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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 University of Maryland College Park MD USA Electrical and Computer Engineering Department Institute of Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

Many animals are known to maintain an internal estimate of their orientation in the environment. In the absence of external sensory cues, this estimate inevitably exhibits drift. When sensory information is available, associations between sensory landmarks and the internal estimate can be used to correct for drift. In this paper we present a neuromorphic system to model such associations between sensory landmarks in the environment (as provided by sonar) and the activity of a hardware-based head direction cell system (HDS) that continuously integrates angular velocity signals to maintain an estimate of the orientation. These associations are shown to correct for drift errors that are encountered in the HDS.

关键词： High definition video Robot sensing systems Neurons Navigation Sonar detection Neuromorphics

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Strategies for pathway-based analysis of genome-wide SNP data

Strategies for pathway-based analysis of genome-wide SNP dat...

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2011 Defense Science Research Conference and Expo, DSR 2011

作者： Patumcharoenpol, P. Chan, J. Prom-On, S. Meechai, A. Bioinformatics and Systems Biology Program King Mongkut's University of Technology Thonburi Bangkok Thailand School of Information Technology King Mongkut's University of Technology Thonburi Bangkok Thailand Computer Engineering Department King Mongkut's University of Technology Thonburi Bangkok Thailand Department of Chemical Engineering King Mongkut's University of Technology Thonburi Bangkok Thailand Biological Engineering Program King Mongkut's University of Technology Thonburi Bangkok Thailand

ISBN: (纸本)9781424492763

Numerous genome-wide association studies (GWAS) have been performed in order to determine the susceptible loci of diseases. However, most diseases still cannot be explained by a single locus. Pathway-based methods address this problem by combining those small effects into groups of related genes or pathways. However, because pathway-based approaches consist of multiple steps, there is much room for improvement. This paper presents an improved method for translating list of SNPs from GWAS into list of genes. We incrementally adjusted and compared different modifications applied to Parkinson's disease (PD) genome-wide SNP data and then used GSEA-P to analyze the resulting list of genes. After careful adjustments, we are able to identify more relevant pathways that were not found previously. © 2011 IEEE.

关键词： Genes

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A Radial Basis Function Spike Model for Indirect Learning via Integrate-and-Fire Sampling and Reconstruction Techniques

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Advances in Artificial Neural systems 2012年第1期2012卷

作者： X. Zhang G. Foderaro C. Henriquez A. M. J. VanDongen S. Ferrari Laboratory for Intelligent Systems and Control (LISC) Department of Mechanical Engineering and Materials Science Duke University Durham NC 27708 USAduke.edu Department of Biomedical Engineering and Department of Computer Science Duke University Durham NC 27708 USAduke.edu Program in Neuroscience & Behavioral Disorders Duke-NUS Graduate Medical School Singapore Singapore

This paper presents a deterministic and adaptive spike model derived from radial basis functions and a leaky integrate-and-fire sampler developed for training spiking neural networks without direct weight manipulation. Several algorithms have been proposed for training spiking neural networks through biologically-plausible learning mechanisms, such as spike-timing-dependent synaptic plasticity and Hebbian plasticity. These algorithms typically rely on the ability to update the synaptic strengths, or weights, directly, through a weight update rule in which the weight increment can be decided and implemented based on the training equations. However, in several potential applications of adaptive spiking neural networks, including neuroprosthetic devices and CMOS/memristor nanoscale neuromorphic chips, the weights cannot be manipulated directly and, instead, tend to change over time by virtue of the pre- and postsynaptic neural activity. This paper presents an indirect learning method that induces changes in the synaptic weights by modulating spike-timing-dependent plasticity by means of controlled input spike trains. In place of the weights, the algorithm manipulates the input spike trains used to stimulate the input neurons by determining a sequence of spike timings that minimize a desired objective function and, indirectly, induce the desired synaptic plasticity in the network.

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Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results 11

Improving protein-RNA interface prediction by combining sequ...

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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Xue, Li C. Walia, Rasna EL-Manzalawy, Yasser Dobbs, Drena Honavar, Vasant Bioinformatics and Computational Biology Program Iowa State University Ames IA 50011 United States Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 United States Department of Computer Science Iowa State University Ames IA 50011 United States Department of Systems and Computer Engineering Al-Azhar University Cairo Egypt

ISBN: (纸本)9781450307963

Protein-RNA interactions play important roles in cellular processes like protein synthesis, RNA processing, and gene expression regulation. Reliable identification of the interfaces involved in RNA-protein interactions is essential for comprehending the mechanisms and the functional implications of these interactions and provides a valuable guide for rational drug discovery and design. Because the determination of 3D structures of protein-RNA complexes has various technical limitations and is typically costly, reliable in silico interface prediction methods that require only the sequence information are urgently needed. We present HomPRIP, a homologous sequence based method for predicting protein-RNA interfaces, based on our conservation analysis of protein-RNA interfaces. We test Hom-PRIP on a benchmark dataset of 199 proteins and compare it with the state-of-the-art protein-RNA interface prediction methods. Our results show that HomPRIP can reliably identify protein-RNA interface residues in 71% of test proteins with at least one putative sequence homolog passing the similarity thresholds of HomPRIP. Moreover, to facilitate predictions for proteins with no identified homologs, we develop HomPRIP-NB, a method combining the HomPRIP predictor and a Naive Bayes (NB) classifier trained using evolutionary information derived from alignments against the NCBI nr database. Our results suggest that HomPRIP-NB significantly outperforms the state-of-the-art machine learning methods for predicting protein-RNA interface residues. Copyright © 2011 ACM.

关键词： Proteins

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Synthesis and Second-Order Nonlinear Optical Properties of New Coumaromethacrylate-Methylmethacrylate Copolymers

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MRS Online Proceedings Library 2011年第1期173卷 601-606页

作者： R. A. Henry J. M. Hoover A. Knoesen S. T. Kowel G. A. Lindsay M. A. Mortazavi Research Department Chemistry Division China Lake USA Department of Electrical Engineering and Computer Science Organized Research Program on Polymeric Ultrathin Film Systems University of California Davis USA

The synthesis and second-order nonlinear optical (NLO) properties of a new family of optically nonlinear coumarin dye-containing polymers is reported. Polymerizable coumaromethacrylate (CMA) monomers having various alkyl spacers (C2 to C5) between the polymerizable group and the chromophore were prepared and copolymerized with methylmethacrylate (MMA) and other vinyl monomers. The CMA copolymers had high chromophoric content (up to 18 × 1020) and glass transitions as high as 132°C. Spin cast films were prepared on BK7 substrates and oriented by corona-onset poling at elevated temperatures (COPET). The poled CMA copolymer films were characterized for spectroscopic absorption and second harmonic properties. A comparison of the nonlinear optical properties of poled CMA-MMA copolymers to poled guest-host systems is made. Relative to guest/host systems, CMA-MMA copolymer films exhibit larger and much more stable second-order nonlinear optical properties.

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Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study 11

Ranking docked models of protein-protein complexes using pre...

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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Xue, Li C. Jordan, Rafael A. El-Manzalawy, Yasser Dobbs, Drena Honavar, Vasant Bioinformatics and Computational Biology Program Iowa State University Ames IA 50011 United States Department of Genetics Development and Cell Biology Iowa State University Ames 50011 United States Department of Computer Science Iowa State University Ames IA 50011 United States Department of Computer Science Pontificia Universidad Javeriana Cali Colombia Department of Systems and Computer Engineering AI-Azhar University Cairo Egypt

ISBN: (纸本)9781450307963

Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting proteinprotein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://***/DockRank/. Copyright © 2011 ACM.

关键词： Proteins

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Automatic Generation of Balletic Motions

Automatic Generation of Balletic Motions

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IEEE/ACM International Conference on Cyber-Physical systems (ICCPS)

作者： Amy LaViers Magnus Egerstedt Yushan Chen Calin Belta School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA Department of Electrical and Computer Engineering Boston University Boston MA USA Department of Mechanical Engineering Division of Systems Engineering and the Bioinformatics Graduate Program Boston University MA USA

As cyber-physical systems become more prevalent, specifications for these systems must be formulated in a more nuanced manner. This paper presents a particular instantiation of such specification by proposing a framework that endows robotic motions with a sense of aesthetic style. Drawing inspiration from classical ballet, poses are cast as discrete states and movements as the transitions between these states. Thus, a given movement style is encoded in the availability of transitions at each state, and the dynamics of a complex physical trajectory are abstracted as a system which moves between these states. Using Linear Temporal Logic (LTL), we are able to further constrain the set of possible sequences through the transition system and thus prevent it from evolving through a sequence of states that is physically impossible or aesthetically undesirable. Our overarching objective is to facilitate subtle degrees of control over systems as such subtleties are required, more and more, to interact in a social and aesthetically driven world.

关键词： Automata Leg Legged locomotion Humans Trajectory Hip

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Validation of a Device for Fluorescence Sensing of Rare Circulating Cells with Diffusive Light in an Optical Flow Phantom Model

Validation of a Device for Fluorescence Sensing of Rare Circ...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society

作者： Eric Zettergren Dwayne Vickers Judith Runnels Charles P. Lin Mark J. Niedre Department of Electrical and Computer Engineering Northeastern University Department of Chemical Engineering Northeastern University Advanced Microscopy Program Center for Systems Biology and Wellman Center for Photomedicine Massachusetts General Hospital

ISBN: (纸本)9781424441211

Detection and quantification of rare circulating cells in biological tissues is an important problem and has many applications in biomedical research. Current methods normally involve extraction of blood samples and counting of cells ex vivo, or the use of microscopy-based fluorescence in vivo flow cytometry. The goal of this work is to develop an instrument for non-invasively enumerating very rare circulating cells in small animals with diffuse light with several orders of magnitude sensitivity improvement versus current approaches. In this work, we describe the design of our system and show that single, fluorescent microspheres can be detected in limb-mimicking optical flow phantoms with varying optical properties chosen to simulate in vivo conditions. Further, we demonstrate single cell counting capabilities using fluorescently (Vybrant-DiD) labeled Jurkat and Multiple Myeloma cells. Ongoing work includes in vivo testing and characterization of our system in mice.

关键词： Imaging Phantom Optic Flow Cell Count diffuse light in vivo test Optical properties TISSUES (BIOLOGY) EX-VIVO Fluorescence Myeloma cell blood specimen

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A parallel architecture for ray-tracing with an embedded intersection algorithm

A parallel architecture for ray-tracing with an embedded int...

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IEEE International Symposium on Circuits and systems (ISCAS)

作者： Alexandre S. Nery Nadia Nedjah Felipe M.G. França Lech Jozwiak LAM-Computer Architecture and Microelectronics Laboratory Systems Engineering and Computer Science Program COPPE Universidade Federal do Rio de Janeiro Brazil Department of Electrical Engineering-Electronic Systems Eindhovan University of Technology Netherlands Department of Electronics Engineering and Telecommunications-Faculty of Engineering Universidade do Estado do Rio de Janeiro (UERJ) Brazil

Real time rendering of three-dimensional scenes in Ray Tracing is a hard problem. However, parallel implementations have been enabling real time performance, as the algorithm can be highly parallelized. Thus, a custom parallel design in hardware is likely to achieve a good performance. In this paper, we further improve the GridRT architecture overall performance by embedding the ray-triangle intersection computation into the precessing elements that form the architecture. Low cost and high rendering performance are the main concerns in this novel design. The results show that the execution time of each intersection computation is reduced by at least 50%, while the area cost is practically unchanged or even reduced when compared to the original GridRT implementation.

关键词： Ray tracing Registers Equations USA Councils Mathematical model Parallel architectures

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MLEA： A Solution for Users of Android in UTPVirtual

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computer Technology and Application 2011年第5期2卷 406-412页

作者： Gisela Torres de Clunie Sergio Crespo Coelho da Silva Pinto Aris Linet Castillo Lucas Monteiro Braz Tasia Serrao Norman Rangel Jeanette Riley Olinda de Barraza Kexy Rodriguez Computer Systems Engineering Department Technological University of Panama Panama 0819 Panama Computer Science Research and Graduate Program in Applied Computing University of the Sinos Valley （UNISINOS） RS 93022-000 Brazil CIDITIC Technological University of Panama Panama 0819 Panama

This paper describes a design of an educational platform for a mobile learning architecture, which is a state of the an topic in distance education. The product will allow users to interact in an efficient, flexible, and transparent fashion with a web-based education environment, in this case Module Object-Oriented Dynamic Learning Environment （Moodle）, using Android mobile devices. In order to provide a strong and lasting architecture, the Service Oriented Architecture （SOA） methodology is used given that it allows easy software re-utilization as well as integration of heterogeneous services. The architecture is based on web services implemented with Representational State Transfer （REST）, as it has been demonstrated to be lighter and less consuming than other protocols, for devices with limited resources such as mobile devices. Web services provide the communication means between the server side and the client side of the architecture, whereas agents are used to deliver the services itself. The authors propose the development of an environment that facilitates the integration of various educational resources to support m-learning. An important aspect of the proposal is the offering of a tool to provide customized alerts for students and teachers, enabling them to remain updated about activities taking place in the courses.

关键词： Distance learning virtual education m-learning service oriented architecture （SOA） mobile learning mobile computing interoperability representational state transfer （REST）.

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