检索结果-内蒙古大学图书馆

Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

引用

Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain. Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

来源：评论

学校读者我要写书评

暂无评论

Polygenic risk modeling for prediction of epithelial ovarian cancer risk (vol 30, pg 349, 2021)

引用

EUROPEAN JOURNAL OF HUMAN GENETICS 2022年第5期30卷 630-631页

作者： Dareng, Eileen O. Tyrer, Jonathan P. Barnes, Daniel R. Jones, Michelle R. Yang, Xin Aben, Katja K. H. Adank, Muriel A. Agata, Simona Andrulis, Irene L. Anton-Culver, Hoda Antonenkova, Natalia N. Aravantinos, Gerasimos Arun, Banu K. Augustinsson, Annelie Balmana, Judith Bandera, Elisa V. Barkardottir, Rosa B. Barrowdale, Daniel Beckmann, Matthias W. Beeghly-Fadiel, Alicia Benitez, Javier Bermisheva, Marina Bernardini, Marcus Q. Bjorge, Line Black, Amanda Bogdanova, Natalia V. Bonanni, Bernardo Borg, Ake Brenton, James D. Budzilowska, Agnieszka Butzow, Ralf Buys, Saundra S. Cai, Hui Caligo, Maria A. Campbell, Ian Cannioto, Rikki Cassingham, Hayley Chang-Claude, Jenny Chanock, Stephen J. Chen, Kexin Chiew, Yoke-Eng Chung, Wendy K. Claes, Kathleen B. M. Colonna, Sarah Cook, Linda S. Couch, Fergus J. Daly, Mary B. Dao, Fanny Davies, Eleanor de la Hoya, Miguel de Putter, Robin Dennis, Joe DePersia, Allison Devilee, Peter Diez, Orland Ding, Yuan Chun Doherty, Jennifer A. Domchek, Susan M. Dork, Thilo du Bois, Andreas Durst, Matthias Eccles, Diana M. Eliassen, Heather A. Engel, Christoph Evans, Gareth D. Fasching, Peter A. Flanagan, James M. Fortner, Renee T. Machackova, Eva Friedman, Eitan Ganz, Patricia A. Garber, Judy Gensini, Francesca Giles, Graham G. Glendon, Gord Godwin, Andrew K. Goodman, Marc T. Greene, Mark H. Gronwald, Jacek Hahnen, Eric Haiman, Christopher A. Hakansson, Niclas Hamann, Ute Hansen, Thomas V. O. Harris, Holly R. Hartman, Mikael Heitz, Florian Hildebrandt, Michelle A. T. Hogdall, Estrid Hogdall, Claus K. Hopper, John L. Huang, Ruea-Yea Huff, Chad Hulick, Peter J. Huntsman, David G. Imyanitov, Evgeny N. Isaacs, Claudine Jakubowska, Anna James, Paul A. Janavicius, Ramunas Jensen, Allan Johannsson, Oskar Th. John, Esther M. Jones, Michael E. Kang, Daehee Karlan, Beth Y. Karnezis, Anthony Kelemen, Linda E. Khusnutdinova, Elza Kiemeney, Lambertus A. Kim, Byoung-Gie Kjaer, Susanne K. Komenaka, Ian Kupryjanczyk, Jolanta Kurian, Allison W. Kwong, Ava Lambrechts, Diether Larson, Melissa C. Lazaro, Conxi L University of Cambridge Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care Cambridge UK University of Cambridge Centre for Cancer Genetic Epidemiology Department of Oncology Cambridge UK Center for Bioinformatics and Functional Genomics Cedars-Sinai Medical Center Los Angeles CA USA Radboud University Medical Center Radboud Institute for Health Sciences Nijmegen The Netherlands Netherlands Comprehensive Cancer Organisation Utrecht The Netherlands The Netherlands Cancer Institute—Antoni van Leeuwenhoek hospital Family Cancer Clinic Amsterdam The Netherlands Veneto Institute of Oncology IOV—IRCCS Immunology and Molecular Oncology Unit Padua Italy Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Fred A. Litwin Center for Cancer Genetics Toronto ON Canada University of Toronto Department of Molecular Genetics Toronto ON Canada University of California Irvine Department of Epidemiology Genetic Epidemiology Research Institute Irvine CA USA N.N. Alexandrov Research Institute of Oncology and Medical Radiology Minsk Belarus ‘Agii Anargiri’ Cancer Hospital Athens Greece University of Texas MD Anderson Cancer Center Department of Breast Medical Oncology Houston TX USA Lund University Department of Cancer Epidemiology Clinical Sciences Lund Sweden Vall d’Hebron Institute of Oncology Hereditary cancer Genetics Group Barcelona Spain University Hospital of Vall d’Hebron Department of Medical Oncology Barcelona Spain Rutgers Cancer Institute of New Jersey Cancer Prevention and Control Program New Brunswick NJ USA Landspitali University Hospital Department of Pathology Reykjavik Iceland University of Iceland BMC (Biomedical Centre) Faculty of Medicine Reykjavik Iceland University Hospital Erlangen Friedrich-Alexander-University Erlangen-Nuremberg Department of Gynecology and Obstetrics Comprehensive Cancer Center ER-EMN Erlangen Germany Vanderbilt University School of Medicine Division of Epidemiology Department

Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, “select and shrink for summary statistics” (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestries; 7,669 women of East Asian ancestries; 1,072 women of African ancestries, and in 18,915 BRCA1 and 12,337 BRCA2 pathogenic variant carriers of European ancestries. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38 (95% CI: 1.28–1.48, AUC: 0.588) per unit standard deviation, in women of European ancestries; 1.14 (95% CI: 1.08–1.19, AUC: 0.538) in women of East Asian ancestries; 1.38 (95% CI: 1.21–1.58, AUC: 0.593) in women of African ancestries; hazard ratios of 1.36 (95% CI: 1.29–1.43, AUC: 0.592) in BRCA1 pathogenic variant carriers and 1.49 (95% CI: 1.35–1.64, AUC: 0.624) in BRCA2 pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.

关键词： Clinical genetics Genetic markers Risk factors Biomedicine general Human Genetics bioinformatics Gene Expression Cytogenetics

来源：评论

学校读者我要写书评

暂无评论

Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries (vol 55, pg 89, 2023)

引用

NATURE GENETICS 2023年第3期55卷 519-520页

作者： Fernandez-Rozadilla, Ceres Timofeeva, Maria Chen, Zhishan Law, Philip Thomas, Minta Schmit, Stephanie Diez-Obrero, Virginia Hsu, Li Fernandez-Tajes, Juan Palles, Claire Sherwood, Kitty Briggs, Sarah Svinti, Victoria Donnelly, Kevin Farrington, Susan Blackmur, James Vaughan-Shaw, Peter Shu, Xiao-ou Long, Jirong Cai, Qiuyin Guo, Xingyi Lu, Yingchang Broderick, Peter Studd, James Huyghe, Jeroen Harrison, Tabitha Conti, David Dampier, Christopher Devall, Mathew Schumacher, Fredrick Melas, Marilena Rennert, Gad Obon-Santacana, Mireia Martin-Sanchez, Vicente Moratalla-Navarro, Ferran Oh, Jae Hwan Kim, Jeongseon Jee, Sun Ha Jung, Keum Ji Kweon, Sun-Seog Shin, Min-Ho Shin, Aesun Ahn, Yoon-Ok Kim, Dong-Hyun Oze, Isao Wen, Wanqing Matsuo, Keitaro Matsuda, Koichi Tanikawa, Chizu Ren, Zefang Gao, Yu-Tang Jia, Wei-Hua Hopper, John Jenkins, Mark Win, Aung Ko Pai, Rish Figueiredo, Jane Haile, Robert Gallinger, Steven Woods, Michael Newcomb, Polly Duggan, David Cheadle, Jeremy Kaplan, Richard Maughan, Timothy Kerr, Rachel Kerr, David Kirac, Iva Bohm, Jan Mecklin, Lukka-Pekka Jousilahti, Pekka Knekt, Paul Aaltonen, Lauri Rissanen, Harri Pukkala, Eero Eriksson, Johan Cajuso, Tatiana Hanninen, Ulrika Kondelin, Johanna Palin, Kimmo Tanskanen, Tomas Renkonen-Sinisalo, Laura Zanke, Brent Mannisto, Satu Albanes, Demetrius Weinstein, Stephanie Ruiz-Narvaez, Edward Palmer, Julie Buchanan, Daniel Platz, Elizabeth Visvanathan, Kala Ulrich, Cornelia Siegel, Erin Brezina, Stefanie Gsur, Andrea Campbell, Peter Chang-Claude, Jenny Hoffmeister, Michael Brenner, Hermann Slattery, Martha Potter, John Tsilidis, Konstantinos Schulze, Matthias Gunter, Marc Murphy, Neil Castells, Antoni Castellvi-Bel, Sergi Moreira, Leticia Arndt, Volker Shcherbina, Anna Stern, Mariana Pardamean, Bens Bishop, Timothy Giles, Graham Southey, Melissa Idos, Gregory McDonnell, Kevin Abu-Ful, Zomoroda Greenson, Joel Shulman, Katerina Lejbkowicz, Flavio Offit, Kenneth Su, Yu-Ru Steinfelder, Robert Keku, Temitope van Guelpen, Bethany Hudson, Thomas Hampel, Heather Pearlman, Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA Division of Genetics and Epidemiology Institute of Cancer Research London UK Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA Genomic Medicine Institute Cleveland Clinic Cleveland OH USA Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain Department of Biostatistics School of Public Health University of Washington Seattle WA USA Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK Department of Public Health Richard Doll Building University of Oxford Oxford UK Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA Department of Populat

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.

关键词： Colorectal cancer Epigenomics Genome-wide association studies Transcriptomics

来源：评论

学校读者我要写书评

暂无评论

Author Correction: Possible association of 16p11.2 copy number variation with altered lymphocyte and neutrophil counts

引用

npj Genomic Medicine 2023年第1期8卷 1页

作者： Giuliana Giannuzzi Nicolas Chatron Katrin Mannik Chiara Auwerx Sylvain Pradervand Gilles Willemin Jacqueline Chrast Eleonora Porcu Katrin Männik Alexandre Reymond Damien Sanlaville Caroline Schluth-Bolard Marie C. Sadler Zoltan Kutalik Kendra Hoekzema Evan E. Eichler Xander Nuttle Yann Herault Cédric Le Caignec Mathilde Nizon Bertrand Isidor Brigitte Gilbert-Dussardier Sandra Martin Sébastien Jacquemont Armand Bottani Marion Gérard Sacha Weber Aurélia Jacquette Catherine Vincent-Delorme Aurora Currò Francesca Mari Alessandra Renieri Alfredo Brusco Giovanni Battista Ferrero Center for Integrative Genomics University of Lausanne Lausanne Switzerland Department of Biosciences University of Milan Milan Italy Service de génétique Hospices Civils de Lyon Lyon France University of Lyon Université Claude Bernard Lyon 1 CNRS UMR-5310 INSERM U-1217 Institut NeuroMyoGène F-69008 Lyon France Department of Computational Biology University of Lausanne Lausanne Switzerland Center for Primary Care and Public Health University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland Department of Genome Sciences University of Washington Seattle WA USA Howard Hughes Medical Institute University of Washington Seattle WA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Department of Neurology Harvard Medical School Boston MA USA Program in Medical and Population Genetics and Stanley Center for Psychiatric Research Broad Institute Cambridge MA USA University of Strasbourg CNRS INSERM PHENOMIN-ICS Institute of Genetics and Molecular and Cellular Biology Illkirch France Service de Génétique Médicale CHU de Nantes Nantes France Service de Génétique CHU de Poitiers Poitiers France Centre Hospitalier Universitaire Vaudois University of Lausanne Lausanne Switzerland University of Montreal Montreal Canada Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Service de Génétique Medicale CHU de Caen Caen France Service de Génétique Clinique CHU Paris-GH La Pitié Salpêtrière Paris France Service de Génétique Clinique CHU de Lille Lille France Medical Genetics University of Siena Siena Italy Department of Medical Sciences University of Turin Turin Italy Department of Clinical and Biological Sciences University of Turin Turin Italy

来源：评论

学校读者我要写书评

暂无评论

Correction to: Microbial function and genital inflammation in young South African women at high risk of HIV infection

引用

Microbiome 2022年第1期10卷 42页

作者： Arghavan Alisoltani Monalisa T Manhanzva Matthys Potgieter Christina Balle Liam Bell Elizabeth Ross Arash Iranzadeh Michelle du Plessis Nina Radzey Zac McDonald Bridget Calder Imane Allali Nicola Mulder Smritee Dabee Shaun Barnabas Hoyam Gamieldien Adam Godzik Jonathan M Blackburn David L Tabb Linda-Gail Bekker Heather B Jaspan Jo-Ann S Passmore Lindi Masson Division of Medical Virology Department of Pathology University of Cape Town Cape Town 7925 South Africa. Division of Biomedical Sciences University of California Riverside School of Medicine Riverside CA 92521 USA. Computational Biology Division Department of Integrative Biomedical Sciences University of Cape Town Cape Town 7925 South Africa. Division of Chemical and Systems Biology Department of Integrative Biomedical Sciences University of Cape Town Cape Town 7925 South Africa. Division of Immunology Department of Pathology University of Cape Town Cape Town 7925 South Africa. Centre for Proteomic and Genomic Research Cape Town 7925 South Africa. Laboratory of Human Pathologies Biology Department of Biology and Genomic Center of Human Pathologies Mohammed V University Rabat Morocco. Institute of Infectious Disease and Molecular Medicine (IDM) University of Cape Town Cape Town 7925 South Africa. Centre for Infectious Diseases Research (CIDRI) in Africa Wellcome Trust Centre University of Cape Town Cape Town 7925 South Africa. Seattle Children's Research Institute University of Washington Seattle WA 98101 USA. Bioinformatics Unit South African Tuberculosis Bioinformatics Initiative Stellenbosch University Stellenbosch 7602 South Africa. DST-NRF Centre of Excellence for Biomedical Tuberculosis Research Stellenbosch University Stellenbosch 7602 South Africa. Desmond Tutu HIV Centre University of Cape Town Cape Town 7925 South Africa. Centre for the AIDS Programme of Research in South Africa Durban 4013 South Africa. National Health Laboratory Service Cape Town 7925 South Africa. Division of Medical Virology Department of Pathology University of Cape Town Cape Town 7925 South Africa. Lindi.Masson@burnet.edu.au. Institute of Infectious Disease and Molecular Medicine (IDM) University of Cape Town Cape Town 7925 South Africa. Lindi.Masson@burnet.edu.au. Centre for the AIDS Programme of Research in South Africa Durban 4013 South Africa. Lindi.Ma

来源：评论

学校读者我要写书评

暂无评论

TACO： Taxonomic prediction of unknown OTUs through OTU co-abundance networks

引用

Frontiers of Electrical and Electronic Engineering in China 2016年第3期4卷 149-158页

作者： Zohreh Baharvand Irannia Ting Chen Program in Computational Biology and Bioinformatics Department of Biological Sciences University of Southern California Los Angeles CA 90089 USA Bioinformatics Division TNLIST Tsinghua University Beijing 100084 China

Background： A main goal of metagenomics is taxonomic characterization of microbial communities. Although sequence comparison has been the main method for the taxonomic classification, there is not a clear agreement on similarity calculation and similarity thresholds, especially at higher taxonomic levels such as phylum and class. Thus taxonomic classification of novel metagenomic sequences without close homologs in the biological databases poses a challenge. Methods： In this study, we propose to use the co-abundant associations between taxa/operational taxonomic units （OTU） across complex and diverse communities to assist taxonomic classification. We developed a Markov Random Field model to predict taxa of unknown microorganisms using co-abundant associations. Results： Although such associations are intrinsically functional associations, we demonstrate that they are strongly correlated with taxonomic associations and can be combined with sequence comparison methods to predict taxonomic origins of unknown microorganisms at phylum and class levels. Conclusions： With the ever-increasing accumulation of sequence data from microbial communities, we now take the first step to explore these associations for taxonomic identification beyond sequence similarity. Availability and Implementation： Source codes of TACO are freely available at the following URL： https：//***/ baharvand/OTU-Taxonomy-Identification implemented in C＋＋, supported on Linux and MS Windows.

关键词： metagenomics 16s rRNA gene taxonomic profiling taxonomic prediction Markov Random Field OTUco-abundance network

来源：评论

学校读者我要写书评

暂无评论

Author Correction: Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

引用

Genome medicine 2022年第1期14卷 128页

作者： Ruth Johnson Yi Ding Vidhya Venkateswaran Arjun Bhattacharya Kristin Boulier Alec Chiu Sergey Knyazev Tommer Schwarz Malika Freund Lingyu Zhan Kathryn S Burch Christa Caggiano Brian Hill Nadav Rakocz Brunilda Balliu Christopher T Denny Jae Hoon Sul Noah Zaitlen Valerie A Arboleda Eran Halperin Sriram Sankararaman Manish J Butte Clara Lajonchere Daniel H Geschwind Bogdan Pasaniuc Department of Computer Science University of California Los Angeles Los Angeles CA 90095 USA. ruthjohnson@g.ucla.edu. Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. ruthjohnson@g.ucla.edu. Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles CA 90095 USA. Department of Oral Biology School of Dentistry University of California Los Angeles Los Angeles CA 90095 USA. Institute for Quantitative and Computational Biosciences David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Department of Medicine Division of Cardiology University of California Los Angeles Los Angeles CA 90095 USA. Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Department of Genetics Stanford School of Medicine Stanford CA 94305 USA. Molecular Biology Institute David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Program in Neurogenetics Department of Neurology David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Department of Computer Science University of California Los Angeles Los Angeles CA 90095 USA. Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA. Division of Hematology/Oncology Department of Pediatrics Gwynne Hazen Cherry Memorial Laboratories University of California Los Angeles Los Angeles CA 90095 USA. Molecular Biology Institute University of California Los Angeles Los Angeles CA 90095 USA. Jonsson Comprehensive Cancer Center University of California Los Angeles Los Angeles CA 90095

来源：评论

学校读者我要写书评

暂无评论

Hypostatic jammed packings of frictionless nonspherical particles

引用

Physical Review E 2018年第1期97卷 012909-012909页

作者： Kyle VanderWerf Weiwei Jin Mark D. Shattuck Corey S. O'Hern Department of Physics Yale University New Haven Connecticut 06520 USA Department of Mechanics and Engineering Science Peking University Beijing 100871 China Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form packings with fewer contacts than degrees of freedom (hypostatic packings) and which have equal numbers of contacts and degrees of freedom (isostatic packings), and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naive constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and cir-polygons, we developed an interparticle potential that gives continuous forces and torques as a function of the particle coordinates. We show that the packing fraction and coordination number at jamming onset obey a masterlike form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity A, which is proportional to the ratio of the squared perimeter to the area of the particle. Further, the eigenvalue spectra of the dynamical matrix for packings of different particle shapes collapse when plotted at the same A. For hypostatic packings of nonspherical particles, we verify that the number of “quartic” modes along which the potential energy increases as the fourth power of the perturbation amplitude matches the number of missing contacts relative to the isostatic value. We show that the fourth derivatives of the total potential energy in the directions of the quartic modes remain nonzero as the pressure of the packings is decreased to zero. In addition, we calculate the principal curvatures of the inequality constraints for each contact in circulo-line packings and identify specific types of contacts with inequality constraints that possess convex curvature. These contacts can constrain multiple degrees of freedom and allow hypostatic packings of nonspherical particles to be mechanically stable.

关键词： Granular materials Granular packing Jamming

来源：评论

学校读者我要写书评

暂无评论

The role of deformability in determining the structural and mechanical properties of bubbles and emulsions

arXiv

引用

arXiv 2019年

作者： Boromand, Arman Signoriello, Alexandra Lowensohn, Janna Orellana, Carlos S. Weeks, Eric R. Ye, Fangfu Shattuck, Mark D. O’Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Beijing National Laboratory for Condensed Matter Physics CAS Key Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Physics Emory University AtlantaGA30322 United States School of Physical Sciences University of Chinese Academy of Sciences Beijing China Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

We perform computational studies of jammed particle packings in two dimensions undergoing isotropic compression using the well-characterized soft particle (SP) model and deformable particle (DP) model that we developed for bubbles and emulsions. In the SP model, circular particles are allowed to overlap, generating purely repulsive forces. In the DP model, particles minimize their perimeter, while deforming at fixed area to avoid overlap during compression. We compare the structural and mechanical properties of jammed packings generated using the SP and DP models as a function of the packing fraction ρ, instead of the reduced number density φ. We show that near jamming onset the excess contact number ∆z = z−zJ and shear modulus G scale as ∆ρ0.5 in the large system limit for both models, where ∆ρ = ρ−ρJ and zJ ≈4 and ρJ ≈0.842 are the values at jamming onset. ∆z and G for the SP and DP models begin to differ for ρ & 0.88. In this regime, ∆z∼G can be described by a sum of two power-laws in ∆ρ, i.e. ∆z∼G ∼C0∆ρ0.5+C1∆ρ1.0 to lowest order. We show that the ratio C1/C0 is much larger for the DP model compared to to that for the SP model. We also characterize the void space in jammed packings as a function of ρ. We find that the DP model can describe the formation of Plateau borders as ρ → 1. We further show that the results for z and the shape factor A versus ρ for the DP model agree with recent experimental studies of foams and emulsions. Copyright © 2019, The Authors. All rights reserved.

关键词： Jamming

来源：评论

学校读者我要写书评

暂无评论

Corrigendum to: Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome

引用

Open forum infectious diseases 2020年第9期7卷 ofaa381页

作者： Ornella Sortino Nittaya Phanuphak Alexandra Schuetz Alexandra M Ortiz Nitiya Chomchey Yasmine Belkaid Jacquice Davis Harry A Mystakelis Mariam Quiñones Claire Deleage Brian Ingram Rungsun Rerknimitr Suteeraporn Pinyakorn Adam Rupert Merlin L Robb Jintanat Ananworanich Jason Brenchley Irini Sereti Clinical Research Directorate Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute. National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. SEARCH/Thai Red Cross AIDS Research Centre Bangkok Thailand. The Henry M. Jackson Foundation for the Advancement of Military Medicine Bethesda Maryland. United States Military HIV Research Program Walter Reed Army Institute of Research Silver Spring Maryland. Armed Forces Research Institute of Medical Sciences Bangkok Thailand. Metaorganism Immunity Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. Microbiome Program National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. Bioinformatics and Computational Biosciences Branch Office of Cyber Infrastructure and Computational Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda Maryland. Metabolon Inc. Research Triangle Park North Carolina. Department of Global Health University of Amsterdam Amsterdam the Netherlands.

[This corrects the article DOI: 10.1093/ofid/ofz367.].

关键词：

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：