Olfactory Coding in the Insect Brain: Molecular Receptive Ranges, Spatial and Temporal Coding
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Neural Coding and the Statistical Modeling of Neuronal Responses By
Neural coding and the statistical modeling of neuronal responses by Jonathan Pillow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Center for Neural Science New York University Jan 2005 Eero P. Simoncelli TABLE OF CONTENTS LIST OF FIGURES v INTRODUCTION 1 1 Characterization of macaque retinal ganglion cell responses using spike-triggered covariance 5 1.1NeuralCharacterization.................... 9 1.2One-DimensionalModelsandtheSTA............ 12 1.3Multi-DimensionalModelsandSTCAnalysis........ 16 1.4 Separability and Subspace STC ................ 21 1.5 Subunit model . ....................... 23 1.6ModelValidation........................ 25 1.7Methods............................. 28 2 Estimation of a Deterministic IF model 37 2.1Leakyintegrate-and-firemodel................. 40 2.2Simulationresultsandcomparison............... 41 ii 2.3Recoveringthelinearkernel.................. 42 2.4Recoveringakernelfromneuraldata............. 44 2.5Discussion............................ 46 3 Estimation of a Stochastic, Recurrent IF model 48 3.1TheModel............................ 52 3.2TheEstimationProblem.................... 54 3.3ComputationalMethodsandNumericalResults....... 57 3.4TimeRescaling......................... 60 3.5Extensions............................ 61 3.5.1 Interneuronalinteractions............... 62 3.5.2 Nonlinear input ..................... 63 3.6Discussion............................ 64 AppendixA:ProofofLog-ConcavityofModelLikelihood..... 65 AppendixB:ComputingtheLikelihoodGradient........ -
Neural Oscillations As a Signature of Efficient Coding in the Presence of Synaptic Delays Matthew Chalk1*, Boris Gutkin2,3, Sophie Dene` Ve2
RESEARCH ARTICLE Neural oscillations as a signature of efficient coding in the presence of synaptic delays Matthew Chalk1*, Boris Gutkin2,3, Sophie Dene` ve2 1Institute of Science and Technology Austria, Klosterneuburg, Austria; 2E´ cole Normale Supe´rieure, Paris, France; 3Center for Cognition and Decision Making, National Research University Higher School of Economics, Moscow, Russia Abstract Cortical networks exhibit ’global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ’prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code. DOI: 10.7554/eLife.13824.001 *For correspondence: Introduction [email protected] Oscillations are a prominent feature of cortical activity. In sensory areas, one typically observes Competing interests: The ’global oscillations’ in the gamma-band range (30–80 Hz), alongside single neuron responses that authors declare that no are irregular and sparse (Buzsa´ki and Wang, 2012; Yu and Ferster, 2010). -
Local Field Potential Decoding of the Onset and Intensity of Acute Pain In
www.nature.com/scientificreports OPEN Local feld potential decoding of the onset and intensity of acute pain in rats Received: 25 January 2018 Qiaosheng Zhang1, Zhengdong Xiao2,3, Conan Huang1, Sile Hu2,3, Prathamesh Kulkarni1,3, Accepted: 8 May 2018 Erik Martinez1, Ai Phuong Tong1, Arpan Garg1, Haocheng Zhou1, Zhe Chen 3,4 & Jing Wang1,4 Published: xx xx xxxx Pain is a complex sensory and afective experience. The current defnition for pain relies on verbal reports in clinical settings and behavioral assays in animal models. These defnitions can be subjective and do not take into consideration signals in the neural system. Local feld potentials (LFPs) represent summed electrical currents from multiple neurons in a defned brain area. Although single neuronal spike activity has been shown to modulate the acute pain, it is not yet clear how ensemble activities in the form of LFPs can be used to decode the precise timing and intensity of pain. The anterior cingulate cortex (ACC) is known to play a role in the afective-aversive component of pain in human and animal studies. Few studies, however, have examined how neural activities in the ACC can be used to interpret or predict acute noxious inputs. Here, we recorded in vivo extracellular activity in the ACC from freely behaving rats after stimulus with non-noxious, low-intensity noxious, and high-intensity noxious stimuli, both in the absence and chronic pain. Using a supervised machine learning classifer with selected LFP features, we predicted the intensity and the onset of acute nociceptive signals with high degree of precision. -
The Effect of Sensory Processing on the Work Performance of Call Centre Agents in a South African Context
The effect of sensory processing on the work performance of call centre agents in a South African context Annemarie Lombard Student Number: ARCANN002 e Town ap y of C SUBMITTED TO THE UNIVERSITY OF CAPE TOWN Department of Health & Rehabilitation Sciences In fulfilmentUniversit of the requirements for the degree of Doctor of Philosophy in Occupational Therapy February 2012 Supervisor: Emeritus Associate Professor R. Watson Co-supervisor: Associate Professor M. Duncan Department of Health & Rehabilitation Sciences The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the University ofof Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University Declaration I, Annemarie Lombard, hereby declare that the work on which this dissertation/thesis is based is my original work (except where acknowledgements indicate otherwise), and that neither the whole work nor any part of it has been, is being, or is to be submitted for another degree at this or any other university. I empower the university to reproduce for the purpose of research either the whole or any portion of the contents in any manner whatsoever. Signature: e Town ap Date: 25th May 2012 y of C Universit Introduction Page i Acknowledgements This study was an epic journey made possible by the support of so many people to whom I am forever grateful: To God, our Heavenly Father who gave me the dream, allowed me the journey, and continues to give me the strength and courage to follow it. -
An Optogenetic Approach to Understanding the Neural Circuits of Fear Joshua P
Controlling the Elements: An Optogenetic Approach to Understanding the Neural Circuits of Fear Joshua P. Johansen, Steffen B.E. Wolff, Andreas Lüthi, and Joseph E. LeDoux Neural circuits underlie our ability to interact in the world and to learn adaptively from experience. Understanding neural circuits and how circuit structure gives rise to neural firing patterns or computations is fundamental to our understanding of human experience and behavior. Fear conditioning is a powerful model system in which to study neural circuits and information processing and relate them to learning and behavior. Until recently, technological limitations have made it difficult to study the causal role of specific circuit elements during fear conditioning. However, newly developed optogenetic tools allow researchers to manipulate individual circuit components such as anatom- ically or molecularly defined cell populations, with high temporal precision. Applying these tools to the study of fear conditioning to control specific neural subpopulations in the fear circuit will facilitate a causal analysis of the role of these circuit elements in fear learning and memory. By combining this approach with in vivo electrophysiological recordings in awake, behaving animals, it will also be possible to determine the functional contribution of specific cell populations to neural processing in the fear circuit. As a result, the application of optogenetics to fear conditioning could shed light on how specific circuit elements contribute to neural coding and to fear learning and memory. Furthermore, this approach may reveal general rules for how circuit structure and neural coding within circuits gives rise to sensory experience and behavior. Key Words: Electrophysiology, fear conditioning, learning and circuits and the identification of sites of neural plasticity in these memory, neural circuits, neural plasticity, optogenetics circuits. -
Identification of Human Gustatory Cortex by Activation Likelihood Estimation
r Human Brain Mapping 32:2256–2266 (2011) r Identification of Human Gustatory Cortex by Activation Likelihood Estimation Maria G. Veldhuizen,1,2 Jessica Albrecht,3 Christina Zelano,4 Sanne Boesveldt,3 Paul Breslin,3,5 and Johan N. Lundstro¨m3,6,7* 1Affective Sensory Neuroscience, John B. Pierce Laboratory, New Haven, Connecticut 2Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 3Monell Chemical Senses Center, Philadelphia, Pennsylvania 4Department of Neurology, Northwestern University, Chicago, Illinois 5Department of Nutritional Sciences, Rutgers University School of Environmental and Biological Sciences, New Brunswick, New Jersey 6Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania 7Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden r r Abstract: Over the last two decades, neuroimaging methods have identified a variety of taste-responsive brain regions. Their precise location, however, remains in dispute. For example, taste stimulation activates areas throughout the insula and overlying operculum, but identification of subregions has been inconsistent. Furthermore, literature reviews and summaries of gustatory brain activations tend to reiterate rather than resolve this ambiguity. Here, we used a new meta-analytic method [activation likelihood estimation (ALE)] to obtain a probability map of the location of gustatory brain activation across 15 studies. The map of activa- tion likelihood values can also serve as a source of independent coordinates for future region-of-interest anal- yses. We observed significant cortical activation probabilities in: bilateral anterior insula and overlying frontal operculum, bilateral mid dorsal insula and overlying Rolandic operculum, and bilateral posterior insula/parietal operculum/postcentral gyrus, left lateral orbitofrontal cortex (OFC), right medial OFC, pre- genual anterior cingulate cortex (prACC) and right mediodorsal thalamus. -
6 Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans
Mario de Bono, William R. Schafer, Alexander Gottschalk 6 Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans 6.1 Introduction – the nematode as a genetic model in systems neurosciencesystems neuroscience Elucidating the mechanisms by which nervous systems process information and gen- erate behavior is among the fundamental problems of biology. The complexity of our brain and plasticity of our behaviors make it challenging to understand even simple human actions in terms of molecular mechanisms and neural activity. However the molecular machines and operational features of our neural circuits are often found in invertebrates, so that studying flies and worms provides an effective way to gain insights into our nervous system. Caenorhabditis elegans offers special opportunities to study behavior. Each of the 302 neurons in its nervous system can be identified and imaged in live animals [1, 2], and manipulated transgenically using specific promoters or promoter combinations [3, 4, 5, 6]. The chemical synapses and gap junctions made by every neuron are known from electron micrograph reconstruction [1]. Importantly, forward genetics can be used to identify molecules that modulate C. elegans’ behavior. Forward genetic dis- section of behavior is powerful because it requires no prior knowledge. It allows mol- ecules to be identified regardless of in vivo concentration, and focuses attention on genes that are functionally important. The identity and expression patterns of these molecules then provide entry points to study the molecular mechanisms and neural circuits controlling the behavior. Genetics does not provide the temporal resolution required to study neural circuit function directly. -
Decoding Odor Quality and Intensity in the Drosophila Brain
RESEARCH ARTICLE elifesciences.org Decoding odor quality and intensity in the Drosophila brain Antonia Strutz1, Jan Soelter2, Amelie Baschwitz1, Abu Farhan1, Veit Grabe1, Jürgen Rybak1, Markus Knaden1, Michael Schmuker2†, Bill S Hansson1, Silke Sachse1* 1Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany; 2Department for Biology, Pharmacy and Chemistry, Free University Berlin, Neuroinformatics and Theoretical Neuroscience, Berlin, Germany Abstract To internally reflect the sensory environment, animals create neural maps encoding the external stimulus space. From that primary neural code relevant information has to be extracted for accurate navigation. We analyzed how different odor features such as hedonic valence and intensity are functionally integrated in the lateral horn (LH) of the vinegar fly, Drosophila melanogaster. We characterized an olfactory-processing pathway, comprised of inhibitory projection neurons (iPNs) that target the LH exclusively, at morphological, functional and behavioral levels. We demonstrate that iPNs are subdivided into two morphological groups encoding positive hedonic valence or intensity information and conveying these features into separate domains in the LH. Silencing iPNs severely diminished flies' attraction behavior. Moreover, functional imaging disclosed a LH region tuned to repulsive odors comprised exclusively of third-order neurons. We provide evidence for a feature-based map in the LH, and elucidate its role as the center for integrating behaviorally relevant olfactory information. DOI: 10.7554/eLife.04147.001 *For correspondence: ssachse@ ice.mpg.de Present address: †School of Introduction Engineering and Informatics, To navigate the environment in a way that optimizes their survival and reproduction, animals have University of Sussex, Brighton, evolved sensory systems. These have three essential tasks: First, the external world has to be trans- United Kingdom lated into an internal representation in the form of an accurate neural map. -
Exploring the Function of Neural Oscillations in Early Sensory Systems
FOCUSED REVIEW published: 15 May 2010 doi: 10.3389/neuro.01.010.2010 Exploring the function of neural oscillations in early sensory systems Kilian Koepsell1*, Xin Wang 2, Judith A. Hirsch 2 and Friedrich T. Sommer1* 1 Redwood Center for Theoretical Neuroscience, University of California, Berkeley, CA, USA 2 Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA Neuronal oscillations appear throughout the nervous system, in structures as diverse as the cerebral cortex, hippocampus, subcortical nuclei and sense organs. Whether neural rhythms contribute to normal function, are merely epiphenomena, or even interfere with physiological processing are topics of vigorous debate. Sensory pathways are ideal for investigation of oscillatory activity because their inputs can be defined. Thus, we will focus on sensory systems Edited by: S. Murray Sherman, as we ask how neural oscillations arise and how they might encode information about the University of Chicago, USA stimulus. We will highlight recent work in the early visual pathway that shows how oscillations Reviewed by: can multiplex different types of signals to increase the amount of information that spike trains Michael J. Friedlander, Baylor College of Medicine, USA encode and transmit. Last, we will describe oscillation-based models of visual processing and Jose-Manuel Alonso, Sociedad Espanola explore how they might guide further research. de Neurociencia, Spain; University of Connecticut, USA; State University Keywords: LGN, retina, visual coding, oscillations, multiplexing of New York, USA Naoum P. Issa, University of Chicago, USA NEURAL OSCILLATIONS IN EARLY However, the autocorrelograms are subject to *Correspondence: SENSORY SYSTEMS confounds caused by the refractory period and Oscillatory neural activity has been observed spectral peaks often fail to reveal weak rhythms. -
Localized Olfactory Representation in Mushroom Bodies of Drosophila Larvae
Localized olfactory representation in mushroom bodies of Drosophila larvae Liria M. Masuda-Nakagawaa,1, Nanae¨ Gendreb, Cahir J. O’Kanec, and Reinhard F. Stockerb aInstitute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan; bDepartment of Biology, University of Fribourg, Chemin du Muse´e 10, CH-1700 Fribourg, Switzerland; and cDepartment of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, United Kingdom Edited by Obaid Siddiqi, Tata Institute for Fundamental Research, Bangalore, India, and approved May 4, 2009 (received for review January 7, 2009) Odor discrimination in higher brain centers is essential for behav- of spatial stereotypy of odor representations in PNs in the calyx ioral responses to odors. One such center is the mushroom body has not yet been functionally defined, and the complexity of the (MB) of insects, which is required for odor discrimination learning. adult calyx makes it difficult to visualize the representation of The calyx of the MB receives olfactory input from projection odor qualities in single identified cells. neurons (PNs) that are targets of olfactory sensory neurons (OSNs) Drosophila larvae, which can perceive a wide variety of odors in the antennal lobe (AL). In the calyx, olfactory information is (14) and perform odor discrimination learning (15, 16), have an transformed from broadly-tuned representations in PNs to sparse olfactory system with the same basic architecture as adults but representations in MB neurons (Kenyon cells). However, the extent numerically much simpler. It contains only 21 unique OSNs (17), of stereotypy in olfactory representations in the calyx is unknown. -
Cortical Feedback and Gating in Olfactory Pattern Completion and Separation
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.05.370494; this version posted November 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Cortical feedback and gating in olfactory pattern completion and separation Gaia Tavonia,b,1,2, David E. Chen Kersena,c,1, and Vijay Balasubramaniana,b,c aComputational Neuroscience Initiative; bDepartment of Physics and Astronomy; cDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 A central question in neuroscience is how context changes percep- reflect coordination between the OB and cortical areas during tion of sensory stimuli. In the olfactory system, for example, exper- learning. However, the precise mechanism by which centrifu- iments show that task demands can drive merging and separation gal feedback to the OB can effect change in cortical odor of cortical odor responses, which underpin olfactory generalization representation remains unclear. and discrimination. Here, we propose a simple statistical mecha- Interestingly, the structural organization of these feedfor- nism for this effect, based on unstructured feedback from the cen- ward and feedback projections is highly disordered. MC/TCs tral brain to the olfactory bulb, representing the context associated project to the cortex in an apparently random fashion (22, 56– with an odor, and sufficiently selective cortical gating of sensory in- 58), while centrifugal feedback fibers are distributed dif- puts. Strikingly, the model predicts that both pattern separation and fusely over the OB without any discernible spatial segregation completion should increase when odors are initially more similar, an (25, 30). -
A Resource for the Drosophila Antennal Lobe Provided by The
TOOLS AND RESOURCES A resource for the Drosophila antennal lobe provided by the connectome of glomerulus VA1v Jane Anne Horne1, Carlie Langille1, Sari McLin1, Meagan Wiederman1, Zhiyuan Lu1,2, C Shan Xu2, Stephen M Plaza2, Louis K Scheffer2, Harald F Hess2, Ian A Meinertzhagen1,2* 1Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, Canada; 2Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States Abstract Using FIB-SEM we report the entire synaptic connectome of glomerulus VA1v of the right antennal lobe in Drosophila melanogaster. Within the glomerulus we densely reconstructed all neurons, including hitherto elusive local interneurons. The fruitless-positive, sexually dimorphic VA1v included >11,140 presynaptic sites with ~38,050 postsynaptic dendrites. These connected input olfactory receptor neurons (ORNs, 51 ipsilateral, 56 contralateral), output projection neurons (18 PNs), and local interneurons (56 of >150 previously reported LNs). ORNs are predominantly presynaptic and PNs predominantly postsynaptic; newly reported LN circuits are largely an equal mixture and confer extensive synaptic reciprocity, except the newly reported LN2V with input from ORNs and outputs mostly to monoglomerular PNs, however. PNs were more numerous than previously reported from genetic screens, suggesting that the latter failed to reach saturation. We report a matrix of 192 bodies each having >50 connections; these form 88% of the glomerulus’ pre/postsynaptic sites. DOI: https://doi.org/10.7554/eLife.37550.001 *For correspondence: [email protected] Competing interests: The Introduction authors declare that no A striking convergence in advanced brains has endowed those structures of the brains in insects and competing interests exist.