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Correction to: Meeting report from the fourth meeting of the computational Modeling in Biology Network (COMBINE)

Standards in genomic sciences 2018年第1期13卷 17页

作者： Dagmar Waltemath Frank T Bergmann Claudine Chaouiya Tobias Czauderna Padraig Gleeson Carole Goble Martin Golebiewski Michael Hucka Nick Juty Olga Krebs Nicolas Le Novère Huaiyu Mi Ion I Moraru Chris J Myers David Nickerson Brett G Olivier Nicolas Rodriguez Falk Schreiber Lucian Smith Fengkai Zhang Eric Bonnet 1Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany. 2Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA. 4Instituto Gulbenkian de Ciência - IGC Rua da Quinta Grande Oeiras Portugal. 3IPK Gatersleben Gatersleben Germany. 5Department of Neuroscience Physiology and Pharmacology University College London London UK. 6School of Computer Science The University of Manchester Manchester UK. 7Heidelberg Institute for Theoretical Studies Heidelberg Germany. 8EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge UK. 14The Babraham Institute Babraham Research Campus Cambridge UK. 9Department of preventive medicine Keck School of Medicine University of Southern California Los Angeles CA USA. 10Center for Cell Analysis and Modeling University of Connecticut Health Center Farmington CT USA. 11Department of Electrical and Computer Engineering University of Utah Salt Lake City USA. 12Auckland Bioengineering Institute University of Auckland Auckland New Zealand. 13Systems Bioinformatics VU University Amsterdam Amsterdam The Netherlands. 15Martin Luther University Halle-Wittenberg Halle Germany. 16Monash University Melbourne Australia. Computational Biology Unit Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases NIH Bethesda MD USA. 18Institut Curie Paris France. INSERM U900 75248 Paris France. 20Mines ParisTech 77300 Fontainebleau Paris France.

[This corrects the article DOI: 10.4056/sigs.5279417.].

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Reports of the AAAI 2014 conference workshops

Reports of the AAAI 2014 conference workshops

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作者： Albrecht, Stefano V. Barreto, André M. S. Braziunas, Darius Buckeridge, David L. Cuayáhuitl, Heriberto Dethlefs, Nina Endres, Markus Farahmand, Amir-Massoud Fox, Mark Frommberger, Lutz Ganzfried, Sam Guillet, Sébastien Gil, Yolanda Hunter, Lawrence E. Jhala, Arnav Kersting, Kristian Konidaris, George Lecue, Freddy McIlraith, Sheila Natarajan, Sriraam Noorian, Zeinab Poole, David Ronfard, Rémi Saffiotti, Alessandro Shaban-Nejad, Arash Srivastava, Biplav Tesauro, Gerald Uceda-Sosa, Rosario Van Den Broeck, Guy Van Otterlo, Martijn Wallace, Byron C. Weng, Paul Wiens, Jenna Zhang, Jie School of Informatics University of Edinburgh United Kingdom Department of Applied and Computational Mathematics Brazilian National Laboratory Brazil Big Data Group Kobo Inc. Brazil Department of Epidemiology and Biostatistics McGill University Canada School of Mathematical and Computer Sciences Heriot-Watt University in Edinburgh United Kingdom University of Augsburg Germany Carnegie Mellon University United States University of Toronto Canada Cognitive Systems Group University of Bremen Germany LIARA UQAC Chicoutimi Canada Information Sciences Institute University of Southern California Computer Science Department United States Center for Computational Pharmacology University of Colorado School of Medicine United States Department of Computational Media University of California Santa Cruz United States Computer Science Department Technical University of Dortmund Germany MIT Computer Science and Artificial Intelligence Laboratory CambridgeMA United States IBM Research - Smarter Cities Technology Centre Dubline Ireland School of Informatics and Computing Indiana University United States Department of Computer Science University of Saskatchewan Canada University of British Columbia Canada INRIA University of Grenoble France Orebro University Sweden McGill Clinical and Health Informatics Group McGill University Canada IBM Research United States Cognitive Computing Department IBM Research Yorktown HeightsNY United States Computer Science Department Katholieke Universiteit Leuven Belgium Cognitive Artificial Intelligence Department Radboud University Nijmegen Netherlands University of Texas Austin United States Pierre and Marie Curie University Paris France University of Michigan United States School of Computer Engineering Nanyang Technological University Singapore

The AAAI-14 Workshop program was held Sunday and Monday, July 27-28, 2014, at the Québec City Convention Centre in Québec, Canada. The AAAI-14 workshop program included 15 workshops covering a wide range of topics in artificial intelligence. The titles of the workshops were Artificial Intelligence and Robotics;Artificial Intelligence Applied to Assistive Technologies and Smart Environments;Cognitive Computing for Augmented Human Intelligence;computer Poker and Imperfect Information;Discovery Informatics;Incentives and Trust in Electronic Communities;Intelligent Cinematography and Editing;Machine Learning for Interactive Systems: Bridging the Gap Between Perception, Action, and Communication;Modern Artificial Intelligence for Health Analytics;Multiagent Interaction Without Prior Coordination;Multidisciplinary Workshop on Advances in Preference Handling;Semantic Cities - Beyond Open Data to Models, Standards, and Reasoning;Sequential Decision Making with Big Data;Statistical Relational AI;and the World Wide Web and Public Health Intelligence. This article presents short summaries of those events. © 2015, Association for the Advancement of Artificial Intelligence. All rights reserved.

关键词： Decision making

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Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations

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Human molecular genetics 2017年第2期26卷 454-465页

作者： Wei Jie Seow Keitaro Matsuo Chao Agnes Hsiung Kouya Shiraishi Minsun Song Hee Nam Kim Maria Pik Wong Yun-Chul Hong H Dean Hosgood Zhaoming Wang I-Shou Chang Jiu-Cun Wang Nilanjan Chatterjee Margaret Tucker Hu Wei Tetsuya Mitsudomi Wei Zheng Jin Hee Kim Baosen Zhou Neil E Caporaso Demetrius Albanes Min-Ho Shin Lap Ping Chung She-Juan An Ping Wang Hong Zheng Yasushi Yatabe Xu-Chao Zhang Young Tae Kim Xiao-Ou Shu Young-Chul Kim Bryan A Bassig Jiang Chang James Chung Man Ho Bu-Tian Ji Michiaki Kubo Yataro Daigo Hidemi Ito Yukihide Momozawa Kyota Ashikawa Yoichiro Kamatani Takayuki Honda Hiromi Sakamoto Hideo Kunitoh Koji Tsuta Shun-Ichi Watanabe Hiroshi Nokihara Yohei Miyagi Haruhiko Nakayama Shingo Matsumoto Masahiro Tsuboi Koichi Goto Zhihua Yin Jianxin Shi Atsushi Takahashi Akiteru Goto Yoshihiro Minamiya Kimihiro Shimizu Kazumi Tanaka Tangchun Wu Fusheng Wei Jason Y Y Wong Fumihiko Matsuda Jian Su Yeul Hong Kim In-Jae Oh Fengju Song Victor Ho Fun Lee Wu-Chou Su Yuh-Min Chen Gee-Chen Chang Kuan-Yu Chen Ming-Shyan Huang Pan-Chyr Yang Hsien-Chih Lin Yong-Bing Xiang Adeline Seow Jae Yong Park Sun-Seog Kweon Chien-Jen Chen Haixin Li Yu-Tang Gao Chen Wu Biyun Qian Daru Lu Jianjun Liu Hyo-Sung Jeon Chin-Fu Hsiao Jae Sook Sung Ying-Huang Tsai Yoo Jin Jung Huan Guo Zhibin Hu Wen-Chang Wang Charles C Chung Charles Lawrence Laurie Burdett Meredith Yeager Kevin B Jacobs Amy Hutchinson Sonja I Berndt Xingzhou He Wei Wu Junwen Wang Yuqing Li Jin Eun Choi Kyong Hwa Park Sook Whan Sung Li Liu Chang Hyun Kang Lingmin Hu Chung-Hsing Chen Tsung-Ying Yang Jun Xu Peng Guan Wen Tan Chih-Liang Wang Alan Dart Loon Sihoe Ying Chen Yi Young Choi Jen-Yu Hung Jun Suk Kim Ho-Il Yoon Qiuyin Cai Chien-Chung Lin In Kyu Park Ping Xu Jing Dong Christopher Kim Qincheng He Reury-Perng Perng Chih-Yi Chen Roel Vermeulen Junjie Wu Wei-Yen Lim Kun-Chieh Chen John K C Chan Minjie Chu Yao-Jen Li Jihua Li Hongyan Chen Chong-Jen Yu Li Jin Yen-Li Lo Ying-Hsiang Chen Joseph F Fraumeni Jie Liu Taiki Yamaji Yang Yang Belynda Hicks Kathleen Wyatt Shengchao A Li Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA. Saw Swee Hock School of Public Health National University of Singapore and National University Health System Singapore. Division of Molecular Medicine Aichi Cancer Center Research Institute Nagoya Japan. Institute of Population Health Sciences National Health Research Institutes Zhunan Taiwan. Division of Genome Biology National Cancer Center Research Institute Tokyo Japan. Department of Statistics Sookmyung Women's University Seoul Republic of Korea. Department of Preventive Medicine Chonnam National University Medical School Gwangju Republic of Korea. Department of Pathology The University of Hong Kong Queen Mary Hospital Hong Kong. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea. Department of Epidemiology and Population Health Albert Einstein College of Medicine Bronx NY USA. Department of Computational Biology St. Jude Children's Research Hospital Memphis TN 38105 USA. National Institute of Cancer Research National Health Research Institutes Zhunan Taiwan. Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences Fudan University Shanghai People's Republic of China. State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai People's Republic of China. Division of Thoracic Surgery Kinki University School of Medicine Sayama Japan. Division of Epidemiology Department of Medicine Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center Nashville TN USA. Department of Integrative Bioscience & Biotechnology Sejong University Seoul Republic of Korea. Department of Epidemiology School of Public Health China Medical University Shenyang People's Republic of China. Guangdong Lung Cancer Institute Medical Research Center and Cancer Center of Guangdong General Hospital Guangdong Academy of Medical Sciences Guangzhou People's Republic

To evaluate associations by EGFR mutation status for lung adenocarcinoma risk among never-smoking Asian women, we conducted a meta-analysis of 11 loci previously identified in genome-wide association studies (GWAS). Genotyping in an additional 10,780 never-smoking cases and 10,938 never-smoking controls from Asia confirmed associations with eight known single nucleotide polymorphisms (SNPs). Two new signals were observed at genome-wide significance (P < 5 × 10-8), namely, rs7216064 (17q24.3, BPTF), for overall lung adenocarcinoma risk, and rs3817963 (6p21.3, BTNL2) which is specific to cases with EGFR mutations. In further sub-analyses by EGFR status, rs9387478 (ROS1/DCBLD1) and rs2179920 (HLA-DPB1) showed stronger estimated associations in EGFR-positive compared to EGFR-negative cases. Comparison of the overall associations with published results in Western populations revealed that the majority of these findings were distinct, underscoring the importance of distinct contributing factors for smoking and non-smoking lung cancer. Our results extend the catalogue of regions associated with lung adenocarcinoma in non-smoking Asian women and highlight the importance of how the germline could inform risk for specific tumour mutation patterns, which could have important translational implications.

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Conformational Dynamics of apo‐GlnBP Revealed by Experimental and computational Analysis

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Angewandte Chemie 2016年第45期128卷

作者： Yitao Feng Lu Zhang Shaowen Wu Zhijun Liu Xin Gao Xu Zhang Maili Liu Jianwei Liu Xuhui Huang Wenning Wang Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Department of Chemistry and Institutes of Biomedical Sciences Fudan University Shanghai P.R. China Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong National Center for Protein Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai China King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Center (CBRC) Computer Electrical and Mathematical Sciences and Engineering (CEMSE) Division Thuwal 23955 Saudi Arabia Key Laboratory of Magnetic and Resonance in Biological Systems State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Centre for Magnetic Resonance Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan China Division of Biomedical Engineering Center of Systems Biology and Human Health Institute for Advance Study and School of Science The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong

The glutamine binding protein (GlnBP) binds l ‐glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo‐ and holo‐GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single‐molecule FRET techniques to decipher the conformational dynamics of apo‐GlnBP. The NMR residual dipolar couplings of apo‐GlnBP were in good agreement with a MD‐derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four‐state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP.

关键词： FRET Konformationsdynamik Moleküldynamik NMR-Spektroskopie Proteinfaltung

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pH‐Sensing Hydrogel Fibers: Flexible pH‐Sensing Hydrogel Fibers for Epidermal Applications (Adv. Healthcare Mater. 6/2016)

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Advanced Healthcare Materials 2016年第6期5卷

作者： Ali Tamayol Mohsen Akbari Yael Zilberman Mattia Comotto Emal Lesha Ludovic Serex Sara Bagherifard Yu Chen Guoqing Fu Shideh Kabiri Ameri Weitong Ruan Eric L. Miller Mehmet R. Dokmeci Sameer Sonkusale Ali Khademhosseini Biomaterials Innovation Research Center (BIRC) Department of Medicine Brigham and Women's Hospital Harvard Medical School Cambridge MA 02139 USA Harvard‐MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge MA 02139 USA Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA Department of Mechanical Engineering University of Victoria Victoria V8P 5C2 Canada Nanoscale Integrated Sensors and Circuits Laboratory (Nanolab) Department of Electrical and Computer Engineering Tufts University Medford MA 02155 USA Department of Biomedical Engineering Tufts University Medford MA 02155 USA Department of Mechanical Engineering Politecnico di Milano Milan 20156 Italy Department of Electrical and Computer Engineering Tufts University Medford 02155 USA Department of Physics King Abdulaziz University Jeddah 21569 Saudi Arabia Department of Bioindustrial Technologies College of Animal Bioscience and Technology Konkuk University Seoul South Korea

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The Chinese ‘‘HumanFlesh’’ Web:the first decade and beyond

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Chinese Science Bulletin 2014年第26期59卷 3352-3361页

作者： Fei-Yue Wang Daniel Zeng Qingpeng Zhang James A. Hendler Jianping Cao The State Key Laboratory of Management and Control for Complex Systems Institute of Automation Chinese Academy of Sciences Department of Management Information Systems The University of Arizona Tucson Department of Systems Engineering and Engineering Management City University of Hong Kong Tetherless World Constellation Department of Computer Science Rensselaer Polytechnic Institute Troy The Research Center for Computational Experiments and Parallel Systems National University of Defense Technology

Human flesh search(HFS), a Web-enabled crowdsourcing phenomenon, originated in China a decade ago. In this article, we present the first comprehensive empirical analysis of HFS, focusing on the scope of HFS activities, the patterns of HFS crowd collaboration process, and the characteristics of HFS participant networks. A survey of HFS participants was conducted to provide an in-depth understanding of the HFS community and various factors that motivate these participants to contribute. This article also advocates a new stream of Web science and social computing research that will be important in predicting the future growth and use of the World Wide Web.

关键词：中国人网址肉 Web功能实证分析参与者共同体万维网

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Comparison of blind source separation algorithms for optical heart rate monitoring

Comparison of blind source separation algorithms for optical...

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EAI International Conference on Wireless Mobile Communication and Healthcare (Mobihealth)

作者： Eirini Christinaki Giorgos Giannakakis Franco Chiarugi Matthew Pediaditis Galateia Iatraki Dimitris Manousos Kostas Marias Manolis Tsiknakis Foundation for Research and Technology Institute of Computer Science Greece Computational Medicine Laboratory Institute of Computer Science Foundation for Research and Technology - Hellas Heraklion Crete Greece Department of Informatics Engineering Technological Educational Institute of Crete Greece

Monitoring of physiological signals of an individual via remote and contactless means is an important scientific challenge, whose resolution will enable the development of novel, non-intrusive mHealth and wellness-management systems and services. In this paper, the performance of three blind source separation algorithms for the optical estimation of the heart rate have been studied. The objective is to perform a comparative evaluation of their accuracy and convergence capability, for the optical estimation of the heart rate.

关键词： Cameras Heart rate Estimation Biomedical monitoring Source separation Optical pulses

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A visualization for the dynamic behaviors of the mixture of water mass for northwestern pacific near Japan

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International Journal of Modeling, Simulation, and Scientific Computing 2015年第2期6卷 213-214页

作者： Kun Zhao Satoshi Nakada Naohisa Sakamoto Koji Koyamada Chandrajit Bajaj Yoichi Ishikawa Toshiyuki Awaji Teiji In Sei-Ichi Saitoh Graduate School of Engineering Kyoto University KyotoKyoto Prefecture606-8501Japan Institute for the Promotion of Excellence in Higher Education Kyoto University KyotoKyoto Prefecture606-8501Japan Department of Computer Science The Institute for Computational Engineering and Sciences University of Texas at Austin AustinTexas78712USA Department of Geophysics Division of Earth and Planetary Sciences Kyoto University KyotoKyoto Prefecture606-8501Japan Data Research Center for Marine-Earth Sciences Japan Agency for Marine-Earth Science and Technology Yokosuka Kanakawa Prefecture237-0061Japan Japan Marine Science Foundation Tokyo Tokyo Metropolis110-0008Japan Laboratory of Marine Bioresource and Environment Sensing Faculty of Fisheries Sciences Hokkaido University SapporoHokkaido Prefecture060-0808Japan

(1)This article,published on 20 June 2013,had the following title:A VASUALIZATION FOR THE DYNAMIC BEHAVIORS OF THE MIXTURE OF WATER MASS FOR NORTHWESTERN PACIFIC NEAR JAPAN Here“VASUALIZATION”should be“VISUALIZATIO... 详细信息

关键词： northwestern dynamic NORTH

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Offload Destination Selection to Enable Distributed Computation on Battlefields

Offload Destination Selection to Enable Distributed Computat...

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MILCOM, Military Communications Conference

作者： Tamim Sookoor David Doria David Bruno Dale Shires Brian Swenson Lori Pollock Computational Sciences Division U.S. Army Research Laboratory Maryland USA School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta Georgia USA Department of Computer and Information Sciences University of Delaware Newark Delaware USA

The tactical edge (battlefields, disaster relief operations, etc.) is an ideal domain for utilizing mobile devices for computation. However, these situations require jobs to complete in a timely manner. Efficiently offloading computation can ensure timely job completion, but access to cloud computing infrastructure is typically limited, unreliable, or unavailable. As an alternative, we propose using vehicle-mounted high performance computers, called Tactical HPCs (T-HPCs), as offload targets. A common scenario includes multiple offload targets with different computation capabilities, multiple clients wanting to offload computations, and wireless ad-hoc connectivity. While offloading strategies exist, currently none address the requirements of task scheduling in this setting. This paper presents an algorithm for offloading tasks from multiple sources while taking into account the computation capabilities and current utilization of available offload targets. In addition, distributed scheduling avoids a single point of failure which could be disastrous on the tactical edge. We report the results of simulations showing that our method reduces job completion time compared to alternative offloading schemes.

关键词： Smart phones Resource management Clouds Schedules Processor scheduling Servers

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High-order continuum kinetic method for modeling plasma dynamics in phase space

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AIP Conference Proceedings 2014年第1期1639卷 146-149页

作者： G. V. Vogman P. Colella U. Shumlak Applied Science & Technology Program University of California Berkeley Berkeley CA 94720 USA Computational Research Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA and Department of Electrical Engineering & Computer Science University of California Berkeley CA 94720 USA Aerospace & Energetic Research Program University of Washington Seattle WA 98195 USA

Continuum methods offer a high-fidelity means of simulating plasma kinetics. While computationally intensive, these methods are advantageous because they can be cast in conservation-law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Advances in continuum method capabilities for modeling kinetic phenomena in plasmas require the development of validation tools in higher dimensional phase space and an ability to handle non-cartesian geometries. To that end, a new benchmark for validating Vlasov-Poisson simulations in 3D (x,vx,vy) is presented [1]. The benchmark is based on the Dory-Guest-Harris instability and is successfully used to validate a continuum finite volume algorithm. To address challenges associated with non-cartesian geometries, unique features of cylindrical phase space coordinates are described. Preliminary results of continuum kinetic simulations in 4D (r,z,vr,vz) phase space are presented.

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