topographic mapping labels.},
	Author = {Cheng, H J and Nakamoto, M and Bergemann, A D and Flanagan, J G},
	Date-Added = {2017-05-06 00:25:11 +0000},
	Date-Modified = {2017-05-06 00:25:11 +0000},
	Journal = {Cell},
	Journal-Full = {Cell},
	Mesh = {Amino Acid Sequence; Animals; Brain Mapping; Chickens; Ephrin-A2; Mice; Molecular Sequence Data; Proteins; Retinal Ganglion Cells; Sequence Homology, Amino Acid; Superior Colliculi},
	Month = {Aug},
	Number = {3},
	Pages = {371-81},
	Pmid = {7634327},
	Pst = {ppublish},
	Title = {Complementary gradients in expression and binding of ELF-1 and Mek4 in development of the topographic retinotectal projection map},
	Volume = {82},
	Year = {1995},
	File = {papers/Cheng_Cell1995.pdf}}

@article{Flanagan:1998,
	Abstract = {The Eph receptors are the largest known family of receptor tyrosine kinases. Initially all of them were identified as orphan receptors without known ligands, and their specific functions were not well understood. During the past few years, a corresponding family of ligands has been identified, called the ephrins, and specific functions have now been identified in neural development. The ephrins and Eph receptors are implicated as positional labels that may guide the development of neural topographic maps. They have also been implicated in pathway selection by axons, the guidance of cell migration, and the establishment of regional pattern in the nervous system. The ligands are anchored to cell surfaces, and most of the functions so far identified can be interpreted as precise guidance of cell or axon movement. This large family of ligands and receptors may make a major contribution to the accurate spatial patterning of connections and cell position in the nervous system.},
	Author = {Flanagan, J G and Vanderhaeghen, P},
	Date-Added = {2017-05-06 00:24:27 +0000},
	Date-Modified = {2017-05-06 00:24:27 +0000},
	Doi = {10.1146/annurev.neuro.21.1.309},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Mesh = {Animals; Central Nervous System; Ephrin-A2; Ephrin-B1; Ephrin-B3; Membrane Proteins; Receptor Protein-Tyrosine Kinases; Transcription Factors},
	Pages = {309-45},
	Pmid = {9530499},
	Pst = {ppublish},
	Title = {The ephrins and Eph receptors in neural development},
	Volume = {21},
	Year = {1998},
	File = {papers/Flanagan_AnnuRevNeurosci1998.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.neuro.21.1.309}}

@article{Mackarehtschian:1999,
	Abstract = {The development of axonal connections between thalamic nuclei and their cortical target areas occurs in a highly specific manner. To explore the mechanisms of thalamocortical axon pathfinding, we investigated the expression of several members of the ephrin and Eph gene families in the forebrain. The Eph ligand ephrin-A5 was expressed in three distinct gradients during the development of the telencephalon. The first gradient occurred in the cortical ventricular zone and established ephrin-A5 as one of the earliest markers distinguishing cells residing in the anterior versus posterior cortical neuroepithelium. The second gradient was apparent in the subplate and occurred in spatial opposition to a distinct gradient for the low-affinity NGF receptor p75. This finding reveals that different regions of the early subplate are molecularly heterogeneous. Third, we confirmed that ephrin-A5 is expressed in a bi-directional gradient in the cortical plate, with highest levels in the somatomotor cortex. Three putative receptors for ephrin-A5 -- EphA3, EphA4 and EphA5 -- showed distinct expression patterns in the developing thalamus. The graded distributions of ephrin-A5 in the developing subplate and cortex and the expression of its receptors in the thalamus are consistent with the notion that the Eph ligands and their receptors may function in the topographic mapping of thalamic axons to specific cortical areas.},
	Author = {Mackarehtschian, K and Lau, C K and Caras, I and McConnell, S K},
	Date-Added = {2017-05-06 00:05:56 +0000},
	Date-Modified = {2017-05-06 00:05:56 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Benzoxazines; Brain Chemistry; Cerebral Cortex; Coloring Agents; DNA Probes; Ephrin-A4; Ephrin-A5; Female; Gene Expression Regulation, Developmental; In Situ Hybridization; Ligands; Membrane Proteins; Oxazines; Pregnancy; Prosencephalon; RNA, Messenger; Rats; Rats, Long-Evans; Receptor Protein-Tyrosine Kinases; Receptor, Nerve Growth Factor},
	Month = {Sep},
	Number = {6},
	Pages = {601-10},
	Pmid = {10498278},
	Pst = {ppublish},
	Title = {Regional differences in the developing cerebral cortex revealed by ephrin-A5 expression},
	Volume = {9},
	Year = {1999},
	File = {papers/Mackarehtschian_CerebCortex1999.pdf}}

@article{Donoghue:1999a,
	Abstract = {The mature cerebral cortex is divided into morphologically distinct, functionally dedicated and stereotypically connected cortical areas. How might such functional domains arise during development? To investigate possible intrinsic programs within the embryonic cerebral cortex we examined patterns of gene expression early in corticogenesis. We performed these studies using the developing macaque monkey because of the size, complexity, areal make-up and the extended nature of its cortical development. Here, we present results for two types of molecules. (i) Transcription factors -- gene products that bind DNA and activate transcription, directing cellular fates through cascades of gene expression. We find that the transcription factors TBr-1, Lhx-2, Emx-1 and a novel POU domain-containing gene are differentially expressed within the forming primate forebrain, and are present in gradients across the neocortex. (ii) The EphA receptor tyrosine kinases -- gene products that mediate cellular recognition in many embryonic systems. Individual members of this family are expressed during primate corticogenesis in pronounced gradients and/or well-defined compartments with distinct boundaries. Together, these results suggest that at least two modes of grouping cells within the neocortex exist: the graded patterning of cells across its full anteroposterior extent and the parcellation of cells into defined domains. Moreover, emergence of molecular differences between regions of the cortical plate, prior to the arrival of afferent and formation of efferent connections, suggests that the initial cellular parcellation in the telencephalon is cell-autonomously regulated. This initial independence from peripheral influences supports the existence of an intrinsic protomap that may function both to differentially attract and respond to specific afferents, thus predicting the functional map of the mature cortex.},
	Author = {Donoghue, M J and Rakic, P},
	Date-Added = {2017-05-06 00:01:28 +0000},
	Date-Modified = {2017-05-06 00:01:28 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Antisense Elements (Genetics); Brain Chemistry; Cloning, Molecular; DNA-Binding Proteins; Ephrin-A1; Female; Gene Expression Regulation, Developmental; Gene Expression Regulation, Enzymologic; Homeodomain Proteins; In Situ Hybridization; Macaca mulatta; Neocortex; Neurons; Pregnancy; Prosencephalon; Proteins; Receptor Protein-Tyrosine Kinases; Transcription Factors},
	Month = {Sep},
	Number = {6},
	Pages = {586-600},
	Pmid = {10498277},
	Pst = {ppublish},
	Title = {Molecular gradients and compartments in the embryonic primate cerebral cortex},
	Volume = {9},
	Year = {1999},
	File = {papers/Donoghue_CerebCortex1999.pdf}}

@article{Vanderhaeghen:2000,
	Abstract = {The neocortical primary somatosensory area (S1) consists of a map of the body surface. The cortical area devoted to different regions, such as parts of the face or hands, reflects their functional importance. Here we investigated the role of genetically determined positional labels in neocortical mapping. Ephrin-A5 was expressed in a medial > lateral gradient across S1, whereas its receptor EphA4 was in a matching gradient across the thalamic ventrobasal (VB) complex, which provides S1 input. Ephrin-A5 had topographically specific effects on VB axon guidance in vitro. Ephrin-A5 gene disruption caused graded, topographically specific distortion in the S1 body map, with medial regions contracted and lateral regions expanded, changing relative areas up to 50% in developing and adult mice. These results provide evidence for within-area thalamocortical mapping labels and show that a genetic difference can cause a lasting change in relative scale of different regions within a topographic map.},
	Author = {Vanderhaeghen, P and Lu, Q and Prakash, N and Fris{\'e}n, J and Walsh, C A and Frostig, R D and Flanagan, J G},
	Date-Added = {2017-05-05 22:02:45 +0000},
	Date-Modified = {2017-05-05 22:02:45 +0000},
	Doi = {10.1038/73929},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Age Factors; Animals; Axons; Brain Mapping; Cell Line; Ephrin-A5; Gene Expression Regulation, Developmental; Membrane Proteins; Mice; Mice, Inbred C57BL; Mutagenesis; RNA, Messenger; Somatosensory Cortex; Thalamus; Transfection},
	Month = {Apr},
	Number = {4},
	Pages = {358-65},
	Pmid = {10725925},
	Pst = {ppublish},
	Title = {A mapping label required for normal scale of body representation in the cortex},
	Volume = {3},
	Year = {2000},
	File = {papers/Vanderhaeghen_NatNeurosci2000.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/73929}}

@article{Lyckman:2001,
	Abstract = {Ascending sensory information reaches primary sensory cortical areas via thalamic relay neurons that are organized into modality-specific compartments or nuclei. Although the sensory relay nuclei of the thalamus show consistent modality-specific segregation of afferents, we now show in a wild-type mouse strain that the visual pathway can be surgically "rewired" so as to induce permanent retinal innervation of auditory thalamic cell groups. Applying the same rewiring paradigm to a transgenic mouse lacking the EphA receptor family ligands ephrin-A2 and ephrin-A5 results in more extensive rewiring than in the wild-type strain. We also show for the first time that ephrin-A2 and ephrin-A5 define a distinct border between visual and auditory thalamus. In the absence of this ephrin-A2/A5 border and after rewiring surgery, retinal afferents are better able to invade and innervate the deafferented auditory thalamus. These data suggest that signals that induce retinal axons to innervate the denervated auditory thalamus may compete with barriers, such as the ephrins, that serve to contain them within the normal target. The present findings thus show that the targeting of retinothalamic projections can be surgically manipulated in the mouse and that such plasticity can be controlled by proteins known to regulate topographic mapping.},
	Author = {Lyckman, A W and Jhaveri, S and Feldheim, D A and Vanderhaeghen, P and Flanagan, J G and Sur, M},
	Date-Added = {2017-05-05 22:01:38 +0000},
	Date-Modified = {2017-05-05 22:01:38 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Animals, Newborn; Auditory Pathways; Axons; Ephrin-A2; Ephrin-A5; Fluorescent Dyes; Geniculate Bodies; Inferior Colliculi; Ligands; Membrane Proteins; Mice; Mice, Inbred Strains; Mice, Knockout; Neuronal Plasticity; Organ Specificity; RNA, Messenger; Retina; Thalamus; Transcription Factors; Visual Pathways},
	Month = {Oct},
	Number = {19},
	Pages = {7684-90},
	Pmid = {11567058},
	Pst = {ppublish},
	Title = {Enhanced plasticity of retinothalamic projections in an ephrin-A2/A5 double mutant},
	Volume = {21},
	Year = {2001},
	File = {papers/Lyckman_JNeurosci2001.pdf}}

@article{Prakash:2000,
	Abstract = {The molecular mechanisms that coordinate the functional organization of the mammalian neocortex are largely unknown. We tested the involvement of a putative guidance label, ephrin-A5, in the functional organization of the somatosensory cortex by quantifying the functional representations of individual whiskers in vivo in adult ephrin-A5 knock-out mice, using intrinsic signal optical imaging. In wild-type mice ephrin-A5 is expressed in a gradient in the somatosensory cortex during development. In adult ephrin-A5 knock-out mice, we found a spatial gradient of change in the amount of cortical territory shared by individual whisker functional representations across the somatosensory cortex, as well as a gradient of change in the distance between the functional representations. Both gradients of change were in correspondence with the developmental expression gradient of ephrin-A5 in wild-type mice. These changes involved malformations of the cortical spacing of the thalamocortical components, without concurrent malformations of the intracortical components of individual whisker functional representations. Overall, these results suggest that a developmental guidance label, such as ephrin-A5, is involved in establishing certain spatial relationships of the functional organization of the adult neocortex, and they underscore the advantage of investigating gene manipulation using in vivo functional imaging.},
	Author = {Prakash, N and Vanderhaeghen, P and Cohen-Cory, S and Fris{\'e}n, J and Flanagan, J G and Frostig, R D},
	Date-Added = {2017-05-05 22:00:47 +0000},
	Date-Modified = {2017-05-05 22:00:47 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Age Factors; Animals; Axons; Brain Mapping; Ephrin-A5; Membrane Proteins; Mice; Mice, Inbred C57BL; Mice, Knockout; Neural Pathways; Optics and Photonics; Somatosensory Cortex; Thalamus; Vibrissae},
	Month = {Aug},
	Number = {15},
	Pages = {5841-7},
	Pmid = {10908626},
	Pst = {ppublish},
	Title = {Malformation of the functional organization of somatosensory cortex in adult ephrin-A5 knock-out mice revealed by in vivo functional imaging},
	Volume = {20},
	Year = {2000},
	File = {papers/Prakash_JNeurosci2000.pdf}}

@article{Pollard:2006,
	Abstract = {The developmental and evolutionary mechanisms behind the emergence of human-specific brain features remain largely unknown. However, the recent ability to compare our genome to that of our closest relative, the chimpanzee, provides new avenues to link genetic and phenotypic changes in the evolution of the human brain. We devised a ranking of regions in the human genome that show significant evolutionary acceleration. Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal-Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal-Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology.},
	Author = {Pollard, Katherine S and Salama, Sofie R and Lambert, Nelle and Lambot, Marie-Alexandra and Coppens, Sandra and Pedersen, Jakob S and Katzman, Sol and King, Bryan and Onodera, Courtney and Siepel, Adam and Kern, Andrew D and Dehay, Colette and Igel, Haller and Ares, Jr, Manuel and Vanderhaeghen, Pierre and Haussler, David},
	Date-Added = {2017-05-05 21:57:52 +0000},
	Date-Modified = {2017-05-05 21:59:46 +0000},
	Doi = {10.1038/nature05113},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {Neocortex; isocortex; Evolution},
	Mesh = {Aging; Animals; Base Sequence; Cell Adhesion Molecules, Neuronal; Cerebral Cortex; Evolution, Molecular; Extracellular Matrix Proteins; Gene Expression Profiling; Gene Expression Regulation, Developmental; Humans; Macaca; Molecular Sequence Data; Mutation; Neocortex; Nerve Tissue Proteins; Nucleic Acid Conformation; Organ Specificity; RNA Stability; RNA, Untranslated; Serine Endopeptidases; Time Factors},
	Month = {Sep},
	Number = {7108},
	Pages = {167-72},
	Pmid = {16915236},
	Pst = {ppublish},
	Title = {An RNA gene expressed during cortical development evolved rapidly in humans},
	Volume = {443},
	Year = {2006},
	File = {papers/Pollard_Nature2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature05113}}

@article{Lee:2013a,
	Abstract = {The hypothesized negative relationship between growth rate and lifespan has proved very difficult to test robustly because of potentially confounding variables, particularly nutrient availability and final size. Here we provide, to our knowledge, the first rigorous experimental test of this hypothesis, and find dramatic changes in lifespan in the predicted direction in response to both upward and downward manipulations of growth rates. We used brief (less than 4% of median lifespan) exposure to relatively cold or warm temperatures early in life to deflect juvenile three-spined sticklebacks Gasterosteus aculeatus from their normal growth trajectories; this induced catch-up or slowed-down growth when ambient temperatures were restored, and all groups attained the same average adult size. Catch-up growth led to a reduction in median lifespan of 14.5 per cent, while slowed-down growth extended lifespan by 30.6 per cent. These lifespan effects were independent of eventual size attained or reproductive investment in adult life. Photoperiod manipulations showed that the effects of compensatory growth on lifespan were also influenced by time available for growth prior to breeding, being more extreme when less time was available. These results demonstrate the growth-lifespan trade-off. While growing more slowly can increase longevity, the optimal resolution of the growth-lifespan trade-off is influenced by time constraints in a seasonal environment.},
	Author = {Lee, Who-Seung and Monaghan, Pat and Metcalfe, Neil B},
	Date-Added = {2017-05-05 21:48:59 +0000},
	Date-Modified = {2017-05-05 21:48:59 +0000},
	Doi = {10.1098/rspb.2012.2370},
	Journal = {Proc Biol Sci},
	Journal-Full = {Proceedings. Biological sciences},
	Mesh = {Animals; Environment; Female; Genetic Fitness; Longevity; Male; Photoperiod; Reproduction; Scotland; Seasons; Smegmamorpha; Temperature},
	Month = {Feb},
	Number = {1752},
	Pages = {20122370},
	Pmc = {PMC3574304},
	Pmid = {23235704},
	Pst = {epublish},
	Title = {Experimental demonstration of the growth rate--lifespan trade-off},
	Volume = {280},
	Year = {2013},
	File = {papers/Lee_ProcBiolSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rspb.2012.2370}}

@article{Mizuno:2014,
	Abstract = {Thalamocortical (TC) connectivity is reorganized by thalamic inputs during postnatal development; however, the dynamic characteristics of TC reorganization and the underlying mechanisms remain unexplored. We addressed this question using dendritic refinement of layer 4 (L4) stellate neurons in mouse barrel cortex (barrel cells) as a model; dendritic refinement of L4 neurons is a critical component of TC reorganization through which postsynaptic L4 neurons acquire their dendritic orientation toward presynaptic TC axon termini. Simultaneous labeling of TC axons and individual barrel cell dendrites allowed in vivo time-lapse imaging of dendritic refinement in the neonatal cortex. The barrel cells reinforced the dendritic orientation toward TC axons by dynamically moving their branches. In N-methyl-D-aspartate receptor (NMDAR)-deficient barrel cells, this dendritic motility was enhanced, and the orientation bias was not reinforced. Our data suggest that L4 neurons have "fluctuating" dendrites during TC reorganization and that NMDARs cell autonomously regulate these dynamics to establish fine-tuned circuits.},
	Author = {Mizuno, Hidenobu and Luo, Wenshu and Tarusawa, Etsuko and Saito, Yoshikazu M and Sato, Takuya and Yoshimura, Yumiko and Itohara, Shigeyoshi and Iwasato, Takuji},
	Date-Added = {2017-05-05 21:35:01 +0000},
	Date-Modified = {2017-05-05 21:35:01 +0000},
	Doi = {10.1016/j.neuron.2014.02.026},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Animals, Newborn; Cerebral Cortex; Dendrites; Excitatory Amino Acid Agonists; Excitatory Postsynaptic Potentials; Female; Gene Expression Regulation, Developmental; In Vitro Techniques; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Models, Biological; N-Methylaspartate; Nerve Tissue Proteins; Neural Pathways; Neurons; Receptors, N-Methyl-D-Aspartate; Thalamus; alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid},
	Month = {Apr},
	Number = {2},
	Pages = {365-79},
	Pmid = {24685175},
	Pst = {ppublish},
	Title = {NMDAR-regulated dynamics of layer 4 neuronal dendrites during thalamocortical reorganization in neonates},
	Volume = {82},
	Year = {2014},
	File = {papers/Mizuno_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.02.026}}

@article{Barbas:1997,
	Abstract = {Cortical areas are linked through pathways which originate and terminate in specific layers. The factors underlying which layers are involved in specific connections are not well understood. Here we tested whether cortical structure can predict the pattern as well as the relative distribution of projection neurons and axonal terminals in cortical layers, studied with retrograde and anterograde tracers. We used the prefrontal cortices in the rhesus monkey as a model system because their laminar organization varies systematically, ranging from areas that have only three identifiable layers, to those that have six layers. We rated each prefrontal area based on the number and definition of its cortical layers (level 1, lowest; level 5, highest). The structural model accurately predicted the laminar pattern of connections in approximately 80% of the cases. Thus, projection neurons from a higher-level cortex originated mostly in the upper layers and their axons terminated predominantly in the deep layers (4-6) of a lower-level cortex. Conversely, most projection neurons from a lower-level area originated in the deep layers and their axons terminated predominantly in the upper layers (1-3) of a higher-level area. In addition, the structural model accurately predicted that the proportion of projection neurons or axonal terminals in the upper to the deep layers would vary as a function of the number of levels between the connected cortices. The power of this structural model lies in its potential to predict patterns of connections in the human cortex, where invasive procedures are precluded.},
	Author = {Barbas, H and Rempel-Clower, N},
	Date = {1997 Oct-Nov},
	Date-Added = {2017-05-05 20:59:22 +0000},
	Date-Modified = {2017-05-05 20:59:22 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Axonal Transport; Axons; Brain Mapping; Cerebral Cortex; Humans; Macaca mulatta; Models, Anatomic; Neurons; Prefrontal Cortex; Wheat Germ Agglutinin-Horseradish Peroxidase Conjugate},
	Number = {7},
	Pages = {635-46},
	Pmid = {9373019},
	Pst = {ppublish},
	Title = {Cortical structure predicts the pattern of corticocortical connections},
	Volume = {7},
	Year = {1997},
	File = {papers/Barbas_CerebCortex1997.pdf}}

@article{Barrett:2015,
	Abstract = {Intuition suggests that perception follows sensation and therefore bodily feelings originate in the body. However, recent evidence goes against this logic: interoceptive experience may largely reflect limbic predictions about the expected state of the body that are constrained by ascending visceral sensations. In this Opinion article, we introduce the Embodied Predictive Interoception Coding model, which integrates an anatomical model of corticocortical connections with Bayesian active inference principles, to propose that agranular visceromotor cortices contribute to interoception by issuing interoceptive predictions. We then discuss how disruptions in interoceptive predictions could function as a common vulnerability for mental and physical illness.},
	Author = {Barrett, Lisa Feldman and Simmons, W Kyle},
	Date-Added = {2017-05-05 19:10:48 +0000},
	Date-Modified = {2017-05-05 19:13:47 +0000},
	Doi = {10.1038/nrn3950},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {ppc; Neocortex; isocortex; topographic map; Motor Cortex; behavior; review; grants; Perception; wholeBrain},
	Mesh = {Awareness; Bayes Theorem; Brain; Cognition; Emotions; Humans; Mental Disorders; Nerve Net; Perception},
	Month = {Jul},
	Number = {7},
	Pages = {419-29},
	Pmc = {PMC4731102},
	Pmid = {26016744},
	Pst = {ppublish},
	Title = {Interoceptive predictions in the brain},
	Volume = {16},
	Year = {2015},
	File = {papers/Barrett_NatRevNeurosci2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn3950}}

@book{Thompson:1917,
	Address = {Cambridge},
	Annote = {LDR    00694cam  22002291  4500
001    9651821
005    20170113093446.0
008    810622s1917    enka          000 0 eng  
035    $9(DLC)   18001383
906    $a7$bcbc$coclcrpl$du$encip$f19$gy-gencatlg
010    $a   18001383 
035    $a(OCoLC)14786876
040    $aDLC$cDNLM$dMNS$dDLC
050 00 $aQP84$b.T4
060 0  $aQH 511$bT469o 1917
100 1  $aThompson, D'Arcy Wentworth,$d1860-1948.
245 10 $aOn growth and form.
260    $aCambridge [Eng.]$bUniversity press,$c1917.
300    $axv, 793 p.$bill. ;$c22 cm.
650  0 $aGrowth.
985    $eOCLC REPLACEMENT
991    $bc-GenColl$hQP84$i.T4$p00000383296$tCopy 1$wOCLCREP
},
	Author = {Thompson, D'Arcy Wentworth},
	Call-Number = {QP84},
	Date-Added = {2017-05-05 19:07:39 +0000},
	Date-Modified = {2017-05-05 19:07:39 +0000},
	Genre = {Growth},
	Library-Id = {18001383},
	Publisher = {University press},
	Title = {On growth and form},
	Year = {1917},
	File = {papers/Thompson_1917.pdf},
	Bdsk-File-2 = {papers/Thompson_1917.epub},
	Bdsk-File-3 = {papers/Thompson_1917.mobi},
	Bdsk-File-4 = {papers/Thompson_1917a.pdf}}

@article{Uziel:2002,
	Abstract = {Axon guidance cues of the ephrin ligand family have been hypothesized to regulate the formation of thalamocortical connections, but in vivo evidence for such a role has not been examined directly. To test whether ephrin-mediated repulsive cues participate in sorting the projections originating from distinct thalamic nuclei, we analyzed the organization of somatosensory and anterior cingulate afferents postnatally in mice lacking ephrin-A5 gene expression. Projections from ventrobasal and laterodorsal nuclei to their respective sensory and limbic cortical areas developed normally. However, a portion of limbic thalamic neurons from the laterodorsal nucleus also formed additional projections to somatosensory cortical territories, thus maintaining inappropriate dual projections to multiple cortical regions. These results suggest that ephrin-A5 is not required for the formation of normal cortical projections from the appropriate thalamic nuclei, but rather acts as a guidance cue that restricts limbic thalamic axons from inappropriate neocortical regions.},
	Author = {Uziel, Daniela and M{\"u}hlfriedel, Sven and Zarbalis, Kostas and Wurst, Wolfgang and Levitt, Pat and Bolz, J{\"u}rgen},
	Date-Added = {2017-05-05 19:04:13 +0000},
	Date-Modified = {2017-05-05 19:04:13 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Cell Count; Cerebral Cortex; Ephrin-A5; Fluorescent Dyes; Gyrus Cinguli; Homozygote; Limbic System; Mice; Mice, Knockout; Nervous System Malformations; Neurons; Thalamic Nuclei; Thalamus},
	Month = {Nov},
	Number = {21},
	Pages = {9352-7},
	Pmid = {12417660},
	Pst = {ppublish},
	Title = {Miswiring of limbic thalamocortical projections in the absence of ephrin-A5},
	Volume = {22},
	Year = {2002},
	File = {papers/Uziel_JNeurosci2002.pdf}}

@article{Donoghue:1982,
	Abstract = {The first motor (MI) cortex of the rat was identified as the region from which movements could be evoked by the lowest intensity of electrical stimulation. The location of this region was correlated with cytoarchitecture in the frontal and parietal cortex. Two frontal areas can be discerned in Nissl-stained sections: (1) the medial agranular field, marked by a pale-staining layer III and a compact layer II, and (2) the lateral agranular field, which has more homogeneous superficial layers and a broad layer V containing large, densely staining cells. Both of these regions project to the spinal cord and can therefore be included in the somatic sensorimotor cortex. MI in the rat coincides with the lateral agranular field but also overlaps with part of the adjacent granular cortex of the first somatic sensory (SI) representation. We conclude that the rat MI cortex can be identified by microstimulation techniques and by cytoarchitecture in the rat.},
	Author = {Donoghue, J P and Wise, S P},
	Date-Added = {2017-05-05 19:02:45 +0000},
	Date-Modified = {2017-05-05 19:02:45 +0000},
	Doi = {10.1002/cne.902120106},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Brain Mapping; Cytoplasmic Granules; Electric Stimulation; Forelimb; Frontal Lobe; Hindlimb; Mechanoreceptors; Motor Activity; Motor Cortex; Neurons; Parietal Lobe; Rats; Somatosensory Cortex; Spinal Cord; Synaptic Transmission},
	Month = {Nov},
	Number = {1},
	Pages = {76-88},
	Pmid = {6294151},
	Pst = {ppublish},
	Title = {The motor cortex of the rat: cytoarchitecture and microstimulation mapping},
	Volume = {212},
	Year = {1982},
	File = {papers/Donoghue_JCompNeurol1982.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902120106}}

@article{Kozanian:2015,
	Abstract = {Functional sensory and motor areas in the developing mammalian neocortex are formed through a complex interaction of cortically intrinsic mechanisms, such as gene expression, and cortically extrinsic mechanisms such as those mediated by thalamic input from the senses. Both intrinsic and extrinsic mechanisms are believed to be involved in cortical patterning and the establishment of areal boundaries in early development; however, the nature of the interaction between intrinsic and extrinsic processes is not well understood. In a previous study, we used a perinatal bilateral enucleation mouse model to test some aspects of this interaction by reweighting sensory input to the developing cortex. Visual deprivation at birth resulted in a shift of intraneocortical connections (INCs) that aligned with ectopic ephrin A5 expression in the same location ten days later at postnatal day (P) 10. A prevailing question remained: Does visual deprivation first induce a change in gene expression, followed by a shift in INCs, or vice versa? In the present study, we address this question by investigating the neuroanatomy and patterns of gene expression in post-natal day (P) 1 and 4 mice following bilateral enucleation at birth. Our results demonstrate a rapid reduction in dorsal lateral geniculate nucleus (dLGN) size and ephrin A5 gene expression 24-hours post-enucleation, with more profound effects apparent at P4. The reduced nuclear size and diminished gene expression mirrors subtle changes in ephrin A5 expression evident in P1 and P4 enucleated neocortex, 11 and 8 days prior to natural eye opening, respectively. Somatosensory and visual INCs were indistinguishable between P1 and P4 mice bilaterally enucleated at birth, indicating that perinatal bilateral enucleation initiates a rapid change in gene expression (within one day) followed by an alteration of sensory INCs later on (second postnatal week). With these results, we gain a deeper understanding of how gene expression and sensory input together regulate cortical arealization and plasticity during early development.},
	Author = {Kozanian, Olga O and Abbott, Charles W and Huffman, Kelly J},
	Date-Added = {2017-05-05 18:50:54 +0000},
	Date-Modified = {2017-05-05 18:50:54 +0000},
	Doi = {10.1371/journal.pone.0140391},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Animals; Embryo, Mammalian; Embryonic Development; Ephrin-A5; Eye Enucleation; Female; Gene Expression Regulation, Developmental; Geniculate Bodies; Mice; Neocortex; Pregnancy; Somatosensory Cortex; Thalamus; Vision, Ocular; Visual Cortex},
	Number = {10},
	Pages = {e0140391},
	Pmc = {PMC4599918},
	Pmid = {26452243},
	Pst = {epublish},
	Title = {Rapid Changes in Cortical and Subcortical Brain Regions after Early Bilateral Enucleation in the Mouse},
	Volume = {10},
	Year = {2015},
	File = {papers/Kozanian_PLoSOne2015.PDF}}

@article{Shipp:2005,
	Abstract = {The agranular cortex is an important landmark-anatomically, as the architectural flag of mammalian motor cortex, and historically, as a spur to the development of theories of localization of function. But why, exactly, do agranularity and motor function go together? To address this question, it should be noted that not only does motor cortex lack granular layer four, it also has a relatively thinner layer three. Therefore, it is the two layers which principally constitute the ascending pathways through the sensory (granular) cortex that have regressed in motor cortex: simply stated, motor cortex does not engage in serial reprocessing of incoming sensory data. But why should a granular architecture not be demanded by the downstream relay of motor instructions through the motor cortex? The scant anatomical evidence available regarding laminar patterns suggests that the pathways from frontal and premotor areas to the primary motor cortex actually bear a greater resemblance to the descending, or feedback connections of sensory cortex that avoid the granular layer. The action of feedback connections is generally described as "modulatory" at a cellular level, or "selective" in terms of systems analysis. By contrast, ascending connections may be labelled "driving" or "instructive". Where the motor cortex uses driving inputs, they are most readily identified as sensory signals instructing the visual location of targets and the kinaesthetic state of the body. Visual signals may activate motor concepts, e.g. "mirror neurons", and the motor plan must select the appropriate muscles and forces to put the plan into action, if the decision to move is taken. This, perhaps, is why "driving" motor signals might be inappropriate-the optimal selection and its execution are conditional upon both kinaesthetic and motivational factors. The argument, summarized above, is constructed in honour of Korbinian Brodmann's centenary, and follows two of the fundamental principles of his school of thought: that uniformities in cortical structure, and development imply global conservation of some aspects of function, whereas regional variations in architecture can be used to chart the "organs" of the cortex, and perhaps to understand their functional differences.},
	Author = {Shipp, Stewart},
	Date-Added = {2017-05-05 18:50:27 +0000},
	Date-Modified = {2017-05-05 18:50:27 +0000},
	Doi = {10.1098/rstb.2005.1630},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Mesh = {Brain Mapping; Feedback, Physiological; Humans; Models, Neurological; Motor Cortex; Neural Pathways; Visual Cortex},
	Month = {Apr},
	Number = {1456},
	Pages = {797-814},
	Pmc = {PMC1569485},
	Pmid = {15937013},
	Pst = {ppublish},
	Title = {The importance of being agranular: a comparative account of visual and motor cortex},
	Volume = {360},
	Year = {2005},
	File = {papers/Shipp_PhilosTransRSocLondBBiolSci2005.pdf}}

@article{Sigalas:2015,
	Abstract = {UNLABELLED: Nicotinic acetylcholine receptors (nAChRs) play an important role in the modulation of many cognitive functions but their role in integrated network activity remains unclear. This is at least partly because of the complexity of the cholinergic circuitry and the difficulty in comparing results from in vivo studies obtained under diverse experimental conditions and types of anesthetics. Hence the role of nAChRs in the synchronization of cortical activity during slow-wave sleep is still controversial, with some studies showing they are involved in ACh-dependent EEG desynchronization, and others suggesting that this effect is mediated exclusively by muscarinic receptors. Here we use an in vitro model of endogenous network activity, in the form of recurring self-maintained depolarized states (Up states), which allows us to examine the role of high-affinity nAChRs on network dynamics in a simpler form of the cortical microcircuit. We find that mice lacking nAChRs containing the β2-subunit (β2-nAChRs) have longer and more frequent Up states, and that this difference is eliminated when β2-nAChRs in wild-type mice are blocked. We further show that endogenously released ACh can modulate Up/Down states through the activation of both β2- and α7-containing nAChRs, but through distinct mechanisms: α7-nAChRs affect only the termination of spontaneous Up states, while β2-nAChRs also regulate their generation. Finally we provide evidence that the effects of β2-subunit-containing, but not α7-subunit-containing nAChRs, are mediated through GABAB receptors. To our knowledge this is the first study documenting direct nicotinic modulation of Up/Down state activity.
SIGNIFICANCE STATEMENT: Through our experiments we were able to uncover a clear and previously disputed effect of nicotinic signaling in synchronized activity of neuronal networks of the cortex. We show that both high-affinity receptors (containing the β2-subunit, β2-nAChRs) and low-affinity receptors (containing the α7-subunit, α7-nAChRs) can regulate cortical network function exhibited in the form of Up/Down states. We further show that the effects of β2-nAChRs, but not α7-nAChRs, are mediated through the activation of GABAB receptors. These results suggest a possible synthesis of seemingly contradictory results in the literature and could be valuable for informing computational models of cortical function and for guiding the search for therapeutic interventions.},
	Author = {Sigalas, Charalambos and Rigas, Pavlos and Tsakanikas, Panagiotis and Skaliora, Irini},
	Date-Added = {2017-05-05 18:50:13 +0000},
	Date-Modified = {2017-05-05 18:50:13 +0000},
	Doi = {10.1523/JNEUROSCI.5222-14.2015},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {barrel cortex; cholinergic; network activity; oscillations; persistent activity; β2-nAChR},
	Mesh = {Animals; Cells, Cultured; Cerebral Cortex; Excitatory Postsynaptic Potentials; In Vitro Techniques; Mice; Mice, Knockout; Neurons; Nicotine; Patch-Clamp Techniques; Receptors, Nicotinic; alpha7 Nicotinic Acetylcholine Receptor},
	Month = {Aug},
	Number = {32},
	Pages = {11196-208},
	Pmid = {26269630},
	Pst = {ppublish},
	Title = {High-Affinity Nicotinic Receptors Modulate Spontaneous Cortical Up States In Vitro},
	Volume = {35},
	Year = {2015},
	File = {papers/Sigalas_JNeurosci2015.pdf}}

@article{Koukouli:2016,
	Abstract = {The prefrontal cortex (PFC) plays an important role in cognitive processes, including access to consciousness. The PFC receives significant cholinergic innervation and nicotinic acetylcholine receptors (nAChRs) contribute greatly to the effects of acetylcholine signaling. Using in vivo two-photon imaging of both awake and anesthetized mice, we recorded spontaneous, ongoing neuronal activity in layer II/III in the PFC of WT mice and mice deleted for different nAChR subunits. As in humans, this activity is characterized by synchronous ultraslow fluctuations and neuronal synchronicity is disrupted by light general anesthesia. Both the α7 and β2 nAChR subunits play an important role in the generation of ultraslow fluctuations that occur to a different extent during quiet wakefulness and light general anesthesia. The β2 subunit is specifically required for synchronized activity patterns. Furthermore, chronic application of mecamylamine, an antagonist of nAChRs, disrupts the generation of ultraslow fluctuations. Our findings provide new insight into the ongoing spontaneous activity in the awake and anesthetized state, and the role of cholinergic neurotransmission in the orchestration of cognitive functions.},
	Author = {Koukouli, Fani and Rooy, Marie and Changeux, Jean-Pierre and Maskos, Uwe},
	Date-Added = {2017-05-05 18:50:02 +0000},
	Date-Modified = {2017-05-05 18:50:02 +0000},
	Doi = {10.1073/pnas.1614417113},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {anesthesia; consciousness; nicotinic receptor; prefrontal cortex; ultraslow fluctuations},
	Month = {Dec},
	Number = {51},
	Pages = {14823-14828},
	Pmc = {PMC5187677},
	Pmid = {27911815},
	Pst = {ppublish},
	Title = {Nicotinic receptors in mouse prefrontal cortex modulate ultraslow fluctuations related to conscious processing},
	Volume = {113},
	Year = {2016},
	File = {papers/Koukouli_ProcNatlAcadSciUSA2016.pdf}}

@article{Cancedda:2012,
	Abstract = {The Italian Space Agency, in line with its scientific strategies and the National Utilization Plan for the International Space Station (ISS), contracted Thales Alenia Space Italia to design and build a spaceflight payload for rodent research on ISS: the Mice Drawer System (MDS). The payload, to be integrated inside the Space Shuttle middeck during transportation and inside the Express Rack in the ISS during experiment execution, was designed to function autonomously for more than 3 months and to involve crew only for maintenance activities. In its first mission, three wild type (Wt) and three transgenic male mice over-expressing pleiotrophin under the control of a bone-specific promoter (PTN-Tg) were housed in the MDS. At the time of launch, animals were 2-months old. MDS reached the ISS on board of Shuttle Discovery Flight 17A/STS-128 on August 28(th), 2009. MDS returned to Earth on November 27(th), 2009 with Shuttle Atlantis Flight ULF3/STS-129 after 91 days, performing the longest permanence of mice in space. Unfortunately, during the MDS mission, one PTN-Tg and two Wt mice died due to health status or payload-related reasons. The remaining mice showed a normal behavior throughout the experiment and appeared in excellent health conditions at landing. During the experiment, the mice health conditions and their water and food consumption were daily checked. Upon landing mice were sacrificed, blood parameters measured and tissues dissected for subsequent analysis. To obtain as much information as possible on microgravity-induced tissue modifications, we organized a Tissue Sharing Program: 20 research groups from 6 countries participated. In order to distinguish between possible effects of the MDS housing conditions and effects due to the near-zero gravity environment, a ground replica of the flight experiment was performed at the University of Genova. Control tissues were collected also from mice maintained on Earth in standard vivarium cages.},
	Author = {Cancedda, Ranieri and Liu, Yi and Ruggiu, Alessandra and Tavella, Sara and Biticchi, Roberta and Santucci, Daniela and Schwartz, Silvia and Ciparelli, Paolo and Falcetti, Giancarlo and Tenconi, Chiara and Cotronei, Vittorio and Pignataro, Salvatore},
	Date-Added = {2017-05-05 18:49:35 +0000},
	Date-Modified = {2017-05-05 18:49:35 +0000},
	Doi = {10.1371/journal.pone.0032243},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Animals; Bone and Bones; Equipment Design; Female; Humans; Male; Mice; Space Flight; Time Factors; Weightlessness Simulation},
	Number = {5},
	Pages = {e32243},
	Pmc = {PMC3362598},
	Pmid = {22666312},
	Pst = {ppublish},
	Title = {The Mice Drawer System (MDS) experiment and the space endurance record-breaking mice},
	Volume = {7},
	Year = {2012},
	File = {papers/Cancedda_PLoSOne2012.PDF}}

@article{Hawrylycz:2016,
	Abstract = {The scientific mission of the Project MindScope is to understand neocortex, the part of the mammalian brain that gives rise to perception, memory, intelligence, and consciousness. We seek to quantitatively evaluate the hypothesis that neocortex is a relatively homogeneous tissue, with smaller functional modules that perform a common computational function replicated across regions. We here focus on the mouse as a mammalian model organism with genetics, physiology, and behavior that can be readily studied and manipulated in the laboratory. We seek to describe the operation of cortical circuitry at the computational level by comprehensively cataloging and characterizing its cellular building blocks along with their dynamics and their cell type-specific connectivities. The project is also building large-scale experimental platforms (i.e., brain observatories) to record the activity of large populations of cortical neurons in behaving mice subject to visual stimuli. A primary goal is to understand the series of operations from visual input in the retina to behavior by observing and modeling the physical transformations of signals in the corticothalamic system. We here focus on the contribution that computer modeling and theory make to this long-term effort.},
	Author = {Hawrylycz, Michael and Anastassiou, Costas and Arkhipov, Anton and Berg, Jim and Buice, Michael and Cain, Nicholas and Gouwens, Nathan W and Gratiy, Sergey and Iyer, Ramakrishnan and Lee, Jung Hoon and Mihalas, Stefan and Mitelut, Catalin and Olsen, Shawn and Reid, R Clay and Teeter, Corinne and de Vries, Saskia and Waters, Jack and Zeng, Hongkui and Koch, Christof and {MindScope}},
	Date-Added = {2017-05-05 18:48:49 +0000},
	Date-Modified = {2017-05-05 18:48:49 +0000},
	Doi = {10.1073/pnas.1512901113},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {computation; neocortex; neural coding; simulation; visual system},
	Month = {Jul},
	Number = {27},
	Pages = {7337-44},
	Pmc = {PMC4941493},
	Pmid = {27382147},
	Pst = {ppublish},
	Title = {Inferring cortical function in the mouse visual system through large-scale systems neuroscience},
	Volume = {113},
	Year = {2016},
	File = {papers/Hawrylycz_ProcNatlAcadSciUSA2016.pdf}}

@article{Chen:2008a,
	Abstract = {Pyramidal neurons in the deep layers of the cerebral cortex can be classified into two major classes: callosal projection neurons and long-range subcortical neurons. We and others have shown that a gene expressed specifically by subcortical projection neurons, Fezf2, is required for the formation of axonal projections to the spinal cord, tectum, and pons. Here, we report that Fezf2 regulates a decision between subcortical vs. callosal projection neuron fates. Fezf2(-/-) neurons adopt the fate of callosal projection neurons as assessed by their axonal projections, electrophysiological properties, and acquisition of Satb2 expression. Ctip2 is a major downstream effector of Fezf2 in regulating the extension of axons toward subcortical targets and can rescue the axonal phenotype of Fezf2 mutants. When ectopically expressed, either Fezf2 or Ctip2 can alter the axonal targeting of corticocortical projection neurons and cause them to project to subcortical targets, although Fezf2 can promote a subcortical projection neuron fate in the absence of Ctip2 expression.},
	Author = {Chen, Bin and Wang, Song S and Hattox, Alexis M and Rayburn, Helen and Nelson, Sacha B and McConnell, Susan K},
	Date-Added = {2017-05-05 18:48:06 +0000},
	Date-Modified = {2017-05-05 18:48:06 +0000},
	Doi = {10.1073/pnas.0804918105},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Axons; DNA-Binding Proteins; Gene Expression Regulation; Mice; Mice, Mutant Strains; Nerve Tissue Proteins; Phenotype; Pyramidal Cells; Repressor Proteins; Tumor Suppressor Proteins},
	Month = {Aug},
	Number = {32},
	Pages = {11382-7},
	Pmc = {PMC2495013},
	Pmid = {18678899},
	Pst = {ppublish},
	Title = {The Fezf2-Ctip2 genetic pathway regulates the fate choice of subcortical projection neurons in the developing cerebral cortex},
	Volume = {105},
	Year = {2008},
	File = {papers/Chen_ProcNatlAcadSciUSA2008.pdf}}

@article{Hattox:2007,
	Abstract = {Layer V pyramidal neurons are anatomically and physiologically heterogeneous and project to multiple intracortical and subcortical targets. However, because most physiological studies of layer V pyramidal neurons have been carried out on unidentified cells, we know little about how anatomical and physiological properties relate to subcortical projection site. Here we combine neuroanatomical tract tracing with whole cell recordings in mouse somatosensory cortex to test whether neurons with the same projection target form discrete subpopulations and whether they have stereotyped physiological properties. Our findings indicate that corticothalamic and -trigeminal neurons are two largely nonoverlapping subpopulations, whereas callosal and corticostriatal neurons overlap extensively. The morphology as well as the intrinsic membrane and firing properties of corticothalamic and corticotrigeminal neurons differ from those of callosal and corticostriatal neurons. In addition, we find that each class of projection neuron exhibits a unique compliment of hyperpolarizing and depolarizing afterpotentials that further suggests that cortical neurons with different subcortical targets are distinct from one another.},
	Author = {Hattox, Alexis M and Nelson, Sacha B},
	Date-Added = {2017-05-05 18:47:26 +0000},
	Date-Modified = {2017-05-05 18:47:53 +0000},
	Doi = {10.1152/jn.00397.2007},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Mesh = {Action Potentials; Animals; Corpus Callosum; Electrophysiology; Image Processing, Computer-Assisted; Immunohistochemistry; Mice; Mice, Inbred C57BL; Microscopy, Confocal; Nerve Tissue Proteins; Neural Pathways; Nuclear Proteins; Patch-Clamp Techniques; Pyramidal Cells; Somatosensory Cortex; Thalamus; Trigeminal Nerve},
	Month = {Dec},
	Number = {6},
	Pages = {3330-40},
	Pmid = {17898147},
	Pst = {ppublish},
	Title = {Layer V neurons in mouse cortex projecting to different targets have distinct physiological properties},
	Volume = {98},
	Year = {2007},
	File = {papers/Hattox_JNeurophysiol2007a.pdf}}

@article{Sestan:2001,
	Abstract = {The visual cortex in primates is parcellated into cytoarchitectonically, physiologically, and connectionally distinct areas: the striate cortex (V1) and the extrastriate cortex, consisting of V2 and numerous higher association areas [1]. The innervation of distinct visual cortical areas by the thalamus is especially segregated in primates, such that the lateral geniculate (LG) nucleus specifically innervates striate cortex, whereas pulvinar projections are confined to extrastriate cortex [2--8]. The molecular bases for the parcellation of the visual cortex and thalamus, as well as the establishment of reciprocal connections between distinct compartments within these two structures, are largely unknown. Here, we show that prospective visual cortical areas and corresponding thalamic nuclei in the embryonic rhesus monkey (Macaca mulatta) can be defined by combinatorial expression of genes encoding Eph receptor tyrosine kinases and their ligands, the ephrins, prior to obvious cytoarchitectonic differentiation within the cortical plate and before the establishment of reciprocal connections between the cortical plate and thalamus. These results indicate that molecular patterns of presumptive visual compartments in both the cortex and thalamus can form independently of one another and suggest a role for EphA family members in both compartment formation and axon guidance within the visual thalamocortical system.},
	Author = {Sestan, N and Rakic, P and Donoghue, M J},
	Date-Added = {2017-05-05 18:47:03 +0000},
	Date-Modified = {2017-05-05 18:47:03 +0000},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Mesh = {Animals; Gene Expression Regulation, Developmental; Macaca; Nerve Tissue Proteins; Receptor Protein-Tyrosine Kinases; Thalamus; Visual Cortex},
	Month = {Jan},
	Number = {1},
	Pages = {39-43},
	Pmid = {11166178},
	Pst = {ppublish},
	Title = {Independent parcellation of the embryonic visual cortex and thalamus revealed by combinatorial Eph/ephrin gene expression},
	Volume = {11},
	Year = {2001},
	File = {papers/Sestan_CurrBiol2001.pdf}}

@article{Bopp:2014,
	Abstract = {One of the hallmarks of neocortical circuits is the predominance of recurrent excitation between pyramidal neurons, which is balanced by recurrent inhibition from smooth GABAergic neurons. It has been previously described that in layer 2/3 of primary visual cortex (V1) of cat and monkey, pyramidal cells filled with horseradish peroxidase connect approximately in proportion to the spiny (excitatory, 95% and 81%, respectively) and smooth (GABAergic, 5% and 19%, respectively) dendrites found in the neuropil. By contrast, a recent ultrastructural study of V1 in a single mouse found that smooth neurons formed 51% of the targets of the superficial layer pyramidal cells. This suggests that either the neuropil of this particular mouse V1 had a dramatically different composition to that of V1 in cat and monkey, or that smooth neurons were specifically targeted by the pyramidal cells in that mouse. We tested these hypotheses by examining similar cells filled with biocytin in a sample of five mice. We found that the average composition of the neuropil in V1 of these mice was similar to that described for cat and monkey V1, but that the superficial layer pyramidal cells do form proportionately more synapses with smooth dendrites than the equivalent neurons in cat or monkey. These distributions may underlie the distinct differences in functional architecture of V1 between rodent and higher mammals.},
	Author = {Bopp, Rita and Ma{\c c}arico da Costa, Nuno and Kampa, Bj{\"o}rn M and Martin, Kevan A C and Roth, Morgane M},
	Date-Added = {2017-05-05 18:45:28 +0000},
	Date-Modified = {2017-05-05 18:45:28 +0000},
	Doi = {10.1371/journal.pbio.1001932},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Mesh = {Animals; Axons; Cats; Dendritic Spines; Electroporation; GABAergic Neurons; Haplorhini; Mice; Models, Neurological; Presynaptic Terminals; Pyramidal Cells; Visual Cortex},
	Month = {Aug},
	Number = {8},
	Pages = {e1001932},
	Pmc = {PMC4138028},
	Pmid = {25137065},
	Pst = {epublish},
	Title = {Pyramidal cells make specific connections onto smooth (GABAergic) neurons in mouse visual cortex},
	Volume = {12},
	Year = {2014},
	File = {papers/Bopp_PLoSBiol2014.PDF}}

@article{Alcamo:2008,
	Abstract = {Satb2 is a DNA-binding protein that regulates chromatin organization and gene expression. In the developing brain, Satb2 is expressed in cortical neurons that extend axons across the corpus callosum. To assess the role of Satb2 in neurons, we analyzed mice in which the Satb2 locus was disrupted by insertion of a LacZ gene. In mutant mice, beta-galactosidase-labeled axons are absent from the corpus callosum and instead descend along the corticospinal tract. Satb2 mutant neurons acquire expression of Ctip2, a transcription factor that is necessary and sufficient for the extension of subcortical projections by cortical neurons. Conversely, ectopic expression of Satb2 in neural stem cells markedly decreases Ctip2 expression. Finally, we find that Satb2 binds directly to regulatory regions of Ctip2 and induces changes in chromatin structure. These data suggest that Satb2 functions as a repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex.},
	Author = {Alcamo, Elizabeth A and Chirivella, Laura and Dautzenberg, Marcel and Dobreva, Gergana and Fari{\~n}as, Isabel and Grosschedl, Rudolf and McConnell, Susan K},
	Date-Added = {2017-05-05 18:44:08 +0000},
	Date-Modified = {2017-05-05 18:45:16 +0000},
	Doi = {10.1016/j.neuron.2007.12.012},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Animals, Newborn; Bromodeoxyuridine; Cells, Cultured; Cerebral Cortex; Chromatin Immunoprecipitation; Electrophoretic Mobility Shift Assay; Embryo, Mammalian; Gene Expression Regulation, Developmental; Matrix Attachment Region Binding Proteins; Mice; Mice, Transgenic; Mutation; Nerve Tissue Proteins; Neural Pathways; Neurons; Stem Cells; Transcription Factors},
	Month = {Feb},
	Number = {3},
	Pages = {364-77},
	Pmid = {18255030},
	Pst = {ppublish},
	Title = {Satb2 regulates callosal projection neuron identity in the developing cerebral cortex},
	Volume = {57},
	Year = {2008},
	File = {papers/Alcamo_Neuron2008.pdf},
	Bdsk-File-2 = {papers/Alcamo_Neuron2008a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2007.12.012}}

@article{Rosa:2005,
	Abstract = {In this paper, we review evidence from comparative studies of primate cortical organization, highlighting recent findings and hypotheses that may help us to understand the rules governing evolutionary changes of the cortical map and the process of formation of areas during development. We argue that clear unequivocal views of cortical areas and their homologies are more likely to emerge for "core" fields, including the primary sensory areas, which are specified early in development by precise molecular identification steps. In primates, the middle temporal area is probably one of these primordial cortical fields. Areas that form at progressively later stages of development correspond to progressively more recent evolutionary events, their development being less firmly anchored in molecular specification. The certainty with which areal boundaries can be delimited, and likely homologies can be assigned, becomes increasingly blurred in parallel with this evolutionary/developmental sequence. For example, while current concepts for the definition of cortical areas have been vindicated in allowing a clarification of the organization of the New World monkey "third tier" visual cortex (the third and dorsomedial areas, V3 and DM), our analyses suggest that more flexible mapping criteria may be needed to unravel the organization of higher-order visual association and polysensory areas.},
	Author = {Rosa, Marcello G P and Tweedale, Rowan},
	Date-Added = {2017-05-05 18:42:44 +0000},
	Date-Modified = {2017-05-05 18:42:44 +0000},
	Doi = {10.1098/rstb.2005.1626},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Mesh = {Anatomy, Comparative; Animals; Biological Evolution; Brain Mapping; Models, Biological; Physiology, Comparative; Primates; Visual Cortex; Visual Perception},
	Month = {Apr},
	Number = {1456},
	Pages = {665-91},
	Pmc = {PMC1874231},
	Pmid = {15937007},
	Pst = {ppublish},
	Title = {Brain maps, great and small: lessons from comparative studies of primate visual cortical organization},
	Volume = {360},
	Year = {2005},
	File = {papers/Rosa_PhilosTransRSocLondBBiolSci2005.pdf}}

@article{Villar-Cervino:2013,
	Abstract = {Cajal-Retzius (CR) cells play a fundamental role in the development of the mammalian cerebral cortex. They control the formation of cortical layers by regulating the migration of pyramidal cells through the release of Reelin. The function of CR cells critically depends on their regular distribution throughout the surface of the cortex, but little is known about the events controlling this phenomenon. Using time-lapse video microscopy in vivo and in vitro, we found that movement of CR cells is regulated by repulsive interactions, which leads to their random dispersion throughout the cortical surface. Mathematical modeling reveals that contact repulsion is both necessary and sufficient for this process, which demonstrates that complex neuronal assemblies may emerge during development through stochastic events. At the molecular level, we found that contact repulsion is mediated by Eph/ephrin interactions. Our observations reveal a mechanism that controls the even distribution of neurons in the developing brain.},
	Author = {Villar-Cervi{\~n}o, Verona and Molano-Maz{\'o}n, Manuel and Catchpole, Timothy and Valdeolmillos, Miguel and Henkemeyer, Mark and Mart{\'\i}nez, Luis M and Borrell, V{\'\i}ctor and Mar{\'\i}n, Oscar},
	Date-Added = {2017-05-05 16:52:27 +0000},
	Date-Modified = {2017-05-05 16:52:27 +0000},
	Doi = {10.1016/j.neuron.2012.11.023},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Age Factors; Animals; Body Patterning; Calbindin 2; Cell Movement; Cerebral Cortex; Embryo, Mammalian; Gene Expression Regulation, Developmental; Green Fluorescent Proteins; Mice; Mice, Inbred C57BL; Mice, Transgenic; Microscopy, Confocal; Nerve Tissue Proteins; Neurons; Organ Culture Techniques; Receptor, EphB1; Receptor, EphB2; Receptor, EphB3; S100 Calcium Binding Protein G},
	Month = {Feb},
	Number = {3},
	Pages = {457-71},
	Pmc = {PMC3569744},
	Pmid = {23395373},
	Pst = {ppublish},
	Title = {Contact repulsion controls the dispersion and final distribution of Cajal-Retzius cells},
	Volume = {77},
	Year = {2013},
	File = {papers/Villar-Cerviño_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.11.023}}

@article{Tessier-Lavigne:1995,
	Author = {Tessier-Lavigne, M},
	Date-Added = {2017-05-05 16:24:40 +0000},
	Date-Modified = {2017-05-05 16:25:53 +0000},
	Journal = {Cell},
	Journal-Full = {Cell},
	Keywords = {review; Development; Protein-Tyrosine Kinases; Ephrin-A2; circuit formation; Brain Mapping; Animals; Proteins;Neurons;Axons},
	Mesh = {Animals; Axons; Brain Mapping; Ephrin-A2; Neurons; Protein-Tyrosine Kinases; Proteins},
	Month = {Aug},
	Number = {3},
	Pages = {345-8},
	Pmid = {7634322},
	Pst = {ppublish},
	Title = {Eph receptor tyrosine kinases, axon repulsion, and the development of topographic maps},
	Volume = {82},
	Year = {1995},
	File = {papers/Tessier-Lavigne_Cell1995.pdf}}

@article{Lieberoth:2009,
	Abstract = {Although carbohydrates have been implicated in cell interactions in the nervous system, the molecular bases of their functions have remained largely obscure. Here, we show that promotion or inhibition of neurite outgrowth of cerebellar or dorsal root ganglion neurons, respectively, induced by the mucin-type adhesion molecule CD24 depends on alpha2,3-linked sialic acid and Lewis(x) present on glia-specific CD24 glycoforms. Alpha2,3-sialyl residues of CD24 bind to a structural motif in the first fibronectin type III domain of the adhesion molecule L1. Following the observation that the adhesion molecules TAG-1 and Contactin show sequence homologies with fucose-specific lectins, we obtained evidence that TAG-1 and Contactin mediate Lewis(x)-dependent CD24-induced effects on neurite outgrowth. Thus, L1, TAG-1, and Contactin function as lectin-like neuronal receptors. Their cis interactions with neighboring adhesion molecules, e.g., Caspr1 and Caspr2, and with their triggered signal transduction pathways elicit cell type-specific promotion or inhibition of neurite outgrowth induced by glial CD24 in a glycan-dependent trans interaction.},
	Author = {Lieberoth, Annika and Splittstoesser, Frauke and Katagihallimath, Nainesh and Jakovcevski, Igor and Loers, Gabriele and Ranscht, Barbara and Karagogeos, Domna and Schachner, Melitta and Kleene, Ralf},
	Date-Added = {2017-05-04 23:34:33 +0000},
	Date-Modified = {2017-05-04 23:34:33 +0000},
	Doi = {10.1523/JNEUROSCI.4361-08.2009},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Animals, Newborn; Antigens, CD15; Antigens, CD24; Binding Sites; Cell Adhesion Molecules, Neuronal; Cells, Cultured; Cerebellum; Contactin 2; Contactins; Cricetinae; Cricetulus; Dose-Response Relationship, Drug; Enzyme-Linked Immunosorbent Assay; Ganglia, Spinal; Glycosylation; Immunoprecipitation; Leukocyte L1 Antigen Complex; Locomotion; Mice; Mice, Inbred C57BL; Mice, Knockout; Neurites; Neurons; Peptides; Protein Binding; Recovery of Function; Sialic Acids; Spinal Cord Injuries; Transfection},
	Month = {May},
	Number = {20},
	Pages = {6677-90},
	Pmid = {19458237},
	Pst = {ppublish},
	Title = {Lewis(x) and alpha2,3-sialyl glycans and their receptors TAG-1, Contactin, and L1 mediate CD24-dependent neurite outgrowth},
	Volume = {29},
	Year = {2009},
	File = {papers/Lieberoth_JNeurosci2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4361-08.2009}}

@article{Vernes:2008,
	Abstract = {BACKGROUND: Rare mutations affecting the FOXP2 transcription factor cause a monogenic speech and language disorder. We hypothesized that neural pathways downstream of FOXP2 influence more common phenotypes, such as specific language impairment.
METHODS: We performed genomic screening for regions bound by FOXP2 using chromatin immunoprecipitation, which led us to focus on one particular gene that was a strong candidate for involvement in language impairments. We then tested for associations between single-nucleotide polymorphisms (SNPs) in this gene and language deficits in a well-characterized set of 184 families affected with specific language impairment.
RESULTS: We found that FOXP2 binds to and dramatically down-regulates CNTNAP2, a gene that encodes a neurexin and is expressed in the developing human cortex. On analyzing CNTNAP2 polymorphisms in children with typical specific language impairment, we detected significant quantitative associations with nonsense-word repetition, a heritable behavioral marker of this disorder (peak association, P=5.0x10(-5) at SNP rs17236239). Intriguingly, this region coincides with one associated with language delays in children with autism.
CONCLUSIONS: The FOXP2-CNTNAP2 pathway provides a mechanistic link between clinically distinct syndromes involving disrupted language.},
	Author = {Vernes, Sonja C and Newbury, Dianne F and Abrahams, Brett S and Winchester, Laura and Nicod, J{\'e}r{\^o}me and Groszer, Matthias and Alarc{\'o}n, Maricela and Oliver, Peter L and Davies, Kay E and Geschwind, Daniel H and Monaco, Anthony P and Fisher, Simon E},
	Date-Added = {2017-05-04 23:31:28 +0000},
	Date-Modified = {2017-05-04 23:31:28 +0000},
	Doi = {10.1056/NEJMoa0802828},
	Journal = {N Engl J Med},
	Journal-Full = {The New England journal of medicine},
	Mesh = {Child; Chromatin Immunoprecipitation; Down-Regulation; Female; Forkhead Transcription Factors; Gene Expression Regulation; Genetic Markers; Genome-Wide Association Study; Haplotypes; Humans; Language Development Disorders; Male; Membrane Proteins; Nerve Tissue Proteins; Phenotype; Polymerase Chain Reaction; Polymorphism, Single Nucleotide},
	Month = {Nov},
	Number = {22},
	Pages = {2337-45},
	Pmc = {PMC2756409},
	Pmid = {18987363},
	Pst = {ppublish},
	Title = {A functional genetic link between distinct developmental language disorders},
	Volume = {359},
	Year = {2008},
	File = {papers/Vernes_NEnglJMed2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1056/NEJMoa0802828}}

@article{Strauss:2006,
	Abstract = {Contactin-associated protein-like 2 (CASPR2) is encoded by CNTNAP2 and clusters voltage-gated potassium channels (K(v)1.1) at the nodes of Ranvier. We report a homozygous mutation of CNTNAP2 in Old Order Amish children with cortical dysplasia, focal epilepsy, relative macrocephaly, and diminished deep-tendon reflexes. Intractable focal seizures began in early childhood, after which language regression, hyperactivity, impulsive and aggressive behavior, and mental retardation developed in all children. Resective surgery did not prevent the recurrence of seizures. Temporal-lobe specimens showed evidence of abnormalities of neuronal migration and structure, widespread astrogliosis, and reduced expression of CASPR2.},
	Author = {Strauss, Kevin A and Puffenberger, Erik G and Huentelman, Matthew J and Gottlieb, Steven and Dobrin, Seth E and Parod, Jennifer M and Stephan, Dietrich A and Morton, D Holmes},
	Date-Added = {2017-05-04 23:20:58 +0000},
	Date-Modified = {2017-05-04 23:20:58 +0000},
	Doi = {10.1056/NEJMoa052773},
	Journal = {N Engl J Med},
	Journal-Full = {The New England journal of medicine},
	Mesh = {Child; Child, Preschool; Electroencephalography; Epilepsies, Partial; Gene Expression; Homozygote; Humans; Magnetic Resonance Angiography; Membrane Proteins; Mutation; Nerve Tissue Proteins; Phenotype; Reflex, Stretch; Secondary Prevention; Seizures; Temporal Lobe},
	Month = {Mar},
	Number = {13},
	Pages = {1370-7},
	Pmid = {16571880},
	Pst = {ppublish},
	Title = {Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2},
	Volume = {354},
	Year = {2006},
	File = {papers/Strauss_NEnglJMed2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1056/NEJMoa052773}}

@article{Baudouin:2010,
	Author = {Baudouin, St{\'e}phane and Scheiffele, Peter},
	Date-Added = {2017-05-04 23:08:18 +0000},
	Date-Modified = {2017-05-04 23:08:18 +0000},
	Doi = {10.1016/j.cell.2010.05.024},
	Journal = {Cell},
	Journal-Full = {Cell},
	Mesh = {Animals; Cell Adhesion Molecules, Neuronal; Humans; Protein Binding; Protein Isoforms; Receptors, Cell Surface; Synapses},
	Month = {May},
	Number = {5},
	Pages = {908, 908.e1},
	Pmid = {20510934},
	Pst = {ppublish},
	Title = {SnapShot: Neuroligin-neurexin complexes},
	Volume = {141},
	Year = {2010},
	File = {papers/Baudouin_Cell2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cell.2010.05.024}}

@article{Lepe-Zuniga:1987,
	Author = {Lepe-Zuniga, J L and Zigler, Jr, J S and Gery, I},
	Date-Added = {2017-05-04 21:46:52 +0000},
	Date-Modified = {2017-05-04 21:46:52 +0000},
	Journal = {J Immunol Methods},
	Journal-Full = {Journal of immunological methods},
	Mesh = {Culture Media; HEPES; Hydrogen Peroxide; Piperazines},
	Month = {Oct},
	Number = {1},
	Pages = {145},
	Pmid = {3655381},
	Pst = {ppublish},
	Title = {Toxicity of light-exposed Hepes media},
	Volume = {103},
	Year = {1987}}

@article{Moreno-Juan:2017,
	Abstract = {The cerebral cortex is organized into specialized sensory areas, whose initial territory is determined by intracortical molecular determinants. Yet, sensory cortical area size appears to be fine tuned during development to respond to functional adaptations. Here we demonstrate the existence of a prenatal sub-cortical mechanism that regulates the cortical areas size in mice. This mechanism is mediated by spontaneous thalamic calcium waves that propagate among sensory-modality thalamic nuclei up to the cortex and that provide a means of communication among sensory systems. Wave pattern alterations in one nucleus lead to changes in the pattern of the remaining ones, triggering changes in thalamic gene expression and cortical area size. Thus, silencing calcium waves in the auditory thalamus induces Rorβ upregulation in a neighbouring somatosensory nucleus preluding the enlargement of the barrel-field. These findings reveal that embryonic thalamic calcium waves coordinate cortical sensory area patterning and plasticity prior to sensory information processing.},
	Annote = {- evidence for thalamocortical inputs in regulating size of cortical areas through 
- evidence for prenatal thalamic waves is all from in vitro thalamic slice recordings in gcamp6 expression thalamic cell populations. In slice the wave travel between thalamic nuclei

quote: 
>Our finding that thalamic waves emerge before peripheral input reaches the thalamus (see also ref. 46) indicates that they might be intrinsically generated in this structure.

ref 46 is Pouchelon:2012 (Eur J Neurosci). However the referenced paper is a review of only somatosensory system axon growth. No information on functional innervation of thalamic nuclei by the brainstem. 

Confusingly, the next sentence in reference to their brain slice thalamic waves:  
>spontaneous calcium waves persist in the absence of retinal input, although their pattern and frequency is altered if no axons from this organ are received.

So peripheral input is functionally influencing the thalamus in their model then?
},
	Author = {Moreno-Juan, Ver{\'o}nica and Filipchuk, Anton and Ant{\'o}n-Bola{\~n}os, Noelia and Mezzera, Cecilia and Gezelius, Henrik and Andr{\'e}s, Belen and Rodr{\'\i}guez-Malmierca, Luis and Sus{\'\i}n, Rafael and Schaad, Olivier and Iwasato, Takuji and Sch{\"u}le, Roland and Rutlin, Michael and Nelson, Sacha and Ducret, Sebastien and Valdeolmillos, Miguel and Rijli, Filippo M and L{\'o}pez-Bendito, Guillermina},
	Date-Added = {2017-05-04 20:45:39 +0000},
	Date-Modified = {2018-01-25 01:19:19 +0000},
	Doi = {10.1038/ncomms14172},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Month = {Feb},
	Pages = {14172},
	Pmc = {PMC5296753},
	Pmid = {28155854},
	Pst = {epublish},
	Title = {Prenatal thalamic waves regulate cortical area size prior to sensory processing},
	Volume = {8},
	Year = {2017},
	File = {papers/Moreno-Juan_NatCommun2017.pdf}}

@article{Bray:1979,
	Abstract = {Evidence is presented that (a) the growth cone of cultured neurons can exert mechanical tension, and (b) that the direction of advance of the growth cone is determined by the tension existing between it and the rest of the cell. (a) The evidence that growth cones can pull comes from a vectorial analysis of the outlines of individually isolated sensory neurons. The angles formed in these outgrowths are very close to those of tension-generated networks anchored at their free ends and these values are restored shortly after an experimental displacement. The relative mechanical tension on each segment of an outgrowth can be calculated by standard methods and is found to decrease at each branch point. It appears to be correlated with the diameter of the fibre so that thicker fibres maintain more tension than thinner ones. (b) The influence of tension on the direction of advance of the growth cone is shown by 2 kinds of experient. If a growing neurite is pulled to one side with a microelectrode then the direction of its advance is changed immediately according to the new stress. If the mechanical tension on the growth cone of a neurite is released by amputation or displacement the growth cone is found to have a high probability of branching shortly afterwards. The ability of the growth cone to exert tension is discussed in relation to evidence that microspikes have contractile properties and in terms of the distribution of microfilaments within the neurite. It is suggested that the exertion of tension by a growth cone could serve to guide the neurite along paths of high adhesivity both in vitro and in vivo.},
	Author = {Bray, D},
	Date-Added = {2017-05-03 23:05:39 +0000},
	Date-Modified = {2017-05-03 23:05:39 +0000},
	Journal = {J Cell Sci},
	Journal-Full = {Journal of cell science},
	Mesh = {Animals; Cells, Cultured; Chickens; Microscopy, Electron, Scanning; Neurons; Stress, Mechanical},
	Month = {Jun},
	Pages = {391-410},
	Pmid = {479327},
	Pst = {ppublish},
	Title = {Mechanical tension produced by nerve cells in tissue culture},
	Volume = {37},
	Year = {1979},
	File = {papers/Bray_JCellSci1979.pdf}}

@article{Chklovskii:2004a,
	Abstract = {In mammalian visual cortex, neurons are organized according to their functional properties into multiple maps such as retinotopic, ocular dominance, orientation preference, direction of motion, and others. What determines the organization of cortical maps? We argue that cortical maps reflect neuronal connectivity in intracortical circuits. Because connecting distant neurons requires costly wiring (i.e., axons and dendrites), there is an evolutionary pressure to place connected neurons as close to each other as possible. Then, cortical maps may be viewed as solutions that minimize wiring cost for given intracortical connectivity. These solutions can help us in inferring intracortical connectivity and, ultimately, in understanding the function of the visual system.},
	Author = {Chklovskii, Dmitri B and Koulakov, Alexei A},
	Date-Added = {2017-05-02 18:52:58 +0000},
	Date-Modified = {2017-05-02 18:52:58 +0000},
	Doi = {10.1146/annurev.neuro.27.070203.144226},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Mesh = {Animals; Axons; Brain Mapping; Dendrites; Humans; Nerve Net; Neural Pathways; Visual Cortex; Visual Fields; Visual Pathways},
	Pages = {369-92},
	Pmid = {15217337},
	Pst = {ppublish},
	Title = {Maps in the brain: what can we learn from them?},
	Volume = {27},
	Year = {2004},
	File = {papers/Chklovskii_AnnuRevNeurosci2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.neuro.27.070203.144226}}

@article{Zalesky:2012,
	Abstract = {Numerous studies have demonstrated that brain networks derived from neuroimaging data have nontrivial topological features, such as small-world organization, modular structure and highly connected hubs. In these studies, the extent of connectivity between pairs of brain regions has often been measured using some form of statistical correlation. This article demonstrates that correlation as a measure of connectivity in and of itself gives rise to networks with non-random topological features. In particular, networks in which connectivity is measured using correlation are inherently more clustered than random networks, and as such are more likely to be small-world networks. Partial correlation as a measure of connectivity also gives rise to networks with non-random topological features. Partial correlation networks are inherently less clustered than random networks. Network measures in correlation networks should be benchmarked against null networks that respect the topological structure induced by correlation measurements. Prevalently used random rewiring algorithms do not yield appropriate null networks for some network measures. Null networks are proposed to explicitly normalize for the inherent topological structure found in correlation networks, resulting in more conservative estimates of small-world organization. A number of steps may be needed to normalize each network measure individually and control for distinct features (e.g. degree distribution). The main conclusion of this article is that correlation can and should be used to measure connectivity, however appropriate null networks should be used to benchmark network measures in correlation networks.},
	Author = {Zalesky, Andrew and Fornito, Alex and Bullmore, Ed},
	Date-Added = {2017-04-29 23:07:08 +0000},
	Date-Modified = {2017-04-29 23:07:08 +0000},
	Doi = {10.1016/j.neuroimage.2012.02.001},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Mesh = {Brain; Brain Mapping; Humans; Magnetic Resonance Imaging; Neural Pathways},
	Month = {May},
	Number = {4},
	Pages = {2096-106},
	Pmid = {22343126},
	Pst = {ppublish},
	Title = {On the use of correlation as a measure of network connectivity},
	Volume = {60},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2012.02.001}}

@article{Fornito:2012,
	Abstract = {Schizophrenia is frequently characterized as a disorder of brain connectivity. Neuroimaging has played a central role in supporting this view, with nearly two decades of research providing abundant evidence of structural and functional connectivity abnormalities in the disorder. In recent years, our understanding of how schizophrenia affects brain networks has been greatly advanced by attempts to map the complete set of inter-regional interactions comprising the brain's intricate web of connectivity; i.e., the human connectome. Imaging connectomics refers to the use of neuroimaging techniques to generate these maps which, combined with the application of graph theoretic methods, has enabled relatively comprehensive mapping of brain network connectivity and topology in unprecedented detail. Here, we review the application of these techniques to the study of schizophrenia, focusing principally on magnetic resonance imaging (MRI) research, while drawing attention to key methodological issues in the field. The published findings suggest that schizophrenia is associated with a widespread and possibly context-independent functional connectivity deficit, upon which are superimposed more circumscribed, context-dependent alterations associated with transient states of hyper- and/or hypo-connectivity. In some cases, these changes in inter-regional functional coupling dynamics can be related to measures of intra-regional dysfunction. Topological disturbances of functional brain networks in schizophrenia point to reduced local network connectivity and modular structure, as well as increased global integration and network robustness. Some, but not all, of these functional abnormalities appear to have an anatomical basis, though the relationship between the two is complex. By comprehensively mapping connectomic disturbances in patients with schizophrenia across the entire brain, this work has provided important insights into the highly distributed character of neural abnormalities in the disorder, and the potential functional consequences that these disturbances entail.},
	Author = {Fornito, Alex and Zalesky, Andrew and Pantelis, Christos and Bullmore, Edward T},
	Date-Added = {2017-04-29 23:06:44 +0000},
	Date-Modified = {2017-04-29 23:06:44 +0000},
	Doi = {10.1016/j.neuroimage.2011.12.090},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Mesh = {Brain Mapping; Connectome; Humans; Magnetic Resonance Imaging; Neural Pathways; Schizophrenia},
	Month = {Oct},
	Number = {4},
	Pages = {2296-314},
	Pmid = {22387165},
	Pst = {ppublish},
	Title = {Schizophrenia, neuroimaging and connectomics},
	Volume = {62},
	Year = {2012},
	File = {papers/Fornito_Neuroimage2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2011.12.090}}

@article{Chang:2017,
	Abstract = {Mirror self-recognition (MSR) is generally considered to be an intrinsic cognitive ability found only in humans and a few species of great apes. Rhesus monkeys do not spontaneously show MSR, but they have the ability to use a mirror as an instrument to find hidden objects. The mechanism underlying the transition from simple mirror use to MSR remains unclear. Here we show that rhesus monkeys could show MSR after learning precise visual-proprioceptive association for mirror images. We trained head-fixed monkeys on a chair in front of a mirror to touch with spatiotemporal precision a laser pointer light spot on an adjacent board that could only be seen in the mirror. After several weeks of training, when the same laser pointer light was projected to the monkey's face, a location not used in training, all three trained monkeys successfully touched the face area marked by the light spot in front of a mirror. All trained monkeys passed the standard face mark test for MSR both on the monkey chair and in their home cage. Importantly, distinct from untrained control monkeys, the trained monkeys showed typical mirror-induced self-directed behaviors in their home cage, such as using the mirror to explore normally unseen body parts. Thus, bodily self-consciousness may be a cognitive ability present in many more species than previously thought, and acquisition of precise visual-proprioceptive association for the images in the mirror is critical for revealing the MSR ability of the animal.},
	Author = {Chang, Liangtang and Zhang, Shikun and Poo, Mu-Ming and Gong, Neng},
	Date-Added = {2017-04-25 23:25:40 +0000},
	Date-Modified = {2017-04-25 23:25:40 +0000},
	Doi = {10.1073/pnas.1620764114},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {bodily self-consciousness; instrumental mirror use; mirror self-recognition; rhesus monkey; visual-proprioceptive association},
	Month = {Mar},
	Number = {12},
	Pages = {3258-3263},
	Pmc = {PMC5373394},
	Pmid = {28193875},
	Pst = {ppublish},
	Title = {Spontaneous expression of mirror self-recognition in monkeys after learning precise visual-proprioceptive association for mirror images},
	Volume = {114},
	Year = {2017},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1620764114}}

@article{Swartz:2017,
	Abstract = {Identifying biological mechanisms through which the experience of adversity emerges as individual risk for mental illness is an important step toward developing strategies for personalized treatment and, ultimately, prevention. Preclinical studies have identified epigenetic modification of gene expression as one such mechanism. Recent clinical studies have suggested that epigenetic modification, particularly methylation of gene regulatory regions, also acts to shape human brain function associated with risk for mental illness. However, it is not yet clear whether differential gene methylation as a function of adversity contributes to the emergence of individual risk for mental illness. Using prospective longitudinal epigenetic, neuroimaging and behavioral data from 132 adolescents, we demonstrate that changes in gene methylation associated with lower socioeconomic status (SES) predict changes in risk-related brain function. Specifically, we find that lower SES during adolescence is associated with an increase in methylation of the proximal promoter of the serotonin transporter gene, which predicts greater increases in threat-related amygdala reactivity. We subsequently demonstrate that greater increases in amygdala reactivity moderate the association between a positive family history for depression and the later manifestation of depressive symptoms. These initial results suggest a specific biological mechanism through which adversity contributes to altered brain function, which in turn moderates the emergence of general liability as individual risk for mental illness. If replicated, this prospective pathway may represent a novel target biomarker for intervention and prevention among high-risk individuals.},
	Author = {Swartz, J R and Hariri, A R and Williamson, D E},
	Date-Added = {2017-04-25 00:10:58 +0000},
	Date-Modified = {2017-04-25 00:10:58 +0000},
	Doi = {10.1038/mp.2016.82},
	Journal = {Mol Psychiatry},
	Journal-Full = {Molecular psychiatry},
	Month = {Feb},
	Number = {2},
	Pages = {209-214},
	Pmc = {PMC5122474},
	Pmid = {27217150},
	Pst = {ppublish},
	Title = {An epigenetic mechanism links socioeconomic status to changes in depression-related brain function in high-risk adolescents},
	Volume = {22},
	Year = {2017},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/mp.2016.82}}

@article{McGowan:2009,
	Abstract = {Maternal care influences hypothalamic-pituitary-adrenal (HPA) function in the rat through epigenetic programming of glucocorticoid receptor expression. In humans, childhood abuse alters HPA stress responses and increases the risk of suicide. We examined epigenetic differences in a neuron-specific glucocorticoid receptor (NR3C1) promoter between postmortem hippocampus obtained from suicide victims with a history of childhood abuse and those from either suicide victims with no childhood abuse or controls. We found decreased levels of glucocorticoid receptor mRNA, as well as mRNA transcripts bearing the glucocorticoid receptor 1F splice variant and increased cytosine methylation of an NR3C1 promoter. Patch-methylated NR3C1 promoter constructs that mimicked the methylation state in samples from abused suicide victims showed decreased NGFI-A transcription factor binding and NGFI-A-inducible gene transcription. These findings translate previous results from rat to humans and suggest a common effect of parental care on the epigenetic regulation of hippocampal glucocorticoid receptor expression.},
	Author = {McGowan, Patrick O and Sasaki, Aya and D'Alessio, Ana C and Dymov, Sergiy and Labont{\'e}, Benoit and Szyf, Moshe and Turecki, Gustavo and Meaney, Michael J},
	Date-Added = {2017-04-25 00:01:42 +0000},
	Date-Modified = {2017-04-25 00:01:42 +0000},
	Doi = {10.1038/nn.2270},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Adult; Adult Survivors of Child Abuse; Base Sequence; Cell Line; DNA Methylation; Epigenesis, Genetic; Female; Hippocampus; Humans; Male; Middle Aged; Molecular Sequence Data; Promoter Regions, Genetic; Receptors, Glucocorticoid; Suicide; Young Adult},
	Month = {Mar},
	Number = {3},
	Pages = {342-8},
	Pmc = {PMC2944040},
	Pmid = {19234457},
	Pst = {ppublish},
	Title = {Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse},
	Volume = {12},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.2270}}

@article{Costa:2010,
	Abstract = {The cortical column has been an invaluable concept to explain the functional organization of the neocortex. While this idea was born out of experiments that cleverly combined electrophysiological recordings with anatomy, no one has 'seen' the anatomy of a column. All we know is that when we record through the cortex of primates, ungulates, and carnivores in a trajectory perpendicular to its surface there is a remarkable constancy in the receptive field properties of the neurons regarding one set of stimulus features. There is no obvious morphological analog for this functional architecture, in fact much of the anatomical data seems to challenge it. Here we describe historically the origins of the concept of the cortical column and the struggles of the pioneers to define the columnar architecture. We suggest that in the concept of a 'canonical circuit' we may find the means to reconcile the structure of neocortex with its functional architecture. The canonical microcircuit respects the known connectivity of the neocortex, and it is flexible enough to change transiently the architecture of its network in order to perform the required computations.},
	Author = {da Costa, Nuno Ma{\c c}arico and Martin, Kevan A C},
	Date-Added = {2017-04-24 20:04:33 +0000},
	Date-Modified = {2017-04-24 20:04:33 +0000},
	Doi = {10.3389/fnana.2010.00016},
	Journal = {Front Neuroanat},
	Journal-Full = {Frontiers in neuroanatomy},
	Keywords = {Daisy; bouton cluster; canonical microcircuit; cortical column; neuroanatomy},
	Pages = {16},
	Pmc = {PMC2904586},
	Pmid = {20640245},
	Pst = {epublish},
	Title = {Whose Cortical Column Would that Be?},
	Volume = {4},
	Year = {2010},
	File = {papers/Costa_FrontNeuroanat2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fnana.2010.00016}}

@article{Fiebig:2017,
	Abstract = {A dominant theory of working memory (WM), referred to as the persistent activity hypothesis, holds that recurrently connected neural networks, presumably located in the prefrontal cortex, encode and maintain WM memory items through sustained elevated activity. Reexamination of experimental data has shown that prefrontal cortex activity in single units during delay periods is much more variable than predicted by such a theory and associated computational models. Alternative models of WM maintenance based on synaptic plasticity, such as short-term nonassociative (non-Hebbian) synaptic facilitation, have been suggested but cannot account for encoding of novel associations. Here we test the hypothesis that a recently identified fast-expressing form of Hebbian synaptic plasticity (associative short-term potentiation) is a possible mechanism for WM encoding and maintenance. Our simulations using a spiking neural network model of cortex reproduce a range of cognitive memory effects in the classical multi-item WM task of encoding and immediate free recall of word lists. Memory reactivation in the model occurs in discrete oscillatory bursts rather than as sustained activity. We relate dynamic network activity as well as key synaptic characteristics to electrophysiological measurements. Our findings support the hypothesis that fast Hebbian short-term potentiation is a key WM mechanism.
SIGNIFICANCE STATEMENT: Working memory (WM) is a key component of cognition. Hypotheses about the neural mechanism behind WM are currently under revision. Reflecting recent findings of fast Hebbian synaptic plasticity in cortex, we test whether a cortical spiking neural network model with such a mechanism can learn a multi-item WM task (word list learning). We show that our model can reproduce human cognitive phenomena and achieve comparable memory performance in both free and cued recall while being simultaneously compatible with experimental data on structure, connectivity, and neurophysiology of the underlying cortical tissue. These findings are directly relevant to the ongoing paradigm shift in the WM field.},
	Author = {Fiebig, Florian and Lansner, Anders},
	Date-Added = {2017-04-24 19:05:29 +0000},
	Date-Modified = {2017-04-24 19:05:29 +0000},
	Doi = {10.1523/JNEUROSCI.1989-16.2017},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Hebbian plasticity; primacy; recency; short-term potentiation; word list learning; working memory},
	Month = {Jan},
	Number = {1},
	Pages = {83-96},
	Pmc = {PMC5214637},
	Pmid = {28053032},
	Pst = {ppublish},
	Title = {A Spiking Working Memory Model Based on Hebbian Short-Term Potentiation},
	Volume = {37},
	Year = {2017},
	File = {papers/Fiebig_JNeurosci2017.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.1989-16.2017}}

@article{Ramaswamy:2015,
	Author = {Ramaswamy, Srikanth and Courcol, Jean-Denis and Abdellah, Marwan and Adaszewski, Stanislaw R and Antille, Nicolas and Arsever, Selim and Atenekeng, Guy and Bilgili, Ahmet and Brukau, Yury and Chalimourda, Athanassia and Chindemi, Giuseppe and Delalondre, Fabien and Dumusc, Raphael and Eilemann, Stefan and Gevaert, Michael Emiel and Gleeson, Padraig and Graham, Joe W and Hernando, Juan B and Kanari, Lida and Katkov, Yury and Keller, Daniel and King, James G and Ranjan, Rajnish and Reimann, Michael W and R{\"o}ssert, Christian and Shi, Ying and Shillcock, Julian C and Telefont, Martin and Van Geit, Werner and Diaz, Jafet Villafranca and Walker, Richard and Wang, Yun and Zaninetta, Stefano M and DeFelipe, Javier and Hill, Sean L and Muller, Jeffrey and Segev, Idan and Sch{\"u}rmann, Felix and Muller, Eilif B and Markram, Henry},
	Date-Added = {2017-04-24 18:39:12 +0000},
	Date-Modified = {2017-04-24 18:39:12 +0000},
	Doi = {10.3389/fncir.2015.00044},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {experimental data; ion channels; microcircuit; models; morphologies; neocortex; neurons; synapses},
	Mesh = {Animals; Cooperative Behavior; Information Systems; Neocortex; Rats; Somatosensory Cortex},
	Pages = {44},
	Pmc = {PMC4597797},
	Pmid = {26500503},
	Pst = {epublish},
	Title = {The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex},
	Volume = {9},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fncir.2015.00044}}

@article{Kaneko:2013,
	Abstract = {In spite of recent progress in brain sciences, the local circuit of the cerebral neocortex, including motor areas, still remains elusive. Morphological works on excitatory cortical circuitry from thalamocortical (TC) afferents to corticospinal neurons (CSNs) in motor-associated areas are reviewed here. First, TC axons of motor thalamic nuclei have been re-examined by the single-neuron labeling method. There are middle layer (ML)-targeting and layer (L) 1-preferring TC axon types in motor-associated areas, being analogous to core and matrix types, respectively, of Jones (1998) in sensory areas. However, the arborization of core-like motor TC axons spreads widely and disregards the columnar structure that is the basis of information processing in sensory areas, suggesting that motor areas adopt a different information-processing framework such as area-wide laminar organization. Second, L5 CSNs receive local excitatory inputs not only from L2/3 pyramidal neurons but also from ML spiny neurons, the latter directly processing cerebellar information of core-like TC neurons (TCNs). In contrast, basal ganglia information is targeted to apical dendrites of L2/3 and L5 pyramidal neurons through matrix TCNs. Third, L6 corticothalamic neurons (CTNs) are most densely innervated by ML spiny neurons located just above CTNs. Since CTNs receive only weak connections from L2/3 and L5 pyramidal neurons, the TC recurrent circuit composed of TCNs, ML spiny neurons and CTNs appears relatively independent of the results of processing in L2/3 and L5. It is proposed that two circuits sharing the same TC projection and ML neurons are embedded in the neocortex: one includes L2/3 and L5 neurons, processes afferent information in a feedforward way and sends the processed information to other cortical areas and subcortical regions; and the other circuit participates in a dynamical system of the TC recurrent circuit and may serve as the basis of autonomous activity of the neocortex.},
	Author = {Kaneko, Takeshi},
	Date-Added = {2017-04-24 18:31:01 +0000},
	Date-Modified = {2017-04-24 18:31:01 +0000},
	Doi = {10.3389/fncir.2013.00075},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {corticospinal projection neurons; corticothalamic projection neurons; excitatory connection; local circuit; microcircuit; motor cortex; pyramidal neurons; thalamocortical projection},
	Mesh = {Animals; Excitatory Postsynaptic Potentials; Humans; Motor Cortex; Nerve Net; Neural Pathways; Neurons; Rats},
	Pages = {75},
	Pmc = {PMC3664775},
	Pmid = {23754982},
	Pst = {epublish},
	Title = {Local connections of excitatory neurons in motor-associated cortical areas of the rat},
	Volume = {7},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fncir.2013.00075}}

@article{Zhang:2004d,
	Abstract = {Layer V pyramidal neurons in the rat medial prefrontal cortex (PFC) were examined with whole cell patch-clamp recording in acute slices from postnatal day 1 (P1) to P36. In the first few days after birth, layer V pyramidal neurons had low resting potentials, high-input resistance, and long membrane time constant. During the next 2 wk, the resting potential shifted by -14 mV, while the input resistance and time constant decreased by 15- and 4-fold, respectively. Between P3 and P21, the surface area of the cell body doubled, while the total lengths of apical and basal dendrites increased by 5- and 13-fold, respectively. Action potentials (APs) were observed at all aged tested. The peak amplitude of APs increased by 30 mV during the first 3 wk, while AP rise time and half-maximum duration shortened significantly. Compared with neurons at P21 or older, neurons in the first week required much smaller currents to reach their maximum firing frequencies, but the maximum frequencies were lower than those at older ages. Stimulation of layer II/III induced monosynaptic responses in neurons older than P5. Paired-pulse responses showed a short-term depression at P7, which shifted progressive to facilitation at older ages. These results demonstrate that, similar to other neurons in the brain, layer V pyramidal neurons in the PFC undergo a period of rapid development during the first 3 wk after birth. These findings suggest that the intrinsic properties of neurons and the properties of synaptic inputs develop concomitantly during early life.},
	Author = {Zhang, Zhong-wei},
	Date-Added = {2017-04-24 18:27:39 +0000},
	Date-Modified = {2017-04-24 18:27:39 +0000},
	Doi = {10.1152/jn.00855.2003},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Mesh = {Action Potentials; Aging; Animals; Dendrites; Electrophysiology; Female; Histocytochemistry; In Vitro Techniques; Lysine; Male; Membrane Potentials; Patch-Clamp Techniques; Prefrontal Cortex; Pyramidal Cells; Rats; Rats, Sprague-Dawley; Synapses},
	Month = {Mar},
	Number = {3},
	Pages = {1171-82},
	Pmid = {14602839},
	Pst = {ppublish},
	Title = {Maturation of layer V pyramidal neurons in the rat prefrontal cortex: intrinsic properties and synaptic function},
	Volume = {91},
	Year = {2004},
	File = {papers/Zhang_JNeurophysiol2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.00855.2003}}

@article{Sherman:2016,
	Abstract = {Several challenges to current views of thalamocortical processing are offered here. Glutamatergic pathways in thalamus and cortex are divided into two distinct classes: driver and modulator. We suggest that driver inputs are the main conduits of information and that modulator inputs modify how driver inputs are processed. Different driver sources reveal two types of thalamic relays: first order relays receive subcortical driver input (for example, retinal input to the lateral geniculate nucleus), whereas higher order relays (for example, pulvinar) receive driver input from layer 5 of cortex and participate in cortico-thalamo-cortical (or transthalamic) circuits. These transthalamic circuits represent an unappreciated aspect of cortical functioning, which I discuss here. Direct corticocortical connections are often paralleled by transthalamic ones. Furthermore, driver inputs to thalamus, both first and higher order, typically arrive via branching axons, and the transthalamic branch often innervates subcortical motor centers, leading to the suggestion that these inputs to thalamus serve as efference copies.},
	Author = {Sherman, S Murray},
	Date-Added = {2017-04-20 21:10:29 +0000},
	Date-Modified = {2017-04-20 21:10:29 +0000},
	Doi = {10.1038/nn.4269},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Animals; Cerebral Cortex; Glutamic Acid; Humans; Nerve Net; Neural Pathways; Thalamus},
	Month = {Apr},
	Number = {4},
	Pages = {533-41},
	Pmid = {27021938},
	Pst = {ppublish},
	Title = {Thalamus plays a central role in ongoing cortical functioning},
	Volume = {19},
	Year = {2016},
	File = {papers/Sherman_NatNeurosci2016.pdf}}

@article{Allen:2016,
	Abstract = {KEY POINTS: The lateral posterior and posterior thalamic nuclei have been implicated in aspects of visually guided behaviour and reflex responses to light, including those dependent on melanopsin photoreception. Here we investigated the extent and basic properties of visually evoked activity across the mouse lateral posterior and posterior thalamus. We show that a subset of retinal projections to these regions derive from melanopsin-expressing retinal ganglion cells and find many cells that exhibit melanopsin-dependent changes in firing. We also show that subsets of cells across these regions integrate signals from both eyes in various ways and that, within the lateral posterior thalamus, visual responses are retinotopically ordered.
ABSTRACT: In addition to the primary thalamocortical visual relay in the lateral geniculate nuclei, a number of other thalamic regions contribute to aspects of visual processing. Thus, the lateral posterior thalamic nuclei (LP/pulvinar) appear important for various functions including determining visual saliency, visually guided behaviours and, alongside dorsal portions of the posterior thalamic nuclei (Po), multisensory processing of information related to aversive stimuli. However, despite the growing importance of mice as a model for understanding visual system organisation, at present we know very little about the basic visual response properties of cells in the mouse LP or Po. Prompted by earlier suggestions that melanopsin photoreception might be important for certain functions of these nuclei, we first employ specific viral tracing to show that a subset of retinal projections to the LP derive from melanopsin-expressing retinal ganglion cells. We next use multielectrode electrophysiology to demonstrate that LP and dorsal Po cells exhibit a variety of responses to simple visual stimuli including two distinct classes that express melanopsin-dependent changes in firing (together comprising ∼25% of neurons we recorded). We also show that subgroups of LP/Po cells integrate signals from both eyes in various ways and that, within the LP, visual responses are retinotopically ordered. Together our data reveal a diverse population of visually responsive neurons across the LP and dorsal Po whose properties align with some of the established functions of these nuclei and suggest new possible routes through which melanopsin photoreception could contribute to reflex light responses and/or higher order visual processing.},
	Author = {Allen, Annette E and Procyk, Christopher A and Howarth, Michael and Walmsley, Lauren and Brown, Timothy M},
	Date-Added = {2017-04-20 21:02:16 +0000},
	Date-Modified = {2017-04-20 21:02:16 +0000},
	Doi = {10.1113/JP271707},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Animals; Evoked Potentials, Visual; Lateral Thalamic Nuclei; Mice; Mice, Inbred C57BL; Posterior Thalamic Nuclei; Retinal Ganglion Cells; Rod Opsins; Visual Pathways},
	Month = {Apr},
	Number = {7},
	Pages = {1911-29},
	Pmc = {PMC4818601},
	Pmid = {26842995},
	Pst = {ppublish},
	Title = {Visual input to the mouse lateral posterior and posterior thalamic nuclei: photoreceptive origins and retinotopic order},
	Volume = {594},
	Year = {2016},
	File = {papers/Allen_JPhysiol2016.pdf}}

@article{Warner:2015,
	Abstract = {BACKGROUND: Conscious vision is believed to depend upon an intact primary visual cortex (V1), although injury in early life is often accompanied by the preservation of visual capacity, unlike in adulthood. The middle temporal area (MT) receives input from the retinorecipient koniocellular layers of the lateral geniculate nucleus (LGN) and the more recently described medial subdivision of the inferior pulvinar (PIm) of the thalamus, pathways that potentially contribute to preservation of vision after early damage to V1.
RESULTS: We examined the potential of these pathways to the long-term preservation of vision after permanent lesions of primate V1 in early and adult life by using a combination of neural tracing and diffusion MRI. We show that early-life V1 lesions lead to less pruning of the retina-pulvinar-MT pathway than is observed in control or adult lesion animals.
CONCLUSIONS: These findings suggest that sustained visual input through the pulvinar to MT following a lesion of V1 in early life has the capacity to afford improved visual outcomes.},
	Author = {Warner, Claire E and Kwan, William C and Wright, David and Johnston, Leigh A and Egan, Gary F and Bourne, James A},
	Date-Added = {2017-04-20 20:54:32 +0000},
	Date-Modified = {2017-04-20 20:54:32 +0000},
	Doi = {10.1016/j.cub.2014.12.028},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Mesh = {Age Factors; Animals; Callithrix; Diffusion Magnetic Resonance Imaging; Female; Male; Neuroanatomical Tract-Tracing Techniques; Pulvinar; Vision, Ocular; Visual Cortex; Visual Pathways},
	Month = {Feb},
	Number = {4},
	Pages = {424-34},
	Pmid = {25601551},
	Pst = {ppublish},
	Title = {Preservation of vision by the pulvinar following early-life primary visual cortex lesions},
	Volume = {25},
	Year = {2015},
	File = {papers/Warner_CurrBiol2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2014.12.028}}

@article{Spitzer:2015,
	Abstract = {Among the many forms of brain plasticity, changes in synaptic strength and changes in synapse number are particularly prominent. However, evidence for neurotransmitter respecification or switching has been accumulating steadily, both in the developing nervous system and in the adult brain, with observations of transmitter addition, loss, or replacement of one transmitter with another. Natural stimuli can drive these changes in transmitter identity, with matching changes in postsynaptic transmitter receptors. Strikingly, they often convert the synapse from excitatory to inhibitory or vice versa, providing a basis for changes in behavior in those cases in which it has been examined. Progress has been made in identifying the factors that induce transmitter switching and in understanding the molecular mechanisms by which it is achieved. There are many intriguing questions to be addressed.},
	Author = {Spitzer, Nicholas C},
	Date-Added = {2017-04-19 19:20:51 +0000},
	Date-Modified = {2017-04-19 19:20:51 +0000},
	Doi = {10.1016/j.neuron.2015.05.028},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Brain; Humans; Neuronal Plasticity; Neurons; Neurotransmitter Agents; Synapses; Synaptic Potentials},
	Month = {Jun},
	Number = {5},
	Pages = {1131-44},
	Pmc = {PMC4458710},
	Pmid = {26050033},
	Pst = {ppublish},
	Title = {Neurotransmitter Switching? No Surprise},
	Volume = {86},
	Year = {2015},
	File = {papers/Spitzer_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.05.028}}

@article{Guemez-Gamboa:2014,
	Abstract = {Activity-dependent neurotransmitter switching engages genetic programs regulating transmitter synthesis, but the mechanism by which activity is transduced is unknown. We suppressed activity in single neurons in the embryonic spinal cord to determine whether glutamate-gamma-aminobutyric acid (GABA) switching is cell autonomous. Transmitter respecification did not occur, suggesting that it is homeostatically regulated by the level of activity in surrounding neurons. Graded increase in the number of silenced neurons in cultures led to graded decrease in the number of neurons expressing GABA, supporting non-cell-autonomous transmitter switching. We found that brain-derived neurotrophic factor (BDNF) is expressed in the spinal cord during the period of transmitter respecification and that spike activity causes release of BDNF. Activation of TrkB receptors triggers a signaling cascade involving JNK-mediated activation of cJun that regulates tlx3, a glutamate/GABA selector gene, accounting for calcium-spike BDNF-dependent transmitter switching. Our findings identify a molecular mechanism for activity-dependent respecification of neurotransmitter phenotype in developing spinal neurons.},
	Author = {Guemez-Gamboa, Alicia and Xu, Lin and Meng, Da and Spitzer, Nicholas C},
	Date-Added = {2017-04-19 19:20:49 +0000},
	Date-Modified = {2017-04-19 19:20:49 +0000},
	Doi = {10.1016/j.neuron.2014.04.029},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Brain-Derived Neurotrophic Factor; Calcium; Cells, Cultured; Female; Glutamic Acid; JNK Mitogen-Activated Protein Kinases; Neurons; Phosphorylation; Proto-Oncogene Proteins c-jun; Signal Transduction; Spinal Cord; Xenopus laevis; gamma-Aminobutyric Acid},
	Month = {Jun},
	Number = {5},
	Pages = {1004-16},
	Pmc = {PMC4072120},
	Pmid = {24908484},
	Pst = {ppublish},
	Title = {Non-cell-autonomous mechanism of activity-dependent neurotransmitter switching},
	Volume = {82},
	Year = {2014},
	File = {papers/Guemez-Gamboa_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.04.029}}

@article{Devor:2013,
	Abstract = {The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative has focused scientific attention on the necessary tools to understand the human brain and mind. Here, we outline our collective vision for what we can achieve within a decade with properly targeted efforts and discuss likely technological deliverables and neuroscience progress.},
	Author = {Devor, Anna and Bandettini, Peter A and Boas, David A and Bower, James M and Buxton, Richard B and Cohen, Lawrence B and Dale, Anders M and Einevoll, Gaute T and Fox, Peter T and Franceschini, Maria Angela and Friston, Karl J and Fujimoto, James G and Geyer, Mark A and Greenberg, Joel H and Halgren, Eric and H{\"a}m{\"a}l{\"a}inen, Matti S and Helmchen, Fritjof and Hyman, Bradley T and Jasanoff, Alan and Jernigan, Terry L and Judd, Lewis L and Kim, Seong-Gi and Kleinfeld, David and Kopell, Nancy J and Kutas, Marta and Kwong, Kenneth K and Larkum, Matthew E and Lo, Eng H and Magistretti, Pierre J and Mandeville, Joseph B and Masliah, Eliezer and Mitra, Partha P and Mobley, William C and Moskowitz, Michael A and Nimmerjahn, Axel and Reynolds, John H and Rosen, Bruce R and Salzberg, Brian M and Schaffer, Chris B and Silva, Gabriel A and So, Peter T C and Spitzer, Nicholas C and Tootell, Roger B and Van Essen, David C and Vanduffel, Wim and Vinogradov, Sergei A and Wald, Lawrence L and Wang, Lihong V and Weber, Bruno and Yodh, Arjun G},
	Date-Added = {2017-04-19 19:20:48 +0000},
	Date-Modified = {2017-04-19 19:20:48 +0000},
	Doi = {10.1016/j.neuron.2013.09.008},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Biomedical Research; Brain Mapping; Humans; Neurosciences},
	Month = {Oct},
	Number = {2},
	Pages = {270-4},
	Pmc = {PMC3864648},
	Pmid = {24139032},
	Pst = {ppublish},
	Title = {The challenge of connecting the dots in the B.R.A.I.N},
	Volume = {80},
	Year = {2013},
	File = {papers/Devor_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.09.008}}

@article{Demarque:2010,
	Abstract = {Genetic programs, environmental factors, and electrical activity interact to drive the maturation of the brain. Although the cascade of transcription factors that leads to specification of the serotonergic phenotype has been well characterized, its interactions with electrical activity are not known. Here we show that spontaneous calcium spike activity in the hindbrain of developing Xenopus laevis larvae modulates the specification of serotonergic neurons via regulation of expression of the Lmx1b transcription factor. Activity acts downstream of Nkx2.2 but upstream of Lmx1b, leading to regulation of the serotonergic phenotype. Using global manipulation of activity and targeted alteration of Lmx1b expression, we also demonstrate that changes in the number of serotonergic neurons change larval swimming behavior. The results link activity-dependent regulation of a transcription factor to transmitter specification and altered behavior.},
	Author = {Demarque, Micha{\"e}l and Spitzer, Nicholas C},
	Date-Added = {2017-04-19 19:20:45 +0000},
	Date-Modified = {2017-04-19 19:20:45 +0000},
	Doi = {10.1016/j.neuron.2010.06.006},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Animals; Behavior, Animal; Bromodeoxyuridine; Calcium; Electroporation; Embryo, Nonmammalian; Gene Expression Regulation, Developmental; Green Fluorescent Proteins; Homeodomain Proteins; Membrane Potentials; Neurons; Otx Transcription Factors; Potassium Channels, Inwardly Rectifying; RNA, Messenger; Raphe Nuclei; Serotonin; Sodium Channels; Statistics, Nonparametric; Swimming; Transcription Factors; Tryptophan Hydroxylase; Xenopus Proteins; Xenopus laevis; gamma-Aminobutyric Acid},
	Month = {Jul},
	Number = {2},
	Pages = {321-34},
	Pmc = {PMC2913149},
	Pmid = {20670838},
	Pst = {ppublish},
	Title = {Activity-dependent expression of Lmx1b regulates specification of serotonergic neurons modulating swimming behavior},
	Volume = {67},
	Year = {2010},
	File = {papers/Demarque_Neuron2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2010.06.006}}

@article{Desarmenien:1991,
	Abstract = {The delayed rectifier current of embryonic Xenopus spinal neurons plays the central role in developmental conversion of calcium-dependent action potentials to sodium-dependent spikes. During its maturation, this potassium current undergoes a pronounced increase in rate of activation. The mechanism underlying the change in kinetics was analyzed with whole-cell voltage clamp of neurons cultured under various conditions. Calcium is necessary at an early stage of development, to permit influx that triggers subsequent release of calcium from intracellular stores. Its action is prevented by depletion of protein kinase C and mimicked by stimulation of the kinase. Calcium influx through voltage-dependent channels at early stages of development regulates the differentiation of potassium current kinetics and modulation of the ionic dependence of action potentials.},
	Author = {Desarmenien, M G and Spitzer, N C},
	Date-Added = {2017-04-19 19:20:43 +0000},
	Date-Modified = {2017-04-19 19:20:43 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Calcium; Cell Aging; Chlorides; Electric Conductivity; Neurons; Potassium; Protein Kinase C; Sodium; Spinal Cord; Xenopus},
	Month = {Nov},
	Number = {5},
	Pages = {797-805},
	Pmid = {1742026},
	Pst = {ppublish},
	Title = {Role of calcium and protein kinase C in development of the delayed rectifier potassium current in Xenopus spinal neurons},
	Volume = {7},
	Year = {1991}}

@article{Pattabiraman:2014,
	Abstract = {Elucidating the genetic control of cerebral cortical (pallial) development is essential for understanding function, evolution, and disorders of the brain. Transcription factors (TFs) that embryonically regulate pallial regionalization are expressed in gradients, raising the question of how discrete domains are generated. We provide evidence that small enhancer elements active in protodomains integrate broad transcriptional information. CreER(T2) and GFP expression from 14 different enhancer elements in stable transgenic mice allowed us to define a comprehensive regional fate map of the pallium. We explored transcriptional mechanisms that control the activity of the enhancers using informatics, in vivo occupancy by TFs that regulate cortical patterning (CoupTFI, Pax6, and Pbx1), and analysis of enhancer activity in Pax6 mutants. Overall, the results provide insights into how broadly expressed patterning TFs regulate the activity of small enhancer elements that drive gene expression in pallial protodomains that fate map to distinct cortical regions.},
	Author = {Pattabiraman, Kartik and Golonzhka, Olga and Lindtner, Susan and Nord, Alex S and Taher, Leila and Hoch, Renee and Silberberg, Shanni N and Zhang, Dongji and Chen, Bin and Zeng, HongKui and Pennacchio, Len A and Puelles, Luis and Visel, Axel and Rubenstein, John L R},
	Date-Added = {2017-04-19 19:16:56 +0000},
	Date-Modified = {2017-04-19 19:16:56 +0000},
	Doi = {10.1016/j.neuron.2014.04.014},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Binding Sites; COUP Transcription Factor I; Cerebral Cortex; Enhancer Elements, Genetic; Eye Proteins; Gene Expression Regulation, Developmental; Hippocampus; Homeodomain Proteins; Humans; Mice; Mice, Transgenic; PAX6 Transcription Factor; Paired Box Transcription Factors; Repressor Proteins; Transcription Factors; Transcription, Genetic},
	Month = {Jun},
	Number = {5},
	Pages = {989-1003},
	Pmc = {PMC4104757},
	Pmid = {24814534},
	Pst = {ppublish},
	Title = {Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex},
	Volume = {82},
	Year = {2014},
	File = {papers/Pattabiraman_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.04.014}}

@article{Eckler:2015,
	Abstract = {We recently published genetic lineage-tracing experiments using the Fezf2 and Cux2 loci. These experiments demonstrated that at both the clonal and population levels Fezf2(+) RGCs are multipotent and that at the population level Cux2(+) RGCs are multipotent. Here, we extend our work on the lineages of Fezf2(+) and Cux2(+) RGCs. Clonal analysis of E10.5 neocortical progenitors suggests that most, if not all, Cux2(+) and Fezf2(+) RGCs generate diverse projection neuron subtypes located throughout layers 2-6. These results support our previous conclusion that both Fezf2(+) and Cux2(+) RGCs are multipotent neocortical progenitors. This Matters Arising Response paper addresses the Gil-Sanz et al. (2015) Matters Arising paper, published concurrently in Neuron.},
	Author = {Eckler, Matthew J and Nguyen, Ton D and McKenna, William L and Fastow, Ben L and Guo, Chao and Rubenstein, John L R and Chen, Bin},
	Date-Added = {2017-04-19 19:16:13 +0000},
	Date-Modified = {2017-04-19 19:16:13 +0000},
	Doi = {10.1016/j.neuron.2015.04.020},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Cell Lineage; Gene Expression Regulation, Developmental; Homeodomain Proteins; Multipotent Stem Cells; Neocortex; Nerve Tissue Proteins; Neurogenesis; Neurons; Oligodendroglia},
	Month = {May},
	Number = {4},
	Pages = {1100-8},
	Pmc = {PMC4441766},
	Pmid = {25996137},
	Pst = {ppublish},
	Title = {Cux2-positive radial glial cells generate diverse subtypes of neocortical projection neurons and macroglia},
	Volume = {86},
	Year = {2015},
	File = {papers/Eckler_Neuron2015.pdf},
	Bdsk-File-2 = {papers/Eckler_Neuron2015a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.04.020}}

@article{Thompson:2009,
	Abstract = {The effects of prenatal exposure to drugs on brain development are complex and are modulated by the timing, dose and route of drug exposure. It is difficult to assess these effects in clinical cohorts as these are beset with problems such as multiple exposures and difficulties in documenting use patterns. This can lead to misinterpretation of research findings by the general public, the media and policy makers, who may mistakenly assume that the legal status of a drug correlates with its biological impact on fetal brain development and long-term clinical outcomes. It is important to close the gap between what science tells us about the impact of prenatal drug exposure on the fetus and the mother and what we do programmatically with regard to at-risk populations.},
	Author = {Thompson, Barbara L and Levitt, Pat and Stanwood, Gregg D},
	Date-Added = {2017-04-19 18:27:12 +0000},
	Date-Modified = {2017-04-19 18:27:12 +0000},
	Doi = {10.1038/nrn2598},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Alcohols; Amphetamine; Antidepressive Agents; Brain; Child; Crack Cocaine; Drug-Related Side Effects and Adverse Reactions; Female; Humans; Maternal-Fetal Exchange; Methamphetamine; Nicotine; Pregnancy; Pregnancy Complications; Prenatal Exposure Delayed Effects; Substance-Related Disorders},
	Month = {Apr},
	Number = {4},
	Pages = {303-12},
	Pmc = {PMC2777887},
	Pmid = {19277053},
	Pst = {ppublish},
	Title = {Prenatal exposure to drugs: effects on brain development and implications for policy and education},
	Volume = {10},
	Year = {2009},
	File = {papers/Thompson_NatRevNeurosci2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2598}}

@article{Holmes:2001,
	Abstract = {BACKGROUND: The frequency of major malformations, growth retardation, and hypoplasia of the midface and fingers, known as the anticonvulsant embryopathy, is increased in infants exposed to anticonvulsant drugs in utero. However, whether the abnormalities are caused by the maternal epilepsy itself or by exposure to anticonvulsant drugs is not known.
METHODS: We screened 128,049 pregnant women at delivery to identify three groups of infants: those exposed to anticonvulsant drugs, those unexposed to anticonvulsant drugs but with a maternal history of seizures, and those unexposed to anticonvulsant drugs with no maternal history of seizures (control group). The infants were examined systematically for the presence of major malformations, signs of hypoplasia of the midface and fingers, microcephaly, and small body size.
RESULTS: The combined frequency of anticonvulsant embryopathy was higher in 223 infants exposed to one anticonvulsant drug than in 508 control infants (20.6 percent vs. 8.5 percent; odds ratio, 2.8; 95 percent confidence interval, 1.1 to 9.7). The frequency was also higher in 93 infants exposed to two or more anticonvulsant drugs than in the controls (28.0 percent vs. 8.5 percent; odds ratio, 4.2; 95 percent confidence interval, 1.1 to 5.1). The 98 infants whose mothers had a history of epilepsy but took no anticonvulsant drugs during the pregnancy did not have a higher frequency of those abnormalities than the control infants.
CONCLUSIONS: A distinctive pattern of physical abnormalities in infants of mothers with epilepsy is associated with the use of anticonvulsant drugs during pregnancy, rather than with epilepsy itself.},
	Author = {Holmes, L B and Harvey, E A and Coull, B A and Huntington, K B and Khoshbin, S and Hayes, A M and Ryan, L M},
	Date-Added = {2017-04-19 18:26:24 +0000},
	Date-Modified = {2017-04-19 18:26:24 +0000},
	Doi = {10.1056/NEJM200104123441504},
	Journal = {N Engl J Med},
	Journal-Full = {The New England journal of medicine},
	Mesh = {Abnormalities, Drug-Induced; Anticonvulsants; Carbamazepine; Case-Control Studies; Congenital Abnormalities; Epilepsy; Face; Female; Fetal Growth Retardation; Fingers; Humans; Infant, Newborn; Logistic Models; Phenobarbital; Phenytoin; Pregnancy; Pregnancy Complications; Valproic Acid},
	Month = {Apr},
	Number = {15},
	Pages = {1132-8},
	Pmid = {11297704},
	Pst = {ppublish},
	Title = {The teratogenicity of anticonvulsant drugs},
	Volume = {344},
	Year = {2001},
	Bdsk-Url-1 = {http://dx.doi.org/10.1056/NEJM200104123441504}}

@article{Manent:2007,
	Abstract = {PURPOSE: The management of epilepsy during pregnancy entails a number of concerns. While seizures may affect adversely maternal and fetal outcome, antiepileptic drugs (AEDs) may increase the incidence of congenital abnormalities and possibly affect postnatal cognitive development in the offspring. Experimental animal studies can aid in assessing teratogenic features associated with individual AEDs and/or with seizures, and to identify the mechanisms involved. The purpose of this study was to investigate the consequences of prenatal exposure to (a) different AEDs and (b) maternal seizures on brain maturational processes in rats.
METHODS: Pregnant rats received from embryonic days 14 to 19 intraperitoneal injections of carbamazepine (20 mg/kg/day), vigabatrin (200 mgkg/day), and valproate (100 mg/kg/day) at doses not widely different from those used clinically. Pups exposed to AEDs in utero were analyzed postnatally. Animals born to "kindled" pregnant animals that had experienced one generalized convulsive seizure per day during the same gestational period were analyzed in parallel.
RESULTS: Prenatal exposure to vigabatrin and valproate, which act on GABA signaling, induced hippocampal and cortical dysplasias, which were likely to result from a neuronal migration defect and neuronal death. By contrast, offspring of rats exposed to carbamazepine (which at the dose used produced low plasma concentrations) or to generalized convulsive seizures showed no clear-cut evidence of dysplasias.
CONCLUSIONS: We suggest that AEDs that increase the extracellular concentration of GABA might induce severe neuronal migration disorders. Drugs acting through other molecular targets would also perturb cortical maturation. The potential clinical relevance of these results should be a subject of future research.},
	Author = {Manent, Jean-Bernard and Jorquera, Isabel and Mazzucchelli, Iolanda and Depaulis, Antoine and Perucca, Emilio and Ben-Ari, Yehezkel and Represa, Alfonso},
	Date-Added = {2017-04-19 18:22:58 +0000},
	Date-Modified = {2017-04-19 18:22:58 +0000},
	Doi = {10.1111/j.1528-1167.2007.01056.x},
	Journal = {Epilepsia},
	Journal-Full = {Epilepsia},
	Mesh = {Abnormalities, Drug-Induced; Animals; Anticonvulsants; Carbamazepine; Cerebral Cortex; Female; Fetus; GABA Agents; Hippocampus; Kindling, Neurologic; Maternal-Fetal Exchange; Pregnancy; Pregnancy Complications; Rats; Seizures; Valproic Acid; Vigabatrin; gamma-Aminobutyric Acid},
	Month = {Apr},
	Number = {4},
	Pages = {684-93},
	Pmid = {17437411},
	Pst = {ppublish},
	Title = {Fetal exposure to GABA-acting antiepileptic drugs generates hippocampal and cortical dysplasias},
	Volume = {48},
	Year = {2007},
	File = {papers/Manent_Epilepsia2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1528-1167.2007.01056.x}}

@article{Ballesteros-Yanez:2010,
	Abstract = {The neuronal nicotinic acetylcholine receptors (nAChRs) are allosteric membrane proteins involved in multiple cognitive processes, including attention, learning, and memory. The most abundant form of heterooligomeric nAChRs in the brain contains the beta2- and alpha4- subunits and binds nicotinic agonists with high affinity. In the present study, we investigated in the mouse the consequences of the deletion of one of the nAChR components: the beta2-subunit (beta2(-/-)) on the microanatomy of cortical pyramidal cells. Using an intracellular injection method, complete basal dendritic arbors of 650 layer III pyramidal neurons were sampled from seven cortical fields, including primary sensory, motor, and associational areas, in both beta2(-/-) and WT animals. We observed that the pyramidal cell phenotype shows significant quantitative differences among different cortical areas in mutant and WT mice. In WT mice, the density of dendritic spines was rather similar in all cortical fields, except in the prelimbic/infralimbic cortex, where it was significantly higher. In the absence of the beta2-subunit, the most significant reduction in the density of spines took place in this high-order associational field. Our data suggest that the beta2-subunit is involved in the dendritic morphogenesis of pyramidal neurons and, in particular, in the circuits that contribute to the high-order functional connectivity of the cerebral cortex.},
	Author = {Ballesteros-Y{\'a}{\~n}ez, Inmaculada and Benavides-Piccione, Ruth and Bourgeois, Jean-Pierre and Changeux, Jean-Pierre and DeFelipe, Javier},
	Date-Added = {2017-04-18 20:27:46 +0000},
	Date-Modified = {2017-04-18 20:27:46 +0000},
	Doi = {10.1073/pnas.1006269107},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Cerebral Cortex; Dendrites; Dendritic Cells; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Models, Biological; Mutation; Neurons; Phenotype; Pyramidal Cells; Receptors, Nicotinic},
	Month = {Jun},
	Number = {25},
	Pages = {11567-72},
	Pmc = {PMC2895077},
	Pmid = {20534523},
	Pst = {ppublish},
	Title = {Alterations of cortical pyramidal neurons in mice lacking high-affinity nicotinic receptors},
	Volume = {107},
	Year = {2010},
	File = {papers/Ballesteros-Yáñez_ProcNatlAcadSciUSA2010.pdf}}

@article{Ichinohe:2012,
	Abstract = {Structures associated with the small-scale module called "minicolumn" can be observed frequently in the cerebral cortex. However, the description of functional characteristics remains obscure. A significant confounding factor is the marked variability both in the definition of a minicolumn and in the diagnostic markers for identifying a minicolumn (see for review, Jones, 2000; DeFelipe et al., 2002; Rockland and Ichinohe, 2004). Within a minicolumn, cell columns are easily visualized by conventional Nissl staining. Dendritic bundles were first discovered with Golgi methods, but are more easily seen with microtubule-associated protein 2 immunohistochemistry. Myelinated axon bundles can be seen by Tau immunohistochemistry or myelin staining. Axon bundles of double bouquet cell can be seen by calbindin immunohistochemistry. The spatial interrelationship among these morphological elements is more complex than expected and is neither clear nor unanimously agreed upon. In this review, I would like to focus first on the minicolumnar structure found in layers 1 and 2 of the rat granular retrosplenial cortex. This modular structure was first discovered as a combination of prominent apical dendritic bundles from layer 2 pyramidal neurons and spatially matched thalamocortical patchy inputs (Wyss et al., 1990). Further examination showed more intricate components of this modular structure, which will be reviewed in this paper. Second, the postnatal development of this structure and potential molecular players for its formation will be reviewed. Thirdly, I will discuss how this modular organization is transformed in mutant rodents with a disorganized layer structure in the cerebral cortex (i.e., reeler mouse and shaking rat Kawasaki). Lastly, the potential significance of this type of module will be discussed.},
	Author = {Ichinohe, Noritaka},
	Date-Added = {2017-04-18 20:17:18 +0000},
	Date-Modified = {2017-04-18 20:17:18 +0000},
	Doi = {10.3389/fnana.2011.00069},
	Journal = {Front Neuroanat},
	Journal-Full = {Frontiers in neuroanatomy},
	Keywords = {cortical modular organization; corticocortical; dendritic bundle; input and recipient matching; thalamocortical},
	Pages = {69},
	Pmc = {PMC3254062},
	Pmid = {22275884},
	Pst = {epublish},
	Title = {Small-scale module of the rat granular retrosplenial cortex: an example of the minicolumn-like structure of the cerebral cortex},
	Volume = {5},
	Year = {2012},
	File = {papers/Ichinohe_FrontNeuroanat2012.pdf}}

@article{Murakami:2015,
	Abstract = {Due to recent advances of genetic manipulation, mouse brain has become a useful model for studying brain function, which demands whole brain functional mapping techniques in the mouse brain. In the present study, to finely map visual responsive areas in the mouse brain, we combined high-resolution wide-field optical imaging with transgenic mice containing the genetically encoded Ca(2+) indicator, GCaMP3. With the high signal amplitude of GCaMP3 expressing in excitatory neurons, this system allowed neural activity to be observed with relatively fine spatial resolution and cell-type specificity. To evaluate this system, we examined whether non-visual areas exhibited a visual response over the entire surface of the mouse hemisphere. We found that two association areas, the retrosplenial area (RS) and secondary motor/anterior cingulate area (M2/AC), were significantly responsive to drifting gratings. Examination using gratings with distinct spatiotemporal frequency parameters revealed that the RS strongly responded to high-spatial and low-temporal frequency gratings. The M2/AC exhibited a response property similar to that of the RS, though it was not statistically significant. Finally, we performed cellular imaging using two-photon microscopy to examine orientation and direction selectivity of individual neurons, and found that a minority of neurons in the RS clearly showed visual responses sharply selective for orientation and direction. These results suggest that neurons in RS encode visual information of fine spatial details in images. Thus, the present study shows the usefulness of the functional mapping method using a combination of wide-field and two-photon Ca(2+) imaging, which allows for whole brain mapping with high spatiotemporal resolution and cell-type specificity.},
	Author = {Murakami, Tomonari and Yoshida, Takashi and Matsui, Teppei and Ohki, Kenichi},
	Date-Added = {2017-04-18 20:16:45 +0000},
	Date-Modified = {2017-04-18 20:16:45 +0000},
	Doi = {10.3389/fnmol.2015.00020},
	Journal = {Front Mol Neurosci},
	Journal-Full = {Frontiers in molecular neuroscience},
	Keywords = {GCaMP3; retrosplenial area; transgenic mouse; visual response; wide-field Ca2+ imaging},
	Pages = {20},
	Pmc = {PMC4458613},
	Pmid = {26106292},
	Pst = {epublish},
	Title = {Wide-field Ca(2+) imaging reveals visually evoked activity in the retrosplenial area},
	Volume = {8},
	Year = {2015},
	File = {papers/Murakami_FrontMolNeurosci2015.pdf}}

@article{Donoghue:1988,
	Abstract = {Somatotopic representation patterns in the motor cortex (MI) of rats that had a unilateral forelimb amputation on the first postnatal day were examined after 2-4 months of survival. Intracortical electrical stimulation and recording techniques were used to map the somatic representation in MI and in the somatic sensory cortex (SI). In normal rats, vibrissa, forelimb, and hindlimb areas comprise the bulk of the MI representation. Stimulation within the forelimb area elicits elbow, wrist, or digit movements at the lowest current intensities. The proximal limb representation appears to be contained within the distal forelimb area, since shoulder movements are nearly always evoked by stimulating at higher current intensities at some distal forelimb sites. In agreement with previous studies, the distal forelimb representation overlapped the adjacent part of the granular SI cortex. Following removal of the forelimb at birth, 3 novel features of MI organization were observed. First, the areas from which stimulation evoked movements of the vibrissa or the shoulder musculature were larger than normal. Stimulation thresholds were lower than those required for comparable movements in normal rats throughout these areas, suggesting that nerve section had not simply unmasked a high-threshold representation. Second, vibrissa movements were more commonly paired with movements of the proximal forelimb muscles at the same site. Third, stimulation in the adjacent granular SI cortex failed to evoke shoulder or trunk movements, although receptive-field mapping in this region showed that cells were responsive to cutaneous stimulation of the trunk and shoulder region. These results indicate that several organizational features develop differently in MI following perinatal nerve injury: certain remaining muscle groups have enlarged cortical representations, there is a strengthening of some normally weak connections from MI to the proximal musculature, and muscles are grouped in unusual combinations. These data demonstrate that the formation of MI representation patterns is strongly influenced by nerve injury during the perinatal period.},
	Author = {Donoghue, J P and Sanes, J N},
	Date-Added = {2017-04-18 19:58:46 +0000},
	Date-Modified = {2017-04-18 19:58:46 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Amputation; Animals; Animals, Newborn; Brain Mapping; Denervation; Differential Threshold; Female; Forelimb; Motor Cortex; Movement; Rats; Rats, Inbred Strains; Reference Values; Somatosensory Cortex; Vibrissae},
	Month = {Sep},
	Number = {9},
	Pages = {3221-32},
	Pmid = {3171676},
	Pst = {ppublish},
	Title = {Organization of adult motor cortex representation patterns following neonatal forelimb nerve injury in rats},
	Volume = {8},
	Year = {1988},
	File = {papers/Donoghue_JNeurosci1988.pdf}}

@article{Tennant:2011,
	Abstract = {The organization of forelimb representation areas of the monkey, cat, and rat motor cortices has been studied in depth, but its characterization in the mouse lags far behind. We used intracortical microstimulation (ICMS) and cytoarchitectonics to characterize the general organization of the C57BL/6 mouse motor cortex, and the forelimb representation in more detail. We found that the forelimb region spans a large area of frontal cortex, bordered primarily by vibrissa, neck, shoulder, and hindlimb representations. It included a large caudal forelimb area, dominated by digit representation, and a small rostral forelimb area, containing elbow and wrist representations. When the entire motor cortex was mapped, the forelimb was found to be the largest movement representation, followed by head and hindlimb representations. The ICMS-defined motor cortex spanned cytoarchitecturally identified lateral agranular cortex (AGl) and also extended into medial agranular cortex. Forelimb and hindlimb representations extended into granular cortex in a region that also had cytoarchitectural characteristics of AGl, consistent with the primary motor-somatosensory overlap zone (OL) characterized in rats. Thus, the mouse motor cortex has homologies with the rat in having 2 forelimb representations and an OL but is distinct in the predominance of digit representations.},
	Author = {Tennant, Kelly A and Adkins, Deanna L and Donlan, Nicole A and Asay, Aaron L and Thomas, Nagheme and Kleim, Jeffrey A and Jones, Theresa A},
	Date-Added = {2017-04-18 19:20:36 +0000},
	Date-Modified = {2017-04-18 19:20:36 +0000},
	Doi = {10.1093/cercor/bhq159},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Brain Mapping; Electric Stimulation; Forelimb; Male; Mice; Mice, Inbred C57BL; Motor Cortex},
	Month = {Apr},
	Number = {4},
	Pages = {865-76},
	Pmc = {PMC3059888},
	Pmid = {20739477},
	Pst = {ppublish},
	Title = {The organization of the forelimb representation of the C57BL/6 mouse motor cortex as defined by intracortical microstimulation and cytoarchitecture},
	Volume = {21},
	Year = {2011},
	File = {papers/Tennant_CerebCortex2011.pdf}}

@article{Belanger:2011,
	Abstract = {The energy requirements of the brain are very high, and tight regulatory mechanisms operate to ensure adequate spatial and temporal delivery of energy substrates in register with neuronal activity. Astrocytes-a type of glial cell-have emerged as active players in brain energy delivery, production, utilization, and storage. Our understanding of neuroenergetics is rapidly evolving from a "neurocentric" view to a more integrated picture involving an intense cooperativity between astrocytes and neurons. This review focuses on the cellular aspects of brain energy metabolism, with a particular emphasis on the metabolic interactions between neurons and astrocytes.},
	Author = {B{\'e}langer, Mireille and Allaman, Igor and Magistretti, Pierre J},
	Date-Added = {2017-04-17 23:16:55 +0000},
	Date-Modified = {2017-04-17 23:16:55 +0000},
	Doi = {10.1016/j.cmet.2011.08.016},
	Journal = {Cell Metab},
	Journal-Full = {Cell metabolism},
	Mesh = {Astrocytes; Brain; Energy Metabolism; Glycogen; Lactic Acid; Models, Biological; Neurons; Oxidative Stress; Regional Blood Flow},
	Month = {Dec},
	Number = {6},
	Pages = {724-38},
	Pmid = {22152301},
	Pst = {ppublish},
	Title = {Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation},
	Volume = {14},
	Year = {2011},
	File = {papers/Bélanger_CellMetab2011.pdf}}

@article{Raichle:2002,
	Author = {Raichle, Marcus E and Gusnard, Debra A},
	Date-Added = {2017-04-17 17:36:54 +0000},
	Date-Modified = {2017-04-17 17:36:54 +0000},
	Doi = {10.1073/pnas.172399499},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Brain; Energy Metabolism; Humans},
	Month = {Aug},
	Number = {16},
	Pages = {10237-9},
	Pmc = {PMC124895},
	Pmid = {12149485},
	Pst = {ppublish},
	Title = {Appraising the brain's energy budget},
	Volume = {99},
	Year = {2002},
	File = {papers/Raichle_ProcNatlAcadSciUSA2002.pdf}}

@article{Parkes:2001,
	Abstract = {A shape can be more difficult to identify when other shapes are near it. For example, when several grating patches are viewed parafoveally, observers are unable to report the orientation of the central patch. This phenomenon, known as 'crowding,' has historically been confused with lateral masking, in which one stimulus attenuates signals generated by another stimulus. Here we show that despite their inability to report the orientation of an individual patch, observers can reliably estimate the average orientation, demonstrating that the local orientation signals are combined rather than lost. Our results imply that crowding is distinct from ordinary masking, and is perhaps related to texture perception. Under crowded conditions, the orientation signals in primary visual cortex are pooled before they reach consciousness.},
	Author = {Parkes, L and Lund, J and Angelucci, A and Solomon, J A and Morgan, M},
	Date-Added = {2017-04-12 17:55:10 +0000},
	Date-Modified = {2017-04-12 17:55:10 +0000},
	Doi = {10.1038/89532},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Algorithms; Form Perception; Humans; Models, Biological; Visual Fields},
	Month = {Jul},
	Number = {7},
	Pages = {739-44},
	Pmid = {11426231},
	Pst = {ppublish},
	Title = {Compulsory averaging of crowded orientation signals in human vision},
	Volume = {4},
	Year = {2001},
	File = {papers/Parkes_NatNeurosci2001.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/89532}}

@article{King:1993,
	Abstract = {Neglect in human and non-human primates has been demonstrated following unilateral lesions of both posterior parietal and prefrontal areas. While it has now been well established that a unilateral lesion of the rodent analog of dorsolateral prefrontal cortex, medial agranular cortex (AGm), results in neglect, the effects of unilateral damage restricted to rodent posterior parietal cortex (PPC) have not been examined in detail. The current study assessed rats with unilateral lesions of PPC or AGm on their ability to orient to unilateral and bilateral stimulation. Since it has been proposed in both the primate and rodent literatures that frontal areas may be responsible for the perception of near space while parietal areas may be responsible for far space, stimuli were presented at two different distances. Lesions of PPC and AGm resulted in severe neglect relative to control operates, with both PPC and AGm operates manifesting severe hemi-inattention and allesthesia relative to control operates. After behavioral recovery from neglect there was no evidence of extinction to bilateral simultaneous stimulation. While neglect to visual stimuli predominated in unilateral PPC operates, unilateral AGm operates had severe neglect in all modalities. In addition, while both left and right PPC operates showed contralesional neglect, AGm operates demonstrated the lateralized differences in neglect reported in previous studies. All groups demonstrated an approximately equivalent level of neglect to stimuli presented at the two different distances, and thus failed to support the suggestion of a peripersonal-extrapersonal dichotomy between frontal and parietal areas in rodents.},
	Author = {King, V R and Corwin, J V},
	Date-Added = {2017-04-08 00:47:52 +0000},
	Date-Modified = {2017-04-08 00:47:52 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Mesh = {Animals; Attention; Brain Mapping; Distance Perception; Dominance, Cerebral; Extinction, Psychological; Food Deprivation; Male; Motivation; Neural Pathways; Orientation; Parietal Lobe; Prefrontal Cortex; Rats; Sound Localization; Touch},
	Month = {Apr},
	Number = {2},
	Pages = {117-31},
	Pmid = {8323710},
	Pst = {ppublish},
	Title = {Comparisons of hemi-inattention produced by unilateral lesions of the posterior parietal cortex or medial agranular prefrontal cortex in rats: neglect, extinction, and the role of stimulus distance},
	Volume = {54},
	Year = {1993},
	File = {papers/King_BehavBrainRes1993.pdf}}

@article{Kesner:1989,
	Abstract = {Animals with medial prefrontal cortex or parietal cortex lesions and sham-operated and non-operated controls were tested for the acquisition of an adjacent arm task that accentuated the importance of egocentric spatial localization and a cheese board task that accentuated the importance of allocentric spatial localization. Results indicated that relative to controls, animals with medial-prefrontal cortex lesions are impaired on the adjacent arm task but displayed facilitation on the cheese board task. In contrast, relative to controls, rats with parietal cortex lesions are impaired on the cheese board task but show no impairment on the adjacent arm task. The data suggest a double dissociation of function between medial prefrontal cortex and parietal cortex in terms of coding of egocentric versus allocentric spatial information.},
	Author = {Kesner, R P and Farnsworth, G and DiMattia, B V},
	Date-Added = {2017-04-08 00:45:29 +0000},
	Date-Modified = {2017-04-08 00:45:29 +0000},
	Journal = {Behav Neurosci},
	Journal-Full = {Behavioral neuroscience},
	Mesh = {Animals; Appetitive Behavior; Attention; Brain Mapping; Discrimination Learning; Frontal Lobe; Male; Memory; Mental Recall; Orientation; Parietal Lobe; Rats; Rats, Inbred Strains; Reaction Time; Retention (Psychology)},
	Month = {Oct},
	Number = {5},
	Pages = {956-61},
	Pmid = {2803562},
	Pst = {ppublish},
	Title = {Double dissociation of egocentric and allocentric space following medial prefrontal and parietal cortex lesions in the rat},
	Volume = {103},
	Year = {1989}}

@article{King:1992,
	Abstract = {Studies of spatial behavior in both the human and non-human primate have generally focused on the role of the posterior parietal and prefrontal cortices and have indicated that destruction of these regions produce allocentric and egocentric deficits, respectively. The present study examined the role of the rodent analogs of these regions, the posterior parietal (PPC) and medial agranular (AGm) cortices, in egocentric and allocentric spatial processing, and whether spatial processing in rodents is organized in a hemispatial and/or lateralized manner as has been found in the primate. Eighty male rats receiving either a unilateral or bilateral lesion of AGm or PPC were examined on an egocentric (adjacent arm) or an allocentric (cheeseboard) maze task. The results indicated that PPC and AGm have dissociable spatial functions. Bilateral AGm destruction resulted in egocentric spatial deficits, and unilateral AGm operates demonstrated an intermediate deficit. In contrast, bilateral PPC operates demonstrated a severe deficit in allocentric processing. In addition, there were lateralized differences in the performance of unilateral PPC operates. While right PPC lesions resulted in a significant deficit on the allocentric task, no such deficit was seen in left PPC operates. In addition, neither unilateral AGm nor unilateral PPC operates demonstrated a hemispatial impairment on either the egocentric or allocentric tasks.},
	Author = {King, V R and Corwin, J V},
	Date-Added = {2017-04-08 00:42:49 +0000},
	Date-Modified = {2017-04-08 00:42:49 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Mesh = {Animals; Brain Mapping; Dominance, Cerebral; Hippocampus; Male; Mental Recall; Motivation; Neural Pathways; Neurons; Orientation; Parietal Lobe; Prefrontal Cortex; Rats; Retention (Psychology); Social Environment},
	Month = {Sep},
	Number = {1-2},
	Pages = {53-68},
	Pmid = {1449649},
	Pst = {ppublish},
	Title = {Spatial deficits and hemispheric asymmetries in the rat following unilateral and bilateral lesions of posterior parietal or medial agranular cortex},
	Volume = {50},
	Year = {1992},
	File = {papers/King_BehavBrainRes1992.pdf}}

@article{Dawson:1986,
	Abstract = {Unilateral lesions in such brain regions as medial frontal cortex and superior colliculus produce polysensory neglect contralateral to the lesion. Since the pineal gland is an unpaired brain structure, both electrophysiologically and hormonally responsive to visual and auditory stimulation, it may modulate bilateral sensory attention mechanisms. Long-Evans male rats were given pineal or sham lesions and were tested behaviourally. Sensory assessment revealed that in comparison to sham animals rats with pineal lesion exhibited unilateral visual and auditory neglect to stimuli presented on either side of the body. Animals with pineal lesions were more likely than sham-lesioned animals to demonstrate visual allesthesis and, compared to sham-lesioned rats, showed extinction on the left side to bilateral simultaneous visual stimulation. This is the first report that midline neuroendocrine damage can produce bilateral sensory inattention.},
	Author = {Dawson, K A and Crowne, D P and Richardson, C M},
	Date-Added = {2017-04-08 00:39:53 +0000},
	Date-Modified = {2017-04-08 00:39:53 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Mesh = {Animals; Attention; Auditory Perception; Brain Mapping; Male; Orientation; Pineal Gland; Rats; Reflex; Visual Fields; Visual Perception},
	Month = {Feb},
	Number = {2},
	Pages = {187-90},
	Pmid = {3964408},
	Pst = {ppublish},
	Title = {Pineal lesion produces bilateral visual and auditory inattention in the rat},
	Volume = {19},
	Year = {1986}}

@article{Crowne:1986,
	Abstract = {Rats were given unilateral aspiration lesions of parietal, medial frontal, or dorsolateral frontal (motor) cortex and then tested for visual, auditory and tactile neglect, and for circling. All medial frontal lesion animals showed contralateral neglect in each modality and circled ipsiversively. The parietal lesion rats initially displayed contralateral visual and auditory neglect as severe as that in the medial frontal group. Three weeks after the lesions, the parietal group had a smaller residual deficit on the visual test than the medial frontal group. In the first week, parietal animals responded less than the medial frontals to stroking the vibrissae but were more responsive to mild pinching of a toe contralateral to the lesion side. In striking contrast to the medial frontal animals, the parietal group circled strongly to the contralateral side. No rat with a motor cortex lesion neglected or circled preferentially. Like medial frontal cortex, unilateral parietal lesions also produce neglect and circling, but there are important features distinguishing unilateral lesion effects in these two regions.},
	Author = {Crowne, D P and Richardson, C M and Dawson, K A},
	Date-Added = {2017-04-08 00:39:51 +0000},
	Date-Modified = {2017-04-08 00:39:51 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Mesh = {Acoustic Stimulation; Animals; Frontal Lobe; Male; Orientation; Parietal Lobe; Photic Stimulation; Physical Stimulation; Rats; Sensation; Stereotyped Behavior; Visual Fields},
	Month = {Dec},
	Number = {3},
	Pages = {227-31},
	Pmid = {3790245},
	Pst = {ppublish},
	Title = {Parietal and frontal eye field neglect in the rat},
	Volume = {22},
	Year = {1986},
	File = {papers/Crowne_BehavBrainRes1986.pdf}}

@article{Reep:1994,
	Abstract = {Anatomical and functional findings support the contention that there is a distinct posterior parietal cortical area (PPC) in the rat, situated between the rostrally adjacent hindlimb sensorimotor area and the caudally adjacent secondary visual areas. The PPC is distinguished from these areas by receiving thalamic afferents from the lateral dorsal (LD), lateral posterior (LP), and posterior (Po) nuclei, in the absence of input from the ventrobasal complex (VB) or dorsal lateral geniculate (DLG) nuclei. Behavioral studies have demonstrated that PPC is involved in spatial orientation and directed attention. In the present study we used fluorescent retrograde axonal tracers primarily to investigate the cortical connections of PPC, in order to determine the organization of the circuitry by which PPC is likely to participate in these functions, and also to determine how the topography of its thalamic connections differs from that of neighboring cortical areas. The cortical connections of PPC involve the ventrolateral (VLO) and medial (MO) orbital areas, medial agranular cortex (area Fr2), portions of somatic sensory areas Par1 and Par2, secondary visual areas Oc2M and Oc2L, auditory area Te1, and retrosplenial cortex. The secondary visual areas Oc2L and Oc2M have cortical connections which are similar to those of PPC, but are restricted within orbital cortex to area VLO, and within area Fr2 to its caudal portion, and do not involve auditory area Te1. The cortical connections of hindlimb cortex are largely restricted to somatic sensory and motor areas. Retrosplenial cortex, which is medially adjacent to PPC, has cortical connections that are prominent with visual cortex, do not involve somatic sensory or auditory cortex, and include the presubiculum. We conclude that PPC is distinguished by its pattern of cortical connections with the somatic sensory, auditory and visual areas, and with areas Fr2, and VLO/MO, in addition to its exclusive thalamic connectivity with LD, LP and Po. Because recent behavioral studies indicate that PPC, Fr2 and VLO are involved in directed attention and spatial learning, we suggest that the interconnections among these three cortical areas represent a major component of the circuitry for these functions in rats.},
	Author = {Reep, R L and Chandler, H C and King, V and Corwin, J V},
	Date-Added = {2017-04-08 00:31:37 +0000},
	Date-Modified = {2017-04-08 00:31:37 +0000},
	Journal = {Exp Brain Res},
	Journal-Full = {Experimental brain research},
	Mesh = {Animals; Cerebral Cortex; Fluorescent Dyes; Hindlimb; Neural Pathways; Parietal Lobe; Rats; Somatosensory Cortex; Stereotaxic Techniques; Stilbamidines; Thalamus; Visual Cortex},
	Number = {1},
	Pages = {67-84},
	Pmid = {7813654},
	Pst = {ppublish},
	Title = {Rat posterior parietal cortex: topography of corticocortical and thalamic connections},
	Volume = {100},
	Year = {1994},
	File = {papers/Reep_ExpBrainRes1994.pdf}}

@article{Mountcastle:1975,
	Abstract = {Experiments were made on the posterior parietal association cortical areas 5 and in 17 hemispheres of 11 monkeys, 6 M. mulatta and 5 M. arctoides. The electrical signs of the activity of single cortical cells were recorded with microelectrodes in waking animals as they carried out certain behavioral acts in response to a series of sensory cues. The behavioral paradigms were one for detection alone, and a second for detection plus projection of the arm to contact a stationary or moving target placed at arm's length. Of the 125 microelectrode penetrations made, 1,451 neurons were identified in terms of the correlation of their activity with the behavioral acts and their sensitivity or lack of it to sensory stimuli delivered passively; 180 were studied quantitatively. The locations of cortical neurons were identified in serial sections; 94 penetrations and 1,058 neurons were located with certainty. About two-thirds of the neurons of area 5 were activated by passive rotation of the limbs at their joints; of these, 82% were related to single, contralateral joints, 10% to two or more contralateral joints, 6% to ipsilateral, and 2% to joints on both sides of the body. A few of the latter were active during complex bodily postures. A large proportion of area 5 neurons were relatively insensitive to passive joint rotations, as compared with similar neurons of the postcentral gyrus, but were driven to high rates of discharge when the same joint was rotated during an active movement of the animal...},
	Author = {Mountcastle, V B and Lynch, J C and Georgopoulos, A and Sakata, H and Acuna, C},
	Date-Added = {2017-04-07 18:13:36 +0000},
	Date-Modified = {2017-04-07 18:13:36 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Mesh = {Animals; Brain Mapping; Exploratory Behavior; Eye Movements; Haplorhini; Joints; Macaca; Mechanoreceptors; Models, Neurological; Motor Skills; Neural Pathways; Neurons; Orientation; Parietal Lobe; Posture; Proprioception; Skin; Space Perception; Time Factors; Visual Perception},
	Month = {Jul},
	Number = {4},
	Pages = {871-908},
	Pmid = {808592},
	Pst = {ppublish},
	Title = {Posterior parietal association cortex of the monkey: command functions for operations within extrapersonal space},
	Volume = {38},
	Year = {1975},
	File = {papers/Mountcastle_JNeurophysiol1975.pdf}}

@article{Andersen:1997,
	Abstract = {Recent experiments are reviewed that indicate that sensory signals from many modalities, as well as efference copy signals from motor structures, converge in the posterior parietal cortex in order to code the spatial locations of goals for movement. These signals are combined using a specific gain mechanism that enables the different coordinate frames of the various input signals to be combined into common, distributed spatial representations. These distributed representations can be used to convert the sensory locations of stimuli into the appropriate motor coordinates required for making directed movements. Within these spatial representations of the posterior parietal cortex are neural activities related to higher cognitive functions, including attention. We review recent studies showing that the encoding of intentions to make movements is also among the cognitive functions of this area.},
	Author = {Andersen, R A and Snyder, L H and Bradley, D C and Xing, J},
	Date-Added = {2017-04-07 18:07:19 +0000},
	Date-Modified = {2017-04-07 18:07:19 +0000},
	Doi = {10.1146/annurev.neuro.20.1.303},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Mesh = {Animals; Movement; Parietal Lobe; Space Perception},
	Pages = {303-30},
	Pmid = {9056716},
	Pst = {ppublish},
	Title = {Multimodal representation of space in the posterior parietal cortex and its use in planning movements},
	Volume = {20},
	Year = {1997},
	File = {papers/Andersen_AnnuRevNeurosci1997.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.neuro.20.1.303}}

@article{Aziz-Zadeh:2006,
	Abstract = {A cortical network consisting of the inferior frontal, rostral inferior parietal, and posterior superior temporal cortices has been implicated in representing actions in the primate brain and is critical to imitation in humans. This neural circuitry may be an evolutionary precursor of neural systems associated with language. However, language is predominantly lateralized to the left hemisphere, whereas the degree of lateralization of the imitation circuitry in humans is unclear. We conducted a functional magnetic resonance imaging study of imitation of finger movements with lateralized stimuli and responses. During imitation, activity in the inferior frontal and rostral inferior parietal cortex, although fairly bilateral, was stronger in the hemisphere ipsilateral to the visual stimulus and response hand. This ipsilateral pattern is at variance with the typical contralateral activity of primary visual and motor areas. Reliably increased signal in the right superior temporal sulcus (STS) was observed for both left-sided and right-sided imitation tasks, although subthreshold activity was also observed in the left STS. Overall, the data indicate that visual and motor components of the human mirror system are not left-lateralized. The left hemisphere superiority for language, then, must be have been favored by other types of language precursors, perhaps auditory or multimodal action representations.},
	Author = {Aziz-Zadeh, Lisa and Koski, Lisa and Zaidel, Eran and Mazziotta, John and Iacoboni, Marco},
	Date-Added = {2017-04-05 01:54:49 +0000},
	Date-Modified = {2017-04-05 01:54:49 +0000},
	Doi = {10.1523/JNEUROSCI.2921-05.2006},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Adolescent; Adult; Brain Mapping; Dominance, Cerebral; Female; Fingers; Frontal Lobe; Humans; Imitative Behavior; Language; Male; Middle Aged; Movement; Nerve Net; Neurons; Parietal Lobe; Psychomotor Performance; Subtraction Technique; Temporal Lobe},
	Month = {Mar},
	Number = {11},
	Pages = {2964-70},
	Pmid = {16540574},
	Pst = {ppublish},
	Title = {Lateralization of the human mirror neuron system},
	Volume = {26},
	Year = {2006},
	File = {papers/Aziz-Zadeh_JNeurosci2006.pdf}}

@article{Takano:2014,
	Abstract = {The mirror system in the brain is considered to be a neural basis of sociality, but previous studies have been limited to primates. Here we report an experimental task to examine the mirror system in rats. We show that a rat could reach to a pellet and grasp and eat it in front of another rat that was observing the reaching, which indicates that the task will enable us to start exploring the rat mirror system.},
	Author = {Takano, Yuji and Ukezono, Masatoshi},
	Date-Added = {2017-04-04 23:47:31 +0000},
	Date-Modified = {2017-04-04 23:47:31 +0000},
	Doi = {10.1038/srep06652},
	Journal = {Sci Rep},
	Journal-Full = {Scientific reports},
	Mesh = {Animals; Behavior, Animal; Brain; Psychomotor Performance; Rats; Social Behavior},
	Month = {Oct},
	Pages = {6652},
	Pmc = {PMC4200406},
	Pmid = {25323637},
	Pst = {epublish},
	Title = {An experimental task to examine the mirror system in rats},
	Volume = {4},
	Year = {2014},
	File = {papers/Takano_SciRep2014.pdf}}

@article{Williams:2006a,
	Abstract = {An association between autistic spectrum disorder and imitative impairment might result from dysfunction in mirror neurons (MNs) that serve to relate observed actions to motor codings. To explore this hypothesis, we employed a functional magnetic resonance imaging (fMRI) protocol previously used to identify the neural substrate of imitation, and human MN function, to compare 16 adolescent males of normal intelligence with autistic spectrum disorder (ASD) and age, sex and IQ matched controls. In the control group, in accord with previous findings, we identified activity attributable to MNs in areas of the right parietal lobe. Activity in this area was less extensive in the ASD group and was absent during non-imitative action execution. Broca's area was minimally active during imitation in controls. Differential patterns of activity during imitation and action observation in ASD and controls were most evident in an area at the right temporo-parietal junction also associated with a 'theory of mind' (ToM) function. ASD participants also failed to show modulation of left amygdala activity during imitation that was evident in the controls. This may have implications for understanding the imitation of emotional stimuli in ASD. Overall, we suggest that ASD is associated with altered patterns of brain activity during imitation, which could stem from poor integration between areas serving visual, motor, proprioceptive and emotional functions. Such poor integration is likely to adversely affect the development of ToM through imitation as well as other aspects of social cognitive function in ASD.},
	Author = {Williams, Justin H G and Waiter, Gordon D and Gilchrist, Anne and Perrett, David I and Murray, Alison D and Whiten, Andrew},
	Date-Added = {2017-04-04 23:41:18 +0000},
	Date-Modified = {2017-04-04 23:41:18 +0000},
	Doi = {10.1016/j.neuropsychologia.2005.06.010},
	Journal = {Neuropsychologia},
	Journal-Full = {Neuropsychologia},
	Mesh = {Adolescent; Amygdala; Asperger Syndrome; Autistic Disorder; Brain; Brain Mapping; Dominance, Cerebral; Female; Humans; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Imitative Behavior; Magnetic Resonance Imaging; Male; Nerve Net; Neurons; Orientation; Parietal Lobe; Personal Construct Theory; Psychomotor Performance; Reference Values; Somatosensory Cortex; Temporal Lobe},
	Number = {4},
	Pages = {610-21},
	Pmid = {16140346},
	Pst = {ppublish},
	Title = {Neural mechanisms of imitation and 'mirror neuron' functioning in autistic spectrum disorder},
	Volume = {44},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuropsychologia.2005.06.010}}

@article{Bernier:2007,
	Abstract = {Imitation ability has consistently been shown to be impaired in individuals with autism. A dysfunctional execution/observation matching system has been proposed to account for this impairment. The EEG mu rhythm is believed to reflect an underlying execution/observation matching system. This study investigated evidence of differential mu rhythm attenuation during the observation, execution, and imitation of movements and examined its relation to behaviorally assessed imitation abilities. Fourteen high-functioning adults with autism spectrum disorder (ASD) and 15 IQ- and age-matched typical adults participated. On the behavioral imitation task, adults with ASD demonstrated significantly poorer performance compared to typical adults in all domains of imitation ability. On the EEG task, both groups demonstrated significant attenuation of the mu rhythm when executing an action. However, when observing movement, the individuals with ASD showed significantly reduced attenuation of the mu wave. Behaviorally assessed imitation skills were correlated with degree of mu wave attenuation during observation of movement. These findings suggest that there is execution/observation matching system dysfunction in individuals with autism and that this matching system is related to degree of impairment in imitation abilities.},
	Author = {Bernier, R and Dawson, G and Webb, S and Murias, M},
	Date-Added = {2017-04-04 23:40:36 +0000},
	Date-Modified = {2017-04-04 23:40:36 +0000},
	Doi = {10.1016/j.bandc.2007.03.004},
	Journal = {Brain Cogn},
	Journal-Full = {Brain and cognition},
	Mesh = {Adult; Autistic Disorder; Brain; Electroencephalography; Hand Strength; Humans; Imitative Behavior; Male; Neurophysiology; Periodicity},
	Month = {Aug},
	Number = {3},
	Pages = {228-37},
	Pmc = {PMC2709976},
	Pmid = {17451856},
	Pst = {ppublish},
	Title = {EEG mu rhythm and imitation impairments in individuals with autism spectrum disorder},
	Volume = {64},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.bandc.2007.03.004}}

@article{Pineda:2005,
	Abstract = {Existing evidence indicates that mu and other alpha-like rhythms are independent phenomena because of differences in source generation, sensitivity to sensory events, bilateral coherence, frequency, and power. Although mu suppression and enhancement echo sensorimotor processing in frontoparietal networks, they are also sensitive to cognitive and affective influences and likely reflect more than an idling brain state. Mu rhythms are present at early stages of human development and in other mammalian species. They exhibit adaptive and dynamically changing properties, including frequency acceleration and posterior-to-anterior shifts in focus. Furthermore, individuals can learn to control mu rhythms volitionally in a very short period of time. This raises questions about the mu rhythm's open neural architecture and ability to respond to cognitive, affective, and motor imagery, implying an even greater developmental and functional role than has previously been ascribed to it. Recent studies have suggested that mu rhythms reflect downstream modulation of motor cortex by prefrontal mirror neurons, i.e., cells that may play a critical role in imitation learning and the ability to understand the actions of others. It is proposed that mu rhythms represent an important information processing function that links perception and action-specifically, the transformation of "seeing" and "hearing" into "doing." In a broader context, this transformation function results from an entrainment/gating mechanism in which multiple alpha networks (visual-, auditory-, and somatosensory-centered domains), typically producing rhythmic oscillations in a locally independent manner, become coupled and entrained. A global or 'diffuse and distributed alpha system' comes into existence when these independent sources of alpha become coherently engaged in transforming perception to action.},
	Author = {Pineda, Jaime A},
	Date-Added = {2017-04-04 22:57:22 +0000},
	Date-Modified = {2017-04-04 22:57:22 +0000},
	Doi = {10.1016/j.brainresrev.2005.04.005},
	Journal = {Brain Res Brain Res Rev},
	Journal-Full = {Brain research. Brain research reviews},
	Mesh = {Animals; Brain; Brain Mapping; Electroencephalography; Hearing; Humans; Mental Processes; Vision, Ocular},
	Month = {Dec},
	Number = {1},
	Pages = {57-68},
	Pmid = {15925412},
	Pst = {ppublish},
	Title = {The functional significance of mu rhythms: translating "seeing" and "hearing" into "doing"},
	Volume = {50},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.brainresrev.2005.04.005}}

@article{Oberman:2005,
	Abstract = {Autism spectrum disorders (ASD) are largely characterized by deficits in imitation, pragmatic language, theory of mind, and empathy. Previous research has suggested that a dysfunctional mirror neuron system may explain the pathology observed in ASD. Because EEG oscillations in the mu frequency (8-13 Hz) over sensorimotor cortex are thought to reflect mirror neuron activity, one method for testing the integrity of this system is to measure mu responsiveness to actual and observed movement. It has been established that mu power is reduced (mu suppression) in typically developing individuals both when they perform actions and when they observe others performing actions, reflecting an observation/execution system which may play a critical role in the ability to understand and imitate others' behaviors. This study investigated whether individuals with ASD show a dysfunction in this system, given their behavioral impairments in understanding and responding appropriately to others' behaviors. Mu wave suppression was measured in ten high-functioning individuals with ASD and ten age- and gender-matched control subjects while watching videos of (1) a moving hand, (2) a bouncing ball, and (3) visual noise, or (4) moving their own hand. Control subjects showed significant mu suppression to both self and observed hand movement. The ASD group showed significant mu suppression to self-performed hand movements but not to observed hand movements. These results support the hypothesis of a dysfunctional mirror neuron system in high-functioning individuals with ASD.},
	Author = {Oberman, Lindsay M and Hubbard, Edward M and McCleery, Joseph P and Altschuler, Eric L and Ramachandran, Vilayanur S and Pineda, Jaime A},
	Date-Added = {2017-04-04 22:19:14 +0000},
	Date-Modified = {2017-04-04 22:19:14 +0000},
	Doi = {10.1016/j.cogbrainres.2005.01.014},
	Journal = {Brain Res Cogn Brain Res},
	Journal-Full = {Brain research. Cognitive brain research},
	Mesh = {Adolescent; Adult; Alpha Rhythm; Autistic Disorder; Case-Control Studies; Child; Electroencephalography; Female; Humans; Imitative Behavior; Inhibition (Psychology); Male; Mental Processes; Middle Aged; Movement; Neurons; Psychomotor Performance; Spectrum Analysis; Visual Perception},
	Month = {Jul},
	Number = {2},
	Pages = {190-8},
	Pmid = {15993757},
	Pst = {ppublish},
	Title = {EEG evidence for mirror neuron dysfunction in autism spectrum disorders},
	Volume = {24},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cogbrainres.2005.01.014}}

@article{Evans:2013,
	Abstract = {Within the framework of the radical pair mechanism, magnetic fields may alter the rate and yields of chemical reactions involving spin-correlated radical pairs as intermediates. Such effects have been studied in detail in a variety of chemical systems both experimentally and theoretically. In recent years, there has been growing interest in whether such magnetic field effects (MFEs) also occur in biological systems, a question driven most notably by the increasing body of evidence for the involvement of such effects in the magnetic compass sense of animals. The blue-light photoreceptor cryptochrome is placed at the centre of this debate and photoexcitation of its bound flavin cofactor has indeed been shown to result in the formation of radical pairs. Here, we review studies of MFEs on free flavins in model systems as well as in blue-light photoreceptor proteins and discuss the properties that are crucial in determining the magnetosensitivity of these systems.},
	Author = {Evans, Emrys W and Dodson, Charlotte A and Maeda, Kiminori and Biskup, Till and Wedge, C J and Timmel, Christiane R},
	Date-Added = {2017-03-06 22:26:23 +0000},
	Date-Modified = {2017-03-06 22:26:23 +0000},
	Doi = {10.1098/rsfs.2013.0037},
	Journal = {Interface Focus},
	Journal-Full = {Interface focus},
	Keywords = {cryptochrome; magnetic compass; magnetic field effect; photolyase; radical pair mechanism},
	Month = {Oct},
	Number = {5},
	Pages = {20130037},
	Pmc = {PMC3915827},
	Pmid = {24511388},
	Pst = {ppublish},
	Title = {Magnetic field effects in flavoproteins and related systems},
	Volume = {3},
	Year = {2013},
	File = {papers/Evans_InterfaceFocus2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rsfs.2013.0037}}

@article{Torii:2009,
	Abstract = {The cerebral cortex is a laminated sheet of neurons composed of the arrays of intersecting radial columns. During development, excitatory projection neurons originating from the proliferative units at the ventricular surface of the embryonic cerebral vesicles migrate along elongated radial glial fibres to form a cellular infrastructure of radial (vertical) ontogenetic columns in the overlaying cortical plate. However, a subpopulation of these clonally related neurons also undergoes a short lateral shift and transfers from their parental to the neighbouring radial glial fibres, and intermixes with neurons originating from neighbouring proliferative units. This columnar organization acts as the primary information processing unit in the cortex. The molecular mechanisms, role and significance of this lateral dispersion for cortical development are not understood. Here we show that an Eph receptor A (EphA) and ephrin A (Efna) signalling-dependent shift in the allocation of clonally related neurons is essential for the proper assembly of cortical columns. In contrast to the relatively uniform labelling of the developing cortical plate by various molecular markers and retrograde tracers in wild-type mice, we found alternating labelling of columnar compartments in Efna knockout mice that are caused by impaired lateral dispersion of migrating neurons rather than by altered cell production or death. Furthermore, in utero electroporation showed that lateral dispersion depends on the expression levels of EphAs and ephrin-As during neuronal migration. This so far unrecognized mechanism for lateral neuronal dispersion seems to be essential for the proper intermixing of neuronal types in the cortical columns, which, when disrupted, might contribute to neuropsychiatric disorders associated with abnormal columnar organization.},
	Author = {Torii, Masaaki and Hashimoto-Torii, Kazue and Levitt, Pat and Rakic, Pasko},
	Date-Added = {2017-02-23 22:15:12 +0000},
	Date-Modified = {2017-02-23 22:15:12 +0000},
	Doi = {10.1038/nature08362},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Cell Movement; Cerebral Cortex; Ephrins; Mice; Mice, Knockout; Neocortex; Neurons; Organogenesis; Rats; Receptors, Eph Family; Signal Transduction},
	Month = {Sep},
	Number = {7263},
	Pages = {524-8},
	Pmc = {PMC2874978},
	Pmid = {19759535},
	Pst = {ppublish},
	Title = {Integration of neuronal clones in the radial cortical columns by EphA and ephrin-A signalling},
	Volume = {461},
	Year = {2009},
	File = {papers/Torii_Nature2009.pdf},
	Bdsk-File-2 = {papers/Torii_Nature2009a.pdf}}

@article{Kania:2016,
	Abstract = {Eph receptor Tyr kinases and their membrane-tethered ligands, the ephrins, elicit short-distance cell-cell signalling and thus regulate many developmental processes at the interface between pattern formation and morphogenesis, including cell sorting and positioning, and the formation of segmented structures and ordered neural maps. Their roles extend into adulthood, when ephrin-Eph signalling regulates neuronal plasticity, homeostatic events and disease processes. Recently, new insights have been gained into the mechanisms of ephrin-Eph signalling in different cell types, and into the physiological importance of ephrin-Eph in different organs and in disease, raising questions for future research directions.},
	Author = {Kania, Artur and Klein, R{\"u}diger},
	Date-Added = {2017-02-23 22:15:03 +0000},
	Date-Modified = {2017-02-23 22:15:03 +0000},
	Doi = {10.1038/nrm.2015.16},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Mesh = {Animals; Ephrins; Growth and Development; Humans; Receptors, Eph Family; Signal Transduction},
	Month = {Apr},
	Number = {4},
	Pages = {240-56},
	Pmid = {26790531},
	Pst = {ppublish},
	Title = {Mechanisms of ephrin-Eph signalling in development, physiology and disease},
	Volume = {17},
	Year = {2016},
	File = {papers/Kania_NatRevMolCellBiol2016.pdf}}

@article{Shibuki:2003,
	Abstract = {We used autofluorescence of mitochondrial flavoproteins to image cortical neural activity in the rat. Green autofluorescence in blue light was examined in slices obtained from rat cerebral cortex. About half of the basal autofluorescence was modulated by the presence or absence of O2 or glucose in the medium. Repetitive electrical stimulation at 20 Hz for 1 s produced a localized fluorescence increase in the slices. The amplitude of the increase was 27 +/- 2 % (mean +/- S.D., n = 35). Tetrodotoxin or diphenyleneiodonium, an inhibitor of flavoproteins, blocked the autofluorescence responses. The autofluorescence responses were not observed in slices perfused with calcium-, glucose- or O2-free medium. In the primary somatosensory cortex of rats anaesthetized with urethane (1.5 g kg-1, I.P.), an activity-dependent increase in autofluorescence of 20 +/- 4 % (n = 6) was observed after electrical cortical stimulation at 100 Hz for 1 s, and an increase of 2.6 +/- 0.5 % (n = 33) after vibratory skin stimulation at 50 Hz for 1 s applied to the plantar hindpaw. These responses were large enough to allow visualization of the neural activity without having to average a number of trials. The distribution of the fluorescence responses after electrical or vibratory skin stimulation was comparable to that of the cortical field potentials in the same rats. The fluorescence responses were followed by an increase in arterial blood flow. The former were resistant to an inhibitor of nitric oxide synthase, while the latter was inhibited. Thus, activity-dependent changes in the autofluorescence of flavoproteins are useful for functional brain imaging in vivo.},
	Author = {Shibuki, Katsuei and Hishida, Ryuichi and Murakami, Hiroatsu and Kudoh, Masaharu and Kawaguchi, Tadashi and Watanabe, Masatoshi and Watanabe, Shunsuke and Kouuchi, Takeshi and Tanaka, Ryuichi},
	Date-Added = {2017-02-20 19:54:00 +0000},
	Date-Modified = {2017-02-20 19:54:00 +0000},
	Doi = {10.1113/jphysiol.2003.040709},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Anesthesia; Animals; Calcium; Cerebrovascular Circulation; Electric Stimulation; Evoked Potentials, Somatosensory; Flavoproteins; Fluorescence; Fluorescent Dyes; Green Fluorescent Proteins; Hemodynamics; Heterocyclic Compounds, 3-Ring; Image Interpretation, Computer-Assisted; Luminescent Proteins; Male; Rats; Rats, Wistar; Somatosensory Cortex; Vibration},
	Month = {Jun},
	Number = {Pt 3},
	Pages = {919-27},
	Pmc = {PMC2342977},
	Pmid = {12730344},
	Pst = {ppublish},
	Title = {Dynamic imaging of somatosensory cortical activity in the rat visualized by flavoprotein autofluorescence},
	Volume = {549},
	Year = {2003},
	File = {papers/Shibuki_JPhysiol2003.pdf}}

@article{Husson:2007,
	Abstract = {Neuronal autofluorescence, which results from the oxidation of flavoproteins in the electron transport chain, has recently been used to map cortical responses to sensory stimuli. This approach could represent a substantial improvement over other optical imaging methods because it is a direct (i.e., nonhemodynamic) measure of neuronal metabolism. However, its application to functional imaging has been limited because strong responses have been reported only in rodents. In this study, we demonstrate that autofluorescence imaging (AFI) can be used to map the functional organization of primary visual cortex in both mouse and cat. In cat area 17, orientation preference maps generated by AFI had the classic pinwheel structure and matched those generated by intrinsic signal imaging in the same imaged field. The spatiotemporal profile of the autofluorescence signal had several advantages over intrinsic signal imaging, including spatially restricted fluorescence throughout its response duration, reduced susceptibility to vascular artifacts, an improved spatial response profile, and a faster time course. These results indicate that AFI is a robust and useful measure of large-scale cortical activity patterns in visual mammals.},
	Author = {Husson, T Robert and Mallik, Atul K and Zhang, Jing X and Issa, Naoum P},
	Date-Added = {2017-02-20 19:53:52 +0000},
	Date-Modified = {2017-02-20 19:53:52 +0000},
	Doi = {10.1523/JNEUROSCI.2156-07.2007},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Brain Mapping; Cats; Female; Flavoproteins; Fluorescence; Mice; Photic Stimulation; Reaction Time; Retinoscopy; Visual Cortex},
	Month = {Aug},
	Number = {32},
	Pages = {8665-75},
	Pmid = {17687044},
	Pst = {ppublish},
	Title = {Functional imaging of primary visual cortex using flavoprotein autofluorescence},
	Volume = {27},
	Year = {2007},
	File = {papers/Husson_JNeurosci2007.pdf}}

@article{Michael:2014,
	Abstract = {Large-scale brain activity patterns can be visualized by optical imaging of intrinsic signals (OIS) based on activity-dependent changes in the blood oxygenation level. Another method, flavoprotein autofluorescence imaging (AFI), exploits the mitochondrial flavoprotein autofluorescence, which is enhanced during neuronal activity. In birds, topographic mapping of visual space has been shown in the visual wulst, the avian homologue of the mammalian visual cortex by using OIS. We here applied the AFI method to visualize topographic maps in the visual wulst because with OIS, which depends on blood flow changes, blood vessel artifacts often obscure brain activity maps. We then compared both techniques quantitatively in zebra finches and in C57Bl/6J mice using the same setup and stimulation conditions. In addition to experiments with craniotomized animals, we also examined mice with intact skull (in zebra finches, intact skull imaging is not feasible probably due to the skull construction). In craniotomized animals, retinotopic maps were obtained by both methods in both species. Using AFI, artifacts caused by blood vessels were generally reduced, the magnitude of neuronal activity significantly higher and the retinotopic map quality better than that obtained by OIS in both zebra finches and mice. In contrast, our measurements in non-craniotomized mice did not reveal any quantitative differences between the two methods. Our results thus suggest that AFI is the method of choice for investigations of visual processing in zebra finches. In mice, however, if researchers decide to use the advantages of imaging through the intact skull, they will not be able to exploit the higher signals obtainable by the AFI-method.},
	Author = {Michael, Neethu and Bischof, Hans-Joachim and L{\"o}wel, Siegrid},
	Date-Added = {2017-02-20 19:53:44 +0000},
	Date-Modified = {2017-02-20 19:53:44 +0000},
	Doi = {10.1371/journal.pone.0085225},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Animals; Female; Finches; Flavoproteins; Male; Mice; Optical Imaging; Visual Cortex},
	Number = {1},
	Pages = {e85225},
	Pmc = {PMC3882276},
	Pmid = {24400130},
	Pst = {epublish},
	Title = {Flavoprotein autofluorescence imaging of visual system activity in zebra finches and mice},
	Volume = {9},
	Year = {2014},
	File = {papers/Michael_PLoSOne2014.PDF}}

@article{Matos:2015,
	Abstract = {BACKGROUND: Adenosine A2A receptors (A2AR) modulate dopamine and glutamate signaling and thereby may influence some of the psychomotor and cognitive processes associated with schizophrenia. Because astroglial A2AR regulate the availability of glutamate, we hypothesized that they might play an unprecedented role in some of the processes leading to the development of schizophrenia, which we investigated using a mouse line with a selective deletion of A2AR in astrocytes (Gfa2-A2AR knockout [KO] mice].
METHODS: We examined Gfa2-A2AR KO mice for behaviors thought to recapitulate some features of schizophrenia, namely enhanced MK-801 psychomotor response (positive symptoms) and decreased working memory (cognitive symptoms). In addition, we probed for neurochemical alterations in the glutamatergic circuitry, evaluating glutamate uptake and release and the levels of key proteins defining glutamatergic signaling (glutamate transporter-I [GLT-I], N-methyl-D-aspartate receptors [NMDA-R] and α-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors [AMPA-R]) to provide a mechanistic understanding of the phenotype encountered.
RESULTS: We show that Gfa2-A2AR KO mice exhibited enhanced MK-801 psychomotor response and decreased working memory; this was accompanied by a disruption of glutamate homeostasis characterized by aberrant GLT-I activity, increased presynaptic glutamate release, NMDA-R 2B subunit upregulation, and increased internalization of AMPA-R. Accordingly, selective GLT-I inhibition or blockade of GluR1/2 endocytosis prevented the psychomotor and cognitive phenotypes in Gfa2-A2AR KO mice, namely in the nucleus accumbens.
CONCLUSIONS: These results show that the dysfunction of astrocytic A2AR, by controlling GLT-I activity, triggers an astrocyte-to-neuron wave of communication resulting in disrupted glutamate homeostasis, thought to underlie several endophenotypes relevant to schizophrenia.},
	Author = {Matos, Marco and Shen, Hai-Ying and Augusto, Elisabete and Wang, Yumei and Wei, Catherine J and Wang, Yu Tian and Agostinho, Paula and Boison, Detlev and Cunha, Rodrigo A and Chen, Jiang-Fan},
	Date-Added = {2017-01-19 20:37:58 +0000},
	Date-Modified = {2017-01-19 20:37:58 +0000},
	Doi = {10.1016/j.biopsych.2015.02.026},
	Journal = {Biol Psychiatry},
	Journal-Full = {Biological psychiatry},
	Keywords = {A(2A)R; Adenosine; Astrocytes; GLT-I; NMDA-R; Schizophrenia},
	Mesh = {Animals; Astrocytes; Cognition Disorders; Disease Models, Animal; Dizocilpine Maleate; Excitatory Amino Acid Antagonists; Excitatory Amino Acid Transporter 2; Gene Expression Regulation; Glial Fibrillary Acidic Protein; Glutamic Acid; Homeostasis; Kainic Acid; Locomotion; Mice; Mice, Inbred C57BL; Mice, Transgenic; Psychomotor Disorders; Pyrimidines; Receptor, Adenosine A2A; Receptors, N-Methyl-D-Aspartate; Synaptosomes; Time Factors; Triazoles},
	Month = {Dec},
	Number = {11},
	Pages = {763-74},
	Pmc = {PMC4714966},
	Pmid = {25869810},
	Pst = {ppublish},
	Title = {Deletion of adenosine A2A receptors from astrocytes disrupts glutamate homeostasis leading to psychomotor and cognitive impairment: relevance to schizophrenia},
	Volume = {78},
	Year = {2015},
	File = {papers/Matos_BiolPsychiatry2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.biopsych.2015.02.026}}

@article{Silva:2013,
	Abstract = {Consumption of certain substances during pregnancy can interfere with brain development, leading to deleterious long-term neurological and cognitive impairments in offspring. To test whether modulators of adenosine receptors affect neural development, we exposed mouse dams to a subtype-selective adenosine type 2A receptor (A2AR) antagonist or to caffeine, a naturally occurring adenosine receptor antagonist, during pregnancy and lactation. We observed delayed migration and insertion of γ-aminobutyric acid (GABA) neurons into the hippocampal circuitry during the first postnatal week in offspring of dams treated with the A2AR antagonist or caffeine. This was associated with increased neuronal network excitability and increased susceptibility to seizures in response to a seizure-inducing agent. Adult offspring of mouse dams exposed to A2AR antagonists during pregnancy and lactation displayed loss of hippocampal GABA neurons and some cognitive deficits. These results demonstrate that exposure to A2AR antagonists including caffeine during pregnancy and lactation in rodents may have adverse effects on the neural development of their offspring.},
	Author = {Silva, Carla G and M{\'e}tin, Christine and Fazeli, Walid and Machado, Nuno J and Darmopil, Sanja and Launay, Pierre-Serge and Ghestem, Antoine and Nesa, Marie-Pascale and Bassot, Emilie and Szab{\'o}, Eszter and Baqi, Younis and M{\"u}ller, Christa E and Tom{\'e}, Angelo R and Ivanov, Anton and Isbrandt, Dirk and Zilberter, Yuri and Cunha, Rodrigo A and Esclapez, Monique and Bernard, Christophe},
	Date-Added = {2017-01-19 20:36:44 +0000},
	Date-Modified = {2017-01-19 20:36:44 +0000},
	Doi = {10.1126/scitranslmed.3006258},
	Journal = {Sci Transl Med},
	Journal-Full = {Science translational medicine},
	Mesh = {Aging; Animals; Animals, Newborn; Brain; Caffeine; Cell Movement; Cognition Disorders; Disease Susceptibility; Female; Fetus; GABAergic Neurons; Glutamates; Green Fluorescent Proteins; Haplorhini; Hippocampus; Mice; Nerve Net; Pregnancy; Purinergic P1 Receptor Antagonists; Rats; Receptors, Adenosine A2; Seizures; Telencephalon},
	Month = {Aug},
	Number = {197},
	Pages = {197ra104},
	Pmid = {23926202},
	Pst = {ppublish},
	Title = {Adenosine receptor antagonists including caffeine alter fetal brain development in mice},
	Volume = {5},
	Year = {2013},
	File = {papers/Silva_SciTranslMed2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/scitranslmed.3006258}}

@article{Aden:2000,
	Abstract = {Maternal caffeine intake has been suggested to influence the offspring. We have studied the effects of maternal caffeine intake on adenosine and GABA receptors, targets for caffeine, during development of the rat brain. Caffeine (0.3 g/L) was added to the drinking water of rat dams during pregnancy and early postnatal life. Adenosine A1 and A2A and GABAA receptor development was studied using receptor autoradiography and in situ hybridization. Pups were examined on embryonic d 14 (E14), E18, E21, 2 h after birth (P2h), P24h, postnatal d 3 (P3), P7, P14, and P21. Adenosine A, receptor mRNA was detected at E14 and receptors at E18. A1 mRNA levels increased from the level reached at E18 between P3 and P14 (maximally a doubling), whereas A, receptors, studied by [3H]-1,3-dipropyl-8-cyclopentyl xanthine binding, increased later and to a much larger extent (about 10-fold) postnatally. Caffeine treatment had no significant effect on adenosine A1 receptors or on A1 receptor mRNA. A2A mRNA had reached adult levels by E18, whereas receptor levels were low or undetectable before birth and increased dramatically until P14. Caffeine did not influence A2A receptors or A2A receptor mRNA at any stage during development. [3H]-flunitrazepam binding, representing GABAA receptors, showed large regional variations during ontogeny, but there were no clear differences between the caffeine-exposed and the nonexposed pups. Thus, exposure to a low dose of caffeine during gestation and postnatal life had only minor effects on development of adenosine A, and A2A receptors and GABAA receptors in the rat brain.},
	Author = {Ad{\'e}n, U and Herlenius, E and Tang, L Q and Fredholm, B B},
	Date-Added = {2017-01-19 20:35:56 +0000},
	Date-Modified = {2017-01-19 20:35:56 +0000},
	Doi = {10.1203/00006450-200008000-00010},
	Journal = {Pediatr Res},
	Journal-Full = {Pediatric research},
	Mesh = {Adenosine; Animals; Animals, Newborn; Autoradiography; Brain; Caffeine; Female; Gene Expression Regulation, Developmental; In Situ Hybridization; Phenethylamines; Pregnancy; Prenatal Exposure Delayed Effects; Rats; Rats, Wistar; Receptors, GABA-A; Receptors, Purinergic P1; Tritium; Xanthines},
	Month = {Aug},
	Number = {2},
	Pages = {177-83},
	Pmid = {10926292},
	Pst = {ppublish},
	Title = {Maternal caffeine intake has minor effects on adenosine receptor ontogeny in the rat brain},
	Volume = {48},
	Year = {2000},
	File = {papers/Adén_PediatrRes2000.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1203/00006450-200008000-00010}}

@article{Schwalfenberg:2013,
	Abstract = {Background. Increasing concern is evident about contamination of foodstuffs and natural health products. Methods. Common off-the-shelf varieties of black, green, white, and oolong teas sold in tea bags were used for analysis in this study. Toxic element testing was performed on 30 different teas by analyzing (i) tea leaves, (ii) tea steeped for 3-4 minutes, and (iii) tea steeped for 15-17 minutes. Results were compared to existing preferred endpoints. Results. All brewed teas contained lead with 73% of teas brewed for 3 minutes and 83% brewed for 15 minutes having lead levels considered unsafe for consumption during pregnancy and lactation. Aluminum levels were above recommended guidelines in 20% of brewed teas. No mercury was found at detectable levels in any brewed tea samples. Teas contained several beneficial elements such as magnesium, calcium, potassium, and phosphorus. Of trace minerals, only manganese levels were found to be excessive in some black teas. Conclusions. Toxic contamination by heavy metals was found in most of the teas sampled. Some tea samples are considered unsafe. There are no existing guidelines for routine testing or reporting of toxicant levels in "naturally" occurring products. Public health warnings or industry regulation might be indicated to protect consumer safety.},
	Author = {Schwalfenberg, Gerry and Genuis, Stephen J and Rodushkin, Ilia},
	Date-Added = {2017-01-19 20:34:51 +0000},
	Date-Modified = {2017-01-19 20:34:51 +0000},
	Doi = {10.1155/2013/370460},
	Journal = {J Toxicol},
	Journal-Full = {Journal of toxicology},
	Pages = {370460},
	Pmc = {PMC3821942},
	Pmid = {24260033},
	Pst = {ppublish},
	Title = {The benefits and risks of consuming brewed tea: beware of toxic element contamination},
	Volume = {2013},
	Year = {2013},
	File = {papers/Schwalfenberg_JToxicol2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1155/2013/370460}}

@article{Aden:2003,
	Abstract = {BACKGROUND AND PURPOSE: Cerebral hypoxic ischemia (HI) is an important cause of brain injury in the newborn infant. Adenosine is believed to protect against HI brain damage. However, the roles of the different adenosine receptors are unclear, particularly in young animals. We examined the role of adenosine A2A receptors (A2AR) using 7-day-old A2A knockout (A2AR(-/-)) mice in a model of HI.
METHODS: HI was induced in 7-day-old CD1 mice by exposure to 8% oxygen for 30 minutes after occlusion of the left common carotid artery. The resulting unilateral focal lesion was evaluated with the use of histopathological scoring and measurements of residual brain areas at 5 days, 3 weeks, and 3 months after HI. Behavioral evaluation of brain injury by locomotor activity, rotarod, and beam-walking test was made 3 weeks and 3 months after HI. Cortical cerebral blood flow, assessed by laser-Doppler flowmetry, and rectal temperature were measured during HI.
RESULTS: Reduction in cortical cerebral blood flow during HI and rectal temperature did not differ between wild-type (A2AR(+/+)) and knockout mice. In the A2AR(-/-) animals, brain injury was aggravated compared with wild-type mice. The A2AR(-/-) mice subjected to HI displayed increased forward locomotion and impaired rotarod performance in adulthood compared with A2AR(+/+) mice subjected to HI, whereas beam-walking performance was similarly defective in both groups.
CONCLUSIONS: These results suggest that, in contrast to the situation in adult animals, A2AR play an important protective role in neonatal HI brain injury.},
	Author = {Ad{\'e}n, Ulrika and Halldner, Linda and Lagercrantz, Hugo and Dalmau, Ishar and Ledent, Catherine and Fredholm, Bertil B},
	Date-Added = {2017-01-19 20:33:07 +0000},
	Date-Modified = {2017-01-19 20:33:07 +0000},
	Doi = {10.1161/01.STR.0000060204.67672.8B},
	Journal = {Stroke},
	Journal-Full = {Stroke},
	Mesh = {Animals; Animals, Newborn; Atmosphere Exposure Chambers; Behavior, Animal; Blood Flow Velocity; Body Temperature; Brain; Carotid Arteries; Cerebrovascular Circulation; Disease Models, Animal; Disease Progression; Hypoxia, Brain; Hypoxia-Ischemia, Brain; Laser-Doppler Flowmetry; Ligation; Mice; Mice, Knockout; Receptor, Adenosine A2A; Receptors, Purinergic P1; Survival Rate},
	Month = {Mar},
	Number = {3},
	Pages = {739-44},
	Pmid = {12624301},
	Pst = {ppublish},
	Title = {Aggravated brain damage after hypoxic ischemia in immature adenosine A2A knockout mice},
	Volume = {34},
	Year = {2003},
	File = {papers/Adén_Stroke2003.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1161/01.STR.0000060204.67672.8B}}

@article{Kinkead:2009,
	Abstract = {STUDY OBJECTIVES: Neonatal maternal separation (NMS) disrupts development of cardiorespiratory regulation. Adult male rats previously subjected to NMS are hypertensive and show a hypoxic ventilatory response greater than that of controls. These results have been obtained in awake or anesthetised animals, and the consequences of NMS on respiratory control during normal sleep are unknown. This study tested the following.
HYPOTHESES: NMS augments respiratory variability across sleep-wake states, and NMS-related enhancement of the hypoxic ventilatory response occurs during sleep.
METHODS: Two groups of adult rats were used: controls (no treatment) and rats subjected to NMS. Ventilatory activity, coefficient of variation, and hypoxic ventilatory response were compared between groups and across sleep-wake states.
SUBJECTS: Male Sprague Dawley rats-NMS: n=11; controls: n=10. Pups subjected to NMS were isolated from their mother for 3 hours per day from postnatal days 3 to 12. Controls were undisturbed.
MEASUREMENTS AND RESULTS: At adulthood, sleep-wake states were monitored by telemetry, and ventilatory activity was measured using whole-body plethysmography. Sleep and breathing were measured for 2.5 hours (in the morning) while the rats were breathing room air. Data were analysed in 20-second epochs. Rats were then exposed to a brief (90-sec) hypoxic episode (nadir = 12% O2) to measure the hypoxic ventilatory response. The coefficient of variability for tidal volume and breathing frequency decreased during sleep but remained more elevated in NMS rats than in controls. During non-rapid eye movement sleep, the breathing-frequency response to hypoxia of NMS rats was significantly greater than that of controls.
CONCLUSION: Neonatal maternal separation results in persistent disruption of respiratory control during sleep.},
	Author = {Kinkead, Richard and Montandon, Gaspard and Bairam, Aida and Lajeunesse, Yves and Horner, Richard},
	Date-Added = {2017-01-19 20:32:11 +0000},
	Date-Modified = {2017-01-19 20:32:11 +0000},
	Journal = {Sleep},
	Journal-Full = {Sleep},
	Mesh = {Animals; Animals, Newborn; Behavior, Animal; Electroencephalography; Electromyography; Hypoxia; Male; Maternal Deprivation; Plethysmography, Whole Body; Pulmonary Ventilation; Rats; Rats, Sprague-Dawley; Respiration; Respiratory Mechanics; Sleep; Sleep Apnea Syndromes; Telemetry; Tidal Volume; Time Factors; Wakefulness},
	Month = {Dec},
	Number = {12},
	Pages = {1611-20},
	Pmc = {PMC2786045},
	Pmid = {20041597},
	Pst = {ppublish},
	Title = {Neonatal maternal separation disrupts regulation of sleep and breathing in adult male rats},
	Volume = {32},
	Year = {2009}}

@article{Montandon:2009,
	Abstract = {Caffeine is commonly used clinically to treat apnoeas and unstable breathing associated with premature birth. Caffeine antagonizes adenosine receptors and acts as an efficient respiratory stimulant in neonates. Owing to its persistent effects on adenosine receptor expression in the brain, neonatal caffeine administration also has significant effects on maturation of the respiratory control system. However, since adenosine receptors are critically involved in sleep regulation, and sleep also modulates breathing, we tested the hypothesis that neonatal caffeine treatment disrupts regulation of sleep and breathing in the adult rat. Neonatal caffeine treatment (15 mg kg(-1) day(-1)) was administered from postnatal days 3-12. At adulthood (8-10 weeks old), sleep and breathing were measured with a telemetry system and whole-body plethysmography respectively. In adult rats treated with caffeine during the neonatal period, sleep time was reduced, sleep onset latency was increased, and non-rapid eye movement (non-REM) sleep was fragmented compared to controls. Ventilation at rest was higher in caffeine-treated adult rats compared to controls across sleep/wake states. Hypercapnic ventilatory responses were significantly reduced in caffeine-treated rats compared to control rats across sleep/wake states. Additional experiments in adult anaesthetized rats showed that at similar levels of arterial blood gases, phrenic nerve activity was enhanced in caffeine-treated rats. This study demonstrates that administration of caffeine in the neonatal period alters respiratory control system activity in awake and sleeping rats, as well as in the anaesthetized rats, and also has persistent disrupting effects on sleep that are apparent in adult rats.},
	Author = {Montandon, Gaspard and Horner, Richard L and Kinkead, Richard and Bairam, Aida},
	Date-Added = {2017-01-19 20:32:09 +0000},
	Date-Modified = {2017-01-19 20:32:09 +0000},
	Doi = {10.1113/jphysiol.2009.171918},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Age Factors; Animals; Animals, Newborn; Blood Gas Analysis; Caffeine; Male; Pulmonary Ventilation; Rats; Rats, Sprague-Dawley; Sleep; Time Factors; Wakefulness},
	Month = {Nov},
	Number = {Pt 22},
	Pages = {5493-507},
	Pmc = {PMC2793879},
	Pmid = {19770189},
	Pst = {ppublish},
	Title = {Caffeine in the neonatal period induces long-lasting changes in sleep and breathing in adult rats},
	Volume = {587},
	Year = {2009},
	File = {papers/Montandon_JPhysiol2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1113/jphysiol.2009.171918}}

@article{Ma:2016,
	Abstract = {Although modern techniques such as two-photon microscopy can now provide cellular-level three-dimensional imaging of the intact living brain, the speed and fields of view of these techniques remain limited. Conversely, two-dimensional wide-field optical mapping (WFOM), a simpler technique that uses a camera to observe large areas of the exposed cortex under visible light, can detect changes in both neural activity and haemodynamics at very high speeds. Although WFOM may not provide single-neuron or capillary-level resolution, it is an attractive and accessible approach to imaging large areas of the brain in awake, behaving mammals at speeds fast enough to observe widespread neural firing events, as well as their dynamic coupling to haemodynamics. Although such wide-field optical imaging techniques have a long history, the advent of genetically encoded fluorophores that can report neural activity with high sensitivity, as well as modern technologies such as light emitting diodes and sensitive and high-speed digital cameras have driven renewed interest in WFOM. To facilitate the wider adoption and standardization of WFOM approaches for neuroscience and neurovascular coupling research, we provide here an overview of the basic principles of WFOM, considerations for implementation of wide-field fluorescence imaging of neural activity, spectroscopic analysis and interpretation of results.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'.},
	Author = {Ma, Ying and Shaik, Mohammed A and Kim, Sharon H and Kozberg, Mariel G and Thibodeaux, David N and Zhao, Hanzhi T and Yu, Hang and Hillman, Elizabeth M C},
	Date-Added = {2017-01-19 20:30:19 +0000},
	Date-Modified = {2017-01-19 20:30:19 +0000},
	Doi = {10.1098/rstb.2015.0360},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Keywords = {GCaMP; fluorescence; haemodynamics; neurovascular coupling; optical imaging; spectroscopy},
	Month = {Oct},
	Number = {1705},
	Pmc = {PMC5003860},
	Pmid = {27574312},
	Pst = {ppublish},
	Title = {Wide-field optical mapping of neural activity and brain haemodynamics: considerations and novel approaches},
	Volume = {371},
	Year = {2016},
	File = {papers/Ma_PhilosTransRSocLondBBiolSci2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1098/rstb.2015.0360}}

@article{Button:2013,
	Abstract = {A study with low statistical power has a reduced chance of detecting a true effect, but it is less well appreciated that low power also reduces the likelihood that a statistically significant result reflects a true effect. Here, we show that the average statistical power of studies in the neurosciences is very low. The consequences of this include overestimates of effect size and low reproducibility of results. There are also ethical dimensions to this problem, as unreliable research is inefficient and wasteful. Improving reproducibility in neuroscience is a key priority and requires attention to well-established but often ignored methodological principles.},
	Author = {Button, Katherine S and Ioannidis, John P A and Mokrysz, Claire and Nosek, Brian A and Flint, Jonathan and Robinson, Emma S J and Munaf{\`o}, Marcus R},
	Date-Added = {2017-01-19 20:24:24 +0000},
	Date-Modified = {2017-01-19 20:24:24 +0000},
	Doi = {10.1038/nrn3475},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Humans; Neurosciences; Probability; Reproducibility of Results; Sample Size},
	Month = {May},
	Number = {5},
	Pages = {365-76},
	Pmid = {23571845},
	Pst = {ppublish},
	Title = {Power failure: why small sample size undermines the reliability of neuroscience},
	Volume = {14},
	Year = {2013},
	File = {papers/Button_NatRevNeurosci2013.pdf}}

@article{Adolphs:1995,
	Abstract = {We have previously reported that bilateral amygdala damage in humans compromises the recognition of fear in facial expressions while leaving intact recognition of face identity (Adolphs et al., 1994). The present study aims at examining questions motivated by this finding. We addressed the possibility that unilateral amygdala damage might be sufficient to impair recognition of emotional expressions. We also obtained further data on our subject with bilateral amygdala damage, in order to elucidate possible mechanisms that could account for the impaired recognition of expressions of fear. The results show that bilateral, but not unilateral, damage to the human amygdala impairs the processing of fearful facial expressions. This impairment appears to result from an insensitivity to the intensity of fear expressed by faces. We also confirmed a double dissociation between the recognition of facial expressions of fear, and the recognition of identity of a face: these two processes can be impaired independently, lending support to the idea that they are subserved in part by anatomically separate neural systems. Based on our data, and on what is known about the amygdala's connectivity, we propose that the amygdala is required to link visual representations of facial expressions, on the one hand, with representations that constitute the concept of fear, on the other. Preliminary data suggest the amygdala's role extends to both recognition and recall of fearful facial expressions.},
	Author = {Adolphs, R and Tranel, D and Damasio, H and Damasio, A R},
	Date-Added = {2016-12-02 18:40:54 +0000},
	Date-Modified = {2016-12-02 18:40:54 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Amygdala; Art; Brain Damage, Chronic; Brain Diseases; Emotions; Face; Facial Expression; Fear; Humans; Magnetic Resonance Imaging; Neuropsychological Tests; Pattern Recognition, Visual; Social Behavior},
	Month = {Sep},
	Number = {9},
	Pages = {5879-91},
	Pmid = {7666173},
	Pst = {ppublish},
	Title = {Fear and the human amygdala},
	Volume = {15},
	Year = {1995},
	File = {papers/Adolphs_JNeurosci1995.pdf}}

@article{Smit-Rigter:2016,
	Abstract = {Mitochondria buffer intracellular Ca(2+) and provide energy [1]. Because synaptic structures with high Ca(2+) buffering [2-4] or energy demand [5] are often localized far away from the soma, mitochondria are actively transported to these sites [6-11]. Also, the removal and degradation of mitochondria are tightly regulated [9, 12, 13], because dysfunctional mitochondria are a source of reactive oxygen species, which can damage the cell [14]. Deficits in mitochondrial trafficking have been proposed to contribute to the pathogenesis of Parkinson's disease, schizophrenia, amyotrophic lateral sclerosis, optic atrophy, and Alzheimer's disease [13, 15-19]. In neuronal cultures, about a third of mitochondria are motile, whereas the majority remains stationary for several days [8, 20]. Activity-dependent mechanisms cause mitochondria to stop at synaptic sites [7, 8, 20, 21], which affects synapse function and maintenance. Reducing mitochondrial content in dendrites decreases spine density [22, 23], whereas increasing mitochondrial content or activity increases it [7]. These bidirectional interactions between synaptic activity and mitochondrial trafficking suggest that mitochondria may regulate synaptic plasticity. Here we investigated the dynamics of mitochondria in relation to axonal boutons of neocortical pyramidal neurons for the first time in vivo. We find that under these circumstances practically all mitochondria are stationary, both during development and in adulthood. In adult visual cortex, mitochondria are preferentially localized at putative boutons, where they remain for several days. Retinal-lesion-induced cortical plasticity increases turnover of putative boutons but leaves mitochondrial turnover unaffected. We conclude that in visual cortex in vivo, mitochondria are less dynamic than in vitro, and that structural plasticity does not affect mitochondrial dynamics.},
	Author = {Smit-Rigter, Laura and Rajendran, Rajeev and Silva, Catia A P and Spierenburg, Liselot and Groeneweg, Femke and Ruimschotel, Emma M and van Versendaal, Danielle and van der Togt, Chris and Eysel, Ulf T and Heimel, J Alexander and Lohmann, Christian and Levelt, Christiaan N},
	Date-Added = {2016-12-02 18:40:11 +0000},
	Date-Modified = {2016-12-02 18:40:11 +0000},
	Doi = {10.1016/j.cub.2016.07.033},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Month = {Oct},
	Number = {19},
	Pages = {2609-2616},
	Pmid = {27641766},
	Pst = {ppublish},
	Title = {Mitochondrial Dynamics in Visual Cortex Are Limited In Vivo and Not Affected by Axonal Structural Plasticity},
	Volume = {26},
	Year = {2016},
	File = {papers/Smit-Rigter_CurrBiol2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2016.07.033}}

@article{Winnubst:2015,
	Abstract = {Spontaneous activity fine-tunes neuronal connections in the developing brain. To explore the underlying synaptic plasticity mechanisms, we monitored naturally occurring changes in spontaneous activity at individual synapses with whole-cell patch-clamp recordings and simultaneous calcium imaging in the mouse visual cortex in vivo. Analyzing activity changes across large populations of synapses revealed a simple and efficient local plasticity rule: synapses that exhibit low synchronicity with nearby neighbors (<12 μm) become depressed in their transmission frequency. Asynchronous electrical stimulation of individual synapses in hippocampal slices showed that this is due to a decrease in synaptic transmission efficiency. Accordingly, experimentally increasing local synchronicity, by stimulating synapses in response to spontaneous activity at neighboring synapses, stabilized synaptic transmission. Finally, blockade of the high-affinity proBDNF receptor p75(NTR) prevented the depression of asynchronously stimulated synapses. Thus, spontaneous activity drives local synaptic plasticity at individual synapses in an "out-of-sync, lose-your-link" fashion through proBDNF/p75(NTR) signaling to refine neuronal connectivity. VIDEO ABSTRACT.},
	Author = {Winnubst, Johan and Cheyne, Juliette E and Niculescu, Dragos and Lohmann, Christian},
	Date-Added = {2016-12-02 18:37:43 +0000},
	Date-Modified = {2016-12-02 18:37:43 +0000},
	Doi = {10.1016/j.neuron.2015.06.029},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Calcium; Computer Simulation; Electric Stimulation; Excitatory Amino Acid Antagonists; In Vitro Techniques; Luminescent Proteins; Mice; Mice, Inbred C57BL; Mice, Transgenic; Models, Biological; Nerve Net; Neuronal Plasticity; Neurons; Organ Culture Techniques; Patch-Clamp Techniques; Quinoxalines; Signal Transduction; Visual Cortex},
	Month = {Jul},
	Number = {2},
	Pages = {399-410},
	Pmid = {26182421},
	Pst = {ppublish},
	Title = {Spontaneous Activity Drives Local Synaptic Plasticity In Vivo},
	Volume = {87},
	Year = {2015},
	File = {papers/Winnubst_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.06.029}}

@article{Niculescu:2014,
	Abstract = {The presence of direct, cytoplasmatic, communication between neurons in the brain of vertebrates has been demonstrated a long time ago. These gap junctions have been characterized in many brain areas in terms of subunit composition, biophysical properties, neuronal connectivity patterns, and developmental regulation. Although interesting findings emerged, showing that different subunits are specifically regulated during development, or that excitatory and inhibitory neuronal networks exhibit various electrical connectivity patterns, gap junctions did not receive much further interest. Originally, it was believed that gap junctions represent simple passageways for electrical and biochemical coordination early in development. Today, we know that gap junction connectivity is tightly regulated, following independent developmental patterns for excitatory and inhibitory networks. Electrical connections are important for many specific functions of neurons, and are, for example, required for the development of neuronal stimulus tuning in the visual system. Here, we integrate the available data on neuronal connectivity and gap junction properties, as well as the most recent findings concerning the functional implications of electrical connections in the developing thalamus and neocortex.},
	Author = {Niculescu, Dragos and Lohmann, Christian},
	Date-Added = {2016-12-02 18:35:44 +0000},
	Date-Modified = {2016-12-02 18:35:44 +0000},
	Doi = {10.1093/cercor/bht175},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {connexin; electrical synapse; gap junctions; neocortex; thalamus},
	Mesh = {Animals; Connexins; Gap Junctions; Neocortex; Nerve Net; Neurons; Thalamus},
	Month = {Dec},
	Number = {12},
	Pages = {3097-106},
	Pmc = {PMC4224240},
	Pmid = {23843439},
	Pst = {ppublish},
	Title = {Gap junctions in developing thalamic and neocortical neuronal networks},
	Volume = {24},
	Year = {2014},
	File = {papers/Niculescu_CerebCortex2014.pdf}}

@article{Lohmann:2014,
	Abstract = {The brain is programmed to drive behaviour by precisely wiring the appropriate neuronal circuits. Wiring and rewiring of neuronal circuits largely depends on the orchestrated changes in the strengths of synaptic contacts. Here, we review how the rules of synaptic plasticity change during development of the brain, from birth to independence. We focus on the changes that occur at the postsynaptic side of excitatory glutamatergic synapses in the rodent hippocampus and neocortex. First we summarize the current data on the structure of synapses and the developmental expression patterns of the key molecular players of synaptic plasticity, N-methyl-d-aspartate (NMDA) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, as well as pivotal kinases (Ca(2+)/calmodulin-dependent protein kinase II, protein kinase A, protein kinase C) and phosphatases (PP1, PP2A, PP2B). In the second part we relate these findings to important characteristics of the emerging network. We argue that the concerted and gradual shifts in the usage of plasticity molecules comply with the changing need for (re)wiring neuronal circuits.},
	Author = {Lohmann, Christian and Kessels, Helmut W},
	Date-Added = {2016-12-02 18:35:00 +0000},
	Date-Modified = {2016-12-02 18:35:00 +0000},
	Doi = {10.1113/jphysiol.2012.235119},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Animals; Brain; Humans; N-Methylaspartate; Nerve Net; Neuronal Plasticity; Phosphoric Monoester Hydrolases; Protein Kinases; alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid},
	Month = {Jan},
	Number = {1},
	Pages = {13-31},
	Pmc = {PMC3903349},
	Pmid = {24144877},
	Pst = {ppublish},
	Title = {The developmental stages of synaptic plasticity},
	Volume = {592},
	Year = {2014},
	File = {papers/Lohmann_JPhysiol2014.pdf}}

@article{Leighton:2016,
	Abstract = {In order to accurately process incoming sensory stimuli, neurons must be organized into functional networks, with both genetic and environmental factors influencing the precise arrangement of connections between cells. Teasing apart the relative contributions of molecular guidance cues, spontaneous activity and visual experience during this maturation is on-going. During development of the sensory system, the first, rough organization of connections is created by molecular factors. These connections are then modulated by the intrinsically generated activity of neurons, even before the senses have become operational. Spontaneous waves of depolarizations sweep across the nervous system, placing them in a prime position to strengthen correct connections and weaken others, shaping synapses into a useful network. A large body of work now support the idea that, rather than being a mere side-effect of the system, spontaneous activity actually contains information which readies the nervous system so that, as soon as the senses become active, sensory information can be utilized by the animal. An example is the neonatal mouse. As soon as the eyelids first open, neurons in the cortex respond to visual information without the animal having previously encountered structured sensory input (Cang et al., 2005b; Rochefort et al., 2011; Zhang et al., 2012; Ko et al., 2013). In vivo imaging techniques have advanced considerably, allowing observation of the natural activity in the brain of living animals down to the level of the individual synapse. New (opto)genetic methods make it possible to subtly modulate the spatio-temporal properties of activity, aiding our understanding of how these characteristics relate to the function of spontaneous activity. Such experiments have had a huge impact on our knowledge by permitting direct testing of ideas about the plasticity mechanisms at play in the intact system, opening up a provocative range of fresh questions. Here, we intend to outline the most recent descriptions of spontaneous activity patterns in rodent developing sensory areas, as well as the inferences we can make about the information content of those activity patterns and ideas about the plasticity rules that allow this activity to shape the young brain.},
	Author = {Leighton, Alexandra H and Lohmann, Christian},
	Date = {2016},
	Date-Added = {2016-12-02 18:34:52 +0000},
	Date-Modified = {2016-12-02 18:34:52 +0000},
	Doi = {10.3389/fncir.2016.00071},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {auditory system development; developmental biology; plasticity mechanisms; spontaneous activity; synaptic plasticity; visual system development},
	Pages = {71},
	Pmc = {PMC5011135},
	Pmid = {27656131},
	Pst = {epublish},
	Title = {The Wiring of Developing Sensory Circuits-From Patterned Spontaneous Activity to Synaptic Plasticity Mechanisms},
	Volume = {10},
	Year = {2016},
	File = {papers/Leighton_FrontNeuralCircuits2016.pdf}}

@article{Ramamurthi:1988,
	Abstract = {After a survey of the anatomical and physiological basis of operative treatment of behaviour disorders by stereotactic lesions in the amygdala and the posterior medial hypothalamus the author describes his own experiences with 603 operations for control of conservatively untreatable aggressiveness. In 481 cases bilateral amygdalotomies and in 122 mostly secondary posteromedian hypothalamotomies have been performed. Initially excellent or moderate improvement was achieved in 76%. After a follow-up of more than three years this figure only slightly decreased to 70%. The group of patients who did not positively respond (30%) needs further study to discover the reasons for failure.},
	Author = {Ramamurthi, B},
	Date-Added = {2016-12-01 21:12:44 +0000},
	Date-Modified = {2016-12-01 21:12:44 +0000},
	Journal = {Acta Neurochir Suppl (Wien)},
	Journal-Full = {Acta neurochirurgica. Supplementum},
	Mesh = {Adolescent; Aggression; Amygdala; Attention Deficit Disorder with Hyperactivity; Child; Child Behavior Disorders; Epilepsy; Follow-Up Studies; Humans; Hypothalamus; Neurocognitive Disorders; Neuropsychological Tests; Postoperative Complications; Psychomotor Agitation; Stereotaxic Techniques; Violence},
	Pages = {152-7},
	Pmid = {3066131},
	Pst = {ppublish},
	Title = {Stereotactic operation in behaviour disorders. Amygdalotomy and hypothalamotomy},
	Volume = {44},
	Year = {1988}}

@article{Kano:2009,
	Abstract = {The discovery of cannabinoid receptors and subsequent identification of their endogenous ligands (endocannabinoids) in early 1990s have greatly accelerated research on cannabinoid actions in the brain. Then, the discovery in 2001 that endocannabinoids mediate retrograde synaptic signaling has opened up a new era for cannabinoid research and also established a new concept how diffusible messengers modulate synaptic efficacy and neural activity. The last 7 years have witnessed remarkable advances in our understanding of the endocannabinoid system. It is now well accepted that endocannabinoids are released from postsynaptic neurons, activate presynaptic cannabinoid CB(1) receptors, and cause transient and long-lasting reduction of neurotransmitter release. In this review, we aim to integrate our current understanding of functions of the endocannabinoid system, especially focusing on the control of synaptic transmission in the brain. We summarize recent electrophysiological studies carried out on synapses of various brain regions and discuss how synaptic transmission is regulated by endocannabinoid signaling. Then we refer to recent anatomical studies on subcellular distribution of the molecules involved in endocannabinoid signaling and discuss how these signaling molecules are arranged around synapses. In addition, we make a brief overview of studies on cannabinoid receptors and their intracellular signaling, biochemical studies on endocannabinoid metabolism, and behavioral studies on the roles of the endocannabinoid system in various aspects of neural functions.},
	Author = {Kano, Masanobu and Ohno-Shosaku, Takako and Hashimotodani, Yuki and Uchigashima, Motokazu and Watanabe, Masahiko},
	Date-Added = {2016-11-15 20:43:47 +0000},
	Date-Modified = {2016-11-15 20:43:47 +0000},
	Doi = {10.1152/physrev.00019.2008},
	Journal = {Physiol Rev},
	Journal-Full = {Physiological reviews},
	Mesh = {Animals; Cannabinoid Receptor Modulators; Endocannabinoids; Humans; Receptors, Cannabinoid; Signal Transduction; Synapses; Synaptic Transmission},
	Month = {Jan},
	Number = {1},
	Pages = {309-80},
	Pmid = {19126760},
	Pst = {ppublish},
	Title = {Endocannabinoid-mediated control of synaptic transmission},
	Volume = {89},
	Year = {2009},
	File = {papers/Kano_PhysiolRev2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/physrev.00019.2008}}

@article{Berchtold:2000,
	Abstract = {Mammalian skeletal muscle shows an enormous variability in its functional features such as rate of force production, resistance to fatigue, and energy metabolism, with a wide spectrum from slow aerobic to fast anaerobic physiology. In addition, skeletal muscle exhibits high plasticity that is based on the potential of the muscle fibers to undergo changes of their cytoarchitecture and composition of specific muscle protein isoforms. Adaptive changes of the muscle fibers occur in response to a variety of stimuli such as, e.g., growth and differentition factors, hormones, nerve signals, or exercise. Additionally, the muscle fibers are arranged in compartments that often function as largely independent muscular subunits. All muscle fibers use Ca(2+) as their main regulatory and signaling molecule. Therefore, contractile properties of muscle fibers are dependent on the variable expression of proteins involved in Ca(2+) signaling and handling. Molecular diversity of the main proteins in the Ca(2+) signaling apparatus (the calcium cycle) largely determines the contraction and relaxation properties of a muscle fiber. The Ca(2+) signaling apparatus includes 1) the ryanodine receptor that is the sarcoplasmic reticulum Ca(2+) release channel, 2) the troponin protein complex that mediates the Ca(2+) effect to the myofibrillar structures leading to contraction, 3) the Ca(2+) pump responsible for Ca(2+) reuptake into the sarcoplasmic reticulum, and 4) calsequestrin, the Ca(2+) storage protein in the sarcoplasmic reticulum. In addition, a multitude of Ca(2+)-binding proteins is present in muscle tissue including parvalbumin, calmodulin, S100 proteins, annexins, sorcin, myosin light chains, beta-actinin, calcineurin, and calpain. These Ca(2+)-binding proteins may either exert an important role in Ca(2+)-triggered muscle contraction under certain conditions or modulate other muscle activities such as protein metabolism, differentiation, and growth. Recently, several Ca(2+) signaling and handling molecules have been shown to be altered in muscle diseases. Functional alterations of Ca(2+) handling seem to be responsible for the pathophysiological conditions seen in dystrophinopathies, Brody's disease, and malignant hyperthermia. These also underline the importance of the affected molecules for correct muscle performance.},
	Author = {Berchtold, M W and Brinkmeier, H and M{\"u}ntener, M},
	Date-Added = {2016-11-15 20:42:46 +0000},
	Date-Modified = {2016-11-15 20:42:46 +0000},
	Journal = {Physiol Rev},
	Journal-Full = {Physiological reviews},
	Mesh = {Animals; Calcium; Calcium Signaling; Calcium-Transporting ATPases; Humans; Muscle Fibers, Skeletal; Muscle, Skeletal; Troponin},
	Month = {Jul},
	Number = {3},
	Pages = {1215-65},
	Pmid = {10893434},
	Pst = {ppublish},
	Title = {Calcium ion in skeletal muscle: its crucial role for muscle function, plasticity, and disease},
	Volume = {80},
	Year = {2000},
	File = {papers/Berchtold_PhysiolRev2000.pdf}}

@article{Tang:2014,
	Abstract = {Voltage-gated calcium (CaV) channels catalyse rapid, highly selective influx of Ca(2+) into cells despite a 70-fold higher extracellular concentration of Na(+). How CaV channels solve this fundamental biophysical problem remains unclear. Here we report physiological and crystallographic analyses of a calcium selectivity filter constructed in the homotetrameric bacterial NaV channel NaVAb. Our results reveal interactions of hydrated Ca(2+) with two high-affinity Ca(2+)-binding sites followed by a third lower-affinity site that would coordinate Ca(2+) as it moves inward. At the selectivity filter entry, Site 1 is formed by four carboxyl side chains, which have a critical role in determining Ca(2+) selectivity. Four carboxyls plus four backbone carbonyls form Site 2, which is targeted by the blocking cations Cd(2+) and Mn(2+), with single occupancy. The lower-affinity Site 3 is formed by four backbone carbonyls alone, which mediate exit into the central cavity. This pore architecture suggests a conduction pathway involving transitions between two main states with one or two hydrated Ca(2+) ions bound in the selectivity filter and supports a 'knock-off' mechanism of ion permeation through a stepwise-binding process. The multi-ion selectivity filter of our CaVAb model establishes a structural framework for understanding the mechanisms of ion selectivity and conductance by vertebrate CaV channels.},
	Author = {Tang, Lin and Gamal El-Din, Tamer M and Payandeh, Jian and Martinez, Gilbert Q and Heard, Teresa M and Scheuer, Todd and Zheng, Ning and Catterall, William A},
	Date-Added = {2016-10-20 21:29:41 +0000},
	Date-Modified = {2016-10-20 21:29:41 +0000},
	Doi = {10.1038/nature12775},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Bacterial Proteins; Binding Sites; Biocatalysis; Calcium; Calcium Channels; Cations, Divalent; Crystallography, X-Ray; Electric Conductivity; Ion Channel Gating; Models, Biological; Models, Molecular; Structure-Activity Relationship; Substrate Specificity},
	Month = {Jan},
	Number = {7481},
	Pages = {56-61},
	Pmc = {PMC3877713},
	Pmid = {24270805},
	Pst = {ppublish},
	Title = {Structural basis for Ca2+ selectivity of a voltage-gated calcium channel},
	Volume = {505},
	Year = {2014},
	File = {papers/Tang_Nature2014.pdf}}

@article{Davies:2003,
	Abstract = {Ethanol is a chemically simple compound that produces many well-known effects in humans. The prevailing idea for many years was that ethanol and other alcohols exerted their effects on the central nervous system (CNS) by non-selectively disrupting the lipid bilayers of neurons. However, in recent years, there has been an accumulation of evidence pointing to the importance of ligand-gated ion channels (LGICs) in mediating the effects of ethanol. Of these LGICs, gamma-aminobutyric acid type A (GABAA) receptors appear to occupy a central role in mediating the effects of ethanol in the CNS. GABA is the primary inhibitory neurotransmitter in the mammalian CNS, and activation of GABAA receptors by GABA tends to decrease neuronal excitability. This article reviews several aspects of GABAA receptor and ethanol interactions, including the evidence for short- and long-term modulation of GABAA receptors by ethanol and evidence for a GABAA receptor-related genetic component of alcoholism.},
	Author = {Davies, Martin},
	Date-Added = {2016-10-20 20:41:05 +0000},
	Date-Modified = {2016-10-20 20:41:05 +0000},
	Journal = {J Psychiatry Neurosci},
	Journal-Full = {Journal of psychiatry \& neuroscience : JPN},
	Mesh = {Alcoholism; Animals; Brain; Cell Membrane; Ethanol; Female; Fetal Alcohol Spectrum Disorders; Humans; Pregnancy; Receptors, GABA-A; Self Administration},
	Month = {Jul},
	Number = {4},
	Pages = {263-74},
	Pmc = {PMC165791},
	Pmid = {12921221},
	Pst = {ppublish},
	Title = {The role of GABAA receptors in mediating the effects of alcohol in the central nervous system},
	Volume = {28},
	Year = {2003},
	File = {papers/Davies_JPsychiatryNeurosci2003.pdf}}

@article{Mihic:1997,
	Abstract = {Volatile anaesthetics have historically been considered to act in a nonspecific manner on the central nervous system. More recent studies, however, have revealed that the receptors for inhibitory neurotransmitters such as gamma-aminobutyric acid (GABA) and glycine are sensitive to clinically relevant concentrations of inhaled anaesthetics. The function of GABA(A) and glycine receptors is enhanced by a number of anaesthetics and alcohols, whereas activity of the related GABA rho1 receptor is reduced. We have used this difference in pharmacology to investigate the molecular basis for modulation of these receptors by anaesthetics and alcohols. By using chimaeric receptor constructs, we have identified a region of 45 amino-acid residues that is both necessary and sufficient for the enhancement of receptor function. Within this region, two specific amino-acid residues in transmembrane domains 2 and 3 are critical for allosteric modulation of both GABA(A) and glycine receptors by alcohols and two volatile anaesthetics. These observations support the idea that anaesthetics exert a specific effect on these ion-channel proteins, and allow for the future testing of specific hypotheses of the action of anaesthetics.},
	Author = {Mihic, S J and Ye, Q and Wick, M J and Koltchine, V V and Krasowski, M D and Finn, S E and Mascia, M P and Valenzuela, C F and Hanson, K K and Greenblatt, E P and Harris, R A and Harrison, N L},
	Date-Added = {2016-10-20 20:39:53 +0000},
	Date-Modified = {2016-10-20 20:39:53 +0000},
	Doi = {10.1038/38738},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Alanine; Amino Acid Sequence; Anesthetics, Inhalation; Anesthetics, Intravenous; Animals; Binding Sites; Cell Line; Electrophysiology; Enflurane; Ethanol; Glycine; Humans; Molecular Sequence Data; Mutagenesis; Propofol; Receptors, GABA-A; Receptors, Glycine; Recombinant Fusion Proteins; Sequence Homology, Amino Acid; Serine; Tryptophan; Xenopus},
	Month = {Sep},
	Number = {6649},
	Pages = {385-9},
	Pmid = {9311780},
	Pst = {ppublish},
	Title = {Sites of alcohol and volatile anaesthetic action on GABA(A) and glycine receptors},
	Volume = {389},
	Year = {1997},
	File = {papers/Mihic_Nature1997.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/38738}}

@article{Picciotto:2000,
	Abstract = {Molecular cloning has elucidated the sequence of a family of acetylcholine receptor subunits that are activated by nicotine. Subsequent studies on the localization of individual subunits and the physiological properties of nicotinic subunit combinations in vitro, have led to identification of subunit compositions of nicotinic receptors that may function in vivo, as the native receptor. A particular challenge for the field has been to use these molecular data to determine which individual nicotinic receptor subtype is responsible for mediating each of the behavioral effects of nicotine. Human and animal studies have shown that nicotine is reinforcing and likely responsible for the addictive properties of tobacco. In addition, nicotine has been shown to have effects on locomotion, cognition, affect, and pain sensitivity. Recent studies combining the techniques of molecular biology, pharmacology, electrophysiology, and behavioral analysis to analyze knock out mice that lack individual subunits of the nicotinic acetylcholine receptor, have helped identify the role of specific nicotinic subunits in some of these complex behaviors. These studies could ultimately be useful in designing specific nicotinic receptor agonists and antagonists that may have uses in the clinic.},
	Author = {Picciotto, M R and Caldarone, B J and King, S L and Zachariou, V},
	Date-Added = {2016-10-20 20:37:26 +0000},
	Date-Modified = {2016-10-20 20:37:26 +0000},
	Doi = {10.1016/S0893-133X(99)00146-3},
	Journal = {Neuropsychopharmacology},
	Journal-Full = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology},
	Mesh = {Animals; Behavior; Humans; Mice; Mice, Knockout; Models, Neurological; Molecular Biology; Receptors, Nicotinic},
	Month = {May},
	Number = {5},
	Pages = {451-65},
	Pmid = {10731620},
	Pst = {ppublish},
	Title = {Nicotinic receptors in the brain. Links between molecular biology and behavior},
	Volume = {22},
	Year = {2000},
	File = {papers/Picciotto_Neuropsychopharmacology2000.pdf}}

@article{Chavas:2003,
	Abstract = {Functional GABA synapses are usually assumed to be inhibitory. However, we show here that inhibitory and excitatory GABA connections coexist in the cerebellar interneuron network. The reversal potential of GABAergic currents (E(GABA)) measured in interneurons is relatively depolarized and contrasts with the hyperpolarized value found in Purkinje cells (-58 and -85 mV respectively). This finding is not correlated to a specific developmental stage and is maintained in the adult animal. E(GABA) in interneurons is close to the mean membrane potential (-56.5 mV, as measured with a novel "equal firing potential" method), and both parameters vary enough among cells so that the driving force for GABA currents can be either inward or outward. Indeed, using noninvasive cell-attached recordings, we demonstrate inhibitory, excitatory, and sequential inhibitory and excitatory responses to interneuron stimulation [results obtained both in juvenile (postnatal days 12-14) and subadult (postnatal days 20-25) animals]. In hyperpolarized cells, single synaptic GABA currents can trigger spikes or trains of spikes, and subthreshold stimulations enhance the responsiveness to subsequent excitatory stimulation over at least 30 msec. We suggest that the coexistence of excitatory and inhibitory GABA synapses could either buffer the mean firing rate of the interneuron network or introduce different types of correlation between neighboring interneurons, or both.},
	Author = {Chavas, Jo{\"e}l and Marty, Alain},
	Date-Added = {2016-10-20 17:48:52 +0000},
	Date-Modified = {2016-10-20 17:48:52 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Action Potentials; Age Factors; Animals; Cerebellum; Electric Stimulation; Excitatory Postsynaptic Potentials; Gramicidin; In Vitro Techniques; Interneurons; Membrane Potentials; Nerve Net; Neural Inhibition; Patch-Clamp Techniques; Potassium; Purkinje Cells; Rats; Receptors, GABA-A; Sodium; Synapses; gamma-Aminobutyric Acid},
	Month = {Mar},
	Number = {6},
	Pages = {2019-31},
	Pmid = {12657660},
	Pst = {ppublish},
	Title = {Coexistence of excitatory and inhibitory GABA synapses in the cerebellar interneuron network},
	Volume = {23},
	Year = {2003},
	File = {papers/Chavas_JNeurosci2003.pdf}}

@article{Takeuchi:1960,
	Author = {Takeuchi, A and Takeuchi, N},
	Date-Added = {2016-10-19 21:20:31 +0000},
	Date-Modified = {2016-10-19 21:21:21 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {MYONEURAL JUNCTION/physiology},
	Mesh = {Neuromuscular Junction; Permeability},
	Month = {Nov},
	Pages = {52-67},
	Pmc = {PMC1359785},
	Pmid = {13774972},
	Pst = {ppublish},
	Title = {On the permeability of end-plate membrane during the action of transmitter},
	Volume = {154},
	Year = {1960}}

@article{McPartland:2001,
	Abstract = {The endocannabinoid system exerts an important neuromodulatory role in mammals. Knockout mice lacking cannabinoid (CB) receptors exhibit significant morbidity. The endocannabinoid system also appears to be phylogenetically ancient--it occurs in mammals, birds, amphibians, fish, sea urchins, leeches, mussels, and even the most primitive animal with a nerve network, the Hydra. The presence of CB receptors, however, has not been examined in terrestrial invertebrates (or any member of the Ecdysozoa). Surprisingly, we found no specific binding of the synthetic CB ligands [(3)H]CP55,940 and [(3)H]SR141716A in a panel of insects: Apis mellifera, Drosophila melanogaster, Gerris marginatus, Spodoptera frugiperda, and Zophobas atratus. A lack of functional CB receptors was confirmed by the inability of tetrahydrocannabinol (THC) and HU210 to activate G-proteins in insect tissues, utilizing a guanosine-5'-O-(3-[(35)]thio)-triphosphate (GTP gamma S) assay. No orthologs of human CB receptors were located in the Drosophila genome, nor did we find orthologs of fatty acid amide hydrolase. This loss of CB receptors appears to be unique in the field of comparative neurobiology. No other known mammalian neuroreceptor is understood to be missing in insects. We hypothesized that CB receptors were lost in insects because of a dearth of ligands; endogenous CB ligands are metabolites of arachidonic acid, and insects produce little or no arachidonic acid or endocannabinoid ligands, such as anandamide.},
	Author = {McPartland, J and Di Marzo, V and De Petrocellis, L and Mercer, A and Glass, M},
	Date-Added = {2016-10-18 19:24:41 +0000},
	Date-Modified = {2016-10-18 19:24:41 +0000},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Amino Acid Sequence; Animals; Bees; Beetles; Cannabinoid Receptor Modulators; Cats; Gas Chromatography-Mass Spectrometry; Humans; Insects; Ligands; Malpighian Tubules; Molecular Sequence Data; Rats; Receptors, Cannabinoid; Receptors, Drug},
	Month = {Aug},
	Number = {4},
	Pages = {423-9},
	Pmid = {11447587},
	Pst = {ppublish},
	Title = {Cannabinoid receptors are absent in insects},
	Volume = {436},
	Year = {2001}}

@article{Jeffries:2014,
	Abstract = {Long-chain fatty acid amides are cell-signaling lipids identified in mammals and, recently, in invertebrates, as well. Many details regarding fatty acid amide metabolism remain unclear. Herein, we demonstrate that Drosophila melanogaster is an excellent model system for the study long-chain fatty acid amide metabolism as we have quantified the endogenous levels of N-acylglycines, N-acyldopamines, N-acylethanolamines, and primary fatty acid amides by LC/QTOF-MS. Growth of D. melanogaster on media supplemented with [1-(13)C]-palmitate lead to a family of (13)C-palmitate-labeled fatty acid amides in the fly heads. The [1-(13)C]-palmitate feeding studies provide insight into the biosynthesis of the fatty acid amides.},
	Author = {Jeffries, Kristen A and Dempsey, Daniel R and Behari, Anita L and Anderson, Ryan L and Merkler, David J},
	Date-Added = {2016-10-18 19:24:02 +0000},
	Date-Modified = {2016-10-18 19:24:02 +0000},
	Doi = {10.1016/j.febslet.2014.02.051},
	Journal = {FEBS Lett},
	Journal-Full = {FEBS letters},
	Keywords = {Biosynthetic pathway; Drosophila melanogaster; Endogenous quantification; Heavy-labeled precursor; Long-chain fatty acid amide; Model system},
	Mesh = {Animals; Drosophila melanogaster; Ethanolamines; Lipid Metabolism; Palmitic Acids},
	Month = {May},
	Number = {9},
	Pages = {1596-602},
	Pmc = {PMC4023565},
	Pmid = {24650760},
	Pst = {ppublish},
	Title = {Drosophila melanogaster as a model system to study long-chain fatty acid amide metabolism},
	Volume = {588},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.febslet.2014.02.051}}

@article{Tomaso:1996,
	Author = {di Tomaso, E and Beltramo, M and Piomelli, D},
	Date-Added = {2016-10-18 19:19:52 +0000},
	Date-Modified = {2016-10-18 19:19:52 +0000},
	Doi = {10.1038/382677a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Amidohydrolases; Animals; Arachidonic Acids; Brain Chemistry; Cacao; Candy; Cannabinoids; Cells, Cultured; Endocannabinoids; Ethanolamines; Gas Chromatography-Mass Spectrometry; Polyunsaturated Alkamides; Rats},
	Month = {Aug},
	Number = {6593},
	Pages = {677-8},
	Pmid = {8751435},
	Pst = {ppublish},
	Title = {Brain cannabinoids in chocolate},
	Volume = {382},
	Year = {1996},
	File = {papers/Tomaso_Nature1996.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/382677a0}}

@article{Pacher:2006,
	Abstract = {The recent identification of cannabinoid receptors and their endogenous lipid ligands has triggered an exponential growth of studies exploring the endocannabinoid system and its regulatory functions in health and disease. Such studies have been greatly facilitated by the introduction of selective cannabinoid receptor antagonists and inhibitors of endocannabinoid metabolism and transport, as well as mice deficient in cannabinoid receptors or the endocannabinoid-degrading enzyme fatty acid amidohydrolase. In the past decade, the endocannabinoid system has been implicated in a growing number of physiological functions, both in the central and peripheral nervous systems and in peripheral organs. More importantly, modulating the activity of the endocannabinoid system turned out to hold therapeutic promise in a wide range of disparate diseases and pathological conditions, ranging from mood and anxiety disorders, movement disorders such as Parkinson's and Huntington's disease, neuropathic pain, multiple sclerosis and spinal cord injury, to cancer, atherosclerosis, myocardial infarction, stroke, hypertension, glaucoma, obesity/metabolic syndrome, and osteoporosis, to name just a few. An impediment to the development of cannabinoid medications has been the socially unacceptable psychoactive properties of plant-derived or synthetic agonists, mediated by CB(1) receptors. However, this problem does not arise when the therapeutic aim is achieved by treatment with a CB(1) receptor antagonist, such as in obesity, and may also be absent when the action of endocannabinoids is enhanced indirectly through blocking their metabolism or transport. The use of selective CB(2) receptor agonists, which lack psychoactive properties, could represent another promising avenue for certain conditions. The abuse potential of plant-derived cannabinoids may also be limited through the use of preparations with controlled composition and the careful selection of dose and route of administration. The growing number of preclinical studies and clinical trials with compounds that modulate the endocannabinoid system will probably result in novel therapeutic approaches in a number of diseases for which current treatments do not fully address the patients' need. Here, we provide a comprehensive overview on the current state of knowledge of the endocannabinoid system as a target of pharmacotherapy.},
	Author = {Pacher, P{\'a}l and B{\'a}tkai, S{\'a}ndor and Kunos, George},
	Date-Added = {2016-10-18 19:16:16 +0000},
	Date-Modified = {2016-10-18 19:16:16 +0000},
	Doi = {10.1124/pr.58.3.2},
	Journal = {Pharmacol Rev},
	Journal-Full = {Pharmacological reviews},
	Mesh = {Animals; Cannabinoid Receptor Modulators; Endocannabinoids; Humans; Metabolic Diseases; Models, Biological},
	Month = {Sep},
	Number = {3},
	Pages = {389-462},
	Pmc = {PMC2241751},
	Pmid = {16968947},
	Pst = {ppublish},
	Title = {The endocannabinoid system as an emerging target of pharmacotherapy},
	Volume = {58},
	Year = {2006},
	File = {papers/Pacher_PharmacolRev2006.pdf}}

@article{Gertsch:2010,
	Abstract = {It is intriguing that during human cultural evolution man has detected plant natural products that appear to target key protein receptors of important physiological systems rather selectively. Plants containing such secondary metabolites usually belong to unique chemotaxa, induce potent pharmacological effects and have typically been used for recreational and medicinal purposes or as poisons. Cannabis sativa L. has a long history as a medicinal plant and was fundamental in the discovery of the endocannabinoid system. The major psychoactive Cannabis constituent Delta(9)-tetrahydrocannabinol (Delta(9)-THC) potently activates the G-protein-coupled cannabinoid receptor CB(1) and also modulates the cannabinoid receptor CB(2). In the last few years, several other non-cannabinoid plant constituents have been reported to bind to and functionally interact with CB receptors. Moreover, certain plant natural products, from both Cannabis and other plants, also target other proteins of the endocannabinoid system, such as hydrolytic enzymes that control endocannabinoid levels. In this commentary we summarize and critically discuss recent findings.},
	Author = {Gertsch, J{\"u}rg and Pertwee, Roger G and Di Marzo, Vincenzo},
	Date-Added = {2016-10-18 18:10:49 +0000},
	Date-Modified = {2016-10-18 18:10:49 +0000},
	Doi = {10.1111/j.1476-5381.2010.00745.x},
	Journal = {Br J Pharmacol},
	Journal-Full = {British journal of pharmacology},
	Mesh = {Animals; Biological Products; Cannabinoids; Cannabis; Fatty Acids; Flavonoids; Humans; Molecular Structure; Phenols; Polyphenols; Receptors, Cannabinoid; Terpenes},
	Month = {Jun},
	Number = {3},
	Pages = {523-9},
	Pmc = {PMC2931553},
	Pmid = {20590562},
	Pst = {ppublish},
	Title = {Phytocannabinoids beyond the Cannabis plant - do they exist?},
	Volume = {160},
	Year = {2010},
	File = {papers/Gertsch_BrJPharmacol2010.pdf}}

@article{Singh:2013,
	Abstract = {Autism is a common and heritable neuropsychiatric disorder that can be categorized into two types: syndromic and nonsyndromic, the former of which are associated with other neurological disorders or syndromes. Molecular and functional links between syndromic and nonsyndromic autism genes were lacking until studies aimed at understanding the role of trans-synaptic adhesion molecule neuroligin, which is associated with nonsyndromic autism, provided important connections. Here, we integrate data from these studies into a model of how neuroligin functions to control synaptic connectivity in the central nervous system and how neuroligin dysfunction may participate in the pathophysiology of autism. Understanding the complex functional interactions between neuroligins and other autism-associated proteins at the synapse is crucial to understand the pathology of autism. This understanding might bring us closer to development of therapeutic approaches for autism.},
	Author = {Singh, Sandeep K and Eroglu, Cagla},
	Date-Added = {2016-08-04 15:10:18 +0000},
	Date-Modified = {2016-08-04 15:15:08 +0000},
	Doi = {10.1126/scisignal.2004102},
	Journal = {Sci Signal},
	Journal-Full = {Science signaling},
	Keywords = {autism; Autistic Disorder; heritability},
	Mesh = {Activated-Leukocyte Cell Adhesion Molecule; Animals; Autistic Disorder; Humans; Synapses; Synaptic Transmission; Syndrome},
	Month = {Jul},
	Number = {283},
	Pages = {re4},
	Pmc = {PMC4000534},
	Pmid = {23838185},
	Pst = {epublish},
	Title = {Neuroligins provide molecular links between syndromic and nonsyndromic autism},
	Volume = {6},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/scisignal.2004102}}

@article{Torre-Ubieta:2016,
	Abstract = {Progress in understanding the genetic etiology of autism spectrum disorders (ASD) has fueled remarkable advances in our understanding of its potential neurobiological mechanisms. Yet, at the same time, these findings highlight extraordinary causal diversity and complexity at many levels ranging from molecules to circuits and emphasize the gaps in our current knowledge. Here we review current understanding of the genetic architecture of ASD and integrate genetic evidence, neuropathology and studies in model systems with how they inform mechanistic models of ASD pathophysiology. Despite the challenges, these advances provide a solid foundation for the development of rational, targeted molecular therapies.},
	Author = {de la Torre-Ubieta, Luis and Won, Hyejung and Stein, Jason L and Geschwind, Daniel H},
	Date-Added = {2016-08-04 14:41:44 +0000},
	Date-Modified = {2016-08-04 14:41:44 +0000},
	Doi = {10.1038/nm.4071},
	Journal = {Nat Med},
	Journal-Full = {Nature medicine},
	Month = {Apr},
	Number = {4},
	Pages = {345-61},
	Pmid = {27050589},
	Pst = {ppublish},
	Title = {Advancing the understanding of autism disease mechanisms through genetics},
	Volume = {22},
	Year = {2016},
	File = {papers/Torre-Ubieta_NatMed2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nm.4071}}

@article{Sandin:2014,
	Abstract = {IMPORTANCE: Autism spectrum disorder (ASD) aggregates in families, but the individual risk and to what extent this is caused by genetic factors or shared or nonshared environmental factors remains unresolved.
OBJECTIVE: To provide estimates of familial aggregation and heritability of ASD.
DESIGN, SETTING, AND PARTICIPANTS: A population-based cohort including 2,049,973 Swedish children born 1982 through 2006. We identified 37,570 twin pairs, 2,642,064 full sibling pairs, 432,281 maternal and 445,531 paternal half sibling pairs, and 5,799,875 cousin pairs. Diagnoses of ASD to December 31, 2009 were ascertained.
MAIN OUTCOMES AND MEASURES: The relative recurrence risk (RRR) measures familial aggregation of disease. The RRR is the relative risk of autism in a participant with a sibling or cousin who has the diagnosis (exposed) compared with the risk in a participant with no diagnosed family member (unexposed). We calculated RRR for both ASD and autistic disorder adjusting for age, birth year, sex, parental psychiatric history, and parental age. We estimated how much of the probability of developing ASD can be related to genetic (additive and dominant) and environmental (shared and nonshared) factors.
RESULTS: In the sample, 14,516 children were diagnosed with ASD, of whom 5689 had autistic disorder. The RRR and rate per 100,000 person-years for ASD among monozygotic twins was estimated to be 153.0 (95% CI, 56.7-412.8; rate, 6274 for exposed vs 27 for unexposed ); for dizygotic twins, 8.2 (95% CI, 3.7-18.1; rate, 805 for exposed vs 55 for unexposed); for full siblings, 10.3 (95% CI, 9.4-11.3; rate, 829 for exposed vs 49 for unexposed); for maternal half siblings, 3.3 (95% CI, 2.6-4.2; rate, 492 for exposed vs 94 for unexposed); for paternal half siblings, 2.9 (95% CI, 2.2-3.7; rate, 371 for exposed vs 85 for unexposed); and for cousins, 2.0 (95% CI, 1.8-2.2; rate, 155 for exposed vs 49 for unexposed). The RRR pattern was similar for autistic disorder but of slightly higher magnitude.We found support for a disease etiology including only additive genetic and nonshared environmental effects. The ASD heritability was estimated to be 0.50 (95% CI, 0.45-0.56) and the autistic disorder heritability was estimated to 0.54 (95% CI, 0.44-0.64).
CONCLUSIONS AND RELEVANCE: Among children born in Sweden, the individual risk of ASD and autistic disorder increased with increasing genetic relatedness. Heritability of ASD and autistic disorder were estimated to be approximately 50%. These findings may inform the counseling of families with affected children.},
	Author = {Sandin, Sven and Lichtenstein, Paul and Kuja-Halkola, Ralf and Larsson, Henrik and Hultman, Christina M and Reichenberg, Abraham},
	Date-Added = {2016-08-04 14:22:15 +0000},
	Date-Modified = {2016-08-04 14:22:15 +0000},
	Doi = {10.1001/jama.2014.4144},
	Journal = {JAMA},
	Journal-Full = {JAMA},
	Mesh = {Adolescent; Adult; Autistic Disorder; Child; Child, Preschool; Cohort Studies; Female; Genetic Predisposition to Disease; Humans; Male; Maternal Age; Paternal Age; Registries; Risk; Sweden; Twins, Monozygotic; Young Adult},
	Month = {May},
	Number = {17},
	Pages = {1770-7},
	Pmc = {PMC4381277},
	Pmid = {24794370},
	Pst = {ppublish},
	Title = {The familial risk of autism},
	Volume = {311},
	Year = {2014},
	File = {papers/Sandin_JAMA2014a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1001/jama.2014.4144}}

@article{Tan:2010,
	Abstract = {Recent genetic studies have implicated a number of candidate genes in the pathogenesis of Autism Spectrum Disorder (ASD). Polymorphisms of CNTNAP2 (contactin-associated like protein-2), a member of the neurexin family, have already been implicated as a susceptibility gene for autism by at least 3 separate studies. We investigated variation in white and grey matter morphology using structural MRI and diffusion tensor imaging. We compared volumetric differences in white and grey matter and fractional anisotropy values in control subjects characterised by genotype at rs7794745, a single nucleotide polymorphism in CNTNAP2. Homozygotes for the risk allele showed significant reductions in grey and white matter volume and fractional anisotropy in several regions that have already been implicated in ASD, including the cerebellum, fusiform gyrus, occipital and frontal cortices. Male homozygotes for the risk alleles showed greater reductions in grey matter in the right frontal pole and in FA in the right rostral fronto-occipital fasciculus compared to their female counterparts who showed greater reductions in FA of the anterior thalamic radiation. Thus a risk allele for autism results in significant cerebral morphological variation, despite the absence of overt symptoms or behavioural abnormalities. The results are consistent with accumulating evidence of CNTNAP2's function in neuronal development. The finding suggests the possibility that the heterogeneous manifestations of ASD can be aetiologically characterised into distinct subtypes through genetic-morphological analysis.},
	Author = {Tan, Geoffrey C Y and Doke, Thomas F and Ashburner, John and Wood, Nicholas W and Frackowiak, Richard S J},
	Date-Added = {2016-08-04 00:17:26 +0000},
	Date-Modified = {2016-08-04 00:17:26 +0000},
	Doi = {10.1016/j.neuroimage.2010.02.018},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Mesh = {Anisotropy; Cerebellum; Child; Child Development Disorders, Pervasive; Endophenotypes; Female; Frontal Lobe; Genetic Predisposition to Disease; Genotype; Humans; Image Interpretation, Computer-Assisted; Magnetic Resonance Imaging; Male; Membrane Proteins; Nerve Tissue Proteins; Neural Pathways; Occipital Lobe; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Polymorphism, Single Nucleotide},
	Month = {Nov},
	Number = {3},
	Pages = {1030-42},
	Pmc = {PMC2941042},
	Pmid = {20176116},
	Pst = {ppublish},
	Title = {Normal variation in fronto-occipital circuitry and cerebellar structure with an autism-associated polymorphism of CNTNAP2},
	Volume = {53},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2010.02.018}}

@article{Abrahams:2007,
	Abstract = {Despite the well established role of the frontal and posterior perisylvian cortices in many facets of human-cognitive specializations, including language, little is known about the developmental patterning of these regions in the human brain. We performed a genome-wide analysis of human cerebral patterning during midgestation, a critical epoch in cortical regionalization. A total of 345 genes were identified as differentially expressed between superior temporal gyrus (STG) and the remaining cerebral cortex. Gene ontology categories representing transcription factors were enriched in STG, whereas cell-adhesion and extracellular matrix molecules were enriched in the other cortical regions. Quantitative RT-PCR or in situ hybridization was performed to validate differential expression in a subset of 32 genes, most of which were confirmed. LIM domain-binding 1 (LDB1), which we show to be enriched in the STG, is a recently identified interactor of LIM domain only 4 (LMO4), a gene known to be involved in the asymmetric pattering of the perisylvian region in the developing human brain. Protocadherin 17 (PCDH17), a neuronal cell adhesion molecule, was highly enriched in focal regions of the human prefrontal cortex. Contactin associated protein-like 2 (CNTNAP2), in which mutations are known to cause autism, epilepsy, and language delay, showed a remarkable pattern of anterior-enriched cortical expression in human that was not observed in mouse or rat. These data highlight the importance of expression analysis of human brain and the utility of cross-species comparisons of gene expression. Genes identified here provide a foundation for understanding molecular aspects of human-cognitive specializations and the disorders that disrupt them.},
	Author = {Abrahams, B S and Tentler, D and Perederiy, J V and Oldham, M C and Coppola, G and Geschwind, D H},
	Date-Added = {2016-08-04 00:16:17 +0000},
	Date-Modified = {2016-08-04 00:16:17 +0000},
	Doi = {10.1073/pnas.0706128104},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Cerebral Cortex; Cognition; Female; Gene Expression Regulation, Developmental; Genome, Human; Humans; Knowledge; Oligonucleotide Array Sequence Analysis; Pregnancy; Pregnancy Trimester, Second; Reverse Transcriptase Polymerase Chain Reaction},
	Month = {Nov},
	Number = {45},
	Pages = {17849-54},
	Pmc = {PMC2077018},
	Pmid = {17978184},
	Pst = {ppublish},
	Title = {Genome-wide analyses of human perisylvian cerebral cortical patterning},
	Volume = {104},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0706128104}}

@article{Scott-Van-Zeeland:2010,
	Abstract = {Genetic studies are rapidly identifying variants that shape risk for disorders of human cognition, but the question of how such variants predispose to neuropsychiatric disease remains. Noninvasive human brain imaging allows assessment of the brain in vivo, and the combination of genetics and imaging phenotypes remains one of the only ways to explore functional genotype-phenotype associations in human brain. Common variants in contactin-associated protein-like 2 (CNTNAP2), a neurexin superfamily member, have been associated with several allied neurodevelopmental disorders, including autism and specific language impairment, and CNTNAP2 is highly expressed in frontal lobe circuits in the developing human brain. Using functional neuroimaging, we have demonstrated a relationship between frontal lobar connectivity and common genetic variants in CNTNAP2. These data provide a mechanistic link between specific genetic risk for neurodevelopmental disorders and empirical data implicating dysfunction of long-range connections within the frontal lobe in autism. The convergence between genetic findings and cognitive-behavioral models of autism provides evidence that genetic variation at CNTNAP2 predisposes to diseases such as autism in part through modulation of frontal lobe connectivity.},
	Author = {Scott-Van Zeeland, Ashley A and Abrahams, Brett S and Alvarez-Retuerto, Ana I and Sonnenblick, Lisa I and Rudie, Jeffrey D and Ghahremani, Dara and Mumford, Jeanette A and Poldrack, Russell A and Dapretto, Mirella and Geschwind, Daniel H and Bookheimer, Susan Y},
	Date-Added = {2016-08-04 00:12:55 +0000},
	Date-Modified = {2016-08-04 00:12:55 +0000},
	Doi = {10.1126/scitranslmed.3001344},
	Journal = {Sci Transl Med},
	Journal-Full = {Science translational medicine},
	Mesh = {Autistic Disorder; Frontal Lobe; Genetic Predisposition to Disease; Humans; Magnetic Resonance Imaging; Membrane Proteins; Nerve Tissue Proteins; Neural Pathways; Risk Factors},
	Month = {Nov},
	Number = {56},
	Pages = {56ra80},
	Pmc = {PMC3065863},
	Pmid = {21048216},
	Pst = {ppublish},
	Title = {Altered functional connectivity in frontal lobe circuits is associated with variation in the autism risk gene CNTNAP2},
	Volume = {2},
	Year = {2010},
	File = {papers/Scott-VanZeeland_SciTranslMed2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/scitranslmed.3001344}}

@article{Lu:2015,
	Author = {Lu, Ju and Zuo, Yi},
	Date-Added = {2016-08-03 16:50:13 +0000},
	Date-Modified = {2016-08-03 16:50:13 +0000},
	Doi = {10.1038/nature15211},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Male; Memory; Motor Cortex; Neuronal Plasticity; Synapses},
	Month = {Sep},
	Number = {7569},
	Pages = {324-5},
	Pmid = {26352474},
	Pst = {ppublish},
	Title = {Neuroscience: Forgetfulness illuminated},
	Volume = {525},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature15211}}

@article{Xu:2009,
	Abstract = {Novel motor skills are learned through repetitive practice and, once acquired, persist long after training stops. Earlier studies have shown that such learning induces an increase in the efficacy of synapses in the primary motor cortex, the persistence of which is associated with retention of the task. However, how motor learning affects neuronal circuitry at the level of individual synapses and how long-lasting memory is structurally encoded in the intact brain remain unknown. Here we show that synaptic connections in the living mouse brain rapidly respond to motor-skill learning and permanently rewire. Training in a forelimb reaching task leads to rapid (within an hour) formation of postsynaptic dendritic spines on the output pyramidal neurons in the contralateral motor cortex. Although selective elimination of spines that existed before training gradually returns the overall spine density back to the original level, the new spines induced during learning are preferentially stabilized during subsequent training and endure long after training stops. Furthermore, we show that different motor skills are encoded by different sets of synapses. Practice of novel, but not previously learned, tasks further promotes dendritic spine formation in adulthood. Our findings reveal that rapid, but long-lasting, synaptic reorganization is closely associated with motor learning. The data also suggest that stabilized neuronal connections are the foundation of durable motor memory.},
	Author = {Xu, Tonghui and Yu, Xinzhu and Perlik, Andrew J and Tobin, Willie F and Zweig, Jonathan A and Tennant, Kelly and Jones, Theresa and Zuo, Yi},
	Date-Added = {2016-08-03 16:50:01 +0000},
	Date-Modified = {2016-08-03 16:50:01 +0000},
	Doi = {10.1038/nature08389},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Aging; Animals; Dendrites; Forelimb; Memory; Mice; Motor Cortex; Motor Skills; Neuronal Plasticity; Psychomotor Performance; Pyramidal Cells; Seeds; Synapses; Time Factors},
	Month = {Dec},
	Number = {7275},
	Pages = {915-9},
	Pmc = {PMC2844762},
	Pmid = {19946267},
	Pst = {ppublish},
	Title = {Rapid formation and selective stabilization of synapses for enduring motor memories},
	Volume = {462},
	Year = {2009},
	File = {papers/Xu_Nature2009.pdf},
	Bdsk-File-2 = {papers/Xu_Nature2009a.pdf},
	Bdsk-File-3 = {papers/Xu_Nature2009.mov},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature08389}}

@article{Fu:2012,
	Abstract = {Many lines of evidence suggest that memory in the mammalian brain is stored with distinct spatiotemporal patterns. Despite recent progresses in identifying neuronal populations involved in memory coding, the synapse-level mechanism is still poorly understood. Computational models and electrophysiological data have shown that functional clustering of synapses along dendritic branches leads to nonlinear summation of synaptic inputs and greatly expands the computing power of a neural network. However, whether neighbouring synapses are involved in encoding similar memory and how task-specific cortical networks develop during learning remain elusive. Using transcranial two-photon microscopy, we followed apical dendrites of layer 5 pyramidal neurons in the motor cortex while mice practised novel forelimb skills. Here we show that a third of new dendritic spines (postsynaptic structures of most excitatory synapses) formed during the acquisition phase of learning emerge in clusters, and that most such clusters are neighbouring spine pairs. These clustered new spines are more likely to persist throughout prolonged learning sessions, and even long after training stops, than non-clustered counterparts. Moreover, formation of new spine clusters requires repetition of the same motor task, and the emergence of succedent new spine(s) accompanies the strengthening of the first new spine in the cluster. We also show that under control conditions new spines appear to avoid existing stable spines, rather than being uniformly added along dendrites. However, succedent new spines in clusters overcome such a spatial constraint and form in close vicinity to neighbouring stable spines. Our findings suggest that clustering of new synapses along dendrites is induced by repetitive activation of the cortical circuitry during learning, providing a structural basis for spatial coding of motor memory in the mammalian brain.},
	Author = {Fu, Min and Yu, Xinzhu and Lu, Ju and Zuo, Yi},
	Date-Added = {2016-08-03 16:49:59 +0000},
	Date-Modified = {2016-08-03 16:49:59 +0000},
	Doi = {10.1038/nature10844},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Dendritic Spines; Forelimb; Learning; Mice; Models, Neurological; Motor Cortex; Psychomotor Performance; Pyramidal Cells; Synapses},
	Month = {Mar},
	Number = {7387},
	Pages = {92-5},
	Pmc = {PMC3292711},
	Pmid = {22343892},
	Pst = {epublish},
	Title = {Repetitive motor learning induces coordinated formation of clustered dendritic spines in vivo},
	Volume = {483},
	Year = {2012},
	File = {papers/Fu_Nature2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature10844}}

@article{Ho:2011,
	Abstract = {Estimation of demographic history from nucleotide sequences represents an important component of many studies in molecular ecology. For example, knowledge of a population's history can allow us to test hypotheses about the impact of climatic and anthropogenic factors. In the past, demographic analysis was typically limited to relatively simple population models, such as exponential or logistic growth. More flexible approaches are now available, including skyline-plot methods that are able to reconstruct changes in population sizes through time. This technical review focuses on these skyline-plot methods. We describe some general principles relating to sampling design and data collection. We then provide an outline of the methodological framework, which is based on coalescent theory, before tracing the development of the various skyline-plot methods and describing their key features. The performance and properties of the methods are illustrated using two simulated data sets.},
	Author = {Ho, Simon Y W and Shapiro, Beth},
	Date-Added = {2016-07-07 22:53:08 +0000},
	Date-Modified = {2016-07-07 22:53:08 +0000},
	Doi = {10.1111/j.1755-0998.2011.02988.x},
	Journal = {Mol Ecol Resour},
	Journal-Full = {Molecular ecology resources},
	Mesh = {Demography; Genetics, Population; Humans; Models, Genetic; Sequence Analysis, DNA; Statistics as Topic},
	Month = {May},
	Number = {3},
	Pages = {423-34},
	Pmid = {21481200},
	Pst = {ppublish},
	Title = {Skyline-plot methods for estimating demographic history from nucleotide sequences},
	Volume = {11},
	Year = {2011},
	File = {papers/Ho_MolEcolResour2011.pdf}}

@article{Green:2010,
	Abstract = {Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.},
	Author = {Green, Richard E and Krause, Johannes and Briggs, Adrian W and Maricic, Tomislav and Stenzel, Udo and Kircher, Martin and Patterson, Nick and Li, Heng and Zhai, Weiwei and Fritz, Markus Hsi-Yang and Hansen, Nancy F and Durand, Eric Y and Malaspinas, Anna-Sapfo and Jensen, Jeffrey D and Marques-Bonet, Tomas and Alkan, Can and Pr{\"u}fer, Kay and Meyer, Matthias and Burbano, Hern{\'a}n A and Good, Jeffrey M and Schultz, Rigo and Aximu-Petri, Ayinuer and Butthof, Anne and H{\"o}ber, Barbara and H{\"o}ffner, Barbara and Siegemund, Madlen and Weihmann, Antje and Nusbaum, Chad and Lander, Eric S and Russ, Carsten and Novod, Nathaniel and Affourtit, Jason and Egholm, Michael and Verna, Christine and Rudan, Pavao and Brajkovic, Dejana and Kucan, Zeljko and Gusic, Ivan and Doronichev, Vladimir B and Golovanova, Liubov V and Lalueza-Fox, Carles and de la Rasilla, Marco and Fortea, Javier and Rosas, Antonio and Schmitz, Ralf W and Johnson, Philip L F and Eichler, Evan E and Falush, Daniel and Birney, Ewan and Mullikin, James C and Slatkin, Montgomery and Nielsen, Rasmus and Kelso, Janet and Lachmann, Michael and Reich, David and P{\"a}{\"a}bo, Svante},
	Date-Added = {2016-07-07 22:53:02 +0000},
	Date-Modified = {2016-07-07 22:53:02 +0000},
	Doi = {10.1126/science.1188021},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {African Continental Ancestry Group; Animals; Asian Continental Ancestry Group; Base Sequence; Bone and Bones; DNA, Mitochondrial; European Continental Ancestry Group; Evolution, Molecular; Extinction, Biological; Female; Fossils; Gene Dosage; Gene Flow; Genetic Variation; Genome; Genome, Human; Haplotypes; Hominidae; Humans; Pan troglodytes; Polymorphism, Single Nucleotide; Selection, Genetic; Sequence Alignment; Sequence Analysis, DNA; Time},
	Month = {May},
	Number = {5979},
	Pages = {710-22},
	Pmid = {20448178},
	Pst = {ppublish},
	Title = {A draft sequence of the Neandertal genome},
	Volume = {328},
	Year = {2010},
	File = {papers/Green_Science2010.pdf}}

@article{Carninci:2005,
	Abstract = {This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.},
	Author = {Carninci, P and Kasukawa, T and Katayama, S and Gough, J and Frith, M C and Maeda, N and Oyama, R and Ravasi, T and Lenhard, B and Wells, C and Kodzius, R and Shimokawa, K and Bajic, V B and Brenner, S E and Batalov, S and Forrest, A R R and Zavolan, M and Davis, M J and Wilming, L G and Aidinis, V and Allen, J E and Ambesi-Impiombato, A and Apweiler, R and Aturaliya, R N and Bailey, T L and Bansal, M and Baxter, L and Beisel, K W and Bersano, T and Bono, H and Chalk, A M and Chiu, K P and Choudhary, V and Christoffels, A and Clutterbuck, D R and Crowe, M L and Dalla, E and Dalrymple, B P and de Bono, B and Della Gatta, G and di Bernardo, D and Down, T and Engstrom, P and Fagiolini, M and Faulkner, G and Fletcher, C F and Fukushima, T and Furuno, M and Futaki, S and Gariboldi, M and Georgii-Hemming, P and Gingeras, T R and Gojobori, T and Green, R E and Gustincich, S and Harbers, M and Hayashi, Y and Hensch, T K and Hirokawa, N and Hill, D and Huminiecki, L and Iacono, M and Ikeo, K and Iwama, A and Ishikawa, T and Jakt, M and Kanapin, A and Katoh, M and Kawasawa, Y and Kelso, J and Kitamura, H and Kitano, H and Kollias, G and Krishnan, S P T and Kruger, A and Kummerfeld, S K and Kurochkin, I V and Lareau, L F and Lazarevic, D and Lipovich, L and Liu, J and Liuni, S and McWilliam, S and Madan Babu, M and Madera, M and Marchionni, L and Matsuda, H and Matsuzawa, S and Miki, H and Mignone, F and Miyake, S and Morris, K and Mottagui-Tabar, S and Mulder, N and Nakano, N and Nakauchi, H and Ng, P and Nilsson, R and Nishiguchi, S and Nishikawa, S and Nori, F and Ohara, O and Okazaki, Y and Orlando, V and Pang, K C and Pavan, W J and Pavesi, G and Pesole, G and Petrovsky, N and Piazza, S and Reed, J and Reid, J F and Ring, B Z and Ringwald, M and Rost, B and Ruan, Y and Salzberg, S L and Sandelin, A and Schneider, C and Sch{\"o}nbach, C and Sekiguchi, K and Semple, C A M and Seno, S and Sessa, L and Sheng, Y and Shibata, Y and Shimada, H and Shimada, K and Silva, D and Sinclair, B and Sperling, S and Stupka, E and Sugiura, K and Sultana, R and Takenaka, Y and Taki, K and Tammoja, K and Tan, S L and Tang, S and Taylor, M S and Tegner, J and Teichmann, S A and Ueda, H R and van Nimwegen, E and Verardo, R and Wei, C L and Yagi, K and Yamanishi, H and Zabarovsky, E and Zhu, S and Zimmer, A and Hide, W and Bult, C and Grimmond, S M and Teasdale, R D and Liu, E T and Brusic, V and Quackenbush, J and Wahlestedt, C and Mattick, J S and Hume, D A and Kai, C and Sasaki, D and Tomaru, Y and Fukuda, S and Kanamori-Katayama, M and Suzuki, M and Aoki, J and Arakawa, T and Iida, J and Imamura, K and Itoh, M and Kato, T and Kawaji, H and Kawagashira, N and Kawashima, T and Kojima, M and Kondo, S and Konno, H and Nakano, K and Ninomiya, N and Nishio, T and Okada, M and Plessy, C and Shibata, K and Shiraki, T and Suzuki, S and Tagami, M and Waki, K and Watahiki, A and Okamura-Oho, Y and Suzuki, H and Kawai, J and Hayashizaki, Y and {FANTOM Consortium} and {RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)}},
	Date-Added = {2016-07-07 22:52:56 +0000},
	Date-Modified = {2016-07-07 22:52:56 +0000},
	Doi = {10.1126/science.1112014},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {3' Untranslated Regions; Animals; Base Sequence; Conserved Sequence; DNA, Complementary; Genome; Genome, Human; Genomics; Humans; Mice; Promoter Regions, Genetic; Proteins; RNA; RNA Splicing; RNA, Untranslated; Regulatory Sequences, Ribonucleic Acid; Terminator Regions, Genetic; Transcription Initiation Site; Transcription, Genetic},
	Month = {Sep},
	Number = {5740},
	Pages = {1559-63},
	Pmid = {16141072},
	Pst = {ppublish},
	Title = {The transcriptional landscape of the mammalian genome},
	Volume = {309},
	Year = {2005},
	File = {papers/Carninci_Science2005.pdf}}

@article{Shapiro:2002,
	Author = {Shapiro, Beth and Sibthorpe, Dean and Rambaut, Andrew and Austin, Jeremy and Wragg, Graham M and Bininda-Emonds, Olaf R P and Lee, Patricia L M and Cooper, Alan},
	Date-Added = {2016-07-07 22:52:33 +0000},
	Date-Modified = {2016-07-07 22:52:33 +0000},
	Doi = {10.1126/science.295.5560.1683},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Biological Evolution; Birds; Columbidae; DNA, Mitochondrial; Flight, Animal; Likelihood Functions; Phylogeny},
	Month = {Mar},
	Number = {5560},
	Pages = {1683},
	Pmid = {11872833},
	Pst = {ppublish},
	Title = {Flight of the dodo},
	Volume = {295},
	Year = {2002},
	File = {papers/Shapiro_Science2002.pdf}}

@article{Eklund:2016,
	Abstract = {The most widely used task functional magnetic resonance imaging (fMRI) analyses use parametric statistical methods that depend on a variety of assumptions. In this work, we use real resting-state data and a total of 3 million random task group analyses to compute empirical familywise error rates for the fMRI software packages SPM, FSL, and AFNI, as well as a nonparametric permutation method. For a nominal familywise error rate of 5%, the parametric statistical methods are shown to be conservative for voxelwise inference and invalid for clusterwise inference. Our results suggest that the principal cause of the invalid cluster inferences is spatial autocorrelation functions that do not follow the assumed Gaussian shape. By comparison, the nonparametric permutation test is found to produce nominal results for voxelwise as well as clusterwise inference. These findings speak to the need of validating the statistical methods being used in the field of neuroimaging.},
	Author = {Eklund, Anders and Nichols, Thomas E and Knutsson, Hans},
	Date-Added = {2016-07-07 22:51:33 +0000},
	Date-Modified = {2016-07-07 22:51:33 +0000},
	Doi = {10.1073/pnas.1602413113},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {cluster inference; fMRI; false positives; permutation test; statistics},
	Month = {Jun},
	Pmid = {27357684},
	Pst = {aheadofprint},
	Title = {Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates},
	Year = {2016},
	File = {papers/Eklund_ProcNatlAcadSciUSA2016.pdf}}

@article{Drummond:2005,
	Abstract = {We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.},
	Author = {Drummond, A J and Rambaut, A and Shapiro, B and Pybus, O G},
	Date-Added = {2016-07-07 22:51:03 +0000},
	Date-Modified = {2016-07-07 22:51:03 +0000},
	Doi = {10.1093/molbev/msi103},
	Journal = {Mol Biol Evol},
	Journal-Full = {Molecular biology and evolution},
	Mesh = {Algorithms; Animals; Bayes Theorem; Bison; DNA, Mitochondrial; Egypt; Evolution, Molecular; Genetics, Population; Hepacivirus; Hepatitis C; Humans; Markov Chains; Models, Genetic; Monte Carlo Method; Population Density; Population Dynamics; Time Factors},
	Month = {May},
	Number = {5},
	Pages = {1185-92},
	Pmid = {15703244},
	Pst = {ppublish},
	Title = {Bayesian coalescent inference of past population dynamics from molecular sequences},
	Volume = {22},
	Year = {2005},
	File = {papers/Drummond_MolBiolEvol2005.pdf}}

@article{Kirkby:2013,
	Abstract = {Correlated spontaneous activity in the developing nervous system is robust to perturbations in the circuits that generate it, suggesting that mechanisms exist to ensure its maintenance. We examine this phenomenon in the developing retina, where blockade of cholinergic circuits that mediate retinal waves during the first postnatal week leads to the generation of "recovered" waves through a distinct, gap junction-mediated circuit. Unlike cholinergic waves, these recovered waves were modulated by dopaminergic and glutamatergic signaling, and required the presence of the gap junction protein connexin 36. Moreover, in contrast to cholinergic waves, recovered waves were stimulated by ambient light via activation of melanopsin-expressing intrinsically photosensitive retinal ganglion cells. The involvement of intrinsically photosensitive retinal ganglion cells in this reconfiguration of wave-generating circuits offers an avenue of retinal circuit plasticity during development that was previously unknown.},
	Author = {Kirkby, Lowry A and Feller, Marla B},
	Date-Added = {2016-07-07 17:34:20 +0000},
	Date-Modified = {2016-07-07 17:34:20 +0000},
	Doi = {10.1073/pnas.1222150110},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {degenerate circuit; dopamine; retinal development},
	Mesh = {Animals; Connexins; Electrophysiological Processes; Gap Junctions; Light Signal Transduction; Mice; Mice, Inbred C57BL; Mice, Knockout; Microscopy, Interference; Retina; Retinal Ganglion Cells; Rod Opsins; Synaptic Transmission},
	Month = {Jul},
	Number = {29},
	Pages = {12090-5},
	Pmc = {PMC3718101},
	Pmid = {23821744},
	Pst = {ppublish},
	Title = {Intrinsically photosensitive ganglion cells contribute to plasticity in retinal wave circuits},
	Volume = {110},
	Year = {2013},
	File = {papers/Kirkby_ProcNatlAcadSciUSA2013.pdf}}

@article{Smith:2015,
	Abstract = {Stimulus discrimination depends on the selectivity and variability of neural responses, as well as the size and correlation structure of the responsive population. For direction discrimination in visual cortex, only the selectivity of neurons has been well characterized across development. Here we show in ferrets that at eye opening, the cortical response to visual stimulation exhibits several immaturities, including a high density of active neurons that display prominent wave-like activity, a high degree of variability and strong noise correlations. Over the next three weeks, the population response becomes increasingly sparse, wave-like activity disappears, and variability and noise correlations are markedly reduced. Similar changes were observed in identified neuronal populations imaged repeatedly over days. Furthermore, experience with a moving stimulus was capable of driving a reduction in noise correlations over a matter of hours. These changes in variability and correlation contribute significantly to a marked improvement in direction discriminability over development.},
	Author = {Smith, Gordon B and Sederberg, Audrey and Elyada, Yishai M and Van Hooser, Stephen D and Kaschube, Matthias and Fitzpatrick, David},
	Date-Added = {2016-07-07 17:19:04 +0000},
	Date-Modified = {2016-07-07 17:19:04 +0000},
	Doi = {10.1038/nn.3921},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Age Factors; Animals; Discrimination (Psychology); Female; Ferrets; Motion Perception; Nerve Net; Neurons; Optical Imaging; Visual Cortex},
	Month = {Feb},
	Number = {2},
	Pages = {252-61},
	Pmc = {PMC4334116},
	Pmid = {25599224},
	Pst = {ppublish},
	Title = {The development of cortical circuits for motion discrimination},
	Volume = {18},
	Year = {2015},
	File = {papers/Smith_NatNeurosci2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.3921}}

@article{McCormick:2015,
	Abstract = {Cortical and thalamocortical activity is highly state dependent, varying between patterns that are conducive to accurate sensory-motor processing, to states in which the brain is largely off-line and generating internal rhythms irrespective of the outside world. The generation of rhythmic activity occurs through the interaction of stereotyped patterns of connectivity together with intrinsic membrane and synaptic properties. One common theme in the generation of rhythms is the interaction of a positive feedback loop (e.g., recurrent excitation) with negative feedback control (e.g., inhibition, adaptation, or synaptic depression). The operation of these state-dependent activities has wide ranging effects from enhancing or blocking sensory-motor processing to the generation of pathological rhythms associated with psychiatric or neurological disorders.},
	Author = {McCormick, David A and McGinley, Matthew J and Salkoff, David B},
	Date-Added = {2016-07-06 23:27:49 +0000},
	Date-Modified = {2016-07-06 23:27:49 +0000},
	Doi = {10.1016/j.conb.2014.10.003},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Mesh = {Action Potentials; Animals; Cerebral Cortex; Feedback, Physiological; Humans; Models, Neurological; Neural Pathways; Periodicity; Thalamus},
	Month = {Apr},
	Pages = {133-40},
	Pmc = {PMC4375098},
	Pmid = {25460069},
	Pst = {ppublish},
	Title = {Brain state dependent activity in the cortex and thalamus},
	Volume = {31},
	Year = {2015},
	File = {papers/McCormick_CurrOpinNeurobiol2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.conb.2014.10.003}}

@article{McCormick:2014,
	Author = {McCormick, David A and Nusbaum, Michael P},
	Date-Added = {2016-07-06 23:27:48 +0000},
	Date-Modified = {2016-07-06 23:27:48 +0000},
	Doi = {10.1016/j.conb.2014.10.010},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Mesh = {Animals; Behavior; Humans; Nerve Net; Neurons; Neurotransmitter Agents},
	Month = {Dec},
	Pages = {iv-vii},
	Pmc = {PMC4450677},
	Pmid = {25457725},
	Pst = {ppublish},
	Title = {Editorial overview: neuromodulation: tuning the properties of neurons, networks and behavior},
	Volume = {29},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.conb.2014.10.010}}

@article{Zagha:2014,
	Abstract = {How the brain takes in information, makes a decision, and acts on this decision is strongly influenced by the ongoing and constant fluctuations of state. Understanding the nature of these brain states and how they are controlled is critical to making sense of how the nervous system operates, both normally and abnormally. While broadly projecting neuromodulatory systems acting through metabotropic pathways have long been appreciated to be critical for determining brain state, more recent investigations have revealed a prominent role for fast acting neurotransmitter pathways for temporally and spatially precise control of neural processing. Corticocortical and thalamocortical glutamatergic projections can rapidly and precisely control brain state by changing both the nature of ongoing activity and by controlling the gain and precision of neural responses.},
	Author = {Zagha, Edward and McCormick, David A},
	Date-Added = {2016-07-06 23:27:46 +0000},
	Date-Modified = {2016-07-06 23:27:46 +0000},
	Doi = {10.1016/j.conb.2014.09.010},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Mesh = {Animals; Brain; Humans; Neural Pathways; Neurons},
	Month = {Dec},
	Pages = {178-86},
	Pmc = {PMC4254046},
	Pmid = {25310628},
	Pst = {ppublish},
	Title = {Neural control of brain state},
	Volume = {29},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.conb.2014.09.010}}

@article{McGinley:2015a,
	Abstract = {The state of the brain and body constantly varies on rapid and slow timescales. These variations contribute to the apparent noisiness of sensory responses at both the neural and the behavioral level. Recent investigations of rapid state changes in awake, behaving animals have provided insight into the mechanisms by which optimal sensory encoding and behavioral performance are achieved. Fluctuations in state, as indexed by pupillometry, impact both the "signal" (sensory evoked response) and the "noise" (spontaneous activity) of cortical responses. By taking these fluctuations into account, neural response (co)variability is significantly reduced, revealing the brain to be more reliable and predictable than previously thought.},
	Author = {McGinley, Matthew J and Vinck, Martin and Reimer, Jacob and Batista-Brito, Renata and Zagha, Edward and Cadwell, Cathryn R and Tolias, Andreas S and Cardin, Jessica A and McCormick, David A},
	Date-Added = {2016-07-01 15:31:16 +0000},
	Date-Modified = {2016-07-01 15:31:16 +0000},
	Doi = {10.1016/j.neuron.2015.09.012},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Animals; Brain; Humans; Motor Activity; Nerve Net; Neurons; Time Factors; Wakefulness},
	Month = {Sep},
	Number = {6},
	Pages = {1143-61},
	Pmc = {PMC4718218},
	Pmid = {26402600},
	Pst = {ppublish},
	Title = {Waking State: Rapid Variations Modulate Neural and Behavioral Responses},
	Volume = {87},
	Year = {2015},
	File = {papers/McGinley_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.09.012}}

@article{McGinley:2015,
	Abstract = {The neural correlates of optimal states for signal detection task performance are largely unknown. One hypothesis holds that optimal states exhibit tonically depolarized cortical neurons with enhanced spiking activity, such as occur during movement. We recorded membrane potentials of auditory cortical neurons in mice trained on a challenging tone-in-noise detection task while assessing arousal with simultaneous pupillometry and hippocampal recordings. Arousal measures accurately predicted multiple modes of membrane potential activity, including rhythmic slow oscillations at low arousal, stable hyperpolarization at intermediate arousal, and depolarization during phasic or tonic periods of hyper-arousal. Walking always occurred during hyper-arousal. Optimal signal detection behavior and sound-evoked responses, at both sub-threshold and spiking levels, occurred at intermediate arousal when pre-decision membrane potentials were stably hyperpolarized. These results reveal a cortical physiological signature of the classically observed inverted-U relationship between task performance and arousal and that optimal detection exhibits enhanced sensory-evoked responses and reduced background synaptic activity.},
	Author = {McGinley, Matthew J and David, Stephen V and McCormick, David A},
	Date-Added = {2016-07-01 15:31:14 +0000},
	Date-Modified = {2016-07-01 15:31:14 +0000},
	Doi = {10.1016/j.neuron.2015.05.038},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Arousal; Auditory Cortex; Auditory Perception; Membrane Potentials; Mice; Neurons; Signal Detection, Psychological},
	Month = {Jul},
	Number = {1},
	Pages = {179-92},
	Pmc = {PMC4631312},
	Pmid = {26074005},
	Pst = {ppublish},
	Title = {Cortical Membrane Potential Signature of Optimal States for Sensory Signal Detection},
	Volume = {87},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.05.038}}

@article{Brockmann:2011,
	Abstract = {The coactivation of prefrontal and hippocampal networks in oscillatory rhythms is critical for precise information flow in mnemonic and executive tasks, yet the mechanisms governing its development are still unknown. Here, we demonstrate that already in neonatal rats, patterns of discontinuous oscillatory activity precisely entrain the firing of prefrontal neurons and have distinct spatial and temporal organization over cingulate and prelimbic cortices. Moreover, we show that hippocampal theta bursts drive the generation of neonatal prefrontal oscillations by phase-locking the neuronal firing via axonal pathways. Consequently, functional impairment of the hippocampus reduces the prefrontal activity. With ongoing maturation continuous theta-gamma oscillations emerge and mutually entrain the prejuvenile prefrontal-hippocampal networks. Thus, theta-modulated communication within developing prefrontal-hippocampal networks may be relevant for circuitry refinement and maturation of functional units underlying information storage at adulthood.},
	Author = {Brockmann, Marco D and P{\"o}schel, Beatrice and Cichon, Nicole and Hanganu-Opatz, Ileana L},
	Date-Added = {2016-07-01 15:29:23 +0000},
	Date-Modified = {2016-07-01 15:29:23 +0000},
	Doi = {10.1016/j.neuron.2011.05.041},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Age Factors; Amino Acids; Analysis of Variance; Anesthetics, Local; Animals; Animals, Newborn; Biological Clocks; Electric Stimulation; Fourier Analysis; GABA Plasma Membrane Transport Proteins; Hippocampus; Lidocaine; N-Methylaspartate; Neural Pathways; Neurons; Parvalbumins; Prefrontal Cortex; Rats},
	Month = {Jul},
	Number = {2},
	Pages = {332-47},
	Pmid = {21791291},
	Pst = {ppublish},
	Title = {Coupled oscillations mediate directed interactions between prefrontal cortex and hippocampus of the neonatal rat},
	Volume = {71},
	Year = {2011},
	File = {papers/Brockmann_Neuron2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2011.05.041}}

@article{Cichon:2014,
	Abstract = {Flexible communication within the brain, which relies on oscillatory activity, is not confined to adult neuronal networks. Experimental evidence has documented the presence of discontinuous patterns of oscillatory activity already during early development. Their highly variable spatial and time-frequency organization has been related to region specificity. However, it might be equally due to the absence of unitary criteria for classifying the early activity patterns, since they have been mainly characterized by visual inspection. Therefore, robust and unbiased methods for categorizing these discontinuous oscillations are needed for increasingly complex data sets from different labs. Here, we introduce an unsupervised detection and classification algorithm for the discontinuous activity patterns of rodents during early development. For this, in a first step time windows with discontinuous oscillations vs. epochs of network "silence" were identified. In a second step, the major features of detected events were identified and processed by principal component analysis for deciding on their contribution to the classification of different oscillatory patterns. Finally, these patterns were categorized using an unsupervised cluster algorithm. The results were validated on manually characterized neonatal spindle bursts (SB), which ubiquitously entrain neocortical areas of rats and mice, and prelimbic nested gamma spindle bursts (NG). Moreover, the algorithm led to satisfactory results for oscillatory events that, due to increased similarity of their features, were more difficult to classify, e.g., during the pre-juvenile developmental period. Based on a linear classification, the optimal number of features to consider increased with the difficulty of detection. This algorithm allows the comparison of neonatal and pre-juvenile oscillatory patterns in their spatial and temporal organization. It might represent a first step for the unbiased elucidation of activity patterns during development.},
	Author = {Cichon, Nicole B and Denker, Michael and Gr{\"u}n, Sonja and Hanganu-Opatz, Ileana L},
	Date-Added = {2016-07-01 15:27:21 +0000},
	Date-Modified = {2016-07-01 15:27:21 +0000},
	Doi = {10.3389/fncir.2014.00050},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {development; high-frequency oscillations; network oscillations; prefrontal cortex; principal component analysis; synchrony},
	Mesh = {Action Potentials; Algorithms; Animals; Animals, Newborn; Neocortex; Nerve Net; Neurons; Rats; Rats, Wistar},
	Pages = {50},
	Pmc = {PMC4034041},
	Pmid = {24904296},
	Pst = {epublish},
	Title = {Unsupervised classification of neocortical activity patterns in neonatal and pre-juvenile rodents},
	Volume = {8},
	Year = {2014},
	File = {papers/Cichon_FrontNeuralCircuits2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fncir.2014.00050}}

@article{Hoy:2015,
	Abstract = {The laminar structure and conserved cellular organization of mouse visual cortex provide a useful model to determine the mechanisms underlying the development of visual system function. However, the normal development of many receptive field properties has not yet been thoroughly quantified, particularly with respect to layer identity and in the absence of anesthesia. Here, we use multisite electrophysiological recording in the awake mouse across an extended period of development, starting at eye opening, to measure receptive field properties and behavioral-state modulation of responsiveness. We find selective responses for orientation, direction, and spatial frequency at eye opening, which are similar across cortical layers. After this initial similarity, we observe layer-specific maturation of orientation selectivity, direction selectivity, and linearity over the following week. Developmental increases in selectivity are most robust and similar between layers 2-4, whereas layers 5 and 6 undergo distinct refinement patterns. Finally, we studied layer-specific behavioral-state modulation of cortical activity and observed a striking reorganization in the effects of running on response gain. During week 1 after eye opening, running increases responsiveness in layers 4 and 5, whereas in adulthood, the effects of running are most pronounced in layer 2/3. Together, these data demonstrate that response selectivity is present in all layers of the primary visual cortex (V1) at eye opening in the awake mouse and identify the features of basic V1 function that are further shaped over this early developmental period in a layer-specific manner.},
	Author = {Hoy, Jennifer L and Niell, Cristopher M},
	Date-Added = {2016-07-01 15:14:41 +0000},
	Date-Modified = {2016-07-01 15:14:41 +0000},
	Doi = {10.1523/JNEUROSCI.3174-14.2015},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {V1; development; gain modulation; mouse; orientation selectivity; receptive field},
	Mesh = {Animals; Brain Mapping; Eye Movements; Female; Male; Mice; Mice, Inbred C57BL; Neurons; Running; Spatial Navigation; Visual Cortex; Visual Fields; Wakefulness},
	Month = {Feb},
	Number = {8},
	Pages = {3370-83},
	Pmc = {PMC4339350},
	Pmid = {25716837},
	Pst = {ppublish},
	Title = {Layer-specific refinement of visual cortex function after eye opening in the awake mouse},
	Volume = {35},
	Year = {2015},
	File = {papers/Hoy_JNeurosci2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.3174-14.2015}}

@article{Alivisatos:2013a,
	Abstract = {Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.},
	Author = {Alivisatos, A Paul and Andrews, Anne M and Boyden, Edward S and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Fraser, Scott E and Lippincott-Schwartz, Jennifer and Looger, Loren L and Masmanidis, Sotiris and McEuen, Paul L and Nurmikko, Arto V and Park, Hongkun and Peterka, Darcy S and Reid, Clay and Roukes, Michael L and Scherer, Axel and Schnitzer, Mark and Sejnowski, Terrence J and Shepard, Kenneth L and Tsao, Doris and Turrigiano, Gina and Weiss, Paul S and Xu, Chris and Yuste, Rafael and Zhuang, Xiaowei},
	Date-Added = {2016-07-01 12:27:41 +0000},
	Date-Modified = {2016-07-01 12:27:41 +0000},
	Doi = {10.1021/nn4012847},
	Journal = {ACS Nano},
	Journal-Full = {ACS nano},
	Mesh = {Animals; Brain Mapping; Humans; Models, Neurological; Nanomedicine; Nanoparticles; Nanotechnology; Nervous System Physiological Phenomena},
	Month = {Mar},
	Number = {3},
	Pages = {1850-66},
	Pmc = {PMC3665747},
	Pmid = {23514423},
	Pst = {ppublish},
	Title = {Nanotools for neuroscience and brain activity mapping},
	Volume = {7},
	Year = {2013},
	File = {papers/Alivisatos_ACSNano2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1021/nn4012847}}

@article{Fenlon:2015a,
	Abstract = {BACKGROUND: Autism spectrum disorders (ASD) are a group of poorly understood behavioural disorders, which have increased in prevalence in the past two decades. Animal models offer the opportunity to understand the biological basis of these disorders. Studies comparing different mouse strains have identified the inbred BTBR T + tf/J (BTBR) strain as a mouse model of ASD based on its anti-social and repetitive behaviours. Adult BTBR mice have complete agenesis of the corpus callosum, reduced cortical thickness and changes in early neurogenesis. However, little is known about the development or ultimate organisation of cortical areas devoted to specific sensory and motor functions in these mice that may also contribute to their behavioural phenotype.
RESULTS: In this study, we performed diffusion tensor imaging and tractography, together with histological analyses to investigate the emergence of functional areas in the cerebral cortex and their connections in BTBR mice and age-matched C57Bl/6 control mice. We found evidence that neither the anterior commissure nor the hippocampal commissure compensate for the loss of callosal connections, indicating that no interhemispheric neocortical connectivity is present in BTBR mice. We also found that both the primary visual and somatosensory cortical areas are shifted medially in BTBR mice compared to controls and that cortical thickness is differentially altered in BTBR mice between cortical areas and throughout development.
CONCLUSIONS: We demonstrate that interhemispheric connectivity and cortical area formation are altered in an age- and region-specific manner in BTBR mice, which may contribute to the behavioural deficits previously observed in this strain. Some of these developmental patterns of change are also present in human ASD patients, and elucidating the aetiology driving cortical changes in BTBR mice may therefore help to increase our understanding of this disorder.},
	Author = {Fenlon, Laura R and Liu, Sha and Gobius, Ilan and Kurniawan, Nyoman D and Murphy, Skyle and Moldrich, Randal X and Richards, Linda J},
	Date-Added = {2016-07-01 12:08:40 +0000},
	Date-Modified = {2016-07-01 12:10:18 +0000},
	Doi = {10.1186/s13064-015-0033-y},
	Journal = {Neural Dev},
	Journal-Full = {Neural development},
	Keywords = {development; corpus callosum; connectivity; neocortex; cerebral; activity-development;},
	Mesh = {Agenesis of Corpus Callosum; Aging; Animals; Anterior Cerebellar Commissure; Autism Spectrum Disorder; Cerebral Cortex; Diffusion Tensor Imaging; Disease Models, Animal; Fornix, Brain; Mice; Mice, Inbred C57BL; Mice, Inbred Strains; Mice, Neurologic Mutants; Phenotype; Somatosensory Cortex; Visual Cortex},
	Pages = {10},
	Pmc = {PMC4412039},
	Pmid = {25879444},
	Pst = {epublish},
	Title = {Formation of functional areas in the cerebral cortex is disrupted in a mouse model of autism spectrum disorder},
	Volume = {10},
	Year = {2015},
	File = {papers/Fenlon_NeuralDev2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1186/s13064-015-0033-y}}

@article{Fenlon:2015,
	Abstract = {The corpus callosum connects the two cortical hemispheres of the mammalian brain and is susceptible to structural defects during development, which often result in significant neuropsychological dysfunction. To date, such individuals have been studied primarily with regards to the integrity of the callosal tract at the midline. However, the mechanisms regulating the contralateral targeting of the corpus callosum, after midline crossing has occurred, are less well understood. Recent evidence suggests that defects in contralateral targeting can occur in isolation from midline-tract malformations, and may have significant functional implications. We propose that contralateral targeting is a crucially important and relatively under-investigated event in callosal development, and that defects in this process may constitute an undiagnosed phenotype in several neurological disorders.},
	Author = {Fenlon, Laura R and Richards, Linda J},
	Date-Added = {2016-07-01 12:08:15 +0000},
	Date-Modified = {2016-07-01 12:10:18 +0000},
	Doi = {10.1016/j.tins.2015.02.007},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {autism; brain development; callosal dysgenesis; contralateral targeting; corpus callosum; schizophrenia; development; corpus callosum; connectivity; neocortex; cerebral; activity-development;},
	Mesh = {Animals; Corpus Callosum; Functional Laterality; Humans; Mental Disorders; Neuroimaging},
	Month = {May},
	Number = {5},
	Pages = {264-72},
	Pmid = {25841797},
	Pst = {ppublish},
	Title = {Contralateral targeting of the corpus callosum in normal and pathological brain function},
	Volume = {38},
	Year = {2015},
	File = {papers/Fenlon_TrendsNeurosci2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tins.2015.02.007}}

@article{Kozberg:2016,
	Abstract = {UNLABELLED: In the adult brain, increases in neural activity lead to increases in local blood flow. However, many prior measurements of functional hemodynamics in the neonatal brain, including functional magnetic resonance imaging (fMRI) in human infants, have noted altered and even inverted hemodynamic responses to stimuli. Here, we demonstrate that localized neural activity in early postnatal mice does not evoke blood flow increases as in the adult brain, and elucidate the neural and metabolic correlates of these altered functional hemodynamics as a function of developmental age. Using wide-field GCaMP imaging, the development of neural responses to somatosensory stimulus is visualized over the entire bilaterally exposed cortex. Neural responses are observed to progress from tightly localized, unilateral maps to bilateral responses as interhemispheric connectivity becomes established. Simultaneous hemodynamic imaging confirms that spatiotemporally coupled functional hyperemia is not present during these early stages of postnatal brain development, and develops gradually as cortical connectivity is established. Exploring the consequences of this lack of functional hyperemia, measurements of oxidative metabolism via flavoprotein fluorescence suggest that neural activity depletes local oxygen to below baseline levels at early developmental stages. Analysis of hemoglobin oxygenation dynamics at the same age confirms oxygen depletion for both stimulus-evoked and resting-state neural activity. This state of unmet metabolic demand during neural network development poses new questions about the mechanisms of neurovascular development and its role in both normal and abnormal brain development. These results also provide important insights for the interpretation of fMRI studies of the developing brain.
SIGNIFICANCE STATEMENT: This work demonstrates that the postnatal development of neuronal connectivity is accompanied by development of the mechanisms that regulate local blood flow in response to neural activity. Novel in vivo imaging reveals that, in the developing mouse brain, strong and localized GCaMP neural responses to stimulus fail to evoke local blood flow increases, leading to a state in which oxygen levels become locally depleted. These results demonstrate that the development of cortical connectivity occurs in an environment of altered energy availability that itself may play a role in shaping normal brain development. These findings have important implications for understanding the pathophysiology of abnormal developmental trajectories, and for the interpretation of functional magnetic resonance imaging data acquired in the developing brain.},
	Author = {Kozberg, Mariel G and Ma, Ying and Shaik, Mohammed A and Kim, Sharon H and Hillman, Elizabeth M C},
	Date-Added = {2016-07-01 12:05:59 +0000},
	Date-Modified = {2016-07-01 12:05:59 +0000},
	Doi = {10.1523/JNEUROSCI.2363-15.2016},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {GCaMP imaging; fMRI; flavoprotein fluorescence; functional hyperemia; neurovascular coupling; oxygen consumption; postnatal neural development},
	Month = {Jun},
	Number = {25},
	Pages = {6704-17},
	Pmid = {27335402},
	Pst = {ppublish},
	Title = {Rapid Postnatal Expansion of Neural Networks Occurs in an Environment of Altered Neurovascular and Neurometabolic Coupling},
	Volume = {36},
	Year = {2016},
	File = {papers/Kozberg_JNeurosci2016.pdf}}

@article{Wise:1978,
	Author = {Wise, S P and Jones, E G},
	Date-Added = {2016-05-13 20:02:41 +0000},
	Date-Modified = {2016-05-13 20:02:41 +0000},
	Doi = {10.1002/cne.901780202},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Age Factors; Animals; Corpus Striatum; Functional Laterality; Neural Pathways; Rats; Somatosensory Cortex; Thalamic Nuclei; Thalamus},
	Month = {Mar},
	Number = {2},
	Pages = {187-208},
	Pmid = {627623},
	Pst = {ppublish},
	Title = {Developmental studies of thalamocortical and commissural connections in the rat somatic sensory cortex},
	Volume = {178},
	Year = {1978},
	File = {papers/Wise_JCompNeurol1978.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901780202}}

@article{Wise:1977,
	Abstract = {The retrograde, horseradish peroxidase technique has been used to demonstrate the cells of origin of corticofugal fiber systems arising in the rat somatic sensory cortex and projecting to the striatum, diencephalon, brainstem, and spinal cord. Correlative experiments conducted with the anterograde, autoradiographic method have been used to confirm the terminal distribution of many of these fiber systems. Corticofugal pathways directed to subcortical structures arise in the first and second somatic sensory areas exclusively from pyramidal cells of the infragranular layers, V and VI. Fibers which descend to the midbrain, pons, medulla and spinal cord arise exclusively from the largest pyramidal cells, the somata of which are found in the deep part of layer V (layer VB). There is some evidence for a sublaminar organization of the different classes of efferent cells within this layer. Fibers projecting to the diencephalon arise from somata situated throughout layer VI and to a lesser extent in layer V. Corticostriatal fibers arise only from cells with somata in layer V, but the somata are more superficially situated than those of the other classes of corticofugal neurons. The laminar distribution of the somata of corticofugal neurons differs considerably from that of commissural and ipsilateral corticocortical neurons.},
	Author = {Wise, S P and Jones, E G},
	Date-Added = {2016-05-13 20:02:38 +0000},
	Date-Modified = {2016-05-13 20:02:38 +0000},
	Doi = {10.1002/cne.901750202},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Autoradiography; Brain Mapping; Cats; Corpus Striatum; Diencephalon; Haplorhini; Medulla Oblongata; Mesencephalon; Neural Pathways; Neurons, Efferent; Pons; Pyramidal Tracts; Rats; Somatosensory Cortex; Tectum Mesencephali; Thalamus},
	Month = {Sep},
	Number = {2},
	Pages = {129-57},
	Pmid = {408380},
	Pst = {ppublish},
	Title = {Cells of origin and terminal distribution of descending projections of the rat somatic sensory cortex},
	Volume = {175},
	Year = {1977},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901750202}}

@article{Wise:1976,
	Abstract = {Anterograde and retrograde tracing experiments have been used to demonstrate the origin and terminal distribution of commissural fibers in the first somatosensory cortex (SI) of the rat. The commissural fibers originate from pyramidal cells of all layers, but predominantly from layers III and V. The fibers terminate in a series of approximately vertical bands. In each of these there are concentrations of terminals extending from the inner portion of the molecular layer to the deep portion of layer III as well as in the superficial part of layer V, and in layer VI. Discrete vertical bands of cortex are reciprocally connected across the midline to give both the origin and terminal regions of the projection a patchy or "columnar" appearance. The commissural fibers arise from and terminate in areas of the cortex that lie between and alongside the aggregations of granule cells that distinguish SI of the rat. No commissural fibers terminate within the aggregations of layer IV cells themselves but the more superficial terminal ramifications may come to overlie these aggregations. A heterotopic projection to the contralateral second somatosensory cortex has been observed and is similar in form to the homotopic projection to SI. Many commissural fibers have crossed the midline in the corpus callosum by the day of birth but lie in the underlying white matter and do not enter the cortical plate until at least the third postnatal day. During the first postnatal week these fibers grow somewhat diffusely into the maturing cortex and their topographic and laminar pattern of distribution attains its adult characteristics by the end of the first week. Commissural axons, thus, arise from immature cells but the maturation of cell form seems to precede the ingrowth of these axons and the acquisition of commissural synapses.},
	Author = {Wise, S P and Jones, E G},
	Date-Added = {2016-05-13 20:02:37 +0000},
	Date-Modified = {2016-05-13 20:02:37 +0000},
	Doi = {10.1002/cne.901680302},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Animals, Newborn; Brain Mapping; Corpus Callosum; Neural Pathways; Rats; Somatosensory Cortex},
	Month = {Aug},
	Number = {3},
	Pages = {313-43},
	Pmid = {950383},
	Pst = {ppublish},
	Title = {The organization and postnatal development of the commissural projection of the rat somatic sensory cortex},
	Volume = {168},
	Year = {1976},
	File = {papers/Wise_JCompNeurol1976.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901680302}}

@article{Mohajerani:2013,
	Abstract = {Using millisecond-timescale voltage-sensitive dye imaging in lightly anesthetized or awake adult mice, we show that a palette of sensory-evoked and hemisphere-wide activity motifs are represented in spontaneous activity. These motifs can reflect multiple modes of sensory processing, including vision, audition and touch. We found similar cortical networks with direct cortical activation using channelrhodopsin-2. Regional analysis of activity spread indicated modality-specific sources, such as primary sensory areas, a common posterior-medial cortical sink where sensory activity was extinguished within the parietal association area and a secondary anterior medial sink within the cingulate and secondary motor cortices for visual stimuli. Correlation analysis between functional circuits and intracortical axonal projections indicated a common framework corresponding to long-range monosynaptic connections between cortical regions. Maps of intracortical monosynaptic structural connections predicted hemisphere-wide patterns of spontaneous and sensory-evoked depolarization. We suggest that an intracortical monosynaptic connectome shapes the ebb and flow of spontaneous cortical activity.},
	Author = {Mohajerani, Majid H and Chan, Allen W and Mohsenvand, Mostafa and LeDue, Jeffrey and Liu, Rui and McVea, David A and Boyd, Jamie D and Wang, Yu Tian and Reimers, Mark and Murphy, Timothy H},
	Date-Added = {2016-04-04 23:31:45 +0000},
	Date-Modified = {2016-04-04 23:31:45 +0000},
	Doi = {10.1038/nn.3499},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Acoustic Stimulation; Animals; Auditory Cortex; Axons; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Nerve Net; Photic Stimulation; Visual Cortex},
	Month = {Oct},
	Number = {10},
	Pages = {1426-35},
	Pmc = {PMC3928052},
	Pmid = {23974708},
	Pst = {ppublish},
	Title = {Spontaneous cortical activity alternates between motifs defined by regional axonal projections},
	Volume = {16},
	Year = {2013},
	File = {papers/Mohajerani_NatNeurosci2013.pdf},
	Bdsk-File-2 = {papers/Mohajerani_NatNeurosci2013a.pdf}}

@article{Feinberg:2015,
	Abstract = {More than twenty types of retinal ganglion cells conduct visual information from the eye to the rest of the brain. Each retinal ganglion cell type tessellates the retina in a regular mosaic, so that every point in visual space is processed for visual primitives such as contrast and motion. This information flows to two principal brain centres: the visual cortex and the superior colliculus. The superior colliculus plays an evolutionarily conserved role in visual behaviours, but its functional architecture is poorly understood. Here we report on population recordings of visual responses from neurons in the mouse superior colliculus. Many neurons respond preferentially to lines of a certain orientation or movement axis. We show that cells with similar orientation preferences form large patches that span the vertical thickness of the retinorecipient layers. This organization is strikingly different from the randomly interspersed orientation preferences in the mouse's visual cortex; instead, it resembles the orientation columns observed in the visual cortices of large mammals. Notably, adjacent superior colliculus orientation columns have only limited receptive field overlap. This is in contrast to the organization of visual cortex, where each point in the visual field activates neurons with all preferred orientations. Instead, the superior colliculus favours specific contour orientations within ∼30$\,^{\circ}$ regions of the visual field, a finding with implications for behavioural responses mediated by this brain centre.},
	Author = {Feinberg, Evan H and Meister, Markus},
	Date-Added = {2016-03-21 23:37:59 +0000},
	Date-Modified = {2016-03-21 23:37:59 +0000},
	Doi = {10.1038/nature14103},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Brain Mapping; Calcium; Female; Male; Mice; Mice, Inbred C57BL; Motion; Neurons; Orientation; Photic Stimulation; Superior Colliculi; Visual Cortex; Visual Fields; Wakefulness},
	Month = {Mar},
	Number = {7542},
	Pages = {229-32},
	Pmid = {25517100},
	Pst = {ppublish},
	Title = {Orientation columns in the mouse superior colliculus},
	Volume = {519},
	Year = {2015},
	File = {papers/Feinberg_Nature2015.pdf},
	Bdsk-File-2 = {papers/Feinberg_Nature2015b.pdf},
	Bdsk-File-3 = {papers/Feinberg_Nature2015.jpg},
	Bdsk-File-4 = {papers/Feinberg_Nature2015a.jpg},
	Bdsk-File-5 = {papers/Feinberg_Nature2015b.jpg},
	Bdsk-File-6 = {papers/Feinberg_Nature2015c.jpg},
	Bdsk-File-7 = {papers/Feinberg_Nature2015d.jpg},
	Bdsk-File-8 = {papers/Feinberg_Nature2015e.jpg},
	Bdsk-File-9 = {papers/Feinberg_Nature2015f.jpg},
	File0 = {papers/Feinberg_Nature2015g.jpg}}

@article{Guadiana:2013,
	Abstract = {The formation of primary cilia is a highly choreographed process that can be disrupted in developing neurons by overexpressing neuromodulatory G-protein-coupled receptors GPCRs or by blocking intraflagellar transport. Here, we examined the effects of overexpressing the ciliary GPCRs, 5HT6 and SSTR3, on cilia structure and the differentiation of neocortical neurons. Neuronal overexpression of 5HT6 and SSTR3 was achieved by electroporating mouse embryo cortex in utero with vectors encoding these receptors. We found that overexpression of ciliary GPCRs in cortical neurons, especially 5HT6, induced the formation of long (>30 μm) and often forked cilia. These changes were associated with increased levels of intraflagellar transport proteins and accelerated ciliogenesis in neonatal neocortex, the induction of which required Kif3a, an anterograde motor critical for cilia protein trafficking and growth. GPCR overexpression also altered the complement of signaling molecules within the cilia. We found that SSTR3 and type III adenylyl cyclase (ACIII), proteins normally enriched in neuronal cilia, were rarely detected in 5HT6-elongated cilia. Intriguingly, the changes in cilia structure were accompanied by changes in neuronal morphology. Specifically, disruption of normal ciliogenesis in developing neocortical neurons, either by overexpressing cilia GPCRs or a dominant-negative form of Kif3a, significantly impaired dendrite outgrowth. Remarkably, coexpression of ACIII with 5HT6 restored ACIII to cilia, normalized cilia structure, and restored dendrite outgrowth, effects that were not observed in neurons coexpressing ACIII and dominant-negative form of Kif3a. Collectively, our data suggest the formation of neuronal dendrites in developing neocortex requires structurally normal cilia enriched with ACIII.},
	Author = {Guadiana, Sarah M and Semple-Rowland, Susan and Daroszewski, Daniel and Madorsky, Irina and Breunig, Joshua J and Mykytyn, Kirk and Sarkisian, Matthew R},
	Date-Added = {2016-03-18 17:31:34 +0000},
	Date-Modified = {2016-03-18 17:31:34 +0000},
	Doi = {10.1523/JNEUROSCI.2906-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Adenylyl Cyclases; Animals; Cells, Cultured; Cilia; Dendrites; Female; Kinesin; Male; Mice; NIH 3T3 Cells; Neocortex; Neurogenesis; Neurons; Pregnancy; Receptors, Serotonin},
	Month = {Feb},
	Number = {6},
	Pages = {2626-38},
	Pmid = {23392690},
	Pst = {ppublish},
	Title = {Arborization of dendrites by developing neocortical neurons is dependent on primary cilia and type 3 adenylyl cyclase},
	Volume = {33},
	Year = {2013},
	File = {papers/Guadiana_JNeurosci2013.pdf}}

@article{Breunig:2015,
	Abstract = {As the list of putative driver mutations in glioma grows, we are just beginning to elucidate the effects of dysregulated developmental signaling pathways on the transformation of neural cells. We have employed a postnatal, mosaic, autochthonous glioma model that captures the first hours and days of gliomagenesis in more resolution than conventional genetically engineered mouse models of cancer. We provide evidence that disruption of the Nf1-Ras pathway in the ventricular zone at multiple signaling nodes uniformly results in rapid neural stem cell depletion, progenitor hyperproliferation, and gliogenic lineage restriction. Abolishing Ets subfamily activity, which is upregulated downstream of Ras, rescues these phenotypes and blocks glioma initiation. Thus, the Nf1-Ras-Ets axis might be one of the select molecular pathways that are perturbed for initiation and maintenance in glioma.},
	Author = {Breunig, Joshua J and Levy, Rachelle and Antonuk, C Danielle and Molina, Jessica and Dutra-Clarke, Marina and Park, Hannah and Akhtar, Aslam Abbasi and Kim, Gi Bum and Hu, Xin and Bannykh, Serguei I and Verhaak, Roel G W and Danielpour, Moise},
	Date-Added = {2016-03-18 17:31:15 +0000},
	Date-Modified = {2016-03-18 17:31:15 +0000},
	Doi = {10.1016/j.celrep.2015.06.012},
	Journal = {Cell Rep},
	Journal-Full = {Cell reports},
	Month = {Jul},
	Number = {2},
	Pages = {258-71},
	Pmid = {26146073},
	Pst = {ppublish},
	Title = {Ets Factors Regulate Neural Stem Cell Depletion and Gliogenesis in Ras Pathway Glioma},
	Volume = {12},
	Year = {2015},
	File = {papers/Breunig_CellRep2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.celrep.2015.06.012}}

@article{Zeisel:2015,
	Abstract = {The mammalian cerebral cortex supports cognitive functions such as sensorimotor integration, memory, and social behaviors. Normal brain function relies on a diverse set of differentiated cell types, including neurons, glia, and vasculature. Here, we have used large-scale single-cell RNA sequencing (RNA-seq) to classify cells in the mouse somatosensory cortex and hippocampal CA1 region. We found 47 molecularly distinct subclasses, comprising all known major cell types in the cortex. We identified numerous marker genes, which allowed alignment with known cell types, morphology, and location. We found a layer I interneuron expressing Pax6 and a distinct postmitotic oligodendrocyte subclass marked by Itpr2. Across the diversity of cortical cell types, transcription factors formed a complex, layered regulatory code, suggesting a mechanism for the maintenance of adult cell type identity.},
	Author = {Zeisel, Amit and Mu{\~n}oz-Manchado, Ana B and Codeluppi, Simone and L{\"o}nnerberg, Peter and La Manno, Gioele and Jur{\'e}us, Anna and Marques, Sueli and Munguba, Hermany and He, Liqun and Betsholtz, Christer and Rolny, Charlotte and Castelo-Branco, Gon{\c c}alo and Hjerling-Leffler, Jens and Linnarsson, Sten},
	Date-Added = {2016-03-17 21:14:22 +0000},
	Date-Modified = {2016-03-17 21:15:48 +0000},
	Doi = {10.1126/science.aaa1934},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {mouse; mice; technique; Methods; RNAseq},
	Mesh = {Animals; CA1 Region, Hippocampal; Eye Proteins; Gene Expression; Genetic Markers; Homeodomain Proteins; Inositol 1,4,5-Trisphosphate Receptors; Interneurons; Mice; Oligodendroglia; Paired Box Transcription Factors; Phylogeny; Repressor Proteins; Sequence Analysis, RNA; Single-Cell Analysis; Somatosensory Cortex; Transcription Factors; Transcriptome},
	Month = {Mar},
	Number = {6226},
	Pages = {1138-42},
	Pmid = {25700174},
	Pst = {ppublish},
	Title = {Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq},
	Volume = {347},
	Year = {2015},
	File = {papers/Zeisel_Science2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.aaa1934}}

@article{Perez-Cadahia:2011,
	Abstract = {Immediate-early genes have important roles in processes such as brain development, learning, and responses to drug abuse. Further, immediate-early genes play an essential role in cellular responses that contribute to long-term neuronal plasticity. Neuronal plasticity is a characteristic of the nervous system that is not limited to the first stages of brain development but persists in adulthood and seems to be an inherent feature of everyday brain function. The plasticity refers to the neuron's capability of showing short- or long-lasting phenotypic changes in response to different stimuli and cellular scenarios. In this review, we focus on the immediate-early genes encoding transcription factors (AP-1 and Egr) that are relevant for neuronal responses. Our current understanding of the mechanisms involved in the induction of the immediate-early genes is presented.},
	Author = {P{\'e}rez-Cadah{\'\i}a, Beatriz and Drobic, Bojan and Davie, James R},
	Date-Added = {2016-03-17 21:12:26 +0000},
	Date-Modified = {2016-03-17 21:13:09 +0000},
	Doi = {10.1139/O10-138},
	Journal = {Biochem Cell Biol},
	Journal-Full = {Biochemistry and cell biology = Biochimie et biologie cellulaire},
	Keywords = {Immediate-Early; gene; IEG; Transcription Factors; activity-development; activity manipulation},
	Mesh = {Animals; Brain; Early Growth Response Protein 1; Genes, Immediate-Early; Humans; Nervous System Physiological Phenomena; Neuronal Plasticity; Neurons; Signal Transduction; Transcription Factor AP-1; Transcription Factors; Transcriptional Activation},
	Month = {Feb},
	Number = {1},
	Pages = {61-73},
	Pmid = {21326363},
	Pst = {ppublish},
	Title = {Activation and function of immediate-early genes in the nervous system},
	Volume = {89},
	Year = {2011},
	File = {papers/Pérez-Cadahía_BiochemCellBiol2011.pdf}}

@article{Meyza:2015,
	Abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized, in part, by an inability to adequately respond to social cues. Patients diagnosed with ASD are often devoid of empathy and impaired in understanding other people's emotional perspective. The neuronal correlates of this impairment are not fully understood. Replicating such a behavioral phenotype in a mouse model of autism would allow us insight into the neuronal background of the problem. Here we tested BTBR T(+)Itpr3(tf)/J (BTBR) and c57BL/6J (B6) mice in two behavioral paradigms: the Transfer of Emotional Information test and the Social Proximity test. In both tests BTBR mice displayed asocial behavior. We analyzed c-Fos protein expression in several brain regions after each of these tests, and found that, unlike B6 mice, BTBR mice react to a stressed cagemate exposure in the Transfer of Emotional Information test with no increase of c-Fos expression in either the prefrontal cortex or the amygdala. However, after Social Proximity exposure we observed a strong increase in c-Fos expression in the CA3 field of the hippocampus and two hypothalamic regions of BTBR brains. This response was accompanied by a strong activation of periaqueductal regions related to defensiveness, which suggests that BTBR mice find unavoidable social interaction highly aversive.},
	Author = {Meyza, Ksenia and Nikolaev, Tomasz and Kondrakiewicz, Kacper and Blanchard, D Caroline and Blanchard, Robert J and Knapska, Ewelina},
	Date-Added = {2016-03-17 21:12:03 +0000},
	Date-Modified = {2016-03-17 21:12:03 +0000},
	Doi = {10.3389/fnbeh.2015.00199},
	Journal = {Front Behav Neurosci},
	Journal-Full = {Frontiers in behavioral neuroscience},
	Keywords = {BTBR; autism; c-Fos; empathy; mouse model},
	Pages = {199},
	Pmc = {PMC4526814},
	Pmid = {26300749},
	Pst = {epublish},
	Title = {Neuronal correlates of asocial behavior in a BTBR T (+) Itpr3(tf)/J mouse model of autism},
	Volume = {9},
	Year = {2015},
	File = {papers/Meyza_FrontBehavNeurosci2015.pdf}}

@article{Darmanis:2015,
	Abstract = {The human brain is a tissue of vast complexity in terms of the cell types it comprises. Conventional approaches to classifying cell types in the human brain at single cell resolution have been limited to exploring relatively few markers and therefore have provided a limited molecular characterization of any given cell type. We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained during surgical procedures where otherwise normal tissue was removed to gain access to deeper hippocampal pathology in patients with medical refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain. We were able to divide neurons into individual communities and show that these communities preserve the categorization of interneuron subtypes that is typically observed with the use of classic interneuron markers. We then used single cell RNA sequencing on fetal human cortical neurons to identify genes that are differentially expressed between fetal and adult neurons and those genes that display an expression gradient that reflects the transition between replicating and quiescent fetal neuronal populations. Finally, we observed the expression of major histocompatibility complex type I genes in a subset of adult neurons, but not fetal neurons. The work presented here demonstrates the applicability of single cell RNA sequencing on the study of the adult human brain and constitutes a first step toward a comprehensive cellular atlas of the human brain.},
	Author = {Darmanis, Spyros and Sloan, Steven A and Zhang, Ye and Enge, Martin and Caneda, Christine and Shuer, Lawrence M and Hayden Gephart, Melanie G and Barres, Ben A and Quake, Stephen R},
	Date-Added = {2016-03-17 21:11:49 +0000},
	Date-Modified = {2016-03-17 21:11:49 +0000},
	Doi = {10.1073/pnas.1507125112},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {RNAseq; human brain; interneurons; neurons; single cells},
	Mesh = {Adult; Brain; HLA Antigens; Humans; Neurons; Sequence Analysis, RNA; Single-Cell Analysis; Transcriptome},
	Month = {Jun},
	Number = {23},
	Pages = {7285-90},
	Pmc = {PMC4466750},
	Pmid = {26060301},
	Pst = {ppublish},
	Title = {A survey of human brain transcriptome diversity at the single cell level},
	Volume = {112},
	Year = {2015},
	File = {papers/Darmanis_ProcNatlAcadSciUSA2015.pdf}}

@article{Zhang:2014a,
	Abstract = {The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function. To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex. We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain. For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase. This dataset will provide a powerful new resource for understanding the development and function of the brain. To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain.},
	Author = {Zhang, Ye and Chen, Kenian and Sloan, Steven A and Bennett, Mariko L and Scholze, Anja R and O'Keeffe, Sean and Phatnani, Hemali P and Guarnieri, Paolo and Caneda, Christine and Ruderisch, Nadine and Deng, Shuyun and Liddelow, Shane A and Zhang, Chaolin and Daneman, Richard and Maniatis, Tom and Barres, Ben A and Wu, Jian Qian},
	Date-Added = {2016-03-17 21:06:04 +0000},
	Date-Modified = {2016-03-17 21:06:54 +0000},
	Doi = {10.1523/JNEUROSCI.1860-14.2014},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {alternative splicing; astrocytes; microglia; oligodendrocytes; transcriptome; vascular cells; Methods; RNAseq; technique},
	Mesh = {Alternative Splicing; Animals; Cerebral Cortex; Databases, Nucleic Acid; Endothelium, Vascular; Mice; Neuroglia; Neurons; Sequence Analysis, RNA; Transcriptome},
	Month = {Sep},
	Number = {36},
	Pages = {11929-47},
	Pmc = {PMC4152602},
	Pmid = {25186741},
	Pst = {ppublish},
	Title = {An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex},
	Volume = {34},
	Year = {2014},
	File = {papers/Zhang_JNeurosci2014.pdf}}

@article{Schmolesky:1998,
	Abstract = {The onset latencies of single-unit responses evoked by flashing visual stimuli were measured in the parvocellular (P) and magnocellular (M) layers of the dorsal lateral geniculate nucleus (LGNd) and in cortical visual areas V1, V2, V3, V4, middle temporal area (MT), medial superior temporal area (MST), and in the frontal eye field (FEF) in individual anesthetized monkeys. Identical procedures were carried out to assess latencies in each area, often in the same monkey, thereby permitting direct comparisons of timing across areas. This study presents the visual flash-evoked latencies for cells in areas where such data are common (V1 and V2), and are therefore a good standard, and also in areas where such data are sparse (LGNd M and P layers, MT, V4) or entirely lacking (V3, MST, and FEF in anesthetized preparation). Visual-evoked onset latencies were, on average, 17 ms shorter in the LGNd M layers than in the LGNd P layers. Visual responses occurred in V1 before any other cortical area. The next wave of activation occurred concurrently in areas V3, MT, MST, and FEF. Visual response latencies in areas V2 and V4 were progressively later and more broadly distributed. These differences in the time course of activation across the dorsal and ventral streams provide important temporal constraints on theories of visual processing.},
	Author = {Schmolesky, M T and Wang, Y and Hanes, D P and Thompson, K G and Leutgeb, S and Schall, J D and Leventhal, A G},
	Date-Added = {2016-03-14 19:27:14 +0000},
	Date-Modified = {2016-03-14 19:29:40 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {neurophysiology; Classical/physiology; monkey; visual system; visual cortex; retina; LGN; Thalamic Nuclei; topographic map; Stimulation; conduction velocity; retina; response latency},
	Mesh = {Animals; Evoked Potentials, Visual; Macaca; Neurons; Photic Stimulation; Signal Transduction; Time Factors; Vision, Ocular; Visual Cortex},
	Month = {Jun},
	Number = {6},
	Pages = {3272-8},
	Pmid = {9636126},
	Pst = {ppublish},
	Title = {Signal timing across the macaque visual system},
	Volume = {79},
	Year = {1998},
	File = {papers/Schmolesky_JNeurophysiol1998.pdf}}

@article{Rash:2016,
	Abstract = {Cortical columns are basic cellular and functional units of the cerebral cortex that are malformed in many brain disorders, but how they initially develop is not well understood. Using an optogenetic sensor in the mouse embryonic forebrain, we demonstrate that Ca(2+) fluxes propagate bidirectionally within the elongated fibers of radial glial cells (RGCs), providing a novel communication mechanism linking the proliferative and postmitotic zones before the onset of synaptogenesis. Our results indicate that Ca(2+) activity along RGC fibers provides feedback information along the radial migratory pathway, influencing neurogenesis and migration during early column development. Furthermore, we find that this columnar Ca(2+) propagation is induced by Notch and fibroblast growth factor activities classically implicated in cortical expansion and patterning. Thus, cortical morphogens and growth factors may influence cortical column assembly in part by regulating long-distance Ca(2+) communication along the radial axis of cortical development.},
	Author = {Rash, Brian G and Ackman, James B and Rakic, Pasko},
	Date-Added = {2016-03-14 19:25:35 +0000},
	Date-Modified = {2016-03-14 19:25:35 +0000},
	Doi = {10.1126/sciadv.1501733},
	Journal = {Sci Adv},
	Journal-Full = {Science advances},
	Keywords = {Calcium; GCaMP; migration; neuron; radial glial cells},
	Month = {Feb},
	Number = {2},
	Pages = {e1501733},
	Pmc = {PMC4771444},
	Pmid = {26933693},
	Pst = {epublish},
	Title = {Bidirectional radial Ca(2+) activity regulates neurogenesis and migration during early cortical column formation},
	Volume = {2},
	Year = {2016},
	File = {papers/Rash_SciAdv2016.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/sciadv.1501733}}

@article{Chen:2011a,
	Abstract = {The taste system is one of our fundamental senses, responsible for detecting and responding to sweet, bitter, umami, salty, and sour stimuli. In the tongue, the five basic tastes are mediated by separate classes of taste receptor cells each finely tuned to a single taste quality. We explored the logic of taste coding in the brain by examining how sweet, bitter, umami, and salty qualities are represented in the primary taste cortex of mice. We used in vivo two-photon calcium imaging to demonstrate topographic segregation in the functional architecture of the gustatory cortex. Each taste quality is represented in its own separate cortical field, revealing the existence of a gustotopic map in the brain. These results expose the basic logic for the central representation of taste.},
	Author = {Chen, Xiaoke and Gabitto, Mariano and Peng, Yueqing and Ryba, Nicholas J P and Zuker, Charles S},
	Date-Added = {2016-03-14 19:24:33 +0000},
	Date-Modified = {2016-03-14 19:24:48 +0000},
	Doi = {10.1126/science.1204076},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {Animals; Appetitive Behavior; Avoidance Learning; Brain Mapping; Cerebral Cortex; Discrimination (Psychology); Male; Mice; Mice, Inbred C57BL; Optogenetics; Stereotaxic Techniques; Taste; Taste Perception; Wakefulness},
	Mesh = {Afferent Pathways; Animals; Brain Mapping; Cerebral Cortex; Cycloheximide; Mice; Mice, Inbred C57BL; Mice, Knockout; Molecular Imaging; Neurons; Sodium Chloride; Sodium Glutamate; Sweetening Agents; Taste; Taste Buds},
	Month = {Sep},
	Number = {6047},
	Pages = {1262-6},
	Pmc = {PMC3523322},
	Pmid = {21885776},
	Pst = {ppublish},
	Title = {A gustotopic map of taste qualities in the mammalian brain},
	Volume = {333},
	Year = {2011},
	File = {papers/Chen_Science2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1204076}}

@article{Peng:2015,
	Abstract = {Taste is responsible for evaluating the nutritious content of food, guiding essential appetitive behaviours, preventing the ingestion of toxic substances, and helping to ensure the maintenance of a healthy diet. Sweet and bitter are two of the most salient sensory percepts for humans and other animals; sweet taste allows the identification of energy-rich nutrients whereas bitter warns against the intake of potentially noxious chemicals. In mammals, information from taste receptor cells in the tongue is transmitted through multiple neural stations to the primary gustatory cortex in the brain. Recent imaging studies have shown that sweet and bitter are represented in the primary gustatory cortex by neurons organized in a spatial map, with each taste quality encoded by distinct cortical fields. Here we demonstrate that by manipulating the brain fields representing sweet and bitter taste we directly control an animal's internal representation, sensory perception, and behavioural actions. These results substantiate the segregation of taste qualities in the cortex, expose the innate nature of appetitive and aversive taste responses, and illustrate the ability of gustatory cortex to recapitulate complex behaviours in the absence of sensory input.},
	Author = {Peng, Yueqing and Gillis-Smith, Sarah and Jin, Hao and Tr{\"a}nkner, Dimitri and Ryba, Nicholas J P and Zuker, Charles S},
	Date-Added = {2016-03-14 19:23:44 +0000},
	Date-Modified = {2016-03-14 19:23:59 +0000},
	Doi = {10.1038/nature15763},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {Animals; Appetitive Behavior; Avoidance Learning; Brain Mapping; Cerebral Cortex; Discrimination (Psychology); Male; Mice; Mice, Inbred C57BL; Optogenetics; Stereotaxic Techniques; Taste; Taste Perception; Wakefulness},
	Mesh = {Animals; Appetitive Behavior; Avoidance Learning; Brain Mapping; Cerebral Cortex; Discrimination (Psychology); Male; Mice; Mice, Inbred C57BL; Optogenetics; Stereotaxic Techniques; Taste; Taste Perception; Wakefulness},
	Month = {Nov},
	Number = {7579},
	Pages = {512-5},
	Pmc = {PMC4712381},
	Pmid = {26580015},
	Pst = {ppublish},
	Title = {Sweet and bitter taste in the brain of awake behaving animals},
	Volume = {527},
	Year = {2015},
	File = {papers/Peng_Nature2015.pdf}}

@article{Zhang:2003c,
	Abstract = {Mammals can taste a wide repertoire of chemosensory stimuli. Two unrelated families of receptors (T1Rs and T2Rs) mediate responses to sweet, amino acids, and bitter compounds. Here, we demonstrate that knockouts of TRPM5, a taste TRP ion channel, or PLCbeta2, a phospholipase C selectively expressed in taste tissue, abolish sweet, amino acid, and bitter taste reception, but do not impact sour or salty tastes. Therefore, despite relying on different receptors, sweet, amino acid, and bitter transduction converge on common signaling molecules. Using PLCbeta2 taste-blind animals, we then examined a fundamental question in taste perception: how taste modalities are encoded at the cellular level. Mice engineered to rescue PLCbeta2 function exclusively in bitter-receptor expressing cells respond normally to bitter tastants but do not taste sweet or amino acid stimuli. Thus, bitter is encoded independently of sweet and amino acids, and taste receptor cells are not broadly tuned across these modalities.},
	Author = {Zhang, Yifeng and Hoon, Mark A and Chandrashekar, Jayaram and Mueller, Ken L and Cook, Boaz and Wu, Dianqing and Zuker, Charles S and Ryba, Nicholas J P},
	Date-Added = {2016-03-14 19:22:34 +0000},
	Date-Modified = {2016-03-14 19:23:08 +0000},
	Journal = {Cell},
	Journal-Full = {Cell},
	Keywords = {Action Potentials; Animals; Cell Membrane; Cells, Cultured; Citric Acid; Female; GTP-Binding Proteins; Glutamic Acid; Isoenzymes; Male; Membrane Proteins; Mice; Mice, Knockout; Neurons, Afferent; Phospholipase C beta; Quinine; Receptors, Cell Surface; Sensory Receptor Cells; Signal Transduction; Sucrose; TRPM Cation Channels; Taste; Taste Buds; Type C Phospholipases},
	Mesh = {Action Potentials; Animals; Cell Membrane; Cells, Cultured; Citric Acid; Female; GTP-Binding Proteins; Glutamic Acid; Isoenzymes; Male; Membrane Proteins; Mice; Mice, Knockout; Neurons, Afferent; Phospholipase C beta; Quinine; Receptors, Cell Surface; Sensory Receptor Cells; Signal Transduction; Sucrose; TRPM Cation Channels; Taste; Taste Buds; Type C Phospholipases},
	Month = {Feb},
	Number = {3},
	Pages = {293-301},
	Pmid = {12581520},
	Pst = {ppublish},
	Title = {Coding of sweet, bitter, and umami tastes: different receptor cells sharing similar signaling pathways},
	Volume = {112},
	Year = {2003},
	File = {papers/Zhang_Cell2003.pdf}}

@article{Sekar:2016,
	Abstract = {Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia.},
	Author = {Sekar, Aswin and Bialas, Allison R and de Rivera, Heather and Davis, Avery and Hammond, Timothy R and Kamitaki, Nolan and Tooley, Katherine and Presumey, Jessy and Baum, Matthew and Van Doren, Vanessa and Genovese, Giulio and Rose, Samuel A and Handsaker, Robert E and {Schizophrenia Working Group of the Psychiatric Genomics Consortium} and Daly, Mark J and Carroll, Michael C and Stevens, Beth and McCarroll, Steven A},
	Date-Added = {2016-01-29 22:14:49 +0000},
	Date-Modified = {2016-01-29 22:14:49 +0000},
	Doi = {10.1038/nature16549},
	Journal = {Nature},
	Journal-Full = {Nature},
	Month = {Jan},
	Pmid = {26814963},
	Pst = {aheadofprint},
	Title = {Schizophrenia risk from complex variation of complement component 4},
	Year = {2016},
	File = {papers/Sekar_Nature2016.pdf}}

@article{Azevedo:2009,
	Abstract = {The human brain is often considered to be the most cognitively capable among mammalian brains and to be much larger than expected for a mammal of our body size. Although the number of neurons is generally assumed to be a determinant of computational power, and despite the widespread quotes that the human brain contains 100 billion neurons and ten times more glial cells, the absolute number of neurons and glial cells in the human brain remains unknown. Here we determine these numbers by using the isotropic fractionator and compare them with the expected values for a human-sized primate. We find that the adult male human brain contains on average 86.1 +/- 8.1 billion NeuN-positive cells ("neurons") and 84.6 +/- 9.8 billion NeuN-negative ("nonneuronal") cells. With only 19% of all neurons located in the cerebral cortex, greater cortical size (representing 82% of total brain mass) in humans compared with other primates does not reflect an increased relative number of cortical neurons. The ratios between glial cells and neurons in the human brain structures are similar to those found in other primates, and their numbers of cells match those expected for a primate of human proportions. These findings challenge the common view that humans stand out from other primates in their brain composition and indicate that, with regard to numbers of neuronal and nonneuronal cells, the human brain is an isometrically scaled-up primate brain.},
	Author = {Azevedo, Frederico A C and Carvalho, Ludmila R B and Grinberg, Lea T and Farfel, Jos{\'e} Marcelo and Ferretti, Renata E L and Leite, Renata E P and Jacob Filho, Wilson and Lent, Roberto and Herculano-Houzel, Suzana},
	Date-Added = {2016-01-19 23:38:02 +0000},
	Date-Modified = {2016-01-19 23:38:02 +0000},
	Doi = {10.1002/cne.21974},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Aged; Antigens, Nuclear; Brain; Cerebral Cortex; Humans; Immunohistochemistry; Male; Middle Aged; Nerve Tissue Proteins; Neuroglia; Neurons},
	Month = {Apr},
	Number = {5},
	Pages = {532-41},
	Pmid = {19226510},
	Pst = {ppublish},
	Title = {Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain},
	Volume = {513},
	Year = {2009},
	File = {papers/Azevedo_JCompNeurol2009.pdf}}

@article{Llinas:2012,
	Author = {Llin{\'a}s, Rodolfo and Sugimori, Mutsuyuki},
	Date-Added = {2016-01-13 18:53:15 +0000},
	Date-Modified = {2016-01-13 18:53:15 +0000},
	Journal = {Cerebellum},
	Journal-Full = {Cerebellum (London, England)},
	Mesh = {Animals; Cerebellum; Dendrites; Electrophysiological Phenomena; Electrophysiology; Humans; Purkinje Cells; Tetrodotoxin},
	Month = {Sep},
	Number = {3},
	Pages = {612-28},
	Pmid = {23035258},
	Pst = {ppublish},
	Title = {Probing the functional properties of mammalian dendrites. 1980},
	Volume = {11},
	Year = {2012}}

@article{Llinas:1980a,
	Abstract = {1. Intradendritic recordings from Purkinje cells in vitro indicate that white matter stimulation produces large synaptic responses by the activation of the climbing fibre afferent, but antidromic potentials do not actively invade the dendritic tree. 2. Climbing fibre responses may be reversed in a manner similar to that observed at the somatic level. However, the reversal does not show the biphasicity often seen at somatic level. 3. Input resistance of these dendrites was found to range from 15 to 30 M omega. The non-linear properties seen at the somatic level for depolarizing currents are also encountered here. However, there seems to be less anomalous rectification. 4. Detailed analysis of repetitive firing of Purkinje cells elicited by outward DC current shows that, as in the case of the antidromic invasion, the fast somatic potentials (s.s.) do not invade the dendrite actively. However, the dendritic spike bursts (d.s.b.s) interposed between the s.s. potentials are most prominent at dendritic level. 5. Two types of voltage-dependent Ca responses were observed. At low stimulus level a plateau-like depolarization is accompanied by a prominent conductance change; further depolarization produces large dendritic action potentials. These two classes of response are TTX-resistant but are blocked by Cd, Co, Mn or D600, or by the removal of extracellular Ca. 6. Following blockage of the Ca conductance, plateau potentials produced by a non-inactivating Na conductance are observed mainly near the soma indicating that this voltage-dependent conductance is probably associated with the somatic membrane. 7. Spontaneous firing in Purkinje cell dendrites is very similar to that observed at the soma. However, the amplitude of these bursts is larger at dendritic level. It is further concluded that these TTX-insensitive spikes are generated at multiple sites along the dendritic tree. 8. Six ionic conductances seem to be involved in Purkinje cell electroresponsiveness: (a) an inactivating and (b) a non-inactivating Na conductance at or near the soma, (c) a spike- and (d) a plateau-generating Ca conductance, and (e) voltage-dependent and (f) Ca-dependent K currents. 9. The possible role of these conductances in Purkinje cell integration is discussed.},
	Author = {Llin{\'a}s, R and Sugimori, M},
	Date-Added = {2016-01-13 18:53:12 +0000},
	Date-Modified = {2016-01-13 18:53:12 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Action Potentials; Animals; Calcium; Dendrites; Electric Conductivity; Guinea Pigs; In Vitro Techniques; Membrane Potentials; Neurons, Afferent; Purkinje Cells; Sodium; Synapses},
	Month = {Aug},
	Pages = {197-213},
	Pmc = {PMC1282967},
	Pmid = {7441553},
	Pst = {ppublish},
	Title = {Electrophysiological properties of in vitro Purkinje cell dendrites in mammalian cerebellar slices},
	Volume = {305},
	Year = {1980}}

@article{Llinas:1980,
	Abstract = {1. The electrical activity of Purkinje cells was studied in guinea-pig cerebellar slices in vitro. Intracellular recordings from Purkinje cell somata were obtained under direct vision, and antidromic, synaptic and direct electroresponsiveness was demonstrated. Synaptic potentials produced by the activation of the climbing fibre afferent could be reversed by direct membrane depolarization. 2. Input resistance of impaled neurones ranged from 10 to 19 M omega and demonstrated non-linearities in both hyperpolarizing and depolarizing directions. 3. Direct activation of a Purkinje cell indicated that repetitive firing of fast somatic spikes (s.s.) occurs, after a threshold, with a minimum spike frequency of about 30 spikes/sec, resembling the '2-class' response of crab nerve (Hodgkin, 1948). 4. As the amplitude of the stimulus was increased, a second form of electroresponsiveness characterized by depolarizing spike bursts (d.s.b.) was observed and was often accomppanied by momentary inactivation of the s.s. potentials. Upon application of tetrodotoxin (TTX) or removal of Na+ ions from the superfusion fluid, the s.s. potentials were abolished while the burst responses remained intact. However, Ca conductance blockers such as Co, Cd, Mn and D600, or the replacement of Ca by Mg, completely abolish d.s.b.s. 5. If Ca conductance was blocked, or Ca removed from the superfusion fluid without blockage of Na conductance, two types of Na-dependent electroresponsiveness were seen: (a) the s.s. potentials and (b) slow rising all-or-none responses which reached plateau at approximately -15 mV and could last for several seconds. These all-or-none Na-dependent plateau depolarizations outlasted the stimulus and were accompanied by a large increase in membrane conductance. Within certain limits the rate of rise and amplitude of the plateau were independent of stimulus strength. The latency, however, was shortened as stimulus amplitude was increased. These potentials were blocked by TTX or by Na-free solutions. 6. Substitution of extracellular Ca by Ba or intracellular injection of tetraethylammonium generated prolonged action potentials lasting for several seconds and showing a plateau more ositive than those obtained in norrmal circumstances by either non-inactivating Na or Ca currents. 7. Spontaneous firing of the Purkinje cell was characterized by burst-like activity consisting of both s.s. and d.s.b. responses. Addition of TTX to the bath left the basic spontaneous activity and its frequency unaltered, indicating tha Ca spiking and Ca-dependent K conductance changes are the main events underlying this oscillatory behaviour. 8...},
	Author = {Llin{\'a}s, R and Sugimori, M},
	Date-Added = {2016-01-13 18:53:07 +0000},
	Date-Modified = {2016-01-13 18:53:07 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Action Potentials; Animals; Barium; Calcium; Electric Conductivity; Guinea Pigs; In Vitro Techniques; Membrane Potentials; Purkinje Cells; Sodium; Synapses; Tetraethylammonium Compounds},
	Month = {Aug},
	Pages = {171-95},
	Pmc = {PMC1282966},
	Pmid = {7441552},
	Pst = {ppublish},
	Title = {Electrophysiological properties of in vitro Purkinje cell somata in mammalian cerebellar slices},
	Volume = {305},
	Year = {1980}}

@article{Jan:1976,
	Abstract = {The anatomy and physiology of the Drosophila larval neuromuscular junction were studied. 2. The dependence of muscle resting potentials on [K+]o and [Na+]o follows the Goldman-Hodgkin-Katz equation (PNa/PK=0-23). Chloride ions distribute passively across the membrane. 3. The mean specific membrane resistance of muscle fibres is 4-3 X 10(3) omega cm2, and the mean specific membrane capacitance is 7-1 muF/cm2. The muscle fibre is virtually isopotential. 4. Transmitter release is quantal. Both the miniature excitatory junctional potential and the evoked release follow the Poisson distribution. 5. Transmitter release depends on approximately the fourth power of [Ca2+]o. If Sr2+ replaces Ca2+, it depends on approximately the fourth power of [Sr2+]o. Mg2+ reduces transmitter release without altering the fourth power dependence on [Ca2+]o.},
	Author = {Jan, L Y and Jan, Y N},
	Date-Added = {2016-01-13 18:52:38 +0000},
	Date-Modified = {2016-01-13 18:52:38 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Animals; Calcium; Chlorides; Drosophila melanogaster; Hydrogen-Ion Concentration; Larva; Magnesium; Membrane Potentials; Neuromuscular Junction; Osmolar Concentration; Potassium; Sodium; Strontium; Synaptic Transmission},
	Month = {Oct},
	Number = {1},
	Pages = {189-214},
	Pmc = {PMC1307637},
	Pmid = {11339},
	Pst = {ppublish},
	Title = {Properties of the larval neuromuscular junction in Drosophila melanogaster},
	Volume = {262},
	Year = {1976}}

@article{Katz:1967,
	Abstract = {1. The axo-axonic giant synapse in the stellate ganglion of the squid has been used to study synaptic transmission.2. When nerve impulses have been eliminated with tetrodotoxin, synaptic transfer of potential changes can still be obtained by applying brief depolarizing pulses to the presynaptic terminal.3. Suitably matched pulses are as effective as the normal presynaptic spike in evoking post-synaptic potentials. The synaptic delay and the time course of the post-synaptic potential are very similar to that in the normal preparation.4. The synaptic transfer (input/output) characteristic has been studied under different experimental conditions. With brief (1-2 msec) current pulses, post-synaptic response becomes detectable when the presynaptic depolarization exceeds about 30 mV. The post-synaptic potential increases about tenfold with 10 mV increments of presynaptic depolarization.5. Calcium increases, magnesium reduces the slope of the synaptic transfer curve. The influences on this curve of (i) duration of the pulse, (ii) preceding level of membrane potential, (iii) position of recording electrode, (iv) rate of repetitive stimulation are described.6. After loading the synaptic terminal with tetraethylammonium ions, large inside-positive potentials can be produced in the terminal and maintained for many milliseconds.7. By raising the internal potential to a sufficiently high level, synaptic transfer becomes suppressed during the pulse, and the post-synaptic response is delayed until the end of the pulse.8. This observation is in accord with a prediction of the ;calcium hypothesis', viz. that inward movement of a positively charged Ca compound, or of the calcium ion itself, constitutes one of the essential links in the ;electro-secretory' coupling process of the axon terminal.},
	Author = {Katz, B and Miledi, R},
	Date-Added = {2016-01-13 18:51:22 +0000},
	Date-Modified = {2016-01-13 18:51:22 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Mesh = {Action Potentials; Animals; Axons; Calcium; Electric Stimulation; In Vitro Techniques; Iontophoresis; Mollusca; Neuromuscular Junction; Neurotransmitter Agents; Stellate Ganglion; Synapses; Synaptic Transmission; Tetraethylammonium Compounds; Tetrodotoxin},
	Month = {Sep},
	Number = {2},
	Pages = {407-36},
	Pmc = {PMC1365564},
	Pmid = {4383089},
	Pst = {ppublish},
	Title = {A study of synaptic transmission in the absence of nerve impulses},
	Volume = {192},
	Year = {1967}}

@article{Coombs:1955,
	Author = {Coombs, J S and Eccles, J C and Fatt, P},
	Date-Added = {2016-01-13 18:50:41 +0000},
	Date-Modified = {2016-10-20 17:00:12 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {neurons; GABA; receptor; Ion Channel Gating; neurophysiology; voltage-clamp},
	Mesh = {Neurons; Synaptic Potentials},
	Month = {Nov},
	Number = {2},
	Pages = {326-74},
	Pmc = {PMC1363415},
	Pmid = {13278905},
	Pst = {ppublish},
	Title = {The specific ionic conductances and the ionic movements across the motoneuronal membrane that produce the inhibitory post-synaptic potential},
	Volume = {130},
	Year = {1955},
	File = {papers/Coombs_JPhysiol1955.pdf}}

@article{Fatt:1953,
	Author = {Fatt, P and Katz, B},
	Date-Added = {2016-01-13 18:50:05 +0000},
	Date-Modified = {2016-10-20 17:41:24 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {MUSCLES/physiology; SHELLFISH},
	Mesh = {Animals; Mollusca; Muscles; Shellfish},
	Month = {Apr},
	Number = {1-2},
	Pages = {171-204},
	Pmc = {PMC1366030},
	Pmid = {13062231},
	Pst = {ppublish},
	Title = {The electrical properties of crustacean muscle fibres},
	Volume = {120},
	Year = {1953},
	File = {papers/Fatt_JPhysiol1953.pdf}}

@article{Hodgkin:1952e,
	Author = {Hodgkin, A L and Huxley, A F},
	Date-Added = {2016-01-13 18:12:26 +0000},
	Date-Modified = {2016-01-13 18:14:55 +0000},
	Journal = {Proc R Soc Lond B Biol Sci},
	Journal-Full = {Proceedings of the Royal Society of London. Series B, Biological sciences},
	Keywords = {AXONS},
	Mesh = {Axons; Nerve Fibers},
	Month = {Oct},
	Number = {899},
	Pages = {177-83},
	Pmid = {13003922},
	Pst = {ppublish},
	Title = {Propagation of electrical signals along giant nerve fibers},
	Volume = {140},
	Year = {1952}}

@article{Hodgkin:1952d,
	Author = {Hodgkin, A L and Huxley, A F},
	Date-Added = {2016-01-13 18:12:24 +0000},
	Date-Modified = {2016-01-13 18:14:48 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {AXONS},
	Mesh = {Axons; Humans},
	Month = {Aug},
	Number = {4},
	Pages = {500-44},
	Pmc = {PMC1392413},
	Pmid = {12991237},
	Pst = {ppublish},
	Title = {A quantitative description of membrane current and its application to conduction and excitation in nerve},
	Volume = {117},
	Year = {1952},
	File = {papers/Hodgkin_JPhysiol1952a.pdf}}

@article{Hodgkin:1952c,
	Author = {Hodgkin, A L and Huxley, A F},
	Date-Added = {2016-01-13 18:12:23 +0000},
	Date-Modified = {2016-01-13 18:14:41 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {AXONS; SODIUM/effects},
	Mesh = {Animals; Axons; Ions; Loligo; Membrane Potentials; Sodium; Sodium, Dietary},
	Month = {Apr},
	Number = {4},
	Pages = {497-506},
	Pmc = {PMC1392212},
	Pmid = {14946715},
	Pst = {ppublish},
	Title = {The dual effect of membrane potential on sodium conductance in the giant axon of Loligo},
	Volume = {116},
	Year = {1952},
	File = {papers/Hodgkin_JPhysiol1952b.pdf}}

@article{Hodgkin:1952b,
	Author = {Hodgkin, A L and Huxley, A F},
	Date-Added = {2016-01-13 18:12:21 +0000},
	Date-Modified = {2016-01-13 18:14:34 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {AXONS},
	Mesh = {Animals; Axons; Humans; Loligo},
	Month = {Apr},
	Number = {4},
	Pages = {473-96},
	Pmc = {PMC1392209},
	Pmid = {14946714},
	Pst = {ppublish},
	Title = {The components of membrane conductance in the giant axon of Loligo},
	Volume = {116},
	Year = {1952},
	File = {papers/Hodgkin_JPhysiol1952c.pdf}}

@article{Hodgkin:1952a,
	Author = {Hodgkin, A L and Huxley, A F},
	Date-Added = {2016-01-13 18:12:19 +0000},
	Date-Modified = {2016-01-13 18:14:28 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {AXONS; POTASSIUM/effects; SODIUM/effects},
	Mesh = {Animals; Axons; Ions; Loligo; Potassium; Sodium; Sodium, Dietary},
	Month = {Apr},
	Number = {4},
	Pages = {449-72},
	Pmc = {PMC1392213},
	Pmid = {14946713},
	Pst = {ppublish},
	Title = {Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo},
	Volume = {116},
	Year = {1952},
	File = {papers/Hodgkin_JPhysiol1952d.pdf}}

@article{Hodgkin:1952,
	Author = {Hodgkin, A L and Huxley, A F and Katz, B},
	Date-Added = {2016-01-13 18:12:18 +0000},
	Date-Modified = {2016-01-13 18:14:20 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {AXONS},
	Mesh = {Animals; Axons; Loligo},
	Month = {Apr},
	Number = {4},
	Pages = {424-48},
	Pmc = {PMC1392219},
	Pmid = {14946712},
	Pst = {ppublish},
	Title = {Measurement of current-voltage relations in the membrane of the giant axon of Loligo},
	Volume = {116},
	Year = {1952},
	File = {papers/Hodgkin_JPhysiol1952.pdf}}

@article{Hodgkin:1939,
	Author = {Hodgkin, A L and Huxley, A F},
	Date-Added = {2016-01-11 19:48:09 +0000},
	Date-Modified = {2016-01-11 19:50:53 +0000},
	Doi = {10.1038/144710a0},
	Journal = {Nature},
	Keywords = {Action Potentials; squid giant axon; neurophysiology; Classical/physiology},
	Pages = {710-711},
	Title = {Action Potentials Recorded from Inside a Nerve Fibre},
	Volume = {144},
	Year = {1939},
	File = {papers/Hodgkin_Nature1939.pdf}}

@article{Hodgkin:1949b,
	Author = {Hodgkin, A L and Katz, B},
	Date-Added = {2016-01-11 19:19:06 +0000},
	Date-Modified = {2016-01-11 19:19:53 +0000},
	Journal = {J Exp Biol},
	Journal-Full = {The Journal of experimental biology},
	Keywords = {NERVOUS SYSTEM},
	Mesh = {Axons; Calcium; Calcium, Dietary; Nerve Fibers; Nervous System},
	Month = {Oct},
	Number = {3},
	Pages = {292-4, pl},
	Pmid = {15395900},
	Pst = {ppublish},
	Title = {The effect of calcium on the axoplasm of giant nerve fibers},
	Volume = {26},
	Year = {1949}}

@article{Hodgkin:1949a,
	Author = {Hodgkin, A L and Katz, B},
	Date-Added = {2016-01-11 19:18:58 +0000},
	Date-Modified = {2016-01-11 19:20:07 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {NERVOUS SYSTEM},
	Mesh = {Animals; Axons; Decapodiformes; Nervous System; Temperature},
	Month = {Aug},
	Number = {1-2},
	Pages = {240-9},
	Pmc = {PMC1392577},
	Pmid = {15394322},
	Pst = {ppublish},
	Title = {The effect of temperature on the electrical activity of the giant axon of the squid},
	Volume = {109},
	Year = {1949}}

@article{Hodgkin:1949,
	Author = {Hodgkin, A L and Katz, B},
	Date-Added = {2016-01-11 19:18:07 +0000},
	Date-Modified = {2016-01-11 19:20:21 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {NEURONS; SODIUM},
	Mesh = {Animals; Axons; Decapodiformes; Ions; Neurons; Sodium; Sodium, Dietary},
	Month = {Mar},
	Number = {1},
	Pages = {37-77},
	Pmc = {PMC1392331},
	Pmid = {18128147},
	Pst = {ppublish},
	Title = {The effect of sodium ions on the electrical activity of giant axon of the squid},
	Volume = {108},
	Year = {1949},
	File = {papers/HODGKIN_JPhysiol1949.pdf}}

@article{Root:2014,
	Abstract = {The lateral habenula (LHb) is involved in reward, aversion, addiction and depression through descending interactions with several brain structures, including the ventral tegmental area (VTA). The VTA provides reciprocal inputs to LHb, but their actions are unclear. Here we show that the majority of rat and mouse VTA neurons innervating LHb coexpress markers for both glutamate signaling (vesicular glutamate transporter 2; VGluT2) and GABA signaling (glutamic acid decarboxylase; GAD, and vesicular GABA transporter; VGaT). A single axon from these mesohabenular neurons coexpresses VGluT2 protein and VGaT protein and, surprisingly, establishes symmetric and asymmetric synapses on LHb neurons. In LHb slices, light activation of mesohabenular fibers expressing channelrhodopsin2 driven by VGluT2 (Slc17a6) or VGaT (Slc32a1) promoters elicits release of both glutamate and GABA onto single LHb neurons. In vivo light activation of mesohabenular terminals inhibits or excites LHb neurons. Our findings reveal an unanticipated type of VTA neuron that cotransmits glutamate and GABA and provides the majority of mesohabenular inputs.},
	Author = {Root, David H and Mejias-Aponte, Carlos A and Zhang, Shiliang and Wang, Hui-Ling and Hoffman, Alexander F and Lupica, Carl R and Morales, Marisela},
	Date-Added = {2016-01-07 20:54:13 +0000},
	Date-Modified = {2016-01-07 20:54:13 +0000},
	Doi = {10.1038/nn.3823},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Animals; Axons; Glutamic Acid; Habenula; Male; Neural Pathways; Rats, Sprague-Dawley; Reward; Synapses; Ventral Tegmental Area; Vesicular Glutamate Transport Protein 2; gamma-Aminobutyric Acid},
	Month = {Nov},
	Number = {11},
	Pages = {1543-51},
	Pmid = {25242304},
	Pst = {ppublish},
	Title = {Single rodent mesohabenular axons release glutamate and GABA},
	Volume = {17},
	Year = {2014},
	File = {papers/Root_NatNeurosci2014.pdf},
	Bdsk-File-2 = {papers/Root_NatNeurosci2014a.pdf}}

@article{Pei:2015,
	Abstract = {Direction selectivity of direction-selective ganglion cells (DSGCs) in the retina results from patterned excitatory and inhibitory inputs onto DSGCs during motion stimuli. The inhibitory inputs onto DSGCs are directionally tuned to the antipreferred (null) direction and therefore potently suppress spiking during motion in the null direction. However, whether direction-selective inhibition is indispensable for direction selectivity is unclear. Here, we selectively eliminated the directional tuning of inhibitory inputs onto DSGCs by disrupting GABA release from the presynaptic interneuron starburst amacrine cell in the mouse retina. We found that, even without directionally tuned inhibition, direction selectivity can still be implemented in a subset of On-Off DSGCs by direction-selective excitation and a temporal offset between excitation and isotropic inhibition. Our results therefore demonstrate the concerted action of multiple synaptic mechanisms for robust direction selectivity in the retina. Significance statement: The direction-selective circuit in the retina has been a classic model to study neural computations by the brain. An important but unresolved question is how direction selectivity is implemented by directionally tuned excitatory and inhibitory mechanisms. Here we specifically removed the direction tuning of inhibition from the circuit. We found that direction tuning of inhibition is important but not indispensable for direction selectivity of DSGCs' spiking activity, and that the residual direction selectivity is implemented by direction-selective excitation and temporal offset between excitation and inhibition. Our results highlight the concerted actions of synaptic excitation and inhibition required for robust direction selectivity in the retina and provide critical insights into how patterned excitation and inhibition collectively implement sensory processing.},
	Author = {Pei, Zhe and Chen, Qiang and Koren, David and Giammarinaro, Benno and Acaron Ledesma, Hector and Wei, Wei},
	Date-Added = {2015-12-15 18:44:22 +0000},
	Date-Modified = {2015-12-15 18:44:22 +0000},
	Doi = {10.1523/JNEUROSCI.0933-15.2015},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {direction selectivity; retina; starburst amacrine cell; synaptic excitation; synaptic inhibition; vesicular GABA transporter},
	Month = {Sep},
	Number = {38},
	Pages = {13219-32},
	Pmc = {PMC4579379},
	Pmid = {26400950},
	Pst = {ppublish},
	Title = {Conditional Knock-Out of Vesicular GABA Transporter Gene from Starburst Amacrine Cells Reveals the Contributions of Multiple Synaptic Mechanisms Underlying Direction Selectivity in the Retina},
	Volume = {35},
	Year = {2015},
	File = {papers/Pei_JNeurosci2015.pdf}}

@article{Catania:2002,
	Abstract = {We investigated naked mole-rat somatosensory cortex to determine how brain areas are modified in mammals with unusual and extreme sensory specializations. Naked mole-rats (Heterocephalus glaber) have numerous anatomical specializations for a subterranean existence, including rows of sensory hairs along the body and tail, reduced eyes, and ears sensitive to low frequencies. However, chief among their adaptations are behaviorally important, enlarged incisors permanently exterior to the oral cavity that are used for digging, object manipulation, social interactions, and feeding. Here we report an extraordinary brain organization where nearly one-third (31%) of primary somatosensory cortex is devoted to the representations of the upper and lower incisors. In addition, somatosensory cortex is greatly enlarged (as a proportion of total neocortical area) compared with closely related laboratory rats. Finally, somatosensory cortex in naked mole-rats encompasses virtually all of the neocortex normally devoted to vision. These findings indicate that major cortical remodeling has occurred in naked mole-rats, paralleling the anatomical and behavioral specializations related to fossorial life.},
	Author = {Catania, Kenneth C and Remple, Michael S},
	Date-Added = {2015-12-14 01:08:16 +0000},
	Date-Modified = {2015-12-14 01:08:16 +0000},
	Doi = {10.1073/pnas.072097999},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Brain; Brain Mapping; Models, Anatomic; Mole Rats; Rats; Rats, Long-Evans; Somatosensory Cortex; Tooth; Touch},
	Month = {Apr},
	Number = {8},
	Pages = {5692-7},
	Pmc = {PMC122833},
	Pmid = {11943853},
	Pst = {ppublish},
	Title = {Somatosensory cortex dominated by the representation of teeth in the naked mole-rat brain},
	Volume = {99},
	Year = {2002},
	File = {papers/Catania_ProcNatlAcadSciUSA2002.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.072097999}}

@article{Crish:2006,
	Abstract = {Naked mole-rats are fossorial rodents native to eastern Africa that spend their lives in extensive subterranean burrows where visual cues are poor. Not surprisingly, they have a degenerated eye and optic nerve, suggesting they have poor visual abilities. However, little is known about their central visual system. To investigate the organization of their central visual system, we injected a neuronal tracer into the eyes of naked mole-rats and mice to compare the neural structures mediating vision. We found that the superior colliculus and lateral geniculate nucleus were severely atrophied in the naked mole-rat. The olivary pretectal nucleus was reduced but still retained its characteristic morphology, possibly indicating a role in light detection. In addition, the suprachiasmatic nucleus is well innervated and resembles the same structure in other rodents. The naked mole-rat appears to have selectively lost structures that mediate form vision while retaining structures needed for minimal entrainment of circadian rhythms. Similar results have been reported for other mole-rat species. Taken together, these data suggest that light detection may still play an important role in the lives of these "blind" animals: most likely for circadian entrainment or setting seasonal rhythms.},
	Author = {Crish, Samuel D and Dengler-Crish, Christine M and Catania, Kenneth C},
	Date-Added = {2015-12-14 01:06:27 +0000},
	Date-Modified = {2015-12-14 01:06:27 +0000},
	Doi = {10.1002/ar.a.20288},
	Journal = {Anat Rec A Discov Mol Cell Evol Biol},
	Journal-Full = {The anatomical record. Part A, Discoveries in molecular, cellular, and evolutionary biology},
	Mesh = {Adaptation, Ocular; Animals; Eye; Female; Male; Mice; Mice, Inbred C57BL; Mole Rats; Ocular Physiological Phenomena; Rats; Superior Colliculi; Vision, Ocular; Visual Pathways},
	Month = {Feb},
	Number = {2},
	Pages = {205-12},
	Pmid = {16419086},
	Pst = {ppublish},
	Title = {Central visual system of the naked mole-rat (Heterocephalus glaber)},
	Volume = {288},
	Year = {2006},
	File = {papers/Crish_AnatRecADiscovMolCellEvolBiol2006.pdf}}

@article{Guertin:2009,
	Abstract = {At the beginning of the 20th century, Thomas Graham Brown conducted experiments that after a long hiatus changed views on the neural control of locomotion. His seminal work supported by subsequent evidence generated largely from the 1960s onwards showed that across species walking, flying, and swimming are controlled largely by a neuronal network that has been referred to as the central pattern generator (CPG) for locomotion. In mammals, this caudally localized spinal cord network was found to generate the basic command signals sent to muscles of the limbs for locomotor rhythm and pattern generation. This article constitutes a comprehensive review summarizing key findings on the organization and properties of this network.},
	Author = {Guertin, Pierre A},
	Date-Added = {2015-12-12 00:27:55 +0000},
	Date-Modified = {2015-12-12 00:28:57 +0000},
	Doi = {10.1016/j.brainresrev.2009.08.002},
	Journal = {Brain Res Rev},
	Journal-Full = {Brain research reviews},
	Keywords = {Locomotion; behavior; Swimming; SPINAL CORD; rat; rodent, development},
	Mesh = {Animals; Brain; Humans; Locomotion; Models, Neurological; Nerve Net; Neurons; Spinal Cord},
	Month = {Dec},
	Number = {1},
	Pages = {45-56},
	Pmid = {19720083},
	Pst = {ppublish},
	Title = {The mammalian central pattern generator for locomotion},
	Volume = {62},
	Year = {2009},
	File = {papers/Guertin_BrainResRev2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.brainresrev.2009.08.002}}

@article{Nishimaru:2000,
	Abstract = {It is well known that in the neonatal rat spinal cord preparation, alternating rhythmic bursts in the left and right ventral roots in a given lumbar segment can be induced by bath-application of N-methyl-D-aspartate or 5-hydroxytryptamine. Alternation between L2 and L5 ventral roots on the same side, representing the activity of flexor and extensor muscles, respectively, can be observed as well. In the prenatal period in the rat, alternation between the left and right ventral roots is established between embryonic day (E) 16.5 and E18.5. The alternation between the L2 and L5 ventral roots emerges at E20.5. Recent findings show that locomotor-like rhythmic activity with similar characteristics can be induced in the neonatal mouse preparation. In the lumbar spinal cord in the neonatal mouse, it is likely that the rhythm-generating network is distributed throughout the lumbar region with a rostro-caudal gradient, a situation similar to that in the neonatal and fetal rat spinal cord. With this review we hope to highlight the dramatic changes that neuronal networks generating locomotor-like activity undergo during the prenatal development of the rat. Moreover, the distribution of the neuronal network generating the locomotor rhythm in the neonatal rat and mouse spinal cord is compared.},
	Author = {Nishimaru, H and Kudo, N},
	Date-Added = {2015-12-11 23:40:58 +0000},
	Date-Modified = {2015-12-11 23:41:08 +0000},
	Journal = {Brain Res Bull},
	Journal-Full = {Brain research bulletin},
	Keywords = {Locomotion; behavior; Swimming; SPINAL CORD; rat; rodent; development},
	Mesh = {Animals; Animals, Newborn; Embryo, Mammalian; In Vitro Techniques; Locomotion; Lumbar Vertebrae; Mice; Nerve Net; Periodicity; Rats; Spinal Cord},
	Month = {Nov},
	Number = {5},
	Pages = {661-9},
	Pmid = {11165801},
	Pst = {ppublish},
	Title = {Formation of the central pattern generator for locomotion in the rat and mouse},
	Volume = {53},
	Year = {2000},
	File = {papers/Nishimaru_BrainResBull2000.pdf}}

@article{Clarac:1992,
	Abstract = {In studies of central nervous system networks, it is synaptic transmission to the postsynaptic soma-dendritic membrane that has received the most attention, in particular in relation to the analysis of sensory-motor integration. Sensory transmission is gated during ongoing movements in both invertebrates and vertebrates, such that it may be depressed in one phase of a cyclic movement and facilitated in another, in order to optimize the execution of the ongoing motor task. This presynaptic modulation is not limited to sensory afferents, but also occurs in synapses of both excitatory and inhibitory premotor interneurons. The modulation can be mediated by the release of different transmitters at axo-axonal synapses, which activate different types of receptors. In addition, presynaptic sensory axons can be coupled via gap junctions, which under certain conditions may mediate a presynaptic facilitation.},
	Author = {Clarac, F and el Manira, A and Cattaert, D},
	Date-Added = {2015-12-11 23:39:02 +0000},
	Date-Modified = {2015-12-11 23:39:58 +0000},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Keywords = {Locomotion; behavior; Swimming; SPINAL CORD; rat; rodent},
	Mesh = {Action Potentials; Afferent Pathways; Animals; Astacoidea; Cats; Chloride Channels; Electric Stimulation; GTP-Binding Proteins; Ion Channel Gating; Locomotion; Membrane Proteins; Models, Neurological; Motor Activity; Receptors, GABA-A; Sensation; Signal Transduction; Synaptic Transmission},
	Month = {Dec},
	Number = {6},
	Pages = {764-9},
	Pmid = {1335811},
	Pst = {ppublish},
	Title = {Presynaptic control as a mechanism of sensory-motor integration},
	Volume = {2},
	Year = {1992}}

@article{Cazalets:1992,
	Abstract = {1. The role of serotonin (5-HT) and excitatory amino-acids (EAAs) in the activation of the neural networks (i.e. the central pattern generators) that organize locomotion in mammals was investigated in an isolated brainstem-spinal cord preparation from the newborn rat. 2. The neuroactive substances were bath applied and the activity of fictive locomotion was recorded in the ventral roots. 3. Serotonin initiated an alternating pattern of right and left action potential bursts. The period of this rhythm was dose dependent, i.e. it decreased from around 10 s at 2 x 10(-5) M to 5 s at 10(-4) M. The effects of serotonin were blocked by a 5-HT1 antagonist (propranolol) and by 5-HT2 antagonists (ketanserin, cyproheptadine, mianserin). 5-HT3 antagonists were ineffective. The effects of methoxytryptamine, a non-selective 5-HT agonist, mimicked the 5-HT effects. 4. The endogenous EAAs, glutamate and aspartate, also triggered an alternating rhythmic pattern. Their effects were blocked by 2-amino-5-phosphonovaleric acid (AP-5; a N-methyl-D-aspartate (NMDA) receptor blocker) and 6,7-dinitro-quinoxaline-2,3-dione (a non-NMDA receptor blocker). 5. Several EAA agonists (N-methyl-D,L-aspartate (NMA) and kainate) initiated rhythmic activity. The period of the induced rhythm (from 3 to 1 s) was similar with both of these substances but in a range of concentrations which was ten times lower in the case of kainate (10(-6) to 5 x 10(-6) M) than in that of NMA (10(-5) to 4 x 10(-5) M). alpha-Amino-3-hydroxy-5-methylisoxazole-4-propionate and quisqualate occasionally triggered some episodes of fictive locomotion with a threshold at 6 x 10(-7) and 10(-5) M, respectively.},
	Author = {Cazalets, J R and Sqalli-Houssaini, Y and Clarac, F},
	Date-Added = {2015-12-11 23:39:00 +0000},
	Date-Modified = {2015-12-11 23:39:52 +0000},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {Locomotion; behavior; Swimming; SPINAL CORD; rat; rodent},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Aspartic Acid; Brain Stem; Dose-Response Relationship, Drug; Glutamates; Glutamic Acid; Kainic Acid; Locomotion; N-Methylaspartate; Nerve Net; Quisqualic Acid; Rats; Rats, Wistar; Serotonin; Spinal Cord},
	Month = {Sep},
	Pages = {187-204},
	Pmc = {PMC1175639},
	Pmid = {1362441},
	Pst = {ppublish},
	Title = {Activation of the central pattern generators for locomotion by serotonin and excitatory amino acids in neonatal rat},
	Volume = {455},
	Year = {1992},
	File = {papers/Cazalets_JPhysiol1992.pdf}}

@article{Cazalets:1990,
	Abstract = {Swimming behaviour was studied in neonate rats by carrying out electromyographic recordings. The study showed that the early swimming pattern was characterized by highly instable temporal parameters. A decrease was found to occur with age in the variability of the instantaneous period in each leg and in that of the antiphase pattern. Moreover, a dissociation occurred during development between the foreleg and the backleg activity. While patterns involving the forelegs always remained extremely instable, a considerable improvement was found to occur with time in the hindlimb activity.},
	Author = {Cazalets, J R and Menard, I and Cr{\'e}mieux, J and Clarac, F},
	Date-Added = {2015-12-11 23:36:28 +0000},
	Date-Modified = {2015-12-11 23:38:04 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Keywords = {Locomotion; rat; rodent; behavior; Swimming; development},
	Mesh = {Afferent Pathways; Animals; Animals, Newborn; Central Nervous System; Electromyography; Forelimb; Hindlimb; Locomotion; Motor Activity; Muscle Contraction; Muscles; Neuromuscular Junction; Rats; Rats, Inbred Strains; Reaction Time; Swimming},
	Month = {Nov},
	Number = {3},
	Pages = {215-25},
	Pmid = {2285479},
	Pst = {ppublish},
	Title = {Variability as a characteristic of immature motor systems: an electromyographic study of swimming in the newborn rat},
	Volume = {40},
	Year = {1990},
	File = {papers/Cazalets_BehavBrainRes1990.pdf}}

@article{Newsome:1985,
	Abstract = {Physiological experiments have produced evidence that the middle temporal visual area (MT) of the monkey is selectively involved in the analysis of visual motion. We tested this hypothesis by studying the effects of small chemical lesions of MT on eye movements made in response to moving as opposed to stationary visual targets. We observed two deficits for eye movements made to moving targets: a monkey's ability to match the speed of his smooth pursuit eye movements to the speed of the moving target was impaired, and a monkey's ability to adjust the amplitude of a saccadic eye movement to compensate for target motion was impaired. In contrast, saccades to stationary targets were unaffected by the MT lesions, suggesting that monkeys with MT lesions had more difficulty responding to moving than to stationary stimuli. These results provide the first behavioral evidence that neural processing in MT contributes to the cortical analysis of visual motion.},
	Author = {Newsome, W T and Wurtz, R H and D{\"u}rsteler, M R and Mikami, A},
	Date-Added = {2015-11-18 03:11:53 +0000},
	Date-Modified = {2015-11-18 03:12:33 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {visual system; Neocortex; monkey; function; behavior; topographic map; vision; Motion Perception},
	Mesh = {Animals; Cerebral Cortex; Female; Ibotenic Acid; Macaca mulatta; Motion Perception; Oxazoles; Psychomotor Performance; Saccades; Temporal Lobe; Visual Perception},
	Month = {Mar},
	Number = {3},
	Pages = {825-40},
	Pmid = {3973698},
	Pst = {ppublish},
	Title = {Deficits in visual motion processing following ibotenic acid lesions of the middle temporal visual area of the macaque monkey},
	Volume = {5},
	Year = {1985}}

@article{Zhu:2015,
	Abstract = {Recently, we created a family of engineered G protein-coupled receptors (GPCRs) called DREADD (designer receptors exclusively activated by designer drugs) which can precisely control three major GPCR signaling pathways (Gq, Gi, and Gs). DREADD technology has been successfully applied in a variety of in vivo studies to control GPCR signaling, and here we describe recent advances of DREADD technology and discuss its potential application in drug discovery, gene therapy, and tissue engineering.},
	Author = {Zhu, Hu and Roth, Bryan L},
	Date-Added = {2015-11-17 21:44:18 +0000},
	Date-Modified = {2015-11-17 21:44:42 +0000},
	Doi = {10.1093/ijnp/pyu007},
	Journal = {Int J Neuropsychopharmacol},
	Journal-Full = {The international journal of neuropsychopharmacology / official scientific journal of the Collegium Internationale Neuropsychopharmacologicum (CINP)},
	Keywords = {GPCRs; GsD; chemogenetics; hM3Dq; hM4Di; DREADD; activity manipulation; Methods},
	Mesh = {Animals; Genetic Techniques; Humans; Neurons; Receptors, G-Protein-Coupled; Signal Transduction},
	Month = {Jan},
	Number = {1},
	Pmc = {PMC4368861},
	Pmid = {25522378},
	Pst = {epublish},
	Title = {DREADD: a chemogenetic GPCR signaling platform},
	Volume = {18},
	Year = {2015},
	File = {papers/Zhu_IntJNeuropsychopharmacol2015.pdf}}

@article{Armbruster:2007,
	Abstract = {We evolved muscarinic receptors in yeast to generate a family of G protein-coupled receptors (GPCRs) that are activated solely by a pharmacologically inert drug-like and bioavailable compound (clozapine-N-oxide). Subsequent screening in human cell lines facilitated the creation of a family of muscarinic acetylcholine GPCRs suitable for in vitro and in situ studies. We subsequently created lines of telomerase-immortalized human pulmonary artery smooth muscle cells stably expressing all five family members and found that each one faithfully recapitulated the signaling phenotype of the parent receptor. We also expressed a G(i)-coupled designer receptor in hippocampal neurons (hM(4)D) and demonstrated its ability to induce membrane hyperpolarization and neuronal silencing. We have thus devised a facile approach for designing families of GPCRs with engineered ligand specificities. Such reverse-engineered GPCRs will prove to be powerful tools for selectively modulating signal-transduction pathways in vitro and in vivo.},
	Author = {Armbruster, Blaine N and Li, Xiang and Pausch, Mark H and Herlitze, Stefan and Roth, Bryan L},
	Date-Added = {2015-11-17 21:39:57 +0000},
	Date-Modified = {2015-11-17 21:40:42 +0000},
	Doi = {10.1073/pnas.0700293104},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {Methods; Grants; activity manipulation; DREADD},
	Mesh = {Animals; Cell Line, Transformed; Clozapine; Designer Drugs; Epitopes; Evolution, Molecular; G Protein-Coupled Inwardly-Rectifying Potassium Channels; Hippocampus; Humans; Hydrolysis; Ligands; Models, Molecular; Mutant Proteins; Myocytes, Smooth Muscle; Neurons; Phosphatidylinositols; Protein Engineering; Pulmonary Artery; Rats; Receptor, Muscarinic M3; Receptor, Muscarinic M4; Receptors, G-Protein-Coupled; Saccharomyces cerevisiae},
	Month = {Mar},
	Number = {12},
	Pages = {5163-8},
	Pmc = {PMC1829280},
	Pmid = {17360345},
	Pst = {ppublish},
	Title = {Evolving the lock to fit the key to create a family of G protein-coupled receptors potently activated by an inert ligand},
	Volume = {104},
	Year = {2007},
	File = {papers/Armbruster_ProcNatlAcadSciUSA2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0700293104}}

@article{Rogan:2011,
	Abstract = {A significant challenge for neuroscientists is to determine how both electrical and chemical signals affect the activity of cells and circuits and how the nervous system subsequently translates that activity into behavior. Remote, bidirectional manipulation of those signals with high spatiotemporal precision is an ideal approach to addressing that challenge. Neuroscientists have recently developed a diverse set of tools that permit such experimental manipulation with varying degrees of spatial, temporal, and directional control. These tools use light, peptides, and small molecules to primarily activate ion channels and G protein-coupled receptors (GPCRs) that in turn activate or inhibit neuronal firing. By monitoring the electrophysiological, biochemical, and behavioral effects of such activation/inhibition, researchers can better understand the links between brain activity and behavior. Here, we review the tools that are available for this type of experimentation. We describe the development of the tools and highlight exciting in vivo data. We focus primarily on designer GPCRs (receptors activated solely by synthetic ligands, designer receptors exclusively activated by designer drugs) and microbial opsins (e.g., channelrhodopsin-2, halorhodopsin, Volvox carteri channelrhodopsin) but also describe other novel techniques that use orthogonal receptors, caged ligands, allosteric modulators, and other approaches. These tools differ in the direction of their effect (activation/inhibition, hyperpolarization/depolarization), their onset and offset kinetics (milliseconds/minutes/hours), the degree of spatial resolution they afford, and their invasiveness. Although none of these tools is perfect, each has advantages and disadvantages, which we describe, and they are all still works in progress. We conclude with suggestions for improving upon the existing tools.},
	Author = {Rogan, Sarah C and Roth, Bryan L},
	Date-Added = {2015-11-17 21:38:18 +0000},
	Date-Modified = {2015-11-17 21:38:42 +0000},
	Doi = {10.1124/pr.110.003020},
	Journal = {Pharmacol Rev},
	Journal-Full = {Pharmacological reviews},
	Keywords = {Methods; Grants; activity manipulation; DREADD},
	Mesh = {Animals; Designer Drugs; Humans; Ligands; Light; Neurons; Opsins; Peptides; Receptors, G-Protein-Coupled; Signal Transduction},
	Month = {Jun},
	Number = {2},
	Pages = {291-315},
	Pmc = {PMC3082452},
	Pmid = {21415127},
	Pst = {ppublish},
	Title = {Remote control of neuronal signaling},
	Volume = {63},
	Year = {2011},
	File = {papers/Rogan_PharmacolRev2011.pdf}}

@article{Dong:2010,
	Abstract = {Recently we have perfected a chemical-genetic approach to gain precise spatio-temporal control of cellular signaling. This approach entails the cell-type specific expression of mutant G-protein coupled receptors which have been evolved to be activated by the pharmacologically inert drug-like small molecule clozapine N-oxide. We have named these mutant GPCRs DREADDs (Designer Receptors Exclusively Activated by Designer Drugs). In this paper we will first review recent applications of this technology for the remote control of neuronal and non-neuronal signaling. Next, we will also introduce new variants which could be useful for the control of cellular signaling in discrete cellular compartments. Finally, we will suggest future basic science and therapeutic applications of this general technology.},
	Author = {Dong, Shuyun and Allen, John A and Farrell, Martilias and Roth, Bryan L},
	Date-Added = {2015-11-17 21:35:01 +0000},
	Date-Modified = {2015-11-17 21:37:40 +0000},
	Doi = {10.1039/c002568m},
	Journal = {Mol Biosyst},
	Journal-Full = {Molecular bioSystems},
	Keywords = {Methods; Grants; activity manipulation; DREADD},
	Mesh = {Animals; Cell Physiological Phenomena; Chemistry Techniques, Analytical; Combinatorial Chemistry Techniques; Genetic Techniques; Growth and Development; Humans; Models, Biological; Organ Specificity; Time Factors},
	Month = {Aug},
	Number = {8},
	Pages = {1376-80},
	Pmid = {20532295},
	Pst = {ppublish},
	Title = {A chemical-genetic approach for precise spatio-temporal control of cellular signaling},
	Volume = {6},
	Year = {2010},
	File = {papers/Dong_MolBiosyst2010.pdf}}

@article{Vardy:2015,
	Abstract = {DREADDs are chemogenetic tools widely used to remotely control cellular signaling, neuronal activity, and behavior. Here we used a structure-based approach to develop a new Gi-coupled DREADD using the kappa-opioid receptor as a template (KORD) that is activated by the pharmacologically inert ligand salvinorin B (SALB). Activation of virally expressed KORD in several neuronal contexts robustly attenuated neuronal activity and modified behaviors. Additionally, co-expression of the KORD and the Gq-coupled M3-DREADD within the same neuronal population facilitated the sequential and bidirectional remote control of behavior. The availability of DREADDs activated by different ligands provides enhanced opportunities for investigating diverse physiological systems using multiplexed chemogenetic actuators.},
	Author = {Vardy, Eyal and Robinson, J Elliott and Li, Chia and Olsen, Reid H J and DiBerto, Jeffrey F and Giguere, Patrick M and Sassano, Flori M and Huang, Xi-Ping and Zhu, Hu and Urban, Daniel J and White, Kate L and Rittiner, Joseph E and Crowley, Nicole A and Pleil, Kristen E and Mazzone, Christopher M and Mosier, Philip D and Song, Juan and Kash, Thomas L and Malanga, C J and Krashes, Michael J and Roth, Bryan L},
	Date-Added = {2015-11-16 19:08:47 +0000},
	Date-Modified = {2015-11-16 19:09:21 +0000},
	Doi = {10.1016/j.neuron.2015.03.065},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {DREADD; Methods; Grants; activity manipulation},
	Mesh = {Animals; Behavior, Animal; Diterpenes; Ligands; Mice, Inbred C57BL; Neurons; Receptors, Opioid, kappa; Signal Transduction},
	Month = {May},
	Number = {4},
	Pages = {936-46},
	Pmc = {PMC4441592},
	Pmid = {25937170},
	Pst = {ppublish},
	Title = {A New DREADD Facilitates the Multiplexed Chemogenetic Interrogation of Behavior},
	Volume = {86},
	Year = {2015},
	File = {papers/Vardy_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.03.065}}

@article{Robinson:2014,
	Abstract = {An essential aspect of episodic memory is the formation of associations between neutral sensory cues in the environment. In light of recent evidence that this critical aspect of learning does not require the hippocampus, we tested the involvement of the retrosplenial cortex (RSC) in this process using a chemogenetic approach that allowed us to temporarily silence neurons along the entire rostrocaudal extent of the RSC. A viral vector containing the gene for a synthetic inhibitory G-protein-coupled receptor (hM4Di) was infused into RSC. When the receptor was later activated by systemic injection of clozapine-N-oxide, neural activity in RSC was transiently silenced (confirmed using a patch-clamp procedure). Rats expressing hM4Di and control rats were trained in a sensory preconditioning procedure in which a tone and light were paired on some trials and a white noise stimulus was presented alone on the other trials during the Preconditioning phase. Thus, rats were given the opportunity to form an association between a tone and a light in the absence of reinforcement. Later, the light was paired with food. During the test phase when the auditory cues were presented alone, controls exhibited more conditioned responding during presentation of the tone compared with the white noise reflecting the prior formation of a tone-light association. Silencing RSC neurons during the Preconditioning phase prevented the formation of an association between the tone and light and eliminated the sensory preconditioning effect. These findings indicate that RSC may contribute to episodic memory formation by linking essential sensory stimuli during learning.},
	Author = {Robinson, Siobhan and Todd, Travis P and Pasternak, Anna R and Luikart, Bryan W and Skelton, Patrick D and Urban, Daniel J and Bucci, David J},
	Date-Added = {2015-11-16 19:04:26 +0000},
	Date-Modified = {2015-11-16 19:04:50 +0000},
	Doi = {10.1523/JNEUROSCI.1349-14.2014},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {DREADD; episodic; hippocampus; learning; parahippocampal; retrosplenial; activity manipulation; Methods; behavior},
	Mesh = {Animals; Association Learning; Cerebral Cortex; Clozapine; Conditioning (Psychology); Cues; Male; Neurons; Rats; Rats, Long-Evans},
	Month = {Aug},
	Number = {33},
	Pages = {10982-8},
	Pmc = {PMC4131013},
	Pmid = {25122898},
	Pst = {ppublish},
	Title = {Chemogenetic silencing of neurons in retrosplenial cortex disrupts sensory preconditioning},
	Volume = {34},
	Year = {2014},
	File = {papers/Robinson_JNeurosci2014.pdf}}

@article{Fotowat:2009,
	Abstract = {Drosophila melanogaster exhibits a robust escape response to objects approaching on a collision course. Although a pair of large command interneurons called the giant fibers (GFs) have been postulated to trigger such behaviors, their role has not been directly demonstrated. Here, we show that escape from visual stimuli like those generated by approaching predators does not rely on the activation of the GFs and consists of a more complex and less stereotyped motor sequence than that evoked by the GFs. Instead, the timing of escape is tightly correlated with the activity of previously undescribed descending interneurons that signal a threshold angular size of the approaching object. The activity pattern of these interneurons shares features with those of visual escape circuits of several species, including pigeons, frogs, and locusts, and may therefore have evolved under similar constraints. These results show that visually evoked escapes in Drosophila can rely on at least two descending neuronal pathways: the GFs and the novel pathway we characterize electrophysiologically. These pathways exhibit very different patterns of sensory activity and are associated with two distinct motor programs.},
	Author = {Fotowat, Haleh and Fayyazuddin, Amir and Bellen, Hugo J and Gabbiani, Fabrizio},
	Date-Added = {2015-11-16 17:16:11 +0000},
	Date-Modified = {2015-11-16 17:17:12 +0000},
	Doi = {10.1152/jn.00073.2009},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {behavior; function; vision; visual system; Drosophila melanogaster; aversive; looming response},
	Mesh = {Action Potentials; Animals; Animals, Genetically Modified; Biomechanical Phenomena; Drosophila Proteins; Drosophila melanogaster; Escape Reaction; Interneurons; Lighting; Microelectrodes; Muscles; Mutation; Neural Pathways; Neurons; Photic Stimulation; Psychomotor Performance; Receptors, Nicotinic; Visual Perception},
	Month = {Aug},
	Number = {2},
	Pages = {875-85},
	Pmc = {PMC3817277},
	Pmid = {19474177},
	Pst = {ppublish},
	Title = {A novel neuronal pathway for visually guided escape in Drosophila melanogaster},
	Volume = {102},
	Year = {2009},
	File = {papers/Fotowat_JNeurophysiol2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.00073.2009}}

@article{Ball:1971,
	Abstract = {Twenty-four infants ranging in age from 2 to 11 weeks responded to symmetrically expanding shadows, which optically specify an approaching object, with an integrated avoidance response and upset. This response did not occur for asymmetrically expanding shadows nor for contracting shadows that specify an object on a miss path and a receding object. The response was observed in all the infants regardless of age, and the addition of kinetic depth information to the displays did not increase the intensity or likelihood of the response. In a second experiment, seven infants defensively reacted to the approach of a real object except when it was on a miss path.},
	Author = {Ball, W and Tronick, E},
	Date-Added = {2015-11-16 17:11:18 +0000},
	Date-Modified = {2015-11-16 17:19:56 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {infant; human; behavior; aversive; vision; visual system; activity-development; looming response},
	Mesh = {Avoidance Learning; Distance Perception; Psychology, Child},
	Month = {Feb},
	Number = {3973},
	Pages = {818-20},
	Pmid = {5541165},
	Pst = {ppublish},
	Title = {Infant responses to impending collision: optical and real},
	Volume = {171},
	Year = {1971}}

@article{Biagi:2015,
	Abstract = {In adults, motion perception is mediated by an extensive network of occipital, parietal, temporal, and insular cortical areas. Little is known about the neural substrate of visual motion in infants, although behavioural studies suggest that motion perception is rudimentary at birth and matures steadily over the first few years. Here, by measuring Blood Oxygenated Level Dependent (BOLD) responses to flow versus random-motion stimuli, we demonstrate that the major cortical areas serving motion processing in adults are operative by 7 wk of age. Resting-state correlations demonstrate adult-like functional connectivity between the motion-selective associative areas, but not between primary cortex and temporo-occipital and posterior-insular cortices. Taken together, the results suggest that the development of motion perception may be limited by slow maturation of the subcortical input and of the cortico-cortical connections. In addition they support the existence of independent input to primary (V1) and temporo-occipital (V5/MT+) cortices very early in life.},
	Author = {Biagi, Laura and Crespi, Sofia Allegra and Tosetti, Michela and Morrone, Maria Concetta},
	Date-Added = {2015-11-15 17:17:08 +0000},
	Date-Modified = {2015-11-15 17:22:47 +0000},
	Doi = {10.1371/journal.pbio.1002260},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Keywords = {human; infant; visual system; Visual Cortex; BEHAVIOR; Motion Perception; topographic map; fMRI; connectivity; network analysis; activity-development},
	Month = {Sep},
	Number = {9},
	Pages = {e1002260},
	Pmc = {PMC4587790},
	Pmid = {26418729},
	Pst = {epublish},
	Title = {BOLD Response Selective to Flow-Motion in Very Young Infants},
	Volume = {13},
	Year = {2015},
	File = {papers/Biagi_PLoSBiol2015.pdf}}

@article{Oh:2014,
	Abstract = {Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease.},
	Author = {Oh, Seung Wook and Harris, Julie A and Ng, Lydia and Winslow, Brent and Cain, Nicholas and Mihalas, Stefan and Wang, Quanxin and Lau, Chris and Kuan, Leonard and Henry, Alex M and Mortrud, Marty T and Ouellette, Benjamin and Nguyen, Thuc Nghi and Sorensen, Staci A and Slaughterbeck, Clifford R and Wakeman, Wayne and Li, Yang and Feng, David and Ho, Anh and Nicholas, Eric and Hirokawa, Karla E and Bohn, Phillip and Joines, Kevin M and Peng, Hanchuan and Hawrylycz, Michael J and Phillips, John W and Hohmann, John G and Wohnoutka, Paul and Gerfen, Charles R and Koch, Christof and Bernard, Amy and Dang, Chinh and Jones, Allan R and Zeng, Hongkui},
	Date-Added = {2015-11-14 01:08:48 +0000},
	Date-Modified = {2015-11-14 01:14:11 +0000},
	Doi = {10.1038/nature13186},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {connectivity; Methods; Computational Biology; Graph theory; network; Neocortex; Thalamic Nuclei; topographic map; mouse; Mice},
	Mesh = {Animals; Atlases as Topic; Axons; Brain; Cerebral Cortex; Connectome; Corpus Striatum; Male; Mice; Mice, Inbred C57BL; Models, Neurological; Neuroanatomical Tract-Tracing Techniques; Thalamus},
	Month = {Apr},
	Number = {7495},
	Pages = {207-14},
	Pmid = {24695228},
	Pst = {ppublish},
	Title = {A mesoscale connectome of the mouse brain},
	Volume = {508},
	Year = {2014},
	File = {papers/Oh_Nature2014.pdf},
	Bdsk-File-2 = {papers/Oh_Nature2014a.pdf}}

@article{Markowitz:2015,
	Abstract = {Time-locked sequences of neural activity can be found throughout the vertebrate forebrain in various species and behavioral contexts. From "time cells" in the hippocampus of rodents to cortical activity controlling movement, temporal sequence generation is integral to many forms of learned behavior. However, the mechanisms underlying sequence generation are not well known. Here, we describe a spatial and temporal organization of the songbird premotor cortical microcircuit that supports sparse sequences of neural activity. Multi-channel electrophysiology and calcium imaging reveal that neural activity in premotor cortex is correlated with a length scale of 100 µm. Within this length scale, basal-ganglia-projecting excitatory neurons, on average, fire at a specific phase of a local 30 Hz network rhythm. These results show that premotor cortical activity is inhomogeneous in time and space, and that a mesoscopic dynamical pattern underlies the generation of the neural sequences controlling song.},
	Author = {Markowitz, Jeffrey E and Liberti, 3rd, William A and Guitchounts, Grigori and Velho, Tarciso and Lois, Carlos and Gardner, Timothy J},
	Date-Added = {2015-11-13 22:57:01 +0000},
	Date-Modified = {2015-11-13 22:57:01 +0000},
	Doi = {10.1371/journal.pbio.1002158},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Month = {Jun},
	Number = {6},
	Pages = {e1002158},
	Pmc = {PMC4454690},
	Pmid = {26039895},
	Pst = {epublish},
	Title = {Mesoscopic patterns of neural activity support songbird cortical sequences},
	Volume = {13},
	Year = {2015},
	File = {papers/Markowitz_PLoSBiol2015.pdf}}

@article{Hagihara:2015,
	Abstract = {Neuronal activity is important for the functional refinement of neuronal circuits in the early visual system. At the level of the cerebral cortex, however, it is still unknown whether the formation of fundamental functions such as orientation selectivity depends on neuronal activity, as it has been difficult to suppress activity throughout development. Using genetic silencing of cortical activity starting before the formation of orientation selectivity, we found that the orientation selectivity of neurons in the mouse visual cortex formed and matured normally despite a strong suppression of both spontaneous and visually evoked activity throughout development. After the orientation selectivity formed, the distribution of the preferred orientations of neurons was reorganized. We found that this process required spontaneous activity, but not visually evoked activity. Thus, the initial formation and maturation of orientation selectivity is largely independent of neuronal activity, and the initial selectivity is subsequently modified depending on neuronal activity.},
	Author = {Hagihara, Kenta M and Murakami, Tomonari and Yoshida, Takashi and Tagawa, Yoshiaki and Ohki, Kenichi},
	Date-Added = {2015-11-13 22:16:11 +0000},
	Date-Modified = {2015-11-13 22:52:04 +0000},
	Doi = {10.1038/nn.4155},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {visual system; Visual Cortex; activity manipulation; activity-dependent; activity-development; topographic map; Orientation; direction; mouse; mice; spontaneous activity},
	Month = {Nov},
	Pmid = {26523644},
	Pst = {aheadofprint},
	Title = {Neuronal activity is not required for the initial formation and maturation of visual selectivity},
	Year = {2015},
	File = {papers/Hagihara_NatNeurosci2015a.pdf},
	Bdsk-File-2 = {papers/Hagihara_NatNeurosci2015.pdf}}

@article{Aston-Jones:2013,
	Abstract = {Optogenetics with microbial opsin genes, and pharmacogenetics with designer receptors, represent potent and versatile experimental modalities that can be integrated with each other as well as with a rich diversity of synergistic methods to provide fundamental opportunities in neuroscience research. The 7th Annual Brain Research Meeting in New Orleans in October 2012, Optogenetics and Pharmacogenetics in Neuronal Function and Dysfunction, brought together leading researchers that have developed and used these tools to explore a wide range of questions in nervous system function and dysfunction. This special issue of Brain Research includes articles by speakers in this meeting and others, which together synthesize and summarize the state of the art for optogenetics and designer receptors. This article is part of a Special Issue entitled Optogenetics (7th BRES).},
	Author = {Aston-Jones, Gary and Deisseroth, Karl},
	Date-Added = {2015-09-30 19:26:18 +0000},
	Date-Modified = {2015-11-16 19:08:04 +0000},
	Doi = {10.1016/j.brainres.2013.01.026},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {Methods; technique; activity manipulation; Grants; DREADD},
	Mesh = {Animals; Autonomic Pathways; Brain; Cognition; Humans; Motivation; Optogenetics; Pharmacogenetics; Receptors, Cell Surface; Signal Transduction},
	Month = {May},
	Pages = {1-5},
	Pmc = {PMC3663045},
	Pmid = {23422677},
	Pst = {ppublish},
	Title = {Recent advances in optogenetics and pharmacogenetics},
	Volume = {1511},
	Year = {2013},
	File = {papers/Aston-Jones_BrainRes2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.brainres.2013.01.026}}

@article{DePuy:2013,
	Abstract = {The C1 neurons are a nodal point for blood pressure control and other autonomic responses. Here we test whether these rostral ventrolateral medullary catecholaminergic (RVLM-CA) neurons use glutamate as a transmitter in the dorsal motor nucleus of the vagus (DMV). After injecting Cre-dependent adeno-associated virus (AAV2) DIO-Ef1α-channelrhodopsin2(ChR2)-mCherry (AAV2) into the RVLM of dopamine-β-hydroxylase Cre transgenic mice (DβH(Cre/0)), mCherry was detected exclusively in RVLM-CA neurons. Within the DMV >95% mCherry-immunoreactive(ir) axonal varicosities were tyrosine hydroxylase (TH)-ir and the same proportion were vesicular glutamate transporter 2 (VGLUT2)-ir. VGLUT2-mCherry colocalization was virtually absent when AAV2 was injected into the RVLM of DβH(Cre/0);VGLUT2(flox/flox) mice, into the caudal VLM (A1 noradrenergic neuron-rich region) of DβH(Cre/0) mice or into the raphe of ePet(Cre/0) mice. Following injection of AAV2 into RVLM of TH-Cre rats, phenylethanolamine N-methyl transferase and VGLUT2 immunoreactivities were highly colocalized in DMV within EYFP-positive or EYFP-negative axonal varicosities. Ultrastructurally, mCherry terminals from RVLM-CA neurons in DβH(Cre/0) mice made predominantly asymmetric synapses with choline acetyl-transferase-ir DMV neurons. Photostimulation of ChR2-positive axons in DβH(Cre/0) mouse brain slices produced EPSCs in 71% of tested DMV preganglionic neurons (PGNs) but no IPSCs. Photostimulation (20 Hz) activated PGNs up to 8 spikes/s (current-clamp). EPSCs were eliminated by tetrodotoxin, reinstated by 4-aminopyridine, and blocked by ionotropic glutamate receptor blockers. In conclusion, VGLUT2 is expressed by RVLM-CA (C1) neurons in rats and mice regardless of the presence of AAV2, the C1 neurons activate DMV parasympathetic PGNs monosynaptically and this connection uses glutamate as an ionotropic transmitter.},
	Author = {DePuy, Seth D and Stornetta, Ruth L and Bochorishvili, Genrieta and Deisseroth, Karl and Witten, Ilana and Coates, Melissa and Guyenet, Patrice G},
	Date-Added = {2015-09-30 19:26:14 +0000},
	Date-Modified = {2015-09-30 19:26:14 +0000},
	Doi = {10.1523/JNEUROSCI.4269-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Excitatory Postsynaptic Potentials; Glutamine; Immunohistochemistry; Medulla Oblongata; Mice; Mice, Transgenic; Neurons; Patch-Clamp Techniques; Synaptic Transmission; Vagus Nerve; Vesicular Glutamate Transport Protein 2},
	Month = {Jan},
	Number = {4},
	Pages = {1486-97},
	Pmc = {PMC3727439},
	Pmid = {23345223},
	Pst = {ppublish},
	Title = {Glutamatergic neurotransmission between the C1 neurons and the parasympathetic preganglionic neurons of the dorsal motor nucleus of the vagus},
	Volume = {33},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4269-12.2013}}

@article{Alivisatos:2013,
	Author = {Alivisatos, A Paul and Chun, Miyoung and Church, George M and Deisseroth, Karl and Donoghue, John P and Greenspan, Ralph J and McEuen, Paul L and Roukes, Michael L and Sejnowski, Terrence J and Weiss, Paul S and Yuste, Rafael},
	Date-Added = {2015-09-30 19:26:12 +0000},
	Date-Modified = {2015-09-30 19:26:12 +0000},
	Doi = {10.1126/science.1236939},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Brain Diseases; Brain Mapping; Hippocampus; Humans; Neural Pathways; Neurons},
	Month = {Mar},
	Number = {6125},
	Pages = {1284-5},
	Pmc = {PMC3722427},
	Pmid = {23470729},
	Pst = {ppublish},
	Title = {Neuroscience. The brain activity map},
	Volume = {339},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1236939}}

@article{Gazzaniga:2005,
	Abstract = {Forty-five years ago, Roger Sperry, Joseph Bogen and I embarked on what are now known as the modern split-brain studies. These experiments opened up new frontiers in brain research and gave rise to much of what we know about hemispheric specialization and integration. The latest developments in split-brain research build on the groundwork laid by those early studies. Split-brain methodology, on its own and in conjunction with neuroimaging, has yielded insights into the remarkable regional specificity of the corpus callosum as well as into the integrative role of the callosum in the perception of causality and in our perception of an integrated sense of self.},
	Author = {Gazzaniga, Michael S},
	Date-Added = {2015-09-30 00:32:59 +0000},
	Date-Modified = {2015-09-30 00:33:45 +0000},
	Doi = {10.1038/nrn1723},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {mirror symmetry; hemisphere; hemispherectomy; Corpus Callosum; human; BEHAVIOR; Perception; Perceptual Disorders; sensory map},
	Mesh = {Animals; Cerebral Cortex; Corpus Callosum; Dominance, Cerebral; Humans; Neurosciences},
	Month = {Aug},
	Number = {8},
	Pages = {653-9},
	Pmid = {16062172},
	Pst = {ppublish},
	Title = {Forty-five years of split-brain research and still going strong},
	Volume = {6},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn1723}}

@article{Burbridge:2014,
	Abstract = {The elaboration of nascent synaptic connections into highly ordered neural circuits is an integral feature of the developing vertebrate nervous system. In sensory systems, patterned spontaneous activity before the onset of sensation is thought to influence this process, but this conclusion remains controversial, largely due to the inherent difficulty recording neural activity in early development. Here, we describe genetic and pharmacological manipulations of spontaneous retinal activity, assayed in vivo, that demonstrate a causal link between retinal waves and visual circuit refinement. We also report a decoupling of downstream activity in retinorecipient regions of the developing brain after retinal wave disruption. Significantly, we show that the spatiotemporal characteristics of retinal waves affect the development of specific visual circuits. These results conclusively establish retinal waves as necessary and instructive for circuit refinement in the developing nervous system and reveal how neural circuits adjust to altered patterns of activity prior to experience.},
	Author = {Burbridge, Timothy J and Xu, Hong-Ping and Ackman, James B and Ge, Xinxin and Zhang, Yueyi and Ye, Mei-Jun and Zhou, Z Jimmy and Xu, Jian and Contractor, Anis and Crair, Michael C},
	Date-Added = {2015-09-04 20:43:26 +0000},
	Date-Modified = {2015-09-04 20:43:26 +0000},
	Doi = {10.1016/j.neuron.2014.10.051},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Action Potentials; Age Factors; Analysis of Variance; Animals; Animals, Newborn; Calcium; Cyclic AMP; Cyclic GMP; Cyclooxygenase Inhibitors; Eye Proteins; Functional Laterality; Homeodomain Proteins; In Vitro Techniques; Meclofenamic Acid; Mice; Mice, Transgenic; Paired Box Transcription Factors; RNA, Messenger; Receptors, Nicotinic; Repressor Proteins; Retina; Retinal Ganglion Cells; Visual Pathways},
	Month = {Dec},
	Number = {5},
	Pages = {1049-64},
	Pmc = {PMC4258148},
	Pmid = {25466916},
	Pst = {ppublish},
	Title = {Visual circuit development requires patterned activity mediated by retinal acetylcholine receptors},
	Volume = {84},
	Year = {2014},
	File = {papers/Burbridge_Neuron2014.pdf},
	Bdsk-File-2 = {papers/Burbridge_Neuron2014a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.10.051}}

@article{Wefers:2000,
	Abstract = {Binocular interactions play a prominent role in shaping the axonal arbors of geniculocortical fibers and the arbors of Y cells in the retinogeniculate pathway of the fetal cat. Fiber interactions between the two eyes have also been suggested to regulate the formation of retinal projections to the dorsal lateral geniculate nucleus (dlgn) of the fetal monkey, but whether this reflects structural refinements of retinal arbors has not been established. To address this issue, we quantified the morphologic properties of individual fibers in two macaque monkeys at embryonic day (E) 110 and E121 that had an eye removed at E69 and E61, respectively. Fibers were labeled by DiI crystals into the fixed optic tract and were visualized by confocal microscopy. Three measurements were made: the number of branch points within the axon terminal arbor, the total arborization length, and the incidence of axonal side branches on the preterminal axon within the confines of the geniculate. There were no significant differences with respect to these parameters between the prenatal enucleates and normal monkeys of comparable age. This was the case for retinal fibers innervating the magnocellular and the parvocellular segments of the dlgn. The arbors stemming from the remaining eye were widely distributed in the dlgn, with some terminating in territories normally innervated by the other (enucleated) eye. These results lend support to the hypothesis that the expanded projection from the remaining eye to the lateral geniculate nucleus of the prenatally enucleated monkey is due to the maintenance of a contingent of retinal fibers normally eliminated by ganglion cell death.},
	Author = {Wefers, C J and Dehay, C and Berland, M and Kennedy, H and Chalupa, L M},
	Date-Added = {2015-09-02 00:40:04 +0000},
	Date-Modified = {2015-09-02 00:40:04 +0000},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Axons; Carbocyanines; Cell Size; Dendrites; Eye Enucleation; Fluorescent Dyes; Geniculate Bodies; Macaca fascicularis; Retina; Vision, Binocular; Vision, Monocular; Visual Pathways},
	Month = {Nov},
	Number = {3},
	Pages = {362-9},
	Pmid = {11054699},
	Pst = {ppublish},
	Title = {Binocular competition does not regulate retinogeniculate arbor size in fetal monkey},
	Volume = {427},
	Year = {2000}}

@article{Polleux:1998b,
	Abstract = {In the homozygous (but not the heterozygous) reeler mutant, disruption of neuron migration leads to a major perturbation of the cortical environment that in turn could modify (1) the specification of neuronal fate and (2) the proliferation dynamics of cortical precursors. To investigate these issues, tritiated thymidine injections during cortical neurogenesis were coupled with postnatal injections of a retrograde tracer in the spinal cord to accurately measure the neurogenesis of corticospinal neurons in the heterozygous and homozygous mutant. The homozygous reeler shows (1) strict conservation of area-specific timetables of corticospinal neuron generation; (2) neurons with the appropriate birthdates show an enhanced probability of projecting to the spinal cord; (3) during early stages of corticogenesis, there is a reduced rate of neuron production followed at later stages by an increased rate of neuron production; and (4) these changes in the rate of neuron production were shown to be at least partially attributable to changes in the proportions of differentiative divisions. Taken together, our results show that in the developing cortex, the neurogenesis and specification of a given neuronal phenotype are partially controlled by the postmigratory compartment. On the other hand, neither areal identity nor the chronology of production of layer-specific neuronal phenotype seems to depend on the integrity of the cellular environment.},
	Author = {Polleux, F and Dehay, C and Kennedy, H},
	Date-Added = {2015-09-02 00:39:57 +0000},
	Date-Modified = {2015-09-02 00:39:57 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Afferent Pathways; Animals; Animals, Newborn; Cell Count; Cell Death; Cell Division; Female; Male; Mice; Mice, Inbred BALB C; Mice, Neurologic Mutants; Neocortex; Neurons; Pyramidal Tracts; Somatosensory Cortex; Thymidine; Tritium},
	Month = {Dec},
	Number = {23},
	Pages = {9910-23},
	Pmid = {9822747},
	Pst = {ppublish},
	Title = {Neurogenesis and commitment of corticospinal neurons in reeler},
	Volume = {18},
	Year = {1998}}

@article{Snider:1999,
	Abstract = {In the fetal monkey the projections from the two eyes are initially completely intermingled within the dorsal lateral geniculate nucleus (DLGN) before separating into eye-specific layers (). To assess the cellular basis of this developmental process, we examined the morphological properties of individual retinogeniculate axons in prenatal monkeys of known gestational ages. The period studied spanned the time from when binocular overlap has been reported to be maximum, circa embryonic (E) day 77 through E112, when the segregation process is already largely completed in the caudal portion of the nucleus. Retinogeniculate fibers were labeled by making small deposits of DiI crystals into the fixed optic tract. After adequate time was allowed for diffusion of the tracer, fibers were visualized by confocal microscopy, and morphometric measures were made from photomontages. This revealed that retinogeniculate fibers in the embryonic monkey undergo continuous growth and elaboration during binocular overlap and subsequent segregation. Importantly, very few side-branches were found along the preterminal axon throughout the developmental period studied. Thus, restructuring of retinogeniculate fibers does not underlie the formation of eye-restricted projections in the primate. Rather, the results support the hypothesis that binocular segregation in the embryonic monkey is caused by the loss of retinal fibers that initially innervate inappropriate territories ().},
	Author = {Snider, C J and Dehay, C and Berland, M and Kennedy, H and Chalupa, L M},
	Date-Added = {2015-09-02 00:39:45 +0000},
	Date-Modified = {2015-09-02 00:39:45 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Axons; Embryonic and Fetal Development; Geniculate Bodies; Macaca fascicularis; Microscopy, Confocal; Retina; Vision, Binocular; Visual Pathways},
	Month = {Jan},
	Number = {1},
	Pages = {220-8},
	Pmid = {9870952},
	Pst = {ppublish},
	Title = {Prenatal development of retinogeniculate axons in the macaque monkey during segregation of binocular inputs},
	Volume = {19},
	Year = {1999}}

@article{Lukaszewicz:2006,
	Abstract = {Regionalization of cell cycle kinetics of cortical precursors has been described in nonhuman primates and rodents indicating a fate map of areas as distinct proliferative programs in the germinal zones of the neocortex. It remains to be understood how proliferative gradients during corticogenesis are transcribed into a stepwise function to form adult areal borders. Here we have used the monkey areas 17 and 18, which show striking cytoarchitectonic differences, as a model system for studying how developmental events establish areal boundaries in the adult. We present data indicating that the events that are involved in the formation of a sharp border separating 2 areas involve an orchestration of diverse phenomena including differential rates of proliferation, migration, and tangential expansion.},
	Author = {Lukaszewicz, Agn{\`e}s and Cortay, V{\'e}ronique and Giroud, Pascale and Berland, Michel and Smart, Iain and Kennedy, Henry and Dehay, Colette},
	Date-Added = {2015-09-02 00:39:23 +0000},
	Date-Modified = {2015-09-02 00:39:23 +0000},
	Doi = {10.1093/cercor/bhk011},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Body Patterning; Cell Differentiation; Cell Proliferation; Haplorhini; Neocortex; Nerve Net; Neurons; Organogenesis},
	Month = {Jul},
	Pages = {i26-34},
	Pmid = {16766704},
	Pst = {ppublish},
	Title = {The concerted modulation of proliferation and migration contributes to the specification of the cytoarchitecture and dimensions of cortical areas},
	Volume = {16 Suppl 1},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhk011}}

@article{Markov:2014,
	Abstract = {Retrograde tracer injections in 29 of the 91 areas of the macaque cerebral cortex revealed 1,615 interareal pathways, a third of which have not previously been reported. A weight index (extrinsic fraction of labeled neurons [FLNe]) was determined for each area-to-area pathway. Newly found projections were weaker on average compared with the known projections; nevertheless, the 2 sets of pathways had extensively overlapping weight distributions. Repeat injections across individuals revealed modest FLNe variability given the range of FLNe values (standard deviation <1 log unit, range 5 log units). The connectivity profile for each area conformed to a lognormal distribution, where a majority of projections are moderate or weak in strength. In the G29 × 29 interareal subgraph, two-thirds of the connections that can exist do exist. Analysis of the smallest set of areas that collects links from all 91 nodes of the G29 × 91 subgraph (dominating set analysis) confirms the dense (66%) structure of the cortical matrix. The G29 × 29 subgraph suggests an unexpectedly high incidence of unidirectional links. The directed and weighted G29 × 91 connectivity matrix for the macaque will be valuable for comparison with connectivity analyses in other species, including humans. It will also inform future modeling studies that explore the regularities of cortical networks.},
	Author = {Markov, N T and Ercsey-Ravasz, M M and Ribeiro Gomes, A R and Lamy, C and Magrou, L and Vezoli, J and Misery, P and Falchier, A and Quilodran, R and Gariel, M A and Sallet, J and Gamanut, R and Huissoud, C and Clavagnier, S and Giroud, P and Sappey-Marinier, D and Barone, P and Dehay, C and Toroczkai, Z and Knoblauch, K and Van Essen, D C and Kennedy, H},
	Date-Added = {2015-09-02 00:38:54 +0000},
	Date-Modified = {2015-09-02 00:38:54 +0000},
	Doi = {10.1093/cercor/bhs270},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {connection; cortex; graph; monkey; network},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Diffusion Magnetic Resonance Imaging; Image Processing, Computer-Assisted; Macaca fascicularis; Macaca mulatta; Models, Neurological; Neural Pathways; Neuroimaging; Neuronal Tract-Tracers},
	Month = {Jan},
	Number = {1},
	Pages = {17-36},
	Pmc = {PMC3862262},
	Pmid = {23010748},
	Pst = {ppublish},
	Title = {A weighted and directed interareal connectivity matrix for macaque cerebral cortex},
	Volume = {24},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhs270}}

@article{Kennedy:2012,
	Abstract = {Variability of gene expression of cortical precursors may partially reflect the operation of the gene regulatory network and determines the boundaries of the state space within which self-organization of the cortex can unfold. In primates, including humans, the outer subventricular zone, a primate-specific germinal zone, generates a large contingent of the projection neurons participating in the interareal network. The number of projection neurons in individual pathways largely determines the network properties as well as the hierarchical organization of the cortex. Mathematical modeling of cell-cycle kinetics of cortical precursors in the germinal zones reveals how multiple control loops ensure the generation of precise numbers of different categories of projection neurons and allow partial simulation of cortical self-organization. We show that molecular manipulation of the cell cycle of cortical precursors shifts the trajectory of the cortical precursor within its state space, increases the diversity in the cortical lineage tree, and explores changes in phylogenetic complexity. These results explore how self-organization underlies the complexity of the cortex and suggest evolutionary mechanisms.},
	Author = {Kennedy, Henry and Dehay, Colette},
	Date-Added = {2015-09-02 00:38:45 +0000},
	Date-Modified = {2015-09-02 00:38:45 +0000},
	Doi = {10.1016/B978-0-444-53860-4.00016-7},
	Journal = {Prog Brain Res},
	Journal-Full = {Progress in brain research},
	Mesh = {Animals; Biological Evolution; Cell Cycle; Cerebral Cortex; Humans; Nerve Net; Neurons; Primates},
	Pages = {341-60},
	Pmid = {22230635},
	Pst = {ppublish},
	Title = {Self-organization and interareal networks in the primate cortex},
	Volume = {195},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/B978-0-444-53860-4.00016-7}}

@article{Kennedy:2007,
	Abstract = {The primate neocortex is characterized by a highly expanded supragranular layer (SGL). The interareal connectivity of the neurons in the SLG largely determines the cortical hierarchy that constrains information flow through the cortex. Interareal connectivity is made by precise numbers of connections, raising the possibility that the physiology of a target area is dictated by the numbers of connections and hierarchical distance in each of the pathways that it receives. The developmental mechanisms ensuring the precision of these interareal networks is in part determined by (i) the numbers of SGL neurons generated by the OSVZ, a primate-specific germinal zone. Neuron generation rate in the OSVZ is determined by regulation of the G1 phase of the cell-cycle. This regulation is area-specific and is linked to thalamic projections to the OSVZ; (ii) Prolonged pre- and postnatal pruning of connections originating from the SGL when the infant monkey visually explores its environment. Remodelling serves to sharpen initial patterns of connections and establishes the adult hierarchy. These results suggest that primate cortical networks underlying high-level function undergo prolonged self-organization via regressive phenomena in the cortical plate (axon elimination) and progressive phenomena (directed growth of cortical axons).},
	Author = {Kennedy, Henry and Douglas, Rodney and Knoblauch, Kenneth and Dehay, Colette},
	Date-Added = {2015-09-02 00:38:36 +0000},
	Date-Modified = {2015-09-02 00:38:36 +0000},
	Journal = {Novartis Found Symp},
	Journal-Full = {Novartis Foundation symposium},
	Mesh = {Animals; Body Patterning; Cerebral Cortex; Embryo, Mammalian; Models, Biological; Models, Neurological; Nerve Net; Neural Pathways; Neurons; Primates},
	Pages = {178-94 discussion 195-8, 276-81},
	Pmid = {18494259},
	Pst = {ppublish},
	Title = {Self-organization and pattern formation in primate cortical networks},
	Volume = {288},
	Year = {2007}}

@article{Dehay:2007,
	Abstract = {The spatio-temporal timing of the last round of mitosis, followed by the migration of neuroblasts to the cortical plate leads to the formation of the six-layered cortex that is subdivided into functionally defined cortical areas. Whereas many of the cellular and molecular mechanisms have been established in rodents, there are a number of unique features that require further elucidation in primates. Recent findings both in rodents and in primates indicate that regulation of the cell cycle, specifically of the G1 phase has a crucial role in controlling area-specific rates of neuron production and the generation of cytoarchitectonic maps.},
	Author = {Dehay, Colette and Kennedy, Henry},
	Date-Added = {2015-09-02 00:38:28 +0000},
	Date-Modified = {2015-09-02 00:38:28 +0000},
	Doi = {10.1038/nrn2097},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Animals; Cell Communication; Cell Cycle; Cell Cycle Proteins; Cell Differentiation; Cell Proliferation; Cerebral Cortex; G1 Phase; Humans; Neurons; Signal Transduction; Stem Cells},
	Month = {Jun},
	Number = {6},
	Pages = {438-50},
	Pmid = {17514197},
	Pst = {ppublish},
	Title = {Cell-cycle control and cortical development},
	Volume = {8},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2097}}

@article{Molnar:2006a,
	Abstract = {This review aims to provide examples of how both comparative and genetic analyses contribute to our understanding of the rules for cortical development and evolution. Genetic studies have helped us to realize the evolutionary rules of telencephalic organization in vertebrates. The control of the establishment of conserved telencephalic subdivisions and the formation of boundaries between these subdivisions has been examined and the very specific alterations at the striatocortical junction have been revealed. Comparative studies and genetic analyses both demonstrate the differential origin and migratory pattern of the two basic neuron types of the cerebral cortex. GABAergic interneurons are mostly generated in the subpallium and a common mechanism governs their migration to the dorsal cortex in both mammals and sauropsids. The pyramidal neurons are generated within the cortical germinal zone and migrate radially, the earliest generated cell layers comprising preplate cells. Reelin-positive Cajal-Retzius cells are a general feature of all vertebrates studied so far; however, there is a considerable amplification of the Reelin signalling with cortical complexity, which might have contributed to the establishment of the basic mammalian pattern of cortical development. Based on numerous recent observations we shall present the argument that specialization of the mitotic compartments may constitute a major drive behind the evolution of the mammalian cortex. Comparative developmental studies have revealed distinct features in the early compartments of the developing macaque brain, drawing our attention to the limitations of some of the current model systems for understanding human developmental abnormalities of the cortex. Comparative and genetic aspects of cortical development both reveal the workings of evolution.},
	Author = {Moln{\'a}r, Zolt{\'a}n and M{\'e}tin, Christine and Stoykova, Anastassia and Tarabykin, Victor and Price, David J and Francis, Fiona and Meyer, Gundela and Dehay, Colette and Kennedy, Henry},
	Date-Added = {2015-09-02 00:38:22 +0000},
	Date-Modified = {2015-09-02 00:38:22 +0000},
	Doi = {10.1111/j.1460-9568.2006.04611.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Mesh = {Animals; Biological Evolution; Cell Differentiation; Cerebral Cortex; Humans; Models, Neurological; Neurons},
	Month = {Feb},
	Number = {4},
	Pages = {921-34},
	Pmc = {PMC1931431},
	Pmid = {16519657},
	Pst = {ppublish},
	Title = {Comparative aspects of cerebral cortical development},
	Volume = {23},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1460-9568.2006.04611.x}}

@article{Dehay:1996a,
	Abstract = {Prenatal bilateral enucleation induces cortex, which normally would have become striate cortex, to follow a default developmental pathway and to take on the cytoarchitectonic appearance of extrastriate cortex (default extrastriate cortex, Dehay et al. [1996] J. Comp. Neurol. 367:70-89). We have investigated if this manipulation influences the cortical expression of acetylcholinesterase (AChE) and cytochrome oxidase (CO). Early enucleation (before embryonic day 81; E81) had only minor effects on the distribution of AChE and CO in the striate cortex. In animals that underwent operation, the striate cortex CO blobs were significantly more closely spaced on the operculum compared with the calcarine. After early enucleation, there was a periodic distribution of CO dense patches in default extrastriate cortex. These CO patches had a center-to-center spacing that was considerably smaller than that of CO stripes in normal area V2, but was somewhat larger than that of the CO blobs in striate cortex. Although the CO stripes characteristic of normal area V2 could not be detected, there were some high-frequency CO patches, similar to those found in default extrastriate cortex. Early enucleation caused a failure to form the transient AChE bands running perpendicular to the striate border, which are normally present in the fetus and early neonate. Late enucleation did not alter AChE expression in extrastriate cortex. The relatively minor effects of early enucleation in the reduced striate cortex contrast with the changes in expression of these enzymes in extrastriate cortex, which accompany large shifts in the location of the striate border. This suggests a massive reorganisation of cortical phenotype in extrastriate cortex.},
	Author = {Dehay, C and Giroud, P and Berland, M and Killackey, H P and Kennedy, H},
	Date-Added = {2015-09-02 00:38:12 +0000},
	Date-Modified = {2015-09-02 00:38:12 +0000},
	Doi = {10.1002/(SICI)1096-9861(19961216)376:3\&lt;386::AID-CNE3\&gt;3.0.CO;2-Z},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Acetylcholinesterase; Animals; Electron Transport Complex IV; Eye Enucleation; Female; Macaca; Neuronal Plasticity; Phenotype; Pregnancy; Vision, Monocular; Visual Cortex},
	Month = {Dec},
	Number = {3},
	Pages = {386-402},
	Pmid = {8956106},
	Pst = {ppublish},
	Title = {Phenotypic characterisation of respecified visual cortex subsequent to prenatal enucleation in the monkey: development of acetylcholinesterase and cytochrome oxidase patterns},
	Volume = {376},
	Year = {1996},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1096-9861(19961216)376:3%5C&lt;386::AID-CNE3%5C&gt;3.0.CO;2-Z}}

@article{Barone:1996,
	Abstract = {In experiments combining retrograde tracers and histochemistry, we have looked at the prenatal development of the cortical pathway linking areas V2 and V4. Transient expression of acetylcholinesterase in fetal area V2 reveals the separate compartments that project to V4 (temporal directed pathway) and V5 (parietal directed pathway). During early stages of pathway formation, V2 neurons projecting to area V4 are clustered in the appropriate compartments. During the phase of rapid axonal growth, there is a selective increase of connections originating from the appropriate compartments leading to a strongly clustered organization at the peak of connectivity. During this phase, injections involving the white matter also showed clustering, but this was somewhat reduced in comparison to that of gray matter injections. The growth phase is followed by an elimination phase during which there is a tendency for a preferential loss of intercluster connections, which may sharpen the early formed pattern. These results demonstrate the primary role of axonal guidance and target recognition mechanisms followed by a limited extent of selective elimination during the formation of functional cortical pathways in the primate isocortex. Compared to previous findings, these results suggest that the developmental restriction of callosal connections is not a universal model of cortical development. In the present report, the directed growth and early specification of feed-forward connections contrast with the prolonged remodelling of monkey feedback projections, suggesting two distinct developmental strategies of pathway formation in the monkey.},
	Author = {Barone, P and Dehay, C and Berland, M and Kennedy, H},
	Date-Added = {2015-09-02 00:38:04 +0000},
	Date-Modified = {2015-09-02 00:38:04 +0000},
	Doi = {10.1002/(SICI)1096-9861(19961007)374:1\&lt;1::AID-CNE1\&gt;3.0.CO;2-7},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Acetylcholinesterase; Animals; Animals, Newborn; Electron Transport Complex IV; Embryonic and Fetal Development; Macaca fascicularis; Microinjections; Neural Pathways; Neurons; Visual Cortex},
	Month = {Oct},
	Number = {1},
	Pages = {1-20},
	Pmid = {8891943},
	Pst = {ppublish},
	Title = {Role of directed growth and target selection in the formation of cortical pathways: prenatal development of the projection of area V2 to area V4 in the monkey},
	Volume = {374},
	Year = {1996},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1096-9861(19961007)374:1%5C&lt;1::AID-CNE1%5C&gt;3.0.CO;2-7}}

@article{Dehay:1996,
	Abstract = {Bilateral enucleation was performed at different fetal ages during corticogenesis, and the brains were prepared for histological examination. Early-enucleated fetuses (operated prior to embryonic day 77) showed morphological changes at the level of the thalamus and the cortex. In the thalamus, there was a loss of lamination and a decrease in size of the lateral geniculate nucleus. There was a decrease in the size of the inferior pulvinar, but there was no change in the lateral pulvinar. The border of striate cortex was as sharp in the enucleates as it was in the normal monkeys. In three of the four early enucleates, we observed an interdigitation of striate and extrastriate cortex. In three of the early enucleates, we observed a small island of nonstriate cortex near the striate border that was surrounded entirely by striate cortex. Enucleation led to an age-related reduction of striate cortex. This reduction was greater in the operculum than in the calcarine fissure. The reduction of striate cortex was accompanied by an increase in the dimensions of extrastriate visual cortex, so that the overall dimensions of the neocortex remained invariant. The extrastriate cortex in the enucleated animals presented a uniform cytoarchitecture and was indistinguishable from area 18 in the normal animal. There were changes in the gyral pattern that were restricted mainly to the cortex on the operculum. A deepening of minor dimples as well as the induction of a variable number of supplementary sulci led to an increase in the convolution of the occipital lobe. These results are discussed with respect to the specification of cortical areas. They demonstrate that the reduction in striate cortex was not accompanied by an equivalent reduction in the neocortex; rather, there was a border shift, and a large volume of cortex that was destined to become striate cortex appears to be cytoarchitectonically normal extrastriate cortex.},
	Author = {Dehay, C and Giroud, P and Berland, M and Killackey, H and Kennedy, H},
	Date-Added = {2015-09-02 00:37:46 +0000},
	Date-Modified = {2015-09-02 00:37:46 +0000},
	Doi = {10.1002/(SICI)1096-9861(19960325)367:1\&lt;70::AID-CNE6\&gt;3.0.CO;2-G},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Aging; Animals; Animals, Newborn; Eye Enucleation; Fetus; Macaca fascicularis; Neuronal Plasticity; Thalamus; Visual Cortex},
	Month = {Mar},
	Number = {1},
	Pages = {70-89},
	Pmid = {8867284},
	Pst = {ppublish},
	Title = {Contribution of thalamic input to the specification of cytoarchitectonic cortical fields in the primate: effects of bilateral enucleation in the fetal monkey on the boundaries, dimensions, and gyrification of striate and extrastriate cortex},
	Volume = {367},
	Year = {1996},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1096-9861(19960325)367:1%5C&lt;70::AID-CNE6%5C&gt;3.0.CO;2-G}}

@article{Barone:1995,
	Abstract = {The pre- and postnatal developmental changes of the cortical afferents to area 17 were studied in the macaque monkey. Paired injections of the retrograde tracers fast blue and diamidino yellow were made in area 17. Quantitative techniques were used to examine the spatial patterns of labeling in three distinct locations of the extrastriate cortex that correspond to known visual areas. In the adult, each cortical region has a characteristic laminar distribution. In the fetus the proportion of supragranular layer neurons in all cortical regions was much higher than in the adult. The present study shows that despite the very high levels of labeled supragranular layer neurons, there is some early areal specialization so that the adult configuration does not emerge from a uniform distribution. The developmental decline in the proportion of labeled supragranular neurons is complete by 1 month after birth. Each injection of tracer gave rise in each cortical area to dense labeling in a restricted region (projection zone). Areal measurements of projection zones in the supra- and infragranular layers showed that the developmental decrease in the proportion of labeled supragranular layer neurons is accompanied by a relative change of the dimensions of supra- and infragranular projection zones: the supragranular projection zone in the fetus is larger than the infragranular projection zone and vice versa in the adult. In the fetus, the two projection zones corresponding to each of the two tracers overlap in the supragranular layers whereas they are largely separated in the infragranular layers. During development there is a progressive decrease in the overlap of the supragranular projection zones and an increase in the overlap in the infragranular layers. Again, the adult configuration is achieved 1 month after birth. This developmental inversion of the areal dimensions of the projection zones in supra- and infragranular layers is accompanied by a drastic decrease in the proportion of double-labeled neurons located in supragranular layers. These results clearly show that early in development, axonal projections to area V1 are modified in very different ways according to whether they originate from supra- or infragranular layers. This developmental process lasts for about 80 d. These findings show that in the primate there is a prolonged remodeling of axonal projections that is a highly characteristic feature of this species.},
	Author = {Barone, P and Dehay, C and Berland, M and Bullier, J and Kennedy, H},
	Date = {1995 Jan-Feb},
	Date-Added = {2015-09-02 00:37:36 +0000},
	Date-Modified = {2015-09-02 00:37:36 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Amidines; Animals; Animals, Newborn; Axons; Female; Fluorescent Dyes; Histocytochemistry; Macaca fascicularis; Neural Pathways; Neurons, Afferent; Pregnancy; Visual Cortex; Visual Pathways},
	Number = {1},
	Pages = {22-38},
	Pmid = {7719128},
	Pst = {ppublish},
	Title = {Developmental remodeling of primate visual cortical pathways},
	Volume = {5},
	Year = {1995}}

@article{Meissirel:1993,
	Abstract = {Anterograde transport of wheat germ agglutinin conjugated to horseradish peroxidase (WGA-HRP) was used to study transient axons from the visual cortex in the pyramidal tract. Injections at birth restricted to the visual cortex labeled axons in the vicinity of the pontine nuclei. Two to eight days after birth, axons from the occipital cortex were found posterior to the pontine nucleus, their caudalmost stable target. Transient corticospinal axons from the presumptive primary visual cortex did not grow caudal to the pyramidal decussation. Innervation of more distal targets preceded innervation of proximal targets. Innervation of the pontine nucleus is initiated around 68 hours after birth, when the transient extension in the medullary pyramidal tract has attained its maximum caudal extent. Innervation of the superior colliculus begins 9 days after birth. Retrograde tracers were used to follow the developmental changes in the cortical distribution of the parent neurons giving rise to axons in the pyramidal tract. In the adult, labeled neurons following injection of retrograde tracer in the pyramidal tract occupied less than a third of the neocortex and were centred on the anterior part of the coronal and spleniocruciate gyri. In the immature brain, labeled neurons covered more than two-thirds of the neocortex. Areal density measurements in the neonate showed that peak labeling was centred in the anterior coronal and spleniocruciate gyri, where corticospinal cells in the adult are located. There was a marked rostral-caudal gradient so that labeled neurons were very scarce towards the occipital pole. These results, showing transient neocortical axons in the pyramidal tract in a carnivore, suggest that this may be a common feature of mammalian development. The finding that the adult pattern of corticospinal projections does not emerge from a uniform distribution is discussed with respect to the areal specification of cortical connectivity.},
	Author = {Meissirel, C and Dehay, C and Kennedy, H},
	Date-Added = {2015-09-02 00:37:28 +0000},
	Date-Modified = {2015-09-02 00:37:28 +0000},
	Doi = {10.1002/cne.903380205},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Animals, Newborn; Ferrets; Neural Pathways; Occipital Lobe; Pons; Pyramidal Tracts; Time Factors; Visual Cortex},
	Month = {Dec},
	Number = {2},
	Pages = {193-213},
	Pmid = {8308167},
	Pst = {ppublish},
	Title = {Transient cortical pathways in the pyramidal tract of the neonatal ferret},
	Volume = {338},
	Year = {1993},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.903380205}}

@article{Dehay:1993,
	Abstract = {An as-yet unresolved issue in developmental neurobiology is whether the discrete areas that form the mammalian cortex emerge from a uniform cortical plate or whether they are already specified in the germinal zone. A feature of the primate striate cortex is that the number of neurons per unit area is twice that of anywhere else in the cerebral cortex. Here we take advantage of this unique structural feature to investigate whether the extra striate cortical cells are due to increased neuron production during neurogenesis. We labelled precursors undergoing terminal cell division with 3H-thymidine and allowed them to migrate to the cortical plate. Cell counts revealed that their rate of production in the germinal zone of striate cortex is higher than in that given rise to extrastriate cortex. Also, we used 3H-thymidine pulse injections to investigate cell cycle dynamics and found that this phase of increased production of striate cortical cells is associated with changes in the parameters of the cell cycle. These results show that cortical area identity is at least partially determined at the level of the ventricular zone.},
	Author = {Dehay, C and Giroud, P and Berland, M and Smart, I and Kennedy, H},
	Date-Added = {2015-09-02 00:37:21 +0000},
	Date-Modified = {2015-09-02 00:37:21 +0000},
	Doi = {10.1038/366464a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Brain; Cell Cycle; Cell Movement; Embryonic and Fetal Development; Fetus; Macaca fascicularis; Neurons; S Phase; Thymidine; Visual Cortex},
	Month = {Dec},
	Number = {6454},
	Pages = {464-6},
	Pmid = {8247154},
	Pst = {ppublish},
	Title = {Modulation of the cell cycle contributes to the parcellation of the primate visual cortex},
	Volume = {366},
	Year = {1993},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/366464a0}}

@article{Kennedy:1990,
	Author = {Kennedy, H and Dehay, C and Horsburgh, G},
	Date-Added = {2015-09-02 00:37:14 +0000},
	Date-Modified = {2015-09-02 00:37:14 +0000},
	Doi = {10.1038/348494a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Electron Transport Complex IV; Primates; Visual Cortex; Visual Perception},
	Month = {Dec},
	Number = {6301},
	Pages = {494},
	Pmid = {2174128},
	Pst = {ppublish},
	Title = {Striate cortex periodicity},
	Volume = {348},
	Year = {1990},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/348494a0}}

@article{Kennedy:1993a,
	Abstract = {Environmental control of gene expression can occur early or late during development, and this is relevant to understanding species differences in cortical specification. Experiments in the developing visual system of the primate show that the areal limits of striate cortex are specified by the thalamic inputs, so that afferent specification of cortex appears as a general feature of mammalian development. Primates differ from nonprimates in that thalamic afferents control very early stages of corticogenesis when symmetrical cell division is forming the pool of striate neuron precursors. Other cortical features are specified much later in primates than in nonprimates. We speculate that the early specification of certain features and the late specification of others contribute to the sophistication of the cerebral cortex characteristic of primates.},
	Author = {Kennedy, H and Dehay, C},
	Date-Added = {2015-09-02 00:37:09 +0000},
	Date-Modified = {2015-09-02 00:37:09 +0000},
	Journal = {Perspect Dev Neurobiol},
	Journal-Full = {Perspectives on developmental neurobiology},
	Mesh = {Afferent Pathways; Animals; Anophthalmos; Cell Differentiation; Cerebral Cortex; Embryonic and Fetal Development; Eye Enucleation; Gene Expression Regulation; Humans; Morphogenesis; Primates; Rodentia; Species Specificity; Thalamus; Time Factors; Visual Cortex},
	Number = {2},
	Pages = {93-9},
	Pmid = {8087537},
	Pst = {ppublish},
	Title = {The importance of developmental timing in cortical specification},
	Volume = {1},
	Year = {1993}}

@article{Kennedy:1993,
	Abstract = {The developmental basis for the localization of function in the mammalian cortex remains a controversial issue. The newly formed rodent cortex displays a considerable uniformity in terms of its connectivity. This contrasts with the primate, where even the first formed connections can show a high degree of areal specificity. An important clue to understanding these species differences can be obtained by examining how and when the sensory periphery exerts its organizing influence on the developing cortex. In rodents the developmental timetable ensures that the organizational control of the periphery persists late in development, when neurons are forming their first connections. By contrast, in primates the late onset and prolonged duration of corticogenesis result in the periphery being able to exert its influence much earlier, during the phase of precursor proliferation. Differences and similarities between primate and rodent corticogenesis are highly informative. In rodents, recent results with molecular markers show that regional differences in developmental potential exist in the cerebral cortex before innervation from the periphery. Similar findings are predicted in primates. It is to be expected that a more complete understanding of the rules governing the emergence of distinct cortical areas will come from resolving how afferent specification acts within the confines of such regional specializations.},
	Author = {Kennedy, H and Dehay, C},
	Date = {1993 May-Jun},
	Date-Added = {2015-09-02 00:37:04 +0000},
	Date-Modified = {2015-09-02 00:37:04 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Mesh = {Animals; Cerebral Cortex; Humans; Mice; Primates; Rodentia; Species Specificity},
	Number = {3},
	Pages = {171-86},
	Pmid = {8324368},
	Pst = {ppublish},
	Title = {Cortical specification of mice and men},
	Volume = {3},
	Year = {1993}}

@article{Dehay:1988a,
	Abstract = {Cytochrome oxidase (CytOx) is known to preferentially stain those regions of the visual cortex which receive direct projections from the thalamus. The pattern of CytOx stain has been used to investigate the maturation of thalamic input to areas V1 and V2 in the newborn monkey. In both areas, the intensity of CytOx activity was similar in newborns and adults. The distribution of CytOx in area V2 was not found to vary with age. In area V1, the only difference in CytOx activity in newborns was a relative immaturity of staining in layer 4C. The callosal connections of visual areas V1 and V2 were investigated by the axonal transport of wheat germ agglutinin conjugated to horseradish peroxidase and free horseradish peroxidase. In the adult, V1 was found to be reciprocally callosally connected for a distance of 1-2.5 mm from the V1/V2 border, whilst V2 was connected for a distance of 3-8 mm from the border. In both areas, callosal connections showed a certain degree of clustering, particularly in V2 which contained 97-98% of the total number of callosal connections of these two areas. In the newborn, the number, tangential extent and clustered distribution of callosal connections were as in the adult. In the newborn, as in the adult, callosal connections coincided with regions of high CytOx activity in area V2. The results showing a relative maturity of the tangential distribution of callosal projecting neurons on the one hand, and an immaturity of thalamic projections on the other, are discussed in terms of: (1) the maturational status of the newborn monkey compared to other mammals at the moment of birth and (2) the possible role of visual experience in shaping cortical connections.},
	Author = {Dehay, C and Kennedy, H},
	Date-Added = {2015-09-02 00:36:55 +0000},
	Date-Modified = {2015-09-02 00:36:55 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Mesh = {Aging; Animals; Animals, Newborn; Brain Mapping; Corpus Callosum; Macaca fascicularis; Thalamic Nuclei; Visual Cortex; Visual Pathways},
	Month = {Aug},
	Number = {3},
	Pages = {237-44},
	Pmid = {3166701},
	Pst = {ppublish},
	Title = {The maturational status of thalamocortical and callosal connections of visual areas V1 and V2 in the newborn monkey},
	Volume = {29},
	Year = {1988}}

@article{Kennedy:1988,
	Abstract = {The efferent and afferent connections of the V1/V2 border with the contralateral hemisphere have been examined using anatomical tracers. The V1/V2 border was found to exchange connections with the contralateral V2 area as well as a restricted strip of V1 lying adjacent to the V1/V2 border. Besides these homotopic projections, two heterotopic projections were found to V3/V3A and V5. Anterograde tracing of callosal connections showed that terminals in these heterotopic sites were focused in layer 4, the recipient layer of projections originating from the ipsilateral V1/V2 border. Bilateral injections of fluorescent dyes showed that these heterotopic targets of the V1/V2 border are connected to the homologous ipsilateral V1/V2 border region. The laminar location of callosal projecting neurons as well as their terminals were characteristic for each cortical region. The laminar pattern of callosal connectivity was found to differ markedly from that of associational visual pathways. Two principal hypotheses are suggested by these results. First, the fact that V1 in part is reciprocally callosally connected in all mammals supports the notion that this interhemispheric pathway completes long-range intrinsic cortical connections. Second, the convergence of inter- and intrahemispheric pathways could provide the anatomical basis for the modulation of the sensory processing within one hemisphere by ongoing activity in the contralateral hemisphere.},
	Author = {Kennedy, H and Dehay, C},
	Date-Added = {2015-09-02 00:36:50 +0000},
	Date-Modified = {2015-09-02 00:36:50 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Mesh = {Animals; Brain Mapping; Corpus Callosum; Dominance, Cerebral; Macaca fascicularis; Visual Cortex; Visual Pathways; Visual Perception},
	Month = {Aug},
	Number = {3},
	Pages = {225-36},
	Pmid = {3166700},
	Pst = {ppublish},
	Title = {Functional implications of the anatomical organization of the callosal projections of visual areas V1 and V2 in the macaque monkey},
	Volume = {29},
	Year = {1988}}

@article{Dehay:1988,
	Abstract = {We have examined the anatomical features of ipsilateral transient cortical projections to areas 17, 18, and 19 in the kitten with the use of axonal tracers Fast Blue and WGA-HRP. Injections of tracers in any of the three primary visual areas led to retrograde labeling in frontal, parietal, and temporal cortices. Retrogradely labeled cells were not randomly distributed, but instead occurred preferentially at certain loci. The pattern of retrograde labeling was not influenced by the area injected. The main locus of transiently projecting neurons was an isolated region in the ectosylvian gyrus, probably corresponding to auditory area A1. Other groups of transiently projecting neurons had more variable locations in the frontoparietal cortex. The laminar distribution of neurons sending a transient projection to the visual cortex is characteristic and different from that of parent neurons of other cortical pathways at the same age. In the frontoparietal cortex, transiently projecting neurons were located mainly in layer 1 and the upper part of layers 2 and 3. In the ectosylvian gyrus, nearly all the neurons are located in layers 2 and 3. In addition, a few transiently projecting neurons are found in layer 6 and in the white matter. Transiently projecting neurons have a pyramidal morphology except for the occasional spindle-shaped cell of layer 1 and multipolar cells observed in the white matter. Anterograde studies were used to investigate the location of transient fibers in the visual cortex. Injections of WGA-HRP at the site of origin of transient projections gave rise to few retrogradely labeled cells in areas 17, 18, and 19, demonstrating that transient projections to these areas are not reciprocal. Although labeled axons were found over a wide area of the posterior cortex, they were more numerous over certain regions, including areas 17, 18, and 19, and absent from other more lateral cortical regions. Transient projecting fibers were present in all cortical layers at birth. Plotting the location of transient fibers in numerous sections and at all ages showed that these fibers are not more plentiful in the white matter than they are in the gray matter. We found no evidence that the white/gray matter border constituted a physical barrier to the growth of transient axons. Comparison of the organization of this transient pathway to that of other transient connections is discussed with respect to the development of the cortex.},
	Author = {Dehay, C and Kennedy, H and Bullier, J},
	Date-Added = {2015-09-02 00:36:44 +0000},
	Date-Modified = {2015-09-02 00:36:44 +0000},
	Doi = {10.1002/cne.902720106},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Aging; Amidines; Animals; Auditory Cortex; Brain Mapping; Cats; Fluorescent Dyes; Horseradish Peroxidase; Motor Cortex; Neuronal Plasticity; Somatosensory Cortex; Visual Cortex; Wheat Germ Agglutinin-Horseradish Peroxidase Conjugate; Wheat Germ Agglutinins},
	Month = {Jun},
	Number = {1},
	Pages = {68-89},
	Pmid = {2454978},
	Pst = {ppublish},
	Title = {Characterization of transient cortical projections from auditory, somatosensory, and motor cortices to visual areas 17, 18, and 19 in the kitten},
	Volume = {272},
	Year = {1988},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902720106}}

@article{Kennedy:1989,
	Abstract = {Area 17 in the neonate of numerous species receives projections from cortical areas that do not project to area 17 in the adult. To investigate if this were the case in the developing primate, we have made injections of retrograde tracers in area 17 of newborn monkeys (Macaca irus) and examined the areal distribution of labeled neurons. Neurons projecting to area 17 were found to be restricted to those cortical regions that project to area 17 in the adult. The projection to area 17 in the neonate did appear to be very different in that in the superior temporal sulcus there was a large contingent of labeled neurons in supragranular layers. This constitutes a transient projection because in the adult area 17 projecting neurons in this cortical region originate almost exclusively from infragranular layers. To test if a change in the laminar distribution of area 17 projecting neurons in extrastriate cortex is a general feature of postnatal development, we have computed in neonates and adults the proportion of area 17 afferent neurons in infra- and supragranular layers for each cortical region that projects to area 17. This revealed (i) that in the adult the laminar distribution of area 17 afferents is characteristic for each cortical area and (ii) that this distribution emerges during development from an immature state in which labeled neurons are more numerous in supragranular layers. These results show that there is an extensive remodeling of the neuronal circuitry connecting visual cortical areas during postnatal development in the monkey and that the transient connectivity of primate area 17 is very different from that observed in other mammalian species.},
	Author = {Kennedy, H and Bullier, J and Dehay, C},
	Date-Added = {2015-09-02 00:36:41 +0000},
	Date-Modified = {2015-09-02 00:36:41 +0000},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Aging; Animals; Animals, Newborn; Axonal Transport; Cerebral Cortex; Horseradish Peroxidase; Macaca; Neurons; Visual Cortex; Wheat Germ Agglutinin-Horseradish Peroxidase Conjugate; Wheat Germ Agglutinins},
	Month = {Oct},
	Number = {20},
	Pages = {8093-7},
	Pmc = {PMC298221},
	Pmid = {2479015},
	Pst = {ppublish},
	Title = {Transient projection from the superior temporal sulcus to area 17 in the newborn macaque monkey},
	Volume = {86},
	Year = {1989}}

@article{Dehay:1989,
	Abstract = {In several species, the peripheral input from the eyes partly determines the pattern of interconnections between the visual areas of the two cerebral hemispheres through the fibre tract termed the corpus callosum. In the macaque monkey, the neurons projecting through the callosum are largely restricted to area 18 throughout ontogeny, whereas area 17 is characterized by few or no callosal projections. Here, we show that suppressing the peripheral input by prenatal removal of the eyes leads to a marked reduction in the extent of area 17, resulting in a large shift in the position of the histologically identifiable boundary between the two areas. Even so, the boundary continues to separate an area rich with callosal connections (area 18) from one poor in such projections (area 17), indicating there is no effect on the callosal connectivity of area 17. In contrast, in area 18, eye removal results in many more neurons with callosal projections than in normal animals. The results suggest that the factors that determine the parcellation of cortical areas also specify their connectivity.},
	Author = {Dehay, C and Horsburgh, G and Berland, M and Killackey, H and Kennedy, H},
	Date-Added = {2015-09-02 00:36:34 +0000},
	Date-Modified = {2015-09-02 00:36:34 +0000},
	Doi = {10.1038/337265a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Corpus Callosum; Electron Transport Complex IV; Eye; Macaca fascicularis; Neurons; Ocular Physiological Phenomena; Reference Values; Retina; Visual Cortex; Visual Fields},
	Month = {Jan},
	Number = {6204},
	Pages = {265-7},
	Pmid = {2536139},
	Pst = {ppublish},
	Title = {Maturation and connectivity of the visual cortex in monkey is altered by prenatal removal of retinal input},
	Volume = {337},
	Year = {1989},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/337265a0}}

@article{Seabrook:2013,
	Abstract = {Neurons in layer VI of visual cortex represent one of the largest sources of nonretinal input to the dorsal lateral geniculate nucleus (dLGN) and play a major role in modulating the gain of thalamic signal transmission. However, little is known about how and when these descending projections arrive and make functional connections with dLGN cells. Here we used a transgenic mouse to visualize corticogeniculate projections to examine the timing of cortical innervation in dLGN. Corticogeniculate innervation occurred at postnatal ages and was delayed compared with the arrival of retinal afferents. Cortical fibers began to enter dLGN at postnatal day 3 (P3) to P4, a time when retinogeniculate innervation is complete. However, cortical projections did not fully innervate dLGN until eye opening (P12), well after the time when retinal inputs from the two eyes segregate to form nonoverlapping eye-specific domains. In vitro thalamic slice recordings revealed that newly arriving cortical axons form functional connections with dLGN cells. However, adult-like responses that exhibited paired pulse facilitation did not fully emerge until 2 weeks of age. Finally, surgical or genetic elimination of retinal input greatly accelerated the rate of corticogeniculate innervation, with axons invading between P2 and P3 and fully innervating dLGN by P8 to P10. However, recordings in genetically deafferented mice showed that corticogeniculate synapses continued to mature at the same rate as controls. These studies suggest that retinal and cortical innervation of dLGN is highly coordinated and that input from retina plays an important role in regulating the rate of corticogeniculate innervation.},
	Author = {Seabrook, Tania A and El-Danaf, Rana N and Krahe, Thomas E and Fox, Michael A and Guido, William},
	Date-Added = {2015-09-02 00:05:58 +0000},
	Date-Modified = {2015-09-02 00:05:58 +0000},
	Doi = {10.1523/JNEUROSCI.5271-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Age Factors; Analysis of Variance; Animals; Animals, Newborn; Basic Helix-Loop-Helix Transcription Factors; Cholera Toxin; Excitatory Postsynaptic Potentials; Eye Enucleation; Gene Expression Regulation, Developmental; Geniculate Bodies; Green Fluorescent Proteins; Mice; Mice, Inbred C57BL; Mice, Transgenic; Myelin Basic Protein; Nerve Tissue Proteins; Retina; Vesicular Glutamate Transport Protein 1; Visual Cortex; Visual Pathways},
	Month = {Jun},
	Number = {24},
	Pages = {10085-97},
	Pmc = {PMC3682386},
	Pmid = {23761904},
	Pst = {ppublish},
	Title = {Retinal input regulates the timing of corticogeniculate innervation},
	Volume = {33},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.5271-12.2013}}

@article{Yilmaz:2013,
	Abstract = {Much of brain science is concerned with understanding the neural circuits that underlie specific behaviors. While the mouse has become a favorite experimental subject, the behaviors of this species are still poorly explored. For example, the mouse retina, like that of other mammals, contains ∼20 different circuits that compute distinct features of the visual scene [1, 2]. By comparison, only a handful of innate visual behaviors are known in this species--the pupil reflex [3], phototaxis [4], the optomotor response [5], and the cliff response [6]--two of which are simple reflexes that require little visual processing. We explored the behavior of mice under a visual display that simulates an approaching object, which causes defensive reactions in some other species [7, 8]. We show that mice respond to this stimulus either by initiating escape within a second or by freezing for an extended period. The probability of these defensive behaviors is strongly dependent on the parameters of the visual stimulus. Directed experiments identify candidate retinal circuits underlying the behavior and lead the way into detailed study of these neural pathways. This response is a new addition to the repertoire of innate defensive behaviors in the mouse that allows the detection and avoidance of aerial predators.},
	Author = {Yilmaz, Melis and Meister, Markus},
	Date-Added = {2015-08-31 20:29:28 +0000},
	Date-Modified = {2015-08-31 20:30:36 +0000},
	Doi = {10.1016/j.cub.2013.08.015},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {mouse; mice; visual system; behavior; function; Escape Reaction; aversive; Retina; Retinal Ganglion Cells; Visual Cortex; superior colliculus},
	Month = {Oct},
	Number = {20},
	Pages = {2011-5},
	Pmc = {PMC3809337},
	Pmid = {24120636},
	Pst = {ppublish},
	Title = {Rapid innate defensive responses of mice to looming visual stimuli},
	Volume = {23},
	Year = {2013},
	File = {papers/Yilmaz_CurrBiol2013.pdf},
	Bdsk-File-2 = {papers/Yilmaz_CurrBiol2013a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2013.08.015}}

@article{Zhao:2014,
	Abstract = {Neural circuits in the brain often receive inputs from multiple sources, such as the bottom-up input from early processing stages and the top-down input from higher-order areas. Here we study the function of top-down input in the mouse superior colliculus (SC), which receives convergent inputs from the retina and visual cortex. Neurons in the superficial SC display robust responses and speed tuning to looming stimuli that mimic approaching objects. The looming-evoked responses are reduced by almost half when the visual cortex is optogenetically silenced in awake, but not in anesthetized, mice. Silencing the cortex does not change the looming speed tuning of SC neurons, or the response time course, except at the lowest tested speed. Furthermore, the regulation of SC responses by the corticotectal input is organized retinotopically. This effect we revealed may thus provide a potential substrate for the cortex, an evolutionarily new structure, to modulate SC-mediated visual behaviors.},
	Author = {Zhao, Xinyu and Liu, Mingna and Cang, Jianhua},
	Date-Added = {2015-08-31 20:09:43 +0000},
	Date-Modified = {2015-08-31 20:31:03 +0000},
	Doi = {10.1016/j.neuron.2014.08.037},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {mouse; mice; visual system; behavior; function; Escape Reaction; aversive; Retina; Retinal Ganglion Cells; Visual Cortex; superior colliculus},
	Mesh = {Animals; Evoked Potentials, Visual; Mice; Mice, Inbred C57BL; Mice, Transgenic; Photic Stimulation; Superior Colliculi; Visual Cortex; Visual Pathways; Wakefulness},
	Month = {Oct},
	Number = {1},
	Pages = {202-13},
	Pmc = {PMC4184914},
	Pmid = {25220812},
	Pst = {ppublish},
	Title = {Visual cortex modulates the magnitude but not the selectivity of looming-evoked responses in the superior colliculus of awake mice},
	Volume = {84},
	Year = {2014},
	File = {papers/Zhao_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.08.037}}

@article{Striem-Amit:2015,
	Abstract = {Is visual input during critical periods of development crucial for the emergence of the fundamental topographical mapping of the visual cortex? And would this structure be retained throughout life-long blindness or would it fade as a result of plastic, use-based reorganization? We used functional connectivity magnetic resonance imaging based on intrinsic blood oxygen level-dependent fluctuations to investigate whether significant traces of topographical mapping of the visual scene in the form of retinotopic organization, could be found in congenitally blind adults. A group of 11 fully and congenitally blind subjects and 18 sighted controls were studied. The blind demonstrated an intact functional connectivity network structural organization of the three main retinotopic mapping axes: eccentricity (centre-periphery), laterality (left-right), and elevation (upper-lower) throughout the retinotopic cortex extending to high-level ventral and dorsal streams, including characteristic eccentricity biases in face- and house-selective areas. Functional connectivity-based topographic organization in the visual cortex was indistinguishable from the normally sighted retinotopic functional connectivity structure as indicated by clustering analysis, and was found even in participants who did not have a typical retinal development in utero (microphthalmics). While the internal structural organization of the visual cortex was strikingly similar, the blind exhibited profound differences in functional connectivity to other (non-visual) brain regions as compared to the sighted, which were specific to portions of V1. Central V1 was more connected to language areas but peripheral V1 to spatial attention and control networks. These findings suggest that current accounts of critical periods and experience-dependent development should be revisited even for primary sensory areas, in that the connectivity basis for visual cortex large-scale topographical organization can develop without any visual experience and be retained through life-long experience-dependent plasticity. Furthermore, retinotopic divisions of labour, such as that between the visual cortex regions normally representing the fovea and periphery, also form the basis for topographically-unique plastic changes in the blind.},
	Author = {Striem-Amit, Ella and Ovadia-Caro, Smadar and Caramazza, Alfonso and Margulies, Daniel S and Villringer, Arno and Amedi, Amir},
	Date-Added = {2015-08-28 23:53:42 +0000},
	Date-Modified = {2015-08-28 23:58:36 +0000},
	Doi = {10.1093/brain/awv083},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {blindness; development; plasticity; vision; activity-development; connectivity; functional connectivity; Neocortex; Visual Cortex; extrastriate; topographic map; resting-state fMRI; Grants},
	Mesh = {Adult; Blindness; Case-Control Studies; Functional Neuroimaging; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Retina; Visual Cortex; Visual Pathways; Young Adult},
	Month = {Jun},
	Number = {Pt 6},
	Pages = {1679-95},
	Pmid = {25869851},
	Pst = {ppublish},
	Title = {Functional connectivity of visual cortex in the blind follows retinotopic organization principles},
	Volume = {138},
	Year = {2015},
	File = {papers/Striem-Amit_Brain2015.pdf}}

@article{Balkema:1981,
	Abstract = {Mice of the mutant strain pearl (pe/pe) differ from the wild strain by a single gene mutation, which leads to a lightening of the coat color. We tested this strain to see if this mutant gene also expressed itself in one or more visual abnormalities. Pearl mice were found to lack totally the optokinetic nystagmus reflex that was present in every normal mouse that we examined. This lack of optokinetic nystagmus was not due to oculomotor defects, since postrotatory nystagmus was normal. As described for other pigmentation mutants, we found that pearl mutants had a reduced ipsilateral projection to the lateral geniculate nucleus, superior colliculus, and visual cortex. We recorded from single cells in the superior colliculus and found response properties and light sensitivities to be normal over the luminance range at which optokinetic nystagmus was tested. However, at very dim backgrounds (scotopic levels), the incremental sensitivities of these cells in pearl mice were about 100 times lower than those of normal mice. This reduction in sensitivity was restricted to scotopic backgrounds and was not due to abnormalities in either the time course of dark adaptation or the receptive field sizes of single cells. In recordings of the electroretinographic response, both the waveforms and the normalized magnitudes of the A and B waves of pearl were indistinguishable from those of normal mice, which seems to indicate that the cause of pearl's sensitivity defect is located central to the main electrical events in the photoreceptors. The normality of many aspects of the visual system of pearl mice contrasts sharply with the complete absence of optokinetic nystagmus, with the reduced ipsilateral projection, and with the reduced dark sensitivity of the cells in the superior colliculus.},
	Author = {Balkema, Jr, G W and Pinto, L H and Dr{\"a}ger, U C and Vanable, Jr, J W},
	Date-Added = {2015-08-28 21:54:55 +0000},
	Date-Modified = {2015-08-28 21:56:53 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {vision; Visual Cortex; superior colliculus; behavior; Motor Activity;},
	Mesh = {Animals; Electric Conductivity; Eye Movements; Mice; Mice, Mutant Strains; Mutation; Neurons; Photic Stimulation; Retina; Retinal Degeneration; Superior Colliculi; Visual Cortex; Visual Perception},
	Month = {Nov},
	Number = {11},
	Pages = {1320-9},
	Pmid = {7310489},
	Pst = {ppublish},
	Title = {Characterization of abnormalities in the visual system of the mutant mouse pearl},
	Volume = {1},
	Year = {1981}}

@article{Schneider:1969,
	Author = {Schneider, G E},
	Date-Added = {2015-08-28 21:51:31 +0000},
	Date-Modified = {2015-08-28 21:53:38 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {vision; visual cortex; superior colliculus; behavior; Motor Activity},
	Mesh = {Animals; Cerebral Cortex; Cricetinae; Discrimination (Psychology); Orientation; Tectum Mesencephali; Vision, Ocular; Visual Cortex},
	Month = {Feb},
	Number = {3870},
	Pages = {895-902},
	Pmid = {5763873},
	Pst = {ppublish},
	Title = {Two visual systems},
	Volume = {163},
	Year = {1969},
	Bdsk-Url-1 = {http://www.sciencemag.org/content/163/3870/895.citation}}

@article{Prusky:2000,
	Abstract = {We have developed a simple computer-based discrimination task that enables the quick determination of visual acuities in rodents. A grating is displayed randomly on one of two monitors at the wide end of a trapezoidal-shaped tank containing shallow water. Animals are trained to swim toward the screens, and at a fixed distance, choose the screen displaying the grating and escape to a submerged platform hidden below it. Both mice and rats learn the task quickly. Performance falls below 70% when the spatial frequency is increased beyond 0.5 cycles in most C57BU6 mice, and around 1.0 cycles per degree (cpd) in Long-Evans rats.},
	Author = {Prusky, G T and West, P W and Douglas, R M},
	Date-Added = {2015-08-28 17:37:22 +0000},
	Date-Modified = {2015-08-28 17:38:04 +0000},
	Journal = {Vision Res},
	Journal-Full = {Vision research},
	Keywords = {mouse; mice; vision; behavior; Methods; technique; visual system; Visual Cortex; superior colliculus},
	Mesh = {Adaptation, Physiological; Animals; Behavior, Animal; Mice; Mice, Inbred C57BL; Psychophysics; Rats; Rats, Long-Evans; Visual Acuity},
	Number = {16},
	Pages = {2201-9},
	Pmid = {10878281},
	Pst = {ppublish},
	Title = {Behavioral assessment of visual acuity in mice and rats},
	Volume = {40},
	Year = {2000},
	File = {papers/Prusky_VisionRes2000.pdf}}

@article{Laramee:2014,
	Abstract = {In the mouse, visual extrastriate areas are located within distinct acallosal zones. It has been proposed that the striate-extrastriate and callosal projections are interdependent. In visually deprived mice, the normal patterns of callosal and striate-extrastriate projections are disrupted. It remains unknown whether visual deprivation affects the topography of V1-extrastriate projections and their relationship with callosal projections. Two anterograde tracers were injected in V1 and multiple retrograde tracer injections were performed in the contralateral hemisphere of intact and enucleated C57BL/6 mice and in ZRDCT/An mice to determine the effects of prenatal and postnatal afferent sensory activity on the topography of V1-extrastriate and callosal projections. Greater topographic anomalies were found in striate-extrastriate projections of anophthalmic than enucleated mice. In enucleated mice, the relationship between striate-extrastriate projections and callosal zones was highly variable. In anophthalmic mice, there was also a greater overlap between these projections. These results suggest that the prenatal afferent sensory activity regulates some aspects of the distribution of V1-extrastriate and callosal projections, in addition to the development of a normal topographic representation in extrastriate areas.},
	Author = {Laram{\'e}e, Marie-Eve and Bronchti, Gilles and Boire, Denis},
	Date-Added = {2015-08-27 16:30:30 +0000},
	Date-Modified = {2017-05-05 18:43:55 +0000},
	Doi = {10.1007/s00429-013-0623-6},
	Journal = {Brain Struct Funct},
	Journal-Full = {Brain structure \& function},
	Keywords = {activity manipulation; activity-dependent; Activity-development; Sensory Deprivation; spontaneous activity; retinal waves; cortical circuits; connectivity; hemisphere; symmetry; extrastriate; Neocortex; Cerebral Cortex; Visual Cortex; mice; mouse; eye; currOpinRvw},
	Mesh = {Animals; Anophthalmos; Corpus Callosum; Eye Enucleation; Mice; Mice, Inbred C57BL; Visual Cortex; Visual Pathways},
	Month = {Nov},
	Number = {6},
	Pages = {2051-70},
	Pmid = {23942645},
	Pst = {ppublish},
	Title = {Primary visual cortex projections to extrastriate cortices in enucleated and anophthalmic mice},
	Volume = {219},
	Year = {2014},
	File = {papers/Laramée_BrainStructFunct2014.pdf}}

@article{Craddock:2013,
	Abstract = {At macroscopic scales, the human connectome comprises anatomically distinct brain areas, the structural pathways connecting them and their functional interactions. Annotation of phenotypic associations with variation in the connectome and cataloging of neurophenotypes promise to transform our understanding of the human brain. In this Review, we provide a survey of magnetic resonance imaging--based measurements of functional and structural connectivity. We highlight emerging areas of development and inquiry and emphasize the importance of integrating structural and functional perspectives on brain architecture.},
	Author = {Craddock, R Cameron and Jbabdi, Saad and Yan, Chao-Gan and Vogelstein, Joshua T and Castellanos, F Xavier and Di Martino, Adriana and Kelly, Clare and Heberlein, Keith and Colcombe, Stan and Milham, Michael P},
	Date-Added = {2015-06-22 22:25:31 +0000},
	Date-Modified = {2015-06-22 22:25:31 +0000},
	Doi = {10.1038/nmeth.2482},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Mesh = {Brain; Connectome; Humans; Magnetic Resonance Imaging; Phenotype},
	Month = {Jun},
	Number = {6},
	Pages = {524-39},
	Pmc = {PMC4096321},
	Pmid = {23722212},
	Pst = {ppublish},
	Title = {Imaging human connectomes at the macroscale},
	Volume = {10},
	Year = {2013},
	File = {papers/Craddock_NatMethods2013.pdf}}

@article{Madisen:2015,
	Abstract = {UNLABELLED: An increasingly powerful approach for studying brain circuits relies on targeting genetically encoded sensors and effectors to specific cell types. However, current approaches for this are still limited in functionality and specificity. Here we utilize several intersectional strategies to generate multiple transgenic mouse lines expressing high levels of novel genetic tools with high specificity. We developed driver and double reporter mouse lines and viral vectors using the Cre/Flp and Cre/Dre double recombinase systems and established a new, retargetable genomic locus, TIGRE, which allowed the generation of a large set of Cre/tTA-dependent reporter lines expressing fluorescent proteins, genetically encoded calcium, voltage, or glutamate indicators, and optogenetic effectors, all at substantially higher levels than before. High functionality was shown in example mouse lines for GCaMP6, YCX2.60, VSFP Butterfly 1.2, and Jaws. These novel transgenic lines greatly expand the ability to monitor and manipulate neuronal activities with increased specificity.
VIDEO ABSTRACT: },
	Author = {Madisen, Linda and Garner, Aleena R and Shimaoka, Daisuke and Chuong, Amy S and Klapoetke, Nathan C and Li, Lu and van der Bourg, Alexander and Niino, Yusuke and Egolf, Ladan and Monetti, Claudio and Gu, Hong and Mills, Maya and Cheng, Adrian and Tasic, Bosiljka and Nguyen, Thuc Nghi and Sunkin, Susan M and Benucci, Andrea and Nagy, Andras and Miyawaki, Atsushi and Helmchen, Fritjof and Empson, Ruth M and Kn{\"o}pfel, Thomas and Boyden, Edward S and Reid, R Clay and Carandini, Matteo and Zeng, Hongkui},
	Date-Added = {2015-06-22 19:24:49 +0000},
	Date-Modified = {2015-06-22 19:24:49 +0000},
	Doi = {10.1016/j.neuron.2015.02.022},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Gene Targeting; Hippocampus; Integrases; Mice; Mice, Transgenic; Neurons; Optogenetics; Organ Culture Techniques; Visual Cortex},
	Month = {Mar},
	Number = {5},
	Pages = {942-58},
	Pmc = {PMC4365051},
	Pmid = {25741722},
	Pst = {ppublish},
	Title = {Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance},
	Volume = {85},
	Year = {2015},
	File = {papers/Madisen_Neuron2015.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2015.02.022}}

@article{Daw:2007a,
	Abstract = {Feedforward inhibitory GABAergic transmission is critical for mature cortical circuit function; in the neonate, however, GABA is depolarizing and believed to have a different role. Here we show that the GABAA receptor-mediated conductance is depolarizing in excitatory (stellate) cells in neonatal (postnatal day [P]3-5) layer IV barrel cortex, but GABAergic transmission at this age is not engaged by thalamocortical input in the feedforward circuit and has no detectable circuit function. However, recruitment occurs at P6-7 as a result of coordinated increases in thalamic drive to fast-spiking interneurons, fast-spiking interneuron-stellate cell connectivity and hyperpolarization of the GABAA receptor-mediated response. Thus, GABAergic circuits are not engaged by thalamocortical input in the neonate, but are poised for a remarkably coordinated development of feedforward inhibition at the end of the first postnatal week, which has profound effects on circuit function at this critical time in development.},
	Author = {Daw, Michael I and Ashby, Michael C and Isaac, John T R},
	Date-Added = {2015-04-08 23:02:15 +0000},
	Date-Modified = {2015-04-08 23:03:28 +0000},
	Doi = {10.1038/nn1866},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {plasticity; development; barrels; Somatosensory Cortex; interneurons; GABA;},
	Mesh = {Action Potentials; Age Factors; Animals; Animals, Newborn; Bicuculline; Cerebral Cortex; Dose-Response Relationship, Radiation; Electric Stimulation; Excitatory Postsynaptic Potentials; GABA Antagonists; Green Fluorescent Proteins; In Vitro Techniques; Interneurons; Mice; Mice, Transgenic; Neural Pathways; Patch-Clamp Techniques; Thalamus},
	Month = {Apr},
	Number = {4},
	Pages = {453-61},
	Pmid = {17351636},
	Pst = {ppublish},
	Title = {Coordinated developmental recruitment of latent fast spiking interneurons in layer IV barrel cortex},
	Volume = {10},
	Year = {2007},
	File = {papers/Daw_NatNeurosci2007a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn1866}}

@article{Cruz-Martin:2010,
	Abstract = {Fragile X syndrome (FXS) causes mental impairment and autism through transcriptional silencing of the Fmr1 gene, resulting in the loss of the RNA-binding protein fragile X mental retardation protein (FMRP). Cortical pyramidal neurons in affected individuals and Fmr1 knock-out (KO) mice have an increased density of dendritic spines. The mutant mice also show defects in synaptic and experience-dependent circuit plasticity, which are known to be mediated in part by dendritic spine dynamics. We used in vivo time-lapse imaging with two-photon microscopy through cranial windows in male and female neonatal mice to test the hypothesis that dynamics of dendritic protrusions are altered in KO mice during early postnatal development. We find that layer 2/3 neurons from wild-type mice exhibit a rapid decrease in dendritic spine dynamics during the first 2 postnatal weeks, as immature filopodia are replaced by mushroom spines. In contrast, KO mice show a developmental delay in the downregulation of spine turnover and in the transition from immature to mature spine subtypes. Blockade of metabotropic glutamate receptor (mGluR) signaling, which reverses some adult phenotypes of KO mice, accentuated this immature protrusion phenotype in KO mice. Thus, absence of FMRP delays spine stabilization and dysregulated mGluR signaling in FXS may partially normalize this early synaptic defect.},
	Author = {Cruz-Mart{\'\i}n, Alberto and Crespo, Michelle and Portera-Cailliau, Carlos},
	Date-Added = {2015-04-08 22:35:31 +0000},
	Date-Modified = {2015-04-08 22:55:49 +0000},
	Doi = {10.1523/JNEUROSCI.0577-10.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {plasticity; Structure-Activity Relationship; structural remodeling; autism; Autistic Disorder; Grants; mouse; in vivo; two-photon imaging; spines; synapse formation; Somatosensory Cortex; Neocortex; development},
	Mesh = {Animals; Animals, Newborn; Dendritic Spines; Disease Models, Animal; Excitatory Amino Acid Antagonists; Fragile X Mental Retardation Protein; Fragile X Syndrome; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Pseudopodia; Pyridines; Receptors, Metabotropic Glutamate},
	Month = {Jun},
	Number = {23},
	Pages = {7793-803},
	Pmc = {PMC2903441},
	Pmid = {20534828},
	Pst = {ppublish},
	Title = {Delayed stabilization of dendritic spines in fragile X mice},
	Volume = {30},
	Year = {2010},
	File = {papers/Cruz-Martín_JNeurosci2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0577-10.2010}}

@article{Zuo:2005a,
	Abstract = {Synapse formation and elimination occur throughout life, but the magnitude of such changes at distinct developmental stages remains unclear. Using transgenic mice overexpressing yellow fluorescent protein and transcranial two-photon microscopy, we repeatedly imaged dendritic spines on the apical dendrites of layer 5 pyramidal neurons. In young adolescent mice (1-month-old), 13%-20% of spines were eliminated and 5%-8% formed over 2 weeks in barrel, motor, and frontal cortices, indicating a cortical-wide spine loss during this developmental period. As animals mature, there is also a substantial loss of dendritic filopodia involved in spinogenesis. In adult mice (4-6 months old), 3%-5% of spines were eliminated and formed over 2 weeks in various cortical regions. Over 18 months, only 26% of spines were eliminated and 19% formed in adult barrel cortex. Thus, after a concurrent loss of spines and spine precursors in diverse regions of young adolescent cortex, spines become stable and a majority of them can last throughout life.},
	Author = {Zuo, Yi and Lin, Aerie and Chang, Paul and Gan, Wen-Biao},
	Date-Added = {2015-04-08 22:28:15 +0000},
	Date-Modified = {2015-04-08 22:29:02 +0000},
	Doi = {10.1016/j.neuron.2005.04.001},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {plasticity; Neocortex; Somatosensory Cortex; barrels; structural remodeling; Structure-Activity Relationship; spines; in vivo; two-photon imaging},
	Mesh = {Aging; Animals; Cerebral Cortex; Dendritic Spines; Green Fluorescent Proteins; Imaging, Three-Dimensional; Mice; Mice, Transgenic},
	Month = {Apr},
	Number = {2},
	Pages = {181-9},
	Pmid = {15848798},
	Pst = {ppublish},
	Title = {Development of long-term dendritic spine stability in diverse regions of cerebral cortex},
	Volume = {46},
	Year = {2005},
	File = {papers/Zuo_Neuron2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2005.04.001}}

@article{Carvell:1996,
	Abstract = {The importance of early tactile experience in the development of discriminative somatomotor function was assessed by examining the proficiency and movement strategies of rats raised without normal sensory inputs provided by their mystacial vibrissae. Infant-trimmed animals had their whiskers clipped daily from birth to 45 d of age, after which they were allowed to regrow for 60-70 d before initiation of behavioral training, which lasted as long as several months. Adult-trimmed animals had their whiskers trimmed for comparable periods during adulthood. Rats were tested on one of two tactile discriminations, rough versus smooth or rough versus rough, that differed with respect to the overall size of their surface features. Whisker movements during task performance were examined in detail using video-based motion analysis software. Infant-trimmed animals performed rough versus smooth discriminations as well as adult-trimmed rats or normally reared animals. Except for one subject, infant-trimmed rats were severely impaired in their ability to distinguish rough versus rough surfaces. Deficits persisted in spite of months of training with the regrown vibrissae. The animals that failed to master this task displayed whisking patterns that notably lacked frequencies in the normal range of 6-12 Hz. Thus, abnormal tactile experience early in life substantially, and perhaps permanently, impairs sensorimotor integration underlying active touch.},
	Author = {Carvell, G E and Simons, D J},
	Date-Added = {2015-04-08 22:25:18 +0000},
	Date-Modified = {2015-04-08 22:25:43 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {plasticity; Sensory Deprivation; structural remodeling; Structure-Activity Relationship; Somatosensory Cortex; Neocortex; sensory map; topographic map},
	Mesh = {Animals; Animals, Newborn; Behavior, Animal; Discrimination (Psychology); Female; Pregnancy; Rats; Rats, Sprague-Dawley; Sensory Deprivation; Somatosensory Cortex; Time Factors; Touch},
	Month = {Apr},
	Number = {8},
	Pages = {2750-7},
	Pmid = {8786450},
	Pst = {ppublish},
	Title = {Abnormal tactile experience early in life disrupts active touch},
	Volume = {16},
	Year = {1996},
	File = {papers/Carvell_JNeurosci1996.pdf}}

@article{Hofer:2009,
	Abstract = {Sensory experiences exert a powerful influence on the function and future performance of neuronal circuits in the mammalian neocortex. Restructuring of synaptic connections is believed to be one mechanism by which cortical circuits store information about the sensory world. Excitatory synaptic structures, such as dendritic spines, are dynamic entities that remain sensitive to alteration of sensory input throughout life. It remains unclear, however, whether structural changes at the level of dendritic spines can outlast the original experience and thereby provide a morphological basis for long-term information storage. Here we follow spine dynamics on apical dendrites of pyramidal neurons in functionally defined regions of adult mouse visual cortex during plasticity of eye-specific responses induced by repeated closure of one eye (monocular deprivation). The first monocular deprivation episode doubled the rate of spine formation, thereby increasing spine density. This effect was specific to layer-5 cells located in binocular cortex, where most neurons increase their responsiveness to the non-deprived eye. Restoring binocular vision returned spine dynamics to baseline levels, but absolute spine density remained elevated and many monocular deprivation-induced spines persisted during this period of functional recovery. However, spine addition did not increase again when the same eye was closed for a second time. This absence of structural plasticity stands out against the robust changes of eye-specific responses that occur even faster after repeated deprivation. Thus, spines added during the first monocular deprivation experience may provide a structural basis for subsequent functional shifts. These results provide a strong link between functional plasticity and specific synaptic rearrangements, revealing a mechanism of how prior experiences could be stored in cortical circuits.},
	Author = {Hofer, Sonja B and Mrsic-Flogel, Thomas D and Bonhoeffer, Tobias and H{\"u}bener, Mark},
	Date-Added = {2015-04-08 22:18:30 +0000},
	Date-Modified = {2015-04-08 22:20:25 +0000},
	Doi = {10.1038/nature07487},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {plasticity; Sensory Deprivation; structural remodeling; Structure-Activity Relationship; Visual Cortex; Neocortex; sensory map; topographic map},
	Mesh = {Animals; Dendrites; Mice; Mice, Inbred C57BL; Models, Neurological; Neural Pathways; Neuronal Plasticity; Pyramidal Cells; Vision, Binocular; Vision, Monocular; Visual Cortex},
	Month = {Jan},
	Number = {7227},
	Pages = {313-7},
	Pmid = {19005470},
	Pst = {ppublish},
	Title = {Experience leaves a lasting structural trace in cortical circuits},
	Volume = {457},
	Year = {2009},
	File = {papers/Hofer_Nature2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature07487}}

@article{Hofer:2010,
	Abstract = {Recent advances in multi-electrode recording and imaging techniques have made it possible to observe the activity of large populations of neurons. However, to take full advantage of these techniques, new methods for the analysis of population responses must be developed. In this paper, we present an algorithm for optimizing population decoding with distance metrics. To demonstrate the utility of this algorithm under experimental conditions, we evaluate its performance in decoding both population spike trains and calcium signals with different correlation structures. Our results demonstrate that the optimized decoder outperforms other simple population decoders and suggest that optimization could serve as a tool for quantifying the potential contribution of individual cells to the population code.},
	Author = {Hofer, Sonja B and Mrsic-Flogel, Thomas D and Horvath, Domonkos and Grothe, Benedikt and Lesica, Nicholas A},
	Date-Added = {2015-02-25 16:28:01 +0000},
	Date-Modified = {2015-02-25 16:28:01 +0000},
	Doi = {10.1016/j.neunet.2010.04.007},
	Journal = {Neural Netw},
	Journal-Full = {Neural networks : the official journal of the International Neural Network Society},
	Mesh = {Action Potentials; Algorithms; Animals; Computer Simulation; Electrophysiology; Gerbillinae; Nerve Net; Neural Networks (Computer); Neurons; Neurophysiology; Signal Processing, Computer-Assisted},
	Month = {Aug},
	Number = {6},
	Pages = {728-32},
	Pmid = {20488662},
	Pst = {ppublish},
	Title = {Optimization of population decoding with distance metrics},
	Volume = {23},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neunet.2010.04.007}}

@article{Mrsic-Flogel:2012,
	Author = {Mrsic-Flogel, Thomas D and Bonhoeffer, Tobias},
	Date-Added = {2015-02-25 16:27:47 +0000},
	Date-Modified = {2015-02-25 16:27:47 +0000},
	Doi = {10.1038/486041a},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Cell Communication; Cell Lineage; Electric Conductivity; Electrical Synapses; Female; Gap Junctions; Male; Neocortex; Neurons; Visual Cortex},
	Month = {Jun},
	Number = {7401},
	Pages = {41-2},
	Pmid = {22678277},
	Pst = {epublish},
	Title = {Neuroscience: Sibling neurons bond to share sensations},
	Volume = {486},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/486041a}}

@article{Han:2013,
	Author = {Han, Yunyun and Mrsic-Flogel, Thomas},
	Date-Added = {2015-02-25 16:27:40 +0000},
	Date-Modified = {2015-02-25 16:27:40 +0000},
	Doi = {10.1038/nn.3507},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Afferent Pathways; Animals; Auditory Cortex; Cerebral Cortex; Female; Linear Models; Male; Nerve Net; Neurons; Orientation; Sensory Receptor Cells; Thalamus; Visual Cortex; Visual Fields; Visual Pathways},
	Month = {Sep},
	Number = {9},
	Pages = {1166-8},
	Pmid = {23982448},
	Pst = {ppublish},
	Title = {A finely tuned cortical amplifier},
	Volume = {16},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.3507}}

@article{Pecka:2014,
	Abstract = {At eye opening, neurons in primary visual cortex (V1) are selective for stimulus features, but circuits continue to refine in an experience-dependent manner for some weeks thereafter. How these changes contribute to the coding of visual features embedded in complex natural scenes remains unknown. Here we show that normal visual experience after eye opening is required for V1 neurons to develop a sensitivity for the statistical structure of natural stimuli extending beyond the boundaries of their receptive fields (RFs), which leads to improvements in coding efficiency for full-field natural scenes (increased selectivity and information rate). These improvements are mediated by an experience-dependent increase in the effectiveness of natural surround stimuli to hyperpolarize the membrane potential specifically during RF-stimulus epochs triggering action potentials. We suggest that neural circuits underlying surround modulation are shaped by the statistical structure of visual input, which leads to more selective coding of features in natural scenes.},
	Author = {Pecka, Michael and Han, Yunyun and Sader, Elie and Mrsic-Flogel, Thomas D},
	Date-Added = {2015-02-25 16:27:32 +0000},
	Date-Modified = {2015-02-25 16:29:37 +0000},
	Doi = {10.1016/j.neuron.2014.09.010},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {visual system; Visual Cortex; sensory coding; excitatory; Patch-Clamp Techniques; Mouse; in vivo; sensory map;},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Mice, Inbred C57BL; Models, Neurological; Nervous System; Neurons; Photic Stimulation; Visual Cortex; Visual Fields; Visual Pathways; Visual Perception},
	Month = {Oct},
	Number = {2},
	Pages = {457-69},
	Pmc = {PMC4210638},
	Pmid = {25263755},
	Pst = {ppublish},
	Title = {Experience-dependent specialization of receptive field surround for selective coding of natural scenes},
	Volume = {84},
	Year = {2014},
	File = {papers/Pecka_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.09.010}}

@article{Cossell:2015,
	Abstract = {The strength of synaptic connections fundamentally determines how neurons influence each other's firing. Excitatory connection amplitudes between pairs of cortical neurons vary over two orders of magnitude, comprising only very few strong connections among many weaker ones. Although this highly skewed distribution of connection strengths is observed in diverse cortical areas, its functional significance remains unknown: it is not clear how connection strength relates to neuronal response properties, nor how strong and weak inputs contribute to information processing in local microcircuits. Here we reveal that the strength of connections between layer 2/3 (L2/3) pyramidal neurons in mouse primary visual cortex (V1) obeys a simple rule--the few strong connections occur between neurons with most correlated responses, while only weak connections link neurons with uncorrelated responses. Moreover, we show that strong and reciprocal connections occur between cells with similar spatial receptive field structure. Although weak connections far outnumber strong connections, each neuron receives the majority of its local excitation from a small number of strong inputs provided by the few neurons with similar responses to visual features. By dominating recurrent excitation, these infrequent yet powerful inputs disproportionately contribute to feature preference and selectivity. Therefore, our results show that the apparently complex organization of excitatory connection strength reflects the similarity of neuronal responses, and suggest that rare, strong connections mediate stimulus-specific response amplification in cortical microcircuits.},
	Author = {Cossell, Lee and Iacaruso, Maria Florencia and Muir, Dylan R and Houlton, Rachael and Sader, Elie N and Ko, Ho and Hofer, Sonja B and Mrsic-Flogel, Thomas D},
	Date-Added = {2015-02-25 16:25:50 +0000},
	Date-Modified = {2015-02-25 16:26:48 +0000},
	Doi = {10.1038/nature14182},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {visual system; Visual Cortex; functional connectivity; excitatory; Patch-Clamp Techniques; optical imaging; calcium imaging; Mouse; in vivo; sensory map;},
	Month = {Feb},
	Number = {7539},
	Pages = {399-403},
	Pmid = {25652823},
	Pst = {ppublish},
	Title = {Functional organization of excitatory synaptic strength in primary visual cortex},
	Volume = {518},
	Year = {2015},
	File = {papers/Cossell_Nature2015.pdf}}

@article{Harris:2013a,
	Abstract = {The sensory cortex contains a wide array of neuronal types, which are connected together into complex but partially stereotyped circuits. Sensory stimuli trigger cascades of electrical activity through these circuits, causing specific features of sensory scenes to be encoded in the firing patterns of cortical populations. Recent research is beginning to reveal how the connectivity of individual neurons relates to the sensory features they encode, how differences in the connectivity patterns of different cortical cell classes enable them to encode information using different strategies, and how feedback connections from higher-order cortex allow sensory information to be integrated with behavioural context.},
	Author = {Harris, Kenneth D and Mrsic-Flogel, Thomas D},
	Date-Added = {2015-02-25 16:05:04 +0000},
	Date-Modified = {2015-02-25 16:06:01 +0000},
	Doi = {10.1038/nature12654},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {review literature; behavior; sensory map; connectivity; neuron;; Visual Cortex; visual system},
	Mesh = {Animals; Auditory Cortex; Cerebral Cortex; Interneurons; Models, Neurological; Neural Pathways; Sensory Receptor Cells; Somatosensory Cortex; Visual Cortex},
	Month = {Nov},
	Number = {7474},
	Pages = {51-8},
	Pmid = {24201278},
	Pst = {ppublish},
	Title = {Cortical connectivity and sensory coding},
	Volume = {503},
	Year = {2013},
	File = {papers/Harris_Nature2013.pdf}}

@article{Mitra:1999,
	Abstract = {Modern imaging techniques for probing brain function, including functional magnetic resonance imaging, intrinsic and extrinsic contrast optical imaging, and magnetoencephalography, generate large data sets with complex content. In this paper we develop appropriate techniques for analysis and visualization of such imaging data to separate the signal from the noise and characterize the signal. The techniques developed fall into the general category of multivariate time series analysis, and in particular we extensively use the multitaper framework of spectral analysis. We develop specific protocols for the analysis of fMRI, optical imaging, and MEG data, and illustrate the techniques by applications to real data sets generated by these imaging modalities. In general, the analysis protocols involve two distinct stages: "noise" characterization and suppression, and "signal" characterization and visualization. An important general conclusion of our study is the utility of a frequency-based representation, with short, moving analysis windows to account for nonstationarity in the data. Of particular note are 1) the development of a decomposition technique (space-frequency singular value decomposition) that is shown to be a useful means of characterizing the image data, and 2) the development of an algorithm, based on multitaper methods, for the removal of approximately periodic physiological artifacts arising from cardiac and respiratory sources.},
	Author = {Mitra, P P and Pesaran, B},
	Date-Added = {2015-01-27 09:52:05 +0000},
	Date-Modified = {2015-01-27 11:22:12 +0000},
	Doi = {10.1016/S0006-3495(99)77236-X},
	Journal = {Biophys J},
	Journal-Full = {Biophysical journal},
	Keywords = {Brain; Fourier Analysis; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Magnetoencephalography; Multivariate Analysis; Computational Biology; optical imaging; neurophysiology; Mathematics; technique},
	Mesh = {Brain; Fourier Analysis; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Magnetoencephalography; Multivariate Analysis},
	Month = {Feb},
	Number = {2},
	Pages = {691-708},
	Pmc = {PMC1300074},
	Pmid = {9929474},
	Pst = {ppublish},
	Title = {Analysis of dynamic brain imaging data},
	Volume = {76},
	Year = {1999},
	File = {papers/Mitra_BiophysJ1999.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0006-3495(99)77236-X}}

@article{Sengupta:1999,
	Abstract = {The singular value decomposition is a matrix decomposition technique widely used in the analysis of multivariate data, such as complex space-time images obtained in both physical and biological systems. In this paper, we examine the distribution of singular values of low-rank matrices corrupted by additive noise. Past studies have been limited to uniform uncorrelated noise. Using diagrammatic and saddle point integration techniques, we extend these results to heterogeneous and correlated noise sources. We also provide perturbative estimates of error bars on the reconstructed low-rank matrix obtained by truncating a singular value decomposition.},
	Author = {Sengupta, A M and Mitra, P P},
	Date-Added = {2015-01-27 08:00:32 +0000},
	Date-Modified = {2015-01-27 08:00:32 +0000},
	Journal = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics},
	Journal-Full = {Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics},
	Month = {Sep},
	Number = {3},
	Pages = {3389-92},
	Pmid = {11970154},
	Pst = {ppublish},
	Title = {Distributions of singular values for some random matrices},
	Volume = {60},
	Year = {1999},
	File = {papers/Sengupta_PhysRevEStatPhysPlasmasFluidsRelatInterdiscipTopics1999.pdf}}

@article{Ben-Ari:2012a,
	Author = {Ben-Ari, Yehezkel},
	Date-Added = {2015-01-13 15:47:39 +0000},
	Date-Modified = {2015-01-13 15:47:39 +0000},
	Doi = {10.3389/fncel.2012.00045},
	Journal = {Front Cell Neurosci},
	Journal-Full = {Frontiers in cellular neuroscience},
	Pages = {45},
	Pmc = {PMC3494101},
	Pmid = {23162428},
	Pst = {epublish},
	Title = {The Yin and Yen of GABA in Brain Development and Operation in Health and Disease},
	Volume = {6},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fncel.2012.00045}}

@article{Ben-Ari:2012,
	Abstract = {DURING BRAIN DEVELOPMENT, THERE IS A PROGRESSIVE REDUCTION OF INTRACELLULAR CHLORIDE ASSOCIATED WITH A SHIFT IN GABA POLARITY: GABA depolarizes and occasionally excites immature neurons, subsequently hyperpolarizing them at later stages of development. This sequence, which has been observed in a wide range of animal species, brain structures and preparations, is thought to play an important role in activity-dependent formation and modulation of functional circuits. This sequence has also been considerably reinforced recently with new data pointing to an evolutionary preserved rule. In a recent "Hypothesis and Theory Article," the excitatory action of GABA in early brain development is suggested to be "an experimental artefact" (Bregestovski and Bernard, 2012). The authors suggest that the excitatory action of GABA is due to an inadequate/insufficient energy supply in glucose-perfused slices and/or to the damage produced by the slicing procedure. However, these observations have been repeatedly contradicted by many groups and are inconsistent with a large body of evidence including the fact that the developmental shift is neither restricted to slices nor to rodents. We summarize the overwhelming evidence in support of both excitatory GABA during development, and the implications this has in developmental neurobiology.},
	Author = {Ben-Ari, Yehezkel and Woodin, Melanie A and Sernagor, Evelyne and Cancedda, Laura and Vinay, Laurent and Rivera, Claudio and Legendre, Pascal and Luhmann, Heiko J and Bordey, Angelique and Wenner, Peter and Fukuda, Atsuo and van den Pol, Anthony N and Gaiarsa, Jean-Luc and Cherubini, Enrico},
	Date-Added = {2015-01-13 15:47:36 +0000},
	Date-Modified = {2015-01-13 15:47:36 +0000},
	Doi = {10.3389/fncel.2012.00035},
	Journal = {Front Cell Neurosci},
	Journal-Full = {Frontiers in cellular neuroscience},
	Keywords = {GABA; brain slices; chloride homeostasis; development; energy substrates; giant depolarizing potentials},
	Pages = {35},
	Pmc = {PMC3428604},
	Pmid = {22973192},
	Pst = {epublish},
	Title = {Refuting the challenges of the developmental shift of polarity of GABA actions: GABA more exciting than ever!},
	Volume = {6},
	Year = {2012},
	File = {papers/Ben-Ari_FrontCellNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fncel.2012.00035}}

@article{Deidda:2015,
	Abstract = {Hyperpolarizing and inhibitory GABA regulates critical periods for plasticity in sensory cortices. Here we examine the role of early, depolarizing GABA in the control of plasticity mechanisms. We report that brief interference with depolarizing GABA during early development prolonged critical-period plasticity in visual cortical circuits without affecting the overall development of the visual system. The effects on plasticity were accompanied by dampened inhibitory neurotransmission, downregulation of brain-derived neurotrophic factor (BDNF) expression and reduced density of extracellular matrix perineuronal nets. Early interference with depolarizing GABA decreased perinatal BDNF signaling, and a pharmacological increase of BDNF signaling during GABA interference rescued the effects on plasticity and its regulators later in life. We conclude that depolarizing GABA exerts a long-lasting, selective modulation of plasticity of cortical circuits by a strong crosstalk with BDNF.},
	Author = {Deidda, Gabriele and Allegra, Manuela and Cerri, Chiara and Naskar, Shovan and Bony, Guillaume and Zunino, Giulia and Bozzi, Yuri and Caleo, Matteo and Cancedda, Laura},
	Date-Added = {2015-01-13 15:44:16 +0000},
	Date-Modified = {2015-01-13 15:44:16 +0000},
	Doi = {10.1038/nn.3890},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Month = {Jan},
	Number = {1},
	Pages = {87-96},
	Pmid = {25485756},
	Pst = {ppublish},
	Title = {Early depolarizing GABA controls critical-period plasticity in the rat visual cortex},
	Volume = {18},
	Year = {2015},
	File = {papers/Deidda_NatNeurosci2015.pdf}}

@article{Liegeois:2010,
	Abstract = {Hemispherectomy (disconnection or removal of an entire cerebral hemisphere) is a rare surgical procedure used for the relief of drug-resistant epilepsy in children. After hemispherectomy, contralateral hemiplegia persists whereas gross expressive and receptive language functions can be remarkably spared. Motor speech deficits have rarely been examined systematically, thus limiting the accuracy of postoperative prognosis. We describe the speech profiles of hemispherectomized participants characterizing their intelligibility, articulation, phonological speech errors, dysarthric features, and execution and sequencing of orofacial speech and non-speech movements. Thirteen participants who had undergone hemispherectomy (six left, seven right; nine with congenital, four with acquired hemiplegia; operated between four months and 13 years) were investigated. Results showed that all participants were intelligible but showed a mild dysarthric profile characterized by neuromuscular asymmetry and reduced quality and coordination of movements, features that are characteristic of adult-onset unilateral upper motor neuron dysarthria, flaccid-ataxic variant. In addition, one left and four right hemispherectomy cases presented with impaired production of speech and non-speech sequences. No participant showed evidence of verbal or oral dyspraxia. It is concluded that mild dysarthria is persistent after left or right hemispherectomy, irrespective of age at onset of hemiplegia. These results indicate incomplete functional re-organization for the control of fine speech motor movements throughout childhood, and provide no evidence of hemispheric differences.},
	Author = {Li{\'e}geois, Fr{\'e}d{\'e}rique and Morgan, Angela T and Stewart, Lorna H and Helen Cross, J and Vogel, Adam P and Vargha-Khadem, Faraneh},
	Date-Added = {2014-12-12 20:31:05 +0000},
	Date-Modified = {2014-12-12 20:31:14 +0000},
	Doi = {10.1016/j.bandl.2009.12.004},
	Journal = {Brain Lang},
	Journal-Full = {Brain and language},
	Keywords = {HEMIPLEGIA; NEUROSURGERY; SPEECH; hemipshere; hemispherectomy; cerebral; cortex; cortical; human},
	Mesh = {Adolescent; Child; Child, Preschool; Dysarthria; Epilepsy; Female; Hemiplegia; Hemispherectomy; Humans; Infant; Language Development; Male; Neuronal Plasticity; Postoperative Complications; Recovery of Function; Speech; Speech Articulation Tests; Speech Intelligibility; Speech Perception; Young Adult},
	Month = {Aug},
	Number = {2},
	Pages = {126-34},
	Pmid = {20096448},
	Pst = {ppublish},
	Title = {Speech and oral motor profile after childhood hemispherectomy},
	Volume = {114},
	Year = {2010},
	File = {papers/Liégeois_BrainLang2010.pdf}}

@article{Basser:1962,
	Author = {Basser, L S},
	Date-Added = {2014-12-12 20:09:58 +0000},
	Date-Modified = {2016-01-13 18:16:44 +0000},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {HEMIPLEGIA; NEUROSURGERY; SPEECH; hemipshere; hemispherectomy; cerebral; cortex; cortical; human},
	Mesh = {Hemiplegia; Neurosurgery; Speech},
	Month = {Sep},
	Pages = {427-60},
	Pmid = {13969875},
	Pst = {ppublish},
	Title = {Hemiplegia of early onset and the faculty of speech with special reference to the effects of hemispherectomy},
	Volume = {85},
	Year = {1962},
	File = {papers/BASSER_Brain1962.pdf}}

@article{Ackman:2014c,
	Abstract = {The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity during early development that is vital for the formation and refinement of neural circuits. Identifying the source and flow of this activity locally and globally is critical for understanding principles guiding self-organization in the developing brain. Here we use whole brain transcranial optical imaging at high spatial and temporal resolution to demonstrate that dynamical patterns of neuronal activity in developing mouse neocortex consist of spatially discrete domains that are coordinated in an age, areal, and behavior- dependent fashion. Ongoing cortical activity displays mirror-symmetric activation patterns across the cerebral hemispheres and stereotyped network architectures that are shaped during development, with parietal-sensorimotor subnetworks functionally connected to occipital regions through frontal-medial cortical areas. This study provides the first broad description of population activity in the developing neocortex at a scope and scale that bridges the microscopic and macroscopic spatiotemporal resolutions provided by traditional neurophysiological and functional neuroimaging techniques. Mesoscale maps of cortical population dynamics within animal models will be crucial for future efforts to understand and treat neurodevelopmental disorders.},
	Author = {Ackman, James B and Zeng, Hongkui and Crair, Michael C},
	Date-Added = {2014-12-10 16:14:44 +0000},
	Date-Modified = {2017-12-01 02:11:23 +0000},
	Doi = {10.1101/012237},
	Journal = {bioRxiv},
	Month = {Dec},
	Title = {Structured dynamics of neural activity across developing neocortex},
	Year = {2014},
	File = {papers/Ackman_bioRxiv2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1101/012237}}

@article{Sakaki:1997,
	Abstract = {Depletion of intracellular Ca2+ stores induces a capacitative Ca2+ influx in non-neural cells. It has been unknown whether the capacitative Ca2+ influx occurs in the cells of nervous systems. We found the capacitative Ca2+ influx in the neural retina of early embryonic chick with Fura-2 fluorescence measurements. A Ca(2+)-free medium containing thapsigargin (500 nM), an inhibitor of Ca(2+)-ATPase of intracellular Ca2+ stores, was applied to the neural retina of embryonic day 3 (E3) chick. A rise in intracellular Ca2+ concentration was evoked after the reintroduction of extracellular Ca2+, and this Ca2+ rise was suppressed by Zn2+ (1 mM) and Ni2+ (5 mM). The developmental changes in the Ca2+ rise induced by thapsigargin (250 nM) were studied from E3 to E13. The thapsigargin-induced Ca2+ rise was largest at E3, declined rapidly toward E6, and then decreased gradually until E13, when the Ca2+ rise almost disappeared. This developmental profile correlated with the decline in the mitotic activities of the retinal cells studied by Prada et al. The fluorescence imaging with the vertical slice of the E9 retina showed that the site at which the thapsigargin-induced Ca2+ rise was largest was the most outer layer of the retina, where proliferating cells are located. This spatial distribution and the above developmental profile may suggest that the capacitative Ca2+ influx occurs at the early period of neurogenesis when the cells have mitotic activities.},
	Author = {Sakaki, Y and Sugioka, M and Fukuda, Y and Yamashita, M},
	Date-Added = {2014-12-09 21:38:47 +0000},
	Date-Modified = {2014-12-09 21:38:47 +0000},
	Journal = {J Neurobiol},
	Journal-Full = {Journal of neurobiology},
	Mesh = {Animals; Calcium; Chick Embryo; Electric Conductivity; Enzyme Inhibitors; Fluorescent Dyes; Fura-2; Neurons; Retina; Thapsigargin},
	Month = {Jan},
	Number = {1},
	Pages = {62-8},
	Pmid = {8989663},
	Pst = {ppublish},
	Title = {Capacitative Ca2+ influx in the neural retina of chick embryo},
	Volume = {32},
	Year = {1997},
	File = {papers/Sakaki_JNeurobiol1997.pdf}}

@article{Rash:2001,
	Abstract = {In many vertebrate and invertebrate systems, pioneering axons play a crucial role in establishing large axon tracts. Previous studies have addressed whether the first axons to cross the midline to from the corpus callosum arise from neurons in either the cingulate cortex (Koester and O'Leary [1994] J. Neurosci. 11:6608-6620) or the rostrolateral neocortex (Ozaki and Wahlsten [1998] J. Comp. Neurol. 400:197-206). However, these studies have not provided a consensus on which populations pioneer the corpus callosum. We have found that neurons within the cingulate cortex project axons that cross the midline and enter the contralateral hemisphere at E15.5. By using different carbocyanine dyes injected into either the cingulate cortex or the neocortex of the same brain, we found that cingulate axons crossed the midline before neocortical axons and projected into the contralateral cortex. Furthermore, the first neocortical axons to reach the midline crossed within the tract formed by these cingulate callosal axons, and appeared to fasciculate with them as they crossed the midline. These data indicate that axons from the cingulate cortex might pioneer a pathway for later arriving neocortical axons that form the corpus callosum. We also found that a small number of cingulate axons project to the septum as well as to the ipsilateral hippocampus via the fornix. In addition, we found that neurons in the cingulate cortex projected laterally to the rostrolateral neocortex at least 1 day before the neocortical axons reach the midline. Because the rostrolateral neocortex is the first neocortical region to develop, it sends the first neocortical axons to the midline to form the corpus callosum. We postulate that, together, both laterally and medially projecting cingulate axons may pioneer a path for the medially directed neocortical axons, thus helping to guide these axons toward and across the midline during the formation of the corpus callosum.},
	Author = {Rash, B G and Richards, L J},
	Date-Added = {2014-10-15 19:41:49 +0000},
	Date-Modified = {2014-10-15 19:41:49 +0000},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Age Factors; Animals; Carbocyanines; Cell Communication; Cell Differentiation; Corpus Callosum; Efferent Pathways; Female; Fetus; Fluorescent Dyes; Fornix, Brain; Functional Laterality; Growth Cones; Gyrus Cinguli; Hippocampus; Mice; Mice, Inbred C57BL; Neocortex; Pyridinium Compounds; Septal Nuclei},
	Month = {May},
	Number = {2},
	Pages = {147-57},
	Pmid = {11331522},
	Pst = {ppublish},
	Title = {A role for cingulate pioneering axons in the development of the corpus callosum},
	Volume = {434},
	Year = {2001}}

@article{Lee:2014,
	Abstract = {Sensory processing is dependent upon behavioral state. In mice, locomotion is accompanied by changes in cortical state and enhanced visual responses. Although recent studies have begun to elucidate intrinsic cortical mechanisms underlying this effect, the neural circuits that initially couple locomotion to cortical processing are unknown. The mesencephalic locomotor region (MLR) has been shown to be capable of initiating running and is associated with the ascending reticular activating system. Here, we find that optogenetic stimulation of the MLR in awake, head-fixed mice can induce both locomotion and increases in the gain of cortical responses. MLR stimulation below the threshold for overt movement similarly changed cortical processing, revealing that MLR's effects on cortex are dissociable from locomotion. Likewise, stimulation of MLR projections to the basal forebrain also enhanced cortical responses, suggesting a pathway linking the MLR to cortex. These studies demonstrate that the MLR regulates cortical state in parallel with locomotion.},
	Author = {Lee, A Moses and Hoy, Jennifer L and Bonci, Antonello and Wilbrecht, Linda and Stryker, Michael P and Niell, Cristopher M},
	Date-Added = {2014-10-09 12:55:29 +0000},
	Date-Modified = {2014-10-09 12:55:29 +0000},
	Doi = {10.1016/j.neuron.2014.06.031},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Brain Stem; Locomotion; Mesencephalon; Mice; Neural Pathways; Neurons; Photic Stimulation; Visual Cortex},
	Month = {Jul},
	Number = {2},
	Pages = {455-66},
	Pmc = {PMC4151326},
	Pmid = {25033185},
	Pst = {ppublish},
	Title = {Identification of a brainstem circuit regulating visual cortical state in parallel with locomotion},
	Volume = {83},
	Year = {2014},
	File = {papers/Lee_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.06.031}}

@article{Homae:2010,
	Abstract = {Human cognition and behaviors are subserved by global networks of neural mechanisms. Although the organization of the brain is a subject of interest, the process of development of global cortical networks in early infancy has not yet been clarified. In the present study, we explored developmental changes in these networks from several days to 6 months after birth by examining spontaneous fluctuations in brain activity, using multichannel near-infrared spectroscopy. We set up 94 measurement channels over the frontal, temporal, parietal, and occipital regions of the infant brain. The obtained signals showed complex time-series properties, which were characterized as 1/f fluctuations. To reveal the functional connectivity of the cortical networks, we calculated the temporal correlations of continuous signals between all the pairs of measurement channels. We found that the cortical network organization showed regional dependency and dynamic changes in the course of development. In the temporal, parietal, and occipital regions, connectivity increased between homologous regions in the two hemispheres and within hemispheres; in the frontal regions, it decreased progressively. Frontoposterior connectivity changed to a "U-shaped" pattern within 6 months: it decreases from the neonatal period to the age of 3 months and increases from the age of 3 months to the age of 6 months. We applied cluster analyses to the correlation coefficients and showed that the bilateral organization of the networks begins to emerge during the first 3 months of life. Our findings suggest that these developing networks, which form multiple clusters, are precursors of the functional cerebral architecture.},
	Author = {Homae, Fumitaka and Watanabe, Hama and Otobe, Takayuki and Nakano, Tamami and Go, Tohshin and Konishi, Yukuo and Taga, Gentaro},
	Date-Added = {2014-10-08 17:17:19 +0000},
	Date-Modified = {2014-10-09 12:54:32 +0000},
	Doi = {10.1523/JNEUROSCI.5618-09.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {resting-state connectivity; fMRI; network analysis; Graph theory; default mode network; human; development; birth},
	Mesh = {Age Factors; Brain Mapping; Cerebral Cortex; Female; Humans; Infant; Infant, Newborn; Male; Nerve Net},
	Month = {Apr},
	Number = {14},
	Pages = {4877-82},
	Pmid = {20371807},
	Pst = {ppublish},
	Title = {Development of global cortical networks in early infancy},
	Volume = {30},
	Year = {2010},
	File = {papers/Homae_JNeurosci2010.pdf}}

@article{Smyser:2010,
	Abstract = {Application of resting state functional connectivity magnetic resonance imaging (fcMRI) to the study of prematurely born infants enables assessment of the earliest forms of cerebral connectivity and characterization of its early development in the human brain. We obtained 90 longitudinal fcMRI data sets from a cohort of preterm infants aged from 26 weeks postmenstrual age (PMA) through term equivalent age at PMA-specific time points. Utilizing seed-based correlation analysis, we identified resting state networks involving varied cortical regions, the thalamus, and cerebellum. Identified networks demonstrated a regionally variable age-specific pattern of development, with more mature forms consisting of localized interhemispheric connections between homotopic counterparts. Anatomical distance was found to play a critical role in the rate of connection development. Prominent differences were noted between networks identified in term control versus premature infants at term equivalent, including in the thalamocortical connections critical for neurodevelopment. Putative precursors of the default mode network were detected in term control infants but were not identified in preterm infants, including those at term equivalent. Identified patterns of network maturation reflect the intricate relationship of structural and functional processes present throughout this important developmental period and are consistent with prior investigations of neurodevelopment in this population.},
	Author = {Smyser, Christopher D and Inder, Terrie E and Shimony, Joshua S and Hill, Jason E and Degnan, Andrew J and Snyder, Abraham Z and Neil, Jeffrey J},
	Date-Added = {2014-10-08 16:30:40 +0000},
	Date-Modified = {2014-10-08 16:34:33 +0000},
	Doi = {10.1093/cercor/bhq035},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {resting-state connectivity; fMRI; Human; network analysis; Graph theory; mirror symmetry; hemisphere; axon guidance; default mode network},
	Mesh = {Brain; Female; Humans; Image Interpretation, Computer-Assisted; Infant, Newborn; Magnetic Resonance Imaging; Male; Nerve Net; Neurogenesis; Pregnancy; Premature Birth},
	Month = {Dec},
	Number = {12},
	Pages = {2852-62},
	Pmc = {PMC2978240},
	Pmid = {20237243},
	Pst = {ppublish},
	Title = {Longitudinal analysis of neural network development in preterm infants},
	Volume = {20},
	Year = {2010},
	File = {papers/Smyser_CerebCortex2010.pdf}}

@article{Colonnese:2014,
	Abstract = {The ability to generate behaviorally appropriate cortical network states is central to sensory perception and plasticity, but little is known about the timing and mechanisms of their development. I paired intracellular and extracellular recordings in the visual cortex of awake infant rats to determine the synaptic and circuit mechanisms regulating the development of a key network state, the persistent and stable subthreshold membrane potential (Vm) depolarization associated with wakefulness/alertness in cortical networks, called the "desynchronized" or "activated" state. Current-clamp recordings reveal that the desynchronized state is absent during the first 2 postnatal weeks, despite behavioral wakefulness. During this period, Vm remains at the resting membrane potential >80% of the time, regardless of behavioral state. Vm dynamics during spontaneous or light-evoked activity were highly variable, contained long-duration supratheshold plateau potentials, and high spike probability, suggesting an unstable and hyperexcitable early cortical network. Voltage-clamp recordings reveal that effective feedforward inhibition is absent at these early ages despite the presence of feedback inhibition. Stable membrane depolarization during wakefulness finally emerges 1-2 d before eye opening and is statistically indistinguishable from that in adults within days. Reduced cortical excitability, fast feedforward inhibition, and the slow cortical oscillation appear simultaneously with stable depolarization, suggesting that an absence of inhibitory balance during early development prevents the expression of the active state and hence a normal wakeful state in early cortex. These observations identify feedforward inhibition as a potential key regulator of cortical network activity development.},
	Author = {Colonnese, Matthew T},
	Date-Added = {2014-10-03 14:37:13 +0000},
	Date-Modified = {2014-10-03 14:37:13 +0000},
	Doi = {10.1523/JNEUROSCI.3659-13.2014},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Action Potentials; Age Factors; Animals; Animals, Newborn; Cerebral Cortex; Cortical Synchronization; Eye; Female; Light; Male; Nerve Net; Neural Inhibition; Neurons; Patch-Clamp Techniques; Rats; Rats, Long-Evans; Sleep; Visual Pathways; Wakefulness},
	Month = {Apr},
	Number = {16},
	Pages = {5477-85},
	Pmc = {PMC3988407},
	Pmid = {24741038},
	Pst = {ppublish},
	Title = {Rapid developmental emergence of stable depolarization during wakefulness by inhibitory balancing of cortical network excitability},
	Volume = {34},
	Year = {2014},
	File = {papers/Colonnese_JNeurosci2014.pdf}}

@article{Colonnese:2012,
	Abstract = {The immature brain spontaneously expresses unique patterns of electrical activity that are believed to contribute to the development of neuronal networks. Certain electrographic features of this activity, particularly modulation on an infraslow time scale, resemble activity patterns observed in the mature brain at 'rest', loosely defined as the absence of an investigator imposed task. However, it is not clear whether the immature activity patterns observed at rest are precursors of the spontaneous neuronal activity that forms resting state networks in the adult. Here, we review recent studies that have explored the generative mechanisms of resting state activity during development in the primary sensory systems of premature human neonates and neonatal rodents. The remarkable hypothesis suggested by this work is that while resting state activity during the pre- and possibly near-term period can bear superficial resemblance to adult activity it is fundamentally different in terms of function and origin. During early development spontaneous thalamocortical activity in primary sensory regions is determined largely by transitory generators in the sensory periphery. This is in contrast to the adult, where spontaneous activity generated within thalamocortex, particularly by cortico-cortical connections, dominates. We therefore suggest a conservative interpretation of developmental mapping studies which are based on indirect measurement of activity (e.g. fMRI), or on the partitioning of EEG frequency using bands derived from adult studies. The generative mechanisms for brain activity at early ages are likely different from those of adults, and may play very different roles; for example in circuit formation as opposed to attention.},
	Author = {Colonnese, Matthew and Khazipov, Rustem},
	Date-Added = {2014-10-03 14:32:38 +0000},
	Date-Modified = {2014-10-03 14:36:15 +0000},
	Doi = {10.1016/j.neuroimage.2012.02.046},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Keywords = {review literature; resting-state fMRI; default mode network; development; Human},
	Mesh = {Animals; Brain; Brain Mapping; Humans; Magnetic Resonance Imaging; Rest},
	Month = {Oct},
	Number = {4},
	Pages = {2212-21},
	Pmid = {22387472},
	Pst = {ppublish},
	Title = {Spontaneous activity in developing sensory circuits: Implications for resting state fMRI},
	Volume = {62},
	Year = {2012},
	File = {papers/Colonnese_Neuroimage2012.pdf}}

@article{Newman:2006,
	Abstract = {Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets.},
	Author = {Newman, M E J},
	Date-Added = {2014-10-02 19:57:45 +0000},
	Date-Modified = {2014-10-02 19:58:32 +0000},
	Doi = {10.1073/pnas.0601602103},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {Graph theory; network analysis; Theoretical; Mathematics},
	Month = {Jun},
	Number = {23},
	Pages = {8577-82},
	Pmc = {PMC1482622},
	Pmid = {16723398},
	Pst = {ppublish},
	Title = {Modularity and community structure in networks},
	Volume = {103},
	Year = {2006},
	File = {papers/Newman_ProcNatlAcadSciUSA2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0601602103}}

@article{Bonacich:2007,
	Author = {Bonacich, P},
	Date-Added = {2014-10-01 22:01:09 +0000},
	Date-Modified = {2014-10-01 22:04:10 +0000},
	Journal = {Social Networks},
	Keywords = {Graph theory; network analysis; Mathematics; Theoretical},
	Pages = {555--564},
	Title = {Some unique properties of eigenvector centrality},
	Volume = {29},
	Year = {2007},
	File = {papers/Bonacich_SocialNetworks2007.pdf}}

@article{Bonacich:1972,
	Author = {Bonacich, P},
	Date-Added = {2014-10-01 21:53:37 +0000},
	Date-Modified = {2014-10-01 21:56:19 +0000},
	Journal = {Sociological Methodology},
	Keywords = {Graph theory; network analysis; Mathematics; Theoretical},
	Pages = {176--185},
	Title = {Technique for Analyzing Overlapping Memberships},
	Volume = {4},
	Year = {1972},
	File = {papers/Bonacich_SociologicalMethodology1972.pdf}}

@article{Bonacich:1987,
	Author = {Bonacich, P},
	Date-Added = {2014-10-01 21:51:14 +0000},
	Date-Modified = {2014-10-01 21:52:27 +0000},
	Journal = {American Journal of Sociology},
	Keywords = {Graph theory; network analysis; Mathematics; Theoretical},
	Pages = {1170-1182},
	Title = {Power and Centrality: A Family of Measures},
	Volume = {92},
	Year = {1987},
	File = {papers/Bonacich_AmericanJournalofSociology1987.pdf}}

@article{Lohmann:2010,
	Abstract = {Functional magnetic resonance data acquired in a task-absent condition ("resting state") require new data analysis techniques that do not depend on an activation model. In this work, we introduce an alternative assumption- and parameter-free method based on a particular form of node centrality called eigenvector centrality. Eigenvector centrality attributes a value to each voxel in the brain such that a voxel receives a large value if it is strongly correlated with many other nodes that are themselves central within the network. Google's PageRank algorithm is a variant of eigenvector centrality. Thus far, other centrality measures - in particular "betweenness centrality" - have been applied to fMRI data using a pre-selected set of nodes consisting of several hundred elements. Eigenvector centrality is computationally much more efficient than betweenness centrality and does not require thresholding of similarity values so that it can be applied to thousands of voxels in a region of interest covering the entire cerebrum which would have been infeasible using betweenness centrality. Eigenvector centrality can be used on a variety of different similarity metrics. Here, we present applications based on linear correlations and on spectral coherences between fMRI times series. This latter approach allows us to draw conclusions of connectivity patterns in different spectral bands. We apply this method to fMRI data in task-absent conditions where subjects were in states of hunger or satiety. We show that eigenvector centrality is modulated by the state that the subjects were in. Our analyses demonstrate that eigenvector centrality is a computationally efficient tool for capturing intrinsic neural architecture on a voxel-wise level.},
	Author = {Lohmann, Gabriele and Margulies, Daniel S and Horstmann, Annette and Pleger, Burkhard and Lepsien, Joeran and Goldhahn, Dirk and Schloegl, Haiko and Stumvoll, Michael and Villringer, Arno and Turner, Robert},
	Date-Added = {2014-10-01 21:12:08 +0000},
	Date-Modified = {2014-10-01 21:13:28 +0000},
	Doi = {10.1371/journal.pone.0010232},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {Graph theory; network analysis; fMRI; resting-state connectivity; Human},
	Mesh = {Algorithms; Brain Mapping; Humans; Hunger; Magnetic Resonance Imaging; Models, Neurological; Neural Pathways; Satiety Response},
	Number = {4},
	Pages = {e10232},
	Pmc = {PMC2860504},
	Pmid = {20436911},
	Pst = {epublish},
	Title = {Eigenvector centrality mapping for analyzing connectivity patterns in fMRI data of the human brain},
	Volume = {5},
	Year = {2010},
	File = {papers/Lohmann_PLoSOne2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0010232}}

@article{Kamada:1989,
	Author = {Kamada, T. and Kawai, S},
	Date-Added = {2014-10-01 20:02:32 +0000},
	Date-Modified = {2014-10-01 20:03:56 +0000},
	Journal = {Information Processing Letters},
	Number = {1},
	Pages = {7-15},
	Title = {An Algorithm for Drawing General Undirected Graphs},
	Volume = {31},
	Year = {1989},
	File = {papers/Kamada_InformationProcessingLetters1989.pdf}}

@article{Fruchterman:1991,
	Author = {Fruchterman, T.M.J. and Reingold, E.M.},
	Date-Added = {2014-10-01 20:00:19 +0000},
	Date-Modified = {2014-10-01 20:01:56 +0000},
	Journal = {Software - Practice and Experience},
	Number = {11},
	Pages = {1129-1164},
	Title = {Graph Drawing by Force-directed Placement},
	Volume = {21},
	Year = {1991},
	File = {papers/Fruchterman_Software-PracticeandExperience1991.pdf}}

@article{Stevens:2009,
	Abstract = {This study examined how the mutual interactions of functionally integrated neural networks during resting-state fMRI differed between adolescence and adulthood. Independent component analysis (ICA) was used to identify functionally connected neural networks in 100 healthy participants aged 12-30 years. Hemodynamic timecourses that represented integrated neural network activity were analyzed with tools that quantified system "causal density" estimates, which indexed the proportion of significant Granger causality relationships among system nodes. Mutual influences among networks decreased with age, likely reflecting stronger within-network connectivity and more efficient between-network influences with greater development. Supplemental tests showed that this normative age-related reduction in causal density was accompanied by fewer significant connections to and from each network, regional increases in the strength of functional integration within networks, and age-related reductions in the strength of numerous specific system interactions. The latter included paths between lateral prefrontal-parietal circuits and "default mode" networks. These results contribute to an emerging understanding that activity in widely distributed networks thought to underlie complex cognition influences activity in other networks.},
	Author = {Stevens, Michael C and Pearlson, Godfrey D and Calhoun, Vince D},
	Date-Added = {2014-09-26 21:18:24 +0000},
	Date-Modified = {2014-09-26 21:19:08 +0000},
	Doi = {10.1002/hbm.20673},
	Journal = {Hum Brain Mapp},
	Journal-Full = {Human brain mapping},
	Keywords = {resting-state fMRI; connectivity; development; human; default mode network; Human; Child; development},
	Mesh = {Adolescent; Adolescent Development; Adult; Aging; Brain; Child; Female; Humans; Magnetic Resonance Imaging; Male; Neural Pathways; Regression Analysis; Rest; Young Adult},
	Month = {Aug},
	Number = {8},
	Pages = {2356-66},
	Pmid = {19172655},
	Pst = {ppublish},
	Title = {Changes in the interaction of resting-state neural networks from adolescence to adulthood},
	Volume = {30},
	Year = {2009},
	File = {papers/Stevens_HumBrainMapp2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/hbm.20673}}

@article{Cao:2014,
	Abstract = {Human brain function undergoes complex transformations across the lifespan. We employed resting-state functional MRI and graph-theory approaches to systematically chart the lifespan trajectory of the topological organization of human whole-brain functional networks in 126 healthy individuals ranging in age from 7 to 85 years. Brain networks were constructed by computing Pearson's correlations in blood-oxygenation-level-dependent temporal fluctuations among 1024 parcellation units followed by graph-based network analyses. We observed that the human brain functional connectome exhibited highly preserved non-random modular and rich club organization over the entire age range studied. Further quantitative analyses revealed linear decreases in modularity and inverted-U shaped trajectories of local efficiency and rich club architecture. Regionally heterogeneous age effects were mainly located in several hubs (e.g., default network, dorsal attention regions). Finally, we observed inverse trajectories of long- and short-distance functional connections, indicating that the reorganization of connectivity concentrates and distributes the brain's functional networks. Our results demonstrate topological changes in the whole-brain functional connectome across nearly the entire human lifespan, providing insights into the neural substrates underlying individual variations in behavior and cognition. These results have important implications for disease connectomics because they provide a baseline for evaluating network impairments in age-related neuropsychiatric disorders.},
	Author = {Cao, Miao and Wang, Jin-Hui and Dai, Zheng-Jia and Cao, Xiao-Yan and Jiang, Li-Li and Fan, Feng-Mei and Song, Xiao-Wei and Xia, Ming-Rui and Shu, Ni and Dong, Qi and Milham, Michael P and Castellanos, F Xavier and Zuo, Xi-Nian and He, Yong},
	Date-Added = {2014-09-26 21:15:20 +0000},
	Date-Modified = {2014-09-26 21:16:24 +0000},
	Doi = {10.1016/j.dcn.2013.11.004},
	Journal = {Dev Cogn Neurosci},
	Journal-Full = {Developmental cognitive neuroscience},
	Keywords = {Functional connectomics; Graph theory; Lifespan trajectory; Rich club; network analysis; resting-state fMRI; human; adult; development; Child},
	Mesh = {Adolescent; Adult; Age Factors; Aged; Aged, 80 and over; Aging; Brain; Brain Mapping; Child; Cognition; Connectome; Female; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Nerve Net; Sex Factors},
	Month = {Jan},
	Pages = {76-93},
	Pmid = {24333927},
	Pst = {ppublish},
	Title = {Topological organization of the human brain functional connectome across the lifespan},
	Volume = {7},
	Year = {2014},
	File = {papers/Cao_DevCognNeurosci2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.dcn.2013.11.004}}

@article{He:2009,
	Abstract = {The characterization of topological architecture of complex brain networks is one of the most challenging issues in neuroscience. Slow (<0.1 Hz), spontaneous fluctuations of the blood oxygen level dependent (BOLD) signal in functional magnetic resonance imaging are thought to be potentially important for the reflection of spontaneous neuronal activity. Many studies have shown that these fluctuations are highly coherent within anatomically or functionally linked areas of the brain. However, the underlying topological mechanisms responsible for these coherent intrinsic or spontaneous fluctuations are still poorly understood. Here, we apply modern network analysis techniques to investigate how spontaneous neuronal activities in the human brain derived from the resting-state BOLD signals are topologically organized at both the temporal and spatial scales. We first show that the spontaneous brain functional networks have an intrinsically cohesive modular structure in which the connections between regions are much denser within modules than between them. These identified modules are found to be closely associated with several well known functionally interconnected subsystems such as the somatosensory/motor, auditory, attention, visual, subcortical, and the "default" system. Specifically, we demonstrate that the module-specific topological features can not be captured by means of computing the corresponding global network parameters, suggesting a unique organization within each module. Finally, we identify several pivotal network connectors and paths (predominantly associated with the association and limbic/paralimbic cortex regions) that are vital for the global coordination of information flow over the whole network, and we find that their lesions (deletions) critically affect the stability and robustness of the brain functional system. Together, our results demonstrate the highly organized modular architecture and associated topological properties in the temporal and spatial brain functional networks of the human brain that underlie spontaneous neuronal dynamics, which provides important implications for our understanding of how intrinsically coherent spontaneous brain activity has evolved into an optimal neuronal architecture to support global computation and information integration in the absence of specific stimuli or behaviors.},
	Author = {He, Yong and Wang, Jinhui and Wang, Liang and Chen, Zhang J and Yan, Chaogan and Yang, Hong and Tang, Hehan and Zhu, Chaozhe and Gong, Qiyong and Zang, Yufeng and Evans, Alan C},
	Date-Added = {2014-09-26 20:52:03 +0000},
	Date-Modified = {2014-09-26 20:53:42 +0000},
	Doi = {10.1371/journal.pone.0005226},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {resting-state fMRI; human; Spontaneous activity; default mode network; connectivity; graph theory; network analysis},
	Mesh = {Brain; Humans; Reproducibility of Results},
	Number = {4},
	Pages = {e5226},
	Pmc = {PMC2668183},
	Pmid = {19381298},
	Pst = {ppublish},
	Title = {Uncovering intrinsic modular organization of spontaneous brain activity in humans},
	Volume = {4},
	Year = {2009},
	File = {papers/He_PLoSOne2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0005226}}

@article{Andrews-Hanna:2010,
	Abstract = {One of the most consistent observations in human functional imaging is that a network of brain regions referred to as the "default network" increases its activity during passive states. Here we explored the anatomy and function of the default network across three studies to resolve divergent hypotheses about its contributions to spontaneous cognition and active forms of decision making. Analysis of intrinsic activity revealed the network comprises multiple, dissociated components. A midline core (posterior cingulate and anterior medial prefrontal cortex) is active when people make self-relevant, affective decisions. In contrast, a medial temporal lobe subsystem becomes engaged when decisions involve constructing a mental scene based on memory. During certain experimentally directed and spontaneous acts of future-oriented thought, these dissociated components are simultaneously engaged, presumably to facilitate construction of mental models of personally significant events.},
	Author = {Andrews-Hanna, Jessica R and Reidler, Jay S and Sepulcre, Jorge and Poulin, Renee and Buckner, Randy L},
	Date-Added = {2014-09-26 20:10:24 +0000},
	Date-Modified = {2014-09-26 20:12:28 +0000},
	Doi = {10.1016/j.neuron.2010.02.005},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {resting-state fMRI; default mode network; human; network analysis; graph theory; Adult; connectivity},
	Mesh = {Adolescent; Adult; Analysis of Variance; Brain; Brain Mapping; Cluster Analysis; Cognition; Emotions; Female; Humans; Image Processing, Computer-Assisted; Imagination; Magnetic Resonance Imaging; Male; Memory; Nerve Net; Neuropsychological Tests},
	Month = {Feb},
	Number = {4},
	Pages = {550-62},
	Pmc = {PMC2848443},
	Pmid = {20188659},
	Pst = {ppublish},
	Title = {Functional-anatomic fractionation of the brain's default network},
	Volume = {65},
	Year = {2010},
	File = {papers/Andrews-Hanna_Neuron2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2010.02.005}}

@article{Thomason:2014,
	Abstract = {The human brain undergoes dramatic maturational changes during late stages of fetal and early postnatal life. The importance of this period to the establishment of healthy neural connectivity is apparent in the high incidence of neural injury in preterm infants, in whom untimely exposure to ex-uterine factors interrupts neural connectivity. Though the relevance of this period to human neuroscience is apparent, little is known about functional neural networks in human fetal life. Here, we apply graph theoretical analysis to examine human fetal brain connectivity. Utilizing resting state functional magnetic resonance imaging (fMRI) data from 33 healthy human fetuses, 19 to 39 weeks gestational age (GA), our analyses reveal that the human fetal brain has modular organization and modules overlap functional systems observed postnatally. Age-related differences between younger (GA <31 weeks) and older (GA≥31 weeks) fetuses demonstrate that brain modularity decreases, and connectivity of the posterior cingulate to other brain networks becomes more negative, with advancing GA. By mimicking functional principles observed postnatally, these results support early emerging capacity for information processing in the human fetal brain. Current technical limitations, as well as the potential for fetal fMRI to one day produce major discoveries about fetal origins or antecedents of neural injury or disease are discussed.},
	Author = {Thomason, Moriah E and Brown, Jesse A and Dassanayake, Maya T and Shastri, Rupal and Marusak, Hilary A and Hernandez-Andrade, Edgar and Yeo, Lami and Mody, Swati and Berman, Susan and Hassan, Sonia S and Romero, Roberto},
	Date-Added = {2014-09-26 18:19:58 +0000},
	Date-Modified = {2014-09-26 18:19:58 +0000},
	Doi = {10.1371/journal.pone.0094423},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Number = {5},
	Pages = {e94423},
	Pmc = {PMC4006774},
	Pmid = {24788455},
	Pst = {epublish},
	Title = {Intrinsic functional brain architecture derived from graph theoretical analysis in the human fetus},
	Volume = {9},
	Year = {2014},
	File = {papers/Thomason_PLoSOne2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0094423}}

@article{Thomason:2013,
	Abstract = {Compelling evidence indicates that psychiatric and developmental disorders are generally caused by disruptions in the functional connectivity (FC) of brain networks. Events occurring during development, and in particular during fetal life, have been implicated in the genesis of such disorders. However, the developmental timetable for the emergence of neural FC during human fetal life is unknown. We present the results of resting-state functional magnetic resonance imaging performed in 25 healthy human fetuses in the second and third trimesters of pregnancy (24 to 38 weeks of gestation). We report the presence of bilateral fetal brain FC and regional and age-related variation in FC. Significant bilateral connectivity was evident in half of the 42 areas tested, and the strength of FC between homologous cortical brain regions increased with advancing gestational age. We also observed medial to lateral gradients in fetal functional brain connectivity. These findings improve understanding of human fetal central nervous system development and provide a basis for examining the role of insults during fetal life in the subsequent development of disorders in neural FC.},
	Author = {Thomason, Moriah E and Dassanayake, Maya T and Shen, Stephen and Katkuri, Yashwanth and Alexis, Mitchell and Anderson, Amy L and Yeo, Lami and Mody, Swati and Hernandez-Andrade, Edgar and Hassan, Sonia S and Studholme, Colin and Jeong, Jeong-Won and Romero, Roberto},
	Date-Added = {2014-09-26 17:28:35 +0000},
	Date-Modified = {2014-09-26 17:29:34 +0000},
	Doi = {10.1126/scitranslmed.3004978},
	Journal = {Sci Transl Med},
	Journal-Full = {Science translational medicine},
	Keywords = {human; fetal; fMRI; resting-state connectivity; default mode network; hemisphere; activity-development; wholeBrain},
	Mesh = {Brain; Female; Humans; Magnetic Resonance Imaging; Neural Pathways; Pregnancy},
	Month = {Feb},
	Number = {173},
	Pages = {173ra24},
	Pmc = {PMC3618956},
	Pmid = {23427244},
	Pst = {ppublish},
	Title = {Cross-hemispheric functional connectivity in the human fetal brain},
	Volume = {5},
	Year = {2013},
	File = {papers/Thomason_SciTranslMed2013.pdf},
	Bdsk-File-2 = {papers/Thomason_SciTranslMed2013a.pdf}}

@article{Zuo:2012,
	Abstract = {The network architecture of functional connectivity within the human brain connectome is poorly understood at the voxel level. Here, using resting state functional magnetic resonance imaging data from 1003 healthy adults, we investigate a broad array of network centrality measures to provide novel insights into connectivity within the whole-brain functional network (i.e., the functional connectome). We first assemble and visualize the voxel-wise (4 mm) functional connectome as a functional network. We then demonstrate that each centrality measure captures different aspects of connectivity, highlighting the importance of considering both global and local connectivity properties of the functional connectome. Beyond "detecting functional hubs," we treat centrality as measures of functional connectivity within the brain connectome and demonstrate their reliability and phenotypic correlates (i.e., age and sex). Specifically, our analyses reveal age-related decreases in degree centrality, but not eigenvector centrality, within precuneus and posterior cingulate regions. This implies that while local or (direct) connectivity decreases with age, connections with hub-like regions within the brain remain stable with age at a global level. In sum, these findings demonstrate the nonredundancy of various centrality measures and raise questions regarding their underlying physiological mechanisms that may be relevant to the study of neurodegenerative and psychiatric disorders.},
	Author = {Zuo, Xi-Nian and Ehmke, Ross and Mennes, Maarten and Imperati, Davide and Castellanos, F Xavier and Sporns, Olaf and Milham, Michael P},
	Date-Added = {2014-09-23 16:31:59 +0000},
	Date-Modified = {2014-09-23 16:34:14 +0000},
	Doi = {10.1093/cercor/bhr269},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {resting-state fMRI; connectivity; graph theory; network analysis; Human; adult},
	Mesh = {Adult; Aging; Algorithms; Brain; Brain Mapping; Female; Humans; Magnetic Resonance Imaging; Male; Nerve Net; Neural Pathways; Sex Characteristics},
	Month = {Aug},
	Number = {8},
	Pages = {1862-75},
	Pmid = {21968567},
	Pst = {ppublish},
	Title = {Network centrality in the human functional connectome},
	Volume = {22},
	Year = {2012},
	File = {papers/Zuo_CerebCortex2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhr269}}

@article{Heuvel:2009,
	Abstract = {During rest, multiple cortical brain regions are functionally linked forming resting-state networks. This high level of functional connectivity within resting-state networks suggests the existence of direct neuroanatomical connections between these functionally linked brain regions to facilitate the ongoing interregional neuronal communication. White matter tracts are the structural highways of our brain, enabling information to travel quickly from one brain region to another region. In this study, we examined both the functional and structural connections of the human brain in a group of 26 healthy subjects, combining 3 Tesla resting-state functional magnetic resonance imaging time-series with diffusion tensor imaging scans. Nine consistently found functionally linked resting-state networks were retrieved from the resting-state data. The diffusion tensor imaging scans were used to reconstruct the white matter pathways between the functionally linked brain areas of these resting-state networks. Our results show that well-known anatomical white matter tracts interconnect at least eight of the nine commonly found resting-state networks, including the default mode network, the core network, primary motor and visual network, and two lateralized parietal-frontal networks. Our results suggest that the functionally linked resting-state networks reflect the underlying structural connectivity architecture of the human brain.},
	Author = {van den Heuvel, Martijn P and Mandl, Ren{\'e} C W and Kahn, Ren{\'e} S and Hulshoff Pol, Hilleke E},
	Date-Added = {2014-09-23 16:23:45 +0000},
	Date-Modified = {2014-09-23 16:24:41 +0000},
	Doi = {10.1002/hbm.20737},
	Journal = {Hum Brain Mapp},
	Journal-Full = {Human brain mapping},
	Keywords = {resting-state fMRI; connectivity; network analysis; graph theory; human; adult},
	Mesh = {Adolescent; Adult; Brain; Brain Mapping; Diffusion Magnetic Resonance Imaging; Female; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Models, Neurological; Nerve Fibers, Myelinated; Nerve Net; Neural Pathways; Oxygen; Rest; Young Adult},
	Month = {Oct},
	Number = {10},
	Pages = {3127-41},
	Pmid = {19235882},
	Pst = {ppublish},
	Title = {Functionally linked resting-state networks reflect the underlying structural connectivity architecture of the human brain},
	Volume = {30},
	Year = {2009},
	File = {papers/Heuvel_HumBrainMapp2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/hbm.20737}}

@article{Damoiseaux:2006,
	Abstract = {Functional MRI (fMRI) can be applied to study the functional connectivity of the human brain. It has been suggested that fluctuations in the blood oxygenation level-dependent (BOLD) signal during rest reflect the neuronal baseline activity of the brain, representing the state of the human brain in the absence of goal-directed neuronal action and external input, and that these slow fluctuations correspond to functionally relevant resting-state networks. Several studies on resting fMRI have been conducted, reporting an apparent similarity between the identified patterns. The spatial consistency of these resting patterns, however, has not yet been evaluated and quantified. In this study, we apply a data analysis approach called tensor probabilistic independent component analysis to resting-state fMRI data to find coherencies that are consistent across subjects and sessions. We characterize and quantify the consistency of these effects by using a bootstrapping approach, and we estimate the BOLD amplitude modulation as well as the voxel-wise cross-subject variation. The analysis found 10 patterns with potential functional relevance, consisting of regions known to be involved in motor function, visual processing, executive functioning, auditory processing, memory, and the so-called default-mode network, each with BOLD signal changes up to 3%. In general, areas with a high mean percentage BOLD signal are consistent and show the least variation around the mean. These findings show that the baseline activity of the brain is consistent across subjects exhibiting significant temporal dynamics, with percentage BOLD signal change comparable with the signal changes found in task-related experiments.},
	Author = {Damoiseaux, J S and Rombouts, S A R B and Barkhof, F and Scheltens, P and Stam, C J and Smith, S M and Beckmann, C F},
	Date-Added = {2014-09-23 16:15:01 +0000},
	Date-Modified = {2014-09-23 16:22:19 +0000},
	Doi = {10.1073/pnas.0601417103},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {resting-state fMRI; connectivity; default mode network; network; human},
	Mesh = {Brain; Brain Mapping; Health; Humans; Magnetic Resonance Imaging; Rest},
	Month = {Sep},
	Number = {37},
	Pages = {13848-53},
	Pmc = {PMC1564249},
	Pmid = {16945915},
	Pst = {ppublish},
	Title = {Consistent resting-state networks across healthy subjects},
	Volume = {103},
	Year = {2006},
	File = {papers/Damoiseaux_ProcNatlAcadSciUSA2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0601417103}}

@article{Salvador:2005,
	Abstract = {We investigated large-scale systems organization of the whole human brain using functional magnetic resonance imaging (fMRI) data acquired from healthy volunteers in a no-task or 'resting' state. Images were parcellated using a prior anatomical template, yielding regional mean time series for each of 90 regions (major cortical gyri and subcortical nuclei) in each subject. Significant pairwise functional connections, defined by the group mean inter-regional partial correlation matrix, were mostly either local and intrahemispheric or symmetrically interhemispheric. Low-frequency components in the time series subtended stronger inter-regional correlations than high-frequency components. Intrahemispheric connectivity was generally related to anatomical distance by an inverse square law; many symmetrical interhemispheric connections were stronger than predicted by the anatomical distance between bilaterally homologous regions. Strong interhemispheric connectivity was notably absent in data acquired from a single patient, minimally conscious following a brainstem lesion. Multivariate analysis by hierarchical clustering and multidimensional scaling consistently defined six major systems in healthy volunteers-- corresponding approximately to four neocortical lobes, medial temporal lobe and subcortical nuclei- - that could be further decomposed into anatomically and functionally plausible subsystems, e.g. dorsal and ventral divisions of occipital cortex. An undirected graph derived by thresholding the healthy group mean partial correlation matrix demonstrated local clustering or cliquishness of connectivity and short mean path length compatible with prior data on small world characteristics of non-human cortical anatomy. Functional MRI demonstrates a neurophysiological architecture of the normal human brain that is anatomically sensible, strongly symmetrical, disrupted by acute brain injury, subtended predominantly by low frequencies and consistent with a small world network topology.},
	Author = {Salvador, Raymond and Suckling, John and Coleman, Martin R and Pickard, John D and Menon, David and Bullmore, Ed},
	Date-Added = {2014-09-23 16:01:55 +0000},
	Date-Modified = {2014-09-23 16:02:57 +0000},
	Doi = {10.1093/cercor/bhi016},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {resting-state fMRI; connectivity; graph theory; network analysis; Neocortex; Human; default mode network},
	Mesh = {Adult; Algorithms; Brain; Brain Stem; Cerebral Cortex; Cerebrovascular Circulation; Cluster Analysis; Echo-Planar Imaging; Female; Functional Laterality; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Middle Aged; Models, Neurological; Multivariate Analysis; Nerve Net},
	Month = {Sep},
	Number = {9},
	Pages = {1332-42},
	Pmid = {15635061},
	Pst = {ppublish},
	Title = {Neurophysiological architecture of functional magnetic resonance images of human brain},
	Volume = {15},
	Year = {2005},
	File = {papers/Salvador_CerebCortex2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhi016}}

@article{Fair:2009,
	Abstract = {The mature human brain is organized into a collection of specialized functional networks that flexibly interact to support various cognitive functions. Studies of development often attempt to identify the organizing principles that guide the maturation of these functional networks. In this report, we combine resting state functional connectivity MRI (rs-fcMRI), graph analysis, community detection, and spring-embedding visualization techniques to analyze four separate networks defined in earlier studies. As we have previously reported, we find, across development, a trend toward 'segregation' (a general decrease in correlation strength) between regions close in anatomical space and 'integration' (an increased correlation strength) between selected regions distant in space. The generalization of these earlier trends across multiple networks suggests that this is a general developmental principle for changes in functional connectivity that would extend to large-scale graph theoretic analyses of large-scale brain networks. Communities in children are predominantly arranged by anatomical proximity, while communities in adults predominantly reflect functional relationships, as defined from adult fMRI studies. In sum, over development, the organization of multiple functional networks shifts from a local anatomical emphasis in children to a more "distributed" architecture in young adults. We argue that this "local to distributed" developmental characterization has important implications for understanding the development of neural systems underlying cognition. Further, graph metrics (e.g., clustering coefficients and average path lengths) are similar in child and adult graphs, with both showing "small-world"-like properties, while community detection by modularity optimization reveals stable communities within the graphs that are clearly different between young children and young adults. These observations suggest that early school age children and adults both have relatively efficient systems that may solve similar information processing problems in divergent ways.},
	Author = {Fair, Damien A and Cohen, Alexander L and Power, Jonathan D and Dosenbach, Nico U F and Church, Jessica A and Miezin, Francis M and Schlaggar, Bradley L and Petersen, Steven E},
	Date-Added = {2014-09-22 20:50:37 +0000},
	Date-Modified = {2014-09-22 20:53:22 +0000},
	Doi = {10.1371/journal.pcbi.1000381},
	Journal = {PLoS Comput Biol},
	Journal-Full = {PLoS computational biology},
	Keywords = {resting-state fMRI; connectivity; graph theory; network analysis; human; development; Child; Adult; default mode network},
	Mesh = {Adolescent; Adult; Brain; Child; Humans; Magnetic Resonance Imaging; Models, Neurological; Nerve Net; Neural Pathways},
	Month = {May},
	Number = {5},
	Pages = {e1000381},
	Pmc = {PMC2671306},
	Pmid = {19412534},
	Pst = {ppublish},
	Title = {Functional brain networks develop from a "local to distributed" organization},
	Volume = {5},
	Year = {2009},
	File = {papers/Fair_PLoSComputBiol2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1000381}}

@article{Gao:2009,
	Abstract = {Several lines of evidence have implicated the existence of the brain's default network during passive or undirected mental states. Nevertheless, results on the emergence of the default network in very young pediatric subjects are lacking. Using resting functional magnetic resonance imaging in healthy pediatric subjects between 2 weeks and 2 years of age, we describe the temporal evolution of the default network in a critical, previously unstudied, period of early human brain development. Our results demonstrate that a primitive and incomplete default network is present in 2-week-olds, followed by a marked increase in the number of brain regions exhibiting connectivity, and the percent of connection at 1 year of age. By 2 years of age, the default network becomes similar to that observed in adults, including medial prefrontal cortex (MPFC), posterior cingulate cortex/retrosplenial (PCC/Rsp), inferior parietal lobule, lateral temporal cortex, and hippocampus regions. While the anatomical representations of the default network highly depend on age, the PCC/Rsp is consistently observed at in both age groups and is central to the most and strongest connections of the default network, suggesting that PCC/Rsp may serve as the main "hub" of the default network as this region does in adults. In addition, although not as remarkable as the PCC/Rsp, the MPFC also emerges as a potential secondary hub starting from 1 year of age. These findings reveal the temporal development of the default network in the critical period of early brain development and offer new insights into the emergence of brain default network.},
	Author = {Gao, Wei and Zhu, Hongtu and Giovanello, Kelly S and Smith, J Keith and Shen, Dinggang and Gilmore, John H and Lin, Weili},
	Date-Added = {2014-09-22 20:28:02 +0000},
	Date-Modified = {2014-09-22 20:28:02 +0000},
	Doi = {10.1073/pnas.0811221106},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Adult; Age Distribution; Brain; Child, Preschool; Female; Humans; Infant; Infant, Newborn; Male; Nerve Net},
	Month = {Apr},
	Number = {16},
	Pages = {6790-5},
	Pmc = {PMC2672537},
	Pmid = {19351894},
	Pst = {ppublish},
	Title = {Evidence on the emergence of the brain's default network from 2-week-old to 2-year-old healthy pediatric subjects},
	Volume = {106},
	Year = {2009},
	File = {papers/Gao_ProcNatlAcadSciUSA2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0811221106}}

@article{Goldman-Rakic:1988,
	Author = {Goldman-Rakic, P S},
	Date-Added = {2014-09-22 20:17:48 +0000},
	Date-Modified = {2014-09-22 20:17:48 +0000},
	Doi = {10.1146/annurev.ne.11.030188.001033},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Mesh = {Animals; Association; Cerebral Cortex; Cognition; Humans; Neural Pathways; Primates; Psychomotor Performance},
	Pages = {137-56},
	Pmid = {3284439},
	Pst = {ppublish},
	Title = {Topography of cognition: parallel distributed networks in primate association cortex},
	Volume = {11},
	Year = {1988},
	File = {papers/Goldman-Rakic_AnnuRevNeurosci1988.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.ne.11.030188.001033}}

@article{Shi:2012,
	Abstract = {Recently, an increasing body of evidence suggests that developmental abnormalities related to schizophrenia may occur as early as the neonatal stage. Impairments of brain gray matter and wiring problems of axonal fibers are commonly suspected to be responsible for the disconnection hypothesis in schizophrenia adults, but significantly less is known in neonates. In this study, we investigated 26 neonates who were at genetic risk for schizophrenia and 26 demographically matched healthy neonates using both morphological and white matter networks to examine possible brain connectivity abnormalities. The results showed that both populations exhibited small-world network topology. Morphological network analysis indicated that the brain structural associations of the high-risk neonates tended to have globally lower efficiency, longer connection distance, and less number of hub nodes and edges with relatively higher betweenness. Subgroup analysis showed that male neonates were significantly disease-affected, while the female neonates were not. White matter network analysis, however, showed that the fiber networks were globally unaffected, although several subcortical-cortical connections had significantly less number of fibers in high-risk neonates. This study provides new lines of evidence in support of the disconnection hypothesis, reinforcing the notion that the genetic risk of schizophrenia induces alterations in both gray matter structural associations and white matter connectivity.},
	Author = {Shi, Feng and Yap, Pew-Thian and Gao, Wei and Lin, Weili and Gilmore, John H and Shen, Dinggang},
	Date-Added = {2014-09-22 20:12:06 +0000},
	Date-Modified = {2014-09-22 20:12:54 +0000},
	Doi = {10.1016/j.neuroimage.2012.05.026},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Keywords = {structural connectivity; DTI; infant; Human; development; Schizophrenia; graph theory; network analysis},
	Mesh = {Brain; Diffusion Magnetic Resonance Imaging; Female; Genetic Predisposition to Disease; Humans; Image Interpretation, Computer-Assisted; Infant, Newborn; Male; Neural Pathways; Risk Factors; Schizophrenia},
	Month = {Sep},
	Number = {3},
	Pages = {1622-33},
	Pmc = {PMC3408572},
	Pmid = {22613620},
	Pst = {ppublish},
	Title = {Altered structural connectivity in neonates at genetic risk for schizophrenia: a combined study using morphological and white matter networks},
	Volume = {62},
	Year = {2012},
	File = {papers/Shi_Neuroimage2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2012.05.026}}

@article{Hagmann:2010,
	Abstract = {From toddler to late teenager, the macroscopic pattern of axonal projections in the human brain remains largely unchanged while undergoing dramatic functional modifications that lead to network refinement. These functional modifications are mediated by increasing myelination and changes in axonal diameter and synaptic density, as well as changes in neurochemical mediators. Here we explore the contribution of white matter maturation to the development of connectivity between ages 2 and 18 y using high b-value diffusion MRI tractography and connectivity analysis. We measured changes in connection efficacy as the inverse of the average diffusivity along a fiber tract. We observed significant refinement in specific metrics of network topology, including a significant increase in node strength and efficiency along with a decrease in clustering. Major structural modules and hubs were in place by 2 y of age, and they continued to strengthen their profile during subsequent development. Recording resting-state functional MRI from a subset of subjects, we confirmed a positive correlation between structural and functional connectivity, and in addition observed that this relationship strengthened with age. Continuously increasing integration and decreasing segregation of structural connectivity with age suggests that network refinement mediated by white matter maturation promotes increased global efficiency. In addition, the strengthening of the correlation between structural and functional connectivity with age suggests that white matter connectivity in combination with other factors, such as differential modulation of axonal diameter and myelin thickness, that are partially captured by inverse average diffusivity, play an increasingly important role in creating brain-wide coherence and synchrony.},
	Author = {Hagmann, P and Sporns, O and Madan, N and Cammoun, L and Pienaar, R and Wedeen, V J and Meuli, R and Thiran, J-P and Grant, P E},
	Date-Added = {2014-09-22 20:08:39 +0000},
	Date-Modified = {2014-09-22 20:10:57 +0000},
	Doi = {10.1073/pnas.1009073107},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {graph theory; network analysis; structural connectivity; resting-state fMRI; DTI; Human; Child; Development},
	Mesh = {Adolescent; Adolescent Development; Axons; Cerebral Cortex; Child; Child Development; Child, Preschool; Female; Follow-Up Studies; Humans; Infant; Magnetic Resonance Imaging; Male; Myelin Sheath; Synapses},
	Month = {Nov},
	Number = {44},
	Pages = {19067-72},
	Pmc = {PMC2973853},
	Pmid = {20956328},
	Pst = {ppublish},
	Title = {White matter maturation reshapes structural connectivity in the late developing human brain},
	Volume = {107},
	Year = {2010},
	File = {papers/Hagmann_ProcNatlAcadSciUSA2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1009073107}}

@article{Supekar:2009,
	Abstract = {The ontogeny of large-scale functional organization of the human brain is not well understood. Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children (ages 7-9 y) and 22 young-adults (ages 19-22 y). Comparison of network properties, including path-length, clustering-coefficient, hierarchy, and regional connectivity, revealed that although children and young-adults' brains have similar "small-world" organization at the global level, they differ significantly in hierarchical organization and interregional connectivity. We found that subcortical areas were more strongly connected with primary sensory, association, and paralimbic areas in children, whereas young-adults showed stronger cortico-cortical connectivity between paralimbic, limbic, and association areas. Further, combined analysis of functional connectivity with wiring distance measures derived from white-matter fiber tracking revealed that the development of large-scale brain networks is characterized by weakening of short-range functional connectivity and strengthening of long-range functional connectivity. Importantly, our findings show that the dynamic process of over-connectivity followed by pruning, which rewires connectivity at the neuronal level, also operates at the systems level, helping to reconfigure and rebalance subcortical and paralimbic connectivity in the developing brain. Our study demonstrates the usefulness of network analysis of brain connectivity to elucidate key principles underlying functional brain maturation, paving the way for novel studies of disrupted brain connectivity in neurodevelopmental disorders such as autism.},
	Author = {Supekar, Kaustubh and Musen, Mark and Menon, Vinod},
	Date-Added = {2014-09-22 20:03:33 +0000},
	Date-Modified = {2014-09-22 20:07:33 +0000},
	Doi = {10.1371/journal.pbio.1000157},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Keywords = {resting-state fMRI; connectivity; graph theory; network analysis; Human; Child; development; default mode network},
	Mesh = {Brain; Brain Mapping; Cerebral Cortex; Child; Female; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Models, Neurological; Nerve Net; Neural Pathways; Young Adult},
	Month = {Jul},
	Number = {7},
	Pages = {e1000157},
	Pmc = {PMC2705656},
	Pmid = {19621066},
	Pst = {ppublish},
	Title = {Development of large-scale functional brain networks in children},
	Volume = {7},
	Year = {2009},
	File = {papers/Supekar_PLoSBiol2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pbio.1000157}}

@article{Uddin:2011,
	Abstract = {Brain structural and functional development, throughout childhood and into adulthood, underlies the maturation of increasingly sophisticated cognitive abilities. High-level attentional and cognitive control processes rely on the integrity of, and dynamic interactions between, core neurocognitive networks. The right fronto-insular cortex (rFIC) is a critical component of a salience network (SN) that mediates interactions between large-scale brain networks involved in externally oriented attention [central executive network (CEN)] and internally oriented cognition [default mode network (DMN)]. How these systems reconfigure and mature with development is a critical question for cognitive neuroscience, with implications for neurodevelopmental pathologies affecting brain connectivity. Using functional and effective connectivity measures applied to fMRI data, we examine interactions within and between the SN, CEN, and DMN. We find that functional coupling between key network nodes is stronger in adults than in children, as are causal links emanating from the rFIC. Specifically, the causal influence of the rFIC on nodes of the SN and CEN was significantly greater in adults compared with children. Notably, these results were entirely replicated on an independent dataset of matched children and adults. Developmental changes in functional and effective connectivity were related to structural connectivity along these links. Diffusion tensor imaging tractography revealed increased structural integrity in adults compared with children along both within- and between-network pathways associated with the rFIC. These results suggest that structural and functional maturation of rFIC pathways is a critical component of the process by which human brain networks mature during development to support complex, flexible cognitive processes in adulthood.},
	Author = {Uddin, Lucina Q and Supekar, Kaustubh S and Ryali, Srikanth and Menon, Vinod},
	Date-Added = {2014-09-22 19:46:26 +0000},
	Date-Modified = {2014-09-22 19:47:35 +0000},
	Doi = {10.1523/JNEUROSCI.4465-11.2011},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {resting-state fMRI; connectivity; human; Child; default mode network; Attention; Decision Making; graph theory; network analysis},
	Mesh = {Brain; Brain Mapping; Child; Cognition; Diffusion Tensor Imaging; Female; Frontal Lobe; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Nerve Net; Young Adult},
	Month = {Dec},
	Number = {50},
	Pages = {18578-89},
	Pmc = {PMC3641286},
	Pmid = {22171056},
	Pst = {ppublish},
	Title = {Dynamic reconfiguration of structural and functional connectivity across core neurocognitive brain networks with development},
	Volume = {31},
	Year = {2011},
	File = {papers/Uddin_JNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4465-11.2011}}

@article{Hwang:2013,
	Abstract = {Functional hubs are brain regions that play a crucial role in facilitating communication among parallel, distributed brain networks. The developmental emergence and stability of hubs, however, is not well understood. The current study used measures of network topology drawn from graph theory to investigate the development of functional hubs in 99 participants, 10-20 years of age. We found that hub architecture was evident in late childhood and was stable from adolescence to early adulthood. Connectivity between hub and non-hub ("spoke") regions, however, changed with development. From childhood to adolescence, the strength of connections between frontal hubs and cortical and subcortical spoke regions increased. From adolescence to adulthood, hub-spoke connections with frontal hubs were stable, whereas connectivity between cerebellar hubs and cortical spoke regions increased. Our findings suggest that a developmentally stable functional hub architecture provides the foundation of information flow in the brain, whereas connections between hubs and spokes continue to develop, possibly supporting mature cognitive function.},
	Author = {Hwang, Kai and Hallquist, Michael N and Luna, Beatriz},
	Date-Added = {2014-09-22 19:43:42 +0000},
	Date-Modified = {2014-09-22 19:44:06 +0000},
	Doi = {10.1093/cercor/bhs227},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {adolescents; brain networks; development; functional connectivity; graph theory; default mode network; human; resting-state fMRI},
	Mesh = {Adolescent; Brain; Child; Humans; Magnetic Resonance Imaging; Models, Neurological; Nerve Net; Neural Pathways; Rest; Young Adult},
	Month = {Oct},
	Number = {10},
	Pages = {2380-93},
	Pmc = {PMC3767958},
	Pmid = {22875861},
	Pst = {ppublish},
	Title = {The development of hub architecture in the human functional brain network},
	Volume = {23},
	Year = {2013},
	File = {papers/Hwang_CerebCortex2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhs227}}

@article{Fransson:2011,
	Abstract = {The functional network topology of the adult human brain has recently begun to be noninvasively mapped using resting-state functional connectivity magnetic resonance imaging and described using mathematical tools originating from graph theory. Previous studies have revealed the existence of disproportionally connected brain regions, so called cortical hubs, which act as information convergence zones and supposedly capture key aspects of how the brain's architecture supports human behavior and how it is affected by disease. In this study, we present results showing that cortical hubs and their associated cortical networks are largely confined to primary sensory and motor brain regions in the infant brain. Our findings in infants stand in stark contrast to the situation found in adults where the majority of cortical hubs and hub-related networks are located in heteromodal association cortex. Our findings suggest that the functional network architecture in infants is linked to support tasks that are of a perception-action nature.},
	Author = {Fransson, Peter and Aden, Ulrika and Blennow, Mats and Lagercrantz, Hugo},
	Date-Added = {2014-09-22 19:18:16 +0000},
	Date-Modified = {2014-09-22 19:19:57 +0000},
	Doi = {10.1093/cercor/bhq071},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {human; infant; Child; fMRI; default mode network; resting-state connectivity; network analysis; graph theory},
	Mesh = {Adult; Aging; Brain Mapping; Brain Waves; Cerebral Cortex; Cohort Studies; Female; Humans; Infant; Magnetic Resonance Imaging; Male; Nerve Net; Neural Pathways; Neuropsychological Tests; Young Adult},
	Month = {Jan},
	Number = {1},
	Pages = {145-54},
	Pmid = {20421249},
	Pst = {ppublish},
	Title = {The functional architecture of the infant brain as revealed by resting-state fMRI},
	Volume = {21},
	Year = {2011},
	File = {papers/Fransson_CerebCortex2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhq071}}

@article{Buckner:2009,
	Abstract = {Recent evidence suggests that some brain areas act as hubs interconnecting distinct, functionally specialized systems. These nexuses are intriguing because of their potential role in integration and also because they may augment metabolic cascades relevant to brain disease. To identify regions of high connectivity in the human cerebral cortex, we applied a computationally efficient approach to map the degree of intrinsic functional connectivity across the brain. Analysis of two separate functional magnetic resonance imaging datasets (each n = 24) demonstrated hubs throughout heteromodal areas of association cortex. Prominent hubs were located within posterior cingulate, lateral temporal, lateral parietal, and medial/lateral prefrontal cortices. Network analysis revealed that many, but not all, hubs were located within regions previously implicated as components of the default network. A third dataset (n = 12) demonstrated that the locations of hubs were present across passive and active task states, suggesting that they reflect a stable property of cortical network architecture. To obtain an accurate reference map, data were combined across 127 participants to yield a consensus estimate of cortical hubs. Using this consensus estimate, we explored whether the topography of hubs could explain the pattern of vulnerability in Alzheimer's disease (AD) because some models suggest that regions of high activity and metabolism accelerate pathology. Positron emission tomography amyloid imaging in AD (n = 10) compared with older controls (n = 29) showed high amyloid-beta deposition in the locations of cortical hubs consistent with the possibility that hubs, while acting as critical way stations for information processing, may also augment the underlying pathological cascade in AD.},
	Author = {Buckner, Randy L and Sepulcre, Jorge and Talukdar, Tanveer and Krienen, Fenna M and Liu, Hesheng and Hedden, Trey and Andrews-Hanna, Jessica R and Sperling, Reisa A and Johnson, Keith A},
	Date-Added = {2014-09-22 13:30:12 +0000},
	Date-Modified = {2014-09-22 13:30:12 +0000},
	Doi = {10.1523/JNEUROSCI.5062-08.2009},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Adolescent; Aged; Aged, 80 and over; Alzheimer Disease; Brain Mapping; Cerebral Cortex; Female; Humans; Male; Middle Aged; Nerve Net; Neural Pathways; Young Adult},
	Month = {Feb},
	Number = {6},
	Pages = {1860-73},
	Pmc = {PMC2750039},
	Pmid = {19211893},
	Pst = {ppublish},
	Title = {Cortical hubs revealed by intrinsic functional connectivity: mapping, assessment of stability, and relation to Alzheimer's disease},
	Volume = {29},
	Year = {2009},
	File = {papers/Buckner_JNeurosci2009.pdf},
	Bdsk-File-2 = {papers/Buckner_JNeurosci2009a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.5062-08.2009}}

@article{Fox:2007a,
	Abstract = {The majority of functional neuroscience studies have focused on the brain's response to a task or stimulus. However, the brain is very active even in the absence of explicit input or output. In this Article we review recent studies examining spontaneous fluctuations in the blood oxygen level dependent (BOLD) signal of functional magnetic resonance imaging as a potentially important and revealing manifestation of spontaneous neuronal activity. Although several challenges remain, these studies have provided insight into the intrinsic functional architecture of the brain, variability in behaviour and potential physiological correlates of neurological and psychiatric disease.},
	Author = {Fox, Michael D and Raichle, Marcus E},
	Date-Added = {2014-09-19 14:37:27 +0000},
	Date-Modified = {2014-09-19 14:38:00 +0000},
	Doi = {10.1038/nrn2201},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {resting-state fMRI; default mode network; functional connectivity;},
	Mesh = {Animals; Brain; Brain Mapping; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Oxygen},
	Month = {Sep},
	Number = {9},
	Pages = {700-11},
	Pmid = {17704812},
	Pst = {ppublish},
	Title = {Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging},
	Volume = {8},
	Year = {2007},
	File = {papers/Fox_NatRevNeurosci2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2201}}

@article{Barch:2013,
	Abstract = {Understanding how brain systems interact to produce complex behaviors is a central goal of cognitive neuroscience. Palaniyappan and colleagues enhance our understanding of how interactions among brain systems contribute to individual differences in function and psychopathology by examining causal interactions among the salience and central executive systems in schizophrenia.},
	Author = {Barch, Deanna M},
	Date-Added = {2014-09-19 14:00:06 +0000},
	Date-Modified = {2014-09-19 14:00:06 +0000},
	Doi = {10.1016/j.tics.2013.09.004},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Brain; Brain Mapping; Female; Humans; Male; Neural Pathways; Schizophrenia},
	Month = {Dec},
	Number = {12},
	Pages = {603-5},
	Pmc = {PMC3858486},
	Pmid = {24080424},
	Pst = {ppublish},
	Title = {Brain network interactions in health and disease},
	Volume = {17},
	Year = {2013},
	File = {papers/Barch_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.004}}

@article{Uddin:2013,
	Abstract = {In recent work, O'Reilly and colleagues demonstrate relatively intact interhemispheric functional connectivity in a macaque brain in the absence of major commissural fibers. This work adds to a growing body of literature challenging the notion that structural and functional brain connectivity metrics are related in a straightforward manner.},
	Author = {Uddin, Lucina Q},
	Date-Added = {2014-09-19 14:00:03 +0000},
	Date-Modified = {2014-09-19 14:00:03 +0000},
	Doi = {10.1016/j.tics.2013.09.011},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Animals; Brain Mapping; Brain Waves; Connectome; Female; Macaca mulatta; Male},
	Month = {Dec},
	Number = {12},
	Pages = {600-2},
	Pmc = {PMC3858496},
	Pmid = {24094797},
	Pst = {ppublish},
	Title = {Complex relationships between structural and functional brain connectivity},
	Volume = {17},
	Year = {2013},
	File = {papers/Uddin_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.011}}

@article{Zanto:2013,
	Abstract = {A recent study shows that the fronto-parietal network (FPN), and subregions therein, alters its functional connectivity with nodes of other networks based on task goals. Moreover, FPN patterns of connectivity not only reflect engagement of specific tasks, but also serve as a code that can be transferred to facilitate learning novel tasks.},
	Author = {Zanto, Theodore P and Gazzaley, Adam},
	Date-Added = {2014-09-19 14:00:00 +0000},
	Date-Modified = {2014-09-19 14:00:00 +0000},
	Doi = {10.1016/j.tics.2013.10.001},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Adaptation, Physiological; Brain; Brain Mapping; Female; Humans; Male; Neural Pathways; Psychomotor Performance},
	Month = {Dec},
	Number = {12},
	Pages = {602-3},
	Pmc = {PMC3873155},
	Pmid = {24129332},
	Pst = {ppublish},
	Title = {Fronto-parietal network: flexible hub of cognitive control},
	Volume = {17},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.10.001}}

@article{Singer:2013,
	Abstract = {Recent discoveries on the organisation of the cortical connectome together with novel data on the dynamics of neuronal interactions require an extension of classical concepts on information processing in the cerebral cortex. These new insights justify considering the brain as a complex, self-organised system with nonlinear dynamics in which principles of distributed, parallel processing coexist with serial operations within highly interconnected networks. The observed dynamics suggest that cortical networks are capable of providing an extremely high-dimensional state space in which a large amount of evolutionary and ontogenetically acquired information can coexist and be accessible to rapid parallel search.},
	Author = {Singer, Wolf},
	Date-Added = {2014-09-19 13:59:57 +0000},
	Date-Modified = {2014-09-19 13:59:57 +0000},
	Doi = {10.1016/j.tics.2013.09.006},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {cerebral cortex; nonlinear dynamics; oscillations; reservoir computing; synchrony},
	Mesh = {Cerebral Cortex; Computer Simulation; Humans; Models, Neurological; Nerve Net; Nonlinear Dynamics},
	Month = {Dec},
	Number = {12},
	Pages = {616-26},
	Pmid = {24139950},
	Pst = {ppublish},
	Title = {Cortical dynamics revisited},
	Volume = {17},
	Year = {2013},
	File = {papers/Singer_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.006}}

@article{Harmelech:2013,
	Abstract = {When the brain is 'at rest', spatiotemporal activity patterns emerge spontaneously, that is, in the absence of an overt task. However, what these patterns reveal about cortical function remains elusive. In this article, we put forward the hypothesis that the correlation patterns among these spontaneous fluctuations (SPs) reflect the profile of individual a priori cognitive biases, coded as synaptic efficacies in cortical networks. Thus, SPs offer a new means for mapping personal traits in both neurotypical and atypical cases. Three sets of observations and related empirical evidence provide support for this hypothesis. First, SPs correspond to activation patterns that occur during typical task performance. Second, individual differences in SPs reflect individual biases and abnormalities. Finally, SPs can be actively remodeled in a long-term manner by focused and intense cortical training.},
	Author = {Harmelech, Tal and Malach, Rafael},
	Date-Added = {2014-09-19 13:59:53 +0000},
	Date-Modified = {2014-09-19 13:59:53 +0000},
	Doi = {10.1016/j.tics.2013.09.014},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {BOLD-fMRI; a priori biases; cortex; human; resting state; spontaneous activity},
	Mesh = {Animals; Bias (Epidemiology); Brain Mapping; Cerebral Cortex; Cognition; Humans; Neuroimaging; Neurons; Rest},
	Month = {Dec},
	Number = {12},
	Pages = {606-15},
	Pmid = {24182697},
	Pst = {ppublish},
	Title = {Neurocognitive biases and the patterns of spontaneous correlations in the human cortex},
	Volume = {17},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.014}}

@article{Menon:2013,
	Abstract = {The human brain undergoes protracted developmental changes during which it constructs functional networks that engender complex cognitive abilities. Understanding brain function ultimately depends on knowledge of how dynamic interactions between distributed brain regions mature with age to produce sophisticated cognitive systems. This review summarizes recent progress in our understanding of the ontogeny of functional brain networks. Here I describe how complementary methods for probing functional connectivity are providing unique insights into the emergence and maturation of distinct functional networks from childhood to adulthood. I highlight six emerging principles governing the development of large-scale functional networks and discuss how they inform cognitive and affective function in typically developing children and in children with neurodevelopmental disorders.},
	Author = {Menon, Vinod},
	Date-Added = {2014-09-19 13:59:51 +0000},
	Date-Modified = {2014-09-19 13:59:51 +0000},
	Doi = {10.1016/j.tics.2013.09.015},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Animals; Brain; Brain Mapping; Developmental Disabilities; Humans; Models, Neurological; Nerve Net; Neural Pathways},
	Month = {Dec},
	Number = {12},
	Pages = {627-40},
	Pmid = {24183779},
	Pst = {ppublish},
	Title = {Developmental pathways to functional brain networks: emerging principles},
	Volume = {17},
	Year = {2013},
	File = {papers/Menon_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.015}}

@article{Buckner:2013,
	Abstract = {The human cerebral cortex is vastly expanded relative to other primates and disproportionately occupied by distributed association regions. Here we offer a hypothesis about how association networks evolved their prominence and came to possess circuit properties vital to human cognition. The rapid expansion of the cortical mantle may have untethered large portions of the cortex from strong constraints of molecular gradients and early activity cascades that lead to sensory hierarchies. What fill the gaps between these hierarchies are densely interconnected networks that widely span the cortex and mature late into development. Limitations of the tethering hypothesis are discussed as well as its broad implications for understanding critical features of the human brain as a byproduct of size scaling.},
	Author = {Buckner, Randy L and Krienen, Fenna M},
	Date-Added = {2014-09-19 13:59:47 +0000},
	Date-Modified = {2014-09-19 13:59:47 +0000},
	Doi = {10.1016/j.tics.2013.09.017},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {cerebellum; cortical circuits; default network; prefrontal cortex; prospection; social cognition},
	Mesh = {Animals; Biological Evolution; Brain; Brain Mapping; Cognition; Humans; Neural Pathways},
	Month = {Dec},
	Number = {12},
	Pages = {648-65},
	Pmid = {24210963},
	Pst = {ppublish},
	Title = {The evolution of distributed association networks in the human brain},
	Volume = {17},
	Year = {2013},
	File = {papers/Buckner_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.017}}

@article{Kim:2013,
	Abstract = {Mapping of neural connectivity across the mammalian brain is a daunting and exciting prospect. Current approaches can be divided into three classes: macroscale, focusing on coarse inter-regional connectivity; mesoscale, involving a finer focus on neurons and projections; and microscale, reconstructing full details of all synaptic contacts. It remains to be determined how to bridge the datasets or insights from the different levels of study. Here we review recent light-microscopy-based approaches that may help in integration across scales.},
	Author = {Kim, Sung-Yon and Chung, Kwanghun and Deisseroth, Karl},
	Date-Added = {2014-09-19 13:59:45 +0000},
	Date-Modified = {2014-09-19 13:59:45 +0000},
	Doi = {10.1016/j.tics.2013.10.005},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Animals; Brain; Brain Mapping; Humans; Microscopy; Neural Pathways},
	Month = {Dec},
	Number = {12},
	Pages = {596-9},
	Pmid = {24210964},
	Pst = {ppublish},
	Title = {Light microscopy mapping of connections in the intact brain},
	Volume = {17},
	Year = {2013},
	File = {papers/Kim_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.10.005}}

@article{Rubinov:2013,
	Abstract = {Pathoconnectomics, the mapping of abnormal brain networks, is a popular current framework for the study of brain dysfunction in psychiatric disorders. In this review we evaluate the conceptual foundations of this framework, describe the construction and analysis of empirical models of brain networks or connectomes, and summarize recent reports of the large-scale whole-brain connectome organization of two candidate brain-network disorders, schizophrenia and autism. We consider the evidence for the abnormal brain-network nature of psychiatric disorders and find it inconclusive. For instance, although there is some evidence for more random whole-brain network organization in schizophrenia and autism, future studies need to determine if these and other observed brain-network abnormalities represent sufficient phenotypes of psychiatric disorders, in order to validate pathoconnectomics as a scientific and clinical framework.},
	Author = {Rubinov, Mikail and Bullmore, Ed},
	Date-Added = {2014-09-19 13:59:41 +0000},
	Date-Modified = {2014-09-19 13:59:41 +0000},
	Doi = {10.1016/j.tics.2013.10.007},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {MRI; complex networks; connectomics; endophenotype; psychiatry},
	Mesh = {Brain; Humans; Mental Disorders; Microscopy; Nerve Net; Neural Pathways; Neuroimaging},
	Month = {Dec},
	Number = {12},
	Pages = {641-7},
	Pmid = {24238779},
	Pst = {ppublish},
	Title = {Fledgling pathoconnectomics of psychiatric disorders},
	Volume = {17},
	Year = {2013},
	File = {papers/Rubinov_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.10.007}}

@article{Heuvel:2013,
	Abstract = {Virtually all domains of cognitive function require the integration of distributed neural activity. Network analysis of human brain connectivity has consistently identified sets of regions that are critically important for enabling efficient neuronal signaling and communication. The central embedding of these candidate 'brain hubs' in anatomical networks supports their diverse functional roles across a broad range of cognitive tasks and widespread dynamic coupling within and across functional networks. The high level of centrality of brain hubs also renders them points of vulnerability that are susceptible to disconnection and dysfunction in brain disorders. Combining data from numerous empirical and computational studies, network approaches strongly suggest that brain hubs play important roles in information integration underpinning numerous aspects of complex cognitive function.},
	Author = {van den Heuvel, Martijn P and Sporns, Olaf},
	Date-Added = {2014-09-19 12:27:08 +0000},
	Date-Modified = {2014-09-19 12:31:02 +0000},
	Doi = {10.1016/j.tics.2013.09.012},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {resting-state fMRI; connectivity; connectomics; default mode network; graph theory; review literature; Human; network analysis; network modelling; wholeBrain},
	Mesh = {Brain; Cognition; Humans; Nerve Net; Neural Pathways},
	Month = {Dec},
	Number = {12},
	Pages = {683-96},
	Pmid = {24231140},
	Pst = {ppublish},
	Title = {Network hubs in the human brain},
	Volume = {17},
	Year = {2013},
	File = {papers/Heuvel_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.012}}

@article{Brown:2001,
	Abstract = {'Independent component analysis' is a technique of data transformation that finds independent sources of activity in recorded mixtures of sources. It can be used to recover fluctuations of membrane potential from individual neurons in multiple-detector optical recordings. There are some examples in which more than 100 neurons can be separated simultaneously. Independent component analysis automatically separates overlapping action potentials, recovers action potentials of different sizes from the same neuron, removes artifacts and finds the position of each neuron on the detector array. One limitation is that the number of sources--neurons and artifacts--must be equal to or less than the number of simultaneous recordings. Independent component analysis also has many other applications in neuroscience including, removal of artifacts from EEG data, identification of spatially independent brain regions in fMRI recordings and determination of population codes in multi-unit recordings.},
	Author = {Brown, G D and Yamada, S and Sejnowski, T J},
	Date-Added = {2014-09-19 04:09:19 +0000},
	Date-Modified = {2014-09-19 04:27:27 +0000},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {wholeBrain; Mathematics; Analysis of Variance; Methods; optical imaging},
	Mesh = {Action Potentials; Algorithms; Animals; Brain; Electroencephalography; Humans; Linear Models; Membrane Potentials; Models, Neurological; Neurons},
	Month = {Jan},
	Number = {1},
	Pages = {54-63},
	Pmid = {11163888},
	Pst = {ppublish},
	Title = {Independent component analysis at the neural cocktail party},
	Volume = {24},
	Year = {2001},
	File = {papers/Brown_TrendsNeurosci2001.pdf}}

@article{Liang:2011,
	Abstract = {Intrinsic connectional architecture of the brain is a crucial element in understanding the governing principle of brain organization. To date, enormous effort has been focused on addressing this issue in humans by combining resting-state functional magnetic resonance imaging (rsfMRI) with other techniques. However, this research area is significantly underexplored in animals, perhaps because of confounding effects of anesthetic agents used in most animal experiments on functional connectivity. To bridge this gap, we have systematically investigated the intrinsic connectional architecture in the rodent brain by using a previously established awake-animal imaging model. First, group independent component analysis was applied to the rsfMRI data to extract elementary functional clusters of the brain. The connectional relationships between these clusters, as evaluated by partial correlation analysis, were then used to construct a graph of whole-brain neural network. This network exhibited the typical features of small-worldness and strong community structures seen in the human brain. Finally, the whole-brain network was segregated into community structures using a graph-based analysis. The results of this work provided a functional atlas of intrinsic connectional architecture of the rat brain at both intraregion and interregion levels. More importantly, the current work revealed that functional networks in rats are organized in a nontrivial manner and conserve fundamental topological properties that are also seen in the human brain. Given the high psychopathological relevance of network organization of the brain, this study demonstrated the feasibility of studying mechanisms and therapies of multiple neurological and psychiatric diseases through translational research.},
	Author = {Liang, Zhifeng and King, Jean and Zhang, Nanyin},
	Date-Added = {2014-09-18 21:25:02 +0000},
	Date-Modified = {2014-09-18 21:25:30 +0000},
	Doi = {10.1523/JNEUROSCI.4557-10.2011},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {resting-state fMRI; default mode network; rat; in vivo; functional connectivity; Motor Activity; awake},
	Mesh = {Animals; Brain; Brain Mapping; Magnetic Resonance Imaging; Nerve Net; Neural Pathways; Neurons; Rats; Rats, Long-Evans},
	Month = {Mar},
	Number = {10},
	Pages = {3776-83},
	Pmc = {PMC3073070},
	Pmid = {21389232},
	Pst = {ppublish},
	Title = {Uncovering intrinsic connectional architecture of functional networks in awake rat brain},
	Volume = {31},
	Year = {2011},
	File = {papers/Liang_JNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4557-10.2011}}

@article{Hutchison:2010,
	Abstract = {The rodent brain is organized into functional networks that can be studied through examination of synchronized low-frequency spontaneous fluctuations (LFFs) of the functional magnetic resonance imaging -blood-oxygen-level-dependent (BOLD) signal. In this study, resting networks of LFFs were estimated from the whole-brain BOLD signals using independent component analysis (ICA). ICA provides a hypothesis-free technique for determining the functional connectivity map that does not require a priori selection of a seed region. Twenty Long-Evans rats were anesthetized with isoflurane (1%, n = 10) or ketamine/xylazine (50/6 mg . kg(-1) . h(-1) ip, n = 10) and imaged for 5-10 min in a 9.4 T MR scanner without experimental stimulation or task requirement. Independent, synchronous LFFs of BOLD signals were found to exist in clustered, bilaterally symmetric regions of both cortical and subcortical structures, including primary and secondary somatosensory cortices, motor cortices, visual cortices, posterior and anterior cingulate cortices, hippocampi, caudate-putamen, and thalamic and hypothalamic nuclei. The somatosensory and motor cortices typically demonstrated both symmetric and asymmetric components with unique frequency profiles. Similar independent network components were found under isoflurane and ketamine/xylazine anesthesia. The report demonstrates, for the first time, 12 independent resting networks that are bilaterally synchronous in different cortical and subcortical areas of the rat brain.},
	Author = {Hutchison, R Matthew and Mirsattari, Seyed M and Jones, Craig K and Gati, Joseph S and Leung, L Stan},
	Date-Added = {2014-09-18 21:06:38 +0000},
	Date-Modified = {2014-09-18 21:08:30 +0000},
	Doi = {10.1152/jn.00141.2010},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {resting-state fMRI; default mode network; rat; in vivo; functional connectivity},
	Mesh = {Anesthesia; Animals; Brain; Brain Mapping; Functional Laterality; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Oxygen; Principal Component Analysis; Rats; Rats, Long-Evans; Rest},
	Month = {Jun},
	Number = {6},
	Pages = {3398-406},
	Pmid = {20410359},
	Pst = {ppublish},
	Title = {Functional networks in the anesthetized rat brain revealed by independent component analysis of resting-state FMRI},
	Volume = {103},
	Year = {2010},
	File = {papers/Hutchison_JNeurophysiol2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.00141.2010}}

@article{Lu:2007,
	Abstract = {Synchronized low-frequency spontaneous fluctuations of the functional MRI (fMRI) signal have recently been applied to investigate large-scale neuronal networks of the brain in the absence of specific task instructions. However, the underlying neural mechanisms of these fluctuations remain largely unknown. To this end, electrophysiological recordings and resting-state fMRI measurements were conducted in alpha-chloralose-anesthetized rats. Using a seed-voxel analysis strategy, region-specific, anesthetic dose-dependent fMRI resting-state functional connectivity was detected in bilateral primary somatosensory cortex (S1FL) of the resting brain. Cortical electroencephalographic signals were also recorded from bilateral S1FL; a visual cortex locus served as a control site. Results demonstrate that, unlike the evoked fMRI response that correlates with power changes in the gamma bands, the resting-state fMRI signal correlates with the power coherence in low-frequency bands, particularly the delta band. These data indicate that hemodynamic fMRI signal differentially registers specific electrical oscillatory frequency band activity, suggesting that fMRI may be able to distinguish the ongoing from the evoked activity of the brain.},
	Author = {Lu, Hanbing and Zuo, Yantao and Gu, Hong and Waltz, James A and Zhan, Wang and Scholl, Clara A and Rea, William and Yang, Yihong and Stein, Elliot A},
	Date-Added = {2014-09-18 21:03:49 +0000},
	Date-Modified = {2014-09-18 21:04:47 +0000},
	Doi = {10.1073/pnas.0705791104},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {resting-state fMRI; default mode network; rat; in vivo; Anesthesia; EEG; sleep; Delta Rhythm; wholeBrain},
	Mesh = {Animals; Magnetic Resonance Imaging; Nerve Net; Rats},
	Month = {Nov},
	Number = {46},
	Pages = {18265-9},
	Pmc = {PMC2084331},
	Pmid = {17991778},
	Pst = {ppublish},
	Title = {Synchronized delta oscillations correlate with the resting-state functional MRI signal},
	Volume = {104},
	Year = {2007},
	File = {papers/Lu_ProcNatlAcadSciUSA2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0705791104}}

@article{Nitz:2009,
	Abstract = {The registration of spatial information by neurons of the parietal cortex takes on many forms. In most experiments, spatially modulated parietal activity patterns are found to take as their frame of reference some part of the body such as the retina. However, recent findings obtained in single neuron recordings from both rat and monkey parietal cortex suggest that the frame of reference utilized by parietal cortex may also be abstract or arbitrary in nature. Evidence in rats comes from work indicating that parietal activity in freely behaving rodents is organized according to the space defined by routes taken through an environment. In monkeys, evidence for an object-centered frame of reference has recently been presented. The present work reviews single neuron recording experiments in parietal cortex of freely behaving rats and considers the potential contribution of parietal cortex in solving navigational tasks. It is proposed that parietal cortex, in interaction with the hippocampus, plays a critical role in the selection of the most appropriate route between two points and, in addition, produces a route-based positional signal capable of guiding sensorimotor transitions.},
	Author = {Nitz, Douglas},
	Date-Added = {2014-09-16 16:13:07 +0000},
	Date-Modified = {2014-09-16 16:13:12 +0000},
	Doi = {10.1016/j.nlm.2008.08.007},
	Journal = {Neurobiol Learn Mem},
	Journal-Full = {Neurobiology of learning and memory},
	Keywords = {rat; Posterior parietal cortex; ppc; Spatial Behavior; navigation; Motor Activity; grid cells; Decision Making; goal directed behavior; retrosplenial cortex},
	Mesh = {Action Potentials; Animals; Exploratory Behavior; Haplorhini; Hippocampus; Maze Learning; Memory; Motor Activity; Neurons; Parietal Lobe; Rats; Space Perception; Spatial Behavior},
	Month = {Feb},
	Number = {2},
	Pages = {179-85},
	Pmid = {18804545},
	Pst = {ppublish},
	Title = {Parietal cortex, navigation, and the construction of arbitrary reference frames for spatial information},
	Volume = {91},
	Year = {2009},
	File = {papers/Nitz_NeurobiolLearnMem2009.pdf}}

@article{Calton:2009,
	Abstract = {The ability of an organism to accurately navigate from one place to another requires integration of multiple spatial constructs, including the determination of one's position and direction in space relative to allocentric landmarks, movement velocity, and the perceived location of the goal of the movement. In this review, we propose that while limbic areas are important for the sense of spatial orientation, the posterior parietal cortex is responsible for relating this sense with the location of a navigational goal and in formulating a plan to attain it. Hence, the posterior parietal cortex is important for the computation of the correct trajectory or route to be followed while navigating. Prefrontal and motor areas are subsequently responsible for executing the planned movement. Using this theory, we are able to bridge the gap between the rodent and primate literatures by suggesting that the allocentric role of the rodent PPC is largely analogous to the egocentric role typically emphasized in primates, that is, the integration of spatial orientation with potential goals in the planning of goal-directed movements.},
	Author = {Calton, Jeffrey L and Taube, Jeffrey S},
	Date-Added = {2014-09-16 15:16:53 +0000},
	Date-Modified = {2014-09-16 15:21:15 +0000},
	Doi = {10.1016/j.nlm.2008.09.015},
	Journal = {Neurobiol Learn Mem},
	Journal-Full = {Neurobiology of learning and memory},
	Keywords = {rat; Posterior parietal cortex; ppc; Spatial Behavior; navigation; Motor Activity; grid cells; Decision Making; goal directed behavior; retrosplenial cortex},
	Mesh = {Action Potentials; Animals; Cognition; Frontal Lobe; Goals; Hippocampus; Maze Learning; Neural Pathways; Neurons; Orientation; Parietal Lobe; Primates; Space Perception; Spatial Behavior},
	Month = {Feb},
	Number = {2},
	Pages = {186-96},
	Pmc = {PMC2666283},
	Pmid = {18929674},
	Pst = {ppublish},
	Title = {Where am I and how will I get there from here? A role for posterior parietal cortex in the integration of spatial information and route planning},
	Volume = {91},
	Year = {2009},
	File = {papers/Calton_NeurobiolLearnMem2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.nlm.2008.09.015}}

@article{Whitlock:2008,
	Abstract = {The navigational system of the mammalian cortex comprises a number of interacting brain regions. Grid cells in the medial entorhinal cortex and place cells in the hippocampus are thought to participate in the formation of a dynamic representation of the animal's current location, and these cells are presumably critical for storing the representation in memory. To traverse the environment, animals must be able to translate coordinate information from spatial maps in the entorhinal cortex and hippocampus into body-centered representations that can be used to direct locomotion. How this is done remains an enigma. We propose that the posterior parietal cortex is critical for this transformation.},
	Author = {Whitlock, Jonathan R and Sutherland, Robert J and Witter, Menno P and Moser, May-Britt and Moser, Edvard I},
	Date-Added = {2014-09-16 14:54:21 +0000},
	Date-Modified = {2014-09-16 14:55:00 +0000},
	Doi = {10.1073/pnas.0804216105},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {Posterior parietal cortex; ppc; rat; grid cells; hippocampus; Spatial Behavior; navigation; Entorhinal Cortex;},
	Mesh = {Animals; Behavior, Animal; Brain Mapping; Entorhinal Cortex; Hippocampus; Memory; Parietal Lobe; Rats; Spatial Behavior},
	Month = {Sep},
	Number = {39},
	Pages = {14755-62},
	Pmc = {PMC2567440},
	Pmid = {18812502},
	Pst = {ppublish},
	Title = {Navigating from hippocampus to parietal cortex},
	Volume = {105},
	Year = {2008},
	File = {papers/Whitlock_ProcNatlAcadSciUSA2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0804216105}}

@article{Nitz:2006,
	Abstract = {Quick and efficient traversal of learned routes is critical to the survival of many animals. Routes can be defined by both the ordering of navigational epochs, such as continued forward motion or execution of a turn, and the distances separating them. The neural substrates conferring the ability to fluidly traverse complex routes are not well understood, but likely entail interactions between frontal, parietal, and rhinal cortices and the hippocampus. This paper demonstrates that posterior parietal cortical neurons map both individual and multiple navigational epochs with respect to their order in a route. In direct contrast to spatial firing patterns of hippocampal neurons, parietal neurons discharged in a place- and direction-independent fashion. Parietal route maps were scalable and versatile in that they were independent of the size and spatial configuration of navigational epochs. The results provide a framework in which to consider parietal function in spatial cognition.},
	Author = {Nitz, Douglas A},
	Date-Added = {2014-09-16 14:51:10 +0000},
	Date-Modified = {2014-09-16 14:51:44 +0000},
	Doi = {10.1016/j.neuron.2006.01.037},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Posterior parietal cortex; ppc; rat; grid cells; hippocampus; Spatial Behavior; navigation; Entorhinal Cortex;},
	Mesh = {Action Potentials; Animals; Behavior, Animal; Brain Mapping; Male; Maze Learning; Neurons; Parietal Lobe; Rats; Rats, Sprague-Dawley; Space Perception; Spatial Behavior; Speech Perception},
	Month = {Mar},
	Number = {5},
	Pages = {747-56},
	Pmid = {16504949},
	Pst = {ppublish},
	Title = {Tracking route progression in the posterior parietal cortex},
	Volume = {49},
	Year = {2006},
	File = {papers/Nitz_Neuron2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2006.01.037}}

@article{McNaughton:1994,
	Abstract = {Neural activity related to unrestrained movement through space was studied in rat sensorimotor and posterior parietal cortices during performance of an eight-arm, radial maze task. Nearly half of the cells exhibited movement-related activity that discriminated among three basic modes of locomotion: left turns, right turns, and forward motion. Correlates ranged from strong excitation (relative to the still condition) to strong inhibition, and were distributed among the movement modes in a variety of different ways. For example, cells that discriminated between clockwise and counterclockwise turns did so with either antagonistic responses or simple excitation or inhibition. Others showed either excitation or inhibition relative to both turning and the still condition, and hence were selective for forward motion. Many cells exhibited somatosensory responsiveness; however, in agreement with findings of others, motion correlates could rarely be sensibly explained by the somatosensory response. Moreover, movement correlates sometimes varied considerably with spatial context. Some cells exhibited more complex motion correlates, such as an apparent dependence on the nature of the preceding movement. Irrespective of the specific sensory or motor determinants of cell activity, which varied considerably among cells, the posterior neocortex of the rat appears to generate a robust and redundant internal representation of body motion through space. Such a representation could be useful in constructing "cognitive maps" of the environment.},
	Author = {McNaughton, B L and Mizumori, S J and Barnes, C A and Leonard, B J and Marquis, M and Green, E J},
	Date = {1994 Jan-Feb},
	Date-Added = {2014-09-16 14:49:48 +0000},
	Date-Modified = {2014-09-16 14:50:32 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {Posterior parietal cortex; ppc; rat; grid cells; hippocampus; Spatial Behavior; navigation; Entorhinal Cortex;},
	Mesh = {Animals; Cerebral Cortex; Electrodes, Implanted; Electrophysiology; Male; Motor Cortex; Movement; Orientation; Rats; Rats, Inbred F344; Somatosensory Cortex; Space Perception},
	Number = {1},
	Pages = {27-39},
	Pmid = {8180489},
	Pst = {ppublish},
	Title = {Cortical representation of motion during unrestrained spatial navigation in the rat},
	Volume = {4},
	Year = {1994}}

@article{Torrealba:2008,
	Abstract = {Spatial cognition is a complex higher function in mammals and is involved in a variety of tasks that can be explored in the laboratory. In this review we will discuss the role of the posterior parietal/anteromedial cortex of rodents, also known as the parietal association cortex, and the hippocampal formation in spatial navigation. We will also discuss other higher associational functions of the posterior parietal/anteromedial cortex as they relate to Dr. Pinto-Hamuy's contribution to understanding behavioral functions.},
	Author = {Torrealba, Fernando and Vald{\'e}s, Jos{\'e} Luis},
	Date-Added = {2014-09-15 15:48:41 +0000},
	Date-Modified = {2014-09-15 15:56:33 +0000},
	Doi = {/S0716-97602008000400002},
	Journal = {Biol Res},
	Journal-Full = {Biological research},
	Keywords = {Posterior parietal cortex; ppc; connectivity; review literature; Spatial Behavior; navigation; grid cells; hippocampus; Neocortex; Association cortex; Motor Activity; Motor Cortex; Visual Cortex; Posterior Thalamic Nuclei; thalamus},
	Mesh = {Animals; Cognition; Memory; Parietal Lobe; Rats; Space Perception; Spatial Behavior},
	Number = {4},
	Pages = {369-77},
	Pmid = {19621117},
	Pst = {ppublish},
	Title = {The parietal association cortex of the rat},
	Volume = {41},
	Year = {2008},
	File = {papers/Torrealba_BiolRes2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/0716-97602008000400002}}

@article{Massimini:2004,
	Abstract = {During much of sleep, virtually all cortical neurons undergo a slow oscillation (<1 Hz) in membrane potential, cycling from a hyperpolarized state of silence to a depolarized state of intense firing. This slow oscillation is the fundamental cellular phenomenon that organizes other sleep rhythms such as spindles and slow waves. Using high-density electroencephalogram recordings in humans, we show here that each cycle of the slow oscillation is a traveling wave. Each wave originates at a definite site and travels over the scalp at an estimated speed of 1.2-7.0 m/sec. Waves originate more frequently in prefrontal-orbitofrontal regions and propagate in an anteroposterior direction. Their rate of occurrence increases progressively reaching almost once per second as sleep deepens. The pattern of origin and propagation of sleep slow oscillations is reproducible across nights and subjects and provides a blueprint of cortical excitability and connectivity. The orderly propagation of correlated activity along connected pathways may play a role in spike timing-dependent synaptic plasticity during sleep.},
	Author = {Massimini, Marcello and Huber, Reto and Ferrarelli, Fabio and Hill, Sean and Tononi, Giulio},
	Date-Added = {2014-09-12 14:56:06 +0000},
	Date-Modified = {2014-09-12 14:56:49 +0000},
	Doi = {10.1523/JNEUROSCI.1318-04.2004},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Synapses;24 Pubmed search results 2008;Electroencephalography;research support, non-u.s. gov't;Adult;21 Neurophysiology;Neuronal Plasticity;Synaptic Transmission;Humans;Male;Cerebral Cortex;Membrane Potentials;Sleep},
	Mesh = {Adult; Cerebral Cortex; Electroencephalography; Humans; Male; Membrane Potentials; Neuronal Plasticity; Sleep; Synapses; Synaptic Transmission},
	Month = {Aug},
	Number = {31},
	Pages = {6862-70},
	Pmid = {15295020},
	Pst = {ppublish},
	Title = {The sleep slow oscillation as a traveling wave},
	Volume = {24},
	Year = {2004},
	File = {papers/Massimini_JNeurosci2004.pdf}}

@article{Hamburger:1963b,
	Author = {Hamburger, V},
	Date-Added = {2014-09-11 20:30:27 +0000},
	Date-Modified = {2014-09-11 20:30:27 +0000},
	Doi = {10.1126/science.142.3597.1367},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Month = {Dec},
	Number = {3597},
	Pages = {1367},
	Pmid = {17752414},
	Pst = {ppublish},
	Title = {Embryology},
	Volume = {142},
	Year = {1963},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.142.3597.1367}}

@article{Hamburger:1963a,
	Author = {Hamburger, V and Balaban, M},
	Date-Added = {2014-09-11 20:30:24 +0000},
	Date-Modified = {2016-01-13 18:16:29 +0000},
	Journal = {Dev Biol},
	Journal-Full = {Developmental biology},
	Keywords = {EMBRYO; PERIODICITY; SPINAL CORD; Motor Activity; development},
	Mesh = {Embryo, Nonmammalian; Periodicity; Spinal Cord},
	Month = {Mar},
	Pages = {533-45},
	Pmid = {13952299},
	Pst = {ppublish},
	Title = {Observations and experiments on spontaneous rhythmical behavior in the chick embryo},
	Volume = {6},
	Year = {1963},
	File = {papers/HAMBURGER_DevBiol1963.pdf}}

@article{Hamburger:1963,
	Author = {Hamburger, V},
	Date-Added = {2014-09-11 20:30:22 +0000},
	Date-Modified = {2016-01-13 18:16:04 +0000},
	Journal = {Q Rev Biol},
	Journal-Full = {The Quarterly review of biology},
	Keywords = {BEHAVIOR, ANIMAL; BRAIN ELECTROPHYSIOLOGY; CHICK EMBRYO; ELECTROPHYSIOLOGY; EMBRYO; EXPERIMENTAL LAB STUDY; FISHES; MOVEMENT; NEURONS; PERIODICITY; PHYSIOLOGY, COMPARATIVE; REFLEX; SALAMANDERS; SPINAL CORD; Motor Activity; spontaneous activity; development},
	Mesh = {Animals; Behavior, Animal; Brain; Chick Embryo; Electrophysiology; Embryo, Nonmammalian; Fishes; Movement; Neurons; Periodicity; Physiology, Comparative; Reflex; Research; Spinal Cord; Urodela},
	Month = {Dec},
	Pages = {342-65},
	Pmid = {14111168},
	Pst = {ppublish},
	Title = {SOME ASPECTS OF THE EMBRYOLOGY OF BEHAVIOR},
	Volume = {38},
	Year = {1963},
	File = {papers/HAMBURGER_QRevBiol1963.pdf}}

@article{Corner:1977,
	Author = {Corner, M A},
	Date-Added = {2014-09-11 20:17:03 +0000},
	Date-Modified = {2014-09-11 20:28:53 +0000},
	Journal = {Prog Neurobiol},
	Journal-Full = {Progress in neurobiology},
	Keywords = {sleep; review literature; behavior; development; Embryo and Fetal Development; Mammals; Chick Embryo; Fishes/growth &development; Motor Activity; Spinal Cord},
	Mesh = {Age Factors; Animals; Animals, Newborn; Anura; Brachyura; Chickens; Cockroaches; Fetus; Fishes; Lizards; Mollusca; Motor Activity; Muscle Contraction; Muscles; Phylogeny; Rats; Sheep; Sleep; Swimming; Wasps},
	Number = {4},
	Pages = {279-95},
	Pmid = {335440},
	Pst = {ppublish},
	Title = {Sleep and the beginnings of behavior in the animal kingdom--studies of ultradian motility cycles in early life},
	Volume = {8},
	Year = {1977},
	File = {papers/Corner_ProgNeurobiol1977.pdf}}

@article{Gramsbergen:1976,
	Abstract = {The development of the electroencephalogram (EEG) and, especially, behavioral state-specific EEG patterns was studied in white and black hooded rats of the Lister strain, aged 9-30 days. Movements of the rat were recorded and the behavioral state was monitored by means of a push-button device. The EEG was collected when the rat was in State 1 (regular respiration, absence of movements, and, after the 14th day when the rat eye opens, eyes closed), State 2 (irregular respiration, continual occurrence of twitches, and, after the 14th day, eyes closed), and in State 4 (irregular respiration, presence of gross body movements, and, after the 14th day, eyes opened). The EEG of rats on the 9th and 10th day did not reveal behavioral state-specific patterns. The amplitudes of the EEG were low and only low frequencies occurred. Between the 10th and 13th day an EEG pattern specific for State 1 containing high amplitudes developed. From the 14th day onwards spindles (frequencies from 14-18 Hz) occurred in the EEG during State 1. From the 14th day onwards, the EEG from the visual cortex during State 2 showed a regular and continually occurring 5-Hz rhythm. Bursts with 5-Hz waves were recorded from the visual cortex only intermittently during State 4. The EEG frequencies during the bursts varied between 5 and 7 Hz from the 17th day onwards. Computer analysis of the amplitude distributions showed a considerable increase in the power after the 10th day. The analysis of the frequency spectra indicated that the power increase occurs expecially in the higher frequencies of the EEG signal. Visual analysis as well as computer analysis of the EEG did not reveal systematic changes in the EEG after the 18th day when the EEG was similar to that recorded at older ages.},
	Author = {Gramsbergen, A},
	Date-Added = {2014-09-11 19:59:44 +0000},
	Date-Modified = {2014-09-11 20:00:24 +0000},
	Doi = {10.1002/dev.420090604},
	Journal = {Dev Psychobiol},
	Journal-Full = {Developmental psychobiology},
	Keywords = {EEG; neurophysiology; rat; in vivo; Cerebral Cortex; sleep; development; spontaneous activity; cortical oscillations},
	Mesh = {Age Factors; Animals; Behavior, Animal; Brain; Computers; Electroencephalography; Motor Activity; Motor Cortex; Rats; Respiration; Somatosensory Cortex; Visual Cortex},
	Month = {Nov},
	Number = {6},
	Pages = {501-15},
	Pmid = {1001836},
	Pst = {ppublish},
	Title = {The development of the EEG in the rat},
	Volume = {9},
	Year = {1976},
	File = {papers/Gramsbergen_DevPsychobiol1976.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/dev.420090604}}

@article{Connors:1984a,
	Abstract = {Epilepsy is characterized by highly synchronized paroxysmal bursts of activity within a large population of cortical neurones. Because such spontaneous, synchronized discharges can occur even in isolated blocks of neocortex, mechanisms for initiating and coordinating this activity must reside within the cortex itself. However, the specific cellular properties and local neural circuitry responsible for such behaviour are unknown. In a previous study of neocortex in vitro, we found that treatment with the convulsants penicillin and bicuculline led to synchronized bursts which were driven by unusually large and long-lasting excitatory synaptic conductances. I now report evidence that synchronized bursts are initiated by a small, spacially discrete subpopulation of cells located in the area comprising layer IV and upper layer V. Neural elements in these layers appear to project paroxysmal synaptic excitation radially, onto the neurones of other layers.},
	Author = {Connors, B W},
	Date = {1984 Aug 23-29},
	Date-Added = {2014-09-11 19:33:37 +0000},
	Date-Modified = {2014-09-11 19:34:41 +0000},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {epilepsy; seizure; GABA; in vitro; Neocortex; spontaneous activity; cortical oscillations},
	Mesh = {Animals; Bicuculline; Cerebral Cortex; Electric Conductivity; Evoked Potentials; Glutamates; Glutamic Acid; Guinea Pigs; Kinetics; Neurons},
	Number = {5979},
	Pages = {685-7},
	Pmid = {6147755},
	Pst = {ppublish},
	Title = {Initiation of synchronized neuronal bursting in neocortex},
	Volume = {310},
	Year = {1984},
	File = {papers/Connors_Nature1984.pdf}}

@article{Woolf:1991,
	Author = {Woolf, N J},
	Date-Added = {2014-09-11 19:10:19 +0000},
	Date-Modified = {2014-09-11 19:12:36 +0000},
	Journal = {Prog Neurobiol},
	Journal-Full = {Progress in neurobiology},
	Keywords = {sleep; review literature; Acetylcholine; cortical oscillations; spontaneous activity; Cerebral Cortex; thalamus; Brain Stem; midbrain},
	Mesh = {Acetylcholine; Afferent Pathways; Animals; Arousal; Behavior; Brain; Brain Mapping; Choline O-Acetyltransferase; Cholinergic Fibers; Cognition; Efferent Pathways; Mammals; Motor Activity; Neurons; Rats; Sensation; Sleep; Spinal Cord},
	Number = {6},
	Pages = {475-524},
	Pmid = {1763188},
	Pst = {ppublish},
	Title = {Cholinergic systems in mammalian brain and spinal cord},
	Volume = {37},
	Year = {1991},
	File = {papers/Woolf_ProgNeurobiol1991.pdf}}

@article{Sanchez-Vives:2000a,
	Abstract = {Contrast adaptation is a psychophysical phenomenon, the neuronal bases of which reside largely in the primary visual cortex. The cellular mechanisms of contrast adaptation were investigated in the cat primary visual cortex in vivo through intracellular recording and current injections. Visual cortex cells, and to a much less extent, dorsal lateral geniculate nucleus (dLGN) neurons, exhibited a reduction in firing rate during prolonged presentations of a high-contrast visual stimulus, a process we termed high-contrast adaptation. In a majority of cortical and dLGN cells, the period of adaptation to high contrast was followed by a prolonged (5-80 sec) period of reduced responsiveness to a low-contrast stimulus (postadaptation suppression), an effect that was associated, and positively correlated, with a hyperpolarization of the membrane potential and an increase in apparent membrane conductance. In simple cells, the period of postadaptation suppression was not consistently associated with a decrease in the grating modulated component of the evoked synaptic barrages (the F1 component). The generation of the hyperpolarization appears to be at least partially intrinsic to the recorded cells, because the induction of neuronal activity with the intracellular injection of current resulted in both a hyperpolarization of the membrane potential and a decrease in the spike response to either current injections or visual stimuli. Conversely, high-contrast visual stimulation could suppress the response to low-intensity sinusoidal current injection. We conclude that control of the membrane potential by intrinsic neuronal mechanisms contributes importantly to the adaptation of neuronal responsiveness to varying levels of contrast. This feedback mechanism, internal to cortical neurons, provides them with the ability to continually adjust their responsiveness as a function of their history of synaptic and action potential activity.},
	Author = {Sanchez-Vives, M V and Nowak, L G and McCormick, D A},
	Date-Added = {2014-09-11 17:58:19 +0000},
	Date-Modified = {2014-09-11 17:58:49 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {sleep; slow oscillations; Neocortex; cat; spontaneous activity; in vivo; Anesthesia},
	Mesh = {Adaptation, Ocular; Animals; Cats; Contrast Sensitivity; Electric Stimulation; Electrophysiology; Evoked Potentials, Visual; Membrane Potentials; Neurons; Photic Stimulation; Potassium Channels; Signal Transduction; Visual Cortex},
	Month = {Jun},
	Number = {11},
	Pages = {4267-85},
	Pmid = {10818163},
	Pst = {ppublish},
	Title = {Membrane mechanisms underlying contrast adaptation in cat area 17 in vivo},
	Volume = {20},
	Year = {2000},
	File = {papers/Sanchez-Vives_JNeurosci2000.pdf}}

@article{Krosigk:1993,
	Abstract = {Spindle waves are a prototypical example of synchronized oscillations, a common feature of neuronal activity in thalamic and cortical systems in sleeping and waking animals. Spontaneous spindle waves recorded from slices of the ferret lateral geniculate nucleus were generated by rebound burst firing in relay cells. This rebound burst firing resulted from inhibitory postsynaptic potentials arriving from the perigeniculate nucleus, the cells of which were activated by burst firing in relay neurons. Reduction of gamma-aminobutyric acidA (GABAA) receptor-mediated inhibition markedly enhanced GABAB inhibitory postsynaptic potentials in relay cells and subsequently generated a slowed and rhythmic population activity resembling that which occurs during an absence seizure. Pharmacological block of GABAB receptors abolished this seizure-like activity but not normal spindle waves, suggesting that GABAB antagonists may be useful in the treatment of absence seizures.},
	Author = {von Krosigk, M and Bal, T and McCormick, D A},
	Date-Added = {2014-09-11 14:29:58 +0000},
	Date-Modified = {2014-09-11 14:29:58 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Baclofen; Bicuculline; Calcium; Epilepsy, Absence; Ferrets; Geniculate Bodies; Membrane Potentials; Neurons; Potassium; Receptors, Amino Acid; Receptors, GABA-A; Receptors, Glutamate; Receptors, Kainic Acid; Receptors, N-Methyl-D-Aspartate},
	Month = {Jul},
	Number = {5119},
	Pages = {361-4},
	Pmid = {8392750},
	Pst = {ppublish},
	Title = {Cellular mechanisms of a synchronized oscillation in the thalamus},
	Volume = {261},
	Year = {1993}}

@article{Steriade:1993d,
	Abstract = {Sleep is characterized by synchronized events in billions of synaptically coupled neurons in thalamocortical systems. The activation of a series of neuromodulatory transmitter systems during awakening blocks low-frequency oscillations, induces fast rhythms, and allows the brain to recover full responsiveness. Analysis of cortical and thalamic networks at many levels, from molecules to single neurons to large neuronal assemblies, with a variety of techniques, ranging from intracellular recordings in vivo and in vitro to computer simulations, is beginning to yield insights into the mechanisms of the generation, modulation, and function of brain oscillations.},
	Author = {Steriade, M and McCormick, D A and Sejnowski, T J},
	Date-Added = {2014-09-11 14:29:55 +0000},
	Date-Modified = {2014-09-11 18:37:40 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Arousal; Cerebral Cortex; Electroencephalography; Sleep; Thalamus},
	Month = {Oct},
	Number = {5134},
	Pages = {679-85},
	Pmid = {8235588},
	Pst = {ppublish},
	Title = {Thalamocortical oscillations in the sleeping and aroused brain},
	Volume = {262},
	Year = {1993},
	File = {papers/Steriade_Science1993.pdf}}

@article{Blumenfeld:2000,
	Abstract = {Absence seizures (3-4 Hz) and sleep spindles (6-14 Hz) occur mostly during slow-wave sleep and have been hypothesized to involve the same corticothalamic network. However, the mechanism by which this network transforms from one form of activity to the other is not well understood. Here we examine this question using ferret lateral geniculate nucleus slices and stimulation of the corticothalamic tract. A feedback circuit, meant to mimic the cortical influence in vivo, was arranged such that thalamic burst firing resulted in stimulation of the corticothalamic tract. Stimuli were either single shocks to mimic normal action potential firing by cortical neurons or high-frequency bursts (six shocks at 200 Hz) to simulate increased cortical firing, such as during seizures. With one corticothalamic stimulus per thalamic burst, 6-10 Hz oscillations resembling spindle waves were generated. However, if the stimulation was a burst, the network immediately transformed into a 3-4 Hz paroxysmal oscillation. This transition was associated with a strong increase in the burst firing of GABAergic perigeniculate neurons. In addition, thalamocortical neurons showed a transition from fast (100-150 msec) IPSPs to slow ( approximately 300 msec) IPSPs. The GABA(B) receptor antagonist CGP 35348 blocked the slow IPSPs and converted the 3-4 Hz paroxysmal oscillations back to 6-10 Hz spindle waves. Conversely, the GABA(A) receptor antagonist picrotoxin blocked spindle frequency oscillations resulting in 3-4 Hz oscillations with either single or burst stimuli. We suggest that differential activation of thalamic GABA(A) and GABA(B) receptors in response to varying corticothalamic input patterns may be critical in setting the oscillation frequency of thalamocortical network interactions.},
	Author = {Blumenfeld, H and McCormick, D A},
	Date-Added = {2014-09-11 14:28:46 +0000},
	Date-Modified = {2014-09-11 14:28:46 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Cerebral Cortex; Electric Stimulation; Evoked Potentials; Female; Ferrets; GABA Antagonists; Geniculate Bodies; Male; Microelectrodes; Nerve Net; Neural Conduction; Neurons; Organophosphorus Compounds; Picrotoxin; Reaction Time; Thalamus; gamma-Aminobutyric Acid},
	Month = {Jul},
	Number = {13},
	Pages = {5153-62},
	Pmid = {10864972},
	Pst = {ppublish},
	Title = {Corticothalamic inputs control the pattern of activity generated in thalamocortical networks},
	Volume = {20},
	Year = {2000}}

@article{McCormick:2001,
	Abstract = {The highly interconnected networks of the mammalian forebrain can generate a wide variety of synchronized activities, including those underlying epileptic seizures, which often appear as a transformation of otherwise normal brain rhythms. The cerebral cortex and hippocampus are particularly prone to the generation of the large, synchronized bursts of activity underlying many forms of seizures owing to strong recurrent excitatory connections, the presence of intrinsically burst-generating neurons, ephaptic interactions among closely spaced neurons, and synaptic plasticity. The simplest form of epileptiform activity in these structures is the interictal spike, a synchronized burst of action potentials generated by recurrent excitation, followed by a period of hyperpolarization, in a localized pool of pyramidal neurons. Seizures can also be generated in response to a loss of balance between excitatory and inhibitory influences and can take the form of either tonic depolarizations or repetitive, rhythmic burst discharges, either as clonic or spike-wave activity, again mediated both by intrinsic membrane properties and synaptic interactions. The interaction of the cerebral cortex and the thalamus, in conjunction with intrathalamic communication, can also generate spike waves similar to those occurring during human absence seizure discharges. Although epileptic syndromes and their causes are diverse, the cellular mechanisms of seizure generation appear to fall into only two categories: rhythmic or tonic "runaway" excitation or the synchronized and rhythmic interplay between excitatory and inhibitory neurons and membrane conductances.},
	Author = {McCormick, D A and Contreras, D},
	Date-Added = {2014-09-11 14:28:36 +0000},
	Date-Modified = {2014-09-11 14:28:36 +0000},
	Doi = {10.1146/annurev.physiol.63.1.815},
	Journal = {Annu Rev Physiol},
	Journal-Full = {Annual review of physiology},
	Mesh = {Animals; Brain; Electroencephalography; Epilepsy; Humans; Neural Pathways; Neurons},
	Pages = {815-46},
	Pmid = {11181977},
	Pst = {ppublish},
	Title = {On the cellular and network bases of epileptic seizures},
	Volume = {63},
	Year = {2001},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.physiol.63.1.815}}

@article{McCormick:2002,
	Abstract = {The cerebral cortex and thalamus can both generate cyclical oscillations of neuronal activity. Within the thalamus, sleep spindles are generated as a recurrent interaction between thalamocortical and thalamic reticular cells. Abnormally strong activation of the inhibitory thalamic reticular neurons can result in the transformation of this normal rhythm into one that resembles that underlying absence seizures. The cerebral cortex can generate periodic activity at < 1 Hz through recurrent excitation that is controlled by inhibition. Again, loss of inhibitory control allows this normal activity to become epileptiform. Together, the cerebral cortex and thalamus can form cyclical loops of activity that may contribute to some forms of epileptic seizures. It is proposed that hypsarrhythmic activity that is characteristic of children with infantile spasms may be generated through abnormal, locally synchronized bursts of activity within the cerebral cortex.},
	Author = {McCormick, David A},
	Date-Added = {2014-09-11 14:28:28 +0000},
	Date-Modified = {2014-09-11 14:28:28 +0000},
	Journal = {Int Rev Neurobiol},
	Journal-Full = {International review of neurobiology},
	Mesh = {Cerebral Cortex; Electroencephalography; Epilepsy, Absence; Humans; Oscillometry; Periodicity; Reference Values; Thalamus},
	Pages = {99-114},
	Pmid = {12040908},
	Pst = {ppublish},
	Title = {Cortical and subcortical generators of normal and abnormal rhythmicity},
	Volume = {49},
	Year = {2002}}

@article{Huguenard:2007,
	Abstract = {The circuitry within the thalamus creates an intrinsic oscillatory unit whose function depends critically on reciprocal synaptic connectivity between excitatory thalamocortical relay neurons and inhibitory thalamic reticular neurons along with a robust post-inhibitory rebound mechanism in relay neurons. Feedforward and feedback connections between cortex and thalamus reinforce the thalamic oscillatory activity into larger thalamocortical networks to generate sleep spindles and spike-wave discharge of generalized absence epilepsy. The degree of synchrony within the thalamic network seems to be crucial in determining whether normal (spindle) or pathological (spike-wave) oscillations occur, and recent studies show that regulation of excitability in the reticular nucleus leads to dynamical modulation of the state of the thalamic circuit and provide a basis for explaining how a variety of unrelated genetic alterations might lead to the spike-wave phenotype. In addition, given the central role of the reticular nucleus in generating spike-wave discharge, these studies have suggested specific interventions that would prevent seizures while still allowing normal spindle generation to occur. This review is part of the INMED/TINS special issue Physiogenic and pathogenic oscillations: the beauty and the beast, based on presentations at the annual INMED/TINS symposium (http://inmednet.com).},
	Author = {Huguenard, John R and McCormick, David A},
	Date-Added = {2014-09-11 14:27:32 +0000},
	Date-Modified = {2014-09-11 14:27:32 +0000},
	Doi = {10.1016/j.tins.2007.05.007},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Mesh = {Animals; Biological Clocks; Nonlinear Dynamics; Prosencephalon; Thalamus},
	Month = {Jul},
	Number = {7},
	Pages = {350-6},
	Pmid = {17544519},
	Pst = {ppublish},
	Title = {Thalamic synchrony and dynamic regulation of global forebrain oscillations},
	Volume = {30},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tins.2007.05.007}}

@article{Frohlich:2010,
	Abstract = {Local field potentials and the underlying endogenous electric fields (EFs) are traditionally considered to be epiphenomena of structured neuronal network activity. Recently, however, externally applied EFs have been shown to modulate pharmacologically evoked network activity in rodent hippocampus. In contrast, very little is known about the role of endogenous EFs during physiological activity states in neocortex. Here, we used the neocortical slow oscillation in vitro as a model system to show that weak sinusoidal and naturalistic EFs enhance and entrain physiological neocortical network activity with an amplitude threshold within the range of in vivo endogenous field strengths. Modulation of network activity by positive and negative feedback fields based on the network activity in real-time provide direct evidence for a feedback loop between neuronal activity and endogenous EF. This significant susceptibility of active networks to EFs that only cause small changes in membrane potential in individual neurons suggests that endogenous EFs could guide neocortical network activity.},
	Author = {Fr{\"o}hlich, Flavio and McCormick, David A},
	Date-Added = {2014-09-11 14:27:22 +0000},
	Date-Modified = {2014-09-11 14:27:22 +0000},
	Doi = {10.1016/j.neuron.2010.06.005},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Computer Simulation; Electric Stimulation; Evoked Potentials; Ferrets; Male; Models, Neurological; Neocortex; Nerve Net; Neurons; Nonlinear Dynamics; Oscillometry},
	Month = {Jul},
	Number = {1},
	Pages = {129-43},
	Pmc = {PMC3139922},
	Pmid = {20624597},
	Pst = {ppublish},
	Title = {Endogenous electric fields may guide neocortical network activity},
	Volume = {67},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2010.06.005}}

@article{Foust:2010,
	Abstract = {Purkinje neurons are the output cells of the cerebellar cortex and generate spikes in two distinct modes, known as simple and complex spikes. Revealing the point of origin of these action potentials, and how they conduct into local axon collaterals, is important for understanding local and distal neuronal processing and communication. By using a recent improvement in voltage-sensitive dye imaging technique that provided exceptional spatial and temporal resolution, we were able to resolve the region of spike initiation as well as follow spike propagation into axon collaterals for each action potential initiated on single trials. All fast action potentials, for both simple and complex spikes, whether occurring spontaneously or in response to a somatic current pulse or synaptic input, initiated in the axon initial segment. At discharge frequencies of less than approximately 250 Hz, spikes propagated faithfully through the axon and axon collaterals, in a saltatory manner. Propagation failures were only observed for very high frequencies or for the spikelets associated with complex spikes. These results demonstrate that the axon initial segment is a critical decision point in Purkinje cell processing and that the properties of axon branch points are adjusted to maintain faithful transmission.},
	Author = {Foust, Amanda and Popovic, Marko and Zecevic, Dejan and McCormick, David A},
	Date-Added = {2014-09-11 14:27:18 +0000},
	Date-Modified = {2014-09-11 14:27:18 +0000},
	Doi = {10.1523/JNEUROSCI.0552-10.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Action Potentials; Animals; Axons; Biophysics; Cerebellum; Electric Stimulation; Green Fluorescent Proteins; Guanine Nucleotide Exchange Factors; Mice; Mice, Transgenic; Nerve Fibers; Neuropeptides; Patch-Clamp Techniques; Purkinje Cells; Voltage-Sensitive Dye Imaging; tau Proteins},
	Month = {May},
	Number = {20},
	Pages = {6891-902},
	Pmc = {PMC2990270},
	Pmid = {20484631},
	Pst = {ppublish},
	Title = {Action potentials initiate in the axon initial segment and propagate through axon collaterals reliably in cerebellar Purkinje neurons},
	Volume = {30},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0552-10.2010}}

@article{Tahvildari:2012,
	Abstract = {The neocortex depends upon a relative balance of recurrent excitation and inhibition for its operation. During spontaneous Up states, cortical pyramidal cells receive proportional barrages of excitatory and inhibitory synaptic potentials. Many of these synaptic potentials arise from the activity of nearby neurons, although the identity of these cells is relatively unknown, especially for those underlying the generation of inhibitory synaptic events. To address these fundamental questions, we developed an in vitro submerged slice preparation of the mouse entorhinal cortex that generates robust and regular spontaneous recurrent network activity in the form of the slow oscillation. By performing whole-cell recordings from multiple cell types identified with green fluorescent protein expression and electrophysiological and/or morphological properties, we show that distinct functional subpopulations of neurons exist in the entorhinal cortex, with large variations in contribution to the generation of balanced excitation and inhibition during the slow oscillation. The most active neurons during the slow oscillation are excitatory pyramidal and inhibitory fast spiking interneurons, receiving robust barrages of both excitatory and inhibitory synaptic potentials. Weak action potential activity was observed in stellate excitatory neurons and somatostatin-containing interneurons. In contrast, interneurons containing neuropeptide Y, vasoactive intestinal peptide, or the 5-hydroxytryptamine (serotonin) 3a receptor, were silent. Our data demonstrate remarkable functional specificity in the interactions between different excitatory and inhibitory cortical neuronal subtypes, and suggest that it is the large recurrent interaction between pyramidal neurons and fast spiking interneurons that is responsible for the generation of persistent activity that characterizes the depolarized states of the cortex.},
	Author = {Tahvildari, Babak and W{\"o}lfel, Markus and Duque, Alvaro and McCormick, David A},
	Date-Added = {2014-09-11 14:26:46 +0000},
	Date-Modified = {2014-09-11 14:26:46 +0000},
	Doi = {10.1523/JNEUROSCI.1181-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Biological Clocks; Cerebral Cortex; Excitatory Postsynaptic Potentials; Female; Humans; Inhibitory Postsynaptic Potentials; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neural Inhibition; Neurons; Organ Culture Techniques; Reaction Time},
	Month = {Aug},
	Number = {35},
	Pages = {12165-79},
	Pmc = {PMC3466092},
	Pmid = {22933799},
	Pst = {ppublish},
	Title = {Selective functional interactions between excitatory and inhibitory cortical neurons and differential contribution to persistent activity of the slow oscillation},
	Volume = {32},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.1181-12.2012}}

@article{Killackey:1995,
	Abstract = {The primary somatosensory cortex of small rodents is an isomorphic representation of the body surface. Similar representations are characteristic of the subcortical pathways, leading from the periphery to the cortex, and these representations develop in a sequence that begins at the periphery, and that ends in the cortex. Furthermore, central representations at all levels of the neural axis are altered by perinatal perturbations of the peripheral surface. This has led to the hypothesis that the periphery plays an instructional role in the formation of central neuronal structures. The morphology of this discrete organization has been examined thoroughly during the development of the thalamocortical projections. The mechanism(s) that underlies the formation of these representations remains unclear although some recent evidence suggests the involvement of activity-dependent processes that are modulated by 5-HT.},
	Author = {Killackey, H P and Rhoades, R W and Bennett-Clarke, C A},
	Date-Added = {2014-09-10 19:09:09 +0000},
	Date-Modified = {2014-09-10 19:37:03 +0000},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {development; activity-dependent; spontaneous activity; Sensory Deprivation; barrels; Somatosensory Cortex; topographic map; Serotonin; rat},
	Mesh = {Animals; Brain Mapping; Humans; Somatosensory Cortex},
	Month = {Sep},
	Number = {9},
	Pages = {402-7},
	Pmid = {7482806},
	Pst = {ppublish},
	Title = {The formation of a cortical somatotopic map},
	Volume = {18},
	Year = {1995},
	File = {papers/Killackey_TrendsNeurosci1995.pdf}}

@article{Vertes:1984,
	Author = {Vertes, R P},
	Date-Added = {2014-09-10 18:14:59 +0000},
	Date-Modified = {2014-09-10 18:19:25 +0000},
	Journal = {Prog Neurobiol},
	Journal-Full = {Progress in neurobiology},
	Keywords = {review literature; sleep; Spinal Cord; Brain Stem; Motor Activity; spontaneous activity},
	Mesh = {Animals; Brain Mapping; Brain Stem; Cardiovascular Physiological Phenomena; Cats; Cortical Synchronization; Eye Movements; Geniculate Bodies; Hippocampus; Humans; Locus Coeruleus; Muscle Contraction; Muscle Tonus; Occipital Lobe; Pons; Rats; Respiration; Reticular Formation; Sleep, REM},
	Number = {3},
	Pages = {241-88},
	Pmid = {6382442},
	Pst = {ppublish},
	Title = {Brainstem control of the events of REM sleep},
	Volume = {22},
	Year = {1984},
	File = {papers/Vertes_ProgNeurobiol1984.pdf}}

@article{Jouvet-Mounier:1970,
	Author = {Jouvet-Mounier, D and Astic, L and Lacote, D},
	Date-Added = {2014-09-10 15:19:30 +0000},
	Date-Modified = {2014-09-10 15:20:36 +0000},
	Doi = {10.1002/dev.420020407},
	Journal = {Dev Psychobiol},
	Journal-Full = {Developmental psychobiology},
	Keywords = {sleep; rat; cat; Guinea Pigs; development; behavior; Motor Activity; spontaneous activity; state},
	Mesh = {Age Factors; Animals; Animals, Newborn; Attention; Behavior, Animal; Cats; Circadian Rhythm; Electroencephalography; Guinea Pigs; Rats; Sleep; Sleep Stages; Wakefulness; Weaning},
	Number = {4},
	Pages = {216-39},
	Pmid = {5527153},
	Pst = {ppublish},
	Title = {Ontogenesis of the states of sleep in rat, cat, and guinea pig during the first postnatal month},
	Volume = {2},
	Year = {1970},
	File = {papers/Jouvet-Mounier_DevPsychobiol1970.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/dev.420020407}}

@article{Stelzner:1975,
	Author = {Stelzner, D J and Ershler, W B and Weber, E D},
	Date-Added = {2014-09-10 15:09:11 +0000},
	Date-Modified = {2014-09-10 15:10:49 +0000},
	Journal = {Exp Neurol},
	Journal-Full = {Experimental neurology},
	Keywords = {development; spontaneous activity; Spinal Cord; Brain; Cerebral Cortex; behavior; Motor Activity; rat;},
	Mesh = {Acute Disease; Age Factors; Animals; Animals, Newborn; Chronic Disease; Female; Gliosis; Locomotion; Motor Skills; Neural Pathways; Posture; Rats; Red Nucleus; Reflex, Abnormal; Spinal Cord; Spinal Cord Injuries},
	Month = {Jan},
	Number = {1},
	Pages = {156-77},
	Pmid = {1109335},
	Pst = {ppublish},
	Title = {Effects of spinal transection in neonatal and weanling rats: survival of function},
	Volume = {46},
	Year = {1975},
	File = {papers/Stelzner_ExpNeurol1975.pdf}}

@article{Altman:1975,
	Abstract = {In laboratory rats (Rattus norvegicus) aged 1 to 21 days emergence of postural and locomotor skills was studied in the open field and in experimental situations with homing used as motivation. Righting is mediated initially by curving and rocking of the trunk, later head and shoulder are rotated, and lastly the hindlimbs turn and provide co-ordinated support. Pivoting prodominates during the second half of the first week, crawling during most of the second week, and walking or running by the end of the second week. Balancing on narrow paths and compensating for lateral displacement on rotating rods mature later, as do various skills (climbing up or down on inclined surfaces, rods and ropes, and jumping across gaps) that require substantial hindlimb co-ordiantion.},
	Author = {Altman, J and Sudarshan, K},
	Date-Added = {2014-09-10 14:30:39 +0000},
	Date-Modified = {2014-09-10 14:31:31 +0000},
	Journal = {Anim Behav},
	Journal-Full = {Animal behaviour},
	Keywords = {development; Motor Activity; behavior; Locomotion; rat},
	Mesh = {Animals; Animals, Newborn; Female; Forelimb; Head; Hindlimb; Housing, Animal; Locomotion; Male; Motor Skills; Movement; Orientation; Posture; Rats},
	Month = {Nov},
	Number = {4},
	Pages = {896-920},
	Pmid = {1200422},
	Pst = {ppublish},
	Title = {Postnatal development of locomotion in the laboratory rat},
	Volume = {23},
	Year = {1975},
	File = {papers/Altman_AnimBehav1975.pdf}}

@article{Narayanan:1971,
	Author = {Narayanan, C H and Fox, M W and Hamburger, V},
	Date-Added = {2014-09-09 02:31:40 +0000},
	Date-Modified = {2014-09-10 14:57:16 +0000},
	Journal = {Behaviour},
	Journal-Full = {Behaviour},
	Keywords = {development; rat; fetal; Embryo; spontaneous activity; Motor Activity; Spinal Cord; sleep; behavior},
	Mesh = {Animals; Embryonic and Fetal Development; Female; Fetus; Motor Activity; Pregnancy; Pregnancy, Animal; Rats; Rats, Inbred Strains},
	Number = {1},
	Pages = {100-34},
	Pmid = {5157515},
	Pst = {ppublish},
	Title = {Prenatal development of spontaneous and evoked activity in the rat (Rattus norvegicus albinus)},
	Volume = {40},
	Year = {1971},
	File = {papers/Narayanan_Behaviour1971.pdf}}

@article{Blumberg:1994,
	Abstract = {Twitches of the limbs during REM sleep in adult mammals result from descending motor activation from the brainstem. In contrast, many spontaneous movements in embryos appear similar to REM-related twitches and result from the local firing of spinal motor neurons. To determine which mechanism produces twitches in neonates, we analyzed twitching in 5- and 8-day-old rat pups that had spinal cords transected in the lower thoracic region. This transection separated motor units controlling forelimb movements from motor units controlling hindlimb movements. Spinal transection did not significantly affect the amount of forelimb twitching. In contrast, the amount of hindlimb twitching in transected pups was reduced by only 35%-50%. Given that hindlimb twitching was not eliminated by spinal transection, it is concluded that there are 2 independent mechanisms producing twitches at these ages.},
	Author = {Blumberg, M S and Lucas, D E},
	Date-Added = {2014-09-08 20:28:18 +0000},
	Date-Modified = {2014-09-08 20:28:45 +0000},
	Journal = {Behav Neurosci},
	Journal-Full = {Behavioral neuroscience},
	Keywords = {Spinal Cord; Motor Activity; Motor Neurons; development; spontaneous activity; Movement; rat},
	Mesh = {Animals; Animals, Newborn; Brain Stem; Female; Forelimb; Hindlimb; Male; Motor Activity; Motor Neurons; Neural Pathways; Rats; Sleep, REM; Spinal Cord},
	Month = {Dec},
	Number = {6},
	Pages = {1196-202},
	Pmid = {7893412},
	Pst = {ppublish},
	Title = {Dual mechanisms of twitching during sleep in neonatal rats},
	Volume = {108},
	Year = {1994},
	File = {papers/Blumberg_BehavNeurosci1994.pdf}}

@article{Robinson:2000,
	Abstract = {Spontaneous motor activity (SMA) is a ubiquitous feature of fetal and infant behavior. Although SMA appears random, successive limb movements often occur in bouts. Bout organization was evident at all ages in fetal (embryonic day [E] 17-21) and infant (postnatal day [P] 1-9) rats, with nearly all bouts comprising 1-4 movements of different limbs. A computational model of SMA, including spontaneous activity of spinal motor neurons, intrasegmental and intersegmental interactions, recurrent inhibition, and descending influences, produced bouts with the same structure as that observed in perinatal rats. Consistent with the model, bouts were not eliminated on E20 after cervical spinal transection, suggesting that the brain is not necessary to produce bout organization. These investigations provide a foundation for understanding the contributions of SMA to neuromuscular and motor development.},
	Author = {Robinson, S R and Blumberg, M S and Lane, M S and Kreber, L A},
	Date-Added = {2014-09-08 20:24:42 +0000},
	Date-Modified = {2014-09-08 20:24:56 +0000},
	Journal = {Behav Neurosci},
	Journal-Full = {Behavioral neuroscience},
	Keywords = {Spinal Cord; Motor Activity; Motor Neurons; development; spontaneous activity; Movement; rat},
	Mesh = {Animals; Animals, Newborn; Female; Fetal Movement; Male; Motor Activity; Motor Neurons; Neuromuscular Junction; Pregnancy; Rats; Rats, Sprague-Dawley; Spinal Cord},
	Month = {Apr},
	Number = {2},
	Pages = {328-36},
	Pmid = {10832794},
	Pst = {ppublish},
	Title = {Spontaneous motor activity in fetal and infant rats is organized into discrete multilimb bouts},
	Volume = {114},
	Year = {2000},
	File = {papers/Robinson_BehavNeurosci2000.pdf}}

@article{Sokoloff:2000,
	Abstract = {In infant rats, huddling improves surface-to-volume ratios and provides metabolic savings during cold exposure. It is unclear, however, whether endothermy is also a necessary component of huddling. In the present experiment, huddles composed of infant Norway rats (2- or 8-day-olds), which produce heat endogenously, or Syrian golden hamsters (8-day-olds), which do not produce heat endogenously, were exposed to decreases in air temperature. Behavioral and physiological responses were monitored throughout the test. Rats, especially at 8 days of age, were better able to thermoregulate using huddling than hamsters, due in part to endogenous heat production. Furthermore, 8-day-old rats exhibited behavioral responses that promote heat retention, suggesting that both physiological and behavioral mechanisms contribute to effective thermoregulation during huddling in the cold.},
	Author = {Sokoloff, G and Blumberg, M S and Adams, M M},
	Date-Added = {2014-09-08 20:24:40 +0000},
	Date-Modified = {2014-09-08 20:25:30 +0000},
	Journal = {Behav Neurosci},
	Journal-Full = {Behavioral neuroscience},
	Keywords = {Thermodynamics; thermoregulation; development; spontaneous activity; Movement; rat},
	Mesh = {Adipose Tissue, Brown; Animals; Animals, Newborn; Body Temperature Regulation; Cricetinae; Energy Metabolism; Mesocricetus; Oxygen Consumption; Rats; Social Environment; Vocalization, Animal},
	Month = {Jun},
	Number = {3},
	Pages = {585-93},
	Pmid = {10883808},
	Pst = {ppublish},
	Title = {A comparative analysis of huddling in infant Norway rats and Syrian golden hamsters: does endothermy modulate behavior?},
	Volume = {114},
	Year = {2000}}

@article{Schouenborg:2004,
	Abstract = {The study of plasticity in the central nervous system is a major and very dynamic neuroscience research field with enormous clinical potential. Considerable advances in this field have been made during the past 10 years. It now appears that most circuits in the brain and spinal cord show plasticity and that they can be modified by experience. Knowledge of the mechanisms of plasticity in the nervous system is therefore essential for the understanding of how the nervous system is wired during development and how it adapts in response to changes in the body and environment. Recent findings indicate that functional sensorimotor modules probe the sensory signals from the body that are generated as a consequence of module specific activity and use this sensory feedback to calibrate the strength in its input-output connections. This experience-dependent signal adapts the circuitry in the sensorimotor module to the body anatomy and biomechanics.},
	Author = {Schouenborg, Jens},
	Date-Added = {2014-09-08 20:21:33 +0000},
	Date-Modified = {2014-09-08 20:22:21 +0000},
	Doi = {10.1016/j.conb.2004.10.009},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Keywords = {Spinal Cord; Motor Activity; Motor Neurons; development; spontaneous activity; Movement},
	Mesh = {Adaptation, Physiological; Animals; Central Nervous System; Feedback; Humans; Learning; Movement; Neural Pathways; Neuronal Plasticity; Sensation; Synaptic Transmission},
	Month = {Dec},
	Number = {6},
	Pages = {693-7},
	Pmid = {15582370},
	Pst = {ppublish},
	Title = {Learning in sensorimotor circuits},
	Volume = {14},
	Year = {2004},
	File = {papers/Schouenborg_CurrOpinNeurobiol2004.pdf}}

@article{Varela:2001,
	Abstract = {The emergence of a unified cognitive moment relies on the coordination of scattered mosaics of functionally specialized brain regions. Here we review the mechanisms of large-scale integration that counterbalance the distributed anatomical and functional organization of brain activity to enable the emergence of coherent behaviour and cognition. Although the mechanisms involved in large-scale integration are still largely unknown, we argue that the most plausible candidate is the formation of dynamic links mediated by synchrony over multiple frequency bands.},
	Author = {Varela, F and Lachaux, J P and Rodriguez, E and Martinerie, J},
	Date-Added = {2014-09-03 13:17:07 +0000},
	Date-Modified = {2014-09-03 13:18:55 +0000},
	Doi = {10.1038/35067550},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {synchrony; review literature; neurophysiology; in vivo; EEG; LFP; Cerebral Cortex; Neocortex; technique; Methods; Theoretical; Computational Biology},
	Mesh = {Animals; Attention; Brain; Cognition; Electrophysiology; Learning; Nerve Net},
	Month = {Apr},
	Number = {4},
	Pages = {229-39},
	Pmid = {11283746},
	Pst = {ppublish},
	Title = {The brainweb: phase synchronization and large-scale integration},
	Volume = {2},
	Year = {2001},
	File = {papers/Varela_NatRevNeurosci2001.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/35067550}}

@article{Collins:2001,
	Abstract = {We have measured intracellular free calcium ([Ca(2+)]i) using Fura-2 or Ca(2+)-sensitive microelectrodes in voltage-clamped neurones of the snail, Helix aspersa. Caffeine-induced transient increases in [Ca(2+)]i were normally followed by a brief fall of [Ca(2+)]i below its pre-caffeine level. We investigated the cause of this undershoot by raising [Ca(2+)]i; and by inhibiting the plasma membrane or endoplasmic reticulum Ca ATPases (PMCA or SERCA respectively). When the cell membrane potential was decreased from -60 to -25mV, steady-state [Ca(2+)]i increased. The caffeine-induced transients were smaller while the undershoots were larger than in control conditions. When the PMCA was inhibited by high pH the steady-state [Ca(2+)]i increased by 100-400nM. The caffeine-induced [Ca(2+)]i increase and the subsequent undershoot both became larger. Injection of orthovanadate, which inhibits the PMCA and increases [Ca(2+)]i, did not block either effect of caffeine. But when the SERCA was inhibited by cyclopiazonic acid the undershoot disappeared. The phosphodiesterase inhibitor IBMX did not influence the undershoot. These results suggest that the undershoot is generated by the Ca(2+)] ATPase of the stores rather than that of the plasma membrane. Since the undershoot increased as [Ca(2+)]i increased, we conclude that at higher levels of [Ca(2+)]i the stores refill more rapidly.},
	Author = {Collins, R O and Thomas, R C},
	Date-Added = {2014-09-03 13:14:40 +0000},
	Date-Modified = {2014-09-03 13:14:40 +0000},
	Doi = {10.1054/ceca.2001.0209},
	Journal = {Cell Calcium},
	Journal-Full = {Cell calcium},
	Mesh = {Animals; Caffeine; Calcium; Calcium-Transporting ATPases; Enzyme Inhibitors; Helix (Snails); Hydrogen-Ion Concentration; Indoles; Intracellular Fluid; Membrane Potentials; Neurons; Phosphodiesterase Inhibitors; Sarcoplasmic Reticulum},
	Month = {Jul},
	Number = {1},
	Pages = {41-8},
	Pmid = {11396986},
	Pst = {ppublish},
	Title = {The effect of calcium pump inhibitors on the response of intracellular calcium to caffeine in snail neurones},
	Volume = {30},
	Year = {2001},
	File = {papers/Collins_CellCalcium2001.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1054/ceca.2001.0209}}

@article{Rolston:2009,
	Abstract = {Commercially available data acquisition systems for multielectrode recording from freely moving animals are expensive, often rely on proprietary software, and do not provide detailed, modifiable circuit schematics. When used in conjunction with electrical stimulation, they are prone to prolonged, saturating stimulation artifacts that prevent the recording of short-latency evoked responses. Yet electrical stimulation is integral to many experimental designs, and critical for emerging brain-computer interfacing and neuroprosthetic applications. To address these issues, we developed an easy-to-use, modifiable, and inexpensive system for multielectrode neural recording and stimulation. Setup costs are less than US{\$}10,000 for 64 channels, an order of magnitude lower than comparable commercial systems. Unlike commercial equipment, the system recovers rapidly from stimulation and allows short-latency action potentials (<1 ms post-stimulus) to be detected, facilitating closed-loop applications and exposing neural activity that would otherwise remain hidden. To illustrate this capability, evoked activity from microstimulation of the rodent hippocampus is presented. System noise levels are similar to existing platforms, and extracellular action potentials and local field potentials can be recorded simultaneously. The system is modular, in banks of 16 channels, and flexible in usage: while primarily designed for in vivo use, it can be combined with commercial preamplifiers to record from in vitro multielectrode arrays. The system's open-source control software, NeuroRighter, is implemented in C#, with an easy-to-use graphical interface. As C# functions in a managed code environment, which may impact performance, analysis was conducted to ensure comparable speed to C++ for this application. Hardware schematics, layout files, and software are freely available. Since maintaining wired headstage connections with freely moving animals is difficult, we describe a new method of electrode-headstage coupling using neodymium magnets.},
	Author = {Rolston, John D and Gross, Robert E and Potter, Steve M},
	Date-Added = {2014-09-03 13:13:44 +0000},
	Date-Modified = {2014-09-03 13:13:44 +0000},
	Doi = {10.3389/neuro.16.012.2009},
	Journal = {Front Neuroeng},
	Journal-Full = {Frontiers in neuroengineering},
	Keywords = {data acquisition system; hippocampus; local field potential; microstimulation; multi-electrode array; population spike; recording; stimulation artifact},
	Pages = {12},
	Pmc = {PMC2722905},
	Pmid = {19668698},
	Pst = {epublish},
	Title = {A low-cost multielectrode system for data acquisition enabling real-time closed-loop processing with rapid recovery from stimulation artifacts},
	Volume = {2},
	Year = {2009},
	File = {papers/Rolston_FrontNeuroeng2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/neuro.16.012.2009}}

@article{Brickley:1998,
	Abstract = {Spatiotemporal correlations in the pattern of spontaneous and evoked retinal ganglion cell (RGC) activity are believed to influence the topographic organization of connections throughout the developing visual system. We have tested this hypothesis by examining the effects of interfering with these potential activity cues during development on the functional organization of binocular maps in the Xenopus frog optic tectum. Paired recordings combined with cross-correlation analyses demonstrated that exposing normal frogs to a continuous 1 Hz of stroboscopic illumination synchronized the firing of all three classes of RGC projecting to the tectum and induced similar patterns of temporally correlated activity across both lobes of the nucleus. Embryonic and eye-rotated larval animals were reared until early adulthood under equivalent stroboscopic conditions. The maps formed by each RGC class in the contralateral tectum showed normal topography and stratification after strobe rearing, but with consistently enlarged multiunit receptive fields. Maps of the ipsilateral eye, formed by crossed isthmotectal axons, showed significant disorder and misalignment with direct visual input from the retina, and in the eye-rotated animals complete compensatory reorientation of these maps usually induced by this procedure failed to occur. These findings suggest that refinement of retinal arbors in the tectum and the ability of crossed isthmotectal arbors to establish binocular convergence with these retinal afferents are disrupted when they all fire together. Our data thus provide direct experimental evidence that spatiotemporal activity patterns within and between the two eyes regulate the precision of their developing connections.},
	Author = {Brickley, S G and Dawes, E A and Keating, M J and Grant, S},
	Date-Added = {2014-09-03 13:09:34 +0000},
	Date-Modified = {2014-09-03 13:12:12 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {activity manipulation; activity-development; development; Xenopus; visual system; optic tectum; neurophysiology; topographic map; ocular dominance; frog},
	Mesh = {Aging; Animals; Brain Mapping; Electrophysiology; Embryo, Nonmammalian; Larva; Neuronal Plasticity; Ocular Physiological Phenomena; Photic Stimulation; Retina; Retinal Ganglion Cells; Rotation; Superior Colliculi; Time Factors; Vision, Binocular; Xenopus},
	Month = {Feb},
	Number = {4},
	Pages = {1491-504},
	Pmid = {9454857},
	Pst = {ppublish},
	Title = {Synchronizing retinal activity in both eyes disrupts binocular map development in the optic tectum},
	Volume = {18},
	Year = {1998},
	File = {papers/Brickley_JNeurosci1998.pdf}}

@article{Leinekugel:1997,
	Abstract = {We asked whether GABA(A) and NMDA receptors may act in synergy in neonatal hippocampal slices, at a time when GABA exerts a depolarizing action. The GABA(A) receptor agonist isoguvacine reduced the voltage-dependent Mg2+ block of single NMDA channels recorded in cell-attached configuration from P(2-5) CA3 pyramidal neurons and potentiated the Ca2+ influx through NMDA channels. The synaptic response evoked by electrical stimulation of stratum radiatum was mediated by a synergistic interaction between GABA(A) and NMDA receptors. Network-driven Giant Depolarizing Potentials, which are a typical feature of the neonatal hippocampal network, provided coactivation of GABA(A) and NMDA receptors and were associated with spontaneous and synchronous Ca2+ increases in CA3 pyramidal neurons. Thus, at the early stages of development, GABA is a major excitatory transmitter that acts in synergy with NMDA receptors. This provides in neonatal neurons a hebbian stimulation that may be involved in neuronal plasticity and network formation in the developing hippocampus.},
	Author = {Leinekugel, X and Medina, I and Khalilov, I and Ben-Ari, Y and Khazipov, R},
	Date-Added = {2014-09-03 13:07:24 +0000},
	Date-Modified = {2014-09-03 13:08:40 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {activity-dependent; development; hippocampus; rat; in vitro; GABA},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Calcium; Calcium Channels; GABA-A Receptor Agonists; Hippocampus; Ion Channel Gating; Isonicotinic Acids; Magnesium; Male; Membrane Potentials; Neuronal Plasticity; Rats; Rats, Wistar; Receptors, GABA-A; Receptors, N-Methyl-D-Aspartate; Synapses},
	Month = {Feb},
	Number = {2},
	Pages = {243-55},
	Pmid = {9052795},
	Pst = {ppublish},
	Title = {Ca2+ oscillations mediated by the synergistic excitatory actions of GABA(A) and NMDA receptors in the neonatal hippocampus},
	Volume = {18},
	Year = {1997},
	File = {papers/Leinekugel_Neuron1997.pdf}}

@article{Akerman:2006a,
	Abstract = {Neurotransmission during development regulates synaptic maturation in neural circuits, but the contribution of different neurotransmitter systems is unclear. We investigated the role of GABAA receptor-mediated Cl- conductances in the development of synaptic responses in the Xenopus visual system. Intracellular Cl- concentration ([Cl-]i) was found to be high in immature tectal neurons and then falls over a period of several weeks. GABAergic synapses are present at early stages of tectal development and, when activated by optic nerve stimulation or visual stimuli, induce sustained depolarizing Cl- conductances that facilitate retinotectal transmission by NMDA receptors. To test whether depolarizing GABAergic inputs cooperate with NMDA receptors during activity-dependent maturation of glutamatergic synapses, we prematurely reduced [Cl-]i in tectal neurons in vivo by expressing the Cl- transporter KCC2. This blocked the normal developmental increase in AMPA receptor-mediated retinotectal transmission and increased GABAergic synaptic input to tectal neurons. Therefore, depolarizing GABAergic transmission plays a pivotal role in the maturation of excitatory transmission and controls the balance of excitation and inhibition in the developing retinotectal circuit.},
	Author = {Akerman, Colin J and Cline, Hollis T},
	Date-Added = {2014-09-03 13:04:33 +0000},
	Date-Modified = {2014-09-03 13:05:52 +0000},
	Doi = {10.1523/JNEUROSCI.0319-06.2006},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Chloride Channels; GABA; development; Xenopus; frog; in vivo; activity-dependent},
	Mesh = {Animals; Cell Membrane; Chloride Channels; Electric Conductivity; Excitatory Postsynaptic Potentials; Larva; Membrane Potentials; Neural Inhibition; Synaptic Transmission; Visual Pathways; Xenopus laevis; gamma-Aminobutyric Acid},
	Month = {May},
	Number = {19},
	Pages = {5117-30},
	Pmid = {16687503},
	Pst = {ppublish},
	Title = {Depolarizing GABAergic conductances regulate the balance of excitation to inhibition in the developing retinotectal circuit in vivo},
	Volume = {26},
	Year = {2006},
	File = {papers/Akerman_JNeurosci2006a.pdf}}

@article{Munz:2014,
	Abstract = {We examined how correlated firing controls axon remodeling, using in vivo time-lapse imaging and electrophysiological analysis of individual retinal ganglion cell (RGC) axons that were visually stimulated either synchronously or asynchronously relative to neighboring inputs in the Xenopus laevis optic tectum. RGCs stimulated out of synchrony rapidly lost the ability to drive tectal postsynaptic partners while their axons grew and added many new branches. In contrast, synchronously activated RGCs produced fewer new branches, but these were more stable. The effects of synchronous activation were prevented by the inhibition of neurotransmitter release and N-methyl-D-aspartate receptor (NMDAR) blockade, which is consistent with a role for synaptic NMDAR activation in the stabilization of axonal branches and suppression of further exploratory branch addition.},
	Author = {Munz, Martin and Gobert, Delphine and Schohl, Anne and Poqu{\'e}russe, Jessie and Podgorski, Kaspar and Spratt, Perry and Ruthazer, Edward S},
	Date-Added = {2014-09-02 15:39:41 +0000},
	Date-Modified = {2014-09-02 15:40:21 +0000},
	Doi = {10.1126/science.1251593},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {activity-dependent; Xenopus; frog; hebbian; development; optic tectum; visual system},
	Mesh = {Animals; Axons; Electrical Synapses; Neuronal Plasticity; Photic Stimulation; Psychological Theory; Receptors, N-Methyl-D-Aspartate; Retinal Ganglion Cells; Superior Colliculi; Synaptic Transmission; Time-Lapse Imaging; Xenopus laevis},
	Month = {May},
	Number = {6186},
	Pages = {904-9},
	Pmid = {24855269},
	Pst = {ppublish},
	Title = {Rapid Hebbian axonal remodeling mediated by visual stimulation},
	Volume = {344},
	Year = {2014},
	File = {papers/Munz_Science2014.pdf}}

@article{Schwartz:2001,
	Abstract = {The population of neurons participating in an epileptiform event varies from moment to moment. Most techniques currently used to localize epileptiform events in vivo have spatial and/or temporal sampling limitations. Here we show in an animal model that optical imaging based on intrinsic signals is an excellent method for in vivo mapping of clinically relevant epileptiform events, such as interictal spikes, ictal onsets, ictal spread and secondary homotopic foci. In addition, a decrease in the optical signal correlates spatially with a decrease in neuronal activity recorded from cortex surrounding an epileptic focus. Optical mapping of epilepsy might be a useful adjunct in the surgical treatment of neocortical epilepsy, which critically depends on the precise localization of intrinsically epileptogenic neurons.},
	Author = {Schwartz, T H and Bonhoeffer, T},
	Date-Added = {2014-08-29 18:48:38 +0000},
	Date-Modified = {2014-08-29 18:49:24 +0000},
	Doi = {10.1038/nm0901-1063},
	Journal = {Nat Med},
	Journal-Full = {Nature medicine},
	Keywords = {optical physiology; optical imaging; intrinsic signal; in vivo; ferret; epilepsy; seizure; wholeBrain},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Electrophysiology; Epilepsies, Partial; Ferrets; Optics and Photonics},
	Month = {Sep},
	Number = {9},
	Pages = {1063-7},
	Pmid = {11533712},
	Pst = {ppublish},
	Title = {In vivo optical mapping of epileptic foci and surround inhibition in ferret cerebral cortex},
	Volume = {7},
	Year = {2001},
	File = {papers/Schwartz_NatMed2001.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nm0901-1063}}

@article{Suarez:2014,
	Abstract = {Bilateral integration of sensory and associative brain processing is achieved by precise connections between homologous regions in the two hemispheres via the corpus callosum. These connections form postnatally, and unilateral deprivation of sensory or spontaneous cortical activity during a critical period severely disrupts callosal wiring. However, little is known about how this early activity affects precise circuit formation. Here, using in utero electroporation of reporter genes, optogenetic constructs, and direct disruption of activity in callosal neurons combined with whisker ablations, we show that balanced interhemispheric activity, and not simply intact cortical activity in either hemisphere, is required for functional callosal targeting. Moreover, bilateral ablation of whiskers in symmetric or asymmetric configurations shows that spatially symmetric interhemispheric activity is required for appropriate callosal targeting. Our findings reveal a principle governing axon targeting, where spatially balanced activity between regions is required to establish their appropriate connectivity.},
	Author = {Su{\'a}rez, Rodrigo and Fenlon, Laura R and Marek, Roger and Avitan, Lilach and Sah, Pankaj and Goodhill, Geoffrey J and Richards, Linda J},
	Date-Added = {2014-08-29 18:12:23 +0000},
	Date-Modified = {2014-08-29 18:42:02 +0000},
	Doi = {10.1016/j.neuron.2014.04.040},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Corpus Callosum; Neocortex; Cerebral Cortex; development; activity-development; mirror symmetry; wholeBrain},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Corpus Callosum; Female; Functional Laterality; Mice; Neural Pathways; Pregnancy},
	Month = {Jun},
	Number = {6},
	Pages = {1289-98},
	Pmid = {24945772},
	Pst = {ppublish},
	Title = {Balanced interhemispheric cortical activity is required for correct targeting of the corpus callosum},
	Volume = {82},
	Year = {2014},
	File = {papers/Suárez_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.04.040}}

@article{Brandes:2001,
	Author = {Ulrik Brandes},
	Date-Added = {2014-08-27 21:06:11 +0000},
	Date-Modified = {2014-08-27 21:07:09 +0000},
	Journal = {Journal of Mathematical Sociology},
	Keywords = {network analysis; graph theory; Mathematics; Theoretical; Computational Biology},
	Pages = {163--177},
	Title = {A Faster Algorithm for Betweenness Centrality},
	Volume = {25},
	Year = {2001},
	File = {papers/Brandes_JournalofMathematicalSociology2001.pdf}}

@article{Sporns:2005,
	Abstract = {The connection matrix of the human brain (the human "connectome") represents an indispensable foundation for basic and applied neurobiological research. However, the network of anatomical connections linking the neuronal elements of the human brain is still largely unknown. While some databases or collations of large-scale anatomical connection patterns exist for other mammalian species, there is currently no connection matrix of the human brain, nor is there a coordinated research effort to collect, archive, and disseminate this important information. We propose a research strategy to achieve this goal, and discuss its potential impact.},
	Author = {Sporns, Olaf and Tononi, Giulio and K{\"o}tter, Rolf},
	Date-Added = {2014-08-27 20:55:40 +0000},
	Date-Modified = {2014-08-27 20:58:44 +0000},
	Doi = {10.1371/journal.pcbi.0010042},
	Journal = {PLoS Comput Biol},
	Journal-Full = {PLoS computational biology},
	Keywords = {connectivity; connectome; connectomics; network analysis; graph theory; Human; wholeBrain},
	Mesh = {Animals; Brain; Humans; Nerve Net; Neurons; Synapses},
	Month = {Sep},
	Number = {4},
	Pages = {e42},
	Pmc = {PMC1239902},
	Pmid = {16201007},
	Pst = {ppublish},
	Title = {The human connectome: A structural description of the human brain},
	Volume = {1},
	Year = {2005},
	File = {papers/Sporns_PLoSComputBiol2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.0010042}}

@article{Smith:2013,
	Abstract = {Spontaneous fluctuations in activity in different parts of the brain can be used to study functional brain networks. We review the use of resting-state functional MRI (rfMRI) for the purpose of mapping the macroscopic functional connectome. After describing MRI acquisition and image-processing methods commonly used to generate data in a form amenable to connectomics network analysis, we discuss different approaches for estimating network structure from that data. Finally, we describe new possibilities resulting from the high-quality rfMRI data being generated by the Human Connectome Project and highlight some upcoming challenges in functional connectomics.},
	Author = {Smith, Stephen M and Vidaurre, Diego and Beckmann, Christian F and Glasser, Matthew F and Jenkinson, Mark and Miller, Karla L and Nichols, Thomas E and Robinson, Emma C and Salimi-Khorshidi, Gholamreza and Woolrich, Mark W and Barch, Deanna M and U{\u g}urbil, Kamil and Van Essen, David C},
	Date-Added = {2014-08-27 20:40:21 +0000},
	Date-Modified = {2014-08-27 20:41:34 +0000},
	Doi = {10.1016/j.tics.2013.09.016},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {connectomics; network modelling; resting-state fMRI; human; default mode network; wholeBrain},
	Mesh = {Animals; Brain; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Nerve Net; Neural Pathways; Oxygen; Rest},
	Month = {Dec},
	Number = {12},
	Pages = {666-82},
	Pmc = {PMC4004765},
	Pmid = {24238796},
	Pst = {ppublish},
	Title = {Functional connectomics from resting-state fMRI},
	Volume = {17},
	Year = {2013},
	File = {papers/Smith_TrendsCognSci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2013.09.016}}

@article{Nadel:1990,
	Author = {Nadel, L},
	Date-Added = {2014-08-27 16:13:14 +0000},
	Date-Modified = {2014-08-27 17:50:41 +0000},
	Journal = {Ann N Y Acad Sci},
	Journal-Full = {Annals of the New York Academy of Sciences},
	Keywords = {goal directed behavior; rat; rodent; learning; memory; development; behavior; Locomotion; Motor Activity},
	Mesh = {Animals; Cognition; Cues; Exploratory Behavior; Female; Hippocampus; Humans; Male; Models, Neurological; Neuronal Plasticity; Orientation; Rats; Spatial Behavior},
	Pages = {613-26; discussion 626-36},
	Pmid = {2075964},
	Pst = {ppublish},
	Title = {Varieties of spatial cognition. Psychobiological considerations},
	Volume = {608},
	Year = {1990},
	File = {papers/Nadel_AnnNYAcadSci1990.pdf}}

@article{Zhang:2014,
	Abstract = {Top-down modulation of sensory processing allows the animal to select inputs most relevant to current tasks. We found that the cingulate (Cg) region of the mouse frontal cortex powerfully influences sensory processing in the primary visual cortex (V1) through long-range projections that activate local γ-aminobutyric acid-ergic (GABAergic) circuits. Optogenetic activation of Cg neurons enhanced V1 neuron responses and improved visual discrimination. Focal activation of Cg axons in V1 caused a response increase at the activation site but a decrease at nearby locations (center-surround modulation). Whereas somatostatin-positive GABAergic interneurons contributed preferentially to surround suppression, vasoactive intestinal peptide-positive interneurons were crucial for center facilitation. Long-range corticocortical projections thus act through local microcircuits to exert spatially specific top-down modulation of sensory processing.},
	Author = {Zhang, Siyu and Xu, Min and Kamigaki, Tsukasa and Hoang Do, Johnny Phong and Chang, Wei-Cheng and Jenvay, Sean and Miyamichi, Kazunari and Luo, Liqun and Dan, Yang},
	Date-Added = {2014-08-27 15:52:21 +0000},
	Date-Modified = {2014-08-27 15:52:21 +0000},
	Doi = {10.1126/science.1254126},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Animals, Genetically Modified; Discrimination (Psychology); GABAergic Neurons; Gyrus Cinguli; Interneurons; Mice; Mice, Inbred C57BL; Neural Inhibition; Photic Stimulation; Somatostatin; Visual Cortex; Visual Perception},
	Month = {Aug},
	Number = {6197},
	Pages = {660-5},
	Pmid = {25104383},
	Pst = {ppublish},
	Title = {Selective attention. Long-range and local circuits for top-down modulation of visual cortex processing},
	Volume = {345},
	Year = {2014},
	File = {papers/Zhang_Science2014.pdf}}

@article{An:2014,
	Abstract = {Self-generated neuronal activity originating from subcortical regions drives early spontaneous motor activity, which is a hallmark of the developing sensorimotor system. However, the neural activity patterns and role of primary motor cortex (M1) in these early movements are still unknown. Combining voltage-sensitive dye imaging (VSDI) with simultaneous extracellular multielectrode recordings in postnatal day 3 (P3)-P5 rat primary somatosensory cortex (S1) and M1 in vivo, we observed that tactile forepaw stimulation induced spindle bursts in S1 and gamma and spindle bursts in M1. Approximately 40% of the spontaneous gamma and spindle bursts in M1 were driven by early motor activity, whereas 23.7% of the M1 bursts triggered forepaw movements. Approximately 35% of the M1 bursts were uncorrelated to movements and these bursts had significantly fewer spikes and shorter burst duration. Focal electrical stimulation of layer V neurons in M1 mimicking physiologically relevant 40 Hz gamma or 10 Hz spindle burst activity reliably elicited forepaw movements. We conclude that M1 is already involved in somatosensory information processing during early development. M1 is mainly activated by tactile stimuli triggered by preceding spontaneous movements, which reach M1 via S1. Only a fraction of M1 activity transients trigger motor responses directly. We suggest that both spontaneously occurring and sensory-evoked gamma and spindle bursts in M1 contribute to the maturation of corticospinal and sensorimotor networks required for the refinement of sensorimotor coordination.},
	Author = {An, Shuming and Kilb, Werner and Luhmann, Heiko J},
	Date-Added = {2014-08-20 19:13:39 +0000},
	Date-Modified = {2014-08-20 19:14:01 +0000},
	Doi = {10.1523/JNEUROSCI.4539-13.2014},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; in vivo; motor; neocortex; rat; somatosensory; wholeBrain},
	Month = {Aug},
	Number = {33},
	Pages = {10870-83},
	Pmid = {25122889},
	Pst = {ppublish},
	Title = {Sensory-evoked and spontaneous gamma and spindle bursts in neonatal rat motor cortex},
	Volume = {34},
	Year = {2014},
	File = {papers/An_JNeurosci2014.pdf}}

@article{Spitzer:2012,
	Abstract = {For many years it has been assumed that the identity of the transmitters expressed by neurons is stable and unchanging. Recent work, however, shows that electrical activity can respecify neurotransmitter expression during development and in the mature nervous system, and an understanding is emerging of the molecular mechanisms underlying activity-dependent transmitter respecification. Changes in postsynaptic neurotransmitter receptor expression accompany and match changes in transmitter specification, thus enabling synaptic transmission. The functional roles of neurotransmitter respecification are beginning to be understood and appear to involve homeostatic synaptic regulation, which in turn influences behaviour. Activation of this novel form of plasticity by sensorimotor stimuli may provide clinical benefits.},
	Author = {Spitzer, Nicholas C},
	Date-Added = {2014-08-20 18:41:44 +0000},
	Date-Modified = {2014-08-20 18:42:35 +0000},
	Doi = {10.1038/nrn3154},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {review literature; Spontaneous activity; development; Neurotransmitters/*physiology; wholeBrain},
	Mesh = {Animals; Calcium Signaling; Cell Differentiation; Cell Movement; Homeostasis; Models, Biological; Motor Activity; Neurons; Neurotransmitter Agents; Receptors, Neurotransmitter; Synapses},
	Month = {Feb},
	Number = {2},
	Pages = {94-106},
	Pmid = {22251956},
	Pst = {epublish},
	Title = {Activity-dependent neurotransmitter respecification},
	Volume = {13},
	Year = {2012},
	File = {papers/Spitzer_NatRevNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn3154}}

@article{Christensen:2013,
	Abstract = {IMPORTANCE: Valproate is used for the treatment of epilepsy and other neuropsychological disorders and may be the only treatment option for women of childbearing potential. However, prenatal exposure to valproate may increase the risk of autism.
OBJECTIVE: To determine whether prenatal exposure to valproate is associated with an increased risk of autism in offspring.
DESIGN, SETTING, AND PARTICIPANTS: Population-based study of all children born alive in Denmark from 1996 to 2006. National registers were used to identify children exposed to valproate during pregnancy and diagnosed with autism spectrum disorders (childhood autism [autistic disorder], Asperger syndrome, atypical autism, and other or unspecified pervasive developmental disorders). We analyzed the risks associated with all autism spectrum disorders as well as childhood autism. Data were analyzed by Cox regression adjusting for potential confounders (maternal age at conception, paternal age at conception, parental psychiatric history, gestational age, birth weight, sex, congenital malformations, and parity). Children were followed up from birth until the day of autism spectrum disorder diagnosis, death, emigration, or December 31, 2010, whichever came first.
MAIN OUTCOMES AND MEASURES: Absolute risk (cumulative incidence) and the hazard ratio (HR) of autism spectrum disorder and childhood autism in children after exposure to valproate in pregnancy.
RESULTS: Of 655,615 children born from 1996 through 2006, 5437 were identified with autism spectrum disorder, including 2067 with childhood autism. The mean age of the children at end of follow-up was 8.84 years (range, 4-14; median, 8.85). The estimated absolute risk after 14 years of follow-up was 1.53% (95% CI, 1.47%-1.58%) for autism spectrum disorder and 0.48% (95% CI, 0.46%-0.51%) for childhood autism. Overall, the 508 children exposed to valproate had an absolute risk of 4.42% (95% CI, 2.59%-7.46%) for autism spectrum disorder (adjusted HR, 2.9 [95% CI, 1.7-4.9]) and an absolute risk of 2.50% (95% CI, 1.30%-4.81%) for childhood autism (adjusted HR, 5.2 [95% CI, 2.7-10.0]). When restricting the cohort to the 6584 children born to women with epilepsy, the absolute risk of autism spectrum disorder among 432 children exposed to valproate was 4.15% (95% CI, 2.20%-7.81%) (adjusted HR, 1.7 [95% CI, 0.9-3.2]), and the absolute risk of childhood autism was 2.95% (95% CI, 1.42%-6.11%) (adjusted HR, 2.9 [95% CI, 1.4-6.0]) vs 2.44% (95% CI, 1.88%-3.16%) for autism spectrum disorder and 1.02% (95% CI, 0.70%-1.49%) for childhood autism among 6152 children not exposed to valproate.
CONCLUSIONS AND RELEVANCE: Maternal use of valproate during pregnancy was associated with a significantly increased risk of autism spectrum disorder and childhood autism in the offspring, even after adjusting for maternal epilepsy. For women of childbearing potential who use antiepileptic medications, these findings must be balanced against the treatment benefits for women who require valproate for epilepsy control.},
	Author = {Christensen, Jakob and Gr{\o}nborg, Therese Koops and S{\o}rensen, Merete Juul and Schendel, Diana and Parner, Erik Thorlund and Pedersen, Lars Henning and Vestergaard, Mogens},
	Date-Added = {2014-08-20 18:39:43 +0000},
	Date-Modified = {2014-08-20 18:40:18 +0000},
	Doi = {10.1001/jama.2013.2270},
	Journal = {JAMA},
	Journal-Full = {JAMA : the journal of the American Medical Association},
	Keywords = {development; Human; fetal; infant; Child; epilepsy; spontaneous activity; Drug; wholeBrain},
	Mesh = {Adolescent; Adult; Anticonvulsants; Autistic Disorder; Child; Child Development Disorders, Pervasive; Child, Preschool; Denmark; Epilepsy; Female; Follow-Up Studies; Humans; Incidence; Male; Maternal Age; Mental Disorders; Pregnancy; Pregnancy Complications; Prenatal Exposure Delayed Effects; Registries; Risk; Valproic Acid; Young Adult},
	Month = {Apr},
	Number = {16},
	Pages = {1696-703},
	Pmid = {23613074},
	Pst = {ppublish},
	Title = {Prenatal valproate exposure and risk of autism spectrum disorders and childhood autism},
	Volume = {309},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1001/jama.2013.2270}}

@article{Meador:2013,
	Abstract = {BACKGROUND: Many women of childbearing potential take antiepileptic drugs, but the cognitive effects of fetal exposure are uncertain. We aimed to assess effects of commonly used antiepileptic drugs on cognitive outcomes in children up to 6 years of age.
METHODS: In this prospective, observational, assessor-masked, multicentre study, we enrolled pregnant women with epilepsy on antiepileptic drug monotherapy (carbamazepine, lamotrigine, phenytoin, or valproate) between October, 1999, and February, 2004, at 25 epilepsy centres in the UK and the USA. Our primary outcome was intelligence quotient (IQ) at 6 years of age (age-6 IQ) in all children, assessed with linear regression adjusted for maternal IQ, antiepileptic drug type, standardised dose, gestational birth age, and use of periconceptional folate. We also assessed multiple cognitive domains and compared findings with outcomes at younger ages. This study is registered with ClinicalTrials.gov, number NCT00021866.
FINDINGS: We included 305 mothers and 311 children (six twin pairs) in the primary analysis. 224 children completed 6 years of follow-up (6-year-completer sample). Multivariate analysis of all children showed that age-6 IQ was lower after exposure to valproate (mean 97, 95% CI 94-101) than to carbamazepine (105, 102-108; p=0·0015), lamotrigine (108, 105-110; p=0·0003), or phenytoin (108, 104-112; p=0·0006). Children exposed to valproate did poorly on measures of verbal and memory abilities compared with those exposed to the other antiepileptic drugs and on non-verbal and executive functions compared with lamotrigine (but not carbamazepine or phenytoin). High doses of valproate were negatively associated with IQ (r=-0·56, p<0·0001), verbal ability (r=-0·40, p=0·0045), non-verbal ability (r=-0·42, p=0·0028), memory (r=-0·30, p=0·0434), and executive function (r=-0·42, p=0·0004), but other antiepileptic drugs were not. Age-6 IQ correlated with IQs at younger ages, and IQ improved with age for infants exposed to any antiepileptic drug. Compared with a normative sample (173 [93%] of 187 children), right-handedness was less frequent in children in our study overall (185 [86%] of 215; p=0·0404) and in the lamotrigine (59 [83%] of 71; p=0·0287) and valproate (38 [79%] of 40; p=0·0089) groups. Verbal abilities were worse than non-verbal abilities in children in our study overall and in the lamotrigine and valproate groups. Mean IQs were higher in children exposed to periconceptional folate (108, 95% CI 106-111) than they were in unexposed children (101, 98-104; p=0·0009).
INTERPRETATION: Fetal valproate exposure has dose-dependent associations with reduced cognitive abilities across a range of domains at 6 years of age. Reduced right-handedness and verbal (vs non-verbal) abilities might be attributable to changes in cerebral lateralisation induced by exposure to antiepileptic drugs. The positive association of periconceptional folate with IQ is consistent with other recent studies.},
	Author = {Meador, Kimford J and Baker, Gus A and Browning, Nancy and Cohen, Morris J and Bromley, Rebecca L and Clayton-Smith, Jill and Kalayjian, Laura A and Kanner, Andres and Liporace, Joyce D and Pennell, Page B and Privitera, Michael and Loring, David W and {NEAD Study Group}},
	Date-Added = {2014-08-20 18:38:00 +0000},
	Date-Modified = {2014-08-20 18:39:13 +0000},
	Doi = {10.1016/S1474-4422(12)70323-X},
	Journal = {Lancet Neurol},
	Journal-Full = {The Lancet. Neurology},
	Keywords = {development; Human; fetal; infant; Child; epilepsy; spontaneous activity; Drug; wholeBrain},
	Mesh = {Adult; Anticonvulsants; Child; Child Development; Child, Preschool; Cognition; Epilepsy; Female; Humans; Infant; Infant, Newborn; Male; Observation; Phenytoin; Pregnancy; Pregnancy Complications; Prenatal Exposure Delayed Effects; Prospective Studies; Triazines},
	Month = {Mar},
	Number = {3},
	Pages = {244-52},
	Pmc = {PMC3684942},
	Pmid = {23352199},
	Pst = {ppublish},
	Title = {Fetal antiepileptic drug exposure and cognitive outcomes at age 6 years (NEAD study): a prospective observational study},
	Volume = {12},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S1474-4422(12)70323-X}}

@article{Bassett:2008,
	Abstract = {The complex organization of connectivity in the human brain is incompletely understood. Recently, topological measures based on graph theory have provided a new approach to quantify large-scale cortical networks. These methods have been applied to anatomical connectivity data on nonhuman species, and cortical networks have been shown to have small-world topology, associated with high local and global efficiency of information transfer. Anatomical networks derived from cortical thickness measurements have shown the same organizational properties of the healthy human brain, consistent with similar results reported in functional networks derived from resting state functional magnetic resonance imaging (MRI) and magnetoencephalographic data. Here we show, using anatomical networks derived from analysis of inter-regional covariation of gray matter volume in MRI data on 259 healthy volunteers, that classical divisions of cortex (multimodal, unimodal, and transmodal) have some distinct topological attributes. Although all cortical divisions shared nonrandom properties of small-worldness and efficient wiring (short mean Euclidean distance between connected regions), the multimodal network had a hierarchical organization, dominated by frontal hubs with low clustering, whereas the transmodal network was assortative. Moreover, in a sample of 203 people with schizophrenia, multimodal network organization was abnormal, as indicated by reduced hierarchy, the loss of frontal and the emergence of nonfrontal hubs, and increased connection distance. We propose that the topological differences between divisions of normal cortex may represent the outcome of different growth processes for multimodal and transmodal networks and that neurodevelopmental abnormalities in schizophrenia specifically impact multimodal cortical organization.},
	Author = {Bassett, Danielle S and Bullmore, Edward and Verchinski, Beth A and Mattay, Venkata S and Weinberger, Daniel R and Meyer-Lindenberg, Andreas},
	Date-Added = {2014-08-19 16:51:42 +0000},
	Date-Modified = {2014-08-19 17:03:45 +0000},
	Doi = {10.1523/JNEUROSCI.1929-08.2008},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {human; fMRI; graph theory; network analysis; Theoretical; wholeBrain; MRI; DTI},
	Mesh = {Adult; Brain Mapping; Case-Control Studies; Cerebral Cortex; Female; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Middle Aged; Models, Neurological; Neural Pathways; Schizophrenia},
	Month = {Sep},
	Number = {37},
	Pages = {9239-48},
	Pmc = {PMC2878961},
	Pmid = {18784304},
	Pst = {ppublish},
	Title = {Hierarchical organization of human cortical networks in health and schizophrenia},
	Volume = {28},
	Year = {2008},
	File = {papers/Bassett_JNeurosci2008.pdf}}

@url{Csardi:2013,
	Author = {Csardi, G.},
	Date-Added = {2014-08-15 17:00:20 +0000},
	Date-Modified = {2014-09-30 20:20:54 +0000},
	Keywords = {Software},
	Title = {igraph, The network analysis package},
	Url = {http://igraph.org},
	Year = {2013},
	Bdsk-Url-1 = {http://igraph.org/}}

@url{Clauset:2004,
	Author = {Clauset, A. and Newman, M. E. J. and Moore, C.},
	Date-Added = {2014-08-15 16:57:32 +0000},
	Date-Modified = {2014-08-15 17:00:02 +0000},
	Keywords = {Software},
	Title = {Finding community structure in very large networks},
	Url = {http://arxiv.org/pdf/cond-mat/0408187v2.pdf},
	Year = {2004},
	File = {papers/Clauset_2004.pdf},
	Bdsk-Url-1 = {http://arxiv.org/pdf/cond-mat/0408187v2.pdf}}

@webpage{Dollar:2014,
	Author = {Doll{\'a}r, P.},
	Date-Added = {2014-08-15 16:55:17 +0000},
	Date-Modified = {2014-08-15 17:02:03 +0000},
	Keywords = {Software},
	Lastchecked = {2014-08},
	Title = {Piotr's Image and Video Matlab Toolbox},
	Url = {http://vision.ucsd.edu/~pdollar/toolbox/doc/index.html},
	Year = {2014},
	Bdsk-Url-1 = {http://vision.ucsd.edu/~pdollar/toolbox/doc/index.html}}

@inproceedings{Lucas:1981,
	Author = {Lucas, B. D. and Kanade, T.},
	Booktitle = {International Joint Conference on Artificial Intelligence},
	Date-Added = {2014-08-15 16:16:56 +0000},
	Date-Modified = {2014-08-15 16:19:42 +0000},
	Keywords = {Software},
	Pages = {674-697},
	Title = {An Iterative image registration technique with an application to stereo vision},
	Year = {1981},
	File = {papers/Lucas_1981.pdf}}

@url{Ackman:2014b,
	Author = {Ackman, James B},
	Date-Added = {2014-08-15 15:47:46 +0000},
	Date-Modified = {2014-08-15 17:19:28 +0000},
	Keywords = {wholeBrain; Software},
	Lastchecked = {2014-08},
	Title = {wholeBrainDX, Image analysis suite for whole brain calcium imaging},
	Url = {https://github.com/ackman678/wholeBrainDX},
	Year = {2014},
	Bdsk-Url-1 = {https://github.com/ackman678/wholeBrainDX}}

@article{Newman:2004,
	Author = {Newman, M. E. J.},
	Date-Added = {2014-08-11 23:45:12 +0000},
	Date-Modified = {2014-08-11 23:47:08 +0000},
	Doi = {10.1103/PhysRevE.69.066133},
	Issue = {6},
	Journal = {Phys. Rev. E},
	Month = {Jun},
	Numpages = {5},
	Pages = {066133},
	Publisher = {American Physical Society},
	Title = {Fast algorithm for detecting community structure in networks},
	Url = {http://link.aps.org/doi/10.1103/PhysRevE.69.066133},
	Volume = {69},
	Year = {2004},
	File = {papers/Newman_Phys.Rev.E2004.pdf},
	Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevE.69.066133},
	Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.69.066133}}

@article{Gaspar:2003,
	Abstract = {New genetic models that target the serotonin system show that transient alterations in serotonin homeostasis cause permanent changes to adult behaviour and modify the fine wiring of brain connections. These findings have revived a long-standing interest in the developmental role of serotonin. Molecular genetic approaches are now showing us that different serotonin receptors, acting at different developmental stages, modulate different developmental processes such as neurogenesis, apoptosis, axon branching and dendritogenesis. Our understanding of the specification of the serotonergic phenotype is improving. In addition, studies have revealed that serotonergic traits are dissociable, as there are populations of neurons that contain serotonin but do not synthesize it.},
	Author = {Gaspar, Patricia and Cases, Olivier and Maroteaux, Luc},
	Date-Added = {2014-08-08 18:11:15 +0000},
	Date-Modified = {2014-08-08 18:11:15 +0000},
	Doi = {10.1038/nrn1256},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Aging; Animals; Behavior, Animal; Cell Aging; Embryo, Mammalian; Homeostasis; Humans; Mental Disorders; Mice; Molecular Biology; Neurons; Receptors, Serotonin; Serotonin},
	Month = {Dec},
	Number = {12},
	Pages = {1002-12},
	Pmid = {14618156},
	Pst = {ppublish},
	Title = {The developmental role of serotonin: news from mouse molecular genetics},
	Volume = {4},
	Year = {2003},
	File = {papers/Gaspar_NatRevNeurosci2003.pdf}}

@article{Lebrand:1998,
	Abstract = {Neurons in first-order sensory thalamic nuclei have been shown to express functional plasma membrane serotonin (SERT) and vesicular monoamine (VMAT2) transporters during early postnatal development. In the present study, we provide an extensive description of the spatial and the temporal patterns of VMAT2 and SERT expression, during early embryonic development and postnatal life, by using in situ hybridization and immunocytochemistry. VMAT2 and SERT genes are transiently expressed in a wide population of non-monoaminergic neurons in the central and peripheral nervous system with a large overlap in the temporal and spatial pattern of expression of both genes. A selective pattern of expression of both genes was observed in the thalamus with expression limited to the dorsal thalamus and more particularly to primary sensory relay nuclei that convey point to point projection maps. Transient expression of the transporters was also observed in sensory cranial nerves, in the hippocampus, cerebral cortex, septum, and amygdala. VMAT2 and SERT gene expression was not necessarily linked, as some neural populations expressed only VMAT2, while others only contained SERT. Since VMAT2 serves to transport catecholamines besides serotonin, we examined the developmental expression of the plasma membrane dopamine and norepinephrine transporters but found no transient expression of these genes. Despite minor temporal disparities, VMAT2 and SERT extinguished almost simultaneously during the second and third weeks of post-natal life. These expressions did not seem to be dependent on peripheral neural inputs, since monocular enucleations and infraorbital nerve cuts effected on the day of birth, did not modify the period of transporter expression or of extinction.},
	Author = {Lebrand, C and Cases, O and Wehrl{\'e}, R and Blakely, R D and Edwards, R H and Gaspar, P},
	Date-Added = {2014-08-08 18:10:54 +0000},
	Date-Modified = {2014-08-08 18:10:54 +0000},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Animals; Brain Chemistry; Carrier Proteins; Cell Membrane; Dopamine Plasma Membrane Transport Proteins; Eye Enucleation; Gene Expression Regulation, Developmental; Membrane Glycoproteins; Membrane Transport Proteins; Mice; Mice, Inbred C3H; Nerve Tissue Proteins; Neurons, Afferent; Neuropeptides; Neurotransmitter Agents; Norepinephrine Plasma Membrane Transport Proteins; Prosencephalon; RNA, Messenger; Rats; Rats, Sprague-Dawley; Serotonin; Symporters; Thalamus; Time Factors; Trigeminal Nerve; Vesicular Biogenic Amine Transport Proteins; Vesicular Monoamine Transport Proteins; Vision, Monocular},
	Month = {Nov},
	Number = {4},
	Pages = {506-24},
	Pmid = {9826275},
	Pst = {ppublish},
	Title = {Transient developmental expression of monoamine transporters in the rodent forebrain},
	Volume = {401},
	Year = {1998},
	File = {papers/Lebrand_JCompNeurol1998.pdf}}

@article{Lebrand:1996,
	Abstract = {Serotonin (5-HT) has been shown to affect the development and patterning of the mouse barrelfield. We show that the dense transient 5-HT innervation of the somatosensory, visual, and auditory cortices originates in the thalamus rather than in the raphe: 5-HT is detected in thalamocortical fibers and most 5-HT cortical labeling disappears after thalamic lesions. Thalamic neurons do not synthesize 5-HT but take up exogenous 5-HT through 5-HT high affinity uptake sites located on thalamocortical axons and terminals. 3H-5-HT injected into the cortex is retrogradely transported to thalamic neurons. In situ hybridization shows a transient expression of the genes encoding the serotonin transporter and the vesicular monoamine transporter in thalamic sensory neurons. In these glutamatergic neurons, internalized 5-HT might thus be stored and used as a "borrowed transmitter" for extraneuronal signaling or could exert an intraneuronal control on thalamic maturation.},
	Author = {Lebrand, C and Cases, O and Adelbrecht, C and Doye, A and Alvarez, C and El Mestikawy, S and Seif, I and Gaspar, P},
	Date-Added = {2014-08-08 18:10:17 +0000},
	Date-Modified = {2014-08-08 18:12:12 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Age Factors; Animals; Antibody Specificity; Biological Transport; Carrier Proteins; Cerebral Cortex; Gene Expression; Immunohistochemistry; In Situ Hybridization; Membrane Glycoproteins; Membrane Transport Proteins; Mice; Mice, Inbred C57BL; Nerve Tissue Proteins; Neurons, Afferent; Neuropeptides; Neurotransmitter Agents; RNA, Messenger; Rats; Rats, Sprague-Dawley; Serotonin; Serotonin Plasma Membrane Transport Proteins; Synaptic Vesicles; Thalamus; Time Factors; Tritium; Vesicular Biogenic Amine Transport Proteins; Vesicular Monoamine Transport Proteins; barrel cortex; topographic map; Visual Cortex; Auditory Cortex; wholeBrain},
	Month = {Nov},
	Number = {5},
	Pages = {823-35},
	Pmid = {8938116},
	Pst = {ppublish},
	Title = {Transient uptake and storage of serotonin in developing thalamic neurons},
	Volume = {17},
	Year = {1996},
	File = {papers/Lebrand_Neuron1996.pdf}}

@article{Newman:2000,
	Abstract = {The small-world network model is a simple model of the structure of social networks, which possesses characteristics of both regular lattices and random graphs. The model consists of a one-dimensional lattice with a low density of shortcuts added between randomly selected pairs of points. These shortcuts greatly reduce the typical path length between any two points on the lattice. We present a mean-field solution for the average path length and for the distribution of path lengths in the model. This solution is exact in the limit of large system size and either a large or small number of shortcuts.},
	Author = {Newman, M E and Moore, C and Watts, D J},
	Date-Added = {2014-08-06 18:24:59 +0000},
	Date-Modified = {2014-08-06 18:24:59 +0000},
	Journal = {Phys Rev Lett},
	Journal-Full = {Physical review letters},
	Mesh = {Computer Simulation; Humans; Mathematics; Models, Theoretical; Neural Networks (Computer); Social Behavior},
	Month = {Apr},
	Number = {14},
	Pages = {3201-4},
	Pmid = {11019047},
	Pst = {ppublish},
	Title = {Mean-field solution of the small-world network model},
	Volume = {84},
	Year = {2000},
	File = {papers/Newman_PhysRevLett2000.pdf}}

@article{Humphries:2008,
	Abstract = {BACKGROUND: Many technological, biological, social, and information networks fall into the broad class of 'small-world' networks: they have tightly interconnected clusters of nodes, and a shortest mean path length that is similar to a matched random graph (same number of nodes and edges). This semi-quantitative definition leads to a categorical distinction ('small/not-small') rather than a quantitative, continuous grading of networks, and can lead to uncertainty about a network's small-world status. Moreover, systems described by small-world networks are often studied using an equivalent canonical network model--the Watts-Strogatz (WS) model. However, the process of establishing an equivalent WS model is imprecise and there is a pressing need to discover ways in which this equivalence may be quantified.
METHODOLOGY/PRINCIPAL FINDINGS: We defined a precise measure of 'small-world-ness' S based on the trade off between high local clustering and short path length. A network is now deemed a 'small-world' if S>1--an assertion which may be tested statistically. We then examined the behavior of S on a large data-set of real-world systems. We found that all these systems were linked by a linear relationship between their S values and the network size n. Moreover, we show a method for assigning a unique Watts-Strogatz (WS) model to any real-world network, and show analytically that the WS models associated with our sample of networks also show linearity between S and n. Linearity between S and n is not, however, inevitable, and neither is S maximal for an arbitrary network of given size. Linearity may, however, be explained by a common limiting growth process.
CONCLUSIONS/SIGNIFICANCE: We have shown how the notion of a small-world network may be quantified. Several key properties of the metric are described and the use of WS canonical models is placed on a more secure footing.},
	Author = {Humphries, Mark D and Gurney, Kevin},
	Date-Added = {2014-08-06 18:22:59 +0000},
	Date-Modified = {2014-08-06 18:22:59 +0000},
	Doi = {10.1371/journal.pone.0002051},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Mesh = {Metric System; Models, Biological},
	Number = {4},
	Pages = {e0002051},
	Pmc = {PMC2323569},
	Pmid = {18446219},
	Pst = {epublish},
	Title = {Network 'small-world-ness': a quantitative method for determining canonical network equivalence},
	Volume = {3},
	Year = {2008},
	File = {papers/Humphries_PLoSOne2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0002051}}

@article{Sporns:2004,
	Abstract = {Recent research has revealed general principles in the structural and functional organization of complex networks which are shared by various natural, social and technological systems. This review examines these principles as applied to the organization, development and function of complex brain networks. Specifically, we examine the structural properties of large-scale anatomical and functional brain networks and discuss how they might arise in the course of network growth and rewiring. Moreover, we examine the relationship between the structural substrate of neuroanatomy and more dynamic functional and effective connectivity patterns that underlie human cognition. We suggest that network analysis offers new fundamental insights into global and integrative aspects of brain function, including the origin of flexible and coherent cognitive states within the neural architecture.},
	Author = {Sporns, Olaf and Chialvo, Dante R and Kaiser, Marcus and Hilgetag, Claus C},
	Date-Added = {2014-08-06 17:59:01 +0000},
	Date-Modified = {2014-08-06 17:59:01 +0000},
	Doi = {10.1016/j.tics.2004.07.008},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Brain; Cognition; Humans; Nerve Net},
	Month = {Sep},
	Number = {9},
	Pages = {418-25},
	Pmid = {15350243},
	Pst = {ppublish},
	Title = {Organization, development and function of complex brain networks},
	Volume = {8},
	Year = {2004},
	File = {papers/Sporns_TrendsCognSci2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tics.2004.07.008}}

@article{Lim:2013,
	Abstract = {Human brain maturation is characterized by the prolonged development of structural and functional properties of large-scale networks that extends into adulthood. However, it is not clearly understood which features change and which remain stable over time. Here, we examined structural connectivity based on diffusion tensor imaging (DTI) in 121 participants between 4 and 40 years of age. DTI data were analyzed for small-world parameters, modularity, and the number of fiber tracts at the level of streamlines. First, our findings showed that the number of fiber tracts, small-world topology, and modular organization remained largely stable despite a substantial overall decrease in the number of streamlines with age. Second, this decrease mainly affected fiber tracts that had a large number of streamlines, were short, within modules and within hemispheres; such connections were affected significantly more often than would be expected given their number of occurrences in the network. Third, streamline loss occurred earlier in females than in males. In summary, our findings suggest that core properties of structural brain connectivity, such as the small-world and modular organization, remain stable during brain maturation by focusing streamline loss to specific types of fiber tracts.},
	Author = {Lim, Sol and Han, Cheol E and Uhlhaas, Peter J and Kaiser, Marcus},
	Date-Added = {2014-08-05 13:08:30 +0000},
	Date-Modified = {2014-08-05 13:09:21 +0000},
	Doi = {10.1093/cercor/bht333},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {brain connectivity; connectome; maturation; network analysis; tractography; resting state; default mode network; technique; Methods; computation biology; Theoretical; graph theory; human; fmri; Software; neonate; Cerebral Cortex; Neocortex; wholeBrain},
	Month = {Dec},
	Pmid = {24343892},
	Pst = {aheadofprint},
	Title = {Preferential Detachment During Human Brain Development: Age- and Sex-Specific Structural Connectivity in Diffusion Tensor Imaging (DTI) Data},
	Year = {2013},
	File = {papers/Lim_CerebCortex2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bht333}}

@article{Heuvel:2014,
	Abstract = {The human connectome is the result of an elaborate developmental trajectory. Acquiring diffusion-weighted imaging and resting-state fMRI, we studied connectome formation during the preterm phase of macroscopic connectome genesis. In total, 27 neonates were scanned at week 30 and/or week 40 gestational age (GA). Examining the architecture of the neonatal anatomical brain network revealed a clear presence of a small-world modular organization before term birth. Analysis of neonatal functional connectivity (FC) showed the early formation of resting-state networks, suggesting that functional networks are present in the preterm brain, albeit being in an immature state. Moreover, structural and FC patterns of the neonatal brain network showed strong overlap with connectome architecture of the adult brain (85 and 81%, respectively). Analysis of brain development between week 30 and week 40 GA revealed clear developmental effects in neonatal connectome architecture, including a significant increase in white matter microstructure (P < 0.01), small-world topology (P < 0.01) and interhemispheric FC (P < 0.01). Computational analysis further showed that developmental changes involved an increase in integration capacity of the connectivity network as a whole. Taken together, we conclude that hallmark organizational structures of the human connectome are present before term birth and subject to early development.},
	Author = {van den Heuvel, Martijn P and Kersbergen, Karina J and de Reus, Marcel A and Keunen, Kristin and Kahn, Ren{\'e} S and Groenendaal, Floris and de Vries, Linda S and Benders, Manon J N L},
	Date-Added = {2014-08-05 13:07:41 +0000},
	Date-Modified = {2014-08-05 13:09:49 +0000},
	Doi = {10.1093/cercor/bhu095},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {connectome; development; functional connectivity; neonatal; structural connectivity; resting state; default mode network; technique; Methods; computation biology; Theoretical; graph theory; human; fmri; Software; neonate; Cerebral Cortex; Neocortex; wholeBrain},
	Month = {May},
	Pmid = {24833018},
	Pst = {aheadofprint},
	Title = {The Neonatal Connectome During Preterm Brain Development},
	Year = {2014},
	File = {papers/Heuvel_CerebCortex2014.pdf}}

@article{Doria:2010,
	Abstract = {The functions of the resting state networks (RSNs) revealed by functional MRI remain unclear, but it has seemed possible that networks emerge in parallel with the development of related cognitive functions. We tested the alternative hypothesis: that the full repertoire of resting state dynamics emerges during the period of rapid neural growth before the normal time of birth at term (around 40 wk of gestation). We used a series of independent analytical techniques to map in detail the development of different networks in 70 infants born between 29 and 43 wk of postmenstrual age (PMA). We characterized and charted the development of RSNs from recognizable but often fragmentary elements at 30 wk of PMA to full facsimiles of adult patterns at term. Visual, auditory, somatosensory, motor, default mode, frontoparietal, and executive control networks developed at different rates; however, by term, complete networks were present, several of which were integrated with thalamic activity. These results place the emergence of RSNs largely during the period of rapid neural growth in the third trimester of gestation, suggesting that they are formed before the acquisition of cognitive competencies in later childhood.},
	Author = {Doria, Valentina and Beckmann, Christian F and Arichi, Tomoki and Merchant, Nazakat and Groppo, Michela and Turkheimer, Federico E and Counsell, Serena J and Murgasova, Maria and Aljabar, Paul and Nunes, Rita G and Larkman, David J and Rees, Geraint and Edwards, A David},
	Date-Added = {2014-08-05 13:06:37 +0000},
	Date-Modified = {2014-08-05 13:09:57 +0000},
	Doi = {10.1073/pnas.1007921107},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {resting state; default mode network; technique; Methods; computation biology; Theoretical; graph theory; human; fmri; Software; neonate; Cerebral Cortex; Neocortex; wholeBrain},
	Mesh = {Bias (Epidemiology); Brain; Female; Gestational Age; Humans; Infant; Nerve Net; Pregnancy; Pregnancy Trimester, Third; Premature Birth; Regression Analysis; Rest},
	Month = {Nov},
	Number = {46},
	Pages = {20015-20},
	Pmc = {PMC2993415},
	Pmid = {21041625},
	Pst = {ppublish},
	Title = {Emergence of resting state networks in the preterm human brain},
	Volume = {107},
	Year = {2010},
	File = {papers/Doria_ProcNatlAcadSciUSA2010.pdf}}

@article{Ko:2014,
	Abstract = {In primary visual cortex (V1), connectivity between layer 2/3 (L2/3) excitatory neurons undergoes extensive reorganization after the onset of visual experience whereby neurons with similar feature selectivity form functional microcircuits (Ko et al., 2011, 2013). It remains unknown whether visual experience is required for the developmental refinement of intracortical circuitry or whether this maturation is guided intrinsically. Here, we correlated the connectivity between V1 L2/3 neurons assayed by simultaneous whole-cell recordings in vitro to their response properties measured by two-photon calcium imaging in vivo in dark-reared mice. We found that neurons with similar responses to oriented gratings or natural movies became preferentially connected in the absence of visual experience. However, the relationship between connectivity and similarity of visual responses to natural movies was not as strong in dark-reared as in normally reared mice. Moreover, dark rearing prevented the normally occurring loss of connections between visually nonresponsive neurons after eye opening (Ko et al., 2013). Therefore, our data suggest that the absence of visual input does not prevent the emergence of functionally specific recurrent connectivity in cortical circuits; however, visual experience is required for complete microcircuit maturation.},
	Author = {Ko, Ho and Mrsic-Flogel, Thomas D and Hofer, Sonja B},
	Date-Added = {2014-07-28 15:16:50 +0000},
	Date-Modified = {2014-07-28 15:16:50 +0000},
	Doi = {10.1523/JNEUROSCI.0875-14.2014},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {experience-dependent; functional microcircuit organization; microcircuit development; mouse visual cortex; synaptic connectivity; two-photon imaging},
	Month = {Jul},
	Number = {29},
	Pages = {9812-6},
	Pmid = {25031418},
	Pst = {ppublish},
	Title = {Emergence of feature-specific connectivity in cortical microcircuits in the absence of visual experience},
	Volume = {34},
	Year = {2014},
	File = {papers/Ko_JNeurosci2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0875-14.2014}}

@article{Nasiriavanaki:2014,
	Abstract = {The increasing use of mouse models for human brain disease studies presents an emerging need for a new functional imaging modality. Using optical excitation and acoustic detection, we developed a functional connectivity photoacoustic tomography system, which allows noninvasive imaging of resting-state functional connectivity in the mouse brain, with a large field of view and a high spatial resolution. Bilateral correlations were observed in eight functional regions, including the olfactory bulb, limbic, parietal, somatosensory, retrosplenial, visual, motor, and temporal regions, as well as in several subregions. The borders and locations of these regions agreed well with the Paxinos mouse brain atlas. By subjecting the mouse to alternating hyperoxic and hypoxic conditions, strong and weak functional connectivities were observed, respectively. In addition to connectivity images, vascular images were simultaneously acquired. These studies show that functional connectivity photoacoustic tomography is a promising, noninvasive technique for functional imaging of the mouse brain.},
	Author = {Nasiriavanaki, Mohammadreza and Xia, Jun and Wan, Hanlin and Bauer, Adam Quentin and Culver, Joseph P and Wang, Lihong V},
	Date-Added = {2014-07-28 14:38:23 +0000},
	Date-Modified = {2014-07-28 14:39:12 +0000},
	Doi = {10.1073/pnas.1311868111},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {RSFC; fcPAT; hyperoxia; hypoxia; mouse brain functional imaging; wholeBrain; topographic map; parcellation; optical physiology},
	Mesh = {Algorithms; Animals; Anoxia; Brain; Brain Mapping; Disease Models, Animal; Electrodes; Equipment Design; Hemodynamics; Hemoglobins; Hyperoxia; Image Processing, Computer-Assisted; Lasers; Male; Mice; Neural Pathways; Normal Distribution; Photoacoustic Techniques},
	Month = {Jan},
	Number = {1},
	Pages = {21-6},
	Pmc = {PMC3890828},
	Pmid = {24367107},
	Pst = {ppublish},
	Title = {High-resolution photoacoustic tomography of resting-state functional connectivity in the mouse brain},
	Volume = {111},
	Year = {2014},
	File = {papers/Nasiriavanaki_ProcNatlAcadSciUSA2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.1311868111}}

@article{Mohns:2008,
	Abstract = {The neonatal hippocampus exhibits regularly recurring waves of synchronized neuronal activity in vitro. Because active sleep (AS), characterized by bursts of phasic motor activity in the form of myoclonic twitching, may provide conditions that are conducive to activity-dependent development of hippocampal circuits, we hypothesized that the waves of synchronous neuronal activity that have been observed in vitro would be associated with AS-related twitching. Using unanesthetized 1- to 12-d-old rats, we report here that the majority of neurons in CA1 and the dentate gyrus (DG) are significantly more active during AS than during either quiet sleep or wakefulness. Neuronal activity typically occurs in phasic bursts, during which most neurons are significantly cross-correlated both within and across the CA1 and DG fields. All AS-active neurons increase their firing rates during periods of myoclonic twitching of the limbs, and a subset of these neurons exhibit a burst of activity immediately after limb twitches, suggesting that the twitches themselves provide sensory feedback to the infant hippocampus, as occurs in the infant spinal cord and neocortex. Finally, the synchronous bursts of neuronal activity are coupled to the emergence of the AS-related hippocampal gamma rhythm during the first postnatal week, as well as the emergence of the AS-related theta rhythm during the second postnatal week. We hypothesize that the phasic motor events of active sleep provide the developing hippocampus with discrete sensory stimulation that contributes to the development and refinement of hippocampal circuits as well as the development of synchronized interactions between hippocampus and neocortex.},
	Author = {Mohns, Ethan J and Blumberg, Mark S},
	Date-Added = {2014-07-25 15:34:41 +0000},
	Date-Modified = {2014-07-25 15:34:41 +0000},
	Doi = {10.1523/JNEUROSCI.1967-08.2008},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Hippocampus; Male; Neurons; Rats; Rats, Sprague-Dawley; Sleep; Theta Rhythm},
	Month = {Oct},
	Number = {40},
	Pages = {10134-44},
	Pmc = {PMC2678192},
	Pmid = {18829971},
	Pst = {ppublish},
	Title = {Synchronous bursts of neuronal activity in the developing hippocampus: modulation by active sleep and association with emerging gamma and theta rhythms},
	Volume = {28},
	Year = {2008},
	File = {papers/Mohns_JNeurosci2008.pdf}}

@article{Karlsson:2005,
	Abstract = {Sleep is a poorly understood behavior that predominates during infancy but is studied almost exclusively in adults. One perceived impediment to investigations of sleep early in ontogeny is the absence of state-dependent neocortical activity. Nonetheless, in infant rats, sleep is reliably characterized by the presence of tonic (i.e., muscle atonia) and phasic (i.e., myoclonic twitching) components; the neural circuitry underlying these components, however, is unknown. Recently, we described a medullary inhibitory area (MIA) in week-old rats that is necessary but not sufficient for the normal expression of atonia. Here we report that the infant MIA receives projections from areas containing neurons that exhibit state-dependent activity. Specifically, neurons within these areas, including the subcoeruleus (SubLC), pontis oralis (PO), and dorsolateral pontine tegmentum (DLPT), exhibit discharge profiles that suggest causal roles in the modulation of muscle tone and the production of myoclonic twitches. Indeed, lesions in the SubLC and PO decreased the expression of muscle atonia without affecting twitching (resulting in "REM sleep without atonia"), whereas lesions of the DLPT increased the expression of atonia while decreasing the amount of twitching. Thus, the neural substrates of infant sleep are strikingly similar to those of adults, a surprising finding in light of theories that discount the contribution of supraspinal neural elements to sleep before the onset of state-dependent neocortical activity.},
	Author = {Karlsson, Karl A E and Gall, Andrew J and Mohns, Ethan J and Seelke, Adele M H and Blumberg, Mark S},
	Date-Added = {2014-07-25 15:32:42 +0000},
	Date-Modified = {2014-07-25 15:32:42 +0000},
	Doi = {10.1371/journal.pbio.0030143},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Mesh = {Aging; Animals; Animals, Newborn; Female; Locus Coeruleus; Male; Medulla Oblongata; Muscle Tonus; Neurons; Pons; Rats; Rats, Sprague-Dawley; Sleep},
	Month = {May},
	Number = {5},
	Pages = {e143},
	Pmc = {PMC1079781},
	Pmid = {15826218},
	Pst = {ppublish},
	Title = {The neural substrates of infant sleep in rats},
	Volume = {3},
	Year = {2005},
	File = {papers/Karlsson_PLoSBiol2005.pdf}}

@article{Mohns:2006,
	Abstract = {Recent findings in infant rats suggest that the preoptic area (POA) and/or basal forebrain (BF) contribute to developmental changes in sleep and wake organization between postnatal day 2 (P2) and P9. To examine the contributions of these forebrain areas to sleep and wakefulness, separate lesions of the POA or BF, or combined lesions (POA + BF), were performed at P9, and precollicular transections were performed at P2. In addition, modafinil, a drug of unknown mechanism of action the effects of which on sleep and wakefulness have been hypothesized to result from inhibition of POA activity, was administered at P2 and P9. Finally, extracellular neuronal activity was recorded from the POA and BF. POA lesions decreased sleep bout durations and increased wake bout durations. BF lesions inhibited sleep bout durations to a lesser extent, while leaving wake bout durations unaffected. POA + BF lesions produced a combination of these effects, resulting in short bouts of sleep and wakefulness similar to those of transected P8 rats. Even at P2, transections decreased sleep bout durations. The finding, however, that the sleep-inhibiting and wake-promoting effects of modafinil were more potent at P9 than at P2 suggests increasing sleep-wake modulation by the POA between these two ages. Finally, neuronal recordings confirmed the presence of state-dependent neurons within the infant POA and BF. We propose that the POA, in addition to promoting sleep, inhibits wakefulness via direct and indirect inhibitory connections with wake-promoting neurons in the BF, and that this inhibitory influence increases across early development.},
	Author = {Mohns, Ethan J and Karlsson, Karl A E and Blumberg, Mark S},
	Date-Added = {2014-07-25 15:31:44 +0000},
	Date-Modified = {2014-07-25 15:31:44 +0000},
	Doi = {10.1111/j.1460-9568.2006.04652.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Mesh = {Animals; Animals, Newborn; Benzhydryl Compounds; Central Nervous System Stimulants; Electromyography; Male; Neurons; Preoptic Area; Prosencephalon; Rats; Rats, Sprague-Dawley; Sleep; Wakefulness},
	Month = {Mar},
	Number = {5},
	Pages = {1301-10},
	Pmc = {PMC2645537},
	Pmid = {16553791},
	Pst = {ppublish},
	Title = {The preoptic hypothalamus and basal forebrain play opposing roles in the descending modulation of sleep and wakefulness in infant rats},
	Volume = {23},
	Year = {2006},
	File = {papers/Mohns_EurJNeurosci2006.pdf}}

@article{Woolsey:1978,
	Author = {Woolsey, T A},
	Date-Added = {2014-07-25 15:19:46 +0000},
	Date-Modified = {2014-07-25 15:19:46 +0000},
	Journal = {Brain Behav Evol},
	Journal-Full = {Brain, behavior and evolution},
	Mesh = {Bibliography as Topic; History, 20th Century; Psychophysiology; United States},
	Number = {4},
	Pages = {307-24},
	Pmid = {359102},
	Pst = {ppublish},
	Title = {C. N. Woolsey--scientist and artist: a complete bibliography (1933--1974)},
	Volume = {15},
	Year = {1978},
	File = {papers/Woolsey_BrainBehavEvol1978.pdf}}

@book{Harlow:1958,
	Annote = {http://hdl.handle.net/10079/bibid/5224793

From http://braininfo.rprc.washington.edu/Source.aspx?ID=90&questID=1350:  

>This paper discusses and illustrates the topographic representation of somesthetic and motor functions in the cerebral cortex of several nonhuman species. Somesthetic function was mapped in anesthetized animals on the basis of evoked potentials elicited in the cortex by light touch stimulation of the skin. Motor function was mapped also in anesthetized animals on the basis of movements elicited by electrical stimulation of the cortex. The report provides summary diagrams in which the size and locations of cortical areas related to specific skin areas are mapped on the cortical surface. The primary somesthetic area (area SI of Woolsey-1958), second somatic sensory area (area SII of Woolsey-1958), primary motor cortex (area MI of Woolsey-1958) and supplementary motor cortex (area MII of Woolsey-1958) are illustrated for the rat, rabbit, cat and macaque with highly detailed illustrations of the primary somesthetic and motor areas in the macaque.},
	Author = {Harlow, H.F. and Woolsey, C.N.},
	Date-Added = {2014-07-25 14:58:38 +0000},
	Date-Modified = {2018-01-16 22:24:29 +0000},
	Keywords = {Somatosensory Cortex; topographic map; neurophysiology; Neocortex; mouse; rat;},
	Lccn = {58013447},
	Publisher = {University of Wisconsin Press},
	Title = {Biological and biochemical bases of behavior},
	Url = {http://books.google.com/books?id=L8M0AAAAMAAJ},
	Year = {1958},
	File = {papers/Harlow_1958.pdf},
	Bdsk-Url-1 = {http://books.google.com/books?id=L8M0AAAAMAAJ},
	Bdsk-Url-2 = {http://braininfo.rprc.washington.edu/Source.aspx?ID=90&questID=1350}}

@article{Wong-Riley:1980,
	Abstract = {The posteromedial barrel subfield of the somatosensory cortex of mice was examined histochemically for cytochrome oxidase activity (cytochrome c oxidase; ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1). In normal mice a high enzymatic activity was found within the barrel hollows, rather than in the sides and septa. Electron microscopic examination indicated that within the hollows reactive mitochondria reside in many dendrites, in some axonal terminals, and in a few neuronal perikarya. After neonatal cauterization of selected row(s) of vibrissae, the corresponding row(s) of barrels appeared as narrowed fused band(s) and their cytochrome oxidase activity was much reduced. Removal of vibrissae in the adult, by either cauterization or repeated plucking, did not cause size changes of cortical barrels. However, there was a significant decrease in the oxidative enzymatic activity within these barrels. Thus, the deprivation of sensory input through damage to, or removal of, the peripheral sensory organ induces an enzymatic response in neurons that are at least two to three synapses away from the periphery.},
	Author = {Wong-Riley, M T and Welt, C},
	Date-Added = {2014-07-25 14:28:21 +0000},
	Date-Modified = {2014-07-25 14:28:21 +0000},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Mesh = {Animals; Electron Transport Complex IV; Hair; Mechanoreceptors; Mice; Neural Pathways; Somatosensory Cortex},
	Month = {Apr},
	Number = {4},
	Pages = {2333-7},
	Pmc = {PMC348709},
	Pmid = {6246540},
	Pst = {ppublish},
	Title = {Histochemical changes in cytochrome oxidase of cortical barrels after vibrissal removal in neonatal and adult mice},
	Volume = {77},
	Year = {1980},
	File = {papers/Wong-Riley_ProcNatlAcadSciUSA1980.pdf}}

@article{Woolsey:1967,
	Author = {Woolsey, T A},
	Date-Added = {2014-07-25 14:12:38 +0000},
	Date-Modified = {2014-07-25 14:12:38 +0000},
	Journal = {Johns Hopkins Med J},
	Journal-Full = {The Johns Hopkins medical journal},
	Mesh = {Anatomy, Comparative; Animals; Cerebral Cortex; Electrophysiology; Evoked Potentials; Golgi Apparatus; Mice; Rabbits; Rodentia; Sensation; Vestibulocochlear Nerve; Visual Perception},
	Month = {Aug},
	Number = {2},
	Pages = {91-112},
	Pmid = {6032827},
	Pst = {ppublish},
	Title = {Somatosensory, auditory and visual cortical areas of the mouse},
	Volume = {121},
	Year = {1967},
	File = {papers/Woolsey_JohnsHopkinsMedJ1967.pdf}}

@article{Woolsey:1970a,
	Author = {Woolsey, T A and Van der Loos, H},
	Date-Added = {2014-07-25 14:06:21 +0000},
	Date-Modified = {2014-07-25 14:06:43 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {Histological Techniques;Sensation;Biometry;Terminology;K;Electrodes;Hair;Animal;Evoked Potentials;Cerebral Cortex/*cytology/physiology;Surface Properties;Mice;16 Barrels},
	Mesh = {Animals; Biometry; Cerebral Cortex; Electrodes; Evoked Potentials; Hair; Histological Techniques; Mice; Sensation; Surface Properties; Terminology as Topic},
	Month = {Jan},
	Number = {2},
	Pages = {205-42},
	Pmid = {4904874},
	Pst = {ppublish},
	Title = {The structural organization of layer IV in the somatosensory region (SI) of mouse cerebral cortex. The description of a cortical field composed of discrete cytoarchitectonic units},
	Volume = {17},
	Year = {1970},
	File = {papers/Woolsey_BrainRes1970.pdf}}

@article{Narboux-Neme:2008,
	Abstract = {The serotonin transporter gene (SLC6A4; synonyms, SERT, 5-HTT) is expressed much more broadly during development than in adulthood. To obtain a full picture of all sites of SERT expression during development we used a new mouse model where Cre recombinase was inserted into the gene encoding the serotonin transporter. Two reporter mouse lines, ROSA26R and the Tau(mGFP), allowed to map all the cells that express SERT at any point during development. Combined LacZ histochemistry and GFP immunolabelling showed neuronal cell bodies and axon fiber tracts. Earliest recombination in embryos was visible in the periphery in the heart and liver by E10.5 followed by recombination in the brain in raphe serotonergic neurons by E12.5. Further, recombination in non-serotonin neurons was visible in the choroid plexus, roof plate, and neural crest derivatives; by E15.5, recombination was found in the dorsal thalamus, cingulate cortex, CA3 field of the hippocampus, retinal ganglion cells, superior olivary nucleus and cochlear nucleus. Postnatally, SERT mediated recombination was visible in the medial prefrontal cortex and layer VI neurons in the isocortex. Recombined cells were co-labelled with Neu-N, but not with GAD67, and were characterized by long range projections (corpus callosum, fornix, thalamocortical). This fate map of serotonin transporter expressing cells emphasizes the broad expression of SERT in non-serotonin neurons during development and clarifies the localization of SERT expression in the hippocampus and limbic cortex. The identification of targets of SSRIs and serotonin releasers during embryonic and early postnatal life helps understanding the very diverse physiological consequences of administration of these drugs during development.},
	Author = {Narboux-N{\^e}me, Nicolas and Pavone, Luigi Michele and Avallone, Luigi and Zhuang, Xiaoxi and Gaspar, Patricia},
	Date-Added = {2014-07-25 13:43:02 +0000},
	Date-Modified = {2014-07-25 13:43:59 +0000},
	Doi = {10.1016/j.neuropharm.2008.08.020},
	Journal = {Neuropharmacology},
	Journal-Full = {Neuropharmacology},
	Keywords = {grant; ideas; thalamocortical; Thalamic Nuclei; Neocortex; barrels; Somatosensory Cortex; topographic map},
	Mesh = {Animals; Embryo, Mammalian; Gene Expression Regulation, Developmental; Green Fluorescent Proteins; Integrases; Mice; Mice, Transgenic; Neurons; Raphe Nuclei; Serotonin; Serotonin Plasma Membrane Transport Proteins; Serotonin Uptake Inhibitors; tau Proteins},
	Month = {Nov},
	Number = {6},
	Pages = {994-1005},
	Pmid = {18789954},
	Pst = {ppublish},
	Title = {Serotonin transporter transgenic (SERTcre) mouse line reveals developmental targets of serotonin specific reuptake inhibitors (SSRIs)},
	Volume = {55},
	Year = {2008},
	File = {papers/Narboux-Nême_Neuropharmacology2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuropharm.2008.08.020}}

@article{Zhuang:2005,
	Abstract = {We used a knock-in strategy to generate two lines of mice expressing Cre recombinase under the transcriptional control of the dopamine transporter promoter (DAT-cre mice) or the serotonin transporter promoter (SERT-cre mice). In DAT-cre mice, immunocytochemical staining of adult brains for the dopamine-synthetic enzyme tyrosine hydroxylase and for Cre recombinase revealed that virtually all dopaminergic neurons in the ventral midbrain expressed Cre. Crossing DAT-cre mice with ROSA26-stop-lacZ or ROSA26-stop-YFP reporter mice revealed a near perfect correlation between staining for tyrosine hydroxylase and beta-galactosidase or YFP. YFP-labeled fluorescent dopaminergic neurons could be readily identified in live slices. Crossing SERT-cre mice with the ROSA26-stop-lacZ or ROSA26-stop-YFP reporter mice similarly revealed a near perfect correlation between staining for serotonin-synthetic enzyme tryptophan hydroxylase and beta-galactosidase or YFP. Additional Cre expression in the thalamus and cortex was observed, reflecting the known pattern of transient SERT expression during early postnatal development. These findings suggest a general strategy of using neurotransmitter transporter promoters to drive selective Cre expression and thus control mutations in specific neurotransmitter systems. Crossed with fluorescent-gene reporters, this strategy tags neurons by neurotransmitter status, providing new tools for electrophysiology and imaging.},
	Author = {Zhuang, Xiaoxi and Masson, Justine and Gingrich, Jay A and Rayport, Stephen and Hen, Ren{\'e}},
	Date-Added = {2014-07-25 13:38:19 +0000},
	Date-Modified = {2014-07-25 13:38:19 +0000},
	Doi = {10.1016/j.jneumeth.2004.09.020},
	Journal = {J Neurosci Methods},
	Journal-Full = {Journal of neuroscience methods},
	Mesh = {Animals; Brain; Chimera; Dopamine; Dopamine Plasma Membrane Transport Proteins; Female; Gene Expression Regulation; Gene Targeting; Genes, Reporter; Integrases; Male; Membrane Glycoproteins; Membrane Transport Proteins; Mice; Mice, Inbred C57BL; Mice, Transgenic; Molecular Biology; Nerve Tissue Proteins; Neurochemistry; Neurons; Promoter Regions, Genetic; Recombinant Fusion Proteins; Serotonin; Serotonin Plasma Membrane Transport Proteins; Tyrosine 3-Monooxygenase; beta-Galactosidase},
	Month = {Apr},
	Number = {1},
	Pages = {27-32},
	Pmid = {15763133},
	Pst = {ppublish},
	Title = {Targeted gene expression in dopamine and serotonin neurons of the mouse brain},
	Volume = {143},
	Year = {2005},
	File = {papers/Zhuang_JNeurosciMethods2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jneumeth.2004.09.020}}

@article{Li:2013b,
	Abstract = {A dynamic interplay between intrinsic regional molecular cues and extrinsic factors from the thalamus shape multiple features of early cortical development. It remains uncertain and controversial, however, whether the initial formation of cortical columns depends on neuronal activity, and there is little evidence that cortical lamination or neuronal differentiation is influenced by extrinsic activity. We examined the role of thalamic-derived factors in cortical development by selectively eliminating glutamatergic synaptic transmission from thalamocortical neurons in mice and found that eliminating thalamocortical neurotransmission prevented the formation of "barrel" columns in somatosensory cortex. Interestingly, based on cytoarchitectonic criteria and genetic markers, blocking thalamocortical neurotransmission also perturbed the development of superficial cortical lamina and the morphologic development of neurons. These experiments demonstrate that barrels and aspects of the layer-dependent pattern of cortical cytoarchitecture, gene expression, and neuronal differentiation depend on thalamocortical neurotransmission, extending the apparent influence of extrinsic, presumably activity-dependent factors, on cortical development.},
	Author = {Li, Hong and Fertuzinhos, Sofia and Mohns, Ethan and Hnasko, Thomas S and Verhage, Matthijs and Edwards, Robert and Sestan, Nenad and Crair, Michael C},
	Date-Added = {2014-07-25 13:37:09 +0000},
	Date-Modified = {2014-07-25 13:37:09 +0000},
	Doi = {10.1016/j.neuron.2013.06.043},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Evoked Potentials, Somatosensory; Glutamic Acid; Mice; Neural Pathways; Neurons; Somatosensory Cortex; Synaptic Transmission; Thalamus},
	Month = {Sep},
	Number = {5},
	Pages = {970-86},
	Pmc = {PMC3768017},
	Pmid = {24012009},
	Pst = {ppublish},
	Title = {Laminar and columnar development of barrel cortex relies on thalamocortical neurotransmission},
	Volume = {79},
	Year = {2013},
	File = {papers/Li_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.06.043}}

@article{Kobayashi:1963,
	Author = {Kobayashi, T},
	Date-Added = {2014-07-11 13:17:40 +0000},
	Date-Modified = {2014-07-11 13:33:27 +0000},
	Journal = {Am J Physiol},
	Journal-Full = {The American journal of physiology},
	Keywords = {BODY WEIGHT; BRAIN; GROWTH; mouse; mice; Cerebral Cortex; postnatal; development; human},
	Mesh = {Body Weight; Brain; Growth},
	Month = {Feb},
	Pages = {343-6},
	Pmid = {14033949},
	Pst = {ppublish},
	Title = {Brain-to-body ratios and time of maturation of the mouse brain},
	Volume = {204},
	Year = {1963},
	File = {papers/KOBAYASHI_AmJPhysiol1963.pdf}}

@article{Bai:2008,
	Abstract = {During forebrain development the lateral cortical stream (LCS) supplies neurons to structures in the ventral telencephalon including the amygdala and piriform cortex. In the current study, we used spatially directed in utero electroporation and RNAi to investigate mechanisms of migration to the ventral telencephalon. Cells labeled by in utero electroporation of the lateral ventricular zone migrated into the LCS, and entered the lateral neocortex, piriform cortex and amygdala, where they differentiated primarily as pyramidal neurons. RNAi of DCX or LIS1 disrupted migration into amygdala and piriform cortex and caused many neurons to accumulate in the external and amygdalar capsules. RNAi of LIS1 and DCX had similar as well as distinguishable effects on the pattern of altered migration. Combinatorial RNAi of LIS1 and DCX further suggested interaction in the functions of LIS1 and DCX on the morphology and migration of migrating neurons in the LCS. Together, these results confirm that the LCS contributes pyramidal neurons to ventral forebrain structures and reveals that DCX and LIS1 have important functions in this major migratory pathway in the developing forebrain.},
	Author = {Bai, Jilin and Ramos, Raddy L and Paramasivam, Murugan and Siddiqi, Faez and Ackman, James B and LoTurco, Joseph J},
	Date-Added = {2014-06-23 18:26:21 +0000},
	Date-Modified = {2014-06-23 18:26:21 +0000},
	Doi = {10.1159/000109859},
	Journal = {Dev Neurosci},
	Journal-Full = {Developmental neuroscience},
	Mesh = {Amygdala; Animals; Cell Differentiation; Cell Movement; Electroporation; Female; Gene Expression Regulation, Developmental; Microtubule-Associated Proteins; Nerve Tissue Proteins; Neural Pathways; Neuropeptides; Olfactory Pathways; Prosencephalon; Pyramidal Cells; RNA Interference; Rats; Rats, Wistar; Stem Cells},
	Number = {1-3},
	Pages = {144-56},
	Pmid = {18075262},
	Pst = {ppublish},
	Title = {The role of DCX and LIS1 in migration through the lateral cortical stream of developing forebrain},
	Volume = {30},
	Year = {2008},
	File = {papers/Bai_DevNeurosci2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1159/000109859}}

@article{Golding:2014,
	Abstract = {Inhibitory interneurons (INs) critically control the excitability and plasticity of neuronal networks, but whether activity can direct INs into specific circuits during development is unknown. Here, we report that in the dorsal lateral geniculate nucleus (dLGN), which relays retinal input to the cortex, circuit activity is required for the migration, molecular differentiation, and functional integration of INs. We first characterize the prenatal origin and molecular identity of dLGN INs, revealing their recruitment from an Otx2(+) neuronal pool located in the adjacent ventral LGN. Using time-lapse and electrophysiological recordings, together with genetic and pharmacological perturbation of retinal waves, we show that retinal activity directs the navigation and circuit incorporation of dLGN INs during the first postnatal week, thereby regulating the inhibition of thalamocortical circuits. These findings identify an input-dependent mechanism regulating IN migration and circuit inhibition, which may account for the progressive recruitment of INs into expanding excitatory circuits during evolution.},
	Author = {Golding, Bruno and Pouchelon, Gabrielle and Bellone, Camilla and Murthy, Sahana and Di Nardo, Ariel A and Govindan, Subashika and Ogawa, Masahuro and Shimogori, Tomomi and L{\"u}scher, Christian and Dayer, Alexandre and Jabaudon, Denis},
	Date-Added = {2014-04-08 16:06:10 +0000},
	Date-Modified = {2014-04-08 16:06:10 +0000},
	Doi = {10.1016/j.neuron.2014.01.032},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Month = {Mar},
	Number = {5},
	Pages = {1057-69},
	Pmid = {24607228},
	Pst = {ppublish},
	Title = {Retinal input directs the recruitment of inhibitory interneurons into thalamic visual circuits},
	Volume = {81},
	Year = {2014},
	File = {papers/Golding_Neuron2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2014.01.032}}

@article{Chen:2013a,
	Abstract = {Fluorescent calcium sensors are widely used to image neural activity. Using structure-based mutagenesis and neuron-based screening, we developed a family of ultrasensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo. In layer 2/3 pyramidal neurons of the mouse visual cortex, GCaMP6 reliably detected single action potentials in neuronal somata and orientation-tuned synaptic calcium transients in individual dendritic spines. The orientation tuning of structurally persistent spines was largely stable over timescales of weeks. Orientation tuning averaged across spine populations predicted the tuning of their parent cell. Although the somata of GABAergic neurons showed little orientation tuning, their dendrites included highly tuned dendritic segments (5-40-µm long). GCaMP6 sensors thus provide new windows into the organization and dynamics of neural circuits over multiple spatial and temporal scales.},
	Author = {Chen, Tsai-Wen and Wardill, Trevor J and Sun, Yi and Pulver, Stefan R and Renninger, Sabine L and Baohan, Amy and Schreiter, Eric R and Kerr, Rex A and Orger, Michael B and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S},
	Date-Added = {2014-03-28 15:24:26 +0000},
	Date-Modified = {2014-03-28 15:25:08 +0000},
	Doi = {10.1038/nature12354},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {technique; Methods; gene; calcium imaging; in vivo; Mouse; optical physiology},
	Mesh = {Action Potentials; Animals; Calcium; Calcium-Binding Proteins; Cells, Cultured; Dendritic Spines; Fluorescent Dyes; GABAergic Neurons; Luminescent Proteins; Mice; Molecular Imaging; Mutagenesis; Protein Engineering; Pyramidal Cells; Visual Cortex},
	Month = {Jul},
	Number = {7458},
	Pages = {295-300},
	Pmc = {PMC3777791},
	Pmid = {23868258},
	Pst = {ppublish},
	Title = {Ultrasensitive fluorescent proteins for imaging neuronal activity},
	Volume = {499},
	Year = {2013},
	File = {papers/Chen_Nature2013a.pdf}}

@article{Zingg:2014,
	Abstract = {Numerous studies have examined the neuronal inputs and outputs of many areas within the mammalian cerebral cortex, but how these areas are organized into neural networks that communicate across the entire cortex is unclear. Over 600 labeled neuronal pathways acquired from tracer injections placed across the entire mouse neocortex enabled us to generate a cortical connectivity atlas. A total of 240 intracortical connections were manually reconstructed within a common neuroanatomic framework, forming a cortico-cortical connectivity map that facilitates comparison of connections from different cortical targets. Connectivity matrices were generated to provide an overview of all intracortical connections and subnetwork clusterings. The connectivity matrices and cortical map revealed that the entire cortex is organized into four somatic sensorimotor, two medial, and two lateral subnetworks that display unique topologies and can interact through select cortical areas. Together, these data provide a resource that can be used to further investigate cortical networks and their corresponding functions.},
	Author = {Zingg, Brian and Hintiryan, Houri and Gou, Lin and Song, Monica Y and Bay, Maxwell and Bienkowski, Michael S and Foster, Nicholas N and Yamashita, Seita and Bowman, Ian and Toga, Arthur W and Dong, Hong-Wei},
	Date-Added = {2014-03-18 00:58:16 +0000},
	Date-Modified = {2014-03-18 00:58:16 +0000},
	Doi = {10.1016/j.cell.2014.02.023},
	Journal = {Cell},
	Journal-Full = {Cell},
	Month = {Feb},
	Number = {5},
	Pages = {1096-111},
	Pmid = {24581503},
	Pst = {ppublish},
	Title = {Neural networks of the mouse neocortex},
	Volume = {156},
	Year = {2014},
	File = {papers/Zingg_Cell2014a.pdf},
	Bdsk-File-2 = {papers/Zingg_Cell2014b.pdf},
	Bdsk-File-3 = {papers/Zingg_Cell2014.xlsx},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cell.2014.02.023}}

@article{Rash:2011,
	Abstract = {The processes regulating cortical surface area expansion during development and evolution are unknown. We show that loss of function of all fibroblast growth factor receptors (FgfRs) expressed at the earliest stages of cortical development causes severe deficits in surface area growth by embryonic day 12.5 (E12.5) in the mouse. In FgfR mutants, accelerated production of neurons led to severe loss of radial progenitors and premature termination of neurogenesis. Nevertheless, these mutants showed remarkably little change in cortical layer structure. Birth-dating experiments indicated that a greater proportion of layer fates was generated during early neurogenic stages, revealing that FgfR activity normally slows the temporal progression of cortical layer fates. Electroporation of a dominant-negative FgfR at E11.5 increased cortical neurogenesis in normal mice--an effect that was blocked by simultaneous activation of the Notch pathway. Together with changes in the expression of Notch pathway genes in FgfR mutant embryos, these findings indicate that Notch lies downstream of FgfR signaling in the same pathway regulating cortical neurogenesis and begin to establish a mechanism for regulating cortical surface expansion.},
	Author = {Rash, Brian G and Lim, H David and Breunig, Joshua J and Vaccarino, Flora M},
	Date-Added = {2014-02-28 19:42:16 +0000},
	Date-Modified = {2014-02-28 19:44:58 +0000},
	Doi = {10.1523/JNEUROSCI.4439-11.2011},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; Cerebral Cortex; Neocortex; radial glia; neurogenesis; Mouse},
	Mesh = {Age Factors; Analysis of Variance; Animals; Brain; Bromodeoxyuridine; Caspase 3; Cell Count; Cell Differentiation; Cells, Cultured; Cerebral Cortex; DNA-Binding Proteins; Electroporation; Embryo, Mammalian; Eye Proteins; Fatty Acid-Binding Proteins; Fibroblast Growth Factors; Gene Expression Regulation, Developmental; Green Fluorescent Proteins; Homeodomain Proteins; Ki-67 Antigen; Mice; Mice, Transgenic; Mutation; Nerve Tissue Proteins; Neurogenesis; Neurons; Paired Box Transcription Factors; Receptors, Fibroblast Growth Factor; Receptors, Notch; Repressor Proteins; Signal Transduction; Stem Cells; T-Box Domain Proteins; Transcription Factors},
	Month = {Oct},
	Number = {43},
	Pages = {15604-17},
	Pmc = {PMC3235689},
	Pmid = {22031906},
	Pst = {ppublish},
	Title = {FGF signaling expands embryonic cortical surface area by regulating Notch-dependent neurogenesis},
	Volume = {31},
	Year = {2011},
	File = {papers/Rash_JNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4439-11.2011}}

@article{Rash:2013,
	Abstract = {Gyrification allows an expanded cortex with greater functionality to fit into a smaller cranium. However, the mechanisms of gyrus formation have been elusive. We show that ventricular injection of FGF2 protein at embryonic day 11.5-before neurogenesis and before the formation of intrahemispheric axonal connections-altered the overall size and shape of the cortex and induced the formation of prominent, bilateral gyri and sulci in the rostrolateral neocortex. We show increased tangential growth of the rostral ventricular zone (VZ) but decreased Wnt3a and Lef1 expression in the cortical hem and adjacent hippocampal promordium and consequent impaired growth of the caudal cortical primordium, including the hippocampus. At the same time, we observed ectopic Er81 expression, increased proliferation of Tbr2-expressing (Tbr2(+)) intermediate neuronal progenitors (INPs), and elevated Tbr1(+) neurogenesis in the regions that undergo gyrification, indicating region-specific actions of FGF2 on the VZ and subventricular zone (SVZ). However, the relative number of basal radial glia-recently proposed to be important in gyrification-appeared to be unchanged. These findings are consistent with the hypothesis that increased radial unit production together with rapid SVZ growth and heightened localized neurogenesis can cause cortical gyrification in lissencephalic species. These data also suggest that the position of cortical gyri can be molecularly specified in mice. In contrast, a different ligand, FGF8b, elicited surface area expansion throughout the cortical primordium but no gyrification. Our findings demonstrate that individual members of the diverse Fgf gene family differentially regulate global as well as regional cortical growth rates while maintaining cortical layer structure.},
	Author = {Rash, Brian G and Tomasi, Simone and Lim, H David and Suh, Carol Y and Vaccarino, Flora M},
	Date-Added = {2014-02-28 19:33:06 +0000},
	Date-Modified = {2014-02-28 19:34:43 +0000},
	Doi = {10.1523/JNEUROSCI.3621-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; Cerebral Cortex; Neocortex; Mouse; radial glia; neurogenesis},
	Mesh = {Animals; Antimetabolites; Axons; Brain Chemistry; Bromodeoxyuridine; Cell Count; Cerebral Cortex; Cerebral Ventricles; DNA, Complementary; Densitometry; Dependovirus; Female; Fibroblast Growth Factor 2; Green Fluorescent Proteins; Immunohistochemistry; In Situ Hybridization; Lymphoid Enhancer-Binding Factor 1; Mice; Neocortex; Pregnancy; RNA; Real-Time Polymerase Chain Reaction; Wnt3A Protein},
	Month = {Jun},
	Number = {26},
	Pages = {10802-14},
	Pmc = {PMC3693057},
	Pmid = {23804101},
	Pst = {ppublish},
	Title = {Cortical gyrification induced by fibroblast growth factor 2 in the mouse brain},
	Volume = {33},
	Year = {2013},
	File = {papers/Rash_JNeurosci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.3621-12.2013}}

@article{Shitamukai:2011,
	Abstract = {Radial glia cells function as neural stem cells in the developing brain and generate self-renewing and differentiating daughter cells by asymmetric cell divisions. During these divisions, the apical process or basal process of the elongated epithelial structure is asymmetrically partitioned into daughter cells, depending on developmental contexts. However, in mammalian neurogenesis, the relationship between these subcellular structures and self-renewability is largely unknown. We induced oblique cleavages of radial glia cells to split the apical and basal processes into two daughters, and investigated the fate and morphology of the daughters in slice cultures. We observed that the more basal daughter cell that inherits the basal process self-renews outside of the ventricular zone (VZ), while the more apical daughter cell differentiates. These self-renewing progenitors, termed "outer VZ progenitors," retain the basal but not the apical process, as recently reported for the outer subventricular zone (OSVZ) progenitors in primates (Fietz et al., 2010; Hansen et al., 2010); to self-renew, they require clonal Notch signaling between sibling cells. We also found a small endogenous population of outer VZ progenitors in the mouse embryonic neocortex, consistent with a low frequency of oblique radial glia divisions. Our results describe the general role of the basal process in the self-renewal of neural progenitors and implicate the loss of the apical junctions during oblique divisions as a possible mechanism for generating OSVZ progenitors. We propose that mouse outer VZ progenitors, induced by oblique cleavages, provide a model to study both progenitor self-renewal and OSVZ progenitors.},
	Author = {Shitamukai, Atsunori and Konno, Daijiro and Matsuzaki, Fumio},
	Date-Added = {2014-02-28 19:30:03 +0000},
	Date-Modified = {2014-02-28 19:31:20 +0000},
	Doi = {10.1523/JNEUROSCI.4773-10.2011},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; radial glia; cortical columns; Cerebral Cortex; Neocortex},
	Mesh = {Analysis of Variance; Animals; Cell Differentiation; Cell Lineage; Cells, Cultured; Immunohistochemistry; Mice; Mice, Inbred ICR; Neocortex; Neuroglia; Neurons; Stem Cells},
	Month = {Mar},
	Number = {10},
	Pages = {3683-95},
	Pmid = {21389223},
	Pst = {ppublish},
	Title = {Oblique radial glial divisions in the developing mouse neocortex induce self-renewing progenitors outside the germinal zone that resemble primate outer subventricular zone progenitors},
	Volume = {31},
	Year = {2011},
	File = {papers/Shitamukai_JNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4773-10.2011}}

@article{Blumberg:2013a,
	Abstract = {BACKGROUND: During active (or REM) sleep, infant mammals exhibit myoclonic twitches of skeletal muscles throughout the body, generating jerky, discrete movements of the distal limbs. Hundreds of thousands of limb twitches are produced daily, and sensory feedback from these movements is a substantial driver of infant brain activity, suggesting that they contribute to motor learning and sensorimotor integration. It is not known whether the production of twitches is random or spatiotemporally structured, or whether the patterning of twitching changes with age; such information is critical for understanding how twitches contribute to development.
RESULTS: We used high-speed videography and 3D motion tracking to assess the spatiotemporal structure of twitching at forelimb joints in 2- and 8-day-old rats. At both ages, twitches exhibited highly structured spatiotemporal properties at multiple timescales, including synergistic and multijoint movements within and across forelimbs. Hierarchical cluster analysis and latent class analysis revealed developmental changes in twitching quantity and patterning. Critically, we found evidence for a selectionist process whereby movement patterns at the early age compete for retention and expression over development.
CONCLUSIONS: These findings indicate that twitches are not produced randomly but are highly structured at multiple timescales. This structure has important implications for understanding brain and spinal mechanisms that produce twitching, and the role that sensory feedback from twitching plays in sensorimotor system development. We propose that twitches represent a heretofore-overlooked form of motor exploration that helps animals probe the biomechanics of their limbs, build motor synergies, and lay a foundation for complex, automatic, and goal-directed wake movements.},
	Author = {Blumberg, Mark S and Coleman, Cassandra M and Gerth, Ashlynn I and McMurray, Bob},
	Date-Added = {2014-02-25 21:00:07 +0000},
	Date-Modified = {2014-02-25 21:01:55 +0000},
	Doi = {10.1016/j.cub.2013.08.055},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {development; Rats; sleep; sensory-motor; spontaneous activity;},
	Month = {Nov},
	Number = {21},
	Pages = {2100-9},
	Pmc = {PMC3823644},
	Pmid = {24139739},
	Pst = {ppublish},
	Title = {Spatiotemporal structure of REM sleep twitching reveals developmental origins of motor synergies},
	Volume = {23},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2013.08.055}}

@article{Blumberg:2013,
	Abstract = {It is still not known how the 'rudimentary' movements of fetuses and infants are transformed into the coordinated, flexible and adaptive movements of adults. In addressing this important issue, we consider a behavior that has been perennially viewed as a functionless by-product of a dreaming brain: the jerky limb movements called myoclonic twitches. Recent work has identified the neural mechanisms that produce twitching as well as those that convey sensory feedback from twitching limbs to the spinal cord and brain. In turn, these mechanistic insights have helped inspire new ideas about the functional roles that twitching might play in the self-organization of spinal and supraspinal sensorimotor circuits. Striking support for these ideas is coming from the field of developmental robotics: when twitches are mimicked in robot models of the musculoskeletal system, the basic neural circuitry undergoes self-organization. Mutually inspired biological and synthetic approaches promise not only to produce better robots, but also to solve fundamental problems concerning the developmental origins of sensorimotor maps in the spinal cord and brain.},
	Author = {Blumberg, Mark S and Marques, Hugo Gravato and Iida, Fumiya},
	Date-Added = {2014-02-25 20:59:56 +0000},
	Date-Modified = {2014-02-25 21:01:33 +0000},
	Doi = {10.1016/j.cub.2013.04.075},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {toread; development; Rats; sleep; sensory-motor; spontaneous activity; review; wholeBrain},
	Mesh = {Animals; Brain; Feedback, Sensory; Fetal Movement; Humans; Motor Activity; Movement; Musculoskeletal Development; Rats; Robotics; Sleep; Spinal Cord},
	Month = {Jun},
	Number = {12},
	Pages = {R532-7},
	Pmc = {PMC3709969},
	Pmid = {23787051},
	Pst = {ppublish},
	Title = {Twitching in sensorimotor development from sleeping rats to robots},
	Volume = {23},
	Year = {2013},
	File = {papers/Blumberg_CurrBiol2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2013.04.075}}

@article{Ackman:2014,
	Abstract = {The initial structural and functional development of visual circuits in reptiles, birds, and mammals happens independent of sensory experience. After eye opening, visual experience further refines and elaborates circuits that are critical for normal visual function. Innate genetic programs that code for gradients of molecules provide gross positional information for developing nerve cells, yet much of the cytoarchitectural complexity and synaptogenesis of neurons depends on calcium influx, neurotransmitter release, and neural activity before the onset of vision. In fact, specific spatiotemporal patterns of neural activity, or 'retinal waves', emerge amidst the development of the earliest connections made between excitable cells in the developing eye. These patterns of spontaneous activity, which have been observed in all amniote retinae examined to date, may be an evolved adaptation for species with long gestational periods before the onset of functional vision, imparting an informational robustness and redundancy to guide development of visual maps across the nervous system. Recent experiments indicate that retinal waves play a crucial role in the development of interconnections between different parts of the visual system, suggesting that these spontaneous patterns serve as a template-matching mechanism to prepare higher-order visually associative circuits for the onset of visuomotor learning and behavior. Key questions for future studies include determining the exact sources and nature of spontaneous activity during development, characterizing the interactions between neural activity and transcriptional gene regulation, and understanding the extent of circuit connectivity governed by retinal waves within and between sensory-motor systems.},
	Author = {Ackman, James B and Crair, Michael C},
	Date-Added = {2014-02-25 20:58:36 +0000},
	Date-Modified = {2014-02-25 20:58:36 +0000},
	Doi = {10.1016/j.conb.2013.11.011},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Month = {Feb},
	Pages = {166-175},
	Pmc = {PMC3957181},
	Pmid = {24492092},
	Pst = {ppublish},
	Title = {Role of emergent neural activity in visual map development},
	Volume = {24C},
	Year = {2014},
	File = {papers/Ackman_CurrOpinNeurobiol2014.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.conb.2013.11.011}}

@article{Fogassi:2005,
	Abstract = {Inferior parietal lobule (IPL) neurons were studied when monkeys performed motor acts embedded in different actions and when they observed similar acts done by an experimenter. Most motor IPL neurons coding a specific act (e.g., grasping) showed markedly different activations when this act was part of different actions (e.g., for eating or for placing). Many motor IPL neurons also discharged during the observation of acts done by others. Most responded differentially when the same observed act was embedded in a specific action. These neurons fired during the observation of an act, before the beginning of the subsequent acts specifying the action. Thus, these neurons not only code the observed motor act but also allow the observer to understand the agent's intentions.},
	Author = {Fogassi, Leonardo and Ferrari, Pier Francesco and Gesierich, Benno and Rozzi, Stefano and Chersi, Fabian and Rizzolatti, Giacomo},
	Date-Added = {2014-01-29 16:00:24 +0000},
	Date-Modified = {2014-01-29 16:00:58 +0000},
	Doi = {10.1126/science.1106138},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {mirror neuron; mirror symmetry; learning; behavior; monkey; Posterior parietal cortex},
	Mesh = {Animals; Comprehension; Electrophysiology; Food; Goals; Haplorhini; Intention; Microelectrodes; Motor Activity; Motor Cortex; Neurons; Parietal Lobe; Psychomotor Performance; Visual Perception},
	Month = {Apr},
	Number = {5722},
	Pages = {662-7},
	Pmid = {15860620},
	Pst = {ppublish},
	Title = {Parietal lobe: from action organization to intention understanding},
	Volume = {308},
	Year = {2005},
	File = {papers/Fogassi_Science2005.pdf}}

@article{Hohl:2013,
	Abstract = {We have used a new approach to study the neural decoding function that converts the population response in extrastriate area MT into estimates of target motion to drive smooth pursuit eye movement. Experiments reveal significant trial-by-trial correlations between the responses of MT neurons and the initiation of pursuit. The preponderance of significant correlations and the relatively low reduction in noise between MT and the behavioral output support the hypothesis of a sensory origin for at least some of the trial-by-trial variation in pursuit initiation. The finding of mainly positive MT-pursuit correlations, whether the target speed is faster or slower than the neuron's preferred speed, places strong constraints on the neural decoding computation. We propose that decoding is based on normalizing a weighted population vector of opponent motion responses; normalization comes from neurons uncorrelated with those used to compute the weighted population vector.},
	Author = {Hohl, Sonja S and Chaisanguanthum, Kris S and Lisberger, Stephen G},
	Date-Added = {2014-01-29 15:38:49 +0000},
	Date-Modified = {2014-01-29 15:39:41 +0000},
	Doi = {10.1016/j.neuron.2013.05.026},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Eye Movements; Saccades; monkey; sensory-motor; visual system; function; behavior},
	Mesh = {Action Potentials; Animals; Eye Movements; Macaca mulatta; Male; Models, Neurological; Motion Perception; Neurons; Photic Stimulation; Pursuit, Smooth; Reaction Time; Visual Cortex},
	Month = {Jul},
	Number = {1},
	Pages = {167-79},
	Pmc = {PMC3757094},
	Pmid = {23849202},
	Pst = {ppublish},
	Title = {Sensory population decoding for visually guided movements},
	Volume = {79},
	Year = {2013},
	File = {papers/Hohl_Neuron2013.pdf},
	Bdsk-File-2 = {papers/Hohl_Neuron2013a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.05.026}}

@article{Lee:2013,
	Abstract = {Sensory inputs control motor behavior with a strength, or gain, that can be modulated according to the movement conditions. In smooth pursuit eye movements, the response to a brief perturbation of target motion is larger during pursuit of a moving target than during fixation of a stationary target. As a step toward identifying the locus and mechanism of gain modulation, we test whether it acts on signals that are in visual or motor coordinates. Monkeys tracked targets that moved at 15$\,^{\circ}$/s in one of eight directions, including left, right, up, down, and the four oblique directions. In eight-ninths of the trials, the target underwent a brief perturbation that consisted of a single cycle of a 10 Hz sine wave of amplitude $\pm$5$\,^{\circ}$/s in one of the same eight directions. Even for oblique directions of baseline target motion, the magnitude of the eye velocity response to the perturbation was largest for a perturbation near the axis of target motion and smallest for a perturbation along the orthogonal axis. Computational modeling reveals that our data are reproduced when the strength of visual-motor transmission is modulated in sensory coordinates, and there is a static motor bias that favors horizontal eye movements. A network model shows how the output from the smooth eye movement region of the frontal eye fields (FEF(SEM)) could implement gain control by shifting the peak of a visual population response along the axes of preferred image speed and direction.},
	Author = {Lee, Joonyeol and Yang, Jin and Lisberger, Stephen G},
	Date-Added = {2014-01-29 15:35:25 +0000},
	Date-Modified = {2014-01-29 15:35:38 +0000},
	Doi = {10.1523/JNEUROSCI.4846-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {sensory-motor; Eye Movements; Saccades; monkey; visual system; function; behavior; Cerebellum},
	Mesh = {Algorithms; Animals; Data Interpretation, Statistical; Functional Laterality; Haplorhini; Individuality; Male; Models, Neurological; Movement; Nerve Net; Normal Distribution; Parietal Lobe; Photic Stimulation; Psychomotor Performance; Pursuit, Smooth; Retina; Synaptic Transmission; Visual Pathways; Visual Perception},
	Month = {May},
	Number = {22},
	Pages = {9420-30},
	Pmc = {PMC3705569},
	Pmid = {23719810},
	Pst = {ppublish},
	Title = {Control of the gain of visual-motor transmission occurs in visual coordinates for smooth pursuit eye movements},
	Volume = {33},
	Year = {2013},
	File = {papers/Lee_JNeurosci2013.pdf}}

@article{Lisberger:2010,
	Abstract = {Smooth-pursuit eye movements transform 100 ms of visual motion into a rapid initiation of smooth eye movement followed by sustained accurate tracking. Both the mean and variation of the visually driven pursuit response can be accounted for by the combination of the mean tuning curves and the correlated noise within the sensory representation of visual motion in extrastriate visual area MT. Sensory-motor and motor circuits have both housekeeping and modulatory functions, implemented in the cerebellum and the smooth eye movement region of the frontal eye fields. The representation of pursuit is quite different in these two regions of the brain, but both regions seem to control pursuit directly with little or no noise added downstream. Finally, pursuit exhibits a number of voluntary characteristics that happen on short timescales. These features make pursuit an excellent exemplar for understanding the general properties of sensory-motor processing in the brain.},
	Author = {Lisberger, Stephen G},
	Date-Added = {2014-01-29 15:32:09 +0000},
	Date-Modified = {2014-01-29 15:33:14 +0000},
	Doi = {10.1016/j.neuron.2010.03.027},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {sensory-motor; Eye Movements; Saccades; monkey; visual system; review literature; function; behavior; Cerebellum},
	Mesh = {Animals; Eye Movements; Humans; Motion Perception; Photic Stimulation; Pursuit, Smooth; Visual Pathways},
	Month = {May},
	Number = {4},
	Pages = {477-91},
	Pmc = {PMC2887486},
	Pmid = {20510853},
	Pst = {ppublish},
	Title = {Visual guidance of smooth-pursuit eye movements: sensation, action, and what happens in between},
	Volume = {66},
	Year = {2010},
	File = {papers/Lisberger_Neuron2010.pdf}}

@article{Oertel-Knochel:2011,
	Abstract = {The hemispheres of the human brain are anatomically and functionally asymmetric, and many cognitive and motor functions such as language and handedness are lateralized. This review examines anatomical, psychological, and physiological approaches to the understanding of separate hemispheric functions and their integration. The concept of hemispheric laterality plays a central role in current neuropsychological and pathophysiological models of schizophrenia. Reduced hemispheric asymmetry has also been reported for other mental disorders, for example, bipolar disorder. Recent research reflects an increasing interest in the molecular and population genetics of laterality and its potential link with animal models of schizophrenia. The authors review the principles of laterality and brain asymmetry and discuss the evidence for changes in asymmetry in schizophrenia and other mental disorders.},
	Author = {Oertel-Kn{\"o}chel, Viola and Linden, David E J},
	Date-Added = {2014-01-28 02:34:55 +0000},
	Date-Modified = {2014-01-28 13:43:48 +0000},
	Doi = {10.1177/1073858410386493},
	Journal = {Neuroscientist},
	Journal-Full = {The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry},
	Keywords = {Schizophrenia; review literature; human; neurological disorder; Genetic; Functional Laterality; lateralization; mirror symmetry; hemisphere},
	Mesh = {Animals; Cerebrum; Functional Laterality; Humans; Schizophrenia},
	Month = {Oct},
	Number = {5},
	Pages = {456-67},
	Pmid = {21518811},
	Pst = {ppublish},
	Title = {Cerebral asymmetry in schizophrenia},
	Volume = {17},
	Year = {2011},
	File = {papers/Oertel-Knöchel_Neuroscientist2011.pdf}}

@article{Dragovic:2005,
	Abstract = {OBJECTIVE: The prevalence of various anomalous handedness subtypes in schizophrenia patients remains ambiguous. Although current literature favours the notion that the shift in lateral preferences seen is because of an increase of mixed-handedness, several studies suggest that exclusive left handedness is more prevalent than in the general population.
METHOD: Over 40 studies with reported prevalence data on various handedness subtypes in a schizophrenia population were evaluated by meta-analysis. Combined odds ratios for the three common handedness subtypes (left, mixed, and right) were separately calculated.
RESULTS: Each of the three atypical hand dominance patterns were significantly greater in schizophrenia patients than in control subjects, showing that the leftward shift in handedness distribution is not entirely because of an increase in mixed-handedness alone.
CONCLUSION: An increase of exclusive left-handedness is at variance with the prevailing assertion that the handedness shift in schizophrenia patients is because of a diffuse and bilateral hemispheric insult.},
	Author = {Dragovic, M and Hammond, G},
	Date-Added = {2014-01-27 21:07:13 +0000},
	Date-Modified = {2014-01-27 21:08:09 +0000},
	Doi = {10.1111/j.1600-0447.2005.00519.x},
	Journal = {Acta Psychiatr Scand},
	Journal-Full = {Acta psychiatrica Scandinavica},
	Keywords = {Functional Laterality; lateralization; handedness; Schizophrenia; behavior; Human; review literature},
	Mesh = {Functional Laterality; Humans; Psychiatric Status Rating Scales; Schizophrenia},
	Month = {Jun},
	Number = {6},
	Pages = {410-9},
	Pmid = {15877707},
	Pst = {ppublish},
	Title = {Handedness in schizophrenia: a quantitative review of evidence},
	Volume = {111},
	Year = {2005},
	File = {papers/Dragovic_ActaPsychiatrScand2005.pdf}}

@article{Sommer:2001,
	Abstract = {BACKGROUND: Cerebral lateralisation appears to be decreased in schizophrenia. Results of studies investigating this, however, are equivocal.
AIMS: To review quantitatively the literature on decreased lateralisation in schizophrenia.
METHOD: Meta-analyses were conducted on 19 studies on handedness, 10 dichotic listening studies and 39 studies investigating anatomical asymmetry in schizophrenia.
RESULTS: The prevalence of mixed- and left-handedness ('non-right-handedness') was significantly higher in patients with schizophrenia as compared to healthy controls, and also as compared to psychiatric controls. The analysis of dichotic listening studies revealed no significant difference in lateralisation in schizophrenia. However, when analysis was restricted to studies using consonant-vowel or fused word tasks, significantly decreased lateralisation in schizophrenia emerged. Asymmetry of the planum temporale and the Sylvian fissure was significantly decreased in schizophrenia, while asymmetry of the temporal horn of the lateral ventricle was not.
CONCLUSION: Strong evidence is provided for decreased cerebral lateralisation in schizophrenia.},
	Author = {Sommer, I and Ramsey, N and Kahn, R and Aleman, A and Bouma, A},
	Date-Added = {2014-01-27 20:45:24 +0000},
	Date-Modified = {2014-01-27 21:02:27 +0000},
	Journal = {Br J Psychiatry},
	Journal-Full = {The British journal of psychiatry : the journal of mental science},
	Keywords = {Grants; Schizophrenia; Functional Laterality; lateralization; Cerebral Cortex; behavior; handedness; Human; review literature; wholeBrain},
	Mesh = {Brain; Dichotic Listening Tests; Functional Laterality; Humans; Schizophrenia; Schizophrenic Psychology; Speech Perception},
	Month = {Apr},
	Pages = {344-51},
	Pmid = {11282814},
	Pst = {ppublish},
	Title = {Handedness, language lateralisation and anatomical asymmetry in schizophrenia: meta-analysis},
	Volume = {178},
	Year = {2001},
	File = {papers/Sommer_BrJPsychiatry2001.pdf}}

@article{Crawley:2008a,
	Abstract = {Comprehensive behavioral analyses of transgenic and knockout mice have successfully identified the functional roles of many genes in the brain. Over the past 10 years, strategies for mouse behavioral phenotyping have evolved to maximize the scope and replicability of findings from a cohort of mutant mice, minimize the interpretation of procedural artifacts, and provide robust translational tools to test hypotheses and develop treatments. This Primer addresses experimental design issues and offers examples of high-throughput batteries, learning and memory tasks, and anxiety-related tests.},
	Author = {Crawley, Jacqueline N},
	Date-Added = {2014-01-27 20:08:27 +0000},
	Date-Modified = {2014-01-27 20:10:12 +0000},
	Doi = {10.1016/j.neuron.2008.03.001},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Mice, Neurologic Mutants;Behavior, Animal;Female;Phenotype;research support, n.i.h., intramural;Animals;Disease Models, Animal;Male;review;Mice; Schizophrenia; Methods; wholeBrain},
	Mesh = {Animals; Behavior, Animal; Disease Models, Animal; Female; Male; Mice; Mice, Neurologic Mutants; Phenotype},
	Month = {Mar},
	Number = {6},
	Pages = {809-18},
	Pmid = {18367082},
	Pst = {ppublish},
	Title = {Behavioral phenotyping strategies for mutant mice},
	Volume = {57},
	Year = {2008},
	File = {papers/Crawley_Neuron2008a.pdf}}

@article{Crawley:1999,
	Abstract = {Rigorous experimental design can minimize the high risk of false positives and false negatives in the behavioral phenotyping of a new transgenic or knockout mouse. Use of well established, quantitative, reproducible behavioral tasks, appropriate Ns, correct statistical methods, consideration of background genes contributed by the parental strains, and attention to litter and gender issues, will maximize meaningful comparisons of -/-, +/-, and +/+ genotypes. Strategies developed and used by our laboratory are described in this review. Preliminary observations evaluate general health and neurological reflexes. Sensory abilities and motor functions are extensively quantitated. Specific tests include observations of home cage behaviors, body weight, body temperature, appearance of the fur and whiskers, righting reflex, acoustic startle, eye blink, pupil constriction, vibrissae reflex, pinna reflex, Digiscan open field locomotion, rotarod motor coordination, hanging wire, footprint pathway, visual cliff, auditory threshold, pain threshold, and olfactory acuity. Hypothesis testing then focuses on at least three well-validated tasks within each relevant behavioral domain. Specific tests for mice are described herein for the domains of learning and memory, feeding, nociception, and behaviors relevant to discrete symptoms of human anxiety, depression, schizophrenia, and drug addiction. An example of our approach is illustrated in the behavioral phenotyping of C/EBPdelta knockout mice, which appear to be normal on general health, neurological reflexes, sensory and motor tasks, and the Morris water task, but show remarkably enhanced performance on contextual fear conditioning.},
	Author = {Crawley, J N},
	Date-Added = {2014-01-27 20:04:38 +0000},
	Date-Modified = {2014-01-27 20:05:48 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {mouse; mice; behavior; Phenotype; Schizophrenia; Methods; review literature; Grants; wholeBrain},
	Mesh = {Animals; Behavior, Animal; Health; Humans; Mice; Mice, Knockout; Mice, Transgenic; Phenotype; Psychomotor Performance; Research Design; Sensation},
	Month = {Jul},
	Number = {1},
	Pages = {18-26},
	Pmid = {10448192},
	Pst = {ppublish},
	Title = {Behavioral phenotyping of transgenic and knockout mice: experimental design and evaluation of general health, sensory functions, motor abilities, and specific behavioral tests},
	Volume = {835},
	Year = {1999},
	File = {papers/Crawley_BrainRes1999.pdf}}

@article{Pletnikov:2008,
	Abstract = {A strong candidate gene for schizophrenia and major mental disorders, disrupted-in-schizophrenia 1 (DISC1) was first described in a large Scottish family in which a balanced chromosomal translocation segregates with schizophrenia and other psychiatric illnesses. The translocation mutation may result in loss of DISC1 function via haploinsufficiency or dominant-negative effects of a predicted mutant DISC1 truncated protein product. DISC1 has been implicated in neurodevelopment, including maturation of the cerebral cortex. To evaluate the neuronal and behavioral effects of mutant DISC1, the Tet-off system under the regulation of the CAMKII promoter was used to generate transgenic mice with inducible expression of mutant human DISC1 (hDISC1) limited to forebrain regions, including cerebral cortex, hippocampus and striatum. Expression of mutant hDISC1 was not associated with gross neurodevelopmental abnormalities, but led to a mild enlargement of the lateral ventricles and attenuation of neurite outgrowth in primary cortical neurons. These morphological changes were associated with decreased protein levels of endogenous mouse DISC1, LIS1 and SNAP-25. Compared to their sex-matched littermate controls, mutant hDISC1 transgenic male mice exhibited spontaneous hyperactivity in the open field and alterations in social interaction, and transgenic female mice showed deficient spatial memory. The results show that the neuronal and behavioral effects of mutant hDISC1 are consistent with a dominant-negative mechanism, and are similar to some features of schizophrenia. The present mouse model may facilitate the study of aspects of the pathogenesis of schizophrenia.},
	Author = {Pletnikov, M V and Ayhan, Y and Nikolskaia, O and Xu, Y and Ovanesov, M V and Huang, H and Mori, S and Moran, T H and Ross, C A},
	Date-Added = {2014-01-27 19:54:14 +0000},
	Date-Modified = {2014-01-27 19:54:44 +0000},
	Doi = {10.1038/sj.mp.4002079},
	Journal = {Mol Psychiatry},
	Journal-Full = {Molecular psychiatry},
	Keywords = {Schizophrenia; Grants; behavior; gene; mice; Mouse},
	Mesh = {Animals; Animals, Newborn; Behavior, Animal; Behavioral Symptoms; Brain; Disease Models, Animal; Female; Gene Expression Regulation, Developmental; Humans; Lateral Ventricles; Male; Mice; Mice, Transgenic; Molecular Weight; Mutation; Nerve Tissue Proteins; Schizophrenia},
	Month = {Feb},
	Number = {2},
	Pages = {173-86, 115},
	Pmid = {17848917},
	Pst = {ppublish},
	Title = {Inducible expression of mutant human DISC1 in mice is associated with brain and behavioral abnormalities reminiscent of schizophrenia},
	Volume = {13},
	Year = {2008},
	File = {papers/Pletnikov_MolPsychiatry2008.pdf}}

@article{Carandini:2013,
	Abstract = {The study of perceptual decision-making offers insight into how the brain uses complex, sometimes ambiguous information to guide actions. Understanding the underlying processes and their neural bases requires that one pair recordings and manipulations of neural activity with rigorous psychophysics. Though this research has been traditionally performed in primates, it seems increasingly promising to pursue it at least partly in mice and rats. However, rigorous psychophysical methods are not yet as developed for these rodents as they are for primates. Here we give a brief overview of the sensory capabilities of rodents and of their cortical areas devoted to sensation and decision. We then review methods of psychophysics, focusing on the technical issues that arise in their implementation in rodents. These methods represent a rich set of challenges and opportunities.},
	Author = {Carandini, Matteo and Churchland, Anne K},
	Date-Added = {2014-01-27 16:03:56 +0000},
	Date-Modified = {2014-01-27 16:04:47 +0000},
	Doi = {10.1038/nn.3410},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {mouse; behavior; Functional Laterality; Decision Making; Grants; wholeBrain; Schizophrenia; Methods; review literature; Psychophysics},
	Mesh = {Animals; Brain; Decision Making; Mice; Neural Pathways; Neurons; Perception; Physical Stimulation; Psychophysics; Rats; Signal Detection, Psychological},
	Month = {Jul},
	Number = {7},
	Pages = {824-31},
	Pmid = {23799475},
	Pst = {ppublish},
	Title = {Probing perceptual decisions in rodents},
	Volume = {16},
	Year = {2013},
	File = {papers/Carandini_NatNeurosci2013.pdf}}

@article{Jia:2013,
	Abstract = {Our ability to control complex systems is a fundamental challenge of contemporary science. Recently introduced tools to identify the driver nodes, nodes through which we can achieve full control, predict the existence of multiple control configurations, prompting us to classify each node in a network based on their role in control. Accordingly a node is critical, intermittent or redundant if it acts as a driver node in all, some or none of the control configurations. Here we develop an analytical framework to identify the category of each node, leading to the discovery of two distinct control modes in complex systems: centralized versus distributed control. We predict the control mode for an arbitrary network and show that one can alter it through small structural perturbations. The uncovered bimodality has implications from network security to organizational research and offers new insights into the dynamics and control of complex systems.},
	Author = {Jia, Tao and Liu, Yang-Yu and Cs{\'o}ka, Endre and P{\'o}sfai, M{\'a}rton and Slotine, Jean-Jacques and Barab{\'a}si, Albert-L{\'a}szl{\'o}},
	Date-Added = {2014-01-15 14:33:31 +0000},
	Date-Modified = {2014-01-15 14:34:03 +0000},
	Doi = {10.1038/ncomms3002},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Keywords = {graph theory; Mathematics; models; self organization; network; Game Theory; Methods},
	Pages = {2002},
	Pmid = {23774965},
	Pst = {ppublish},
	Title = {Emergence of bimodality in controlling complex networks},
	Volume = {4},
	Year = {2013},
	File = {papers/Jia_NatCommun2013.pdf}}

@article{Raj:2008,
	Abstract = {Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure. Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others. These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging.},
	Author = {Raj, Arjun and van Oudenaarden, Alexander},
	Date-Added = {2014-01-14 17:44:56 +0000},
	Date-Modified = {2014-01-14 17:45:54 +0000},
	Doi = {10.1016/j.cell.2008.09.050},
	Journal = {Cell},
	Journal-Full = {Cell},
	Keywords = {handedness; gene; Gene Expression; development; Experimental; self organization; Selection (Genetics); Game Theory; asymmetry; lateralization},
	Mesh = {Animals; Bacteria; Eukaryotic Cells; Gene Expression; Humans; Stochastic Processes; Transcription, Genetic},
	Month = {Oct},
	Number = {2},
	Pages = {216-26},
	Pmc = {PMC3118044},
	Pmid = {18957198},
	Pst = {ppublish},
	Title = {Nature, nurture, or chance: stochastic gene expression and its consequences},
	Volume = {135},
	Year = {2008},
	File = {papers/Raj_Cell2008.pdf}}

@article{Cai:2013,
	Abstract = {In the transgenic multicolor labeling strategy called 'Brainbow', Cre-loxP recombination is used to create a stochastic choice of expression among fluorescent proteins, resulting in the indelible marking of mouse neurons with multiple distinct colors. This method has been adapted to non-neuronal cells in mice and to neurons in fish and flies, but its full potential has yet to be realized in the mouse brain. Here we present several lines of mice that overcome limitations of the initial lines, and we report an adaptation of the method for use in adeno-associated viral vectors. We also provide technical advice about how best to image Brainbow-expressing tissue.},
	Author = {Cai, Dawen and Cohen, Kimberly B and Luo, Tuanlian and Lichtman, Jeff W and Sanes, Joshua R},
	Date-Added = {2014-01-08 21:07:08 +0000},
	Date-Modified = {2014-01-08 21:07:08 +0000},
	Doi = {10.1038/nmeth.2450},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Month = {May},
	Number = {6},
	Pages = {540-7},
	Pmc = {PMC3713494},
	Pmid = {23817127},
	Pst = {ppublish},
	Title = {Improved tools for the Brainbow toolbox},
	Volume = {10},
	Year = {2013},
	File = {papers/Cai_NatMethods2013.pdf}}

@article{Kohl:2004,
	Abstract = {Fever is a common clinical complaint in adults and children with a variety of infectious illnesses, as well as a frequently reported adverse event following immunization. Although the level of measured temperature indicative of a "fever" was first defined in 1868, it remains unclear what role fever has as a physiologic reaction to invading substances, how best to measure body temperature and compare measurements from different body sites, and, consequently, how to interpret fever data derived from vaccine safety trials or immunization safety surveillance. However, even with many aspects of the societal, medical, economic, and epidemiologic meanings of fever as an adverse event following immunization (AEFI) still elusive, it is a generally benign--albeit common--clinical sign. By standardizing the definition and means of assessment of fever in vaccine safety studies, thereby permitting comparability of data, we hope to arrive at an improved understanding of its importance as an AEFI.},
	Author = {Kohl, Katrin S and Marcy, S Michael and Blum, Michael and Connell Jones, Marcy and Dagan, Ron and Hansen, John and Nalin, David and Rothstein, Edward and {Brighton Collaboration Fever Working Group}},
	Date-Added = {2013-12-12 17:13:47 +0000},
	Date-Modified = {2013-12-12 17:14:10 +0000},
	Doi = {10.1086/422454},
	Journal = {Clin Infect Dis},
	Journal-Full = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
	Keywords = {health, child, infant, flu, influenza, vaccination, epilepsy, seizures},
	Mesh = {Adult; Child; Fever; Humans; Infant; Seizures, Febrile; Vaccination},
	Month = {Aug},
	Number = {3},
	Pages = {389-94},
	Pmid = {15307007},
	Pst = {ppublish},
	Title = {Fever after immunization: current concepts and improved future scientific understanding},
	Volume = {39},
	Year = {2004},
	File = {papers/Kohl_ClinInfectDis2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1086/422454}}

@article{Koplan:1979,
	Abstract = {Using decision analysis, we estimated the benefits, risks and costs of routine childhood immunization against pertussis. Without an immunization program, we predict that there would be a 71-fold increase in cases and an almost fourfold increase in deaths (2.0 to 7.6) per cohort of one million children. With a vaccination program, we predict 0.1 case of encephalitis associated with pertussis and five cases of post-vaccination encephalitis; without a program, there would be only 2.3 cases of encephalitis associated with pertussis. Community vaccination would reduce by 61 per cent the costs related to pertussis. Our analysis supports continuation of vaccination in routine childhood immunization programs, but suggests the need for more reliable data on complications from the vaccine, further study of the epidemiology of pertussis and development of a less toxic vaccine.},
	Author = {Koplan, J P and Schoenbaum, S C and Weinstein, M C and Fraser, D W},
	Date-Added = {2013-12-12 17:03:47 +0000},
	Date-Modified = {2013-12-12 17:04:10 +0000},
	Doi = {10.1056/NEJM197910253011703},
	Journal = {N Engl J Med},
	Journal-Full = {The New England journal of medicine},
	Keywords = {health, child, infant, flu, influenza, vaccination, epilepsy, seizures},
	Mesh = {Child; Child, Preschool; Cost-Benefit Analysis; Decision Theory; Encephalitis; Encephalomyelitis, Acute Disseminated; Europe; Humans; Infant; Infant, Newborn; Models, Theoretical; National Health Programs; Personal Health Services; Pertussis Vaccine; Risk; United States; Vaccination; Whooping Cough},
	Month = {Oct},
	Number = {17},
	Pages = {906-11},
	Pmid = {39253},
	Pst = {ppublish},
	Title = {Pertussis vaccine--an analysis of benefits, risks and costs},
	Volume = {301},
	Year = {1979},
	File = {papers/Koplan_NEnglJMed1979.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1056/NEJM197910253011703}}

@article{Nelson:1976,
	Abstract = {We examined the frequency of development of afebrile seizures in 1706 children who had experienced at least one febrile seizure and were followed to the age of seven years. Epilepsy developed by seven years of age in 20 per 1000 (2 per cent), and another 10 per 1000 had at least one afebrile seizure that did not meet our definition of epilepsy. In children whose neurologic or developmental status was suspect or abnormal before any seizure and whose first seizure was complex (longer than 15 minutes, multiple or focal) epilepsy developed at a rate 18 times higher than in children with no febrile seizures (92 vs. 5 per 1000; P less than 0.001). In the largest group with febrile seizures, those previously normal with noncomplex first febrile seizures, epilepsy developed in 11 per 1000; this rate, although moderate, was greater than that for children with no febrile seizures (P = 0.027). Prior neurologic and developmental status and characteristics of the first febrile seizure are important predictors of epilepsy after febrile seizures.},
	Author = {Nelson, K B and Ellenberg, J H},
	Date-Added = {2013-12-12 16:30:41 +0000},
	Date-Modified = {2013-12-12 16:30:55 +0000},
	Doi = {10.1056/NEJM197611042951901},
	Journal = {N Engl J Med},
	Journal-Full = {The New England journal of medicine},
	Keywords = {health, child, infant, flu, influenza, vaccination, epilepsy, seizures},
	Mesh = {Age Factors; Child; Child, Preschool; Epilepsy; Female; Follow-Up Studies; Humans; Infant; Male; Recurrence; Risk; Time Factors},
	Month = {Nov},
	Number = {19},
	Pages = {1029-33},
	Pmid = {972656},
	Pst = {ppublish},
	Title = {Predictors of epilepsy in children who have experienced febrile seizures},
	Volume = {295},
	Year = {1976},
	File = {papers/Nelson_NEnglJMed1976.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1056/NEJM197611042951901}}

@article{Klein:2010,
	Abstract = {OBJECTIVE: In February 2008, we alerted the Advisory Committee on Immunization Practices to preliminary evidence of a twofold increased risk of febrile seizures after the combination measles-mumps-rubella-varicella (MMRV) vaccine when compared with separate measles-mumps-rubella (MMR) and varicella vaccines. Now with data on twice as many vaccine recipients, our goal was to reexamine seizure risk after MMRV vaccine.
METHODS: Using 2000-2008 Vaccine Safety Datalink data, we assessed seizures and fever visits among children aged 12 to 23 months after MMRV and separate MMR + varicella vaccines. We compared seizure risk after MMRV vaccine to that after MMR + varicella vaccines by using Poisson regression as well as with supplementary regressions that incorporated chart-review results and self-controlled analyses.
RESULTS: MMRV vaccine recipients (83,107) were compared with recipients of MMR + varicella vaccines (376,354). Seizure and fever significantly clustered 7 to 10 days after vaccination with all measles-containing vaccines but not after varicella vaccination alone. Seizure risk during days 7 to 10 was higher after MMRV than after MMR + varicella vaccination (relative risk: 1.98 [95% confidence interval: 1.43-2.73]). Supplementary analyses yielded similar results. The excess risk for febrile seizures 7 to 10 days after MMRV compared with separate MMR + varicella vaccination was 4.3 per 10,000 doses (95% confidence interval: 2.6-5.6).
CONCLUSIONS: Among 12- to 23-month-olds who received their first dose of measles-containing vaccine, fever and seizure were elevated 7 to 10 days after vaccination. Vaccination with MMRV results in 1 additional febrile seizure for every 2300 doses given instead of separate MMR + varicella vaccines. Providers who recommend MMRV should communicate to parents that it increases the risk of fever and seizure over that already associated with measles-containing vaccines.},
	Author = {Klein, Nicola P and Fireman, Bruce and Yih, W Katherine and Lewis, Edwin and Kulldorff, Martin and Ray, Paula and Baxter, Roger and Hambidge, Simon and Nordin, James and Naleway, Allison and Belongia, Edward A and Lieu, Tracy and Baggs, James and Weintraub, Eric and {Vaccine Safety Datalink}},
	Date-Added = {2013-12-12 15:49:08 +0000},
	Date-Modified = {2013-12-12 16:29:51 +0000},
	Doi = {10.1542/peds.2010-0665},
	Journal = {Pediatrics},
	Journal-Full = {Pediatrics},
	Keywords = {health, child, infant, flu, influenza, vaccination, epilepsy, seizures},
	Mesh = {Age Distribution; Chickenpox Vaccine; Cohort Studies; Databases, Factual; Female; Follow-Up Studies; Humans; Incidence; Infant; Male; Measles-Mumps-Rubella Vaccine; Retrospective Studies; Seizures, Febrile; Severity of Illness Index; Sex Distribution; Time Factors; Vaccination; Vaccines, Combined},
	Month = {Jul},
	Number = {1},
	Pages = {e1-8},
	Pmid = {20587679},
	Pst = {ppublish},
	Title = {Measles-mumps-rubella-varicella combination vaccine and the risk of febrile seizures},
	Volume = {126},
	Year = {2010},
	File = {papers/Klein_Pediatrics2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1542/peds.2010-0665}}

@article{Chen:2013,
	Abstract = {In the mammalian neocortex, segregated processing streams are thought to be important for forming sensory representations of the environment, but how local information in primary sensory cortex is transmitted to other distant cortical areas during behaviour is unclear. Here we show task-dependent activation of distinct, largely non-overlapping long-range projection neurons in the whisker region of primary somatosensory cortex (S1) in awake, behaving mice. Using two-photon calcium imaging, we monitored neuronal activity in anatomically identified S1 neurons projecting to secondary somatosensory (S2) or primary motor (M1) cortex in mice using their whiskers to perform a texture-discrimination task or a task that required them to detect the presence of an object at a certain location. Whisking-related cells were found among S2-projecting (S2P) but not M1-projecting (M1P) neurons. A higher fraction of S2P than M1P neurons showed touch-related responses during texture discrimination, whereas a higher fraction of M1P than S2P neurons showed touch-related responses during the detection task. In both tasks, S2P and M1P neurons could discriminate similarly between trials producing different behavioural decisions. However, in trials producing the same decision, S2P neurons performed better at discriminating texture, whereas M1P neurons were better at discriminating location. Sensory stimulus features alone were not sufficient to elicit these differences, suggesting that selective transmission of S1 information to S2 and M1 is driven by behaviour.},
	Author = {Chen, Jerry L and Carta, Stefano and Soldado-Magraner, Joana and Schneider, Bernard L and Helmchen, Fritjof},
	Date-Added = {2013-12-10 14:52:26 +0000},
	Date-Modified = {2013-12-10 14:53:29 +0000},
	Doi = {10.1038/nature12236},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {calcium imaging; optical physiology; neurophysiology; in vivo; mouse; Somatosensory Cortex; barrels; Motor Cortex; behavior; function; connectivity},
	Mesh = {Afferent Pathways; Animals; Behavior, Animal; Calcium; Discrimination (Psychology); Mice; Neurons; Somatosensory Cortex; Vibrissae},
	Month = {Jul},
	Number = {7458},
	Pages = {336-40},
	Pmid = {23792559},
	Pst = {ppublish},
	Title = {Behaviour-dependent recruitment of long-range projection neurons in somatosensory cortex},
	Volume = {499},
	Year = {2013},
	File = {papers/Chen_Nature2013.pdf}}

@article{Ramnani:2006,
	Abstract = {Evidence has been accumulating that the primate cerebellum contributes not only to motor control, but also to higher 'cognitive' function. However, there is no consensus about how the cerebellum processes such information. The answer to this puzzle can be found in the nature of cerebellar connections to areas of the cerebral cortex (particularly the prefrontal cortex) and in the uniformity of its intrinsic cellular organization, which implies uniformity in information processing regardless of the area of origin in the cerebral cortex. With this in mind, the relatively well-developed models of how the cerebellum processes information from the motor cortex might be extended to explain how it could also process information from the prefrontal cortex.},
	Author = {Ramnani, Narender},
	Date-Added = {2013-10-09 15:51:22 +0000},
	Date-Modified = {2013-10-09 15:52:26 +0000},
	Doi = {10.1038/nrn1953},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {review literature; Cerebellar Cortex; Cerebellum; function; Cerebral Cortex; Thalamic Nuclei; thalamus; Neocortex; Motor Activity/physiology; Motor Cortex; behavior;},
	Mesh = {Animals; Cerebellum; Cerebral Cortex; Humans; Nerve Net; Neural Pathways},
	Month = {Jul},
	Number = {7},
	Pages = {511-22},
	Pmid = {16791141},
	Pst = {ppublish},
	Title = {The primate cortico-cerebellar system: anatomy and function},
	Volume = {7},
	Year = {2006},
	File = {papers/Ramnani_NatRevNeurosci2006.pdf}}

@article{Altman:1969a,
	Author = {Altman, J},
	Date-Added = {2013-10-09 15:27:38 +0000},
	Date-Modified = {2013-10-09 15:27:38 +0000},
	Doi = {10.1002/cne.901360303},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Mesh = {Age Factors; Animals; Animals, Newborn; Autoradiography; Cell Differentiation; Cell Movement; Cerebellar Cortex; Neurons; Purkinje Cells; Rats; Thymidine; Tritium},
	Month = {Jul},
	Number = {3},
	Pages = {269-93},
	Pmid = {5788129},
	Pst = {ppublish},
	Title = {Autoradiographic and histological studies of postnatal neurogenesis. 3. Dating the time of production and onset of differentiation of cerebellar microneurons in rats},
	Volume = {136},
	Year = {1969},
	File = {papers/Altman_JCompNeurol1969.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901360303}}

@article{Ahrens:2013,
	Abstract = {Brain function relies on communication between large populations of neurons across multiple brain areas, a full understanding of which would require knowledge of the time-varying activity of all neurons in the central nervous system. Here we use light-sheet microscopy to record activity, reported through the genetically encoded calcium indicator GCaMP5G, from the entire volume of the brain of the larval zebrafish in vivo at 0.8 Hz, capturing more than 80% of all neurons at single-cell resolution. Demonstrating how this technique can be used to reveal functionally defined circuits across the brain, we identify two populations of neurons with correlated activity patterns. One circuit consists of hindbrain neurons functionally coupled to spinal cord neuropil. The other consists of an anatomically symmetric population in the anterior hindbrain, with activity in the left and right halves oscillating in antiphase, on a timescale of 20 s, and coupled to equally slow oscillations in the inferior olive.},
	Author = {Ahrens, Misha B and Orger, Michael B and Robson, Drew N and Li, Jennifer M and Keller, Philipp J},
	Date-Added = {2013-09-28 16:09:18 +0000},
	Date-Modified = {2013-09-28 16:09:55 +0000},
	Doi = {10.1038/nmeth.2434},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Keywords = {wholeBrain; calcium imaging; calcium sensor; technique; Microscopy; Methods; Zebrafish; in vivo},
	Mesh = {Animals; Brain; Microscopy; Zebrafish},
	Month = {May},
	Number = {5},
	Pages = {413-20},
	Pmid = {23524393},
	Pst = {ppublish},
	Title = {Whole-brain functional imaging at cellular resolution using light-sheet microscopy},
	Volume = {10},
	Year = {2013},
	File = {papers/Ahrens_NatMethods2013.pdf},
	Bdsk-File-2 = {papers/Ahrens_NatMethods2013a.pdf},
	Bdsk-File-3 = {papers/Ahrens_NatMethods2013.zip}}

@article{Kloppel:2007,
	Abstract = {The neuronal correlates of handedness are still poorly understood. Here we used event-related functional magnetic resonance imaging to investigate the impact of handedness on neuronal activation of the primary sensorimotor cortex, supplementary motor area and dorsal premotor cortex during simple unilateral and bilateral finger movements. In 16 right-handed and 16 left-handed individuals, we mapped changes in regional neuronal activity while participants responded to four symbolic cues presented in a pseudorandom order. According to pre-specified cues, they pressed a button with their right, left or both index fingers or withheld a response. For unilateral right index finger button presses, reaction times, motor and premotor activity were the same for both right- and left-handers. Compared with right-handers, left-handers had shorter reaction times with unilateral left index finger button presses, along with greater activation of the supplementary motor area and right frontal opercular cortex. Simultaneous bilateral compared with unilateral button presses led to a relative increase of activity in the right and left dorsal premotor cortex and the right primary sensorimotor cortex in right but not left-handers. Neither right nor left-handers showed any tendency during bilateral button presses towards faster responses with the dominant hand and the reaction times were equal in the two groups. Therefore, we conclude that the relative increase of activity in dorsal premotor and right primary sensorimotor cortices in right-handers represents a genuine difference in bimanual motor control related to handedness.},
	Author = {Kl{\"o}ppel, Stefan and van Eimeren, Thilo and Glauche, Volkmar and Vongerichten, Anna and M{\"u}nchau, Alexander and Frackowiak, Richard S J and B{\"u}chel, Christian and Weiller, Cornelius and Siebner, Hartwig R},
	Date-Added = {2013-09-25 20:49:10 +0000},
	Date-Modified = {2013-09-25 20:49:32 +0000},
	Doi = {10.1016/j.neuroimage.2006.08.038},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb; language; fMRI},
	Mesh = {Adult; Female; Functional Laterality; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Motor Cortex; Movement},
	Month = {Jan},
	Number = {1},
	Pages = {274-80},
	Pmid = {17056278},
	Pst = {ppublish},
	Title = {The effect of handedness on cortical motor activation during simple bilateral movements},
	Volume = {34},
	Year = {2007},
	File = {papers/Klöppel_Neuroimage2007.pdf}}

@article{Li:2013a,
	Abstract = {Mapping cortical hemispheric asymmetries in infants would increase our understanding of the origins and developmental trajectories of hemispheric asymmetries. We analyze longitudinal cortical hemispheric asymmetries in 73 healthy subjects at birth, 1, and 2 years of age using surface-based morphometry of magnetic resonance images with a specific focus on the vertex position, sulcal depth, mean curvature, and local surface area. Prominent cortical asymmetries are found around the peri-Sylvian region and superior temporal sulcus (STS) at birth that evolve modestly from birth to 2 years of age. Sexual dimorphisms of cortical asymmetries are present at birth, with males having the larger magnitudes and sizes of the clusters of asymmetries than females that persist from birth to 2 years of age. The left supramarginal gyrus (SMG) is significantly posterior to the right SMG, and the maximum position difference increases from 10.2 mm for males (6.9 mm for females) at birth to 12.0 mm for males (8.4 mm for females) by 2 years of age. The right STS and parieto-occipital sulcus are significantly larger and deeper than those in the left hemisphere, and the left planum temporale is significantly larger and deeper than that in the right hemisphere at all 3 ages. Our results indicate that early hemispheric structural asymmetries are inherent and gender related.},
	Author = {Li, Gang and Nie, Jingxin and Wang, Li and Shi, Feng and Lyall, Amanda E and Lin, Weili and Gilmore, John H and Shen, Dinggang},
	Date-Added = {2013-09-25 20:46:53 +0000},
	Date-Modified = {2013-09-25 20:47:26 +0000},
	Doi = {10.1093/cercor/bhs413},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb; language; MRI},
	Month = {Jan},
	Pmid = {23307634},
	Pst = {aheadofprint},
	Title = {Mapping Longitudinal Hemispheric Structural Asymmetries of the Human Cerebral Cortex From Birth to 2 Years of Age},
	Year = {2013},
	File = {papers/Li_CerebCortex2013.pdf}}

@article{Hill:2010,
	Abstract = {We have established a population average surface-based atlas of human cerebral cortex at term gestation and used it to compare infant and adult cortical shape characteristics. Accurate cortical surface reconstructions for each hemisphere of 12 healthy term gestation infants were generated from structural magnetic resonance imaging data using a novel segmentation algorithm. Each surface was inflated, flattened, mapped to a standard spherical configuration, and registered to a target atlas sphere that reflected shape characteristics of all 24 contributing hemispheres using landmark constrained surface registration. Population average maps of sulcal depth, depth variability, three-dimensional positional variability, and hemispheric depth asymmetry were generated and compared with previously established maps of adult cortex. We found that cortical structure in term infants is similar to the adult in many respects, including the pattern of individual variability and the presence of statistically significant structural asymmetries in lateral temporal cortex, including the planum temporale and superior temporal sulcus. These results indicate that several features of cortical shape are minimally influenced by the postnatal environment.},
	Author = {Hill, Jason and Dierker, Donna and Neil, Jeffrey and Inder, Terrie and Knutsen, Andrew and Harwell, John and Coalson, Timothy and Van Essen, David},
	Date-Added = {2013-09-25 20:44:54 +0000},
	Date-Modified = {2013-09-25 20:45:23 +0000},
	Doi = {10.1523/JNEUROSCI.4682-09.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb; language; neuroimaging; fMRI},
	Mesh = {Atlases as Topic; Cerebral Cortex; Female; Humans; Image Processing, Computer-Assisted; Infant, Newborn; Magnetic Resonance Imaging; Male},
	Month = {Feb},
	Number = {6},
	Pages = {2268-76},
	Pmc = {PMC2836191},
	Pmid = {20147553},
	Pst = {ppublish},
	Title = {A surface-based analysis of hemispheric asymmetries and folding of cerebral cortex in term-born human infants},
	Volume = {30},
	Year = {2010},
	File = {papers/Hill_JNeurosci2010.pdf}}

@article{Bishop:2013,
	Abstract = {In most people, language is processed predominantly by the left hemisphere of the brain, but we do not know how or why. A popular view is that developmental language disorders result from a poorly lateralized brain, but until recently, evidence has been weak and indirect. Modern neuroimaging methods have made it possible to study normal and abnormal development of lateralized function in the developing brain and have confirmed links with language and literacy impairments. However, there is little evidence that weak cerebral lateralization has common genetic origins with language and literacy impairments. Our understanding of the association between atypical language lateralization and developmental disorders may benefit if we reconceptualize the nature of cerebral asymmetry to recognize its multidimensionality and consider variation in lateralization over developmental time. Contrary to popular belief, cerebral lateralization may not be a highly heritable, stable characteristic of individuals; rather, weak lateralization may be a consequence of impaired language learning.},
	Author = {Bishop, Dorothy V M},
	Date-Added = {2013-09-25 20:40:06 +0000},
	Date-Modified = {2013-09-25 20:40:11 +0000},
	Doi = {10.1126/science.1230531},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; mouse; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb; language},
	Mesh = {Animals; Cerebral Cortex; Cognition Disorders; Dyslexia; Forkhead Transcription Factors; Functional Laterality; Genetic Predisposition to Disease; Humans; Language Development; Language Development Disorders; Mitochondrial Proteins; Nerve Tissue Proteins; Neuronal Plasticity; Polymorphism, Single Nucleotide; Repressor Proteins; Ribosomal Proteins; Ultrasonography, Doppler, Transcranial},
	Month = {Jun},
	Number = {6138},
	Pages = {1230531},
	Pmid = {23766329},
	Pst = {ppublish},
	Title = {Cerebral asymmetry and language development: cause, correlate, or consequence?},
	Volume = {340},
	Year = {2013},
	File = {papers/Bishop_Science2013.pdf}}

@article{Mento:2010,
	Abstract = {In recent years, magnetic resonance imaging has allowed researchers to individuate the earlier morphological development of the right hemisphere compared with the left hemisphere during late-gestational development. Anatomical asymmetry, however, does not necessarily mean functional asymmetry, and whether the anatomical differences between hemispheres at this early age are paralleled by functional specialisations remains unknown. In this study, the presence of lateralised electrical brain activity related to both pitch detection and discrimination was investigated in 34 prematurely-born infants [24-34 gestational weeks (GWs)] all tested at the same post-conceptional age of 35 weeks. By means of a frequency-change oddball experimental paradigm, with 'standard' tones at 1000 Hz (P = 90%) and 'deviant' tones at 2000 Hz (P = 10%), we were able to record higher right event-related potential activity in the interval windows between 350 and 650 ms after stimulus onset. An explorative hierarchical cluster analysis confirmed the different distribution of the hemispheric asymmetry score in newborns < 30 weeks old. Here, we show electrophysiological evidence of the early functional right lateralisation for pitch processing (detection and discrimination) arising by 30 GWs, but not before, in preterm newborns despite the longer environmental sensorial experience of newborns < 30 GWs. Generally, these findings suggest that the earlier right structural maturation in foetal epochs seems to be paralleled by a right functional development.},
	Author = {Mento, Giovanni and Suppiej, Agnese and Alto{\`e}, Gianmarco and Bisiacchi, Patrizia S},
	Date-Added = {2013-09-25 20:37:05 +0000},
	Date-Modified = {2013-09-25 20:37:35 +0000},
	Doi = {10.1111/j.1460-9568.2010.07076.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb; language; infant; EEG; neurophysiology},
	Mesh = {Brain; Electroencephalography; Female; Functional Laterality; Gestational Age; Humans; Infant, Newborn; Infant, Premature; Magnetic Resonance Imaging; Pitch Perception; Pregnancy},
	Month = {Feb},
	Number = {3},
	Pages = {565-74},
	Pmid = {20105238},
	Pst = {ppublish},
	Title = {Functional hemispheric asymmetries in humans: electrophysiological evidence from preterm infants},
	Volume = {31},
	Year = {2010},
	File = {papers/Mento_EurJNeurosci2010.pdf}}

@article{Ward:1987,
	Abstract = {The relation between morphological variation of the corpus callosum and variation in the degree of paw preference was investigated in 129/J and BALB/cCF mice. A positive relationship explaining 24% of the variance of paw preference was found in 129/J mice; no such relationship exists in BALB/cCF mice. It is suggested that, since the genetic dissimilarity between these two inbred strains is comparable in magnitude with the genetic dissimilarity between unrelated human subjects, genetic variation may have been an uncontrolled source of heterogeneity in previous human neuropsychological studies.},
	Author = {Ward, R and Tremblay, L and Lassonde, M},
	Date-Added = {2013-09-25 20:04:01 +0000},
	Date-Modified = {2013-09-25 20:04:08 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {Cerebral Cortex; asymmetry; lateralization; hemisphere; behavior; forelimb; handedness; Corpus Callosum},
	Mesh = {Animals; Corpus Callosum; Female; Forelimb; Functional Laterality; Genetic Variation; Genotype; Male; Mice; Mice, Inbred BALB C; Mice, Inbred Strains; Sex Factors; Species Specificity},
	Month = {Oct},
	Number = {1},
	Pages = {84-8},
	Pmid = {3690305},
	Pst = {ppublish},
	Title = {The relationship between callosal variation and lateralization in mice is genotype-dependent},
	Volume = {424},
	Year = {1987},
	File = {papers/Ward_BrainRes1987.pdf}}

@article{Fride:1990,
	Abstract = {Cerebral lateralization has been suggested to play a regulatory role in immune function. In this study, several measures of immune function were evaluated in mice selectively bred for either a strong (HI) or weak (LO) degree of behavioral asymmetry (paw preference) and compared to an unselected control population (HET). Both HI and LO animals had fewer spleen cells but higher degrees of [3H]thymidine incorporation into DNA (on a per cell basis) than HET mice. However, only HI mice had lower immune functions compared to HET controls manifest as reduced mixed leukocyte reaction (MLR), cytotoxic T lymphocyte (CTL) activity, and natural killer (NK) cell activity. These findings indicate that although both extremes in the degree of paw preference may be associated with deviations from the norm, a high degree of behavioral lateralization is associated with decreased immune responsiveness in this animal model.},
	Author = {Fride, E and Collins, R L and Skolnick, P and Arora, P K},
	Date-Added = {2013-09-25 20:01:58 +0000},
	Date-Modified = {2013-09-25 20:02:30 +0000},
	Journal = {Brain Behav Immun},
	Journal-Full = {Brain, behavior, and immunity},
	Keywords = {Cerebral Cortex; asymmetry; lateralization; hemisphere; behavior; forelimb; handedness; Corpus Callosum},
	Mesh = {Animals; Behavior, Animal; Functional Laterality; Immune System; Killer Cells, Natural; Lymphocyte Culture Test, Mixed; Male; Mice; Psychoneuroimmunology; Species Specificity; T-Lymphocytes, Cytotoxic},
	Month = {Jun},
	Number = {2},
	Pages = {129-38},
	Pmid = {2144194},
	Pst = {ppublish},
	Title = {Immune function in lines of mice selected for high or low degrees of behavioral asymmetry},
	Volume = {4},
	Year = {1990}}

@article{Betancur:1991,
	Abstract = {The brain is known to modulate the immune system in an asymmetrical way. In mice, there is an association between handedness and immune response and it has also been shown that hemicortical ablation has opposite effects on some immune parameters. An association between autoantibody production and paw preference was previously observed in female mice, but not in males, suggesting that the association between immune reactivity and functional brain asymmetry is a sex-dependent phenomenon. In three independent experiments, natural killer (NK) cell activity, lymphocyte subset distribution, and mitogen-induced lymphoproliferation were assessed in male C3H/OuJIco mice selected for handedness and after unilateral cortical ablation. Handedness was shown to be associated with NK cell activity but not with lymphocyte subset distribution or lymphoproliferation. Left-handers exhibited lower NK cell activity compared to right-handed or ambidextrous animals. In contrast to previous results in female mice, mitogen-induced lymphoproliferation was not associated with handedness in males. Left cortical ablations depressed NK cell activity, while right lesions had no effect. Neither left or right lesions affected lymphocyte subsets. No interaction between paw preference and side of the lesion was found in the modulation of NK cell activity. These and previous data show that the association between paw preference and immune reactivity varies according to the sex of the animal and the immunological parameters studied. This indicates that the brain may modulate different components of the immune system in different ways, through mechanisms apparently involving sex hormones.},
	Author = {Betancur, C and Neveu, P J and Vitiello, S and Le Moal, M},
	Date-Added = {2013-09-25 20:01:52 +0000},
	Date-Modified = {2013-09-25 20:02:30 +0000},
	Journal = {Brain Behav Immun},
	Journal-Full = {Brain, behavior, and immunity},
	Keywords = {Cerebral Cortex; asymmetry; lateralization; hemisphere; behavior; forelimb; handedness; Corpus Callosum},
	Mesh = {Animals; Brain Damage, Chronic; Cerebral Cortex; Cytotoxicity, Immunologic; Dominance, Cerebral; Functional Laterality; Humans; Killer Cells, Natural; Lymphocyte Activation; Male; Mice; Mice, Inbred C3H; Sex Characteristics; T-Lymphocyte Subsets},
	Month = {Jun},
	Number = {2},
	Pages = {162-9},
	Pmid = {1893219},
	Pst = {ppublish},
	Title = {Natural killer cell activity is associated with brain asymmetry in male mice},
	Volume = {5},
	Year = {1991},
	File = {papers/Betancur_BrainBehavImmun1991.pdf}}

@article{Manhaes:2003,
	Abstract = {In the present work, the hypothesis that the ontogenetic development of the corpus callosum (CC) affects the establishment of behavioral lateralization was tested by studying paw preference performance in adult Swiss mice that were subjected to mid-sagittal transection of the CC on the first postnatal day. Magnitude and direction of laterality were evaluated independently. No significant differences between groups were found for the magnitude of paw preference. On the other hand, the transected group presented a significant populational bias favoring the left paw that was not present in the control groups. These results lend support to the hypothesis that the development of the CC plays a role in the establishment of the normal pattern of behavioral lateralization.},
	Author = {Manh{\~a}es, Alex C and Krahe, Thomas E and Caparelli-D{\'a}quer, Egas and Ribeiro-Carvalho, Anderson and Schmidt, Sergio L and Filgueiras, Cl{\'a}udio C},
	Date-Added = {2013-09-25 20:00:13 +0000},
	Date-Modified = {2013-09-25 20:01:12 +0000},
	Journal = {Neurosci Lett},
	Journal-Full = {Neuroscience letters},
	Keywords = {Cerebral Cortex; asymmetry; lateralization; hemisphere; behavior; forelimb; handedness; Corpus Callosum},
	Mesh = {Animals; Animals, Newborn; Cell Differentiation; Corpus Callosum; Denervation; Forelimb; Functional Laterality; Growth Cones; Male; Mice; Motor Cortex; Movement},
	Month = {Sep},
	Number = {2},
	Pages = {69-72},
	Pmid = {12902020},
	Pst = {ppublish},
	Title = {Neonatal transection of the corpus callosum affects paw preference lateralization of adult Swiss mice},
	Volume = {348},
	Year = {2003},
	File = {papers/Manhães_NeurosciLett2003.pdf}}

@article{Gruber:1991,
	Abstract = {Ward et al. (Brain Research 424 (1987) 84-88) have reported that reduced size of the corpus callosum (CC) was associated with a lower degree of paw preference in the mouse strain 129/J but not in the strain BALB/cCF. Both strains show individually different degrees of development of the CC but mice completely lacking CC occur rarely. The mouse strain I/LnJ shows complete agenesis of the CC. Thus, we have compared the degree of paw lateralization by means of a food reaching task in two samples of I/LnJ mice (n1 = 81, n2 = 93) with that of two common mouse strains which show a normal CC (C57BL/6JIbm, n = 44; DBA/2JZur, n = 48). The two samples of I/LnJ mice were tested in different laboratories. The first sample of I/LnJ mice had a mean age of 36 weeks. As compared to the control mice, the males but not the females showed a significantly reduced degree of paw preference. Both, callosal and acallosal mice showed a preference for left choices. The replication sample of I/LnJ mice contained only animals between 6 and 8 weeks old. All of them were ambilateral. There was no side preference and no gender difference. We conclude that congenital absence of the CC is a factor which may substantially interfere with the development of paw lateralization. However, depending on age and gender, about half of the acallosal mice develop a paw preference.},
	Author = {Gruber, D and Waanders, R and Collins, R L and Wolfer, D P and Lipp, H P},
	Date-Added = {2013-09-25 19:25:52 +0000},
	Date-Modified = {2013-09-25 19:27:50 +0000},
	Journal = {Behav Brain Res},
	Journal-Full = {Behavioural brain research},
	Keywords = {Cerebral Cortex; lateralization; asymmetry; hemisphere; forelimb; behavior; handedness; Corpus Callosum},
	Mesh = {Agenesis of Corpus Callosum; Animals; Behavior, Animal; Brain; Corpus Callosum; Female; Foot; Functional Laterality; Male; Mice; Mice, Inbred BALB C; Mice, Inbred DBA; Mice, Neurologic Mutants},
	Month = {Dec},
	Number = {1},
	Pages = {9-16},
	Pmid = {1786116},
	Pst = {ppublish},
	Title = {Weak or missing paw lateralization in a mouse strain (I/LnJ) with congenital absence of the corpus callosum},
	Volume = {46},
	Year = {1991},
	File = {papers/Gruber_BehavBrainRes1991.pdf}}

@article{Rogers:2009,
	Abstract = {Hand preferences of primates are discussed as part of the broad perspective of brain lateralization in animals, and compared with paw preferences in non-primates. Previously, it has been suggested that primates are more likely to express a species-typical hand preference on complex tasks, especially in the case of coordinated hand use in using tools. I suggest that population-level hand preferences are manifested when the task demands the obligate use of the processing specialization of one hemisphere, and that this depends on the nature of the task rather than its complexity per se. Depending on the species, simple reaching tasks may not demand the obligate use of a specialized hemisphere and so do not constrain limb/hand use. In such cases, individuals may show hand preferences that are associated with consistent differences in behaviour. The individual's hand preference is associated with the expression of behaviour controlled by the hemisphere contralateral to the preferred hand (fear and reactivity in left-handed individuals versus proactivity in right-handed individuals). Recent findings of differences in brain structure between left- and right-handed primates (e.g. somatosensory cortex in marmosets) have been discussed and related to potential evolutionary advances.},
	Author = {Rogers, Lesley J},
	Date-Added = {2013-09-25 13:13:42 +0000},
	Date-Modified = {2013-09-25 13:15:37 +0000},
	Doi = {10.1098/rstb.2008.0225},
	Journal = {Philos Trans R Soc Lond B Biol Sci},
	Journal-Full = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	Keywords = {cerebral cortex; asymmetry; hemisphere; lateralization; handedness; forelimb; behavior},
	Mesh = {Animals; Brain; Choice Behavior; Feeding Behavior; Forelimb; Functional Laterality; Hand; Humans; Individuality; Species Specificity; Tool Use Behavior; Vertebrates},
	Month = {Apr},
	Number = {1519},
	Pages = {943-54},
	Pmc = {PMC2666076},
	Pmid = {19064357},
	Pst = {ppublish},
	Title = {Hand and paw preferences in relation to the lateralized brain},
	Volume = {364},
	Year = {2009},
	File = {papers/Rogers_PhilosTransRSocLondBBiolSci2009.pdf}}

@article{Galaburda:2006a,
	Abstract = {All four genes thus far linked to developmental dyslexia participate in brain development, and abnormalities in brain development are increasingly reported in dyslexia. Comparable abnormalities induced in young rodent brains cause auditory and cognitive deficits, underscoring the potential relevance of these brain changes to dyslexia. Our perspective on dyslexia is that some of the brain changes cause phonological processing abnormalities as well as auditory processing abnormalities; the latter, we speculate, resolve in a proportion of individuals during development, but contribute early on to the phonological disorder in dyslexia. Thus, we propose a tentative pathway between a genetic effect, developmental brain changes, and perceptual and cognitive deficits associated with dyslexia.},
	Author = {Galaburda, Albert M and LoTurco, Joseph and Ramus, Franck and Fitch, R Holly and Rosen, Glenn D},
	Date-Added = {2013-09-25 12:40:21 +0000},
	Date-Modified = {2013-09-25 12:41:09 +0000},
	Doi = {10.1038/nn1772},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {cerebral cortex; lateralization; asymmetry; Dyslexia; neurological disorder; gene; mouse; rat; learning; behavior; hemisphere},
	Mesh = {Animals; Behavior; Cognition Disorders; Disease Models, Animal; Dyslexia; Humans; Models, Molecular},
	Month = {Oct},
	Number = {10},
	Pages = {1213-7},
	Pmid = {17001339},
	Pst = {ppublish},
	Title = {From genes to behavior in developmental dyslexia},
	Volume = {9},
	Year = {2006},
	File = {papers/Galaburda_NatNeurosci2006.pdf}}

@article{Collins:1968,
	Author = {Collins, R L},
	Date-Added = {2013-09-25 12:30:14 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {J Hered},
	Journal-Full = {The Journal of heredity},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; mouse; behavior; Forelimb; forelimb},
	Mesh = {Animals; Behavior, Animal; Functional Laterality; Genetics; Hybridization, Genetic; Inbreeding; Male; Mice},
	Month = {Jan-Feb},
	Number = {1},
	Pages = {9-12},
	Pmid = {5656926},
	Pst = {ppublish},
	Title = {On the inheritance of handedness. I. Laterality in inbred mice},
	Volume = {59},
	Year = {1968},
	File = {papers/Collins_JHered1968.pdf}}

@article{Sun:2006a,
	Abstract = {In the human brain, distinct functions tend to be localized in the left or right hemispheres, with language ability usually localized predominantly in the left and spatial recognition in the right. Furthermore, humans are perhaps the only mammals who have preferential handedness, with more than 90% of the population more skillful at using the right hand, which is controlled by the left hemisphere. How is a distinct function consistently localized in one side of the human brain? Because of the convergence of molecular and neurological analysis, we are beginning to consider the puzzle of brain asymmetry and handedness at a molecular level.},
	Author = {Sun, Tao and Walsh, Christopher A},
	Date-Added = {2013-09-25 00:16:54 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Doi = {10.1038/nrn1930},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; mouse; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb},
	Mesh = {Animals; Brain; Dominance, Cerebral; Functional Laterality; Humans},
	Month = {Aug},
	Number = {8},
	Pages = {655-62},
	Pmid = {16858393},
	Pst = {ppublish},
	Title = {Molecular approaches to brain asymmetry and handedness},
	Volume = {7},
	Year = {2006},
	File = {papers/Sun_NatRevNeurosci2006.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn1930}}

@article{Biddle:1993,
	Abstract = {Lateralization of paw preference in laboratory mice in a single-paw reaching task has been used as a model system for left- and right-hand usage. Given a set number of paw reaches for food from a centrally placed food tube, an individual mouse will exhibit a reliable number of left and right paw reaches. Within any single inbred strain, there are approximately equal numbers of left-pawed and right-pawed mice. Nevertheless, significant strain differences have been reported for the degree of lateralization of paw preference. We report here a systematic survey of paw preference in 12 inbred strains of the mouse in which the degree of lateralization falls into two groups of weakly lateralized and highly lateralized paw preference. The genetic inference is that a single major gene may control some function, and alternate alleles at this locus are expressed as weakly and highly lateralized paw preference. Reciprocal crosses indicate the trait is additive with no maternal or X-linked effects. The direction of paw preference has previously appeared to be genetically neutral, but in some strains there is evidence of significant deviation of the numbers of mice to the left and right of equal paw usage, independent of degree of lateralization, and this suggests that direction of left-right paw usage may be a separate genetic trait in the mouse model.},
	Author = {Biddle, F G and Coffaro, C M and Ziehr, J E and Eales, B A},
	Date-Added = {2013-09-25 00:15:43 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {Genome},
	Journal-Full = {Genome / National Research Council Canada = G{\'e}nome / Conseil national de recherches Canada},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; mouse; behavior; forelimb},
	Mesh = {Animals; Female; Functional Laterality; Genetic Variation; Male; Mice; Mice, Inbred Strains},
	Month = {Oct},
	Number = {5},
	Pages = {935-43},
	Pmid = {8270204},
	Pst = {ppublish},
	Title = {Genetic variation in paw preference (handedness) in the mouse},
	Volume = {36},
	Year = {1993},
	File = {papers/Biddle_Genome1993.pdf}}

@article{Signore:1991,
	Abstract = {Mice from a pool of inbred strains (384 males and 329 females) were tested for handedness according to Collins' protocol in order to assess the reliability of this measurement. As previously reported by Collins these data revealed that a) approximately half of the mice were right-handed and half left-handed, b) most of the mice were strongly lateralized and c) females were more lateralized than males. The study of the psychometric characteristics of the test suggested that this measurement of behavioral asymmetry is both stable and observer independent. The test of paw preference also appeared to measure preexisting lateralization and was not a function of training during the test.},
	Author = {Signore, P and Nosten-Bertrand, M and Chaoui, M and Roubertoux, P L and Marchaland, C and Perez-Diaz, F},
	Date-Added = {2013-09-25 00:02:10 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {Physiol Behav},
	Journal-Full = {Physiology \& behavior},
	Keywords = {cerebral cortex; lateralization; asymmetry; hemisphere; Grants; mouse; behavior; forelimb},
	Mesh = {Animals; Appetitive Behavior; Cerebral Cortex; Dominance, Cerebral; Female; Male; Mice; Mice, Inbred Strains; Psychomotor Performance; Sex Characteristics; Species Specificity},
	Month = {Apr},
	Number = {4},
	Pages = {701-4},
	Pmid = {1881972},
	Pst = {ppublish},
	Title = {An assessment of handedness in mice},
	Volume = {49},
	Year = {1991},
	File = {papers/Signore_PhysiolBehav1991.pdf}}

@article{Li:2013,
	Author = {Li, Qingsong and Bian, Shan and Liu, Bingfang and Hong, Janet and Toth, Miklos and Sun, Tao},
	Date-Added = {2013-09-24 19:34:34 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Doi = {10.1038/cr.2013.106},
	Journal = {Cell Res},
	Journal-Full = {Cell research},
	Keywords = {Laterality; behavior; cerebral cortex; asymmetry; hemisphere; proposal; Grants; forelimb},
	Month = {Sep},
	Number = {9},
	Pages = {1147-9},
	Pmc = {PMC3760628},
	Pmid = {23917527},
	Pst = {ppublish},
	Title = {Establishing brain functional laterality in adult mice through unilateral gene manipulation in the embryonic cortex},
	Volume = {23},
	Year = {2013},
	File = {papers/Li_CellRes2013.pdf}}

@article{Mountcastle:1997,
	Abstract = {The modular organization of nervous systems is a widely documented principle of design for both vertebrate and invertebrate brains of which the columnar organization of the neocortex is an example. The classical cytoarchitectural areas of the neocortex are composed of smaller units, local neural circuits repeated iteratively within each area. Modules may vary in cell type and number, in internal and external connectivity, and in mode of neuronal processing between different large entities; within any single large entity they have a basic similarity of internal design and operation. Modules are most commonly grouped into entities by sets of dominating external connections. This unifying factor is most obvious for the heterotypical sensory and motor areas of the neocortex. Columnar defining factors in homotypical areas are generated, in part, within the cortex itself. The set of all modules composing such an entity may be fractionated into different modular subsets by different extrinsic connections. Linkages between them and subsets in other large entities form distributed systems. The neighborhood relations between connected subsets of modules in different entities result in nested distributed systems that serve distributed functions. A cortical area defined in classical cytoarchitectural terms may belong to more than one and sometimes to several distributed systems. Columns in cytoarchitectural areas located at some distance from one another, but with some common properties, may be linked by long-range, intracortical connections.},
	Author = {Mountcastle, V B},
	Date-Added = {2013-09-18 16:44:17 +0000},
	Date-Modified = {2013-09-18 16:44:58 +0000},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {Neocortex; Cerebral Cortex; isocortex; cortical columns; topographic map; Anatomy; function},
	Mesh = {Animals; Brain Mapping; Cell Division; Cell Movement; Cerebral Cortex; Humans; Models, Neurological; Neurons},
	Month = {Apr},
	Pages = {701-22},
	Pmid = {9153131},
	Pst = {ppublish},
	Title = {The columnar organization of the neocortex},
	Volume = {120 ( Pt 4)},
	Year = {1997},
	File = {papers/Mountcastle_Brain1997.pdf}}

@article{Mountcastle:1957a,
	Abstract = {THE METHOD of single unit analysis has now been applied to three primary sensory receiving areas of the cerebral cortex (4, 14, -15, 16, 20, 21, 22, 23, 25). Among these studies, considerable attention has been given to the somatic sensory areas, for Li et al. in an extensive series of investigations
(20, 21, 22, 23) have described the responses of neurons in this region to electrical stimulation of the specific relay nucleus of the thalamus, as well as to stimulation of those thalamic nuclei they designate as unspecific, or diffusely projecting. The discharge properties of neurons of the somatic sensory areas in response to peripheral nerve volleys have been detailed by Amassian (4), and he has also given the first description of the neuronal activity of a sensory association area (5). Preliminary reports of similar studies have appeared from the Paris laboratories of Albe-Fessard (2, 3, 11).
In the present investigation we wished to study the functional organiza- tion of the first somatic sensory cortex by the method of single unit analysis, and to determine as precisely as possi ble the firing patterns of cortical Cells activated by stimuli delivered to the related sense organs. We wished also to determine which modality components of somatic sensibility project upon the somatic sensory cortex, as well as to gain some idea of the functional organization of that projection. Our purposes required that the activity of cortical cells be observed over considerable periods of time in a stable fash- ion. It appears from the published records that the technique of intracellu- lar recording from cortical cells has not yet reached the stage of perfection required, for only Phillips (26, 27), dealing with the motor cortex, has been able to study cortical neurons for considerable periods of time after im- palement without deterioration of resting or action potentials. His beautiful records, however, give examples of what may be hoped for with this tech- nique. We have, therefore, persisted in the method of extracellular recording. A chamber has been developed by one of us (12) with which it is possible to obliterate cortical pulsations without the risk of direct pressure injury, yet allowing free lateral movement of the electrode carrier.},
	Author = {Mountcastle, V B and Davies, P W and Berman, A L},
	Date-Added = {2013-09-18 16:37:27 +0000},
	Date-Modified = {2013-09-18 19:20:13 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {CEREBRAL CORTEX/physiology; cortical columns; Neocortex; Anatomy; function; topographic map; Somatosensory Cortex; cat; Classical/physiology},
	Mesh = {Cerebral Cortex},
	Month = {Jul},
	Number = {4},
	Pages = {374-407},
	Pmid = {13439409},
	Pst = {ppublish},
	Title = {Response properties of neurons of cat's somatic sensory cortex to peripheral stimuli},
	Volume = {20},
	Year = {1957},
	File = {papers/MOUNTCASTLE_JNeurophysiol1957a.pdf}}

@article{Mountcastle:1957,
	Abstract = {THE PRESENT PAPER describes some observations upon the modality and topographical attributes of single neurons of the first somatic sensory area of the cat's cerebral cortex, the analogue of the cortex of the postcentral gy- rus in the primate brain. These data, together with others upon the response latencies of the cells of different layers of the cortex to peripheral stimuli, support an hypothesis of the functional organization of this cortical area. This is that the neurons which lie in narrow vertical columns, or cylinders, extending from layer II through layer VI make up an elementary unit of organization, for they are activated by stimulation of the same single class of peripheral receptors, from almost identical peripheral receptive fields, at latencies which are not significantly different for the cells of the various lay- ers. It is emphasized that this pattern of organization obtains only for the early repetitiv `e responses of cortical neurons to brief peripheral stimuli. These neurons may be rela ted in quite different organization patterns when analyzed in terms of later discharges. A report of these experiments was made to the American Physiological Society in September, 1955 (10, 17).},
	Author = {Mountcastle, V B},
	Date-Added = {2013-09-18 16:34:47 +0000},
	Date-Modified = {2013-09-18 19:20:27 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {CEREBRAL CORTEX/physiology; cortical columns; Neocortex; Anatomy; function; topographic map; Somatosensory Cortex; cat; Classical/physiology},
	Mesh = {Cerebral Cortex},
	Month = {Jul},
	Number = {4},
	Pages = {408-34},
	Pmid = {13439410},
	Pst = {ppublish},
	Title = {Modality and topographic properties of single neurons of cat's somatic sensory cortex},
	Volume = {20},
	Year = {1957},
	File = {papers/MOUNTCASTLE_JNeurophysiol1957.pdf}}

@article{Gu:2013,
	Abstract = {Fluorescence imaging is one of the most versatile and widely used visualization methods in biomedical research. However, tissue autofluorescence is a major obstacle confounding interpretation of in vivo fluorescence images. The unusually long emission lifetime (5-13 μs) of photoluminescent porous silicon nanoparticles can allow the time-gated imaging of tissues in vivo, completely eliminating shorter-lived (<10 ns) emission signals from organic chromophores or tissue autofluorescence. Here using a conventional animal imaging system not optimized for such long-lived excited states, we demonstrate improvement of signal to background contrast ratio by >50-fold in vitro and by >20-fold in vivo when imaging porous silicon nanoparticles. Time-gated imaging of porous silicon nanoparticles accumulated in a human ovarian cancer xenograft following intravenous injection is demonstrated in a live mouse. The potential for multiplexing of images in the time domain by using separate porous silicon nanoparticles engineered with different excited state lifetimes is discussed.},
	Author = {Gu, Luo and Hall, David J and Qin, Zhengtao and Anglin, Emily and Joo, Jinmyoung and Mooney, David J and Howell, Stephen B and Sailor, Michael J},
	Date-Added = {2013-09-13 17:27:37 +0000},
	Date-Modified = {2013-09-13 17:28:04 +0000},
	Doi = {10.1038/ncomms3326},
	Journal = {Nat Commun},
	Journal-Full = {Nature communications},
	Keywords = {technique; Methods; in vivo; Microscopy; Dyes},
	Month = {Aug},
	Pages = {2326},
	Pmid = {23933660},
	Pst = {ppublish},
	Title = {In vivo time-gated fluorescence imaging with biodegradable luminescent porous silicon nanoparticles},
	Volume = {4},
	Year = {2013},
	File = {papers/Gu_NatCommun2013.pdf}}

@article{Reimann:2013,
	Abstract = {Brain activity generates extracellular voltage fluctuations recorded as local field potentials (LFPs). It is known that the relevant microvariables, the ionic currents across membranes, jointly generate the macrovariables, the extracellular voltage, but neither the detailed biophysical knowledge nor the required computational power have been available to model these processes. We simulated the LFP in a model of the rodent neocortical column composed of >12,000 reconstructed, multicompartmental, and spiking cortical layer 4 and 5 pyramidal neurons and basket cells, including five million dendritic and somatic compartments with voltage- and ion-dependent currents, realistic connectivity, and probabilistic AMPA, NMDA, and GABA synapses. We found that, depending on a number of factors, the LFP reflects local and cross-layer processing. Active currents dominate the generation of LFPs, not synaptic ones. Spike-related currents impact the LFP not only at higher frequencies but below 50 Hz. This work calls for re-evaluating the genesis of LFPs.},
	Author = {Reimann, Michael W and Anastassiou, Costas A and Perin, Rodrigo and Hill, Sean L and Markram, Henry and Koch, Christof},
	Date-Added = {2013-09-13 17:06:15 +0000},
	Date-Modified = {2013-09-13 17:07:13 +0000},
	Doi = {10.1016/j.neuron.2013.05.023},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Mathematics; models; Electroencephalography; LFP; EEG; neurophysiology; field potential; Neocortex; Methods},
	Month = {Jul},
	Number = {2},
	Pages = {375-90},
	Pmc = {PMC3732581},
	Pmid = {23889937},
	Pst = {ppublish},
	Title = {A biophysically detailed model of neocortical local field potentials predicts the critical role of active membrane currents},
	Volume = {79},
	Year = {2013},
	File = {papers/Reimann_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.05.023}}

@article{Zembrzycki:2013,
	Abstract = {The primary somatosensory cortex (S1) contains a complete body map that mirrors the subcortical maps developed by peripheral sensory input projecting to the sensory hindbrain, the thalamus and then S1. Peripheral changes during development alter these maps through 'bottom-up' plasticity. Unknown is how S1 size influences map organization and whether an altered S1 map feeds back to affect subcortical maps. We show that the size of S1 in mice is significantly reduced by cortex-specific deletion of Pax6, resulting in a reduced body map and loss of body representations by an exclusion of later-differentiating sensory thalamocortical input. An initially normal sensory thalamus was repatterned to match the aberrant S1 map by apoptotic deletion of thalamic neurons representing body parts with axons excluded from S1. Deleted representations were rescued by altering competition between thalamocortical axons using sensory deprivation or increasing the size of S1. Thus, S1 size determined the resolution and completeness of body maps and engaged 'top-down' plasticity that repatterned the sensory thalamus to match S1.},
	Author = {Zembrzycki, Andreas and Chou, Shen-Ju and Ashery-Padan, Ruth and Stoykova, Anastassia and O'Leary, Dennis D M},
	Date-Added = {2013-09-13 17:01:05 +0000},
	Date-Modified = {2013-09-13 17:01:44 +0000},
	Doi = {10.1038/nn.3454},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {mouse; topographic map; Somatosensory Cortex; connectivity; parcellation; Neocortex},
	Month = {Aug},
	Number = {8},
	Pages = {1060-7},
	Pmc = {PMC3769112},
	Pmid = {23831966},
	Pst = {ppublish},
	Title = {Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits},
	Volume = {16},
	Year = {2013},
	File = {papers/Zembrzycki_NatNeurosci2013.pdf}}

@article{Ke:2013,
	Abstract = {We report a water-based optical clearing agent, SeeDB, which clears fixed brain samples in a few days without quenching many types of fluorescent dyes, including fluorescent proteins and lipophilic neuronal tracers. Our method maintained a constant sample volume during the clearing procedure, an important factor for keeping cellular morphology intact, and facilitated the quantitative reconstruction of neuronal circuits. Combined with two-photon microscopy and an optimized objective lens, we were able to image the mouse brain from the dorsal to the ventral side. We used SeeDB to describe the near-complete wiring diagram of sister mitral cells associated with a common glomerulus in the mouse olfactory bulb. We found the diversity of dendrite wiring patterns among sister mitral cells, and our results provide an anatomical basis for non-redundant odor coding by these neurons. Our simple and efficient method is useful for imaging intact morphological architecture at large scales in both the adult and developing brains.},
	Author = {Ke, Meng-Tsen and Fujimoto, Satoshi and Imai, Takeshi},
	Date-Added = {2013-09-13 17:00:01 +0000},
	Date-Modified = {2013-09-13 17:00:36 +0000},
	Doi = {10.1038/nn.3447},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {Microscopy; technique; Methods; Imaging},
	Month = {Aug},
	Number = {8},
	Pages = {1154-61},
	Pmid = {23792946},
	Pst = {ppublish},
	Title = {SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction},
	Volume = {16},
	Year = {2013},
	File = {papers/Ke_NatNeurosci2013.pdf}}

@article{Harris:2013,
	Abstract = {Sensory cortices receive inputs not only from thalamus but also from higher-order cortical regions. Here, Zagha et al. (2013) show that motor cortical inputs can switch barrel cortex into a desynchronized state that enables more faithful representation of subtle sensory stimuli.},
	Author = {Harris, Kenneth D},
	Date-Added = {2013-09-13 16:57:34 +0000},
	Date-Modified = {2013-09-13 16:58:53 +0000},
	Doi = {10.1016/j.neuron.2013.07.034},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {in vivo; mouse; Somatosensory Cortex; Motor Cortex; neurophysiology; Patch-Clamp Techniques; state; multimodal; spontaneous activity; review literature},
	Month = {Aug},
	Number = {3},
	Pages = {408-10},
	Pmc = {PMC3739006},
	Pmid = {23931991},
	Pst = {ppublish},
	Title = {Top-down control of cortical state},
	Volume = {79},
	Year = {2013},
	File = {papers/Harris_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.07.034}}

@article{Zagha:2013,
	Abstract = {Long-range corticocortical communication may have important roles in context-dependent sensory processing, yet we know very little about how these pathways influence their target regions. We studied the influence of primary motor cortex activity on primary somatosensory cortex in the mouse whisker system. We show that primary motor and somatosensory cortices undergo coherent, context-dependent changes in network state. Moreover, we show that motor cortex activity can drive changes in somatosensory cortex network state. A series of experiments demonstrate the involvement of the direct corticocortical feedback pathway, providing temporally precise and spatially targeted modulation of network dynamics. Cortically mediated changes in network state significantly impact sensory coding, with activated states increasing the reliability of responses to complex stimuli. By influencing network state, corticocortical communication from motor cortex may ensure that during active exploration the relevant sensory region is primed for enhanced sensory discrimination.},
	Author = {Zagha, Edward and Casale, Amanda E and Sachdev, Robert N S and McGinley, Matthew J and McCormick, David A},
	Date-Added = {2013-09-13 16:57:29 +0000},
	Date-Modified = {2013-09-13 16:58:40 +0000},
	Doi = {10.1016/j.neuron.2013.06.008},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {in vivo; mouse; Somatosensory Cortex; Motor Cortex; neurophysiology; Patch-Clamp Techniques; state; multimodal; spontaneous activity;},
	Month = {Aug},
	Number = {3},
	Pages = {567-78},
	Pmc = {PMC3742632},
	Pmid = {23850595},
	Pst = {ppublish},
	Title = {Motor cortex feedback influences sensory processing by modulating network state},
	Volume = {79},
	Year = {2013},
	File = {papers/Zagha_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.06.008}}

@article{Olcese:2013,
	Abstract = {Multisensory integration (MI) is crucial for sensory processing, but it is unclear how MI is organized in cortical microcircuits. Whole-cell recordings in a mouse visuotactile area located between primary visual and somatosensory cortices revealed that spike responses were less bimodal than synaptic responses but displayed larger multisensory enhancement. MI was layer and cell type specific, with multisensory enhancement being rare in the major class of inhibitory interneurons and in the output infragranular layers. Optogenetic manipulation of parvalbumin-positive interneuron activity revealed that the scarce MI of interneurons enables MI in neighboring pyramids. Finally, single-cell resolution calcium imaging revealed a gradual merging of modalities: unisensory neurons had higher densities toward the borders of the primary cortices, but were located in unimodal clusters in the middle of the cortical area. These findings reveal the role of different neuronal subcircuits in the synaptic process of MI in the rodent parietal cortex.},
	Author = {Olcese, Umberto and Iurilli, Giuliano and Medini, Paolo},
	Date-Added = {2013-09-13 16:55:06 +0000},
	Date-Modified = {2013-09-13 16:56:09 +0000},
	Doi = {10.1016/j.neuron.2013.06.010},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {in vivo; mouse; Patch-Clamp Techniques; calcium imaging; Somatosensory Cortex; motor; multimodal; topographic map},
	Month = {Aug},
	Number = {3},
	Pages = {579-93},
	Pmid = {23850594},
	Pst = {ppublish},
	Title = {Cellular and synaptic architecture of multisensory integration in the mouse neocortex},
	Volume = {79},
	Year = {2013},
	File = {papers/Olcese_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.06.010}}

@article{Partanen:2013,
	Abstract = {Learning, the foundation of adaptive and intelligent behavior, is based on plastic changes in neural assemblies, reflected by the modulation of electric brain responses. In infancy, auditory learning implicates the formation and strengthening of neural long-term memory traces, improving discrimination skills, in particular those forming the prerequisites for speech perception and understanding. Although previous behavioral observations show that newborns react differentially to unfamiliar sounds vs. familiar sound material that they were exposed to as fetuses, the neural basis of fetal learning has not thus far been investigated. Here we demonstrate direct neural correlates of human fetal learning of speech-like auditory stimuli. We presented variants of words to fetuses; unlike infants with no exposure to these stimuli, the exposed fetuses showed enhanced brain activity (mismatch responses) in response to pitch changes for the trained variants after birth. Furthermore, a significant correlation existed between the amount of prenatal exposure and brain activity, with greater activity being associated with a higher amount of prenatal speech exposure. Moreover, the learning effect was generalized to other types of similar speech sounds not included in the training material. Consequently, our results indicate neural commitment specifically tuned to the speech features heard before birth and their memory representations.},
	Author = {Partanen, Eino and Kujala, Teija and N{\"a}{\"a}t{\"a}nen, Risto and Liitola, Auli and Sambeth, Anke and Huotilainen, Minna},
	Date-Added = {2013-09-13 16:32:38 +0000},
	Date-Modified = {2013-09-13 16:32:38 +0000},
	Doi = {10.1073/pnas.1302159110},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {event-related potentials; mismatch negativity},
	Month = {Sep},
	Number = {37},
	Pages = {15145-50},
	Pmid = {23980148},
	Pst = {ppublish},
	Title = {Learning-induced neural plasticity of speech processing before birth},
	Volume = {110},
	Year = {2013},
	File = {papers/Partanen_ProcNatlAcadSciUSA2013.pdf}}

@article{Borjigin:2013,
	Abstract = {The brain is assumed to be hypoactive during cardiac arrest. However, the neurophysiological state of the brain immediately following cardiac arrest has not been systematically investigated. In this study, we performed continuous electroencephalography in rats undergoing experimental cardiac arrest and analyzed changes in power density, coherence, directed connectivity, and cross-frequency coupling. We identified a transient surge of synchronous gamma oscillations that occurred within the first 30 s after cardiac arrest and preceded isoelectric electroencephalogram. Gamma oscillations during cardiac arrest were global and highly coherent; moreover, this frequency band exhibited a striking increase in anterior-posterior-directed connectivity and tight phase-coupling to both theta and alpha waves. High-frequency neurophysiological activity in the near-death state exceeded levels found during the conscious waking state. These data demonstrate that the mammalian brain can, albeit paradoxically, generate neural correlates of heightened conscious processing at near-death.},
	Author = {Borjigin, Jimo and Lee, Uncheol and Liu, Tiecheng and Pal, Dinesh and Huff, Sean and Klarr, Daniel and Sloboda, Jennifer and Hernandez, Jason and Wang, Michael M and Mashour, George A},
	Date-Added = {2013-09-13 16:25:07 +0000},
	Date-Modified = {2013-09-13 16:25:07 +0000},
	Doi = {10.1073/pnas.1308285110},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {consciousness; global hypoxia; global ischemia; near-death experience},
	Month = {Aug},
	Number = {35},
	Pages = {14432-7},
	Pmc = {PMC3761619},
	Pmid = {23940340},
	Pst = {ppublish},
	Title = {Surge of neurophysiological coherence and connectivity in the dying brain},
	Volume = {110},
	Year = {2013},
	File = {papers/Borjigin_ProcNatlAcadSciUSA2013.pdf}}

@article{Berger:2007,
	Abstract = {Cortical dynamics can be imaged at high spatiotemporal resolution with voltage-sensitive dyes (VSDs) and calcium-sensitive dyes (CaSDs). We combined these two imaging techniques using epifluorescence optics together with whole cell recordings to measure the spatiotemporal dynamics of activity in the mouse somatosensory barrel cortex in vitro and in the supragranular layers in vivo. The two optical signals reported distinct aspects of cortical function. VSD fluorescence varied linearly with membrane potential and was dominated by subthreshold postsynaptic potentials, whereas the CaSD signal predominantly reflected local action potential firing. Combining VSDs and CaSDs allowed us to monitor the synaptic drive and the spiking activity of a given area at the same time in the same preparation. The spatial extent of the two dye signals was different, with VSD signals spreading further than CaSD signals, reflecting broad subthreshold and narrow suprathreshold receptive fields. Importantly, the signals from the dyes were differentially affected by pharmacological manipulations, stimulation strength, and depth of isoflurane anesthesia. Combined VSD and CaSD measurements can therefore be used to specify the temporal and spatial relationships between subthreshold and suprathreshold activity of the neocortex.},
	Author = {Berger, Thomas and Borgdorff, Aren and Crochet, Sylvain and Neubauer, Florian B and Lefort, Sandrine and Fauvet, Bruno and Ferezou, Isabelle and Carleton, Alan and L{\"u}scher, Hans-Rudolf and Petersen, Carl C H},
	Date-Added = {2013-09-10 16:45:21 +0000},
	Date-Modified = {2013-09-10 16:46:01 +0000},
	Doi = {10.1152/jn.01178.2006},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {calcium imaging; Multiphoton; Microscopy; technical report; voltage sensor; neurophysiology},
	Mesh = {Analysis of Variance; Animals; Brain Mapping; Fluorescent Dyes; Image Processing, Computer-Assisted; Larva; Membrane Potentials; Mice; Mice, Inbred C57BL; Microscopy, Fluorescence; Nerve Net; Nonlinear Dynamics; Patch-Clamp Techniques; Photic Stimulation; Somatosensory Cortex; Vibrissae; Xenopus},
	Month = {May},
	Number = {5},
	Pages = {3751-62},
	Pmid = {17360827},
	Pst = {ppublish},
	Title = {Combined voltage and calcium epifluorescence imaging in vitro and in vivo reveals subthreshold and suprathreshold dynamics of mouse barrel cortex},
	Volume = {97},
	Year = {2007},
	File = {papers/Berger_JNeurophysiol2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.01178.2006}}

@article{Vogelstein:2010,
	Abstract = {Fluorescent calcium indicators are becoming increasingly popular as a means for observing the spiking activity of large neuronal populations. Unfortunately, extracting the spike train of each neuron from a raw fluorescence movie is a nontrivial problem. This work presents a fast nonnegative deconvolution filter to infer the approximately most likely spike train of each neuron, given the fluorescence observations. This algorithm outperforms optimal linear deconvolution (Wiener filtering) on both simulated and biological data. The performance gains come from restricting the inferred spike trains to be positive (using an interior-point method), unlike the Wiener filter. The algorithm runs in linear time, and is fast enough that even when simultaneously imaging >100 neurons, inference can be performed on the set of all observed traces faster than real time. Performing optimal spatial filtering on the images further refines the inferred spike train estimates. Importantly, all the parameters required to perform the inference can be estimated using only the fluorescence data, obviating the need to perform joint electrophysiological and imaging calibration experiments.},
	Author = {Vogelstein, Joshua T and Packer, Adam M and Machado, Timothy A and Sippy, Tanya and Babadi, Baktash and Yuste, Rafael and Paninski, Liam},
	Date-Added = {2013-09-10 14:51:05 +0000},
	Date-Modified = {2013-09-10 14:51:55 +0000},
	Doi = {10.1152/jn.01073.2009},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {methods; technical report; calcium imaging; Multiphoton; Computers},
	Mesh = {Action Potentials; Algorithms; Calcium Signaling; Computer Simulation; Fluorescent Dyes; Microscopy, Fluorescence; Microscopy, Video; Models, Neurological; Neurons; Normal Distribution; Poisson Distribution; Signal Processing, Computer-Assisted; Time Factors},
	Month = {Dec},
	Number = {6},
	Pages = {3691-704},
	Pmc = {PMC3007657},
	Pmid = {20554834},
	Pst = {ppublish},
	Title = {Fast nonnegative deconvolution for spike train inference from population calcium imaging},
	Volume = {104},
	Year = {2010},
	File = {papers/Vogelstein_JNeurophysiol2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.01073.2009}}

@article{Ko:2013,
	Abstract = {Sensory processing occurs in neocortical microcircuits in which synaptic connectivity is highly structured and excitatory neurons form subnetworks that process related sensory information. However, the developmental mechanisms underlying the formation of functionally organized connectivity in cortical microcircuits remain unknown. Here we directly relate patterns of excitatory synaptic connectivity to visual response properties of neighbouring layer 2/3 pyramidal neurons in mouse visual cortex at different postnatal ages, using two-photon calcium imaging in vivo and multiple whole-cell recordings in vitro. Although neural responses were already highly selective for visual stimuli at eye opening, neurons responding to similar visual features were not yet preferentially connected, indicating that the emergence of feature selectivity does not depend on the precise arrangement of local synaptic connections. After eye opening, local connectivity reorganized extensively: more connections formed selectively between neurons with similar visual responses and connections were eliminated between visually unresponsive neurons, but the overall connectivity rate did not change. We propose a sequential model of cortical microcircuit development based on activity-dependent mechanisms of plasticity whereby neurons first acquire feature preference by selecting feedforward inputs before the onset of sensory experience--a process that may be facilitated by early electrical coupling between neuronal subsets--and then patterned input drives the formation of functional subnetworks through a redistribution of recurrent synaptic connections.},
	Author = {Ko, Ho and Cossell, Lee and Baragli, Chiara and Antolik, Jan and Clopath, Claudia and Hofer, Sonja B and Mrsic-Flogel, Thomas D},
	Date-Added = {2013-09-10 14:10:22 +0000},
	Date-Modified = {2013-09-10 14:12:25 +0000},
	Doi = {10.1038/nature12015},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {activity-development; topographic map; visual system; Visual Cortex; Multiphoton; calcium imaging; Patch-Clamp Techniques; in vivo; mouse; currOpinRvw},
	Mesh = {Animals; Animals, Newborn; Eye; Eyelids; Mice; Mice, Inbred C57BL; Models, Neurological; Movement; Neural Pathways; Neuronal Plasticity; Pyramidal Cells; Synapses; Visual Cortex; Visual Perception},
	Month = {Apr},
	Number = {7443},
	Pages = {96-100},
	Pmid = {23552948},
	Pst = {ppublish},
	Title = {The emergence of functional microcircuits in visual cortex},
	Volume = {496},
	Year = {2013},
	File = {papers/Ko_Nature2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature12015}}

@article{Van-Hooser:2012,
	Abstract = {Visual experience plays a critical role in the development of direction-selective responses in ferret visual cortex. In visually naive animals, presentation of a bidirectional "training" stimulus induces rapid increases in the direction-selective responses of single neurons that can be predicted by small but significant direction biases that are present in neighboring neurons at the onset of stimulation. In this study we used in vivo two-photon imaging of calcium signals to further explore the contribution of visual experience to the emergence of direction- selective responses in ferret visual cortex. The first set of experiments was designed to determine whether visual experience is required for the development of the initial neighborhood bias. In animals that were dark-reared until the time of eye opening, we found that individual neurons exhibited weak direction-selective responses accompanied by a reduced but statistically significant neighborhood bias, indicating that both features arise without the need for visual experience. The second set of experiments used a unidirectional training stimulus to assess the relative roles of the neighborhood bias and visual experience in determining the direction preference that cortical neurons acquire during direction training. We found that neurons became more responsive to the trained direction even when they were located in regions of the cortex with an initial neighborhood bias for the direction opposite the training stimulus. Together, these results suggest an adaptive developmental strategy for the elaboration of direction-selective responses, one in which experience-independent mechanisms provide a symmetry-breaking seed for the instructive effects of visual experience.},
	Author = {Van Hooser, Stephen D and Li, Ye and Christensson, Maria and Smith, Gordon B and White, Leonard E and Fitzpatrick, David},
	Date-Added = {2013-08-28 14:55:59 +0000},
	Date-Modified = {2013-08-28 14:57:57 +0000},
	Doi = {10.1523/JNEUROSCI.0230-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {topographic map; visual system; ferret; Visual Cortex; calcium imaging; optical physiology; currOpinRvw; activity-development;},
	Mesh = {Animals; Female; Ferrets; Male; Molecular Imaging; Motion Perception; Neurons; Photic Stimulation; Visual Cortex; Visual Perception},
	Month = {May},
	Number = {21},
	Pages = {7258-66},
	Pmc = {PMC3368384},
	Pmid = {22623671},
	Pst = {ppublish},
	Title = {Initial neighborhood biases and the quality of motion stimulation jointly influence the rapid emergence of direction preference in visual cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/VanHooser_JNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0230-12.2012}}

@article{Soto:2012,
	Abstract = {Spontaneous activity is thought to regulate synaptogenesis in many parts of the developing nervous system. In vivo evidence for this regulation, however, is scarce and comes almost exclusively from experiments in which normal activity was reduced or blocked completely. Thus, whether spontaneous activity itself promotes synaptogenesis or plays a purely permissive role remains uncertain. In addition, how activity influences synapse dynamics to shape connectivity and whether its effects among neurons are uniform or cell-type-dependent is unclear. In mice lacking the cone-rod homeobox gene (Crx), photoreceptors fail to establish normal connections with bipolar cells (BCs). Here, we find that retinal ganglion cells (RGCs) in Crx⁻/⁻ mice become rhythmically hyperactive around the time of eye opening as a result of increased spontaneous glutamate release from BCs. This elevated neurotransmission enhances synaptogenesis between BCs and RGCs, without altering the overall circuit architecture. Using live imaging, we discover that spontaneous activity selectively regulates the rate of synapse formation, not elimination, in this circuit. Reconstructions of the connectivity patterns of three BC types with a shared RGC target further revealed that neurotransmission specifically promotes the formation of multisynaptic appositions from one BC type without affecting the maintenance or elimination of connections from the other two. Although hyperactivity in Crx⁻/⁻ mice persists, synapse numbers do not increase beyond 4 weeks of age, suggesting closure of a critical period for synaptic refinement in the inner retina. Interestingly, despite their hyperactivity, RGC axons maintain normal eye-specific territories and cell-type-specific layers in the dorsal lateral geniculate nucleus.},
	Author = {Soto, Florentina and Ma, Xiaofeng and Cecil, Jacob L and Vo, Bradly Q and Culican, Susan M and Kerschensteiner, Daniel},
	Date-Added = {2013-08-28 14:29:07 +0000},
	Date-Modified = {2013-08-28 14:29:52 +0000},
	Doi = {10.1523/JNEUROSCI.0194-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {spontaneous activity; activity-dependent; Retina; Glutamate; bipolar cells; Retinal Ganglion Cells; retinal waves; currOpinRvw},
	Mesh = {Action Potentials; Age Factors; Animals; Animals, Newborn; Biophysics; Calcium Channels; Calcium-Binding Protein, Vitamin D-Dependent; Cholera Toxin; Choline O-Acetyltransferase; Electric Stimulation; Excitatory Postsynaptic Potentials; Eye; Female; Gene Expression Regulation, Developmental; Geniculate Bodies; Guanylate Kinase; Homeodomain Proteins; Injections, Intraocular; Luminescent Proteins; Membrane Proteins; Mice; Mice, Inbred C57BL; Mice, Transgenic; Neurogenesis; Neurons; Neurotransmitter Agents; Patch-Clamp Techniques; Peanut Agglutinin; Periodicity; Presynaptic Terminals; Receptors, Dopamine D4; Retina; Retinal Ganglion Cells; Rhodopsin; Synapses; Trans-Activators; Transfection; Vesicular Glutamate Transport Protein 1; Visual Pathways},
	Month = {Apr},
	Number = {16},
	Pages = {5426-39},
	Pmc = {PMC3353326},
	Pmid = {22514306},
	Pst = {ppublish},
	Title = {Spontaneous activity promotes synapse formation in a cell-type-dependent manner in the developing retina},
	Volume = {32},
	Year = {2012},
	File = {papers/Soto_JNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0194-12.2012}}

@article{Kuhl:2010,
	Abstract = {The last decade has produced an explosion in neuroscience research examining young children's early processing of language. Noninvasive, safe functional brain measurements have now been proven feasible for use with children starting at birth. The phonetic level of language is especially accessible to experimental studies that document the innate state and the effect of learning on the brain. The neural signatures of learning at the phonetic level can be documented at a remarkably early point in development. Continuity in linguistic development from infants' earliest brain responses to phonetic stimuli is reflected in their language and prereading abilities in the second, third, and fifth year of life, a finding with theoretical and clinical impact. There is evidence that early mastery of the phonetic units of language requires learning in a social context. Neuroscience on early language learning is beginning to reveal the multiple brain systems that underlie the human language faculty.},
	Author = {Kuhl, Patricia K},
	Date-Added = {2013-08-28 14:07:15 +0000},
	Date-Modified = {2013-08-28 14:07:53 +0000},
	Doi = {10.1016/j.neuron.2010.08.038},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {development; Cerebral Cortex; Language Development Disorders; Dyslexia; function; human; review literature; currOpinRvw},
	Mesh = {Brain; Cognition; Computer Simulation; Critical Period (Psychology); Evoked Potentials; Humans; Interpersonal Relations; Language; Language Development; Verbal Learning},
	Month = {Sep},
	Number = {5},
	Pages = {713-27},
	Pmc = {PMC2947444},
	Pmid = {20826304},
	Pst = {ppublish},
	Title = {Brain mechanisms in early language acquisition},
	Volume = {67},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2010.08.038}}

@article{Antonini:1993a,
	Abstract = {If vision in one eye is blurred or occluded during a critical period in postnatal development, neurons in the visual cortex lose their responses to stimulation through that eye within a few days. Anatomical changes in the nerve terminals that provide input to the visual cortex have previously been observed only after weeks of deprivation, suggesting that synapses become physiologically ineffective before the branches on which they sit are withdrawn. Reconstruction of single geniculocortical axonal arbors in the cat after either brief or prolonged monocular occlusion revealed striking axonal rearrangements in both instances. Rapid withdrawal of the branches of deprived-eye arbors suggests that axonal branches bearing synapses respond quickly to changing patterns of neuronal activity.},
	Author = {Antonini, A and Stryker, M P},
	Date-Added = {2013-08-27 20:36:05 +0000},
	Date-Modified = {2013-08-27 20:36:05 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Animals; Axons; Cats; Geniculate Bodies; Neuronal Plasticity; Neurons, Afferent; Photic Stimulation; Vision, Ocular; Visual Cortex},
	Month = {Jun},
	Number = {5115},
	Pages = {1819-21},
	Pmid = {8511592},
	Pst = {ppublish},
	Title = {Rapid remodeling of axonal arbors in the visual cortex},
	Volume = {260},
	Year = {1993}}

@article{Antonini:1993,
	Abstract = {This study analyzes the morphological changes in geniculocortical axons terminating in the primary visual cortex of the cat, during the period in which, in normal development, the terminals in layer IV undergo an eye-specific segregation. Geniculocortical afferent fibers were filled anterogradely by the Phaseolus lectin (PHA-L) injected into the main laminae of the LGN. After standard immunohistochemical procedures, single axons were serially reconstructed in two or three dimensions. Experiments were performed in normal kittens and in kittens in which retinal activity was continuously blocked by repeated intraocular injections of TTX. In normal kittens, arbors were reconstructed at four different ages (19, 23, 30-31, and 39 days postnatally) spanning the period during which the geniculocortical projection segregates into eye-specific columns in layer IV (LeVay et al., 1978). Results reveal that sparse but widely extending branches characteristic of young arbors are eliminated during normal development at the same time as selected portions of the arbor grow considerably in length and complexity. The terminal arborizations also subdivide into distinct patches of terminals, consistent with the segregation of left and right eye afferents. In TTX-treated animals, axonal arbors reconstructed at postnatal days 23, 29, and 39 show a complexity and extent of terminal arborization similar to that of normal animals, though more variable in size and degree of elaboration. No progressive changes are evident with age. Further, the majority of arbors reconstructed from TTX-treated animals lack the patchy organization typical of normal animals.},
	Author = {Antonini, A and Stryker, M P},
	Date-Added = {2013-08-27 20:36:00 +0000},
	Date-Modified = {2013-08-27 20:37:51 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {visual system; cat; retina; Thalamic Nuclei; LGN; activity manipulation; spontaneous activity; retinal waves; Anatomy; currOpinRvw},
	Mesh = {Afferent Pathways; Animals; Axons; Cats; Geniculate Bodies; Immunoenzyme Techniques; Immunohistochemistry; Phytohemagglutinins; Retina; Tetrodotoxin; Visual Cortex},
	Month = {Aug},
	Number = {8},
	Pages = {3549-73},
	Pmid = {8340819},
	Pst = {ppublish},
	Title = {Development of individual geniculocortical arbors in cat striate cortex and effects of binocular impulse blockade},
	Volume = {13},
	Year = {1993}}

@article{Furman:2013,
	Abstract = {Prior to eye opening, waves of spontaneous activity sweep across the developing retina. These "retinal waves", together with genetically encoded molecular mechanisms, mediate the formation of visual maps in the brain. However, the specific role of wave activity in synapse development in retino-recipient brain regions is unclear. Here, we compare the functional development of synapses and the morphological development of neurons in the superior colliculus (SC) of wild-type mice (WT) and transgenic mice (β2-TG) in which retinal wave propagation is spatially truncated (Xu et al., 2011). We use two recently developed brain slice preparations to examine neurons and synapses in the binocular vs. mainly-monocular SC. We find that retinocollicular synaptic strength is reduced whereas the number of retinal inputs is increased in the binocular SC of β2-TG mice in comparison to WT mice. In contrast, in the mainly-monocular SC, the number of retinal inputs is normal in β2-TG mice, but transiently, synapses are abnormally strong, possibly due to enhanced activity-dependent competition between local, 'small' retinal domains. These findings demonstrate that retinal wave size plays an instructive role in the synaptic and morphological development of SC neurons, possibly through a competitive process among retinofugal axons.},
	Author = {Furman, Moran and Xu, Hong-Ping and Crair, Michael C},
	Date-Added = {2013-08-27 20:19:20 +0000},
	Date-Modified = {2013-08-27 20:21:27 +0000},
	Doi = {10.1152/jn.01066.2012},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {retinal waves; spontaneous activity; synapses; Patch-Clamp Techniques; in vitro; mice; mouse; Neurophysiology; activity-dependent; development; retinal waves; superior colliculus; vision; currOpinRvw},
	Month = {Jun},
	Pmid = {23741047},
	Pst = {aheadofprint},
	Title = {Competition driven by retinal waves promotes the morphological and functional synaptic development of neurons in the superior colliculus},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.01066.2012}}

@article{Furman:2012,
	Abstract = {In the developing visual system of mammals, retinal axons from the two eyes compete for postsynaptic partners. After eye opening, this process is regulated in part by homeostatically constrained competition for synaptic connectivity with target neurons. However, prior to eye opening, the functional and synaptic basis of binocular map development is unclear. To examine the role of binocular interactions during early stages of visual map development, we performed in vitro patch-clamp recordings from the superior colliculus (SC) of neonatal mice. Using newly designed slice preparations, we compared retinocollicular synapse development in the medial SC, which receives binocular input, and the lateral SC, which is predominantly monocular. Surprisingly, we found that at P6-7, when eye-specific segregation has just emerged, retinocollicular synapses were stronger and more mature and dendritic arbors were more elaborate in the medial than the lateral SC. Furthermore, monocular enucleation of the ipsilateral eye at P0 selectively reduced synaptic strength and dendritic branching in the medial SC and abolished the differences normally observed between the two slices at P6-7. This specifically implicates binocular interactions in the development of retinocollicular connectivity prior to eye opening. Our findings contrast with the predictions of a constrained-connectivity model of binocular map development and suggest instead that binocular competition prior to eye opening enhances retinocollicular synaptic strength and the morphological development of retino-recipient neurons.},
	Author = {Furman, Moran and Crair, Michael C},
	Date-Added = {2013-08-27 20:19:16 +0000},
	Date-Modified = {2013-08-27 20:21:35 +0000},
	Doi = {10.1152/jn.00943.2011},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {retinal waves; spontaneous activity; synapses; Patch-Clamp Techniques; in vitro; mice; mouse; Neurophysiology; activity-dependent; development; retinal waves; superior colliculus; vision; currOpinRvw},
	Mesh = {Animals; Animals, Newborn; Brain Mapping; Eye; Female; Male; Mice; Mice, Inbred C57BL; Neuronal Plasticity; Organ Culture Techniques; Retina; Superior Colliculi; Synapses; Vision, Binocular; Visual Pathways},
	Month = {Jun},
	Number = {11},
	Pages = {3200-16},
	Pmid = {22402661},
	Pst = {ppublish},
	Title = {Synapse maturation is enhanced in the binocular region of the retinocollicular map prior to eye opening},
	Volume = {107},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1152/jn.00943.2011}}

@article{Turrigiano:2011,
	Abstract = {Maintaining the proper balance between excitation and inhibition is critical for the normal function of cortical circuits. This balance is thought to be maintained by an array of homeostatic mechanisms that regulate neuronal and circuit excitability, including mechanisms that target excitatory and inhibitory synapses, and mechanisms that target intrinsic neuronal excitability. In this review, I discuss where and when these mechanisms are used in complex microcircuits, what is currently known about the signaling pathways that underlie them, and how these different ways of achieving network stability cooperate and/or compete. An important challenge for the field of homeostatic plasticity is to assemble our understanding of these individual mechanisms into a coherent view of how microcircuit stability is maintained during experience-dependent circuit refinement.},
	Author = {Turrigiano, Gina},
	Date-Added = {2013-08-27 20:12:28 +0000},
	Date-Modified = {2013-08-27 20:15:22 +0000},
	Doi = {10.1146/annurev-neuro-060909-153238},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Keywords = {Visual Cortex; plasticity; homeostatic plasticity; neurophysiology; currOpinRvw},
	Mesh = {Animals; Cerebral Cortex; Homeostasis; Models, Neurological; Nerve Net; Neurons; Synapses},
	Pages = {89-103},
	Pmid = {21438687},
	Pst = {ppublish},
	Title = {Too many cooks? Intrinsic and synaptic homeostatic mechanisms in cortical circuit refinement},
	Volume = {34},
	Year = {2011},
	File = {papers/Turrigiano_AnnuRevNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev-neuro-060909-153238}}

@article{Levelt:2012,
	Abstract = {In many regions of the developing brain, neuronal circuits undergo defined phases of enhanced plasticity, termed critical periods. Work in the rodent visual cortex has led to important insights into the cellular and molecular mechanisms regulating the timing of the critical period. Although there is little doubt that the maturation of specific inhibitory circuits plays a key role in the opening of the critical period in the visual cortex, it is less clear what puts an end to it. In this review, we describe the established mechanisms and point out where more experimental work is needed. We also show that plasticity in the visual cortex is present well before, and long after, the peak of the critical period.},
	Author = {Levelt, Christiaan N and H{\"u}bener, Mark},
	Date-Added = {2013-08-27 20:08:58 +0000},
	Date-Modified = {2013-08-27 20:09:57 +0000},
	Doi = {10.1146/annurev-neuro-061010-113813},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Keywords = {activity-development; visual system; Visual Cortex; plasticity; Critical Period; currOpinRvw},
	Mesh = {Aging; Animals; Critical Period (Psychology); Dominance, Ocular; Humans; Models, Neurological; Neural Inhibition; Neuronal Plasticity; Signal Transduction; Synaptic Transmission; Visual Cortex},
	Pages = {309-30},
	Pmid = {22462544},
	Pst = {ppublish},
	Title = {Critical-period plasticity in the visual cortex},
	Volume = {35},
	Year = {2012},
	File = {papers/Levelt_AnnuRevNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev-neuro-061010-113813}}

@article{Syed:2004a,
	Abstract = {Spontaneous rhythmic waves in the developing mammalian retina are thought to propagate among differentiated neurons in the inner retina (IR) and play an important role in activity-dependent visual development. Here we report a new form of rhythmic Ca(2+) wave in the ventricular zone (VZ) of the developing rabbit retina. Ca(2+) imaging from two-photon optical sections near the ventricular surface of the whole-mount retina showed rhythmic Ca(2+) transients propagating laterally as waves. The VZ waves had a distinctively slow Ca(2+) dynamics (lasting approximately 20 s) but shared a similar frequency and propagation speed with the IR waves. Simultaneous Ca(2+) imaging in VZ and multi-electrode array recording in the ganglion cell layer (GCL) revealed close spatiotemporal correlation between spontaneous VZ and IR waves, suggesting a common source of initiation and/or regulation of the two waves. Pharmacological studies further showed that all drugs that blocked IR waves also blocked VZ waves. However, the muscarinic antagonist atropine selectively blocked VZ but not IR waves at this developmental stage, indicating that IR waves were not dependent on VZ waves, but VZ waves likely relied on the initiation of IR waves. Eliciting IR waves with puffs of nicotinic or non-N-methyl-d-aspartate agonists in GCL produced atropine-sensitive waves in the VZ, demonstrating a unique, retrograde signaling pathway from IR to VZ. Thus differentiated neurons in the IR use spontaneous, rhythmic waves to send both forward signals to the central visual targets and retrograde messages to the developing cells in the VZ.},
	Author = {Syed, Mohsin Md and Lee, Seunghoon and He, Shigang and Zhou, Z Jimmy},
	Date-Added = {2013-08-14 20:09:04 +0000},
	Date-Modified = {2013-08-14 20:09:44 +0000},
	Doi = {10.1152/jn.01129.2003},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {retinal waves, spontaneous activity; activity-development; calcium imaging; retina; visual system},
	Mesh = {Animals; Atropine; Axons; Calcium; Calcium Signaling; Cell Differentiation; Cholinergic Antagonists; Electrodes; Excitatory Amino Acid Agonists; Female; GABA Antagonists; Image Processing, Computer-Assisted; Microscopy, Fluorescence; Muscarinic Antagonists; Neurotransmitter Agents; Pregnancy; Rabbits; Retina; Retinal Ganglion Cells; Synaptic Transmission},
	Month = {May},
	Number = {5},
	Pages = {1999-2009},
	Pmid = {14681336},
	Pst = {ppublish},
	Title = {Spontaneous waves in the ventricular zone of developing mammalian retina},
	Volume = {91},
	Year = {2004},
	File = {papers/Syed_JNeurophysiol2004.pdf}}

@article{Copenhagen:1996,
	Abstract = {Propagated waves of excitation in developing neural tissues may be a critical feature of maturation. Recent findings shed new light on the mechanisms underlying these waves.},
	Author = {Copenhagen, D R},
	Date-Added = {2013-08-14 16:25:40 +0000},
	Date-Modified = {2013-08-14 16:26:17 +0000},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {retinal waves; Spontaneous activity; review},
	Mesh = {Animals; Retina; Signal Transduction},
	Month = {Nov},
	Number = {11},
	Pages = {1368-70},
	Pmid = {8939594},
	Pst = {ppublish},
	Title = {Retinal development: on the crest of an exciting wave},
	Volume = {6},
	Year = {1996},
	File = {papers/Copenhagen_CurrBiol1996.pdf}}

@article{Zhou:1998,
	Abstract = {Spontaneous, rhythmic waves of excitation in the developing mammalian retina play a critical role in the formation of precise neuronal connectivity in the visual system. However, it is not known what circuits in the retina are responsible for the production of these waves. Using patch-clamp recordings in the whole-mount neonatal rabbit retina, this study reports that the displaced starburst amacrine cell, a unique cholinergic interneuron in the ganglion cell layer of the retina, undergoes rhythmic bursts of membrane depolarization with a frequency and duration similar to those of spontaneous retinal waves. Simultaneous patch-clamp recordings from pairs of neighboring starburst and ganglion cells show that the rhythmic activity in starburst cells is closely correlated with that in ganglion cells, and that the excitation in both cell types is most likely driven by synaptic input. However, in contrast to ganglion cells, displaced starburst cells usually do not generate spontaneous somatic action potentials. Instead, they seem to use subthreshold potentials (at least at the soma) to mediate the rhythmic excitation. The results suggest that acetylcholine is likely released rhythmically in the developing retina. Thus, starburst amacrine cells form the first identified network of retinal interneurons that directly participate in spontaneous rhythmic activities in the developing retina.},
	Author = {Zhou, Z J},
	Date-Added = {2013-08-14 14:43:31 +0000},
	Date-Modified = {2013-08-14 14:44:20 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Rabbits; spontaneous activity; retina; visual system; activity-development; retinal waves; in vitro; Patch-Clamp Techniques},
	Mesh = {Action Potentials; Animals; Cholinergic Fibers; Fluorescent Dyes; Isoquinolines; Patch-Clamp Techniques; Periodicity; Rabbits; Retina; Retinal Ganglion Cells; Synapses},
	Month = {Jun},
	Number = {11},
	Pages = {4155-65},
	Pmid = {9592095},
	Pst = {ppublish},
	Title = {Direct participation of starburst amacrine cells in spontaneous rhythmic activities in the developing mammalian retina},
	Volume = {18},
	Year = {1998}}

@article{Miller:1972,
	Author = {Miller, D J},
	Date-Added = {2013-08-08 15:23:33 +0000},
	Date-Modified = {2013-08-08 15:24:25 +0000},
	Journal = {Child Dev},
	Journal-Full = {Child development},
	Keywords = {entrainment; development; human; infant; visual system; habituation; learning; memory},
	Mesh = {Attention; Child Development; Color Perception; Fixation, Ocular; Form Perception; Habituation, Psychophysiologic; Humans; Infant; Male; Memory; Orientation; Probability; Visual Perception},
	Month = {Jun},
	Number = {2},
	Pages = {481-93},
	Pmid = {5034730},
	Pst = {ppublish},
	Title = {Visual habituation in the human infant},
	Volume = {43},
	Year = {1972},
	File = {papers/Miller_ChildDev1972.pdf}}

@article{Lau:2008,
	Abstract = {BACKGROUND: Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalian brain, significant resources are applied to the mapping and visualization of data. This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL\6J adult mouse brain.
RESULTS: Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 microm3, allowing co-display of several experiments as well as 179 reference neuro-anatomical structures. Brain Explorer also allows viewing of the original ISH images referenced from any point in a 3D data set. Anatomic and spatial homology searches can be performed from the application to find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies.
CONCLUSION: These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.},
	Author = {Lau, Christopher and Ng, Lydia and Thompson, Carol and Pathak, Sayan and Kuan, Leonard and Jones, Allan and Hawrylycz, Mike},
	Date-Added = {2013-08-08 12:55:28 +0000},
	Date-Modified = {2013-08-08 12:56:11 +0000},
	Doi = {10.1186/1471-2105-9-153},
	Journal = {BMC Bioinformatics},
	Journal-Full = {BMC bioinformatics},
	Keywords = {neuroinformatics; visualization; technical report; Methods; Programming Languages; Software; Computational Biology; connectivity;},
	Mesh = {Animals; Brain; Computer Graphics; Computer Simulation; Gene Expression; Gene Expression Profiling; Mice; Mice, Inbred C57BL; Models, Anatomic; Models, Biological; Nerve Tissue Proteins; Oligonucleotide Array Sequence Analysis; Software; Tissue Distribution; User-Computer Interface},
	Pages = {153},
	Pmc = {PMC2375125},
	Pmid = {18366675},
	Pst = {epublish},
	Title = {Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain},
	Volume = {9},
	Year = {2008},
	File = {papers/Lau_BMCBioinformatics2008.pdf}}

@article{Inamura:2011,
	Abstract = {Neuronal differentiation is a crucial event during neural development. Recent studies have characterized the development of the diencephalon; however, the origins of the primarily GABAergic prethalamic nuclei, including the zona incerta (ZI), ventral lateral geniculate nucleus (vLG) and reticular thalamic nucleus (RT), remain unclear. Here we characterize Olig2 lineage cells in the developing prethalamus using mice in which tamoxifen-induced recombination permanently labels Olig2-expressing cells. We show that GABAergic neurons in the prethalamic nuclei, including the RT, ZI and vLG, originate from prethalamic Olig2 lineage cells. Based on these data and on those derived from short-term lineage-tracing data using Olig3-lacZ mice and previous reports, we suggest that vLG cells originate from the ventricular zone of the thalamus, zona limitans intrathalamica and prethalamus.},
	Author = {Inamura, Naoko and Ono, Katsuhiko and Takebayashi, Hirohide and Zalc, Bernard and Ikenaka, Kazuhiro},
	Date-Added = {2013-08-07 13:38:36 +0000},
	Date-Modified = {2013-08-07 13:39:45 +0000},
	Doi = {10.1159/000328974},
	Journal = {Dev Neurosci},
	Journal-Full = {Developmental neuroscience},
	Keywords = {development; visual system; thalamus; migration; Gene Expression; GABA; Interneurons},
	Mesh = {Animals; Basic Helix-Loop-Helix Transcription Factors; Cell Differentiation; Cell Lineage; Cell Movement; Female; GABAergic Neurons; Gene Expression Regulation, Developmental; Geniculate Bodies; Immunohistochemistry; In Situ Hybridization; Mice; Mice, Transgenic; Models, Animal; Nerve Tissue Proteins; Stem Cells; Subthalamus; Tamoxifen; Ventral Thalamic Nuclei},
	Number = {2},
	Pages = {118-29},
	Pmid = {21865661},
	Pst = {ppublish},
	Title = {Olig2 lineage cells generate GABAergic neurons in the prethalamic nuclei, including the zona incerta, ventral lateral geniculate nucleus and reticular thalamic nucleus},
	Volume = {33},
	Year = {2011},
	File = {papers/Inamura_DevNeurosci2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1159/000328974}}

@article{Arcelli:1997,
	Abstract = {The present study evaluated the occurrence, distribution, and number of GABAergic neurons in the thalamus of different mammalian species (bat, mouse, rat, guinea pig, rabbit, cat, monkey, humans), by means of light microscopical immunoenzymatic localization of GABA or of its biosynthetic enzyme glutamic acid decarboxylase and by ultrastructural immunogold detection of GABA. Our data demonstrated that: 1) GABAergic local circuit neurons were detected in the thalamic visual domain in all the species analyzed, whereas in other thalamic nuclei their presence and number varied among species; 2) the number of GABAergic local circuit neurons progressively increased in the dorsal thalamus of species with more complex behavior; 3) the presence of local circuit neurons conferred a similar intrinsic organization to the dorsal thalamic nuclei, characterized by complex synaptic arrangements; 4) in the reticular thalamic nucleus, whose neurons were GABA-immunoreactive in all the examined species, the cellular density decreased from the bat to humans. These findings strongly suggest that thalamic GABAergic local circuit neurons are not directly related to the ability to perform specific sensorimotor tasks, but they are likely to reflect an increasing complexity of the local information processing that occurs at thalamic level.},
	Author = {Arcelli, P and Frassoni, C and Regondi, M C and De Biasi, S and Spreafico, R},
	Date-Added = {2013-08-07 13:09:38 +0000},
	Date-Modified = {2013-08-07 13:11:41 +0000},
	Journal = {Brain Res Bull},
	Journal-Full = {Brain research bulletin},
	Keywords = {development; visual system; thalamus; Primates; rodent; GABA; interneurons},
	Mesh = {Animals; Cats; Guinea Pigs; Mammals; Rabbits; Rats; Synapses; Thalamic Nuclei; Thalamus; gamma-Aminobutyric Acid},
	Number = {1},
	Pages = {27-37},
	Pmid = {8978932},
	Pst = {ppublish},
	Title = {GABAergic neurons in mammalian thalamus: a marker of thalamic complexity?},
	Volume = {42},
	Year = {1997},
	File = {papers/Arcelli_BrainResBull1997.pdf}}

@article{Rakic:2009,
	Abstract = {In the past three decades, mounting evidence has revealed that specification of the basic cortical neuronal classes starts at the time of their final mitotic divisions in the embryonic proliferative zones. This early cell determination continues during the migration of the newborn neurons across the widening cerebral wall, and it is in the cortical plate that they attain their final positions and establish species-specific cytoarchitectonic areas. Here, the development and evolutionary expansion of the neocortex is viewed in the context of the radial unit and protomap hypotheses. A broad spectrum of findings gave insight into the pathogenesis of cortical malformations and the biological bases for the evolution of the modern human neocortex. We examine the history and evidence behind the concept of early specification of neurons and provide the latest compendium of genes and signaling molecules involved in neuronal fate determination and specification.},
	Author = {Rakic, Pasko and Ayoub, Albert E and Breunig, Joshua J and Dominguez, Martin H},
	Date-Added = {2013-08-07 12:51:08 +0000},
	Date-Modified = {2013-08-07 12:52:24 +0000},
	Doi = {10.1016/j.tins.2009.01.007},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {review literature; Molecular Biology; Gene Expression; Cerebral Cortex; topographic map; Visual Cortex; visual system; patterning; development; Grants},
	Mesh = {Animals; Body Patterning; Brain Mapping; Cell Movement; Cerebral Cortex; Gene Expression Regulation, Developmental; Humans; Models, Neurological; Neural Pathways; Neurogenesis; Neuronal Plasticity; Neurons},
	Month = {May},
	Number = {5},
	Pages = {291-301},
	Pmc = {PMC3601545},
	Pmid = {19380167},
	Pst = {ppublish},
	Title = {Decision by division: making cortical maps},
	Volume = {32},
	Year = {2009},
	File = {papers/Rakic_TrendsNeurosci2009.pdf}}

@article{Akrouh:2013,
	Abstract = {The developing retina generates spontaneous glutamatergic (stage III) waves of activity that sequentially recruit neighboring ganglion cells with opposite light responses (ON and OFF RGCs). This activity pattern is thought to help establish parallel ON and OFF pathways in downstream visual areas. The circuits that produce stage III waves and desynchronize ON and OFF RGC firing remain obscure. Using dual patch-clamp recordings, we find that ON and OFF RGCs receive sequential excitatory input from ON and OFF cone bipolar cells (CBCs), respectively. This input sequence is generated by crossover circuits, in which ON CBCs control glutamate release from OFF CBCs via diffusely stratified inhibitory amacrine cells. In addition, neighboring ON CBCs communicate directly and indirectly through lateral glutamatergic transmission and gap junctions, both of which are required for wave initiation and propagation. Thus, intersecting lateral excitatory and vertical inhibitory circuits give rise to precisely patterned stage III retinal waves.},
	Author = {Akrouh, Alejandro and Kerschensteiner, Daniel},
	Date-Added = {2013-07-15 14:14:55 +0000},
	Date-Modified = {2013-08-28 14:10:43 +0000},
	Doi = {10.1016/j.neuron.2013.05.012},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {retinal waves; spontaneous activity; development; retina; Retinal Ganglion Cells; bipolar cells; currOpinRvw},
	Month = {Jul},
	Pmid = {23830830},
	Pst = {aheadofprint},
	Title = {Intersecting Circuits Generate Precisely Patterned Retinal Waves},
	Year = {2013},
	File = {papers/Akrouh_Neuron2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2013.05.012}}

@article{Rivlin-Etzion:2012,
	Abstract = {Direction selectivity in the retina is mediated by direction-selective ganglion cells. These cells are part of a circuit in which they are asymmetrically wired to inhibitory neurons. Thus, they respond strongly to an image moving in the preferred direction and weakly to an image moving in the opposite (null) direction. Here, we demonstrate that adaptation with short visual stimulation of a direction-selective ganglion cell using drifting gratings can reverse this cell's directional preference by 180$\,^{\circ}$. This reversal is robust, long lasting, and independent of the animal's age. Our findings indicate that, even within circuits that are hardwired, the computation of direction can be altered by dynamic circuit mechanisms that are guided by visual stimulation.},
	Author = {Rivlin-Etzion, Michal and Wei, Wei and Feller, Marla B},
	Date-Added = {2013-07-15 14:13:03 +0000},
	Date-Modified = {2013-07-15 14:14:03 +0000},
	Doi = {10.1016/j.neuron.2012.08.041},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Retina; development; Retinal Ganglion Cells; direction; topographic map; neurophysiology; inhibition},
	Mesh = {Adaptation, Physiological; Animals; Female; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Motion Perception; Photic Stimulation; Reaction Time; Retinal Ganglion Cells},
	Month = {Nov},
	Number = {3},
	Pages = {518-25},
	Pmc = {PMC3496185},
	Pmid = {23141064},
	Pst = {ppublish},
	Title = {Visual stimulation reverses the directional preference of direction-selective retinal ganglion cells},
	Volume = {76},
	Year = {2012},
	File = {papers/Rivlin-Etzion_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.08.041}}

@article{Gitton:1999,
	Abstract = {In the H-2Z1 mouse line, postnatal expression of the lacZ containing transgene in the cerebral cortex is restricted to layer IV neurons of the somatosensory area. We have used H-2Z1 embryos in previous heterotopic transplantation experiments to investigate the chronology of determination of areal identity. From the onset of neurogenesis, the cortex was regionalized in domains fated to express or not the somatosensory area-specific transgene. Determination occured 1 day later. In the present study, we show that, in vivo, H-2Z1 expression coincides with invasion of the cortical plate by thalamic afferents. We therefore investigated the role of thalamic innervation in the onset of H-2Z1 expression. For this purpose, we examined the pattern of H-2Z1 expression in perinatal cortical explant, in reeler mutant and MaoA deficient mice, or in animals which had received neonatal lesions affecting the somatosensory cortex or the thalamocortical projection. We found that, around birth, a switch occurs in the control of H-2Z1 expression: whereas H-2Z1 expression developed autonomously in embryonic parietal cortex in the absence of thalamic fibers, a transient requirement for a thalamic axon derived signal was observed postnatally. This property has interesting implications for the plasticity of cortical areas in development and evolution.},
	Author = {Gitton, Y and Cohen-Tannoudji, M and Wassef, M},
	Date-Added = {2013-07-15 14:11:08 +0000},
	Date-Modified = {2013-07-15 14:12:10 +0000},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {genes; technique; ideas; Thalamic Nuclei; marker; Somatosensory Cortex; mouse; development; Neocortex;},
	Mesh = {Animals; Animals, Newborn; Axons; Biological Markers; Cells, Cultured; Denervation; Female; Gene Expression Regulation, Developmental; Gene Expression Regulation, Enzymologic; Genes, Reporter; Lac Operon; Lip; Male; Mice; Mice, Inbred C57BL; Mice, Inbred CBA; Mice, Neurologic Mutants; Mice, Transgenic; Monoamine Oxidase; Neural Pathways; Parietal Lobe; Somatosensory Cortex; Thalamus; Transgenes; beta-Galactosidase},
	Month = {Sep},
	Number = {6},
	Pages = {611-20},
	Pmid = {10498279},
	Pst = {ppublish},
	Title = {Role of thalamic axons in the expression of H-2Z1, a mouse somatosensory cortex specific marker},
	Volume = {9},
	Year = {1999},
	File = {papers/Gitton_CerebCortex1999.pdf}}

@article{Song:2005a,
	Abstract = {The oocyte is a highly differentiated cell. It makes organelles specialized to its unique functions and progresses through a series of developmental stages to acquire a fertilization competent phenotype. This review will integrate the biology of the oocyte with what is known about oocyte-specific gene regulation and transcription factors involved in oocyte development. We propose that oogenesis is reliant on a dynamic gene regulatory network that includes oocyte-specific transcriptional regulators.},
	Author = {Song, Jia L and Wessel, Gary M},
	Date-Added = {2013-07-05 21:11:54 +0000},
	Date-Modified = {2013-07-05 21:13:06 +0000},
	Doi = {10.1111/j.1432-0436.2005.07301005.x},
	Journal = {Differentiation},
	Journal-Full = {Differentiation; research in biological diversity},
	Keywords = {development; Transcription; gene; Environment; Regeneration; Stem Cells},
	Mesh = {Animals; Basic Helix-Loop-Helix Transcription Factors; DNA-Binding Proteins; Female; Gene Expression Regulation, Developmental; Homeodomain Proteins; Humans; Octamer Transcription Factor-3; Oocytes; Oogenesis; Organ Specificity; Ovary; Ovum; Pregnancy; RNA, Ribosomal; Transcription Factors; Transcription, Genetic; Xenopus Proteins},
	Month = {Feb},
	Number = {1},
	Pages = {1-17},
	Pmid = {15733063},
	Pst = {ppublish},
	Title = {How to make an egg: transcriptional regulation in oocytes},
	Volume = {73},
	Year = {2005},
	File = {papers/Song_Differentiation2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1432-0436.2005.07301005.x}}

@article{Dimos:2008,
	Abstract = {The generation of pluripotent stem cells from an individual patient would enable the large-scale production of the cell types affected by that patient's disease. These cells could in turn be used for disease modeling, drug discovery, and eventually autologous cell replacement therapies. Although recent studies have demonstrated the reprogramming of human fibroblasts to a pluripotent state, it remains unclear whether these induced pluripotent stem (iPS) cells can be produced directly from elderly patients with chronic disease. We have generated iPS cells from an 82-year-old woman diagnosed with a familial form of amyotrophic lateral sclerosis (ALS). These patient-specific iPS cells possess properties of embryonic stem cells and were successfully directed to differentiate into motor neurons, the cell type destroyed in ALS.},
	Author = {Dimos, John T and Rodolfa, Kit T and Niakan, Kathy K and Weisenthal, Laurin M and Mitsumoto, Hiroshi and Chung, Wendy and Croft, Gist F and Saphier, Genevieve and Leibel, Rudy and Goland, Robin and Wichterle, Hynek and Henderson, Christopher E and Eggan, Kevin},
	Date-Added = {2013-07-05 20:54:00 +0000},
	Date-Modified = {2013-07-05 21:11:18 +0000},
	Doi = {10.1126/science.1158799},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {Stem Cells; Pluripotent Stem Cells; development; gene; Regeneration},
	Mesh = {Aged, 80 and over; Amyotrophic Lateral Sclerosis; Cell Differentiation; Cell Line; Embryonic Stem Cells; Female; Fibroblasts; Gene Expression; Humans; Motor Neurons; Neuroglia; Nuclear Reprogramming; Pluripotent Stem Cells; Retroviridae; Spinal Cord; Superoxide Dismutase; Transcription Factors; Transduction, Genetic},
	Month = {Aug},
	Number = {5893},
	Pages = {1218-21},
	Pmid = {18669821},
	Pst = {ppublish},
	Title = {Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons},
	Volume = {321},
	Year = {2008},
	File = {papers/Dimos_Science2008.pdf}}

@article{King:2000,
	Abstract = {Many animals with laterally placed eyes, such as chameleons, move their eyes independently of one another. In contrast, primates with frontally placed eyes and binocular vision must move them together so that both eyes are aimed at the same point in visual space. Is binocular coordination an innate feature of how our brains are wired, or have we simply learned to move our eyes together? This question sparked a controversy in the 19(th) century between two eminent German scientists, Ewald Hering and Hermann von Helmholtz. Hering took the position that binocular coordination was innate and vigorously challenged von Helmholtz's view that it was learned. Hering won the argument and his hypothesis, known as Hering's Law of Equal Innervation, became generally accepted. New evidence suggests, however, that similar to chameleons, primates may program movements of each eye independently. Binocular coordination is achieved by a neural network at the motor periphery comprised of motoneurons and specialized interneurons located near or in the cranial nerve nuclei that innervate the extraocular muscles. It is assumed that this network must be trained and calibrated during infancy and probably throughout life in order to maintain the precise binocular coordination characteristic of primate eye movements despite growth, aging effects, and injuries to the eye movement neuromuscular system. Malfunction of this network or its ability to adaptively learn may be a contributing cause of strabismus.},
	Author = {King, W M and Zhou, W},
	Date-Added = {2013-07-01 21:14:53 +0000},
	Date-Modified = {2013-07-01 21:15:50 +0000},
	Journal = {Anat Rec},
	Journal-Full = {The Anatomical record},
	Keywords = {currOpinRvw; Activity-development; visual system; motor; Saccades; binocular disparity; mirror symmetry},
	Mesh = {Animals; Eye Movements; Lizards; Motor Neurons; Oculomotor Muscles; Primates; Strabismus; Vision, Binocular},
	Month = {Aug},
	Number = {4},
	Pages = {153-61},
	Pmid = {10944576},
	Pst = {ppublish},
	Title = {New ideas about binocular coordination of eye movements: is there a chameleon in the primate family tree?},
	Volume = {261},
	Year = {2000},
	File = {papers/King_AnatRec2000.pdf}}

@article{Medina:2000,
	Abstract = {Recent data on the expression of several homeobox genes in the embryonic telencephalon of mammals, birds and reptiles support the homology of a part of the avian pallium, named the Wulst, and at least the more-medial and superior parts of mammalian neocortex. This conclusion is also supported by previous embryological, topological and hodological data. Furthermore, new evidence on the connections and electrophysiological properties of specific subfields within the avian Wulst, and on the thalamic territories that project to these fields, supports the more-specific conclusion that a primary visual area and a primary somatosensory-somatomotor area are present in the avian Wulst; these areas are likely to be homologous to their counterparts in mammals. In spite of this, developmental, morphological and comparative evidence indicate that some structural and physiological traits that appear to be similar in the Wulst and neocortex (such as the lamination or binocularity) evolved independently in birds and mammals.},
	Author = {Medina, L and Reiner, A},
	Date-Added = {2013-06-14 18:49:31 +0000},
	Date-Modified = {2013-06-14 18:50:50 +0000},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {neocortex; cerebral cortex; turtle; Evolution; Visual Cortex; birds; reptiles; mammals; review literature},
	Mesh = {Animals; Biological Evolution; Birds; Brain; Gene Expression Regulation; Genes, Homeobox; Mammals; Models, Neurological; Neocortex; Nerve Net; Species Specificity},
	Month = {Jan},
	Number = {1},
	Pages = {1-12},
	Pmid = {10631781},
	Pst = {ppublish},
	Title = {Do birds possess homologues of mammalian primary visual, somatosensory and motor cortices?},
	Volume = {23},
	Year = {2000},
	File = {papers/Medina_TrendsNeurosci2000.pdf}}

@article{Mulligan:1990,
	Abstract = {The projection from the dorsal lateral geniculate complex to the visual cortex in Pseudemys and Chrysemys turtles was examined by using the anterograde transport of horseradish peroxidase (HRP) in vitro and the retrograde transport of HRP in vivo. In vitro HRP injections into the lateral forebrain bundle were used to fill geniculocortical axons anterogradely, which were then analyzed in cortical wholemount preparations. Geniculocortical axons gain access to the visual cortex along its entire rostral-caudal extent. They course in slightly curved trajectories for up to 2 mm from the lateral edge of the cortex through both the lateral (or pallial thickening) and medial parts of Desan's cortical area D2. Single axons are of fine caliber. They tend to cross each other and sometimes branch in the pallial thickening, but are generally unbranched in the medial part of D2. They bear small, fusiform varicosities at irregular intervals along their lengths. Although axons show small variations in the number of varicosities per 100 microns segment, no consistent variation in varicosity number as a function of distance could be detected. These results indicate that geniculocortical axons project to the visual cortex in an orderly pattern. The retrograde transport experiments provide some clue as to the significance of this pattern. Small, ionotophoretic injections of HRP in the visual cortex retrogradely labeled neurons in the dorsal lateral geniculate complex. Injections in the rostral visual cortex retrogradely labeled neurons in the caudal pole of the geniculate complex. Injections at progressively more caudal loci within the visual cortex labeled neurons at progressively more rostral loci within the geniculate complex. Thus, there is a representation of the rostral-caudal axis of the geniculate complex along the caudal-rostral axis of the visual cortex. Consistent with the anterograde transport experiments that showed individual geniculocortical axons coursing through both lateral and medial parts of the visual cortex, HRP injections restricted to the medial edge of the visual cortex retrogradely labeled neurons along the entire dorsal-ventral axis of the geniculate complex at the appropriate rostral-caudal position. The neurophysiological studies of Mazurskaya ('72: J. Evol. Biochem. Physiol. 8:550-555; respond to a small, moving stimulus anywhere in visual space, implying a convergence of inputs from all points in visual space somewhere along the retinogeniculocortical pathway. The experiments reported here suggest a convergence in the geniculocortical projections of information along the vertical meridians, or azimuth lines, of visual space onto neurons lying along lateral to medial transects through the visual cortex.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {Mulligan, K A and Ulinski, P S},
	Date-Added = {2013-06-14 16:44:25 +0000},
	Date-Modified = {2013-06-14 16:50:21 +0000},
	Doi = {10.1002/cne.902960403},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {Visual Cortex; Turtles; in vivo; visual system; topographic map; Anatomy; connectivity; Histocytochemistry; tracer},
	Mesh = {Animals; Geniculate Bodies; Horseradish Peroxidase; Nerve Endings; Turtles; Visual Cortex; Visual Pathways},
	Month = {Jun},
	Number = {4},
	Pages = {531-47},
	Pmid = {2358551},
	Pst = {ppublish},
	Title = {Organization of geniculocortical projections in turtles: isoazimuth lamellae in the visual cortex},
	Volume = {296},
	Year = {1990},
	File = {papers/Mulligan_JCompNeurol1990a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902960403}}

@article{Cosans:1990,
	Abstract = {The spatial pattern of projections within turtle visual cortex was studied by using focal injections of horseradish peroxidase into visual cortex in an in vitro wholebrain preparation. Injections anterogradely filled the axons of many layer 2 neurons, which could be followed for 200-500 microns from the injection sites. Axons were typically unbranched, relatively straight, and bore small varicosities at irregular intervals. They radiated from the injection sites in all directions, but showed some preference toward orientations along the lateral-medial axis of the cortex. Earlier work (Mulligan and Ulinski, '90) had demonstrated that turtle visual cortex contains a series of isoazimuth lamellae, each representing an individual azimuth of visual space and oriented perpendicular to the rostral-caudal axis of the cortex. The present study provides evidence for intrinsic projections both along isoazimuth lamellae and between adjacent lamellae. These projections may play roles in the elaboration of wide receptive fields of cortical neurons.},
	Author = {Cosans, C E and Ulinski, P S},
	Date-Added = {2013-06-14 16:44:21 +0000},
	Date-Modified = {2013-06-14 16:46:30 +0000},
	Doi = {10.1002/cne.902960404},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {Visual Cortex; Turtles; in vivo; visual system; topographic map; Anatomy; connectivity},
	Mesh = {Animals; Axons; Horseradish Peroxidase; Turtles; Visual Cortex},
	Month = {Jun},
	Number = {4},
	Pages = {548-58},
	Pmid = {2358552},
	Pst = {ppublish},
	Title = {Spatial organization of axons in turtle visual cortex: intralamellar and interlamellar projections},
	Volume = {296},
	Year = {1990},
	File = {papers/Cosans_JCompNeurol1990.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902960404}}

@article{Schutte:1995,
	Abstract = {Centrifugal fibers innervating the retina have been shown in all classes of vertebrate, except for mammals where conventional tract-tracing methods have not been able to unmistakably demonstrate their existence. In a previous study, a unilateral, intravitreal injection of 5,7-dihydroxytryptamine was used to reveal indoleamine-accumulating centrifugal fibers which were visualized by an immunoreaction against serotonin. In the present study, I employed a modification of this method to stain retinopetal neurons in the rat. Terminals were located preferentially in the outer retina; labeled fibers could be traced back along an ipsilateral pathway to somata in the dorso-caudal portions of the chiasm or the medio-lateral preoptic area, and thence towards the suprachiasmatic nuclei. The unique beaded appearance of the fibers distinguishes them from retinal ganglion cell axons. The labeling of central cell bodies strongly suggests that they possess terminals in the retina. Thus, at least some mammalian retinas receive centrifugal innervation. This indoleamine-accumulating retinopetal pathway may be involved in retinal melatonin synthesis, coordination of circadian rhythms, and interocular phenomena.},
	Author = {Sch{\"u}tte, M},
	Date = {1995 Nov-Dec},
	Date-Added = {2013-06-14 16:17:23 +0000},
	Date-Modified = {2013-06-14 16:19:16 +0000},
	Journal = {Vis Neurosci},
	Journal-Full = {Visual neuroscience},
	Keywords = {retinopetal; retino-retinal; retino-retino; connectivity; visual system; Serotonin; retina; mirror symmetry; Binocular;},
	Mesh = {5,7-Dihydroxytryptamine; Animals; Immunologic Techniques; Male; Nerve Fibers; Neurons; Optic Nerve; Preoptic Area; Rats; Rats, Inbred Strains; Retina; Serotonin; Suprachiasmatic Nucleus; Visual Pathways},
	Number = {6},
	Pages = {1083-92},
	Pmid = {8962828},
	Pst = {ppublish},
	Title = {Centrifugal innervation of the rat retina},
	Volume = {12},
	Year = {1995},
	File = {papers/Schütte_VisNeurosci1995.pdf}}

@article{Ulinski:1988,
	Abstract = {Organization of retinal projections to the dorsal lateral geniculate complex in turtles has been studied by means of light and electron microscopic axon tracing techniques. Orthograde degeneration studies with Fink-Heimer methods following restricted retinal lesions show the entire retina has a topologically organized projection to the contralateral dorsal lateral geniculate complex. The nasotemporal axis of the retina projects along the rostrocaudal axis of the geniculate complex; the dorsoventral axis of the retina projects along the dorsoventral axis of the geniculate complex. The projection to the ipsilateral dorsal lateral geniculate complex originates from the ventral, temporal and nasal edges of the retina. The nasotemporal axis of the ipsilateral retina projects along the rostrocaudal axis of the geniculate complex. It was not possible to determine the orientation of the dorsoventral axis of the ipsilateral retina on the geniculate complex. Light microscopic autoradiographic tracing experiments and electron microscopic degeneration experiments show the retinogeniculate projection has a laminar organization. Retinogeniculate terminals are found in both the neuropile and cell plate throughout all three subnuclei of the dorsal lateral geniculate complex but have a distinctive distribution in each subnucleus. In the subnucleus ovalis, they are frequent in both the neuropile and cell plate which forms the rostral pole of the complex. In the dorsal subnucleus, they are most prevalent in the outer part of the neuropile layer, less frequent in the inner part of the neuropile, and rare in the cell plate. In the ventral subnucleus, they are frequent in the outer part of the neuropile but are also common in the inner part of the neuropile and cell plate. These observations point to several principles of geniculate organization in turtles. First, the complex receives projections from the entire contralateral retina and a segment of the ipsilateral retina. It thus has monocular and binocular segments that together receive a topologically organized representation of the binocular visual space and the contralateral monocular visual space. Second, the three geniculate subnuclei receive information from different, specialized regions of the retina and visual space. Subnucleus ovalis receives information from the frontal binocular visual field. The ventral subnucleus receives information from the caudal binocular field. The dorsal subnucleus receives input from the contralateral monocular field. Third, there is a lamination of retinal inputs in the geniculate complex which differs in character within the three subnuclei.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {Ulinski, P S and Nautiyal, J},
	Date-Added = {2013-06-14 16:07:31 +0000},
	Date-Modified = {2013-06-14 16:08:38 +0000},
	Doi = {10.1002/cne.902760107},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {turtle; anatomy; connectivity; topographic map; visual system; LGN; retina; Visual Cortex;},
	Mesh = {Animals; Functional Laterality; Geniculate Bodies; Microscopy, Electron; Nerve Degeneration; Nerve Endings; Retina; Turtles; Visual Pathways},
	Month = {Oct},
	Number = {1},
	Pages = {92-112},
	Pmid = {3192765},
	Pst = {ppublish},
	Title = {Organization of retinogeniculate projections in turtles of the genera Pseudemys and Chrysemys},
	Volume = {276},
	Year = {1988},
	File = {papers/Ulinski_JCompNeurol1988.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902760107}}

@article{Warren:2008,
	Abstract = {We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.},
	Author = {Warren, Wesley C and Hillier, LaDeana W and Marshall Graves, Jennifer A and Birney, Ewan and Ponting, Chris P and Gr{\"u}tzner, Frank and Belov, Katherine and Miller, Webb and Clarke, Laura and Chinwalla, Asif T and Yang, Shiaw-Pyng and Heger, Andreas and Locke, Devin P and Miethke, Pat and Waters, Paul D and Veyrunes, Fr{\'e}d{\'e}ric and Fulton, Lucinda and Fulton, Bob and Graves, Tina and Wallis, John and Puente, Xose S and L{\'o}pez-Ot{\'\i}n, Carlos and Ord{\'o}{\~n}ez, Gonzalo R and Eichler, Evan E and Chen, Lin and Cheng, Ze and Deakin, Janine E and Alsop, Amber and Thompson, Katherine and Kirby, Patrick and Papenfuss, Anthony T and Wakefield, Matthew J and Olender, Tsviya and Lancet, Doron and Huttley, Gavin A and Smit, Arian F A and Pask, Andrew and Temple-Smith, Peter and Batzer, Mark A and Walker, Jerilyn A and Konkel, Miriam K and Harris, Robert S and Whittington, Camilla M and Wong, Emily S W and Gemmell, Neil J and Buschiazzo, Emmanuel and Vargas Jentzsch, Iris M and Merkel, Angelika and Schmitz, Juergen and Zemann, Anja and Churakov, Gennady and Kriegs, Jan Ole and Brosius, Juergen and Murchison, Elizabeth P and Sachidanandam, Ravi and Smith, Carly and Hannon, Gregory J and Tsend-Ayush, Enkhjargal and McMillan, Daniel and Attenborough, Rosalind and Rens, Willem and Ferguson-Smith, Malcolm and Lef{\`e}vre, Christophe M and Sharp, Julie A and Nicholas, Kevin R and Ray, David A and Kube, Michael and Reinhardt, Richard and Pringle, Thomas H and Taylor, James and Jones, Russell C and Nixon, Brett and Dacheux, Jean-Louis and Niwa, Hitoshi and Sekita, Yoko and Huang, Xiaoqiu and Stark, Alexander and Kheradpour, Pouya and Kellis, Manolis and Flicek, Paul and Chen, Yuan and Webber, Caleb and Hardison, Ross and Nelson, Joanne and Hallsworth-Pepin, Kym and Delehaunty, Kim and Markovic, Chris and Minx, Pat and Feng, Yucheng and Kremitzki, Colin and Mitreva, Makedonka and Glasscock, Jarret and Wylie, Todd and Wohldmann, Patricia and Thiru, Prathapan and Nhan, Michael N and Pohl, Craig S and Smith, Scott M and Hou, Shunfeng and Nefedov, Mikhail and de Jong, Pieter J and Renfree, Marilyn B and Mardis, Elaine R and Wilson, Richard K},
	Date-Added = {2013-06-13 15:43:25 +0000},
	Date-Modified = {2013-06-13 15:43:25 +0000},
	Doi = {10.1038/nature06936},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Animals; Base Composition; Dentition; Evolution, Molecular; Female; Genome; Genomic Imprinting; Humans; Immunity; Male; Mammals; MicroRNAs; Milk Proteins; Phylogeny; Platypus; Receptors, Odorant; Repetitive Sequences, Nucleic Acid; Reptiles; Sequence Analysis, DNA; Spermatozoa; Venoms; Zona Pellucida},
	Month = {May},
	Number = {7192},
	Pages = {175-83},
	Pmc = {PMC2803040},
	Pmid = {18464734},
	Pst = {ppublish},
	Title = {Genome analysis of the platypus reveals unique signatures of evolution},
	Volume = {453},
	Year = {2008},
	File = {papers/Warren_Nature2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature06936}}

@article{Hall:1970,
	Abstract = {The telencephalic projections of the turtle thalamus were studied using the Fink-Heimer ('67) technique for staining dezenerated axons and their terminals. Large thalamic lesions produced terminal degeneration in the basal telencephalic nuclei, the core of the dorsal ventricular ridge and the outer half of layer I in general cortex. A variety of control lesions confirmed that these projections arisc in the thalamus. Circumscribed thalamic lesions revealed first, that there is some degree of spatial organization in the turtlc's thalamocortical projection system and second, that at least one sensory relay nucleus, the dorsal lateral geniculate, projects to general cortex. Detailed comparisons of the turtle's thalamotelencephalic projections with thosc present in two primitive mammalian species, the hedgehog and the opos- sum, provided a basis for identifying probablc homologies in thc forebrains of reptilcs and mnmmals.},
	Author = {Hall, W C and Ebner, F F},
	Date-Added = {2013-06-12 19:25:55 +0000},
	Date-Modified = {2013-06-12 19:27:40 +0000},
	Doi = {10.1002/cne.901400107},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {turtle; Visual Cortex; anatomy; LGN; thalamus; connectivity; Histological Techniques; Classical; projection; topographic map},
	Mesh = {Anatomy, Comparative; Animals; Cerebral Cortex; Geniculate Bodies; Insectivora; Nerve Degeneration; Neural Pathways; Opossums; Telencephalon; Thalamus; Turtles},
	Month = {Sep},
	Number = {1},
	Pages = {101-22},
	Pmid = {5459208},
	Pst = {ppublish},
	Title = {Thalamotelencephalic projections in the turtle (Pseudemys scripta)},
	Volume = {140},
	Year = {1970},
	File = {papers/Hall_JCompNeurol1970.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901400107}}

@article{Prechtl:1997,
	Abstract = {The computations involved in the processing of a visual scene invariably involve the interactions among neurons throughout all of visual cortex. One hypothesis is that the timing of neuronal activity, as well as the amplitude of activity, provides a means to encode features of objects. The experimental data from studies on cat [Gray, C. M., Konig, P., Engel, A. K. & Singer, W. (1989) Nature (London) 338, 334-337] support a view in which only synchronous (no phase lags) activity carries information about the visual scene. In contrast, theoretical studies suggest, on the one hand, the utility of multiple phases within a population of neurons as a means to encode independent visual features and, on the other hand, the likely existence of timing differences solely on the basis of network dynamics. Here we use widefield imaging in conjunction with voltage-sensitive dyes to record electrical activity from the virtually intact, unanesthetized turtle brain. Our data consist of single-trial measurements. We analyze our data in the frequency domain to isolate coherent events that lie in different frequency bands. Low frequency oscillations (<5 Hz) are seen in both ongoing activity and activity induced by visual stimuli. These oscillations propagate parallel to the afferent input. Higher frequency activity, with spectral peaks near 10 and 20 Hz, is seen solely in response to stimulation. This activity consists of plane waves and spiral-like waves, as well as more complex patterns. The plane waves have an average phase gradient of approximately pi/2 radians/mm and propagate orthogonally to the low frequency waves. Our results show that large-scale differences in neuronal timing are present and persistent during visual processing.},
	Author = {Prechtl, J C and Cohen, L B and Pesaran, B and Mitra, P P and Kleinfeld, D},
	Date-Added = {2013-06-12 18:57:37 +0000},
	Date-Modified = {2013-06-12 18:59:50 +0000},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {turtle; voltage sensor; optical imaging; optical physiology; neurophysiology; in vivo; visual cortex; next},
	Mesh = {Animals; Cats; Cerebral Cortex; Electrophysiology; Photic Stimulation; Turtles; Vision, Ocular},
	Month = {Jul},
	Number = {14},
	Pages = {7621-6},
	Pmc = {PMC23872},
	Pmid = {9207142},
	Pst = {ppublish},
	Title = {Visual stimuli induce waves of electrical activity in turtle cortex},
	Volume = {94},
	Year = {1997},
	File = {papers/Prechtl_ProcNatlAcadSciUSA1997.pdf}}

@article{Rutishauser:2013,
	Abstract = {Brain activity often consists of interactions between internal-or on-going-and external-or sensory-activity streams, resulting in complex, distributed patterns of neural activity. Investigation of such interactions could benefit from closed-loop experimental protocols in which one stream can be controlled depending on the state of the other. We describe here methods to present rapid and precisely timed visual stimuli to awake animals, conditional on features of the animal's on-going brain state; those features are the presence, power and phase of oscillations in local field potentials (LFP). The system can process up to 64 channels in real time. We quantified its performance using simulations, synthetic data and animal experiments (chronic recordings in the dorsal cortex of awake turtles). The delay from detection of an oscillation to the onset of a visual stimulus on an LCD screen was 47.5ms and visual-stimulus onset could be locked to the phase of ongoing oscillations at any frequency ≤40Hz. Our software's architecture is flexible, allowing on-the-fly modifications by experimenters and the addition of new closed-loop control and analysis components through plugins. The source code of our system "StimOMatic" is available freely as open-source.},
	Author = {Rutishauser, Ueli and Kotowicz, Andreas and Laurent, Gilles},
	Date-Added = {2013-06-12 18:44:04 +0000},
	Date-Modified = {2013-06-12 18:50:44 +0000},
	Doi = {10.1016/j.jneumeth.2013.02.020},
	Journal = {J Neurosci Methods},
	Journal-Full = {Journal of neuroscience methods},
	Keywords = {technique; Methods; next; neurophysiology; hardware; Programming Languages; visual system; in vivo; Electrophysiology},
	Month = {Apr},
	Number = {1},
	Pages = {139-55},
	Pmid = {23473800},
	Pst = {ppublish},
	Title = {A method for closed-loop presentation of sensory stimuli conditional on the internal brain-state of awake animals},
	Volume = {215},
	Year = {2013},
	File = {papers/Rutishauser_JNeurosciMethods2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jneumeth.2013.02.020}}

@article{Kriegstein:1986,
	Abstract = {We have examined the synaptic physiology of the isolated dorsal cortex of the turtle, Pseudemys scripta elegans. Electrical stimulation of afferent pathways elicited distinct, stereotyped responses in pyramidal and stellate neurons. Single shocks evoked a long-lasting barrage of excitatory postsynaptic potentials (EPSPs) in stellate cells, and led to a burst of several action potentials. Under the same circumstances, pyramidal cells displayed a small amount of short-latency excitation, but this was accompanied by a profound and prolonged set of inhibitory post-synaptic potentials (IPSPs). Synaptic excitation of the distal dendrites of pyramidal cells could evoke dendritic action potentials that were visible at the soma as small all-or-none spikes rising from the hyperpolarized level of the IPSP. There appeared to be two mechanistically different types of IPSPs in pyramidal cells. The first occurred at short latency, could produce a very large conductance increase, reversed polarity at -71 mV, and was chloride-dependent. The second was generally smaller and more protracted, had a relatively negative reversal potential of -85 to -95 mV, and was insensitive to chloride injection. Focal application of small doses of the putative inhibitory neurotransmitter gamma-aminobutyric acid (GABA) onto the somata of pyramidal cells caused a conductance increase and hyperpolarization. This response had features in common with the short-latency IPSP, including an identical reversal potential. Application of large doses of GABA to the somata of pyramidal cells or smaller doses to their dendrites elicited multiphasic or purely depolarizing responses that were at least partly due to time- or space-dependent shifts of the equilibrium potential of the response. Bicuculline methiodide, a potent GABA antagonist, depressed both the responses to GABA and the short-latency IPSP, but not the long-latency IPSP; synchronized epileptiform burst discharges also resulted. These findings, together with responses to locally applied electric shocks and the excitatory amino acid glutamate, suggested that inhibition of pyramidal cells was generated intrinsically by stellate cells, and that the cortical circuit provides pathways for both feedforward and feedback GABAergic inhibition. The data also suggest that pyramidal cells are mutually excitatory. These features are similar to the basic intrinsic circuitry in the telencephalic cortices of mammals.},
	Author = {Kriegstein, A R and Connors, B W},
	Date-Added = {2013-06-12 18:38:19 +0000},
	Date-Modified = {2013-06-12 18:39:23 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {neurophysiology; Patch-Clamp Techniques; Turtles; physiology; Synapses; Visual Cortex},
	Mesh = {Animals; Bicuculline; Chlorides; Electrophysiology; Evoked Potentials; Glutamates; Glutamic Acid; Intracellular Fluid; Membrane Potentials; Pyramidal Tracts; Synapses; Turtles; Visual Cortex; gamma-Aminobutyric Acid},
	Month = {Jan},
	Number = {1},
	Pages = {178-91},
	Pmid = {2868076},
	Pst = {ppublish},
	Title = {Cellular physiology of the turtle visual cortex: synaptic properties and intrinsic circuitry},
	Volume = {6},
	Year = {1986},
	File = {papers/Kriegstein_JNeurosci1986.pdf}}

@article{Wu:2008,
	Abstract = {The development of voltage-sensitive dyes (VSD) and fast optical imaging techniques have brought us a new tool for examining spatiotemporal patterns of population neuronal activity in the neocortex. Propagating waves have been observed during almost every type of cortical processing examined by VSD imaging or electrode arrays. These waves provide subthreshold depolarization to individual neurons and increase their spiking probability. Therefore, the propagation of the waves sets up a spatiotemporal framework for increased excitability in neuronal populations, which can help to determine when and where the neurons are likely to fire. In this review, first discussed is propagating waves observed in various systems and possible mechanisms for generating and sustaining these waves. Then discussed are wave dynamics as an emergent behavior of the population activity that can, in turn, influence the activity of individual neurons. The functions of spontaneous and sensory-evoked waves remain to be explored. An important next step will be to examine the interaction between dynamics of propagating waves and functions in the cortex, and to verify if cortical processing can be modified when these waves are altered.},
	Author = {Wu, Jian-Young and Xiaoying Huang and Chuan Zhang},
	Date-Added = {2013-06-12 18:28:17 +0000},
	Date-Modified = {2013-06-12 18:29:40 +0000},
	Doi = {10.1177/1073858408317066},
	Journal = {Neuroscientist},
	Journal-Full = {The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry},
	Keywords = {waves; Visual Cortex; visual system; optical imaging; neurophysiology; voltage sensor; review literature},
	Mesh = {Action Potentials; Animals; Electrophysiology; Evoked Potentials; Fluorescent Dyes; Humans; Neocortex; Nerve Net; Neural Pathways; Neurons; Optics and Photonics; Sensory Receptor Cells},
	Month = {Oct},
	Number = {5},
	Pages = {487-502},
	Pmc = {PMC2679998},
	Pmid = {18997124},
	Pst = {ppublish},
	Title = {Propagating waves of activity in the neocortex: what they are, what they do},
	Volume = {14},
	Year = {2008},
	File = {papers/Wu_Neuroscientist2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1177/1073858408317066}}

@article{Senseman:1999,
	Abstract = {The network behavior of cortical cells during the processing of a light flash was characterized in an isolated, but functionally intact, turtle visual system. Rapid changes in intracellular membrane potential were monitored optically using a voltage-sensitive dye (VSD). Spatially coherent changes in membrane potential were determined by subjecting high-speed movies of the VSD signals to Karhunen-Lo{\'e}ve decomposition. In all experimental trials analyzed (n > 50), coherent activity was restricted to a small number of similar spatial patterns or modes. At least four modes (M(1,1), M(1,2), M(2,1), and M(2,2)) have an organizational structure similar to the normal modes of a vibrating membrane (drum). This empirical observation of modal activity provides a useful framework for analyzing the macroscopic behavior of cortical networks.},
	Author = {Senseman, D M and Robbins, K A},
	Date-Added = {2013-06-12 18:23:26 +0000},
	Date-Modified = {2013-06-12 18:25:41 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Turtles; Visual Cortex; waves; neurophysiology; optical imaging; voltage sensor; Computational Biology; Computer Simulation; technique; next},
	Mesh = {Animals; Cerebral Cortex; Evoked Potentials, Visual; Mathematics; Membrane Potentials; Models, Neurological; Nerve Net; Photic Stimulation; Turtles; Visual Perception},
	Month = {May},
	Number = {10},
	Pages = {RC3},
	Pmid = {10234049},
	Pst = {ppublish},
	Title = {Modal behavior of cortical neural networks during visual processing},
	Volume = {19},
	Year = {1999},
	File = {papers/Senseman_JNeurosci1999.pdf}}

@article{Senseman:2002,
	Abstract = {In the pond turtle, Pseudemys scripta elegans, visually evoked cortical waves propagate at different velocities within the primary visual area compared with waves that pass into the secondary visual area. In an effort to separate intra- and intercortical wave motions, movies of visually evoked cortical waves recorded by high-speed voltage-sensitive dye (VSD) imaging were subjected to Karhunen-Lo{\'e}ve (KL) decomposition. This procedure decomposes the VSD movies into a series of basis images that capture different spatial patterns of coherent activity. Most of the energy of the compound wave motion (>95%) was captured by the three largest basis images, M(1,1), M(1,2), and M(2,1). Based on visual comparison with maps of wave front latency, KL basis image M(1,2) appears to capture the spread of depolarization within the primary visual area, whereas KL basis image M(2,1) appears to capture the spread of depolarization from the primary into the secondary visual area. The contribution of different basis images to the intra- and intercortical wave motions was tested by reconstructing the response using different combinations of KL basis images. Only KL basis images M(1,1) and M(1,2) were needed to reconstruct intracortical wave motion, while basis images M(1,1) and M(2,1) were needed to reconstruct intercortical wave motion. It was also found that the direction and speed of wave propagation could be deduced by visual inspection of the basis image projections on to the original data set. The relative advantage of KL decomposition for the analysis of complex wave motions captured by VSD imaging is discussed.},
	Author = {Senseman, David M and Robbins, Kay A},
	Date-Added = {2013-06-12 18:10:55 +0000},
	Date-Modified = {2013-06-12 18:17:17 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {computation biology; models; Computer Simulation; neurophysiology; optical imaging; voltage sensor; Visual Cortex; visual system; next},
	Mesh = {Animals; Coloring Agents; Evoked Potentials, Visual; Image Processing, Computer-Assisted; Membrane Potentials; Models, Neurological; Photic Stimulation; Reaction Time; Turtles; Visual Cortex},
	Month = {Mar},
	Number = {3},
	Pages = {1499-514},
	Pmid = {11877522},
	Pst = {ppublish},
	Title = {High-speed VSD imaging of visually evoked cortical waves: decomposition into intra- and intercortical wave motions},
	Volume = {87},
	Year = {2002},
	File = {papers/Senseman_JNeurophysiol2002.pdf}}

@article{Robbins:2004,
	Abstract = {Waves have long been thought to be a fundamental mechanism for communicating information within a medium and are widely observed in biological systems. However, a quantitative analysis of biological waves is confounded by the variability and complexity of the response. This paper proposes a robust technique for extracting wave structure from experimental data by calculating "wave subspaces" from the KL decomposition of the data set. If a wave subspace contains a substantial portion of the data set energy during a particular time interval, one can deduce the structure of the wave and potentially isolate its information content. This paper uses the wave subspace technique to extract and compare wave structure in data from three different preparations of the turtle visual cortex. The paper demonstrates that wave subspace caricatures from the three cortical preparations have qualitative similarities. In the numerical model, where information about the underlying dynamics is available, wave subspace landmarks are related to activation and changes in behavior of other dynamic variables besides membrane potential.},
	Author = {Robbins, Kay A and Senseman, David M},
	Date = {2004 May-Jun},
	Date-Added = {2013-06-12 18:09:28 +0000},
	Date-Modified = {2013-06-12 18:10:31 +0000},
	Doi = {10.1023/B:JCNS.0000025689.01581.26},
	Journal = {J Comput Neurosci},
	Journal-Full = {Journal of computational neuroscience},
	Keywords = {computation biology; models; Computer Simulation; Mathematics; Visual Cortex; Turtles; visual system; wave},
	Mesh = {Animals; Computer Simulation; Dose-Response Relationship, Radiation; Evoked Potentials, Visual; Geniculate Bodies; Membrane Potentials; Models, Neurological; Neurons; Photic Stimulation; Principal Component Analysis; Reaction Time; Receptors, AMPA; Receptors, GABA; Receptors, N-Methyl-D-Aspartate; Space Perception; Time Factors; Turtles; Visual Cortex; Visual Pathways},
	Number = {3},
	Pages = {267-98},
	Pmid = {15114050},
	Pst = {ppublish},
	Title = {Extracting wave structure from biological data with application to responses in turtle visual cortex},
	Volume = {16},
	Year = {2004},
	File = {papers/Robbins_JComputNeurosci2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1023/B:JCNS.0000025689.01581.26}}

@article{Nenadic:2003,
	Abstract = {This article describes a large-scale model of turtle visual cortex that simulates the propagating waves of activity seen in real turtle cortex. The cortex model contains 744 multicompartment models of pyramidal cells, stellate cells, and horizontal cells. Input is provided by an array of 201 geniculate neurons modeled as single compartments with spike-generating mechanisms and axons modeled as delay lines. Diffuse retinal flashes or presentation of spots of light to the retina are simulated by activating groups of geniculate neurons. The model is limited in that it does not have a retina to provide realistic input to the geniculate, and the cortex and does not incorporate all of the biophysical details of real cortical neurons. However, the model does reproduce the fundamental features of planar propagating waves. Activation of geniculate neurons produces a wave of activity that originates at the rostrolateral pole of the cortex at the point where a high density of geniculate afferents enter the cortex. Waves propagate across the cortex with velocities of 4 microm/ms to 70 microm/ms and occasionally reflect from the caudolateral border of the cortex.},
	Author = {Nenadic, Zoran and Ghosh, Bijoy K and Ulinski, Philip},
	Date = {2003 Mar-Apr},
	Date-Added = {2013-06-12 17:53:07 +0000},
	Date-Modified = {2013-06-12 18:05:54 +0000},
	Journal = {J Comput Neurosci},
	Journal-Full = {Journal of computational neuroscience},
	Keywords = {computation biology; Computer Simulation; models; Turtles; neurophysiology; waves; Visual Cortex; visual system; Mathematics; technique; next},
	Mesh = {Algorithms; Animals; Axons; Computer Simulation; Demography; Dendrites; Excitatory Postsynaptic Potentials; Geniculate Bodies; Membrane Potentials; Models, Neurological; Neurons; Photic Stimulation; Pyramidal Cells; Reaction Time; Receptors, AMPA; Receptors, GABA-A; Receptors, GABA-B; Receptors, N-Methyl-D-Aspartate; Synapses; Time Factors; Turtles; Visual Cortex; Visual Pathways},
	Number = {2},
	Pages = {161-84},
	Pmid = {12567015},
	Pst = {ppublish},
	Title = {Propagating waves in visual cortex: a large-scale model of turtle visual cortex},
	Volume = {14},
	Year = {2003},
	File = {papers/Nenadic_JComputNeurosci2003.pdf},
	Bdsk-File-2 = {papers/Nenadic_JComputNeurosci2003a.pdf}}

@article{Godecke:1996,
	Abstract = {In the mammalian visual cortex, many neurons are driven binocularly and response properties such as orientation preference or spatial frequency tuning are virtually identical for the two eyes. A precise match of orientation is essential in order to detect disparity and is therefore a prerequisite for stereoscopic vision. It is not clear whether this match is accomplished by activity-dependent mechanisms together with the common visual experience normally received by the eyes, or whether the visual system relies on other, perhaps even innate, cues to achieve this task. Here we test whether visual experience is responsible for the match in a reverse-suturing experiment in which kittens were raised so that both eyes were never able to see at the same time. A comparison of the layout of the two maps formed under these conditions showed them to be virtually identical. Considering that the two eyes never had common visual experience, this indicates that correlated visual input is not required for the alignment of orientation preference maps.},
	Author = {G{\"o}decke, I and Bonhoeffer, T},
	Date-Added = {2013-06-10 19:48:54 +0000},
	Date-Modified = {2013-06-10 19:50:54 +0000},
	Doi = {10.1038/379251a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {cat; kitten; spontaneous activity; activity manipulation; activity-development; development; Visual Cortex; Neocortex; visual system; topographic map},
	Mesh = {Animals; Brain Mapping; Cats; Ocular Physiological Phenomena; Ophthalmologic Surgical Procedures; Orientation; Sensory Deprivation; Sutures; Vision, Binocular; Vision, Ocular; Visual Cortex},
	Month = {Jan},
	Number = {6562},
	Pages = {251-4},
	Pmid = {8538789},
	Pst = {ppublish},
	Title = {Development of identical orientation maps for two eyes without common visual experience},
	Volume = {379},
	Year = {1996},
	File = {papers/Gödecke_Nature1996.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/379251a0}}

@article{Toth:1989,
	Abstract = {In juvenile and adult Xenopus laevis, in adult Bufo marinus and Rana esculenta frogs retino-retinal projections were traced by filling the central stump of one optic nerve, cut 2-3 mm from the eye, with horse-radish peroxidase (HRP) or cobaltic-lysine complex (CLC). The presence of retino-retinal projections was confirmed in all 3 species both in the juvenile and the adult. Up to 12 ganglion cells per retina were found to be filled retrogradely with HRP together with optic axons filled anterogradely with CLC. These findings suggest that (1) a small proportion of ganglion cells project, erroneously, to the opposite retina and (2) this erroneous retino-retinal projection persists throughout the whole lifespan of the animals.},
	Author = {T{\'o}th, P and Straznicky, C},
	Date-Added = {2013-06-10 18:42:13 +0000},
	Date-Modified = {2013-06-10 19:17:29 +0000},
	Journal = {Neurosci Lett},
	Journal-Full = {Neuroscience letters},
	Keywords = {retino-retinal; retino-retino; retinopetal; mirror symmetry; development; activity-development; frog; Amphibia; growth; retina; visual system; tracer; anatomy; connectivity},
	Mesh = {Animals; Axons; Bufo marinus; Cobalt; Horseradish Peroxidase; Lysine; Neural Pathways; Optic Nerve; Rana esculenta; Retina; Retinal Ganglion Cells; Xenopus laevis},
	Month = {Sep},
	Number = {1-2},
	Pages = {43-7},
	Pmid = {2510094},
	Pst = {ppublish},
	Title = {Retino-retinal projections in three anuran species},
	Volume = {104},
	Year = {1989},
	File = {papers/Tóth_NeurosciLett1989.pdf}}

@article{Sarnaik:2013,
	Abstract = {The convergence of eye-specific thalamic inputs to visual cortical neurons forms the basis of binocular vision. Inputs from the same eye that signal light increment (On) and decrement (Off) are spatially segregated into subregions, giving rise to cortical receptive fields (RFs) that are selective for stimulus orientation. Here we map RFs of binocular neurons in the mouse primary visual cortex using spike-triggered average. We find that subregions of the same sign (On-On and Off-Off) preferentially overlap between the 2 monocular RFs, leading to binocularly matched orientation tuning. We further demonstrate that such subregion correspondence and the consequent matching of RF orientation are disrupted in mice reared in darkness during development. Surprisingly, despite the lack of all postnatal visual experience, a substantial degree of subregion correspondence still remains. In addition, dark-reared mice show normal monocular RF structures and binocular overlap. These results thus reveal the specific roles of experience-dependent and -independent processes in binocular convergence and refinement of On and Off inputs onto single cortical neurons.},
	Author = {Sarnaik, Rashmi and Wang, Bor-Shuen and Cang, Jianhua},
	Date-Added = {2013-06-10 17:03:05 +0000},
	Date-Modified = {2013-08-28 14:53:55 +0000},
	Doi = {10.1093/cercor/bht027},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {spontaneous activity; topographic map; mouse; neurophysiology; activity-development; currOpinRvw; Orientation; Visual Cortex; visual system; currOpinRvw},
	Month = {Feb},
	Pmid = {23389996},
	Pst = {aheadofprint},
	Title = {Experience-Dependent and Independent Binocular Correspondence of Receptive Field Subregions in Mouse Visual Cortex},
	Year = {2013},
	File = {papers/Sarnaik_CerebCortex2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bht027}}

@article{Huberman:2005,
	Abstract = {Axon guidance cues contributing to the development of eye-specific visual projections to the lateral geniculate nucleus (LGN) have not previously been identified. Here we show that gradients of ephrin-As and their receptors (EphAs) direct retinal ganglion cell (RGC) axons from the two eyes into their stereotyped pattern of layers in the LGN. Overexpression of EphAs in ferret RGCs using in vivo electroporation induced axons from both eyes to misproject within the LGN. The effects of EphA overexpression were competition-dependent and restricted to the early postnatal period. These findings represent the first demonstration of eye-specific pathfinding mediated by axon guidance cues and, taken with other reports, indicate that ephrin-As can mediate several mapping functions within individual target structures.},
	Author = {Huberman, Andrew D and Murray, Karl D and Warland, David K and Feldheim, David A and Chapman, Barbara},
	Date-Added = {2013-06-10 16:30:29 +0000},
	Date-Modified = {2013-06-10 16:36:56 +0000},
	Doi = {10.1038/nn1505},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {ferret; Anatomy; topographic map; Genes; development; activity-development; Spontaneous activity},
	Mesh = {Aging; Animals; Animals, Newborn; Axons; Electroporation; Ephrin-A3; Ephrin-A5; Female; Ferrets; Geniculate Bodies; Green Fluorescent Proteins; Luminescent Agents; Male; Receptor, EphA3; Receptor, EphA5; Receptors, Eph Family; Retinal Ganglion Cells; Synaptic Transmission; Visual Pathways},
	Month = {Aug},
	Number = {8},
	Pages = {1013-21},
	Pmc = {PMC2652399},
	Pmid = {16025110},
	Pst = {ppublish},
	Title = {Ephrin-As mediate targeting of eye-specific projections to the lateral geniculate nucleus},
	Volume = {8},
	Year = {2005},
	File = {papers/Huberman_NatNeurosci2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn1505}}

@article{Cang:2013,
	Abstract = {Brain connections are organized into topographic maps that are precisely aligned both within and across modalities. This alignment facilitates coherent integration of different categories of sensory inputs and allows for proper sensorimotor transformations. Topographic maps are established and aligned by multistep processes during development, including interactions of molecular guidance cues expressed in gradients; spontaneous activity-dependent axonal and dendritic remodeling; and sensory-evoked plasticity driven by experience. By focusing on the superior colliculus, a major site of topographic map alignment for different sensory modalities, this review summarizes current understanding of topographic map development in the mammalian visual system and highlights recent advances in map alignment studies. A major goal looking forward is to reveal the molecular and synaptic mechanisms underlying map alignment and to understand the physiological and behavioral consequences when these mechanisms are disrupted at various scales. Expected final online publication date for the Annual Review of Neuroscience Volume 36 is July 08, 2013. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.},
	Author = {Cang, Jianhua and Feldheim, David A},
	Date-Added = {2013-06-10 13:05:55 +0000},
	Date-Modified = {2013-08-27 02:57:51 +0000},
	Doi = {10.1146/annurev-neuro-062012-170341},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Keywords = {currOpinRvw; spontaneous activity; visual system; retina; superior colliculus; review literature; Visual Cortex; topographic map; activity-development; activity manipulation; Genes; trophic signal; currOpinRvw},
	Month = {Apr},
	Pmid = {23642132},
	Pst = {aheadofprint},
	Title = {Developmental Mechanisms of Topographic Map Formation and Alignment},
	Year = {2013},
	File = {papers/Cang_AnnuRevNeurosci2013.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev-neuro-062012-170341}}

@article{Friauf:1991,
	Abstract = {1. The development of excitatory activation in the visual cortex was studied in fetal and neonatal cats. During fetal and neonatal life, the immature cerebral cortex (the cortical plate) is sandwiched between two synaptic zones: the marginal zone above, and an area just below the cortical plate, the subplate. The subplate is transient and disappears by approximately 2 mo postnatal. Here we have investigated whether the subplate and the cortical plate receive functional synaptic inputs in the fetus, and when the adultlike pattern of excitatory synaptic input to the cortical plate appears during development. 2. Extracellular field potential recording to electrical stimulation of the optic radiation was performed in slices of cerebral cortex maintained in vitro. Laminar profiles of field potentials were converted by the current-source density (CSD) method to identify the spatial and temporal distribution of neuronal excitation within the subplate and the cortical plate. 3. Between embryonic day 47 (E47) and postnatal day 28 (P28; birth, E65), age-related changes occur in the pattern of synaptic activation of neurons in the cortical plate and the subplate. Early in development, at E47, E57, and P0, short-latency (probably monosynaptic) excitation is most obvious in the subplate, and longer latency (presumably polysynaptic) excitation can be seen in the cortical plate. Synaptic excitation in the subplate is no longer apparent at P21 and P28, a time when cell migration is finally complete and the cortical layers have formed. By contrast, excitation in the cortical plate is prominent in postnatal animals, and the temporal and spatial pattern has changed. 4. The adultlike sequence of synaptic activation in the different cortical layers can be seen by P28. It differs from earlier ages in several respects. First, short-latency (probably monosynaptic) excitation can be detected in cortical layer 4. Second, multisynaptic, long-lasting activation is present in layers 2/3 and 5. 5. Our results show that the subplate zone, known from anatomic studies to be a synaptic neurophil during development, receives functional excitatory inputs from axons that course in the developing white matter. Because the only mature neurons present in this zone are the subplate neurons, we conclude that subplate neurons are the principal, if not the exclusive, recipients of this input. The results suggest further that the excitation in the subplate in turn is relayed to neurons of the cortical plate via axon collaterals of subplate neurons.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {Friauf, E and Shatz, C J},
	Date-Added = {2013-05-31 19:22:12 +0000},
	Date-Modified = {2013-08-27 03:06:44 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {neurophysiology; extracellular; electrical recording; development; synapses; Stimulation; in vitro; cat; kitten; Visual Cortex; neocortex;; currOpinRvw},
	Mesh = {Aging; Animals; Animals, Newborn; Electric Stimulation; Fetus; Gestational Age; Membrane Potentials; Neurons; Synapses; Visual Cortex},
	Month = {Dec},
	Number = {6},
	Pages = {2059-71},
	Pmid = {1812236},
	Pst = {ppublish},
	Title = {Changing patterns of synaptic input to subplate and cortical plate during development of visual cortex},
	Volume = {66},
	Year = {1991},
	File = {papers/Friauf_JNeurophysiol1991.pdf}}

@article{McConnell:1989,
	Abstract = {During the development of the nervous system, growing axons must traverse considerable distances to find their targets. In insects, this problem is solved in part by pioneer neurons, which lay down the first axonal pathways when distances are at a minimum. Here the existence of a similar kind of neuron in the developing mammalian telencephalon is described. These are the subplate cells, the first postmitotic neurons of the cerebral cortex. Axons from subplate neurons traverse the internal capsule and invade the thalamus early in fetal life, even before the neurons of cortical layers 5 and 6, which will form the adult subcortical projections, are generated. During postnatal life, after the adult pattern of axonal projections is firmly established, most subplate neurons disappear. These observations raise the possibility that the early axonal scaffold formed by subplate cells may prove essential for the establishment of permanent subcortical projections.},
	Author = {McConnell, S K and Ghosh, A and Shatz, C J},
	Date-Added = {2013-05-31 17:38:19 +0000},
	Date-Modified = {2013-05-31 17:38:25 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {development; subplate neurons; cat; neocortex; cerebral cortex; patterning; topographic map; axon guidance; visual cortex; activity-development},
	Mesh = {Animals; Axonal Transport; Axons; Cats; Cerebral Cortex; Embryonic and Fetal Development; Fluorescent Dyes; Neurons; Superior Colliculi; Thalamus},
	Month = {Sep},
	Number = {4921},
	Pages = {978-82},
	Pmid = {2475909},
	Pst = {ppublish},
	Title = {Subplate neurons pioneer the first axon pathway from the cerebral cortex},
	Volume = {245},
	Year = {1989},
	File = {papers/McConnell_Science1989.pdf}}

@article{Ghosh:1992a,
	Abstract = {During development of the mammalian cerebral cortex, thalamic axons must grow into the telencephalon and select appropriate cortical targets. In order to begin to understand the cellular interactions that are important in cortical target selection by thalamic axons, we have examined the morphology of axons from the lateral geniculate nucleus (LGN) as they navigate their way to the primary visual cortex. The morphology of geniculocortical axons was revealed by placing the lipophilic tracer Dil into the LGN of paraformaldehyde-fixed brains from fetal and neonatal cats between embryonic day 26 (E26; gestation is 65 d) and postnatal day 7 (P7). This morphological approach has led to three major observations. (1) As LGN axons grow within the intermediate zone of the telencephalon toward future visual cortex (E30-40), many give off distinct interstitial axon collaterals that penetrate the subplate of nonvisual cortical areas. These collaterals are transient and are not seen postnatally. (2) There is a prolonged period during which LGN axons are restricted to the visual subplate prior to their ingrowth into the cortical plate; the first LGN axons arrive within visual subplate by E36 but are not detected in layer 6 of visual cortex until about E50. (3) Within the visual subplate, LGN axons extend widespread terminal branches. This represents a marked change in their morphology from the simple growth cones present earlier as LGN axons navigate en route to visual cortex. The presence of interstitial collaterals suggests that there may be ongoing interactions between LGN axons and subplate neurons along the entire intracortical route traversed by the axons. From the extensive branching of LGN axons within the visual subplate during the waiting period, it appears that they are not simply "waiting." Rather, LGN axons may participate in dynamic cellular interactions within the subplate long before they contact their ultimate target neurons in layer 4. These observations confirm the existence of a prolonged waiting period in the development of thalamocortical connections and provide important morphological evidence in support of the previous suggestion that interactions between thalamic axons and subplate neurons are necessary for cortical target selection.},
	Author = {Ghosh, A and Shatz, C J},
	Date-Added = {2013-05-31 17:28:45 +0000},
	Date-Modified = {2013-05-31 17:34:43 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; subplate neurons; cat; neocortex; cerebral cortex; patterning; topographic map; axon guidance; visual cortex; activity-development},
	Mesh = {Aging; Animals; Animals, Newborn; Axons; Carbocyanines; Cats; Fluorescent Dyes; Geniculate Bodies; Gestational Age; Neural Pathways; Telencephalon; Thalamus; Visual Cortex},
	Month = {Jan},
	Number = {1},
	Pages = {39-55},
	Pmid = {1729444},
	Pst = {ppublish},
	Title = {Pathfinding and target selection by developing geniculocortical axons},
	Volume = {12},
	Year = {1992}}

@article{Ghosh:1994,
	Abstract = {To investigate the cellular interactions within the mammalian visual cortex that are important in ocular dominance column formation, we have examined the role of subplate neurons in this process. LGN axons segregate in layer 4 of the cat's visual cortex between the third and sixth postnatal weeks to give rise to the adult pattern of ocular dominance columns. Subplate neurons are a transient population of neurons that sit in the white matter but have extensive projections into the overlying cortex, particularly layer 4, during neonatal life. Many subplate neurons are present at birth, but most are gone by the end of the period of LGN axon segregation. To examine whether these neurons are required for the segregation of LGN axons, we deleted them by intracortical injections of kainic acid either just after LGN axons had grown into layer 4 (first postnatal week) or later, just before the onset of segregation (third postnatal week). The consequences for the patterning of geniculocortical terminals were evaluated by transneuronal transport of 3H-proline injected into one eye at times when segregation would normally be complete. Following deletion of subplate neurons at either age, LGN axons failed to segregate into ocular dominance columns. Following the late deletions only, geniculocortical axons lost their laminar restriction to layer 4 and projected to layers 2 and 3 as well. Deletion of subplate neurons also resulted in long-term changes in the cytoarchitecture of layer 4. These observations suggest that the interactions that mediate segregation of LGN axons within layer 4 of visual cortex are susceptible to influences from subplate neurons. Although the mechanisms by which subplate neurons exert their effect are not yet clear, these experiments strongly suggest that interactions between LGN axons and layer 4 neurons are not sufficient for column formation, and that subplate neurons most likely play a critical role in interactions leading to ocular segregation.},
	Author = {Ghosh, A and Shatz, C J},
	Date-Added = {2013-05-31 17:28:34 +0000},
	Date-Modified = {2013-05-31 17:34:43 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; subplate neurons; cat; neocortex; cerebral cortex; patterning; topographic map; axon guidance; visual cortex; activity-development},
	Mesh = {Aging; Animals; Animals, Newborn; Axons; Cats; Cerebral Cortex; Functional Laterality; Geniculate Bodies; Kainic Acid; Neurons; Neurons, Afferent; Ocular Physiological Phenomena; Time Factors; Visual Cortex},
	Month = {Jun},
	Number = {6},
	Pages = {3862-80},
	Pmid = {8207493},
	Pst = {ppublish},
	Title = {Segregation of geniculocortical afferents during the critical period: a role for subplate neurons},
	Volume = {14},
	Year = {1994}}

@article{McConnell:1994,
	Abstract = {The adult cerebral cortex extends axons to a variety of subcortical targets, including the thalamus and superior colliculus. These descending projections are pioneered during development by the axons of a transient population of subplate neurons (McConnell et al., 1989). We show here that the descending axons of cortical plate neurons appear to be delayed significantly in their outgrowth, compared with those of subplate neurons. To assess the possible role of subplate neurons in the formation of these pathways, subplate neurons were ablated during the embryonic period. In all cases, an axon pathway formed from visual cortex through the internal capsule and into the thalamus. In half of all cases, however, cortical axons failed to invade their normal subcortical targets. In the other half, targets were innervated normally. Subplate neurons are therefore likely to provide important cues that aid the process by which cortical axons grow toward, select, and invade their subcortical targets.},
	Author = {McConnell, S K and Ghosh, A and Shatz, C J},
	Date-Added = {2013-05-31 17:28:27 +0000},
	Date-Modified = {2013-05-31 17:34:43 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; subplate neurons; cat; neocortex; cerebral cortex; patterning; topographic map; axon guidance; visual cortex; activity-development},
	Mesh = {Afferent Pathways; Animals; Animals, Newborn; Axonal Transport; Axons; Carbocyanines; Cats; Cerebral Cortex; Efferent Pathways; Fetus; Fluorescent Dyes; Models, Neurological; Neurons; Temporal Lobe; Thalamus; Visual Cortex},
	Month = {Apr},
	Number = {4},
	Pages = {1892-907},
	Pmid = {7512631},
	Pst = {ppublish},
	Title = {Subplate pioneers and the formation of descending connections from cerebral cortex},
	Volume = {14},
	Year = {1994}}

@article{Ghosh:1992,
	Abstract = {During development of the mammalian visual system, axon terminals of lateral geniculate nucleus (LGN) neurons, initially intermixed within layer 4 of the visual cortex, gradually segregate according to eye preference to form ocular dominance columns. In addition to LGN axons and layer 4 neurons, subplate neurons may also participate in interactions leading to column formation. Deletion of subplate neurons before the formation of ocular dominance columns prevents the segregation of LGN axons within layer 4. Thus, interactions between LGN axons and layer 4 neurons are not sufficient; subplate neurons are also required for formation of ocular dominance columns in the visual cortex.},
	Author = {Ghosh, A and Shatz, C J},
	Date-Added = {2013-05-31 17:28:05 +0000},
	Date-Modified = {2013-05-31 17:34:43 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {development; subplate neurons; cat; neocortex; cerebral cortex; patterning; topographic map; axon guidance; visual cortex; activity-development},
	Mesh = {Animals; Animals, Newborn; Axons; Cats; Cell Death; Kainic Acid; Neurons; Ocular Physiological Phenomena; Visual Cortex; Visual Pathways},
	Month = {Mar},
	Number = {5050},
	Pages = {1441-3},
	Pmid = {1542795},
	Pst = {ppublish},
	Title = {Involvement of subplate neurons in the formation of ocular dominance columns},
	Volume = {255},
	Year = {1992},
	File = {papers/Ghosh_Science1992.pdf}}

@article{Ghosh:1990,
	Abstract = {The neurons of layer 4 in the adult cerebral cortex receive their major ascending inputs from the thalamus. In development, however, thalamic axons arrive at the appropriate cortical area long before their target layer 4 neurons have migrated into the cortical plate. The axons accumulate and wait in the zone below the cortical plate, the subplate, for several weeks before invading the cortical plate. The subplate is a transient zone that contains the first postmitotic neurons of the telencephalon. These neurons mature well before other cortical neurons, and disappear by cell death after the thalamic axons have grown into the overlying cortical plate. The close proximity of growing thalamocortical axons and subplate neurons suggests that they might be involved in interactions important for normal thalamocortical development. Here we show that early in development the deletion of subplate neurons located beneath visual cortex prevents axons from the lateral geniculate nucleus of the thalamus from recognizing and innervating visual cortex, their normal target. In the absence of subplate neurons, lateral geniculate nucleus axons continue to grow in the white matter past visual cortex despite the presence of their target layer 4 neurons. Thus the transient subplate neurons are necessary for appropriate cortical target selection by thalamocortical axons.},
	Author = {Ghosh, A and Antonini, A and McConnell, S K and Shatz, C J},
	Date-Added = {2013-05-31 17:28:01 +0000},
	Date-Modified = {2013-05-31 17:34:43 +0000},
	Doi = {10.1038/347179a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {development; subplate neurons; cat; neocortex; cerebral cortex; patterning; topographic map; axon guidance; visual cortex; activity-development},
	Mesh = {Animals; Axons; Cats; Cell Movement; Cell Survival; Cerebral Cortex; Immunohistochemistry; Kainic Acid; Microtubule-Associated Proteins; Neurons; Thalamus; Visual Cortex},
	Month = {Sep},
	Number = {6289},
	Pages = {179-81},
	Pmid = {2395469},
	Pst = {ppublish},
	Title = {Requirement for subplate neurons in the formation of thalamocortical connections},
	Volume = {347},
	Year = {1990},
	File = {papers/Ghosh_Nature1990.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/347179a0}}

@article{Demas:2012,
	Abstract = {Developing amphibians need vision to avoid predators and locate food before visual system circuits fully mature. Xenopus tadpoles can respond to visual stimuli as soon as retinal ganglion cells (RGCs) innervate the brain, however, in mammals, chicks and turtles, RGCs reach their central targets many days, or even weeks, before their retinas are capable of vision. In the absence of vision, activity-dependent refinement in these amniote species is mediated by waves of spontaneous activity that periodically spread across the retina, correlating the firing of action potentials in neighboring RGCs. Theory suggests that retinorecipient neurons in the brain use patterned RGC activity to sharpen the retinotopy first established by genetic cues. We find that in both wild type and albino Xenopus tadpoles, RGCs are spontaneously active at all stages of tadpole development studied, but their population activity never coalesces into waves. Even at the earliest stages recorded, visual stimulation dominates over spontaneous activity and can generate patterns of RGC activity similar to the locally correlated spontaneous activity observed in amniotes. In addition, we show that blocking AMPA and NMDA type glutamate receptors significantly decreases spontaneous activity in young Xenopus retina, but that blocking GABA(A) receptor blockers does not. Our findings indicate that vision drives correlated activity required for topographic map formation. They further suggest that developing retinal circuits in the two major subdivisions of tetrapods, amphibians and amniotes, evolved different strategies to supply appropriately patterned RGC activity to drive visual circuit refinement.},
	Author = {Demas, James A and Payne, Hannah and Cline, Hollis T},
	Date-Added = {2013-05-31 16:22:46 +0000},
	Date-Modified = {2013-05-31 16:33:28 +0000},
	Doi = {10.1002/dneu.20880},
	Journal = {Dev Neurobiol},
	Journal-Full = {Developmental neurobiology},
	Keywords = {retinal waves; spontaneous activity; Xenopus; vision; Activity-development; development; topographic map; visual system; retina; Retinal Ganglion Cells; currOpinRvw},
	Mesh = {Animals; Electrophysiology; Neurogenesis; Retina; Retinal Ganglion Cells; Vision, Ocular; Visual Pathways; Xenopus},
	Month = {Apr},
	Number = {4},
	Pages = {537-46},
	Pmc = {PMC3157589},
	Pmid = {21312343},
	Pst = {ppublish},
	Title = {Vision drives correlated activity without patterned spontaneous activity in developing Xenopus retina},
	Volume = {72},
	Year = {2012},
	File = {papers/Demas_DevNeurobiol2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/dneu.20880}}

@article{Grzywacz:2000,
	Abstract = {We report on the temporal properties of the spontaneous bursts of activity in the developing turtle retina. Quantitative statistical criteria were used to detect, cluster, and analyze the temporal properties of the bursts. The interburst interval, duration, firing rate, and number of spikes per burst varied widely among cells and from burst to burst in a single cell. Part of this variability was due to the positive correlation between a burst's duration and the interburst interval preceding that burst. This correlation indicated the influence of a refractory period on the bursts' properties. Further evidence of such a refractoriness came from the bursts' auto-covariance function, which gives the tendency of a spike to occur a given amount of time after another spike. This function showed a positive phase (between approximately 10 ms and 10 s) followed by a negative one (between 10 s and more than 100 s), suggestive of burst refractoriness. The bursts seemed to be propagating from cell to cell, because there was a long (symmetrically distributed) delay between the activation of two neighbor cells (median absolute delay = 2.3 s). However, the activity often failed to propagate from one cell to the other (median safety factor = 0.59). The number of spikes per burst in neighbor cells was statistically positively correlated, indicating that the activity in the two cells was driven by the same excitatory process. At least two factors contribute to the excitability during bursts, because the positive phase of the cross-covariance function (similar to auto-covariance but for two cells) had a temporally asymmetric fast component (1-3 ms) followed by a temporally symmetric slow component (1 ms to 10 s).},
	Author = {Grzywacz, N M and Sernagor, E},
	Date = {2000 Mar-Apr},
	Date-Added = {2013-05-31 16:04:51 +0000},
	Date-Modified = {2013-05-31 16:05:54 +0000},
	Journal = {Vis Neurosci},
	Journal-Full = {Visual neuroscience},
	Keywords = {retinal waves; turtle; Retina; visual system; spontaneous activity; development},
	Mesh = {Animals; Cluster Analysis; Electrophysiology; Microelectrodes; Retinal Ganglion Cells; Turtles},
	Number = {2},
	Pages = {229-41},
	Pmid = {10824677},
	Pst = {ppublish},
	Title = {Spontaneous activity in developing turtle retinal ganglion cells: statistical analysis},
	Volume = {17},
	Year = {2000}}

@article{Sernagor:1999,
	Abstract = {Extracellular recordings were obtained from the ganglion cell (GC) layer during correlated spontaneous bursting activity (SBA) in the immature turtle retina. Pharmacological agents were bath-applied, and their effects on burst and correlation parameters were determined. SBA requires synaptic transmission. It was blocked in the presence of curare and mecamylamine, two cholinergic nicotinic antagonists, and enhanced with neostigmine, a cholinesterase inhibitor. SBA was profoundly inhibited during blockade of glutamatergic receptors with the broad spectrum antagonist kynurenate and it vanished with 6,7-dinitroquinoxaline-2-3-dione (DNQX) and 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), two AMPA/kainate receptor antagonists. Blockade of NMDA receptors with D(-)-2-amino-5-phosphonopentanoic acid (D-AP-5) led only to a modest reduction in SBA. Blockade of GABAA receptors with bicuculline prolonged the duration of the bursts. Inhibition of GABA uptake with nipecotic acid led to a decrease in burst rate. Blockade of K+ channels with cesium (Cs+) and tetraethylammonium (TEA) led to a dramatic decrease in excitability. Burst propagation between neighboring GCs was reduced by K+ channel blockade. Gap junction blockade had no consistent effect on bursts or correlation parameters. None of these drugs had a strong effect on the refractory period between bursts. We conclude that correlated SBA in immature turtle GCs requires both cholinergic nicotinic and glutamatergic (mainly through AMPA/kainate receptors) synaptic transmission. GABAergic activity modulates the intensity and the duration of the bursts. Extracellular K+ is involved in lateral activity propagation and increases retinal excitability, which may be required for burst generation.},
	Author = {Sernagor, E and Grzywacz, N M},
	Date-Added = {2013-05-31 16:04:46 +0000},
	Date-Modified = {2013-05-31 16:05:54 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {retinal waves; turtle; Retina; visual system; spontaneous activity; development},
	Mesh = {Action Potentials; Animals; Embryo, Nonmammalian; Embryonic Development; Excitatory Amino Acid Antagonists; Gap Junctions; Potassium; Retinal Ganglion Cells; Synaptic Transmission; Turtles},
	Month = {May},
	Number = {10},
	Pages = {3874-87},
	Pmid = {10234019},
	Pst = {ppublish},
	Title = {Spontaneous activity in developing turtle retinal ganglion cells: pharmacological studies},
	Volume = {19},
	Year = {1999},
	File = {papers/Sernagor_JNeurosci1999.pdf}}

@article{Sernagor:1996,
	Abstract = {BACKGROUND: The role played by early neural activity in shaping retinal functions has not yet been established. In the developing vertebrate retina, ganglion cells fire spontaneous bursts of action potentials before the onset of visual experience. This spontaneous bursting disappears shortly after birth or eye opening. In the present study, we have investigated whether the outgrowth of receptive fields in turtle retinal ganglion cells is affected by early spontaneous bursting or by early visual experience.
RESULTS: Ganglion cells normally stop bursting spontaneously 2-4 weeks post-hatching, the time when receptive-field areas reach adult size. When turtles are reared in the dark, the spontaneous bursting persists. Concomitantly, receptive-field areas expand to more than twice those observed in normal adults. To test whether chronic blockade of spontaneous bursting inhibits the expansion of developing receptive-field areas, we have exposed the retina to curare, a nicotinic cholinergic antagonist, because spontaneous bursting by ganglion cells requires acetylcholine. Curare was released from Elvax, a slow-release polymer that was implanted in the eye. When spontaneous bursting was chronically blocked with curare in hatchlings, dark-induced expansion of receptive fields was abolished. Moreover, receptive fields of ganglion cells exposed to curare in hatchlings reared in normal light and dark cycles were smaller than normal.
CONCLUSIONS: These results strongly suggest that early, acetylcholine-dependent spontaneous bursts of activity control the outgrowth of receptive-field areas in retinal ganglion cells. The onset of visual experience induces the disappearance of the immature spontaneous bursts, resulting in the stabilization of receptive-field areas to their mature size.},
	Author = {Sernagor, E and Grzywacz, N M},
	Date-Added = {2013-05-31 16:04:41 +0000},
	Date-Modified = {2013-05-31 16:06:12 +0000},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {retinal waves; currOpinRvw; turtle; Retina; visual system; spontaneous activity; development},
	Mesh = {Animals; Darkness; Receptors, Cholinergic; Retinal Ganglion Cells; Turtles},
	Month = {Nov},
	Number = {11},
	Pages = {1503-8},
	Pmid = {8939611},
	Pst = {ppublish},
	Title = {Influence of spontaneous activity and visual experience on developing retinal receptive fields},
	Volume = {6},
	Year = {1996},
	File = {papers/Sernagor_CurrBiol1996.pdf}}

@article{Sernagor:1995,
	Abstract = {1. Receptive field properties of adult retinal ganglion cells are well documented, but little is known about their development. We made extracellular recordings of activity from turtle retinal ganglion cells during embryogenesis (stages 22-26), during the first 40 days posthatching, and in adults. 2. From stage 22 the cells fired in spontaneous recurring bursts, and from stage 23 they responded to light. Polar plots of the responses to motion were highly anisotropic in early embryonic cells. More than 40% of embryonic cells exhibited multiaxis anisotropy, and only 6% were statistically isotropic. The incidence of anisotropic cells gradually decreased throughout development. The incidence of isotropic cells and the excitatory receptive field diameters of all ganglion cells gradually increased during development and their maturation coincided with the disappearance of the spontaneous bursts (2-4 wk posthatching). 3. Both sensitivities to stimulus orientation and direction of motion were observed at the earliest stages of development. However, orientation selectivity reached a peak incidence at hatching, whereas directional selectivity completely disappeared, only to reappear in adults. 4. These results show that mature spatiotemporal receptive field properties of retinal ganglion cells emerge from initially highly anisotropic properties, which may reflect an immature, polarized dendritic layout. Their maturation might be mediated by dendritic outgrowth and strengthening of excitatory synaptic connections, which could be induced by spontaneous activity and driven to maturation by exposure to light at birth. Mature directional selectivity seems to require visual experience or the late establishment of a specialized inhibitory synaptic drive.},
	Author = {Sernagor, E and Grzywacz, N M},
	Date-Added = {2013-05-31 16:04:37 +0000},
	Date-Modified = {2013-05-31 16:05:54 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {retinal waves; turtle; Retina; visual system; spontaneous activity; development},
	Mesh = {Animals; Embryo, Nonmammalian; Extracellular Space; Motion Perception; Orientation; Photic Stimulation; Retina; Retinal Ganglion Cells; Space Perception; Time Perception; Turtles; Visual Fields},
	Month = {Apr},
	Number = {4},
	Pages = {1355-64},
	Pmid = {7643153},
	Pst = {ppublish},
	Title = {Emergence of complex receptive field properties of ganglion cells in the developing turtle retina},
	Volume = {73},
	Year = {1995},
	File = {papers/Sernagor_JNeurophysiol1995.pdf}}

@article{Wong:1998,
	Abstract = {Even before birth and the onset of sensory experience, neural activity plays an important role in shaping the vertebrate nervous system. In the embryonic chick visual system, activity in the retina before vision has been implicated in the refinement of retinotopic maps, the elimination of transient projections, and the survival of a full complement of neurons. In this study, we report the detection of a physiological substrate for these phenomena: waves of spontaneous activity in the ganglion cell layer of the embryonic chick retina. The activity is robust and highly patterned, taking the form of large amplitude, rhythmic, and wide-ranging waves of excitation that propagate across the retina. Activity waves are most prominent and organized between embryonic days 13-18, coinciding with the developmental period during which retinal axons refine their connections in their targets. The spatial and temporal features of the patterns observed are consistent with the role of activity patterns in shaping eye-specific projections and retinotopic maps but inconsistent with the hypothesis that they specify lamina-specific projections in the tectum. Antagonists of glutamatergic and glycinergic transmission and of gap junctional communication suppress spontaneous activity, whereas antagonists to GABAergic transmission potentiate it. Based on these results, we propose that spontaneous activity in the ganglion cells is regulated by chemical inputs from both bipolar and amacrine cells and by gap junctional coupling involving ganglion cells.},
	Author = {Wong, W T and Sanes, J R and Wong, R O},
	Date-Added = {2013-05-31 16:00:35 +0000},
	Date-Modified = {2013-05-31 16:00:41 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {retinal waves; currOpinRvw; Chick Embryo; Retina; visual system; spontaneous activity},
	Mesh = {Animals; Chick Embryo; Cholinergic Antagonists; Electrophysiology; Excitatory Amino Acid Antagonists; Fluorescent Dyes; Fura-2; GABA-A Receptor Antagonists; Gap Junctions; Green Fluorescent Proteins; Indicators and Reagents; Luminescent Proteins; Microscopy, Fluorescence; Receptors, Glycine; Retina; Retinal Ganglion Cells; Synaptic Transmission; Time Factors; Transfection; Visual Cortex},
	Month = {Nov},
	Number = {21},
	Pages = {8839-52},
	Pmid = {9786990},
	Pst = {ppublish},
	Title = {Developmentally regulated spontaneous activity in the embryonic chick retina},
	Volume = {18},
	Year = {1998},
	File = {papers/Wong_JNeurosci1998.pdf}}

@article{Catsicas:1998,
	Abstract = {The development of the central nervous system is dependent on spontaneous action potentials and changes in [Ca2+]i occurring in neurons [1-4]. In the mammalian retina, waves of spontaneous electrical activity spread between retinal neurons, raising [Ca2+]i as they pass [5-7]. In the ferret retina, the first spontaneous Ca2+ waves have been reported at postnatal day 2 and are thought to result from the Ca2+ influx associated with bursts of action potentials seen in ganglion cells at this time [5-7]. These waves depend on depolarisation produced by voltage-gated sodium channels, but their initiation and/or propagation also depends upon nicotinic cholinergic synaptic transmission between amacrine cells and ganglion cells [8]. Here, we report contrasting results for the chick retina where Ca2+ transients are seen at times before retinal synapse formation but when there are extensive networks of gap junctions. These Ca2+ transients do not require nicotinic cholinergic transmission but are modulated by acetylcholine (ACh), dopamine and glycine. Furthermore, they propagate into the depth of the retina, suggesting that they are not restricted to ganglion and amacrine cells. The transients are abolished by the gap-junctional blocker octanol. Thus, the Ca2+ transients seen early in chick retinal development are triggered and propagate in the absence of synapses by a mechanism that involves several neurotransmitters and gap junctions.},
	Author = {Catsicas, M and Bonness, V and Becker, D and Mobbs, P},
	Date-Added = {2013-05-31 15:56:33 +0000},
	Date-Modified = {2013-05-31 15:57:08 +0000},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {retinal waves; currOpinRvw; Chick Embryo; Retina; visual system; spontaneous activity},
	Mesh = {Acetylcholine; Action Potentials; Animals; Calcium; Chick Embryo; Dopamine; Gap Junctions; Glycine; Neurons; Retina; Tetrodotoxin},
	Month = {Feb},
	Number = {5},
	Pages = {283-6},
	Pmid = {9501073},
	Pst = {ppublish},
	Title = {Spontaneous Ca2+ transients and their transmission in the developing chick retina},
	Volume = {8},
	Year = {1998},
	File = {papers/Catsicas_CurrBiol1998.pdf}}

@article{Sharma:2010,
	Abstract = {Regulation of progenitor cell fate determines the numbers of neurons in the developing brain. While proliferation of neural progenitors predominates during early central nervous system (CNS) development, progenitor cell fate shifts toward differentiation as CNS circuits develop, suggesting that signals from developing circuits may regulate proliferation and differentiation. We tested whether activity regulates neurogenesis in vivo in the developing visual system of Xenopus tadpoles. Both cell proliferation and the number of musashi1-immunoreactive progenitors in the optic tectum decrease as visual system connections become stronger. Visual deprivation for 2 days increased proliferation of musashi1-immunoreactive radial glial progenitors, while visual experience increased neuronal differentiation. Morpholino-mediated knockdown and overexpression of musashi1 indicate that musashi1 is necessary and sufficient for neural progenitor proliferation in the CNS. These data demonstrate a mechanism by which increased brain activity in developing circuits decreases cell proliferation and increases neuronal differentiation through the downregulation of musashi1 in response to circuit activity.},
	Author = {Sharma, Pranav and Cline, Hollis T},
	Date-Added = {2013-05-30 19:52:07 +0000},
	Date-Modified = {2013-05-30 19:52:07 +0000},
	Doi = {10.1016/j.neuron.2010.09.028},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Adenosine Triphosphatases; Animals; Cell Cycle; Cell Differentiation; Cell Proliferation; Central Nervous System; Immunohistochemistry; Larva; Nerve Tissue Proteins; Neuroglia; Neurons; Photic Stimulation; Ribonucleoproteins; Sensory Deprivation; Stem Cells; Superior Colliculi; Vision, Ocular; Visual Pathways; Xenopus; Xenopus Proteins},
	Month = {Nov},
	Number = {3},
	Pages = {442-55},
	Pmc = {PMC3005332},
	Pmid = {21040846},
	Pst = {ppublish},
	Title = {Visual activity regulates neural progenitor cells in developing xenopus CNS through musashi1},
	Volume = {68},
	Year = {2010},
	File = {papers/Sharma_Neuron2010.pdf}}

@article{Ruthazer:2004,
	Abstract = {The development of orderly topographic maps in the central nervous system (CNS) results from a collaboration of chemoaffinity cues that establish the coarse organization of the projection and activity-dependent mechanisms that fine-tune the map. Using the retinotectal projection as a model system, we describe evidence that biochemical tags and patterned neural activity work in parallel to produce topographically ordered axonal projections. Finally, we review recent experiments in other CNS projections that support the proposition that cooperation between molecular guidance cues and activity-dependent processes constitutes a general paradigm for CNS map formation.},
	Author = {Ruthazer, Edward S and Cline, Hollis T},
	Date-Added = {2013-05-30 19:49:36 +0000},
	Date-Modified = {2013-05-30 19:49:36 +0000},
	Doi = {10.1002/neu.10344},
	Journal = {J Neurobiol},
	Journal-Full = {Journal of neurobiology},
	Mesh = {Animals; Axons; Brain Mapping; Cerebral Cortex; Eye; Models, Neurological; Neurons; Retina; Superior Colliculi; Thalamus; Visual Pathways},
	Month = {Apr},
	Number = {1},
	Pages = {134-46},
	Pmid = {15007832},
	Pst = {ppublish},
	Title = {Insights into activity-dependent map formation from the retinotectal system: a middle-of-the-brain perspective},
	Volume = {59},
	Year = {2004},
	File = {papers/Ruthazer_JNeurobiol2004.pdf}}

@article{Smetters:1994,
	Abstract = {Recent studies have shown that electrical activity, particularly that mediated by NMDA receptors, has a profound effect on the development of specific neuronal connections. Blocking NMDA receptors in the ferret's lateral geniculate nucleus prevents the segregation of retinal afferents into ON and OFF sublaminae. We have now examined the involvement of NMDA receptors in the separation of afferents from the two eyes that occurs in the lateral geniculate nucleus several weeks earlier in development. Blockade of NMDA receptor activity does not appear to interfere with this eye-specific segregation.},
	Author = {Smetters, D K and Hahm, J and Sur, M},
	Date-Added = {2013-05-28 19:49:12 +0000},
	Date-Modified = {2013-05-28 19:51:00 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {Ferrets; LGN; visual system; currOpinRvw},
	Mesh = {Animals; Eye; Ferrets; Geniculate Bodies; Neural Pathways; Organ Specificity; Piperazines; Receptors, N-Methyl-D-Aspartate; Retina; Retinal Ganglion Cells},
	Month = {Sep},
	Number = {1-2},
	Pages = {168-78},
	Pmid = {7834339},
	Pst = {ppublish},
	Title = {An N-methyl-D-aspartate receptor antagonist does not prevent eye-specific segregation in the ferret retinogeniculate pathway},
	Volume = {658},
	Year = {1994}}

@article{Bickford:2010,
	Abstract = {The dorsal lateral geniculate nucleus (dLGN) of the mouse has emerged as a model system in the study of thalamic circuit development. However, there is still a lack of information regarding how and when various types of retinal and nonretinal synapses develop. We examined the synaptic organization of the developing mouse dLGN in the common pigmented C57/BL6 strain, by recording the synaptic responses evoked by electrical stimulation of optic tract axons, and by investigating the ultrastructure of identified synapses. At early postnatal ages (<P12), optic tract evoked responses were primarily excitatory. The full complement of inhibitory responses did not emerge until after eye opening (>P14), when optic tract stimulation routinely evoked an excitatory postsynaptic potential/inhibitory postsynaptic potential (EPSP/IPSP) sequence, with the latter having both a GABA(A) and GABA(B) component. Electrophysiological and ultrastructural observations were consistent. At P7, many synapses were present, but synaptic profiles lacked the ultrastructural features characteristic of the adult dLGN, and little gamma-aminobutyric acid (GABA) could be detected by using immunocytochemical techniques. In contrast, by P14, GABA staining was robust, mature synaptic profiles of retinal and nonretinal origin were easily distinguished, and the size and proportion of synaptic contacts were similar to those of the adult. The emergence of nonretinal synapses coincides with pruning of retinogeniculate connections, and the transition of retinal activity from spontaneous to visually driven. These results indicate that the synaptic architecture of the mouse dLGN is similar to that of other higher mammals, and thus provides further support for its use as a model system for visual system development.},
	Author = {Bickford, Martha E and Slusarczyk, Arkadiusz and Dilger, Emily K and Krahe, Thomas E and Kucuk, Can and Guido, William},
	Date-Added = {2013-05-28 18:27:19 +0000},
	Date-Modified = {2013-05-28 18:28:08 +0000},
	Doi = {10.1002/cne.22223},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {Thalamic Nuclei; visual system; LGN; Patch-Clamp Techniques; Voltage-Gated; Calcium Channels; development; synapse formation; plasticity; in vitro; GABA; Mouse},
	Mesh = {Animals; Animals, Newborn; Cell Differentiation; Electric Stimulation; Excitatory Postsynaptic Potentials; Geniculate Bodies; Inhibitory Postsynaptic Potentials; Mice; Mice, Inbred C57BL; Microscopy, Immunoelectron; Neural Inhibition; Neuronal Plasticity; Organ Culture Techniques; Photic Stimulation; Presynaptic Terminals; Receptors, GABA-A; Receptors, GABA-B; Retinal Ganglion Cells; Synapses; Visual Pathways; gamma-Aminobutyric Acid},
	Month = {Mar},
	Number = {5},
	Pages = {622-35},
	Pmid = {20034053},
	Pst = {ppublish},
	Title = {Synaptic development of the mouse dorsal lateral geniculate nucleus},
	Volume = {518},
	Year = {2010},
	File = {papers/Bickford_JCompNeurol2010.pdf}}

@article{Guido:2008,
	Abstract = {Much of our present understanding about the mechanisms contributing to the activity-dependent refinement of sensory connections comes from experiments done in the retinogeniculate pathway. In recent years the mouse has emerged as a model system of study. This review outlines the major changes in connectivity that occur in this species and a potential mechanism that can account for such remodelling. During early postnatal life when spontaneous activity of retinal ganglion cells sweeps across the retina in waves, retinal projections from the two eyes to the dorsal lateral geniculate nucleus (LGN) segregate to form non-overlapping eye-specific domains. There is a loss of binocular innervation, a pruning of excitatory inputs from a dozen or more to one or two, and the emergence of inhibitory circuitry. Many of these changes underlie the development of precise eye-specific visual maps and receptive field structure of LGN neurons. Retinal activity plays a major role both in the induction and maintenance of this refinement. The activity-dependent influx of Ca(2+) through L-type channels and associated activation of CREB signalling may underlie the pruning and stabilization of developing retinogeniculate connections.},
	Author = {Guido, William},
	Date-Added = {2013-05-28 18:26:31 +0000},
	Date-Modified = {2013-05-28 18:27:09 +0000},
	Doi = {10.1113/jphysiol.2008.157115},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {Thalamic Nuclei; visual system; LGN; Patch-Clamp Techniques; Voltage-Gated; Calcium Channels; development; synapse formation; plasticity; in vitro; review literature},
	Mesh = {Afferent Pathways; Animals; Animals, Newborn; Calcium Channels, L-Type; Geniculate Bodies; Retina; Synapses},
	Month = {Sep},
	Number = {Pt 18},
	Pages = {4357-62},
	Pmc = {PMC2614014},
	Pmid = {18556365},
	Pst = {ppublish},
	Title = {Refinement of the retinogeniculate pathway},
	Volume = {586},
	Year = {2008},
	File = {papers/Guido_JPhysiol2008.pdf}}

@article{Ziburkus:2009,
	Abstract = {The purpose of the present study was to determine whether retinal activity can support long-term changes in synaptic strength in the developing dorsal lateral geniculate nucleus (LGN) of thalamus. To test for this we made use of a rodent in vitro explant preparation in which retinal afferents and the intrinsic circuitry of the LGN remain intact. We repetitively stimulated the optic tract with a tetanus protocol that approximated the temporal features of spontaneous retinal waves. We found the amplitude of extracellular field potentials evoked by retinal stimulation changed significantly after tetanus and that the polarity of these alterations was related to postnatal age. At a time when substantial pruning of retinal connections occurs (postnatal day 1 [P1] to P14), high-frequency stimulation led to an immediate and long-term depression (LTD). However, at times when pruning wanes and adult-like patterns of connectivity are stabilizing (P16 to P30), the identical form of stimulation produced a modest form of potentiation (long-term potentiation [LTP]). The LTD was unaffected by the bath application of gamma-aminobutyric acid type A and N-methyl-D-aspartate receptor antagonists. However, both LTD and LTP were blocked by L-type Ca(2+)-channel antagonists. Thus the Ca(2+) influx associated with L-type channel activation mediates the induction of synaptic plasticity and may signal the pruning and subsequent stabilization of developing retinogeniculate connections.},
	Author = {Ziburkus, Jok{\=u}bas and Dilger, Emily K and Lo, Fu-Sun and Guido, William},
	Date-Added = {2013-05-28 18:22:11 +0000},
	Date-Modified = {2013-05-28 20:01:55 +0000},
	Doi = {10.1152/jn.90618.2008},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {Thalamic Nuclei; visual system; LGN; Patch-Clamp Techniques; Voltage-Gated; Calcium Channels; development; synapse formation; plasticity; in vitro; synaptic; LTP; LTD; currOpinRvw},
	Mesh = {2-Amino-5-phosphonovalerate; Age Factors; Animals; Animals, Newborn; Bicuculline; Biophysics; Calcium Channel Blockers; Dose-Response Relationship, Drug; Electric Stimulation; Excitatory Amino Acid Antagonists; GABA Antagonists; Geniculate Bodies; Long-Term Potentiation; Long-Term Synaptic Depression; Nimodipine; Nitrendipine; Rats; Rats, Long-Evans; Retina; Synapses; Time Factors; Visual Pathways},
	Month = {Dec},
	Number = {6},
	Pages = {3082-90},
	Pmc = {PMC2804430},
	Pmid = {19776360},
	Pst = {ppublish},
	Title = {LTD and LTP at the developing retinogeniculate synapse},
	Volume = {102},
	Year = {2009},
	File = {papers/Ziburkus_JNeurophysiol2009.pdf}}

@article{Lo:2002,
	Abstract = {Using intracellular recordings in an isolated (in vitro) rat brain stem preparation, we examined the synaptic responses of developing relay neurons in the dorsal lateral geniculate nucleus (LGN). In newborn rats, strong stimulation of the optic tract (OT) evoked excitatory postsynaptic potentials (EPSPs) that gave rise to a sustained (300-1,300 ms), slow-decaying (<0.01 mV/s), depolarization (25-40 mV). Riding atop this response was a train of spikes of variable amplitude. We refer to this synaptically evoked event as a plateau potential. Pharmacology experiments indicate the plateau potential was mediated by the activation of high-threshold L-type Ca(2+) channels. Synaptic activation of the plateau potential relied on N-methyl-D-aspartate (NMDA) receptor-mediated activity and the spatial and/or temporal summation of retinally evoked EPSPs. Inhibitory postsynaptic responses (IPSPs) did not prevent the expression of the plateau potential. However, GABA(A) receptor activity modulated the intensity of optic tract stimulation needed to evoke the plateau potential, while GABA(B) receptor activity affected its duration. Expression of the plateau potential was developmentally regulated, showing a much higher incidence at P1-2 (90%) than at P19-20 (1%). This was in part due to the fact that developing relay cells show a greater degree of spatial summation than their mature counterparts, receiving input from as many as 7-12 retinal ganglion cells. Early spontaneous retinal activity is also likely to trigger the plateau potential. Repetitive stimulation of optic tract in a manner that approximated the high-frequency discharge of retinal ganglion cells led to a massive temporal summation of EPSPs and the activation of a sustained depolarization (>1 min) that was blocked by L-type Ca(2+) channel antagonists. These age-related changes in Ca(2+) signaling may contribute to the activity-dependent refinement of retinogeniculate connections.},
	Author = {Lo, Fu-Sun and Ziburkus, Jokubas and Guido, William},
	Date-Added = {2013-05-28 18:19:02 +0000},
	Date-Modified = {2013-05-28 18:21:43 +0000},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {Thalamic Nuclei; visual system; LGN; Patch-Clamp Techniques; Voltage-Gated; Calcium Channels; development; synapse formation; plasticity; GABA; rat; in vitro},
	Mesh = {2-Amino-5-phosphonovalerate; Action Potentials; Animals; Baclofen; Bicuculline; Calcium; Calcium Channel Blockers; Calcium Channels, L-Type; Excitatory Amino Acid Antagonists; Excitatory Postsynaptic Potentials; GABA Antagonists; Geniculate Bodies; Neurons; Nitrendipine; Rats; Rats, Sprague-Dawley; Receptors, GABA; Synapses},
	Month = {Mar},
	Number = {3},
	Pages = {1175-85},
	Pmid = {11877491},
	Pst = {ppublish},
	Title = {Synaptic mechanisms regulating the activation of a Ca(2+)-mediated plateau potential in developing relay cells of the LGN},
	Volume = {87},
	Year = {2002},
	File = {papers/Lo_JNeurophysiol2002.pdf}}

@article{Krahe:2011,
	Abstract = {Monocular deprivation (MD) is a classic paradigm for experience-dependent cortical plasticity. One form is known as homeostatic plasticity, in which neurons innervated by the deprived eye show a remarkable capacity to compensate for degraded visual signals in an attempt to stabilize network activity. Although the evidence supporting homeostatic plasticity in visual cortex is extensive, it remains unclear whether neurons in subcortical visual structures respond to MD in a similar manner. Here we examined whether cells in the dorsal lateral geniculate nucleus (dLGN), the thalamic relay between the retina and visual cortex, show similar forms of experience-dependent homeostatic plasticity following MD. Two-week-old mice were monocularly deprived for a period of 5-7 d and miniature EPSCs (mEPSCs) were obtained from cells located in dLGN regions receiving input from the deprived or nondeprived eye. We found that MD promotes increases in the frequency and amplitude of mEPSCs and were restricted to the monocular segment contralateral to the deprived eye. These changes were accompanied by an increase in the probability of glutamate release at corticothalamic terminals that arise from the deprived visual cortex. Our findings indicate that homeostatic synaptic regulation from MD extends beyond cortical circuitry and shed light on how the brain modulates and integrates activity in the face of altered sensory experience.},
	Author = {Krahe, Thomas E and Guido, William},
	Date-Added = {2013-05-28 18:16:18 +0000},
	Date-Modified = {2013-05-28 18:18:12 +0000},
	Doi = {10.1523/JNEUROSCI.1173-11.2011},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Thalamic Nuclei; visual system; mouse; LGN; Patch-Clamp Techniques; development; plasticity; Sensory Deprivation; homeostatic plasticity},
	Mesh = {Analysis of Variance; Animals; Electric Stimulation; Electrophysiology; Excitatory Postsynaptic Potentials; Geniculate Bodies; Mice; Miniature Postsynaptic Potentials; Neuronal Plasticity; Neurons; Photic Stimulation; Sensory Deprivation; Vision, Monocular; Visual Pathways},
	Month = {May},
	Number = {18},
	Pages = {6842-9},
	Pmc = {PMC3319043},
	Pmid = {21543614},
	Pst = {ppublish},
	Title = {Homeostatic plasticity in the visual thalamus by monocular deprivation},
	Volume = {31},
	Year = {2011},
	File = {papers/Krahe_JNeurosci2011.pdf}}

@article{Dilger:2011,
	Abstract = {In developing cells of the mouse dorsal lateral geniculate nucleus (dLGN), synaptic responses evoked by optic tract (OT) stimulation give rise to long-lasting, high-amplitude depolarizations known as plateau potentials. These events are mediated by L-type Ca2+ channels and occur during early postnatal life, a time when retinogeniculate connections are remodelling. To better understand the relationship between L-type activity and dLGN development we used an in vitro thalamic slice preparation which preserves the retinal connections and intrinsic circuitry in dLGN and examined how synaptic responses evoked by OT stimulation lead to the activation of plateau potentials. By varying the strength and temporal frequency of OT stimulation we identified at least three factors that contribute to the developmental regulation of plateau activity: the degree of retinal convergence, the temporal pattern of retinal stimulation and the emergence of feed-forward inhibition. Before natural eye opening (postnatal day 14), the excitatory synaptic responses of relay cells receiving multiple retinal inputs summated in both the spatial and temporal domains to produce depolarizations sufficient to activate L-type activity. After eye opening, when inhibitory responses are fully developed, plateau activity was rarely evoked even with high temporal rates of OT stimulation. When the bulk of this inhibition was blocked by bath application of bicuculline, the incidence of plateau activity increased significantly. We also made use of a transgenic mouse that lacks the β3 subunit of the L-type Ca2+ channel. These mutants have far fewer membrane-bound Ca2+ channels and attenuated L-type activity. In β3 nulls, L-type plateau activity was rarely observed even at young ages when plateau activity prevails. Thus, in addition to the changing patterns of synaptic connectivity and retinal activity, the expression of L-type Ca2+ channels is a requisite component in the manifestation of plateau activity.},
	Author = {Dilger, Emily K and Shin, Hee-Sup and Guido, William},
	Date-Added = {2013-05-28 18:14:49 +0000},
	Date-Modified = {2013-05-28 18:16:06 +0000},
	Doi = {10.1113/jphysiol.2010.202499},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {Thalamic Nuclei; visual system; mouse; LGN; Patch-Clamp Techniques; Voltage-Gated; Calcium Channels; development; synapse formation; plasticity},
	Mesh = {Animals; Animals, Newborn; Electric Stimulation; Evoked Potentials; Geniculate Bodies; Mice; Mice, Inbred C57BL; Mice, Transgenic; Synapses; Synaptic Potentials; Visual Pathways},
	Month = {Feb},
	Number = {Pt 4},
	Pages = {919-37},
	Pmc = {PMC3060370},
	Pmid = {21173075},
	Pst = {ppublish},
	Title = {Requirements for synaptically evoked plateau potentials in relay cells of the dorsal lateral geniculate nucleus of the mouse},
	Volume = {589},
	Year = {2011},
	File = {papers/Dilger_JPhysiol2011.pdf}}

@article{Bender:2003a,
	Abstract = {The excitatory feedforward projection from layer (L) 4 to L2/3 in rat primary somatosensory (S1) cortex exhibits precise, columnar topography that is critical for columnar processing of whisker inputs. Here, we characterize the development of axonal topography in this projection using single-cell reconstructions in S1 slices. In the mature projection [postnatal day (P) 14-26], axons of L4 cells extending into L2/3 were confined almost entirely to the home barrel column, consistent with previous results. At younger ages (P8-11), however, axonal topography was significantly less columnar, with a large proportion of branches innervating neighboring barrel columns representing adjacent whisker rows. Mature topography developed from this initial state by targeted axonal growth within the home column and by growth of barrel columns themselves. Raising rats with all or a subset of whiskers plucked from P8-9, manipulations that induce reorganization of functional whisker maps and synaptic depression at L4 to L2/3 synapses, did not alter normal anatomical development of L4 to L2/3 axons. Thus, development of this projection does not require normal sensory experience after P8, and deprivation-induced reorganization of whisker maps at this age is unlikely to involve physical remodeling of L4 to L2/3 axons.},
	Author = {Bender, Kevin J and Rangel, Juliana and Feldman, Daniel E},
	Date-Added = {2013-05-28 17:39:15 +0000},
	Date-Modified = {2013-05-28 17:41:23 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {patterning; Somatosensory Cortex; barrels; axon guidance; synapse formation; Neocortex; development},
	Mesh = {Action Potentials; Age Factors; Animals; Axons; Brain Mapping; Dendrites; Electric Stimulation; Lysine; Membrane Potentials; Neuronal Plasticity; Neurons; Patch-Clamp Techniques; Rats; Rats, Long-Evans; Sensory Deprivation; Somatosensory Cortex; Vibrissae},
	Month = {Sep},
	Number = {25},
	Pages = {8759-70},
	Pmc = {PMC3066032},
	Pmid = {14507976},
	Pst = {ppublish},
	Title = {Development of columnar topography in the excitatory layer 4 to layer 2/3 projection in rat barrel cortex},
	Volume = {23},
	Year = {2003},
	File = {papers/Bender_JNeurosci2003a.pdf}}

@article{Kovacs:2007,
	Abstract = {A key feature of memory processes is to link different input signals by association and to preserve this coupling at the level of synaptic connections. Late-phase long-term potentiation (L-LTP), a form of synaptic plasticity thought to encode long-term memory, requires gene transcription and protein synthesis. In this study, we report that a recently cloned coactivator of cAMP-response element-binding protein (CREB), called transducer of regulated CREB activity 1 (TORC1), contributes to this process by sensing the coincidence of calcium and cAMP signals in neurons and by converting it into a transcriptional response that leads to the synthesis of factors required for enhanced synaptic transmission. We provide evidence that TORC1 is involved in L-LTP maintenance at the Schaffer collateral-CA1 synapses in the hippocampus.},
	Author = {Kov{\'a}cs, Kriszti{\'a}n A and Steullet, Pascal and Steinmann, Myriam and Do, Kim Q and Magistretti, Pierre J and Halfon, Olivier and Cardinaux, Jean-Ren{\'e}},
	Date-Added = {2013-05-28 16:59:05 +0000},
	Date-Modified = {2013-05-28 17:00:31 +0000},
	Doi = {10.1073/pnas.0607524104},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {coincidence detector; plasticity; synapses; learning; memory; in vitro},
	Mesh = {Active Transport, Cell Nucleus; Animals; Calcineurin; Cyclic AMP; Cyclic AMP Response Element-Binding Protein; Hippocampus; Long-Term Potentiation; Male; Mice; Neurons; RNA, Messenger; Rats; Synapses; Trans-Activators; Transcription Factors},
	Month = {Mar},
	Number = {11},
	Pages = {4700-5},
	Pmc = {PMC1838663},
	Pmid = {17360587},
	Pst = {ppublish},
	Title = {TORC1 is a calcium- and cAMP-sensitive coincidence detector involved in hippocampal long-term synaptic plasticity},
	Volume = {104},
	Year = {2007},
	File = {papers/Kovács_ProcNatlAcadSciUSA2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0607524104}}

@article{Fino:2010,
	Abstract = {Corticostriatal projections constitute the main input to the basal ganglia, an ensemble of interconnected subcortical nuclei involved in procedural learning. Thus, long-term plasticity at corticostriatal synapses would provide a basic mechanism for the function of basal ganglia in learning and memory. We had previously reported the existence of a corticostriatal anti-Hebbian spike timing-dependent plasticity (STDP) at synapses onto striatal output neurons, the medium-sized spiny neurons. Here, we show that the blockade of GABAergic transmission reversed the time dependence of corticostriatal STDP. We explored the receptors and signalling mechanisms involved in the corticostriatal STDP. Although classical models for STDP propose NMDA receptors as the unique coincidence detector, the involvement of multiple coincidence detectors has also been demonstrated. Here, we show that corticostriatal STDP depends on distinct coincidence detectors. Specifically, long-term potentiation is dependent on NMDA receptor activation, while long-term depression requires distinct coincidence detectors: the phospholipase Cbeta (PLCbeta) and the inositol-trisphosphate receptor (IP3R)-gated calcium stores. Furthermore, we found that PLCbeta activation is controlled by group-I metabotropic glutamate receptors, type-1 muscarinic receptors and voltage-sensitive calcium channel activities. Activation of PLCbeta and IP3Rs leads to robust retrograde endocannabinoid signalling mediated by 2-arachidonoyl-glycerol and cannabinoid CB1 receptors. Interestingly, the same coincidence detectors govern the corticostriatal anti-Hebbian STDP and the Hebbian STDP reported at cortical synapses. Therefore, LTP and LTD induced by STDP at corticostriatal synapses are mediated by independent signalling mechanisms, each one being controlled by distinct coincidence detectors.},
	Author = {Fino, Elodie and Paille, Vincent and Cui, Yihui and Morera-Herreras, Teresa and Deniau, Jean-Michel and Venance, Laurent},
	Date-Added = {2013-05-28 16:54:37 +0000},
	Date-Modified = {2013-05-28 16:58:07 +0000},
	Doi = {10.1113/jphysiol.2010.188466},
	Journal = {J Physiol},
	Journal-Full = {The Journal of physiology},
	Keywords = {coincidence detector; currOpinRvw; synapses; plasticity},
	Mesh = {Animals; Arachidonic Acids; Basal Ganglia; Calcium Channels; Cerebral Cortex; Endocannabinoids; Enzyme Activation; Enzyme Inhibitors; Excitatory Postsynaptic Potentials; Glycerides; Inositol 1,4,5-Trisphosphate Receptors; Neural Pathways; Neuronal Plasticity; Neurotransmitter Agents; Phospholipase C beta; Rats; Receptor, Cannabinoid, CB1; Receptor, Muscarinic M1; Receptors, Metabotropic Glutamate; Receptors, N-Methyl-D-Aspartate; Signal Transduction; Synapses; Time Factors; gamma-Aminobutyric Acid},
	Month = {Aug},
	Number = {Pt 16},
	Pages = {3045-62},
	Pmc = {PMC2956944},
	Pmid = {20603333},
	Pst = {ppublish},
	Title = {Distinct coincidence detectors govern the corticostriatal spike timing-dependent plasticity},
	Volume = {588},
	Year = {2010},
	File = {papers/Fino_JPhysiol2010.pdf}}

@article{Bender:2006,
	Abstract = {Many cortical synapses exhibit spike timing-dependent plasticity (STDP) in which the precise timing of presynaptic and postsynaptic spikes induces synaptic strengthening [long-term potentiation (LTP)] or weakening [long-term depression (LTD)]. Standard models posit a single, postsynaptic, NMDA receptor-based coincidence detector for LTP and LTD components of STDP. We show instead that STDP at layer 4 to layer 2/3 synapses in somatosensory (S1) cortex involves separate calcium sources and coincidence detection mechanisms for LTP and LTD. LTP showed classical NMDA receptor dependence. LTD was independent of postsynaptic NMDA receptors and instead required group I metabotropic glutamate receptors and calcium from voltage-sensitive channels and IP3 receptor-gated stores. Downstream of postsynaptic calcium, LTD required retrograde endocannabinoid signaling, leading to presynaptic LTD expression, and also required activation of apparently presynaptic NMDA receptors. These LTP and LTD mechanisms detected firing coincidence on approximately 25 and approximately 125 ms time scales, respectively, and combined to implement the overall STDP rule. These findings indicate that STDP is not a unitary process and suggest that endocannabinoid-dependent LTD may be relevant to cortical map plasticity.},
	Author = {Bender, Vanessa A and Bender, Kevin J and Brasier, Daniel J and Feldman, Daniel E},
	Date-Added = {2013-05-28 16:31:50 +0000},
	Date-Modified = {2013-05-28 16:32:27 +0000},
	Doi = {10.1523/JNEUROSCI.0176-06.2006},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {coincidence detector; learning; memory; synapses; plasticity; currOpinRvw},
	Mesh = {Action Potentials; Animals; Dizocilpine Maleate; Neuronal Plasticity; Piperidines; Pyrazoles; Rats; Rats, Long-Evans; Receptors, N-Methyl-D-Aspartate; Somatosensory Cortex; Time Factors},
	Month = {Apr},
	Number = {16},
	Pages = {4166-77},
	Pmc = {PMC3071735},
	Pmid = {16624937},
	Pst = {ppublish},
	Title = {Two coincidence detectors for spike timing-dependent plasticity in somatosensory cortex},
	Volume = {26},
	Year = {2006},
	File = {papers/Bender_JNeurosci2006.pdf}}

@article{Duguid:2006,
	Abstract = {Long-term plasticity typically relies on postsynaptic NMDA receptors to detect the coincidence of pre- and postsynaptic activity. Recent studies, however, have revealed forms of plasticity that depend on coincidence detection by presynaptic NMDA receptors. In the amygdala, cortical afferent associative presynaptic long-term potentiation (LTP) requires activation of presynaptic NMDA receptors by simultaneous thalamic and cortical afferents. Surprisingly, both types of afferent can also undergo postsynaptically induced NMDA-receptor-dependent LTP. In the neocortex, spike-timing-dependent long-term depression (LTD) requires simultaneous activation of presynaptic NMDA autoreceptors and retrograde signalling by endocannabinoids. In cerebellar LTD, presynaptic NMDA receptor activation suggests that similar presynaptic mechanisms may exist. Recent studies also indicate the existence of presynaptic coincidence detection that is independent of NMDA receptors, suggesting that such mechanisms have a widespread role in plasticity.},
	Author = {Duguid, Ian and Sj{\"o}str{\"o}m, Per Jesper},
	Date-Added = {2013-05-28 16:05:06 +0000},
	Date-Modified = {2013-05-28 16:06:24 +0000},
	Doi = {10.1016/j.conb.2006.05.008},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Keywords = {currOpinRvw; synapses; plasticity; coincidence detector},
	Mesh = {Action Potentials; Animals; Brain; Humans; Long-Term Potentiation; Neural Pathways; Neuronal Plasticity; Presynaptic Terminals; Receptors, N-Methyl-D-Aspartate; Signal Transduction; Synaptic Transmission; Time Factors},
	Month = {Jun},
	Number = {3},
	Pages = {312-22},
	Pmid = {16713246},
	Pst = {ppublish},
	Title = {Novel presynaptic mechanisms for coincidence detection in synaptic plasticity},
	Volume = {16},
	Year = {2006},
	File = {papers/Duguid_CurrOpinNeurobiol2006.pdf}}

@article{Wree:1983,
	Abstract = {The cerebral cortex of the albino mouse was examined by means of a quantitative method. An image analyzer was used in conjunction with an automatic scanning procedure to determine the grey level index in Nissl-stained sections. Computer plots of various ranges of grey level indices enabled delineation of cortical areas, from which cortical maps were graphically reconstructed. The cortical areal pattern is, in some regions, similar to the commonly used map of Caviness (1975) but differs considerably in other regions, especially in the temporal one. Furthermore, the primary visual cortex of the mouse was shown to be composed of two distinct cytoarchitectonic areas. The results of the study are discussed with respect to the literature on anatomical and functional localizations in the mouse cerebral cortex.},
	Author = {Wree, A and Zilles, K and Schleicher, A},
	Date-Added = {2013-04-23 18:06:37 +0000},
	Date-Modified = {2013-04-23 18:07:00 +0000},
	Journal = {Anat Embryol (Berl)},
	Journal-Full = {Anatomy and embryology},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics; mouse},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Computers; Male; Mice; Temporal Lobe; Visual Cortex},
	Number = {3},
	Pages = {333-53},
	Pmid = {6869850},
	Pst = {ppublish},
	Title = {A quantitative approach to cytoarchitectonics. VIII. The areal pattern of the cortex of the albino mouse},
	Volume = {166},
	Year = {1983},
	File = {papers/Wree_AnatEmbryol(Berl)1983.pdf}}

@article{Campi:2010,
	Abstract = {In this study we examine and describe the neuroanatomical organization of sensory cortex in four rodents: laboratory Norway rats (Long Evans; Rattus norvegicus), wild-caught Norway rats (Rattus norvegicus), wild-caught California ground squirrels (Spermophilus beecheyi), and wild-caught Eastern gray squirrels (Sciurus carolinensis). Specifically, we examined the myeloarchitecture and cytochrome oxidase reactivity for several well-identified areas in visual cortex (areas 17, 18, and 19), somatosensory cortex (areas S1, S2 and PV), and auditory cortex [areas A1+AAF (R) and TA] and compared the percentage of dorsolateral cortex devoted to each of these areas. Our results demonstrate that squirrels have a larger mean percentage of dorsolateral cortex devoted to visual areas than rats. The difference is due to the greater percentage of cortex devoted to known areas such as area 17 and area 18 and not simply to a difference in the number of visual areas, which ultimately makes this distinction even more pronounced. Furthermore, both rat groups have a larger percentage of the dorsolateral cortex devoted to somatosensory and auditory cortical areas. Differences within groups were also observed. The arboreal squirrel had a larger mean percentage of dorsolateral cortex devoted to areas 17 and 18 compared with the terrestrial squirrel. The laboratory Norway rat had a larger percentage of dorsolateral cortex devoted to both somatosensory and auditory areas than the wild-caught Norway rat. Our results indicate that differences in sensory apparatus, use of sensory systems, and niche are reflected in the organization and size of cortical areas.},
	Author = {Campi, Katharine L and Krubitzer, Leah},
	Date-Added = {2013-04-23 18:04:55 +0000},
	Date-Modified = {2013-04-23 18:05:02 +0000},
	Doi = {10.1002/cne.22466},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Mesh = {Analysis of Variance; Animals; Animals, Laboratory; Animals, Wild; Body Weight; Brain Mapping; Circadian Rhythm; Functional Laterality; Life Style; Myelin Sheath; Rats; Rats, Long-Evans; Sciuridae; Species Specificity; Visual Cortex},
	Month = {Nov},
	Number = {22},
	Pages = {4491-512},
	Pmc = {PMC3432265},
	Pmid = {20886618},
	Pst = {ppublish},
	Title = {Comparative studies of diurnal and nocturnal rodents: differences in lifestyle result in alterations in cortical field size and number},
	Volume = {518},
	Year = {2010},
	File = {papers/Campi_JCompNeurol2010.pdf}}

@article{Campi:2011,
	Abstract = {In this study we examine the size of primary sensory areas in the neocortex and the cellular composition of area 17/V1 in three rodent groups: laboratory nocturnal Norway rats (Long-Evans; Rattus norvegicus), wild-caught nocturnal Norway rats (R. norvegicus), and laboratory diurnal Nile grass rats (Arvicanthis niloticus). Specifically, we used areal measures of myeloarchitecture of the primary sensory areas to compare area size and the isotropic fractionator method to estimate the number of neurons and nonneurons in area 17 in each species. Our results demonstrate that the percentage of cortex devoted to area 17 is significantly greater and the percentage of cortex devoted to S1 is significantly smaller in the diurnal Nile grass rat compared with the nocturnal Norway rat groups. Further, the laboratory rodent groups have a greater percentage of cortex devoted to auditory cortex compared with the wild-caught group. We also demonstrate that wild-caught rats have a greater density of neurons in area 17 compared to laboratory-reared animals. However, there were no other clear cellular composition differences in area 17 or differences in the percentage of brain weight devoted to area 17 between nocturnal and diurnal rats. Thus, there are differences in primary sensory area size between diurnal versus nocturnal and laboratory versus wild-caught rat groups and cellular density between wild-caught and laboratory rat groups. Our results demonstrate that the differences in the size and cellular composition of cortical areas do not fit with what would be expected based on brain scaling differences alone, and have a consistent relationship with lifestyle and sensory morphology.},
	Author = {Campi, Katharine L and Collins, Christine E and Todd, William D and Kaas, Jon and Krubitzer, Leah},
	Date-Added = {2013-04-23 18:03:41 +0000},
	Date-Modified = {2013-04-23 18:04:05 +0000},
	Doi = {10.1159/000324862},
	Journal = {Brain Behav Evol},
	Journal-Full = {Brain, behavior and evolution},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics; review literature},
	Mesh = {Adaptation, Ocular; Animals; Animals, Domestic; Circadian Rhythm; Dark Adaptation; Female; Male; Neurons; Rats; Rats, Long-Evans; Species Specificity; Visual Cortex; Visual Pathways; Visual Perception},
	Number = {2},
	Pages = {116-30},
	Pmc = {PMC3094678},
	Pmid = {21525748},
	Pst = {ppublish},
	Title = {Comparison of area 17 cellular composition in laboratory and wild-caught rats including diurnal and nocturnal species},
	Volume = {77},
	Year = {2011},
	File = {papers/Campi_BrainBehavEvol2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1159/000324862}}

@article{Caviness:1975,
	Abstract = {The neocortex of the normal mouse has been subdivided into architectonic fields on the basis of its cellular and fiber patterns. The map of medial, retrohippocampal, frontal and insular regions is little different from that of Brodmann as modified in minor ways by Krieg. The map of parietal, occipital and temporal regions follows closely the major rearrangements introduced to Brodmann's map by Krieg. Krieg's map has been modified to give individual status to the barrel fields and to disignate occipital fields around the full circumference of field 17, and temporal fields circumferentially around field 41.},
	Author = {Caviness, Jr, V S},
	Date-Added = {2013-04-23 17:17:42 +0000},
	Date-Modified = {2013-04-23 17:17:54 +0000},
	Doi = {10.1002/cne.901640207},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Frontal Lobe; Hybridization, Genetic; Mice; Mice, Inbred Strains; Occipital Lobe; Parietal Lobe; Temporal Lobe},
	Month = {Nov},
	Number = {2},
	Pages = {247-63},
	Pmid = {1184785},
	Pst = {ppublish},
	Title = {Architectonic map of neocortex of the normal mouse},
	Volume = {164},
	Year = {1975},
	File = {papers/Caviness_JCompNeurol1975.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.901640207}}

@article{Reep:2009,
	Abstract = {A rodent model of directed attention has been developed based upon behavioral analysis of contralateral neglect, pharmacological manipulations, and anatomical analysis of neural circuitry. In each of these three domains the rodent model exhibits striking similarities to humans. We hypothesize that there is a specific thalamo-cortical-basal ganglia network that subserves spatial attentional functions. Key components of this network are medial agranular and posterior parietal cortex, dorsocentral striatum, and the lateral posterior thalamic nucleus. Several issues need to be addressed before we can hope to realistically understand or model the functions of this network. Among these are the roles of medial versus lateral posterior parietal cortex; cholinergic mechanisms in attention; interhemispheric interactions; the role of synchronous firing at the cortical, striatal, and thalamic levels; interactions between cortical and thalamic projections to the striatum; interactions between cortical and nigral inputs to the thalamus; the role of collicular inputs to the lateral posterior thalamic nucleus; the role of cerebral cortex versus superior colliculus in driving the motor output expressed as orienting behavior during directed attention; the extent to which the circuitry we describe for directed attention also plays a role in other forms of attention.},
	Author = {Reep, Roger L and Corwin, James V},
	Date-Added = {2013-04-17 21:10:26 +0000},
	Date-Modified = {2014-09-16 16:12:55 +0000},
	Doi = {10.1016/j.nlm.2008.08.010},
	Journal = {Neurobiol Learn Mem},
	Journal-Full = {Neurobiology of learning and memory},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics; rat; Posterior parietal cortex; ppc; Spatial Behavior; navigation; Motor Activity; grid cells; Decision Making; goal directed behavior; retrosplenial cortex},
	Mesh = {Acetylcholine; Animals; Attention; Basal Ganglia; Cortical Synchronization; Disease Models, Animal; Functional Laterality; Humans; Motor Activity; Neural Pathways; Neurons; Orientation; Parietal Lobe; Perceptual Disorders; Tectum Mesencephali; Thalamus},
	Month = {Feb},
	Number = {2},
	Pages = {104-13},
	Pmid = {18824116},
	Pst = {ppublish},
	Title = {Posterior parietal cortex as part of a neural network for directed attention in rats},
	Volume = {91},
	Year = {2009},
	File = {papers/Reep_NeurobiolLearnMem2009.pdf}}

@article{Kaas:2011,
	Abstract = {In Prosimian primates, New World monkeys, and Old World monkeys microstimulation with half second trains of electrical pulses identifies separate zones in posterior parietal cortex (PPC) where reaching, defensive, grasping, and other complex movements can be evoked. Each functional zone receives a different pattern of visual and somatosensory inputs, and projects preferentially to functionally matched parts of motor and premotor cortex. As PPC is a relatively small portion of cortex in most mammals, including the close relatives of primates, we suggest that a larger, more significant PPC emerged with the first primates as a region where several ethologically relevant behaviors could be initiated by sensory and intrinsic signals, and mediated via connections with premotor and motor cortex. While several classes of PPC modules appear to be retained by all primates, elaboration and differentiation of these modules likely occurred in some primates, especially humans.},
	Author = {Kaas, Jon H and Gharbawie, Omar A and Stepniewska, Iwona},
	Date-Added = {2013-04-17 21:08:08 +0000},
	Date-Modified = {2013-04-23 17:56:33 +0000},
	Doi = {10.3389/fnana.2011.00034},
	Journal = {Front Neuroanat},
	Journal-Full = {Frontiers in neuroanatomy},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Pages = {34},
	Pmc = {PMC3116136},
	Pmid = {21716641},
	Pst = {ppublish},
	Title = {The organization and evolution of dorsal stream multisensory motor pathways in primates},
	Volume = {5},
	Year = {2011},
	File = {papers/Kaas_FrontNeuroanat2011.pdf}}

@book{Chalupa:2008,
	Address = {Cambridge, Mass.},
	Annote = {LDR    01428cam  2200337 a 4500
001    15090115
005    20090828092700.0
008    071121s2008    mauaf    b    001 0 eng  
906    $a7$bcbc$corignew$d1$eecip$f20$gy-gencatlg
925 0  $aacquire$b2 shelf copies$xpolicy default
955    $ajb04 2007-11-21$ijb04 2007-11-21$ejb04 2007-11-21 to Dewey$aaa07 2007-11-29$aps04 2008-07-08 1 copy rec'd., to CIP ver.$fsc02 2008-07-24 Z-CipVer$gsc02 2008-07-24 to BCCD$alg08 2008-09-09 copy 2 added
010    $a  2007047445
015    $aGBA889303$2bnb
016 7  $a014669647$2Uk
020    $a9780262033817 (hardcover : alk. paper)
020    $a026203381X (hardcover : alk. paper)
035    $a(OCoLC)ocn182662502
035    $a(OCoLC)182662502
040    $aDLC$cDLC$dBTCTA$dBAKER$dYDXCP$dOCLCG$dC#P$dUKM$dDLC
050 00 $aQL737.R6$bE94 2008
082 00 $a573.8/819353$222
245 00 $aEye, retina, and visual system of the mouse /$cedited by Leo M. Chalupa and Robert W. Williams.
260    $aCambridge, Mass. :$bMIT Press,$cc2008.
300    $axii, 754 p., [48] p. of plates :$bill. (some col.) ;$c29 cm.
504    $aIncludes bibliographical references and index.
650  0 $aMice$xSense organs.
650  0 $aEye.
650  0 $aVisual pathways.
700 1  $aChalupa, Leo M.
700 1  $aWilliams, Robert W.,$d1952-
856 41 $3Table of contents only$uhttp://www.loc.gov/catdir/toc/ecip085/2007047445.html
},
	Author = {Chalupa, Leo M and Williams, Robert W.},
	Call-Number = {QL737.R6},
	Date-Added = {2013-04-17 20:54:07 +0000},
	Date-Modified = {2013-04-23 17:56:13 +0000},
	Dewey-Call-Number = {573.8/819353},
	Genre = {Mice},
	Isbn = {9780262033817 (hardcover : alk. paper)},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Library-Id = {2007047445},
	Publisher = {MIT Press},
	Title = {Eye, retina, and visual system of the mouse},
	Url = {http://www.loc.gov/catdir/toc/ecip085/2007047445.html},
	Year = {2008},
	Bdsk-Url-1 = {http://www.loc.gov/catdir/toc/ecip085/2007047445.html}}

@book{Paxinos:1995,
	Address = {San Diego},
	Annote = {LDR    01198cam  2200313 a 4500
001    4906797
005    20030709200427.0
008    940621s1995    caua     b    001 0 eng  
035    $9(DLC)   94026442
906    $a7$bcbc$corignew$d1$eocip$f19$gy-gencatlg
955    $apc05 to ja00 06-21-94; jb09 06-21-94; jb02 06-23-94; aa07 06-23-94; CIP ver. pv06 12-08-94
010    $a   94026442 
020    $a0125476353 (acid-free paper)
040    $aDLC$cDLC$dDLC
050 00 $aQL937$b.R33 1995
082 00 $a599.32/33$220
245 04 $aThe rat nervous system /$cedited by George Paxinos.
250    $a2nd ed.
260    $aSan Diego :$bAcademic Press,$cc1995.
300    $axvii, 1136 p. :$bill. ;$c29 cm.
504    $aIncludes bibliographical references and index.
650  0 $aRats$xAnatomy.
650  0 $aBrain$xAnatomy.
650  0 $aRats$xNervous system.
700 1  $aPaxinos, George,$d1944-
856 42 $3Publisher description$uhttp://www.loc.gov/catdir/description/els032/94026442.html
856 41 $3Table of contents$uhttp://www.loc.gov/catdir/toc/els032/94026442.html
920    $a** LC HAS REQ'D # OF SHELF COPIES **
991    $bc-GenColl$hQL937$i.R33 1995$p00055111315$tCopy 1$wBOOKS
},
	Author = {Paxinos, George},
	Call-Number = {QL937},
	Date-Added = {2013-04-17 20:45:25 +0000},
	Date-Modified = {2013-04-23 17:55:51 +0000},
	Dewey-Call-Number = {599.32/33},
	Edition = {2nd ed},
	Genre = {Rats},
	Isbn = {0125476353 (acid-free paper)},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Library-Id = {94026442},
	Publisher = {Academic Press},
	Title = {The rat nervous system},
	Url = {http://www.loc.gov/catdir/description/els032/94026442.html},
	Year = {1995},
	Bdsk-Url-1 = {http://www.loc.gov/catdir/description/els032/94026442.html}}

@book{Paxinos:2004,
	Address = {Amsterdam},
	Annote = {LDR    01232cam  2200289 a 4500
001    13582666
005    20041223075507.0
008    040504s2004    ne a     b    001 0 eng  
906    $a7$bcbc$corigcop$d2$encip$f20$gy-gencatlg
925 0  $aacquire$b2 shelf copies$xpolicy default
955    $apv21 2004-05-04 Preprocessor two copies to ASCD$ajc41 2004-05-11 sent to Bio-Ag$ajb00 2004-05-12 bk. rec.$cjb17 2004-06-22$djb09 2004-06-30$ejb18 2004-07-28 Copies 1-2 to Dewey$aaa07 2004-07-29
010    $a  2004270372
020    $a0125476388 (alk. paper)
040    $aDLC$cDLC$dDLC
050 00 $aQL937$b.R33 2004
082 00 $a573.8/19352$222
245 04 $aThe rat nervous system /$cedited by George Paxinos.
250    $a3rd ed.
260    $aAmsterdam ;$aBoston :$bElsevier Academic Press,$cc2004.
300    $axvii, 1309 p. :$bill. (some col.) ;$c29 cm.
504    $aIncludes bibliographical references and index.
650  0 $aRats$xAnatomy.
650  0 $aBrain$xAnatomy.
650  0 $aRats$xNervous system.
700 1  $aPaxinos, George,$d1944-
856 41 $3Table of contents$uhttp://www.loc.gov/catdir/toc/els051/2004270372.html
856 42 $3Publisher description$uhttp://www.loc.gov/catdir/description/els051/2004270372.html
},
	Author = {Paxinos, George},
	Call-Number = {QL937},
	Date-Added = {2013-04-17 20:45:19 +0000},
	Date-Modified = {2013-04-23 17:55:42 +0000},
	Dewey-Call-Number = {573.8/19352},
	Edition = {3rd ed},
	Genre = {Rats},
	Isbn = {0125476388 (alk. paper)},
	Keywords = {neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Library-Id = {2004270372},
	Publisher = {Elsevier Academic Press},
	Title = {The rat nervous system},
	Url = {http://www.loc.gov/catdir/toc/els051/2004270372.html},
	Year = {2004},
	Bdsk-Url-1 = {http://www.loc.gov/catdir/toc/els051/2004270372.html}}

@article{Lim:2012,
	Abstract = {We have mapped intracortical activity in vivo independent of sensory input using arbitrary point channelrhodopsin-2 (ChR2) stimulation and regional voltage sensitive dye imaging in B6.Cg-Tg (Thy1-COP4/EYFP)18Gfng/J transgenic mice. Photostimulation of subsets of deep layer pyramidal neurons within forelimb, barrel, or visual primary sensory cortex led to downstream cortical maps that were dependent on synaptic transmission and were similar to peripheral sensory stimulation. ChR2-evoked maps confirmed homotopic connections between hemispheres and intracortical sensory and motor cortex connections. This ability of optogentically activated subpopulations of neurons to drive appropriate downstream maps suggests that mechanisms exist to allow prototypical cortical maps to self-assemble from the stimulation of neuronal subsets. Using this principle of map self-assembly, we employed ChR2 point stimulation to map connections between cortical areas that are not selectively activated by peripheral sensory stimulation or behavior. Representing the functional cortical regions as network nodes, we identified asymmetrical connection weights in individual nodes and identified the parietal association area as a network hub. Furthermore, we found that the strength of reciprocal intracortical connections between primary and secondary sensory areas are unequal, with connections from primary to secondary sensory areas being stronger than the reciprocal.},
	Author = {Lim, Diana H and Mohajerani, Majid H and Ledue, Jeffrey and Boyd, Jamie and Chen, Shangbin and Murphy, Timothy H},
	Date-Added = {2013-04-01 16:18:07 +0000},
	Date-Modified = {2013-04-01 16:18:44 +0000},
	Doi = {10.3389/fncir.2012.00011},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {downloads},
	Pages = {11},
	Pmc = {PMC3304170},
	Pmid = {22435052},
	Pst = {ppublish},
	Title = {In vivo Large-Scale Cortical Mapping Using Channelrhodopsin-2 Stimulation in Transgenic Mice Reveals Asymmetric and Reciprocal Relationships between Cortical Areas},
	Volume = {6},
	Year = {2012},
	File = {papers/Lim_FrontNeuralCircuits2012.pdf}}

@article{Hong:2012,
	Abstract = {Neurons are interconnected with extraordinary precision to assemble a functional nervous system. Compared to axon guidance, far less is understood about how individual pre- and postsynaptic partners are matched. To ensure the proper relay of olfactory information in the fruitfly Drosophila, axons of ∼50 classes of olfactory receptor neurons (ORNs) form one-to-one connections with dendrites of ∼50 classes of projection neurons (PNs). Here, using genetic screens, we identified two evolutionarily conserved, epidermal growth factor (EGF)-repeat containing transmembrane Teneurin proteins, Ten-m and Ten-a, as synaptic-partner-matching molecules between PN dendrites and ORN axons. Ten-m and Ten-a are highly expressed in select PN-ORN matching pairs. Teneurin loss- and gain-of-function cause specific mismatching of select ORNs and PNs. Finally, Teneurins promote homophilic interactions in vitro, and Ten-m co-expression in non-partner PNs and ORNs promotes their ectopic connections in vivo. We propose that Teneurins instruct matching specificity between synaptic partners through homophilic attraction.},
	Author = {Hong, Weizhe and Mosca, Timothy J and Luo, Liqun},
	Date-Added = {2013-04-01 16:18:07 +0000},
	Date-Modified = {2013-04-01 16:18:44 +0000},
	Doi = {10.1038/nature10926},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Axons; Drosophila Proteins; Drosophila melanogaster; Olfactory Pathways; Olfactory Receptor Neurons; Protein Binding; RNA Interference; Receptors, Cell Surface; Smell; Synapses; Tenascin},
	Month = {Apr},
	Number = {7393},
	Pages = {201-7},
	Pmc = {PMC3345284},
	Pmid = {22425994},
	Pst = {epublish},
	Title = {Teneurins instruct synaptic partner matching in an olfactory map},
	Volume = {484},
	Year = {2012},
	File = {papers/Hong_Nature2012.pdf}}

@article{Derecki:2012a,
	Abstract = {Rett syndrome is an X-linked autism spectrum disorder. The disease is characterized in most cases by mutation of the MECP2 gene, which encodes a methyl-CpG-binding protein. Although MECP2 is expressed in many tissues, the disease is generally attributed to a primary neuronal dysfunction. However, as shown recently, glia, specifically astrocytes, also contribute to Rett pathophysiology. Here we examine the role of another form of glia, microglia, in a murine model of Rett syndrome. Transplantation of wild-type bone marrow into irradiation-conditioned Mecp2-null hosts resulted in engraftment of brain parenchyma by bone-marrow-derived myeloid cells of microglial phenotype, and arrest of disease development. However, when cranial irradiation was blocked by lead shield, and microglial engraftment was prevented, disease was not arrested. Similarly, targeted expression of MECP2 in myeloid cells, driven by Lysm(cre) on an Mecp2-null background, markedly attenuated disease symptoms. Thus, through multiple approaches, wild-type Mecp2-expressing microglia within the context of an Mecp2-null male mouse arrested numerous facets of disease pathology: lifespan was increased, breathing patterns were normalized, apnoeas were reduced, body weight was increased to near that of wild type, and locomotor activity was improved. Mecp2(+/-) females also showed significant improvements as a result of wild-type microglial engraftment. These benefits mediated by wild-type microglia, however, were diminished when phagocytic activity was inhibited pharmacologically by using annexin V to block phosphatydilserine residues on apoptotic targets, thus preventing recognition and engulfment by tissue-resident phagocytes. These results suggest the importance of microglial phagocytic activity in Rett syndrome. Our data implicate microglia as major players in the pathophysiology of this devastating disorder, and suggest that bone marrow transplantation might offer a feasible therapeutic approach for it.},
	Author = {Derecki, No{\"e}l C and Cronk, James C and Lu, Zhenjie and Xu, Eric and Abbott, Stephen B G and Guyenet, Patrice G and Kipnis, Jonathan},
	Date-Added = {2013-04-01 16:18:07 +0000},
	Date-Modified = {2013-04-01 16:18:44 +0000},
	Doi = {10.1038/nature10907},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Annexin A5; Apoptosis; Body Weight; Bone Marrow Transplantation; Brain; Disease Models, Animal; Disease Progression; Female; Insulin-Like Growth Factor I; Locomotion; Male; Methyl-CpG-Binding Protein 2; Mice; Mice, Inbred C57BL; Microglia; Phagocytosis; Phosphatidylserines; Respiration; Rett Syndrome; Rotarod Performance Test},
	Month = {Apr},
	Number = {7392},
	Pages = {105-9},
	Pmc = {PMC3321067},
	Pmid = {22425995},
	Pst = {epublish},
	Title = {Wild-type microglia arrest pathology in a mouse model of Rett syndrome},
	Volume = {484},
	Year = {2012},
	File = {papers/Derecki_Nature2012a.pdf}}

@article{Mosca:2012,
	Abstract = {Synapse assembly requires trans-synaptic signals between the pre- and postsynapse, but our understanding of the essential organizational molecules involved in this process remains incomplete. Teneurin proteins are conserved, epidermal growth factor (EGF)-repeat-containing transmembrane proteins with large extracellular domains. Here we show that two Drosophila Teneurins, Ten-m and Ten-a, are required for neuromuscular synapse organization and target selection. Ten-a is presynaptic whereas Ten-m is mostly postsynaptic; neuronal Ten-a and muscle Ten-m form a complex in vivo. Pre- or postsynaptic Teneurin perturbations cause severe synapse loss and impair many facets of organization trans-synaptically and cell autonomously. These include defects in active zone apposition, release sites, membrane and vesicle organization, and synaptic transmission. Moreover, the presynaptic microtubule and postsynaptic spectrin cytoskeletons are severely disrupted, suggesting a mechanism whereby Teneurins organize the cytoskeleton, which in turn affects other aspects of synapse development. Supporting this, Ten-m physically interacts with α-Spectrin. Genetic analyses of teneurin and neuroligin reveal that they have differential roles that synergize to promote synapse assembly. Finally, at elevated endogenous levels, Ten-m regulates target selection between specific motor neurons and muscles. Our study identifies the Teneurins as a key bi-directional trans-synaptic signal involved in general synapse organization, and demonstrates that proteins such as these can also regulate target selection.},
	Author = {Mosca, Timothy J and Hong, Weizhe and Dani, Vardhan S and Favaloro, Vincenzo and Luo, Liqun},
	Date-Added = {2013-04-01 16:18:07 +0000},
	Date-Modified = {2013-04-01 16:18:44 +0000},
	Doi = {10.1038/nature10923},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Biological Markers; Cell Adhesion Molecules, Neuronal; Cytoskeleton; Drosophila Proteins; Drosophila melanogaster; Gene Expression Regulation; Larva; Microtubule-Associated Proteins; Muscles; Neuromuscular Junction; Neurons; Receptors, Cell Surface; Synapses; Synaptic Transmission; Tenascin},
	Month = {Apr},
	Number = {7393},
	Pages = {237-41},
	Pmc = {PMC3326183},
	Pmid = {22426000},
	Pst = {epublish},
	Title = {Trans-synaptic Teneurin signalling in neuromuscular synapse organization and target choice},
	Volume = {484},
	Year = {2012},
	File = {papers/Mosca_Nature2012.pdf}}

@article{Grienberger:2012,
	Abstract = {Calcium ions generate versatile intracellular signals that control key functions in all types of neurons. Imaging calcium in neurons is particularly important because calcium signals exert their highly specific functions in well-defined cellular subcompartments. In this Primer, we briefly review the general mechanisms of neuronal calcium signaling. We then introduce the calcium imaging devices, including confocal and two-photon microscopy as well as miniaturized devices that are used in freely moving animals. We provide an overview of the classical chemical fluorescent calcium indicators and of the protein-based genetically encoded calcium indicators. Using application examples, we introduce new developments in the field, such as calcium imaging in awake, behaving animals and the use of calcium imaging for mapping single spine sensory inputs in cortical neurons in vivo. We conclude by providing an outlook on the prospects of calcium imaging for the analysis of neuronal signaling and plasticity in various animal models.},
	Author = {Grienberger, Christine and Konnerth, Arthur},
	Date-Added = {2013-04-01 16:18:07 +0000},
	Date-Modified = {2013-04-01 16:18:44 +0000},
	Doi = {10.1016/j.neuron.2012.02.011},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {downloads},
	Mesh = {Aequorin; Animals; Calcium; Calcium Channels; Calcium Signaling; Diagnostic Imaging; Humans; Luminescent Agents; Neurons; Photons; Receptors, Ionotropic Glutamate},
	Month = {Mar},
	Number = {5},
	Pages = {862-85},
	Pmid = {22405199},
	Pst = {ppublish},
	Title = {Imaging calcium in neurons},
	Volume = {73},
	Year = {2012},
	File = {papers/Grienberger_Neuron2012.pdf}}

@article{McGinley:2012,
	Abstract = {Broadband transient sounds, such as clicks and consonants, activate a traveling wave in the cochlea. This wave evokes firing in auditory nerve fibers that are tuned to high frequencies several milliseconds earlier than in fibers tuned to low frequencies. Despite this substantial traveling wave delay, octopus cells in the brainstem receive broadband input and respond to clicks with submillisecond temporal precision. The dendrites of octopus cells lie perpendicular to the tonotopically organized array of auditory nerve fibers, placing the earliest arriving inputs most distally and the latest arriving closest to the soma. Here, we test the hypothesis that the topographic arrangement of synaptic inputs on dendrites of octopus cells allows octopus cells to compensate the traveling wave delay. We show that in mice the full cochlear traveling wave delay is 1.6 ms. Because the dendrites of each octopus cell spread across approximately one-third of the tonotopic axis, a click evokes a soma-directed sweep of synaptic input lasting 0.5 ms in individual octopus cells. Morphologically and biophysically realistic, computational models of octopus cells show that soma-directed sweeps with durations matching in vivo measurements result in the largest and sharpest somatic EPSPs. A low input resistance and activation of a low-voltage-activated potassium conductance that are characteristic of octopus cells are important determinants of sweep sensitivity. We conclude that octopus cells have dendritic morphologies and biophysics tailored to accomplish the precise encoding of broadband transient sounds.},
	Author = {McGinley, Matthew J and Liberman, M Charles and Bal, Ramazan and Oertel, Donata},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1523/JNEUROSCI.0272-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Acoustic Stimulation; Animals; Auditory Pathways; Brain Waves; Cochlea; Cochlear Nerve; Cochlear Nucleus; Dendrites; Excitatory Postsynaptic Potentials; Female; Humans; Male; Mice; Mice, Inbred CBA; Mice, Inbred ICR; Models, Neurological},
	Month = {Jul},
	Number = {27},
	Pages = {9301-11},
	Pmc = {PMC3417346},
	Pmid = {22764237},
	Pst = {ppublish},
	Title = {Generating synchrony from the asynchronous: compensation for cochlear traveling wave delays by the dendrites of individual brainstem neurons},
	Volume = {32},
	Year = {2012},
	File = {papers/McGinley_JNeurosci2012.pdf}}

@article{Nataraj:2011,
	Abstract = {Different neocortical regions are functionally specialized, but whether this specialization is reflected in the forms of plasticity present during developmental critical periods (CPs) is largely unknown. In rodent visual cortex, we recently showed that a form of intrinsic plasticity [LTP of intrinsic excitability (LTP-IE)] in the monocular region of the primary visual cortex (V1M) plays an important role in modulating cortical responsiveness following visual deprivation. Here we ask whether LTP-IE is present and similarly regulated by visual experience in the binocular region of the primary visual cortex (V1B), where inputs from the two eyes compete during the CP. In contrast to V1M, where LTP-IE is present throughout the CP, in V1B LTP-IE was only transiently expressed at the onset of the CP. Also distinct from V1M, brief monocular deprivation (MD) was unable to modulate LTP-IE magnitude in V1B, and even binocular deprivation (the equivalent of MD in V1M) could only influence LTP-IE expression during a narrow time window at the peak of the CP. Finally, we asked whether these differences depend on differences in sensory activation of the two areas during development. MD of ipsilateral inputs from before eye opening (to reduce competitive interactions) did not affect the pattern of LTP-IE expression in V1B. Further, the differences in plasticity in the two cortical areas persisted when animals were reared in the dark to remove all patterned visual input. Thus neocortical LTP-IE expression shows dramatic regional and temporal differentiation, and these differences are not driven by differences in sensory experience.},
	Author = {Nataraj, Kiran and Turrigiano, Gina},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-08-27 20:02:04 +0000},
	Doi = {10.1523/JNEUROSCI.4455-11.2011},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads; currOpinRvw},
	Mesh = {Age Factors; Analysis of Variance; Animals; Animals, Newborn; Biophysics; Critical Period (Psychology); Dark Adaptation; Electric Stimulation; Female; Functional Laterality; Long-Term Potentiation; Lysine; Male; Patch-Clamp Techniques; Rats; Rats, Long-Evans; Sensory Deprivation; Time Factors; Visual Cortex},
	Month = {Dec},
	Number = {49},
	Pages = {17932-40},
	Pmc = {PMC3272675},
	Pmid = {22159108},
	Pst = {ppublish},
	Title = {Regional and temporal specificity of intrinsic plasticity mechanisms in rodent primary visual cortex},
	Volume = {31},
	Year = {2011},
	File = {papers/Nataraj_JNeurosci2011.pdf}}

@article{Grant:2012,
	Abstract = {In this review we discuss recent advances in the understanding of corticothalamic axon guidance; patterning of the early telencephalon, the sequence and choreography of the development of projections from subplate, layers 5 and 6. These cortical subpopulations display different axonal outgrowth kinetics and innervate distinct thalamic nuclei in a temporal pattern determined by cortical layer identity and subclass specificity. Guidance by molecular cues, structural cues, and activity-dependent mechanisms contribute to this development. There is a substantial rearrangement of the corticofugal connectivity outside the thalamus at the border of and within the reticular thalamic nucleus, a region that shares some of the characteristics of the cortical subplate during development. The early transient circuits are not well understood, nor the extent to which this developmental pattern may be driven by peripheral sensory activity. We hypothesize that transient circuits during embryonic and early postnatal development are critical in the matching of the cortical and thalamic representations and forming the cortical circuits in the mature brain.},
	Author = {Grant, Eleanor and Hoerder-Suabedissen, Anna and Moln{\'a}r, Zolt{\'a}n},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.3389/fnins.2012.00053},
	Journal = {Front Neurosci},
	Journal-Full = {Frontiers in neuroscience},
	Keywords = {downloads},
	Pages = {53},
	Pmc = {PMC3343305},
	Pmid = {22586359},
	Pst = {ppublish},
	Title = {Development of the corticothalamic projections},
	Volume = {6},
	Year = {2012},
	File = {papers/Grant_FrontNeurosci2012.pdf}}

@article{Blandina:2012,
	Abstract = {Histamine axons originate from a single source, the tuberomamillary nucleus (TMN) of the posterior hypothalamus, to innervate almost all central nervous system (CNS) regions. This feature, a compact cell group with widely distributed fibers, resembles that of other amine systems, such as noradrenaline or serotonin, and is consistent with a function for histamine over a host of physiological processes, including the regulation of the sleep-wake cycle, appetite, endocrine homeostasis, body temperature, pain perception, learning, memory, and emotion. An important question is whether these diverse physiological roles are served by different histamine neuronal subpopulation. While the histamine system is generally regarded as one single functional unit that provides histamine throughout the brain, evidence is beginning to accumulate in favor of heterogeneity of histamine neurons. The aim of this review is to summarize experimental evidence demonstrating that histamine neurons are heterogeneous, organized into functionally distinct circuits, impinging on different brain regions, and displaying selective control mechanisms. This could imply independent functions of subsets of histamine neurons according to their respective origin and terminal projections.},
	Author = {Blandina, Patrizio and Munari, Leonardo and Provensi, Gustavo and Passani, Maria B},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.3389/fnsys.2012.00033},
	Journal = {Front Syst Neurosci},
	Journal-Full = {Frontiers in systems neuroscience},
	Keywords = {downloads},
	Pages = {33},
	Pmc = {PMC3343474},
	Pmid = {22586376},
	Pst = {ppublish},
	Title = {Histamine neurons in the tuberomamillary nucleus: a whole center or distinct subpopulations?},
	Volume = {6},
	Year = {2012},
	File = {papers/Blandina_FrontSystNeurosci2012.pdf}}

@article{Stanley:2012,
	Abstract = {Medical applications of nanotechnology typically focus on drug delivery and biosensors. Here, we combine nanotechnology and bioengineering to demonstrate that nanoparticles can be used to remotely regulate protein production in vivo. We decorated a modified temperature-sensitive channel, TRPV1, with antibody-coated iron oxide nanoparticles that are heated in a low-frequency magnetic field. When local temperature rises, TRPV1 gates calcium to stimulate synthesis and release of bioengineered insulin driven by a Ca(2+)-sensitive promoter. Studying tumor xenografts expressing the bioengineered insulin gene, we show that exposure to radio waves stimulates insulin release from the tumors and lowers blood glucose in mice. We further show that cells can be engineered to synthesize genetically encoded ferritin nanoparticles and inducibly release insulin. These approaches provide a platform for using nanotechnology to activate cells.},
	Author = {Stanley, Sarah A and Gagner, Jennifer E and Damanpour, Shadi and Yoshida, Mitsukuni and Dordick, Jonathan S and Friedman, Jeffrey M},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1126/science.1216753},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {downloads},
	Mesh = {Animals; Bioengineering; Blood Glucose; Calcium; Embryonic Stem Cells; Epitopes; Ferric Compounds; Ferritins; HEK293 Cells; Hot Temperature; Humans; Insulin; Male; Metal Nanoparticles; Mice; Mice, Nude; Neoplasm Transplantation; Neoplasms, Experimental; PC12 Cells; Radio Waves; Rats; Recombinant Fusion Proteins; TRPV Cation Channels; Transfection; Transplantation, Heterologous},
	Month = {May},
	Number = {6081},
	Pages = {604-8},
	Pmid = {22556257},
	Pst = {ppublish},
	Title = {Radio-wave heating of iron oxide nanoparticles can regulate plasma glucose in mice},
	Volume = {336},
	Year = {2012},
	File = {papers/Stanley_Science2012.pdf}}

@article{Swindell:2006a,
	Abstract = {Rx is a homeobox-containing gene that is critical for vertebrate eye development. Its expression domain delineates a field of cells from which the retina and the ventral hypothalamus develop. The 5' upstream regulatory sequences of the medaka fish Rx gene are functionally conserved during evolution to a degree that they direct gene expression into the Rx-expressing field of cells in mice. Using these sequences, we made a Cre line that can be used for inactivation of gene expression in the developing retina.},
	Author = {Swindell, Eric C and Bailey, Travis J and Loosli, Felix and Liu, Chaomei and Amaya-Manzanares, Felipe and Mahon, Kathleen A and Wittbrodt, Joachim and Jamrich, Milan},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1002/dvg.20225},
	Journal = {Genesis},
	Journal-Full = {Genesis (New York, N.Y. : 2000)},
	Keywords = {downloads},
	Mesh = {Alleles; Animals; Eye Proteins; Gene Expression Regulation, Developmental; Genes, Homeobox; Genes, Reporter; Green Fluorescent Proteins; Homeodomain Proteins; Integrases; Lac Operon; Mice; Mice, Transgenic; Oryzias; Retina},
	Month = {Aug},
	Number = {8},
	Pages = {361-3},
	Pmid = {16850473},
	Pst = {ppublish},
	Title = {Rx-Cre, a tool for inactivation of gene expression in the developing retina},
	Volume = {44},
	Year = {2006},
	File = {papers/Swindell_Genesis2006a.pdf}}

@article{Li:2012a,
	Abstract = {A fundamental feature of the mammalian neocortex is its columnar organization. In the visual cortex, functional columns consisting of neurons with similar orientation preferences have been characterized extensively, but how these columns are constructed during development remains unclear. The radial unit hypothesis posits that the ontogenetic columns formed by clonally related neurons migrating along the same radial glial fibre during corticogenesis provide the basis for functional columns in adult neocortex. However, a direct correspondence between the ontogenetic and functional columns has not been demonstrated. Here we show that, despite the lack of a discernible orientation map in mouse visual cortex, sister neurons in the same radial clone exhibit similar orientation preferences. Using a retroviral vector encoding green fluorescent protein to label radial clones of excitatory neurons, and in vivo two-photon calcium imaging to measure neuronal response properties, we found that sister neurons preferred similar orientations whereas nearby non-sister neurons showed no such relationship. Interestingly, disruption of gap junction coupling by viral expression of a dominant-negative mutant of Cx26 (also known as Gjb2) or by daily administration of a gap junction blocker, carbenoxolone, during the first postnatal week greatly diminished the functional similarity between sister neurons, suggesting that the maturation of ontogenetic into functional columns requires intercellular communication through gap junctions. Together with the recent finding of preferential excitatory connections among sister neurons, our results support the radial unit hypothesis and unify the ontogenetic and functional columns in the visual cortex.},
	Author = {Li, Ye and Lu, Hui and Cheng, Pei-lin and Ge, Shaoyu and Xu, Huatai and Shi, Song-Hai and Dan, Yang},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-08-28 16:41:13 +0000},
	Doi = {10.1038/nature11110},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {development; visual system; Selection; Cooperative Behavior; topographic map; Visual Cortex},
	Mesh = {Animals; Animals, Newborn; Carbenoxolone; Cell Communication; Clone Cells; Connexins; Female; Gap Junctions; Male; Mice; Mice, Inbred C57BL; Models, Neurological; Neurons; Visual Cortex},
	Month = {Jun},
	Number = {7401},
	Pages = {118-21},
	Pmc = {PMC3375857},
	Pmid = {22678292},
	Pst = {epublish},
	Title = {Clonally related visual cortical neurons show similar stimulus feature selectivity},
	Volume = {486},
	Year = {2012},
	File = {papers/Li_Nature2012.pdf}}

@article{Yu:2012a,
	Abstract = {Radial glial cells are the primary neural progenitor cells in the developing neocortex. Consecutive asymmetric divisions of individual radial glial progenitor cells produce a number of sister excitatory neurons that migrate along the elongated radial glial fibre, resulting in the formation of ontogenetic columns. Moreover, sister excitatory neurons in ontogenetic columns preferentially develop specific chemical synapses with each other rather than with nearby non-siblings. Although these findings provide crucial insight into the emergence of functional columns in the neocortex, little is known about the basis of this lineage-dependent assembly of excitatory neuron microcircuits at single-cell resolution. Here we show that transient electrical coupling between radially aligned sister excitatory neurons regulates the subsequent formation of specific chemical synapses in the neocortex. Multiple-electrode whole-cell recordings showed that sister excitatory neurons preferentially form strong electrical coupling with each other rather than with adjacent non-sister excitatory neurons during early postnatal stages. This preferential coupling allows selective electrical communication between sister excitatory neurons, promoting their action potential generation and synchronous firing. Interestingly, although this electrical communication largely disappears before the appearance of chemical synapses, blockade of the electrical communication impairs the subsequent formation of specific chemical synapses between sister excitatory neurons in ontogenetic columns. These results suggest a strong link between lineage-dependent transient electrical coupling and the assembly of precise excitatory neuron microcircuits in the neocortex.},
	Author = {Yu, Yong-Chun and He, Shuijin and Chen, She and Fu, Yinghui and Brown, Keith N and Yao, Xing-Hua and Ma, Jian and Gao, Kate P and Sosinsky, Gina E and Huang, Kun and Shi, Song-Hai},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1038/nature10958},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Action Potentials; Animals; Animals, Newborn; Cell Lineage; Electric Conductivity; Electrical Synapses; Gap Junctions; Meclofenamic Acid; Mice; Models, Neurological; Neocortex; Neurons; Synaptic Transmission},
	Month = {Jun},
	Number = {7401},
	Pages = {113-7},
	Pmc = {PMC3599787},
	Pmid = {22678291},
	Pst = {epublish},
	Title = {Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly},
	Volume = {486},
	Year = {2012},
	File = {papers/Yu_Nature2012.pdf}}

@article{Rushmore:2006,
	Abstract = {Visuospatial neglect is a common neurological syndrome caused by unilateral brain damage to the posterior and inferior parietal cerebral cortex, and is characterized by an inability to respond or orient to stimuli presented in the contralesional hemifield. Neglect has been elicited in experimental models of the rat, cat and monkey, and is thought to result in part from a pathological state of inhibition exerted on the damaged hemisphere by the hyperexcited intact hemisphere. We sought to test this theory by assessing neural activity levels in multiple brain structures during neglect using 2-deoxyglucose (2DG) as a metabolic marker of neural activity. Neglect was induced in two ways: (i) by cooling deactivation of posterior parietal cortex or (ii) in conjunction with broader cortical blindness produced by unilateral lesion of all contiguous visual cortical areas spanning occipital, parietal and temporal regions. The direction and magnitude of changes in 2DG uptake were measured in cerebral cortex and midbrain structures. Finally, the 2DG uptake was assessed in a group of cats in which the lesion-induced neglect component of blindness was cancelled by cooling of either the contralateral posterior parietal cortex or the contralateral superior colliculus (SC). Overall, we found that (i) both lesion- and cooling-induced neglect are associated with decreases in 2DG uptake in specific ipsilateral cortical and midbrain regions; (ii) levels of 2DG uptake in the intermediate and deep layers of the SC contralateral to both cooling and lesion deactivations are increased; (iii) changes in 2DG uptake were not identified in the contralateral cortex; and (iv) reversal of the lesion-induced neglect component of blindness is associated with a reduction of contralesional 2DG uptake to normal or subnormal levels. These data are in accord with theories of neglect that include mutually suppressive mechanisms between the two hemispheres, and we show that these mechanisms operate at the level of the SC, but are not apparent at the level of cortex. These results suggest that the most effective therapies for visual neglect will be those that act to decrease neural activity in the intermediate layers of the SC contralateral to the brain damage.},
	Author = {Rushmore, R Jarrett and Valero-Cabre, Antoni and Lomber, Stephen G and Hilgetag, Claus C and Payne, Bertram R},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1093/brain/awl140},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {downloads},
	Mesh = {Animals; Blindness, Cortical; Brain Mapping; Cats; Cold Temperature; Deoxyglucose; Disease Models, Animal; Motion Perception; Parietal Lobe; Perceptual Disorders; Superior Colliculi; Visual Field Tests},
	Month = {Jul},
	Number = {Pt 7},
	Pages = {1803-21},
	Pmid = {16731540},
	Pst = {ppublish},
	Title = {Functional circuitry underlying visual neglect},
	Volume = {129},
	Year = {2006},
	File = {papers/Rushmore_Brain2006.pdf}}

@article{Huster:2012,
	Abstract = {The simultaneous recording and analysis of electroencephalography (EEG) and fMRI data in human systems, cognitive and clinical neurosciences is rapidly evolving and has received substantial attention. The significance of multimodal brain imaging is documented by a steadily increasing number of laboratories now using simultaneous EEG-fMRI aiming to achieve both high temporal and spatial resolution of human brain function. Due to recent developments in technical and algorithmic instrumentation, the rate-limiting step in multimodal studies has shifted from data acquisition to analytic aspects. Here, we introduce and compare different methods for data integration and identify the benefits that come with each approach, guiding the reader toward an understanding and informed selection of the integration approach most suitable for addressing a particular research question.},
	Author = {Huster, Ren{\'e} J and Debener, Stefan and Eichele, Tom and Herrmann, Christoph S},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1523/JNEUROSCI.0447-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Algorithms; Brain; Brain Mapping; Electroencephalography; Humans; Image Interpretation, Computer-Assisted; Magnetic Resonance Imaging; Subtraction Technique},
	Month = {May},
	Number = {18},
	Pages = {6053-60},
	Pmid = {22553012},
	Pst = {ppublish},
	Title = {Methods for simultaneous EEG-fMRI: an introductory review},
	Volume = {32},
	Year = {2012},
	File = {papers/Huster_JNeurosci2012.pdf}}

@article{Min:2012,
	Abstract = {Endocannabinoid mediated spike timing-dependent depression (t-LTD) is crucially involved in the development of the sensory neocortex. t-LTD at excitatory synapses in the developing rat barrel cortex requires cannabinoid CB(1) receptor (CB(1)R) activation, as well as activation of NMDA receptors located on the presynaptic terminal, but the exact signaling cascade leading to t-LTD remains unclear. We found that astrocytes are critically involved in t-LTD. Astrocytes gradually increased their Ca(2+) signaling specifically during the induction of t-LTD in a CB(1)R-dependent manner. In this way, astrocytes might act as a memory buffer for previous coincident neuronal activity. Following activation, astrocytes released glutamate, which activated presynaptic NMDA receptors to induce t-LTD. Astrocyte stimulation coincident with afferent activity resulted in long-term depression, indicating that astrocyte activation is sufficient for the induction of synaptic depression. Taken together, our findings describe the retrograde signaling cascade underlying neocortical t-LTD. The critical involvement of astrocytes in this process highlights their importance for experience-dependent sensory remodeling.},
	Author = {Min, Rogier and Nevian, Thomas},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1038/nn.3075},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {downloads},
	Mesh = {2-Amino-5-phosphonovalerate; Animals; Animals, Newborn; Astrocytes; Benzoxazines; Biophysics; Calcium; Calcium Channel Blockers; Dizocilpine Maleate; Electric Stimulation; Excitatory Amino Acid Antagonists; Excitatory Postsynaptic Potentials; Glutamic Acid; Long-Term Synaptic Depression; Morpholines; Naphthalenes; Neocortex; Patch-Clamp Techniques; Piperidines; Probability; Pyrazoles; Rats; Rats, Wistar; Receptor, Cannabinoid, CB1; Signal Transduction; Sodium Channel Blockers; Synapses; Tetrodotoxin; Thalamus; Time Factors},
	Month = {May},
	Number = {5},
	Pages = {746-53},
	Pmid = {22446881},
	Pst = {epublish},
	Title = {Astrocyte signaling controls spike timing-dependent depression at neocortical synapses},
	Volume = {15},
	Year = {2012},
	File = {papers/Min_NatNeurosci2012.pdf}}

@article{Huber:2012,
	Abstract = {The mechanisms linking sensation and action during learning are poorly understood. Layer 2/3 neurons in the motor cortex might participate in sensorimotor integration and learning; they receive input from sensory cortex and excite deep layer neurons, which control movement. Here we imaged activity in the same set of layer 2/3 neurons in the motor cortex over weeks, while mice learned to detect objects with their whiskers and report detection with licking. Spatially intermingled neurons represented sensory (touch) and motor behaviours (whisker movements and licking). With learning, the population-level representation of task-related licking strengthened. In trained mice, population-level representations were redundant and stable, despite dynamism of single-neuron representations. The activity of a subpopulation of neurons was consistent with touch driving licking behaviour. Our results suggest that ensembles of motor cortex neurons couple sensory input to multiple, related motor programs during learning.},
	Author = {Huber, D and Gutnisky, D A and Peron, S and O'Connor, D H and Wiegert, J S and Tian, L and Oertner, T G and Looger, L L and Svoboda, K},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1038/nature11039},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Behavior, Animal; Feedback, Sensory; Hippocampus; Learning; Long-Term Potentiation; Mice; Microscopy; Models, Neurological; Motor Cortex; Neuronal Plasticity; Psychomotor Performance; Rats; Tongue; Touch; Vibrissae},
	Month = {Apr},
	Number = {7395},
	Pages = {473-8},
	Pmid = {22538608},
	Pst = {epublish},
	Title = {Multiple dynamic representations in the motor cortex during sensorimotor learning},
	Volume = {484},
	Year = {2012},
	File = {papers/Huber_Nature2012.pdf}}

@article{Madisen:2012,
	Abstract = {Cell type-specific expression of optogenetic molecules allows temporally precise manipulation of targeted neuronal activity. Here we present a toolbox of four knock-in mouse lines engineered for strong, Cre-dependent expression of channelrhodopsins ChR2-tdTomato and ChR2-EYFP, halorhodopsin eNpHR3.0 and archaerhodopsin Arch-ER2. All four transgenes mediated Cre-dependent, robust activation or silencing of cortical pyramidal neurons in vitro and in vivo upon light stimulation, with ChR2-EYFP and Arch-ER2 demonstrating light sensitivity approaching that of in utero or virally transduced neurons. We further show specific photoactivation of parvalbumin-positive interneurons in behaving ChR2-EYFP reporter mice. The robust, consistent and inducible nature of our ChR2 mice represents a significant advance over previous lines, and the Arch-ER2 and eNpHR3.0 mice are to our knowledge the first demonstration of successful conditional transgenic optogenetic silencing. When combined with the hundreds of available Cre driver lines, this optimized toolbox of reporter mice will enable widespread investigations of neural circuit function with unprecedented reliability and accuracy.},
	Author = {Madisen, Linda and Mao, Tianyi and Koch, Henner and Zhuo, Jia-min and Berenyi, Antal and Fujisawa, Shigeyoshi and Hsu, Yun-Wei A and Garcia, 3rd, Alfredo J and Gu, Xuan and Zanella, Sebastien and Kidney, Jolene and Gu, Hong and Mao, Yimei and Hooks, Bryan M and Boyden, Edward S and Buzs{\'a}ki, Gy{\"o}rgy and Ramirez, Jan Marino and Jones, Allan R and Svoboda, Karel and Han, Xue and Turner, Eric E and Zeng, Hongkui},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1038/nn.3078},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {downloads},
	Mesh = {Action Potentials; Animals; Archaeal Proteins; Brain; Electroporation; Halorhodopsins; Integrases; Light; Luminescent Proteins; Mice; Mice, Transgenic; Neurogenesis; Neurons; Optics and Photonics; Proteins; Rhodopsin; Wakefulness},
	Month = {May},
	Number = {5},
	Pages = {793-802},
	Pmc = {PMC3337962},
	Pmid = {22446880},
	Pst = {epublish},
	Title = {A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing},
	Volume = {15},
	Year = {2012},
	File = {papers/Madisen_NatNeurosci2012.pdf}}

@article{Wester:2012,
	Abstract = {The cortex is organized in vertical and horizontal circuits that determine the spatiotemporal properties of distributed cortical activity. Despite detailed knowledge of synaptic interactions among individual cells in the neocortex, little is known about the rules governing interactions among local populations. Here, we used self-sustained recurrent activity generated in cortex, also known as up-states, in rat thalamocortical slices in vitro to understand interactions among laminar and horizontal circuits. By means of intracellular recordings and fast optical imaging with voltage-sensitive dyes, we show that single thalamic inputs activate the cortical column in a preferential layer 4 (L4) → layer 2/3 (L2/3) → layer 5 (L5) sequence, followed by horizontal propagation with a leading front in supragranular and infragranular layers. To understand the laminar and columnar interactions, we used focal injections of TTX to block activity in small local populations, while preserving functional connectivity in the rest of the network. We show that L2/3 alone, without underlying L5, does not generate self-sustained activity and is inefficient propagating activity horizontally. In contrast, L5 sustains activity in the absence of L2/3 and is necessary and sufficient to propagate activity horizontally. However, loss of L2/3 delays horizontal propagation via L5. Finally, L5 amplifies activity in L2/3. Our results show for the first time that columnar interactions between supragranular and infragranular layers are required for the normal propagation of activity in the neocortex. Our data suggest that supragranular and infragranular circuits, with their specific and complex set of inputs and outputs, work in tandem to determine the patterns of cortical activation observed in vivo.},
	Author = {Wester, Jason C and Contreras, Diego},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1523/JNEUROSCI.5006-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Animals, Newborn; Brain Mapping; Electric Stimulation; Electron Transport Complex IV; Membrane Potentials; Neocortex; Nerve Net; Neural Pathways; Optics and Photonics; Rats; Rats, Sprague-Dawley; Recruitment, Neurophysiological; Sodium Channel Blockers; Tetrodotoxin; Thalamus; Voltage-Sensitive Dye Imaging},
	Month = {Apr},
	Number = {16},
	Pages = {5454-71},
	Pmc = {PMC3415278},
	Pmid = {22514308},
	Pst = {ppublish},
	Title = {Columnar interactions determine horizontal propagation of recurrent network activity in neocortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Wester_JNeurosci2012.pdf}}

@article{Derecki:2012,
	Abstract = {Rett syndrome is an X-linked autism spectrum disorder. The disease is characterized in most cases by mutation of the MECP2 gene, which encodes a methyl-CpG-binding protein. Although MECP2 is expressed in many tissues, the disease is generally attributed to a primary neuronal dysfunction. However, as shown recently, glia, specifically astrocytes, also contribute to Rett pathophysiology. Here we examine the role of another form of glia, microglia, in a murine model of Rett syndrome. Transplantation of wild-type bone marrow into irradiation-conditioned Mecp2-null hosts resulted in engraftment of brain parenchyma by bone-marrow-derived myeloid cells of microglial phenotype, and arrest of disease development. However, when cranial irradiation was blocked by lead shield, and microglial engraftment was prevented, disease was not arrested. Similarly, targeted expression of MECP2 in myeloid cells, driven by Lysm(cre) on an Mecp2-null background, markedly attenuated disease symptoms. Thus, through multiple approaches, wild-type Mecp2-expressing microglia within the context of an Mecp2-null male mouse arrested numerous facets of disease pathology: lifespan was increased, breathing patterns were normalized, apnoeas were reduced, body weight was increased to near that of wild type, and locomotor activity was improved. Mecp2(+/-) females also showed significant improvements as a result of wild-type microglial engraftment. These benefits mediated by wild-type microglia, however, were diminished when phagocytic activity was inhibited pharmacologically by using annexin V to block phosphatydilserine residues on apoptotic targets, thus preventing recognition and engulfment by tissue-resident phagocytes. These results suggest the importance of microglial phagocytic activity in Rett syndrome. Our data implicate microglia as major players in the pathophysiology of this devastating disorder, and suggest that bone marrow transplantation might offer a feasible therapeutic approach for it.},
	Author = {Derecki, No{\"e}l C and Cronk, James C and Lu, Zhenjie and Xu, Eric and Abbott, Stephen B G and Guyenet, Patrice G and Kipnis, Jonathan},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1038/nature10907},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Annexin A5; Apoptosis; Body Weight; Bone Marrow Transplantation; Brain; Disease Models, Animal; Disease Progression; Female; Insulin-Like Growth Factor I; Locomotion; Male; Methyl-CpG-Binding Protein 2; Mice; Mice, Inbred C57BL; Microglia; Phagocytosis; Phosphatidylserines; Respiration; Rett Syndrome; Rotarod Performance Test},
	Month = {Apr},
	Number = {7392},
	Pages = {105-9},
	Pmc = {PMC3321067},
	Pmid = {22425995},
	Pst = {epublish},
	Title = {Wild-type microglia arrest pathology in a mouse model of Rett syndrome},
	Volume = {484},
	Year = {2012},
	File = {papers/Derecki_Nature2012.pdf}}

@article{Simini:2012,
	Abstract = {Introduced in its contemporary form in 1946 (ref. 1), but with roots that go back to the eighteenth century, the gravity law is the prevailing framework with which to predict population movement, cargo shipping volume and inter-city phone calls, as well as bilateral trade flows between nations. Despite its widespread use, it relies on adjustable parameters that vary from region to region and suffers from known analytic inconsistencies. Here we introduce a stochastic process capturing local mobility decisions that helps us analytically derive commuting and mobility fluxes that require as input only information on the population distribution. The resulting radiation model predicts mobility patterns in good agreement with mobility and transport patterns observed in a wide range of phenomena, from long-term migration patterns to communication volume between different regions. Given its parameter-free nature, the model can be applied in areas where we lack previous mobility measurements, significantly improving the predictive accuracy of most of the phenomena affected by mobility and transport processes.},
	Author = {Simini, Filippo and Gonz{\'a}lez, Marta C and Maritan, Amos and Barab{\'a}si, Albert-L{\'a}szl{\'o}},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2014-01-15 14:50:07 +0000},
	Doi = {10.1038/nature10856},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {graph theory; Mathematics; models; self organization; network; Game Theory; Methods},
	Mesh = {Emigration and Immigration; Europe; Internationality; Models, Statistical; Population Density; Population Dynamics; Statistical Distributions; Stochastic Processes; Telephone; Transportation; United States},
	Month = {Apr},
	Number = {7392},
	Pages = {96-100},
	Pmid = {22367540},
	Pst = {epublish},
	Title = {A universal model for mobility and migration patterns},
	Volume = {484},
	Year = {2012},
	File = {papers/Simini_Nature2012.pdf}}

@article{Harvey:2012,
	Abstract = {The posterior parietal cortex (PPC) has an important role in many cognitive behaviours; however, the neural circuit dynamics underlying PPC function are not well understood. Here we optically imaged the spatial and temporal activity patterns of neuronal populations in mice performing a PPC-dependent task that combined a perceptual decision and memory-guided navigation in a virtual environment. Individual neurons had transient activation staggered relative to one another in time, forming a sequence of neuronal activation spanning the entire length of a task trial. Distinct sequences of neurons were triggered on trials with opposite behavioural choices and defined divergent, choice-specific trajectories through a state space of neuronal population activity. Cells participating in the different sequences and at distinct time points in the task were anatomically intermixed over microcircuit length scales (<100 micrometres). During working memory decision tasks, the PPC may therefore perform computations through sequence-based circuit dynamics, rather than long-lived stable states, implemented using anatomically intermingled microcircuits.},
	Author = {Harvey, Christopher D and Coen, Philip and Tank, David W},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2014-09-15 21:57:26 +0000},
	Doi = {10.1038/nature10918},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {Posterior parietal cortex; ppc; Neocortex; Cerebral Cortex; mouse; in vivo; optical physiology; two-photon imaging; optical imaging; synchrony; Theoretical; Decision Making; memory; learning; Hippocampal; grid cells; Spatial Behavior; navigation; Attention},
	Mesh = {Action Potentials; Animals; Decision Making; Male; Maze Learning; Memory; Mice; Mice, Inbred C57BL; Models, Neurological; Parietal Lobe; Photic Stimulation; User-Computer Interface},
	Month = {Apr},
	Number = {7392},
	Pages = {62-8},
	Pmc = {PMC3321074},
	Pmid = {22419153},
	Pst = {epublish},
	Title = {Choice-specific sequences in parietal cortex during a virtual-navigation decision task},
	Volume = {484},
	Year = {2012},
	File = {papers/Harvey_Nature2012.pdf},
	Bdsk-File-2 = {papers/Harvey_Nature2012a.pdf}}

@article{Petersen:2004b,
	Abstract = {The functional and anatomical rearrangements of cortical sensory maps accompanying changes in experience are not well understood. We examined in vivo and in vitro how the sensory map and underlying synaptic connectivity of the developing rat barrel cortex are altered when the sensory input to the cortex is partially deprived. In the nondeprived cortex, both the sensory responses and synaptic connectivity between columns were strengthened through an increase in the synaptic connection probability between L2/3 pyramids in adjacent columns. This was accompanied by a selective growth of L2/3pyramid axonal arbors between spared columns. In contrast, deprived and nondeprived cortical columns became weakly connected in their L2/3 pyramid connections.},
	Author = {Petersen, Carl C H and Brecht, Michael and Hahn, Thomas T G and Sakmann, Bert},
	Date-Added = {2013-04-01 16:16:30 +0000},
	Date-Modified = {2013-04-01 16:17:05 +0000},
	Doi = {10.1126/science.1096750},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {downloads},
	Mesh = {Action Potentials; Animals; Brain Mapping; Electric Stimulation; Excitatory Postsynaptic Potentials; Image Processing, Computer-Assisted; Nerve Net; Neuronal Plasticity; Patch-Clamp Techniques; Pyramidal Cells; Rats; Rats, Wistar; Somatosensory Cortex; Synapses; Synaptic Transmission; Vibrissae},
	Month = {Apr},
	Number = {5671},
	Pages = {739-42},
	Pmid = {15118164},
	Pst = {ppublish},
	Title = {Synaptic changes in layer 2/3 underlying map plasticity of developing barrel cortex},
	Volume = {304},
	Year = {2004},
	File = {papers/Petersen_Science2004.pdf}}

@article{Lee:2012,
	Abstract = {Inhibitory interneurons are essential components of the neural circuits underlying various brain functions. In the neocortex, a large diversity of GABA (γ-aminobutyric acid) interneurons has been identified on the basis of their morphology, molecular markers, biophysical properties and innervation pattern. However, how the activity of each subtype of interneurons contributes to sensory processing remains unclear. Here we show that optogenetic activation of parvalbumin-positive (PV+) interneurons in the mouse primary visual cortex (V1) sharpens neuronal feature selectivity and improves perceptual discrimination. Using multichannel recording with silicon probes and channelrhodopsin-2 (ChR2)-mediated optical activation, we found that increased spiking of PV+ interneurons markedly sharpened orientation tuning and enhanced direction selectivity of nearby neurons. These effects were caused by the activation of inhibitory neurons rather than a decreased spiking of excitatory neurons, as archaerhodopsin-3 (Arch)-mediated optical silencing of calcium/calmodulin-dependent protein kinase IIα (CAMKIIα)-positive excitatory neurons caused no significant change in V1 stimulus selectivity. Moreover, the improved selectivity specifically required PV+ neuron activation, as activating somatostatin or vasointestinal peptide interneurons had no significant effect. Notably, PV+ neuron activation in awake mice caused a significant improvement in their orientation discrimination, mirroring the sharpened V1 orientation tuning. Together, these results provide the first demonstration that visual coding and perception can be improved by increased spiking of a specific subtype of cortical inhibitory interneurons.},
	Author = {Lee, Seung-Hee and Kwan, Alex C and Zhang, Siyu and Phoumthipphavong, Victoria and Flannery, John G and Masmanidis, Sotiris C and Taniguchi, Hiroki and Huang, Z Josh and Zhang, Feng and Boyden, Edward S and Deisseroth, Karl and Dan, Yang},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1038/nature11312},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Calcium-Calmodulin-Dependent Protein Kinase Type 2; Discrimination Learning; Interneurons; Mice; Models, Neurological; Neural Inhibition; Parvalbumins; Rhodopsin; Rhodopsins, Microbial; Visual Cortex; Visual Perception; Wakefulness; gamma-Aminobutyric Acid},
	Month = {Aug},
	Number = {7411},
	Pages = {379-83},
	Pmc = {PMC3422431},
	Pmid = {22878719},
	Pst = {ppublish},
	Title = {Activation of specific interneurons improves V1 feature selectivity and visual perception},
	Volume = {488},
	Year = {2012},
	File = {papers/Lee_Nature2012.pdf}}

@article{Wilson:2012,
	Abstract = {Brain circuits process information through specialized neuronal subclasses interacting within a network. Revealing their interplay requires activating specific cells while monitoring others in a functioning circuit. Here we use a new platform for two-way light-based circuit interrogation in visual cortex in vivo to show the computational implications of modulating different subclasses of inhibitory neurons during sensory processing. We find that soma-targeting, parvalbumin-expressing (PV) neurons principally divide responses but preserve stimulus selectivity, whereas dendrite-targeting, somatostatin-expressing (SOM) neurons principally subtract from excitatory responses and sharpen selectivity. Visualized in vivo cell-attached recordings show that division by PV neurons alters response gain, whereas subtraction by SOM neurons shifts response levels. Finally, stimulating identified neurons while scanning many target cells reveals that single PV and SOM neurons functionally impact only specific subsets of neurons in their projection fields. These findings provide direct evidence that inhibitory neuronal subclasses have distinct and complementary roles in cortical computations.},
	Author = {Wilson, Nathan R and Runyan, Caroline A and Wang, Forea L and Sur, Mriganka},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1038/nature11347},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Dendrites; Electrophysiology; Interneurons; Mice; Models, Neurological; Neural Inhibition; Neural Pathways; Neurons; Parvalbumins; Somatostatin; Visual Cortex},
	Month = {Aug},
	Number = {7411},
	Pages = {343-8},
	Pmid = {22878717},
	Pst = {ppublish},
	Title = {Division and subtraction by distinct cortical inhibitory networks in vivo},
	Volume = {488},
	Year = {2012},
	File = {papers/Wilson_Nature2012.pdf}}

@article{West:2011,
	Abstract = {Activity-dependent plasticity of vertebrate neurons allows the brain to respond to its environment. During brain development, both spontaneous and sensory-driven neural activity are essential for instructively guiding the process of synapse development. These effects of neuronal activity are transduced in part through the concerted regulation of a set of activity-dependent transcription factors that coordinate a program of gene expression required for the formation and maturation of synapses. Here we review the cellular signaling networks that regulate the activity of transcription factors during brain development and discuss the functional roles of specific activity-regulated transcription factors in specific stages of synapse formation, refinement, and maturation. Interestingly, a number of neurodevelopmental disorders have been linked to abnormalities in activity-regulated transcriptional pathways, indicating that these signaling networks are critical for cognitive development and function.},
	Author = {West, Anne E and Greenberg, Michael E},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1101/cshperspect.a005744},
	Journal = {Cold Spring Harb Perspect Biol},
	Journal-Full = {Cold Spring Harbor perspectives in biology},
	Keywords = {downloads},
	Mesh = {Calcium Signaling; Cognition Disorders; Gene Expression Regulation; Humans; Models, Genetic; Neurites; Neuronal Plasticity; Neurons; Synapses; Synaptic Transmission; Transcription Factors},
	Month = {Jun},
	Number = {6},
	Pmc = {PMC3098681},
	Pmid = {21555405},
	Pst = {epublish},
	Title = {Neuronal activity-regulated gene transcription in synapse development and cognitive function},
	Volume = {3},
	Year = {2011},
	File = {papers/West_ColdSpringHarbPerspectBiol2011.pdf}}

@article{Petrof:2012,
	Abstract = {The subgranular layers (layers 5 and 6) of primary sensory cortex provide corticofugal output to thalamus and they also project to the appropriate secondary sensory cortices. Here we injected two combinations of different color retrograde fluorescent markers in the thalamic and cortical targets of these layers from the three primary sensory cortices (somatosensory, auditory, and visual) in mice to examine the degree of overlap between corticothalamic and interareal corticocortical cells in the subgranular layers. We found that, for all three primary sensory cortices, double-labeled cells were extremely rare, indicating that corticothalamic and interareal corticocortical cells in the subgranular layers represent largely independent populations.},
	Author = {Petrof, Iraklis and Viaene, Angela N and Sherman, S Murray},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1002/cne.23006},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {downloads},
	Mesh = {Animals; Cell Count; Fluorescent Dyes; Immunohistochemistry; Mice; Mice, Inbred BALB C; Neurons; Somatosensory Cortex},
	Month = {Jun},
	Number = {8},
	Pages = {1678-86},
	Pmc = {PMC3561675},
	Pmid = {22120996},
	Pst = {ppublish},
	Title = {Two populations of corticothalamic and interareal corticocortical cells in the subgranular layers of the mouse primary sensory cortices},
	Volume = {520},
	Year = {2012},
	File = {papers/Petrof_JCompNeurol2012.pdf}}

@article{Nassi:2009,
	Abstract = {Incoming sensory information is sent to the brain along modality-specific channels corresponding to the five senses. Each of these channels further parses the incoming signals into parallel streams to provide a compact, efficient input to the brain. Ultimately, these parallel input signals must be elaborated on and integrated in the cortex to provide a unified and coherent percept. Recent studies in the primate visual cortex have greatly contributed to our understanding of how this goal is accomplished. Multiple strategies including retinal tiling, hierarchical and parallel processing and modularity, defined spatially and by cell type-specific connectivity, are used by the visual system to recover the intricate detail of our visual surroundings.},
	Author = {Nassi, Jonathan J and Callaway, Edward M},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1038/nrn2619},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Humans; Models, Biological; Primates; Retina; Sensory Receptor Cells; Vision, Ocular; Visual Cortex; Visual Pathways; Visual Perception},
	Month = {May},
	Number = {5},
	Pages = {360-72},
	Pmc = {PMC2771435},
	Pmid = {19352403},
	Pst = {ppublish},
	Title = {Parallel processing strategies of the primate visual system},
	Volume = {10},
	Year = {2009},
	File = {papers/Nassi_NatRevNeurosci2009.pdf}}

@article{Yu:2012,
	Abstract = {In primates, prostriata is a small area located between the primary visual cortex (V1) and the hippocampal formation. Prostriata sends connections to multisensory and high-order association areas in the temporal, parietal, cingulate, orbitofrontal, and frontopolar cortices. It is characterized by a relatively simple histological organization, alluding to an early origin in mammalian evolution. Here we show that prostriata neurons in marmoset monkeys exhibit a unique combination of response properties, suggesting a new pathway for rapid distribution of visual information in parallel with the traditionally recognized dorsal and ventral streams. Whereas the location and known connections of prostriata suggest a high-level association area, its response properties are unexpectedly simple, resembling those found in early stages of the visual processing: neurons have robust, nonadapting responses to simple stimuli, with latencies comparable to those found in V1, and are broadly tuned to stimulus orientation and spatiotemporal frequency. However, their receptive fields are enormous and form a unique topographic map that emphasizes the far periphery of the visual field. These results suggest a specialized circuit through which stimuli in peripheral vision can bypass the elaborate hierarchy of extrastriate visual areas and rapidly elicit coordinated motor and cognitive responses across multiple brain systems.},
	Author = {Yu, Hsin-Hao and Chaplin, Tristan A and Davies, Amanda J and Verma, Richa and Rosa, Marcello G P},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1016/j.cub.2012.05.029},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {downloads},
	Mesh = {Animals; Brain Mapping; Callitrichinae; Limbic System; Visual Pathways; Visual Perception},
	Month = {Jul},
	Number = {14},
	Pages = {1351-7},
	Pmid = {22704993},
	Pst = {ppublish},
	Title = {A specialized area in limbic cortex for fast analysis of peripheral vision},
	Volume = {22},
	Year = {2012},
	File = {papers/Yu_CurrBiol2012.pdf}}

@article{Paul:2012,
	Abstract = {The assembly of neural circuits involves multiple sequential steps such as the specification of cell-types, their migration to proper brain locations, morphological and physiological differentiation, and the formation and maturation of synaptic connections. This intricate and often prolonged process is guided by elaborate genetic mechanisms that regulate each step. Evidence from numerous systems suggests that each cell-type, once specified, is endowed with a genetic program that unfolds in response to, and is regulated by, extrinsic signals, including cell-cell and synaptic interactions. To a large extent, the execution of this intrinsic program is achieved by the expression of specific sets of genes that support distinct developmental processes. Therefore, a comprehensive analysis of the developmental progression of gene expression in synaptic partners of neurons may provide a basis for exploring the genetic mechanisms regulating circuit assembly. Here we examined the developmental gene expression profiles of well-defined cell-types in a stereotyped microcircuit of the cerebellar cortex. We found that the transcriptomes of Purkinje cell and stellate/basket cells are highly dynamic throughout postnatal development. We revealed "phasic expression" of transcription factors, ion channels, receptors, cell adhesion molecules, gap junction proteins, and identified distinct molecular pathways that might contribute to sequential steps of cerebellar inhibitory circuit formation. We further revealed a correlation between genomic clustering and developmental co-expression of hundreds of transcripts, suggesting the involvement of chromatin level gene regulation during circuit formation.},
	Author = {Paul, Anirban and Cai, Ying and Atwal, Gurinder S and Huang, Z Josh},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.3389/fncir.2012.00037},
	Journal = {Front Neural Circuits},
	Journal-Full = {Frontiers in neural circuits},
	Keywords = {downloads},
	Pages = {37},
	Pmc = {PMC3385560},
	Pmid = {22754500},
	Pst = {ppublish},
	Title = {Developmental Coordination of Gene Expression between Synaptic Partners During GABAergic Circuit Assembly in Cerebellar Cortex},
	Volume = {6},
	Year = {2012},
	File = {papers/Paul_FrontNeuralCircuits2012.pdf}}

@article{Thomson:2010,
	Abstract = {This review attempts to summarise some of the major areas of neocortical research as it pertains to neocortical layer 6. After a brief summary of the development of this intriguing layer, the major pyramidal cell classes to be found in layer 6 are described and compared. The connections made and received by these different classes of neurones are then discussed and the possible functions of these connections, with particular reference to the shaping of responses in visual cortex and thalamus. Inhibition in layer 6 is discussed where appropriate, but not in great detail. Many types of interneurones are to be found in each cortical layer and layer 6 is no exception, but the functions of each type remain to be elucidated (Gonchar et al., 2007).},
	Author = {Thomson, Alex M},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.3389/fnana.2010.00013},
	Journal = {Front Neuroanat},
	Journal-Full = {Frontiers in neuroanatomy},
	Keywords = {downloads},
	Pages = {13},
	Pmc = {PMC2885865},
	Pmid = {20556241},
	Pst = {epublish},
	Title = {Neocortical layer 6, a review},
	Volume = {4},
	Year = {2010},
	File = {papers/Thomson_FrontNeuroanat2010.pdf}}

@article{Mahou:2012,
	Abstract = {We achieve simultaneous two-photon excitation of three chromophores with distinct absorption spectra using synchronized pulses from a femtosecond laser and an optical parametric oscillator. The two beams generate separate multiphoton processes, and their spatiotemporal overlap provides an additional two-photon excitation route, with submicrometer overlay of the color channels. We report volume and live multicolor imaging of 'Brainbow'-labeled tissues as well as simultaneous three-color fluorescence and third-harmonic imaging of fly embryos.},
	Author = {Mahou, Pierre and Zimmerley, Maxwell and Loulier, Karine and Matho, Katherine S and Labroille, Guillaume and Morin, Xavier and Supatto, Willy and Livet, Jean and D{\'e}barre, Delphine and Beaurepaire, Emmanuel},
	Date-Added = {2013-04-01 16:14:10 +0000},
	Date-Modified = {2013-04-01 16:15:03 +0000},
	Doi = {10.1038/nmeth.2098},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Keywords = {downloads},
	Mesh = {Animals; Cerebral Cortex; Color; Drosophila melanogaster; Fluorescence; Lasers; Mice; Microscopy, Fluorescence, Multiphoton; Photons; Time Factors},
	Month = {Aug},
	Number = {8},
	Pages = {815-8},
	Pmid = {22772730},
	Pst = {epublish},
	Title = {Multicolor two-photon tissue imaging by wavelength mixing},
	Volume = {9},
	Year = {2012},
	File = {papers/Mahou_NatMethods2012.pdf}}

@article{Clemens:2012,
	Abstract = {Sensory experience plays a critical role in the development of cortical circuits. At the time of eye opening, visual cortical neurons in the ferret exhibit orientation selectivity, but lack direction selectivity, which is a feature of mature cortical neurons in this species. Direction selectivity emerges in the days and weeks following eye opening via a process that requires visual experience. However, the circuit mechanisms that underlie the development of direction selectivity remain unclear. Here, we used microelectrodes to examine the laminar chronology of the development of direction selectivity around the time of eye opening to identify the locations within the cortical circuit that are altered during this process. We found that neurons in layers 4 and 2/3 exhibited weak direction selectivity just before natural eye opening. Layer 4 neurons in animals that had opened their eyes but were younger than postnatal day 35 (PND 35) exhibited modestly increased direction selectivity, but layer 2/3 cells remained as weakly tuned as before eye opening. Animals that had opened their eyes and were PND 35 or older exhibited increased direction selectivity in both layers 4 and 2/3. On average, initial increases in direction selectivity in animals younger than PND 35 were explained by increases in responses to the preferred direction, while subsequent increases in direction selectivity in animals PND 35 or older were explained by decreases in responses to the null direction. These results suggest that all cortical layers are influenced by sensory stimulation during early stages of experience-dependent development.},
	Author = {Clemens, Jared M and Ritter, Neil J and Roy, Arani and Miller, Julie M and Van Hooser, Stephen D},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.3399-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Female; Ferrets; Immunohistochemistry; Male; Microelectrodes; Neurons; Orientation; Photic Stimulation; Visual Cortex; Visual Pathways; Visual Perception},
	Month = {Dec},
	Number = {50},
	Pages = {18177-85},
	Pmc = {PMC3532899},
	Pmid = {23238731},
	Pst = {ppublish},
	Title = {The laminar development of direction selectivity in ferret visual cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Clemens_JNeurosci2012.pdf}}

@article{Stensola:2012,
	Abstract = {The medial entorhinal cortex (MEC) is part of the brain's circuit for dynamic representation of self-location. The metric of this representation is provided by grid cells, cells with spatial firing fields that tile environments in a periodic hexagonal pattern. Limited anatomical sampling has obscured whether the grid system operates as a unified system or a conglomerate of independent modules. Here we show with recordings from up to 186 grid cells in individual rats that grid cells cluster into a small number of layer-spanning anatomically overlapping modules with distinct scale, orientation, asymmetry and theta-frequency modulation. These modules can respond independently to changes in the geometry of the environment. The discrete topography of the grid-map, and the apparent autonomy of the modules, differ from the graded topography of maps for continuous variables in several sensory systems, raising the possibility that the modularity of the grid map is a product of local self-organizing network dynamics.},
	Author = {Stensola, Hanne and Stensola, Tor and Solstad, Trygve and Fr{\o}land, Kristian and Moser, May-Britt and Moser, Edvard I},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2014-09-16 14:36:50 +0000},
	Doi = {10.1038/nature11649},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {rat; grid cells; hippocampus; Spatial Behavior; navigation; Entorhinal Cortex;},
	Mesh = {Animals; Entorhinal Cortex; Environment; Male; Models, Neurological; Orientation; Rats; Rats, Long-Evans; Theta Rhythm},
	Month = {Dec},
	Number = {7427},
	Pages = {72-8},
	Pmid = {23222610},
	Pst = {ppublish},
	Title = {The entorhinal grid map is discretized},
	Volume = {492},
	Year = {2012},
	File = {papers/Stensola_Nature2012.pdf}}

@article{Su:2012,
	Abstract = {Diverse sensory organs, including mammalian taste buds and insect chemosensory sensilla, show a marked compartmentalization of receptor cells; however, the functional impact of this organization remains unclear. Here we show that compartmentalized Drosophila olfactory receptor neurons (ORNs) communicate with each other directly. The sustained response of one ORN is inhibited by the transient activation of a neighbouring ORN. Mechanistically, such lateral inhibition does not depend on synapses and is probably mediated by ephaptic coupling. Moreover, lateral inhibition in the periphery can modulate olfactory behaviour. Together, the results show that integration of olfactory information can occur via lateral interactions between ORNs. Inhibition of a sustained response by a transient response may provide a means of encoding salience. Finally, a CO(2)-sensitive ORN in the malaria mosquito Anopheles can also be inhibited by excitation of an adjacent ORN, suggesting a broad occurrence of lateral inhibition in insects and possible applications in insect control.},
	Author = {Su, Chih-Ying and Menuz, Karen and Reisert, Johannes and Carlson, John R},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1038/nature11712},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Anopheles gambiae; Carbon Dioxide; Dose-Response Relationship, Drug; Drosophila melanogaster; Female; Neural Inhibition; Olfactory Pathways; Olfactory Receptor Neurons; Sensilla; Smell; Synapses; Synaptic Transmission},
	Month = {Dec},
	Number = {7427},
	Pages = {66-71},
	Pmc = {PMC3518700},
	Pmid = {23172146},
	Pst = {ppublish},
	Title = {Non-synaptic inhibition between grouped neurons in an olfactory circuit},
	Volume = {492},
	Year = {2012},
	File = {papers/Su_Nature2012.pdf}}

@article{Yang:2010a,
	Abstract = {Imaging neurons, glia and vasculature in the living brain has become an important experimental tool for understanding how the brain works. Here we describe in detail a protocol for imaging cortical structures at high optical resolution through a thinned-skull cranial window in live mice using two-photon laser scanning microscopy (TPLSM). Surgery can be performed within 30-45 min and images can be acquired immediately thereafter. The procedure can be repeated multiple times allowing longitudinal imaging of the cortex over intervals ranging from days to years. Imaging through a thinned-skull cranial window avoids exposure of the meninges and the cortex, thus providing a minimally invasive approach for studying structural and functional changes of cells under normal and pathological conditions in the living brain.},
	Author = {Yang, Guang and Pan, Feng and Parkhurst, Christopher N and Grutzendler, Jaime and Gan, Wen-Biao},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1038/nprot.2009.222},
	Journal = {Nat Protoc},
	Journal-Full = {Nature protocols},
	Keywords = {downloads},
	Mesh = {Animals; Axons; Cerebral Cortex; Dendrites; Equipment Design; Indicators and Reagents; Luminescent Proteins; Mice; Mice, Transgenic; Microscopy, Confocal; Neurons; Photons; Skull; Synapses},
	Month = {Feb},
	Number = {2},
	Pages = {201-8},
	Pmid = {20134419},
	Pst = {ppublish},
	Title = {Thinned-skull cranial window technique for long-term imaging of the cortex in live mice},
	Volume = {5},
	Year = {2010},
	File = {papers/Yang_NatProtoc2010a.pdf}}

@article{Warner:2012,
	Abstract = {The hierarchical development of the primate visual cortex and associated streams remains somewhat of a mystery. While anatomical, physiological, and psychological studies have demonstrated the early maturation of the dorsal "where"/"how" or motion cortical stream, little is known about the circuitry responsible. The influence of the retinogeniculostriate pathway has been investigated, but little attention has been paid to the role of two more recently described disynaptic retinothalamic projections to the middle temporal (MT) area, an early maturing dorsal stream cortical field, and which bypass the primary visual cortex (V1). These pathways are via the koniocellular layers of the lateral geniculate nucleus (LGN) and the medial portion of the inferior pulvinar (PIm). Both have been demonstrated in the adult nonhuman primate, but their influence during the maturation of the visual cortex is unknown. We used a combination of neural tracing and immunohistochemistry to follow the development of LGN and PIm inputs to area MT in the marmoset monkey. Our results revealed that the early maturation of area MT is likely due to the disynaptic retinopulvinar input and not the retinogeniculate input or the direct projection from V1. Furthermore, from soon after birth to adulthood, there was a dynamic shift in the ratio of input from these three structures to area MT, with an increasing dominance of the direct V1 afference.},
	Author = {Warner, Claire E and Kwan, William C and Bourne, James A},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.3269-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Callithrix; Female; Geniculate Bodies; Male; Neurons; Pulvinar; Visual Cortex; Visual Pathways},
	Month = {Nov},
	Number = {48},
	Pages = {17073-85},
	Pmid = {23197701},
	Pst = {ppublish},
	Title = {The early maturation of visual cortical area MT is dependent on input from the retinorecipient medial portion of the inferior pulvinar},
	Volume = {32},
	Year = {2012},
	File = {papers/Warner_JNeurosci2012.pdf}}

@article{Okun:2012,
	Abstract = {Cortical circuits encode sensory stimuli through the firing of neuronal ensembles, and also produce spontaneous population patterns in the absence of sensory drive. This population activity is often characterized experimentally by the distribution of multineuron "words" (binary firing vectors), and a match between spontaneous and evoked word distributions has been suggested to reflect learning of a probabilistic model of the sensory world. We analyzed multineuron word distributions in sensory cortex of anesthetized rats and cats, and found that they are dominated by fluctuations in population firing rate rather than precise interactions between individual units. Furthermore, cortical word distributions change when brain state shifts, and similar behavior is seen in simulated networks with fixed, random connectivity. Our results suggest that similarity or dissimilarity in multineuron word distributions could primarily reflect similarity or dissimilarity in population firing rate dynamics, and not necessarily the precise interactions between neurons that would indicate learning of sensory features.},
	Author = {Okun, Michael and Yger, Pierre and Marguet, Stephan L and Gerard-Mercier, Florian and Benucci, Andrea and Katzner, Steffen and Busse, Laura and Carandini, Matteo and Harris, Kenneth D},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.1831-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Action Potentials; Animals; Cats; Male; Models, Neurological; Nerve Net; Neurons; Rats; Rats, Sprague-Dawley; Somatosensory Cortex},
	Month = {Nov},
	Number = {48},
	Pages = {17108-19},
	Pmc = {PMC3520056},
	Pmid = {23197704},
	Pst = {ppublish},
	Title = {Population rate dynamics and multineuron firing patterns in sensory cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Okun_JNeurosci2012.pdf}}

@article{Mancini:2012,
	Abstract = {Topographic maps of the receptive surface are a fundamental feature of neural organization in many sensory systems. While touch is finely mapped in the cerebral cortex, it remains controversial how precise any cortical nociceptive map may be. Given that nociceptive innervation density is relatively low on distal skin regions such as the digits, one might conclude that the nociceptive system lacks fine representation of these regions. Indeed, only gross spatial organization of nociceptive maps has been reported so far. However, here we reveal the existence of fine-grained somatotopy for nociceptive inputs to the digits in human primary somatosensory cortex (SI). Using painful nociceptive-selective laser stimuli to the hand, and phase-encoded functional magnetic resonance imaging analysis methods, we observed somatotopic maps of the digits in contralateral SI. These nociceptive maps were highly aligned with maps of non-painful tactile stimuli, suggesting comparable cortical representations for, and possible interactions between, mechanoreceptive and nociceptive signals. Our findings may also be valuable for future studies tracking the time course and the spatial pattern of plastic changes in cortical organization involved in chronic pain.},
	Author = {Mancini, Flavia and Haggard, Patrick and Iannetti, Gian Domenico and Longo, Matthew R and Sereno, Martin I},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.3059-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Brain Mapping; Female; Hand; Humans; Magnetic Resonance Imaging; Male; Nociception; Pain; Physical Stimulation; Skin; Somatosensory Cortex},
	Month = {Nov},
	Number = {48},
	Pages = {17155-62},
	Pmc = {PMC3529201},
	Pmid = {23197708},
	Pst = {ppublish},
	Title = {Fine-grained nociceptive maps in primary somatosensory cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Mancini_JNeurosci2012.pdf}}

@article{Ren:2012,
	Abstract = {Rett syndrome (RTT) is a severe neurological disorder that is associated with mutations in the methyl-CpG binding protein 2 (MECP2) gene. RTT patients suffer from mental retardation and behavioral disorders, including heightened anxiety and state-dependent breathing irregularities, such as hyperventilation and apnea. Many symptoms are recapitulated by the Mecp2-null male mice (Mecp2(-/y)). To characterize developmental progression of the respiratory phenotype and explore underlying mechanisms, we examined Mecp2(-/y) and wild-type (WT) mice from presymptomatic periods to end-stage disease. We monitored breathing patterns of unrestrained mice during wake-sleep states and while altering stress levels using movement restraint or threatening odorant (trimethylthiazoline). Respiratory motor patterns generated by in situ working heart-brainstem preparations (WHBPs) were measured to assess function of brainstem respiratory networks isolated from suprapontine structures. Data revealed two general stages of respiratory dysfunction in Mecp2(-/y) mice. At the early stage, respiratory abnormalities were limited to wakefulness, correlated with markers of stress (increased fecal deposition and blood corticosterone levels), and alleviated by antalarmin (corticotropin releasing hormone receptor 1 antagonist). Furthermore, the respiratory rhythm generated by WHBPs was similar in WT and Mecp2(-/y) mice. During the later stage, respiratory abnormalities were evident during wakefulness and sleep. Also, WHBPs from Mecp2(-/y) showed central apneas. We conclude that, at early disease stages, stress-related modulation from suprapontine structures is a significant factor in the Mecp2(-/y) respiratory phenotype and that anxiolytics may be effective. At later stages, abnormalities of brainstem respiratory networks are a significant cause of irregular breathing patterns and central apneas.},
	Author = {Ren, Jun and Ding, Xiuqing and Funk, Gregory D and Greer, John J},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.2951-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Anxiety; Disease Models, Animal; Male; Methyl-CpG-Binding Protein 2; Mice; Respiration; Respiration Disorders; Rett Syndrome; Wakefulness},
	Month = {Nov},
	Number = {48},
	Pages = {17230-40},
	Pmid = {23197715},
	Pst = {ppublish},
	Title = {Anxiety-related mechanisms of respiratory dysfunction in a mouse model of Rett syndrome},
	Volume = {32},
	Year = {2012},
	File = {papers/Ren_JNeurosci2012.pdf}}

@article{Stevenson:2012,
	Abstract = {How interactions between neurons relate to tuned neural responses is a longstanding question in systems neuroscience. Here we use statistical modeling and simultaneous multi-electrode recordings to explore the relationship between these interactions and tuning curves in six different brain areas. We find that, in most cases, functional interactions between neurons provide an explanation of spiking that complements and, in some cases, surpasses the influence of canonical tuning curves. Modeling functional interactions improves both encoding and decoding accuracy by accounting for noise correlations and features of the external world that tuning curves fail to capture. In cortex, modeling coupling alone allows spikes to be predicted more accurately than tuning curve models based on external variables. These results suggest that statistical models of functional interactions between even relatively small numbers of neurons may provide a useful framework for examining neural coding.},
	Author = {Stevenson, Ian H and London, Brian M and Oby, Emily R and Sachs, Nicholas A and Reimer, Jacob and Englitz, Bernhard and David, Stephen V and Shamma, Shihab A and Blanche, Timothy J and Mizuseki, Kenji and Zandvakili, Amin and Hatsopoulos, Nicholas G and Miller, Lee E and Kording, Konrad P},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1371/journal.pcbi.1002775},
	Journal = {PLoS Comput Biol},
	Journal-Full = {PLoS computational biology},
	Keywords = {downloads},
	Number = {11},
	Pages = {e1002775},
	Pmc = {PMC3499254},
	Pmid = {23166484},
	Pst = {ppublish},
	Title = {Functional connectivity and tuning curves in populations of simultaneously recorded neurons},
	Volume = {8},
	Year = {2012},
	File = {papers/Stevenson_PLoSComputBiol2012.pdf}}

@article{Reichl:2012,
	Abstract = {In the juvenile brain, the synaptic architecture of the visual cortex remains in a state of flux for months after the natural onset of vision and the initial emergence of feature selectivity in visual cortical neurons. It is an attractive hypothesis that visual cortical architecture is shaped during this extended period of juvenile plasticity by the coordinated optimization of multiple visual cortical maps such as orientation preference (OP), ocular dominance (OD), spatial frequency, or direction preference. In part (I) of this study we introduced a class of analytically tractable coordinated optimization models and solved representative examples, in which a spatially complex organization of the OP map is induced by interactions between the maps. We found that these solutions near symmetry breaking threshold predict a highly ordered map layout. Here we examine the time course of the convergence towards attractor states and optima of these models. In particular, we determine the timescales on which map optimization takes place and how these timescales can be compared to those of visual cortical development and plasticity. We also assess whether our models exhibit biologically more realistic, spatially irregular solutions at a finite distance from threshold, when the spatial periodicities of the two maps are detuned and when considering more than 2 feature dimensions. We show that, although maps typically undergo substantial rearrangement, no other solutions than pinwheel crystals and stripes dominate in the emerging layouts. Pinwheel crystallization takes place on a rather short timescale and can also occur for detuned wavelengths of different maps. Our numerical results thus support the view that neither minimal energy states nor intermediate transient states of our coordinated optimization models successfully explain the architecture of the visual cortex. We discuss several alternative scenarios that may improve the agreement between model solutions and biological observations.},
	Author = {Reichl, Lars and Heide, Dominik and L{\"o}wel, Siegrid and Crowley, Justin C and Kaschube, Matthias and Wolf, Fred},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1371/journal.pcbi.1002756},
	Journal = {PLoS Comput Biol},
	Journal-Full = {PLoS computational biology},
	Keywords = {downloads},
	Number = {11},
	Pages = {e1002756},
	Pmc = {PMC3493502},
	Pmid = {23144602},
	Pst = {ppublish},
	Title = {Coordinated optimization of visual cortical maps (II) numerical studies},
	Volume = {8},
	Year = {2012},
	File = {papers/Reichl_PLoSComputBiol2012.pdf}}

@article{Mukamel:2010a,
	Abstract = {Direct recordings in monkeys have demonstrated that neurons in frontal and parietal areas discharge during execution and perception of actions [1-8]. Because these discharges "reflect" the perceptual aspects of actions of others onto the motor repertoire of the perceiver, these cells have been called mirror neurons. Their overlapping sensory-motor representations have been implicated in observational learning and imitation, two important forms of learning [9]. In humans, indirect measures of neural activity support the existence of sensory-motor mirroring mechanisms in homolog frontal and parietal areas [10, 11], other motor regions [12-15], and also the existence of multisensory mirroring mechanisms in nonmotor regions [16-19]. We recorded extracellular activity from 1177 cells in human medial frontal and temporal cortices while patients executed or observed hand grasping actions and facial emotional expressions. A significant proportion of neurons in supplementary motor area, and hippocampus and environs, responded to both observation and execution of these actions. A subset of these neurons demonstrated excitation during action-execution and inhibition during action-observation. These findings suggest that multiple systems in humans may be endowed with neural mechanisms of mirroring for both the integration and differentiation of perceptual and motor aspects of actions performed by self and others.},
	Author = {Mukamel, Roy and Ekstrom, Arne D and Kaplan, Jonas and Iacoboni, Marco and Fried, Itzhak},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1016/j.cub.2010.02.045},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {downloads},
	Mesh = {Animals; Cerebral Cortex; Electrophysiology; Emotions; Facial Expression; Hand; Humans; Imitative Behavior; Motor Activity; Neurons; Psychomotor Performance; Visual Perception},
	Month = {Apr},
	Number = {8},
	Pages = {750-6},
	Pmc = {PMC2904852},
	Pmid = {20381353},
	Pst = {ppublish},
	Title = {Single-neuron responses in humans during execution and observation of actions},
	Volume = {20},
	Year = {2010},
	File = {papers/Mukamel_CurrBiol2010a.pdf}}

@article{Sato:2012b,
	Abstract = {The mammalian neocortex is composed of various types of neurons that reflect its laminar and area structures. It has been suggested that not only intrinsic but also afferent-derived extrinsic factors are involved in neuronal differentiation during development. However, the role and molecular mechanism of such extrinsic factors are almost unknown. Here, we attempted to identify molecules that are expressed in the thalamus and affect cortical cell development. First, thalamus-specific molecules were sought by comparing gene expression profiles of the developing rat thalamus and cortex using microarrays, and by constructing a thalamus-enriched subtraction cDNA library. A systematic screening by in situ hybridization showed that several genes encoding extracellular molecules were strongly expressed in sensory thalamic nuclei. Exogenous and endogenous protein localization further demonstrated that two extracellular molecules, Neuritin-1 (NRN1) and VGF, were transported to thalamic axon terminals. Application of NRN1 and VGF to dissociated cell culture promoted the dendritic growth. An organotypic slice culture experiment further showed that the number of primary dendrites in multipolar stellate neurons increased in response to NRN1 and VGF, whereas dendritic growth of pyramidal neurons was not promoted. These molecules also increased neuronal survival of multipolar neurons. Taken together, these results suggest that the thalamus-specific molecules NRN1 and VGF play an important role in the dendritic growth and survival of cortical neurons in a cell type-specific manner.},
	Author = {Sato, Haruka and Fukutani, Yuma and Yamamoto, Yuji and Tatara, Eiichi and Takemoto, Makoto and Shimamura, Kenji and Yamamoto, Nobuhiko},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.0293-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Antibodies, Blocking; Cell Survival; Cells, Cultured; Cerebral Cortex; DNA Primers; DNA, Complementary; Dendrites; Electroporation; Female; GPI-Linked Proteins; Genetic Vectors; Immunohistochemistry; In Situ Hybridization; Male; Microarray Analysis; Neurons; Neuropeptides; Plasmids; Pregnancy; Presynaptic Terminals; Rats; Rats, Sprague-Dawley; Thalamus; Transfection},
	Month = {Oct},
	Number = {44},
	Pages = {15388-402},
	Pmid = {23115177},
	Pst = {ppublish},
	Title = {Thalamus-derived molecules promote survival and dendritic growth of developing cortical neurons},
	Volume = {32},
	Year = {2012},
	File = {papers/Sato_JNeurosci2012a.pdf}}

@article{State:2012,
	Author = {State, Matthew W and {\v S}estan, Nenad},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1126/science.1224989},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {downloads},
	Mesh = {Child Development Disorders, Pervasive; Child, Preschool; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genetic Loci; Humans; Mutation; Neocortex},
	Month = {Sep},
	Number = {6100},
	Pages = {1301-3},
	Pmid = {22984058},
	Pst = {ppublish},
	Title = {Neuroscience. The emerging biology of autism spectrum disorders},
	Volume = {337},
	Year = {2012},
	File = {papers/State_Science2012.pdf}}

@article{Holmes:2012,
	Abstract = {Cervical dystonia (CD; spasmodic torticollis) can be evoked by inhibition of substantia nigra pars reticulata (SNpr) in the nonhuman primate (Burbaud et al., 1998; Dybdal et al., 2012). Suppression of GABAergic neurons that project from SNpr results in the disinhibition of the targets to which these neurons project. It therefore should be possible to prevent CD by inhibition of the appropriate nigral target region(s). Here we tested the hypothesis that the deep and intermediate layers of the superior colliculus (DLSC), a key target of nigral projections, are required for the emergence of CD. To test this hypothesis, we pretreated the DLSC of four macaques with the GABA(A) agonist muscimol to determine whether this treatment would prevent CD evoked by muscimol infusions in SNpr. Our data supported this hypothesis: inhibition of DLSC attenuated CD evoked by muscimol in SNpr in all four animals. In two of the four subjects, quadrupedal rotations were evoked by muscimol application into SNpr sites that were distinct from those that induced dystonia. We found that inhibition of DLSC did not significantly alter quadrupedal rotations, suggesting that this response is dissociable from the SNpr-evoked CD. Our results are the first to demonstrate a role of DLSC in mediating the expression of CD. Furthermore, these data reveal a functional relationship between SNpr and DLSC in regulating posture and movement in the nonhuman primate, raising the possibility that the nigrotectal pathway has potential as a target for therapeutic interventions for CD.},
	Author = {Holmes, Angela L and Forcelli, Patrick A and DesJardin, Jacqueline T and Decker, Ashley L and Teferra, Menna and West, Elizabeth A and Malkova, Ludise and Gale, Karen},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.2295-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Analysis of Variance; Animals; Bicuculline; Disease Models, Animal; Drug Administration Routes; Female; GABA-A Receptor Agonists; GABA-A Receptor Antagonists; Head Movements; Macaca mulatta; Magnetic Resonance Imaging; Male; Movement; Muscimol; Postural Balance; Sensation Disorders; Substantia Nigra; Superior Colliculi; Torticollis},
	Month = {Sep},
	Number = {38},
	Pages = {13326-32},
	Pmid = {22993447},
	Pst = {ppublish},
	Title = {Superior colliculus mediates cervical dystonia evoked by inhibition of the substantia nigra pars reticulata},
	Volume = {32},
	Year = {2012},
	File = {papers/Holmes_JNeurosci2012.pdf}}

@article{Anastasiades:2012,
	Abstract = {The integration of neurons within the developing cerebral cortex is a prolonged process dependent on a combination of molecular and physiological cues. To examine the latter we used laser scanning photostimulation (LSPS) of caged glutamate in conjunction with whole-cell patch-clamp electrophysiology to probe the integration of pyramidal cells in the sensorimotor regions of the mouse neocortex. In the days immediately after postnatal day 5 (P5) the origin of the LSPS-evoked AMPA receptor (AMPAR)-mediated synaptic inputs were diffuse and poorly defined with considerable variability between cells. Over the subsequent week this coalesced and shifted, primarily influenced by an increased contribution from layers 2/3 cells, which became a prominent motif of the afferent input onto layer 5 pyramidal cells regardless of cortical region. To further investigate this particular emergent translaminar connection, we alternated our mapping protocol between two holding potentials (-70 and +40 mV) allowing us to detect exclusively NMDA receptor (NMDAR)-mediated inputs. This revealed distal MK-801-sensitive synaptic inputs that predict the formation of the mature, canonical layer 2/3 to 5 pathway. However, these were a transient feature and had been almost entirely converted to AMPAR synapses at a later age (P16). To examine the role of activity in the recruitment of early NMDAR synapses, we evoked brief periods (20 min) of rhythmic bursting. Short intense periods of activity could cause a prolonged augmentation of the total input onto pyramidal cells up until P12; a time point when the canonical circuit has been instated and synaptic integration shifts to a more consolidatory phase.},
	Author = {Anastasiades, Paul G and Butt, Simon J B},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1523/JNEUROSCI.1262-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Action Potentials; Age Factors; Animals; Animals, Newborn; Bicuculline; Biophysics; Brain Mapping; Dizocilpine Maleate; Dose-Response Relationship, Drug; Electric Stimulation; Excitatory Amino Acid Antagonists; Excitatory Postsynaptic Potentials; GABA-A Receptor Antagonists; Glutamates; Lasers; Magnesium; Mice; Motor Cortex; Neocortex; Neural Pathways; Patch-Clamp Techniques; Photic Stimulation; Pyramidal Cells; Statistics, Nonparametric; Synapses; Time Factors},
	Month = {Sep},
	Number = {38},
	Pages = {13085-99},
	Pmid = {22993426},
	Pst = {ppublish},
	Title = {A role for silent synapses in the development of the pathway from layer 2/3 to 5 pyramidal cells in the neocortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Anastasiades_JNeurosci2012.pdf}}

@article{Rizo:2012,
	Author = {Rizo, Josep},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1126/science.1228654},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {downloads},
	Mesh = {Optical Tweezers; SNARE Proteins},
	Month = {Sep},
	Number = {6100},
	Pages = {1300-1},
	Pmid = {22984057},
	Pst = {ppublish},
	Title = {Cell biology. Staging membrane fusion},
	Volume = {337},
	Year = {2012},
	File = {papers/Rizo_Science2012.pdf}}

@article{Sherratt:2012,
	Author = {Sherratt, Thomas N and Roberts, Gilbert},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1126/science.1226328},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {downloads},
	Mesh = {Animals; Behavior, Animal; Biological Evolution; Cooperative Behavior; Female; Male; Sexual Behavior, Animal},
	Month = {Sep},
	Number = {6100},
	Pages = {1304-5},
	Pmid = {22984060},
	Pst = {ppublish},
	Title = {Ecology. When paths to cooperation converge},
	Volume = {337},
	Year = {2012},
	File = {papers/Sherratt_Science2012.pdf}}

@article{Capotondo:2012,
	Abstract = {The recent hypothesis that postnatal microglia are maintained independently of circulating monocytes by local precursors that colonize the brain before birth has relevant implications for the treatment of various neurological diseases, including lysosomal storage disorders (LSDs), for which hematopoietic cell transplantation (HCT) is applied to repopulate the recipient myeloid compartment, including microglia, with cells expressing the defective functional hydrolase. By studying wild-type and LSD mice at diverse time-points after HCT, we showed the occurrence of a short-term wave of brain infiltration by a fraction of the transplanted hematopoietic progenitors, independently from the administration of a preparatory regimen and from the presence of a disease state in the brain. However, only the use of a conditioning regimen capable of ablating functionally defined brain-resident myeloid precursors allowed turnover of microglia with the donor, mediated by local proliferation of early immigrants rather than entrance of mature cells from the circulation.},
	Author = {Capotondo, Alessia and Milazzo, Rita and Politi, Letterio Salvatore and Quattrini, Angelo and Palini, Alessio and Plati, Tiziana and Merella, Stefania and Nonis, Alessandro and di Serio, Clelia and Montini, Eugenio and Naldini, Luigi and Biffi, Alessandra},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1073/pnas.1205858109},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {downloads},
	Mesh = {Analysis of Variance; Animals; Cell Differentiation; Cell Movement; Flow Cytometry; Green Fluorescent Proteins; Hematopoietic Stem Cell Transplantation; In Situ Nick-End Labeling; Lysosomal Storage Diseases, Nervous System; Mice; Mice, Knockout; Microglia; Transplantation Conditioning},
	Month = {Sep},
	Number = {37},
	Pages = {15018-23},
	Pmc = {PMC3443128},
	Pmid = {22923692},
	Pst = {ppublish},
	Title = {Brain conditioning is instrumental for successful microglia reconstitution following hematopoietic stem cell transplantation},
	Volume = {109},
	Year = {2012},
	File = {papers/Capotondo_ProcNatlAcadSciUSA2012.pdf}}

@article{Yurovsky:2012,
	Abstract = {The study of cognitive development hinges, largely, on the analysis of infant looking. But analyses of eye gaze data require the adoption of linking hypotheses: assumptions about the relationship between observed eye movements and underlying cognitive processes. We develop a general framework for constructing, testing, and comparing these hypotheses, and thus for producing new insights into early cognitive development. We first introduce the general framework--applicable to any infant gaze experiment--and then demonstrate its utility by analyzing data from a set of experiments investigating the role of attentional cues in infant learning. The new analysis uncovers significantly more structure in these data, finding evidence of learning that was not found in standard analyses and showing an unexpected relationship between cue use and learning rate. Finally, we discuss general implications for the construction and testing of quantitative linking hypotheses. MATLAB code for sample linking hypotheses can be found on the first author's website.},
	Author = {Yurovsky, Daniel and Hidaka, Shohei and Wu, Rachel},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1371/journal.pone.0047419},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {downloads},
	Number = {10},
	Pages = {e47419},
	Pmc = {PMC3482231},
	Pmid = {23110071},
	Pst = {ppublish},
	Title = {Quantitative linking hypotheses for infant eye movements},
	Volume = {7},
	Year = {2012},
	File = {papers/Yurovsky_PLoSOne2012.pdf}}

@article{Margolis:2012,
	Abstract = {Sensory maps are reshaped by experience. It is unknown how map plasticity occurs in vivo in functionally diverse neuronal populations because activity of the same cells has not been tracked over long time periods. Here we used repeated two-photon imaging of a genetic calcium indicator to measure whisker-evoked responsiveness of the same layer 2/3 neurons in adult mouse barrel cortex over weeks, first with whiskers intact, then during continued trimming of all but one whisker. Across the baseline period, neurons displayed heterogeneous yet stable responsiveness. During sensory deprivation, responses to trimmed whisker stimulation globally decreased, whereas responses to spared whisker stimulation increased for the least active neurons and decreased for the most active neurons. These findings suggest that recruitment of inactive, 'silent' neurons is part of a convergent redistribution of population activity underlying sensory map plasticity. Sensory-driven responsiveness is a key property controlling experience-dependent activity changes in individual neurons.},
	Author = {Margolis, David J and L{\"u}tcke, Henry and Schulz, Kristina and Haiss, Florent and Weber, Bruno and K{\"u}gler, Sebastian and Hasan, Mazahir T and Helmchen, Fritjof},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1038/nn.3240},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {downloads},
	Mesh = {Action Potentials; Animals; Brain Mapping; Calcium; Cerebral Cortex; Computer Simulation; Female; Gene Expression Regulation; Luminescent Proteins; Male; Mice; Mice, Inbred C57BL; Models, Biological; Neurons; Neuropil; Optics and Photonics; Physical Stimulation; Sensory Deprivation; Synapsins; Time Factors; Transduction, Genetic; Vibrissae},
	Month = {Nov},
	Number = {11},
	Pages = {1539-46},
	Pmid = {23086335},
	Pst = {ppublish},
	Title = {Reorganization of cortical population activity imaged throughout long-term sensory deprivation},
	Volume = {15},
	Year = {2012},
	File = {papers/Margolis_NatNeurosci2012.pdf}}

@article{Blanco-Hernandez:2012,
	Abstract = {The olfactory system, particularly the olfactory epithelium, presents a unique opportunity to study the regenerative capabilities of the brain, because of its ability to recover after damage. In this study, we ablated olfactory sensory neurons with methimazole and followed the anatomical and functional recovery of circuits expressing genetic markers for I7 and M72 receptors (M72-IRES-tau-LacZ and I7-IRES-tau-GFP). Our results show that 45 days after methimazole-induced lesion, axonal projections to the bulb of M72 and I7 populations are largely reestablished. Furthermore, regenerated glomeruli are re-formed within the same areas as those of control, unexposed mice. This anatomical regeneration correlates with functional recovery of a previously learned odorant-discrimination task, dependent on the cognate ligands for M72 and I7. Following regeneration, mice also recover innate responsiveness to TMT and urine. Our findings show that regeneration of neuronal circuits in the olfactory system can be achieved with remarkable precision and underscore the importance of glomerular organization to evoke memory traces stored in the brain.},
	Author = {Blanco-Hern{\'a}ndez, Eduardo and Valle-Leija, Pablo and Zomosa-Signoret, Viviana and Drucker-Col{\'\i}n, Ren{\'e} and Vidaltamayo, Rom{\'a}n},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1371/journal.pone.0046338},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {downloads},
	Number = {10},
	Pages = {e46338},
	Pmc = {PMC3468571},
	Pmid = {23071557},
	Pst = {ppublish},
	Title = {Odor memory stability after reinnervation of the olfactory bulb},
	Volume = {7},
	Year = {2012},
	File = {papers/Blanco-Hernández_PLoSOne2012.pdf}}

@article{Watakabe:2012,
	Abstract = {We are interested in identifying and characterizing various projection neurons that constitute the neocortical circuit. For this purpose, we developed a novel lentiviral vector that carries the tetracycline transactivator (tTA) and the transgene under the TET Responsive Element promoter (TRE) on a single backbone. By pseudotyping such a vector with modified rabies G-protein, we were able to express palmitoylated-GFP (palGFP) or turboFP635 (RFP) in corticothalamic, corticocortical, and corticopontine neurons of mice. The high-level expression of the transgene achieved by the TET-Off system enabled us to observe characteristic elaboration of neuronal processes for each cell type. At higher magnification, we were able to observe fine structures such as boutons and spines as well. We also injected our retrograde TET-Off vector to the marmoset cortex and proved that it can be used to label the long-distance cortical connectivity of millimeter scale. In conclusion, our novel retrograde tracer provides an attractive option to investigate the morphologies of identified cortical projection neurons of various species.},
	Author = {Watakabe, Akiya and Kato, Shigeki and Kobayashi, Kazuto and Takaji, Masafumi and Nakagami, Yuki and Sadakane, Osamu and Ohtsuka, Masanari and Hioki, Hiroyuki and Kaneko, Takeshi and Okuno, Hiroyuki and Kawashima, Takashi and Bito, Haruhiko and Kitamura, Yoshihiro and Yamamori, Tetsuo},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1371/journal.pone.0046157},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {downloads},
	Number = {10},
	Pages = {e46157},
	Pmc = {PMC3465318},
	Pmid = {23071541},
	Pst = {ppublish},
	Title = {Visualization of cortical projection neurons with retrograde TET-off lentiviral vector},
	Volume = {7},
	Year = {2012},
	File = {papers/Watakabe_PLoSOne2012.pdf}}

@article{Reese:2012,
	Abstract = {The brain is one of the most studied and highly complex systems in the biological world. While much research has concentrated on studying the brain directly, our focus is the structure of the brain itself: at its core an interconnected network of nodes (neurons). A better understanding of the structural connectivity of the brain should elucidate some of its functional properties. In this paper we analyze the connectome of the nematode Caenorhabditis elegans. Consisting of only 302 neurons, it is one of the better-understood neural networks. Using a Laplacian Matrix of the 279-neuron "giant component" of the network, we use an eigenvalue counting function to look for fractal-like self similarity. This matrix representation is also used to plot visualizations of the neural network in eigenfunction coordinates. Small-world properties of the system are examined, including average path length and clustering coefficient. We test for localization of eigenfunctions, using graph energy and spacial variance on these functions. To better understand results, all calculations are also performed on random networks, branching trees, and known fractals, as well as fractals which have been "rewired" to have small-world properties. We propose algorithms for generating Laplacian matrices of each of these graphs.},
	Author = {Reese, Tyler M and Brzoska, Antoni and Yott, Dylan T and Kelleher, Daniel J},
	Date-Added = {2013-04-01 16:12:12 +0000},
	Date-Modified = {2013-04-01 16:12:27 +0000},
	Doi = {10.1371/journal.pone.0040483},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {downloads},
	Number = {10},
	Pages = {e40483},
	Pmc = {PMC3465333},
	Pmid = {23071485},
	Pst = {ppublish},
	Title = {Analyzing self-similar and fractal properties of the C. elegans neural network},
	Volume = {7},
	Year = {2012},
	File = {papers/Reese_PLoSOne2012.pdf}}

@article{Sugar:2011,
	Abstract = {A connectome is an indispensable tool for brain researchers, since it quickly provides comprehensive knowledge of the brain's anatomical connections. Such knowledge lies at the basis of understanding network functions. Our first comprehensive and interactive account of brain connections comprised the rat hippocampal-parahippocampal network. We have now added all anatomical connections with the retrosplenial cortex (RSC) as well as the intrinsic connections of this region, because of the interesting functional overlap between these brain regions. The RSC is involved in a variety of cognitive tasks including memory, navigation, and prospective thinking, yet the exact role of the RSC and the functional differences between its subdivisions remain elusive. The connectome presented here may help to define this role by providing an unprecedented interactive and searchable overview of all connections within and between the rat RSC, parahippocampal region and hippocampal formation.},
	Author = {Sugar, J{\o}rgen and Witter, Menno P and van Strien, Niels M and Cappaert, Natalie L M},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.3389/fninf.2011.00007},
	Journal = {Front Neuroinform},
	Journal-Full = {Frontiers in neuroinformatics},
	Keywords = {downloads},
	Pages = {7},
	Pmc = {PMC3147162},
	Pmid = {21847380},
	Pst = {ppublish},
	Title = {The retrosplenial cortex: intrinsic connectivity and connections with the (para)hippocampal region in the rat. An interactive connectome},
	Volume = {5},
	Year = {2011},
	File = {papers/Sugar_FrontNeuroinform2011.pdf}}

@article{McNaughton:2006,
	Abstract = {The hippocampal formation can encode relative spatial location, without reference to external cues, by the integration of linear and angular self-motion (path integration). Theoretical studies, in conjunction with recent empirical discoveries, suggest that the medial entorhinal cortex (MEC) might perform some of the essential underlying computations by means of a unique, periodic synaptic matrix that could be self-organized in early development through a simple, symmetry-breaking operation. The scale at which space is represented increases systematically along the dorsoventral axis in both the hippocampus and the MEC, apparently because of systematic variation in the gain of a movement-speed signal. Convergence of spatially periodic input at multiple scales, from so-called grid cells in the entorhinal cortex, might result in non-periodic spatial firing patterns (place fields) in the hippocampus.},
	Author = {McNaughton, Bruce L and Battaglia, Francesco P and Jensen, Ole and Moser, Edvard I and Moser, May-Britt},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2014-09-16 14:38:03 +0000},
	Doi = {10.1038/nrn1932},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {rat; grid cells; hippocampus; Spatial Behavior; navigation; Entorhinal Cortex; place cells},
	Mesh = {Animals; Brain Mapping; Cognition; Hippocampus; Humans; Nerve Net; Neural Pathways},
	Month = {Aug},
	Number = {8},
	Pages = {663-78},
	Pmid = {16858394},
	Pst = {ppublish},
	Title = {Path integration and the neural basis of the 'cognitive map'},
	Volume = {7},
	Year = {2006},
	File = {papers/McNaughton_NatRevNeurosci2006.pdf}}

@article{Wagner:2006,
	Abstract = {Retinoic acid is well recognized to promote neuronal differentiation in the embryonic nervous system, but how it influences the postnatal cerebral cortex remains largely unknown. The domain of highest retinoic acid actions in the cortex of the mouse constricts postnatally to a narrow band that includes the dorsal visual stream and the attentional and executive networks. This band of cortex, which is distinguished by the retinoic acid-synthesizing enzyme RALDH3, exhibits signs of delayed maturation and enhanced plasticity compared to the surrounding cortex, as indicated by suppression of parvalbumin, neurofilament, cytochrome oxidase and perineuronal net maturation, and persistence of the embryonic, polysialated form of the neural cell-adhesion molecule PSA-NCAM. During the first postnatal week, the RALDH3-expressing territory translocates in the caudal cortex from the medial limbic lobe to the adjacent neocortex. This topographical shift requires the neurotrophin NT-3 because in mice lacking neuronal NT-3 the RALDH3 enzyme maintains its early postnatal pattern up to adulthood. In the NT-3-null mutants, expression of the markers, whose topography colocalizes with RALDH3 in the normal cortex, matches the abnormal RALDH3 pattern. This indicates that the uneven retinoic acid distribution serves a role in patterning the maturation and to some extent function of the normal postnatal cerebral cortex.},
	Author = {Wagner, Elisabeth and Luo, Tuanlian and Sakai, Yasuo and Parada, Luis F and Dr{\"a}ger, Ursula C},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1111/j.1460-9568.2006.04934.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Keywords = {downloads},
	Mesh = {Aldehyde Oxidoreductases; Animals; Animals, Newborn; Biological Markers; Cell Differentiation; Cerebral Cortex; Electron Transport Complex IV; Gene Expression Regulation, Developmental; Humans; Mice; Mice, Inbred C57BL; Mice, Knockout; Neural Cell Adhesion Molecule L1; Neural Pathways; Neurofilament Proteins; Neuronal Plasticity; Neurons; Neurotrophin 3; Parvalbumins; Protein Transport; Retinal Dehydrogenase; Sialic Acids; Tretinoin},
	Month = {Jul},
	Number = {2},
	Pages = {329-40},
	Pmid = {16836633},
	Pst = {ppublish},
	Title = {Retinoic acid delineates the topography of neuronal plasticity in postnatal cerebral cortex},
	Volume = {24},
	Year = {2006},
	File = {papers/Wagner_EurJNeurosci2006.pdf}}

@article{Grimsley:2011,
	Abstract = {Adult mice are highly vocal animals, with both males and females vocalizing in same sex and cross sex social encounters. Mouse pups are also highly vocal, producing isolation vocalizations when they are cold or removed from the nest. This study examined patterns in the development of pup isolation vocalizations, and compared these to adult vocalizations. In three litters of CBA/CaJ mice, we recorded isolation vocalizations at ages postnatal day 5 (p5), p7, p9, p11, and p13. Adult vocalizations were obtained in a variety of social situations. Altogether, 28,384 discrete vocal signals were recorded using high-frequency-sensitive equipment and analyzed for syllable type, spectral and temporal features, and the temporal sequencing within bouts. We found that pups produced all but one of the 11 syllable types recorded from adults. The proportions of syllable types changed developmentally, but even the youngest pups produced complex syllables with frequency-time variations. When all syllable types were pooled together for analysis, changes in the peak frequency or the duration of syllables were small, although significant, from p5 through p13. However, individual syllable types showed different, large patterns of change over development, requiring analysis of each syllable type separately. Most adult syllables were substantially lower in frequency and shorter in duration. As pups aged, the complexity of vocal bouts increased, with a greater tendency to switch between syllable types. Vocal bouts from older animals, p13 and adult, had significantly more sequential structure than those from younger mice. Overall, these results demonstrate substantial changes in social vocalizations with age. Future studies are required to identify whether these changes result from developmental processes affecting the vocal tract or control of vocalization, or from vocal learning. To provide a tool for further research, we developed a MATLAB program that generates bouts of vocalizations that correspond to mice of different ages.},
	Author = {Grimsley, Jasmine M S and Monaghan, Jessica J M and Wenstrup, Jeffrey J},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1371/journal.pone.0017460},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {downloads},
	Mesh = {Acoustics; Aging; Animals; Animals, Newborn; Female; Male; Mice; Nonlinear Dynamics; Phonetics; Social Behavior; Sound Spectrography; Vocal Cords; Vocalization, Animal},
	Number = {3},
	Pages = {e17460},
	Pmc = {PMC3052362},
	Pmid = {21408007},
	Pst = {epublish},
	Title = {Development of social vocalizations in mice},
	Volume = {6},
	Year = {2011},
	File = {papers/Grimsley_PLoSOne2011.pdf}}

@article{Taniguchi:2013,
	Abstract = {Diverse γ-aminobutyric acid-releasing interneurons regulate the functional organization of cortical circuits and derive from multiple embryonic sources. It remains unclear to what extent embryonic origin influences interneuron specification and cortical integration because of difficulties in tracking defined cell types. Here, we followed the developmental trajectory of chandelier cells (ChCs), the most distinct interneurons that innervate the axon initial segment of pyramidal neurons and control action potential initiation. ChCs mainly derive from the ventral germinal zone of the lateral ventricle during late gestation and require the homeodomain protein Nkx2.1 for their specification. They migrate with stereotyped routes and schedule and achieve specific laminar distribution in the cortex. The developmental specification of this bona fide interneuron type likely contributes to the assembly of a cortical circuit motif.},
	Author = {Taniguchi, Hiroki and Lu, Jiangteng and Huang, Z Josh},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1126/science.1227622},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {downloads},
	Mesh = {Animals; Cell Lineage; Female; Interneurons; Lateral Ventricles; Mice; Mice, Mutant Strains; Neocortex; Neural Stem Cells; Nuclear Proteins; Pyramidal Cells; Transcription Factors; gamma-Aminobutyric Acid},
	Month = {Jan},
	Number = {6115},
	Pages = {70-4},
	Pmid = {23180771},
	Pst = {ppublish},
	Title = {The spatial and temporal origin of chandelier cells in mouse neocortex},
	Volume = {339},
	Year = {2013},
	File = {papers/Taniguchi_Science2013.pdf}}

@article{Haider:2013,
	Abstract = {The activity of the cerebral cortex is thought to depend on the precise relationship between synaptic excitation and inhibition. In the visual cortex, in particular, intracellular measurements have related response selectivity to coordinated increases in excitation and inhibition. These measurements, however, have all been made during anaesthesia, which strongly influences cortical state and therefore sensory processing. The synaptic activity that is evoked by visual stimulation during wakefulness is unknown. Here we measured visually evoked responses--and the underlying synaptic conductances--in the visual cortex of anaesthetized and awake mice. Under anaesthesia, responses could be elicited from a large region of visual space and were prolonged. During wakefulness, responses were more spatially selective and much briefer. Whole-cell patch-clamp recordings of synaptic conductances showed a difference in synaptic inhibition between the two conditions. Under anaesthesia, inhibition tracked excitation in amplitude and spatial selectivity. By contrast, during wakefulness, inhibition was much stronger than excitation and had extremely broad spatial selectivity. We conclude that during wakefulness, cortical responses to visual stimulation are dominated by synaptic inhibition, restricting the spatial spread and temporal persistence of neural activity. These results provide a direct glimpse of synaptic mechanisms that control sensory responses in the awake cortex.},
	Author = {Haider, Bilal and H{\"a}usser, Michael and Carandini, Matteo},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1038/nature11665},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Anesthesia; Animals; Female; Mice; Mice, Inbred C57BL; Models, Neurological; Neural Inhibition; Patch-Clamp Techniques; Photic Stimulation; Synapses; Synaptic Transmission; Time Factors; Visual Cortex; Wakefulness},
	Month = {Jan},
	Number = {7430},
	Pages = {97-100},
	Pmc = {PMC3537822},
	Pmid = {23172139},
	Pst = {ppublish},
	Title = {Inhibition dominates sensory responses in the awake cortex},
	Volume = {493},
	Year = {2013},
	File = {papers/Haider_Nature2013.pdf}}

@article{Lazarenko:2010,
	Abstract = {At surgical depths of anesthesia, inhalational anesthetics cause a loss of motor response to painful stimuli (i.e., immobilization) that is characterized by profound inhibition of spinal motor circuits. Yet, although clearly depressed, the respiratory motor system continues to provide adequate ventilation under these same conditions. Here, we show that isoflurane causes robust activation of CO(2)/pH-sensitive, Phox2b-expressing neurons located in the retrotrapezoid nucleus (RTN) of the rodent brainstem, in vitro and in vivo. In brainstem slices from Phox2b-eGFP mice, the firing of pH-sensitive RTN neurons was strongly increased by isoflurane, independent of prevailing pH conditions. At least two ionic mechanisms contributed to anesthetic activation of RTN neurons: activation of an Na(+)-dependent cationic current and inhibition of a background K(+) current. Single-cell reverse transcription-PCR analysis of dissociated green fluorescent protein-labeled RTN neurons revealed expression of THIK-1 (TWIK-related halothane-inhibited K(+) channel, K(2P)13.1), a channel that shares key properties with the native RTN current (i.e., suppression by inhalational anesthetics, weak rectification, inhibition by extracellular Na(+), and pH-insensitivity). Isoflurane also increased firing rate of RTN chemosensitive neurons in urethane-anesthetized rats, again independent of CO(2) levels. In these animals, isoflurane transiently enhanced activity of the respiratory system, an effect that was most prominent at low levels of respiratory drive and mediated primarily by an increase in respiratory frequency. These data indicate that inhalational anesthetics cause activation of RTN neurons, which serve an important integrative role in respiratory control; the increased drive provided by enhanced RTN neuronal activity may contribute, in part, to maintaining respiratory motor activity under immobilizing anesthetic conditions.},
	Author = {Lazarenko, Roman M and Fortuna, Michal G and Shi, Yingtang and Mulkey, Daniel K and Takakura, Ana C and Moreira, Thiago S and Guyenet, Patrice G and Bayliss, Douglas A},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1523/JNEUROSCI.1956-10.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Analysis of Variance; Anesthetics, Inhalation; Animals; Animals, Newborn; Blood Pressure; Chemoreceptor Cells; Dose-Response Relationship, Drug; Electric Stimulation; Gene Expression Regulation; Green Fluorescent Proteins; Homeodomain Proteins; Hydrogen-Ion Concentration; Ion Channel Gating; Isoflurane; Membrane Potentials; Mice; Mice, Transgenic; Neural Inhibition; Patch-Clamp Techniques; Phrenic Nerve; Potassium Channels, Tandem Pore Domain; Respiration; Respiratory Center; Transcription Factors},
	Month = {Jul},
	Number = {27},
	Pages = {9324-34},
	Pmc = {PMC2910363},
	Pmid = {20610767},
	Pst = {ppublish},
	Title = {Anesthetic activation of central respiratory chemoreceptor neurons involves inhibition of a THIK-1-like background K(+) current},
	Volume = {30},
	Year = {2010},
	File = {papers/Lazarenko_JNeurosci2010.pdf}}

@article{Meyer-Lindenberg:2012,
	Abstract = {Mental health and social life are intimately inter-related, as demonstrated by the frequent social deficits of psychiatric patients and the increased rate of psychiatric disorders in people exposed to social environmental adversity. Here, we review emerging evidence that combines epidemiology, social psychology and neuroscience to bring neural mechanisms of social risk factors for mental illness into focus. In doing so, we discuss existing evidence on the effects of common genetic risk factors in social neural pathways and outline the need for integrative approaches to identify the converging mechanisms of social environmental and genetic risk in brain.},
	Author = {Meyer-Lindenberg, Andreas and Tost, Heike},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1038/nn.3083},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {downloads},
	Mesh = {Brain; Brain Mapping; Calcium Channels; Emotions; Gene-Environment Interaction; Humans; Mental Disorders; Receptors, Oxytocin; Risk Factors; Social Behavior},
	Month = {May},
	Number = {5},
	Pages = {663-8},
	Pmid = {22504349},
	Pst = {epublish},
	Title = {Neural mechanisms of social risk for psychiatric disorders},
	Volume = {15},
	Year = {2012},
	File = {papers/Meyer-Lindenberg_NatNeurosci2012.pdf}}

@article{Halje:2012,
	Abstract = {The standard pharmacological treatment for Parkinson's disease using the dopamine precursor levodopa is unfortunately limited by gradual development of disabling involuntary movements for which the underlying causes are poorly understood. Here we show that levodopa-induced dyskinesia in hemiparkinsonian rats is strongly associated with pronounced 80 Hz local field potential oscillations in the primary motor cortex following levodopa treatment. When this oscillation is interrupted by application of a dopamine antagonist onto the cortical surface the dyskinetic symptoms disappear. The finding that abnormal cortical oscillations are a key pathophysiological mechanism calls for a revision of the prevailing hypothesis that links levodopa-induced dyskinesia to an altered sensitivity to dopamine only in the striatum. Apart from having important implications for the treatment of Parkinson's disease, the discovered pathophysiological mechanism may also play a role in several other psychiatric and neurological conditions involving cortical dysfunction.},
	Author = {Halje, P{\"a}r and Tamt{\`e}, Martin and Richter, Ulrike and Mohammed, Mohsin and Cenci, M Angela and Petersson, Per},
	Date-Added = {2013-04-01 16:09:48 +0000},
	Date-Modified = {2013-04-01 16:10:10 +0000},
	Doi = {10.1523/JNEUROSCI.3047-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Algorithms; Animals; Antiparkinson Agents; Cerebral Cortex; Dyskinesia, Drug-Induced; Electrodes, Implanted; Electroencephalography; Evoked Potentials; Female; Fluorescent Antibody Technique; Levodopa; Microelectrodes; Neostriatum; Neurons; Oxidopamine; Parkinson Disease, Secondary; Proto-Oncogene Proteins c-fos; Rats; Rats, Sprague-Dawley; Receptors, Dopamine D1; Tyrosine 3-Monooxygenase},
	Month = {Nov},
	Number = {47},
	Pages = {16541-51},
	Pmid = {23175810},
	Pst = {ppublish},
	Title = {Levodopa-induced dyskinesia is strongly associated with resonant cortical oscillations},
	Volume = {32},
	Year = {2012},
	File = {papers/Halje_JNeurosci2012.pdf}}

@article{McMullen:2011,
	Abstract = {Many multiphoton imaging applications would benefit from a larger field of view; however, large field of views (>mm) require low magnification objectives which have low light collection efficiencies. We demonstrate a light collection system mounted on a low magnification objective that increases fluorescence collection by as much as 20-fold in scattering tissues. This peripheral detector results in an effective numerical aperture of collection >0.8 with a 3-4 mm field of view.},
	Author = {McMullen, J D and Kwan, A C and Williams, R M and Zipfel, W R},
	Date-Added = {2013-04-01 16:08:21 +0000},
	Date-Modified = {2013-04-01 16:08:49 +0000},
	Doi = {10.1111/j.1365-2818.2010.03419.x},
	Journal = {J Microsc},
	Journal-Full = {Journal of microscopy},
	Keywords = {downloads},
	Mesh = {Abdominal Neoplasms; Animals; Brain; Carcinoma; Mice; Microscopy, Fluorescence; Pathology; Spinal Cord},
	Month = {Feb},
	Number = {2},
	Pages = {119-24},
	Pmid = {21118215},
	Pst = {ppublish},
	Title = {Enhancing collection efficiency in large field of view multiphoton microscopy},
	Volume = {241},
	Year = {2011},
	File = {papers/McMullen_JMicrosc2011.pdf}}

@article{Kwan:2010,
	Abstract = {Neural activity can be captured by state-of-the-art optical imaging methods although the analysis of the resulting data sets is often manual and not standardized. Therefore, laboratories using large-scale calcium imaging eagerly await software toolboxes that can automate the process of identifying cells and inferring spikes. An algorithm proposed and implemented in a recent paper by Mukamel et al. [Neuron 63, 747-760 (2009)] used independent component analysis and offers significant improvements over conventional methods. The approach should be widely applicable, as tested with data obtained from the mouse cerebellum, neocortex, and spinal cord. The emergence of analysis tools in parallel with the rapid advances in optical imaging is an exciting development that will stimulate new discoveries and further elucidate the functions of neural circuits.},
	Author = {Kwan, Alex C},
	Date-Added = {2013-04-01 16:08:21 +0000},
	Date-Modified = {2013-04-01 16:08:49 +0000},
	Doi = {10.2976/1.3284977},
	Journal = {HFSP J},
	Journal-Full = {HFSP journal},
	Keywords = {downloads},
	Month = {Feb},
	Number = {1},
	Pages = {1-5},
	Pmc = {PMC2880024},
	Pmid = {20676302},
	Pst = {ppublish},
	Title = {Toward reconstructing spike trains from large-scale calcium imaging data},
	Volume = {4},
	Year = {2010},
	File = {papers/Kwan_HFSPJ2010.pdf}}

@article{Li:2012,
	Abstract = {The usefulness of genetically encoded probes for optical monitoring of neuronal activity and brain circuits would be greatly advanced by the generation of multiple indicators with non-overlapping color spectra. Most existing indicators are derived from or spectrally convergent on GFP. We generated a bright, red, pH-sensitive fluorescent protein, pHTomato, that can be used in parallel with green probes to monitor neuronal activity. SypHTomato, made by fusing pHTomato to the vesicular membrane protein synaptophysin, reported activity-dependent exocytosis as efficiently as green reporters. When expressed with the GFP-based indicator GCaMP3 in the same neuron, sypHTomato enabled concomitant imaging of transmitter release and presynaptic Ca(2+) transients at single nerve terminals. Expressing sypHTomato and GCaMP3 in separate cells enabled the simultaneous determination of presynaptic vesicular turnover and postsynaptic sub- and supra-threshold responses from a connected pair of neurons. With these new tools, we observed a close size matching between pre- and postsynaptic compartments, as well as interesting target cell-dependent regulation of presynaptic vesicle pools. Lastly, by coupling expression of pHTomato- and GFP-based probes with distinct variants of channelrhodopsin, we provided proof-of-principle for an all-optical approach to multiplex control and tracking of distinct circuit pathways.},
	Author = {Li, Yulong and Tsien, Richard W},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1038/nn.3126},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {downloads},
	Mesh = {Cells, Cultured; Exocytosis; Fluorescent Dyes; HEK293 Cells; Hippocampus; Humans; Hydrogen-Ion Concentration; Luminescent Proteins; Nerve Net; Synaptic Potentials; Synaptic Transmission},
	Month = {Jul},
	Number = {7},
	Pages = {1047-53},
	Pmid = {22634730},
	Pst = {epublish},
	Title = {pHTomato, a red, genetically encoded indicator that enables multiplex interrogation of synaptic activity},
	Volume = {15},
	Year = {2012},
	File = {papers/Li_NatNeurosci2012.pdf}}

@article{Koralek:2012,
	Abstract = {The ability to learn new skills and perfect them with practice applies not only to physical skills but also to abstract skills, like motor planning or neuroprosthetic actions. Although plasticity in corticostriatal circuits has been implicated in learning physical skills, it remains unclear if similar circuits or processes are required for abstract skill learning. Here we use a novel behavioural task in rodents to investigate the role of corticostriatal plasticity in abstract skill learning. Rodents learned to control the pitch of an auditory cursor to reach one of two targets by modulating activity in primary motor cortex irrespective of physical movement. Degradation of the relation between action and outcome, as well as sensory-specific devaluation and omission tests, demonstrate that these learned neuroprosthetic actions are intentional and goal-directed, rather than habitual. Striatal neurons change their activity with learning, with more neurons modulating their activity in relation to target-reaching as learning progresses. Concomitantly, strong relations between the activity of neurons in motor cortex and the striatum emerge. Specific deletion of striatal NMDA receptors impairs the development of this corticostriatal plasticity, and disrupts the ability to learn neuroprosthetic skills. These results suggest that corticostriatal plasticity is necessary for abstract skill learning, and that neuroprosthetic movements capitalize on the neural circuitry involved in natural motor learning.},
	Author = {Koralek, Aaron C and Jin, Xin and Long, 2nd, John D and Costa, Rui M and Carmena, Jose M},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1038/nature10845},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Acoustic Stimulation; Algorithms; Animals; Cues; Learning; Male; Man-Machine Systems; Mice; Motor Cortex; Motor Skills; Movement; Neostriatum; Neuronal Plasticity; Prostheses and Implants; Psychomotor Performance; Rats; Rats, Long-Evans; Receptors, N-Methyl-D-Aspartate; Reward},
	Month = {Mar},
	Number = {7389},
	Pages = {331-5},
	Pmc = {PMC3477868},
	Pmid = {22388818},
	Pst = {epublish},
	Title = {Corticostriatal plasticity is necessary for learning intentional neuroprosthetic skills},
	Volume = {483},
	Year = {2012},
	File = {papers/Koralek_Nature2012.pdf}}

@article{Kinoshita:2012,
	Abstract = {It is generally accepted that the direct connection from the motor cortex to spinal motor neurons is responsible for dexterous hand movements in primates. However, the role of the 'phylogenetically older' indirect pathways from the motor cortex to motor neurons, mediated by spinal interneurons, remains elusive. Here we used a novel double-infection technique to interrupt the transmission through the propriospinal neurons (PNs), which act as a relay of the indirect pathway in macaque monkeys (Macaca fuscata and Macaca mulatta). The PNs were double infected by injection of a highly efficient retrograde gene-transfer vector into their target area and subsequent injection of adeno-associated viral vector at the location of cell somata. This method enabled reversible expression of green fluorescent protein (GFP)-tagged tetanus neurotoxin, thereby permitting the selective and temporal blockade of the motor cortex--PN--motor neuron pathway. This treatment impaired reach and grasp movements, revealing a critical role for the PN-mediated pathway in the control of hand dexterity. Anti-GFP immunohistochemistry visualized the cell bodies and axonal trajectories of the blocked PNs, which confirmed their anatomical connection to motor neurons. This pathway-selective and reversible technique for blocking neural transmission does not depend on cell-specific promoters or transgenic techniques, and is a new and powerful tool for functional dissection in system-level neuroscience studies.},
	Author = {Kinoshita, Masaharu and Matsui, Ryosuke and Kato, Shigeki and Hasegawa, Taku and Kasahara, Hironori and Isa, Kaoru and Watakabe, Akiya and Yamamori, Tetsuo and Nishimura, Yukio and Alstermark, Bror and Watanabe, Dai and Kobayashi, Kazuto and Isa, Tadashi},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1038/nature11206},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Animals; Dependovirus; Green Fluorescent Proteins; Hand; Macaca; Metalloendopeptidases; Motor Cortex; Motor Neurons; Neurosciences; Synaptic Transmission; Tetanus Toxin},
	Month = {Jul},
	Number = {7406},
	Pages = {235-8},
	Pmid = {22722837},
	Pst = {ppublish},
	Title = {Genetic dissection of the circuit for hand dexterity in primates},
	Volume = {487},
	Year = {2012},
	File = {papers/Kinoshita_Nature2012.pdf}}

@article{Park:2009,
	Abstract = {Constructing a rich and continuous visual experience requires computing specific details across views as well as integrating similarities across views. In this paper, we report functional magnetic resonance imaging (fMRI) evidence that these distinct computations may occur in two scene-sensitive regions in the brain, the parahippocampal place area (PPA) and retrosplenial cortex (RSC). Participants saw different snapshot views from panoramic scenes, which represented clearly different views, but appeared to come from the same scene. Using fMRI adaptation, we tested whether the PPA and RSC treated these panoramic views as the same or different. In the panoramic condition, three different views from a single panoramic scene were presented. We did not find any attenuation for panoramic repeats in the PPA, showing viewpoint-specificity. In contrast, RSC showed significant attenuation for the panoramic condition, showing viewpoint-integration. However, when the panoramic views were not presented in a continuous way, both the specificity in the PPA and the integration in RSC were lost. These results demonstrate that the PPA and RSC compute different properties of scenes: the PPA focuses on selective discrimination of different views while RSC focuses on the integration of scenes under the same visual context. These complementary functions of the PPA and RSC enable both specific and integrative representations of scenes across several viewpoints.},
	Author = {Park, Soojin and Chun, Marvin M},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1016/j.neuroimage.2009.04.058},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Keywords = {downloads},
	Mesh = {Adult; Brain Mapping; Cerebral Cortex; Cues; Evoked Potentials, Visual; Female; Hippocampus; Humans; Magnetic Resonance Imaging; Male; Pattern Recognition, Visual; Young Adult},
	Month = {Oct},
	Number = {4},
	Pages = {1747-56},
	Pmc = {PMC2753672},
	Pmid = {19398014},
	Pst = {ppublish},
	Title = {Different roles of the parahippocampal place area (PPA) and retrosplenial cortex (RSC) in panoramic scene perception},
	Volume = {47},
	Year = {2009},
	File = {papers/Park_Neuroimage2009.pdf}}

@article{Tsai:2009a,
	Abstract = {It is well known that the density of neurons varies within the adult brain. In neocortex, this includes variations in neuronal density between different lamina as well as between different regions. Yet the concomitant variation of the microvessels is largely uncharted. Here, we present automated histological, imaging, and analysis tools to simultaneously map the locations of all neuronal and non-neuronal nuclei and the centerlines and diameters of all blood vessels within thick slabs of neocortex from mice. Based on total inventory measurements of different cortical regions ( approximately 10(7) cells vectorized across brains), these methods revealed: (1) In three dimensions, the mean distance of the center of neuronal somata to the closest microvessel was 15 mum. (2) Volume samples within lamina of a given region show that the density of microvessels does not match the strong laminar variation in neuronal density. This holds for both agranular and granular cortex. (3) Volume samples in successive radii from the midline to the ventral-lateral edge, where each volume summed the number of cells and microvessels from the pia to the white matter, show a significant correlation between neuronal and microvessel densities. These data show that while neuronal and vascular densities do not track each other on the 100 mum scale of cortical lamina, they do track each other on the 1-10 mm scale of the cortical mantle. The absence of a disproportionate density of blood vessels in granular lamina is argued to be consistent with the initial locus of functional brain imaging signals.},
	Author = {Tsai, Philbert S and Kaufhold, John P and Blinder, Pablo and Friedman, Beth and Drew, Patrick J and Karten, Harvey J and Lyden, Patrick D and Kleinfeld, David},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1523/JNEUROSCI.3287-09.2009},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Cell Count; Cell Nucleus; Cerebral Cortex; Mice; Mice, Inbred C57BL; Microvessels; Neurons; Rats; Rats, Sprague-Dawley},
	Month = {Nov},
	Number = {46},
	Pages = {14553-70},
	Pmid = {19923289},
	Pst = {ppublish},
	Title = {Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels},
	Volume = {29},
	Year = {2009},
	File = {papers/Tsai_JNeurosci2009.pdf}}

@article{Erzurumlu:2012,
	Abstract = {In primary sensory neocortical areas of mammals, the distribution of sensory receptors is mapped with topographic precision and amplification in proportion to the peripheral receptor density. The visual, somatosensory and auditory cortical maps are established during a critical period in development. Throughout this window in time, the developing cortical maps are vulnerable to deleterious effects of sense organ damage or sensory deprivation. The rodent barrel cortex offers an invaluable model system with which to investigate the mechanisms underlying the formation of topographic maps and their plasticity during development. Five rows of mystacial vibrissa (whisker) follicles on the snout and an array of sinus hairs are represented by layer IV neural modules ('barrels') and thalamocortical axon terminals in the primary somatosensory cortex. Perinatal damage to the whiskers or the sensory nerve innervating them irreversibly alters the structural organization of the barrels. Earlier studies emphasized the role of the sensory periphery in dictating whisker-specific brain maps and patterns. Recent advances in molecular genetics and analyses of genetically altered mice allow new insights into neural pattern formation in the neocortex and the mechanisms underlying critical period plasticity. Here, we review the development and patterning of the barrel cortex and the critical period plasticity.},
	Author = {Erzurumlu, Reha S and Gaspar, Patricia},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1111/j.1460-9568.2012.08075.x},
	Journal = {Eur J Neurosci},
	Journal-Full = {The European journal of neuroscience},
	Keywords = {downloads},
	Mesh = {Afferent Pathways; Animals; Critical Period (Psychology); Humans; Mice; Models, Biological; Neuronal Plasticity; Neurons; Somatosensory Cortex; Vibrissae},
	Month = {May},
	Number = {10},
	Pages = {1540-53},
	Pmc = {PMC3359866},
	Pmid = {22607000},
	Pst = {ppublish},
	Title = {Development and critical period plasticity of the barrel cortex},
	Volume = {35},
	Year = {2012},
	File = {papers/Erzurumlu_EurJNeurosci2012.pdf}}

@article{Hochberg:2012,
	Abstract = {Paralysis following spinal cord injury, brainstem stroke, amyotrophic lateral sclerosis and other disorders can disconnect the brain from the body, eliminating the ability to perform volitional movements. A neural interface system could restore mobility and independence for people with paralysis by translating neuronal activity directly into control signals for assistive devices. We have previously shown that people with long-standing tetraplegia can use a neural interface system to move and click a computer cursor and to control physical devices. Able-bodied monkeys have used a neural interface system to control a robotic arm, but it is unknown whether people with profound upper extremity paralysis or limb loss could use cortical neuronal ensemble signals to direct useful arm actions. Here we demonstrate the ability of two people with long-standing tetraplegia to use neural interface system-based control of a robotic arm to perform three-dimensional reach and grasp movements. Participants controlled the arm and hand over a broad space without explicit training, using signals decoded from a small, local population of motor cortex (MI) neurons recorded from a 96-channel microelectrode array. One of the study participants, implanted with the sensor 5 years earlier, also used a robotic arm to drink coffee from a bottle. Although robotic reach and grasp actions were not as fast or accurate as those of an able-bodied person, our results demonstrate the feasibility for people with tetraplegia, years after injury to the central nervous system, to recreate useful multidimensional control of complex devices directly from a small sample of neural signals.},
	Author = {Hochberg, Leigh R and Bacher, Daniel and Jarosiewicz, Beata and Masse, Nicolas Y and Simeral, John D and Vogel, Joern and Haddadin, Sami and Liu, Jie and Cash, Sydney S and van der Smagt, Patrick and Donoghue, John P},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1038/nature11076},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Aged; Arm; Calibration; Drinking; Female; Hand; Hand Strength; Humans; Male; Man-Machine Systems; Microelectrodes; Middle Aged; Motor Cortex; Movement; Psychomotor Performance; Quadriplegia; Robotics; Time Factors},
	Month = {May},
	Number = {7398},
	Pages = {372-5},
	Pmid = {22596161},
	Pst = {epublish},
	Title = {Reach and grasp by people with tetraplegia using a neurally controlled robotic arm},
	Volume = {485},
	Year = {2012},
	File = {papers/Hochberg_Nature2012.pdf}}

@article{Ahrens:2012,
	Abstract = {A fundamental question in neuroscience is how entire neural circuits generate behaviour and adapt it to changes in sensory feedback. Here we use two-photon calcium imaging to record the activity of large populations of neurons at the cellular level, throughout the brain of larval zebrafish expressing a genetically encoded calcium sensor, while the paralysed animals interact fictively with a virtual environment and rapidly adapt their motor output to changes in visual feedback. We decompose the network dynamics involved in adaptive locomotion into four types of neuronal response properties, and provide anatomical maps of the corresponding sites. A subset of these signals occurred during behavioural adjustments and are candidates for the functional elements that drive motor learning. Lesions to the inferior olive indicate a specific functional role for olivocerebellar circuitry in adaptive locomotion. This study enables the analysis of brain-wide dynamics at single-cell resolution during behaviour.},
	Author = {Ahrens, Misha B and Li, Jennifer M and Orger, Michael B and Robson, Drew N and Schier, Alexander F and Engert, Florian and Portugues, Ruben},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1038/nature11057},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {downloads},
	Mesh = {Adaptation, Physiological; Animals; Animals, Genetically Modified; Brain; Larva; Learning; Locomotion; Models, Neurological; Nerve Net; Neurons; Neuropil; Photic Stimulation; Psychomotor Performance; Single-Cell Analysis; Zebrafish},
	Month = {May},
	Number = {7399},
	Pages = {471-7},
	Pmid = {22622571},
	Pst = {epublish},
	Title = {Brain-wide neuronal dynamics during motor adaptation in zebrafish},
	Volume = {485},
	Year = {2012},
	File = {papers/Ahrens_Nature2012.pdf}}

@article{Allene:2012,
	Abstract = {During early postnatal development, neuronal networks successively produce various forms of spontaneous patterned activity that provide key signals for circuit maturation. Initially, in both rodent hippocampus and neocortex, coordinated activity emerges in the form of synchronous plateau assemblies (SPAs) that are initiated by sparse groups of gap-junction-coupled oscillating neurons. Subsequently, SPAs are replaced by synapse-driven giant depolarizing potentials (GDPs). Whether these sequential changes in mechanistically distinct network activities correlate with modifications in single-cell properties is unknown. To determine this, we studied the morphophysiological fate of single SPA cells as a function of development. We focused on CA3 GABAergic interneurons, which are centrally involved in generating GDPs in the hippocampus. As the network matures, GABAergic neurons are engaged more in GDPs and less in SPAs. Using inducible genetic fate mapping, we show that the individual involvement of GABAergic neurons in SPAs is correlated to their temporal origin. In addition, we demonstrate that the SPA-to-GDP transition is paralleled by a remarkable maturation in the morphophysiological properties of GABAergic neurons. Compared with those involved in GDPs, interneurons participating in SPAs possess immature intrinsic properties, receive synaptic inputs spanning a wide amplitude range, and display large somata as well as membrane protrusions. Thus, a developmental switch in the morphophysiological properties of GABAergic interneurons as they progress from SPAs to GDPs marks the emergence of synapse-driven network oscillations.},
	Author = {Allene, Camille and Picardo, Michel A and Becq, H{\'e}l{\`e}ne and Miyoshi, Goichi and Fishell, Gord and Cossart, Rosa},
	Date-Added = {2013-04-01 16:06:55 +0000},
	Date-Modified = {2013-04-01 16:07:16 +0000},
	Doi = {10.1523/JNEUROSCI.0081-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Animals, Newborn; Female; Gene Knock-In Techniques; Hippocampus; Interneurons; Male; Mice; Mice, Transgenic; Nerve Net; Organ Culture Techniques},
	Month = {May},
	Number = {19},
	Pages = {6688-98},
	Pmc = {PMC3371585},
	Pmid = {22573691},
	Pst = {ppublish},
	Title = {Dynamic changes in interneuron morphophysiological properties mark the maturation of hippocampal network activity},
	Volume = {32},
	Year = {2012},
	File = {papers/Allene_JNeurosci2012.pdf}}

@article{Beurdeley:2012,
	Abstract = {Specific transfer of (orthodenticle homeobox 2) Otx2 homeoprotein into GABAergic interneurons expressing parvalbumin (PV) is necessary and sufficient to open, then close, a critical period (CP) of plasticity in the developing mouse visual cortex. The accumulation of endogenous Otx2 in PV cells suggests the presence of specific Otx2 binding sites. Here, we find that perineuronal nets (PNNs) on the surfaces of PV cells permit the specific, constitutive capture of Otx2. We identify a 15 aa domain containing an arginine-lysine doublet (RK peptide) within Otx2, bearing prototypic traits of a glycosaminoglycan (GAG) binding sequence that mediates Otx2 binding to PNNs, and specifically to chondroitin sulfate D and E, with high affinity. Accordingly, PNN hydrolysis by chondroitinase ABC reduces the amount of endogenous Otx2 in PV cells. Direct infusion of RK peptide similarly disrupts endogenous Otx2 localization to PV cells, reduces PV and PNN expression, and reopens plasticity in adult mice. The closure of one eye during this transient window reduces cortical acuity and is specific to the RK motif, as an Alanine-Alanine variant or a scrambled peptide fails to reactivate plasticity. Conversely, this transient reopening of plasticity in the adult restores binocular vision in amblyopic mice. Thus, one function of PNNs is to facilitate the persistent internalization of Otx2 by PV cells to maintain CP closure. The pharmacological use of the Otx2 GAG binding domain offers a novel, potent therapeutic tool with which to restore cortical plasticity in the mature brain.},
	Author = {Beurdeley, Marine and Spatazza, Julien and Lee, Henry H C and Sugiyama, Sayaka and Bernard, Cl{\'e}mence and Di Nardo, Ariel A and Hensch, Takao K and Prochiantz, Alain},
	Date-Added = {2013-04-01 16:06:07 +0000},
	Date-Modified = {2013-04-01 16:06:22 +0000},
	Doi = {10.1523/JNEUROSCI.0394-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Age Factors; Animals; Extracellular Matrix; GABAergic Neurons; Interneurons; Male; Mice; Mice, Inbred C57BL; Neuronal Plasticity; Otx Transcription Factors; Protein Binding; Visual Cortex},
	Month = {Jul},
	Number = {27},
	Pages = {9429-37},
	Pmc = {PMC3419577},
	Pmid = {22764251},
	Pst = {ppublish},
	Title = {Otx2 binding to perineuronal nets persistently regulates plasticity in the mature visual cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Beurdeley_JNeurosci2012.pdf}}

@article{Guo:2012,
	Abstract = {Topographically organized maps of the sensory receptor epithelia are regarded as cornerstones of cortical organization as well as valuable readouts of diverse biological processes ranging from evolution to neural plasticity. However, maps are most often derived from multiunit activity recorded in the thalamic input layers of anesthetized animals using near-threshold stimuli. Less distinct topography has been described by studies that deviated from the formula above, which brings into question the generality of the principle. Here, we explicitly compared the strength of tonotopic organization at various depths within core and belt regions of the auditory cortex using electrophysiological measurements ranging from single units to delta-band local field potentials (LFP) in the awake and anesthetized mouse. Unit recordings in the middle cortical layers revealed a precise tonotopic organization in core, but not belt, regions of auditory cortex that was similarly robust in awake and anesthetized conditions. In core fields, tonotopy was degraded outside the middle layers or when LFP signals were substituted for unit activity, due to an increasing proportion of recording sites with irregular tuning for pure tones. However, restricting our analysis to clearly defined receptive fields revealed an equivalent tonotopic organization in all layers of the cortical column and for LFP activity ranging from gamma to theta bands. Thus, core fields represent a transition between topographically organized simple receptive field arrangements that extend throughout all layers of the cortical column and the emergence of nontonotopic representations outside the input layers that are further elaborated in the belt fields.},
	Author = {Guo, Wei and Chambers, Anna R and Darrow, Keith N and Hancock, Kenneth E and Shinn-Cunningham, Barbara G and Polley, Daniel B},
	Date-Added = {2013-04-01 16:05:33 +0000},
	Date-Modified = {2013-04-01 16:05:43 +0000},
	Doi = {10.1523/JNEUROSCI.0065-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {downloads},
	Mesh = {Animals; Auditory Cortex; Auditory Pathways; Auditory Perception; Brain Mapping; Electrophysiology; Evoked Potentials, Auditory; Female; Mice; Mice, Inbred CBA; Neural Pathways; Neurons; Signal Processing, Computer-Assisted; Signal Transduction},
	Month = {Jul},
	Number = {27},
	Pages = {9159-72},
	Pmc = {PMC3402176},
	Pmid = {22764225},
	Pst = {ppublish},
	Title = {Robustness of cortical topography across fields, laminae, anesthetic states, and neurophysiological signal types},
	Volume = {32},
	Year = {2012},
	File = {papers/Guo_JNeurosci2012.pdf}}

@article{Sansom:2009,
	Abstract = {In the developing brain, gradients are commonly used to divide neurogenic regions into distinct functional domains. In this article, we discuss the functions of morphogen and gene expression gradients in the assembly of the nervous system in the context of the development of the cerebral cortex. The cerebral cortex is a mammal-specific region of the forebrain that functions at the top of the neural hierarchy to process and interpret sensory information, plan and organize tasks, and to control motor functions. The mature cerebral cortex is a modular structure, consisting of anatomically and functionally distinct areas. Those areas of neurons are generated from a uniform neuroepithelial sheet by two forms of gradients: graded extracellular signals and a set of transcription factor gradients operating across the field of neocortical stem cells. Fgf signaling from the rostral pole of the cerebral cortex sets up gradients of expression of transcription factors by both activating and repressing gene expression. However, in contrast to the spinal cord and the early Drosophila embryo, these gradients are not subsequently resolved into molecularly distinct domains of gene expression. Instead, graded information in stem cells is translated into discrete, region-specific gene expression in the postmitotic neuronal progeny of the stem cells.},
	Author = {Sansom, Stephen N and Livesey, Frederick J},
	Date-Added = {2013-04-01 16:02:24 +0000},
	Date-Modified = {2013-04-23 17:54:57 +0000},
	Doi = {10.1101/cshperspect.a002519},
	Journal = {Cold Spring Harb Perspect Biol},
	Journal-Full = {Cold Spring Harbor perspectives in biology},
	Keywords = {Cerebral Cortex; Neocortex; patterning; topographic map; development; Gene Expression; toread; neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Mesh = {Animals; Brain; Cerebral Cortex; Drosophila; Fibroblast Growth Factors; Gene Expression Regulation, Developmental; Mice; Models, Biological; Motor Cortex; Nervous System; Neurons; Spinal Cord; Stem Cells; Transcription Factors},
	Month = {Aug},
	Number = {2},
	Pages = {a002519},
	Pmc = {PMC2742095},
	Pmid = {20066088},
	Pst = {ppublish},
	Title = {Gradients in the brain: the control of the development of form and function in the cerebral cortex},
	Volume = {1},
	Year = {2009},
	File = {papers/Sansom_ColdSpringHarbPerspectBiol2009.pdf}}

@article{Courchet:2012,
	Abstract = {In this issue of Neuron, Harwell et al. (2012) identify a new role for the secreted molecule Shh and its receptor Boc in synapse formation. These results add an unexpected new player to the expanding list of extracellular cues regulating the spatial specificity of synapse formation.},
	Author = {Courchet, Julien and Polleux, Franck},
	Date-Added = {2013-04-01 15:51:29 +0000},
	Date-Modified = {2013-04-01 15:52:12 +0000},
	Doi = {10.1016/j.neuron.2012.03.008},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {development; patterning; Cerebral Cortex; Neocortex; Laterality},
	Mesh = {Animals; Cerebral Cortex; Gene Expression Regulation, Developmental; Hedgehog Proteins; Nerve Net; Neurons; Pyramidal Tracts},
	Month = {Mar},
	Number = {6},
	Pages = {1055-8},
	Pmid = {22445332},
	Pst = {ppublish},
	Title = {Sonic hedgehog, BOC, and synaptic development: new players for an old game},
	Volume = {73},
	Year = {2012},
	File = {papers/Courchet_Neuron2012.pdf}}

@article{Johansen-Berg:2012,
	Abstract = {How rapidly does learning shape our brains? A new study in this issue of Neuron by Sagi et al. (2012) that uses diffusion magnetic resonance imaging in both humans and rats suggests that just 2 hr of spatial learning is sufficient to change brain structure.},
	Author = {Johansen-Berg, Heidi and Baptista, Cassandra Sampaio and Thomas, Adam G},
	Date-Added = {2013-04-01 15:49:05 +0000},
	Date-Modified = {2013-04-01 15:51:08 +0000},
	Doi = {10.1016/j.neuron.2012.03.001},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread; plasticity; structural remodeling; Structure-Activity Relationship; human; MRI; DTI},
	Mesh = {Animals; Brain; Brain Mapping; Female; Humans; Learning; Male; Neuronal Plasticity},
	Month = {Mar},
	Number = {6},
	Pages = {1058-60},
	Pmc = {PMC3353540},
	Pmid = {22445333},
	Pst = {ppublish},
	Title = {Human structural plasticity at record speed},
	Volume = {73},
	Year = {2012},
	File = {papers/Johansen-Berg_Neuron2012.pdf}}

@article{Eglen:2003,
	Abstract = {A role for spontaneous spiking activity in shaping neuronal circuits has frequently been debated. Analyses of retinotopy in mutant mice with reduced correlated firing among neighboring retinal cells by Grubb et al. and McLaughlin et al. in this issue of Neuron indicate the importance of patterned spontaneous activity for retinotopic map refinement in subcortical visual targets.},
	Author = {Eglen, Stephen J and Demas, Jay and Wong, Rachel O L},
	Date-Added = {2013-04-01 15:47:38 +0000},
	Date-Modified = {2013-04-01 15:48:47 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {spontaneous activity; development; topographic map; patterning; Cerebral Cortex; Neocortex; visual system; retinal waves},
	Mesh = {Action Potentials; Animals; Humans; Neural Pathways; Photic Stimulation; Retina; Retinal Ganglion Cells},
	Month = {Dec},
	Number = {6},
	Pages = {1053-5},
	Pmid = {14687538},
	Pst = {ppublish},
	Title = {Mapping by waves. Patterned spontaneous activity regulates retinotopic map refinement},
	Volume = {40},
	Year = {2003},
	File = {papers/Eglen_Neuron2003.pdf}}

@article{Harwell:2012,
	Abstract = {The precise connectivity of inputs and outputs is critical for cerebral cortex function; however, the cellular mechanisms that establish these connections are poorly understood. Here, we show that the secreted molecule Sonic Hedgehog (Shh) is involved in synapse formation of a specific cortical circuit. Shh is expressed in layer V corticofugal projection neurons and the Shh receptor, Brother of CDO (Boc), is expressed in local and callosal projection neurons of layer II/III that synapse onto the subcortical projection neurons. Layer V neurons of mice lacking functional Shh exhibit decreased synapses. Conversely, the loss of functional Boc leads to a reduction in the strength of synaptic connections onto layer Vb, but not layer II/III, pyramidal neurons. These results demonstrate that Shh is expressed in postsynaptic target cells while Boc is expressed in a complementary population of presynaptic input neurons, and they function to guide the formation of cortical microcircuitry. VIDEO ABSTRACT:},
	Author = {Harwell, Corey C and Parker, Philip R L and Gee, Steven M and Okada, Ami and McConnell, Susan K and Kreitzer, Anatol C and Kriegstein, Arnold R},
	Date-Added = {2013-04-01 15:45:55 +0000},
	Date-Modified = {2013-04-01 15:47:20 +0000},
	Doi = {10.1016/j.neuron.2012.02.009},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread; development; Neocortex; Gene Expression; Cerebral Cortex; patterning; lateralization},
	Mesh = {Age Factors; Animals; Animals, Newborn; Cerebral Cortex; Corpus Callosum; DNA-Binding Proteins; Dendritic Spines; Electric Stimulation; Electroporation; Fluorobenzenes; Functional Laterality; Furans; Gene Expression Regulation, Developmental; Hedgehog Proteins; Immunoglobulin G; Luminescent Proteins; Matrix Attachment Region Binding Proteins; Membrane Potentials; Mice; Mice, Transgenic; Mutation; Nerve Net; Neurons; Nuclear Proteins; Patch-Clamp Techniques; Phosphopyruvate Hydratase; Pyramidal Tracts; RNA, Small Interfering; Receptors, Cell Surface; Repressor Proteins; Rhodopsin; Silver Staining; Stilbamidines; Synapses; Synaptophysin; Transcription Factors; Tumor Suppressor Proteins; gamma-Aminobutyric Acid},
	Month = {Mar},
	Number = {6},
	Pages = {1116-26},
	Pmc = {PMC3551478},
	Pmid = {22445340},
	Pst = {ppublish},
	Title = {Sonic hedgehog expression in corticofugal projection neurons directs cortical microcircuit formation},
	Volume = {73},
	Year = {2012},
	File = {papers/Harwell_Neuron2012.pdf}}

@article{Schutz-Bosbach:2007,
	Abstract = {A direct relationship between perception and action implies bi-directionality, and predicts not only effects of perception on action but also effects of action on perception. Modern theories of social cognition have intensively examined the relation from perception to action and propose that mirroring the observed actions of others underlies action understanding. Here, we suggest that this view is incomplete, as it neglects the perspective of the actor. We will review empirical evidence showing the effects of self-generated action on perceptual judgments. We propose that producing action might prime perception in a way that observers are selectively sensitive to related or similar actions of conspecifics. Therefore, perceptual resonance, not motor resonance, might be decisive for grounding sympathy and empathy and, thus, successful social interactions.},
	Author = {Sch{\"u}tz-Bosbach, Simone and Prinz, Wolfgang},
	Date-Added = {2013-04-01 15:25:56 +0000},
	Date-Modified = {2013-04-01 15:25:56 +0000},
	Doi = {10.1016/j.tics.2007.06.005},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Mesh = {Auditory Perception; Brain Mapping; Cerebral Cortex; Cognition; Concept Formation; Humans; Imagination; Interpersonal Relations; Judgment; Kinesthesis; Motor Activity; Neurons; Perception; Psychomotor Performance; Self Concept; Visual Perception},
	Month = {Aug},
	Number = {8},
	Pages = {349-55},
	Pmid = {17629544},
	Pst = {ppublish},
	Title = {Perceptual resonance: action-induced modulation of perception},
	Volume = {11},
	Year = {2007},
	File = {papers/Schütz-Bosbach_TrendsCognSci2007.pdf}}

@article{Nataraj:2010,
	Abstract = {In visual cortex monocular deprivation (MD) during a critical period (CP) reduces the ability of the deprived eye to activate cortex, but the underlying cellular plasticity mechanisms are incompletely understood. Here we show that MD reduces the intrinsic excitability of layer 5 (L5) pyramidal neurons and enhances long-term potentiation of intrinsic excitability (LTP-IE). Further, MD and LTP-IE induce reciprocal changes in K(v)2.1 current, and LTP-IE reverses the effects of MD on intrinsic excitability. Taken together these data suggest that MD reduces intrinsic excitability by preventing sensory-drive induced LTP-IE. The effects of MD on excitability were correlated with the classical visual system CP, and (like the functional effects of MD) could be rapidly reversed when vision was restored. These data establish LTP-IE as a candidate mechanism mediating loss of visual responsiveness within L5, and suggest that intrinsic plasticity plays an important role in experience-dependent refinement of visual cortical circuits.},
	Author = {Nataraj, Kiran and Le Roux, Nicolas and Nahmani, Marc and Lefort, Sandrine and Turrigiano, Gina},
	Date-Added = {2013-04-01 15:23:07 +0000},
	Date-Modified = {2013-04-01 15:23:17 +0000},
	Doi = {10.1016/j.neuron.2010.09.033},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {downloads},
	Mesh = {Animals; Animals, Newborn; Mice; Neural Inhibition; Neuronal Plasticity; Neurons; Pyramidal Cells; Rats; Rats, Long-Evans; Sensory Deprivation; Visual Cortex; Visual Perception},
	Month = {Nov},
	Number = {4},
	Pages = {750-62},
	Pmc = {PMC2990987},
	Pmid = {21092863},
	Pst = {ppublish},
	Title = {Visual deprivation suppresses L5 pyramidal neuron excitability by preventing the induction of intrinsic plasticity},
	Volume = {68},
	Year = {2010},
	File = {papers/Nataraj_Neuron2010.pdf}}

@article{Zheng:2004,
	Abstract = {Dual patch-clamp recording and Ca2+ uncaging revealed Ca2+-dependent corelease of ACh and GABA from, and the presence of reciprocal nicotinic and GABAergic synapses between, starburst cells in the perinatal rabbit retina. With maturation, the nicotinic synapses between starburst cells dramatically diminished, whereas the GABAergic synapses remained and changed from excitatory to inhibitory, indicating a coordinated conversion of the starburst network excitability from an early hyperexcitatory to a mature nonepileptic state. We show that this transition allows the starburst cells to use their neurotransmitters for two completely different functions. During early development, the starburst network mediates recurrent excitation and spontaneous retinal waves, which are important for visual system development. After vision begins, starburst cells release GABA in a prolonged and Ca2+-dependent manner and inhibit each other laterally via direct GABAergic synapses, which may be important for visual integration, such as the detection of motion direction.},
	Author = {Zheng, Ji-Jian and Lee, Seunghoon and Zhou, Z Jimmy},
	Date-Added = {2013-04-01 15:21:15 +0000},
	Date-Modified = {2013-08-15 13:00:54 +0000},
	Doi = {10.1016/j.neuron.2004.11.015},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {retinal waves; Rabbits; spontaneous activity; Acetylcholine; retina; visual system; in vitro; calcium imaging; Patch-Clamp Techniques},
	Mesh = {Acetylcholine; Aging; Animals; Electrophysiology; Embryo, Mammalian; Nerve Net; Nicotine; Patch-Clamp Techniques; Rabbits; Retina; Synapses; Vision, Ocular; gamma-Aminobutyric Acid},
	Month = {Dec},
	Number = {5},
	Pages = {851-64},
	Pmid = {15572115},
	Pst = {ppublish},
	Title = {A developmental switch in the excitability and function of the starburst network in the mammalian retina},
	Volume = {44},
	Year = {2004},
	File = {papers/Zheng_Neuron2004.pdf}}

@article{Vanderhaeghen:2004,
	Abstract = {Roger Sperry proposed 40 years ago that topographic neural connections are established through complementary expression of chemoaffinity labels in projecting neurons and their final targets. This led to the identification of ephrins as key molecular cues controlling the topography of retinotectal projections. Recent studies have revealed a surprising twist to this model, shedding light on the developmental mechanisms patterning the projections between the thalamus and the cortex: ephrins, unexpectedly expressed in an intermediate target, control the establishment of topography of axonal projections between these two structures. The same cues are re-used later to control the mapping of thalamocortical projections within a given cortical area, which strikingly illustrates how a limited set of genes can contribute to generate several levels of complexity of a neuronal network.},
	Author = {Vanderhaeghen, Pierre and Polleux, Franck},
	Date-Added = {2013-04-01 15:19:28 +0000},
	Date-Modified = {2017-05-05 21:54:52 +0000},
	Doi = {10.1016/j.tins.2004.05.009},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {Research Support, Non-U.S. Gov't;Neurophysiology;Neural Pathways;Research Support, U.S. Gov't, P.H.S.;Animals;Thalamus;Cerebral Cortex;review;Humans},
	Mesh = {Animals; Cerebral Cortex; Humans; Neural Pathways; Thalamus},
	Month = {Jul},
	Number = {7},
	Pages = {384-91},
	Pmid = {15219737},
	Pst = {ppublish},
	Title = {Developmental mechanisms patterning thalamocortical projections: intrinsic, extrinsic and in between},
	Volume = {27},
	Year = {2004},
	File = {papers/Vanderhaeghen_TrendsNeurosci2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tins.2004.05.009}}

@article{Stahl:2004,
	Abstract = {Examining eye movements is an important part of the neurological evaluation of humans; the distribution of the neural circuits that control these movements is such that they are disrupted--often in highly characteristic fashions--by many disease processes. Technical advances have made it possible to measure accurately the eye movements of mice, so it is now possible to use the detective power of eye movement recording to characterize neurological dysfunction in genetically altered strains. Here we introduce analytical tools used in ocular motor research and demonstrate their ability to reveal disorders of the visual pathways, inner ear, and cerebellum.},
	Author = {Stahl, John S},
	Date-Added = {2013-04-01 15:15:48 +0000},
	Date-Modified = {2017-10-27 18:23:27 +0000},
	Doi = {10.1016/j.visres.2004.09.011},
	Journal = {Vision Res},
	Journal-Full = {Vision research},
	Mesh = {Animals; Brain Diseases; Disease Models, Animal; Eye Movements; Mice; Mice, Neurologic Mutants; Nystagmus, Optokinetic; Psychomotor Performance; Reflex, Vestibulo-Ocular; Visual Pathways},
	Month = {Dec},
	Number = {28},
	Pages = {3401-10},
	Pmid = {15536008},
	Pst = {ppublish},
	Title = {Using eye movements to assess brain function in mice},
	Volume = {44},
	Year = {2004},
	File = {papers/Stahl_VisionRes2004.pdf}}

@article{Charrier:2012,
	Abstract = {Structural genomic variations represent a major driving force of evolution, and a burst of large segmental gene duplications occurred in the human lineage during its separation from nonhuman primates. SRGAP2, a gene recently implicated in neocortical development, has undergone two human-specific duplications. Here, we find that both duplications (SRGAP2B and SRGAP2C) are partial and encode a truncated F-BAR domain. SRGAP2C is expressed in the developing and adult human brain and dimerizes with ancestral SRGAP2 to inhibit its function. In the mouse neocortex, SRGAP2 promotes spine maturation and limits spine density. Expression of SRGAP2C phenocopies SRGAP2 deficiency. It underlies sustained radial migration and leads to the emergence of human-specific features, including neoteny during spine maturation and increased density of longer spines. These results suggest that inhibition of SRGAP2 function by its human-specific paralogs has contributed to the evolution of the human neocortex and plays an important role during human brain development.},
	Author = {Charrier, C{\'e}cile and Joshi, Kaumudi and Coutinho-Budd, Jaeda and Kim, Ji-Eun and Lambert, Nelle and de Marchena, Jacqueline and Jin, Wei-Lin and Vanderhaeghen, Pierre and Ghosh, Anirvan and Sassa, Takayuki and Polleux, Franck},
	Date-Added = {2013-04-01 15:15:21 +0000},
	Date-Modified = {2013-04-01 15:15:28 +0000},
	Doi = {10.1016/j.cell.2012.03.034},
	Journal = {Cell},
	Journal-Full = {Cell},
	Keywords = {downloads},
	Mesh = {Animals; Brain; Cell Movement; Dendritic Spines; Evolution, Molecular; GTPase-Activating Proteins; Gene Duplication; Humans; Mice; Molecular Sequence Data; Neurons; Protein Structure, Tertiary; Segmental Duplications, Genomic; Species Specificity},
	Month = {May},
	Number = {4},
	Pages = {923-35},
	Pmc = {PMC3357949},
	Pmid = {22559944},
	Pst = {ppublish},
	Title = {Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation},
	Volume = {149},
	Year = {2012},
	File = {papers/Charrier_Cell2012.pdf}}

@article{Tamietto:2012,
	Abstract = {Nonconscious [1-6], rapid [7, 8], or coarse [9] visual processing of emotional stimuli induces functional activity in a subcortical pathway to the amygdala involving the superior colliculus and pulvinar. Despite evidence in lower mammals [10, 11] and nonhuman primates [12], it remains speculative whether anatomical connections between these structures exist in the human brain [13-15]. It is also unknown whether destruction of the visual cortex, which provides a major input to the amygdala, induces modifications in anatomical connections along this subcortical pathway. We used diffusion tensor imaging to investigate in vivo anatomical connections between human amygdala and subcortical visual structures in ten age-matched controls and in one patient with early unilateral destruction of the visual cortex. We found fiber connections between pulvinar and amygdala and also between superior colliculus and amygdala via the pulvinar in the controls as well as in the patient. Destruction of the visual cortex led to qualitative and quantitative modifications along the pathways connecting these three structures and the changes were confined to the patient's damaged hemisphere. The present findings thus show extensive neural plasticity in the anatomical connections between subcortical visual structures of old evolutionary origin involved in the processing of emotional stimuli.},
	Author = {Tamietto, Marco and Pullens, Pim and de Gelder, Beatrice and Weiskrantz, Lawrence and Goebel, Rainer},
	Date-Added = {2013-04-01 15:11:46 +0000},
	Date-Modified = {2013-04-01 15:13:27 +0000},
	Doi = {10.1016/j.cub.2012.06.006},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {downloads},
	Mesh = {Amygdala; Brain Injuries; Case-Control Studies; Child; Diffusion Tensor Imaging; Humans; Male; Middle Aged; Superior Colliculi; Visual Cortex},
	Month = {Aug},
	Number = {15},
	Pages = {1449-55},
	Pmid = {22748315},
	Pst = {ppublish},
	Title = {Subcortical connections to human amygdala and changes following destruction of the visual cortex},
	Volume = {22},
	Year = {2012},
	File = {papers/Tamietto_CurrBiol2012.pdf},
	Bdsk-File-2 = {papers/Tamietto_CurrBiol2012a.pdf}}

@article{Hoshiko:2012,
	Abstract = {Accumulative evidence indicates that microglial cells influence the normal development of brain synapses. Yet, the mechanisms by which these immune cells target maturating synapses and influence their functional development at early postnatal stages remain poorly understood. Here, we analyzed the role of CX3CR1, a microglial receptor activated by the neuronal chemokine CX3CL1 (or fractalkine) which controls key functions of microglial cells. In the whisker-related barrel field of the mouse somatosensory cortex, we show that the recruitment of microglia to the sites where developing thalamocortical synapses are concentrated (i.e., the barrel centers) occurs only after postnatal day 5 and is controlled by the fractalkine/CX3CR1 signaling pathway. Indeed, at this developmental stage fractalkine is overexpressed within the barrels and CX3CR1 deficiency delays microglial cell recruitment into the barrel centers. Functional analysis of thalamocortical synapses shows that CX3CR1 deficiency also delays the functional maturation of postsynaptic glutamate receptors which normally occurs at these synapses between the first and second postnatal week. These results show that reciprocal interactions between neurons and microglial cells control the functional maturation of cortical synapses.},
	Author = {Hoshiko, Maki and Arnoux, Isabelle and Avignone, Elena and Yamamoto, Nobuhiko and Audinat, Etienne},
	Date-Added = {2013-03-19 14:24:43 +0000},
	Date-Modified = {2013-03-19 14:25:58 +0000},
	Doi = {10.1523/JNEUROSCI.1167-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; microglia; Thalamic Nuclei; Cerebral Cortex; Neocortex; barrels; Somatosensory Cortex},
	Mesh = {Age Factors; Animals; Animals, Newborn; Chemokine CX3CL1; Developmental Disabilities; Electric Stimulation; Excitatory Amino Acid Antagonists; Excitatory Postsynaptic Potentials; Female; GABA Antagonists; Gene Expression Regulation, Developmental; Green Fluorescent Proteins; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Microglia; Receptors, Chemokine; Serotonin Plasma Membrane Transport Proteins; Somatosensory Cortex; Statistics, Nonparametric; Synapses; Thalamus},
	Month = {Oct},
	Number = {43},
	Pages = {15106-11},
	Pmid = {23100431},
	Pst = {ppublish},
	Title = {Deficiency of the microglial receptor CX3CR1 impairs postnatal functional development of thalamocortical synapses in the barrel cortex},
	Volume = {32},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.1167-12.2012}}

@article{Sato:2012a,
	Abstract = {The mammalian neocortex is composed of various types of neurons that reflect its laminar and area structures. It has been suggested that not only intrinsic but also afferent-derived extrinsic factors are involved in neuronal differentiation during development. However, the role and molecular mechanism of such extrinsic factors are almost unknown. Here, we attempted to identify molecules that are expressed in the thalamus and affect cortical cell development. First, thalamus-specific molecules were sought by comparing gene expression profiles of the developing rat thalamus and cortex using microarrays, and by constructing a thalamus-enriched subtraction cDNA library. A systematic screening by in situ hybridization showed that several genes encoding extracellular molecules were strongly expressed in sensory thalamic nuclei. Exogenous and endogenous protein localization further demonstrated that two extracellular molecules, Neuritin-1 (NRN1) and VGF, were transported to thalamic axon terminals. Application of NRN1 and VGF to dissociated cell culture promoted the dendritic growth. An organotypic slice culture experiment further showed that the number of primary dendrites in multipolar stellate neurons increased in response to NRN1 and VGF, whereas dendritic growth of pyramidal neurons was not promoted. These molecules also increased neuronal survival of multipolar neurons. Taken together, these results suggest that the thalamus-specific molecules NRN1 and VGF play an important role in the dendritic growth and survival of cortical neurons in a cell type-specific manner.},
	Author = {Sato, Haruka and Fukutani, Yuma and Yamamoto, Yuji and Tatara, Eiichi and Takemoto, Makoto and Shimamura, Kenji and Yamamoto, Nobuhiko},
	Date-Added = {2013-03-19 14:24:29 +0000},
	Date-Modified = {2013-03-19 14:27:20 +0000},
	Doi = {10.1523/JNEUROSCI.0293-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; rodent; rat; mouse; Visual Cortex; Somatosensory Cortex; thalamus; Gene Expression; Gene Expression Profiling; extrinsic; Growth Factor},
	Mesh = {Animals; Antibodies, Blocking; Cell Survival; Cells, Cultured; Cerebral Cortex; DNA Primers; DNA, Complementary; Dendrites; Electroporation; Female; GPI-Linked Proteins; Genetic Vectors; Immunohistochemistry; In Situ Hybridization; Male; Microarray Analysis; Neurons; Neuropeptides; Plasmids; Pregnancy; Presynaptic Terminals; Rats; Rats, Sprague-Dawley; Thalamus; Transfection},
	Month = {Oct},
	Number = {44},
	Pages = {15388-402},
	Pmid = {23115177},
	Pst = {ppublish},
	Title = {Thalamus-derived molecules promote survival and dendritic growth of developing cortical neurons},
	Volume = {32},
	Year = {2012},
	File = {papers/Sato_JNeurosci2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0293-12.2012}}

@article{Jin:2011,
	Abstract = {Reduced synaptic inhibition is an important factor contributing to posttraumatic epileptogenesis. Axonal sprouting and enhanced excitatory synaptic connectivity onto rodent layer V pyramidal (Pyr) neurons occur in epileptogenic partially isolated (undercut) neocortex. To determine if enhanced excitation also affects inhibitory circuits, we used laser scanning photostimulation of caged glutamate and whole-cell recordings from GAD67-GFP-expressing mouse fast spiking (FS) interneurons and Pyr cells in control and undercut in vitro slices to map excitatory and inhibitory synaptic inputs. Results are 1) the region-normalized excitatory postsynaptic current (EPSC) amplitudes and proportion of uncaging sites from which EPSCs could be evoked (hotspot ratio) "increased" significantly in FS cells of undercut slices; 2) in contrast, these parameters were significantly "decreased" for inhibitory postsynaptic currents (IPSCs) in undercut FS cells; and 3) in rat layer V Pyr neurons, we found significant decreases in IPSCs in undercut versus control Pyr neurons. The decreases were mainly located in layers II and IV, suggesting a reduction in the efficacy of interlaminar synaptic inhibition. Results suggest that there is significant synaptic reorganization in this model of posttraumatic epilepsy, resulting in increased excitatory drive and reduced inhibitory input to FS interneurons that should enhance their inhibitory output and, in part, offset similar alterations in innervation of Pyr cells.},
	Author = {Jin, Xiaoming and Huguenard, John R and Prince, David A},
	Date-Added = {2013-02-19 18:47:04 +0000},
	Date-Modified = {2013-02-19 18:48:48 +0000},
	Doi = {10.1093/cercor/bhq181},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {Epilepsy; inhibition; Development; neurophysiology; Interneurons; Pyramidal Cells; Neocortex; optical physiology; transgenic; mouse; mice; Patch-Clamp Techniques; Stimulation},
	Mesh = {Animals; Brain Damage, Chronic; Disease Models, Animal; Epilepsy; Mice; Mice, Transgenic; Microscopy, Confocal; Neocortex; Neural Inhibition; Neural Pathways; Organ Culture Techniques; Photic Stimulation; Rats; Synaptic Transmission},
	Month = {May},
	Number = {5},
	Pages = {1094-104},
	Pmc = {PMC3077430},
	Pmid = {20855494},
	Pst = {ppublish},
	Title = {Reorganization of inhibitory synaptic circuits in rodent chronically injured epileptogenic neocortex},
	Volume = {21},
	Year = {2011},
	File = {papers/Jin_CerebCortex2011.pdf}}

@article{Tiriac:2012,
	Abstract = {Spontaneous activity in the sensory periphery drives infant brain activity and is thought to contribute to the formation of retinotopic and somatotopic maps. In infant rats during active (or REM) sleep, brainstem-generated spontaneous activity triggers hundreds of thousands of skeletal muscle twitches each day; sensory feedback from the resulting limb movements is a primary activator of forebrain activity. The rodent whisker system, with its precise isomorphic mapping of individual whiskers to discrete brain areas, has been a key contributor to our understanding of somatotopic maps and developmental plasticity. But although whisker movements are controlled by dedicated skeletal muscles, spontaneous whisker activity has not been entertained as a contributing factor to the development of this system. Here we report in 3- to 6-day-old rats that whiskers twitch rapidly and asynchronously during active sleep; furthermore, neurons in whisker thalamus exhibit bursts of activity that are tightly associated with twitches but occur infrequently during waking. Finally, we observed barrel-specific cortical activity during periods of twitching. This is the first report of self-generated, sleep-related twitches in the developing whisker system, a sensorimotor system that is unique for the precision with which it can be experimentally manipulated. The discovery of whisker twitching will allow us to attain a better understanding of the contributions of peripheral sensory activity to somatosensory integration and plasticity in the developing nervous system.},
	Author = {Tiriac, Alexandre and Uitermarkt, Brandt D and Fanning, Alexander S and Sokoloff, Greta and Blumberg, Mark S},
	Date-Added = {2013-02-19 18:45:31 +0000},
	Date-Modified = {2013-02-19 18:46:22 +0000},
	Doi = {10.1016/j.cub.2012.09.009},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {Somatosensory Cortex; topographic map; development; sensory-motor; barrels; Neocortex; Rats},
	Month = {Nov},
	Number = {21},
	Pages = {2075-80},
	Pmc = {PMC3494768},
	Pmid = {23084988},
	Pst = {ppublish},
	Title = {Rapid whisker movements in sleeping newborn rats},
	Volume = {22},
	Year = {2012},
	File = {papers/Tiriac_CurrBiol2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cub.2012.09.009}}

@article{Chen:2012,
	Abstract = {The ability to chronically monitor neuronal activity in the living brain is essential for understanding the organization and function of the nervous system. The genetically encoded green fluorescent protein-based calcium sensor GCaMP provides a powerful tool for detecting calcium transients in neuronal somata, processes, and synapses that are triggered by neuronal activities. Here we report the generation and characterization of transgenic mice that express improved GCaMPs in various neuronal subpopulations under the control of the Thy1 promoter. In vitro and in vivo studies show that calcium transients induced by spontaneous and stimulus-evoked neuronal activities can be readily detected at the level of individual cells and synapses in acute brain slices, as well as chronically in awake, behaving animals. These GCaMP transgenic mice allow investigation of activity patterns in defined neuronal populations in the living brain and will greatly facilitate dissecting complex structural and functional relationships of neural networks.},
	Author = {Chen, Qian and Cichon, Joseph and Wang, Wenting and Qiu, Li and Lee, Seok-Jin R and Campbell, Nolan R and Destefino, Nicholas and Goard, Michael J and Fu, Zhanyan and Yasuda, Ryohei and Looger, Loren L and Arenkiel, Benjamin R and Gan, Wen-Biao and Feng, Guoping},
	Date-Added = {2013-02-19 18:43:41 +0000},
	Date-Modified = {2013-02-19 18:44:39 +0000},
	Doi = {10.1016/j.neuron.2012.07.011},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {in vivo; mouse; mice; transgenic; Transgenes; calcium sensor; calcium imaging; optical physiology; technique},
	Mesh = {Age Factors; Animals; Antigens, Thy-1; Biophysics; Brain; Calcium; Calmodulin; Cell Count; Cell Line, Transformed; Dendrites; Dose-Response Relationship, Drug; Electric Stimulation; Gene Expression Regulation; Green Fluorescent Proteins; Humans; Membrane Potentials; Mice; Mice, Inbred C57BL; Mice, Transgenic; Microscopy, Confocal; Mutation; Myosin-Light-Chain Kinase; Neurons; Odors; Patch-Clamp Techniques; Peptide Fragments; Potassium Chloride; Retina; Transfection},
	Month = {Oct},
	Number = {2},
	Pages = {297-308},
	Pmid = {23083733},
	Pst = {ppublish},
	Title = {Imaging neural activity using Thy1-GCaMP transgenic mice},
	Volume = {76},
	Year = {2012},
	File = {papers/Chen_Neuron2012.pdf},
	Bdsk-File-2 = {papers/Chen_Neuron2012a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.07.011}}

@article{Vogel:2010,
	Abstract = {A full understanding of the development of the brain's functional network architecture requires not only an understanding of developmental changes in neural processing in individual brain regions but also an understanding of changes in inter-regional interactions. Resting state functional connectivity MRI (rs-fcMRI) is increasingly being used to study functional interactions between brain regions in both adults and children. We briefly review methods used to study functional interactions and networks with rs-fcMRI and how these methods have been used to define developmental changes in network functional connectivity. The developmental rs-fcMRI studies to date have found two general properties. First, regional interactions change from being predominately anatomically local in children to interactions spanning longer cortical distances in young adults. Second, this developmental change in functional connectivity occurs, in general, via mechanisms of segregation of local regions and integration of distant regions into disparate subnetworks.},
	Author = {Vogel, Alecia C and Power, Jonathan D and Petersen, Steven E and Schlaggar, Bradley L},
	Date-Added = {2013-01-29 20:46:29 +0000},
	Date-Modified = {2013-01-29 20:47:02 +0000},
	Doi = {10.1007/s11065-010-9145-7},
	Journal = {Neuropsychol Rev},
	Journal-Full = {Neuropsychology review},
	Keywords = {toread; default mode network; resting state; development; fMRI; connectivity},
	Mesh = {Age Factors; Brain; Brain Mapping; Functional Laterality; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Nerve Net; Neural Pathways; Neurons; Oxygen; Synapses},
	Month = {Dec},
	Number = {4},
	Pages = {362-75},
	Pmid = {20976563},
	Pst = {ppublish},
	Title = {Development of the brain's functional network architecture},
	Volume = {20},
	Year = {2010},
	File = {papers/Vogel_NeuropsycholRev2010.pdf}}

@article{Donoghue:1999,
	Abstract = {To identify molecules that may play a role in the initiation of cerebral cortical area formation, we examined the expression of the Eph receptors and their ligands, the ephrins, during primate corticogenesis. We selected the macaque monkey neocortex because of its clear areal subdivisions, large surface area, protracted development (gestation = 165 d), and similarity to the human brain. In situ hybridizations, performed at early [embryonic day 65 (E65)], middle (E80), and late (E95) stages of cortical development, revealed that EphA system family members are expressed in distinct gradients and laminar and areal domains in the embryonic neocortex. Indeed, several regionally restricted molecular patterns are already apparent within the cortical plate at E65, before the formation of thalamocortical connections, suggesting that the initial expression of some EphA system members is regulated by programs intrinsic to cortical cells. For example, EphA3, EphA6, and EphA7 are all selectively expressed within the presumptive visual cortex. However, although EphA6 and EphA7 are present throughout this region, EphA3 is only expressed in the prospective extrastriate cortex, suggesting that cortical cells harbor functional biases that may influence the formation of appropriate synaptic connections. Although several patterns of early gene expression are stable (e.g., EphA3, EphA4, and EphA6), others change as development proceeds (e.g., EphA5, EphA7, ephrin-A2, ephrin-A3, and ephrin-A5), perhaps responding to extrinsic cues. Thus, at E95, after connections between the cortical plate and thalamus have formed, receptor subtypes EphA3, EphA5, EphA6, and EphA7 and the ligand ephrin-A5 are expressed in posterior regions, whereas EphA4 and ephrin-A2 and ephrin-A3 are either uniformly distributed or anteriorly biased. Taken together, our results demonstrate molecular distinctions among cells of the embryonic primate neocortex, revealing hitherto unrecognized compartmentalization early in corticogenesis.},
	Author = {Donoghue, M J and Rakic, P},
	Date-Added = {2013-01-29 20:45:59 +0000},
	Date-Modified = {2013-01-29 20:45:59 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Cerebral Cortex; Embryonic and Fetal Development; Gene Expression Regulation, Developmental; Gestational Age; Humans; In Situ Hybridization; Macaca mulatta; Nerve Tissue Proteins; Organ Specificity; Receptor Protein-Tyrosine Kinases},
	Month = {Jul},
	Number = {14},
	Pages = {5967-79},
	Pmid = {10407035},
	Pst = {ppublish},
	Title = {Molecular evidence for the early specification of presumptive functional domains in the embryonic primate cerebral cortex},
	Volume = {19},
	Year = {1999},
	File = {papers/Donoghue_JNeurosci1999.pdf}}

@article{Lu:2012,
	Abstract = {The default mode network (DMN) in humans has been suggested to support a variety of cognitive functions and has been implicated in an array of neuropsychological disorders. However, its function(s) remains poorly understood. We show that rats possess a DMN that is broadly similar to the DMNs of nonhuman primates and humans. Our data suggest that, despite the distinct evolutionary paths between rodent and primate brain, a well-organized, intrinsically coherent DMN appears to be a fundamental feature in the mammalian brain whose primary functions might be to integrate multimodal sensory and affective information to guide behavior in anticipation of changing environmental contingencies.},
	Author = {Lu, Hanbing and Zou, Qihong and Gu, Hong and Raichle, Marcus E and Stein, Elliot A and Yang, Yihong},
	Date-Added = {2013-01-29 20:26:54 +0000},
	Date-Modified = {2013-04-23 17:55:27 +0000},
	Doi = {10.1073/pnas.1200506109},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {default mode network; resting state; connectivity; wholeBrain; toread; grants; cerebral cortex; mirror symmetry; neocortex; cerebral cortex; areas; parcellation; patterning; topographic map; cytoarchitectonics},
	Mesh = {Animals; Behavior, Animal; Brain; Brain Mapping; Haplorhini; Humans; Magnetic Resonance Imaging; Models, Anatomic; Models, Biological; Neural Pathways; Rats; Species Specificity},
	Month = {Mar},
	Number = {10},
	Pages = {3979-84},
	Pmc = {PMC3309754},
	Pmid = {22355129},
	Pst = {ppublish},
	Title = {Rat brains also have a default mode network},
	Volume = {109},
	Year = {2012},
	File = {papers/Lu_ProcNatlAcadSciUSA2012.pdf},
	Bdsk-File-2 = {papers/Lu_ProcNatlAcadSciUSA2012a.pdf}}

@article{Kron:2012,
	Abstract = {Excitatory-inhibitory imbalance has been identified within specific brain microcircuits in models of Rett syndrome (RTT) and other autism spectrum disorders (ASDs). However, macrocircuit dysfunction across the RTT brain as a whole has not been defined. To approach this issue, we mapped expression of the activity-dependent, immediate-early gene product Fos in the brains of wild-type (Wt) and methyl-CpG-binding protein 2 (Mecp2)-null (Null) mice, a model of RTT, before and after the appearance of overt symptoms (3 and 6 weeks of age, respectively). At 6 weeks, Null mice exhibit significantly less Fos labeling than Wt in limbic cortices and subcortical structures, including key nodes in the default mode network. In contrast, Null mice exhibit significantly more Fos labeling than Wt in the hindbrain, most notably in cardiorespiratory regions of the nucleus tractus solitarius (nTS). Using nTS as a model, whole-cell recordings demonstrated that increased Fos expression in Nulls at 6 weeks of age is associated with synaptic hyperexcitability, including increased frequency of spontaneous and miniature EPSCs and increased amplitude of evoked EPSCs in Nulls. No such effect of genotype on Fos or synaptic function was seen at 3 weeks. In the mutant forebrain, reduced Fos expression, as well as abnormal sensorimotor function, were reversed by the NMDA receptor antagonist ketamine. In light of recent findings that the default mode network is hypoactive in autism, our data raise the possibility that hypofunction within this meta-circuit is a shared feature of RTT and other ASDs and is reversible.},
	Author = {Kron, Miriam and Howell, C James and Adams, Ian T and Ransbottom, Michael and Christian, Diana and Ogier, Michael and Katz, David M},
	Date-Added = {2013-01-29 20:22:24 +0000},
	Date-Modified = {2013-01-29 20:22:57 +0000},
	Doi = {10.1523/JNEUROSCI.2159-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Immediate-Early; gene; default mode network; resting state; Autistic Disorder; autism; Rett Syndrome;},
	Mesh = {Animals; Autonomic Nervous System; Cerebellum; Disease Models, Animal; Excitatory Amino Acid Antagonists; Female; Gene Expression Regulation, Developmental; Genes, fos; Humans; Ketamine; Male; Methyl-CpG-Binding Protein 2; Mice; Mice, Knockout; Miniature Postsynaptic Potentials; Nerve Net; Nerve Tissue Proteins; Organ Specificity; Patch-Clamp Techniques; Prosencephalon; Proto-Oncogene Proteins c-fos; Rett Syndrome; Sensory Gating; Solitary Nucleus; Synaptic Transmission},
	Month = {Oct},
	Number = {40},
	Pages = {13860-72},
	Pmc = {PMC3500840},
	Pmid = {23035095},
	Pst = {ppublish},
	Title = {Brain activity mapping in Mecp2 mutant mice reveals functional deficits in forebrain circuits, including key nodes in the default mode network, that are reversed with ketamine treatment},
	Volume = {32},
	Year = {2012},
	File = {papers/Kron_JNeurosci2012.pdf}}

@article{White:2012,
	Abstract = {Resting-state networks derived from temporal correlations of spontaneous hemodynamic fluctuations have been extensively used to elucidate the functional organization of the brain in adults and infants. We have previously developed functional connectivity diffuse optical tomography methods in adults, and we now apply these techniques to study functional connectivity in newborn infants at the bedside. We present functional connectivity maps in the occipital cortices obtained from healthy term-born infants and premature infants, including one infant with an occipital stroke. Our results suggest that functional connectivity diffuse optical tomography has potential as a valuable clinical tool for the early detection of functional deficits and for providing prognostic information on future development.},
	Author = {White, Brian R and Liao, Steve M and Ferradal, Silvina L and Inder, Terrie E and Culver, Joseph P},
	Date-Added = {2013-01-29 20:19:43 +0000},
	Date-Modified = {2013-01-29 20:20:20 +0000},
	Doi = {10.1016/j.neuroimage.2011.08.094},
	Journal = {Neuroimage},
	Journal-Full = {NeuroImage},
	Keywords = {default mode network; resting state; human; neonatal; fetal; optical imaging; visual cortex; connectivity},
	Mesh = {Brain Injuries; Brain Mapping; Cerebrovascular Circulation; Data Interpretation, Statistical; Diagnostic Imaging; Electroencephalography; Feasibility Studies; Female; Functional Laterality; Humans; Image Processing, Computer-Assisted; Infant, Newborn; Infant, Premature; Male; Models, Anatomic; Neural Pathways; Occipital Lobe; Pilot Projects; Point-of-Care Systems; Prognosis; Stroke; Tomography; Visual Cortex},
	Month = {Feb},
	Number = {3},
	Pages = {2529-38},
	Pmid = {21925609},
	Pst = {ppublish},
	Title = {Bedside optical imaging of occipital resting-state functional connectivity in neonates},
	Volume = {59},
	Year = {2012},
	File = {papers/White_Neuroimage2012.pdf}}

@article{White:2011,
	Abstract = {Functional neuroimaging (e.g., with fMRI) has been difficult to perform in mice, making it challenging to translate between human fMRI studies and molecular and genetic mechanisms. A method to easily perform large-scale functional neuroimaging in mice would enable the discovery of functional correlates of genetic manipulations and bridge with mouse models of disease. To satisfy this need, we combined resting-state functional connectivity mapping with optical intrinsic signal imaging (fcOIS). We demonstrate functional connectivity in mice through highly detailed fcOIS mapping of resting-state networks across most of the cerebral cortex. Synthesis of multiple network connectivity patterns through iterative parcellation and clustering provides a comprehensive map of the functional neuroarchitecture and demonstrates identification of the major functional regions of the mouse cerebral cortex. The method relies on simple and relatively inexpensive camera-based equipment, does not require exogenous contrast agents and involves only reflection of the scalp (the skull remains intact) making it minimally invasive. In principle, fcOIS allows new paradigms linking human neuroscience with the power of molecular/genetic manipulations in mouse models.},
	Author = {White, Brian R and Bauer, Adam Q and Snyder, Abraham Z and Schlaggar, Bradley L and Lee, Jin-Moo and Culver, Joseph P},
	Date-Added = {2013-01-29 20:03:54 +0000},
	Date-Modified = {2013-01-29 20:13:03 +0000},
	Doi = {10.1371/journal.pone.0016322},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {toread; technique; grants; wholeBrain; default mode network; resting state; spontaneous activity; mouse; mice; fMRI; Cerebral Cortex; mirror symmetry},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Equipment Design; Magnetic Resonance Imaging; Methods; Mice; Neural Pathways; Optical Devices},
	Number = {1},
	Pages = {e16322},
	Pmc = {PMC3024435},
	Pmid = {21283729},
	Pst = {epublish},
	Title = {Imaging of functional connectivity in the mouse brain},
	Volume = {6},
	Year = {2011},
	File = {papers/White_PLoSOne2011.pdf},
	Bdsk-File-2 = {papers/White_PLoSOne2011.eps},
	Bdsk-File-3 = {papers/White_PLoSOne2011a.eps},
	Bdsk-File-4 = {papers/White_PLoSOne2011b.eps},
	Bdsk-File-5 = {papers/White_PLoSOne2011c.eps},
	Bdsk-File-6 = {papers/White_PLoSOne2011e.eps},
	Bdsk-File-7 = {papers/White_PLoSOne2011d.eps}}

@article{Denenberg:1991c,
	Abstract = {We have recently developed a computer program for measuring midsagittal sections of the human corpus callosum, similar to one used for the rat. Callosal area, perimeter, axis length, and 99 widths for 104 subjects were entered into a factor analysis in order to define regional clusters. Seven width factors were obtained. Regional widths were found to be sensitive to Sex X Handedness interactions in the anterior body, with right-handed females and left-handed males being larger. In the posterior body males had wider callosa than females. A further analysis within the 'isthmus' region compared consistent and non-consistent right-handed males and females. Consistent right-handed males and both female groups had smaller callosa than non-consistent right-handed males. These findings confirmed the use of consistency of handedness as an important independent variable with respect to human callosal morphology.},
	Author = {Denenberg, V H and Kertesz, A and Cowell, P E},
	Date-Added = {2013-01-29 16:45:35 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {Cerebral Cortex; hemisphere; asymmetry; lateralization; Grants; forelimb},
	Mesh = {Adult; Animals; Brain Mapping; Corpus Callosum; Female; Functional Laterality; Haplorhini; Humans; Male; Sex Characteristics},
	Month = {May},
	Number = {1-2},
	Pages = {126-32},
	Pmid = {1907877},
	Pst = {ppublish},
	Title = {A factor analysis of the human's corpus callosum},
	Volume = {548},
	Year = {1991}}

@article{Denenberg:1991b,
	Abstract = {As an animal swims through the Lashley III maze, an observer types into a Macintosh computer the path taken. The computer program, Observe Software, then breaks the string of choices into two-step sequences and counts the number of such sequences. These data are then sent to a spreadsheet, where the sequences are sorted into forward and backward responses. Forward choices are Correct Path, T Choice Errors and Cul Entry Errors. All backward choices are errors, by definition. They are classified as T Choices, Cul Entries, Cul Exits, and Return to Start. The animal's behavior is then described by the various error classes plus a measure called Learning Index. Examples of learning by rats and mice are presented.},
	Author = {Denenberg, V H and Talgo, N and Carroll, D A and Freter, S and Deni, R},
	Date-Added = {2013-01-29 16:45:09 +0000},
	Date-Modified = {2013-01-29 16:45:09 +0000},
	Journal = {Physiol Behav},
	Journal-Full = {Physiology \& behavior},
	Mesh = {Animals; Escape Reaction; Image Processing, Computer-Assisted; Mental Recall; Mice; Mice, Inbred Strains; Microcomputers; Orientation; Problem Solving; Rats; Rats, Inbred Strains; Software},
	Month = {Oct},
	Number = {4},
	Pages = {857-61},
	Pmid = {1775564},
	Pst = {ppublish},
	Title = {A computer-aided procedure for measuring Lashley III maze performance},
	Volume = {50},
	Year = {1991}}

@article{Denenberg:1991a,
	Abstract = {Previous research found that the corpus callosum of male rats is larger than that of females; handling rats in infancy enhances this sex difference; and female rat pups, when handled in infancy and given 1 injection of testosterone propionate (TP) on Day 4 of life, will have callosa as large as those of males. In 2 experiments, male pups were castrated on Day 1 or received sham surgery; female pups were injected with TP on Day 4 or received an oil injection. Litters were handled or nonhandled. The previous finding that females, when handled and given TP in infancy, have a larger callosum was confirmed; however, a TP effect when administered to nonhandled females was not found. Because handling is known to cause a corticosterone release, these findings were interpreted as evidence of a developmental interaction between adrenal and gonadal hormones at the cortical level.},
	Author = {Denenberg, V H and Fitch, R H and Schrott, L M and Cowell, P E and Waters, N S},
	Date-Added = {2013-01-29 16:43:01 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {Behav Neurosci},
	Journal-Full = {Behavioral neuroscience},
	Keywords = {Cerebral Cortex; hemisphere; asymmetry; lateralization; Grants; forelimb},
	Mesh = {Animals; Animals, Newborn; Arousal; Brain Mapping; Cerebral Cortex; Corpus Callosum; Female; Handling (Psychology); Male; Pregnancy; Rats; Rats, Inbred Strains; Sex Differentiation; Testosterone},
	Month = {Aug},
	Number = {4},
	Pages = {562-6},
	Pmid = {1930724},
	Pst = {ppublish},
	Title = {Corpus callosum: interactive effects of infantile handling and testosterone in the rat},
	Volume = {105},
	Year = {1991}}

@article{Denenberg:1991,
	Abstract = {NZB and BXSB mice were given a battery of behavioral tests including paw preference, water escape, Lashley III maze, and discrimination learning. Their brains were then evaluated for cortical ectopias. The incidence of ectopias was 40.5% in NZBs and 48.5% in BXSBs. In the NZB strain left-pawed ectopic mice (both male and female) had the fastest swimming time in the water escape test, while right-pawed ectopics were the slowest. The same findings were obtained for left- and right-pawed ectopic BXSB males, but not for the females. However, on discrimination learning the BXSB males had the exact opposite pattern: right-pawed ectopics were the best learners while left-pawed ectopics were the worst. Male BXSBs and both male and female NZBs were manifesting autoimmune disease at the time of testing, while female BXSBs were not, suggesting that autoimmunity is a necessary background condition for the differential expression of ectopias and paw preference upon learning processes. The finding that the left-pawed ectopic BXSB mice, who were the poorest learners in the non-spatial discrimination learning test, learned best in the spatial water escape test is in agreement with the Geschwind hypothesis that pathological events during brain development may, in some instances, produce superiority of function.},
	Author = {Denenberg, V H and Sherman, G F and Schrott, L M and Rosen, G D and Galaburda, A M},
	Date-Added = {2013-01-29 16:42:59 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {Brain Res},
	Journal-Full = {Brain research},
	Keywords = {Cerebral Cortex; hemisphere; asymmetry; lateralization; Grants; forelimb},
	Mesh = {Animals; Autoimmune Diseases; Brain; Cerebral Cortex; Discrimination (Psychology); Escape Reaction; Functional Laterality; Learning; Mice; Mice, Inbred Strains; Space Perception},
	Month = {Oct},
	Number = {1},
	Pages = {98-104},
	Pmid = {1799876},
	Pst = {ppublish},
	Title = {Spatial learning, discrimination learning, paw preference and neocortical ectopias in two autoimmune strains of mice},
	Volume = {562},
	Year = {1991},
	File = {papers/Denenberg_BrainRes1991.pdf}}

@article{Waters:1991,
	Abstract = {A lateral paw preference testing unit is described. Mice are allowed access to preferred food with either their left or right forepaw, and the amount eaten with each paw is measured. The unit allows easy measurement and quantification of this behavior, without requiring food deprivation or continuous monitoring of the subjects, and may be performed in the subject's home cage. Its reliability under a number of conditions is reported. The results do not correlate with those obtained using the Collins paw preference test.},
	Author = {Waters, N S and Denenberg, V H},
	Date-Added = {2013-01-29 16:41:46 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Journal = {Physiol Behav},
	Journal-Full = {Physiology \& behavior},
	Keywords = {Cerebral Cortex; hemisphere; asymmetry; lateralization; Grants; forelimb},
	Mesh = {Animals; Appetitive Behavior; Dominance, Cerebral; Mice; Psychomotor Performance; Social Environment},
	Month = {Oct},
	Number = {4},
	Pages = {853-6},
	Pmid = {1775563},
	Pst = {ppublish},
	Title = {A measure of lateral paw preference in the mouse},
	Volume = {50},
	Year = {1991},
	File = {papers/Waters_PhysiolBehav1991.pdf}}

@article{Vyazovskiy:2008a,
	Abstract = {Sleep electroencephalographic (EEG) slow-wave activity is increased after wakefulness and decreases during sleep. Regional sleep EEG differences are thought to be a consequence of activation of specific cortical neuronal circuits during waking. We investigated the relationship between handedness and interhemispheric brain asymmetry. Bilateral EEG recordings were obtained from the frontal and occipital cortex in rats with a clear paw preference in a food-reaching task (right, n = 5; left, n = 5). While still na{\"\i}ve to the task, no waking or sleep EEG asymmetry was present. During the food-reaching task, the waking EEG showed significant, substantial power increases in the frontal hemisphere contralateral to the dominant paw in the low theta range (4.5-6.0 Hz). Moreover, the non-REM sleep EEG following feeding bouts was markedly asymmetric, with significantly higher power in the hemisphere contralateral to the preferred paw in frequencies >1.5 Hz. No asymmetry was evident in the occipital EEG. Correlation analyses revealed a positive association between the hemispheric asymmetry during sleep and the degree of preferred use of the contralateral paw during waking in frequencies <9.0 Hz. Our findings show that handedness is reflected in specific, regional EEG asymmetry during sleep. Neuronal activity induced by preferential use of a particular forelimb led to a local enhancement of EEG power in frequencies within the delta and sigma ranges, supporting the hypothesis of use-dependent local sleep regulation. We conclude that inherent laterality is manifested when animals are exposed to complex behavioral tasks, and sleep plays a role in consolidating the hemispheric dominance of the brain.},
	Author = {Vyazovskiy, V V and Tobler, I},
	Date-Added = {2013-01-29 16:36:04 +0000},
	Date-Modified = {2013-09-25 12:31:24 +0000},
	Doi = {10.1152/jn.01154.2007},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {asymmetry; symmetry; EEG; neurophysiology; sleep; in vivo; rats; Frontal; visual cortex; Cerebral Cortex; asymmetry; hemipshere; Grants; forelimb},
	Mesh = {Animals; Behavior, Animal; Electroencephalography; Functional Laterality; Male; Occipital Lobe; Rats; Rats, Sprague-Dawley; Sleep; Sleep Deprivation; Wakefulness},
	Month = {Feb},
	Number = {2},
	Pages = {969-75},
	Pmid = {18077659},
	Pst = {ppublish},
	Title = {Handedness leads to interhemispheric EEG asymmetry during sleep in the rat},
	Volume = {99},
	Year = {2008},
	File = {papers/Vyazovskiy_JNeurophysiol2008.pdf}}

@article{Dharmaratne:2012,
	Abstract = {BACKGROUND: The alignment of ipsilaterally and contralaterally projecting retinal axons that view the same part of visual space is fundamental to binocular vision. While much progress has been made regarding the mechanisms which regulate contralateral topography, very little is known of the mechanisms which regulate the mapping of ipsilateral axons such that they align with their contralateral counterparts.
RESULTS: Using the advantageous model provided by the mouse retinocollicular pathway, we have performed anterograde tracing experiments which demonstrate that ipsilateral retinal axons begin to form terminal zones (TZs) in the superior colliculus (SC), within the first few postnatal days. These appear mature by postnatal day 11. Importantly, TZs formed by ipsilaterally-projecting retinal axons are spatially offset from those of contralaterally-projecting axons arising from the same retinotopic location from the outset. This pattern is consistent with that required for adult visuotopy. We further demonstrate that a member of the Ten-m/Odz/Teneurin family of homophilic transmembrane glycoproteins, Ten-m3, is an essential regulator of ipsilateral retinocollicular topography. Ten-m3 mRNA is expressed in a high-medial to low-lateral gradient in the developing SC. This corresponds topographically with its high-ventral to low-dorsal retinal gradient. In Ten-m3 knockout mice, contralateral ventrotemporal axons appropriately target rostromedial SC, whereas ipsilateral axons exhibit dramatic targeting errors along both the mediolateral and rostrocaudal axes of the SC, with a caudal shift of the primary TZ, as well as the formation of secondary, caudolaterally displaced TZs. In addition to these dramatic ipsilateral-specific mapping errors, both contralateral and ipsilateral retinocollicular TZs exhibit more subtle changes in morphology.
CONCLUSIONS: We conclude that important aspects of adult visuotopy are established via the differential sensitivity of ipsilateral and contralateral axons to intrinsic guidance cues. Further, we show that Ten-m3 plays a critical role in this process and is particularly important for the mapping of the ipsilateral retinocollicular pathway.},
	Author = {Dharmaratne, Nuwan and Glendining, Kelly A and Young, Timothy R and Tran, Heidi and Sawatari, Atomu and Leamey, Catherine A},
	Date-Added = {2013-01-29 15:24:47 +0000},
	Date-Modified = {2013-01-29 15:25:24 +0000},
	Doi = {10.1371/journal.pone.0043083},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {retinotopy; topographic map; Superior Colliculus; optic tectum; mice; mouse; gene; ipsilateral},
	Number = {9},
	Pages = {e43083},
	Pmc = {PMC3446960},
	Pmid = {23028443},
	Pst = {ppublish},
	Title = {Ten-m3 is required for the development of topography in the ipsilateral retinocollicular pathway},
	Volume = {7},
	Year = {2012},
	File = {papers/Dharmaratne_PLoSOne2012.pdf}}

@article{Wyatt:2012,
	Abstract = {The stability of dendritic spines in the neocortex is profoundly influenced by sensory experience, which determines the magnitude and pattern of neural firing. By optically manipulating the temporal structure of neural activity in vivo using channelrhodopsin-2 and repeatedly imaging dendritic spines along these stimulated neurons over a period of weeks, we show that the specific pattern, rather than the total amount of activity, determines spine stability in awake mice.},
	Author = {Wyatt, Ryan M and Tring, Elaine and Trachtenberg, Joshua T},
	Date-Added = {2013-01-29 15:22:06 +0000},
	Date-Modified = {2013-01-29 15:22:57 +0000},
	Doi = {10.1038/nn.3134},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {Dendrites; spines; neural activity; optogenetics},
	Mesh = {Action Potentials; Amygdala; Animals; Dendritic Spines; Mice; Mice, Transgenic; Neocortex; Neural Pathways; Rhodopsin; Sensory Receptor Cells; Wakefulness},
	Month = {Jul},
	Number = {7},
	Pages = {949-51},
	Pmc = {PMC3386353},
	Pmid = {22706266},
	Pst = {epublish},
	Title = {Pattern and not magnitude of neural activity determines dendritic spine stability in awake mice},
	Volume = {15},
	Year = {2012},
	File = {papers/Wyatt_NatNeurosci2012.pdf}}

@article{Feldheim:1998,
	Abstract = {Visual connections to the mammalian forebrain are known to be patterned by neural activity, but it remains unknown whether the map topography of such higher sensory projections depends on axon guidance labels. Here, we show complementary expression and binding for the receptor EphA5 in mouse retina and its ligands ephrin-A2 and ephrin-A5 in multiple retinal targets, including the major forebrain target, the dorsal lateral geniculate nucleus (dLGN). These ligands can act in vitro as topographically specific repellents for mammalian retinal axons and are necessary for normal dLGN mapping in vivo. The results suggest a general and economic modular mechanism for brain mapping whereby a projecting field is mapped onto multiple targets by repeated use of the same labels. They also indicate the nature of a coordinate system for the mapping of sensory connections to the forebrain.},
	Author = {Feldheim, D A and Vanderhaeghen, P and Hansen, M J and Fris{\'e}n, J and Lu, Q and Barbacid, M and Flanagan, J G},
	Date-Added = {2013-01-29 15:13:39 +0000},
	Date-Modified = {2013-01-29 15:14:58 +0000},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Ephrins; retina; optic tectum; Superior Colliculus; topographic map; retinotopy; Gene Expression; gradients; genetic; axon guidance},
	Mesh = {Aging; Animals; Axons; Brain Mapping; Embryo, Mammalian; Ephrin-A2; Ephrin-A5; Gene Expression Regulation, Developmental; Geniculate Bodies; Membrane Proteins; Mice; Polymerase Chain Reaction; Prosencephalon; Receptor Protein-Tyrosine Kinases; Receptor, EphA5; Retina; Transcription Factors; Visual Pathways},
	Month = {Dec},
	Number = {6},
	Pages = {1303-13},
	Pmid = {9883724},
	Pst = {ppublish},
	Title = {Topographic guidance labels in a sensory projection to the forebrain},
	Volume = {21},
	Year = {1998},
	File = {papers/Feldheim_Neuron1998.pdf}}

@article{Chang:2012,
	Abstract = {Social decisions are crucial for the success of individuals and the groups that they comprise. Group members respond vicariously to benefits obtained by others, and impairments in this capacity contribute to neuropsychiatric disorders such as autism and sociopathy. We examined the manner in which neurons in three frontal cortical areas encoded the outcomes of social decisions as monkeys performed a reward-allocation task. Neurons in the orbitofrontal cortex (OFC) predominantly encoded rewards that were delivered to oneself. Neurons in the anterior cingulate gyrus (ACCg) encoded reward allocations to the other monkey, to oneself or to both. Neurons in the anterior cingulate sulcus (ACCs) signaled reward allocations to the other monkey or to no one. In this network of received (OFC) and foregone (ACCs) reward signaling, ACCg emerged as an important nexus for the computation of shared experience and social reward. Individual and species-specific variations in social decision-making might result from the relative activation and influence of these areas.},
	Author = {Chang, Steve W C and Gari{\'e}py, Jean-Fran{\c c}ois and Platt, Michael L},
	Date-Added = {2013-01-29 14:56:31 +0000},
	Date-Modified = {2013-01-29 14:58:20 +0000},
	Doi = {10.1038/nn.3287},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {monkey; Social Behavior; reward; Cognition; orbitofrontal; Cerebral Cortex; Neocortex; mirror neuron; cingulate; Frontal Lobe; empathy},
	Month = {Dec},
	Number = {2},
	Pages = {243-50},
	Pmid = {23263442},
	Pst = {ppublish},
	Title = {Neuronal reference frames for social decisions in primate frontal cortex},
	Volume = {16},
	Year = {2012},
	File = {papers/Chang_NatNeurosci2012.pdf}}

@article{Buckner:2008,
	Abstract = {Thirty years of brain imaging research has converged to define the brain's default network-a novel and only recently appreciated brain system that participates in internal modes of cognition. Here we synthesize past observations to provide strong evidence that the default network is a specific, anatomically defined brain system preferentially active when individuals are not focused on the external environment. Analysis of connectional anatomy in the monkey supports the presence of an interconnected brain system. Providing insight into function, the default network is active when individuals are engaged in internally focused tasks including autobiographical memory retrieval, envisioning the future, and conceiving the perspectives of others. Probing the functional anatomy of the network in detail reveals that it is best understood as multiple interacting subsystems. The medial temporal lobe subsystem provides information from prior experiences in the form of memories and associations that are the building blocks of mental simulation. The medial prefrontal subsystem facilitates the flexible use of this information during the construction of self-relevant mental simulations. These two subsystems converge on important nodes of integration including the posterior cingulate cortex. The implications of these functional and anatomical observations are discussed in relation to possible adaptive roles of the default network for using past experiences to plan for the future, navigate social interactions, and maximize the utility of moments when we are not otherwise engaged by the external world. We conclude by discussing the relevance of the default network for understanding mental disorders including autism, schizophrenia, and Alzheimer's disease.},
	Author = {Buckner, Randy L and Andrews-Hanna, Jessica R and Schacter, Daniel L},
	Date-Added = {2013-01-29 14:53:12 +0000},
	Date-Modified = {2013-01-29 14:55:37 +0000},
	Doi = {10.1196/annals.1440.011},
	Journal = {Ann N Y Acad Sci},
	Journal-Full = {Annals of the New York Academy of Sciences},
	Keywords = {grants; default mode network; resting state; fMRI; cognition; cingulate; monkey; empathy},
	Mesh = {Animals; Brain; Brain Diseases; Brain Mapping; Humans; Models, Neurological; Nerve Net},
	Month = {Mar},
	Pages = {1-38},
	Pmid = {18400922},
	Pst = {ppublish},
	Title = {The brain's default network: anatomy, function, and relevance to disease},
	Volume = {1124},
	Year = {2008},
	File = {papers/Buckner_AnnNYAcadSci2008.pdf}}

@article{Sommer:2004,
	Abstract = {Neuronal processing in cerebral cortex and signal transmission from cortex to brain stem have been studied extensively, but little is known about the numerous feedback pathways that ascend from brain stem to cortex. In this study, we characterized the signals conveyed through an ascending pathway coursing from the superior colliculus (SC) to the frontal eye field (FEF) via mediodorsal thalamus (MD). Using antidromic and orthodromic stimulation, we identified SC source neurons, MD relay neurons, and FEF recipient neurons of the pathway in Macaca mulatta. The monkeys performed oculomotor tasks, including delayed-saccade tasks, that permitted analysis of signals such as visual activity, delay activity, and presaccadic activity. We found that the SC sends all of these signals into the pathway with no output selectivity, i.e., the signals leaving the SC resembled those found generally within the SC. Visual activity arrived in FEF too late to contribute to short-latency visual responses there, and delay activity was largely filtered out in MD. Presaccadic activity, however, seemed critical because it traveled essentially unchanged from SC to FEF. Signal transmission in the pathway was fast ( approximately 2 ms from SC to FEF) and topographically organized (SC neurons drove MD and FEF neurons having similarly eccentric visual and movement fields). Our analysis of identified neurons in one pathway from brain stem to frontal cortex thus demonstrates that multiple signals are sent from SC to FEF with presaccadic activity being prominent. We hypothesize that a major signal conveyed by the pathway is corollary discharge information about the vector of impending saccades.},
	Author = {Sommer, Marc A and Wurtz, Robert H},
	Date-Added = {2013-01-29 14:50:40 +0000},
	Date-Modified = {2013-01-29 14:53:03 +0000},
	Doi = {10.1152/jn.00738.2003},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {visual system; Superior Colliculus; frontal eye field; Frontal Lobe; connectivity; monkey; Macaca mulatta; pulvinar; neurophysiology},
	Mesh = {Animals; Blinking; Brain Stem; Electric Stimulation; Electrodes; Electrophysiology; Feedback; Fixation, Ocular; Frontal Lobe; Macaca mulatta; Mediodorsal Thalamic Nucleus; Neurons; Photic Stimulation; Psychomotor Performance; Saccades; Superior Colliculi; Visual Fields; Visual Pathways},
	Month = {Mar},
	Number = {3},
	Pages = {1381-402},
	Pmid = {14573558},
	Pst = {ppublish},
	Title = {What the brain stem tells the frontal cortex. I. Oculomotor signals sent from superior colliculus to frontal eye field via mediodorsal thalamus},
	Volume = {91},
	Year = {2004},
	File = {papers/Sommer_JNeurophysiol2004.pdf}}

@article{Namiki:2013,
	Abstract = {Correlated spiking activity prevails in immature cortical networks and is believed to contribute to neuronal circuit maturation; however, its spatiotemporal organization is not fully understood. Using wide-field calcium imaging from acute whole-brain slices of rat pups on postnatal days 1-6, we found that correlated spikes were initiated in the anterior part of the lateral entorhinal cortex and propagated anteriorly to the frontal cortex and posteriorly to the medial entorhinal cortex, forming traveling waves that engaged almost the entire cortex. The waves were blocked by ionotropic glutamatergic receptor antagonists but not by GABAergic receptor antagonists. During wave events, glutamatergic and GABAergic synaptic inputs were balanced and induced UP state-like depolarization. Magnified monitoring with cellular resolution revealed that the layer III neurons were first activated when the waves were initiated. Consistent with this finding, layer III contained a larger number of neurons that were autonomously active, even under a blockade of synaptic transmission. During wave propagation, the layer III neurons constituted a leading front of the wave. The waves did not enter the parasubiculum; however, in some cases, they were reflected at the parasubicular border and propagated back in the opposite direction. During this reflection process, the layer III neurons in the medial entorhinal cortex maintained persistent activity. Thus, our data emphasize the role of layer III in early network behaviors and provide insight into the circuit mechanisms through which cerebral cortical networks maturate.},
	Author = {Namiki, Shigehiro and Norimoto, Hiroaki and Kobayashi, Chiaki and Nakatani, Kei and Matsuki, Norio and Ikegaya, Yuji},
	Date-Added = {2013-01-29 14:49:39 +0000},
	Date-Modified = {2013-08-27 03:10:14 +0000},
	Doi = {10.1523/JNEUROSCI.2522-12.2013},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread; in vitro; multiphoton; calcium imaging; development; oscillations; synchrony; spontaneous activity; wholeBrain; currOpinRvw},
	Month = {Jan},
	Number = {3},
	Pages = {987-1001},
	Pmid = {23325237},
	Pst = {ppublish},
	Title = {Layer III Neurons Control Synchronized Waves in the Immature Cerebral Cortex},
	Volume = {33},
	Year = {2013},
	File = {papers/Namiki_JNeurosci2013.pdf}}

@article{De-la-Rossa:2013,
	Abstract = {The molecular mechanisms that control how progenitors generate distinct subtypes of neurons, and how undifferentiated neurons acquire their specific identity during corticogenesis, are increasingly understood. However, whether postmitotic neurons can change their identity at late stages of differentiation remains unknown. To study this question, we developed an electrochemical in vivo gene delivery method to rapidly manipulate gene expression specifically in postmitotic neurons. Using this approach, we found that the molecular identity, morphology, physiology and functional input-output connectivity of layer 4 mouse spiny neurons could be specifically reprogrammed during the first postnatal week by ectopic expression of the layer 5B output neuron-specific transcription factor Fezf2. These findings reveal a high degree of plasticity in the identity of postmitotic neocortical neurons and provide a proof of principle for postnatal re-engineering of specific neural microcircuits in vivo.},
	Author = {De la Rossa, Andres and Bellone, Camilla and Golding, Bruno and Vitali, Ilaria and Moss, Jonathan and Toni, Nicolas and L{\"u}scher, Christian and Jabaudon, Denis},
	Date-Added = {2013-01-29 14:48:45 +0000},
	Date-Modified = {2013-01-29 14:49:26 +0000},
	Doi = {10.1038/nn.3299},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {toread; development; Neocortex; axon guidance},
	Month = {Jan},
	Number = {2},
	Pages = {193-200},
	Pmid = {23292682},
	Pst = {ppublish},
	Title = {In vivo reprogramming of circuit connectivity in postmitotic neocortical neurons},
	Volume = {16},
	Year = {2013},
	File = {papers/DelaRossa_NatNeurosci2013.pdf}}

@article{Krey:2013,
	Abstract = {L-type voltage gated calcium channels have an important role in neuronal development by promoting dendritic growth and arborization. A point mutation in the gene encoding Ca(V)1.2 causes Timothy syndrome, a neurodevelopmental disorder associated with autism spectrum disorders (ASDs). We report that channels with the Timothy syndrome alteration cause activity-dependent dendrite retraction in rat and mouse neurons and in induced pluripotent stem cell (iPSC)-derived neurons from individuals with Timothy syndrome. Dendrite retraction was independent of calcium permeation through the mutant channel, was associated with ectopic activation of RhoA and was inhibited by overexpression of the channel-associated GTPase Gem. These results suggest that Ca(V)1.2 can activate RhoA signaling independently of Ca(2+) and provide insights into the cellular basis of Timothy syndrome and other ASDs.},
	Author = {Krey, Jocelyn F and Pa{\c s}ca, Sergiu P and Shcheglovitov, Aleksandr and Yazawa, Masayuki and Schwemberger, Rachel and Rasmusson, Randall and Dolmetsch, Ricardo E},
	Date-Added = {2013-01-29 14:47:48 +0000},
	Date-Modified = {2013-01-29 14:48:35 +0000},
	Doi = {10.1038/nn.3307},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {toread; grants; Calcium Channels; neurological disorder; autism; Autistic Disorder; development},
	Month = {Jan},
	Number = {2},
	Pages = {201-9},
	Pmid = {23313911},
	Pst = {ppublish},
	Title = {Timothy syndrome is associated with activity-dependent dendritic retraction in rodent and human neurons},
	Volume = {16},
	Year = {2013},
	File = {papers/Krey_NatNeurosci2013.pdf}}

@article{Glickfeld:2013,
	Abstract = {Neurons in primary sensory cortex have diverse response properties, whereas higher cortical areas are specialized. Specific connectivity may be important for areal specialization, particularly in the mouse, where neighboring neurons are functionally diverse. To examine whether higher visual areas receive functionally specific input from primary visual cortex (V1), we used two-photon calcium imaging to measure responses of axons from V1 arborizing in three areas with distinct spatial and temporal frequency preferences. We found that visual preferences of presynaptic boutons in each area were distinct and matched the average preferences of recipient neurons. This specificity could not be explained by organization within V1 and instead was due to both a greater density and greater response amplitude of functionally matched boutons. Projections from a single layer (layer 5) and from secondary visual cortex were also matched to their target areas. Thus, transmission of specific information to downstream targets may be a general feature of cortico-cortical communication.},
	Author = {Glickfeld, Lindsey L and Andermann, Mark L and Bonin, Vincent and Reid, R Clay},
	Date-Added = {2013-01-29 14:47:03 +0000},
	Date-Modified = {2013-01-29 14:47:41 +0000},
	Doi = {10.1038/nn.3300},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {toread; visual cortex; extrastriate; connectivity; adult; mouse; optical imaging; calcium imaging; multiphoton},
	Month = {Jan},
	Number = {2},
	Pages = {219-26},
	Pmid = {23292681},
	Pst = {ppublish},
	Title = {Cortico-cortical projections in mouse visual cortex are functionally target specific},
	Volume = {16},
	Year = {2013},
	File = {papers/Glickfeld_NatNeurosci2013.pdf}}

@article{Beltramo:2013,
	Abstract = {In the absence of external stimuli, the mammalian neocortex shows intrinsic network oscillations. These dynamics are characterized by translaminar assemblies of neurons whose activity synchronizes rhythmically in space and time. How different cortical layers influence the formation of these spontaneous cellular assemblies is poorly understood. We found that excitatory neurons in supragranular and infragranular layers have distinct roles in the regulation of intrinsic low-frequency oscillations in mice in vivo. Optogenetic activation of infragranular neurons generated network activity that resembled spontaneous events, whereas photoinhibition of these same neurons substantially attenuated slow ongoing dynamics. In contrast, light activation and inhibition of supragranular cells had modest effects on spontaneous slow activity. This study represents, to the best of our knowledge, the first causal demonstration that excitatory circuits located in distinct cortical layers differentially control spontaneous low-frequency dynamics.},
	Author = {Beltramo, Riccardo and D'Urso, Giulia and Dal Maschio, Marco and Farisello, Pasqualina and Bovetti, Serena and Clovis, Yoanne and Lassi, Glenda and Tucci, Valter and De Pietri Tonelli, Davide and Fellin, Tommaso},
	Date-Added = {2013-01-29 14:46:16 +0000},
	Date-Modified = {2013-01-29 14:46:55 +0000},
	Doi = {10.1038/nn.3306},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {toread; slow oscillations; Delta Rhythm; Neocortex; optogenetics; neurophysiology},
	Month = {Jan},
	Number = {2},
	Pages = {227-34},
	Pmid = {23313909},
	Pst = {ppublish},
	Title = {Layer-specific excitatory circuits differentially control recurrent network dynamics in the neocortex},
	Volume = {16},
	Year = {2013},
	File = {papers/Beltramo_NatNeurosci2013.pdf}}

@article{Brecht:2011,
	Abstract = {In this issue, two studies, by Ehrlich et al. and Hill et al., address the role of the frontal motor cortices in behavior of the rat and suggest a potential role for this structure in high-level control of diverse behaviors. Hill et al. show that motor cortical neurons predict whisker movements even without sensory feedback and that their activity reflects efferent control. Surprisingly, Ehrlich et al. report the participation of this same cortical region in the preparation and execution of orienting behaviors.},
	Author = {Brecht, Michael},
	Date-Added = {2013-01-29 14:45:07 +0000},
	Date-Modified = {2013-01-29 14:46:07 +0000},
	Doi = {10.1016/j.neuron.2011.10.002},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread; function; connectivity; rat; Frontal Lobe; frontal eye field; cerebral cortex},
	Mesh = {Animals; Female; Frontal Lobe; Male; Memory; Motor Cortex; Neurons; Orientation; Vibrissae; Visual Pathways},
	Month = {Oct},
	Number = {2},
	Pages = {193-6},
	Pmid = {22017982},
	Pst = {ppublish},
	Title = {Movement, confusion, and orienting in frontal cortices},
	Volume = {72},
	Year = {2011},
	File = {papers/Brecht_Neuron2011.pdf}}

@article{Arvanitis:2008,
	Abstract = {Bidirectional signaling has emerged as an important signature by which Ephs and ephrins control biological functions. Eph/ephrin signaling participates in a wide spectrum of developmental processes, and cross-regulation with other communication pathways lies at the heart of the complexity underlying their function in vivo. Here, we review in vitro and in vivo data describing molecular, functional, and genetic interactions between Eph/ephrin and other cell surface signaling pathways. The complexity of Eph/ephrin function is discussed in terms of the pathways that regulate Eph/ephrin signaling and also the pathways that are regulated by Eph/ephrin signaling.},
	Author = {Arvanitis, Dina and Davy, Alice},
	Date-Added = {2013-01-29 14:42:52 +0000},
	Date-Modified = {2013-01-29 14:44:34 +0000},
	Doi = {10.1101/gad.1630408},
	Journal = {Genes Dev},
	Journal-Full = {Genes \& development},
	Keywords = {review literature; calcium; Ephrins; development; synaptogenesis; grants},
	Mesh = {Animals; Cell Adhesion; Cell Movement; Ephrins; Humans; Receptor Cross-Talk; Receptors, Eph Family; Signal Transduction},
	Month = {Feb},
	Number = {4},
	Pages = {416-29},
	Pmc = {PMC2731651},
	Pmid = {18281458},
	Pst = {ppublish},
	Title = {Eph/ephrin signaling: networks},
	Volume = {22},
	Year = {2008},
	File = {papers/Arvanitis_GenesDev2008.pdf}}

@article{Prigge:2012,
	Abstract = {Channelrhodopsin-2 is a light-gated ion channel and a major tool of optogenetics. It is used to control neuronal activity via blue light. Here we describe the construction of color-tuned high efficiency channelrhodopsins (ChRs), based on chimeras of Chlamydomonas channelrhodopsin-1 and Volvox channelrhodopsin-1. These variants show superb expression and plasma membrane integration, resulting in 3-fold larger photocurrents in HEK cells compared with channelrhodopsin-2. Further molecular engineering gave rise to chimeric variants with absorption maxima ranging from 526 to 545 nm, dovetailing well with maxima of channelrhodopsin-2 derivatives ranging from 461 to 492 nm. Additional kinetic fine-tuning led to derivatives in which the lifetimes of the open state range from 19 ms to 5 s. Finally, combining green- with blue-absorbing variants allowed independent activation of two distinct neural cell populations at 560 and 405 nm. This novel panel of channelrhodopsin variants may serve as an important toolkit element for dual-color cell stimulation in neural circuits.},
	Author = {Prigge, Matthias and Schneider, Franziska and Tsunoda, Satoshi P and Shilyansky, Carrie and Wietek, Jonas and Deisseroth, Karl and Hegemann, Peter},
	Date-Added = {2013-01-21 19:28:41 +0000},
	Date-Modified = {2013-01-21 19:29:04 +0000},
	Doi = {10.1074/jbc.M112.391185},
	Journal = {J Biol Chem},
	Journal-Full = {The Journal of biological chemistry},
	Keywords = {technique; methods; optogenetics},
	Mesh = {Animals; Calcium; Chlamydomonas; Color; Electrophysiology; Genetic Engineering; HEK293 Cells; Hippocampus; Humans; Ions; Kinetics; Light; Models, Neurological; Oocytes; Optogenetics; Recombinant Fusion Proteins; Rhodopsin; Volvox; Xenopus},
	Month = {Sep},
	Number = {38},
	Pages = {31804-12},
	Pmc = {PMC3442514},
	Pmid = {22843694},
	Pst = {ppublish},
	Title = {Color-tuned channelrhodopsins for multiwavelength optogenetics},
	Volume = {287},
	Year = {2012},
	File = {papers/Prigge_JBiolChem2012.pdf}}

@article{Schoppik:2006,
	Abstract = {Saccades modulate the relationship between visual motion and smooth eye movement. Before a saccade, pursuit eye movements reflect a vector average of motion across the visual field. After a saccade, pursuit primarily reflects the motion of the target closest to the endpoint of the saccade. We tested the hypothesis that the saccade produces a spatial weighting of motion around the endpoint of the saccade. Using a moving pursuit stimulus that stepped to a new spatial location just before a targeting saccade, we controlled the distance between the endpoint of the saccade and the position of the moving target. We demonstrate that the smooth eye velocity following the targeting saccade weights the presaccadic visual motion inputs by the distance from their location in space to the endpoint of the saccade, defining the extent of a spatiotemporal filter for driving the eyes. The center of the filter is located at the endpoint of the saccade in space, not at the position of the fovea. The filter is stable in the face of a distracter target, is present for saccades to stationary and moving targets, and affects both the speed and direction of the postsaccadic eye movement. The spatial filter can explain the target-selecting gain change in postsaccadic pursuit, and has intriguing parallels to the process by which perceptual decisions about a restricted region of space are enhanced by attention. The effect of the spatial saccade plan on the pursuit response to a given retinal motion describes the dynamics of a coordinate transformation.},
	Author = {Schoppik, David and Lisberger, Stephen G},
	Date-Added = {2013-01-11 14:12:44 +0000},
	Date-Modified = {2013-01-11 14:13:01 +0000},
	Doi = {10.1523/JNEUROSCI.1719-06.2006},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread},
	Mesh = {Animals; Macaca mulatta; Male; Models, Biological; Motion Perception; Photic Stimulation; Pursuit, Smooth; Saccades; Space Perception},
	Month = {Jul},
	Number = {29},
	Pages = {7607-18},
	Pmc = {PMC2548311},
	Pmid = {16855088},
	Pst = {ppublish},
	Title = {Saccades exert spatial control of motion processing for smooth pursuit eye movements},
	Volume = {26},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.1719-06.2006}}

@article{Schoppik:2008,
	Abstract = {Neural activity in the frontal eye fields controls smooth pursuit eye movements, but the relationship between single neuron responses, cortical population responses, and eye movements is not well understood. We describe an approach to dynamically link trial-to-trial fluctuations in neural responses to parallel variations in pursuit and demonstrate that individual neurons predict eye velocity fluctuations at particular moments during the course of behavior, while the population of neurons collectively tiles the entire duration of the movement. The analysis also reveals the strength of correlations in the eye movement predictions derived from pairs of simultaneously recorded neurons and suggests a simple model of cortical processing. These findings constrain the primate cortical code for movement, suggesting that either a few neurons are sufficient to drive pursuit at any given time or that many neurons operate collectively at each moment with remarkably little variation added to motor command signals downstream from the cortex.},
	Author = {Schoppik, David and Nagel, Katherine I and Lisberger, Stephen G},
	Date-Added = {2013-01-11 14:12:42 +0000},
	Date-Modified = {2013-01-11 14:13:01 +0000},
	Doi = {10.1016/j.neuron.2008.02.015},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread},
	Mesh = {Action Potentials; Animals; Behavior, Animal; Brain Mapping; Cerebral Cortex; Macaca mulatta; Male; Models, Neurological; Neurons; Nonlinear Dynamics; Numerical Analysis, Computer-Assisted; Photic Stimulation; Pursuit, Smooth; Reaction Time; Stereotyped Behavior},
	Month = {Apr},
	Number = {2},
	Pages = {248-60},
	Pmc = {PMC2426736},
	Pmid = {18439409},
	Pst = {ppublish},
	Title = {Cortical mechanisms of smooth eye movements revealed by dynamic covariations of neural and behavioral responses},
	Volume = {58},
	Year = {2008},
	File = {papers/Schoppik_Neuron2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2008.02.015}}

@article{McConnell:1988,
	Abstract = {In the mammalian cerebral cortex, neurons in a given layer are generated at about the same time in development. These cells also tend to share similar sets of morphological and physiological properties and have projection patterns characteristic of that layer. This correspondence between the birthday and eventual fate of a cortical neuron suggests the possibility that the commitment of a cell to a particular laminar position and set of connections may occur very early on in cortical development. The experiments described here constitute an attempt to manipulate the fates of newly generated cortical neurons upon transplantation. The first set of experiments addressed the normal development of neurons in the primary visual cortex (area 17) of the ferret. Injections of 3H-thymidine into newborn ferrets showed that neurons generated after birth are destined to sit in layer 2/3 of the cortex, whereas neurons born on embryonic day (E) 32 populate primarily layers 5 and 6. Many layer 2/3 neurons in adult ferrets could be retrogradely labeled with HRP from visual cortical areas 18 and 19, while about half of the neurons in layer 6 were found to project to the lateral geniculate nucleus (LGN). In the second set of experiments, presumptive layer 2/3 cells were labeled in vivo by injecting ferrets with 3H-thymidine on P1 and P2. Before the cells had a chance to migrate, they were removed from the donor brain, incubated in a fluorescent dye (DAPI or fast blue), and dissociated into a single-cell suspension. The labeled cells were then transplanted into the proliferative zone of a littermate host ferret ("isochronic" transplants). Over the next few weeks, many of these dye-labeled cells underwent changes in their position and morphology that were consistent with a radially directed migration and subsequent differentiation into cortical neurons. The final positions of isochronically transplanted neurons in the host brain were mapped out by using the 3H-thymidine marker after long survival periods. About 97% of radioactively labeled cells had migrated out into the visual cortex, where they attained a compact laminar distribution: 99% were found in layer 2/3, their normal destination. The labeled cells had normal, mostly pyramidal neuronal morphologies and appeared to be well integrated with host neurons when viewed in Nissl-stained sections. Ten isochronically transplanted neurons were successfully labeled after HRP injection into 2 normal target regions, areas 18 and 19.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {McConnell, S K},
	Date-Added = {2012-12-19 17:50:54 +0000},
	Date-Modified = {2012-12-19 17:50:54 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Mesh = {Animals; Cell Movement; Ferrets; Neural Pathways; Neurons; Thymidine; Transplantation; Visual Cortex},
	Month = {Mar},
	Number = {3},
	Pages = {945-74},
	Pmid = {3346731},
	Pst = {ppublish},
	Title = {Fates of visual cortical neurons in the ferret after isochronic and heterochronic transplantation},
	Volume = {8},
	Year = {1988}}

@article{McConnell:1985,
	Abstract = {Cells from the cerebral proliferative zones of newborn ferrets were labeled with tritiated thymidine and a fluorescent dye and were transplanted as a single-cell suspension into the occipital region of newborn ferrets. The transplanted cells became thoroughly integrated into the host environment: many cells migrated through the intermediate zone and into the cortical plate, where they developed as pyramidal neurons. Other transplanted cells came to resemble glial cells. After 1 to 2 months most transplanted neurons had taken up residence in layer 2 + 3, the normal destination of neurons generated on postnatal days 1 and 2. Thus the sequence of morphological differentiation and the eventual laminar position of the isochronically transplanted neurons closely paralleled that of their normal host counterparts.},
	Author = {McConnell, S K},
	Date-Added = {2012-12-19 17:50:31 +0000},
	Date-Modified = {2012-12-19 17:50:31 +0000},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Mesh = {Amidines; Animals; Animals, Newborn; Autoradiography; Cell Differentiation; Cell Movement; Cerebral Cortex; Ferrets; Fluorescent Dyes; Indoles; Neurons},
	Month = {Sep},
	Number = {4719},
	Pages = {1268-71},
	Pmid = {4035355},
	Pst = {ppublish},
	Title = {Migration and differentiation of cerebral cortical neurons after transplantation into the brains of ferrets},
	Volume = {229},
	Year = {1985}}

@article{OLeary:1989a,
	Abstract = {In adult rats, cortical neurons that extend an exon through the pyramidal tract (a major subcortical efferent projection of the neocortex) are limited to layer V of about the rostral two-thirds of the neocortex. In neonates, however, pyramidal tract neurons are distributed throughout the neocortex, but all of those found in certain areas, such as the posterior occipital region (including primary visual cortex) selectively lose their pyramidal tract axon (Stanfield et al., 1982) yet maintain axon collaterals to other subcortical targets (O'Leary and Stanfield, 1985). To determine if the regional location of a developing pyramidal tract neuron critically influences the maintenance or elimination of the axon collaterals it initially extends, pieces of cortex from embryonic day 17 (E17) rat fetuses (exposed to 3H-thymidine on E15) were transplanted heterotopically into the cortex of newborn (PO) rats; rostral cortex was placed into the posterior occipital region (R----O), or posterior occipital cortex into a rostral cortical locale (O----R). The retrograde tracers Fast blue (FB) and Diamidino yellow (DY) were used to assay for the presence of specific populations of cortical projection neurons within the autoradiographically identified transplants. In terms of the extension and maintenance of pyramidal tract axons, the transplanted neurons behave like the host neurons of the recipient cortical region rather than like those of their site of origin. At P40, following FB injections into the pyramidal decussation on P34, pyramidal tract neurons are labeled within the O----R transplants, but none can be labeled within R----O transplants, although in the same R----O cases transplanted neurons are labeled by an injection of DY in the superior colliculus. However, at P13 pyramidal tract neurons can be identified within the R----O transplants, as well as in the host occipital cortex, following injections made on P9, a period when the distribution of pyramidal tract neurons in normal rats is widespread (Stanfield and O'Leary, 1985b). In a second series of host rats, on P34 FB was injected in the pyramidal decussation of the O----R cases, or in the superior colliculus of the R----O cases, and in both groups DY was injected into the region of contralateral cortex homotopic for the new location of the transplant. On P40, in both the O----R and R----O transplants, many neurons singly labeled with FB or DY are found, but no double dye-labeled cells are seen.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {O'Leary, D D and Stanfield, B B},
	Date-Added = {2012-12-19 17:45:09 +0000},
	Date-Modified = {2012-12-19 17:48:55 +0000},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {development; map; topographic map; activity manipulation; Activity-development; gene; cell fate; connectivity},
	Mesh = {Animals; Animals, Newborn; Axons; Cerebral Cortex; Female; Occipital Lobe; Pyramidal Tracts; Rats; Rats, Inbred Strains; Synaptic Transmission; Transplantation, Heterologous},
	Month = {Jul},
	Number = {7},
	Pages = {2230-46},
	Pmid = {2545833},
	Pst = {ppublish},
	Title = {Selective elimination of axons extended by developing cortical neurons is dependent on regional locale: experiments utilizing fetal cortical transplants},
	Volume = {9},
	Year = {1989}}

@article{OLeary:1989,
	Abstract = {The adult mammalian neocortex consists of numerous 'areas' distinguished from one another largely on the basis of distinctions in cytoarchitecture and connections. The developing neocortex, though, lacks many of these area-specific distinctions, and is more uniform across its extent. This less differentiated structure, here termed the 'protocortex' undergoes considerable modification after neurogenesis which results in the emergence of well-defined neocortical areas. To what extent, then, are neocortical areas predetermined? This issue is considered in the context of recent findings on the generation of the neocortex and its subsequent parcellation into distinct areas.},
	Author = {O'Leary, D D},
	Date-Added = {2012-12-19 17:45:04 +0000},
	Date-Modified = {2012-12-19 17:49:01 +0000},
	Journal = {Trends Neurosci},
	Journal-Full = {Trends in neurosciences},
	Keywords = {development; map; topographic map; activity manipulation; Activity-development; gene; cell fate; connectivity},
	Mesh = {Aging; Animals; Cerebral Cortex; Embryonic and Fetal Development},
	Month = {Oct},
	Number = {10},
	Pages = {400-6},
	Pmid = {2479138},
	Pst = {ppublish},
	Title = {Do cortical areas emerge from a protocortex?},
	Volume = {12},
	Year = {1989}}

@article{Steele:1999,
	Abstract = {We investigated the role of NMDA receptors in memory encoding and retrieval. A delayed matching-to-place (DMP) paradigm in the watermaze was used to examine 1-trial spatial memory in rats. Over periods of up to 21 days, 4 daily trials were given to an escape platform hidden in a new location each day, with the memory interval (ITI) varying from 15 sec to 2 hours between trials 1 and 2, but always at 15 sec for the remaining ITIs. Using chronic i.c.v. infusions of D-AP5, acute intrahippocampal infusions, ibotenate hippocampus + dentate lesions and relevant aCSF or sham surgery control groups, we established: (1) the DMP task is hippocampal-dependent; (2) D-AP5 causes a delay-dependent impairment of memory in which the Groups x Delay interaction was significant on two separate measures of performance; (3) this memory impairment also occurs with acute intrahippocampal infusions; (4) the impairment occurs irrespective of whether the animals stay in or are removed from the training context during the memory delay interval; and (5) D-AP5 affects neither the retrieval of information about the spatial layout of the environment, nor memory of where the escape platform had been located on the last day before the start of chronic D-AP5 infusion. LTP in vivo in the dentate gyrus was blocked in the chronically-infused D-AP5 rats and HPLC measurements at sacrifice revealed appropriate intrahippocampal levels. Acute intrahippocampal infusion of radiolabelled D-AP5 revealed relatively restricted diffusion and was used to estimate whole-tissue hippocampal drug concentrations. These results indicate that (1) short-term memory for spatial information is independent of NMDA receptors; (2) the rapid consolidation of spatial information into long-term memory requires activation of hippocampal NMDA receptors; (3) NMDA receptors are not involved in memory retrieval; and (4) the delay-related effects of NMDA receptor antagonists on performance of this task cannot be explained in terms of sensorimotor disturbances. The findings relate to the idea that hippocampal synaptic plasticity is involved in event-memory (Morris and Frey, Phil Trans R Soc Lond B 1997;352:1489-1503) and to a computational model of one-trial DMP performance of Foster et al. (unpublished data).},
	Author = {Steele, R J and Morris, R G},
	Date-Added = {2012-12-12 18:31:17 +0000},
	Date-Modified = {2012-12-12 18:31:17 +0000},
	Doi = {10.1002/(SICI)1098-1063(1999)9:2<118::AID-HIPO4>3.0.CO;2-8},
	Journal = {Hippocampus},
	Journal-Full = {Hippocampus},
	Mesh = {2-Amino-5-phosphonovalerate; Animals; Autoradiography; Behavior, Animal; Chromatography, High Pressure Liquid; Excitatory Amino Acid Antagonists; Hippocampus; Long-Term Potentiation; Male; Maze Learning; Memory, Short-Term; Microinjections; Psychomotor Performance; Rats; Rats, Inbred Strains; Reaction Time; Receptors, N-Methyl-D-Aspartate; Space Perception; Tritium},
	Number = {2},
	Pages = {118-36},
	Pmid = {10226773},
	Pst = {ppublish},
	Title = {Delay-dependent impairment of a matching-to-place task with chronic and intrahippocampal infusion of the NMDA-antagonist D-AP5},
	Volume = {9},
	Year = {1999},
	File = {papers/Steele_Hippocampus1999.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1098-1063(1999)9:2%3C118::AID-HIPO4%3E3.0.CO;2-8}}

@article{Ferrer:1988,
	Abstract = {Retrogradely transported tracers were injected into area 18 of the visual cortex of the adult cat to study the organization of corticocortical projections from area 17 to area 18. All injections, whether very small or relatively large, and irrespective of their exact location in area 18, produced a discontinuous, clustered distribution of labelled cells, mainly in layers II, III and upper IV, in a topographically related region of area 17. The mean centre-centre distance between neighbouring patches was about 750 microns. We conclude that the overall population of cells projecting to area 18 is genuinely distributed in a patchy fashion and that they provide an efficient spatial sample of information from area 17. Comparison of the dimensions of each injection site and of the retrogradely labelled territory suggested that each region in area 18 receives a convergent input from a zone in area 17 whose visual field representation is about 0.8 M-1 deg larger in all directions (where M is the magnification factor in millimetres per degree at the termination site in area 18). Pairs of injection were made in area 18 by placing small volumes of two fluorescent tracers, fast blue and diamidino yellow, side-by-side in either a rostrocaudal or a mediolateral plane, with different distances between them. When the boundaries of the dense central cores of two injection sites were separated, at their closest points, by about 1.6 mm, the two corresponding distributions of labelled cells in area 17 were just non-overlapping, suggesting that each group of cells in area 17 sends a divergent projection in innervate a zone about 0.8 mm larger in all directions in area 18. More closely spaced injections led to overlap of the distributions of labelling by the two dyes, with shared clusters containing a mixture of labelled cells. The proportion of double-labelled cells in these shared clusters never exceeded 4.4% (but was 70% after sequential injection of the two dyes at a single point). We conclude that, although each cluster of cells sends a divergent projection to area 18, the majority of individual axons terminate more discretely, perhaps providing specific inter-connections between functionally corresponding 'columns' in the two areas.},
	Author = {Ferrer, J M and Price, D J and Blakemore, C},
	Date-Added = {2012-12-11 15:58:56 +0000},
	Date-Modified = {2012-12-11 15:58:56 +0000},
	Journal = {Proc R Soc Lond B Biol Sci},
	Journal-Full = {Proceedings of the Royal Society of London. Series B, Containing papers of a Biological character. Royal Society (Great Britain)},
	Mesh = {Animals; Cats; Microscopy, Fluorescence; Neurons; Visual Cortex},
	Month = {Feb},
	Number = {1270},
	Pages = {77-98},
	Pmid = {2895934},
	Pst = {ppublish},
	Title = {The organization of corticocortical projections from area 17 to area 18 of the cat's visual cortex},
	Volume = {233},
	Year = {1988},
	File = {papers/Ferrer_ProcRSocLondBBiolSci1988.pdf}}

@article{King:1988,
	Abstract = {Environmental factors play an important role in certain aspects of the development of sensory systems. But the way in which the maturation of different sensory modalities is coordinated is poorly understood. We have investigated this question neurophysiologically in the mammalian superior colliculus (SC), which contains topographically aligned maps of visual and auditory space. We report here that an essentially normal auditory map, in approximate register with the visual map, is found in the SC of adult ferrets reared with abnormal binaural localization cues. Also, if, early in life, one eye is deviated laterally, there is a compensatory shift in the auditory map, but early eye rotation totally disorders the auditory representation. These results imply that development of the auditory map is affected by visual activity or by information about eye position and that there is definite, but limited, capacity for the auditory map to reorganize so that it remains aligned with the visual map.},
	Author = {King, A J and Hutchings, M E and Moore, D R and Blakemore, C},
	Date-Added = {2012-12-11 15:58:31 +0000},
	Date-Modified = {2012-12-11 15:58:31 +0000},
	Doi = {10.1038/332073a0},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Acoustic Stimulation; Animals; Carnivora; Eye; Ferrets; Hearing; Neurons; Ocular Physiological Phenomena; Superior Colliculi; Vision, Ocular; Visual Fields},
	Month = {Mar},
	Number = {6159},
	Pages = {73-6},
	Pmid = {3347247},
	Pst = {ppublish},
	Title = {Developmental plasticity in the visual and auditory representations in the mammalian superior colliculus},
	Volume = {332},
	Year = {1988},
	File = {papers/King_Nature1988.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/332073a0}}

@article{Stein:2008,
	Abstract = {For thousands of years science philosophers have been impressed by how effectively the senses work together to enhance the salience of biologically meaningful events. However, they really had no idea how this was accomplished. Recent insights into the underlying physiological mechanisms reveal that, in at least one circuit, this ability depends on an intimate dialogue among neurons at multiple levels of the neuraxis; this dialogue cannot take place until long after birth and might require a specific kind of experience. Understanding the acquisition and usage of multisensory integration in the midbrain and cerebral cortex of mammals has been aided by a multiplicity of approaches. Here we examine some of the fundamental advances that have been made and some of the challenging questions that remain.},
	Author = {Stein, Barry E and Stanford, Terrence R},
	Date-Added = {2012-12-11 15:15:04 +0000},
	Date-Modified = {2012-12-11 15:15:04 +0000},
	Doi = {10.1038/nrn2331},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Mesh = {Afferent Pathways; Animals; Brain Mapping; Cerebral Cortex; Humans; Mental Processes; Neurons; Sensation},
	Month = {Apr},
	Number = {4},
	Pages = {255-66},
	Pmid = {18354398},
	Pst = {ppublish},
	Title = {Multisensory integration: current issues from the perspective of the single neuron},
	Volume = {9},
	Year = {2008},
	File = {papers/Stein_NatRevNeurosci2008.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrn2331}}

@article{Mu:2012,
	Abstract = {Visual cues often modulate auditory signal processing, leading to improved sound detection. However, the synaptic and circuit mechanism underlying this cross-modal modulation remains poorly understood. Using larval zebrafish, we first established a cross-modal behavioral paradigm in which a preceding flash enhances sound-evoked escape behavior, which is known to be executed through auditory afferents (VIII(th) nerves) and command-like neurons (Mauthner cells). In vivo recording revealed that the visual enhancement of auditory escape is achieved by increasing sound-evoked Mauthner cell responses. This increase in Mauthner cell responses is accounted for by the increase in the signal-to-noise ratio of sound-evoked VIII(th) nerve spiking and efficacy of VIII(th) nerve-Mauthner cell synapses. Furthermore, the visual enhancement of Mauthner cell response and escape behavior requires light-responsive dopaminergic neurons in the caudal hypothalamus and D1 dopamine receptor activation. Our findings illustrate a cooperative neural mechanism for visual modulation of audiomotor processing that involves dopaminergic neuromodulation.},
	Author = {Mu, Yu and Li, Xiao-quan and Zhang, Bo and Du, Jiu-lin},
	Date-Added = {2012-12-11 14:45:16 +0000},
	Date-Modified = {2012-12-11 14:47:57 +0000},
	Doi = {10.1016/j.neuron.2012.05.035},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {multimodal; Activity-development; activity manipulation; sensory map; Motor Activity; neurophysiology; Zebrafish; development; Auditory Pathways; visual system; plasticity; Dopamine; potentiation; Adaptation; habituation;},
	Mesh = {6-Cyano-7-nitroquinoxaline-2,3-dione; Acoustic Stimulation; Action Potentials; Animals; Apomorphine; Behavior, Animal; Benzazepines; Biotin; Cell Communication; Dopamine Agonists; Dopamine Antagonists; Dopaminergic Neurons; Escape Reaction; Excitatory Amino Acid Agonists; Excitatory Postsynaptic Potentials; Flufenamic Acid; Functional Laterality; Glycyrrhetinic Acid; Hypothalamus; Larva; Light; Locomotion; Microscopy, Confocal; Morpholinos; Patch-Clamp Techniques; Photic Stimulation; Psychoacoustics; Receptors, Dopamine D1; Signal-To-Noise Ratio; Time Factors; Valine; Visual Pathways; Zebrafish},
	Month = {Aug},
	Number = {4},
	Pages = {688-99},
	Pmid = {22920259},
	Pst = {ppublish},
	Title = {Visual input modulates audiomotor function via hypothalamic dopaminergic neurons through a cooperative mechanism},
	Volume = {75},
	Year = {2012},
	File = {papers/Mu_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.05.035}}

@article{Salin:1989,
	Abstract = {We have examined the topography of the afferent connections to area 17 in the cat by means of double retrograde label tracing techniques. Injections of two fluorescent retrograde tracers, diamidino yellow and fast blue, were made with variable separations in area 17 and the spatial distributions of the resulting populations of labeled cells examined in afferent cortical areas and subcortical structures. When injections were separated rostrocaudally, the topographic organizations of the projections were characterized quantitatively with two graphic methods: the labeling density curve and the connectivity graph. The labeling density curve measures labeled neuron density in successive rostrocaudal sections, whereas the connectivity graph provides a two-dimensional model of the topography of a given connectivity. The connectivity graph makes it possible to define two parameters that characterize the topography of the connection: the convergence and the divergence. The convergence is defined as the extent of an afferent structure that contains neurons converging on a line normal to the cortical surface in area 17. The divergence is the extent of area 17 that is innervated by neurons contained in an infinitely small region of the afferent structure. The results show that a number of subcortical structures project to area 17 in a nontopographic manner, i.e., that in each of these structures neurons contained in an infinitely small region send projections to the whole of area 17 and that a line normal to the surface of area 17 is innervated by neurons distributed throughout the afferent structure in question. Nontopographic projections are found from the intralaminar nuclei, the ventral mesencephalic tegmental region, the diagonal band of Broca, and the locus coeruleus. All remaining subcortical structures and cortical areas send topographically organized projections to area 17. The extent of the convergence and divergence, however, varies between structures. Only the projection from the A laminae of the LGN was found to approximate a point-to-point projection with a convergence of 0.4 mm and 2 mm in divergence. Much larger convergence and divergence values are found in the projections from the claustrum and the cortical areas. For example, the divergence reaches 20 mm for the projections from area 20 or from the anterior part of the lateral suprasylvian sulcus. Knowing the convergence and divergence values and the retinotopic organizations of area 17 and a number of its afferents, it becomes possible to test whether connections in the visual system link regions representing the same zone of the visual field.(ABSTRACT TRUNCATED AT 400 WORDS)},
	Author = {Salin, P A and Bullier, J and Kennedy, H},
	Date-Added = {2012-12-11 13:59:40 +0000},
	Date-Modified = {2012-12-11 14:01:33 +0000},
	Doi = {10.1002/cne.902830405},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {mirror symmetry; Corpus Callosum; cat; Histological Techniques; histology; visual system; visual cortex; Neocortex; topographic map; brain mapping; graph theory; toread},
	Mesh = {Afferent Pathways; Animals; Brain Mapping; Cats; Fluorescent Dyes; Visual Cortex; Visual Pathways},
	Month = {May},
	Number = {4},
	Pages = {486-512},
	Pmid = {2745751},
	Pst = {ppublish},
	Title = {Convergence and divergence in the afferent projections to cat area 17},
	Volume = {283},
	Year = {1989},
	File = {papers/Salin_JCompNeurol1989.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.902830405}}

@article{Olavarria:2012,
	Abstract = {Callosal connections form elaborate patterns that bear close association with striate and extrastriate visual areas. Although it is known that retinal input is required for normal callosal development, there is little information regarding the period during which the retina is critically needed and whether this period correlates with the same developmental stage across species. Here we review the timing of this critical period, identified in rodents and ferrets by the effects that timed enucleations have on mature callosal connections, and compare it to other developmental milestones in these species. Subsequently, we compare these events to diffusion tensor imaging (DTI) measurements of water diffusion anisotropy within developing cerebral cortex. We observed that the relationship between the timing of the critical period and the DTI-characterized developmental trajectory is strikingly similar in rodents and ferrets, which opens the possibility of using cortical DTI trajectories for predicting the critical period in species, such as humans, in which this period likely occurs prenatally. Last, we discuss the potential of utilizing DTI to distinguish normal from abnormal cerebral cortical development, both within the context of aberrant connectivity induced by early retinal deafferentation, and more generally as a potential tool for detecting abnormalities associated with neurodevelopmental disorders.},
	Author = {Olavarria, Jaime F and Bock, Andrew S and Leigland, Lindsey A and Kroenke, Christopher D},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:14:04 +0000},
	Doi = {10.1155/2012/250196},
	Journal = {Neural Plast},
	Journal-Full = {Neural plasticity},
	Keywords = {visual system, connectivity, visual cortex, neocortex, histology, spontaneous activity, retina, brain mapping, mirror symmetry, corpus callosum},
	Pages = {250196},
	Pmid = {23213572},
	Pst = {ppublish},
	Title = {Deafferentation-induced plasticity of visual callosal connections: predicting critical periods and analyzing cortical abnormalities using diffusion tensor imaging},
	Volume = {2012},
	Year = {2012},
	File = {papers/Olavarria_NeuralPlast2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1155/2012/250196}}

@article{Laing:2012,
	Abstract = {Previous studies have shown that retinal input plays an important role in the development of interhemispheric callosal connections, but little is known about the role retinal input plays on the development of ipsilateral striate-extrastriate connections and the interplay that might exist between developing ipsilateral and callosal pathways. We analyzed the effects of bilateral enucleation performed at different ages on both the distribution of extrastriate projections originating from restricted loci in medial, acallosal striate cortex, and the overall pattern of callosal connections revealed following multiple tracer injections. As in normal rats, striate-extrastriate projections in rats enucleated at birth consisted of multiple, well-defined fields that were largely confined to acallosal regions throughout extrastriate cortex. However, these projections were highly irregular and variable, and they tended to occupy correspondingly anomalous and variable acallosal regions. Moreover, area 17, but not area 18a, was smaller in enucleates compared to controls, resulting in an increase in the divergence of striate projections. Anomalies in patterns of striate-extrastriate projections were not observed in rats enucleated at postnatal day (P)6, although the size of area 17 was still reduced in these rats. These results indicate that the critical period during which the eyes influence the development of striate-extrastriate, but not the size of striate cortex, ends by P6. Finally, enucleation did not change the time course and definition of the initial invasion of axons into gray matter, suggesting that highly variable striate projections patterns do not result from anomalous pruning of exuberant distributions of 17-18a fibers in gray matter.},
	Author = {Laing, R J and Bock, A S and Lasiene, J and Olavarria, J F},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:20:19 +0000},
	Doi = {10.1002/cne.23096},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {visual system, connectivity, visual cortex, neocortex, histology, spontaneous activity, retina, brain mapping, mirror symmetry, corpus callosum, toread},
	Month = {Oct},
	Number = {14},
	Pages = {3256-76},
	Pmid = {22430936},
	Pst = {ppublish},
	Title = {Role of retinal input on the development of striate-extrastriate patterns of connections in the rat},
	Volume = {520},
	Year = {2012},
	File = {papers/Laing_JCompNeurol2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.23096}}

@article{Bock:2012,
	Abstract = {Retinal input plays an important role in the specification of topographically organized circuits and neuronal response properties, but the mechanism and timing of this effect is not known in most species. A system that shows dramatic dependence on retinal influences is the interhemispheric connection through the corpus callosum. Using ferrets, we analyzed the extent to which development of the visual callosal pattern depends on retinal influences, and explored the period during which these influences are required for normal pattern formation. We studied the mature callosal patterns in normal ferrets and in ferrets bilaterally enucleated (BE) at postnatal day 7 (P7) or P20. Callosal patterns were revealed in tangential sections from unfolded and flattened brains following multiple injections of horseradish peroxidase in the opposite hemisphere. We also estimated the effect of enucleation on the surface areas of striate and extrastriate visual cortex by using magnetic resonance imaging (MRI) data from intact brains. In BEP7 ferrets we found that the pattern of callosal connections was highly anomalous and the sizes of both striate and extrastriate visual cortex were significantly reduced. In contrast, enucleation at P20 had no significant effect on the callosal pattern, but it still caused a reduction in the size of striate and extrastriate visual cortex. Finally, retinal deafferentation had no significant effect on the number of visual callosal neurons. These results indicate that the critical period during which the eyes influence the development of callosal patterns, but not the size of visual cortex, ends by P20 in the ferret.},
	Author = {Bock, A S and Kroenke, C D and Taber, E N and Olavarria, J F},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:20:27 +0000},
	Doi = {10.1002/cne.22738},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {currOpinRvw; visual system; connectivity; visual cortex; neocortex; histology; spontaneous activity; retina; brain mapping; mirror symmetry; corpus callosum; toread},
	Mesh = {Animals; Animals, Newborn; Corpus Callosum; Eye Enucleation; Ferrets; Retina; Visual Cortex; Visual Pathways},
	Month = {Apr},
	Number = {5},
	Pages = {914-32},
	Pmid = {21830218},
	Pst = {ppublish},
	Title = {Retinal input influences the size and corticocortical connectivity of visual cortex during postnatal development in the ferret},
	Volume = {520},
	Year = {2012},
	File = {papers/Bock_JCompNeurol2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.22738}}

@article{Bock:2011a,
	Abstract = {Previous studies have reported that intrahemispheric connections between area 17 (V1, striate cortex) and other cortical visual areas are not point-to-point, but instead have some degree of convergence and divergence. Many pathological conditions can interfere with the normal development of patterns of cortico-cortical connections, but there is little information regarding whether or not early pathological insults can also induce permanent changes in the convergence and divergence of cortical connections. Obtaining this information is important because loss of precision in neural projections can contribute to functional deficits and behavioral impairment. In the present study we investigated whether retinal input is required for the development of normal values of convergence and divergence in the visual callosal pathway. We found that enucleation performed at birth induced significant increases in convergence and divergence compared to control animals. In contrast, values of convergence and divergence in rats enucleated at postnatal day 7 (P7) were similar to those in controls. Previous studies have shown that retinal input during the first postnatal week is required for the specification of the overall distribution and internal topography of visual callosal pathways. Our present results therefore extend these previous finding by showing that retinal input during the first postnatal week also specifies the precision of cortico-cortical projections. These findings raise the possibility that the precision of neural connections may be reduced in other pathological conditions that affect early development of neural connections.},
	Author = {Bock, A S and Olavarria, J F},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:14:04 +0000},
	Doi = {10.1016/j.neulet.2011.07.005},
	Journal = {Neurosci Lett},
	Journal-Full = {Neuroscience letters},
	Keywords = {visual system, connectivity, visual cortex, neocortex, histology, spontaneous activity, retina, brain mapping, mirror symmetry, corpus callosum},
	Mesh = {Animals; Animals, Newborn; Axons; Blindness; Critical Period (Psychology); Disease Models, Animal; Neural Pathways; Rats; Rats, Long-Evans; Visual Cortex; Visual Pathways},
	Month = {Sep},
	Number = {3},
	Pages = {152-6},
	Pmc = {PMC3155624},
	Pmid = {21782890},
	Pst = {ppublish},
	Title = {Neonatal enucleation during a critical period reduces the precision of cortico-cortical projections in visual cortex},
	Volume = {501},
	Year = {2011},
	File = {papers/Bock_NeurosciLett2011.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neulet.2011.07.005}}

@article{Bock:2010,
	Abstract = {Diffusion tensor imaging (DTI) is a technique that non-invasively provides quantitative measures of water translational diffusion, including fractional anisotropy (FA), that are sensitive to the shape and orientation of cellular elements, such as axons, dendrites and cell somas. For several neurodevelopmental disorders, histopathological investigations have identified abnormalities in the architecture of pyramidal neurons at early stages of cerebral cortex development. To assess the potential capability of DTI to detect neuromorphological abnormalities within the developing cerebral cortex, we compare changes in cortical FA with changes in neuronal architecture and connectivity induced by bilateral enucleation at postnatal day 7 (BEP7) in ferrets. We show here that the visual callosal pattern in BEP7 ferrets is more irregular and occupies a significantly greater cortical area compared to controls at adulthood. To determine whether development of the cerebral cortex is altered in BEP7 ferrets in a manner detectable by DTI, cortical FA was compared in control and BEP7 animals on postnatal day 31. Visual cortex, but not rostrally adjacent non-visual cortex, exhibits higher FA than control animals, consistent with BEP7 animals possessing axonal and dendritic arbors of reduced complexity than age-matched controls. Subsequent to DTI, Golgi-staining and analysis methods were used to identify regions, restricted to visual areas, in which the orientation distribution of neuronal processes is significantly more concentrated than in control ferrets. Together, these findings suggest that DTI can be of utility for detecting abnormalities associated with neurodevelopmental disorders at early stages of cerebral cortical development, and that the neonatally enucleated ferret is a useful animal model system for systematically assessing the potential of this new diagnostic strategy.},
	Author = {Bock, Andrew S and Olavarria, Jaime F and Leigland, Lindsey A and Taber, Erin N and Jespersen, Sune N and Kroenke, Christopher D},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:14:04 +0000},
	Doi = {10.3389/fnsys.2010.00149},
	Journal = {Front Syst Neurosci},
	Journal-Full = {Frontiers in systems neuroscience},
	Keywords = {visual system, connectivity, visual cortex, neocortex, histology, spontaneous activity, retina, brain mapping, mirror symmetry, corpus callosum},
	Pages = {149},
	Pmc = {PMC2971465},
	Pmid = {21048904},
	Pst = {epublish},
	Title = {Diffusion tensor imaging detects early cerebral cortex abnormalities in neuronal architecture induced by bilateral neonatal enucleation: an experimental model in the ferret},
	Volume = {4},
	Year = {2010},
	File = {papers/Bock_FrontSystNeurosci2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fnsys.2010.00149}}

@article{Ruthazer:2010a,
	Abstract = {We combined fixed-tissue and time-lapse analyses to investigate the axonal branching phenomena underlying the development of topographically organized ipsilateral projections from area 17 to area 18a in the rat. These complementary approaches allowed us to relate static, large-scale information provided by traditional fixed-tissue analysis to highly dynamic, local, small-scale branching phenomena observed with two-photon time-lapse microscopy in acute slices of visual cortex. Our fixed-tissue data revealed that labeled area 17 fibers invaded area 18a gray matter at topographically restricted sites, reaching superficial layers in significant numbers by postnatal day 6 (P6). Moreover, most parental axons gave rise to only one or occasionally a small number of closely spaced interstitial branches beneath 18a. Our time-lapse data showed that many filopodium-like branches emerged along parental axons in white matter or deep layers in area 18a. Most of these filopodial branches were transient, often disappearing after several minutes to hours of exploratory extension and retraction. These dynamic behaviors decreased significantly from P4, when the projection is first forming, through the second postnatal week, suggesting that the expression of, or sensitivity to, cortical cues promoting new branch addition in the white matter is developmentally down-regulated coincident with gray matter innervation. Together, these data demonstrate that the development of topographically organized corticocortical projections in rats involves extensive exploratory branching along parental axons and invasion of cortex by only a small number of interstitial branches, rather than the widespread innervation of superficial cortical layers by an initially exuberant population of branches.},
	Author = {Ruthazer, Edward S and Bachleda, Amelia R and Olavarria, Jaime F},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:14:04 +0000},
	Doi = {10.1002/cne.22502},
	Journal = {J Comp Neurol},
	Journal-Full = {The Journal of comparative neurology},
	Keywords = {currOpinRvw; visual system; connectivity; visual cortex; neocortex; histology; spontaneous activity; retina; brain mapping; mirror symmetry; corpus callosum},
	Mesh = {Animals; Animals, Newborn; Axons; Brain Mapping; Cell Differentiation; Microscopy, Video; Neural Pathways; Neuronal Tract-Tracers; Rats; Time Factors; Time-Lapse Imaging; Tissue Fixation; Visual Cortex; Visual Pathways},
	Month = {Dec},
	Number = {24},
	Pages = {4963-79},
	Pmid = {21031561},
	Pst = {ppublish},
	Title = {Role of interstitial branching in the development of visual corticocortical connections: a time-lapse and fixed-tissue analysis},
	Volume = {518},
	Year = {2010},
	File = {papers/Ruthazer_JCompNeurol2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/cne.22502}}

@article{Olavarria:2008,
	Abstract = {Visual callosal fibers link cortical loci in opposite hemispheres that represent the same visual field but whose locations are not mirror-symmetric with respect to the brain midline. Presence of the eyes from postnatal day 4 (P4) to P6 is required for this map to be specified. We tested the hypothesis that specification of the callosal map requires the activation of N-methyl-D-aspartate receptors (NMDARs). Our results show that blockade of NMDARs with MK-801 during this critical period did not induce obvious abnormalities in callosal connectivity patterns, suggesting that retinal influences do not operate through NMDAR-mediated processes to specify normal callosal topography. In contrast, we found that interfering with NMDAR function either through MK801-induced blockade of NMDARs starting at P6 or neonatal enucleation significantly increases the length of axon branches and total length of arbors, without major effects on the number of branch tips. Our results further suggest that NMDARs act by altering the initial elaboration of arbors rather than by inhibiting a later-occurring remodeling process. Since the callosal map is present by P6, just as axonal branches of simple architecture grow into gray matter, we suggest that regulation of arbor development by NMDAR-mediated processes is important for maintaining the precision of this map.},
	Author = {Olavarr{\'\i}a, Jaime F and Laing, Robyn and Hiroi, Ryoko and Lasiene, Jurate},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:14:04 +0000},
	Doi = {/S0716-97602008000400007},
	Journal = {Biol Res},
	Journal-Full = {Biological research},
	Keywords = {visual system, connectivity, visual cortex, neocortex, histology, spontaneous activity, retina, brain mapping, mirror symmetry, corpus callosum},
	Mesh = {Animals; Animals, Newborn; Axons; Brain Mapping; Corpus Callosum; Dizocilpine Maleate; Excitatory Amino Acid Antagonists; Eye Enucleation; Rats; Rats, Long-Evans; Receptors, N-Methyl-D-Aspartate; Visual Pathways},
	Number = {4},
	Pages = {413-24},
	Pmid = {19621122},
	Pst = {ppublish},
	Title = {Topography and axon arbor architecture in the visual callosal pathway: effects of deafferentation and blockade of N-methyl-D-aspartate receptors},
	Volume = {41},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/0716-97602008000400007}}

@article{Olavarria:2007,
	Abstract = {Development of the visual callosal projection in rodents goes through an early critical period, from postnatal day (P) 4 to P6, during which retinal input specifies the blueprint for normal topographic connections, and a subsequent period of progressive pathway maturation that is largely complete by the time the eyes open, around P13. This study tests the hypothesis that these developmental stages correlate with age-related changes in the kinetics of synaptic responses mediated by the N-methyl-D-aspartate subclass of glutamate receptors (NMDARs). We used an in vitro slice preparation to perform whole-cell recordings from retrogradely-labeled visual callosal cells, as well from cortical cells with unknown projections. We analyzed age-related changes in the decay time constant of evoked as well as spontaneous excitatory postsynaptic currents mediated by N-methyl-D-aspartate subclass of glutamate receptors (NMDAR-EPSCs) in slices from normal pups and pups enucleated at different postnatal ages. In normal pups we found that the decay time constant of NMDAR-EPSCs increases starting at about P6 and decreases by about P13. In contrast, these changes were not observed in rats enucleated at birth. However, by delaying the age at which enucleation was performed we found that the presence of the eyes until P6, but not until P4, is sufficient for inducing slow NMDAR-EPSC kinetics during the second postnatal week, as observed in normal pups. These results provide evidence that the eyes exert a bidirectional effect on the kinetics of NMDARs: during a P4-P6 critical period, retinal influences induce processes that slow down the kinetics of NMDAR-EPSCs, while, near the age of eye opening, retinal input induces a sudden acceleration of NMDAR-EPSC kinetics. These findings suggest that the retinally-driven processes that specify normal callosal topography during the P4-P6 time window also induce an increase in the decay time constant of NMDAR-EPSCs. This increase in response kinetics may play an important role in the maturation of cortical topographic maps after P6. Using ifenprodil, a noncompetitive NR2B-selective blocker, we obtained evidence that although NR1/NR2B diheteromeric receptors contribute to evoked synaptic responses in both normal and enucleated animals, they are not primarily responsible for either the age-related changes in the kinetics of NMDAR-mediated responses, or the effects that bilateral enucleation has on the kinetics of NMDAR-EPSCs.},
	Author = {Olavarria, J F and van Brederode, J F M and Spain, W J},
	Date-Added = {2012-12-10 20:12:55 +0000},
	Date-Modified = {2012-12-10 20:14:04 +0000},
	Doi = {10.1016/j.neuroscience.2007.07.005},
	Journal = {Neuroscience},
	Journal-Full = {Neuroscience},
	Keywords = {visual system, connectivity, visual cortex, neocortex, histology, spontaneous activity, retina, brain mapping, mirror symmetry, corpus callosum},
	Mesh = {Aging; Animals; Animals, Newborn; Cell Communication; Cell Differentiation; Corpus Callosum; Denervation; Excitatory Amino Acid Antagonists; Excitatory Postsynaptic Potentials; Eye Enucleation; Kinetics; Neuronal Plasticity; Organ Culture Techniques; Patch-Clamp Techniques; Presynaptic Terminals; Rats; Rats, Long-Evans; Receptors, N-Methyl-D-Aspartate; Retina; Synaptic Transmission; Visual Cortex; Visual Pathways},
	Month = {Sep},
	Number = {3},
	Pages = {683-99},
	Pmid = {17706364},
	Pst = {ppublish},
	Title = {Retinal influences induce bidirectional changes in the kinetics of N-methyl-D-aspartate receptor-mediated responses in striate cortex cells during postnatal development},
	Volume = {148},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroscience.2007.07.005}}

@article{Innocenti:1979a,
	Author = {Innocenti, G M and Frost, D O},
	Date-Added = {2012-12-10 20:06:17 +0000},
	Date-Modified = {2012-12-10 20:11:20 +0000},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {visual system; mirror symmetry; Neocortex; visual cortex; activity manipulation; Sensory Deprivation; Spontaneous activity; retina; connectivity; Histological Techniques; Brain Mapping},
	Mesh = {Animals; Blindness; Cats; Corpus Callosum; Efferent Pathways; Horseradish Peroxidase; Retrograde Degeneration; Strabismus; Visual Cortex},
	Month = {Jul},
	Number = {5719},
	Pages = {231-4},
	Pmid = {450139},
	Pst = {ppublish},
	Title = {Effects of visual experience on the maturation of the efferent system to the corpus callosum},
	Volume = {280},
	Year = {1979},
	File = {papers/Innocenti_Nature1979.pdf}}

@article{Nimmervoll:2012,
	Abstract = {During the pre- and neonatal period, the cerebral cortex reveals distinct patterns of spontaneous synchronized activity, which is critically involved in the formation of early networks and in the regulation of neuronal survival and programmed cell death (apoptosis). During this period, the cortex is also highly vulnerable to inflammation and in humans prenatal infection may have a profound impact on neurodevelopment causing long-term neurological deficits. Using in vitro and in vivo multi-electrode array recordings and quantification of caspase-3 (casp-3)-dependent apoptosis, we demonstrate that lipopolysaccharide-induced inflammation causes rapid alterations in the pattern of spontaneous burst activities, which subsequently leads to an increase in apoptosis. We show that these inflammatory effects are specifically initiated by the microglia-derived pro-inflammatory cytokine tumor necrosis factor α and the chemokine macrophage inflammatory protein 2. Our data demonstrate that inflammation-induced modifications in spontaneous network activities influence casp-3-dependent cell death in the developing cerebral cortex.},
	Author = {Nimmervoll, Birgit and White, Robin and Yang, Jenq-Wei and An, Shuming and Henn, Christopher and Sun, Jyh-Jang and Luhmann, Heiko J},
	Date-Added = {2012-11-20 14:55:43 +0000},
	Date-Modified = {2012-11-20 15:00:14 +0000},
	Doi = {10.1093/cercor/bhs156},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {genes; self organization; Competitive Behavior; optical imaging; optical physiology; toread; wholeBrain; Somatosensory Cortex; thalamus; barrels; Mouse; development; synchrony; oscillations; microglia},
	Month = {Jun},
	Pmid = {22700645},
	Pst = {aheadofprint},
	Title = {LPS-Induced Microglial Secretion of TNFα Increases Activity-Dependent Neuronal Apoptosis in the Neonatal Cerebral Cortex},
	Year = {2012},
	File = {papers/Nimmervoll_CerebCortex2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhs156}}

@article{Yang:2012a,
	Abstract = {Neocortical areas are organized in columns, which form the basic structural and functional modules of intracortical information processing. Using voltage-sensitive dye imaging and simultaneous multi-channel extracellular recordings in the barrel cortex of newborn rats in vivo, we found that spontaneously occurring and whisker stimulation-induced gamma bursts followed by longer lasting spindle bursts were topographically organized in functional cortical columns already at the day of birth. Gamma bursts synchronized a cortical network of 300-400 µm in diameter and were coherent with gamma activity recorded simultaneously in the thalamic ventral posterior medial (VPM) nucleus. Cortical gamma bursts could be elicited by focal electrical stimulation of the VPM. Whisker stimulation-induced spindle and gamma bursts and the majority of spontaneously occurring events were profoundly reduced by the local inactivation of the VPM, indicating that the thalamus is important to generate these activity patterns. Furthermore, inactivation of the barrel cortex with lidocaine reduced the gamma activity in the thalamus, suggesting that a cortico-thalamic feedback loop modulates this early thalamic network activity.},
	Author = {Yang, Jenq-Wei and An, Shuming and Sun, Jyh-Jang and Reyes-Puerta, Vicente and Kindler, Jennifer and Berger, Thomas and Kilb, Werner and Luhmann, Heiko J},
	Date-Added = {2012-11-20 14:55:31 +0000},
	Date-Modified = {2012-11-20 14:59:37 +0000},
	Doi = {10.1093/cercor/bhs103},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {genes; self organization; Competitive Behavior; optical imaging; optical physiology; toread; wholeBrain; Somatosensory Cortex; thalamus; barrels; Mouse; development; synchrony; oscillations},
	Month = {May},
	Pmid = {22593243},
	Pst = {aheadofprint},
	Title = {Thalamic Network Oscillations Synchronize Ontogenetic Columns in the Newborn Rat Barrel Cortex},
	Year = {2012},
	File = {papers/Yang_CerebCortex2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhs103}}

@article{Blanton:1990,
	Abstract = {Before synapses form in embryonic turtle cerebral cortex, an endogenous neurotransmitter activates N-methyl-D-aspartate (NMDA) channels on neurons in the cortical plate. Throughout cortical development, these channels exhibit voltage-dependent Mg2+ blockade and are antagonized by D-2-amino-5-phosphonovaleric acid, a selective NMDA receptor antagonist. The activation in situ of these nonsynaptic NMDA channels demonstrates a potential physiological substrate for control of early neuronal differentiation.},
	Author = {Blanton, M G and Lo Turco, J J and Kriegstein, A R},
	Date-Added = {2012-11-15 22:04:30 +0000},
	Date-Modified = {2012-11-15 22:05:41 +0000},
	Journal = {Proc Natl Acad Sci U S A},
	Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America},
	Keywords = {Activity-development; NMDA; Glutamate; Spontaneous activity; Calcium Signaling; Electrophysiology; Turtles; embryology; physiology},
	Mesh = {2-Amino-5-phosphonovalerate; Animals; Axons; Cell Differentiation; Cerebral Cortex; Electric Conductivity; Embryo, Nonmammalian; Glutamates; Glutamic Acid; Magnesium; Neurons; Neurotransmitter Agents; Receptors, N-Methyl-D-Aspartate; Turtles},
	Month = {Oct},
	Number = {20},
	Pages = {8027-30},
	Pmc = {PMC54885},
	Pmid = {1978317},
	Pst = {ppublish},
	Title = {Endogenous neurotransmitter activates N-methyl-D-aspartate receptors on differentiating neurons in embryonic cortex},
	Volume = {87},
	Year = {1990}}

@article{Bassett:2006a,
	Abstract = {Many complex networks have a small-world topology characterized by dense local clustering or cliquishness of connections between neighboring nodes yet a short path length between any (distant) pair of nodes due to the existence of relatively few long-range connections. This is an attractive model for the organization of brain anatomical and functional networks because a small-world topology can support both segregated/specialized and distributed/integrated information processing. Moreover, small-world networks are economical, tending to minimize wiring costs while supporting high dynamical complexity. The authors introduce some of the key mathematical concepts in graph theory required for small-world analysis and review how these methods have been applied to quantification of cortical connectivity matrices derived from anatomical tract-tracing studies in the macaque monkey and the cat. The evolution of small-world networks is discussed in terms of a selection pressure to deliver cost-effective information-processing systems. The authors illustrate how these techniques and concepts are increasingly being applied to the analysis of human brain functional networks derived from electroencephalography/magnetoencephalography and fMRI experiments. Finally, the authors consider the relevance of small-world models for understanding the emergence of complex behaviors and the resilience of brain systems to pathological attack by disease or aberrant development. They conclude that small-world models provide a powerful and versatile approach to understanding the structure and function of human brain systems.},
	Author = {Bassett, Danielle Smith and Bullmore, Ed},
	Date-Added = {2012-11-15 13:34:38 +0000},
	Date-Modified = {2012-11-15 13:34:45 +0000},
	Doi = {10.1177/1073858406293182},
	Journal = {Neuroscientist},
	Journal-Full = {The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry},
	Keywords = {network; technique; Methods; review literature; computation biology; Theoretical; graph theory; human; fmri; Software; toread},
	Mesh = {Animals; Brain; Brain Mapping; Humans; Models, Neurological; Nerve Net},
	Month = {Dec},
	Number = {6},
	Pages = {512-23},
	Pmid = {17079517},
	Pst = {ppublish},
	Title = {Small-world brain networks},
	Volume = {12},
	Year = {2006},
	File = {papers/Bassett_Neuroscientist2006.pdf}}

@article{Bullmore:2009,
	Abstract = {Recent developments in the quantitative analysis of complex networks, based largely on graph theory, have been rapidly translated to studies of brain network organization. The brain's structural and functional systems have features of complex networks--such as small-world topology, highly connected hubs and modularity--both at the whole-brain scale of human neuroimaging and at a cellular scale in non-human animals. In this article, we review studies investigating complex brain networks in diverse experimental modalities (including structural and functional MRI, diffusion tensor imaging, magnetoencephalography and electroencephalography in humans) and provide an accessible introduction to the basic principles of graph theory. We also highlight some of the technical challenges and key questions to be addressed by future developments in this rapidly moving field.},
	Author = {Bullmore, Ed and Sporns, Olaf},
	Date-Added = {2012-11-15 13:33:26 +0000},
	Date-Modified = {2014-08-05 13:06:00 +0000},
	Doi = {10.1038/nrn2575},
	Journal = {Nat Rev Neurosci},
	Journal-Full = {Nature reviews. Neuroscience},
	Keywords = {network; technique; Methods; review literature; computation biology; Theoretical; graph theory; human; fmri; Software},
	Mesh = {Animals; Brain; Brain Mapping; Computer Graphics; Electroencephalography; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Magnetoencephalography; Nerve Net; Neural Networks (Computer)},
	Month = {Mar},
	Number = {3},
	Pages = {186-98},
	Pmid = {19190637},
	Pst = {ppublish},
	Title = {Complex brain networks: graph theoretical analysis of structural and functional systems},
	Volume = {10},
	Year = {2009},
	File = {papers/Bullmore_NatRevNeurosci2009.pdf}}

@article{Lynall:2010,
	Abstract = {Schizophrenia has often been conceived as a disorder of connectivity between components of large-scale brain networks. We tested this hypothesis by measuring aspects of both functional connectivity and functional network topology derived from resting-state fMRI time series acquired at 72 cerebral regions over 17 min from 15 healthy volunteers (14 male, 1 female) and 12 people diagnosed with schizophrenia (10 male, 2 female). We investigated between-group differences in strength and diversity of functional connectivity in the 0.06-0.125 Hz frequency interval, and some topological properties of undirected graphs constructed from thresholded interregional correlation matrices. In people with schizophrenia, strength of functional connectivity was significantly decreased, whereas diversity of functional connections was increased. Topologically, functional brain networks had reduced clustering and small-worldness, reduced probability of high-degree hubs, and increased robustness in the schizophrenic group. Reduced degree and clustering were locally significant in medial parietal, premotor and cingulate, and right orbitofrontal cortical nodes of functional networks in schizophrenia. Functional connectivity and topological metrics were correlated with each other and with behavioral performance on a verbal fluency task. We conclude that people with schizophrenia tend to have a less strongly integrated, more diverse profile of brain functional connectivity, associated with a less hub-dominated configuration of complex brain functional networks. Alongside these behaviorally disadvantageous differences, however, brain networks in the schizophrenic group also showed a greater robustness to random attack, pointing to a possible benefit of the schizophrenia connectome, if less extremely expressed.},
	Author = {Lynall, Mary-Ellen and Bassett, Danielle S and Kerwin, Robert and McKenna, Peter J and Kitzbichler, Manfred and Muller, Ulrich and Bullmore, Ed},
	Date-Added = {2012-11-14 22:00:52 +0000},
	Date-Modified = {2014-01-27 14:57:50 +0000},
	Doi = {10.1523/JNEUROSCI.0333-10.2010},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {connectivity; Schizophrenia; human; fmri; Functional Laterality; network; graph theory; Technique; grant; wholeBrain; Schizophrenia},
	Mesh = {Adult; Brain; Brain Mapping; Cognition; Female; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Models, Neurological; Nerve Net; Neural Pathways; Neuropsychological Tests; Principal Component Analysis; Schizophrenia},
	Month = {Jul},
	Number = {28},
	Pages = {9477-87},
	Pmc = {PMC2914251},
	Pmid = {20631176},
	Pst = {ppublish},
	Title = {Functional connectivity and brain networks in schizophrenia},
	Volume = {30},
	Year = {2010},
	File = {papers/Lynall_JNeurosci2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.0333-10.2010}}

@article{Karlsgodt:2008,
	Abstract = {Schizophrenia has been thought of as a disorder of reduced functional and structural connectivity. Recent advances in neuroimaging techniques such as functional magnetic resonance imaging, structural magnetic resonance imaging, diffusion tensor imaging, and small animal imaging have advanced our ability to investigate this hypothesis. Moreover, the power of longitudinal designs possible with these noninvasive techniques enable the study of not just how connectivity is disrupted in schizophrenia, but when this disruption emerges during development. This article reviews genetic and neurodevelopmental influences on structural and functional connectivity in human populations with or at risk for schizophrenia and in animal models of the disorder. We conclude that the weight of evidence across these diverse lines of inquiry points to a developmental disruption of neural connectivity in schizophrenia and that this disrupted connectivity likely involves susceptibility genes that affect processes involved in establishing intra- and interregional connectivity.},
	Author = {Karlsgodt, Katherine H and Sun, Daqiang and Jimenez, Amy M and Lutkenhoff, Evan S and Willhite, Rachael and van Erp, Theo G M and Cannon, Tyrone D},
	Date-Added = {2012-11-14 21:29:25 +0000},
	Date-Modified = {2012-11-14 21:30:17 +0000},
	Doi = {10.1017/S095457940800062X},
	Journal = {Dev Psychopathol},
	Journal-Full = {Development and psychopathology},
	Keywords = {Schizophrenia; neurological disorder; Cognition; Cognition Disorders; Functional Laterality; asymmetry; mirror symmetry; fMRI; connectivity; human; mouse},
	Mesh = {Adolescent; Adult; Animals; Brain; Brain Mapping; Child; Child Development; Cognition Disorders; Disease Models, Animal; Environment; Genetic Predisposition to Disease; Genotype; Humans; Magnetic Resonance Imaging; Models, Neurological; Neural Conduction; Neurons; Risk Factors; Schizophrenia; Synapses; Young Adult},
	Number = {4},
	Pages = {1297-327},
	Pmid = {18838043},
	Pst = {ppublish},
	Title = {Developmental disruptions in neural connectivity in the pathophysiology of schizophrenia},
	Volume = {20},
	Year = {2008},
	File = {papers/Karlsgodt_DevPsychopathol2008.pdf}}

@article{Bressler:2010,
	Abstract = {An understanding of how the human brain produces cognition ultimately depends on knowledge of large-scale brain organization. Although it has long been assumed that cognitive functions are attributable to the isolated operations of single brain areas, we demonstrate that the weight of evidence has now shifted in support of the view that cognition results from the dynamic interactions of distributed brain areas operating in large-scale networks. We review current research on structural and functional brain organization, and argue that the emerging science of large-scale brain networks provides a coherent framework for understanding of cognition. Critically, this framework allows a principled exploration of how cognitive functions emerge from, and are constrained by, core structural and functional networks of the brain.},
	Author = {Bressler, Steven L and Menon, Vinod},
	Date-Added = {2012-11-14 21:24:24 +0000},
	Date-Modified = {2012-11-14 21:28:09 +0000},
	Doi = {10.1016/j.tics.2010.04.004},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {toread; resting state; default mode network; connectivity; connectome; human; fMRI; function; Functional Laterality; Technique; Methods; Computational Biology; graph theory; network},
	Mesh = {Animals; Brain; Brain Mapping; Cognition; Humans; Neural Pathways; Psychopathology},
	Month = {Jun},
	Number = {6},
	Pages = {277-90},
	Pmid = {20493761},
	Pst = {ppublish},
	Title = {Large-scale brain networks in cognition: emerging methods and principles},
	Volume = {14},
	Year = {2010},
	File = {papers/Bressler_TrendsCognSci2010.pdf}}

@article{Menon:2011,
	Abstract = {The science of large-scale brain networks offers a powerful paradigm for investigating cognitive and affective dysfunction in psychiatric and neurological disorders. This review examines recent conceptual and methodological developments which are contributing to a paradigm shift in the study of psychopathology. I summarize methods for characterizing aberrant brain networks and demonstrate how network analysis provides novel insights into dysfunctional brain architecture. Deficits in access, engagement and disengagement of large-scale neurocognitive networks are shown to play a prominent role in several disorders including schizophrenia, depression, anxiety, dementia and autism. Synthesizing recent research, I propose a triple network model of aberrant saliency mapping and cognitive dysfunction in psychopathology, emphasizing the surprising parallels that are beginning to emerge across psychiatric and neurological disorders.},
	Author = {Menon, Vinod},
	Date-Added = {2012-11-14 21:15:29 +0000},
	Date-Modified = {2012-11-14 21:16:16 +0000},
	Doi = {10.1016/j.tics.2011.08.003},
	Journal = {Trends Cogn Sci},
	Journal-Full = {Trends in cognitive sciences},
	Keywords = {toread; connectivity; connectome; function; Functional Laterality; resting state; default mode network; human; neuroimaging; fMRI; Cognition; Cognition Disorders; neurological disorder},
	Mesh = {Brain; Humans; Models, Neurological; Nerve Net; Psychopathology},
	Month = {Oct},
	Number = {10},
	Pages = {483-506},
	Pmid = {21908230},
	Pst = {ppublish},
	Title = {Large-scale brain networks and psychopathology: a unifying triple network model},
	Volume = {15},
	Year = {2011},
	File = {papers/Menon_TrendsCognSci2011.pdf}}

@article{Courchesne:2005,
	Abstract = {Although it has long been thought that frontal lobe abnormality must play an important part in generating the severe impairment in higher-order social, emotional and cognitive functions in autism, only recently have studies identified developmentally early frontal lobe defects. At the microscopic level, neuroinflammatory reactions involving glial activation, migration defects and excess cerebral neurogenesis and/or defective apoptosis might generate frontal neural pathology early in development. It is hypothesized that these abnormal processes cause malformation and thus malfunction of frontal minicolumn microcircuitry. It is suggested that connectivity within frontal lobe is excessive, disorganized and inadequately selective, whereas connectivity between frontal cortex and other systems is poorly synchronized, weakly responsive and information impoverished. Increased local but reduced long-distance cortical-cortical reciprocal activity and coupling would impair the fundamental frontal function of integrating information from widespread and diverse systems and providing complex context-rich feedback, guidance and control to lower-level systems.},
	Author = {Courchesne, Eric and Pierce, Karen},
	Date-Added = {2012-11-14 20:03:57 +0000},
	Date-Modified = {2012-11-14 20:05:51 +0000},
	Doi = {10.1016/j.conb.2005.03.001},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Keywords = {Autistic Disorder; autism; connectivity; human; mirror symmetry; neurological disorder; function; Frontal Lobe; Neocortex; Cerebral Cortex},
	Mesh = {Autistic Disorder; Frontal Lobe; Humans; Nerve Net},
	Month = {Apr},
	Number = {2},
	Pages = {225-30},
	Pmid = {15831407},
	Pst = {ppublish},
	Title = {Why the frontal cortex in autism might be talking only to itself: local over-connectivity but long-distance disconnection},
	Volume = {15},
	Year = {2005},
	File = {papers/Courchesne_CurrOpinNeurobiol2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.conb.2005.03.001}}

@article{Desgent:2012,
	Abstract = {Early loss of a given sensory input in mammals causes anatomical and functional modifications in the brain via a process called cross-modal plasticity. In the past four decades, several animal models have illuminated our understanding of the biological substrates involved in cross-modal plasticity. Progressively, studies are now starting to emphasise on cell-specific mechanisms that may be responsible for this intermodal sensory plasticity. Inhibitory interneurons expressing γ-aminobutyric acid (GABA) play an important role in maintaining the appropriate dynamic range of cortical excitation, in critical periods of developmental plasticity, in receptive field refinement, and in treatment of sensory information reaching the cerebral cortex. The diverse interneuron population is very sensitive to sensory experience during development. GABAergic neurons are therefore well suited to act as a gate for mediating cross-modal plasticity. This paper attempts to highlight the links between early sensory deprivation, cortical GABAergic interneuron alterations, and cross-modal plasticity, discuss its implications, and further provide insights for future research in the field.},
	Author = {Desgent, S{\'e}bastien and Ptito, Maurice},
	Date-Added = {2012-11-14 19:31:01 +0000},
	Date-Modified = {2012-11-14 19:33:09 +0000},
	Doi = {10.1155/2012/590725},
	Journal = {Neural Plast},
	Journal-Full = {Neural plasticity},
	Keywords = {GABA; interneurons; development; Cerebral Cortex; Neocortex; visual cortex; visual system; multimodal; vision; Sensory Deprivation; plasticity; structural remodeling; Structure-Activity Relationship; Spontaneous activity},
	Pages = {590725},
	Pmc = {PMC3377178},
	Pmid = {22720175},
	Pst = {ppublish},
	Title = {Cortical GABAergic interneurons in cross-modal plasticity following early blindness},
	Volume = {2012},
	Year = {2012},
	File = {papers/Desgent_NeuralPlast2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1155/2012/590725}}

@article{Baumann:2012,
	Author = {Baumann, Kim},
	Date-Added = {2012-11-14 18:49:22 +0000},
	Date-Modified = {2012-11-14 18:50:14 +0000},
	Doi = {10.1038/nrm3456},
	Journal = {Nat Rev Mol Cell Biol},
	Journal-Full = {Nature reviews. Molecular cell biology},
	Keywords = {mirror symmetry; asymmetry;development; patterning;Gene Expression;toread},
	Month = {Nov},
	Number = {11},
	Pages = {682-3},
	Pmid = {23034454},
	Pst = {ppublish},
	Title = {Development: Knowing left from right},
	Volume = {13},
	Year = {2012},
	File = {papers/Baumann_NatRevMolCellBiol2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrm3456}}

@article{Nakamura:2012,
	Abstract = {The left-right (LR) asymmetry of visceral organs is fundamental to their function and position within the body. Over the past decade or so, the molecular mechanisms underlying the establishment of such LR asymmetry have been revealed in many vertebrate and invertebrate model organisms. These studies have identified a gene network that contributes to this process and is highly conserved from sea urchin to mouse. By contrast, some specific steps of the process, such as the symmetry-breaking event and situs-specific organogenesis, appear to have diverged during evolution. Here, we summarize the common and divergent mechanisms by which LR asymmetry is established in vertebrates.},
	Author = {Nakamura, Tetsuya and Hamada, Hiroshi},
	Date-Added = {2012-11-14 18:41:32 +0000},
	Date-Modified = {2012-11-14 18:41:37 +0000},
	Doi = {10.1242/dev.061606},
	Journal = {Development},
	Journal-Full = {Development (Cambridge, England)},
	Keywords = {development; mirror symmetry; asymmetry; Gene Expression; patterning; toread},
	Mesh = {Animals; Body Patterning; Cell Movement; Gene Expression Regulation, Developmental; Invertebrates; Mice; Sea Urchins; Vertebrates},
	Month = {Sep},
	Number = {18},
	Pages = {3257-62},
	Pmid = {22912409},
	Pst = {ppublish},
	Title = {Left-right patterning: conserved and divergent mechanisms},
	Volume = {139},
	Year = {2012},
	File = {papers/Nakamura_Development2012.pdf}}

@article{Vandenberg:2010,
	Abstract = {Consistent laterality is a crucial aspect of embryonic development, physiology, and behavior. While strides have been made in understanding unilaterally expressed genes and the asymmetries of organogenesis, early mechanisms are still poorly understood. One popular model centers on the structure and function of motile cilia and subsequent chiral extracellular fluid flow during gastrulation. Alternative models focus on intracellular roles of the cytoskeleton in driving asymmetries of physiological signals or asymmetric chromatid segregation, at much earlier stages. All three models trace the origin of asymmetry back to the chirality of cytoskeletal organizing centers, but significant controversy exists about how this intracellular chirality is amplified onto cell fields. Analysis of specific predictions of each model and crucial recent data on new mutants suggest that ciliary function may not be a broadly conserved, initiating event in left-right patterning. Many questions about embryonic left-right asymmetry remain open, offering fascinating avenues for further research in cell, developmental, and evolutionary biology.},
	Author = {Vandenberg, Laura N and Levin, Michael},
	Date-Added = {2012-11-14 18:39:32 +0000},
	Date-Modified = {2013-09-25 20:54:06 +0000},
	Doi = {10.1002/dvdy.22450},
	Journal = {Dev Dyn},
	Journal-Full = {Developmental dynamics : an official publication of the American Association of Anatomists},
	Keywords = {development; mirror symmetry; asymmetry; Gene Expression; patterning; cerebral cortex; lateralization; asymmetry; hemisphere; Grants; mouse; behavior; Hand Strength; handedness; Laterality; human; gene; forelimb; language},
	Mesh = {Animals; Body Patterning; Embryonic Development; Humans; Models, Biological},
	Month = {Dec},
	Number = {12},
	Pages = {3131-46},
	Pmid = {21031419},
	Pst = {ppublish},
	Title = {Far from solved: a perspective on what we know about early mechanisms of left-right asymmetry},
	Volume = {239},
	Year = {2010},
	File = {papers/Vandenberg_DevDyn2010.pdf}}

@article{Yost:1998,
	Abstract = {Bilateran animals have external bilateral symmetry along the dorsoventral (DV) and anteroposterior (AP) axes. Internal left-right asymmetries appear to be consistently aligned along the left-right (LR) axis with respect to the other axes. Left-right development is most apparent in the directional looping of the cardiac tube, the coiling and placement of the intestines, the positioning of internal organs such as liver, gallbladder, pancreas, and stomach. In addition, there are obvious morphological asymmetries in the brains of some vertebrates and functional left-right asymmetries in the activities of the brain, as assessed by psychological testing, MRI, and the analysis of lesions. There are several fundamental questions: What are the origins of the left-right axis, and are they highly conserved across metazoans? Once the left-right axis is established by the initial breaking of bilateral symmetry, what is the genetic pathway that perpetrates left-right development? What are the cellular and tissue mechanics that lead to morphogenesis during, for example, the looping of the cardiac tube, the coiling of the gut, or asymmetric brain development? Finally, do the asymmetric developmental pathways of each organ system take register from the same initial event that establishes the left-right axis, or are there separate mechanisms that orient heart, gut, and brain left-right asymmetry with respect to the DV and AP axes? These questions are beginning to be experimentally addressed, and papers in this issue of Developmental Genetics make contributions to several aspects in the burgeoning field of left-right development. Recent reviews have summarized the emerging genes and pathways in vertebrate left-right development [Wood, 1997; Harvey, 1998; Ramsdell and Yost, 1998]. Here, I give an overview of the contributions in this issue to the fundamental questions in left-right development.},
	Author = {Yost, H J},
	Date-Added = {2012-11-14 17:37:21 +0000},
	Date-Modified = {2012-11-14 17:40:53 +0000},
	Doi = {10.1002/(SICI)1520-6408(1998)23:3<159::AID-DVG1>3.0.CO;2-1},
	Journal = {Dev Genet},
	Journal-Full = {Developmental genetics},
	Keywords = {asymmetry; lateralization; Cerebral Cortex; callosal; mirror symmetry; toread},
	Mesh = {Animals; Body Patterning; Brain; Functional Laterality; Humans; Mesoderm; Stereoisomerism},
	Number = {3},
	Pages = {159-63},
	Pmid = {9842710},
	Pst = {ppublish},
	Title = {Left-right development from embryos to brains},
	Volume = {23},
	Year = {1998},
	File = {papers/Yost_DevGenet1998.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/(SICI)1520-6408(1998)23:3%3C159::AID-DVG1%3E3.0.CO;2-1}}

@article{Borodinsky:2004,
	Abstract = {Neurotransmitters are essential for interneuronal signalling, and the specification of appropriate transmitters in differentiating neurons has been related to intrinsic neuronal identity and to extrinsic signalling proteins. Here we show that altering the distinct patterns of Ca2+ spike activity spontaneously generated by different classes of embryonic spinal neurons in vivo changes the transmitter that neurons express without affecting the expression of markers of cell identity. Regulation seems to be homeostatic: suppression of activity leads to an increased number of neurons expressing excitatory transmitters and a decreased number of neurons expressing inhibitory transmitters; the reverse occurs when activity is enhanced. The imposition of specific spike frequencies in vitro does not affect labels of cell identity but again specifies the expression of transmitters that are inappropriate for the markers they express, during an early critical period. The results identify a new role of patterned activity in development of the central nervous system.},
	Author = {Borodinsky, Laura N and Root, Cory M and Cronin, Julia A and Sann, Sharon B and Gu, Xiaonan and Spitzer, Nicholas C},
	Date-Added = {2012-11-13 16:08:31 +0000},
	Date-Modified = {2012-11-14 16:34:47 +0000},
	Doi = {10.1038/nature02518},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {Spontaneous activity; development; Activity-development; Gene Expression; Transcription Factors; Calcium Signaling; Neurophysiology;xenopus; activity manipulation; Differentiation; Transmission; Neurotransmitters},
	Mesh = {Action Potentials; Animals; Calcium; Calcium Signaling; Cell Differentiation; Cells, Cultured; Gene Expression Regulation; Homeostasis; Humans; Neurons; Neurotransmitter Agents; Organ Specificity; Phenotype; Potassium Channels, Inwardly Rectifying; Rats; Sodium Channels; Spinal Cord; Xenopus laevis},
	Month = {Jun},
	Number = {6991},
	Pages = {523-30},
	Pmid = {15175743},
	Pst = {ppublish},
	Title = {Activity-dependent homeostatic specification of transmitter expression in embryonic neurons},
	Volume = {429},
	Year = {2004},
	File = {papers/Borodinsky_Nature2004.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature02518}}

@article{Marek:2010,
	Abstract = {Neuronal differentiation is accomplished through cascades of intrinsic genetic factors initiated in neuronal progenitors by external gradients of morphogens. Activity has been thought to be important only late in development, but recent evidence suggests that activity also regulates early neuronal differentiation. Activity in post-mitotic neurons before synapse formation can regulate phenotypic specification, including neurotransmitter choice, but the mechanisms are not clear. We identified a mechanism that links endogenous calcium spike activity with an intrinsic genetic pathway to specify neurotransmitter choice in neurons in the dorsal embryonic spinal cord of Xenopus tropicalis. Early activity modulated transcription of the GABAergic/glutamatergic selection gene tlx3 through a variant cAMP response element (CRE) in its promoter. The cJun transcription factor bound to this CRE site, modulated transcription and regulated neurotransmitter phenotype via its transactivation domain. Calcium signaled through cJun N-terminal phosphorylation, which integrated activity-dependent and intrinsic neurotransmitter specification. This mechanism provides a basis for early activity to regulate genetic pathways at critical decision points, switching the phenotype of developing neurons.},
	Author = {Marek, Kurt W and Kurtz, Lisa M and Spitzer, Nicholas C},
	Date-Added = {2012-11-13 16:07:23 +0000},
	Date-Modified = {2012-11-13 16:08:05 +0000},
	Doi = {10.1038/nn.2582},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {21 Activity-development;Spontaneous activity;development;10 circuit formation;Synapses;Electric Conductivity;Cell Differentiation;21 Neurophysiology;Animals;Brain;Neurons; Gene Expression; Transcription Factors; Activity-development; Structure-Activity Relationship; axon guidance; cell migration;Xenopus},
	Mesh = {Animals; Base Sequence; Calcium; Calcium Signaling; Electrophoretic Mobility Shift Assay; Gene Expression; Gene Expression Regulation, Developmental; Homeodomain Proteins; Immunohistochemistry; In Situ Hybridization; Molecular Sequence Data; Neurogenesis; Neurons; Neurotransmitter Agents; Promoter Regions, Genetic; Proto-Oncogene Proteins c-jun; Response Elements; Reverse Transcriptase Polymerase Chain Reaction; Xenopus; Xenopus Proteins},
	Month = {Aug},
	Number = {8},
	Pages = {944-50},
	Pmc = {PMC2910808},
	Pmid = {20581840},
	Pst = {ppublish},
	Title = {cJun integrates calcium activity and tlx3 expression to regulate neurotransmitter specification},
	Volume = {13},
	Year = {2010},
	File = {papers/Marek_NatNeurosci2010.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nn.2582}}

@article{Mire:2012,
	Abstract = {Developing axons must control their growth rate to follow the appropriate pathways and establish specific connections. However, the regulatory mechanisms involved remain elusive. By combining live imaging with transplantation studies in mice, we found that spontaneous calcium activity in the thalamocortical system and the growth rate of thalamocortical axons were developmentally and intrinsically regulated. Indeed, the spontaneous activity of thalamic neurons governed axon growth and extension through the cortex in vivo. This activity-dependent modulation of growth was mediated by transcriptional regulation of Robo1 through an NF-κB binding site. Disruption of either the Robo1 or Slit1 genes accelerated the progression of thalamocortical axons in vivo, and interfering with Robo1 signaling restored normal axon growth in electrically silent neurons. Thus, modifications to spontaneous calcium activity encode a switch in the axon outgrowth program that allows the establishment of specific neuronal connections through the transcriptional regulation of Slit1 and Robo1 signaling.},
	Author = {Mire, Erik and Mezzera, Cecilia and Leyva-D{\'\i}az, Eduardo and Paternain, Ana V and Squarzoni, Paola and Bluy, Lisa and Castillo-Paterna, Mar and L{\'o}pez, Mar{\'\i}a Jos{\'e} and Peregr{\'\i}n, Sandra and Tessier-Lavigne, Marc and Garel, Sonia and Galcer{\'a}n, Joan and Lerma, Juan and L{\'o}pez-Bendito, Guillermina},
	Date-Added = {2012-11-13 13:49:58 +0000},
	Date-Modified = {2012-11-13 15:54:38 +0000},
	Doi = {10.1038/nn.3160},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {Spontaneous activity; development; Activity-development; activity manipulation; Structure-Activity Relationship; structural remodeling; axon guidance; synapse formation; Synaptic Transmission; mouse; thalamus; Cerebral Cortex; Neocortex; optical imaging; Transcription Factors; Gene Expression},
	Mesh = {Animals; Axons; Calcium; Calcium Signaling; Cerebral Cortex; Female; Gene Expression Regulation, Developmental; Mice; Nerve Tissue Proteins; Receptors, Immunologic; Thalamus},
	Month = {Aug},
	Number = {8},
	Pages = {1134-43},
	Pmid = {22772332},
	Pst = {epublish},
	Title = {Spontaneous activity regulates Robo1 transcription to mediate a switch in thalamocortical axon growth},
	Volume = {15},
	Year = {2012},
	File = {papers/Mire_NatNeurosci2012.pdf}}

@article{Bouwman:2004,
	Abstract = {Outgrowing axons in the developing nervous system secrete neurotransmitters and neuromodulatory substances, which is considered to stimulate synaptogenesis. However, some synapses develop independent of presynaptic secretion. To investigate the role of secretion in synapse formation and maintenance in vivo, we quantified synapses and their morphology in the neocortical marginal zone of munc18-1 deficient mice which lack both evoked and spontaneous secretion [Science 287 (2000) 864]. Histochemical analyses at embryonic day 18 (E18) showed that the overall organization of the neocortex and the number of cells were similar in mutants and controls. Western blot analysis revealed equal concentrations of pre- and post-synaptic marker proteins in mutants and controls and immunocytochemical analyses indicated that these markers were targeted to the neuropil of the synaptic layer in the mutant neocortex. Electron microscopy revealed that at E16 immature synapses had formed both in mutants and controls. These synapses had a similar synapse diameter, active zone length and contained similar amounts of synaptic vesicles, which were immuno-positive for two synaptic vesicle markers. However, these synapses were three times less abundant in the mutant. Two days later, E18, synapses in the controls had more total and docked vesicles, but not in the mutant. Furthermore, synapses were now five times less abundant in the mutant. In both mutant and controls, synapse-like structures were observed with irregular shaped vesicles on both sides of the synaptic cleft. These 'multivesicular structures' were immuno-positive for synaptic vesicle markers and were four times more abundant in the mutant. We conclude that in the absence of presynaptic secretion immature synapses with a normal morphology form, but fewer in number. These secretion-deficient synapses might fail to mature and instead give rise to multivesicular structures. These two observations suggest that secretion of neurotransmitters and neuromodulatory substances is required for synapse maintenance, not for synaptogenesis. Multivesicular structures may develop out of unstable synapses.},
	Author = {Bouwman, J and Maia, A S and Camoletto, P G and Posthuma, G and Roubos, E W and Oorschot, V M J and Klumperman, J and Verhage, M},
	Date-Added = {2012-11-12 22:33:08 +0000},
	Date-Modified = {2012-11-12 22:34:24 +0000},
	Doi = {10.1016/j.neuroscience.2004.03.027},
	Journal = {Neuroscience},
	Journal-Full = {Neuroscience},
	Keywords = {Anatomy; activity manipulation; transgenic; mouse; synapse formation; axon guidance; Structure-Activity Relationship; Activity-development; development; Spontaneous activity; Synaptic Transmission},
	Mesh = {Animals; Female; Immunohistochemistry; Mice; Mice, Mutant Strains; Microscopy, Electron; Munc18 Proteins; Neocortex; Nerve Tissue Proteins; Neurons; Pregnancy; Synapses; Synaptic Transmission; Synaptic Vesicles; Vesicular Transport Proteins},
	Number = {1},
	Pages = {115-26},
	Pmid = {15145078},
	Pst = {ppublish},
	Title = {Quantification of synapse formation and maintenance in vivo in the absence of synaptic release},
	Volume = {126},
	Year = {2004},
	File = {papers/Bouwman_Neuroscience2004.pdf}}

@article{Yamamoto:2002,
	Abstract = {During development of the central nervous system, growth cones navigate along specific pathways, recognize their targets and then form synaptic connections by elaborating terminal arbors. To date, a number of developmental and in vitro studies have characterized the nature of the guidance cues that underlie various types of axonal behavior, from initial outgrowth to synapse formation, including pathway selection, polarized growth, orientated growth, termination and branching. New approaches in molecular biology have identified several types of guidance cues, most of which are likely to act as local cues. Moreover, recent studies have indicated that axonal responsiveness to guidance cues changes dynamically, which appears to be elicited by environmental factors encountered by the navigating growth cones. This article addresses what molecular cues are responsible for guidance mechanisms including axonal responsiveness, focusing on axonal behavior in the developmental stages.},
	Author = {Yamamoto, Nobuhiko and Tamada, Atsushi and Murakami, Fujio},
	Date-Added = {2012-11-12 22:31:49 +0000},
	Date-Modified = {2012-11-12 22:33:00 +0000},
	Journal = {Prog Neurobiol},
	Journal-Full = {Progress in neurobiology},
	Keywords = {review; toread; Structure-Activity Relationship; Spontaneous activity; axon guidance; development; Activity-development; in vitro; Thalamus; Cerebral Cortex; Neocortex},
	Mesh = {Axons; Brain; Cell Communication; Cell Differentiation; Growth Cones; Nerve Growth Factors; Nerve Tissue Proteins; Neural Pathways; Neuronal Plasticity; Neurons; Signal Transduction; Synapses},
	Month = {Dec},
	Number = {6},
	Pages = {393-407},
	Pmid = {12576293},
	Pst = {ppublish},
	Title = {Wiring of the brain by a range of guidance cues},
	Volume = {68},
	Year = {2002},
	File = {papers/Yamamoto_ProgNeurobiol2002.pdf}}

@article{Mason:2009,
	Author = {Mason, Carol},
	Date-Added = {2012-11-08 22:33:58 +0000},
	Date-Modified = {2012-11-08 22:34:41 +0000},
	Doi = {10.1523/JNEUROSCI.4648-09.2009},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread; development; review literature},
	Mesh = {Animals; Brain; Developmental Biology; History, 20th Century; History, 21st Century; Humans; Neurons; Neurosciences},
	Month = {Oct},
	Number = {41},
	Pages = {12735-47},
	Pmid = {19828784},
	Pst = {ppublish},
	Title = {The development of developmental neuroscience},
	Volume = {29},
	Year = {2009},
	File = {papers/Mason_JNeurosci2009.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.4648-09.2009}}

@article{Sato:2012,
	Abstract = {Electrode recordings and imaging studies have revealed that localized visual stimuli elicit waves of activity that travel across primary visual cortex. Traveling waves are present also during spontaneous activity, but they can be greatly reduced by widespread and intensive visual stimulation. In this Review, we summarize the evidence in favor of these traveling waves. We suggest that their substrate may lie in long-range horizontal connections and that their functional role may involve the integration of information over large regions of space.},
	Author = {Sato, Tatsuo K and Nauhaus, Ian and Carandini, Matteo},
	Date-Added = {2012-11-08 22:32:50 +0000},
	Date-Modified = {2012-11-08 22:33:10 +0000},
	Doi = {10.1016/j.neuron.2012.06.029},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread},
	Mesh = {Animals; Models, Neurological; Nerve Net; Neural Conduction; Neurons; Visual Cortex},
	Month = {Jul},
	Number = {2},
	Pages = {218-29},
	Pmid = {22841308},
	Pst = {ppublish},
	Title = {Traveling waves in visual cortex},
	Volume = {75},
	Year = {2012},
	File = {papers/Sato_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.06.029}}

@article{Priebe:2012,
	Abstract = {Orientation selectivity in the primary visual cortex (V1) is a receptive field property that is at once simple enough to make it amenable to experimental and theoretical approaches and yet complex enough to represent a significant transformation in the representation of the visual image. As a result, V1 has become an area of choice for studying cortical computation and its underlying mechanisms. Here we consider the receptive field properties of the simple cells in cat V1--the cells that receive direct input from thalamic relay cells--and explore how these properties, many of which are highly nonlinear, arise. We have found that many receptive field properties of V1 simple cells fall directly out of Hubel and Wiesel's feedforward model when the model incorporates realistic neuronal and synaptic mechanisms, including threshold, synaptic depression, response variability, and the membrane time constant.},
	Author = {Priebe, Nicholas J and Ferster, David},
	Date-Added = {2012-11-08 22:31:49 +0000},
	Date-Modified = {2012-11-08 22:31:49 +0000},
	Doi = {10.1016/j.neuron.2012.06.011},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Animals; Cats; Models, Neurological; Neurons; Synaptic Transmission; Visual Cortex; Visual Pathways},
	Month = {Jul},
	Number = {2},
	Pages = {194-208},
	Pmc = {PMC3477598},
	Pmid = {22841306},
	Pst = {ppublish},
	Title = {Mechanisms of neuronal computation in mammalian visual cortex},
	Volume = {75},
	Year = {2012},
	File = {papers/Priebe_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.06.011}}

@article{Gilbert:2012,
	Abstract = {The visual cortex has the capacity for experience-dependent change, or cortical plasticity, that is retained throughout life. Plasticity is invoked for encoding information during perceptual learning, by internally representing the regularities of the visual environment, which is useful for facilitating intermediate-level vision--contour integration and surface segmentation. The same mechanisms have adaptive value for functional recovery after CNS damage, such as that associated with stroke or neurodegenerative disease. A common feature to plasticity in primary visual cortex (V1) is an association field that links contour elements across the visual field. The circuitry underlying the association field includes a plexus of long-range horizontal connections formed by cortical pyramidal cells. These connections undergo rapid and exuberant sprouting and pruning in response to removal of sensory input, which can account for the topographic reorganization following retinal lesions. Similar alterations in cortical circuitry may be involved in perceptual learning, and the changes observed in V1 may be representative of how learned information is encoded throughout the cerebral cortex.},
	Author = {Gilbert, Charles D and Li, Wu},
	Date-Added = {2012-11-08 22:30:32 +0000},
	Date-Modified = {2012-11-08 22:30:55 +0000},
	Doi = {10.1016/j.neuron.2012.06.030},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread},
	Mesh = {Animals; Humans; Learning; Neuronal Plasticity; Neurons; Visual Cortex; Visual Perception},
	Month = {Jul},
	Number = {2},
	Pages = {250-64},
	Pmc = {PMC3408614},
	Pmid = {22841310},
	Pst = {ppublish},
	Title = {Adult visual cortical plasticity},
	Volume = {75},
	Year = {2012},
	File = {papers/Gilbert_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.06.030}}

@article{Reid:2012,
	Abstract = {"Receptive Fields, Binocular Interaction and Functional Architecture in the Cat's Visual Cortex" by Hubel and Wiesel (1962) reported several important discoveries: orientation columns, the distinct structures of simple and complex receptive fields, and binocular integration. But perhaps the paper's greatest influence came from the concept of functional architecture (the complex relationship between in vivo physiology and the spatial arrangement of neurons) and several models of functionally specific connectivity. They thus identified two distinct concepts, topographic specificity and functional specificity, which together with cell-type specificity constitute the major determinants of nonrandom cortical connectivity. Orientation columns are iconic examples of topographic specificity, whereby axons within a column connect with cells of a single orientation preference. Hubel and Wiesel also saw the need for functional specificity at a finer scale in their model of thalamic inputs to simple cells, verified in the 1990s. The difficult but potentially more important question of functional specificity between cortical neurons is only now becoming tractable with new experimental techniques.},
	Author = {Reid, R Clay},
	Date-Added = {2012-11-08 22:29:53 +0000},
	Date-Modified = {2012-11-08 22:31:20 +0000},
	Doi = {10.1016/j.neuron.2012.06.031},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {toread},
	Mesh = {Animals; Models, Neurological; Nerve Net; Neurons; Orientation; Visual Cortex; Visual Pathways},
	Month = {Jul},
	Number = {2},
	Pages = {209-17},
	Pmid = {22841307},
	Pst = {ppublish},
	Title = {From functional architecture to functional connectomics},
	Volume = {75},
	Year = {2012},
	File = {papers/Reid_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.06.031}}

@book{finlay:2003,
	Author = {Finlay, B L},
	Date-Added = {2012-11-08 22:04:41 +0000},
	Date-Modified = {2012-11-08 22:27:47 +0000},
	Editor = {Hopkins},
	Keywords = {toread},
	Publisher = {Praeger},
	Title = {The Developmental Neurobiology of Early Vision},
	Year = {2003},
	File = {papers/Finlay_2003.pdf}}

@article{Roffwarg:1966,
	Author = {Roffwarg, H P and Muzio, J N and Dement, W C},
	Date-Added = {2012-11-08 21:46:57 +0000},
	Date-Modified = {2012-11-08 22:03:57 +0000},
	Doi = {10.1126/science.152.3722.604},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {toread; human; sleep; oscillations; synchrony; development; Cerebral Cortex; Neocortex; EEG; Fetal Development/physiology},
	Month = {Apr},
	Number = {3722},
	Pages = {604-19},
	Pmid = {17779492},
	Pst = {ppublish},
	Title = {Ontogenetic development of the human sleep-dream cycle},
	Volume = {152},
	Year = {1966},
	File = {papers/Roffwarg_Science1966.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.152.3722.604}}

@article{Espinosa:2012,
	Abstract = {Hubel and Wiesel began the modern study of development and plasticity of primary visual cortex (V1), discovering response properties of cortical neurons that distinguished them from their inputs and that were arranged in a functional architecture. Their findings revealed an early innate period of development and a later critical period of dramatic experience-dependent plasticity. Recent studies have used rodents to benefit from biochemistry and genetics. The roles of spontaneous neural activity and molecular signaling in innate, experience-independent development have been clarified, as have the later roles of visual experience. Plasticity produced by monocular visual deprivation (MD) has been dissected into stages governed by distinct signaling mechanisms, some of whose molecular players are known. Many crucial questions remain, but new tools for perturbing cortical cells and measuring plasticity at the level of changes in connections among identified neurons now exist. The future for the study of V1 to illuminate cortical development and plasticity is bright.},
	Author = {Espinosa, J Sebastian and Stryker, Michael P},
	Date-Added = {2012-11-08 21:03:43 +0000},
	Date-Modified = {2013-06-10 19:56:04 +0000},
	Doi = {10.1016/j.neuron.2012.06.009},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {topographic map; development; activity-development; review literature; spontaneous activity; experience dependent plasticity; currOpinRvw},
	Mesh = {Animals; Neuronal Plasticity; Neurons; Vision, Ocular; Visual Cortex},
	Month = {Jul},
	Number = {2},
	Pages = {230-49},
	Pmid = {22841309},
	Pst = {ppublish},
	Title = {Development and plasticity of the primary visual cortex},
	Volume = {75},
	Year = {2012},
	File = {papers/Espinosa_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.06.009}}

@article{Takahashi:2011,
	Abstract = {The immature cortex (cortical plate [CP]) and underlying subplate (SP), a transient cell layer just below the CP, play critical roles in the formation of intracerebral connections. The purpose of this study was to examine the diffusion characteristics of the developing cortex and subcortical structures and compare to histology. We obtained high-resolution diffusion spectrum images of postnatal day (P) 0 (newborn), P35 (pediatric), and P100 (adult) cat brains, performed tractography analysis, and correlated with histological findings. Tractography revealed radial organization and radial afferent/efferent tracts not only in the CP but also in external SP at P0. Radial organization persisted only in the cortex but decreased at P35 and P100. Radial organization correlated with radial cellular organization, with highest cellular density at P0 (Cresyl Violet staining). At P0, the internal SP contained abundant corticocortical and projection tractography pathways, crossing at wide angles in areas with no myelination by Luxol Fast Blue staining. At P35 and P100, increased directional coherence of white matter was observed, with fewer local tracts, but more long association pathways. These results suggest that diffusion tractography can differentially characterize internal and external SP zones and their transition into mature cortical pathways.},
	Author = {Takahashi, Emi and Dai, Guangping and Rosen, Glenn D and Wang, Ruopeng and Ohki, Kenichi and Folkerth, Rebecca D and Galaburda, Albert M and Wedeen, Van J and Ellen Grant, P},
	Date-Added = {2012-11-08 21:01:24 +0000},
	Date-Modified = {2012-11-08 21:01:37 +0000},
	Doi = {10.1093/cercor/bhq084},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {toread},
	Mesh = {Animals; Animals, Newborn; Axons; Brain Mapping; Cats; Cell Differentiation; Diffusion Tensor Imaging; Image Processing, Computer-Assisted; Neocortex; Neural Pathways},
	Month = {Jan},
	Number = {1},
	Pages = {200-11},
	Pmc = {PMC3025725},
	Pmid = {20494968},
	Pst = {ppublish},
	Title = {Developing neocortex organization and connectivity in cats revealed by direct correlation of diffusion tractography and histology},
	Volume = {21},
	Year = {2011},
	File = {papers/Takahashi_CerebCortex2011.pdf}}

@article{Rubel:2002,
	Abstract = {The neurons of the cochlear ganglion transmit acoustic information between the inner ear and the brain. These placodally derived neurons must produce a topographically precise pattern of connections in both the inner ear and the brain. In this review, we consider the current state of knowledge concerning the development of these neurons, their peripheral and central connections, and their influences on peripheral and central target cells. Relatively little is known about the cellular and molecular regulation of migration or the establishment of precise topographic connection to the hair cells or cochlear nucleus (CN) neurons. Studies of mice with neurotrophin deletions are beginning to yield increasing understanding of variations in ganglion cell survival and resulting innervation patterns, however. Finally, existing evidence suggests that while ganglion cells have little influence on the differentiation of their hair cell targets, quite the opposite is true in the brain. Ganglion cell innervation and synaptic activity are essential for normal development of neurons in the cochlear nucleus.},
	Author = {Rubel, Edwin W and Fritzsch, Bernd},
	Date-Added = {2012-11-08 21:00:49 +0000},
	Date-Modified = {2012-11-08 21:01:02 +0000},
	Doi = {10.1146/annurev.neuro.25.112701.142849},
	Journal = {Annu Rev Neurosci},
	Journal-Full = {Annual review of neuroscience},
	Keywords = {Non-programmatic; toread; review literature},
	Mesh = {Animals; Auditory Pathways; Cell Communication; Cell Differentiation; Cell Movement; Cochlear Nucleus; Gene Expression Regulation, Developmental; Hair Cells, Auditory; Humans; Nerve Growth Factors; Neurons, Afferent; Spiral Ganglion},
	Pages = {51-101},
	Pmid = {12052904},
	Pst = {ppublish},
	Title = {Auditory system development: primary auditory neurons and their targets},
	Volume = {25},
	Year = {2002},
	File = {papers/Rubel_AnnuRevNeurosci2002.pdf}}

@article{Dunn:2012,
	Abstract = {Sensory circuits use common strategies, such as convergence and divergence, typically at different synapses, to pool or distribute inputs. Inputs from different presynaptic cell types converge onto a common postsynaptic cell, acting together to shape neuronal output (Klausberger and Somogyi, 2008). Also, individual presynaptic cells contact several postsynaptic cell types, generating divergence of signals. Attaining such complex wiring patterns relies on the orchestration of many events across development, including axonal and dendritic growth and synapse formation and elimination (reviewed by Waites et al., 2005; Sanes and Yamagata, 2009). Recent work has focused on how distinct presynaptic cell types form stereotypic connections with an individual postsynaptic cell (Morgan et al., 2011; Williams et al., 2011), but how a single presynaptic cell type diverges to form distinct wiring patterns with multiple postsynaptic cell types during development remains unexplored. Here we take advantage of the compactness of the visual system's first synapse to observe development of such a circuit in mouse retina. By imaging three types of postsynaptic bipolar cells and their common photoreceptor targets across development, we found that distinct bipolar cell types engage in disparate dendritic growth behaviors, exhibit targeted or exploratory approaches to contact photoreceptors, and adhere differently to the synaptotropic model of establishing synaptic territories. Furthermore each type establishes its final connectivity patterns with the same afferents on separate time scales. We propose that such differences in strategy and timeline could facilitate the division of common inputs among multiple postsynaptic cell types to create parallel circuits with diverse function.},
	Author = {Dunn, Felice A and Wong, Rachel O L},
	Date-Added = {2012-11-08 20:59:42 +0000},
	Date-Modified = {2012-11-08 20:59:53 +0000},
	Doi = {10.1523/JNEUROSCI.1581-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread},
	Mesh = {Animals; Axons; Dendrites; Mice; Mice, Transgenic; Retina; Retinal Neurons; Synapses; Visual Pathways},
	Month = {Jul},
	Number = {30},
	Pages = {10306-17},
	Pmc = {PMC3435432},
	Pmid = {22836264},
	Pst = {ppublish},
	Title = {Diverse strategies engaged in establishing stereotypic wiring patterns among neurons sharing a common input at the visual system's first synapse},
	Volume = {32},
	Year = {2012},
	File = {papers/Dunn_JNeurosci2012.pdf}}

@article{Rust:2012,
	Abstract = {Although popular accounts suggest that neurons along the ventral visual processing stream become increasingly selective for particular objects, this appears at odds with the fact that inferior temporal cortical (IT) neurons are broadly tuned. To explore this apparent contradiction, we compared processing in two ventral stream stages (visual cortical areas V4 and IT) in the rhesus macaque monkey. We confirmed that IT neurons are indeed more selective for conjunctions of visual features than V4 neurons and that this increase in feature conjunction selectivity is accompanied by an increase in tolerance ("invariance") to identity-preserving transformations (e.g., shifting, scaling) of those features. We report here that V4 and IT neurons are, on average, tightly matched in their tuning breadth for natural images ("sparseness") and that the average V4 or IT neuron will produce a robust firing rate response (>50% of its peak observed firing rate) to ∼10% of all natural images. We also observed that sparseness was positively correlated with conjunction selectivity and negatively correlated with tolerance within both V4 and IT, consistent with selectivity-building and invariance-building computations that offset one another to produce sparseness. Our results imply that the conjunction-selectivity-building and invariance-building computations necessary to support object recognition are implemented in a balanced manner to maintain sparseness at each stage of processing.},
	Author = {Rust, Nicole C and DiCarlo, James J},
	Date-Added = {2012-11-08 20:59:08 +0000},
	Date-Modified = {2012-11-08 20:59:28 +0000},
	Doi = {10.1523/JNEUROSCI.6125-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread},
	Mesh = {Animals; Form Perception; Macaca mulatta; Male; Neurons; Pattern Recognition, Visual; Photic Stimulation; Visual Cortex; Visual Pathways},
	Month = {Jul},
	Number = {30},
	Pages = {10170-82},
	Pmc = {PMC3485085},
	Pmid = {22836252},
	Pst = {ppublish},
	Title = {Balanced increases in selectivity and tolerance produce constant sparseness along the ventral visual stream},
	Volume = {32},
	Year = {2012},
	File = {papers/Rust_JNeurosci2012.pdf}}

@article{Cohen-Cory:2002,
	Abstract = {Synapse formation and stabilization in the vertebrate central nervous system is a dynamic process, requiring bi-directional communication between pre- and postsynaptic partners. Numerous mechanisms coordinate where and when synapses are made in the developing brain. This review discusses cellular and activity-dependent mechanisms that control the development of synaptic connectivity.},
	Author = {Cohen-Cory, Susana},
	Date-Added = {2012-11-08 20:59:08 +0000},
	Date-Modified = {2012-11-12 22:31:37 +0000},
	Doi = {10.1126/science.1075510},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {toread; Structure-Activity Relationship; development; synapse formation; synapses; Synaptic Transmission; axon guidance; activity manipulation; Spontaneous activity; review literature},
	Mesh = {Animals; Axons; Brain; Cells, Cultured; Dendrites; Nerve Growth Factors; Neuromuscular Junction; Neuronal Plasticity; Neurons; Neurotransmitter Agents; Receptors, Neurotransmitter; Synapses; Synaptic Transmission; Synaptic Vesicles; Visual Cortex; Visual Pathways},
	Month = {Oct},
	Number = {5594},
	Pages = {770-6},
	Pmid = {12399577},
	Pst = {ppublish},
	Title = {The developing synapse: construction and modulation of synaptic structures and circuits},
	Volume = {298},
	Year = {2002},
	File = {papers/Cohen-Cory_Science2002.pdf}}

@article{Economides:2012,
	Abstract = {Misalignment of the eyes can lead to double vision and visual confusion. However, these sensations are rare when strabismus is acquired early in life, because the extra image is suppressed. To explore the mechanism of perceptual suppression in strabismus, the visual fields were mapped binocularly in 14 human subjects with exotropia. Subjects wore red/blue filter glasses to permit dichoptic stimulation while fixating a central target on a tangent screen. A purple stimulus was flashed at a peripheral location; its reported color ("red" or "blue") revealed which eye's image was perceived at that locus. The maps showed a vertical border between the center of gaze for each eye, splitting the visual field into two separate regions. In each region, perception was mediated by only one eye, with suppression of the other eye. Unexpectedly, stimuli falling on the fovea of the deviated eye were seen in all subjects. However, they were perceived in a location shifted by the angle of ocular deviation. This plasticity in the coding of visual direction allows accurate localization of objects everywhere in the visual scene, despite the presence of strabismus.},
	Author = {Economides, John R and Adams, Daniel L and Horton, Jonathan C},
	Date-Added = {2012-11-08 20:57:25 +0000},
	Date-Modified = {2012-11-08 20:57:56 +0000},
	Doi = {10.1523/JNEUROSCI.1435-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread},
	Mesh = {Adolescent; Adult; Child; Exotropia; Female; Fixation, Ocular; Humans; Male; Middle Aged; Photic Stimulation; Vision, Binocular; Visual Fields; Visual Perception},
	Month = {Jul},
	Number = {30},
	Pages = {10286-95},
	Pmc = {PMC3435149},
	Pmid = {22836262},
	Pst = {ppublish},
	Title = {Perception via the deviated eye in strabismus},
	Volume = {32},
	Year = {2012},
	File = {papers/Economides_JNeurosci2012.pdf}}

@article{Liang:2012,
	Abstract = {The neural mechanism of unconsciousness has been a major unsolved question in neuroscience despite its vital role in brain states like coma and anesthesia. The existing literature suggests that neural connections, information integration, and conscious states are closely related. Indeed, alterations in several important neural circuitries and networks during unconscious conditions have been reported. However, how the whole-brain network is topologically reorganized to support different patterns of information transfer during unconscious states remains unknown. Here we directly compared whole-brain neural networks in awake and anesthetized states in rodents. Consistent with our previous report, the awake rat brain was organized in a nontrivial manner and conserved fundamental topological properties in a way similar to the human brain. Strikingly, these topological features were well maintained in the anesthetized brain. Local neural networks in the anesthetized brain were reorganized with altered local network properties. The connectional strength between brain regions was also considerably different between the awake and anesthetized conditions. Interestingly, we found that long-distance connections were not preferentially reduced in the anesthetized condition, arguing against the hypothesis that loss of long-distance connections is characteristic to unconsciousness. These findings collectively show that the integrity of the whole-brain network can be conserved between widely dissimilar physiologic states while local neural networks can flexibly adapt to new conditions. They also illustrate that the governing principles of intrinsic brain organization might represent fundamental characteristics of the healthy brain. With the unique spatial and temporal scales of resting-state fMRI, this study has opened a new avenue for understanding the neural mechanism of (un)consciousness.},
	Author = {Liang, Zhifeng and King, Jean and Zhang, Nanyin},
	Date-Added = {2012-11-08 20:57:25 +0000},
	Date-Modified = {2013-09-26 17:19:03 +0000},
	Doi = {10.1523/JNEUROSCI.1020-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {default mode network; fmri; rat; in vivo; connectivity; wholeBrain; spontaneous activity},
	Mesh = {Anesthesia; Anesthetics, Inhalation; Animals; Brain; Brain Mapping; Consciousness; Image Processing, Computer-Assisted; Isoflurane; Magnetic Resonance Imaging; Male; Nerve Net; Neuroimaging; Rats; Rats, Long-Evans},
	Month = {Jul},
	Number = {30},
	Pages = {10183-91},
	Pmc = {PMC3422560},
	Pmid = {22836253},
	Pst = {ppublish},
	Title = {Intrinsic organization of the anesthetized brain},
	Volume = {32},
	Year = {2012},
	File = {papers/Liang_JNeurosci2012.pdf}}

@article{Mao:2012,
	Abstract = {Brain damage resulting in loss of sensory stimulation can induce reorganization of sensory maps in cerebral cortex. Previous research on recovery from brain damage has focused primarily on adaptive plasticity within the affected modality. Less attention has been paid to maladaptive plasticity that may arise as a result of ectopic innervation from other modalities. Using ferrets in which neonatal midbrain damage results in diversion of retinal projections to the auditory thalamus, we investigated how auditory cortical function is impacted by the resulting ectopic visual activation. We found that, although auditory neurons in cross-modal auditory cortex (XMAC) retained sound frequency tuning, their thresholds were increased, their tuning was broader, and tonotopic order in their frequency maps was disturbed. Multisensory neurons in XMAC also exhibited frequency tuning, but they had longer latencies than normal auditory neurons, suggesting they arise from multisynaptic, non-geniculocortical sources. In a control group of animals with neonatal deafferentation of auditory thalamus but without redirection of retinal axons, tonotopic order and sharp tuning curves were seen, indicating that this aspect of auditory function had developed normally. This result shows that the compromised auditory function in XMAC results from invasion by ectopic visual inputs and not from deafferentation. These findings suggest that the cross-modal plasticity that commonly occurs after loss of sensory input can significantly interfere with recovery from brain damage and that mitigation of maladaptive effects is critical to maximizing the potential for recovery.},
	Author = {Mao, Yu-Ting and Pallas, Sarah L},
	Date-Added = {2012-11-08 20:57:25 +0000},
	Date-Modified = {2012-11-08 20:57:56 +0000},
	Doi = {10.1523/JNEUROSCI.6524-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread},
	Mesh = {Acoustic Stimulation; Animals; Auditory Cortex; Auditory Pathways; Axons; Female; Ferrets; Male; Neuronal Plasticity; Neurons; Thalamus; Visual Pathways},
	Month = {Jul},
	Number = {30},
	Pages = {10338-51},
	Pmc = {PMC3428959},
	Pmid = {22836267},
	Pst = {ppublish},
	Title = {Compromise of auditory cortical tuning and topography after cross-modal invasion by visual inputs},
	Volume = {32},
	Year = {2012},
	File = {papers/Mao_JNeurosci2012.pdf}}

@article{Emsley:2004,
	Abstract = {During the past three decades, research exploring potential neuronal replacement therapies has focused on replacing lost neurons by transplanting cells or grafting tissue into diseased regions of the brain. However, in the last decade, the development of novel approaches has resulted in an explosion of new research showing that neurogenesis, the birth of new neurons, normally occurs in two limited and specific regions of the adult mammalian brain, and that there are significant numbers of multipotent neural precursors in many parts of the adult mammalian brain. Recent advances in our understanding of related events of neural development and plasticity, including the role of radial glia in developmental neurogenesis, and the ability of endogenous precursors present in the adult brain to be induced to produce neurons and partially repopulate brain regions affected by neurodegenerative processes, have led to fundamental changes in the views about how the brain develops, as well as to approaches by which transplanted or endogenous precursors might be used to repair the adult brain. For example, recruitment of new neurons can be induced in a region-specific, layer-specific, and neuronal type-specific manner, and, in some cases, newly recruited neurons can form long-distance connections to appropriate targets. Elucidation of the relevant molecular controls may both allow control over transplanted precursor cells and potentially allow for the development of neuronal replacement therapies for neurodegenerative disease and other CNS injuries that might not require transplantation of exogenous cells.},
	Author = {Emsley, Jason G and Mitchell, Bartley D and Magavi, Sanjay S P and Arlotta, Paola and Macklis, Jeffrey D},
	Date-Added = {2012-11-08 17:31:10 +0000},
	Date-Modified = {2012-11-08 17:31:40 +0000},
	Doi = {10.1602/neurorx.1.4.452},
	Journal = {NeuroRx},
	Journal-Full = {NeuroRx : the journal of the American Society for Experimental NeuroTherapeutics},
	Keywords = {Adult Neurogenesis; transplant regeneration},
	Mesh = {Animals; Cell Death; Cell Differentiation; Cell Movement; Cerebral Cortex; Humans; Nerve Net; Nerve Regeneration; Nerve Tissue; Nervous System Diseases; Signal Transduction; Stem Cell Transplantation},
	Month = {Oct},
	Number = {4},
	Pages = {452-71},
	Pmc = {PMC534952},
	Pmid = {15717047},
	Pst = {ppublish},
	Title = {The repair of complex neuronal circuitry by transplanted and endogenous precursors},
	Volume = {1},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1602/neurorx.1.4.452}}

@article{Maravall:2004,
	Abstract = {In rat barrel cortex, development of layer 2/3 receptive fields can be disrupted by sensory deprivation, with a critical period ending around postnatal day (PND) 14. To determine if experience-dependent plasticity of dendritic morphology could contribute to the reorganization of synaptic inputs, we analyzed dendritic structure in acute brain slices using two-photon laser scanning microscopy (2PLSM) and automated segmentation and analysis software. Layer 2/3 pyramidal cells from control and deprived rats were imaged from PND 9 to PND 20, spanning the critical period. Detailed analyses were performed on basal arbors, which receive the majority of synaptic input from layer 4. Some parameters (number of primary dendrites, volume subtended, aspect ratios) were stable, suggesting that development of several important properties of basal arbors has ceased by age PND 9. However, the spatial organization of secondary branching changed with age and experience. In older neurons there was a larger fraction of branch points farther from the soma. Deprivation from age PND 9 delayed these changes in secondary branching. This effect of deprivation was rapid (detectable at PND 10) and present at all ages observed. Deprivation initiated at PND 15 had no effect on basal branching measured at PND 20. Thus the spatial organization of secondary dendritic branching is experience-dependent and shares a critical period with receptive field plasticity.},
	Author = {Maravall, Miguel and Koh, Ingrid Y Y and Lindquist, W Brent and Svoboda, Karel},
	Date-Added = {2012-11-08 17:25:56 +0000},
	Date-Modified = {2012-11-08 17:28:21 +0000},
	Doi = {10.1093/cercor/bhh026},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {21 Activity-development; development; barrels; Somatosensory Cortex; rat; rodent; spines; Dendrites; structural remodeling; Structure-Activity Relationship; in vitro; multiphoton; Sensory Deprivation},
	Mesh = {Adaptation, Physiological; Aging; Animals; Animals, Newborn; Dendrites; Neocortex; Nerve Net; Neuronal Plasticity; Pyramidal Cells; Rats; Sensory Deprivation},
	Month = {Jun},
	Number = {6},
	Pages = {655-64},
	Pmid = {15054062},
	Pst = {ppublish},
	Title = {Experience-dependent changes in basal dendritic branching of layer 2/3 pyramidal neurons during a critical period for developmental plasticity in rat barrel cortex},
	Volume = {14},
	Year = {2004},
	File = {papers/Maravall_CerebCortex2004.pdf}}

@article{Parvizi:2012,
	Abstract = {Face-selective neural responses in the human fusiform gyrus have been widely examined. However, their causal role in human face perception is largely unknown. Here, we used a multimodal approach of electrocorticography (ECoG), high-resolution functional magnetic resonance imaging (fMRI), and electrical brain stimulation (EBS) to directly investigate the causal role of face-selective neural responses of the fusiform gyrus (FG) in face perception in a patient implanted with subdural electrodes in the right inferior temporal lobe. High-resolution fMRI identified two distinct FG face-selective regions [mFus-faces and pFus-faces (mid and posterior fusiform, respectively)]. ECoG revealed a striking anatomical and functional correspondence with fMRI data where a pair of face-selective electrodes, positioned 1 cm apart, overlapped mFus-faces and pFus-faces, respectively. Moreover, electrical charge delivered to this pair of electrodes induced a profound face-specific perceptual distortion during viewing of real faces. Specifically, the subject reported a "metamorphosed" appearance of faces of people in the room. Several controls illustrate the specificity of the effect to the perception of faces. EBS of mFus-faces and pFus-faces neither produced a significant deficit in naming pictures of famous faces on the computer, nor did it affect the appearance of nonface objects. Further, the appearance of faces remained unaffected during both sham stimulation and stimulation of a pair of nearby electrodes that were not face-selective. Overall, our findings reveal a striking convergence of fMRI, ECoG, and EBS, which together offer a rare causal link between functional subsets of the human FG network and face perception.},
	Author = {Parvizi, Josef and Jacques, Corentin and Foster, Brett L and Withoft, Nathan and Rangarajan, Vinitha and Weiner, Kevin S and Grill-Spector, Kalanit},
	Date-Added = {2012-11-05 19:30:59 +0000},
	Date-Modified = {2012-11-05 19:32:16 +0000},
	Doi = {10.1523/JNEUROSCI.2609-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {visual system; function; fmri; human; epilepsy; seizure; visual map; Perception; Face; Neurophysiology; extracellular; eeg; toread},
	Month = {Oct},
	Number = {43},
	Pages = {14915-20},
	Pmid = {23100414},
	Pst = {ppublish},
	Title = {Electrical stimulation of human fusiform face-selective regions distorts face perception},
	Volume = {32},
	Year = {2012},
	File = {papers/Parvizi_JNeurosci2012.pdf},
	Bdsk-Url-1 = {http://news.sciencemag.org/sciencenow/2012/10/identifying-the-brains-own-facia.html?ref=em}}

@article{Narboux-Neme:2012,
	Abstract = {To assess the impact of synaptic neurotransmitter release on neural circuit development, we analyzed barrel cortex formation after thalamic or cortical ablation of RIM1 and RIM2 proteins, which control synaptic vesicle fusion. Thalamus-specific deletion of RIMs reduced neurotransmission efficacy by 67%. A barrelless phenotype was found with a dissociation of effects on the presynaptic and postsynaptic cellular elements of the barrel. Presynaptically, thalamocortical axons formed a normal whisker map, whereas postsynaptically the cytoarchitecture of layer IV neurons was altered as spiny stellate neurons were evenly distributed and their dendritic trees were symmetric. Strikingly, cortex-specific deletion of the RIM genes did not modify barrel development. Adult mice with thalamic-specific RIM deletion showed a lack of activity-triggered immediate early gene expression and altered sensory-related behaviors. Thus, efficient synaptic release is required at thalamocortical but not at corticocortical synapses for building the whisker to barrel map and for efficient sensory function.},
	Author = {Narboux-N{\^e}me, Nicolas and Evrard, Alexis and Ferezou, Isabelle and Erzurumlu, Reha S and Kaeser, Pascal S and Lain{\'e}, Jeanne and Rossier, Jean and Ropert, Nicole and S{\"u}dhof, Thomas C and Gaspar, Patricia},
	Date-Added = {2012-11-05 18:10:09 +0000},
	Date-Modified = {2012-11-05 18:11:39 +0000},
	Doi = {10.1523/JNEUROSCI.0343-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread; barrels; Somatosensory Cortex; Neocortex; Cerebral Cortex; mouse; Structure-Activity Relationship; activity manipulation; synapse formation; topographic map; sensory map; Sensory Deprivation; transgenic},
	Mesh = {Animals; Axons; Cerebral Cortex; Female; Male; Mice; Neuronal Plasticity; Neurotransmitter Agents; Somatosensory Cortex; Synapses; Synaptic Transmission; Thalamus; Touch; Vibrissae},
	Month = {May},
	Number = {18},
	Pages = {6183-96},
	Pmid = {22553025},
	Pst = {ppublish},
	Title = {Neurotransmitter release at the thalamocortical synapse instructs barrel formation but not axon patterning in the somatosensory cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Narboux-Nême_JNeurosci2012.pdf}}

@article{Barkovich:2012,
	Abstract = {Malformations of the midbrain (MB) and hindbrain (HB) have become topics of considerable interest in the neurology and neuroscience literature in recent years. The combined advances of imaging and molecular biology have improved analyses of structures in these areas of the central nervous system, while advances in genetics have made it clear that malformations of these structures are often associated with dysfunction or malformation of other organ systems. This review focuses upon the importance of communication between clinical researchers and basic scientists in the advancement of knowledge of this group of disorders. Disorders of anteroposterior (AP) patterning, cerebellar hypoplasias, disorders associated with defects of the pial limiting membrane (cobblestone cortex), disorders of the Reelin pathway, and disorders of the primary cilium/basal body organelle (molar tooth malformations) are the main focus of the review.},
	Author = {Barkovich, A James},
	Date-Added = {2012-11-05 18:08:25 +0000},
	Date-Modified = {2012-11-05 18:09:30 +0000},
	Doi = {10.3389/fnana.2012.00007},
	Journal = {Front Neuroanat},
	Journal-Full = {Frontiers in neuroanatomy},
	Keywords = {cortical malformation; development; neurological disorder; Cerebellar Cortex; Cerebellum; optic tectum; midbrain; Superior Colliculus; fmri; human; review; toread; grants; ideas},
	Month = {Jan},
	Pages = {7},
	Pmc = {PMC3294267},
	Pmid = {22408608},
	Pst = {ppublish},
	Title = {Developmental disorders of the midbrain and hindbrain},
	Volume = {6},
	Year = {2012},
	File = {papers/Barkovich_FrontNeuroanat2012.pdf}}

@article{Wang:2012,
	Abstract = {Much of the information used for visual perception and visually guided actions is processed in complex networks of connections within the cortex. To understand how this works in the normal brain and to determine the impact of disease, mice are promising models. In primate visual cortex, information is processed in a dorsal stream specialized for visuospatial processing and guided action and a ventral stream for object recognition. Here, we traced the outputs of 10 visual areas and used quantitative graph analytic tools of modern network science to determine, from the projection strengths in 39 cortical targets, the community structure of the network. We found a high density of the cortical graph that exceeded that shown previously in monkey. Each source area showed a unique distribution of projection weights across its targets (i.e., connectivity profile) that was well fit by a lognormal function. Importantly, the community structure was strongly dependent on the location of the source area: outputs from medial/anterior extrastriate areas were more strongly linked to parietal, motor, and limbic cortices, whereas lateral extrastriate areas were preferentially connected to temporal and parahippocampal cortices. These two subnetworks resemble dorsal and ventral cortical streams in primates, demonstrating that the basic layout of cortical networks is conserved across species.},
	Author = {Wang, Quanxin and Sporns, Olaf and Burkhalter, Andreas},
	Date-Added = {2012-11-05 18:05:37 +0000},
	Date-Modified = {2012-11-05 18:07:54 +0000},
	Doi = {10.1523/JNEUROSCI.6063-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {connectivity; connectome; mouse; Cerebral Cortex; Neocortex; visual system; network; Anatomy; Histological Techniques; Structure-Activity Relationship; graph theory; toread; callosal; visual cortex; Association cortex; function},
	Mesh = {Animals; Brain Mapping; Cerebral Cortex; Female; Iontophoresis; Male; Mice; Mice, Inbred C57BL; Models, Statistical; Neural Pathways; Neuroanatomical Tract-Tracing Techniques; Neuronal Tract-Tracers; Visual Cortex},
	Month = {Mar},
	Number = {13},
	Pages = {4386-99},
	Pmc = {PMC3328193},
	Pmid = {22457489},
	Pst = {ppublish},
	Title = {Network analysis of corticocortical connections reveals ventral and dorsal processing streams in mouse visual cortex},
	Volume = {32},
	Year = {2012},
	File = {papers/Wang_JNeurosci2012.pdf}}

@article{Nicol:2007,
	Abstract = {Spontaneous activity generated in the retina is necessary to establish a precise retinotopic map, but the underlying mechanisms are poorly understood. We demonstrate here that neural activity controls ephrin-A-mediated responses. In the mouse retinotectal system, we show that spontaneous activity of the retinal ganglion cells (RGCs) is needed, independently of synaptic transmission, for the ordering of the retinotopic map and the elimination of exuberant retinal axons. Activity blockade suppressed the repellent action of ephrin-A on RGC growth cones by cyclic AMP (cAMP)-dependent pathways. Unexpectedly, the ephrin-A5-induced retraction required cAMP oscillations rather than sustained increases in intracellular cAMP concentrations. Periodic photo-induced release of caged cAMP in growth cones rescued the response to ephrin-A5 when activity was blocked. These results provide a direct molecular link between spontaneous neural activity and axon guidance mechanisms during the refinement of neural maps.},
	Author = {Nicol, Xavier and Voyatzis, Sylvie and Muzerelle, Aude and Narboux-N{\^e}me, Nicolas and S{\"u}dhof, Thomas C and Miles, Richard and Gaspar, Patricia},
	Date-Added = {2012-11-05 18:01:02 +0000},
	Date-Modified = {2012-11-05 18:03:52 +0000},
	Doi = {10.1038/nn1842},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {Calcium Signaling; Calcium Channels; oscillations; Spontaneous activity; retinal waves; Retinal Ganglion Cells; Ephrins; mouse; Superior Colliculus; optic tectum; retinotopy; topographic map; visual system; development; axon guidance; Structure-Activity Relationship; synapse formation; grants; ideas},
	Mesh = {1-Methyl-3-isobutylxanthine; Action Potentials; Animals; Cyclic AMP; Embryo, Mammalian; Ephrin-A5; Excitatory Amino Acid Antagonists; Growth Cones; Mice; Mice, Knockout; Munc18 Proteins; Organ Culture Techniques; Periodicity; Phosphodiesterase Inhibitors; Quinoxalines; Retina; Retinal Ganglion Cells; Signal Transduction; Tetrodotoxin; Visual Pathways},
	Month = {Mar},
	Number = {3},
	Pages = {340-7},
	Pmid = {17259982},
	Pst = {ppublish},
	Title = {cAMP oscillations and retinal activity are permissive for ephrin signaling during the establishment of the retinotopic map},
	Volume = {10},
	Year = {2007},
	File = {papers/Nicol_NatNeurosci2007.pdf}}

@article{Mukamel:2010,
	Abstract = {Direct recordings in monkeys have demonstrated that neurons in frontal and parietal areas discharge during execution and perception of actions [1-8]. Because these discharges "reflect" the perceptual aspects of actions of others onto the motor repertoire of the perceiver, these cells have been called mirror neurons. Their overlapping sensory-motor representations have been implicated in observational learning and imitation, two important forms of learning [9]. In humans, indirect measures of neural activity support the existence of sensory-motor mirroring mechanisms in homolog frontal and parietal areas [10, 11], other motor regions [12-15], and also the existence of multisensory mirroring mechanisms in nonmotor regions [16-19]. We recorded extracellular activity from 1177 cells in human medial frontal and temporal cortices while patients executed or observed hand grasping actions and facial emotional expressions. A significant proportion of neurons in supplementary motor area, and hippocampus and environs, responded to both observation and execution of these actions. A subset of these neurons demonstrated excitation during action-execution and inhibition during action-observation. These findings suggest that multiple systems in humans may be endowed with neural mechanisms of mirroring for both the integration and differentiation of perceptual and motor aspects of actions performed by self and others.},
	Author = {Mukamel, Roy and Ekstrom, Arne D and Kaplan, Jonas and Iacoboni, Marco and Fried, Itzhak},
	Date-Added = {2012-11-05 17:52:36 +0000},
	Date-Modified = {2012-11-05 17:55:30 +0000},
	Doi = {10.1016/j.cub.2010.02.045},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {sensory-motor; function; mirror neuron; mirror symmetry; Perception; human; Neurophysiology; extracellular; Frontal Lobe; Temporal Lobe; multimodal},
	Mesh = {Animals; Cerebral Cortex; Electrophysiology; Emotions; Facial Expression; Hand; Humans; Imitative Behavior; Motor Activity; Neurons; Psychomotor Performance; Visual Perception},
	Month = {Apr},
	Number = {8},
	Pages = {750-6},
	Pmc = {PMC2904852},
	Pmid = {20381353},
	Pst = {ppublish},
	Title = {Single-neuron responses in humans during execution and observation of actions},
	Volume = {20},
	Year = {2010},
	File = {papers/Mukamel_CurrBiol2010.pdf}}

@article{Mane:2012,
	Abstract = {Spreading depression (SD) is characterized by a sustained near-complete depolarization of neurons, a massive depolarization of glia, and a negative deflection of the extracellular DC potential. These electrophysiological signs are accompanied by an intrinsic optical signal (IOS) which arises from changes in light scattering and absorption. Even though the underlying mechanisms are unclear, the IOS serves as non-invasive tool to define the spatiotemporal dynamics of SD in brain slices. Usually the tissue is illuminated by white light, and light reflectance or transmittance is monitored. Using a polychromatic, fast-switchable light source we now performed temporo-spectral recordings of the IOS associated with hypoxia-induced SD-like depolarization (HSD) in rat hippocampal slices kept in an interface recording chamber. Recording full illumination spectra (320-680 nm) yielded distinct reflectance profiles for the different phases of HSD. Early during hypoxia tissue reflectance decreased within almost the entire spectrum due to cell swelling. HSD was accompanied by a reversible reflectance increase being most pronounced at 400 nm and 460 nm. At 440 nm massive porphyrin absorption (Soret band) was detected. Hypotonic solutions, Ca(2+)-withdrawal and glial poisoning intensified the reflectance increase during HSD, whereas hypertonic solutions dampened it. Replacement of Cl(-) inverted the reflectance increase. Inducing HSD by cyanide distorted the IOS and reflectance at 340-400 nm increased irreversibly. The pronounced changes at short wavelengths (380 nm, 460 nm) and their cyanide sensitivity suggest that block of mitochondrial metabolism contributes to the IOS during HSD. For stable and reliable IOS recordings during HSD wavelengths of 460-560 nm are recommended.},
	Author = {Man{\'e}, Maria and M{\"u}ller, Michael},
	Date-Added = {2012-11-05 17:52:36 +0000},
	Date-Modified = {2012-11-05 17:57:10 +0000},
	Doi = {10.1371/journal.pone.0043981},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {Hypoxia-Ischemia; hypoxic; oscillations; synchrony; Spontaneous activity; Neuron-Glia/*physiology; Neurophysiology; optical imaging; optical physiology; intrinsic signal; glia; excitotoxcity},
	Number = {8},
	Pages = {e43981},
	Pmc = {PMC3430631},
	Pmid = {22952835},
	Pst = {ppublish},
	Title = {Temporo-spectral imaging of intrinsic optical signals during hypoxia-induced spreading depression-like depolarization},
	Volume = {7},
	Year = {2012},
	File = {papers/Mané_PLoSOne2012.pdf}}

@article{Lin:2012,
	Abstract = {Amblyopia, also known as lazy eye, usually occurs during early childhood and results in poor or blurred vision. Recent neuroimaging studies have found cortical structural/functional abnormalities in amblyopia. However, until now, it was still not known whether the spontaneous activity of the brain changes in amblyopia subjects. In the present study, regional homogeneity (ReHo), a measure of the homogeneity of functional magnetic resonance imaging signals, was used for the first time to investigate changes in resting-state local spontaneous brain activity in individuals with anisometropic amblyopia. Compared with age- and gender-matched subjects with normal vision, the anisometropic amblyopia subjects showed decreased ReHo of spontaneous brain activity in the right precuneus, the left medial prefrontal cortex, the left inferior frontal gyrus, and the left cerebellum, and increased ReHo of spontaneous brain activity was found in the bilateral conjunction area of the postcentral and precentral gyri, the left paracentral lobule, the left superior temporal gyrus, the left fusiform gyrus, the conjunction area of the right insula, putamen and the right middle occipital gyrus. The observed decreases in ReHo may reflect decreased visuo-motor processing ability, and the increases in ReHo in the somatosensory cortices, the motor areas and the auditory area may indicate compensatory plasticity in amblyopia.},
	Author = {Lin, Xiaoming and Ding, Kun and Liu, Yong and Yan, Xiaohe and Song, Shaojie and Jiang, Tianzi},
	Date-Added = {2012-11-05 17:52:36 +0000},
	Date-Modified = {2012-11-05 17:59:33 +0000},
	Doi = {10.1371/journal.pone.0043373},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {resting state; default mode network; amblyopia; Spontaneous activity; function; connectivity; fMRI; human; Cerebral Cortex; visual system; sensory-motor; activity manipulation; Sensory Deprivation; plasticity; toread; ideas; grants},
	Number = {8},
	Pages = {e43373},
	Pmc = {PMC3427333},
	Pmid = {22937041},
	Pst = {ppublish},
	Title = {Altered spontaneous activity in anisometropic amblyopia subjects: revealed by resting-state FMRI},
	Volume = {7},
	Year = {2012},
	File = {papers/Lin_PLoSOne2012.pdf}}

@article{Grinevich:2005,
	Abstract = {The mammalian motor cortex typically innervates motor neurons indirectly via oligosynaptic pathways. However, evolution of skilled digit movements in humans, apes, and some monkey species is associated with the emergence of abundant monosynaptic cortical projections onto spinal motor neurons innervating distal limb muscles. Rats perform skilled movements with their whiskers, and we examined the possibility that the rat vibrissa motor cortex (VMC) projects monosynaptically onto facial motor neurons controlling the whisker movements. First, single injections of lentiviruses to VMC sites identified by intracortical microstimulations were used to label a distinct subpopulation of VMC axons or presynaptic terminals by expression of enhanced green fluorescent protein (GFP) or GFP-tagged synaptophysin, respectively. Four weeks after the injections, GFP and synaptophysin-GFP labeling of axons and putative presynaptic terminals was detected in the lateral portion of the facial nucleus (FN), in close proximity to motor neurons identified morphologically and by axonal back-labeling from the whisker follicles. The VMC projections were detected bilaterally, with threefold larger density of labeling in the contralateral FN. Next, multiple VMC injections were used to label a large portion of VMC axons, resulting in overall denser but still laterally restricted FN labeling. Ultrastructural analysis of the GFP-labeled VMC axons confirmed the existence of synaptic contacts onto dendrites and somata of FN motor neurons. These findings provide anatomical demonstration of monosynaptic VMC-to-FN pathway in the rat and show that lentivirus-based expression of GFP and GFP-tagged presynaptic proteins can be used as a high-resolution neuroanatomical tracing method.},
	Author = {Grinevich, Valery and Brecht, Michael and Osten, Pavel},
	Date-Added = {2012-11-05 17:48:40 +0000},
	Date-Modified = {2012-11-05 17:52:11 +0000},
	Doi = {10.1523/JNEUROSCI.2235-05.2005},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {18 Classic Neuroanatomy Physiology;16 Barrels;Technique; Cerebral Cortex; Neocortex; topographic map; sensory-motor; sensory map; Somatosensory Cortex},
	Mesh = {Animals; Axons; Electric Stimulation; Face; Genes, Reporter; Green Fluorescent Proteins; Lentivirus; Motor Cortex; Motor Neurons; Movement; Pyramidal Cells; Rats; Synapses; Vibrissae},
	Month = {Sep},
	Number = {36},
	Pages = {8250-8},
	Pmid = {16148232},
	Pst = {ppublish},
	Title = {Monosynaptic pathway from rat vibrissa motor cortex to facial motor neurons revealed by lentivirus-based axonal tracing},
	Volume = {25},
	Year = {2005},
	File = {papers/Grinevich_JNeurosci2005.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1523/JNEUROSCI.2235-05.2005}}

@article{Komai:2006a,
	Abstract = {Sensory experience is necessary for normal cortical development. This has been shown by sensory deprivation and pharmacological perturbation of the cortex. Because these manipulations affect the cortical network as a whole, the role of postsynaptic cellular properties during experience-dependent development is unclear. Here we addressed the developmental role of somatodendritic excitability, which enables postsynaptic spike timing-dependent forms of plasticity, in rat somatosensory cortex. We used short interfering RNA (siRNA)-based knockdown of Na+ channels to suppress the somatodendritic excitability of small numbers of layer 2/3 pyramidal neurons in the barrel cortex, without altering the ascending sensory pathway. In vivo recordings from siRNA-expressing cells revealed that this manipulation interfered with the normal developmental strengthening of sensory responses. The sensory responsiveness of neighboring cortical neurons was unchanged, indicating that the cortical network was unchanged. We conclude that somatodendritic excitability of the postsynaptic neuron is needed for the regulation of synaptic strength in the developing sensory cortex.},
	Author = {Komai, Shoji and Licznerski, Pawel and Cetin, Ali and Waters, Jack and Denk, Winfried and Brecht, Michael and Osten, Pavel},
	Date-Added = {2012-11-05 17:48:40 +0000},
	Date-Modified = {2012-11-05 17:48:40 +0000},
	Doi = {10.1038/nn1752},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Mesh = {Animals; DNA, Recombinant; Excitatory Postsynaptic Potentials; Green Fluorescent Proteins; Lentivirus; Microscopy, Confocal; Neuronal Plasticity; Pyramidal Cells; RNA Interference; RNA, Small Interfering; Rats; Rats, Wistar; Sensory Deprivation; Sodium Channels; Somatosensory Cortex; Synaptic Transmission},
	Month = {Sep},
	Number = {9},
	Pages = {1125-33},
	Pmid = {16921372},
	Pst = {ppublish},
	Title = {Postsynaptic excitability is necessary for strengthening of cortical sensory responses during experience-dependent development},
	Volume = {9},
	Year = {2006},
	File = {papers/Komai_NatNeurosci2006.pdf}}

@article{Baudouin:2012,
	Abstract = {The genetic heterogeneity of autism poses a major challenge for identifying mechanism-based treatments. A number of rare mutations are associated with autism, and it is unclear whether these result in common neuronal alterations. Monogenic syndromes, such as fragile X, include autism as one of their multifaceted symptoms and have revealed specific defects in synaptic plasticity. We discovered an unexpected convergence of synaptic pathophysiology in a nonsyndromic form of autism with those in fragile X syndrome. Neuroligin-3 knockout mice (a model for nonsyndromic autism) exhibited disrupted heterosynaptic competition and perturbed metabotropic glutamate receptor-dependent synaptic plasticity, a hallmark of fragile X. These phenotypes could be rescued by reexpression of neuroligin-3 in juvenile mice, highlighting the possibility of reverting neuronal circuit alterations in autism after the completion of development.},
	Author = {Baudouin, St{\'e}phane J and Gaudias, Julien and Gerharz, Stefan and Hatstatt, Laetitia and Zhou, Kuikui and Punnakkal, Pradeep and Tanaka, Kenji F and Spooren, Will and Hen, Rene and De Zeeuw, Chris I and Vogt, Kaspar and Scheiffele, Peter},
	Date-Added = {2012-11-05 17:44:14 +0000},
	Date-Modified = {2012-11-05 17:46:47 +0000},
	Doi = {10.1126/science.1224159},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {autism; Autistic Disorder; function; Synaptic Transmission; Neurophysiology; Electrophysiology; Patch-Clamp Techniques; mouse; transgenic; Transgenes; Behavior; connectivity; toread},
	Mesh = {Animals; Autistic Disorder; Cell Adhesion Molecules, Neuronal; Disease Models, Animal; Fragile X Syndrome; Male; Membrane Proteins; Mice; Mice, Inbred C57BL; Mice, Knockout; Nerve Net; Nerve Tissue Proteins; Neuronal Plasticity; Synapses},
	Month = {Oct},
	Number = {6103},
	Pages = {128-32},
	Pmid = {22983708},
	Pst = {ppublish},
	Title = {Shared synaptic pathophysiology in syndromic and nonsyndromic rodent models of autism},
	Volume = {338},
	Year = {2012},
	File = {papers/Baudouin_Science2012.pdf}}

@article{Ragan:2012,
	Abstract = {Here we describe an automated method, named serial two-photon (STP) tomography, that achieves high-throughput fluorescence imaging of mouse brains by integrating two-photon microscopy and tissue sectioning. STP tomography generates high-resolution datasets that are free of distortions and can be readily warped in three dimensions, for example, for comparing multiple anatomical tracings. This method opens the door to routine systematic studies of neuroanatomy in mouse models of human brain disorders.},
	Author = {Ragan, Timothy and Kadiri, Lolahon R and Venkataraju, Kannan Umadevi and Bahlmann, Karsten and Sutin, Jason and Taranda, Julian and Arganda-Carreras, Ignacio and Kim, Yongsoo and Seung, H Sebastian and Osten, Pavel},
	Date-Added = {2012-11-05 17:44:14 +0000},
	Date-Modified = {2012-11-05 17:48:05 +0000},
	Doi = {10.1038/nmeth.1854},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Keywords = {Methods; Technique; multiphoton; mouse; Anatomy; connectivity; histology; Histological Techniques; microscopy; toread},
	Mesh = {Anatomy, Cross-Sectional; Animals; Brain; Image Interpretation, Computer-Assisted; Mice; Mice, Transgenic; Microscopy, Fluorescence, Multiphoton; Pattern Recognition, Automated; Tomography},
	Month = {Mar},
	Number = {3},
	Pages = {255-8},
	Pmc = {PMC3297424},
	Pmid = {22245809},
	Pst = {epublish},
	Title = {Serial two-photon tomography for automated ex vivo mouse brain imaging},
	Volume = {9},
	Year = {2012},
	File = {papers/Ragan_NatMethods2012.pdf}}

@article{Yang:2012,
	Abstract = {The basic circuitry of auditory, visual, somatosensory and other cortical areas is highly stereotyped (Douglas and Martin, 2004). However, it remains unclear whether this anatomical stereotypy implies functional homogeneity, or whether instead different cortical areas are specialized to process the diverse sensory inputs they receive. Here we have used a two alternative forced choice task to assess modality-specific differences in the ability of rats to exploit precise neuronal timing. We delivered pairs of electrical pulses directly to different areas of cortex to determine the minimum timing differences subjects could detect. By stimulating the cortex directly, we isolated differences due to cortical circuitry rather than to sensory transduction and subcortical processing. Surprisingly, the minimum detectable timing differences varied over more than an order of magnitude, ranging from 1 ms in barrel cortex to 15 ms in visual cortex. Furthermore, these modality-specific differences depended upon sensory experience: although animals subjected to whisker clipping initially showed an impaired ability to exploit fine timing in barrel cortical stimulation, behavioral training partially rescued this deficit. Our results suggest that different cortical areas are adapted to the specific structure of the input signals they process, and that precise spike timing may play a more important role for some cortical areas than for others.},
	Author = {Yang, Yang and Zador, Anthony M},
	Date-Added = {2012-11-05 17:39:47 +0000},
	Date-Modified = {2012-11-05 17:43:53 +0000},
	Doi = {10.1523/JNEUROSCI.1411-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {Decision Making; Attention; latency; Behavior; Neurophysiology; mouse; Neocortex; Cerebral Cortex},
	Month = {Oct},
	Number = {43},
	Pages = {15142-7},
	Pmid = {23100435},
	Pst = {ppublish},
	Title = {Differences in Sensitivity to Neural Timing among Cortical Areas},
	Volume = {32},
	Year = {2012},
	File = {papers/Yang_JNeurosci2012.pdf}}

@article{Chan:2012,
	Abstract = {In humans, naturally acquired microchimerism has been observed in many tissues and organs. Fetal microchimerism, however, has not been investigated in the human brain. Microchimerism of fetal as well as maternal origin has recently been reported in the mouse brain. In this study, we quantified male DNA in the human female brain as a marker for microchimerism of fetal origin (i.e. acquisition of male DNA by a woman while bearing a male fetus). Targeting the Y-chromosome-specific DYS14 gene, we performed real-time quantitative PCR in autopsied brain from women without clinical or pathologic evidence of neurologic disease (n = 26), or women who had Alzheimer's disease (n = 33). We report that 63% of the females (37 of 59) tested harbored male microchimerism in the brain. Male microchimerism was present in multiple brain regions. Results also suggested lower prevalence (p = 0.03) and concentration (p = 0.06) of male microchimerism in the brains of women with Alzheimer's disease than the brains of women without neurologic disease. In conclusion, male microchimerism is frequent and widely distributed in the human female brain.},
	Author = {Chan, William F N and Gurnot, C{\'e}cile and Montine, Thomas J and Sonnen, Joshua A and Guthrie, Katherine A and Nelson, J Lee},
	Date-Added = {2012-11-05 17:39:47 +0000},
	Date-Modified = {2012-11-05 17:43:13 +0000},
	Doi = {10.1371/journal.pone.0045592},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {Genomic Imprinting; Fetal Development; Maternal-Fetal Exchange; Maternally-Acquired; Cell Fusion; macrophage; microglia; gene},
	Number = {9},
	Pages = {e45592},
	Pmc = {PMC3458919},
	Pmid = {23049819},
	Pst = {ppublish},
	Title = {Male microchimerism in the human female brain},
	Volume = {7},
	Year = {2012},
	File = {papers/Chan_PLoSOne2012.pdf}}

@article{Johansson:2008,
	Abstract = {Transplanted bone marrow-derived cells (BMDCs) have been reported to fuse with cells of diverse tissues, but the extremely low frequency of fusion has led to the view that such events are biologically insignificant. Nonetheless, in mice with a lethal recessive liver disease (tyrosinaemia), transplantation of wild-type BMDCs restored liver function by cell fusion and prevented death, indicating that cell fusion can have beneficial effects. Here we report that chronic inflammation resulting from severe dermatitis or autoimmune encephalitis leads to robust fusion of BMDCs with Purkinje neurons and formation of hundreds of binucleate heterokaryons per cerebellum, a 10-100-fold higher frequency than previously reported. Single haematopoietic stem-cell transplants showed that the fusogenic cell is from the haematopoietic lineage and parabiosis experiments revealed that fusion can occur without irradiation. Transplantation of rat bone marrow into mice led to activation of dormant rat Purkinje neuron-specific genes in BMDC nuclei after fusion with mouse Purkinje neurons, consistent with nuclear reprogramming. The precise neurological role of these heterokaryons awaits elucidation, but their frequency in brain after inflammation is clearly much higher than previously appreciated.},
	Author = {Johansson, Clas B and Youssef, Sawsan and Koleckar, Kassie and Holbrook, Colin and Doyonnas, Regis and Corbel, Stephane Y and Steinman, Lawrence and Rossi, Fabio M V and Blau, Helen M},
	Date-Added = {2012-11-05 17:39:47 +0000},
	Date-Modified = {2012-11-05 17:40:43 +0000},
	Doi = {10.1038/ncb1720},
	Journal = {Nat Cell Biol},
	Journal-Full = {Nature cell biology},
	Keywords = {Stem Cells; Cell Fusion; macrophage; microglia; neuron; Immune System;},
	Mesh = {Animals; Bone Marrow Cells; Cell Fusion; Dermatitis; Encephalomyelitis, Autoimmune, Experimental; Female; Green Fluorescent Proteins; Hematopoietic Stem Cells; Inflammation; Lipopolysaccharides; Mesenchymal Stem Cell Transplantation; Mice; Mice, Inbred C57BL; Purkinje Cells; Rats; Rats, Sprague-Dawley; Transplantation Chimera},
	Month = {May},
	Number = {5},
	Pages = {575-83},
	Pmid = {18425116},
	Pst = {ppublish},
	Title = {Extensive fusion of haematopoietic cells with Purkinje neurons in response to chronic inflammation},
	Volume = {10},
	Year = {2008},
	File = {papers/Johansson_NatCellBiol2008.pdf}}

@article{Lapray:2010,
	Abstract = {Previous reports indicate that in utero knockdown of doublecortin (DCX) results in the genesis of a subcortical heterotopia reminiscent of the doublecortex observed in female patients with DCX mutations. It has also been shown that these rats display an increased susceptibility to convulsant agents and increased cortical neurons excitability; but it is presently unknown whether they display spontaneous seizures. Furthermore, the link between the size of heterotopia and the clinical manifestation remained to be elucidated. Using video-electrocorticogram recordings, we now report that DCX knockdown induces frequent spontaneous seizures commonly associated with myoclonic jerks in adult rats. Surprisingly, epilepsy occurred even in rats with very small subcortical heterotopias, as revealed by histological analysis of recorded animals. Moreover, the severity of the epileptic manifestations was positively correlated with both the size of the subcortical heterotopia and the age of recorded animals; thus, epileptic features were not detected in immature affected rats. In conclusion, our data demonstrate for the first time that subtle alterations can yield epilepsy and reveal a strong correlation between thicknesses of subcortical heterotopia, age of affected individuals and clinical impairment.},
	Author = {Lapray, Damien and Popova, Irina Y and Kindler, Jennifer and Jorquera, Isabel and Becq, H{\'e}l{\`e}ne and Manent, Jean-Bernard and Luhmann, Heiko J and Represa, Alfonso},
	Date-Added = {2012-11-05 17:38:13 +0000},
	Date-Modified = {2012-11-05 17:39:24 +0000},
	Doi = {10.1093/cercor/bhq014},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {cortical malformation; Epilepsy; development; doublecortin; Seizures; Neurophysiology; rat},
	Mesh = {Animals; Animals, Newborn; Disease Models, Animal; Epilepsy; Female; Gene Knockdown Techniques; Humans; Male; Malformations of Cortical Development; Microtubule-Associated Proteins; Neuropeptides; Rats; Rats, Wistar},
	Month = {Nov},
	Number = {11},
	Pages = {2694-701},
	Pmid = {20164125},
	Pst = {ppublish},
	Title = {Spontaneous epileptic manifestations in a DCX knockdown model of human double cortex},
	Volume = {20},
	Year = {2010},
	File = {papers/Lapray_CerebCortex2010.pdf}}

@article{Grinevich:2009,
	Abstract = {The brain-specific immediate early gene Arc/Arg3.1 is induced in response to a variety of stimuli, including sensory and behavior-linked neural activity. Here we report the generation of transgenic mice, termed TgArc/Arg3.1-d4EGFP, expressing a 4-h half-life form of enhanced green fluorescent protein (d4EGFP) under the control of the Arc/Arg3.1 promoter. We show that d4EGFP-mediated fluorescence faithfully reports Arc/Arg3.1 induction in response to physiological, pathological and pharmacological stimuli, and that this fluorescence permits electrical recording from activated neurons in the live mouse. Moreover, the fluorescent Arc/Arg3.1 indicator revealed activity changes in circumscribed brain areas in distinct modes of stress and in a mouse model of Alzheimer's disease. These findings identify the TgArc/Arg3.1-d4EGFP mouse as a versatile tool to monitor Arc/Arg3.1 induction in neural circuits, both in vitro and in vivo.},
	Author = {Grinevich, Valery and Kolleker, Alexander and Eliava, Marina and Takada, Naoki and Takuma, Hiroshi and Fukazawa, Yugo and Shigemoto, Ryuichi and Kuhl, Dietmar and Waters, Jack and Seeburg, Peter H and Osten, Pavel},
	Date-Added = {2012-11-05 17:33:58 +0000},
	Date-Modified = {2012-11-05 17:35:47 +0000},
	Doi = {10.1016/j.jneumeth.2009.07.015},
	Journal = {J Neurosci Methods},
	Journal-Full = {Journal of neuroscience methods},
	Keywords = {optical physiology; optical imaging; multiphoton; Immediate-Early Proteins; genes; Transcription Factors; Reporter/genetics; Transgenes; transgenic; mouse; in vivo; Technique; ideas; grants},
	Mesh = {Alzheimer Disease; Amyloid beta-Protein Precursor; Animals; Brain; Cytoskeletal Proteins; Disease Models, Animal; Fluorescence; Green Fluorescent Proteins; Humans; Male; Mice; Mice, Transgenic; Nerve Tissue Proteins; Neurons; Presenilin-1; Presenilin-2; Promoter Regions, Genetic; Protease Nexins; Receptors, Cell Surface; Stress, Physiological; Time Factors},
	Month = {Oct},
	Number = {1},
	Pages = {25-36},
	Pmid = {19628007},
	Pst = {ppublish},
	Title = {Fluorescent Arc/Arg3.1 indicator mice: a versatile tool to study brain activity changes in vitro and in vivo},
	Volume = {184},
	Year = {2009},
	File = {papers/Grinevich_JNeurosciMethods2009.pdf}}

@article{Lam:2012,
	Abstract = {A variety of genetically encoded reporters use changes in fluorescence (or F{\"o}rster) resonance energy transfer (FRET) to report on biochemical processes in living cells. The standard genetically encoded FRET pair consists of CFPs and YFPs, but many CFP-YFP reporters suffer from low FRET dynamic range, phototoxicity from the CFP excitation light and complex photokinetic events such as reversible photobleaching and photoconversion. We engineered two fluorescent proteins, Clover and mRuby2, which are the brightest green and red fluorescent proteins to date and have the highest F{\"o}rster radius of any ratiometric FRET pair yet described. Replacement of CFP and YFP with these two proteins in reporters of kinase activity, small GTPase activity and transmembrane voltage significantly improves photostability, FRET dynamic range and emission ratio changes. These improvements enhance detection of transient biochemical events such as neuronal action-potential firing and RhoA activation in growth cones.},
	Author = {Lam, Amy J and St-Pierre, Fran{\c c}ois and Gong, Yiyang and Marshall, Jesse D and Cranfill, Paula J and Baird, Michelle A and McKeown, Michael R and Wiedenmann, J{\"o}rg and Davidson, Michael W and Schnitzer, Mark J and Tsien, Roger Y and Lin, Michael Z},
	Date-Added = {2012-11-05 17:30:58 +0000},
	Date-Modified = {2012-11-05 17:33:08 +0000},
	Doi = {10.1038/nmeth.2171},
	Journal = {Nat Methods},
	Journal-Full = {Nature methods},
	Keywords = {Technique; optical imaging; microscopy; FRET; Transgenes; Reporter/genetics; optical physiology; Neurophysiology;},
	Month = {Oct},
	Number = {10},
	Pages = {1005-12},
	Pmc = {PMC3461113},
	Pmid = {22961245},
	Pst = {ppublish},
	Title = {Improving FRET dynamic range with bright green and red fluorescent proteins},
	Volume = {9},
	Year = {2012},
	File = {papers/Lam_NatMethods2012.pdf}}

@article{Jones:2012,
	Abstract = {Noise is a major concern in circuits processing electrical signals, including neural circuits. There are many factors that influence how noise propagates through neural circuits, and there are few systems in which noise levels have been studied throughout a processing pathway. We recorded intracellularly from multiple stages of a sensory-motor pathway in the locust that detects approaching objects. We found that responses are more variable and that signal-to-noise ratios (SNRs) are lower further from the sensory periphery. SNRs remain low even with the use of stimuli for which the pathway is most selective and for which the neuron representing its final sensory level must integrate many synaptic inputs. Modeling of this neuron shows that variability in the strength of individual synaptic inputs within a large population has little effect on the variability of the spiking output. In contrast, jitter in the timing of individual inputs and spontaneous variability is important for shaping the responses to preferred stimuli. These results suggest that neural noise is inherent to the processing of visual stimuli signaling impending collision and contributes to shaping neural responses along this sensory-motor pathway.},
	Annote = {Model and paper of looming response, large movement detector, nAchR, GABA, nicotinic:

},
	Author = {Jones, Peter W and Gabbiani, Fabrizio},
	Date-Added = {2012-11-05 17:04:45 +0000},
	Date-Modified = {2012-11-05 17:08:24 +0000},
	Doi = {10.1152/jn.00607.2011},
	Journal = {J Neurophysiol},
	Journal-Full = {Journal of neurophysiology},
	Keywords = {Models; looming response; movement detector, nAchR, GABA, nicotinic; noise; Theoretical; Signal Processing; sensory-motor; topographic map; multimodal; locust; Insect; neuron; Electrophysiology; extracellular; Neurophysiology},
	Mesh = {Analysis of Variance; Animals; Computer Simulation; Grasshoppers; Light; Membrane Potentials; Models, Neurological; Motion Perception; Nervous System; Photic Stimulation; Photoreceptor Cells, Invertebrate; Psychophysics; Reaction Time; Signal-To-Noise Ratio; Time Factors; Visual Pathways},
	Month = {Feb},
	Number = {4},
	Pages = {1067-79},
	Pmc = {PMC3289460},
	Pmid = {22114160},
	Pst = {ppublish},
	Title = {Impact of neural noise on a sensory-motor pathway signaling impending collision},
	Volume = {107},
	Year = {2012},
	File = {papers/Jones_JNeurophysiol2012.pdf},
	Bdsk-Url-1 = {http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=144007&file=%5CLGMD%5Cjnphysiol2012%5Cparameter_comparison.rtf}}

@article{Fan:2012,
	Abstract = {The vast majority of prenatal genetic testing requires invasive sampling. However, this poses a risk to the fetus, so one must make a decision that weighs the desire for genetic information against the risk of an adverse outcome due to hazards of the testing process. These issues are not required to be coupled, and it would be desirable to discover genetic information about the fetus without incurring a health risk. Here we demonstrate that it is possible to non-invasively sequence the entire prenatal genome. Our results show that molecular counting of parental haplotypes in maternal plasma by shotgun sequencing of maternal plasma DNA allows the inherited fetal genome to be deciphered non-invasively. We also applied the counting principle directly to each allele in the fetal exome by performing exome capture on maternal plasma DNA before shotgun sequencing. This approach enables non-invasive exome screening of clinically relevant and deleterious alleles that were paternally inherited or had arisen as de novo germline mutations, and complements the haplotype counting approach to provide a comprehensive view of the fetal genome. Non-invasive determination of the fetal genome may ultimately facilitate the diagnosis of all inherited and de novo genetic disease.},
	Author = {Fan, H Christina and Gu, Wei and Wang, Jianbin and Blumenfeld, Yair J and El-Sayed, Yasser Y and Quake, Stephen R},
	Date-Added = {2012-11-05 17:02:31 +0000},
	Date-Modified = {2012-11-05 17:03:47 +0000},
	Doi = {10.1038/nature11251},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {ideas; grants; Genomic Imprinting; Sequence Analysis; Fetal Development; shotgun sequencing; disease; marker},
	Mesh = {Chromosomes, Human; DNA; Exome; Female; Fetus; Genome, Human; Haplotypes; Humans; Male; Pregnancy; Prenatal Diagnosis; Sensitivity and Specificity},
	Month = {Jul},
	Number = {7407},
	Pages = {320-4},
	Pmid = {22763444},
	Pst = {ppublish},
	Title = {Non-invasive prenatal measurement of the fetal genome},
	Volume = {487},
	Year = {2012},
	File = {papers/Fan_Nature2012.pdf}}

@article{Campbell:2012,
	Abstract = {Bone and lung metastases are responsible for the majority of deaths in patients with breast cancer. Following treatment of the primary cancer, emotional and psychosocial factors within this population precipitate time to recurrence and death, however the underlying mechanism(s) remain unclear. Using a mouse model of bone metastasis, we provide experimental evidence that activation of the sympathetic nervous system, which is one of many pathophysiological consequences of severe stress and depression, promotes MDA-231 breast cancer cell colonization of bone via a neurohormonal effect on the host bone marrow stroma. We demonstrate that induction of RANKL expression in bone marrow osteoblasts, following β2AR stimulation, increases the migration of metastatic MDA-231 cells in vitro, independently of SDF1-CXCR4 signaling. We also show that the stimulatory effect of endogenous (chronic stress) or pharmacologic sympathetic activation on breast cancer bone metastasis in vivo can be blocked with the β-blocker propranolol, and by knockdown of RANK expression in MDA-231 cells. These findings indicate that RANKL promotes breast cancer cell metastasis to bone via its pro-migratory effect on breast cancer cells, independently of its effect on bone turnover. The emerging clinical implication, supported by recent epidemiological studies, is that βAR-blockers and drugs interfering with RANKL signaling, such as Denosumab, could increase patient survival if used as adjuvant therapy to inhibit both the early colonization of bone by metastatic breast cancer cells and the initiation of the "vicious cycle" of bone destruction induced by these cells.},
	Author = {Campbell, J Preston and Karolak, Matthew R and Ma, Yun and Perrien, Daniel S and Masood-Campbell, S Kathryn and Penner, Niki L and Munoz, Steve A and Zijlstra, Andries and Yang, Xiangli and Sterling, Julie A and Elefteriou, Florent},
	Date-Added = {2012-11-05 16:58:27 +0000},
	Date-Modified = {2012-11-05 17:00:12 +0000},
	Doi = {10.1371/journal.pbio.1001363},
	Journal = {PLoS Biol},
	Journal-Full = {PLoS biology},
	Keywords = {neuron; Immune System; cancer; metastasis; macrophage; microglia; Cell Fusion; ideas},
	Mesh = {Adrenergic beta-Antagonists; Animals; Bone Marrow Cells; Bone Neoplasms; Cell Movement; Female; Mammary Neoplasms, Experimental; Mice; Osteoblasts; Propranolol; Receptors, Adrenergic, beta-2; Signal Transduction; Stromal Cells; Sympathetic Nervous System},
	Month = {Jul},
	Number = {7},
	Pages = {e1001363},
	Pmc = {PMC3398959},
	Pmid = {22815651},
	Pst = {ppublish},
	Title = {Stimulation of host bone marrow stromal cells by sympathetic nerves promotes breast cancer bone metastasis in mice},
	Volume = {10},
	Year = {2012},
	File = {papers/Campbell_PLoSBiol2012.pdf}}

@article{Poil:2012,
	Abstract = {Criticality has gained widespread interest in neuroscience as an attractive framework for understanding the character and functional implications of variability in brain activity. The metastability of critical systems maximizes their dynamic range, storage capacity, and computational power. Power-law scaling-a hallmark of criticality-has been observed on different levels, e.g., in the distribution of neuronal avalanches in vitro and in vivo, but also in the decay of temporal correlations in behavioral performance and ongoing oscillations in humans. An unresolved issue is whether power-law scaling on different organizational levels in the brain-and possibly in other hierarchically organized systems-can be related. Here, we show that critical-state dynamics of avalanches and oscillations jointly emerge in a neuronal network model when excitation and inhibition is balanced. The oscillatory activity of the model was qualitatively similar to what is typically observed in recordings of human resting-state MEG. We propose that homeostatic plasticity mechanisms tune this balance in healthy brain networks, and that it is essential for critical behavior on multiple levels of neuronal organization with ensuing functional benefits. Based on our network model, we introduce a concept of multi-level criticality in which power-law scaling can emerge on multiple time scales in oscillating networks.},
	Author = {Poil, Simon-Shlomo and Hardstone, Richard and Mansvelder, Huibert D and Linkenkaer-Hansen, Klaus},
	Date-Added = {2012-11-05 16:56:48 +0000},
	Date-Modified = {2012-11-05 16:57:54 +0000},
	Doi = {10.1523/JNEUROSCI.5990-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread; Spontaneous activity; computation biology; Theoretical; oscillations; synchrony; human; MEG; Models},
	Mesh = {Action Potentials; Brain; Computer Simulation; Humans; Models, Neurological; Nerve Net; Neural Inhibition; Neuronal Plasticity; Neurons},
	Month = {Jul},
	Number = {29},
	Pages = {9817-23},
	Pmid = {22815496},
	Pst = {ppublish},
	Title = {Critical-state dynamics of avalanches and oscillations jointly emerge from balanced excitation/inhibition in neuronal networks},
	Volume = {32},
	Year = {2012},
	File = {papers/Poil_JNeurosci2012.pdf}}

@article{Danziger:2012,
	Abstract = {How does visual perception shape the way we coordinate movements? Recent studies suggest that the brain organizes movements based on minimizing reaching errors in the presence of motor and sensory noise. We present an alternative hypothesis in which movement trajectories also result from acquired knowledge about the geometrical properties of the object that the brain is controlling. To test this hypothesis, we asked human subjects to control a simulated kinematic linkage by continuous finger motion, a completely novel experience. This paradigm removed all biases arising from influences of limb dynamics and past experience. Subjects were exposed to two different types of visual feedback; some saw the entire simulated linkage and others saw only the moving extremity. Consistent with our hypothesis, subjects learned to move the simulated linkage along geodesic lines corresponding to the geometrical structure of the observed motion. Thus, optimizing final accuracy is not the unique determinant of trajectory formation.},
	Author = {Danziger, Zachary and Mussa-Ivaldi, Ferdinando A},
	Date-Added = {2012-11-05 16:55:31 +0000},
	Date-Modified = {2012-11-05 16:56:25 +0000},
	Doi = {10.1523/JNEUROSCI.5528-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {motor; map; topographic map; Perception; visual system; Motion Perception;human},
	Mesh = {Biomechanics; Feedback, Sensory; Female; Fingers; Humans; Learning; Male; Motion Perception; Movement; Photic Stimulation; Psychomotor Performance; Visual Perception},
	Month = {Jul},
	Number = {29},
	Pages = {9859-69},
	Pmc = {PMC3437549},
	Pmid = {22815501},
	Pst = {ppublish},
	Title = {The influence of visual motion on motor learning},
	Volume = {32},
	Year = {2012},
	File = {papers/Danziger_JNeurosci2012.pdf}}

@article{Tang:2012,
	Abstract = {Recent computational and experimental work has shown that similar network performance can result from variable sets of synaptic and intrinsic properties. Because temperature is a global perturbation that differentially influences every biological process within the nervous system, one might therefore expect that individual animals would respond differently to temperature. Nonetheless, the phase relationships of the pyloric rhythm of the stomatogastric ganglion (STG) of the crab, Cancer borealis, are remarkably invariant between 7 and 23$\,^{\circ}$C (Tang et al., 2010). Here, we report that, when isolated STG preparations were exposed to more extreme temperature ranges, their networks became nonrhythmic, or "crashed", in a reversible fashion. Animals were acclimated for at least 3 weeks at 7, 11, or 19$\,^{\circ}$C. When networks from the acclimated animals were perturbed by acute physiologically relevant temperature ramps (11-23$\,^{\circ}$C), the network frequency and phase relationships were independent of the acclimation group. At high acute temperatures (>23$\,^{\circ}$C), circuits from the cold-acclimated animals produced less-regular pyloric rhythms than those from warm-acclimated animals. At high acute temperatures, phase relationships between pyloric neurons were more variable from animal to animal than at moderate acute temperatures, suggesting that individual differences across animals in intrinsic circuit parameters are revealed at high temperatures. This shows that individual and variable neuronal circuits can behave similarly in normal conditions, but their behavior may diverge when confronted with extreme external perturbations.},
	Author = {Tang, Lamont S and Taylor, Adam L and Rinberg, Anatoly and Marder, Eve},
	Date-Added = {2012-11-05 16:54:24 +0000},
	Date-Modified = {2012-11-05 16:54:58 +0000},
	Doi = {10.1523/JNEUROSCI.1443-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread; crab; motor; oscillations; synchrony; Spontaneous activity},
	Mesh = {Acclimatization; Animals; Brachyura; Environment; Ganglia, Invertebrate; Neurons; Periodicity; Pylorus; Temperature},
	Month = {Jul},
	Number = {29},
	Pages = {10075-85},
	Pmid = {22815521},
	Pst = {ppublish},
	Title = {Robustness of a rhythmic circuit to short- and long-term temperature changes},
	Volume = {32},
	Year = {2012},
	File = {papers/Tang_JNeurosci2012.pdf}}

@article{Nguyen:2012,
	Abstract = {Mutations in the X-linked gene, methyl-CpG binding protein 2 (Mecp2), underlie a wide range of neuropsychiatric disorders, most commonly, Rett Syndrome (RTT), a severe autism spectrum disorder that affects approximately one in 10,000 female live births. Because mutations in the Mecp2 gene occur in the germ cells with onset of neurological symptoms occurring in early childhood, the role of MeCP2 has been ascribed to brain maturation at a specific developmental window. Here, we show similar kinetics of onset and progression of RTT-like symptoms in mice, including lethality, if MeCP2 is removed postnatally during the developmental stage that coincides with RTT onset, or adult stage. For the first time, we show that brains that lose MeCP2 at these two different stages are actively shrinking, resulting in higher than normal neuronal cell density. Furthermore, we show that mature dendritic arbors of pyramidal neurons are severely retracted and dendritic spine density is dramatically reduced. In addition, hippocampal astrocytes have significantly less complex ramified processes. These changes accompany a striking reduction in the levels of several synaptic proteins, including CaMKII α/β, AMPA, and NMDA receptors, and the synaptic vesicle proteins Vglut and Synapsin, which represent critical modifiers of synaptic function and dendritic arbor structure. Importantly, the mRNA levels of these synaptic proteins remains unchanged, suggesting that MeCP2 likely regulates these synaptic proteins post-transcriptionally, directly or indirectly. Our data suggest a crucial role for MeCP2 in post-transcriptional regulation of critical synaptic proteins involved in maintaining mature neuronal networks during late stages of postnatal brain development.},
	Author = {Nguyen, Minh Vu Chuong and Du, Fang and Felice, Christy A and Shan, Xiwei and Nigam, Aparna and Mandel, Gail and Robinson, John K and Ballas, Nurit},
	Date-Added = {2012-11-05 16:52:21 +0000},
	Date-Modified = {2012-11-05 16:53:19 +0000},
	Doi = {10.1523/JNEUROSCI.1316-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {toread; mutant; mouse; transgenic; autism; Autistic Disorder; Behavior; Dendrites; spines;},
	Mesh = {Animals; Brain; Dendrites; Disease Models, Animal; Gene Expression Regulation; Male; Methyl-CpG-Binding Protein 2; Mice; Mice, Transgenic; Motor Activity; Nerve Net; Neurons; Rett Syndrome; Synapses},
	Month = {Jul},
	Number = {29},
	Pages = {10021-34},
	Pmc = {PMC3461266},
	Pmid = {22815516},
	Pst = {ppublish},
	Title = {MeCP2 is critical for maintaining mature neuronal networks and global brain anatomy during late stages of postnatal brain development and in the mature adult brain},
	Volume = {32},
	Year = {2012},
	File = {papers/Nguyen_JNeurosci2012.pdf}}

@article{Litwin-Kumar:2012,
	Abstract = {Anatomical studies demonstrate that excitatory connections in cortex are not uniformly distributed across a network but instead exhibit clustering into groups of highly connected neurons. The implications of clustering for cortical activity are unclear. We studied the effect of clustered excitatory connections on the dynamics of neuronal networks that exhibited high spike time variability owing to a balance between excitation and inhibition. Even modest clustering substantially changed the behavior of these networks, introducing slow dynamics during which clusters of neurons transiently increased or decreased their firing rate. Consequently, neurons exhibited both fast spiking variability and slow firing rate fluctuations. A simplified model shows how stimuli bias networks toward particular activity states, thereby reducing firing rate variability as observed experimentally in many cortical areas. Our model thus relates cortical architecture to the reported variability in spontaneous and evoked spiking activity.},
	Author = {Litwin-Kumar, Ashok and Doiron, Brent},
	Date-Added = {2012-11-05 16:36:41 +0000},
	Date-Modified = {2012-11-05 16:40:09 +0000},
	Doi = {10.1038/nn.3220},
	Journal = {Nat Neurosci},
	Journal-Full = {Nature neuroscience},
	Keywords = {oscillations; synchrony; connectivity; graph theory; Theoretical; Models; computation biology; Cerebral Cortex; Neocortex; network; Technique},
	Month = {Sep},
	Number = {11},
	Pages = {1498-505},
	Pmid = {23001062},
	Pst = {ppublish},
	Title = {Slow dynamics and high variability in balanced cortical networks with clustered connections},
	Volume = {15},
	Year = {2012},
	File = {papers/Litwin-Kumar_NatNeurosci2012.pdf}}

@article{Wandell:2011,
	Abstract = {A quarter-century ago visual neuroscientists had little information about the number and organization of retinotopic maps in human visual cortex. The advent of functional magnetic resonance imaging (MRI), a non-invasive, spatially-resolved technique for measuring brain activity, provided a wealth of data about human retinotopic maps. Just as there are differences amongst non-human primate maps, the human maps have their own unique properties. Many human maps can be measured reliably in individual subjects during experimental sessions lasting less than an hour. The efficiency of the measurements and the relatively large amplitude of functional MRI signals in visual cortex make it possible to develop quantitative models of functional responses within specific maps in individual subjects. During this last quarter-century, there has also been significant progress in measuring properties of the human brain at a range of length and time scales, including white matter pathways, macroscopic properties of gray and white matter, and cellular and molecular tissue properties. We hope the next 25years will see a great deal of work that aims to integrate these data by modeling the network of visual signals. We do not know what such theories will look like, but the characterization of human retinotopic maps from the last 25years is likely to be an important part of future ideas about visual computations.},
	Author = {Wandell, Brian A and Winawer, Jonathan},
	Date-Added = {2012-11-02 18:18:52 +0000},
	Date-Modified = {2012-11-02 18:20:03 +0000},
	Doi = {10.1016/j.visres.2010.08.004},
	Journal = {Vision Res},
	Journal-Full = {Vision research},
	Keywords = {visual system; fMRI; human; retinotopy; topographic map; visual cortex; Neocortex; function; review literature},
	Mesh = {Brain Mapping; Humans; Magnetic Resonance Imaging; Visual Cortex; Visual Pathways},
	Month = {Apr},
	Number = {7},
	Pages = {718-37},
	Pmc = {PMC3030662},
	Pmid = {20692278},
	Pst = {ppublish},
	Title = {Imaging retinotopic maps in the human brain},
	Volume = {51},
	Year = {2011},
	File = {papers/Wandell_VisionRes2011.pdf}}

@article{Sengpiel:1999,
	Abstract = {Visual search tasks appear to involve spatially selective attention to the target, but evidence for attentional modulation in the visual area with the most precise retinotopic organization V1 has been elusive. Recent imaging studies show that spatial attention can indeed enhance visual responses in human V1.},
	Author = {Sengpiel, F and H{\"u}bener, M},
	Date-Added = {2012-11-02 18:13:41 +0000},
	Date-Modified = {2012-11-02 18:14:21 +0000},
	Journal = {Curr Biol},
	Journal-Full = {Current biology : CB},
	Keywords = {visual system; topographic map; function; human; visual cortex; retinotopy; review literature},
	Mesh = {Animals; Humans; Magnetic Resonance Imaging; Visual Cortex},
	Month = {May},
	Number = {9},
	Pages = {R318-21},
	Pmid = {10419335},
	Pst = {ppublish},
	Title = {Visual attention: spotlight on the primary visual cortex},
	Volume = {9},
	Year = {1999},
	File = {papers/Sengpiel_CurrBiol1999.pdf}}

@article{Hoffmann:2012,
	Abstract = {The absence of the optic chiasm is an extraordinary and extreme abnormality in the nervous system. The abnormality produces highly atypical functional responses in the cortex, including overlapping hemifield representations and bilateral population receptive fields in both striate and extrastriate visual cortex. Even in the presence of these large functional abnormalities, the effect on visual perception and daily life is not easily detected. Here, we demonstrate that in two achiasmic humans the gross topography of the geniculostriate and occipital callosal connections remains largely unaltered. We conclude that visual function is preserved by reorganization of intracortical connections instead of large-scale reorganizations of the visual cortex. Thus, developmental mechanisms of local wiring within cortical maps compensate for the improper gross wiring to preserve function in human achiasma.},
	Author = {Hoffmann, Michael B and Kaule, Falko R and Levin, Netta and Masuda, Yoichiro and Kumar, Anil and Gottlob, Irene and Horiguchi, Hiroshi and Dougherty, Robert F and Stadler, Joerg and Wolynski, Barbara and Speck, Oliver and Kanowski, Martin and Liao, Yaping J and Wandell, Brian A and Dumoulin, Serge O},
	Date-Added = {2012-11-02 18:10:29 +0000},
	Date-Modified = {2012-11-02 18:10:29 +0000},
	Doi = {10.1016/j.neuron.2012.05.026},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Mesh = {Humans; Magnetic Resonance Imaging; Neuronal Plasticity; Optic Chiasm; Visual Pathways},
	Month = {Aug},
	Number = {3},
	Pages = {393-401},
	Pmc = {PMC3427398},
	Pmid = {22884323},
	Pst = {ppublish},
	Title = {Plasticity and stability of the visual system in human achiasma},
	Volume = {75},
	Year = {2012},
	File = {papers/Hoffmann_Neuron2012.pdf},
	Bdsk-File-2 = {papers/Hoffmann_Neuron2012a.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.05.026}}

@article{Goddard:2012,
	Abstract = {Gamma-band (25-140 Hz) oscillations are a hallmark of sensory processing in the forebrain. The optic tectum (OT), a midbrain structure implicated in sensorimotor processing and attention, also exhibits gamma oscillations. However, the origin and mechanisms of these oscillations remain unknown. We discovered that in acute slices of the avian OT, persistent (>100 ms) epochs of large amplitude gamma oscillations can be evoked that closely resemble those recorded in vivo. We found that cholinergic, glutamatergic, and GABAergic mechanisms differentially regulate the structure of the oscillations at various timescales. These persistent oscillations originate in the multisensory layers of the OT and are broadcast to visual layers via the cholinergic nucleus Ipc, providing a potential mechanism for enhancing the processing of visual information within the OT. The finding that the midbrain contains an intrinsic gamma-generating circuit suggests that the OT could use its own oscillatory code to route signals to forebrain networks.},
	Author = {Goddard, C Alex and Sridharan, Devarajan and Huguenard, John R and Knudsen, Eric I},
	Date-Added = {2012-11-02 17:58:35 +0000},
	Date-Modified = {2012-11-02 18:00:11 +0000},
	Doi = {10.1016/j.neuron.2011.11.028},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {optic tectum; visual system; Superior Colliculus; barn owl; multimodal; oscillations; synchrony; Attention; visual map;},
	Mesh = {Animals; Animals, Newborn; Atropine; Attention; Biophysics; Brain Mapping; Chickens; Electric Stimulation; Excitatory Amino Acid Antagonists; GABA Antagonists; GABA Modulators; Mesencephalon; Muscarinic Antagonists; Pentobarbital; Periodicity; Photic Stimulation; Picrotoxin; Receptors, Cholinergic; Receptors, GABA; Receptors, N-Methyl-D-Aspartate; Superior Colliculi; Synaptic Potentials; Valine},
	Month = {Feb},
	Number = {3},
	Pages = {567-80},
	Pmc = {PMC3291715},
	Pmid = {22325207},
	Pst = {ppublish},
	Title = {Gamma oscillations are generated locally in an attention-related midbrain network},
	Volume = {73},
	Year = {2012},
	File = {papers/Goddard_Neuron2012.pdf}}

@article{Park:2006,
	Author = {Park, Chan Young and Dolmetsch, Richard},
	Date-Added = {2012-11-02 17:55:42 +0000},
	Date-Modified = {2012-11-02 17:56:48 +0000},
	Doi = {10.1126/science.1133757},
	Journal = {Science},
	Journal-Full = {Science (New York, N.Y.)},
	Keywords = {development; Calcium Signaling/*physiology; review literature; Transcription Factors; toread},
	Mesh = {Calcium; Calcium Channels; Calcium Signaling; Cell Membrane; Cytoplasm; Humans; Phospholipase C gamma; Protein Binding; Protein Structure, Tertiary; TRPC Cation Channels; Transcription Factors, TFII},
	Month = {Oct},
	Number = {5796},
	Pages = {64-5},
	Pmid = {17023638},
	Pst = {ppublish},
	Title = {Cell signaling. The double life of a transcription factor takes it outside the nucleus},
	Volume = {314},
	Year = {2006},
	File = {papers/Park_Science2006.pdf}}

@article{Gomez-Ospina:2006,
	Abstract = {Voltage-gated calcium channels play a central role in regulating the electrical and biochemical properties of neurons and muscle cells. One of the ways in which calcium channels regulate long-lasting neuronal properties is by activating signaling pathways that control gene expression, but the mechanisms that link calcium channels to the nucleus are not well understood. We report that a C-terminal fragment of Ca(V)1.2, an L-type voltage-gated calcium channel (LTC), translocates to the nucleus and regulates transcription. We show that this calcium channel associated transcription regulator (CCAT) binds to a nuclear protein, associates with an endogenous promoter, and regulates the expression of a wide variety of endogenous genes important for neuronal signaling and excitability. The nuclear localization of CCAT is regulated both developmentally and by changes in intracellular calcium. These findings provide evidence that voltage-gated calcium channels can directly activate transcription and suggest a mechanism linking voltage-gated channels to the function and differentiation of excitable cells.},
	Author = {Gomez-Ospina, Natalia and Tsuruta, Fuminori and Barreto-Chang, Odmara and Hu, Linda and Dolmetsch, Ricardo},
	Date-Added = {2012-11-02 17:45:46 +0000},
	Date-Modified = {2012-11-02 17:47:13 +0000},
	Doi = {10.1016/j.cell.2006.10.017},
	Journal = {Cell},
	Journal-Full = {Cell},
	Keywords = {Calcium Channels; Calcium Signaling; Transcription Factors; oscillations; toread; next; development},
	Mesh = {Amino Acid Sequence; Animals; Calcium Channels, L-Type; Cell Culture Techniques; Cell Line; Cells, Cultured; Cerebral Cortex; Dendrites; Fluorescence Recovery After Photobleaching; Genes, Reporter; Humans; Ion Channel Gating; Luciferases; Myocytes, Cardiac; Neurites; Neurons; PC12 Cells; Rats; Rats, Sprague-Dawley; Transcription Factors; Transfection},
	Month = {Nov},
	Number = {3},
	Pages = {591-606},
	Pmc = {PMC1750862},
	Pmid = {17081980},
	Pst = {ppublish},
	Title = {The C terminus of the L-type voltage-gated calcium channel Ca(V)1.2 encodes a transcription factor},
	Volume = {127},
	Year = {2006},
	File = {papers/Gomez-Ospina_Cell2006.pdf},
	Bdsk-File-2 = {papers/Gomez-Ospina_Cell2006a.pdf},
	Bdsk-File-3 = {papers/Gomez-Ospina_Cell2006b.pdf}}

@article{Dolmetsch:1998,
	Abstract = {Cytosolic calcium ([Ca2+]i) oscillations are a nearly universal mode of signalling in excitable and non-excitable cells. Although Ca2+ is known to mediate a diverse array of cell functions, it is not known whether oscillations contribute to the efficiency or specificity of signalling or are merely an inevitable consequence of the feedback control of [Ca2+]i. We have developed a Ca2+ clamp technique to investigate the roles of oscillation amplitude and frequency in regulating gene expression driven by the proinflammatory transcription factors NF-AT, Oct/OAP and NF-kappaB. Here we report that oscillations reduce the effective Ca2+ threshold for activating transcription factors, thereby increasing signal detection at low levels of stimulation. In addition, specificity is encoded by the oscillation frequency: rapid oscillations stimulate all three transcription factors, whereas infrequent oscillations activate only NF-kappaB. The genes encoding the cytokines interleukin (IL)-2 and IL-8 are also frequency-sensitive in a way that reflects their degree of dependence on NF-AT versus NF-kappaB. Our results provide direct evidence that [Ca2+]i oscillations increase both the efficacy and the information content of Ca2+ signals that lead to gene expression and cell differentiation.},
	Author = {Dolmetsch, R E and Xu, K and Lewis, R S},
	Date-Added = {2012-11-02 17:40:26 +0000},
	Date-Modified = {2012-11-02 17:41:21 +0000},
	Doi = {10.1038/31960},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {development; Spontaneous activity; Calcium Channels; Calcium Signaling/*physiology; Transcription Factors; next; toread},
	Mesh = {Calcium; Calcium Channels; Cell Membrane; Cytosol; DNA-Binding Proteins; Gene Expression Regulation; Genes, Reporter; Humans; Interleukin-2; Interleukin-8; Jurkat Cells; NF-kappa B; NFATC Transcription Factors; Nuclear Proteins; Phosphorylation; Signal Transduction; T-Lymphocytes; Transcription Factors; Transfection},
	Month = {Apr},
	Number = {6679},
	Pages = {933-6},
	Pmid = {9582075},
	Pst = {ppublish},
	Title = {Calcium oscillations increase the efficiency and specificity of gene expression},
	Volume = {392},
	Year = {1998},
	File = {papers/Dolmetsch_Nature1998.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/31960}}

@article{Barreto-Chang:2009,
	Abstract = {Calcium imaging is a common technique that is useful for measuring calcium signals in cultured cells. Calcium imaging techniques take advantage of calcium indicator dyes, which are BAPTA-based organic molecules that change their spectral properties in response to the binding of Ca2+ ions. Calcium indicator dyes fall into two categories, ratio-metric dyes like Fura-2 and Indo-1 and single-wavelength dyes like Fluo-4. Ratio-metric dyes change either their excitation or their emission spectra in response to calcium, allowing the concentration of intracellular calcium to be determined from the ratio of fluorescence emission or excitation at distinct wavelengths. The main advantage of using ratio-metric dyes over single wavelength probes is that the ratio signal is independent of the dye concentration, illumination intensity, and optical path length allowing the concentration of intracellular calcium to be determined independently of these artifacts. One of the most common calcium indicators is Fura-2, which has an emission peak at 505 nM and changes its excitation peak from 340 nm to 380 nm in response to calcium binding. Here we describe the use of Fura-2 to measure intracellular calcium elevations in neurons and other excitable cells.},
	Author = {Barreto-Chang, Odmara L and Dolmetsch, Ricardo E},
	Date-Added = {2012-11-02 17:38:20 +0000},
	Date-Modified = {2012-11-02 17:39:02 +0000},
	Doi = {10.3791/1067},
	Journal = {J Vis Exp},
	Journal-Full = {Journal of visualized experiments : JoVE},
	Keywords = {optical physiology; imaging; Technique; review literature; calcium imaging;},
	Mesh = {Calcium; Calcium Signaling; Cerebral Cortex; Fluorescent Dyes; Fura-2; Microscopy, Fluorescence; Neurons},
	Number = {23},
	Pmc = {PMC2763293},
	Pmid = {19229178},
	Pst = {epublish},
	Title = {Calcium imaging of cortical neurons using Fura-2 AM},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.3791/1067}}

@article{Rana:2010,
	Abstract = {Understanding the complexity of neuronal biology requires the manipulation of cellular processes with high specificity and spatio-temporal precision. The recent development of synthetic photo-activatable proteins designed using the light-oxygen-voltage and phytochrome domains provides a new set of tools for genetically targeted optical control of cell signaling. Their modular design, functional diversity, precisely controlled activity and in vivo applicability offer many advantages for investigating neuronal function. Although designing these proteins is still a considerable challenge, future advances in rational protein design and a deeper understanding of their photoactivation mechanisms will allow the development of the next generation of optogenetic techniques.},
	Author = {Rana, Anshul and Dolmetsch, Ricardo E},
	Date-Added = {2012-11-02 17:37:05 +0000},
	Date-Modified = {2012-11-02 17:38:06 +0000},
	Doi = {10.1016/j.conb.2010.08.018},
	Journal = {Curr Opin Neurobiol},
	Journal-Full = {Current opinion in neurobiology},
	Keywords = {optical physiology; imaging; gene; Technique; review literature; toread; activity manipulation;},
	Mesh = {Animals; Gene Targeting; Humans; Luminescent Proteins; Neurons; Photochemistry; Rhodopsins, Microbial; Signal Transduction; Staining and Labeling},
	Month = {Oct},
	Number = {5},
	Pages = {617-22},
	Pmc = {PMC2993759},
	Pmid = {20850295},
	Pst = {ppublish},
	Title = {Using light to control signaling cascades in live neurons},
	Volume = {20},
	Year = {2010},
	File = {papers/Rana_CurrOpinNeurobiol2010.pdf}}

@article{Ackman:2012,
	Abstract = {The morphological and functional development of the vertebrate nervous system is initially governed by genetic factors and subsequently refined by neuronal activity. However, fundamental features of the nervous system emerge before sensory experience is possible. Thus, activity-dependent development occurring before the onset of experience must be driven by spontaneous activity, but the origin and nature of activity in vivo remains largely untested. Here we use optical methods to show in live neonatal mice that waves of spontaneous retinal activity are present and propagate throughout the entire visual system before eye opening. This patterned activity encompassed the visual field, relied on cholinergic neurotransmission, preferentially initiated in the binocular retina and exhibited spatiotemporal correlations between the two hemispheres. Retinal waves were the primary source of activity in the midbrain and primary visual cortex, but only modulated ongoing activity in secondary visual areas. Thus, spontaneous retinal activity is transmitted through the entire visual system and carries patterned information capable of guiding the activity-dependent development of complex intra- and inter-hemispheric circuits before the onset of vision.},
	Author = {Ackman, James B and Burbridge, Timothy J and Crair, Michael C},
	Date-Added = {2012-10-25 13:10:07 +0000},
	Date-Modified = {2013-05-21 19:47:22 +0000},
	Doi = {10.1038/nature11529},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {Spontaneous activity; Retina; Visual Cortex; visual system; Superior Colliculus; optic tectum; optical imaging; optical physiology; calcium imaging; multiphoton; development; Neocortex; mirror symmetry; currOpinRvw},
	Month = {Oct},
	Number = {7419},
	Pages = {219-25},
	Pmc = {PMC3962269},
	Pmid = {23060192},
	Pst = {ppublish},
	Title = {Retinal waves coordinate patterned activity throughout the developing visual system},
	Volume = {490},
	Year = {2012},
	File = {papers/Ackman_Nature2012.pdf},
	Bdsk-File-2 = {papers/Ackman_Nature2012a.pdf}}

@article{Just:2007,
	Abstract = {The brain activation of a group of high-functioning autistic participants was measured using functional magnetic resonance imaging during the performance of a Tower of London task, in comparison with a control group matched with respect to intelligent quotient, age, and gender. The 2 groups generally activated the same cortical areas to similar degrees. However, there were 3 indications of underconnectivity in the group with autism. First, the degree of synchronization (i.e., the functional connectivity or the correlation of the time series of the activation) between the frontal and parietal areas of activation was lower for the autistic than the control participants. Second, relevant parts of the corpus callosum, through which many of the bilaterally activated cortical areas communicate, were smaller in cross-sectional area in the autistic participants. Third, within the autism group but not within the control group, the size of the genu of the corpus callosum was correlated with frontal-parietal functional connectivity. These findings suggest that the neural basis of altered cognition in autism entails a lower degree of integration of information across certain cortical areas resulting from reduced intracortical connectivity. The results add support to a new theory of cortical underconnectivity in autism, which posits a deficit in integration of information at the neural and cognitive levels.},
	Author = {Just, Marcel Adam and Cherkassky, Vladimir L and Keller, Timothy A and Kana, Rajesh K and Minshew, Nancy J},
	Date-Added = {2012-10-14 04:29:25 +0000},
	Date-Modified = {2012-10-14 04:30:01 +0000},
	Doi = {10.1093/cercor/bhl006},
	Journal = {Cereb Cortex},
	Journal-Full = {Cerebral cortex (New York, N.Y. : 1991)},
	Keywords = {autism; Autistic Disorder; connectivity; default mode network; human; fMRI},
	Mesh = {Adult; Autistic Disorder; Brain Mapping; Cerebral Cortex; Cognition; Corpus Callosum; Female; Humans; Magnetic Resonance Imaging; Male; Neural Pathways},
	Month = {Apr},
	Number = {4},
	Pages = {951-61},
	Pmid = {16772313},
	Pst = {ppublish},
	Title = {Functional and anatomical cortical underconnectivity in autism: evidence from an FMRI study of an executive function task and corpus callosum morphometry},
	Volume = {17},
	Year = {2007},
	File = {papers/Just_CerebCortex2007.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/cercor/bhl006}}

@article{Demonet:2004,
	Abstract = {Developmental dyslexia, or specific reading disability, is a disorder in which children with normal intelligence and sensory abilities show learning deficits for reading. Substantial evidence has established its biological origin and the preponderance of phonological disorders even though important phenotypic variability and comorbidity have been recorded. Diverse theories have been proposed to account for the cognitive and neurological aspects of dyslexia. Findings of genetic studies show that different loci affect specific reading disability although a direct relation has not been established between symptoms and a given genomic locus. In both children and adults with dyslexia, results of neuroimaging studies suggest defective activity and abnormal connectivity between regions crucial for language functions--eg, the left fusiform gyrus for reading--and changes in brain activity associated with performance improvement after various remedial interventions.},
	Author = {D{\'e}monet, Jean-Fran{\c c}ois and Taylor, Margot J and Chaix, Yves},
	Date-Added = {2012-10-13 21:46:13 +0000},
	Date-Modified = {2012-10-13 21:46:39 +0000},
	Doi = {10.1016/S0140-6736(04)16106-0},
	Journal = {Lancet},
	Journal-Full = {Lancet},
	Keywords = {Dyslexia; neurological disorder; human; connectivity; Neocortex; Cerebral Cortex},
	Mesh = {Adult; Brain Mapping; Child; Dyslexia; Humans; Reading},
	Month = {May},
	Number = {9419},
	Pages = {1451-60},
	Pmid = {15121410},
	Pst = {ppublish},
	Title = {Developmental dyslexia},
	Volume = {363},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0140-6736(04)16106-0}}

@article{Egaas:1995,
	Abstract = {OBJECTIVE: To determine via magnetic resonance imaging if the posterior corpus callosum is reduced in the midline cross-sectional area in autistic patients, consistent with previous reports of parietal lobe abnormalities.
DESIGN: Case-control study.
SETTING: Tertiary care facility.
PATIENTS AND OTHER PARTICIPANTS: Fifty-one autistic patients (45 males and six females; age range, 3 to 42 years), including both mentally retarded and nonretarded patients who met several diagnostic criteria for autism were prospectively selected. Fifty-one age-and sex-matched volunteer normal control subjects were also included.
INTERVENTION: None.
MAIN OUTCOME MEASURES: Computer-aided measurement of cross-sectional area, areas of five subregions, and thickness profile.
RESULTS: Overall size reduction, concentrated in posterior subregions.
CONCLUSIONS: Evidence is found of a reduced size of the corpus callosum in autistic patients. This reduction is localized to posterior regions, where parietal lobe fibers are known to project. This finding further supports the idea that parietal lobe involvement may be a consistent feature in autism.},
	Author = {Egaas, B and Courchesne, E and Saitoh, O},
	Date-Added = {2012-10-13 21:43:18 +0000},
	Date-Modified = {2012-10-13 21:44:01 +0000},
	Journal = {Arch Neurol},
	Journal-Full = {Archives of neurology},
	Keywords = {Autistic Disorder; autism; Cerebral Cortex; Neocortex; connectivity; human},
	Mesh = {Adolescent; Adult; Autistic Disorder; Cerebral Cortex; Child; Child, Preschool; Corpus Callosum; Female; Humans; Magnetic Resonance Imaging; Male},
	Month = {Aug},
	Number = {8},
	Pages = {794-801},
	Pmid = {7639631},
	Pst = {ppublish},
	Title = {Reduced size of corpus callosum in autism},
	Volume = {52},
	Year = {1995},
	File = {papers/Egaas_ArchNeurol1995.pdf}}

@article{Castelli:2002,
	Abstract = {Ten able adults with autism or Asperger syndrome and 10 normal volunteers were PET scanned while watching animated sequences. The animations depicted two triangles moving about on a screen in three different conditions: moving randomly, moving in a goal-directed fashion (chasing, fighting), and moving interactively with implied intentions (coaxing, tricking). The last condition frequently elicited descriptions in terms of mental states that viewers attributed to the triangles (mentalizing). The autism group gave fewer and less accurate descriptions of these latter animations, but equally accurate descriptions of the other animations compared with controls. While viewing animations that elicited mentalizing, in contrast to randomly moving shapes, the normal group showed increased activation in a previously identified mentalizing network (medial prefrontal cortex, superior temporal sulcus at the temporo-parietal junction and temporal poles). The autism group showed less activation than the normal group in all these regions. However, one additional region, extrastriate cortex, which was highly active when watching animations that elicited mentalizing, showed the same amount of increased activation in both groups. In the autism group this extrastriate region showed reduced functional connectivity with the superior temporal sulcus at the temporo-parietal junction, an area associated with the processing of biological motion as well as with mentalizing. This finding suggests a physiological cause for the mentalizing dysfunction in autism: a bottleneck in the interaction between higher order and lower order perceptual processes.},
	Author = {Castelli, Fulvia and Frith, Chris and Happ{\'e}, Francesca and Frith, Uta},
	Date-Added = {2012-10-13 21:43:16 +0000},
	Date-Modified = {2012-10-13 21:44:10 +0000},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {Autistic Disorder; autism; Cerebral Cortex; Neocortex; connectivity; human},
	Mesh = {Adult; Asperger Syndrome; Autistic Disorder; Brain; Brain Mapping; Educational Status; Humans; Magnetic Resonance Imaging; Mental Status Schedule; Organ Specificity; Speech; Tomography, Emission-Computed},
	Month = {Aug},
	Number = {Pt 8},
	Pages = {1839-49},
	Pmid = {12135974},
	Pst = {ppublish},
	Title = {Autism, Asperger syndrome and brain mechanisms for the attribution of mental states to animated shapes},
	Volume = {125},
	Year = {2002}}

@article{Pignatelli:2009,
	Abstract = {A significant fraction of the interneurons added in adulthood to the glomerular layer (GL) of the olfactory bulb (OB) are dopaminergic (DA). In the OB, DA neurons are restricted to the GL, but using transgenic mice expressing eGFP under the tyrosine hydroxylase (TH) promoter, we also detected the presence of TH-GFP+ cells in the mitral and external plexiform layers. We hypothesized that these could be adult-generated neurons committed to become DA but not yet entirely differentiated. Accordingly, TH-GFP+ cells outside the GL exhibit functional properties (appearance of pacemaker currents, synaptic connection with the olfactory nerve, intracellular chloride concentration, and other) marking a gradient of maturity toward the dopaminergic phenotype along the mitral-glomerular axis. Finally, we propose that the establishment of a synaptic contact with the olfactory nerve is the key event allowing these cells to complete their differentiation toward the DA phenotype and to reach their final destination.},
	Author = {Pignatelli, Angela and Ackman, James B and Vigetti, Davide and Beltrami, Antonio P and Zucchini, Silvia and Belluzzi, Ottorino},
	Date-Added = {2012-10-02 20:56:24 +0000},
	Date-Modified = {2012-10-02 20:56:24 +0000},
	Doi = {10.1007/s00424-008-0535-0},
	Journal = {Pflugers Arch},
	Journal-Full = {Pfl{\"u}gers Archiv : European journal of physiology},
	Mesh = {Action Potentials; Animals; Chlorides; Dopamine; Eye Proteins; Homeodomain Proteins; Mice; Mice, Transgenic; Neurons; Olfactory Bulb; Paired Box Transcription Factors; Patch-Clamp Techniques; Receptors, Glutamate; Recombinant Fusion Proteins; Repressor Proteins; Tyrosine 3-Monooxygenase},
	Month = {Feb},
	Number = {4},
	Pages = {899-915},
	Pmid = {19011893},
	Pst = {ppublish},
	Title = {A potential reservoir of immature dopaminergic replacement neurons in the adult mammalian olfactory bulb},
	Volume = {457},
	Year = {2009},
	File = {papers/Pignatelli_PflugersArch2009.pdf}}

@article{Wei:2012,
	Abstract = {Neural activity-induced long-term potentiation (LTP) of synaptic transmission is believed to be one of the cellular mechanisms underlying experience-dependent developmental refinement of neural circuits. Although it is well established that visual experience and neural activity are critical for the refinement of retinal circuits, whether and how LTP occurs in the retina remain unknown. Using in vivo perforated whole-cell recording and two-photon calcium imaging, we find that both repeated electrical and visual stimulations can induce LTP at excitatory synapses formed by bipolar cells on retinal ganglion cells in larval but not juvenile zebrafish. LTP induction requires the activation of postsynaptic N-methyl-D-aspartate receptors, and its expression involves arachidonic acid-dependent presynaptic changes in calcium dynamics and neurotransmitter release. Physiologically, both electrical and visual stimulation-induced LTP can enhance visual responses of retinal ganglion cells. Thus, LTP exists in developing retinae with a presynaptic locus and may serve for visual experience-dependent refinement of retinal circuits.},
	Author = {Wei, Hong-Ping and Yao, Yuan-Yuan and Zhang, Rong-Wei and Zhao, Xiao-Feng and Du, Jiu-Lin},
	Date-Added = {2012-09-04 18:21:22 +0000},
	Date-Modified = {2012-09-04 18:23:36 +0000},
	Doi = {10.1016/j.neuron.2012.05.031},
	Journal = {Neuron},
	Journal-Full = {Neuron},
	Keywords = {Long-Term Potentiation; synapse formation; activity manipulation; Zebrafish; in vivo; Synaptic Transmission; 21 Activity-development; calcium imaging; Patch-Clamp Techniques; N-Methyl-D-Aspartate; NMDA; plasticity},
	Month = {Aug},
	Number = {3},
	Pages = {479-89},
	Pmid = {22884331},
	Pst = {ppublish},
	Title = {Activity-induced long-term potentiation of excitatory synapses in developing zebrafish retina in vivo},
	Volume = {75},
	Year = {2012},
	File = {papers/Wei_Neuron2012.pdf},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuron.2012.05.031}}

@article{Hansel:2012,
	Abstract = {Neurons in primary visual cortex (V1) display substantial orientation selectivity even in species where V1 lacks an orientation map, such as in mice and rats. The mechanism underlying orientation selectivity in V1 with such a salt-and-pepper organization is unknown; it is unclear whether a connectivity that depends on feature similarity is required, or a random connectivity suffices. Here we argue for the latter. We study the response to a drifting grating of a network model of layer 2/3 with random recurrent connectivity and feedforward input from layer 4 neurons with random preferred orientations. We show that even though the total feedforward and total recurrent excitatory and inhibitory inputs all have a very weak orientation selectivity, strong selectivity emerges in the neuronal spike responses if the network operates in the balanced excitation/inhibition regime. This is because in this regime the (large) untuned components in the excitatory and inhibitory contributions approximately cancel. As a result the untuned part of the input into a neuron as well as its modulation with orientation and time all have a size comparable to the neuronal threshold. However, the tuning of the F0 and F1 components of the input are uncorrelated and the high-frequency fluctuations are not tuned. This is reflected in the subthreshold voltage response. Remarkably, due to the nonlinear voltage-firing rate transfer function, the preferred orientation of the F0 and F1 components of the spike response are highly correlated.},
	Author = {Hansel, David and van Vreeswijk, Carl},
	Date-Added = {2012-09-04 18:17:35 +0000},
	Date-Modified = {2012-09-04 18:19:51 +0000},
	Doi = {10.1523/JNEUROSCI.6284-11.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {visual system; visual cortex; Neocortex; mouse; rat; Orientation; topographic map; sensory map; function; self organization; oscillations; Neurophysiology; extracellular; Models; Theoretical; Computational Biology; connectivity},
	Mesh = {Action Potentials; Algorithms; Animals; Biophysical Processes; Computer Simulation; Excitatory Postsynaptic Potentials; Models, Neurological; Nerve Net; Neural Inhibition; Neurons; Nonlinear Dynamics; Orientation; Visual Cortex; Visual Pathways},
	Month = {Mar},
	Number = {12},
	Pages = {4049-64},
	Pmid = {22442071},
	Pst = {ppublish},
	Title = {The mechanism of orientation selectivity in primary visual cortex without a functional map},
	Volume = {32},
	Year = {2012},
	File = {papers/Hansel_JNeurosci2012.pdf}}

@article{Triplett:2012,
	Abstract = {The superior colliculus (SC) is a midbrain structure that integrates visual, somatosensory, and auditory inputs to direct head and eye movements. Each of these modalities is topographically mapped and aligned with the others to ensure precise behavioral responses to multimodal stimuli. While it is clear that neural activity is instructive for topographic alignment of inputs from the visual cortex (V1) and auditory system with retinal axons in the SC, there is also evidence that activity-independent mechanisms are used to establish topographic alignment between modalities. Here, we show that the topography of the projection from primary somatosensory cortex (S1) to the SC is established during the first postnatal week. Unlike V1-SC projections, the S1-SC projection does not bifurcate when confronted with a duplicated retinocollicular map, showing that retinal input in the SC does not influence the topography of the S1-SC projection. However, S1-SC topography is disrupted in mice lacking ephrin-As, which we find are expressed in graded patterns along with their binding partners, the EphA4 and EphA7, in both S1 and the somatosensory recipient layer of the SC. Together, these data support a model in which somatosensory inputs into the SC map topographically and establish alignment with visual inputs in the SC using a gradient-matching mechanism.},
	Author = {Triplett, Jason W and Phan, An and Yamada, Jena and Feldheim, David A},
	Date-Added = {2012-09-04 18:13:53 +0000},
	Date-Modified = {2012-09-04 18:17:25 +0000},
	Doi = {10.1523/JNEUROSCI.0240-12.2012},
	Journal = {J Neurosci},
	Journal-Full = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	Keywords = {retinal waves; Spontaneous activity; Superior Colliculus; optic tectum; function; topographic map; sensory map; Somatosensory Cortex; activity manipulation; Gene Expression; Eph Family; Ephrin-A4; multimodal; Mouse; 21 Activity-development; synapse formation; development; 21 Activity-development; visual system; retina},
	Mesh = {Animals; Axons; Brain Mapping; Ephrins; Female; Image Processing, Computer-Assisted; In Situ Hybridization; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Mice, Transgenic; Microscopy, Fluorescence; Motor Cortex; Sensation; Somatosensory Cortex; Superior Colliculi; Visual Cortex; Visual Pathways},
	Month = {Apr},
	Number = {15},
	Pages = {5264-71},
	Pmc = {PMC3342701},
	Pmid = {22496572},
	Pst = {ppublish},
	Title = {Alignment of multimodal sensory input in the superior colliculus through a gradient-matching mechanism},
	Volume = {32},
	Year = {2012},
	File = {papers/Triplett_JNeurosci2012.pdf}}

@article{Gutknecht:2012,
	Abstract = {Brain serotonin (5-HT) is implicated in a wide range of functions from basic physiological mechanisms to complex behaviors, including neuropsychiatric conditions, as well as in developmental processes. Increasing evidence links 5-HT signaling alterations during development to emotional dysregulation and psychopathology in adult age. To further analyze the importance of brain 5-HT in somatic and brain development and function, and more specifically differentiation and specification of the serotonergic system itself, we generated a mouse model with brain-specific 5-HT deficiency resulting from a genetically driven constitutive inactivation of neuronal tryptophan hydroxylase-2 (Tph2). Tph2 inactivation (Tph2-/-) resulted in brain 5-HT deficiency leading to growth retardation and persistent leanness, whereas a sex- and age-dependent increase in body weight was observed in Tph2+/- mice. The conserved expression pattern of the 5-HT neuron-specific markers (except Tph2 and 5-HT) demonstrates that brain 5-HT synthesis is not a prerequisite for the proliferation, differentiation and survival of raphe neurons subjected to the developmental program of serotonergic specification. Furthermore, although these neurons are unable to synthesize 5-HT from the precursor tryptophan, they still display electrophysiological properties characteristic of 5-HT neurons. Moreover, 5-HT deficiency induces an up-regulation of 5-HT(1A) and 5-HT(1B) receptors across brain regions as well as a reduction of norepinephrine concentrations accompanied by a reduced number of noradrenergic neurons. Together, our results characterize developmental, neurochemical, neurobiological and electrophysiological consequences of brain-specific 5-HT deficiency, reveal a dual dose-dependent role of 5-HT in body weight regulation and show that differentiation of serotonergic neuron phenotype is independent from endogenous 5-HT synthesis.},
	Author = {Gutknecht, Lise and Araragi, Naozumi and Merker, S{\"o}ren and Waider, Jonas and Sommerlandt, Frank M J and Mlinar, Boris and Baccini, Gilda and Mayer, Ute and Proft, Florian and Hamon, Michel and Schmitt, Angelika G and Corradetti, Renato and Lanfumey, Laurence and Lesch, Klaus-Peter},
	Date-Added = {2012-08-31 21:14:38 +0000},
	Date-Modified = {2012-08-31 21:14:43 +0000},
	Doi = {10.1371/journal.pone.0043157},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {autism; Autistic Disorder; Serotonin; mouse; mice; development;},
	Number = {8},
	Pages = {e43157},
	Pmc = {PMC3422228},
	Pmid = {22912815},
	Pst = {ppublish},
	Title = {Impacts of Brain Serotonin Deficiency following Tph2 Inactivation on Development and Raphe Neuron Serotonergic Specification},
	Volume = {7},
	Year = {2012},
	File = {papers/Gutknecht_PLoSOne2012.pdf}}

@article{Farook:2012,
	Abstract = {Childhood neurodevelopmental disorders like Angelman syndrome and autism may be the result of underlying defects in neuronal plasticity and ongoing problems with synaptic signaling. Some of these defects may be due to abnormal monoamine levels in different regions of the brain. Ube3a, a gene that causes Angelman syndrome (AS) when maternally deleted and is associated with autism when maternally duplicated has recently been shown to regulate monoamine synthesis in the Drosophila brain. Therefore, we examined monoamine levels in striatum, ventral midbrain, frontal cerebral cortex, cerebellar cortex and hippocampus in Ube3a deficient and Ube3a duplication animals. We found that serotonin (5HT), a monoamine affected in autism, was elevated in the striatum and cortex of AS mice. Dopamine levels were almost uniformly elevated compared to control littermates in the striatum, midbrain and frontal cortex regardless of genotype in Ube3a deficient and Ube3a duplication animals. In the duplication 15q autism mouse model, paternal but not maternal duplication animals showed a decrease in 5HT levels when compared to their wild type littermates, in accordance with previously published data. However, maternal duplication animals show no significant changes in 5HT levels throughout the brain. These abnormal monoamine levels could be responsible for many of the behavioral abnormalities observed in both AS and autism, but further investigation is required to determine if any of these changes are purely dependent on Ube3a levels in the brain.},
	Author = {Farook, M Febin and Decuypere, Michael and Hyland, Keith and Takumi, Toru and Ledoux, Mark S and Reiter, Lawrence T},
	Date-Added = {2012-08-31 21:13:17 +0000},
	Date-Modified = {2012-08-31 21:14:05 +0000},
	Doi = {10.1371/journal.pone.0043030},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {autism; Autistic Disorder; Serotonin; mouse; mice; development;},
	Number = {8},
	Pages = {e43030},
	Pmc = {PMC3420863},
	Pmid = {22916201},
	Pst = {ppublish},
	Title = {Altered serotonin, dopamine and norepinepherine levels in 15q duplication and angelman syndrome mouse models},
	Volume = {7},
	Year = {2012},
	File = {papers/Farook_PLoSOne2012.pdf}}

@article{Ye:2012,
	Abstract = {BACKGROUND: Cross-modal plasticity is characterized as the hypersensitivity of remaining modalities after a sensory function is lost in rodents, which ensures their awareness to environmental changes. Cellular and molecular mechanisms underlying cross-modal sensory plasticity remain unclear. We aim to study the role of different types of neurons in cross-modal plasticity.
METHODOLOGY/PRINCIPAL FINDINGS: In addition to behavioral tasks in mice, whole-cell recordings at the excitatory and inhibitory neurons, and their two-photon imaging, were conducted in piriform cortex. We produced a mouse model of cross-modal sensory plasticity that olfactory function was upregulated by trimming whiskers to deprive their sensory inputs. In the meantime of olfactory hypersensitivity, pyramidal neurons and excitatory synapses were functionally upregulated, as well as GABAergic cells and inhibitory synapses were downregulated in piriform cortex from the mice of cross-modal sensory plasticity, compared with controls. A crosswire connection between barrel cortex and piriform cortex was established in cross-modal plasticity.
CONCLUSION/SIGNIFICANCE: An upregulation of pyramidal neurons and a downregulation of GABAergic neurons strengthen the activities of neuronal networks in piriform cortex, which may be responsible for olfactory hypersensitivity after a loss of whisker tactile input. This finding provides the clues for developing therapeutic strategies to promote sensory recovery and substitution.},
	Author = {Ye, Bing and Huang, Li and Gao, Zilong and Chen, Ping and Ni, Hong and Guan, Sudong and Zhu, Yan and Wang, Jin-Hui},
	Date-Added = {2012-08-31 21:02:04 +0000},
	Date-Modified = {2012-08-31 21:06:00 +0000},
	Doi = {10.1371/journal.pone.0041986},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {optical physiology; optical imaging; calcium imaging; Patch-Clamp Techniques; Neurophysiology; multimodal; Sensory Deprivation; sensory map; Somatosensory Cortex; piriform cortex; Neocortex; GABA; interneurons; mice; Mouse; in vitro},
	Number = {8},
	Pages = {e41986},
	Pmc = {PMC3424151},
	Pmid = {22927919},
	Pst = {ppublish},
	Title = {The functional upregulation of piriform cortex is associated with cross-modal plasticity in loss of whisker tactile inputs},
	Volume = {7},
	Year = {2012},
	File = {papers/Ye_PLoSOne2012.pdf}}

@article{Stetter:2012,
	Abstract = {A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically infeasible, even in simpler systems like dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct structural connectivity from network activity monitored through calcium imaging. We focus in this study on the inference of excitatory synaptic links. Based on information theory, our method requires no prior assumptions on the statistics of neuronal firing and neuronal connections. The performance of our algorithm is benchmarked on surrogate time series of calcium fluorescence generated by the simulated dynamics of a network with known ground-truth topology. We find that the functional network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (bursting or non-bursting). Thus by conditioning with respect to the global mean activity, we improve the performance of our method. This allows us to focus the analysis to specific dynamical regimes of the network in which the inferred functional connectivity is shaped by monosynaptic excitatory connections, rather than by collective synchrony. Our method can discriminate between actual causal influences between neurons and spurious non-causal correlations due to light scattering artifacts, which inherently affect the quality of fluorescence imaging. Compared to other reconstruction strategies such as cross-correlation or Granger Causality methods, our method based on improved Transfer Entropy is remarkably more accurate. In particular, it provides a good estimation of the excitatory network clustering coefficient, allowing for discrimination between weakly and strongly clustered topologies. Finally, we demonstrate the applicability of our method to analyses of real recordings of in vitro disinhibited cortical cultures where we suggest that excitatory connections are characterized by an elevated level of clustering compared to a random graph (although not extreme) and can be markedly non-local.},
	Author = {Stetter, Olav and Battaglia, Demian and Soriano, Jordi and Geisel, Theo},
	Date-Added = {2012-08-31 20:59:59 +0000},
	Date-Modified = {2012-08-31 21:01:15 +0000},
	Doi = {10.1371/journal.pcbi.1002653},
	Journal = {PLoS Comput Biol},
	Journal-Full = {PLoS computational biology},
	Keywords = {graph theory; Theoretical; Computational Biology; Methods; optical imaging; Neurophysiology; calcium imaging; Statistics; Mathematics; network},
	Month = {Aug},
	Number = {8},
	Pages = {e1002653},
	Pmc = {PMC3426566},
	Pmid = {22927808},
	Pst = {ppublish},
	Title = {Model-free reconstruction of excitatory neuronal connectivity from calcium imaging signals},
	Volume = {8},
	Year = {2012},
	File = {papers/Stetter_PLoSComputBiol2012.pdf}}

@article{Carver:2012,
	Abstract = {Examining real-time cortical dynamics is crucial for understanding time perception. Using magnetoencephalography we studied auditory duration discrimination of short (<.5 s) versus long tones (>.5 s) versus a pitch control. Time-frequency analysis of event-related fields showed widespread beta-band (13-30 Hz) desynchronization during all tone presentations. Synthetic aperture magnetometry indicated automatic primarily sensorimotor responses in short and pitch conditions, with activation specific to timing in bilateral inferior frontal gyrus. In the long condition, a right lateralized network was active, including lateral prefrontal cortices, inferior frontal gyrus, supramarginal gyrus and secondary auditory areas. Activation in this network peaked just after attention to tone duration was no longer necessary, suggesting a role in sustaining representation of the interval. These data expand our understanding of time perception by revealing its complex cortical spatiotemporal signature.},
	Author = {Carver, Frederick W and Elvev{\aa}g, Brita and Altamura, Mario and Weinberger, Daniel R and Coppola, Richard},
	Date-Added = {2012-08-31 20:58:06 +0000},
	Date-Modified = {2012-08-31 20:59:48 +0000},
	Doi = {10.1371/journal.pone.0042618},
	Journal = {PLoS One},
	Journal-Full = {PloS one},
	Keywords = {entrainment; 21 Cortical oscillations; 21 Neurophysiology; Theoretical; Stimulation; Perception; Cognition; MEG; Auditory Cortex},
	Number = {8},
	Pages = {e42618},
	Pmc = {PMC3422225},
	Pmid = {22912714},
	Pst = {ppublish},
	Title = {The neuromagnetic dynamics of time perception},
	Volume = {7},
	Year = {2012},
	File = {papers/Carver_PLoSOne2012.pdf}}

@article{Kozorovitskiy:2012,
	Abstract = {Neural activity during development critically shapes postnatal wiring of the mammalian brain. This is best illustrated by the sensory systems, in which the patterned feed-forward excitation provided by sensory organs and experience drives the formation of mature topographic circuits capable of extracting specific features of sensory stimuli. In contrast, little is known about the role of early activity in the development of the basal ganglia, a phylogenetically ancient group of nuclei fundamentally important for complex motor action and reward-based learning. These nuclei lack direct sensory input and are only loosely topographically organized, forming interlocking feed-forward and feed-back inhibitory circuits without laminar structure. Here we use transgenic mice and viral gene transfer methods to modulate neurotransmitter release and neuronal activity in vivo in the developing striatum. We find that the balance of activity between the two inhibitory and antagonist pathways in the striatum regulates excitatory innervation of the basal ganglia during development. These effects indicate that the propagation of activity through a multi-stage network regulates the wiring of the basal ganglia, revealing an important role of positive feedback in driving network maturation.},
	Author = {Kozorovitskiy, Yevgenia and Saunders, Arpiar and Johnson, Caroline A and Lowell, Bradford B and Sabatini, Bernardo L},
	Date-Added = {2012-08-28 14:21:04 +0000},
	Date-Modified = {2012-08-28 14:29:10 +0000},
	Doi = {10.1038/nature11052},
	Journal = {Nature},
	Journal-Full = {Nature},
	Keywords = {activity manipulation; 21 Activity-development; 21 Neurophysiology; striatum; Basal Ganglia; mouse; Patch-Clamp Techniques; synapse formation; gaba; interneurons;},
	Mesh = {Animals; Basal Ganglia; Cerebral Cortex; Feedback, Physiological; Female; Male; Mice; Mice, Transgenic; Models, Neurological; Neostriatum; Neural Inhibition; Neural Pathways; Synapses; Thalamus; Vesicular Inhibitory Amino Acid Transport Proteins; gamma-Aminobutyric Acid},
	Month = {May},
	Number = {7400},
	Pages = {646-50},
	Pmc = {PMC3367801},
	Pmid = {22660328},
	Pst = {epublish},
	Title = {Recurrent network activity drives striatal synaptogenesis},
	Volume = {485},
	Year = {2012},
	File = {papers/Kozorovitskiy_Nature2012.pdf},
	Bdsk-File-2 = {papers/Kozorovitskiy_Nature2012a.pdf}}

@article{Geschwind:1965,
	Author = {Geschwind, N},
	Date-Added = {2012-08-27 16:34:58 +0000},
	Date-Modified = {2012-08-27 16:39:03 +0000},
	Journal = {Brain},
	Journal-Full = {Brain : a journal of neurology},
	Keywords = {neurological disorder; Cognitive neuroscience; human; connectivity; review; Anatomy; mirror symmetry; mirror neuron; sensory-motor; Neocortex; Cerebral Cortex; Agnosia; aphasia; topographic map; multimodal; Association Learning/physiology},
	Mesh = {Agnosia; Animals; Brain; Humans},
	Month = {Jun},
	Number = {2},
	Pages = {237-94},
	Pmid = {5318481},
	Pst = {ppublish},
	Title = {Disconnexion syndromes in animals and man. I},
	Volume = {88},
	Year = {1965},
	File = {papers/Geschwind_Brain1965.pdf}}

