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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center 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 New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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STATE OF THE CLIMATE IN 2021

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BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY 2022年第8期103卷 S1-S1页

作者： Blunden, Jessica NOAA/NESDIS National Centers for Environmental Information Asheville NC United States NOAA NESDIS National Centers for Environmental Information Silver Spring MD United States Met Office Hadley Centre Exeter United Kingdom Cooperative Institute for Satellite Earth System Studies North Carolina State University Asheville NC United States Communications and Outreach NOAA/NESDIS National Centers for Environmental Information Asheville NC United States Innovative Consulting and Management Services LLC NOAA/NESDIS National Centers for Environmental Information Asheville NC United States European Centre for Medium-Range Weather Forecasts Reading United Kingdom CMNS-Earth System Science Interdisciplinary Center University of Maryland College Park MD United States Department of Meteorology National Centre for Earth Observation University of Reading Reading United Kingdom Department of Atmospheric and Planetary Science Hampton University Hampton VA United States National Research Institute for Agriculture Food and Environment (INRAE) CARRTEL Université Savoie Mont Blanc Thonon les Bains France Graduate School of Life and Environmental Sciences Osaka Prefecture University Osaka Sakai Japan University of Bremen Bremen Germany NOAA Global Monitoring Laboratory Boulder CO United States Centro de Investigaciones sobre Desertificación Spanish National Research Council (CIDE CSIC-UV-Generalitat Valenciana) Climate Atmosphere and Ocean Laboratory (Climatoc-Lab) Moncada Valencia Spain Instituto de Geografía Pontificia Universidad Católica de Valparaíso Valparaíso Chile Climatic Research Unit School of Environmental Sciences University of East Anglia Norwich United Kingdom Joint Research Centre of the European Commission Ispra Italy GloH2O Almere Netherlands University of Reading Reading United Kingdom School of Engineering Newcastle University Newcastle-upon-Tyne United Kingdom Université de Paris Cité Institut de physique du globe de Paris CNRS IGN Paris

Editors note: For easy download the posted pdf of the State of the Climate in 2021 is a low-resolution file. A high-resolution copy of the report is available by clickinghere. Please be patient as it may take a few mi... 详细信息

关键词： Greenhouse gases

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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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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Author Correction: Neural complexity is a common denominator of human consciousness across diverse regimes of cortical dynamics

Communications biology

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Communications biology 2023年第1期6卷 41页

作者： Joel Frohlich Jeffrey N Chiang Pedro A M Mediano Mark Nespeca Vidya Saravanapandian Daniel Toker John Dell'Italia Joerg F Hipp Shafali S Jeste Catherine J Chu Lynne M Bird Martin M Monti Department of Psychology University of California Los Angeles 90095 Pritzker Hall Los Angeles CA USA. jfneuro@pm.me. Institute for Neuromodulation and Neurotechnology University Hospital and University of Tuebingen Tuebingen Germany. jfneuro@pm.me. Department of Computational Medicine University of California Los Angeles Los Angeles CA USA. Department of Computing Imperial College London London UK. Department of Psychology University of Cambridge Cambridge UK. Department of Neurosciences University of California San Diego San Diego CA USA. Department of Neurology Rady Children's Hospital San Diego San Diego CA USA. Center for Autism Research and Treatment University of California Los Angeles Semel Institute for Neuroscience Los Angeles CA USA. Department of Psychology University of California Los Angeles 90095 Pritzker Hall Los Angeles CA USA. Institute for Advanced Consciousness Studies Santa Monica CA USA. Roche Pharma Research and Early Development Neuroscience and Rare Diseases Roche Innovation Center Basel Basel Switzerland. Children's Hospital Los Angeles Los Angeles CA USA. Department of Neurology Massachusetts General Hospital Harvard Medical School Boston MA USA. Department of Pediatrics University of California San Diego San Diego CA USA. Division of Genetics/Dysmorphology Rady Children's Hospital - San Diego San Diego CA USA. Deptment of Neurosurgery UCLA Brain Injury Research Center David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA.

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Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

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Human genomics 2016年第1期10 Suppl 1卷 12页

作者： A. K. Srivastava Y. Wang R. Huang C. Skinner T. Thompson L. Pollard T. Wood F. Luo R. Stevenson R. Polimanti J. Gelernter X. Lin I. Y. Lim Y. Wu A. L. Teh L. Chen I. M. Aris S. E. Soh M. T. Tint J. L. MacIsaac F. Yap K. Kwek S. M. Saw M. S. Kobor M. J. Meaney K. M. Godfrey Y. S. Chong J. D. Holbrook Y. S. Lee P. D. Gluckman N. Karnani A. Kapoor D. Lee A. Chakravarti C. Maercker F. Graf M. Boutros G. Stamoulis F. Santoni P. Makrythanasis A. Letourneau M. Guipponi N. Panousis M. Garieri P. Ribaux E. Falconnet C. Borel S. E. Antonarakis S. Kumar J. Curran J. Blangero S. Chatterjee J. Akiyama D. Auer C. Berrios L. Pennacchio T. R. Donti G. Cappuccio M. Miller P. Atwal A. Kennedy A. Cardon C. Bacino L. Emrick J. Hertecant F. Baumer B. Porter M. Bainbridge P. Bonnen B. Graham R. Sutton Q. Sun S. Elsea Z. Hu P. Wang Y. Zhu J. Zhao M. Xiong David A. Bennett A. Hidalgo-Miranda S. Romero-Cordoba S. Rodriguez-Cuevas R. Rebollar-Vega E. Tagliabue M. Iorio E. D’Ippolito S. Baroni B. Kaczkowski Y. Tanaka H. Kawaji A. Sandelin R. Andersson M. Itoh T. Lassmann Y. Hayashizaki P. Carninci A. R. R. Forrest C. A. Semple E. A. Rosenthal B. Shirts L. Amendola C. Gallego M. Horike-Pyne A. Burt P. Robertson P. Beyers C. Nefcy D. Veenstra F. Hisama R. Bennett M. Dorschner D. Nickerson J. Smith K. Patterson D. Crosslin R. Nassir N. Zubair T. Harrison U. Peters G. Jarvik F. Menghi K. Inaki X. Woo P. Kumar K. Grzeda A. Malhotra H. Kim D. Ucar P. Shreckengast K. Karuturi J. Keck J. Chuang E. T. Liu B. Ji A. Tyler G. Ananda G. Carter H. Nikbakht M. Montagne M. Zeinieh A. Harutyunyan M. Mcconechy N. Jabado P. Lavigne J. Majewski J. B. Goldstein M. Overman G. Varadhachary R. Shroff R. Wolff M. Javle A. Futreal D. Fogelman L. Bravo W. Fajardo H. Gomez C. Castaneda C. Rolfo J. A. Pinto K. C. Akdemir L. Chin S. Patterson C. Statz S. Mockus S. N. Nikolaev X. I. Bonilla L. Parmentier B. King F. Bezrukov G. Kaya V. Zoete V. Seplyarskiy H. Sharpe T. McKee K. Popadin N. Basset-Seguin R. Ben Chaabene M. Andrianova C. Verdan K. Grosdemange O. Sumara M. E JCSRI Greenwood Genetic Center Greenwood USA School of Computing Clemson University Clemson USA Biochemical Genetics Laboratory Greenwood Genetic Center Greenwood USA Department Psychiatry Yale Sch Med and VA CT Healthcare Center West Haven USA Department Genetics Yale Sch Med and VA CT Healthcare Center West Haven USA Department Neurobiology Yale Sch Med and VA CT Healthcare Center West Haven USA Singapore Institute for Clinical Sciences Singapore Singapore National University of Singapore Singapore Singapore University of British Columbia Vancouver Canada KK Women’s and Children’s Hospital Singapore Singapore University of Southampton and University Hospital Southampton NHS Foundation Trust Southampton UK University of Auckland Auckland New Zealand McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore USA Esslingen University of Applied Sciences Esslingen Germany German Cancer Research Center Heidelberg Germany Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Geneva University Hospitals-HUG Service of Genetic Medicine Geneva Switzerland GE3 Institute of Genetics and Genomics of Geneva University of Geneva Medical School Geneva Switzerland South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Edinburg USA South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Brownsville USA Institute of Genetic Medicine Johns Hopkins University Baltimore USA Genomics Division Lawrence Berkeley National Laboratory Berkeley USA Molecular and Human Genetics Baylor College of Medicine Houston USA Department of Translational Medical Sciences Federico II University Naples Italy Metabolon Inc Durham USA Section of Pediatric Neurology and Neuroscience Baylor College of Medicine Houston USA Tawam Hospital Abu Dhabi United Arab Emirates Stanford Medical School Stanford USA Sch

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s

关键词： Pulmonary Arterial Hypertension Oral Squamous Cell Carcinoma Deep Neural Network Autosomal Recessive Polycystic Kidney Disease Whole Genome Bisulfite Sequencing

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Performance of the ATLAS track reconstruction algorithms in dense environments in LHC Run 2

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EUROPEAN PHYSICAL JOURNAL C 2017年第10期77卷 1-30页

作者： Aaboudd, M. Aad, G. Abbott, B. Abdallah, J. Abdinov, O. Abeloos, B. Abidi, S. H. AbouZeid, O. S. Abraham, N. L. Abramowicz, H. Abreu, H. Abreu, R. Abulaitia, Y. Acharya, B. Adachi, S. Adamczyk, L. Adelman, J. Adersberger, M. Adye, T. Affolder, A. A. Agatonovic-Jovin, T. Agheorghiesei, C. Aguilar-Saavedra, J. A. Ahlen, S. P. Ahmadov, F. Aielli, G. Akatsuka, S. Akerstedt, H. Akesson, T. P. Akimov, A. V. Alberghia, G. L. Albert, J. Albicocco, P. Verzini, M. J. Alconada Aleksa, M. Aleksandrov, I. N. Alexab, C. Alexander, G. Alexopoulos, T. Alhroob, M. Ali, B. Aliev, M. Alimontia, G. Alison, J. Alkire, S. P. Allbrooke, B. M. M. Allen, B. W. Allport, P. P. Aloisioa, A. Alonso, A. Alonso, F. Alpigiani, C. Alshehri, A. A. Alstaty, M. Gonzalez, B. Alvarez Piqueras, D. Alvarez Alviggia, M. G. Amadio, B. T. Coutinhoa, Y. Amaral Amelung, C. Amidei, D. Dos Santosa, S. P. Amor Amorima, A. Amoroso, S. Amundsen, G. Anastopoulos, C. Ancu, L. S. Andari, N. Andeen, T. Andersb, C. F. Anders, J. K. Anderson, K. J. Andreazza, A. Andreia, V. Angelidakis, S. Angelozzi, I. Angerami, A. Anisenkovc, A. V. Anjos, N. Annovia, A. Antela, C. Antonelli, M. Antonov, A. Antrim, D. J. Anullia, F. Aoki, M. Bella, L. Aperio Arabidze, G. Arai, Y. Araquea, J. P. Ferraza, V. Araujo Arce, A. T. H. Ardell, R. E. Arduh, F. A. Arguin, J. -F. Argyropoulos, S. Arika, M. Armbruster, A. J. Armitage, L. J. Arnaez, O. Arnold, H. Arratia, M. Arslan, O. Artamonov, A. Artoni, G. Artz, S. Asai, S. Asbah, N. Ashkenazi, A. Asquith, L. Assamagan, K. Astalosa, R. Atkinson, M. Atlay, N. B. Augsten, K. Avolio, G. Axen, B. Ayoub, M. K. Azuelosd, G. Baasa, A. E. Baca, M. J. Bachacou, H. Bachasa, K. Backes, M. Backhaus, M. Bagnaiaa, P. Bahrasemani, H. Baines, J. T. Bajic, M. Baker, O. K. Baldinc, E. M. Balek, P. Balli, F. Balunas, W. K. Banas, E. Banerjeee, Sw. Bannoura, A. A. E. Barak, L. Barberio, E. L. Barberisa, D. Barbero, M. Barillari, T. Barisits, M. -S. Barklow, T. Barlow, N. Barnesc, S. L. Barnett, B. M. Barnett, R. M. Barnovska-Blenessya, Z. Baroncellia, A. Barone, Faculté des Sciences Université Mohamed Premier and LPTPM Oujda Morocco. CPPM Aix-Marseille Université and CNRS/IN2P3 Marseille France. Homer L. Dodge Department of Physics and Astronomy University of Oklahoma Norman OK USA. Department of Physics The University of Texas at Arlington Arlington TX USA. Institute of Physics Azerbaijan Academy of Sciences Baku Azerbaijan. LAL Univ. Paris-Sud CNRS/IN2P3 Université Paris-Saclay Orsay France. Department of Physics University of Toronto Toronto ON Canada. Santa Cruz Institute for Particle Physics University of California Santa Cruz Santa Cruz CA USA. Department of Physics and Astronomy University of Sussex Brighton UK. Raymond and Beverly Sackler School of Physics and Astronomy Tel Aviv University Tel Aviv Israel. Department of Physics Technion: Israel Institute of Technology Haifa Israel. Center for High Energy Physics University of Oregon Eugene OR USA. Department of Physics Stockholm University Stockholm Sweden. The Oskar Klein Centre Stockholm Sweden. INFN Gruppo Collegato di Udine Sezione di Trieste Udine Italy. ICTP Trieste Italy. International Center for Elementary Particle Physics and Department of Physics The University of Tokyo Tokyo Japan. Faculty of Physics and Applied Computer Science AGH University of Science and Technology Krakow Poland. Department of Physics Northern Illinois University DeKalb IL USA. Fakultät für Physik Ludwig-Maximilians-Universität München München Germany. Particle Physics Department Rutherford Appleton Laboratory Didcot UK. Institute of Physics University of Belgrade Belgrade Serbia. Department of Physics Alexandru Ioan Cuza University of Iasi Iasi Romania. Laboratório de Instrumentação e Física Experimental de Partículas-LIP Lisbon Portugal. Departamento de Fisica Teorica y del Cosmos and CAFPE Universidad de Granada Granada Spain. Department of Physics Boston University Boston MA USA. Institut für Kern- und Teilchenphysik Technische Universität Dresden Dr

With the increase in energy of the Large Hadron Collider to a centre-of-mass energy of 13 TeV for Run 2, events with dense environments, such as in the cores of highenergy jets, became a focus for new physics searches as well as measurements of the Standard Model. These environments are characterized by charged-particle separations of the order of the tracking detectors sensor granularity. Basic track quantities are compared between 3.2 fb(-1) of data collected by the ATLAS experiment and simulation of protonproton collisions producing high-transverse-momentum jets at a centre-of-mass energy of 13 TeV. The impact of chargedparticle separations and multiplicities on the track reconstruction performance is discussed. The track reconstruction efficiency in the cores of jets with transverse momenta between 200 and 1600 GeV is quantified using a novel, datadriven, method. The method uses the energy loss, dE/ dx, to identify pixel clusters originating from two charged particles. Of the charged particles creating these clusters, themeasured fraction that fail to be reconstructed is 0.061 +/- 0.006 (stat.) +/- 0.014 (syst.) and 0.093 +/- 0.017 (stat.) +/- 0.021 (syst.) for jet transverse momenta of 200-400GeV and 1400-1600GeV, respectively.

关键词： Charged particles

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Population of Merging Compact Binaries Inferred Using Gravitational Waves through GWTC-3

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Physical Review X 2023年第1期13卷 011048-011048页

作者： R. Abbott T. D. Abbott F. Acernese K. Ackley C. Adams N. Adhikari R. X. Adhikari V. B. Adya C. Affeldt D. Agarwal M. Agathos K. Agatsuma N. Aggarwal O. D. Aguiar L. Aiello A. Ain P. Ajith T. Akutsu P. F. de Alarcón S. Akcay S. Albanesi A. Allocca P. A. Altin A. Amato C. Anand S. Anand A. Ananyeva S. B. Anderson W. G. Anderson M. Ando T. Andrade N. Andres T. Andrić S. V. Angelova S. Ansoldi J. M. Antelis S. Antier F. Antonini S. Appert Koji Arai Koya Arai Y. Arai S. Araki A. Araya M. C. Araya J. S. Areeda M. Arène N. Aritomi N. Arnaud M. Arogeti S. M. Aronson K. G. Arun H. Asada Y. Asali G. Ashton Y. Aso M. Assiduo S. M. Aston P. Astone F. Aubin C. Austin S. Babak F. Badaracco M. K. M. Bader C. Badger S. Bae Y. Bae A. M. Baer S. Bagnasco Y. Bai L. Baiotti J. Baird R. Bajpai M. Ball G. Ballardin S. W. Ballmer A. Balsamo G. Baltus S. Banagiri D. Bankar J. C. Barayoga C. Barbieri B. C. Barish D. Barker P. Barneo F. Barone B. Barr L. Barsotti M. Barsuglia D. Barta J. Bartlett M. A. Barton I. Bartos R. Bassiri A. Basti M. Bawaj J. C. Bayley A. C. Baylor M. Bazzan B. Bécsy V. M. Bedakihale M. Bejger I. Belahcene V. Benedetto D. Beniwal T. F. Bennett J. D. Bentley M. BenYaala F. Bergamin B. K. Berger S. Bernuzzi C. P. L. Berry D. Bersanetti A. Bertolini J. Betzwieser D. Beveridge R. Bhandare U. Bhardwaj D. Bhattacharjee S. Bhaumik I. A. Bilenko G. Billingsley S. Bini R. Birney O. Birnholtz S. Biscans M. Bischi S. Biscoveanu A. Bisht B. Biswas M. Bitossi M.-A. Bizouard J. K. Blackburn C. D. Blair D. G. Blair R. M. Blair F. Bobba N. Bode M. Boer G. Bogaert M. Boldrini L. D. Bonavena F. Bondu E. Bonilla R. Bonnand P. Booker B. A. Boom R. Bork V. Boschi N. Bose S. Bose V. Bossilkov V. Boudart Y. Bouffanais A. Bozzi C. Bradaschia P. R. Brady A. Bramley A. Branch M. Branchesi J. Brandt J. E. Brau M. Breschi T. Briant J. H. Briggs A. Brillet M. Brinkmann P. Brockill A. F. Brooks J. Brooks D. D. Brown S. Brunett G. Bruno R. Bruntz J. Bryant T. Bulik H. J. Bulten A. Buonanno R. Buscicchio D. Buskulic C. Buy R. L. Byer L. Cadonati LIGO Laboratory California Institute of Technology Pasadena California 91125 USA Louisiana State University Baton Rouge Louisiana 70803 USA Dipartimento di Farmacia Università di Salerno I-84084 Fisciano Salerno Italy INFN Sezione di Napoli Complesso Universitario di Monte S. Angelo I-80126 Napoli Italy OzGrav School of Physics & Astronomy Monash University Clayton 3800 Victoria Australia LIGO Livingston Observatory Livingston Louisiana 70754 USA University of Wisconsin-Milwaukee Milwaukee Wisconsin 53201 USA OzGrav Australian National University Canberra Australian Capital Territory 0200 Australia Max Planck Institute for Gravitational Physics (Albert Einstein Institute) D-30167 Hannover Germany Leibniz Universität Hannover D-30167 Hannover Germany Inter-University Centre for Astronomy and Astrophysics Pune 411007 India University of Cambridge Cambridge CB2 1TN United Kingdom Theoretisch-Physikalisches Institut Friedrich-Schiller-Universität Jena D-07743 Jena Germany University of Birmingham Birmingham B15 2TT United Kingdom Center for Interdisciplinary Exploration & Research in Astrophysics (CIERA) Northwestern University Evanston Illinois 60208 USA Instituto Nacional de Pesquisas Espaciais 12227-010 São José dos Campos São Paulo Brazil Gravity Exploration Institute Cardiff University Cardiff CF24 3AA United Kingdom INFN Sezione di Pisa I-56127 Pisa Italy International Centre for Theoretical Sciences Tata Institute of Fundamental Research Bengaluru 560089 India Gravitational Wave Science Project National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan Advanced Technology Center National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan Universitat de les Illes Balears IAC3–IEEC E-07122 Palma de Mallorca Spain University College Dublin Dublin 4 Ireland INFN Sezione di Torino I-10125 Torino Italy Università di Napoli “Federico II” Complesso Universitario di Monte S. Angelo I-80126 Napoli

We report on the population properties of compact binary mergers inferred from gravitational-wave observations of these systems during the first three LIGO-Virgo observing runs. The Gravitational-Wave Transient Catalog 3 (GWTC-3) contains signals consistent with three classes of binary mergers: binary black hole, binary neutron star, and neutron star–black hole mergers. We infer the binary neutron star merger rate to be between 10 and 1700 Gpc−3 yr−1 and the neutron star–black hole merger rate to be between 7.8 and 140 Gpc−3 yr−1, assuming a constant rate density in the comoving frame and taking the union of 90% credible intervals for methods used in this work. We infer the binary black hole merger rate, allowing for evolution with redshift, to be between 17.9 and 44 Gpc−3 yr−1 at a fiducial redshift (z=0.2). The rate of binary black hole mergers is observed to increase with redshift at a rate proportional to (1+z)κ with κ=2.9−1.8+1.7 for z≲1. Using both binary neutron star and neutron star–black hole binaries, we obtain a broad, relatively flat neutron star mass distribution extending from 1.2−0.2+0.1 to 2.0−0.3+0.3M⊙. We confidently determine that the merger rate as a function of mass sharply declines after the expected maximum neutron star mass, but cannot yet confirm or rule out the existence of a lower mass gap between neutron stars and black holes. We also find the binary black hole mass distribution has localized over- and underdensities relative to a power-law distribution, with peaks emerging at chirp masses of 8.3−0.5+0.3 and 27.9−1.8+1.9M⊙. While we continue to find that the mass distribution of a binary’s more massive component strongly decreases as a function of primary mass, we observe no evidence of a strongly suppressed merger rate above approximately 60M⊙, which would indicate the presence of a upper mass gap. Observed black hole spins are small, with half of spin magnitudes below χi≈0.25. While the majority of spins are preferentially aligned wi

关键词： Gravitational wave sources Gravitational waves Gravitational wave detection

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Search for continuous gravitational waves from 20 accreting millisecond x-ray pulsars in O3 LIGO data

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Physical Review D 2022年第2期105卷 022002-022002页

作者： R. Abbott T. D. Abbott F. Acernese K. Ackley C. Adams N. Adhikari R. X. Adhikari V. B. Adya C. Affeldt D. Agarwal M. Agathos K. Agatsuma N. Aggarwal O. D. Aguiar L. Aiello A. Ain T. Akutsu S. Albanesi A. Allocca P. A. Altin A. Amato C. Anand S. Anand A. Ananyeva S. B. Anderson W. G. Anderson M. Ando T. Andrade N. Andres T. Andrić S. V. Angelova S. Ansoldi J. M. Antelis S. Antier S. Appert Koji Arai Koya Arai Y. Arai S. Araki A. Araya M. C. Araya J. S. Areeda M. Arène N. Aritomi N. Arnaud S. M. Aronson K. G. Arun H. Asada Y. Asali G. Ashton Y. Aso M. Assiduo S. M. Aston P. Astone F. Aubin C. Austin S. Babak F. Badaracco M. K. M. Bader C. Badger S. Bae Y. Bae A. M. Baer S. Bagnasco Y. Bai L. Baiotti J. Baird R. Bajpai M. Ball G. Ballardin S. W. Ballmer A. Balsamo G. Baltus S. Banagiri D. Bankar J. C. Barayoga C. Barbieri B. C. Barish D. Barker P. Barneo F. Barone B. Barr L. Barsotti M. Barsuglia D. Barta J. Bartlett M. A. Barton I. Bartos R. Bassiri A. Basti M. Bawaj J. C. Bayley A. C. Baylor M. Bazzan B. Bécsy V. M. Bedakihale M. Bejger I. Belahcene V. Benedetto D. Beniwal T. F. Bennett J. D. Bentley M. BenYaala F. Bergamin B. K. Berger S. Bernuzzi D. Bersanetti A. Bertolini J. Betzwieser D. Beveridge R. Bhandare U. Bhardwaj D. Bhattacharjee S. Bhaumik I. A. Bilenko G. Billingsley S. Bini R. Birney O. Birnholtz S. Biscans M. Bischi S. Biscoveanu A. Bisht B. Biswas M. Bitossi M.-A. Bizouard J. K. Blackburn C. D. Blair D. G. Blair R. M. Blair F. Bobba N. Bode M. Boer G. Bogaert M. Boldrini L. D. Bonavena F. Bondu E. Bonilla R. Bonnand P. Booker B. A. Boom R. Bork V. Boschi N. Bose S. Bose V. Bossilkov V. Boudart Y. Bouffanais A. Bozzi C. Bradaschia P. R. Brady A. Bramley A. Branch M. Branchesi J. E. Brau M. Breschi T. Briant J. H. Briggs A. Brillet M. Brinkmann P. Brockill A. F. Brooks J. Brooks D. D. Brown S. Brunett G. Bruno R. Bruntz J. Bryant T. Bulik H. J. Bulten A. Buonanno R. Buscicchio D. Buskulic C. Buy R. L. Byer L. Cadonati G. Cagnoli C. Cahillane J. Calderón Bustillo J. D. Callaghan T. A. Callister E. Ca LIGO Laboratory California Institute of Technology Pasadena California 91125 USA Louisiana State University Baton Rouge Louisiana 70803 USA Dipartimento di Farmacia Università di Salerno I-84084 Fisciano Salerno Italy INFN Sezione di Napoli Complesso Universitario di Monte S. Angelo I-80126 Napoli Italy OzGrav School of Physics & Astronomy Monash University Clayton 3800 Victoria Australia LIGO Livingston Observatory Livingston Louisiana 70754 USA University of Wisconsin-Milwaukee Milwaukee Wisconsin 53201 USA OzGrav Australian National University Canberra Australian Capital Territory 0200 Australia Max Planck Institute for Gravitational Physics (Albert Einstein Institute) D-30167 Hannover Germany Leibniz Universität Hannover D-30167 Hannover Germany Inter-University Centre for Astronomy and Astrophysics Pune 411007 India University of Cambridge Cambridge CB2 1TN United Kingdom Theoretisch-Physikalisches Institut Friedrich-Schiller-Universität Jena D-07743 Jena Germany University of Birmingham Birmingham B15 2TT United Kingdom Center for Interdisciplinary Exploration & Research in Astrophysics (CIERA) Northwestern University Evanston Illinois 60208 USA Instituto Nacional de Pesquisas Espaciais 12227-010 São José dos Campos São Paulo Brazil Gravity Exploration Institute Cardiff University Cardiff CF24 3AA United Kingdom INFN Sezione di Pisa I-56127 Pisa Italy Gravitational Wave Science Project National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan Advanced Technology Center National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan INFN Sezione di Torino I-10125 Torino Italy Università di Napoli “Federico II” Complesso Universitario di Monte S. Angelo I-80126 Napoli Italy Université de Lyon Université Claude Bernard Lyon 1 CNRS Institut Lumière Matière F-69622 Villeurbanne France Department of Physics The University of Tokyo Bunkyo-ku Tokyo 113-0033 Japan Research Center for the Early Un

Results are presented of searches for continuous gravitational waves from 20 accreting millisecond x-ray pulsars with accurately measured spin frequencies and orbital parameters, using data from the third observing run of the advanced LIGO and advanced Virgo detectors. The search algorithm uses a hidden Markov model, where the transition probabilities allow the frequency to wander according to an unbiased random walk, while the J-statistic maximum-likelihood matched filter tracks the binary orbital phase. Three narrow subbands are searched for each target, centered on harmonics of the measured spin frequency. The search yields 16 candidates, consistent with a false alarm probability of 30% per subband and target searched. These candidates, along with one candidate from an additional target-of-opportunity search done for SAX J1808.4−3658, which was in outburst during one month of the observing run, cannot be confidently associated with a known noise source. Additional follow-up does not provide convincing evidence that any are a true astrophysical signal. When all candidates are assumed nonastrophysical, upper limits are set on the maximum wave strain detectable at 95% confidence, h095%. The strictest constraint is h095%=4.7×10−26 from IGR J17062−6143. Constraints on the detectable wave strain from each target lead to constraints on neutron star ellipticity and r-mode amplitude, the strictest of which are ε95%=3.1×10−7 and α95%=1.8×10−5 respectively. This analysis is the most comprehensive and sensitive search of continuous gravitational waves from accreting millisecond x-ray pulsars to date.

关键词： Gravitational waves Binary stars Neutron stars & pulsars

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