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A genomic catalog of Earth's microbiomes (November, 10.1038/s41587-020-0718-6, 2020)

NATURE BIOTECHNOLOGY 2021年第4期39卷 520-520页

作者： Nayfach, Stephen Roux, Simon Seshadri, Rekha Udwary, Daniel Varghese, Neha Schulz, Frederik Wu, Dongying Paez-Espino, David Chen, I-Min Huntemann, Marcel Palaniappan, Krishna Ladau, Joshua Mukherjee, Supratim Reddy, T. B. K. Nielsen, Torben Kirton, Edward Faria, Jose P. Edirisinghe, Janaka N. Henry, Christopher S. Jungbluth, Sean P. Chivian, Dylan Dehal, Paramvir Wood-Charlson, Elisha M. Arkin, Adam P. Tringe, Susannah G. Visel, Axel Woyke, Tanja Mouncey, Nigel J. Ivanova, Natalia N. Kyrpides, Nikos C. Eloe-Fadrosh, Emiley A. DOE Joint Genome Institute Berkeley CA USA Argonne National Laboratory Argonne IL USA Lawrence Berkeley National Laboratory Berkeley CA USA Travessa Alexandre da Conceicao ALGAplus Ilhavo Portugal Department of Marine Biology and Oceanography Institute of Marine Sciences-CSIC Barcelona Spain Scripps Institution of Oceanography University of California San Diego La Jolla CA USA School of Biotechnology and Biomolecular Sciences UNSW Sydney Sydney New South Wales Australia Centre for Microbiology and Environmental Systems Science University of Vienna Vienna Austria Department of Environmental Science Aarhus University Roskilde Denmark Rumen Microbiology Animal Science AgResearch Grasslands Research Centre Palmerston North New Zealand Department of Biology Pennsylvania State University University Park Pennsylvania PA USA Scottish Association for Marine Science Oban UK Department of Earth and Environmental Sciences University of Minnesota Minneapolis MN USA Department of Marine Science University of Texas Austin Austin TX USA Institute of Microbiology of the Czech Academy of Sciences Praha 4 Czech Republic Department of Biology University of Akron Akron OH USA Department of Chemical Engineering & eScience Institute University of Washington Seattle WA USA Department of Biology University of North Alabama Florence AL USA Life and Environmental Sciences and Sierra Nevada Research Institute University of California Merced Merced CA USA Ecole Polytechnique Federale de Lausanne Lausanne Switzerland Department of Soil Science University of Wisconsin-Madison Madison WI USA School of Biological Sciences Georgia Institute of Technology Atlanta GA USA Department of Aquatic Sciences and Assessment Swedish University of Agricultural Sciences Uppsala Sweden Department of Biology Boston University Boston MA USA University of Arkansas for Medical Sciences Little Rock AR USA Biology Department University of Massachusetts Amherst Amherst MA USA

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

关键词： computational biology and bioinformatics Microbiology

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Flexible multiple base station association and activation for downlink heterogeneous networks

arXiv

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arXiv 2017年

作者： Shen, Kaiming Liu, Ya-Feng Ding, David Yiwei Yu, Wei Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto TorontoONM5S 3G4 Canada State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China

This letter shows that the flexible association of possibly multiple base stations (BSs) to each user over multiple frequency bands, along with the joint optimization of BS transmit power that encourages the turning-off of the BSs at off-peak time, can significantly improve the performance of a downlink heterogeneous wireless cellular network. We propose a gradient projection algorithm for optimizing BS association and an iteratively reweighting scheme together with a novel proximal gradient method for optimizing power in order to find the optimal tradeoff between network utility and power consumption. Simulation results reveal significant performance improvement as compared to the conventional single-BS association. Copyright © 2017, The Authors. All rights reserved.

关键词： Chemical activation

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High order fast algorithm for the Caputo fractional derivative

arXiv

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arXiv 2017年

作者： Wang, Kun Huang, Jizu College of Mathematics and Statistics Chongqing University Chongqing401331 China LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China

In the paper, we present a high order fast algorithm with almost optimum memory for the Caputo fractional derivative, which can be expressed as a convolution of u′(t) with the kernel (tn- t)-α. In the fast algorithm, the interval [0, tn-1] is split into nonuniform subintervals. The number of the subintervals is in the order of log n at the n-th time step. The fractional kernel function is approximated by a polynomial function of K-th degree with a uniform absolute error on each subinterval. We save K+1 integrals on each subinterval, which can be written as a convolution of u′(t) with a polynomial base function. As compared with the direct method, the proposed fast algorithm reduces the storage requirement and computational cost from O(n) to O((K + 1) log n) at the n-th time step. We prove that the convergence rate of the fast algorithm is the same as the direct method even a high order direct method is considered. The convergence rate and efficiency of the fast algorithm are illustrated via several numerical examples. Copyright © 2017, The Authors. All rights reserved.

关键词： Polynomial approximation

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On efficient second order stabilized semi-implicit schemes for the cahn-hilliard phase-field equation

arXiv

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arXiv 2017年

作者： Wang, Lin Yu, Haijun School of Mathematical Sciences University of Chinese Academy of Sciences Beijing100049 China NCMIS LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Beijing100190 China

Efficient and energy stable high order time marching schemes are very important but not easy to construct for the study of nonlinear phase dynamics. In this paper, we propose and study two linearly stabilized second order semi-implicit schemes for the Cahn-Hilliard phase-field equation. One uses backward differentiation formula and the other uses Crank- Nicolson method to discretize linear terms. In both schemes, the nonlinear bulk forces are treated explicitly with two second-order stabilization terms. This treatment leads to linear elliptic systems with constant coefficients, for which lots of robust and efficient solvers are available. The discrete energy dissipation properties are proved for both schemes. Rigorous error analysis is carried out to show that, when the time step-size is small enough, second order accuracy in time is obtained with a prefactor controlled by a fixed power of 1/ϵ, where ϵ is the characteristic interface thickness. Numerical results are presented to verify the accuracy and efficiency of proposed *** Codes 65M12, 65M15, 65P40 Copyright © 2017, The Authors. All rights reserved.

关键词： Energy dissipation

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LifeTime and improving European healthcare through cell-based interceptive medicine (vol 587, pg 377, 2020)

引用

NATURE 2021年第7852期592卷 E8-E8页

作者： Rajewsky, Nikolaus Almouzni, Genevieve Gorski, Stanislaw A. Aerts, Stein Amit, Ido Bertero, Michela G. Bock, Christoph Bredenoord, Annelien L. Cavalli, Giacomo Chiocca, Susanna Clevers, Hans De Strooper, Bart Eggert, Angelika Ellenberg, Jan Fernandez, Xose M. Figlerowicz, Marek Gasser, Susan M. Hubner, Norbert Kjems, Jorgen Knoblich, Jurgen A. Krabbe, Grietje Lichter, Peter Linnarsson, Sten Marine, Jean-Christophe Marioni, John C. Marti-Renom, Marc A. Netea, Mihai G. Nickel, Dorthe Nollmann, Marcelo Novak, Halina R. Parkinson, Helen Piccolo, Stefano Pinheiro, Ines Pombo, Ana Popp, Christian Reik, Wolf Roman-Roman, Sergio Rosenstiel, Philip Schultze, Joachim L. Stegle, Oliver Tanay, Amos Testa, Giuseppe Thanos, Dimitris Theis, Fabian J. Torres-Padilla, Maria-Elena Valencia, Alfonso Vallot, Celine van Oudenaarden, Alexander Vidal, Marie Voet, Thierry Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany Charité-Universitätsmedizin Berlin Germany Berlin Institute of Health (BIH) Berlin Germany German Center for Cardiovascular Research (DZHK) Partner Site Berlin Berlin Germany Institute for Biology Humboldt University of Berlin Berlin Germany Cardiovascular and Metabolic Sciences Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany Department of Pediatric Oncology/Hematology Charité-Universitätsmedizin Berlin Berlin Germany Institut Curie CNRS PSL Research University Sorbonne Université Nuclear Dynamics Unit Equipe Labellisée Ligue contre le cancer Paris France VIB Center for Brain and Disease Research Leuven Belgium Department of Human Genetics KU Leuven Leuven Belgium Department of Neurosciences KU Leuven Leuven Belgium UK Dementia Research Institute at UCL University College London London UK Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK Department of Immunology Weizmann Institute of Science Rehovot Israel Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology Barcelona Spain CNAG-CRG Centre for Genomic Regulation Barcelona Institute of Science and Technology Barcelona Spain Universitat Pompeu Fabra Barcelona Spain ICREA Barcelona Spain CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria Department of Laboratory Medicine Medical University of Vienna Vienna Austria Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases Vienna Austria Department of Medical Humanities Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Institute of Human Genetics UMR 9002 CNRS and University of Montpellier Montpellier France Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy Department of Oncology and Hemato

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mathematical and numerical analysis of the time-dependent Maxwell-Schrödinger Equations in the Coulomb gauge

arXiv

引用

arXiv 2017年

作者： Ma, Chupeng Cao, Liqun Huang, Jizu Lin, Yanping Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China Department of Applied Mathematics Hong Kong Polytechnic University Kowloon Hong Kong

In this paper, we consider the initial-boundary value problem for the time-dependent Maxwell-Schrödinger equations in the Coulomb gauge. We first prove the global existence of weak solutions to the equations. Next we propose an energy-conserving fully discrete finite element scheme for the system and prove the existence and uniqueness of solutions to the discrete system. The optimal error estimates for the numerical scheme without any time-step restrictions are then derived. Numerical results are provided to support our theoretical analysis. Copyright © 2017, The Authors. All rights reserved.

关键词： Initial value problems

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Network slicing for service-oriented networks under resource constraints

arXiv

引用

arXiv 2017年

作者： Zhang, Nan Liu, Ya-Feng Farmanbar, Hamid Chang, Tsung-Hui Hong, Mingyi Luo, Zhi-Quan School of Mathematical Sciences Peking University State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing China Huawei Canada Research Center Ottawa Canada Department of Electrical and Computer Engineering University of Minnesota United States Shenzhen Research Institute of Big Data Chinese University of Hong Kong Shenzhen China

To support multiple on-demand services over fixed communication networks, network operators must allow flexible customization and fast provision of their network resources. One effective approach to this end is network virtualization, whereby each service is mapped to a virtual subnetwork providing dedicated on-demand support to network users. In practice, each service consists of a prespecified sequence of functions, called a service function chain (SFC), while each service function in a SFC can only be provided by some given network nodes. Thus, to support a given service, we must select network function nodes according to the SFC and determine the routing strategy through the function nodes in a specified order. A crucial network slicing problem that needs to be addressed is how to optimally localize the service functions in a physical network as specified by the SFCs, subject to link and node capacity constraints. In this paper, we formulate the network slicing problem as a mixed binary linear program and establish its strong NP-hardness. Furthermore, we propose efficient penalty successive upper bound minimization (PSUM) and PSUM-R(ounding) algorithms, and two heuristic algorithms to solve the problem. Simulation results are shown to demonstrate the effectiveness of the proposed algorithms. Copyright © 2017, The Authors. All rights reserved.

关键词： Network function virtualization

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A multilevel, hierarchical sampling technique for spatially correlated random fields ∗

arXiv

引用

arXiv 2017年

作者： Osborn, Sarah Vassilevski, Panayot S. Villa, Umberto Center for Applied Scientific Computing Lawrence Livermore National Laboratory 7000 East Avenue LivermoreCA94551 United States Institute for Computational Engineering and Sciences University of Texas AustinTX United States

We propose an alternative method to generate samples of a spatially correlated random field with applications to large-scale problems for forward propagation of uncertainty. A classical approach for generating these samples is the Karhunen-Loève (KL) decomposition. However, the KL expansion requires solving a dense eigenvalue problem and is therefore computationally infeasible for large-scale problems. Sampling methods based on stochastic partial differential equations provide a highly scalable way to sample Gaussian fields, but the resulting parametrization is mesh dependent. We propose a multilevel decomposition of the stochastic field to allow for scalable, hierarchical sampling based on solving a mixed finite element formulation of a stochastic reaction-diffusion equation with a random, white noise source function. Numerical experiments are presented to demonstrate the scalability of the sampling method as well as numerical results of multilevel Monte Carlo simulations for a subsurface porous media flow application using the proposed sampling method.65C05, 60H15, 35R60, 65N30, 65M75, 65C30 Copyright © 2017, The Authors. All rights reserved.

关键词： Monte Carlo methods

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A monotone finite volume method for time fractional Fokker-Planck equations

arXiv

引用

arXiv 2017年

作者： Jiang, Yingjun Xu, Xuejun Department of Mathematics and Scientific Computing Changsha University of Science and Technology Changsha410076 China Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences P.O. Box 2719 Beijing100190 China School of Mathematical Sciences Tongji University Shanghai China

We develop a monotone finite volume method for the time fractional Fokker-Planck equations and theoretically prove its unconditional stability. We show that the convergence rate of this method is order 1 in space and if the space grid becomes sufficiently fine, the convergence rate can be improved to order 2. Numerical results are given to support our theoretical findings. One characteristic of our method is that it has monotone property such that it keeps the nonnegativity of some physical variables such as density, concentration, etc.65M12, 65M06, 35S1065M12, 65M06, 35S10 Copyright © 2017, The Authors. All rights reserved.

关键词： Finite volume method

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Spectral gap of sparse bistochastic matrices with exchangeable rows

arXiv

引用

arXiv 2018年

作者： Bordenave, Charles Qiu, Yanqi Zhang, Yiwei Institut de Mathématiques de Marseille CNRS Aix-Marseille University 39 Rue Frédéric Joliot Curie Marseille13013 France Institute of Mathematics and Hua Loo-Keng Key Laboratory of Mathematics AMSS Chinese Academy of Sciences Beijing100190 China CNRS Institut de Mathématiques de Toulouse University of Toulouse III School of Mathematics and Statistics Center for Mathematical Sciences Hubei Key Laboratory of Engineering Modeling and Scientific Computing Huazhong University of Sciences and Technology Wuhan430074 China

We consider a random bistochastic matrix of size n of the form MQ where M is a uniformly distributed permutation matrix and Q is a given bistochastic matrix. Under sparsity and regularity assumptions on Q, we prove that the second largest eigenvalue of MQ is essentially bounded by the normalized Hilbert-Schmidt norm of Q when n grows large. We apply this result to random walks on random regular digraphs.60B20, 60C05, 05C80, 05C38 Copyright © 2018, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

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