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Correction to: MISC: missing imputation for single-cell RNA sequencing data

BMC systems biology 2019年第1期13卷 13页

作者： Mary Qu Yang Sherman M Weissman William Yang Jialing Zhang Allon Canaan Renchu Guan Joint Bioinformatics Program University of Arkansas Little Rock George Washington Donaghey College of Engineering & IT and University of Arkansas for Medical Sciences Little Rock AR 72204 USA. mqyang@ualr.edu. Department of Genetics Yale University New Haven CT 06512 USA. sherman.weissman@yale.edu. Department of Genetics Yale University New Haven CT 06512 USA. Department of Computer Science Carnegie Mellon University School of Computer Science Pittsburgh PA 15213 USA. Joint Bioinformatics Program University of Arkansas Little Rock George Washington Donaghey College of Engineering & IT and University of Arkansas for Medical Sciences Little Rock AR 72204 USA. guanrenchu@***. College of Computer Science and Technology Jilin University Changchun 130012 Jilin China. guanrenchu@***.

It was highlighted that the original article [1] contained a typesetting error in the last name of Allon Canaan. This was incorrectly captured as Allon Canaann in the original article which has since been updated.

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From medical records to research papers: A literature analysis pipeline for supporting medical genomic diagnosis processes

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Informatics in Medicine Unlocked 2019年 15卷

作者： López Bello, Fernando Naya, Hugo Raggio, Víctor Rosá, Aiala Basic Sciences Development Program (PEDECIBA www.pedeciba.edu.uy) ICT4V (***) Av. Italia 6201 Parque Tecnológico del LATU Montevideo 11500 Uruguay Bioinformatics Unit Institut Pasteur de Montevideo Montevideo Uruguay Genetics Department Facultad de Medicina Universidad de la República de Uruguay Montevideo Uruguay Computer Science Institute (Instituto de Computación INCO) Engineering School (Facultad de Ingeniería FING) Universidad de la República Montevideo Uruguay

In this paper, we introduce a framework for processing genetics and genomics literature, based on ontologies and lexical resources from the biomedical domain. The main objective is to support the diagnosis process that is done by medical geneticists who extract knowledge from published works. We constructed a pipeline that gathers several genetics- and genomics-related resources and applies natural language processing techniques, which include named entity recognition and relation extraction. Working on a corpus created from PubMed abstracts, we built a knowledge database that can be used for processing medical records written in Spanish. Given a medical record from Uruguayan healthcare patients, we show how we can map it to the database and perform graph queries for relevant knowledge paths. The framework is not an end user application, but an extensible processing structure to be leveraged by external applications, enabling software developers to streamline incorporation of the extracted knowledge. © 2019

关键词： Automated pattern recognition Controlled vocabulary Genomics Medical records Natural language processing Publications

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Measurements of the temperature and E-mode polarization of the cosmic microwave background from the full 500-square-degree SPTpol dataset

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Physical Review D 2025年第12期111卷 123513-123513页

作者： T.-L. Chou P. A. R. Ade A. J. Anderson J. E. Austermann L. Balkenhol J. A. Beall A. N. Bender B. A. Benson F. Bianchini L. E. Bleem J. E. Carlstrom C. L. Chang P. Chaubal H. C. Chiang R. Citron C. Corbett Moran T. M. Crawford A. T. Crites T. de Haan M. A. Dobbs D. Dutcher W. Everett J. Gallicchio E. M. George N. Gupta N. W. Halverson G. P. Holder W. L. Holzapfel J. D. Hrubes N. Huang J. Hubmayr K. D. Irwin L. Knox A. T. Lee D. Li A. Lowitz J. J. McMahon J. Montgomery T. Natoli J. P. Nibarger G. I. Noble V. Novosad Y. Omori S. Padin S. Patil C. Pryke W. Quan C. L. Reichardt J. E. Ruhl B. R. Saliwanchik K. K. Schaffer C. Sievers G. Smecher A. A. Stark C. Tucker T. Veach J. D. Vieira G. Wang N. Whitehorn W. L. K. Wu V. Yefremenko J. A. Zebrowski Department of Astronomy and Astrophysics University of Chicago 5640 South Ellis Avenue Chicago Illinois 60637 USA Kavli Institute for Cosmological Physics University of Chicago 5640 South Ellis Avenue Chicago Illinois 60637 USA Cardiff University Cardiff CF10 3XQ United Kingdom Fermi National Accelerator Laboratory MS209 P.O. Box 500 Batavia Illinois 60510 USA NIST Quantum Devices Group 325 Broadway Mailcode 817.03 Boulder Colorado 80305 USA Department of Physics University of Colorado Boulder Colorado 80309 USA Sorbonne Universit’e CNRS UMR 7095 Institut d’Astrophysique de Paris 98 bis bd Arago 75014 Paris France High Energy Physics Division Argonne National Laboratory 9700 South Cass Avenue Argonne Illinois 60439 USA SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park California 94025 USA Department of Physics University of Chicago 5640 South Ellis Avenue Chicago Illinois 60637 USA Enrico Fermi Institute University of Chicago 5640 South Ellis Avenue Chicago Illinois 60637 USA School of Physics University of Melbourne Parkville Victoria 3010 Australia Department of Physics McGill University 3600 Rue University Montreal Quebec H3A 2T8 Canada School of Mathematics Statistics and Computer Science University of KwaZulu-Natal Durban South Africa University of Chicago 5640 South Ellis Avenue Chicago Illinois 60637 USA Jet Propulsion Laboratory Pasadena California 91109 USA Department of Physics Cornell University Ithaca New York USA Department of Astronomy Cornell University Ithaca New York USA Department of Physics University of California Berkeley California 94720 USA Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA High Energy Accelerator Research Organization (KEK) Tsukuba Ibaraki 305-0801 Japan Canadian Institute for Advanced Research CIFAR Program in Gravity and the Extreme Universe Toronto Ontario M5G 1Z8 Canada Joseph Henry Laboratories of Physics Jadwin Hall Princ

Using the full four-year SPTpol 500 deg2 dataset in both the 95 and 150 GHz frequency bands, we present measurements of the temperature and E-mode polarization of the cosmic microwave background (CMB), as well as the E-mode polarization autopower spectrum (EE) and temperature-E-mode cross-power spectrum (TE) in the angular multipole range 50<ℓ<8000. We find the SPTpol dataset to be self-consistent, passing several internal consistency tests based on maps, frequency bands, bandpowers, and cosmological parameters. The full SPTpol dataset is well-fit by the ΛCDM model, for which we find H0=70.48±2.16 km s−1 Mpc−1 and Ωm=0.271±0.026, when using only the SPTpol data and a Planck-based prior on the optical depth to reionization. The ΛCDM parameter constraints are consistent across the 95 GHz-only, 150 GHz-only, TE-only, and EE-only data splits. Between the ℓ<1000 and ℓ>1000 data splits, the ΛCDM parameter constraints are borderline consistent at the ∼2σ level. This consistency improves when including a parameter AL, the degree of lensing of the CMB inferred from the smearing of acoustic peaks. When marginalized over AL, the ΛCDM parameter constraints from SPTpol are consistent with those from Planck. The power spectra presented here are the most sensitive measurements of the lensed CMB damping tail to date for roughly ℓ>1700 in TE and ℓ>2000 in EE.

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Non-uniform time-scaling of carnatic music transients

arXiv

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arXiv 2017年

作者： Viraraghavan, Venkata Subramanian Pal, Arpan Aravind, R. Murthy, Hema TCS Research and Innovation Embedded Systems and Robotics Bangalore India Department of Electrical Engineering Indian Institute of Technology Madras Singapore Department of Computer Science and Engineering Indian Institute of Technology Madras India

Gamakas are an integral aspect of Carnatic Music, a form of classical music prevalent in South India. They are used in rāgas, which may be seen as melodic scales and/or a set of characteristic melodic phrases. Gamakas exhibit continuous pitch variation often spanning several semitones. In this paper, we study how gamakas scale with tempo and propose a novel approach to change the tempo of Carnatic music pieces. The music signal is viewed as consisting of constant-pitch segments and transients. The transients show continuous pitch variation and we consider their analyses from a theoretical stand-point. We next observe the non-uniform ratios of time-scaling of constantpitch segments, transients and silence in excerpts from nine concert renditions of varn. ams in six rāgas. The results indicate that the changing tempo of Carnatic music does not change the duration of transients significantly. We report listening tests on our algorithm to slow down Carnatic music that is consistent with this observation. Copyright © 2017, The Authors. All rights reserved.

关键词： Music

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Coherently Enhanced Wireless Power Transfer

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Physical Review Letters 2018年第14期120卷 143901-143901页

作者： Alex Krasnok Denis G. Baranov Andrey Generalov Sergey Li Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Department of Physics Chalmers University of Technology 412 96 Gothenburg Sweden Moscow Institute of Physics and Technology Dolgoprudny 141700 Russia Department of Electronics and Nanoengineering Aalto University 02150 Espoo Finland ITMO University St. Petersburg 197101 Russia Photonics Initiative Advanced Science Research Center City University of New York New York 10031 USA Physics Program Graduate Center City University of New York New York 10016 USA Department of Electrical Engineering City College of The City University of New York New York 10031 USA

Extraction of electromagnetic energy by an antenna from impinging external radiation is at the basis of wireless communications and wireless power transfer (WPT). The maximum of transferred energy is ensured when the antenna is conjugately matched, i.e., when it is resonant and it has an equal coupling with free space and its load. This condition, however, can be easily affected by changes in the environment, preventing optimal operation of a WPT system. Here, we introduce the concept of coherently enhanced WPT that allows us to bypass this difficulty and achieve dynamic control of power transfer. The approach relies on coherent excitation of the waveguide connected to the antenna load with a backward propagating signal of specific amplitude and phase. This signal creates a suitable interference pattern at the load resulting in a modification of the local wave impedance, which in turn enables conjugate matching and a largely increased amount of extracted energy. We develop a simple theoretical model describing this concept, demonstrate it with full-wave numerical simulations for the canonical example of a dipole antenna, and verify experimentally in both near-field and far-field regimes.

关键词： Electromagnetism engineering Light propagation, transmission & absorption Photonics

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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

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Nature 2022年第7909期605卷 E3页

作者： Jill E Moore Michael J Purcaro Henry E Pratt Charles B Epstein Noam Shoresh Jessika Adrian Trupti Kawli Carrie A Davis Alexander Dobin Rajinder Kaul Jessica Halow Eric L Van Nostrand Peter Freese David U Gorkin Yin Shen Yupeng He Mark Mackiewicz Florencia Pauli-Behn Brian A Williams Ali Mortazavi Cheryl A Keller Xiao-Ou Zhang Shaimae I Elhajjajy Jack Huey Diane E Dickel Valentina Snetkova Xintao Wei Xiaofeng Wang Juan Carlos Rivera-Mulia Joel Rozowsky Jing Zhang Surya B Chhetri Jialing Zhang Alec Victorsen Kevin P White Axel Visel Gene W Yeo Christopher B Burge Eric Lécuyer David M Gilbert Job Dekker John Rinn Eric M Mendenhall Joseph R Ecker Manolis Kellis Robert J Klein William S Noble Anshul Kundaje Roderic Guigó Peggy J Farnham J Michael Cherry Richard M Myers Bing Ren Brenton R Graveley Mark B Gerstein Len A Pennacchio Michael P Snyder Bradley E Bernstein Barbara Wold Ross C Hardison Thomas R Gingeras John A Stamatoyannopoulos Zhiping Weng University of Massachusetts Medical School Program in Bioinformatics and Integrative Biology Worcester MA USA. The Broad Institute of Harvard and MIT Cambridge MA USA. Department of Genetics School of Medicine Stanford University Palo Alto CA USA. Cold Spring Harbor Laboratory Functional Genomics Cold Spring Harbor NY USA. Altius Institute for Biomedical Sciences Seattle WA USA. Department of Medicine University of Washington School of Medicine Seattle WA USA. Department of Cellular and Molecular Medicine Institute for Genomic Medicine Stem Cell Program Sanford Consortium for Regenerative Medicine University of California San Diego La Jolla CA USA. Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge MA USA. Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA. Ludwig Institute for Cancer Research University of California San Diego La Jolla CA USA. Institute for Human Genetics Department of Neurology University of California San Francisco San Francisco CA USA. Genomics Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA. Department of Developmental and Cell Biology University of California Irvine Irvine CA USA. Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA. Département de Biochimie et Médecine Moléculaire Université de Montréal Montréal Quebec Canada. Division of Experimental Medicine McGill University Montreal Quebec Canada. Institut de Recherches Cliniques de Montréal (IR

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Author Correction: π-HuB: the proteomic navigator of the human body

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Nature 2025年第8046期637卷 E22页

作者： Fuchu He Ruedi Aebersold Mark S Baker Xiuwu Bian Xiaochen Bo Daniel W Chan Cheng Chang Luonan Chen Xiangmei Chen Yu-Ju Chen Heping Cheng Ben C Collins Fernando Corrales Jürgen Cox Weinan E Jennifer E Van Eyk Jia Fan Pouya Faridi Daniel Figeys George Fu Gao Wen Gao Zu-Hua Gao Keisuke Goda Wilson Wen Bin Goh Dongfeng Gu Changjiang Guo Tiannan Guo Yuezhong He Albert J R Heck Henning Hermjakob Tony Hunter Narayanan Gopalakrishna Iyer Ying Jiang Connie R Jimenez Lokesh Joshi Neil L Kelleher Ming Li Yang Li Qingsong Lin Cui Hua Liu Fan Liu Guang-Hui Liu Yansheng Liu Zhihua Liu Teck Yew Low Ben Lu Matthias Mann Anming Meng Robert L Moritz Edouard Nice Guang Ning Gilbert S Omenn Christopher M Overall Giuseppe Palmisano Yaojin Peng Charles Pineau Terence Chuen Wai Poon Anthony W Purcell Jie Qiao Roger R Reddel Phillip J Robinson Paola Roncada Chris Sander Jiahao Sha Erwei Song Sanjeeva Srivastava Aihua Sun Siu Kwan Sze Chao Tang Liujun Tang Ruijun Tian Juan Antonio Vizcaíno Chanjuan Wang Chen Wang Xiaowen Wang Xinxing Wang Yan Wang Tobias Weiss Mathias Wilhelm Robert Winkler Bernd Wollscheid Limsoon Wong Linhai Xie Wei Xie Tao Xu Tianhao Xu Liying Yan Jing Yang Xiao Yang John Yates Tao Yun Qiwei Zhai Bing Zhang Hui Zhang Lihua Zhang Lingqiang Zhang Pingwen Zhang Yukui Zhang Yu Zi Zheng Qing Zhong Yunping Zhu State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. hefc@***. International Academy of Phronesis Medicine (Guangdong) Guangdong China. hefc@***. Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland. aebersold@imsb.biol.ethz.ch. Macquarie Medical School Macquarie University Sydney New South Wales Australia. Institute of Pathology and Southwest Cancer Center Southwest Hospital Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology Ministry of Education of China Chongqing China. Institute of Health Service and Transfusion Medicine Beijing China. Department of Pathology and The Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University Baltimore MD USA. State Key Laboratory of Medical Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing China. Key Laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai China. Department of Nephrology First Medical Center of Chinese PLA General Hospital Nephrology Institute of the Chinese People's Liberation Army State Key Laboratory of Kidney Diseases National Clinical Research Center for Kidney Diseases Beijing Key Laboratory of Kidney Disease Research Beijing China. Institute of Chemistry Academia Sinica Taipei China. National Biomedical Imaging Center State Key Laboratory of Membrane Biology Institute of Molecular Medicine Peking-Tsinghua Center for Life Sciences College of Future Technology Peking University Beijing China. School of Biological Sciences Queen's University of Belfast Belfast UK. Functional Proteomics Laboratory Centro Nacional de Biotecnología-CSIC Madrid Spain. Computational Systems Biochemistry Research Group Ma

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Non-reciprocal hyperbolic propagation over moving metasurfaces

arXiv

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arXiv 2018年

作者： Mazor, Yarden Alu, Andrea Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Department of Electrical Engineering City College of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States

Hyperbolic propagation offers exciting opportunities in nanophotonics, from sub-diffraction imaging to enhanced local density of states. This transport regime is typically induced by strong modulation of conductivity, i.e., with alternating metallic and dielectric material properties. Here, we analyze a moving impedance surface, showing that suitably tailored homogeneous metasurfaces can support one-way hyperbolic propagation when in motion, adding non-reciprocity to hyperbolic propagation phenomena, and without suffering from nonlocal effects stemming from discretization or finite granularity of the surface. Copyright © 2018, The Authors. All rights reserved.

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Angular-Momentum Selectivity and Asymmetry in Highly Confined Wave Propagation along Sheath-Helical Metasurface Tubes

arXiv

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arXiv 2018年

作者： Mazor, Yarden Alù, Andrea Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States Department of Electrical Engineering City College of New York New YorkNY10031 United States

Highly confined surface waves present unique opportunities to enhance light interactions with localized emitters or molecules. Hyperbolic dispersion in metasurfaces allows us to tailor and manipulate surface waves, enhancing the local density of states over broad bandwidths. So far, propagation on this platform was mainly studied in planar geometries, which facilitates the analysis but somehow limits the realm of possibilities. Here we show that "wrapping" hyperbolic metasurfaces into tubes may greatly enrich the wave propagation dynamics along their axis. This system shows strong interaction with fields and sources carrying optical angular momentum, pronounced field asymmetries, and opens pathways to valley-specific excitation and routing. In addition, we demonstrate that various parameter regimes enable strong spin/helicity – momentum locking. Copyright © 2018, The Authors. All rights reserved.

关键词： Surface waves

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Ultrafast magnetic switching of GdFeCo with electronic heat currents

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Physical Review B 2017年第18期95卷 180409(R)-180409(R)页

作者： R. B. Wilson Jon Gorchon Yang Yang Charles-Henri Lambert Sayeef Salahuddin Jeffrey Bokor Department of Mechanical Engineering and Materials Science & Engineering Program University of California Riverside California 92521 USA Department of Electrical Engineering and Computer Sciences University of California Berkeley California 94720 USA Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley California 94720 USA Department of Materials Science and Engineering University of California Berkeley California 94720 USA

We report the magnetic response of Pt/Au/GdFeCo trilayers to optical irradiation of the Pt surface. For trilayers with Au thickness greater than 50 nm, the great majority of energy is absorbed by the Pt layer, creating an initial temperature differential of thousands of kelvin between the Pt/Au layers and the GdFeCo layer. The resulting electronic heat current across the metal multilayer lasts for several picoseconds with energy flux in excess of 2TWm−2 and provides sufficient heating to the GdFeCo electrons to induce deterministic reversal of the magnetic moment.

关键词： Ferrimagnetism Magnetization switching Magneto-optical Kerr effect Multilayer thin films Femtosecond laser irradiation Kerr effect Photoexcitation

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