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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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Molecular dynamic simulation of heat pulse propagation in multiwall carbon nanotubes

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Physical Review B 2007年第15期76卷 155424-155424页

作者： Taejin Kim Mohamed A. Osman Cecilia D. Richards David F. Bahr Robert F. Richard Material Science Program Washington State University Pullman Washington 99164-4620 USA Department of Physics Washington State University Pullman Washington 99164-2814 USA School of Electrical Engineering and Computer Science Washington State University Pullman Washington 99164-2752 USA School of Mechanical and Materials Engineering Washington State University Pullman Washington 99164-2920 USA

The propagation of heat pulses in zigzag and armchair double wall nanotubes (DWNTs) has been investigated using molecular dynamics simulations. It is found that the leading heat wave packets in zigzag (9,0)∕(18,0) and armchair (5,5)∕(10,10) DWNTs move with the speed of longitudinal acoustic (LA) phonon modes. The intensities of the leading heat wave packets in outer and inner shells in DWNTs were found to be five to seven times larger than that of the corresponding single wall nanotubes (SWNTs). The heat energy carried by the leading heat wave packets in zigzag DWNT was about four and five times more than those in armchair DWNT shells. Within the leading LA wave packet, the strain in the inner shell of the DWNTs is stronger than the strain in the outer shell and considerably larger than strain in the corresponding SWNTs. The regions with the largest strain coincide with the regions of high kinetic temperatures within the LA mode wave packets. The higher energy of the LA mode waves in DWNT shells compared to SWNT is attributed to the presence of higher strain fields in DWNTs compared to individual SWNTs. The higher strain in the inner shell of DWNT compared to the outer shell accounts for the three to five times higher kinetic energy of leading wave packets in inner shells compared to those in outer shells. The induced strain fields in zigzag DWNT are distributed over a wider region compared to armchair DWNT, and the strains in inner and outer shells of zigzag DWNT are out phase by 180°.

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Work in progress - evaluation of the University of Maine GK-12 sensors! program

Work in progress - evaluation of the University of Maine GK-...

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Frontiers in Education (FIE) Conference

作者： Brian E. Doore Joseph Arsenault Constance Holden Stephen Godsoe John Vetelino Program Evaluator Center for Research and Evaluation University of Maine Orono ME USA Department of English University of Maine Orono ME USA Department of Spatial Engineering and Information Science University of Maine Orono ME USA Bangor High School Bangor ME USA Department of Electrical and Computer Engineering University of Maine Orono ME USA

Findings from several years of participant feedback about the NSF sponsored GK-12 Sensors! program at the University of Maine are described. The program places graduate Fellows in local K-12 classrooms, with the goal of encouraging students to consider science, technology, engineering, and mathematics professions. Three broad themes are discussed: communication, preparation, and "fit." These factors determine the success of GK-12 Fellow placements, as shown by student and teacher evaluations, Fellow satisfaction, and classroom evaluations. Successful placements strengthen program implementation and status in participating schools while marginal placements can negatively affect both teachers and students and erode support for the GK-12 initiative.

关键词： Feedback Educational institutions engineering profession Mathematics Design methodology Protocols Information science

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Proposal of an ISO/IEEE11073 Platform for Healthcare Telemonitoring: Plug-and-Play Solution with new Use Cases

Proposal of an ISO/IEEE11073 Platform for Healthcare Telemon...

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29th Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBS 2007), vol.16

作者： M. Galarraga I. Martinez L. Serrano P. de Toledo J. Escayola J. Fernandez S. Jimenez-Fernandez S. Led M. Martinez-Espronceda E. Viruete J. Garcia Communications Technologies Group Aragon Institute for Engineering Research University of Zaragoza Spain PST Microelectronics Crolles France France Telecom. CNET Grenoble France Electrical and Electronics Engineering Dept Public University of Navarra Spain Computer Science Department Carlos III University of Madrid Spain Bioengineering and Telemedicine Research Centre (GBT) Technical University Madrid Spain

Remote patient monitoring in e-Health is everyday closer to be a mature technology/service. However, there is still a lack of development in areas such as standardization of the sensor's communication interface, integration into Electronic Healthcare Record systems or incorporation in ambient-intelligent scenarios. This work identifies a set of use cases involved in the personal monitoring scenario and highlights the related features and functionalities, as well as the integration and implementation difficulties found when these are to be implemented in a system based on the ISO/IEEE11073 (X73) standard. It is part of a cooperative research effort devoted to the development of an end-to-end standards-based telemonitoring solution. Standardization committees are working towards adapting the X73 standard to this emerging personal health devices market and use case identification is essential to direct these revisions.

关键词： Proposals Medical services ISO standards Wireless sensor networks Intelligent sensors Standardization Biomedical monitoring Protocols Patient monitoring Prototypes

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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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Oscillator models and collective motion

IEEE Control Systems Magazine

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IEEE Control Systems Magazine 2007年第4期27卷 89-105页

作者： Paley, Derek A. Leonard, Naomi Ehrich Sepulchre, Rodolphe Grünbaum, Daniel Parrish, Julia K. Princeton University Department of Mechanical and Aerospace Engineering Princeton NJ 08544 United States Department of Mechanical and Aerospace Engineering Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 United States Department Electrical Engineering and Computer Science University of Liège Liège Belgium School of Oceanography Department of Biology University of Washington Seattle WA United States Biology Department School of Aquatic and Fishery Sciences University of Washington Seattle WA United States

A description of the so called "particles with coupled oscillator dynamics" (PCOD) is presented which is used to model, analyze and synthesize collective motion. An oscillator model with spatial dynamics is presented to help describe how to design steering control laws while it is being used to study biological collectives. Lastly, both engineering and biological analysis were described.

关键词： Oscillators (mechanical)

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Lattice Boltzmann Algorithms for Fluid Turbulence

Lattice Boltzmann Algorithms for Fluid Turbulence

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DoD High Performance Computing Modernization program Users Group

作者： G. Vahala J. Yepez M. Soe L. Vahala S. Ziegeler Department of Physics The College of William and Mary Williamsburg VA USA U.S. Air Force Research Laboratory MA USA US Air Force Research Laboratory (AFRL) Hanscom Field MA Department of Mathematics and Science Rogers State University Claremore OK USA Department of Electrical & Computer Engineering Old Dominion University Norfolk VA USA High Performance Computing Modernization Program Mississippi State University MS

Lattice Boltzmann algorihms are a mesoscopic representation of nonlinear continuum physics (like Navier-Stokes, magnetohydro dynamics (MHD), Gross- Pitaevskii equations) which are ideal for parallel supercomputers because they transform the difficult nonlinear convective macroscopic derivatives into purely local moments of distribution functions. The macroscopic nonlinearities are recovered by relaxation distribution functions in the collision operator whose dependence on the macroscopic velocity is algebraically nonlinear and thus purely local. Unlike standard computational fluid dynamics codes, there is no loss in parallelization in handling arbitrary geometric boundaries, e.g., using bounce-back rules from kinetic theory. By encoding detailed balance into the collision operator through the introduction of discrete H-function, the lattice Boltzmann algorithm can be made unconditionally stable for arbitrary high Reynolds numbers. It is shown that this approach is a special case of a quantum lattice Boltzmann algorithm that entangles local qubits through unitary collision operators and which is ideally parallelized on quantum computer architectures. Here we consider turbulence simulations using 2,048 PEs on a 1,6003-spatial grid. A connection is found between the rate of change of enstrophy and the onset of laminar-to- turbulent flows.

关键词： Lattice Boltzmann methods Magnetohydrodynamics Distribution functions Quantum computing Quantum entanglement Physics Fluid dynamics Navier-Stokes equations Nonlinear equations Supercomputers

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Design and analysis of an adaptive, global strategy for detecting and mitigating distributed DoS attacks in GRID environments

Design and analysis of an adaptive, global strategy for dete...

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39th Annual Simulation Symposium, 2006

作者： Znati, Taieb Amadei, James Pazehoski, Daniel R. Sweeny, Scott Department of Computer Science Telecommunication Program Department of Electrical and Computer Engineering

ISBN: (纸本)0769525598

Basic protection schemes against Denial-of-Service (DoS) are based on a perimeter-based model, where attacks are dealt with after they occur. This is quite often too late to prevent damage or loss of resources and service. The focus of this paper is to investigate a distributed defense method that can neutralize the attack before it reaches the potential target in mass. In order to effectively implement this method, this paper proposes a progressive, globally deployable sentinel scheme for data sampling, packet inspection, and DoS attack detection and recovery. A simulation framework is developed to study the performance of the proposed scheme. The results show a significant improvement in how the network deals with DoS attacks, in comparison to local DoS detection and prevention schemes. © 2006 IEEE.

关键词： computer crime

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Decision Fusion of Circulating Markers for Breast Cancer Detection in Premenopausal Women

Decision Fusion of Circulating Markers for Breast Cancer Det...

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IEEE Symposium on Bioinformatics and bioengineering (BIBE)

作者： Jonathan L. Jesneck Sayan Mukherjee Loren W. Nolte Anna E. Lokshin Jeffrey R. Marks Joseph Lo Duke Advanced Imaging Labs Institute for Genome Sciences and Policy Department of Computer Science Duke University USA Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh PA USA Division of Hematology/Oncology University of Pittsburgh Cancer Institute Pittsburgh PA USA Division of Hematology/Oncology University of Pittsburgh Cancer Institute Pittsburgh PA Institute for Genome Sciences and Policy Department of Experimental Surgery Medical Center Duke University USA Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC USA

Current mammographic screening for breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions.

关键词： Breast cancer Cancer detection Lesions Proteins Support vector machines Support vector machine classification Mammography Testing Blood Linear regression

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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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