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Comparative cellular analysis of motor cortex in human, marmoset and mouse (vol 598, pg 111, 2021)

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NATURE 2022年第7904期604卷 E8-E8页

作者： Bakken, Trygve E. Jorstad, Nikolas L. Hu, Qiwen Lake, Blue B. Tian, Wei Kalmbach, Brian E. Crow, Megan Hodge, Rebecca D. Krienen, Fenna M. Sorensen, Staci A. Eggermont, Jeroen Yao, Zizhen Aevermann, Brian D. Aldridge, Andrew I. Bartlett, Anna Bertagnolli, Darren Casper, Tamara Castanon, Rosa G. Crichton, Kirsten Daigle, Tanya L. Dalley, Rachel Dee, Nick Dembrow, Nikolai Diep, Dinh Ding, Song-Lin Dong, Weixiu Fang, Rongxin Fischer, Stephan Goldman, Melissa Goldy, Jeff Graybuck, Lucas T. Herb, Brian R. Hou, Xiaomeng Kancherla, Jayaram Kroll, Matthew Lathia, Kanan van Lew, Baldur Li, Yang Eric Liu, Christine S. Liu, Hanqing Lucero, Jacinta D. Mahurkar, Anup McMillen, Delissa Miller, Jeremy A. Moussa, Marmar Nery, Joseph R. Nicovich, Philip R. Niu, Sheng-Yong Orvis, Joshua Osteen, Julia K. Owen, Scott Palmer, Carter R. Pham, Thanh Plongthongkum, Nongluk Poirion, Olivier Reed, Nora M. Rimorin, Christine Rivkin, Angeline Romanow, William J. Sedeno-Cortes, Adriana E. Siletti, Kimberly Somasundaram, Saroja Sulc, Josef Tieu, Michael Torkelson, Amy Tung, Herman Wang, Xinxin Xie, Fangming Yanny, Anna Marie Zhang, Renee Ament, Seth A. Behrens, M. Margarita Bravo, Hector Corrada Chun, Jerold Dobin, Alexander Gillis, Jesse Hertzano, Ronna Hof, Patrick R. Hollt, Thomas Horwitz, Gregory D. Keene, C. Dirk Kharchenko, Peter V. Ko, Andrew L. Lelieveldt, Boudewijn P. Luo, Chongyuan Mukamel, Eran A. Pinto-Duarte, Antonio Preiss, Sebastian Regev, Aviv Ren, Bing Scheuermann, Richard H. Smith, Kimberly Spain, William J. White, Owen R. Koch, Christof Hawrylycz, Michael Tasic, Bosiljka Macosko, Evan Z. McCarroll, Steven A. Ting, Jonathan T. Zeng, Hongkui Zhang, Kun Feng, Guoping Ecker, Joseph R. Linnarsson, Sten Lein, Ed S. Allen Institute for Brain Science Seattle WA USA Department of Physiology and Biophysics University of Washington Seattle WA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Bioengineering University of California San Diego La Jolla CA USA The Salk Institute for Biological Studies La Jolla CA USA Epilepsy Center of Excellence Department of Veterans Affairs Medical Center Seattle WA USA Stanley Institute for Cognitive Genomics Cold Spring Harbor Laboratory Cold Spring Harbor NY USA Department of Genetics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA LKEB Department of Radiology Leiden University Medical Center Leiden The Netherlands Pattern Recognition and Bioinformatics group Delft University of Technology Delft The Netherlands J. Craig Venter Institute La Jolla CA USA Department of Pathology University of California San Diego CA USA Division of Vaccine Discovery La Jolla Institute for Immunology La Jolla CA USA Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA Computer Science and Engineering Program University of California San Diego La Jolla CA USA Howard Hughes Medical Institute The Salk Institute for Biological Studies La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Institute for Genomes Sciences University of Maryland School of Medicine Baltimore MD USA Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA Ludwig Institute for Cancer Research La Jolla CA USA Department of Computer Science University of Maryland College Park College Park MD USA Sanford Burnham Prebys Medical Discovery Institute La Jolla CA USA Biomedical Sciences Program School of Medicine University of California San Diego La Jolla CA USA University of Connecticut Storrs CT USA Department

Shot noise in a strange metal

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arXiv 2022年

作者： Chen, Liyang Lowder, Dale T. Bakali, Emine Andrews, Aaron Maxwell Schrenk, Werner Waas, Monika Svagera, Robert Eguchi, Gaku Prochaska, Lukas Wang, Yiming Setty, Chandan Sur, Shouvik Si, Qimiao Paschen, Silke Natelson, Douglas Applied Physics Graduate Program Rice University 6100 Main St. HoustonTX77005 United States Department of Physics and Astronomy Rice Center for Quantum Materials Rice University 6100 Main St. HoustonTX77005 United States Institute of Solid State Physics TU Wien Wiedner Hauptstraße 8-10 Vienna1040 Austria Institute of Solid State Electronics TU Wien Gußhausstraße 25-25a Gebäude CH Vienna1040 Austria Center for Micro and Nanostructures TU Wien Gußhausstraße 25-25a Gebäude CH Vienna1040 Austria Department of Electrical and Computer Engineering Rice University 6100 Main St. HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University 6100 Main St. HoustonTX77005 United States

Strange-metal behavior has been observed in materials ranging from high-temperature superconductors to heavy fermion metals. In conventional metals, current is carried by quasiparticles;although it has been suggested that quasiparticles are absent in strange metals, direct experimental evidence is lacking. We measured shot noise to probe the granularity of the current-carrying excitations in nanowires of the heavy fermion strange metal YbRh2Si2. When compared with conventional metals, shot noise in these nanowires is strongly suppressed. This suppression cannot be attributed to either electron-phonon or electron-electron interactions in a Fermi liquid, which suggests that the current is not carried by well-defined quasiparticles in the strange-metal regime that we probed. Our work sets the stage for similar studies of other strange metals. Copyright © 2022, The Authors. All rights reserved.

关键词： Nanowires

Experimental investigation of nonlinear dynamics and bifurcation in a quantum-dot laser with optical feedback

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Experimental investigation of nonlinear dynamics and bifurca...

Frontiers in Optics, FiO_2019

作者： Yamasaki, Kazuto Kanno, Kazutaka Matsumoto, Atsushi Naruse, Makoto Yamamoto, Naokatsu Uchida, Atsushi Department of Information and Computer Sciences Saitama University 225 Shimo-Okubo Sakura-ku Saitama City Saitama338–8570 Japan Network System Research Institute National Institute of Information and Communications Technology 4–2–1 Nukui–kita Koganei Tokyo184–8795 Japan Department of Information Physics and Computing Graduate School of Information Science and Technology University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-8656 Japan

We investigate the temporal dynamics of a quantum dot laser with optical feedback by changing the injection current and the optical feedback strength. Chaotic oscillations and low frequency fluctuations are observed f... 详细信息

ISBN: (纸本)9781943580675

关键词： Optical feedback

Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci

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Nature computational science 2023年第7期3卷 658页

作者： Gengjie Jia Yu Li Xue Zhong Kanix Wang Milton Pividori Rabab Alomairy Aniello Esposito Hatem Ltaief Chikashi Terao Masato Akiyama Koichi Matsuda David E Keyes Hae Kyung Im Takashi Gojobori Yoichiro Kamatani Michiaki Kubo Nancy J Cox James Evans Xin Gao Andrey Rzhetsky Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China. jiagengjie@***. Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong People's Republic of China. Department of Medicine and Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN US. Department of Medicine Institute of Genomics and Systems Biology Committee on Genomics Genetics and Systems Biology University of Chicago Chicago IL US. Department of Operations Business Analytics and Information Systems University of Cincinnati Cincinnati OH US. Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA US. Extreme Computing Research Center Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. College of Computer Science and Engineering University of Jeddah Jeddah Saudi Arabia. HPE HPC/AI EMEA Research Laboratory Bristol UK. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Clinical Research Center Shizuoka General Hospital Shizuoka Japan. Department of Applied Genetics The School of Pharmaceutical Sciences University of Shizuoka Shizuoka Japan. Department of Ophthalmology Graduate School of Medical Sciences Kyushu University Fukuoka Japan. Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo Japan. Biological and Environmenta

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

TOI-2458 b: A mini-Neptune consistent with in situ hot Jupiter formation

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arXiv 2024年

作者： Šubjak, Jan Gandolfi, Davide Goffo, Elisa Rapetti, David Jankowski, Dawid Mizuki, Toshiyuki Dai, Fei Serrano, Luisa M. Wilson, Thomas G. Goździewski, Krzysztof Nowak, Grzegorz Jenkins, Jon M. Twicken, Joseph D. Winn, Joshua N. Bieryla, Allyson Ciardi, David R. Cochran, William D. Collins, Karen A. Deeg, Hans J. Garcia, Rafael A. Guenther, Eike W. Hatzes, Artie P. Kabath, Petr Korth, Judith Latham, David W. Livingston, John H. Lund, Michael B. Mathur, Savita Narita, Norio Orell-Miquel, Jaume Palle, Enric Persson, Carina M. Redfield, Seth Schwarz, Richard P. Watanabe, David Ziegler, Carl Astronomical Institute Czech Academy of Sciences Fričova 298 Ondřejov251 65 Czech Republic Center for Astrophysics | Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Dipartimento di Fisica Universita degli Studi di Torino via Pietro Giuria 1 TorinoI-10125 Italy Thuringer Landessternwarte Tautenburg Sternwarte 5 Tautenburg07778 Germany NASA Ames Research Center Moffett FieldCA94035 United States Research Institute for Advanced Computer Science Universities Space Research Association WashingtonDC20024 United States Institute of Astronomy Faculty of Physics Astronomy and Informatics Nicolaus Copernicus University Grudziadzka 5 Toruń87-100 Poland Astrobiology Center of NINS 2-21-1 Osawa Mitaka Tokyo181-8588 Japan National Astronomical Observatory of Japan 2-21-2 Osawa Mitaka Tokyo181-8588 Japan Institute for Astronomy University of Hawai'i 2680 Woodlawn Drive HonoluluHI96822 United States Department of Physics University of Warwick Gibbet Hill Road CoventryCV4 7AL United Kingdom SETI Institute Mountain ViewCA94043 United States Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States NASA Exoplanet Science Institute-Caltech/IPAC PasadenaCA91125 United States McDonald Observatory The University of Texas AustinTX United States Center for Planetary Systems Habitability The University of Texas AustinTX United States C. Via Lactea S/N Tenerife La LagunaE-38205 Spain Dept. de Astrofisica Tenerife La LagunaE-38206 Spain Universite Paris-Saclay Universite Paris Cite CEA CNRS AIM Gif-sur-Yvette91191 France Lund Observatory Division of Astrophysics Department of Physics Lund University Box 118 Lund22100 Sweden Astronomical Science Program Graduate University for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Komaba Institute for Science The University of Tokyo 3-8-1 Komaba Meguro Tokyo153-8902 Japan Chalmers University of Technology Departmen

We report on the discovery and spectroscopic confirmation of TOI-2458 b, a transiting mini-Neptune around an F-type star leaving the mainsequence with a mass of M*= 1.05 ± 0.03Mo, a radius of R*= 1.31 ± 0.03 Ro, an effective temperature of Teff = 6005 ± 50 K, and a metallicity of -0.10 ± 0.05 dex. By combining TESS photometry with high-resolution spectra acquired with the HARPS spectrograph, we found that the transiting planet has an orbital period of ∼3.74 days, a mass of Mp = 13.31±0.99M⊕ and a radius of Rp = 2.83±0.20 R⊕. The host star TOI-2458 shows a short activity cycle of ∼54 days revealed in the HARPS S-index and Hα times series. We took the opportunity to investigate other F stars showing activity cycle periods comparable to that of TOI-2458 and found that they have shorter rotation periods than would be expected based on the gyrochronology predictions. In addition, we determined TOI-2458's stellar inclination angle to be i*= 10.6+13.3 -10.6 degrees. We discuss that both phenomena (fast stellar rotation and planet orbit inclination) could be explained by in situ formation of a hot Jupiter interior to TOI-2458 b. It is plausible that this hot Jupiter was recently engulfed by the star. Analysis of HARPS spectra has identified the presence of another planet with a period of P = 16.55 ± 0.06 days and a minimum mass of Mp sin i = 10.22 ± 1.90M⊕. Using dynamical stability analysis, we constrained the mass of this planet to the range Mc (10, 25)M⊕. © 2024, CC BY.

关键词： Stars

A survey on studying the social networks of students

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arXiv 2019年

作者： Saxena, Akrati Saxena, Pratishtha Reddy, Harita Gera, Ralucca Department of Computer Science School of Computing National University of Singapore Singapore Singapore Department of Computer Science and Engineering Center for Advanced Studies Lucknow India Department of Computer Science and Engineering National Institute of Technology Karnataka India Department of Applied Mathematics Associate Provost for Graduate Education Teaching and Learning Commons Naval Postgraduate School MontereyCA United States

Do studies show that physical and online students’ social networks support education? Analyzing interactions between students in schools and universities can provide a wealth of information. Studies on students’ social networks can help us understand their behavioral dynamics, the correlation between their friendships and academic performance, community and group formation, information diffusion, and so on. Educational goals and holistic development of students with various academic abilities and backgrounds can be achieved by incorporating the findings attained by the studies in terms of knowledge propagation in classroom and spread of delinquent behaviors. Moreover, we use Social Network Analysis (SNA) to identify isolated students, ascertain the group study culture, analyze the spreading of various habits like smoking, drinking, and so on. In this paper, we present a review of the research showing how analysis of students’ social networks can help us identify how improved educational methods can be used to make learning more inclusive at both school and university levels and achieve holistic development of students through expansion of their social networks, as well as control the spread of delinquent behaviors. Copyright © 2019, The Authors. All rights reserved.

关键词： Students

Toward Quantification and Visualization of Active Stress Waves for Myocardial Biomechanical Function Assessment

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Toward Quantification and Visualization of Active Stress Wav...

2019 computing in Cardiology, CinC 2019

作者： Otani, Niels F. Linte, Cristian A. Dang, Dylan Beam, Christopher Mohammadi, Fariba Wentz, Brian Kamrul Hasan, S.M. Shontz, Suzanne M. Schwarz, Karl Q. Thomas, Sabu Rochester Institute of Technology School of Mathematical Sciences RochesterNY United States Mechanical Engineering University of Kansas LawrenceKS United States Bioengineering Graduate Program University of Kansas LawrenceKS United States Center for Imaging Science Rochester Institute of Technology RochesterNY United States Electrical Engineering and Computer Science University of Kansas LawrenceKS United States Division of Cardiology University of Rochester Medical Center RochesterNY United States RochesterNY14467 United States

ISBN: (纸本)9781728169361

Estimating and visualizing myocardial active stress wave patterns is crucial to understanding the mechanical activity of the heart and provides a potential non-invasive method to assess myocardial function. These patterns can be reconstructed by analyzing 2D and/or 3D tissue displacement data acquired using medical imaging. Here we describe an application that utilizes a 3D finite element formulation to reconstruct active stress from displacement data. As a proof of concept, a simple cubic mesh was used to represent a myocardial tissue "sample" consisting of a 10 x 10 x 10 lattice of nodes featuring different fiber directions that rotate with depth, mimicking cardiac transverse isotropy. In the forward model, tissue deformation was generated using a test wave with active stresses that mimic the myocardial contractile forces. The generated deformation field was used as input to an inverse model designed to reconstruct the original active stress distribution. We numerically simulated malfunctioning tissue regions (experiencing limited contractility and hence active stress) within the healthy tissue. We also assessed model sensitivity by adding noise to the deformation field generated using the forward model. The difference image between the original and reconstructed active stress distribution suggests that the model accurately estimates active stress from tissue deformation data with a high signal-to-noise ratio. © 2019 Creative Commons.

关键词： Medical imaging

Tunable nanophotonics enabled by chalcogenide phase-change materials

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arXiv 2020年

作者： Abdollahramezani, Sajjad Hemmatyar, Omid Taghinejad, Hossein Krasnok, Alex Kiarashinejad, Yashar Zandehshahvar, Mohammadreza Alù, Andrea Adibi, Ali School of Electrical and Computer Engineering Georgia Institute of Technology 778 Atlantic Drive NW AtlantaGA30332-0250 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 YorkNY10016 United States

Nanophotonics has garnered intensive attention due to its unique capabilities in molding the flow of light in the subwavelength regime. Metasurfaces (MSs) and photonic integrated circuits (PICs) enable the realization of mass-producible, cost-effective, and highly efficient flat optical components for imaging, sensing, and communications. In order to enable nanophotonics with multi-purpose functionalities, chalcogenide phase-change materials (PCMs) have been introduced as a promising platform for tunable and reconfigurable nanophotonic frameworks. Integration of non-volatile chalcogenide PCMs with unique properties such as drastic optical contrasts, fast switching speeds, and long-term stability grants substantial reconfiguration to the more conventional static nanophotonic platforms. In this review, we discuss state-of-the-art developments as well as emerging trends in tunable MSs and PICs using chalcogenide PCMs. We outline the unique material properties, structural transformation, electro-optic, and thermo-optic effects of well-established classes of chalcogenide PCMs. The emerging deep learning-based approaches for the optimization of reconfigurable MSs and the analysis of light-matter interactions are also discussed. The review is concluded by discussing existing challenges in the realization of adjustable nanophotonics and a perspective on the possible developments in this promising area. Copyright © 2020, The Authors. All rights reserved.

关键词： Phase change materials