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arXiv 2024年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Gandhi, Deep Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Franson, Andrea Gottipati, Anurag Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Khalili, Neda Kofler, Florian LaBella, Dominic Lai, Hollie Anne Van Leemput, Koen Li, Hongwei Bran Maleki, Nazanin McAllister, Aaron S. Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Nandolia, Khanak K. Pavaine, Julija Piraud, Marie Poussaint, Tina Prabhu, Sanjay P. Reitman, Zachary Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Sheth, Nakul Tu, Wenxin Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Zapaishchykova, Anna Bornhorst, Miriam Deutsch, Michelle Fouladi, Maryam Lazow, Margot Mikael, Leonie Hummel, Trent Kann, Benjamin de Blank, Peter Hoffman, Lindsey Aboian, Mariam Nabavizadeh, Ali Packer, Roger Bakas, Spyridon Resnick, Adam Rood, Brian Vossough, Arastoo Linguraru, Marius George Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Neurosurgery University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Sage Bionetworks United States Lab Crestview Radiology Lagos Nigeria McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center DurhamNC United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States C. S. Mott Children’s Hospital University of Michigan MI United States Biomedical Engineering Rutgers University New BrunswickNJ United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Yale University New HavenCT United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Cincinnati Children’s Hospital Medical Center OH United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center DurhamNC United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of De

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge, focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors. © 2024, CC BY.

关键词： Deep learning

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Observation of indirect ionization of W7+ in EBIT plasma

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Journal of physics: Conference Series 2020年第13期1412卷

作者： Q Lu J He H Tian M Li Y Yang K Yao C Chen J Xiao J G Li B Tu Y Zou Institute of Modern Physics Department of Nuclear Science and Technology Fudan University Shanghai 200433 China Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) Fudan University Shanghai 200433 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China Max-Planck-Institute für Kernphysik Saupfercheckweg 1 69117 Heidelberg Germany

In this work, visible and EUV spectra of W7+ have been measured using the high-temperature super-conducting electron-beam ion trap at the Shanghai EBIT laboratory under extremely low-energy conditions. The relevant atomic structure has been calculated by using the flexible atomic code package and the GRASP2K code. A hypothesis for the charge-state evolution of W7+ is proposed based on our results. The occurrence of W7+ ions results from indirect ionization caused by stepwise excitation between some metastable states of lower-charge-state W ions, at the nominal electron beam energy of 59 eV.

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Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

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Physical Review Letters 2018年第14期120卷 143001-143001页

作者： Linfeng Zhang Jiequn Han Han Wang Roberto Car Weinan E Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA and Center for Data Science Beijing International Center for Mathematical Research Peking University Beijing Institute of Big Data Research Beijing 100871 People’s Republic of China

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

关键词： Classical statistical mechanics Density functional theory First-principles calculations Interatomic & molecular potentials Learning Neuronal networks Potential energy surfaces Solid-state chemistry Thermal properties Van der Waals interaction Molecular dynamics

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Volume growth, curvature, and buser-type inequalities in graphs

arXiv

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arXiv 2018年

作者： Benson, Brian Ralli, Peter Tetali, Prasad Department of Mathematics University of California RiversideCA United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States School of Mathematics Georgia Institute of Technology AtlantaGA United States

We study the volume growth of metric balls as a function of the radius in discrete spaces, and focus on the relationship between volume growth and discrete curvature. We improve volume growth bounds under a lower bound on the so-called Ollivier curvature, and discuss similar results under other types of discrete Ricci curvature. Following recent work in the continuous setting of Riemannian manifolds (by the first author), we then bound the eigenvalues of the Laplacian of a graph under bounds on the volume growth. In particular, λ2of the graph can be bounded using a weighted discrete Hardy inequality and the higher eigenvalues of the graph can be bounded by the eigenvalues of a tridiagonal matrix times a multiplicative factor, both of which only depend on the volume growth of the graph. As a direct application, we relate the eigenvalues to the Cheeger isoperimetric constant. Using these methods, we describe classes of graphs for which the Cheeger inequality is tight on the second eigenvalue. We also describe a method for proving Buser's Inequality in graphs, particularly under a lower bound assumption on curvature. Copyright © 2018, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

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Regularized matrix data clustering and its application to image analysis

arXiv

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arXiv 2018年

作者： Gao, Xu Shen, Weining Ombao, Hernando Department of Statistics University of California IrvineCA United States Program on Applied Mathematics & Computational Science King Abdullah University of Science and Technology Saudi Arabia

In this paper, we propose a regularized mixture probabilistic model to cluster matrix data and apply it to brain signals. The approach is able to capture the sparsity (low rank, small/zero values) of the original signals by introducing regularization terms into the likelihood function. Through a modified EM algorithm, our method achieves the optimal solution with low computational cost. Theoretical results are also provided to establish the consistency of the proposed estimators. Simulations show the advantages of the proposed method over other existing methods. We also apply the approach to two real datasets from different experiments. Promising results imply that the proposed method successfully characterizes signals with different patterns while yielding insightful scientific interpretation. Copyright © 2018, The Authors. All rights reserved.

关键词： Matrix algebra

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Metadata for the Flux Density Calibration of the April 2018 Event Horizon Telescope Data

arXiv

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arXiv 2023年

作者： Koay, J.Y. Romero-Cañizales, C. Matthews, L.D. Janssen, M. Blackburn, L. Tilanus, R.P.J. Park, J. Asada, K. Matsushita, S. Baczko, A.-K. Bella, N. La Chan, C.-K. Crew, G.B. Fish, V. Patel, N. Ramakrishnan, V. Rottmann, H. Wagner, J. Wiik, K. Friberg, P. Goddi, C. Issaoun, S. Keating, G. Kim, J. Krichbaum, T.P. Marrone, D. Narayanan, G. Roy, A. Ruíz, I. Sánchez, S. Torne, P. Weintroub, J. Academia Sinica Institute of Astronomy and Astrophysics No.1 Sec. 4 Roosevelt Rd Taipei10617 Taiwan Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road WestfordMA01886 United States Auf dem Hügel 69 Bonn53121 Germany Center for Astrophysics Harvard & Smithsonian 60 Garden St. CambridgeMA02138 United States Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Avenue TucsonAZ85721 United States Department of Astronomy and Space Science Kyung Hee University 1732 Deogyeong-daero Giheung-gu Gyeonggi-do Yongin-si17104 Korea Republic of Department of Astrophysics IMAPP Radboud University P.O. Box 9010 Nijmegen6500 GL Netherlands Data Science Institute University of Arizona 1230 N. Cherry Ave. TucsonAZ85721 United States Program in Applied Mathematics University of Arizona 617 N. Santa Rita TucsonAZ85721 United States Finnish Centre for Astronomy with ESO University of Turku FI-20014 Finland Aalto University Metsähovi Radio Observatory Metsähovintie 114 KylmäläFI-02540 Finland Tuorla Observatory Department of Physics and Astronomy University of Turku Finland East Asian Observatory 660 N. A’ohoku Place HiloHI96720 United States INAF - Osservatorio Astronomico di Cagliari Via della Scienza 5 CA Selargius09047 Italy California Institute of Technology 1200 East California Boulevard PasadenaCA91125 United States Department of Astronomy University of Massachusetts AmherstMA01003 United States Institut de Radioastronomie Millimétrique Avenida Divina Pastora 7 Local 20 GranadaE-18012 Spain

The Event Horizon Telescope (EHT) observations carried out in 2018 April at 1.3 mm wavelengths included 9 stations in the array, comprising 7 single-dish telescopes and 2 phased arrays. The metadata package for the 2018 EHT observing campaign contains calibration tables required for the a-priori amplitude calibration of the 2018 April visibility data. This memo is the official documentation accompanying the release of the 2018 EHT metadata package, providing an overview of the contents of the package. We describe how telescope sensitivities, gain curves and other relevant parameters for each station in the EHT array were collected, processed, and validated to produce the calibration tables. Copyright © 2023, The Authors. All rights reserved.

关键词： Telescopes

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Role of XUV Photons in Atomic High-Order Above-Threshold Ionization Processes in IR+XUV Two-Color Laser Fields

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Chinese physics Letters 2017年第11期34卷 15-19页

作者：张奎刘敏王兵兵郭迎春严宗朝陈京柳晓军 Laboratory of Optical Physics Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing 100190 Department of Physics East China Normal UniversityShanghai 200241 Department of Physics University of New BrunswickFrederictonNew BrunswickCanada State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics Wuhan Institute of Physics and MathematicsChinese Academy of SciencesWuhan 430071 Center for Cold Atom Physics Chinese Academy of SciencesWuhan 430071 HEDPS Center for Applied Physics and TechnologyPeking UniversityBeijing 100871 Institute of Applied Physics and Computational Mathematics Beijing 100088

We investigate the above-threshold ionization of an atom in a combined infrared （IR） and extreme ultraviolet （XUV） two-color laser field and focus on the role of XUV field in the high-order above-threshold ionization （HATI） process. It is demonstrated that, in stark contrast to previous studies, the XUV laser may play a significant role in atomic HATI process, and in particular, the XUV laser can accelerate the ionized electron in a quantized way during the collision between the electron and its parent ion. This process cannot be explained by the elassical three-step model Our results indicate that the previously well-established concept that HATI is an elastic recollision process is broken down.

关键词： ATI Role of XUV Photons in Atomic High-Order Above-Threshold Ionization Processes in IR+XUV Two-Color Laser Fields IR

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center 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 New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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The Effect of Mission Duration on LISA Science Objectives

arXiv

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arXiv 2021年

作者： Seoane, Pau Amaro Sedda, Manuel Arca Babak, Stanislav Berry, Christopher P. L. Berti, Emanuele Bertone, Gianfranco Blas, Diego Bogdanović, Tamara Bonetti, Matteo Breivik, Katelyn Brito, Richard Caldwell, Robert Capelo, Pedro R. Caprini, Chiara Cardoso, Vitor Carson, Zack Chen, Hsin-Yu Chua, Alvin J. K. Dvorkin, Irina Haiman, Zoltan Heisenberg, Lavinia Isi, Maximiliano Karnesis, Nikolaos Kavanagh, Bradley J. Littenberg, Tyson B. Mangiagli, Alberto Marcoccia, Paolo Maselli, Andrea Nardini, Germano Pani, Paolo Peloso, Marco Pieroni, Mauro Ricciardone, Angelo Sesana, Alberto Tamanini, Nicola Toubiana, Alexandre Valiante, Rosa Vretinaris, Stamatis Weir, David J. Yagi, Kent Zimmerman, Aaron Institute of Multidisciplinary Mathematics Universitat Politécnica de Valéncia Spain DESY Zeuthen Germany Institute of Applied Mathematics Academy of Mathematics and Systems Science CAS Beijing China Kavli Institute for Astronomy and Astrophysics Beijing China Astronomisches Rechen-Institut Zentrüm für Astronomie Universität Heidelberg Mönchofstr. 12-14 Heidelberg Germany Université de Paris CNRS Astroparticule et Cosmologie ParisF-75006 France Moscow Institute of Physics and Technology Moscow region Dolgoprudny Russia Department of Physics and Astronomy Northwestern University 1800 Sherman Ave EvanstonIL60201 United States SUPA School of Physics and Astronomy University of Glasgow Kelvin Building University Ave GlasgowG12 8QQ United Kingdom Department of Physics and Astronomy Johns Hopkins University 3400 N. Charles St BaltimoreMD21218 United States Institute for Theoretical Physics University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Theoretical Particle Physics and Cosmology Group Department of Physics King's College London Strand LondonWC2R 2LS United Kingdom Grup de Física Teòrica Departament de Física Universitat Autònoma de Barcelona Bellaterra 08193 Spain The Barcelona Institute of Science and Technology Campus UAB Bellaterra 08193 Spain Center for Relativistic Astrophysics School of Physics Georgia Institute of Technology AtlantaGA30332 United States Università degli Studi di Milano-Bicocca Piazza della Scienza 3 Milano20126 Italy Center for Computational Astrophysics Flatiron Institute New YorkNY10010 United States CENTRA Departamento de Física Instituto Superior Técnico - IST Universidade de Lisboa - UL Avenida Rovisco Pais 1 Lisboa 1049 France Department of Physics and Astronomy HB6127 Wilder Lab Dartmouth College HanoverNH03755 United States Center for Theoretical Astrophysics and Cosmology Institute for Computational Science University of Zurich Winterthurerstrasse 190 ZürichCH-8057

The science objectives of the LISA mission have been defined under the implicit assumption of a 4-yr continuous data stream. Based on the performance of LISA Pathfinder, it is now expected that LISA will have a duty cycle of ≈ 0.75, which would reduce the effective span of usable data to 3 yr. This paper reports the results of a study by the LISA Science Group, which was charged with assessing the additional science return of increasing the mission lifetime. We explore various observational scenarios to assess the impact of mission duration on the main science objectives of the mission. We find that the science investigations most affected by mission duration concern the search for seed black holes at cosmic dawn, as well as the study of stellar-origin black holes and of their formation channels via multi-band and multi-messenger observations. We conclude that an extension to 6 yr of mission operations is recommended. Copyright © 2021, The Authors. All rights reserved.

关键词： Black holes

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Publisher Correction: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

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Nature structural & molecular biology 2024年第2期31卷 390页

作者： S Basu O Shukron D Hall P Parutto A Ponjavic D Shah W Boucher D Lando W Zhang N Reynolds L H Sober A Jartseva R Ragheb X Ma J Cramard R Floyd J Balmer T A Drury A R Carr L-M Needham A Aubert G Communie K Gor M Steindel L Morey E Blanco T Bartke L Di Croce I Berger C Schaffitzel S F Lee T J Stevens D Klenerman B D Hendrich D Holcman E D Laue Department of Biochemistry University of Cambridge Cambridge UK. Wellcome-MRC Cambridge Stem Cell Institute Jeffrey Cheah Biomedical Centre Cambridge UK. Department of Physiology Development and Neuroscience University of Cambridge Cambridge UK. Department of Applied Mathematics and Computational Biology Ecole Normale Supérieure Paris France. Yusuf Hamied Department of Chemistry University of Cambridge Cambridge UK. School of Physics and Astronomy University of Leeds Leeds UK. School of Food Science and Nutrition University of Leeds Leeds UK. Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada. The European Molecular Biology Laboratory EMBL Grenoble France. The European Molecular Biology Laboratory Heidelberg Germany. Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona Spain. Sylvester Comprehensive Cancer Center Department of Human Genetics University of Miami Miller School of Medicine Biomedical Research Building Miami FL USA. Helmholtz Zentrum München German Research Center for Environmental Health Institute of Functional Epigenetics Neuherberg Germany. Institució Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. School of Biochemistry University of Bristol Bristol UK. MRC Laboratory of Molecular Biology Cambridge Biomedical Campus Cambridge UK. Yusuf Hamied Department of Chemistry University of Cambridge Cambridge UK. dk10012@cam.ac.uk. Department of Biochemistry University of Cambridge Cambridge UK. bdh24@cam.ac.uk. Wellcome-MRC Cambridge Stem Cell Institute Jeffrey Cheah Biomedical Centre Cambridge UK. bdh24@cam.ac.uk. Department of Applied Mathematics and Computational Biology Ecole Normale Supérieure Paris France. holcman.david@***. Department of Biochemistry University of Cambridge Cambridge UK. e.d.laue@bioc.cam.ac.uk. Wellcome-MRC Cambridge Stem Cell Institute Jeffrey Cheah Biomedical Centre Cambridge UK. e.d.laue@bioc.cam.ac.uk.

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