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Author Correction: Why rankings of biomedical image analysis competitions should be interpreted with care

Nature communications 2019年第1期10卷 588页

作者： Lena Maier-Hein Matthias Eisenmann Annika Reinke Sinan Onogur Marko Stankovic Patrick Scholz Tal Arbel Hrvoje Bogunovic Andrew P Bradley Aaron Carass Carolin Feldmann Alejandro F Frangi Peter M Full Bram van Ginneken Allan Hanbury Katrin Honauer Michal Kozubek Bennett A Landman Keno März Oskar Maier Klaus Maier-Hein Bjoern H Menze Henning Müller Peter F Neher Wiro Niessen Nasir Rajpoot Gregory C Sharp Korsuk Sirinukunwattana Stefanie Speidel Christian Stock Danail Stoyanov Abdel Aziz Taha Fons van der Sommen Ching-Wei Wang Marc-André Weber Guoyan Zheng Pierre Jannin Annette Kopp-Schneider Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. l.maier-hein@dkfz.de. Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Centre for Intelligent Machines McGill University Montreal QC H3A0G4 Canada. Christian Doppler Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University Vienna 1090 Vienna Austria. Science and Engineering Faculty Queensland University of Technology Brisbane QLD 4001 Australia. Department of Electrical and Computer Engineering Department of Computer Science Johns Hopkins University Baltimore MD 21218 USA. CISTIB - Center for Computational Imaging & Simulation Technologies in Biomedicine The University of Leeds Leeds Yorkshire LS2 9JT UK. Department of Radiology and Nuclear Medicine Medical Image Analysis Radboud University Center 6525 GA Nijmegen The Netherlands. Institute of Information Systems Engineering TU Wien 1040 Vienna Austria. Complexity Science Hub Vienna 1080 Vienna Austria. Heidelberg Collaboratory for Image Processing (HCI Heidelberg University 69120 Heidelberg Germany. Centre for Biomedical Image Analysis Masaryk University 60200 Brno Czech Republic. Electrical Engineering Vanderbilt University Nashville TN 37235-1679 USA. Institute of Medical Informatics Universität zu Lübeck 23562 Lübeck Germany. Division of Medical Image Computing (MIC) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Institute for Advanced Studies Department of Informatics Technical University of Munich 80333 Munich Germany. Information System Institute HES-SO Sierre 3960 Switzerland. Departments of Radiology Nuclear Medicine and Medical Informatics Erasmus MC 3015 GD Rotterdam The Netherlands. Department of Computer Science University of Warwick Coventry CV4 7AL UK. Department of Radiation Oncology Massachusetts General Hospital Boston MA

In the original version of this Article the values in the rightmost column of Table 1 were inadvertently shifted relative to the other columns. This has now been corrected in the PDF and HTML versions of the Article.

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Few-nucleon systems with state-of-the-art chiral nucleon-nucleon forces

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Physical Review C 2016年第4期93卷 044002-044002页

作者： S. Binder A. Calci E. Epelbaum R. J. Furnstahl J. Golak K. Hebeler H. Kamada H. Krebs J. Langhammer S. Liebig P. Maris Ulf-G. Meißner D. Minossi A. Nogga H. Potter R. Roth R. Skibiński K. Topolnicki J. P. Vary H. Witała Department of Physics and Astronomy University of Tennessee Knoxville Tennessee 37996 USA Physics Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA TRIUMF 4004 Wesbrook Mall Vancouver British Columbia V6T 2A3 Canada Institut für Theoretische Physik II Ruhr-Universität Bochum D-44780 Bochum Germany Department of Physics The Ohio State University Columbus Ohio 43210 USA M. Smoluchowski Institute of Physics Jagiellonian University PL-30348 Kraków Poland Institut für Kernphysik Technische Universität Darmstadt 64289 Darmstadt Germany ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH 64291 Darmstadt Germany Department of Physics Faculty of Engineering Kyushu Institute of Technology Kitakyushu 804-8550 Japan Institut für Kernphysik Institute for Advanced Simulation Jülich Center for Hadron Physics and JARA - High Performance Computing Forschungszentrum Jülich D-52425 Jülich Germany Department of Physics and Astronomy Iowa State University Ames Iowa 50011 USA Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics Universität Bonn D-53115 Bonn Germany JARA - High Performance Computing Forschungszentrum Jülich D-52425 Jülich Germany

We apply improved nucleon-nucleon potentials up to fifth order in chiral effective field theory, along with a new analysis of the theoretical truncation errors to study nucleon-deuteron (Nd) scattering and selected low-energy observables in H3,He4, and Li6. Calculations beyond second order differ from experiment well outside the range of quantified uncertainties, providing truly unambiguous evidence for missing three-nucleon forces within the employed framework. The sizes of the required three-nucleon-force contributions agree well with expectations based on Weinberg's power counting. We identify the energy range in elastic Nd scattering best suited to study three-nucleon-force effects and estimate the achievable accuracy of theoretical predictions for various observables.

关键词： Few-body systems Nuclear forces Nucleon-nucleon interactions Chiral symmetry

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Binding in light nuclei: Statistical NN uncertainties vs Computational accuracy

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Journal of Physics: Conference Series 2016年第1期742卷

作者： R. Navarro Pérez A. Nogga J. E. Amaro E. Ruiz Arriola Nuclear and Chemical Science Division Lawrence Livermore National Laboratory Livermore California 94551 USA Forschungszentrum Jülich Institut für Kernphysik (Theorie) Institute for Advanced Simulation Jülich Center for Hadron Physics and JARA - High Performance Computing D-52425 Julich Germany. Departamento de Física Atómica Molecular y Nuclear and Instituto Carlos I de Física Teórica y Computacional Universidad de Granada E-18071 Granada Spain

We analyse the impact of the statistical uncertainties of the the nucleon-nucleon interaction, based on the Granada-2013 np-pp database, on the binding energies of the triton and the alpha particle using a bootstrap method, by solving the Faddeev equations for 3H and the Yakubovsky equations for 4He respectively. We check that in practice about 30 samples prove enough for a reliable error estimate. An extrapolation of the well fulfilled Tjon-line correlation predicts the experimental binding of the alpha particle within uncertainties.

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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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[CrF(O2CtBu)2]9: Synthesis and Characterization of a Regular Homometallic Ring with an Odd Number of Metal Centers and Electrons

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Angewandte Chemie 2016年第31期128卷

作者： Robert J. Woolfson Grigore A. Timco Alessandro Chiesa Inigo J. Vitorica‐Yrezabal Floriana Tuna Tatiana Guidi Eva Pavarini Paolo Santini Stefano Carretta Richard E. P. Winpenny School of Chemistry and Photon Science Institute University of Manchester Oxford Road Manchester M20 4NZ UK Dipartimento di Fisica e Scienze della Terra Università di Parma Parco Area della Scienze 7/A I-43124 Parma Italy ISIS Facility Rutherford Appleton Laboratory Didcot OX11 0QX UK Institute for Advanced Simulation Forschungzentrum Jülich 52425 Jülich Germany JARA High Performance Computing RWTH Aachen University 52062 Aachen Germany

The first regular homometallic ring containing an odd number of metal centers is reported. The ring was synthesized by means of amine‐templated self‐assembly. Extensive physical characterization studies, including magnetic measurements, powder inelastic neutron scattering (INS), and DFT calculations, show that the molecule has a near perfect match to the expected behavior for a frustrated system with the lowest energy pair of S =1/2 spin states separated by only 0.1 meV (0.8 cm −1 ).

关键词： Inelastische Neutronenstreuung Magnetische Eigenschaften Molekularer Magnetismus Spinfrustration Supramolekulare Chemie

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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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Unidirectional phase singularity in ultrathin metamaterials at exceptional points

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Physical Review A 2014年第6期89卷 065801-065801页

作者： Ming Kang Hai-Xu Cui Teng-Fei Li Jing Chen Weiren Zhu Malin Premaratne College of Physics and Materials Science Tianjin Normal University Tianjin 300387 China MOE Key Laboratory of Weak-Light Nonlinear Photonics School of Physics Nankai University Tianjin 300071 China Advanced Computing and Simulation Laboratory (AχL) Department of Electrical and Computer Systems Engineering Monash University Clayton Victoria 3800 Australia

Scattering properties of light in metamaterials are similar to those in open quantum systems. Here we propose an ultrathin tailored metamaterial designed to show that one-way zero reflection yielding to topologically stable phase dislocation is responsible for the exceptional point, one of the most important degeneracies in the non-Hermitian Hamiltonian. In order to bridge the exotic macroscopic optical phenomenon occurring in metamaterials, a phenomenological model under microscopic view is developed and good agreement with the full-blown numerical simulation is found. Our investigation uncovers the capabilities of metamaterials to exhibit extreme optical properties and to provide us with many potential applications such as the suppression of undesired scattering signals in the spectral band ranging from microwaves to visible light.

关键词： Metamaterials

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Scalable replay with partial-order dependencies for message-logging fault tolerance

Scalable replay with partial-order dependencies for message-...

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IEEE International Conference on Cluster computing

作者： Jonathan Lifflander Esteban Meneses Harshitha Menon Phil Miller Sriram Krishnamoorthy Laxmikant V. Kalé Department of Computer Science University of Illinois Urbana-Champaign Center for Simulation and Modeling University of Pittsburgh Department of Computer Science University of Illinois at Urbana-Champaign Advanced Computing Mathematics and Data Division Pacific Northwest National Laboratory

Deterministic replay of a parallel application is commonly used for discovering bugs or to recover from a hard fault with message-logging fault tolerance. For message passing programs, a major source of overhead during forward execution is recording the order in which messages are sent and received. During replay, this ordering must be used to deterministically reproduce the execution. Previous work in replay algorithms often makes minimal assumptions about the programming model and application to maintain generality. However, in many applications, only a partial order must be recorded due to determinism intrinsic in the program, ordering constraints imposed by the execution model, and events that are commutative (their relative execution order during replay does not need to be reproduced exactly). In this paper, we present a novel algebraic framework for reasoning about the minimum dependencies required to represent the partial order for different orderings and interleavings. By exploiting this framework, we improve on an existing scalable message-logging fault tolerance scheme that uses a total order. The improved scheme scales to 131,072 cores on an IBM BlueGene/P with up to 2× lower overhead.

关键词： Fault tolerance Fault tolerant systems Programming Debugging Program processors Electronic mail Benchmark testing

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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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Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization

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Computational biology and chemistry 2015年 57卷 21-8页

作者： Zhi-Qin Zhao Guo-Sheng Han Zu-Guo Yu Jinyan Li Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China. Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia. Electronic address: yuzg1970@***. Advanced Analytics Institute & Centre for Health Technologies University of Technology Sydney Broadway NSW 2007 Australia. Electronic address: jinyan.li@uts.edu.au.

Random walk on heterogeneous networks is a recently emerging approach to effective disease gene prioritization. Laplacian normalization is a technique capable of normalizing the weight of edges in a network. We use this technique to normalize the gene matrix and the phenotype matrix before the construction of the heterogeneous network, and also use this idea to define the transition matrices of the heterogeneous network. Our method has remarkably better performance than the existing methods for recovering known gene-phenotype relationships. The Shannon information entropy of the distribution of the transition probabilities in our networks is found to be smaller than the networks constructed by the existing methods, implying that a higher number of top-ranked genes can be verified as disease genes. In fact, the most probable gene-phenotype relationships ranked within top 3 or top 5 in our gene lists can be confirmed by the OMIM database for many cases. Our algorithms have shown remarkably superior performance over the state-of-the-art algorithms for recovering gene-phenotype relationships. All Matlab codes can be available upon email request.

关键词： Disease genes and phenotypes Heterogeneous network Laplacian normalization Leave-one-out cross-validation Random walk with restart Shannon information entropy

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