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Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010

BMC Bioinformatics 2010年第SUPPL. 4期11卷 I1-I1页

作者： Rouchka, Eric C. Flight, Robert M. Rinehart, Claire Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 United States Neuroscience Training Program University of Louisville Louisville KY 40292 United States Department of Biology Western Kentucky University Bowling Green KY 42101 United States

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Where-what networks for motor invariance without any internal master map

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BMC neuroscience 2010年第1期11卷 1-2页

作者： Juyang Weng Matthew D Luciw Department of Computer Science and Engineering Michigan State University East Lansing MI 48824 USA Cognitive Science Program Michigan State University East Lansing MI 48824 USA Neuroscience Program Michigan State University East Lansing MI 48824 USA

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Characterization of the retinal proteome during rod photoreceptor genesis

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BMC Research Notes 2010年第1期3卷 1-8页

作者： Barnhill, Alison E Hecker, Laura A Kohutyuk, Oksana Buss, Janice E Honavar, Vasant G Greenlee, Heather West Interdepartmental Neuroscience Program Iowa State University Ames IA United States Department of Biomedical Sciences Iowa State University Ames IA United States Bioinformatics and Computational Biology Program Iowa State University Ames IA United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA United States Department of Computer Science Iowa State University Ames IA United States National Animal Disease Center Ames IA 50010 United States Mayo Clinic Department of Ophthalmology Rochester MN 55905 United States

Background. The process of rod photoreceptor genesis, cell fate determination and differentiation is complex and multi-factorial. Previous studies have defined a model of photoreceptor differentiation that relies on intrinsic changes within the presumptive photoreceptor cells as well as changes in surrounding tissue that are extrinsic to the cell. We have used a proteomics approach to identify proteins that are dynamically expressed in the mouse retina during rod genesis and differentiation. Findings. A series of six developmental ages from E13 to P5 were used to define changes in retinal protein expression during rod photoreceptor genesis and early differentiation. Retinal proteins were separated by isoelectric focus point and molecular weight. Gels were analyzed for changes in protein spot intensity across developmental time. Protein spots that peaked in expression at E17, P0 and P5 were picked from gels for identification. There were 239 spots that were picked for identification based on their dynamic expression during the developmental period of maximal rod photoreceptor genesis and differentiation. Of the 239 spots, 60 of them were reliably identified and represented a single protein. Ten proteins were represented by multiple spots, suggesting they were post-translationally modified. Of the 42 unique dynamically expressed proteins identified, 16 had been previously reported to be associated with the developing retina. Conclusions. Our results represent the first proteomics study of the developing mouse retina that includes prenatal development. We identified 26 dynamically expressed proteins in the developing mouse retina whose expression had not been previously associated with retinal development. © 2010 Greenlee et al.;licensee BioMed Central Ltd.

关键词： Protein Spot Mouse Retina Retinal Development Retinal Protein Probability Base Mowse Score

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Decoder remapping to counteract neuron loss in brain-machine interfaces

Decoder remapping to counteract neuron loss in brain-machine...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Rodolphe Heliot Subramaniam Venkatraman Jose M. Carmena CEA LETI MINATEC France Department of Electrical Engineering and Computer Sciences University of California Berkeley CA USA QUALCOMM Inc.orporated USA Department of Electrical Engineering and Computer Sciences Helen Wills Neuroscience Institute and Program in Cognitive Science University of California Berkeley CA USA

Variability of single-unit neural recordings can significantly affect the overall performance achieved by brain machine interfaces (BMI). In this paper, we present a novel technique to adapt a linear filter commonly used in BMI to compensate for loss of neurons from the recorded neural ensemble, thus minimizing loss in performance. We simulate the gains achieved by this technique using a model of the learning process during closed-loop BMI operation. This simulation suggests that we can adapt to the loss of 24% of the neurons controlling a BMI with only 13% drop in performance.

关键词： Neurons Decoding Firing Wiener filter Brain modeling Maximum likelihood detection Nonlinear filters

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A neuromorphic head direction cell system

A neuromorphic head direction cell system

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： Tarek M. Massoud Timothy K. Horiuchi Electrical and Computer Engineering Department Institute of Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

ISBN: (纸本)9781424438273

The head direction (HD) cell system in the brain of mammals is thought to be part of the neural circuitry supporting their spatial navigation capabilities. In this paper we present a neuromorphic VLSI system that mimics the operation of the HD system. Relying on spiking neurons and attractor dynamics, this system can be used to represent and retain the current estimate of head orientation in the environment and integrate angular velocity to update this estimate. The presented system is a first step towards more general odometry systems that could be used for modeling biological navigation systems.

关键词： Neuromorphics Neurons High definition video Navigation Very large scale integration Biological system modeling Brain neuroscience Cognitive science Educational institutions

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Biomimetic evolutionary analysis: Robotically-simulated vertebrates in a predator-prey ecology

Biomimetic evolutionary analysis: Robotically-simulated vert...

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IEEE Symposium on Artificial Life, ALIFE

作者： Nicole Doorly Kira Irving Gianna McArthur Keon Combie Virginia Engel Hassan Sakhtah Elise Stickles Hannah Rosenblum Andres Gutierrez Robert Root Chun Wai Liew John H. Long Mechanical and Aerospace Engineering Department Case Western Reserve University Cleveland OH USA Interdisciplinary Robotics Research Laboratory and the Cognitive Science Program Vassar College Poughkeepsie NY USA Neuroscience Institute Stanford University School of Medicine Stanford CA USA Neuroscience and Behavior Program Vassar College Poughkeepsie NY USA Memorial Sloan Kettering Cancer Care Center New York NY USA Department of Biology Vassar College Poughkeepsie NY USA Biochemistry Program Vassar College Poughkeepsie NY USA College of Medicine Howard University College of Medicine Washington D.C. USA School of Oceanography University of Washington Seattle WA USA Vassar College Poughkeepsie NY USA Department of Mathematics Lafayette College Easton PA USA Computer Science Department Lafayette College Easton PA USA Interdisciplinary Robotics Research Laboratory the Department of Biology and the Cognitive Science Program Vassar College Poughkeepsie NY USA

To test adaptation hypotheses about the evolution of animals, we need information about the behavior of phenotypically-variable individuals in a specific environment. To model behavior of ancient fish-like vertebrates, we previously combined evolutionary robotics and software simulations to create autonomous biomimetic swimmers in a simple aquatic environment competing and foraging for a single source of food. This system allowed us to test the hypothesis that selection for improved forage navigation drove the evolution of stiffer tails. In this paper, we extend our framework to evaluate more complex environments and hypotheses. Specifically, we test the hypothesis that predator-prey dynamics and the need for effective foraging strategies, operating simultaneously, were key selection pressures driving the evolution of morphological and sensory traits in early, fish-like vertebrates. Three evolvable traits were chosen because of their importance in propulsion and predator avoidance: (1) the number of vertebrae in the axial skeleton, (2) the trailing edge span of the caudal fin, and (3) the sensitivity of the sensory lateral line. To produce variable offspring, we used a genetic algorithm that rewarded parents with high fitness, allowing them to mate randomly and combine their mutated gametes. Offspring were then instantiated as autonomous embodied robots, the prey. These prey were chased by a non-evolving autonomous predator. Both kinds of robots were surface swimmers. The prey used a control architecture based on that of living fish: a two-layer subsumption architecture with predator escape over-riding steady swimming during foraging. The performance of six different prey robots in each generation was judged with a relative fitness function that rewarded a combination of high speed, rapid escape acceleration, escape responses, and the ability to stay away from the predator while at the same time staying close to the food source. This approach, which we call biomimet

关键词： Biomimetics Environmental factors Biological system modeling System testing Evolution (biology) Robot sensing systems Animals Navigation Tail Propulsion

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Circuit sharing and the implementation of intelligent systems

Circuit sharing and the implementation of intelligent system...

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2008 AAAI Fall Symposium

作者： Anderson, Michael L. Department of Psychology Franklin and Marshall College Lancaster PA United States Institute for Advanced Computer Studies Neuroscience and Cognitive Science Program University of Maryland College Park MD 20742 United States

ISBN: (纸本)9781577353966

A foundational and highly contested question in cognitive science is whether and to what degree the brain is a modular system. This talk outlines some of the broad architectural implications of the modularity thesis, and reports on an attempt to test for them. The results indicate that the same brain regions contribute to functions across various cognitive domains, but in each domain cooperate with one another in different patterns. This does not appear to be compatible with the modularity thesis. The talk discusses the implications of the finding for the best approach to analyzing, modeling and reproducing cognitive functions in intelligent systems. Copyright © 2008, Association for the Advancement of Artificial Intelligence.

关键词： Intelligent systems

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Spike-based acoustic signal processing chips for detection and localization

Spike-based acoustic signal processing chips for detection a...

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IEEE Biomedical Circuits and Systems (BIOCAS)

作者： Hisham Abdalla Timothy K. Horiuchi Electrical and Computer Engineering Department Institute for Systems Research University of Maryland College Park MD USA Electrical and Computer Engineering Department Institute for Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

Voltage spikes are ubiquitous in biological nervous systems. How spikes can be used to encode signals, facilitate communication, and implement important computations is an important question of contemporary neuroscience. Acoustic processing tasks provide a rich range of applications for this encoding scheme. As a summary of the Ph.D. research of the first author, we present two analog VLSI spike-based example systems that process acoustic information using spikes: a model of the neural signal processing involved in bat echolocation, and a low-power, time-domain acoustic periodicity detector.

关键词： Acoustic signal processing Acoustic signal detection Voltage Biological information theory Nervous system Biology computing Pervasive computing neuroscience Acoustic applications Encoding

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Binaural Spectral Cues for Ultrasonic Localization

Binaural Spectral Cues for Ultrasonic Localization

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2008 IEEE International Symposium on Circuits and Systems (ISCAS 2008), vol.6

作者： Hisham Abdalla Timothy K Horiuchi Electrical and Computer Engineering Department Institute for systems research University of Maryland College Park MD USA Electrical and Computer Engineering dept Insitute for Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

To support our ongoing work in modeling bat echolocation, an artificial bat head was designed and fabricated using a 3D printer, an ultrasonic cochlea-like filter bank with 16 channels was designed with moderate quality (Q) factor, and 128 spiking neurons convert these signals to spike trains. A two-dimensional address-event arbiter is used to transmit these spikes off of the chip. We demonstrate that the population of spiking neurons can be decoded to estimate azimuth and elevation of ultrasonic chirps. This chip was fabricated in a commercially-available 0.5(mu)m CMOS process and consumes approximately 36(mu)W.

关键词： Hafnium

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An information theoretic framework for eukaryotic gradient sensing 19

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20th Annual Conference on Neural Information Processing Systems, NIPS 2006

作者： Kimmel, Joseph M. Salter, Richard M. Thomas, Peter J. Computer Science Program Oberlin College Oberlin OH 44074 United States Department of Mathematics Biology and Cognitive Science Case Western Reserve University Cleveland OH 44106 United States Computational Neuroscience Graduate Program University of Chicago United States Center for Computation and Modeling United States

ISBN: (纸本)9780262195683

Chemical reaction networks by which individual cells gather and process information about their chemical environments have been dubbed "signal transduction" networks. Despite this suggestive terminology, there have been few attempts to analyze chemical signaling systems with the quantitative tools of information theory. Gradient sensing in the social amoeba Dictyostelium discoideum is a well characterized signal transduction system in which a cell estimates the direction of a source of diffusing chemoattractant molecules based on the spatiotemporal sequence of ligand-receptor binding events at the cell membrane. Using Monte Carlo techniques (MCell) we construct a simulation in which a collection of individual ligand particles undergoing Brownian diffusion in a three-dimensional volume interact with receptors on the surface of a static amoeboid cell. Adapting a method for estimation of spike train entropies described by Victor (originally due to Kozachenko and Leonenko), we estimate lower bounds on the mutual information between the transmitted signal (direction of ligand source) and the received signal (spatiotemporal pattern of receptor binding/unbinding events). Hence we provide a quantitative framework for addressing the question: how much could the cell know, and when could it know it? We show that the time course of the mutual information between the cell's surface receptors and the (unknown) gradient direction is consistent with experimentally measured cellular response times. We find that the acquisition of directional information depends strongly on the time constant at which the intracellular response is filtered.

关键词： Ligands

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