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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Khaladkar, Mugdha Bellofatto, Vivian Wang, Jason T. L. Patel, Vandanaben Nakayama, Marvin K. Department of Computer Science New Jersey Institute of Technology Newark NJ 07102 United States Department of Microbiology and Molecular Genetics University of Medicine and Dentistry of New Jersey-New Jersey Medical School International Center for Public Health 225 Warren Street Newark NJ 07103 United States Bioinformatics Program Department of Computer Science New Jersey Institute of Technology NJ 07102 United States

ISBN: (纸本)1424415098

In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures to assess the significance of alignment scores. Experimental results obtained by using the constrained alignment method to search for structural motifs in the untranslated regions of Trypanosoma brucei mRNAs demonstrate the good performance of the proposed method and its superiority over existing methods. ©2007 IEEE.

关键词： RNA

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114th Annual ASEE Conference and Exposition, 2007

作者： Kansaku, Claude Kehr, Linda Lanier, Catherine Oregon Institute of Technology United States Department of Computer Engineering Technology OIT LaunchOIT BalloonSat Program Edge of Space Hign-altitude Balloon Program Klamath County School District United States Ferguson Elementary School Klamath Falls OR United States Edge of Space Program Oregon Department of Education's Science Content and Assessment Panel United States Oregon NASA Space Grant Consortium United States

A university that develops a program with the capability to launch, chase, and recover helium-filled high-altitude balloon satellites (BalloonSats) enables a number of undergraduate research possibilities. The program faculty and the undergraduates served can also form the engine of an exciting and effective vehicle to perform K-12 outreach related to science, technology, engineering, and math (STEM). Nearly identical to weather balloons, low-weight BalloonSats can affordably carry student experiments literally to the edge of space. When the outreach effort is extended and a partnership between the university program and a K-12 classroom forms, the outreach can be transformed from a series of "fire and forget" activities into a genuine, standards-based, educational component. This paper describes the collaboration between Oregon Institute of technology's (OIT's) BalloonSat program (LaunchOIT) and Ferguson Elementary school in Klamath Falls, Oregon (Ferguson school). LaunchOIT is an affiliate of Oregon NASA Space Grant Consortium's1(OSGCs) "LaunchOregon" BalloonSat program. The paper presents some history relating to LaunchOIT, the enabling underpinnings of the OSGC, the OIT-Ferguson school collaboration structure (including some data related to student participants and performance), the benefits of the program collaboration, and how the program looks to sustain itself, particularly considering the auspices of NASA's educational mission as exercised through the National Space Grant College and Fellowship program2(Space Grant) efforts. © American Society for Engineering Education, 2007.

关键词： Meteorological balloons

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A systematic approach to quantifying evolutionary functional trends across the universal tree of life

A systematic approach to quantifying evolutionary functional...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Muso, Taro Malalur, Paresh 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 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

ISBN: (纸本)1424415098

The accumulation of genomic and proteomic data of many organisms presents an opportunity to analyze entire phylogenetic trees in a systematic, quantified manner. The universal tree of life, constructed by genomic data, provides an evolutionary context for proteomic data of individual organisms. Using proteomic information mapped to biological functions, we survey the tree of life for evolutionary trends, where trends are low p-value linear regressions of relative protein diversity against an evolutionary timeline. These trends provide quantified perspectives across evolution that would be otherwise difficult to discern from the large amount of available bioinformatic data. We analyzed 22,762 functions across 167 proteomes for approximately 3.8 million information content calculations. Of particular interest is the rise of protein-protein interactions along the path of mammalian evolution. Of general interest are the numerous uncovered trends that open the door to future queries of focused scope. ©2007 IEEE.

关键词： Information theory

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A study of dynamics and communication mechanism for ICPF actuating tortoise-like micro-robot

A study of dynamics and communication mechanism for ICPF act...

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IEEE International Conference on Robotics and Biomimetics

作者： Rong Nie Lin Nie Desheng Li Department of computer science and application Zhengzhou Institute of Aeronautical Industry Management Zhengzhou Henan China School of Mechanical Engineering and Applied Electronics Technology Beijing University of Technology Beijing China

ISBN: (纸本)9781424417612;1424417619

In the paper, our preliminary work in using ICPF to develop a novel tortoise-like flexible micro-robot with four legs and one tail is reported, which can crawl and swim underwater. ICPF is the abbreviation of ionic conducting polymer gel film which is a kind of smart film and can give large and fast bending displacement in the presence of a low applied voltage in wet condition. For controlling and analyzing easily the robot, we establish the micro-robot's tail dynamic model by applying pseudo-rigid-body-dynamic-model (PRBDM). Then, the frequency analysis of a micro-robot based on PRBDM is investigated. The relation between the robot tail's displacement and the electrical voltage's frequency f is theoretically derived and the simulation result for the tail's displacement is performed. Based on the characteristics of the micro bio-robots actuated by ICPF, a short-distance multi-hop communication mechanism is designed and can be used to constitute a wireless sensor network. In the mechanism, every peer only restores one-hop peers in its routing table, which is so small that the search speed and network efficiency is increased. In addition, data is transmitted by multiple paths. The network resources are made adequate use. The reliability of the network is increased, too. Thus, the network consisted of micro-robots can be established quickly and flexibly.

关键词： Tail Polymer films Conductive films Frequency Leg Polymer gels Low voltage Robot sensing systems Spread spectrum communication Wireless sensor networks

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An information theoretic framework for ontology-based bioinformatics

An information theoretic framework for ontology-based bioinf...

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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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An Energy-Aware Protocol for Data Gathering applications in Wireless Sensor Networks

An Energy-Aware Protocol for Data Gathering Applications in ...

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IEEE International Conference on Communications (ICC)

作者： M. Liu Y. Zheng J. Cao G. Chen L. Chen H. Gong School of Computer Science and Engineering University of Electronic Science and Technology China Internet and Mobile Computing Lab Department of Computing Hong Kong Polytechnic University Hong Kong China State Key Laboratory for Novel Software Technology Nanjing University China

Data gathering is a major function of many applications in wireless sensor networks (WSNs). The most important issue in designing a data gathering algorithm is how to save energy of sensor nodes while meeting the requirement of applications/users such as sensing area coverage. In this paper, we propose a novel hierarchical clustering protocol for long-lived sensor network. EAP achieves a good performance in terms of lifetime by minimizing energy consumption for in-network communications and balancing the energy load among all nodes. EAP introduces a new clustering parameter for cluster head election, which can better handle the heterogeneous energy capacities. Furthermore, it also introduces a simple but efficient approach, namely intra-cluster coverage to cope with the area coverage problem. We evaluate the performance of the proposed protocol using a simple temperature sensing application. Simulation results show that our protocol significantly outperforms LEACH and HEED in terms of network lifetime and the amount of data gathered.

关键词： Wireless application protocol Wireless sensor networks Energy consumption application software Temperature sensors computer networks Clustering algorithms Peer to peer computing Scalability Paper technology

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Fast time-domain edge-diffraction calculations for interactive acoustic simulations

Eurasip Journal on Advances in Signal Processing

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Eurasip Journal on Advances in Signal Processing 2007年 2007卷

作者： Calamia, Paul T. Svensson, U. Peter Program in Architectural Acoustics School of Architecture Rensselaer Polytechnic Institute Troy NY 12180 United States Department of Computer Science Princeton University Princeton NJ 08544 United States Acoustics Research Centre Department of Electronics and Telecommunications Norwegian University of Science and Technology NO-7491 Trondheim Norway

The inclusion of edge diffraction has long been recognized as an improvement to geometrical-acoustics (GA)modeling techniques, particularly for acoustic simulations of complex environments that are represented as collections of finite-sized planar surfaces. One particular benefit of combining edge diffraction with GA components is that the resulting total sound field is continuous when an acoustic source or receiver crosses a specular-zone or shadow-zone boundary, despite the discontinuity experienced by the associated GA *** interactive acoustic simulations which include only GA components, such discontinuities may be heard as clicks or other undesirable audible artifacts, and thus diffraction calculations are important for high perceptual quality as well as physical realism. While exact diffraction calculations are difficult to compute at interactive rates, approximate calculations are possible and sufficient for situations in which the ultimate goal is a perceptually plausible simulation rather than a numerically exact one. In this paper, we describe an edge-subdivision strategy that allows for fast time-domain edge-diffraction calculations with relatively low error when compared with results from a more numerically accurate solution. The tradeoff between computation time and accuracy can be controlled with a number of parameters, allowing the user to choose the speed that is necessary and the error that is tolerable for a specific modeling scenario.

关键词： Edge detection

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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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