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arXiv 2018年

作者： Bevilacqua, Andrea Pitman, E. Bruce Patra, Abani Neri, Augusto Bursik, Marcus Voight, Barry Department of Earth Sciences University at Buffalo BuffaloNY United States Department of Materials Design and Innovation University at Buffalo NY United States Department of Mechanical and Aerospace Engineering University at Buffalo BuffaloNY United States Computational Data Science and Engineering University at Buffalo BuffaloNY United States Sezione di Pisa Istituto Nazionale di Geosica e Vulcanologia Pisa Italy Department of Geosciences Pennsylvania State University University ParkPA United States

We introduce a doubly stochastic method for performing material failure theory based forecasts of volcanic eruptions. The method enhances the well known Failure Forecast Method equation, introducing a new formulation similar to the Hull-White model in financial mathematics. In particular, we incorporate a stochastic noise term in the original equation, and systematically characterize the uncertainty. The model is a stochastic differential equation with mean reverting paths, where the traditional ordinary differential equation defines the mean solution. Our implementation allows the model to make excursions from the classical solutions, by including uncertainty in the estimation. The doubly stochastic formulation is particularly powerful, in that it provides a complete posterior probability distribution, allowing users to determine a worst case scenario with a specified level of confidence. We apply the new method on historical datasets of precursory signals, across a wide range of possible values of convexity in the solutions and amounts of scattering in the observations. The results show the increased forecasting skill of the doubly stochastic formulation of the equations if compared to statistical regression. Copyright © 2018, The Authors. All rights reserved.

关键词： Volcanoes

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Strikingly high fraction of fast rotators in Magellanic Cloud star clusters

arXiv

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arXiv 2025年

作者： Ettorre, Greta Mazzi, Alessandro Girardi, Léo Marigo, Paola Pastorelli, Giada Goudfrooij, Paul Williams, Benjamin F. Bellini, Andrea Bressan, Alessandro Chen, Yang Correnti, Matteo Costa, Guglielmo Dalcanton, Julianne J. Facchini, Pietro Fouesneau, Morgan Nguyen, Chi Thanh Volpato, Guglielmo Dipartimento di Fisica e Astronomia "Galileo Galilei" Università di Padova Vicolo dell’Osservatorio 3 PadovaI-35122 Italy Dipartimento di Fisica e Astronomia "Augusto Righi" Alma Mater Studiorum Università di Bologna Via Gobetti 93/2 BolognaI-40129 Italy INAF - Osservatorio di Astrofisica e Scienza dello Spazio di Bologna Via Gobetti 93/3 Bologna40129 Italy INAF - Osservatorio Astronomico di Padova Vicolo dell’Osservatorio 5 PadovaI-35122 Italy Space Telescope Science Institute 3700 San Martin drive BaltimoreMD21218 United States Department of Astronomy University of Washington Box 351580 SeattleWA98195 United States SISSA International School for Advanced Studies Trieste Italy School of Physics and optoelectronic engineering Anhui University Hefei230601 China National Astronomical Observatories Chinese Academy of Sciences Beijing100101 China INAF - Osservatorio Astronomico di Roma Via Frascati 33 Monteporzio Catone Rome00078 Italy ASI - Space Science Data Center Via del Politecnico RomeI-00133 Italy Université de Lyon Univ Lyon1 ENS de Lyon CNRS Centre de Recherche Astrophysique de Lyon UMR5574 Saint-Genis-LavalF-69230 France Center for Computational Astrophysics Flatiron Institute 162 Fifth Avenue New YorkNY10010 United States Astronomisches Rechen-Institut Zentrum für Astronomie der Universität Heidelberg Mönchhofstr. 12-14 HeidelbergD-69120 Germany Königstuhl 17 Heidelberg69117 Germany INAF - Osservatorio Astronomico di Trieste via Tiepolo 11 Trieste34143 Italy

There has been growing evidence that the rich star clusters in the Magellanic Clouds contain significant fractions of rapidly rotating stars. In this work, we aim to constrain these fractions by studying the colour-magnitude diagrams of four star clusters, selected among those with the most striking signatures of fast rotators. Using isochrones derived from parsec v2.0 stellar tracks, we generate distinct stellar populations, each covering a limited interval of initial rotation rates ωi, referred to as ‘Partial Models’ (PMs). Using optimization algorithms and Monte Carlo Markov Chains, PMs are combined to create the final best-fitting model. In our analysis, we adopt two key assumptions: a uniform age and an isotropic distribution of stellar spin axes within each cluster. The solutions are allowed to explore the entire range of ωi, and different values of age, metallicity, distance and foreground extinction. We find that the rotational velocity distributions in all four clusters reveal a high fraction of stars with ωi close to the break-up value, in all cases. Specifically, the fraction of stars with ωi > 0.7 exceeds 80% in the clusters NGC 419 of the Small Magellanic Cloud (SMC) and NGC 1831 and NGC 1866 of the Large Magellanic Cloud (LMC). For NGC 2203 of the LMC, this fraction is smaller, although it still exceeds 50%, confirming that also this cluster is mainly populated by fast-rotating stars. Copyright © 2025, The Authors. All rights reserved.

关键词： Monte Carlo methods

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Corrigendum to “Single-walled carbon nanotube membranes for optical applications in the extreme ultraviolet rang” [155, (2019) 734–739]

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Carbon 2020年 156卷 576-576页

作者： V.M. Gubarev V.Y. Yakovlev M.G. Sertsu O.F. Yakushev V.M. Krivtsun Yu G. Gladush I.A. Ostanin A. Sokolov F. Schäfers V.V. Medvedev A.G. Nasibulin Moscow Institute of Physics and Technology (State University) Institutskiy pereulok str. 9 Dolgoprudny Moscow Region 141701 Russia Skolkovo Institute of Science and Technology Nobel str. 3 Moscow 121205 Russia Helmholtz Zentrum Berlin (BESSY-II) Albert-Einstein-Strasse 15 D-12489 Berlin Germany P. N. Lebedev Physical Institute of the Russian Academy of Science Moscow Russia Institute for Spectroscopy of the Russian Academy of Science Moscow Troitsk Russia Faculty of Physics Higher School of Economics Old Basmannya 21/4 Moscow Russia Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow Russia Multi-Scale Mechanics (MSM) Faculty of Engineering Technology MESA+ University of Twente Enschede the Netherlands Department of Applied Physics Aalto University 15100 FI-00076 Aalto Finland

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Dynamic load balancing strategies for graph applications on GPUs

arXiv

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arXiv 2017年

作者： Raval, Ananya Nasre, Rupesh Kumar, Vivek Vasudevan, R. Vadhiyar, Sathish Pingali, Keshav Department of Computational and Data Sciences Indian Institute of Science Bangalore Department of Computer Science and Engineering Indian Institute of Technology Madras Institute for Computational Engineering and Sciences University of Texas at Austin United States Department of Computer Science University of Texas at Austin United States

Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this paper, is that of load-imbalance. If the work-assignment to threads uses node-based graph partitioning, it can result in skewed task-distribution, leading to poor load-balance. In contrast, if the work-assignment uses edge-based graph partitioning, the load-balancing is better, but the memory requirement is relatively higher. This makes it unsuitable for large graphs. In this work, we propose three techniques for improved load-balancing of graph applications on GPUs. Each technique brings in unique advantages, and a user may have to employ a specific technique based on the requirement. Using Breadth First Search and Single Source Shortest Paths as our processing kernels, we illustrate the effectiveness of each of the proposed techniques in comparison to the existing node-based and edge-based mechanisms. Copyright © 2017, The Authors. All rights reserved.

关键词： Program processors

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High-depth African genomes inform human migration and health (vol 586, pg 741, 2020)

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NATURE 2021年第7856期592卷 E26-E26页

作者： Choudhury, Ananyo Aron, Shaun Botigue, Laura R. Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Muzny, Donna Metcalf, Ginger Gibbs, Richard A. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Rotimi, Charles Ramsay, Michele Choudhury, Ananyo Choudhury, Ananyo Aron, Shaun Botigue, Laura Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Rotimi, Charles Ramsay, Michele Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Adebamowo, Clement Agongo, Godfred Boua, Romuald P. Oduro, Abraham Sorgho, Hermann Landoure, Guida Cisse, Lassana Diarra, Salimata Samassekou, Oumar Anabwani, Gabriel Matshaba, Mogomotsi Joloba, Moses Kekitiinwa, Adeodata Mardon, Graeme Mpoloka, Sununguko W. Kyobe, Samuel Mlotshwa, Busisiwe Mwesigwa, Savannah Retshabile, Gaone Williams, Lesedi Wonkam, Ambroise Moussa, Ahmed Adu, Dwomoa Ojo, Akinlolu Burke, David Salako, Babatunde O. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Awadalla, Philip Bruat, Vanessa Gbeha, Elias Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa School of Electrical and Information Engineering University of the Witwatersrand Johannesburg South Africa Division of Human Genetics National Health Laboratory Service and School of Pathology Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa Navrongo Health Research Centre Navrongo Ghana Clinical Research Unit of Nanoro Institut de Recherche en Sciences de la Sante Bobo-Dioulasso Burkina Faso Center for Research in Agricultural Genomics (CRAG) Plant and Animal Genomics Program CSIC-IRTA-UAB-UB Barcelona Spain Computational Biology Division and H3ABioNet Department of Integrative Biomedical Sciences IDM University of Cape Town Cape Town South Africa System and Data Engineering Team Abdelmalek Essaadi University ENSA Tangier Morocco Centre for Proteomic and Genomic Research (CPGR) Cape Town South Africa South African National Bioinformatics Institute University of the Western Cape Bellville South Africa Africa Health Research Institute Durban South Africa Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA Department of Agriculture and Food Science Faculty of Agriculture University of Mauritius Reduit Mauritius Department of Digital Technologies Faculty of Information Communication & Digital Technologies University of Mauritius Reduit Mauritius Department of Public Health and Primary Care University of Cambridge Cambridge UK Institute of Human Virology Nigeria Abuja Nigeria Department of Epidemiology and Public Health University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA University of Maryland Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA Institute of Human Virology and Greeneba

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Characterization of temporarily-captured minimoon 2020 CD3 by Keck time-resolved spectrophotometry

arXiv

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arXiv 2020年

作者： Bolin, Bryce T. Fremling, Christoffer Holt, Timothy R. Hankins, Matthew J. Ahumada, Tomás Anand, Shreya Bhalerao, Varun Burdge, Kevin B. Copperwheat, Chris M. Coughlin, Michael Deshmukh, Kunal P. De, Kishalay Kasliwal, Mansi M. Morbidelli, Alessandro Purdum, Josiah N. Quimby, Robert Bodewits, Dennis Chang, Chan-Kao Ip, Wing-Huen Hsu, Chen-Yen Laher, Russ R. Lin, Zhong-Yi Lisse, Carey M. Masci, Frank J. Ngeow, Chow-Choong Tan, Hanjie Zhai, Chengxing Burruss, Rick Dekany, Richard Delacroix, Alexandre Duev, Dmitry A. Graham, Matthew Hale, David Kulkarni, Shrinivas R. Kupfer, Thomas Mahabal, Ashish Mróz, Przemyslaw J. Neill, James D. Riddle, Reed Rodriguez, Hector Smith, Roger M. Soumagnac, Maayane T. Walters, Richard Yan, Lin Zolkower, Jeffry Division of Physics Mathematics and Astronomy California Institute of Technology PasadenaCA91125 United States IPAC Mail Code 100-22 Caltech 1200 E. California Blvd. PasadenaCA91125 United States University of Southern Queensland Computational Engineering and Science Research Centre QLD Australia Southwest Research Institute Department of Space Studies BoulderCO80302 United States Department of Astronomy University of Maryland College ParkMD20742 United States Division of Physics Mathematics and Astronomy California Institute of Technology PasadenaCA91125 United States Department of Physics Indian Institute of Technology Bombay Powai Mumbai400076 India Astrophysics Research Institute Liverpool John Moores University 146 Brownlow Hill LiverpoolL3 5RF United Kingdom School of Physics and Astronomy University of Minnesota MinneapolisMN55455 United States Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai400076 India Université Côte d’Azur Observatoire de la Côte d’Azur CNRS Laboratoire Lagrange Boulevard de l’Observatoire CS 34229 Nice cedex 406304 France Department of Astronomy San Diego State University 5500 Campanile Dr San DiegoCA92182 United States University of Tokyo Institutes for Advanced Study University of Tokyo KashiwaChiba277-8583 Japan Physics Department Leach Science Center Auburn University AuburnAL36832 United States Institute of Astronomy National Central University 32001 Taiwan Johns Hopkins University Applied Physics Laboratory LaurelMD20723 United States Jet Propulsion Laboratory California Institute of Technology 4800 Oak Grove Drive PasadenaCA91109 United States Caltech Optical Observatories California Institute of Technology PasadenaCA91125 United States Kavli Institute for Theoretical Physics University of California Santa BarbaraCA93106 United States Center for Data Driven Discovery California Institute of Technology PasadenaCA

We present rotationally-averaged visible spectrophotometry of minimoon 2020 CD3, the second asteroid known to become temporarily captured by the Earth-Moon system’s gravitational field. The spectrophotometry was taken with Keck I/LRIS between wavelengths 434 nm and 912 nm in B, g, V, R, I and RG850 filters as it was leaving the Earth-Moon system on 2020 March 23 UTC. The broad-band spectrophotometry of 2020 CD3 most closely resembles the spectra of V-type asteroids and some Lunar rock samples with a reddish slope of ∼18%/100 nm between 434 nm and 761 nm corresponding to colors of g-r = 0.62±0.08, r-i = 0.21 ± 0.06 and an absorption band at ∼900 nm corresponding to i-z = -0.54±0.10 (DeMeo et al. 2009;Isaacson et al. 2011). Combining our measured 31.9±0.1 absolute magnitude with an albedo of 0.35 typical for V-type asteroids (DeMeo & Carry 2013), we determine 2020 CD3’s size to be ∼1.0±0.1 m making it the first minimoon and one of the smallest asteroids to be spectrally characterized. We use our time-series photometry to detect periodic lightcurve variations with a −4 false alarm probability corresponding to a lightcurve period of ∼573 s and a lightcurve amplitude of ∼1 mag implying 2020 CD3 possesses a b/a axial ratio of ∼2.5. In addition, we extend the observational arc of 2020 CD3 to 37 days between 2020 February 15 UTC and 2020 March 23 UTC. From the improved orbital solution for 2020 CD3, we estimate its likely duration of its capture to be ∼2 y, and we measure the non-gravitation perturbation on its orbit due to radiation pressure with an area-to-mass ratio of 6.9±2.4×10−4 m2/kg implying a density of 2.1±0.7 g/cm3, broadly compatible with the densities of other meter-scale asteroids (e.g., Micheli et al. 2012;Mommert et al. 2014) and Lunar rock (∼2.4 g/cm3, Kiefer et al. 2012). We searched for pre-discovery observations of 2020 CD3 in the ZTF archive as far back as 2018 October (Masci et al. 2019), but were unable to locate any positive detections. Copyright © 2

关键词： Asteroids

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Compartmental process-based model for estimating ammonia emission from liquid dairy manure storage tank

Compartmental process-based model for estimating ammonia emi...

引用

2017 ASABE Annual International Meeting

作者： Karunarathne, Sampath A. Chung, Matthias Ogejo, Jactone A. Biological Systems Engineering Virginia Tech BlacksburgVA24061 United States Department of Mathematics Virginia Tech BlacksburgVA24061 United States Computational Modeling and Data Analytics Division Academy of Integrated Science Virginia Tech BlacksburgVA24061 United States

The biogeochemical processes responsible for production and emission of ammonia from stored liquid dairy manure are governed by environmental factors (e.g. manure temperature, moisture) and manure characteristics (e.g. total ammoniacal nitrogen concentration, pH). These environmental factors and manure characteristics vary spatially as a result of spatially heterogeneous physical, chemical, and biological properties of manure. Existing process-based models used for estimating ammonia emission do not consider these spatial variations leading to inaccurate estimations. In this study, a one-dimensional compartmental process-based model was developed to (i) estimate spatial variation of temperature and substrate concentration (ii) estimate spatial variations and rates of biogeochemical processes, and (iii) estimate production and emission of ammonia from a liquid manure storage tank. Model performance was evaluated using experimental data obtained from National Air Emissions Monitoring Study. A sensitivity analysis was performed and air temperature, manure pH, wind speed, and manure total ammoniacal nitrogen concentration were identified as the most sensitive model inputs. The model was used to estimate ammonia emission from a liquid dairy manure storage of a dairy farm located in Rockingham County in Virginia. Ammonia emission was estimated under different management and weather scenarios: two different manure storage periods in cold season from November to April and in warm season from May to October using historical weather data of the Rockingham County. Results suggest greater ammonia emission and manure nitrogen loss for the manure storage period in warm season compared to the storage period in cold season.

关键词： Liquids

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Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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NATURE 2021年第7856期592卷 E24-E24页

作者： Feng, Shaohong Stiller, Josefin Deng, Yuan Armstrong, Joel Fang, Qi Reeve, Andrew Hart Xie, Duo Chen, Guangji Guo, Chunxue Faircloth, Brant C. Petersen, Bent Wang, Zongji Zhou, Qi Diekhans, Mark Chen, Wanjun Andreu-Sanchez, Sergio Margaryan, Ashot Howard, Jason Travis Parent, Carole Pacheco, George Sinding, Mikkel-Holger S. Puetz, Lara Cavill, Emily Ribeiro, Angela M. Eckhart, Leopold Fjeldsa, Jon Hosner, Peter A. Brumfield, Robb T. Christidis, Les Bertelsen, Mads F. Sicheritz-Ponten, Thomas Tietze, Dieter Thomas Robertson, Bruce C. Song, Gang Borgia, Gerald Claramunt, Santiago Lovette, Irby J. Cowen, Saul J. Njoroge, Peter Dumbacher, John Philip Ryder, Oliver A. Fuchs, Jerome Bunce, Michael Burt, David W. Cracraft, Joel Meng, Guanliang Hackett, Shannon J. Ryan, Peter G. Jonsson, Knud Andreas Jamieson, Ian G. da Fonseca, Rute R. Braun, Edward L. Houde, Peter Mirarab, Siavash Suh, Alexander Hansson, Bengt Ponnikas, Suvi Sigeman, Hanna Stervander, Martin Frandsen, Paul B. van der Zwan, Henriette van der Sluis, Rencia Visser, Carina Balakrishnan, Christopher N. Clark, Andrew G. Fitzpatrick, John W. Bowman, Reed Chen, Nancy Cloutier, Alison Sackton, Timothy B. Edwards, Scott V. Foote, Dustin J. Shakya, Subir B. Sheldon, Frederick H. Vignal, Alain Soares, Andre E. R. Shapiro, Beth Gonzalez-Solis, Jacob Ferrer-Obiol, Joan Rozas, Julio Riutort, Marta Tigano, Anna Friesen, Vicki Dalen, Love Urrutia, Araxi O. Szekely, Tamas Liu, Yang Campana, Michael G. Corvelo, Andre Fleischer, Robert C. Rutherford, Kim M. Gemmell, Neil J. Dussex, Nicolas Mouritsen, Henrik Thiele, Nadine Delmore, Kira Liedvogel, Miriam Franke, Andre Hoeppner, Marc P. Krone, Oliver Fudickar, Adam M. Mila, Borja Ketterson, Ellen D. Fidler, Andrew Eric Friis, Guillermo Parody-Merino, Angela M. Battley, Phil F. Cox, Murray P. Lima, Nicholas Costa Barroso Prosdocimi, Francisco Parchman, Thomas Lee Schlinger, Barney A. Loiselle, Bette A. Blake, John G. Lim, Haw Chuan Day, Lainy B. Fuxjager, Matthew J. Baldwin, Maude W. Braun, Michael J. Wirthlin, Morgan Dikow, China National GeneBank BGI-Shenzhen Shenzhen China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China BGI-Shenzhen Shenzhen China Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark BGI Education Center University of Chinese Academy of Sciences Shenzhen China MOE Laboratory of Biosystems Homeostasis and Protection Life Sciences Institute Zhejiang University Hangzhou China Department of Neuroscience and Developmental Biology University of Vienna Vienna Austria Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China James D. Watson Institute of Genome Sciences Hangzhou China UC Santa Cruz Genomics Institute UC Santa Cruz Santa Cruz CA USA Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark Center for Macroecology Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark Department of Biological Sciences Louisiana State University Baton Rouge LA USA Museum of Natural Science Louisiana State University Baton Rouge LA USA Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) Faculty of Applied Sciences AIMST University Kedah Malaysia Section for Evolutionary Genomics The GLOBE Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Institute of Molecular Biology National Academy of Sciences Yerevan Armenia University Museum Norwegian University of Science and Technology Trondheim Norway Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Novogene Durham NC USA Duke University Medical Center Durham NC USA The Rockefeller University New York NY USA Howard Hughes Medical Institute Chevy Chase MD USA Department of Dermatology Medical University of Vienna Vienna Austria

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Preface

OpenAccess Series in Informatics

引用

OpenAccess Series in Informatics 2019年 70卷 IX-X页

作者： Eskevich, Maria de Melo, Gerard Fäth, Christian McCrae, John P. Buitelaar, Paul Chiarcos, Christian Klimek, Bettina Dojchinovski, Milan CLARIN ERIC Utrecht Netherlands Department of Computer Science Rutgers University New BrunswickNJ United States Applied Computational Linguistics Goethe University Frankfurt Germany Insight Centre for Data Analytics National University of Ireland Galway Ireland Agile Knowledge Engineering and Semantic Web University of Leipzig Germany

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Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

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science 2020年第6523期370卷 eabc6617页

作者： Warren, Wesley C. Harris, R. Alan Haukness, Marina Fiddes, Ian T. Murali, Shwetha C. Fernandes, Jason Dishuck, Philip C. Storer, Jessica M. Raveendran, Muthuswamy Hillier, LaDeana W. Porubsky, David Mao, Yafei Gordon, David Vollger, Mitchell R. Lewis, Alexandra P. Munson, Katherine M. DeVogelaere, Elizabeth Armstrong, Joel Diekhans, Mark Walker, Jerilyn A. Tomlinson, Chad Graves-Lindsay, Tina A. Kremitzki, Milinn Salama, Sofie R. Audano, Peter A. Escalona, Merly Maurer, Nicholas W. Antonacci, Francesca Mercuri, Ludovica Maggiolini, Flavia A. M. Catacchio, Claudia Rita Underwood, Jason G. O'Connor, David H. Sanders, Ashley D. Korbel, Jan O. Ferguson, Betsy Kubisch, H. Michael Picker, Louis Kalin, Ned H. Rosene, Douglas Levine, Jon Abbott, David H. Gray, Stanton B. Sanchez, Mar M. Kovacs-Balint, Zsofia A. Kemnitz, Joseph W. Thomasy, Sara M. Roberts, Jeffrey A. Kinnally, Erin L. Capitanio, John P. Skene, J. H. Pate Platt, Michael Cole, Shelley A. Green, Richard E. Ventura, Mario Wiseman, Roger W. Paten, Benedict Batzer, Mark A. Rogers, Jeffrey Eichler, Evan E. Department of Animal Sciences Bond Life Sciences Center University of Missouri Columbia MO 65211 USA. Department of Surgery School of Medicine University of Missouri Columbia MO 65211 USA. Institute of Data Science and Informatics University of Missouri Columbia MO 65211 USA. Human Genome Sequencing Center Department of Molecular and Human Genetics Baylor College of Medicine Houston TX 77030 USA. Computational Genomics Laboratory University of California–Santa Cruz Santa Cruz CA 95064 USA. Inscripta Inc. Boulder CO 80301 USA. Department of Genome Sciences University of Washington Seattle WA 98195 USA. Howard Hughes Medical Institute University of Washington Seattle WA 98195 USA. Department of Biomolecular Engineering University of California–Santa Cruz Santa Cruz CA 95064 USA. Department of Biological Sciences Louisiana State University Baton Rouge LA 70803 USA. Institue for Systems Biology Seattle WA 98109 USA. McDonnell Genome Institute Washington University St. Louis MO 63108 USA. Department of Biology University of Bari 'Aldo Moro' 70125 Bari Italy. Pacific Biosciences of California Seattle WA 94025 USA. Department of Pathology and Laboratory Medicine Wisconsin National Primate Research Center University of Wisconsin–Madison Madison WI 53711 USA. European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany. Division of Genetics Oregon National Primate Research Center Oregon Health and Science University Beaverton OR 97006 USA. Tulane National Primate Research Center Covington LA 70433 USA. Oregon National Primate Research Center and Vaccine and Gene Therapy Institute Oregon Health Sciences University Beaverton OR 97006 USA. Department of Psychiatry University of Wisconsin School of Medicine and Public Health Madison WI 53719 USA. Department of Anatomy and Neurobiology Boston University School of Medicine Boston MA 02118 USA. Department of Neuroscience University of Wisconsin Madison WI 53175 USA. Wisconsin N

The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.

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