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Volume 17 Issue 11, November 2014

Neuroscientists have to learn to manage and take advantage of the big waves of data that are being generated. In this special issue on big data, we present a series of Commentaries, Perspectives and Reviews by leading experts on the collection, management, analysis and utility of large data sets in neuroscience.1440–1517


  • Nature Neuroscience presents a special focus issue highlighting big data efforts under way in the field.



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News & Views

  • Fruit flies seek water, but only when they are thirsty. And imbibing is rewarding only to water-deprived individuals. The effects of thirst on water seeking and on formation of associative memories of drinking water each are mediated by distinct sets of dopamine neurons that innervate restricted zones of the mushroom bodies in the fly brain.

    • Meng-Fu Maxwell Shih
    • Josh Dubnau
    News & Views
  • A study finds evidence supporting co-release of glutamate and GABA, excitatory and inhibitory fast neurotransmitters, from a single axon terminal in neurons of the ventral tegmental area that project to the lateral habenula.

    • Naoshige Uchida
    News & Views
  • Cortical neurons reduce spiking responses to repetitive sensory stimulation, but the perceptual impact of this adaptation has been difficult to assess. Work now shows that it has profound consequences for tactile perception.

    • Hongdian Yang
    • Daniel H O'Connor
    News & Views
  • Retrosplenial cortex neurons provide a signal akin to a compass readout. Evidence in humans now demonstrates that these neurons anchor their representations locally, locking to the geometry of a room rather than to the city beyond.

    • Martin J Chadwick
    • Hugo J Spiers
    News & Views
  • Jeremy Bentham distilled animal behavior as avoiding pain and seeking pleasure. Now, using a combination of different methodological approaches, Roy et al. identify a neural mechanism relevant for learning to avoid pain.

    • Falk Eippert
    • Irene Tracey
    News & Views
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  • Neuroscience is poised to collect Big Data sets. In this Commentary, the authors argue that, to exploit its full potential, there need to be ways to standardize, integrate and synthesize diverse types of data and that this will require a cultural shift to a central role for theorists in neuroscience research.

    • Terrence J Sejnowski
    • Patricia S Churchland
    • J Anthony Movshon
  • In this Commentary, Martone and colleagues discuss the potential benefits of sharing small datasets, also called “long-tail” data, in the Neuroscience community. They introduce the pros and cons associated with data sharing, describe the existing attitudes toward such initiative, introduce best practices and offer their views on why and how the field should establish a credit system for sharing “long-tail” data.

    • Adam R Ferguson
    • Jessica L Nielson
    • Maryann E Martone
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  • Due to recent technological developments in acquisition techniques, the field of electron microscopy-based connectomics now produces colossal amounts of data. Here, the authors discuss the practical and analytical challenges associated with such large amounts of data and propose some solutions to surmount them.

    • Jeff W Lichtman
    • Hanspeter Pfister
    • Nir Shavit
  • In this Perspective, the authors discuss the recent surge in the collection of "big behavioral data" and how it might contribute to the understanding of how the brain controls behavior. They also highlight the challenges of making sense of increasing amounts of behavioral data.

    • Alex Gomez-Marin
    • Joseph J Paton
    • Zachary F Mainen
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Review Article

  • This article reviews various next-generation sequencing (NGS) technologies and how they may be applied to the studies of the central nervous system. Specifically, the authors summarize practical information about when and how NGS may be applied to the studies of brain function, highlighting pros and cons of each technique for the unique challenges of studying a mixed population of targets.

    • Jaehoon Shin
    • Guo-li Ming
    • Hongjun Song
    Review Article
  • In this review, the authors discuss the applications of epigenomics approaches to studies of the CNS and critique the tools available to analyze neuroepigenomics data. They also assess the challenges of integrating these data with that of other approaches, such as transcriptomics, proteomics and behavior.

    • Ian Maze
    • Li Shen
    • Eric J Nestler
    Review Article
  • A full understanding of the biology and function of the numerous cell types that comprise the nervous system requires analysis of their transcriptional and translational profiles. In this Review article, the authors discuss the methods for overcoming the challenges that accompany the collection of large proteomic datasets and their integration with other data modalities.

    • Robert R Kitchen
    • Joel S Rozowsky
    • Angus C Nairn
    Review Article
  • Many recent studies have adopted dimensionality reduction to analyze neural population activity and to find features that are not apparent at the level of individual neurons. The authors describe the scientific motivation for population analyses and the dimensionality reduction methods commonly applied to population activity. They also offer practical advice about selecting methods and interpreting their outputs.

    • John P Cunningham
    • Byron M Yu
    Review Article
  • Neuroimagers have collected large datasets and many of these are now available online. In this review the authors discuss the current state of sharing task-based fMRI data and the many challenges it poses.

    • Russell A Poldrack
    • Krzysztof J Gorgolewski
    Review Article
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  • Oligodendrocyte precursor cells (OPCs) retain their proliferative/differentiation capacity throughout life. This study uses in vivo and ex vivo imaging to show a specific temporal window between OPC division and oligodendrocyte differentiation in the postnatal mouse brain that is modulated by the microenvironment. The latency between OPC division and differentiation is shortened by myelin damage, while sensory deprivation reduces the survival of divided OPCs undergoing differentiation.

    • Robert A Hill
    • Kiran D Patel
    • Akiko Nishiyama
  • Radial glial progenitors (RGPs) in the developing mouse cortex generate excitatory neurons during development. This study examines the role of centriole-related protein Sas4, the mutation of which causes microcephaly in human brain, and shows that centrosome and centriole act to anchor RGPs in the ventricular zone during embryonic neurogenesis. By preventing cell death of RGPs without centrioles, the study also shows that cleavage plane orientation of cell division is not essential for radial glial progenitors' self-renewal.

    • Ryan Insolera
    • Hisham Bazzi
    • Song-Hai Shi
  • Using the Drosophila system, this study shows that rewarding and motivational properties of water are mediated by different subsets of dopaminergic neurons. The study also shows a satiety state–dependent effect in which thirst can change water avoidance behavior into water-seeking behavior and demonstrates that water wanting versus liking versus learning are separable at the level of behavior and the underlying neural circuit.

    • Suewei Lin
    • David Owald
    • Scott Waddell
  • The ventral tegmental area (VTA) and lateral habenula (LHb) are reciprocally connected. Here the authors show, using electron microscopy, tract tracing and optogenetics in rodents, that the majority of VTA neurons innervating LHb release both GABA and glutamate at the same synaptic terminals.

    • David H Root
    • Carlos A Mejias-Aponte
    • Marisela Morales
  • This study describes the segregated neural representations at single cell level and in whole brain when mice are presented with positive and negative emotional stimuli given in succession. Using a newly developed technique called tyramide-amplified-immunohistochemistry–fluorescence in situ hybridization (TAI-FISH) to label multiple neuronal populations, the authors demonstrate specific overlap and divergence of neuronal activation pattern to different emotional stimuli.

    • Jianbo Xiu
    • Qi Zhang
    • Hailan Hu
  • The authors devised a new behavioral task to study cooling perception in head-fixed mice. Using whole-cell recordings from layer 2/3 neurons in the somatosensory cortex, they reveal that the same neurons that respond to mechanical stimulation of the skin also respond to its cooling. In addition, they find that both the perception of cooling and the cooling responses in S1 are eliminated in TRPM8 knockout mice.

    • Nevena Milenkovic
    • Wen-Jie Zhao
    • James F A Poulet
  • During adaptation, neocortical responses change as a result of repeated sensory stimulation, but it's unclear how this affects perception. Here the authors use optogenetics to mimic sensory evoked cortical responses with or without adaptation. They find adaptation impairs frequency discrimination but enhances change detection during whisker stimulation.

    • Simon Musall
    • Wolfger von der Behrens
    • Florent Haiss
  • Using in vivo recording of neuronal activities in rat secondary motor cortex and devising a novel task of waiting before performing an action, Murakami et al. show a neural correlate of voluntary action initiation. The study also shows population activity and computational modeling data that correspond to action timing of voluntary action that are consistent with integration-to-bound theories of decision making.

    • Masayoshi Murakami
    • M Inês Vicente
    • Zachary F Mainen
  • Neurofibromatosis type 1 (NF1) is associated with social dysfunction in children. Here the authors show that Nf1 heterozygous mice have deficits in social memory associated with alterations in amygdala plasticity and Map kinase signaling. Global deletion or amygdala-specific pharmacological inhibition of Pak1 rescued social deficits in Nf1 heterozygous mice.

    • Andrei I Molosh
    • Philip L Johnson
    • Anantha Shekhar
  • This recording study shows that attention can increase or decrease correlations between fluctuations in the responses of pairs of neurons, depending on task demands. These results suggest that attention can flexibly modulate such spike count correlations, independent of changes in firing rate and provide constraints on possible neuronal mechanisms.

    • Douglas A Ruff
    • Marlene R Cohen
  • Although head direction cells are known to encode information related to an organism's heading, it is unclear how the brain integrates this with information provided by fixed environmental features. In this study, the authors show that the retrosplenial complex is important for encoding heading and facing direction based on local landmarks and that this process generalizes across different environments that have similar geometry.

    • Steven A Marchette
    • Lindsay K Vass
    • Russell A Epstein
  • This study uses fMRI in humans to find that prediction errors about pain are encoded in the periaqueductal gray. Modeling inter-area connectivity suggests that the ventromedial prefrontal cortex and the putamen pass on a value-related signal to this midbrain structure, which then conveys predictor error signals to prefrontal regions that regulate behavior.

    • Mathieu Roy
    • Daphna Shohamy
    • Tor D Wager
  • This study uses a combination of human fMRI and computational modeling to show that decision-making can be explained by a hierarchical model involving competition between different options at many different levels of representation. These results do not support a model where competition happens only at a final choice stage.

    • Laurence T Hunt
    • Raymond J Dolan
    • Timothy E J Behrens
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  • Big data projects in the neurosciences have been increasing in number in recent years. Nature Neurosciencepresents a collection of Reviews, Perspectives and Commentaries that discuss different kinds of big data in neuroscience, from epigenomics to connectomics and whole-brain activity recordings to big behavioral data. The authors of these pieces tackle tough questions that have come to the forefront during this era of big data, including whether big data will completely change the way neuroscience is done, how much insight will be gained from big data, and what are the best ways to go about conducting such projects.

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