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

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

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Integrated micro-comb sources for quantum optical applications

arXiv

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arXiv 2020年

作者： Kues, Michael Reimer, Christian Lukens, Joseph M. Munro, William J. Weiner, Andrew M. Moss, David J. Morandotti, Roberto School of Engineering University of Glasgow Rankine Building Oakfield Avenue GlasgowG12 8LT United Kingdom Department of Engineering Aarhus University Finlandsgade 22 Aarhus N8200 Denmark John A. Paulson School of Engineering and Applied Sciences Harvard University Cambridge02138 United States Quantum Information Science Group Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN37831 United States NTT Basic Research Laboratories NTT Research Center for Theoretical Quantum Physics NTT Corporation Kanagawa Japan National Institute of Informatics Tokyo Japan School of Electrical and Computer Engineering Purdue Quantum Center Purdue University West LafayetteIN47907 United States Centre for Micro Photonics Swinburne University of Technology HawthornVIC3122 Australia 1650 Blvd. Lionel-Boulet VarennesJ3X1S2 Canada Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of China Chengdu610054 China ITMO University St Petersburg Russia

A key challenge for quantum science and technology is to realise large-scale, precisely controllable, practical systems for non-classical secured communications, metrology and ultimately meaningful quantum simulation and computation. Optical frequency combs represent a powerful approach towards this, since they provide a very high number of temporal and frequency modes which can result in large-scale quantum systems. The generation and control of quantum optical frequency combs will enable a unique, practical and scalable framework for quantum signal and information processing. Here, we review recent progress on the realization of energy-time entangled optical frequency combs and discuss how photonic integration and the use of fiber-optic telecommunications components can enable quantum state control with new functionalities, yielding unprecedented capability. Copyright © 2020, The Authors. All rights reserved.

关键词： Quantum optics

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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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Searching for GEMS: Confirmation of TOI-5573 b, a Cool, Saturn-like Planet Orbiting an M Dwarf*: 收藏
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引用; The Astronomical Journal 2025年第1期170卷 55-55页; 作者： Rachel B. Fernandes Shubham Kanodia Megan Delamer Andrew Hotnisky Te Han Caleb I. Cañas Jessica Libby-Roberts Varghese Reji Arvind F. Gupta Jaime A. Alvarado-Montes Chad F. Bender Cullen H. Blake William D. Cochran Zoë L. de Beurs Scott A. Diddams Jiayin Dong Mark E. Everett Eric B. Ford Samuel Halverson Jesus Higuera Henry A. Kobulnicky Daniel M. Krolikowski Alexander Larsen Andrea S.J. Lin Suvrath Mahadevan Michael W. McElwain Andrew Monson Joe P. Ninan Leonardo A. Paredes Yatrik G. Patel Paul Robertson Gabrielle Ross Arpita Roy Christian Schwab Gudmundur Stefansson Daniel J. Stevens Andrew M. Vanderburg Jason Wright Department of Astronomy & Astrophysics 525 Davey Laboratory 251 Pollock Road Penn State University Park PA 16802 USA rbf5378@psu.edu Center for Exoplanets and Habitable Worlds 525 Davey Laboratory 251 Pollock Road Penn State University Park PA 16802 USA Earth and Planets Laboratory Carnegie Science 5241 Broad Branch Road NW Washington DC 20015 USA Department of Physics & Astronomy The University of California Irvine CA 92697 USA NASA Goddard Space Flight Center 8800 Greenbelt Road Greenbelt MD 20771 USA Department of Astronomy and Astrophysics Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai 400005 India U.S. National Science Foundation National Optical-Infrared Astronomy Research Laboratory 950 N. Cherry Avenue Tucson AZ 85719 USA Australian Astronomical Optics Macquarie University Balaclava Road North Ryde NSW 2109 Australia Astrophysics and Space Technologies Research Centre Macquarie University Balaclava Road North Ryde NSW 2109 Australia Steward Observatory University of Arizona 933 N. Cherry Avenue Tucson AZ 85721 USA Department of Physics and Astronomy University of Pennsylvania 209 S 33rd Street Philadelphia PA 19104 USA McDonald Observatory and Center for Planetary Systems Habitability The University of Texas at Austin Austin TX 78730 USA Department of Earth Atmospheric and Planetary Sciences Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA Electrical Computer & Energy Engineering University of Colorado 425 UCB Boulder CO 80309 USA Department of Physics University of Colorado 2000 Colorado Avenue Boulder CO 80309 USA Center for Computational Astrophysics Flatiron Institute 162 Fifth Avenue New York NY 10010 USA Institute for Computational and Data Sciences Penn State University University Park PA 16802 USA Center for Astrostatistics 525 Davey Laboratory 251 Pollock Road University Park PA 16802 USA Jet Propulsion Laboratory California Institute of Technology; We present the confirmation of TOI-5573 b, a Saturn-sized exoplanet on an 8.79 days orbit around an early M dwarf (3790 K, 0.59 R⊙, 0.61 M⊙, 12.30 Jmag). TOI-5573 b has a mass of 112−19+18 M⊕(0.35 ± 0.06 M; We present the confirmation of TOI-5573 b, a Saturn-sized exoplanet on an 8.79 days orbit around an early M dwarf (3790 K, 0.59 R_⊙, 0.61 M_⊙, 12.30 Jmag). TOI-5573 b has a mass of $11{2}_{-19}^{+18}$ $11 2_{- 19}^{+ 18}$ M_⊕(0.35 ± 0.06 M; 关键词：; 来源：评论; 学校读者我要写书评

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A constraint-reduced MPC algorithm for convex quadratic programming, with a modified active set identification scheme

arXiv

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arXiv 2018年

作者： Paul Laiu, M. Tits, André L. Computational and Applied Mathematics Group Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Department of Electrical and Computer Engineering Institute for Systems Research University of Maryland College ParkMD20742 United States

A constraint-reduced Mehrotra–Predictor–Corrector algorithm for convex quadratic programming is proposed. (At each iteration, such algorithms use only a subset of the inequality constraints in constructing the searc... 详细信息

A constraint-reduced Mehrotra–Predictor–Corrector algorithm for convex quadratic programming is proposed. (At each iteration, such algorithms use only a subset of the inequality constraints in constructing the search direction, resulting in CPU savings.) The proposed algorithm makes use of a regularization scheme to cater to cases where the reduced constraint matrix is rank deficient. Global and local convergence properties are established under arbitrary working-set selection rules subject to satisfaction of a general condition. A modified active-set identification scheme that fulfills this condition is introduced. Numerical tests show great promise for the proposed algorithm, in particular for its active-set identification scheme. While the focus of the present paper is on dense systems, application of the main ideas to large sparse systems is briefly discussed. Copyright © 2018, The Authors. All rights reserved.

关键词： Constraint theory

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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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Learning From Experience: An Automatic pH Neutralization System Using Hybrid Fuzzy System and Neural Network

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Procedia computer Science 2018年 140卷 206-215页

作者： Ethar H.K. Alkamil Seaar Al-Dabooni Ahmed K. Abbas Ralph Flori Donald C. Wunsch Dept. of Geosciences and Geological and Petroleum Engineering Missouri University of Science and Technology Rolla Missouri 65401 USA Dept. of Petroleum Engineering University of Basrah 61004 Iraq Basrah Oil Company Basrah 61004 Iraq Applied Computational Intelligence Laboratory Rolla Missouri 65401 USA Iraqi Drilling Company Basrah 61004 Iraq Dept. of Electrical and Computer Engineering Missouri University of Science and Technology Rolla Missouri 65401 USA

In oil and gas industry, the pH level is one of the most important indicators of mud contamination while drilling. Although the process has simple components, the pH neutralization process is complicated in the mud ci... 详细信息

In oil and gas industry, the pH level is one of the most important indicators of mud contamination while drilling. Although the process has simple components, the pH neutralization process is complicated in the mud circulation system. This difficulty is due to the high nonlinearity of the process. In this paper, the fuzzy neural network (FNN) is integrated to the fuzzy logic controller (FLC) to create a system which identifies pH fluctuation into a drilling mud system, assesses and signals its severity. And then, it automatically actuates a chemical treating fluids valve (CTFV), such as Caustic Soda (CS), for neutralizing the drilling fluid pH level while circulating. In this work, an integrated mud circulation lab-scaled system is used to mimic the pH neutralization (e.g., because of the H2S intrusion) while drilling the hydrogen sulfide bearing zones. The system contains several significant nonlinearities such as sudden pH reduction appearances that stretch the ability of simple controllers in achieving satisfactory performance. The results show, the FLC can be used successfully to stabilize any chosen operating point of the system and to deal with nonlinearities (uncertainties of a model). All derived results are validated by computer simulation of a nonlinear mathematical model of the lab-scaled mud neutralization system. The presented FNN in this work demonstrates a reliable response to neutralize the circulated drilling fluid pH, through a quick, safe, and automatic initiation of appropriate treatment.

关键词： Automatic pH Neutralization System Fuzzy Neural Network

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Predictable and precise template-free CRISPR editing of pathogenic variants (vol 563, pg 646, 2018)

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NATURE 2019年第7746期567卷 E1-E2页

作者： Shen, Max W. Arbab, Mandana Hsu, Jonathan Y. Worstell, Daniel Culbertson, Sannie J. Krabbe, Olga Cassa, Christopher A. Liu, David R. Gifford, David K. Sherwood, Richard I. Computational and Systems Biology Program Massachusetts Institute of Technology Cambridge USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge USA Merkin Institute of Transformative Technologies in Healthcare Broad Institute of Harvard and MIT Cambridge USA Department of Chemistry and Chemical Biology Harvard University Cambridge USA Howard Hughes Medical Institute Harvard University Cambridge USA Department of Biological Engineering Massachusetts Institute of Technology Cambridge USA Molecular Pathology Unit Center for Cancer Research and Center for Computational and Integrative Biology Massachusetts General Hospital Charlestown USA Division of Genetics Department of Medicine Brigham and Women’s Hospital and Harvard Medical School Boston USA Hubrecht Institute for Developmental Biology and Stem Cell Research Royal Netherlands Academy of Arts and Sciences (KNAW) Utrecht The Netherlands Broad Institute of MIT and Harvard Cambridge USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA

In this Article, a data processing error affected Fig. 3e and Extended Data Table 2; these errors have been corrected online.

In this Article, a data processing error affected Fig. 3e and Extended Data Table 2; these errors have been corrected online.

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Dc motor educational kit: A teaching aid in control theory 12th

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12th Portuguese Conference on Automatic Control, CONTROLO 2016

作者： Moreira, António Paulo Costa, Paulo Gonçalves, José Faria, Brígida M. Faculty of Engineering Department of Electrical Engineering and Computers University of Porto Porto Portugal Department of Electrical Engineering Polytechnic Institute of Bragança Bragança Portugal School of Applied Health Technology Polytechnic Institute of Porto Porto Portugal INESC TEC Institute for Systems and Computer Engineering Technology and Science Porto Portugal LIACC - Artificial Intelligence and Computer Science Laboratory Porto Portugal

This paper describes a laboratory control theory experiment supported by the use of a DCMotor Educational Kit. The impact, as a teaching aid, of the proposed laboratory control experiment is evaluated, having in mind ... 详细信息

ISBN: (纸本)9783319436708

This paper describes a laboratory control theory experiment supported by the use of a DCMotor Educational Kit. The impact, as a teaching aid, of the proposed laboratory control experiment is evaluated, having in mind the student’s feedback. The DC motor that is used in the developed educational Kit is the EMG30, being a low cost 12V motor equipped with encoders and a 30:1 reduction gearbox. The experiment is based on real hardware and on simulation, using the SimTwo realistic simulation software. In order to implement the realistic simulation the EMG30model was obtained. Students’ feedback was acquired using a questionnaire and the results confirmed the importance given to these practical experiments. © Springer International Publishing Switzerland 2017.

关键词： DC motors

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Wellcome Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA UK Korea Advanced Institute of Science and Technology Daejeon 34141 South Korea Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Korea Advanced Institute of Science and Technology Daejeon South Korea Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston MA USA Ludwig Center at Harvard Medical School Boston MA USA Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Broad Institute of MIT and Harvard

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