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arXiv 2017年

作者： Yousefi, Siamak Chang, Xiao-Wen Wymeersch, Henk Champagne, Benoit Toussaint, Godfried Department of Electrical and Computer Engineering McGill University MontrealQC Canada School of Computer Science McGill University MontrealQC Canada Department of Signals and Systems Chalmers University of Technology Gothenburg Sweden Computer Science Program New York University Abu Dhabi United Arab Emirates

In this paper, a novel technique for tight outer-approximation of the intersection region of a finite number of ellipses in 2-dimensional (2D) space is proposed. First, the vertices of a tight polygon that contains the convex intersection of the ellipses are found in an efficient manner. To do so, the intersection points of the ellipses that fall on the boundary of the intersection region are determined, and a set of points is generated on the elliptic arcs connecting every two neighbouring intersection points. By finding the tangent lines to the ellipses at the extended set of points, a set of half-planes is obtained, whose intersection forms a polygon. To find the polygon more efficiently, the points are given an order and the intersection of the half-planes corresponding to every two neighbouring points is calculated. If the polygon is convex and bounded, these calculated points together with the initially obtained intersection points will form its vertices. If the polygon is non-convex or unbounded, we can detect this situation and then generate additional discrete points only on the elliptical arc segment causing the issue, and restart the algorithm to obtain a bounded and convex polygon. Finally, the smallest area ellipse that contains the vertices of the polygon is obtained by solving a convex optimization problem. Through numerical experiments, it is illustrated that the proposed technique returns a tighter outer-approximation of the intersection of multiple ellipses, compared to conventional techniques, with only slightly higher computational cost. Copyright © 2017, The Authors. All rights reserved.

关键词： Convex optimization

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery

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Nature communications 2021年第1期12卷 4318页

作者： Bahar Behsaz Edna Bode Alexey Gurevich Yan-Ni Shi Florian Grundmann Deepa Acharya Andrés Mauricio Caraballo-Rodríguez Amina Bouslimani Morgan Panitchpakdi Annabell Linck Changhui Guan Julia Oh Pieter C Dorrestein Helge B Bode Pavel A Pevzner Hosein Mohimani Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Center for Microbiome Innovation University of California at San Diego La Jolla CA USA. Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA. Molecular Biotechnology Department of Biosciences Goethe University Frankfurt Frankfurt am Main Germany. Center for Algorithmic Biotechnology Institute of Translational Biomedicine St. Petersburg State University St Petersburg Russia. Tiny Earth Chemistry Hub University of Wisconsin-Madison Madison WI USA. Collaborative Mass Spectrometry Innovation Center Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. The Jackson Laboratory of Medical Genomics Farmington CT USA. Molecular Biotechnology Department of Biosciences Goethe University Frankfurt Frankfurt am Main Germany. helge.bode@mpi-marburg.mpg.de. Buchmann Institute for Molecular Life Sciences (BMLS) Goethe University Frankfurt & Senckenberg Research Institute Frankfurt am Main Germany. helge.bode@mpi-marburg.mpg.de. Max-Planck-Institute for Terrestrial Microbiology Department for Natural Products in Organismic Interactions Marburg Germany. helge.bode@mpi-marburg.mpg.de. Department of Computer Science and Engineering University of California San Diego La Jolla CA USA. ppevzner@ucsd.edu. Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA. hoseinm@andrew.cmu.edu.

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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The 2021 report of the Lancet Countdown on health and climate change: code red for a healthy future

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The Lancet 2021年第10311期398卷 1619-1662页

作者： Romanello, Marina McGushin, Alice Di Napoli, Claudia Drummond, Paul Hughes, Nick Jamart, Louis Kennard, Harry Lampard, Pete Solano Rodriguez, Baltazar Arnell, Nigel Ayeb-Karlsson, Sonja Belesova, Kristine Cai, Wenjia Campbell-Lendrum, Diarmid Capstick, Stuart Chambers, Jonathan Chu, Lingzhi Ciampi, Luisa Dalin, Carole Dasandi, Niheer Dasgupta, Shouro Davies, Michael Dominguez-Salas, Paula Dubrow, Robert Ebi, Kristie L Eckelman, Matthew Ekins, Paul Escobar, Luis E Georgeson, Lucien Grace, Delia Graham, Hilary Gunther, Samuel H Hartinger, Stella He, Kehan Heaviside, Clare Hess, Jeremy Hsu, Shih-Che Jankin, Slava Jimenez, Marcia P Kelman, Ilan Kiesewetter, Gregor Kinney, Patrick L Kjellstrom, Tord Kniveton, Dominic Lee, Jason K W Lemke, Bruno Liu, Yang Liu, Zhao Lott, Melissa Lowe, Rachel Martinez-Urtaza, Jaime Maslin, Mark McAllister, Lucy McMichael, Celia Mi, Zhifu Milner, James Minor, Kelton Mohajeri, Nahid Moradi-Lakeh, Maziar Morrissey, Karyn Munzert, Simon Murray, Kris A Neville, Tara Nilsson, Maria Obradovich, Nick Sewe, Maquins Odhiambo Oreszczyn, Tadj Otto, Matthias Owfi, Fereidoon Pearman, Olivia Pencheon, David Rabbaniha, Mahnaz Robinson, Elizabeth Rocklöv, Joacim Salas, Renee N Semenza, Jan C Sherman, Jodi Shi, Liuhua Springmann, Marco Tabatabaei, Meisam Taylor, Jonathon Trinanes, Joaquin Shumake-Guillemot, Joy Vu, Bryan Wagner, Fabian Wilkinson, Paul Winning, Matthew Yglesias, Marisol Zhang, Shihui Gong, Peng Montgomery, Hugh Costello, Anthony Hamilton, Ian Institute for Global Health University College London London UK United Kingdom Institute for Sustainable Resources University College London London UK United Kingdom UCL Energy Institute University College London London UK United Kingdom Institute for Environmental Design and Engineering University College London London UK United Kingdom Department of Geography University College London London UK United Kingdom The Bartlett School of Sustainable Construction University College London London UK United Kingdom Centre for Human Health and Performance University College London London UK United Kingdom School of Agriculture Policy and Development University of Reading Reading United Kingdom Department of Meteorology University of Reading Reading United Kingdom The Walker Institute University of Reading Reading United Kingdom Department of Health Sciences University of York York United Kingdom Institute for Environment and Human Security United Nations University Bonn Germany Centre on Climate Change and Planetary Health London School of Hygiene & Tropical Medicine London UK United Kingdom Centre for Mathematical Modelling of Infectious Diseases London School of Hygiene & Tropical Medicine London UK United Kingdom Department of Public Health Environments and Society London School of Hygiene & Tropical Medicine London UK United Kingdom Department of Earth System Science Tsinghua University Beijing China Department of Environment Climate Change and Health World Health Organization Geneva Switzerland Institute for Environmental Sciences World Health Organization Geneva Switzerland Centre for Climate Change and Social Transformations School of Psychology Cardiff University Cardiff United Kingdom Yale Center on Climate Change and Health Yale University New Haven CT United States School of Government University of Birmingham Birmingham United Kingdom Economic analysis of Climate Impacts and Policy Centro Euro-Mediterraneo sui Cambiamenti Climatic

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Decanting the contribution of instruction types and loop structures in the reuse of traces

arXiv

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arXiv 2017年

作者： Coppieters, Andrey M. de Oliveira, Sheila França, Felipe M.G. Pilla, Maurício L. da Costa, Amarildo T. Program of Systems and Computer Engineering Federal University of Rio de Janeiro PO Box 68511 Rio de Janeiro RJ21941-972 Brazil Graduate Program in Computer Sciences Federal University of Pelotas R. Gomes Carneiro 1 PelotasRS/96010-610 Brazil Military Institute of Engineering Praça Gen. Tibúrcio 80 Rio de Janeiro RJ22290-270 Brazil

Reuse has been proposed as a microarchitecture-level mechanism to reduce the amount of executed instructions, collapsing dependencies and freeing resources for other instructions. Previous works have used reuse domains such as memory accesses, integer or not floating point, based on the reusability rate. However, these works have not studied the specific contribution of reusing different subsets of instructions for performance. In this work, we analysed the sensitivity of trace reuse to instruction subsets, comparing their efficiency to their complementary subsets. We also studied the amount of reuse that can be extracted from loops. Our experiments show that disabling trace reuse outside loops does not harm performance but reduces in 12% the number of accesses to the reuse table. Our experiments with reuse subsets show that most of the speedup can be retained even when not reusing all types of instructions previously found in the reuse domain. Copyright © 2017, The Authors. All rights reserved.

关键词： Reusability

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Correction: Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes

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Genetics in medicine : official journal of the American College of Medical Genetics 2020年第8期22卷 1427页

作者： Willie H Chang Pouria Mashouri Alexander X Lozano Brittney Johnstone Mia Husić Annie Olry Sylvie Maiella Tugce B Balci Sarah L Sawyer Peter N Robinson Ana Rath Michael Brudno Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada. Department of Computer Science Princeton University Princeton NJ USA. Faculty of Medicine University of Toronto Toronto ON Canada. Department of Materials Science & Engineering Stanford University Stanford CA USA. Sunnybrook Health Sciences Centre Toronto ON Canada. Orphanet Institut national de la santé et de la recherche médicale Paris France. Medical Genetics Program of Southwestern Ontario London Health Sciences Centre London ON Canada. Department of Genetics Children's Hospital of Eastern Ontario and Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON Canada. The Jackson Laboratory for Genomic Medicine Farmington CT USA. Institute for Systems Genomics University of Connecticut Farmington CT USA. Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada. brudno@cs.toronto.edu. Department of Computer Science University of Toronto Toronto ON Canada. brudno@cs.toronto.edu. Genetics and Genome Biology Program The Hospital for Sick Children Toronto ON Canada. brudno@cs.toronto.edu. University Health Network Toronto ON Canada. brudno@cs.toronto.edu.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Enhancing verification and validation education using active learning tools developed through an academia-industry partnership 123

Enhancing verification and validation education using active...

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123rd ASEE Annual Conference and Exposition

作者： Acharya, Sushil Manohar, Priya Schilling, Walter W. Wu, Peter Y. Robert Morris University PittsburghPA United States Software Engineering Program Milwaukee School of Engineering MilwaukeeWI United States Department of Computer and Information Systems Robert Morris University United States

Imparting real world experiences in a software verification and validation (SV&V) course is often a challenge due to the lack of effective active learning tools. This pedagogical requirement is important because graduates are expected to develop software that meets rigorous quality standards in functional and application domains. Realizing the necessity of such teaching tools, the authors designed and developed eighteen (18) delivery hours of Case Studies, sixteen (16) delivery hours of Class Exercises, and six (6) delivery hours of Video Case Studies for use in courses that impart knowledge on SV&V topics viz. requirements engineering, software reviews, configuration management, and software testing. Four key skill areas sought after by employers, namely communication skills, applied knowledge of methods, applied knowledge of tools, and research exposure are used to drive the development funded by a National Science Foundation grant and perfected through an industry-academia partnership. In this paper, we discuss in detail the four project plans the researchers and their industry counterparts followed over the past two years in the development and eventual dissemination of active learning tools. A course enhancement plan was used to drive activities related to reviewing, enhancing, and modularizing modules, identified by a gap analysis performed by focus groups comprised of industry and academic partners. The course delivery plan was used to drive activities related to developing content delivery strategies. An evaluation and assessment plan was used to drive activities related to periodically evaluating student learning and assessing the project. And finally a course dissemination plan is being used to drive activities related to disseminating course modules and assessment reports. Active learning tools have been disseminated through a workshop and other means to universities and industry partners. © American Society for engineering Education, 2016.

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Author Correction: The interrelation of sleep and mental and physical health is anchored in grey-matter neuroanatomy and under genetic control

Communications biology

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Communications biology 2020年第1期3卷 290页

作者： Masoud Tahmasian Fateme Samea Habibolah Khazaie Mojtaba Zarei Shahrzad Kharabian Masouleh Felix Hoffstaedter Julia Camilleri Peter Kochunov B T Thomas Yeo Simon Bodo Eickhoff Sofie Louise Valk Institute of Medical Science and Technology Shahid Beheshti University Tehran Iran. Sleep Disorders Research Center Kermanshah University of Medical Sciences Kermanshah Iran. Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour) Research Centre Jülich 52425 Jülich Germany. Institute of Systems Neuroscience Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany. Maryland Psychiatric Research Center University of Maryland School of Medicine Baltimore MD 21201 USA. Department of Electrical and Computer Engineering Clinical Imaging Research Centre N.1 Institute for Health and Memory Networks Program National University of Singapore Singapore 119077 Singapore. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA 02114 USA. Centre for Sleep and Cognition National University of Singapore Singapore 119077 Singapore. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore Singapore 119077 Singapore. Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour) Research Centre Jülich 52425 Jülich Germany. svalk@fz-juelich.de. Institute of Systems Neuroscience Heinrich Heine University Düsseldorf 40225 Düsseldorf Germany. svalk@fz-juelich.de.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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