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Quantum Simulation for High-energy Physics

PRX Quantum 2023年第2期4卷 027001-027001页

作者： Christian W. Bauer Zohreh Davoudi A. Baha Balantekin Tanmoy Bhattacharya Marcela Carena Wibe A. de Jong Patrick Draper Aida el-Khadra Nate Gemelke Masanori Hanada Dmitri Kharzeev Henry Lamm Ying-Ying Li Junyu Liu Mikhail Lukin Yannick Meurice Christopher Monroe Benjamin Nachman Guido Pagano John Preskill enrico Rinaldi Alessandro Roggero David I. Santiago Martin J. Savage Irfan Siddiqi George Siopsis David Van Zanten Nathan Wiebe Yukari Yamauchi Kübra Yeter-Aydeniz Silvia Zorzetti Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics Maryland Center for Fundamental Physics and the NSF Institute for Robust Quantum Simulation University of Maryland College Park Maryland 20742 USA Department of Physics University of Wisconsin Madison Wisconsin 53706 USA T-2 Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Fermi National Accelerator Laboratory Batavia Illinois 60510 USA Enrico Fermi Institute University of Chicago Chicago Illinois 60637 USA Kavli Institute for Cosmological Physics University of Chicago Chicago Illinois 60637 USA Department of Physics University of Chicago Chicago Illinois 60637 USA Department of Physics and Illinois Center for the Advanced Study of the Universe and Illinois Quantum Information Science and Technology Center University of Illinois Urbana Illinois 61801 USA QuEra Computing Inc Boston Massachusetts 02135 USA Department of Mathematics University of Surrey Guildford Surrey GU2 7XH United Kingdom Center for Nuclear Theory Department of Physics and Astronomy Stony Brook University New York 11794-3800 USA Department of Physics Brookhaven National Laboratory Upton New York 11973 USA Peng Huanwu Center for Fundamental Theory Hefei Anhui 230026 China Interdisciplinary Center for Theoretical Study University of Science and Technology of China Hefei Anhui 230026 China Pritzker School of Molecular Engineering Chicago Quantum Exchange and Kadanoff Center for Theoretical Physics University of Chicago Illinois 60637 USA qBraid Co. Harper Court 5235 Chicago Illinois 60615 USA Department of Physics Harvard University Cambridge Massachusetts 02138 USA Department of Physics and Astronomy University of Iowa Iowa City Iowa 52242 USA Duke Quantum Center Duke University Durham North Carolina 27701 USA Department of Electrical and Computer Engineering Duke University Durham North Carolina 27708 USA Department of Physics Duke University

It is for the first time that quantum simulation for high-energy physics (HeP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in quantum information sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HeP mission. This Roadmap is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.

关键词： Quantum simulation

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Beyond Low earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health

arXiv

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arXiv 2021年

作者： Scott, Ryan T. Antonsen, erik L. Sanders, Lauren M. Hastings, Jaden J.A. Park, Seung-Min Mackintosh, Graham Reynolds, Robert J. Hoarfrost, Adrienne L. Sawyer, Aenor Greene, Casey S. Glicksberg, Benjamin S. Theriot, Corey A. Berrios, Daniel C. Miller, Jack Babdor, Joel Barker, Richard Baranzini, Sergio e. Beheshti, Afshin Chalk, Stuart Delgado-Aparicio, Guillermo M. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Kalantari, John Khezeli, Kia Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Martin, Hector Garcia Mason, Christopher e. Matar, Mona Mias, George I. Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Parsons-Wingerter, Patricia Prabhu, R.K. Qutub, Amina Ann Rask, Jon Saravia-Butler, Amanda Saria, Suchi Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Yang, Jason H. Zitnik, Marinka Costes, Sylvain V. KBR Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Department of Urology Department of Radiology Stanford University School of Medicine StanfordCA94305 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett FieldCA94035 United States Mortality Research & Consulting Inc. HoustonTX77058 United States Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States UC Space Health Department of Orthopaedic Surgery University of California San Francisco San FranciscoCA94143 United States Center for Health AI Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine Anschutz Medical Campus AuroraCO80045 United States Hasso Plattner Institute for Digital Health at Mount Sinai Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New YorkNY10065 United States Department of Preventive Medicine and Community Health UTMB GalvestonTX77551 United States Human Health and Performance Directorate NASA Johnson Space Center HoustonTX77058 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Data Scienc

Human space exploration beyond low earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable earth-independence, rather than earth-reliance. Promising developments in the fields of artificial intelligence and machine learning for biology and health can address these needs. We propose an appropriately autonomous and intelligent Precision Space Health system that will monitor, aggregate, and assess biomedical statuses;analyze and predict personalized adverse health outcomes;adapt and respond to newly accumulated data;and provide preventive, actionable, and timely insights to individual deep space crew members and iterative decision support to their crew medical officer. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration, on future applications of artificial intelligence in space biology and health. In the next decade, biomonitoring technology, biomarker science, spacecraft hardware, intelligent software, and streamlined data management must mature and be woven together into a Precision Space Health system to enable humanity to thrive in deep space. © 2021, CC BY.

关键词： earth (planet)

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHeMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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Beyond Low earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

arXiv

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arXiv 2021年

作者： Sanders, Lauren M. Yang, Jason H. Scott, Ryan T. Qutub, Amina Ann Martin, Hector Garcia Berrios, Daniel C. Hastings, Jaden J.A. Rask, Jon Mackintosh, Graham Hoarfrost, Adrienne L. Chalk, Stuart Kalantari, John Khezeli, Kia Antonsen, erik L. Babdor, Joel Barker, Richard Baranzini, Sergio e. Beheshti, Afshin Delgado-Aparicio, Guillermo M. Glicksberg, Benjamin S. Greene, Casey S. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Mason, Christopher e. Matar, Mona Mias, George I. Miller, Jack Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Park, Seung-Min Parsons-Wingerter, Patricia Prabhu, R.K. Reynolds, Robert J. Saravia-Butler, Amanda Saria, Suchi Sawyer, Aenor Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik Theriot, Corey A. van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Zitnik, Marinka Costes, Sylvain V. Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Center for Emerging and Re-Emerging Pathogens Department of Microbiology Biochemistry and Molecular Genetics Rutgers New Jersey Medical School NewarkNJ07103 United States KBR Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States AI MATRIX Consortium Department of Biomedical Engineering University of Texas San Antonio and UT Health Sciences San AntonioTX78249 United States Biological Systems and Engineering Division Lawrence Berkeley National Lab. BerkeleyCA94608 United States DOE Agile BioFoundry EmeryvilleCA94608 United States Joint BioEnergy Institute EmeryvilleCA94608 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Office of the Center Director NASA Ames Research Center Moffett Field CA94035 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett Field CA94035 United States Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Center for Individualized Medicine Department of Surgery Department of Quantitative Health Sciences Mayo Clinic RochesterMN55905 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin - Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Data Science Analytics Georgia Institute of Technology Lima15024

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space. © 2021, CC BY.

关键词： Predictive analytics

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ROLe OF SIMULATION IN RAPID PROTOTYPING FOR CONCePT DeVeLOPMeNT

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NAVAL eNGINeeRS JOURNAL 1991年第3期103卷 204-211页

作者： KING, JF BARTON, De J. Fred King:is the manager of the Advanced Technology Department for Unisys in Reston Virginia. He earned his Ph.D. in mathematics from the University of Houston in 1977. He has been principal investigator of research projects in knowledge engineering pattern recognition and heuristic problem-solving. Efforts include the development of a multi-temporal multispectral classifier for identifying graincrops using LANDSAT satellite imagery data for NASA. Also as a member of the research team for a NCI study with Baylor College of Medicine and NASA he helped develop techniques for detection of carcinoma using multispectral microphotometer scans of lung tissue. He established and became technical director of the AI Laboratory for Ford Aerospace where he developed expert scheduling modeling and knowledge acquisition systems for NASA. Since joining Unisys in 1985 he has led the development of object-oriented programming environments blackboard architectures data fusion techniques using neural networks and intelligent data base systems. Douglas E. Barton:is manager of Logistics Information Systems for Unisys in Reston Virginia. He earned his B.A. degree in computer science from the College of William and Mary in 1978 and did postgraduate work in London as a Drapers Company scholar. Since joining Unisys in 1981 his work has concentrated on program management and software engineering of large scale data base management systems and design and implementation of knowledge-based systems in planning and logistics. As chairman of the Logistics Data Subcommittee of the National Security Industrial Association (NSIA) he led an industry initiative which examined concepts in knowledge-based systems in military logistics. His responsibilities also include evaluation development and tailoring of software engineering standards and procedures for data base and knowledge-based systems. He is currently program manager of the Navigation Information Management System which provides support to the Fleet Ballistic Missile Progr

A valuable technique during concept development is rapid prototyping of software for key design components. This approach is particularly useful when the optimum design approach is not readily apparent or several known alternatives need to be rapidly evaluated. A problem inherent in rapid prototyping is the lack of a "target system" with which to interface. Some alternatives are to develop test driver libraries, integrate the prototype with an existing working simulator, or build one for the specific problem. This paper presents a unique approach to concept development using rapid prototyping for concept development and scenario-based simulation for concept verification. The rapid prototyping environment, derived from artificial intelligence technology, is based on a blackboard architecture. The rapid prototype simulation capability is provided through an object-oriented modeling environment. It is shown how both simulation and blackboard technologies are used collectively to rapidly gain insight into a tenacious problem. A specific example will be discussed where this approach was used to evolve the logic of a mission controller for an autonomous underwater vehicle.

关键词： Military engineering

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Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

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The Lancet 2020年第10258期396卷 1204-1222页

作者： Abbafati, Cristiana Abbas, Kaja M. Abbasi, Mohammad Abbasifard, Mitra Abbasi-Kangevari, Mohsen Abbastabar, Hedayat Abd-Allah, Foad Abdelalim, Ahmed Abdollahi, Mohammad Abdollahpour, Ibrahim Abedi, Aidin Abedi, Parisa Abegaz, Kedir Hussein Abolhassani, Hassan Abosetugn, Akine eshete Aboyans, Victor Abrams, elissa M. Abreu, Lucas Guimarães Abrigo, Michael R.M. Abu Haimed, Abdulaziz Khalid Abualhasan, Ahmed Abu-Gharbieh, eman Abu-Raddad, Laith Jamal Abushouk, Abdelrahman I. Acebedo, Alyssa Ackerman, Ilana N. Adabi, Maryam Adair, Tim Adamu, Abdu A. Adebayo, Oladimeji M. Adedeji, Isaac Akinkunmi Adekanmbi, Victor Adelson, Jaimie D. Adeoye, Abiodun Moshood Adetokunboh, Olatunji O. Adham, Davoud Advani, Shailesh M. Afarideh, Mohsen Afshari, Mahdi Afshin, Ashkan Agardh, emilie e. Agarwal, Gina Agasthi, Pradyumna Agesa, Kareha M. Aghaali, Mohammad Aghamir, Seyed Mohammad Kazem Agrawal, Anurag Ahmad, Tauseef Ahmadi, Alireza Ahmadi, Keivan Ahmadi, Mehdi Ahmadieh, Hamid Ahmadpour, ehsan Ahmed, Muktar Beshir Aji, Budi Akalu, Temesgen Yihunie Akinyemi, Rufus Olusola Akinyemiju, Tomi Akombi, Blessing Akunna, Chisom Joyqueenet Alahdab, Fares Al-Aly, Ziyad Alam, Khurshid Alam, Noore Alam, Samiah Alam, Tahiya Alanezi, Fahad Mashhour Alanzi, Turki M. Albertson, Samuel B. Alcalde-Rabanal, Jacqueline elizabeth Alema, Niguse Meles Alemu, Biresaw Wassihun Alemu, Yihun Mulugeta Alhabib, Khalid F. Alhassan, Robert Kaba Ali, Muhammad Ali, Saqib Alicandro, Gianfranco Alijanzadeh, Mehran Alinia, Cyrus Alipour, Vahid Alizade, Hesam Aljunid, Syed Mohamed Alla, François Allebeck, Peter Almadi, Majid Abdulrahman Hamad Almasi, Ali Almasi-Hashiani, Amir Almasri, Nihad A. Al-Mekhlafi, Hesham M. Almulhim, Abdulaziz M. Alonso, Jordi Al-Raddadi, Rajaa M. Altirkawi, Khalid A. Alumran, Arwa Khalid Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Amare, Azmeraw T. Amare, Bekalu Amini, Saeed Amini-Rarani, Mostafa Aminorroaya, Arya Amiri, Fatemeh Amit, Arianna Maever L. Amugsi, Dickson A. Amul, Gianna Gayle Herrera Anbesu, etsay Woldu Ancuceanu, Robert Anderl Department of Juridical and Economic Studies La Sapienza University Rome Italy Department of Infectious Disease Epidemiology London School of Hygiene and Tropical Medicine London United Kingdom Social Determinants of Health Research Center Tehran Iran Department of Neurology Cairo University Cairo Egypt School of Pharmacy Tehran Iran The Institute of Pharmaceutical Sciences (TIPS) Tehran Iran Neuroscience Research Center Isfahan University of Medical Sciences Isfahan Iran Biostatistics Department Near East University Nicosia Cyprus Biostatistics and Health Informatics Madda Walabu University Bale Robe Ethiopia Research Center for Immunodeficiencies Tehran Iran Karolinska University Hospital Huddinge Sweden Department of Cardiology Dupuytren University Hospital Limoges France University of Limoges Limoges France Department of Pediatric Dentistry Federal University of Minas Gerais Belo Horizonte Brazil Department of Research Philippine Institute for Development Studies Quezon City Philippines Department of Healthcare Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Harvard Medical School Boston MA United States Department of Medicine Ain Shams University Cairo Egypt Hamadan University of Medical Sciences Hamadan Iran School of Medicine Cardiff University Cardiff United Kingdom School of Laboratory Medicine and Science University College Hospital Ibadan Ibadan Nigeria Institute of Cardiovascular Diseases University of Ibadan Ibadan Nigeria Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Cape Town South Africa Department of Global Health Stellenbosch University Cape Town South Africa School of Health Ardabil University of Medical Science Ardabil Iran Social Behavioral Research Branch National Institute of Health Bethesda MD United States Department of Oncology Georgetown University Washington DC DC United States Department of Health Metrics Sciences School of Medicine Seattle WA

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw value

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Creation and analysis of biochemical constraint-based models: The COBRA Toolbox v3.0

arXiv

引用

arXiv 2017年

作者： Heirendt, Laurent Arreckx, Sylvain Pfau, Thomas Mendoza, Sebastián N. Richelle, Anne Heinken, Almut Haraldsdóttir, Hulda S. Wachowiak, Jacek Keating, Sarah M. Vlasov, Vanja Magnusdóttir, Stefania Ng, Chiam Yu Preciat, German Žagare, Alise Chan, Siu H.J. Aurich, Maike K. Clancy, Catherine M. Modamio, Jennifer Sauls, John T. Noronha, Alberto Bordbar, Aarash Cousins, Benjamin el Assal, Diana C. Valcarcel, Luis V. Apaolaza, Iñigo Ghaderi, Susan Ahookhosh, Masoud Guebila, Marouen Ben Kostromins, Andrejs Sompairac, Nicolas Le, Hoai M. Ma, Ding Sun, Yuekai Wang, Lin Yurkovich, James T. Oliveira, Miguel A.P. Vuong, Phan T. el Assal, Lemmer P. Kuperstein, Inna Zinovyev, Andrei Scott Hinton, H. Bryant, William A. Aragón Artacho, Francisco J. Planes, Francisco J. Stalidzans, egils Maass, Alejandro Vempala, Santosh Hucka, Michael Saunders, Michael A. Maranas, Costas D. Lewis, Nathan e. Sauter, Thomas Palsson, Bernhard Ø. Thiele, Ines Fleming, Ronan M.T. Luxembourg Centre for Systems Biomedicine University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg Life Sciences Research Unit University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg University of Chile Blanco Encalada 2085 Santiago Chile Department of Pediatrics University of California San Diego School of Medicine San DiegoCA92093 United States Hinxton CambridgeCB10 1SD United Kingdom Department of Chemical Engineering Pennsylvania State University University University ParkPA16802 United States Department of Physics University of California San Diego 9500 Gilman Dr. San DiegoCA92093 United States Bioinformatics and Systems Biology Program University of California San Diego San DiegoCA United States Sinopia Biosciences San DiegoCA United States School of Computer Science Algorithms and Randomness Center Georgia Institute of Technology AtlantaGA United States Biomedical Engineering and Sciences Department TECNUN University of Navarra Paseo de Manuel Lardizabal 13 San Sebastian20018 Spain Institute of Microbiology and Biotechnology University of Latvia Jelgavas iela 1 RigaLV-1004 Latvia Department of Management Science and Engineering Stanford University StanfordCA94305-4026 United States Bioengineering Department University of California San Diego San DiegoCA United States Utah State University Research Foundation 1695 North Research Park Way North LoganUT84341 United States Centre for Integrative Systems Biology and Bioinformatics Department of Life Sciences Imperial College London London United Kingdom Department of Mathematics University of Alicante Spain California Institute of Technology Computing and Mathematical Sciences MC 305-16 1200 E. California Blvd. PasadenaCA91125 United States Mathomics Center for Mathematical Modeling University of Chile Beauchef 851 Santiago Chile Novo Nordisk Foundation Center for Biosustainability University of California San Diego San DiegoCA92093 Uni

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain and experimental design, network visualisation as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios. This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Data integration

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Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and experimental Aspects

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Molecular Cytogenetics 2017年第2期10卷 77-94页

作者： Athel Cornish-Bowden David Rasnick Henry H. Heng Steven Horne Batoul Abdallah Guo Liu Christine J. Ye Mathew Bloomfield Mark D. Vincent C. Marcelo Aldaz Jenny Karlsson Anders Valind Caroline Jansson David Gisselsson Jennifer A. Marshall Graves Aleksei A. Stepanenko Svitlana V. Andreieva Kateryna V. Korets Dmytro O. Mykytenko Stanislav S. Avdieiev Nataliya L. Huleyuk Vladimir P. Baklaushev Oksana A. Kovaleva Vladimir P. Chekhonin Yegor S. Vassetzky Bjorn Bakker Aaron S. Taudt Mirjam e. Belderbos David Porubsky Diana C. J. Spierings Tristan V. de Jong Nancy Halsema Hinke G. Kazemier Karina Hoekstra-Wakker Victor Guryev Peter M. Lansdorp Maria Colomé Tatché Floris Foijer Allan Bradley eveline S. J. M. de Bont Anke van den Berg Thomas Liehr Nicolaas C. Baudoin Joshua M. Nicholson Kimberly Soto Daniela Cimini Isabel Quintanilla Jordi Camps M. Dürrbaum N. Donnelly V. Passerini C. Kruse Z. Storchová B. Habermann Daniele Mandrioli Fiorella Belpoggi ellen K Silbergeld Melissa J Perry Rolf I. Skotheim Marthe Løvf Bjarne Johannessen Andreas M. Hoff Sen Zhao Jonas M. SveeStrømme Anita Sveen Ragnhild A. Lothe R. Hehlmann A. Voskanyan A. Fabarius Alfred Böcking Stefan Biesterfeld Leonid Berynskyy Christof Börgermann Rainer engers Josef Dietz A. Fritz N. Page C. Tye G. Stein J. Stein N. Sehgal R. Berezney J. Vecerova B. Stojkovicz H. Ding J. Xu S. Bhattacharya Xue Gong Sarah Grasedieck Julian Swoboda Jonathan R. Pollack Frank G. Rücker Lars Bullinger Fani-Marlen Roumelioti Maria Chiourea Christina Raftopoulou Sarantis Gagos Peter Duesberg Mat Bloomfield Sunyoung Hwang Hans Tobias Gustafsson Ciara O’Sullivan Aracelli Acevedo-Colina eduardo M. Torres Xinhe Huang Robert C. Dickson Christian Klose Andrej Schevchenko Paola Cavaliere Noah Dephoure Martha R. Stampfer Mark A. LaBarge James C. Garbe Lukas Vrba Bernard Futscher Yi-Hong Zhou Andrew L. Trinh Michelle Digman Directeur de Recherche (Émérite) Centre National de la Recherche Scientifique (CNRS) Marseilles France 549 Fairbanks Ave. Oakland California 94610 USA Wayne State University School of Medicine Detroit MI USA University of Michigan School of Medicine Ann Arbor MI USA Department of Molecular and Cell Biology UC Berkeley Donner Lab Berkeley CA USA Department of Natural Sciences and Mathematics Dominican University of California San Rafael CA USA Department of Medical Oncology London Regional Cancer Program London Ontario N6A 4L6 Canada Department of Epigenetics and Molecular Carcinogenesis University of Texas M.D. Anderson Cancer Center Science Park Smithville TX 78957 USA Department of Laboratory Medicine Division of Clinical Genetics Lund University Lund SE221 84 Sweden Department of Clinical Sciences Division of Oncology and Pathology Lund University Lund SE221 85 Sweden Skåne Regional and Univeristy Laboratories Department of Pathology Lund SE221 85 Sweden School of Life Sciences La Trobe University Melbourne Vic 3168 Australia Department of Functional Genomics Institute of Molecular Biology and Genetics Kyiv 03680 Ukraine Institute of Hereditary Pathology National Academy of Medical Sciences of Ukraine Lviv 79008 Ukraine Federal Research and Clinical Center FMBA of Russia Moscow 115682 Russia R.E. Kavetsky Institute of Experimental Pathology Oncology and Radiobiology Kyiv 03022 Ukraine V. P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology Ministry of Health of the Russian Federation Moscow 119034 Russia Department of Medicinal Nanobiotechnology Pirogov Russian State Medical University Moscow 117997 Russia CNRS UMR8126 Université Paris-Sud 11 Institut de Cancérologie Gustave Roussy Villejuif 94805 France European Research Institute for the Biology of Ageing University of Groningen University Medical Center Groningen A. Deusinglaan 1 NL-9713 AV Groningen The Netherlands Department of Paediatrics University

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Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

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Nature communications 2020年第1期11卷 4499页

作者： Igor Mandric Jeremy Rotman Harry Taegyun Yang Nicolas Strauli Dennis J Montoya William Van Der Wey Jiem R Ronas Benjamin Statz Douglas Yao Velislava Petrova Alex Zelikovsky Roberto Spreafico Sagiv Shifman Noah Zaitlen Maura Rossetti K Mark Ansel eleazar eskin Serghei Mangul Department of Computer Science University of California Los Angeles 404 Westwood Plaza Los Angeles CA 90095 USA. Department of Clinical Pharmacy School of Pharmacy University of Southern California 1540 Alcazar Street Los Angeles CA 90033 USA. Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles 611 Charles E. Young Drive East Los Angeles CA 90095-1570 USA. Biomedical Sciences Graduate Program University of California San Francisco 1675 Owens Street Suite 310 San Francisco CA 94143-0523 USA. Department of Molecular Cell and Developmental Biology University of California Los Angeles 610 Charles E. Young Drive South Los Angeles CA 90095 USA. Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles 609 Charles E. Young Drive East Los Angeles CA 90095 USA. Program in Bioinformatics and Integrative Genomics Harvard Medical School 10 Shattuck Street Suite 514 Boston MA 02115 USA. Wellcome Trust Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA UK. Department of Computer Science Georgia State University 33 Gilmer Street SE Atlanta GA 30303 USA. The Laboratory of Bioinformatics I.M. Sechenov First Moscow State Medical University Moscow 119991 Russia. Institute for Quantitative and Computational Biosciences University of California Los Angeles 611 Charles E. Young Drive East Los Angeles CA 90095 USA. Department of Genetics The Institute of Life Sciences The Hebrew University of Jerusalem Jerusalem 9190401 Israel. Department of Medicine University of California San Francisco 533 Parnassus Avenue San Francisco CA 94143 USA. Immunogenetics Center Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles 1000 Veteran Avenue Los Angeles CA 90095-1652 USA. Sandler Asthma Basic Research Center Department of Microbiology and Immunology University of California San Francisco 513 Parnass

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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Supernova model discrimination with Hyper-Kamiokande

arXiv

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arXiv 2021年

作者： Abe, K. Adrich, P. Aihara, H. Akutsu, R. Alekseev, I. Ali, A. Ameli, F. Anghel, I. Anthony, L.H.V. Antonova, M. Araya, A. Asaoka, Y. Ashida, Y. Aushev, V. Ballester, F. Bandac, I. Barbi, M. Barker, G.J. Barr, G. Batkiewicz-Kwasniak, M. Bellato, M. Berardi, V. Bergevin, M. Bernard, L. Bernardini, e. Berns, L. Bhadra, S. Bian, J. Blanchet, A. Blaszczyk, F.D.M. Blondel, A. Boiano, A. Bolognesi, S. Bonavera, L. Booth, N. Borjabad, S. Boschi, T. Bose, D. Boyd, S.B. Bozza, C. Bravar, A. Bravo-Berguño, D. Bronner, C. Brown, L. Bubak, A. Buchowicz, A. Avanzini, M. Buizza Cafagna, F.S. Calabria, N.F. Calvo-Mozota, J.M. Cao, S. Cartwright, S.L. Carroll, A. Catanesi, M.G. Cebriàn, S. Chabera, M. Chakraborty, S. Checchia, C. Choi, J.H. Choubey, S. Cicerchia, M. Coleman, J. Collazuol, G. Cook, L. Cowan, G. Cuen-Rochin, S. Danilov, M. Lopez, G. Daz de la Fuente, e. de Perio, P. de Rosa, G. Dealtry, T. Densham, C.J. Dergacheva, A. Deshmukh, N. Devi, M.M. Di Lodovico, F. Di Meo, P. Di Palma, I. Doyle, T.A. Drakopoulou, e. Drapier, O. Dumarchez, J. Dunne, P. Dziewiecki, M. eklund, L. el Hedri, S. ellis, J. emery, S. esmaili, A. esteve, R. evangelisti, A. Feely, M. Fedotov, S. Feng, J. Fernandez, P. Fernández-Martinez, e. Ferrario, P. Ferrazzi, B. Feusels, T. Finch, A. Finley, C. Fiorentini, A. Fiorillo, G. Fitton, M. Frankiewicz, K. Friend, M. Fujii, Y. Fukuda, Y. Galinski, G. Gao, J. Garde, C. Garfagnini, A. Garode, S. Gialanella, L. Giganti, C. Gomez-Cadenas, J.J. Gonin, M. González-Nuevo, J. Gorin, A. Gornea, R. Gousy-Leblanc, V. Gramegna, F. Grassi, M. Grella, G. Guigue, M. Gumplinger, P. Hadley, D.R. Harada, M. Hartfiel, B. Hartz, M. Hassani, S. Hastings, N.C. Hayato, Y. Hernando-Morata, J.A. Herrero, V. Hill, J. Hiraide, K. Hirota, S. Holin, A. Horiuchi, S. Hoshina, K. Hultqvist, K. Iacob, F. Ichikawa, A.K. Ibnsalih, W. Idrissi Iijima, T. Ikeda, M. Inomoto, M. Inoue, K. Insler, J. Ioannisian, A. Ishida, T. Ishidoshiro, K. AGH University of Science and Technology Faculty of Computer Science Electronics and Telecommunications Krakow Poland Boston University Department of Physics BostonMA United States University of British Columbia Department of Physics and Astronomy VancouverBC Canada British Columbia Institute of Technology Physics Department BurnabyBC Canada Università della Campania L. Vanvitelli INFN Sezione di Napoli Napoli Italy Carleton University Department of Physics OttawaON Canada University of California Davis Department of Physics DavisCA United States University of California Irvine Department of Physics and Astronomy IrvineCA United States California State University Department of Physics CarsonCA United States Charles University IPNP FMF Prague Czech Republic Chonnam National University Department of Physics Gwangju Korea Republic of Dongshin University Laboratory for High Energy Physics Naju Korea Republic of Donostia International Physics Center Ikerbasque Foundation Basque Country Spain Ecole Polytechnique IN2P3-CNRS Laboratoire Leprince-Ringuet Palaiseau France University of Edinburgh School of Physics and Astronomy Edinburgh United Kingdom ETH Zurich Institute for Particle and Astroparticle Physics Zurich Switzerland University of Geneva Section de Physique DPNC Geneva Switzerland GIST College Gwangju Institute of Science and Technology Gwangju Korea Republic of University of Glasgow School of Physics and Astronomy Glasgow United Kingdom Universidad de Guadalajara CUCEI Departamento de Fisica Jal Guadalajara Mexico Universidad de Guadalajara CUCEA IT.Ph.D. program Jal Guadalajara Mexico H. Niewodniczá nski Institute of Nuclear Physics PAN Cracow Poland University of Hawaii Department of Physics and Astronomy HonoluluHI United States Imperial College London Department of Physics London United Kingdom Indian Institute of Technology Guwahati Guwahati India Indian Institute of Technology Jodhpur Department of Physics Raj

Core-collapse supernovae are among the most magnificent events in the observable universe. They produce many of the chemical elements necessary for life to exist and their remnants-neutron stars and black holes-are interesting astrophysical objects in their own right. However, despite millennia of observations and almost a century of astrophysical study, the explosion mechanism of core-collapse supernovae is not yet well understood. Hyper-Kamiokande is a next-generation neutrino detector that will be able to observe the neutrino flux from the next galactic core-collapse supernova in unprecedented detail. We focus on the first 500 ms of the neutrino burst, corresponding to the accretion phase, and use a newly-developed, high-precision supernova event generator to simulate Hyper-Kamiokande's response to five different supernova models. We show that Hyper-Kamiokande will be able to distinguish between these models with high accuracy for a supernova at a distance of up to 100 kpc. Once the next galactic supernova happens, this ability will be a powerful tool for guiding simulations towards a precise reproduction of the explosion mechanism observed in nature. Copyright © 2021, The Authors. All rights reserved.

关键词： Supernovae

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