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Publisher Correction: On the issue of transparency and reproducibility in nanomedicine

Nature nanotechnology 2019年第8期14卷 811页

作者： Hon S Leong Kimberly S Butler C Jeffrey Brinker May Azzawi Steve Conlan Christine Dufès Andrew Owen Steve Rannard Chris Scott Chunying Chen Marina A Dobrovolskaia Serguei V Kozlov Adriele Prina-Mello Ruth Schmid Peter Wick Fanny Caputo Patrick Boisseau Rachael M Crist Scott E McNeil Bengt Fadeel Lang Tran Steffen Foss Hansen Nanna B Hartmann Lauge P W Clausen Lars M Skjolding Anders Baun Marlene Ågerstrand Zhen Gu Dimitrios A Lamprou Clare Hoskins Leaf Huang Wantong Song Huiliang Cao Xuanyong Liu Klaus D Jandt Wen Jiang Betty Y S Kim Korin E Wheeler Andrew J Chetwynd Iseult Lynch Sayed Moein Moghimi André Nel Tian Xia Paul S Weiss Bruno Sarmento José das Neves Hélder A Santos Luis Santos Samir Mitragotri Steve Little Dan Peer Mansoor M Amiji Maria José Alonso Alke Petri-Fink Sandor Balog Aaron Lee Barbara Drasler Barbara Rothen-Rutishauser Stefan Wilhelm Handan Acar Roger G Harrison Chuanbin Mao Priyabrata Mukherjee Rajagopal Ramesh Lacey R McNally Sara Busatto Joy Wolfram Paolo Bergese Mauro Ferrari Ronnie H Fang Liangfang Zhang Jie Zheng Chuanqi Peng Bujie Du Mengxiao Yu Danielle M Charron Gang Zheng Chiara Pastore Department of Urology Mayo Clinic Rochester MN USA. Department of Physiology and Biomedical Engineering Mayo Clinic Rochester MN USA. Department of Nanobiology Sandia National Laboratories Albuquerque NM USA. Center for Micro-Engineered Materials University of New Mexico Albuquerque Albuquerque NM USA. Departments of Chemical and Biological Engineering University of New Mexico Albuquerque NM USA. Department of Molecular Genetics and Microbiology University of New Mexico Albuquerque NM USA. UNM Comprehensive Cancer Center University of New Mexico Albuquerque NM USA. Cardiovascular Research Group School of Healthcare Science Manchester Metropolitan University Manchester UK. British Society for Nanomedicine Liverpool UK. Institute of Life Science Swansea University Medical School Swansea University Swansea UK. Strathclyde Institute of Pharmacy and Biomedical Sciences University of Strathclyde Glasgow UK. Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Liverpool UK. Department of Chemistry School of Physical Sciences University of Liverpool Liverpool UK. Centre for Cancer Research and Cell Biology Queen's University of Belfast Belfast UK. National Center for Nanoscience and Technology of China Beijing China. Cancer Research Technology Program Nanotechnology Characterization Laboratory Frederick National Laboratory for Cancer Research Frederick MD USA. Laboratory of Animal Sciences Program Center for Advanced Preclinical Research Frederick National Laboratory for Cancer Research Frederick National Laboratory for Cancer Research Frederick MD USA. Trinity Translational Medicine Institute Department of Clinical Medicine Trinity College Dublin Dublin Ireland. Laboratory for Biological Characterisation of Advanced Materials Trinity Translational Medicine Institute Trinity College Dublin Dublin Ireland. Nanomedicine Group Advanced Materials and Bioengineering Research (AMBER) centre Centre

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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Erratum to: The sponge microbiome project

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Gigascience 2018年第12期7卷 giy145页

作者： Lucas Moitinho-Silva Shaun Nielsen Amnon Amir Antonio Gonzalez Gail L Ackermann Carlo Cerrano Carmen Astudillo-Garcia Cole Easson Detmer Sipkema Fang Liu Georg Steinert Giorgos Kotoulas Grace P McCormack Guofang Feng James J Bell Jan Vicente Johannes R Björk Jose M Montoya Julie B Olson Julie Reveillaud Laura Steindler Mari-Carmen Pineda Maria V Marra Micha Ilan Michael W Taylor Paraskevi Polymenakou Patrick M Erwin Peter J Schupp Rachel L Simister Rob Knight Robert W Thacker Rodrigo Costa Russell T Hill Susanna Lopez-Legentil Thanos Dailianis Timothy Ravasi Ute Hentschel Zhiyong Li Nicole S Webster Torsten Thomas Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences The University of New South Wales Sydney 2052 Australia. Department of Pediatrics University of California - San Diego La Jolla CA 92093 USA. Department of Life and Environmental Sciences Polytechnic University of Marche Ancona 60131 Italy. School of Biological Sciences University of Auckland Auckland New Zealand. Halmos College of Natural Sciences and Oceanography Nova Southeastern University Dania Beach FL 33004 USA. Wageningen University Laboratory of Microbiology Stippeneng 4 6708 WE Wageningen The Netherlands. State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200240 P.R. China. Hellenic Centre for Marine Research Institute of Marine Biology Biotechnology and Aquaculture Thalassocosmos 71500 Heraklion Greece. Zoology School of Natural Sciences Ryan Institute National University of Ireland Galway University Rd. Galway Ireland. School of Biological Sciences Victoria University of Wellington Wellington New Zealand. Hawaii Institute of Marine Biology 46-007 Lilipuna Road Kaneohe HI 96744-1346. Galvin Life Science Center University of Notre Dame Notre Dame IN 46556 USA. Ecological Networks and Global Change Group Theoretical and Experimental Ecology Station CNRS and Paul Sabatier University Moulis France. Department of Biological Sciences University of Alabama Tuscaloosa AL 35487 USA. INRA UMR1309 CMAEE Cirad UMR15 CMAEE 34398 Montpellier France. Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa Haifa Israel. Australian Institute of Marine Science (AIMS) Townsville 4810 Queensland Australia. Department of Zoology George S. Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 69978 Israel. Department of Biology and Marine Biology University of North Carolina Wilmington Wilmington NC 28409 USA. Institute for Chemistry and Biolog

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Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas program

arXiv

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arXiv 2019年

作者： Snyder, Michael P. Lin, Shin Posgai, Amanda Atkinson, Mark Regev, Aviv Rood, Jennifer Rozenblatt-Rosen, Orit Gaffney, Leslie Hupalowska, Anna Satija, Rahul Gehlenborg, Nils Shendure, Jay Laskin, Julia Harbury, Pehr Nystrom, Nicholas A. Bar-Joseph, Ziv Zhang, Kun Börner, Katy Lin, Yiing Conroy, Richard Procaccini, Dena Roy, Ananda L. Pillai, Ajay Brown, Marishka Galis, Zorina S. Cai, Long Shendure, Jay Trapnell, Cole Lin, Shin Jackson, Dana Snyder, Michael P. Nolan, Garry Greenleaf, William James Lin, Yiing Plevritis, Sylvia Ahadi, Sara Lee, Hayan Nevins, Stephanie Esplin, Ed Horning, Aaron Bahmani, Amir Zhang, Kun Sun, Xin Jain, Sanjay Hagood, James Kharchenko, Peter Atkinson, Mark Bodenmiller, Bernd Brusko, Todd Clare-Salzler, Michael Nick, Harry Otto, Kevin Posgai, Amanda Wasserfall, Clive Maffioletti, Sergio Caprioli, Richard M. Spraggins, Jeffrey M. Gutierrez, Danielle Patterson, Nathan Heath Neumann, Elizabeth K. Harris, Raymond deCaestecker, Mark de Plas, Raf Van Lau, Ken Cai, Long Yuan, Guo-Cheng Zhu, Qian Dries, Ruben Yin, Peng Saka, Sinem K. Kishi, Jocelyn Y. Wang, Yu Goldaracena, Isabel Laskin, Julia Ye, DongHye Burnum-Johnson, Kristin E. Piehowski, Paul D. Ansong, Charles Zhu, Ying Harbury, Pehr Desai, Tushar Mulye, Jay Chou, Peter Nagendran, Monica Bar-Joseph, Ziv Teichmann, Sarah A. Paten, Benedict Murphy, Robert F. Ma, Jian Kiselev, Vladimir Yu Kingsford, Carl Ricarte, Allyson Ruffalo, Matthew Gehlenborg, Nils Kharchenko, Peter Vella, Margaret McCallum, Chuck Börner, Katy Cross, Leonard E. Friedman, Samuel H. Heiland, Randy Herr, Bruce Macklin, Paul Quardokus, Ellen M. Record, Lisel Sluka, James P. Weber, Griffin M. Nystrom, Nicholas A. Silverstein, Jonathan C. Blood, Philip D. Ropelewski, Alexander J. Shirey, William E. Mabee, Paula Lenhardt, W. Christopher Robasky, Kimberly Michailidis, Stavros Satija, Rahul Marioni, John Regev, Aviv Butler, Andrew Stuart, Tim Fisher, Eyal Ghazanfar, Shila Rood, Jennifer Gaffney, Leslie Ersalan, Gokcen Biancalani, Tommaso Conroy, Richard Procaccini, Dena Roy, Anan School of Medicine Stanford University 300 Pasteur Drive United States Department of Genetics Stanford School of Medicine StanfordCA94305 United States Department of Medicine University of Washington SeattleWA98195 United States Department of Pathology University of Florida Diabetes Institute GainesvilleFL32610 United States Klarman Cell Observatory Broad Institute of MIT and Harvard CambridgeMA02142 United States Howard Hughes Medical Institute Koch Institute of Integrative Cancer Research Department of Biology Massachusetts Institute of Technology CambridgeMA02140 United States New York Genome Center New York CityNY10013 United States New York University New YorkNY10012 United States Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Department of Genome Sciences University of Washington SeattleWA98105 United States Department of Chemistry Purdue University West LafayetteIN47907 United States Department of Biochemistry Stanford University School of Medicine StanfordCA94305 United States Pittsburgh Supercomputing Center Carnegie Mellon University PittsburghPA15213 United States Department of Computational Biology School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Department of Bioengineering University of California San Diego La JollaCA92093 United States Department of Intelligent Systems Engineering School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Surgery Washington University School of Medicine St LouisMO63110 United States Division of Program Coordination Planning and Strategic Initiatives National Institutes of Health BethesdaMD20892 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Caltech-UW TMC Departmen

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings. Copyright © 2019, The Authors. All rights reserved.

关键词： Mapping

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROscience 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROscience 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

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Nature genetics 2018年第12期50卷 1754页

作者： Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Igor Cima Min-Han Tan Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. Department of Computer Science and Engineering and Center for Computational Biology Indraprastha Institute of Information Technology Delhi India. Synthetic Biology Genome Institute of Singapore Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. Department of Pathology Singapore General Hospital Singapore Singapore. Department of Colorectal Surgery Singapore General Hospital Singapore Singapore. Institute of Bioengineering and Nanotechnology Singapore Singapore. Data Analytics Department Institute for Infocomm Research Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. paul.robson@***. The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA. paul.robson@***. Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA. paul.robson@***. Department of Biological Sciences National University of Singapore Singapore Singapore. paul.robson@***. Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. prabhakars@gis.a-star.edu.sg.

In the version of the article published, the author list is not accurate. Igor Cima and Min-Han Tan should have been authors, appearing after Mark Wong in the author list, while Paul Jongjoon Choi should not have been listed as an author. Igor Cima and Min-Han Tan both have the affiliation Institute of bioengineering and Nanotechnology, Singapore, Singapore, and their contributions should have been noted in the Author Contributions section as "I.C. preprocessed Primary Cell Atlas data with inputs from M.-H.T." The following description of the contribution of Paul Jongjoon Choi should not have appeared: "P.J.C. supported the smFISH experiments." In the 'RCA: global panel' section of the Online Methods, the following sentence should have appeared as the second sentence, "An expression atlas of human primary cells (the Primary Cell Atlas) was preprocessed similarly to in ref. 55," with new reference 55 (Cima, I. et al. Tumor-derived circulating endothelial cell clusters in colorectal cancer. science Transl. Med. 8, 345ra89, 2016).

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Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis (vol 50, pg 1072, 2018)

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NATURE GENETICS 2018年第9期50卷 1343-1343页

作者： Waage, Johannes Standl, Marie Curtin, John A. Jessen, Leon E. Thorsen, Jonathan Tian, Chao Schoettler, Nathan Flores, Carlos Abdellaoui, Abdel Ahluwalia, Tarunveer S. Alves, Alexessander C. Amaral, Andre F. S. Anto, Josep M. Arnold, Andreas Barreto-Luis, Amalia Baurecht, Hansjorg van Beijsterveldt, Catharina E. M. Bleecker, Eugene R. Bonas-Guarch, Silvia Boomsma, Dorret I. Brix, Susanne Bunyavanich, Supinda Burchard, Esteban G. Chen, Zhanghua Curjuric, Ivan Custovic, Adnan den Dekker, Herman T. Dharmage, Shyamali C. Dmitrieva, Julia Duijts, Liesbeth Ege, Markus J. Gauderman, W. James Georges, Michel Gieger, Christian Gilliland, Frank Granell, Raquel Gui, Hongsheng Hansen, Torben Heinrich, Joachim Henderson, John Hernandez-Pacheco, Natalia Holt, Patrick Imboden, Medea Jaddoe, Vincent W. V. Jarvelin, Marjo-Riitta Jarvis, Deborah L. Jensen, Kamilla K. Jonsdottir, Ingileif Kabesch, Michael Kaprio, Jaakko Kumar, Ashish Lee, Young-Ae Levin, Albert M. Li, Xingnan Lorenzo-Diaz, Fabian Melen, Erik Mercader, Josep M. Meyers, Deborah A. Myers, Rachel Nicolae, Dan L. Nohr, Ellen A. Palviainen, Teemu Paternoster, Lavinia Pennell, Craig E. Pershagen, Goran Pino-Yanes, Maria Probst-Hensch, Nicole M. Ruschendorf, Franz Simpson, Angela Stefansson, Kari Sunyer, Jordi Sveinbjornsson, Gardar Thiering, Elisabeth Thompson, Philip J. Torrent, Maties Torrents, David Tung, Joyce Y. Wang, Carol A. Weidinger, Stephan Weiss, Scott Willemsen, Gonneke Williams, L. Keoki Ober, Carole Hinds, David A. Ferreira, Manuel A. Bisgaard, Hans Strachan, David P. Bonnelykke, Klaus COPSAC Copenhagen Prospective Studies on Asthma in Childhood Herlev and Gentofte Hospital University of Copenhagen Copenhagen Denmark Institute of Epidemiology Helmholtz Zentrum München-German Research Center for Environmental Health Neuherberg Germany Division of Infection Immunity and Respiratory Medicine University of Manchester Manchester Academic Health Science Centre Manchester University NHS Foundation Trust Manchester UK 23andMe Inc. Mountain View CA USA Department of Human Genetics University of Chicago Chicago IL USA Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Tenerife Spain CIBER de Enfermedades Respiratorias (CIBERES) Instituto de Salud Carlos III Madrid Spain Department of Biological Psychology Netherlands Twin Register VU University Amsterdam The Netherlands Department of Psychiatry Academic Medical Center University of Amsterdam Amsterdam The Netherlands Department of Epidemiology and Biostatistics MRC-PHE Centre for Environment & Health School of Public Health Imperial College London London UK Population Health and Occupational Disease National Heart and Lung Institute Imperial College London London UK ISGlobal Barcelona Spain IMIM (Hospital del Mar Medical Research Institute) Barcelona Spain Universitat Pompeu Fabra (UPF) Barcelona Spain CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain Clinic and Polyclinic of Dermatology University Medicine Greifswald Greifswald Germany Department of Dermatology Venereology and Allergology University-Hospital Schleswig-Hostein Campus Kiel Kiel Germany Divisions of Pharmacogenomics and Genetics Genomics and Precision Medicine Department of Medicine University of Arizona College of Medicine Tucson AZ USA Barcelona Supercomputing Center (BSC) Joint BSC-CRG-IRB Research Program in Computational Biology Barcelona Spain APH Amsterdam Public Health Amsterdam The Netherlands Department of Biotechnology and Biomedicine Technical University of Denma

Allergic rhinitis is the most common clinical presentation of allergy, affecting 400 million people worldwide, with increasing incidence in westernized countries1,2. To elucidate the genetic architecture and understan... 详细信息

Allergic rhinitis is the most common clinical presentation of allergy, affecting 400 million people worldwide, with increasing incidence in westernized countries^1,2. To elucidate the genetic architecture and understand the underlying disease mechanisms, we carried out a meta-analysis of allergic rhinitis in 59,762 cases and 152,358 controls of European ancestry and identified a total of 41 risk loci for allergic rhinitis, including 20 loci not previously associated with allergic rhinitis, which were confirmed in a replication phase of 60,720 cases and 618,527 controls. Functional annotation implicated genes involved in various immune pathways, and fine mapping of the HLA region suggested amino acid variants important for antigen binding. We further performed genome-wide association study (GWAS) analyses of allergic sensitization against inhalant allergens and nonallergic rhinitis, which suggested shared genetic mechanisms across rhinitis-related traits. Future studies of the identified loci and genes might identify novel targets for treatment and prevention of allergic rhinitis.

关键词： Allergy Genome-wide association studies

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25th Annual Computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

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BMC NEUROscience 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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FANTOM5 CAGE profiles of human and mouse samples

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Scientific Data 2017年第1期4卷 170112-170121页

作者： Noguchi, Shuhei Arakawa, Takahiro Fukuda, Shiro Furuno, Masaaki Hasegawa, Akira Hori, Fumi Ishikawa-Kato, Sachi Kaida, Kaoru Kaiho, Ai Kanamori-Katayama, Mutsumi Kawashima, Tsugumi Kojima, Miki Kubosaki, Atsutaka Manabe, Ri-Ichiroh Murata, Mitsuyoshi Nagao-Sato, Sayaka Nakazato, Kenichi Ninomiya, Noriko Nishiyori-Sueki, Hiromi Noma, Shohei Saijyo, Eri Saka, Akiko Sakai, Mizuho Simon, Christophe Suzuki, Naoko Tagami, Michihira Watanabe, Shoko Yoshida, Shigehiro Arner, Peter Axton, Richard A. Babina, Magda Kenneth Baillie, J. Barnett, Timothy C. Beckhouse, Anthony G. Blumenthal, Antje Bodega, Beatrice Bonetti, Alessandro Briggs, James Brombacher, Frank Carlisle, Ailsa J. Clevers, Hans C. Davis, Carrie A. Detmar, Michael Dohi, Taeko Edge, B. Albert S. Edinger, Matthias Ehrlund, Anna Ekwall, Karl Endoh, Mitsuhiro Enomoto, Hideki Eslami, Afsaneh Fagiolini, Michela Fairbairn, Lynsey Farach-Carson, Mary C. Faulkner, Geoffrey J. Ferrai, Carmelo Fisher, Malcolm E. Forrester, Lesley M. Fujita, Rie Furusawa, Jun-Ichi Geijtenbeek, Teunis B. Gingeras, Thomas Goldowitz, Daniel Guhl, Sven Guler, Reto Gustincich, Stefano Ha, Thomas J. Hamaguchi, Masahide Hara, Mitsuko Hasegawa, Yuki Herlyn, Meenhard Heutink, Peter Hitchens, Kelly J. Hume, David A. Ikawa, Tomokatsu Ishizu, Yuri Kai, Chieko Kawamoto, Hiroshi Kawamura, Yuki I. Kempfle, Judith S. Kenna, Tony J. Kere, Juha Khachigian, Levon M. Kitamura, Toshio Klein, Sarah Peter Klinken, S. Knox, Alan J. Kojima, Soichi Koseki, Haruhiko Koyasu, Shigeo Lee, Weonju Lennartsson, Andreas MacKay-Sim, Alan Mejhert, Niklas Mizuno, Yosuke Morikawa, Hiromasa Morimoto, Mitsuru Moro, Kazuyo Morris, Kelly J. Motohashi, Hozumi Mummery, Christine L. Nakachi, Yutaka Nakahara, Fumio Nakamura, Toshiyuki Nakamura, Yukio Nozaki, Tadasuke Ogishima, Soichi Ohkura, Naganari Ohno, Hiroshi Ohshima, Mitsuhiro Okada-Hatakeyama, Mariko Okazaki, Yasushi Orlando, Valerio Ovchinnikov, Dmitry A. Passier, Robert Patrikakis, Margaret Pombo, Ana Pradhan-Bhatt, Swati Qin, Xian-Yang Rehli, Michael Rizzu, Patrizia Roy, S Division of Genomic Technologies RIKEN Center for Life Science Technologies Yokohama Kanagawa 230-0045 Japan RIKEN Omics Science Center Yokohama Kanagawa 230-0045 Japan Department of Medicine Karolinska Institutet Stockholm 14186 Sweden Karolinska University Hospital Center for Metabolism and Endocrinology Stockholm 14186 Sweden Scottish Centre for Regenerative Medicine University of Edinburgh 5 Little France Drive Edinburgh EH164UU United Kingdom Department of Dermatology and Allergy Charite University Medicine Berlin Charitéplatz 1 Berlin 10117 Germany Roslin Institute and Royal School of Veterinary Studies University of Edinburgh Edinburgh EH259RG United Kingdom Australian Infectious Diseases Research Centre University of Queensland St Lucia 4072 QLD Australia School of Chemistry and Molecular Biosciences University of Queensland St Lucia 4072 QLD Australia Bio-Rad Laboratories Pty Ltd Hercules 94547 CA United States University of Queensland Diamantina Institute University of Queensland Woolloongabba 4102 QLD Australia IRCCS Fondazione Santa Lucia Via del Fosso di Fiorano 64 Rome 00143 Italy Australian Institute for Bioengineering and Nanotechnology University of Queensland Brisbane St Lucia 4072 QLD Australia Division of Immunology Institute of Infectious Diseases and Molecular Medicine University of Cape Town Anzio Road Observatory 7925 South Africa Immunology of Infectious Diseases Faculty of Health Sciences South African Medical Research Council University of Cape Town Anzio Road 7925 South Africa International Centre for Genetic Engineering and Biotechnology Cape Town Component Anzio Road 7925 South Africa Hubrecht Institute Royal Netherlands Academy of Arts and Sciences Uppsalalaan 8 3584 Netherlands University Medical Centre Utrecht Postbus 85500 Utrecht 3508 Netherlands Genomics Cold Spring Harbor Laboratory Cold Spring Harbor New York 11797 NY United States Institute of Pharmaceutical Sciences ETH Zurich Vladi

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

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Single-cell morphological analysis for rapid antimicrobial susceptibility test

Single-cell morphological analysis for rapid antimicrobial s...

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International Conference on Solid State Sensors and Actuators (TRANSDUCERS)

作者： J. Choi J. Yoo M. Lee E.-G. Kim J. S. Lee S. Lee S. Joo S. H. Song E.-C. Kim J. C. Lee H. C. Kim Y.-G. Jung S. Kwon Department of Electrical Engineering and Computer Science Seoul National University Seoul Republic of Korea QuantaMatrix Inc. Republic of Korea Interdisciplinary Program of Bioengineering Seoul National University Graduate School Seoul Republic of Korea Department of Laboratory Medicine School of Medicine” Incheon Republic of Korea Department of Laboratory Medicine Seoul National-University Hospital Seoul Republic of Korea Institute of Medical and Biological Engineering Seoul National University Seoul Republic of Korea

A rapid antibiotic susceptibility test (AST) is desperately needed in clinical settings for fast and appropriate antibiotic administration. Traditional ASTs, which rely on cell culture, are not suitable for urgent cases of bacterial infection and antibiotic resistance owing to their relatively long test times. Here, we describe a novel AST called single-cell morphological analysis (SCMA) that can determine antimicrobial susceptibility by automatically analyzing and categorizing morphological changes in single bacterial cells under various antimicrobial conditions. The SCMA was tested with four Clinical and Laboratory Standards Institute standard bacterial strains and 189 clinical samples from hospitals. The results were compared with the gold standard broth microdilution test. The SCMA results were obtained in less than 4 hours with 91.5% categorical agreement and 6.51% minor, 2.56% major, and 1.49% very major discrepancies. Thus, SCMA provides rapid and accurate antimicrobial susceptibility data.

关键词： Microorganisms Antibiotics Strain Immune system Microfluidics Standards Imaging

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