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2007 Information Theory and Applications Workshop, ITA

作者： Alterovitz, Gil Xiang, Michael Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Children's Hospital Informatics Program Boston MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States Department of Biology Massachusetts Institute of Technology Cambridge MA United States

ISBN: (纸本)9780615153148

With myriad information being generated from high-throughput experiments such as microarrays and sequencing technologies, an ever-increasing amount of data is being recorded and analyzed with the help of hierarchical ontologies, such as the Gene Ontology (GO). We have developed a novel framework-based on the well established foundations of information theory - that allows for the evaluation of new types of hypotheses. The framework, encapsulated in Open Biomedical Ontology-Based Exploration and Search (OBOES), has already been applied in the investigation of different kinds of questions. The resulting framework enables the new field of information theoretic ontology-based analysis. We have applied this framework to create methods to re-engineer ontologies, explore fundamental questions on the evolution of biological complexity, determine optimal ontology terms for bioinformatics analysis, and quantify the usefulness of biofluids as proxies for tissues/diseases. In each case, we found that our methods provide novel, significant findings. An open source Java implementation of OBOES is available at: http://***. net.

关键词： Information theory

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Linking protein mass with function via organismal massome networks

Linking protein mass with function via organismal massome ne...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Lyashenko, Eugenia Xiang, Michael Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Children's Hospital Informatics Program at Health Sciences and Technology Harvard Medical School Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States Department of Biomedical Informatics Columbia University New York NY United States

ISBN: (纸本)1424415098

With the human genome sequenced, attention has been shifting to proteins and their function. Several technologies including mass spectrometry and gel electrophoresis have traditionally been used to study proteins. These technologies rely on proteins' masses to characterize and/or identify them. Once identified, the discovered proteins' are often analyzed for their functional relevance. In this paper, we present an alternative approach to studying protein function directly, based on protein mass. By analyzing proteins with similar mass ranges (bins), we discovered that certain biological functions are associated with specific mass bins more frequently than would be expected by chance. Biological functional classes found in this manner could be seen across the three examined organisms: human, worm and fly. We found no sequence-based homology across significant mass-function proteins in the three different organisms. This investigation leads to useful property that the mass-based biological functional classes are preserved across the organisms. Thus, this paper describes a potential constraint for evolution of similar function based on mass constraints. Finally, this work yields a roadmap for experimental design for functional exploration of proteomes in mass-based technologies such as gel electrophoresis and mass spectrometry. ©2007 IEEE.

关键词： Proteins

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Using pitch, amplitude modulation, and spatial cues for separation of harmonic instruments from stereo music recordings

Eurasip Journal on Advances in Signal Processing

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Eurasip Journal on Advances in Signal Processing 2007年 2007卷

作者： Woodruff, John Pardo, Bryan Music Technology Program School of Music Northwestern University Evanston IL 60208 United States Department of Electrical Engineering and Computer Science Northwestern University Evanston IL 60208 United States

Recent work in blind source separation applied to anechoic mixtures of speech allows for improved reconstruction of sources that rarely overlap in a time-frequency representation. While the assumption that speech mixtures do not overlap significantly in time-frequency is reasonable, music mixtures rarely meet this constraint, requiring new approaches. We introduce a method that uses spatial cues from anechoic, stereo music recordings and assumptions regarding the structure of musical source signals to effectively separate mixtures of tonal music. We discuss existing techniques to create partial source signal estimates from regions of the mixture where source signals do not overlap significantly. We use these partial signals within a new demixing framework, in which we estimate harmonic masks for each source, allowing the determination of the number of active sources in important time-frequency frames of the mixture. We then propose a method for distributing energy from time-frequency frames of the mixture to multiple source signals. This allows dealing with mixtures that contain time-frequency frames in which multiple harmonic sources are active without requiring knowledge of source characteristics. Copyright © 2007 Hindawi Publishing Corporation. All rights reserved.

关键词： Harmonic generation

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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis (vol 69, pg 298, 2007)

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CHEMICAL BIOLOGY & DRUG DESIGN 2007年第6期69卷 455-455页

作者： Chellappan, S. Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville MD 20850 USA Chemical Biology Program Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA Biological Engineering Division Department of Electrical Engineering & Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA *Correspondence: Michael K. Gilson *Correspondence: * Michael K. Gilson gilson@umbi.umd.edu http://gilsonlab.umbi.umd.edu[?][?]These authors contributed equally to this study.

There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild-type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.

关键词： AIDS crystal drug design inhibitor protease

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MARKOV DECISION PROCESSES WITH UNCERTAIN TRANSITION RATES: SENSITIVITY AND MAX HYPHEN MIN CONTROL

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Asian Journal of Control 2008年第2期6卷

作者： Suresh Kalyanasundaram Edwin K. P. Chong Ness B. Shroff Motorola India Electronics Limited No. 66/1 Plot 5 Bagmane Techpark C. V. Raman Nagar Post Bangalore 560 093 India. Department of Electrical and Computer Engineering Colorado State University Fort Collins CO 80523-1373 USA. Professor Edwin K. P. Chong received the B.E.(Hons.) degree with First Class Honors from the University of Adelaide South Australia in 1987 graduating top of his class and the M.A. and Ph.D. degrees in 1989 and 1991 respectively both from Princeton University where he held an IBM Fellowship. He joined the School of Electrical and Computer Engineering at Purdue University in 1991 where he was named a University Faculty Scholar in 1999 and promoted to Full Professor in 2001. Since August 2001 he has been a Professor of Electrical and Computer Engineering and Professor of Mathematics at Colorado State University. His current interests are in communication networks and optimization methods. He coauthored the best-selling book An Introduction to Optimization 2nd Edition Wiley-Interscience 2001. He received the NSF CAREER Award in 1995 and the ASEE Frederick Emmons Terman Award in 1998. He coauthored a paper that was awarded Best Paper in the journal Computer Networks 2003. Professor Chong is a Fellow of the IEEE. He was founding chairman of the IEEE Control Systems Society Technical Committee on Discrete Event Systems and until recently served as an IEEE Control Systems Society Distinguished Lecturer. He has been on the editorial board of the IEEE Transactions on Automatic Control. He is currently on the editorial board of the journal Computer Networks. He has also served on the organizing committees of several international conferences. He has been on the program committees for the IEEE Conference on Decision and Control the American Control Conference the IEEE International Symposium on Intelligent Control IEEE Symposium on Computers and Communications and the IEEE Global Telecommunications Conference. He has also served in the executive committees for the IEEE Co

Solution techniques for Markov decision problems rely on exact knowledge of the transition rates, which may be difficult or impossible to obtain. In this paper, we consider Markov decision problems with uncertain transition rates represented as compact sets. We first consider the problem of sensitivity analysis where the aim is to quantify the range of uncertainty of the average per-unit-time reward given the range of uncertainty of the transition rates. We then develop solution techniques for the problem of obtaining the max-min optimal policy, which maximizes the worst-case average per-unit-time reward. In each of these problems, we distinguish between systems that can have their transition rates chosen independently and those where the transition rates depend on each other. Our solution techniques are applicable to Markov decision processes with fixed but unknown transition rates and to those with time-varying transition rates.

关键词： Markov decision processes sensitivity max-min control call admission control policy iteration

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In vivo fiber tracking in the rat brain on a clinical 3T MRI system using a high strength insert gradient coil

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NeuroImage 2007年第3期35卷 1077-1085页

作者： Mayer, Dirk Zahr, Natalie M. Adalsteinsson, Elfar Rutt, Brian Sullivan, Edith V. Pfefferbaum, Adolf Department of Radiology Stanford University School of Medicine Stanford CA United States Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine Stanford CA United States Harvard-MIT Division of Health Sciences and Technology MIT Cambridge MA United States Department of Electrical Engineering and Computer Science MIT Cambridge MA United States Imaging Research Laboratories Robarts Research Institute London Ont. Canada Neuroscience Program SRI International Menlo Park CA 333 Ravenswood Avenue United States

In vivo neuroimaging methods permit longitudinal quantitative examination of the dynamic course of neurodegenerative conditions in humans and animal models and enable assessment of therapeutic efforts in mitigating disease effects on brain systems. The study of conditions affecting white matter, such as multiple sclerosis, demyelinating conditions, and drug and alcohol dependence, can be accomplished with diffusion tensor imaging (DTI), a technique uniquely capable of probing the microstructural integrity of white matter fibers in the living brain. We used a 3T clinical MR scanner equipped with an insert gradient coil that yields an order of magnitude increase in performance over the whole-body hardware to acquire in vivo DTI images of rat brain. The resolution allowed for fiber tracking evaluation of fractional anisotropy (FA) and apparent diffusion coefficients in the genu and splenium of the corpus callosum. A comparison of short (46 min) and long (92 min) acquisition time DTI protocols indicated low but adequate signal-to-noise ratio (SNR = 6.2) of the shorter protocol to conduct quantitative fiber tracking enhanced by multiple acquisitions. As observed in human studies, FA in the rat splenium was higher than in the genu. Advantages of this technology include the use of similar user interface, pulse sequences, and field strength for preclinical animal and clinical human research, enhancing translational capabilities. An additional benefit of scanning at lower field strength, such as 3 T, is the reduction of artifacts due to main field inhomogeneity relative to higher field animal systems. © 2007 Elsevier Inc. All rights reserved.

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Analysis of P-type Poly-Si TFT Degradation under Dynamic Gate Voltage Stress Using the Slicing Model

Analysis of P-type Poly-Si TFT Degradation under Dynamic Gat...

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2007亚洲显示国际会议

作者： Shih-Che Huang Hung-Chuan Tsao Ya-Hsiang Tai Department of Photonics ＆ Institute of Electro-Optical Engineering NCTU HsinchuTaiwanChina 30010 College of Electrical and Computer Engineering Industrial Technology R ＆ D Master Program on Photonics and Display Technologies NCTUHsinchuTaiwanChina 30010 Department of Photonics ＆ Display Institute NCTU HsinchuTaiwanChina 30010

＜正＞In this work,the mobility degradation after gate AC stress in the off region are *** is discovered that the mob- ility increases after AC gate stress condition 0 V to+15 V,which the previously reported model （by Uraoka.Y） may not *** the spatial distribution of the voltage and the flow of the carriers in the channel,we proposed the “slicing model”,that is,replace the original TFT by ten TFTs with shorter channel ***,by applying the circuit simulator,the voltage distribution in the channel under different stages of gate applied voltage may be *** index considering the current flow and the channel voltage at the edge nodes are proposed to describe the degradation in mobili- *** fair linearity between the proposed index and the degradation in mobility reveals the validity of the proposed model.

关键词： Reliability AC Stress Poly-Si TFT

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MODELING AND CONTROL OF ELEVATORS BY STATECHARTS

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Asian Journal of Control 2008年第2期6卷

作者： Yi-Sheng Huang Sheng-Luen Chung Mu-Der Jeng Department of Aeronautical Engineering Chung Cheng Institute of Technology National Defense University Tashi Taoyuan 335 Taiwan R.O.C. Department of Electrical Engineering National Taiwan University of Science and Technology Taipei 106 Taiwan R.O.C. Department of Electrical Engineering National Taiwan Ocean University Kellung 202 Taiwan R.O.C. MuDer Jeng received the Ph.D. degree in computer and systems engineering from Rensselaer Polytechnic Institute Troy NY in 1992. Since August 1992 Dr. Jeng has been with National Taiwan Ocean University Keelung Taiwan where he is currently a full Professor at the Department of Electrical Engineering. His current research interests include Petri nets discrete event systems computer integrated manufacturing semiconductor factory automation embedded systems. Dr. Jeng is the author/co-author of over 120 book chapters journal papers and conference papers. Dr. Jeng received the Franklin V. Taylor Outstanding Paper Award from the IEEE Systems Man and Cybernetics Society in 1993. He was granted the Research Award by the National Science Council of Taiwan annually from 1994 to 2000. He is an Associate Editor for IEEE Transactions on Systems Man and Cybernetics-Part A IEEE Transactions on Robotics and Automation IEEE Transactions on Robotics and serves on the Editorial Board of International Journal of Computer Integrated Manufacturing. He has been a Guest Editor for eight leading journals. Dr. Jeng is the Chair of the Technical Committee on Discrete Event Systems of the IEEE SMC Society and the Founding Chair of the Technical Committee on Semiconductor Factory Automation of the IEEE Robotics and Automation Society. He served as the Exhibitions Chair of 2003 IEEE International Conference on Robotics and Automation and the Special Sessions Chair of 2004 IEEE International Conference on Networking Sensing and Control. He serves as a Program Co-Chair of 2005 IEEE International Conference on Networking Sensing and Control and the Organization Commit

Statechart has been utilized as a visual formalism for the modeling of complex and interactive systems for its illuminating features on describing properties of causality, concurrency, and synchronization. This paper presents the application of satechart to the modeling, design and implementation of an elevator system, whose system behavior involves aggregating complexity of state descriptions, and imposition of underlying control policy. Based on the operational flow of an elevator, we derive the associated statechart model by looking into the inherent hierarchical structure of the elevator. The advantage of the proposed approach is the clear presentation of system behavior in terms of conditions and events that cause the transitions in system dynamics. Implementation of the controlled elevator based on the modeled statechart is also presented.

关键词： Statechart interactive systems elevator

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Enabling a strong U.S. engineering workforce for technological innovation: A national partnership in graduate professional education with industry to enhance U.S. competitiveness and economic development

Enabling a strong U.S. engineering workforce for technologic...

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114th Annual ASEE Conference and Exposition, 2007

作者： Keating, Donald Stanford, Thomas Bardo, John Dunlap, Duane DeLoatch, Eugene Tricamo, Stephen Deoew, Dennis Bertoline, Gary Schuver, Mark McHenry, Albert Lindquist, Timothy Tidwell, Joseph Palmer, Harvey Smith, Mark Morrison, Raymond Egbert, Norm Quick, David Olson, Roger Truesdale, Samuel Noori, Mohamad Sullivan, Edward Rencis, Joseph Purdy, Carla University of South Carolina United States Department of Mechanical Engineering University of South Carolina United States ASEE-Graduate Studies Division Department of Chemical Engineering University of South Carolina United States Western Carolina University United States Kimmel School Western Carolina University United States Morgan State University United States School of Engineering Morgan State University United States ASEE New Jersey Institute of Technology United States Department of Industrial and Manufacturing Engineering Purdue University United States College of Technology Purdue University United States Rolls-Royce-Purdue Master's Degree Program Purdue University United States Arizona State University United States Arizona State University Polytechnic United States Boeing Co. United States JACMET Arizona State University Polytechnic United States ASEE-College Industry Partnership Division Rochester Institute of Technology United States Kate Gleason College of Engineering Rochester Institute of Technology United States Lockheed Martin Aeronautics Co. United States Engineering Integration and Strategy Lockheed Martin Aeronautics Company United States ASEE-Corporate Rolls-Royce Corporation United States Rolls-Royce North American Technologies United States California State Polytechnic University United States College of Engineering California State Polytechnic University United States Graduate Programs and Research College of Engineering California State Polytechnic University United States University of Arkansas United States Department of Mechanical Engineering University of Arkansas Fayetteville United States ASEE-Mechanical Engineering Division ASME Mechanical Engineering Department University of Cincinnati United States Department of Electrical and Computer Engineering University of Cincinnati United States

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An Information Theoretic Framework for Ontology-based Bioinformatics

An Information Theoretic Framework for Ontology-based Bioinf...

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Information Theory and Applications Workshop, ITA

作者： Gil Alterovitz Michael Xiang Marco F. Ramoni Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Biology Massachusetts Institute of Technology Cambridge MA USA Division of Health Sciences and Technology Harvard Medical School and Massachusetts Institute of Technology Boston MA Children's Hospital Informatics Program Boston MA Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA.

With myriad information being generated from high-throughput experiments such as microarrays and sequencing technologies, an ever-increasing amount of data is being recorded and analyzed with the help of hierarchical ontologies, such as the gene ontology (GO). We have developed a novel framework- based on the well established foundations of information theory- that allows for the evaluation of new types of hypotheses. The framework, encapsulated in open biomedical ontology-based exploration and search (OBOES), has already been applied in the investigation of different kinds of questions. The resulting framework enables the new field of information theoretic ontology-based analysis. We have applied this framework to create methods to re-engineer ontologies, explore fundamental questions on the evolution of biological complexity, determine optimal ontology terms for bioinformatics analysis, and quantify the usefulness of biofluids as proxies for tissues/diseases. In each case, we found that our methods provide novel, significant findings. An open source Java implementation of OBOES is available at: http://***.

关键词： Ontologies Bioinformatics Genomics Information analysis Biological information theory Information theory Genetic communication Humans Biochemistry Frequency

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