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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The 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 Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

On derivatives of smooth functions represented in multiwavelet bases

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Journal of Computational Physics: X 2019年 4卷

作者： Anderson, Joel Harrison, Robert J. Sekino, Hideo Sundahl, Bryan Beylkin, Gregory Fann, George I. Jensen, Stig R. Sagert, Irina Institute for Advanced Computational Science Stony Brook University Stony BrookNY11794-5250 United States Department of Applied Mathematics University of Colorado at Boulder UCB 526 BoulderCO80309-0526 United States Computer Science and Mathematics Division Oak Ridge National Laboratory MS6211 1 Bethel Valley Road Oak RidgeTN37831-6367 United States Department of Chemistry Hylleraas Centre for Quantum Molecular Sciences UiT The Arctic University of Norway Mailbox 6050 Langnes N-9037 Tromsø Norway Center for Theoretical Astrophysics Los Alamos National Laboratory Los AlamosNM87545 United States

We construct high-order derivative operators for smooth functions represented via discontinuous multiwavelet bases. The need for such operators arises in order to avoid artifacts when computing functionals involving high-order derivatives of solutions of integral equations. Previously high-order derivatives had to be formed by repeated application of a first-derivative operator that, while uniquely defined, has a spectral norm that grows quadratically with polynomial order and, hence, greatly amplifies numerical noise (truncation error) in the multiwavelet computation. The new constructions proceed via least-squares projection onto smooth bases and provide substantially improved numerical properties as well as permitting direct construction of high-order derivatives. We employ either b-splines or bandlimited exponentials as the intermediate smooth basis, with the former maintaining the concept of approximation order while the latter preserves the pure imaginary spectrum of the first-derivative operator and provides more direct control over the bandlimit and accuracy of computation. We demonstrate the properties of these new operators via several numerical tests as well as application to a problem in nuclear physics. © 2019 The Authors

关键词： Integral equations

A simple approach to reliable and robust a posteriori error estimation for singularly perturbed problems

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arXiv 2018年

作者： Ainsworth, Mark Vejchodský, Tomáš Division of Applied Mathematics Brown University 182 George St ProvidenceRI02912 United States Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Institute of Mathematics Czech Academy of Sciences 115 67 Žitná 25 Prague 1CZ- Czech Republic

A simple flux reconstruction for finite element solutions of reaction-diffusion problems is shown to yield fully computable upper bounds on the energy norm of error in an approximation of singularly perturbed reaction-diffusion problem. The flux reconstruction is based on simple, independent post-processing operations over patches of elements in conjunction with standard Raviart–Thomas vector fields and gives upper bounds even in cases where Galerkin orthogonality might be violated. If Galerkin orthogonality holds, we prove that the corresponding local error indicators are locally efficient and robust with respect to any mesh size and any size of the reaction coefficient, including the singularly perturbed *** Codes 65N15, 65N30, 65J15 Copyright © 2018, The Authors. All rights reserved.

关键词： Finite element method

Galaxy clusters at z∼1 imaged by ALMA with the Sunyaev-Zel’dovich effect

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arXiv 2022年

作者： Kitayama, Tetsu Ueda, Shutaro Okabe, Nobuhiro Akahori, Takuya Hilton, Matt Hughes, John P. Ichinohe, Yuto Kohno, Kotaro Komatsu, Eiichiro Lin, Yen-Ting Miyatake, Hironao Oguri, Masamune Sifón, Cristóbal Takakuwa, Shigehisa Takizawa, Motokazu Tsutsumi, Takahiro van Marrewijk, Joshiwa Wollack, Edward J. Department of Physics Toho University Chiba Funabashi274-8510 Japan No. 1 Section 4 Roosevelt Road Taipei10617 Taiwan Institute of Astronomy National Tsing Hua University Hsinchu30013 Taiwan Department of Physics Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Astrophysical Science Center Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Core Research for Energetic Universe Hiroshima University Department of Physics Hiroshima University 1-3-1 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Physics Program Graduate School of Advanced Science and Engineering Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Mizusawa VLBI observatory National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Operation Division SKA Observatory Jodrell Bank Lower Withington MacclesfieldSK11 9DL United Kingdom Astrophysics Research Centre University of KwaZulu-Natal Westville Campus Durban4041 South Africa School of Mathematics Statistics & Computer Science University of KwaZulu-Natal Westville Campus Durban4041 South Africa Wits Centre for Astrophysics School of Physics University of the Witwatersrand Private Bag 3 Johannesburg2050 South Africa Department of Physics and Astronomy Rutgers The State University of New Jersey PiscatawayNJ08854-8019 United States Department of Physics Rikkyo University 3-34-1 Nishi-Ikebukuro Toshima-ku Tokyo171-8501 Japan Institute of Astronomy School of Science The University of Tokyo 2-21-1 Osawa Mitaka Tokyo181-0015 Japan Research Center for the Early Universe School of Science The University of Tokyo 7-3-1 Hongo Bunkyo Tokyo113-0033 Japan Max-Planck-Institut für Astrophysik Karl-Schwarzschild Str. 1 GarchingD-85741 Germany The University of Tokyo Institutes for Advanced Study The University of Tokyo 5-1-5 Kashiwanoha Chiba277-8583 Japan Nagoya University Nagoya464-8

We present high angular-resolution measurements of the thermal Sunyaev-Zel’dovich effect (SZE) toward two galaxy clusters, RCS J2319+0038 at z = 0.9 and HSC J0947−0119 at z = 1.1, by the Atacama Large Millimeter/submillimeter Array (ALMA) in Band 3. They are supplemented with available Chandra X-ray data, optical data taken by Hyper Suprime-Cam on Subaru, and millimeter-wave SZE data from the Atacama Cosmology Telescope. Taking into account departures from spherical symmetry, we have reconstructed non-parametrically the inner pressure profile of two clusters as well as electron temperature and density profiles for RCS J2319+0038. This is one of the first such measurements for an individual cluster at z >∼ 0.9. We find that the inner pressure profile of both clusters is much shallower than that of local cool-core clusters. Our results consistently suggest that RCS J2319+0038 hosts a weak cool core, where radiative cooling is less significant than in local cool cores. On the other hand, HSC J0947−0119 exhibits an even shallower pressure profile than RCS J2319+0038 and is more likely a non-cool-core cluster. The SZE centroid position is offset by more than 140 h−170kpc from the peaks of galaxy distribution in HSC J0947−0119, suggesting a stronger influence of mergers in this cluster. We conclude that these distant clusters are at a very early stage of developing the cool cores typically found in clusters at lower redshifts. Copyright © 2022, The Authors. All rights reserved.

关键词： Millimeter waves

The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

Multilevel Particle Filters for Lévy-driven stochastic differential equations

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arXiv 2018年

作者： Jasra, Ajay Law, Kody J.H. Osei, Prince Peprah Department of Statistics and Applied Probability National University of Singapore Singapore117546 SG Singapore School of Mathematics University of Manchester United Kingdom Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN37831 United States

We develop algorithms for computing expectations with respect to the laws of models associated to stochastic differential equations (SDEs) driven by pure Lévy processes. We consider filtering such processes and well as pricing of path dependent options. We propose a multilevel particle filter (MLPF) to address the computational issues involved in solving these continuum problems. We show via numerical simulations and theoretical results that under suitable assumptions regarding the discretization of the underlying driving Lévy proccess, our proposed method achieves optimal convergence rates: the cost to obtain MSE O(ϵ2) scales like O(ϵ-2) for our method, as compared with the standard particle filter O(ϵ-3). Copyright © 2018, The Authors. All rights reserved.

关键词： Monte Carlo methods

Using automatic differentiation as a general framework for ptychographic reconstruction

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arXiv 2019年

作者： Kandel, Saugat Maddali, S. Allain, Marc Hruszkewycz, Stephan O. Jacobsen, Chris Nashed, Youssef S.G. Applied Physics Northwestern University EvanstonIL60208 United States Materials Science Division Argonne National Laboratory LemontIL60439 United States Aix Marseille Univ CNRS Centrale Marseille Institut Fresnel Marseille France Advanced Photon Source Argonne National Laboratory LemontIL60439 United States Department of Physics & Astronomy Northwestern University EvanstonIL60208 United States Chemistry of Life Processes Institute Northwestern University EvanstonIL60208 United States Mathematics and Computer Science Division Argonne National Laboratory LemontIL60439 United States

Coherent diffraction imaging methods enable imaging beyond lens-imposed resolution limits. In these methods, the object can be recovered by minimizing an error metric that quantifies the difference between diffraction patterns as observed, and those calculated from a present guess of the object. Efficient minimization methods require analytical calculation of the derivatives of the error metric, which is not always straightforward. This limits our ability to explore variations of basic imaging approaches. In this paper, we propose to substitute analytical derivative expressions with the automatic differentiation method, whereby we can achieve object reconstruction by specifying only the physics-based experimental forward model. We demonstrate the generality of the proposed method through straightforward object reconstruction for a variety of complex ptychographic experimental models. Copyright © 2019, The Authors. All rights reserved.

关键词： Diffraction

Multiwavelength Constraints on the Origin of a Nearby Repeating Fast Radio Burst Source in a Globular Cluster

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arXiv 2023年

作者： Pearlman, Aaron B. Scholz, Paul Bethapudi, Suryarao Hessels, Jason W.T. Kaspi, Victoria M. Kirsten, Franz Nimmo, Kenzie Spitler, Laura G. Fonseca, Emmanuel Meyers, Bradley W. Stairs, Ingrid H. Tan, Chia Min Bhardwaj, Mohit Chatterjee, Shami Cook, Amanda M. Curtin, Alice P. Dong, Fengqiu Adam Eftekhari, Tarraneh Gaensler, B.M. Güver, Tolga Kaczmarek, Jane Leung, Calvin Masui, Kiyoshi W. Michilli, Daniele Prince, Thomas A. Sand, Ketan R. Shin, Kaitlyn Smith, Kendrick M. Tendulkar, Shriharsh P. Department of Physics McGill University MontréalQC Canada Trottier Space Institute McGill University MontréalQC Canada Division of Physics Mathematics and Astronomy California Institute of Technology PasadenaCA United States Dunlap Institute for Astronomy and Astrophysics University of Toronto TorontoON Canada Department of Physics and Astronomy York University TorontoON Canada Max-Planck-Institut für Radioastronomie Bonn Germany Anton Pannekoek Institute for Astronomy University of Amsterdam Amsterdam Netherlands ASTRON Netherlands Institute for Radio Astronomy Dwingeloo Netherlands Department of Space Earth and Environment Chalmers University of Technology Onsala Space Observatory Onsala Sweden MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology CambridgeMA United States Department of Physics and Astronomy West Virginia University MorgantownWV United States Center for Gravitational Waves and Cosmology West Virginia University Chestnut Ridge Research Building MorgantownWV United States International Centre for Radio Astronomy Research Curtin University BentleyWA Australia Department of Physics and Astronomy University of British Columbia VancouverBC Canada McWilliams Center for Cosmology Department of Physics Carnegie Mellon University PittsburghPA United States Cornell Center for Astrophysics and Planetary Science Cornell University IthacaNY United States David A. Dunlap Department of Astronomy and Astrophysics University of Toronto TorontoON Canada Center for Interdisciplinary Exploration and Research in Astrophysics Department of Physics and Astronomy Northwestern University EvanstonIL United States Department of Astronomy and Astrophysics University of California Santa Cruz Santa CruzCA United States Department of Astronomy and Space Sciences Science Faculty Istanbul University Istanbul Turkey Istanbul University Observatory Research and Application Center Istanbul University Istanbul T

The precise origins of fast radio bursts (FRBs) remain unknown. Multiwavelength observations of nearby FRB sources can provide important insights into the enigmatic FRB phenomenon. Here, we present results from a sensitive, broadband X-ray and radio observational campaign of FRB 20200120E, the closest known extragalactic repeating FRB source (located 3.63 Mpc away in an ∼10-Gyr-old globular cluster). We place deep limits on the persistent and prompt X-ray emission from FRB 20200120E, which we use to constrain possible origins for the source. We compare our results with various classes of X-ray sources, transients, and FRB models. We find that FRB 20200120E is unlikely to be associated with ultraluminous X-ray bursts, magnetar-like giant flares, or an SGR 1935+2154-like intermediate flare. Although other types of bright magnetar-like intermediate flares and short X-ray bursts would have been detectable from FRB 20200120E during our observations, we cannot entirely rule them out as a class. We show that FRB 20200120E is unlikely to be powered by an ultraluminous X-ray source or a young extragalactic pulsar embedded in a Crab-like nebula. We also provide new constraints on the compatibility of FRB 20200120E with accretion-based FRB models involving X-ray binaries. These results highlight the power of multiwavelength observations of nearby FRBs for discriminating between FRB models. © 2023, CC BY.

关键词： X-ray astronomy

Approval gap of weighted k-majority tournaments

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arXiv 2018年

作者： Coste, Jeremy Flesch, Breeann McNicholas, Erin M. Laison, Joshua D. Miyata, Dane Fu Foundation School of Engineering and Applied Science Columbia University New YorkNY United States Computer Science Division Western Oregon University Monmouth United States Mathematics Department Willamette University Salem United States Department of Mathematics University of Oregon Eugene United States

A k-majority tournament T on a finite set of vertices V is defined by a set of 2k - 1 linear orders on V, with an edge u → v in T if u > v in a majority of the linear orders. We think of the linear orders as voter preferences and the vertices of T as candidates, with an edge u → v in T if a majority of voters prefer candidate u to candidate v. In this paper we introduce weighted k-majority tournaments, with each edge u → v weighted by the number of voters preferring u. We define the maximum approval gap γw(T), a measure by which any dominating set of T beats the next most popular candidate. This parameter is analogous to previous work on the size of minimum dominating sets of (unweighted) k-majority tournaments. We prove that k/2 ≤ γw(T) ≤ 2k - 1 for any weighted k-majority tournament T, and construct tournaments with γw(T) = q for any rational number k/2 ≤ q ≤ 2k - 1. We also consider the minimum number of vertices m(q;k) in a k-majority tournament with γw(T) = *** Codes 05C20, 05C69, 91B14 Copyright © 2018, The Authors. All rights reserved.

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