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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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A constant revenue model for telecommunication networks

A constant revenue model for telecommunication networks

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International Conference on Networking, International Conference on Systems andInternational Conference on Mobile Communications and Learning Technologies, ICN/ICONS/MCL'06

作者： Sukasdadi, Hapsara R. Verma, Pramode K. Graduate Program in Telecommunication System Department of Electrical and Computer Engineering

ISBN: (纸本)0769525520

It is well known that the quality of service provided by a telecommunication network as measured by the probability of blocking decreases rapidly when the incident traffic exceeds the design limits of the network. A higher probability of blocking results in reduced throughput and loss of revenue for the service provider. This paper presents a mechanism that introduces priority in a telephone system with the objective of providing a defined grade of service to priority traffic carrying a higher price tag. The non-priority traffic carries a lower price tag and a lower grade of service. The proposed pricing scheme maintains the overall revenue associated with the network at a constant level over a wide range of incident traffic. © 2006 IEEE.

关键词： Telecommunication 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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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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Workshop on imaging science development for cancer prevention and preemption

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Cancer Biomarkers 2007年第1期3卷 1-33页

作者： Kelloff, Gary J. Sullivan, Daniel C. Baker, Houston Clarke, Lawrence P. Nordstrom, Robert Tatum, James L. Dorfman, Gary S. Jacobs, Paula Berg, Christine D. Pomper, Martin G. Birrer, Michael J. Tempero, Margaret Higley, Howard R. Petty, Brenda Gumbs Sigman, Caroline C. Maley, Carlo Sharma, Prateek Wax, Adam Ginsberg, Gregory G. Dannenberg, Andrew J. Hawk, Ernest T. Messing, Edward M. Grossman, H. Barton Harisinghani, Mukesh Bigio, Irving J. Griebel, Donna Henson, Donald E. Fabian, Carol J. Ferrara, Katherine Fantini, Sergio Schnall, Mitchell D. Zujewski, Jo Anne Hayes, Wendy Klein, Eric A. DeMarzo, Angelo Ocak, Iclal Ketterling, Jeffrey A. Tempany, Clare Shtern, Faina Parnes, Howard L. Gomez, Jorge Srivastava, Sudhir Szabo, Eva Lam, Stephen Seibel, Eric J. Massion, Pierre McLennan, Geoffrey Cleary, Kevin Suh, Robert Burt, Randall W. Pfeiffer, Ruth M. Hoffman, John M. Roy, Hemant K. Wang, Thomas Limburg, Paul J. El-Deiry, Wafik S. Papadimitrakopoulou, Vali Hittelman, Walter N. MacAulay, Calum Veltri, Robert W. Solomonzz, Diane Jeronimo, Jose Richards-Kortum, Rebecca Johnson, Karen A. Viner, Jaye L. Stratton, Steven P. Rajadhyaksha, Milind Dhawan, Atam NIH/NCI/DCTD Cancer Imaging Program Bethesda MD United States NIH/NCI/DCTD Cancer Imaging Program NCI-Frederick Frederick MD United States NIH/NCI/DCP Early Detection Research Group Bethesda MD United States The Johns Hopkins University School of Medicine Departments of Radiology Pharmacology and Oncology Division of Neuroradiology Baltimore MD United States NIH/NCI/CCR Cell and Cancer Biology Branch Bethesda MD United States University of California San Francisco Department of Medicine Division of Medical Oncology San Francisco CA United States CCS Associates Inc. Mountain View CA United States Wistar Institute Molecular and Cellular Oncogenesis Program Philadelphia PA United States University of Kansas School of Medicine VA Hospital Kansas City MO United States Duke University Department of Biomedical Engineering Medical Physics Program Durham NC United States University of Pennsylvania School of Medicine Department of Gastroenterology Philadelphia PA United States New York Presbyterian Hospital Weill Medical College of Cornell University New York NY United States NIH/NCI/OD Office of Centers for Training and Resources Bethesda MD United States University of Rochester Medical Center Department of Urology Rochester NY United States University of Texas MD Anderson Cancer Center Department of Urology Houston TX United States Massachusetts General Hospital Abdominal Imaging/Interventional Radiology Boston MA United States Boston University Biomedical Engineering Electrical and Computer Engineering and Physics Boston MA United States NIH/NCI/DCP Gastrointestinal and Other Cancers Research Group Bethesda MD United States The George Washington University Cancer Institute Office of Cancer Prevention and Control Washington DC United States University of Kansas Cancer Center Clinical Oncology Kansas City KS United States University of California Davis Department of Biomedical Engineering Davis CA United States Tufts University De

The article provides information on a workshop on the development of imaging systems for cancer prevention and preemption convened by the U.S. National Cancer Institute (NCI) Cancer Imaging program.held in Gaithersburg, Maryland. Doctor Katherine Ferrara of the University of California discussed the function of ultrasound in breast tumor imaging. Ways to close the gap between development and application of imaging approaches were tackled in a roundtable discussion on cervix and skin cancer.

关键词： FORUMS (Discussion & debate) IMAGING systems in medicine CANCER prevention

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Modeling of biochemical pathways: Physical interpretation of network behavior

Modeling of biochemical pathways: Physical interpretation of...

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IEEE 32nd Annual Northeast Bioengineering Conference, 2006

作者： Sarvia, Tricia A. Sun, Ying Biomedical Engineering Program Department of Electrical and Computer Engineering University of Rhode Island Kingston RI 02881 United States

ISBN: (纸本)0780395638

The development of computational models allows one to easily reveal certain behaviors of the biochemical network of interest. In this project we seek to represent the set of rate equations used to describe the dynamics of a system with a common physical model. This allows for the reduction of such complexities that can restrict the model's overall stability. Conclusions from preliminary data have shown that the model produces valid results consistent with experimental data. We also have tested the model's reliability by reversing the reaction's driving potential. It has been concluded that this modeling approach gives logical and consistent results. The next phase of this project would be to apply this approach to a larger biochemical process, such as glycolysis. © 2006 IEEE.

关键词： Medical computing

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Guest editorial nonlinear optimization of communication systems

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IEEE Journal on Selected Areas in Communications 2006年第8期24卷 1421-1423页

作者： Chiang, Mung Low, Steven H. Luo, Zhi-Quan Shroff, Ness B. Yu, Wei Steenstrup, M. Princeton University Department of Electrical Engineering Program in Applied and Computational Mathematics Princeton NJ 08544 United States California Institute of Technology Department of Computer Science Pasadena CA 91125 United States University of Minnesota Department of Electrical and Computer Engineering Minneapolis MN 55455 United States Purdue University School of Electrical and Computer Engineering West Lafayette IN 47907 United States University of Toronto Edward S. Rogers Sr. Department of Electrical and Computer Engineering Toronto Ont. M4S 3G5 Canada

No abstract available

关键词： Communication systems Design optimization Communication system control Optimization methods Protocols Distributed algorithms Power system modeling Nonlinear control systems Lagrangian functions Surges

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Shortening-deactivation and stretch-activation during spontaneous contraction and relaxation of bivalve cardiac muscles

Shortening-deactivation and stretch-activation during sponta...

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IEEE 32nd Annual Northeast Bioengineering Conference, 2006

作者： Pizza, Christopher Donoian, Armen Booker, Shyla Sun, Ying Biomedical Engineering Program Department of Electrical and Computer Engineering University of Rhode Island Kingston RI 02881-0805 United States

ISBN: (纸本)0780395638

Shortening-deactivation and Stretch-activation are well established techniques to study the dynamics of muscles. However, very limited data exists for comparing the two techniques. This study was conducted to perform stretch and release on the same muscle specimen and to determine whether a correlation exists between the two data sets. The entire heart of the clam (Venus mercenaria) was used in a muscle bath preparation. The neurotransmitter 5-hydroxytryptamine (5HT) was used to modulate the cardiac rhythmicity. Stretch-activation and shortening-deactivation at different phases of a spontaneous contraction cycle were introduced by used a computer-controller lever system. A preliminary analysis based on the time integral of the deviation of a perturbed force curve from the normal curve did not show a significant correlation between stretch-activation and shortening-deactivaton. Future study will include additional experiments and more sophisticated model-based analyses. © 2006 IEEE.

关键词： Muscle

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electrically modeled reciprocal inhibitory oscillator

Electrically modeled reciprocal inhibitory oscillator

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IEEE 32nd Annual Northeast Bioengineering Conference, 2006

作者： Keseberg, Christoph Maio-Cannon, Shannon Mackenzie, Christopher Chabot, Eugene DiCecco, John Wu, Jiang Sun, Ying Biomedical Engineering Program Department of Electrical and Computer Engineering University of Rhode Island Kingston RI 02881-0805 United States

ISBN: (纸本)0780395638

A model of the neuronal reciprocal inhibitory oscillator was developed in this study by use of an entirely electronic platform. Neuronal Oscillators were widely studied in previous research due to their important roll as central pattern generators. Our model consisted of two electronic components, the neuron emulator for modeling the electrical activities of a neuron and the artificial synapse for mimicking a synaptic connection between two neurons. The typical bursting patterns of action potentials were demonstrated by connecting two Neuron Emulators with the Artificial Synapse. These electronic devices provided a unique hardware platform for studying reciprocal inhibitory oscillators and other neuronal networks. © 2006 IEEE.

关键词： Oscillators (electronic)

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