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Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics

BMC Bioinformatics 2017年第9期18卷 1-9页

作者： Eric C. Rouchka Juw Won Park Julia H. Chariker David A. Tieri Shreedharkumar Rajurkar Vikas Singh Nishchal K. Verma Yan Cui Mark Farman Bradford Condon Jolanta Jaromczyk Neil Moore Jerzy Jaromczyk Daniel Harris Patrick Calie Eun Kyong Shin Robert L. Davis Arash Shaban-Nejad Joshua M. Mitchell Hunter N. B. Moseley Robert M. Flight Qing Jun Wang Richard M. Higashi Teresa W-M Fan Andrew N. Lane Liangqun Lu Bernie J Daigle Jr. Xi Chen Andrey Smelter Jerzy W. Jaromczyk Bailey K. Phan Nathaniel J. Serpico Ethan G. Toney Li Chen Caroline E. Melton Jennifer R. Mandel Bernie J. Daigle Jr. Hao Chen Kazi I. Zaman Ramin Homayouni Patrick J. Trainor Andrew P. DeFilippis Samantha M. Carlisle Shesh N. Rai Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core 522 East Gray Street Louisville KY 40292 USA Department of Psychological and Brain Sciences University of Louisville Louisville KY 40292 USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville KY 40292 USA Department of Electrical Engineering IIT Kanpur India Department of Microbiology Immunology and Biochemistry University of Tennessee Health Science Center Memphis TN 38103 USA Center for Integrative and Translational Genomics University of Tennessee Health Science Center Memphis TN 38103 USA Department of Plant Pathology University of Kentucky Lexington KY 40546 USA UK Healthcare Genomics University of Kentucky Lexington KY 40536 USA Department of Entomology & Plant Pathology University of Tennessee Knoxville TN 37996 USA Department of Forestry University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40508 USA Department of Biological Sciences Eastern Kentucky University Richmond KY 40475 USA University of Tennessee Health Science Center – Oak-Ridge National Lab (UTHSC-ORNL) Center for Biomedical Informatics Department of Pediatrics Memphis TN 38103 USA Department of Molecular & Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Markey Cancer Center University of Kentucky Lexington KY 40536 USA Center for Environmental and Systems Biochemistry University of Kentucky Lexington KY 40536 USA Institute for Biomedical Informatics University of Kentucky Lexington KY 40536 USA Department of Molecular and Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Department of Statistics University of Kentucky Louisville KY

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A Moment-Based Method for Large-Scale Generalized Eigenvalue Problems

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Applied Numerical Analysis & Computational Mathematics 2004年第2期1卷

作者： Tetsuya Sakurai Hiroto Tadano Yuichi Inadomi Umpei Nagashima Department of Computer Science University of Tsukuba Tsukuba 305-8573 Japan Core Research for Evolutional Science and Technology Japan (CREST) Doctoral Program of Systems and Information Engineering University of Tsukuba Tsukuba 305-8573 Japan Grid Technology Research Center National Institute of Advanced Industrial Science and Technology Tsukuba 305-8568 Japan

In this paper we consider a method for finding several eigenvalues and corresponding eigenvectors of large-scale generalized eigenvalue problems. In this method, a small matrix pencil that has only the desired eigenvalues is derived using complex moments obtained via numerical integration. Since the process to derive the moments can be performed in parallel and we do not need to exchange data between processes, the presented method is suitable for master-worker programming models. We have implemented and tested the proposed method in a grid RPC (remote procedure call) system. Numerical examples illustrate the properties of our approach. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

关键词： Eigenvalue problems moment-based method parallel algorithm

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Book reviews

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Minds and Machines 1995年第1期5卷 109-155页

作者： Weiss, Eric A. Leiber, Justin Duchan, Judith Felson Selfridge, Mallory Dietrich, Eric Facione, Peter A. Day, Timothy Joseph Lammens, Johan M. Feenberg, Andrew Johnson, Deborah G. Levine, Daniel S. Warfield, Ted A. Annals of the History of Computing Kailua U.S.A. Department of Philosophy University of Houston Houston U.S.A. Department of Communicative Disorders and Sciences and Center for Cognitive Science State University of New York at Buffalo Buffalo USA Department of Computer Science and Engineering The University of Connecticut Storrs U.S.A. Program in Philosophy Computers and Systems Science Department of Philosophy State University of New York at Binghamton Binghamton USA College of Arts and Sciences Santa Clara University Santa Clara U.S.A. Department of Philosophy University of Alabama at Birmingham Birmingham U.S.A. Scuola Superiore S. Anna ARTS Lab Pisa Italy Department of Philosophy San Diego State University San Diego U.S.A. Department of Science and Technology Studies Rensselaer Polytechnic Institute Troy U.S.A. Department of Mathematics University of Texas at Arlington Arlington U.S.A. Department of Philosophy Rutgers The State University of New Jersey New Brunswick U.S.A.

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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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A computer-MODEL FOR SHIPBOARD ENERGY ANALYSIS

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NAVAL ENGINEERS JOURNAL 1984年第5期96卷 33-45页

作者： DETOLLA, JP FLEMING, JR Joseph DeTolla:is a ship systems engineer in the Ship Systems Engineering Division SEA 56D5 at the Naval Sea Systems Command. His career with the Navy started in 1965 at the Philadelphia Naval Shipyard Design Division. In 1971 he transferred to the Naval Ship Engineering Center. He has held positions as a fluid systems design engineer and auxiliary systems design integration engineer. Mr. DeTolla has worked extensively in the synthesis and analysis of total energy systems notably the design development of the FFG-7 class waste heat recovery system. He is NA VSEA's machinery group computer supported design project coordinator and is managing the development of a machinery systems data base load forecasting algorithms and design analysis computer programs. Mr. DeTolla has a bachelor of science degree in mechanical engineering from Drexel University and a master of engineering administration degree from George Washington University. He is a registered professional engineer in the District of Columbia and has written several technical papers on waste heat recovery and energy conservation. Jeffrey Fleming:is a senior project engineer in the Energy R&D Office at the David Taylor Naval Ship R&D Center. In his current position as group leader for the future fleet energy conservation portion of the Navy's energy R&D program he is responsible for the identification and development of advanced components and subsystems which will lead to reductions in the fossil fuel consumption of future ships. Over the past several years he has also directed the development and application of total energy computer analysis techniques for the assessment of conventional and advanced shipboard machinery concepts. Mr. Fleming is a 1971 graduate electrical engineer of Virginia Polytechnic Institute and received his MS in electrical engineering from Johns Hopkins University in 1975. Mr. Fleming has authored various technical publications and was the recipient of the Severn Technical Society's “Best Technical Paper of the Year” award in 1

In support of the Navy's efforts to improve the energy usage of future ships and thereby to reduce fleet operating costs, a large scale computer model has been developed by the David Taylor Naval Ship Research and Development Center (DTNSRDC) to analyze the performance of shipboard energy systems for applications other than nuclear or oil-fired steam propulsion plants. This paper discusses the applications and utility of this computer program as a performance analysis tool for design of ship machinery systems. The program is a simulation model that performs a complete thermodynamic analysis of a user-specified energy system. It offers considerable flexibility in analyzing a variety of propulsion, electrical, and auxiliary plant configurations through a component building block structure. Component subroutines that model the performance of shipboard equipment such as engines, boilers, generators, and compressors are available from the program library. Component subroutines are selected and linked in the program to model the desired machinery plant functional configurations. The operation of the defined shipboard energy system may then be simulated over a user-specified scenario of temperature, time, and load profiles. The program output furnishes information on component operating characteristics and fuel demands, which allows evaluation of the total system performance.

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Operational systems, logistics engineering and technology insertion

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NAVAL ENGINEERS JOURNAL 1997年第3期109卷 205-220页

作者： Grubb, MJ Skolnick, A Michael J. Grubb:has perfomzed naval engineering at the Crane Division Naval Surface Warfare Center (NSWC) for more than twenty-five years. He currently the program manager for the Sustainable Hardware and Affordable Readiness Practice Program (SHARP). is a Navy-wide logistics research and development prgram aimed at the successful transiton of proved technologies inot the fleet. SHARP focuses on reducing acquisition performance capability reliability maintainability and readiness of these systems. Mr. Grubb has served as a department director for the past eleven years. His most recent assignment was as director of the Tactical Computer Resources and Test Equipment Department. This organization provided acquisition and in-service engineering support of the Navy's tectical embedded computers priphirals displays and mass memory storage devices. The organization also provided a complete range of product engineering and metrology engineerig services for SSP NevSeaSysCom and the Trident Program. Prior to this appointment Mr. Grubb was deptuy director psysical security programs department and site responsible for program management and system integration of ashore integrated security systems. Mr. Grubb holds a B.S. degree in industrial engineering from Iowa State Universtiy an M.S. degree in industrial engineering from Purdue University and has copleted the course work (Dec.'96 for a master's degree in public and environment affairs at Indiana University-Purdue Univeristy Indianapolis. Dr. Alfred Skolnick operates System Science Consultants (SSC) specilizing in strategic planning technical program definiton technology assessment and engineering analyses on selected matters of national interest. He has taught physics mathematics and management sciences at University of Virginia and Marymount University and is currently adjunct professor of mathematics at Northern Virginia Community College. Form 1985 to 1989 he was president of the American Society of Noval Engineers. Dr. Skolnick served at Applied Physic

In an era of fiscal austerity, downsizing and unforgiving pressure upon human and economic capital, it is an Augean task to identify resources for fresh and creative work. The realities of the day and the practical demands of more immediate fleet needs can often dictate higher priorities. Yet, the Navy must avoid eating its seed corn. Exercising both technical insight and management foresight, the fleet, the R&D community, the Office of the Chief of Naval Operations (OpNav) and the product engineering expertise of the Naval Surface Warfare Center (NSWC) are joined and underway with integrated efforts to marry new, fully demonstrated technologies and operational urgencies. Defense funding today cannot sponsor all work that can be mission-justified over the long term because budgets are insufficient to support product maturation within the classical development cycle. However, by rigorous technical filtering and astute engineering of both marketplace capabilities and currently available components, it is possible in a few select cases to compress and, in effect, integrate advanced development (6.3), engineering development (6.4), weapon procurement (WPN), ship construction (SCN), operation and maintenance (O&M,N) budgetary categories when fleet criticalities and technology opportunities can happily meet. In short, 6.3 funds can be applied directly to ''ripe gateways'' so modern technology is inserted into existing troubled or aging systems, sidestepping the lengthy, traditional development cycle and accelerating practical payoffs to recurrent fleet problems. To produce such constructive results has required a remarkable convergence of sponsor prescience and engineering workforce excellence. The paper describes, extensively, the philosophy of approach, transition strategy, polling of fleet needs, technology assessment, and management team requirements. The process for culling and selecting specific candidate tasks for SHARP sponsorship (matching operational need with t

关键词： Naval vessels

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Direct Comparison of RT-ddPCR and Targeted Amplicon Sequencing for SARS-CoV-2 Mutation Monitoring in Wastewater

SSRN

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SSRN 2022年

作者： Lou, Esther G. Sapoval, Nicolae McCall, Camille Bauhs, Lauren Carlson-Stadler, Russell Kalvapalle, Prashant Lai, Yanlai Palmer, Kyle Penn, Ryker Rich, Whitney Wolken, Madeline Ensor, Katherine B. Hopkins, Loren Treangen, Todd J. Stadler, Lauren B. Department of Civil and Environmental Engineering Rice University 6100 Main Street MS 519 HoustonTX77005 United States Department of Computer Science Rice University 6100 Main Street HoustonTX77005 United States Systems Synthetic and Physical Biology Graduate Program Rice University 6100 Main Street HoustonTX77005 United States Houston Health Department 8000 N. Stadium Dr. HoustonTX77054 United States Department of Statistics Rice University 6100 Main Street MS 138 HoustonTX77005 United States

Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3;hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing. © 2022, The Authors. All rights reserved.

关键词： SARS

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computer-SYSTEM ARCHITECTURE CONCEPTS FOR FUTURE COMBAT systems

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NAVAL ENGINEERS JOURNAL 1990年第3期102卷 43-62页

作者： ZITZMAN, LH FALATKO, SM PAPACH, JL Dr. Lewis H. Zitzman:is the group supervisor of the Advanced Systems Design Group Fleet Systems Department The Johns Hopkins University Applied Physics Laboratory (JHU/APL). He has been employed at JHU/APL since 1972 performing applied research in computer science and in investigating and applying advanced computer technologies to Navy shipboard systems. He is currently chairman of Aegis Computer Architecture Data Bus and Fiber Optics Working Group from which many concepts for this paper were generated. Dr. Zitzman received his B.S. degree in physics from Brigham Young University in 1963 and his M.S. and Ph.D. degrees in physics from the University of Illinois in 1967 and 1972 respectively. Stephen M. Falatko:was a senior engineering analyst in the Combat Systems Engineering Department Comptek Research Incorporated for the majority of this effort. He is currently employed at ManTech Services Corporation. During his eight-year career first at The Johns Hopkins University Applied Physics Laboratory and currently with ManTech Mr. Falatko's work has centered around the development of requirements and specifications for future Navy systems and the application of advanced technology to Navy command and control systems. He is a member of both the Computer Architecture Fiber Optics and Data Bus Working Group and the Aegis Fiber Optics Working Group. Mr. Falatko received his B.S. degree in aerospace engineering with high distinction from the University of Virginia in 1982 and his M.S. degree in applied physics from The Johns Hopkins University in 1985. Mr. Falatko is a member of Tau Beta Pi Sigma Gamma Tau the American Society of Naval Engineers and the U.S. Naval Institute. Janet L. Papach:is a section leader and senior engineering analyst in the Combat Systems Engineering Department Comptek Research Incorporated. She has ten years' experience as an analyst supporting NavSea Spa War and the U.S. Department of State. She currently participates in working group efforts under Aegis Combat System Doctrin

This paper sets forth computer systems architecture concepts for the combat system of the 2010–2030 timeframe that satisfy the needs of the next generation of surface combatants. It builds upon the current Aegis computer systems architecture, expanding that architecture while preserving, and adhering to, the Aegis fundamental principle of thorough systems engineering, dedicated to maintaining a well integrated, highly reliable, and easily operable combat system. The implementation of these proposed computer systems concepts in a coherent architecture would support the future battle force capable combat system and allow the expansion necessary to accommodate evolutionary changes in both the threat environment and the technology then available to effectively counter that threat. Changes to the current Aegis computer architecture must be carefully and effectively managed such that the fleet will retain its combat readiness capability at all times. This paper describes a possible transition approach for evolving the current Aegis computer architecture to a general architecture for the future. The proposed computer systems architecture concepts encompass the use of combinations of physically distributed, microprocessor-based computers, collocated with the equipment they support or embedded within the equipment itself. They draw heavily on widely used and available industry standards, including instruction set architectures (ISAs), backplane busses, microprocessors, computer programming languages and development environments, and local area networks (LANs). In this proposal, LANs, based on fiber optics, will provide the interconnection to support system expandability, redundancy, and higher data throughput rates. A system of cross connected LANs will support a high level of combat system integration, spanning the major warfare areas, and will facilitate the coordination and development of a coherent multi-warfare tactical picture supporting the future combatant command st

关键词： computer Architecture

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Spatio-temporal assessment of whole-body center of mass coordination on standard maximum vertical jump

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Gait & Posture 2022年 97卷 S208-S209页

作者： Rodrigues, C. Correia, M. Abrantes, J. Rodrigues, B. Nadal, J. Faculty of Engineering- University of Porto Biomedical Engineering Program Porto Portugal INESC TEC - Institute for Systems and Computer Engineering- Technology and Science C-BER - Centre for Biomedical Engineering Research Porto Portugal University of Porto Faculty of Engineering Porto Portugal Lusófona University- CICANT - Centre for Research in Applied Communication- Culture and New Technologies MovLab Laboratory of Technologies for Interactions and Interfaces Lisbon Portugal Federal University of Pernambuco Department of Electronic and Systems Recife Brazil Federal University of Rio de Janeiro Biomedical Engineering Program Rio de Janeiro Brazil

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Predictable and precise template-free CRISPR editing of pathogenic variants (vol 563, pg 646, 2018)

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NATURE 2019年第7746期567卷 E1-E2页

作者： Shen, Max W. Arbab, Mandana Hsu, Jonathan Y. Worstell, Daniel Culbertson, Sannie J. Krabbe, Olga Cassa, Christopher A. Liu, David R. Gifford, David K. Sherwood, Richard I. Computational and Systems Biology Program Massachusetts Institute of Technology Cambridge USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge USA Merkin Institute of Transformative Technologies in Healthcare Broad Institute of Harvard and MIT Cambridge USA Department of Chemistry and Chemical Biology Harvard University Cambridge USA Howard Hughes Medical Institute Harvard University Cambridge USA Department of Biological Engineering Massachusetts Institute of Technology Cambridge USA Molecular Pathology Unit Center for Cancer Research and Center for Computational and Integrative Biology Massachusetts General Hospital Charlestown USA Division of Genetics Department of Medicine Brigham and Women’s Hospital and Harvard Medical School Boston USA Hubrecht Institute for Developmental Biology and Stem Cell Research Royal Netherlands Academy of Arts and Sciences (KNAW) Utrecht The Netherlands Broad Institute of MIT and Harvard Cambridge USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA

In this Article, a data processing error affected Fig. 3e and Extended Data Table 2; these errors have been corrected online.

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