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A molecular single-cell lung atlas of lethal COVID-19 (vol 595, pg 114, 2021)

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NATURE 2021年第7882期598卷 E2-E2页

作者： Melms, Johannes C. Biermann, Jana Huang, Huachao Wang, Yiping Nair, Ajay Tagore, Somnath Katsyv, Igor Rendeiro, Andre F. Amin, Amit Dipak Schapiro, Denis Frangieh, Chris J. Luoma, Adrienne M. Filliol, Aveline Fang, Yinshan Ravichandran, Hiranmayi Clausi, Mariano G. Alba, George A. Rogava, Meri Chen, Sean W. Ho, Patricia Montoro, Daniel T. Kornberg, Adam E. Han, Arnold S. Bakhoum, Mathieu F. Anandasabapathy, Niroshana Suarez-Farinas, Mayte Bakhoum, Samuel F. Bram, Yaron Borczuk, Alain Guo, Xinzheng V. Lefkowitch, Jay H. Marboe, Charles Lagana, Stephen M. Del Portillo, Armando Tsai, Emily J. Zorn, Emmanuel Markowitz, Glen S. Schwabe, Robert F. Schwartz, Robert E. Elemento, Olivier Saqi, Anjali Hibshoosh, Hanina Que, Jianwen Izar, Benjamin Department of Medicine Division of Hematology/Oncology Columbia University Irving Medical Center New York NY USA Columbia Center for Translational Immunology Columbia University Irving Medical Center New York NY USA Herbert Irving Comprehensive Cancer Center Columbia University Irving Medical Center New York NY USA Program for Mathematical Genomics Columbia University New York NY USA Columbia Center for Human Development Columbia University Irving Medical Center New York NY USA Division of Digestive and Liver Diseases Columbia University Irving Medical Center New York NY USA Department of Medicine Columbia University Irving Medical Center New York NY USA Institute of Human Nutrition Columbia University New York NY USA Department of Systems Biology Columbia University Irving Medical Center New York NY USA Department of Pathology and Cell Biology Columbia University Irving Medical Center New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Caryl and Israel Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA WorldQuant Initiative for Quantitative Prediction Weill Cornell Medicine New York NY USA Department of Physiology and Biophysics Weill Cornell Medical College New York NY USA Department of Dermatology Weill Cornell Medical College New York NY USA Meyer Cancer Center Weill Cornell Medical College New York NY USA Laboratory of Systems Pharmacology Harvard Medical School Boston MA USA Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Cancer Immunology and Virology Dana-Farber Cancer Center Boston MA USA Human Immune Monitoring Core Columbia University Irving Medical Center New York NY USA Department of Medicine Division of Pulmonary and Critical Care Massachusetts General Hospital Boston MA USA Cell Circu

Species trees from gene trees despite a high rate of lateral genetic transfer: A tight bound (Extended Abstract) 27

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Species trees from gene trees despite a high rate of lateral...

27th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2016

作者： Daskalakis, Constantinos Roch, Sebastien Department of Electrical Engineering and Computer Science MIT United States University of Wisconsin-Madison United States

ISBN: (纸本)9781510819672

Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes which can complicate the reconstruction problem due to the fact that different genes may undergo different evolutionary histories. This is the case in particular in the presence of lateral genetic transfer (LGT), whereby a gene is inherited from a distant species rather than an immediate ancestor. Such an event produces a gene tree which is distinct from (but related to) the species phylogeny. In previous work, a stochastic model of LGT was introduced and it was shown that the species phylogeny can be reconstructed from gene trees despite surprisingly high rates of LGT. Both lower and upper bounds on this rate were obtained, but a large gap remained. Here we close this gap, up to a constant. Specifically, we show that the species phylogeny can be reconstructed perfectly even when each edge of the tree has a constant probability of being the location of an LGT event. Our new reconstruction algorithm builds the tree recursively from the leaves. We also provide a matching bound in the negative direction (up to a constant). © (2016) by SIAM: Society for Industrial and Applied Mathematics.

关键词： Genes

Particle computation: Complexity, algorithms, and logic

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arXiv 2017年

作者： Becker, Aaron T. Demaine, Erik D. Fekete, Sándor P. Lonsford, Jarrett Morris-Wright, Rose Department of Electrical and Computer Engineering University of Houston TX United States Computer Science and Artificial Intelligence Laboratory MIT CambridgeMA United States Department of Computer Science TU Braunschweig Germany Mathematics Brandeis University WalthamMA United States

We investigate algorithmic control of a large swarm of mobile particles (such as robots, sensors, or building material) that move in a 2D workspace using a global input signal (such as gravity or a magnetic field). Upon activation of the field, each particle moves maximally in the same direction until forward progress is blocked by a stationary obstacle or another stationary particle. In an open workspace, this system model is of limited use because it has only two controllable degrees of freedom-all particles receive the same inputs and move uniformly. We show that adding a maze of obstacles to the environment can make the system drastically more complex but also more useful. We provide a wide range of results for a wide range of questions. These can be subdivided into external algorithmic problems, in which particle configurations serve as input for computations that are performed elsewhere, and internal logic problems, in which the particle configurations themselves are used for carrying out computations. For external algorithms, we give both negative and positive results. If we are given a set of stationary obstacles, we prove that it is NP-hard to decide whether a given initial configuration of unit-sized particles can be transformed into a desired target configuration. Moreover, we show that finding a control sequence of minimum length is PSPACE-complete. We also work on the inverse problem, providing constructive algorithms to design workspaces that efficiently implement arbitrary permutations between different configurations. For internal logic, we investigate how arbitrary computations can be implemented. We demonstrate how to encode dual-rail logic to build a universal logic gate that concurrently evaluates and, nand, nor, and or operations. Using many of these gates and appropriate interconnects, we can evaluate any logical expression. However, we establish that simulating the full range of complex interactions present in arbitrary digital circuits encoun

关键词： Nanoparticles

THz-driven electron streak camera based on a multilayer structure

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THz-driven electron streak camera based on a multilayer stru...

Conference on Lasers and Electro-Optics Europe (CLEO EUROPE)

作者： Dongfang Zhang Arya Fallahi Xiaojun Wu Moein Fakhari Huseyin Cankaya Anne-Laure Calendron Chun Zhou Wenqian Ronny Huang Daniel Haynes Francois Lemery Frederike Ahr Wenchao Qiao Nicholas H. Matlis Franz X. Kärtner Department of Physics University of Hamburg Hamburg Germany Center for Free-Electron Laser Science Deutsches Elektronen Synchrotron Hamburg Germany Department of Electrical Engineering & Computer Science MIT Cambridge Massachusetts USA

ISBN: (纸本)9781509067374

Summary form only given. With the development of modem THz technology [1], which can provide electric fields with GV/m gradients, THz-based control and manipulation of the electron bunches has become possible. THz-driven electron acceleration, compression and streaking have attracted much attention recently [2, 3]. Here, we present a novel THz driven electron streak camera that provides sub-fs temporal resolution using a multilayer structure.

关键词： Laser beams Cameras Nonhomogeneous media Electric fields Acceleration Cavity resonators Electron optics

A local universe host for the repeating fast radio burst FRB 20181030A

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arXiv 2021年

作者： Bhardwaj, Mohit Kirichenko, A.Y. Michilli, D. Mayya, Y.D. Kaspi, V.M. Gaensler, B.M. Rahman, M. Tendulkar, S.P. Fonseca, E. Josephy, Alexander Leung, C. Merryfield, Marcus Petroff, Emily Pleunis, Z. Sanghavi, Pranav Scholz, P. Shin, K. Smith, Kendrick M. Stairs, I.H. Department of Physics McGill University 3600 rue University MontréalQCH3A 2T8 Canada McGill Space Institute McGill University 3550 rue University MontréalQCH3A 2A7 Canada Instituto de Astronomía Universidad Nacional Autónoma de México Apdo. Postal 877 Baja California Ensenada22800 Mexico Ioffe Institute 26 Politekhnicheskaya st. St. Petersburg194021 Russia Instituto Nacional de Astrofísica Óptica y Electrónica Luis Enrique Erro 1 Tonantzintla Puebla72840 Mexico Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Department of Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Sidrat Research PO Box 73527 RPO Wychwood TorontoONM6C 4A7 Canada Department of Astronomy and Astrophysics Tata Institute of Fundamental Research Mumbai400005 India National Centre for Radio Astrophysics Post Bag 3 Ganeshkhind Pune411007 India MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Department of Physics Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Lane Department of Computer Science and Electrical Engineering 1220 Evansdale Drive PO Box 6109 MorgantownWV26506 United States Center for Gravitational Waves and Cosmology West Virginia University Chestnut Ridge Research Building MorgantownWV26505 United States Perimeter Institute for Theoretical Physics 31 Caroline Street N WaterlooONN25 2YL Canada Dept. of Physics and Astronomy 6224 Agricultural Road VancouverBCV6T 1Z1 Canada

We report on the host association of FRB 20181030A, a repeating fast radio burst (FRB) with a low dispersion measure (DM, 103.5 pc cm−3) discovered by CHIME/FRB Collaboration et al. (2019a). Using baseband voltage data saved for its repeat bursts, we localize the FRB to a sky area of 5.3 sq. arcmin (90% confidence). Within the FRB localization region, we identify NGC 3252 as the most promising host, with an estimated chance coincidence probability −3. Moreover, we do not find any other galaxy with Mr 26erg s−1Hz−1, at least 1500 times smaller than that of the FRB 20121102A persistent radio source. We also argue that a population of young millisecond magnetars alone cannot explain the observed volumetric rate of repeating FRBs. Finally, FRB 20181030A is a promising source for constraining FRB emission models due to its proximity, and we strongly encourage its multi-wavelength follow-up. Copyright © 2021, The Authors. All rights reserved.

关键词： Galaxies

Erratum: “The First CHIME/FRB Fast Radio Burst Catalog” (2021, ApJS, 257, 59)

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The Astrophysical Journal Supplement Series 2023年第2期264卷 53-53页

作者： The CHIME/FRB Collaboration Mandana Amiri Bridget C. Andersen Kevin Bandura Sabrina Berger Mohit Bhardwaj Michelle M. Boyce P. J. Boyle Charanjot Brar Daniela Breitman Tomas Cassanelli Pragya Chawla Tianyue Chen J.-F. Cliche Amanda Cook Davor Cubranic Alice P. Curtin Meiling Deng Matt Dobbs Fengqiu (Adam) Dong Gwendolyn Eadie Mateus Fandino Emmanuel Fonseca B. M. Gaensler Utkarsh Giri Deborah C. Good Mark Halpern Alex S. Hill Gary Hinshaw Alexander Josephy Jane F. Kaczmarek Zarif Kader Joseph W. Kania Victoria M. Kaspi T. L. Landecker Dustin Lang Calvin Leung Dongzi Li Hsiu-Hsien Lin Kiyoshi W. Masui Ryan Mckinven Juan Mena-Parra Marcus Merryfield Bradley W. Meyers Daniele Michilli Nikola Milutinovic Arash Mirhosseini Moritz Münchmeyer Arun Naidu Laura Newburgh Cherry Ng Chitrang Patel Ue-Li Pen Emily Petroff Tristan Pinsonneault-Marotte Ziggy Pleunis Masoud Rafiei-Ravandi Mubdi Rahman Scott M. Ransom Andre Renard Pranav Sanghavi Paul Scholz J. Richard Shaw Kaitlyn Shin Seth R. Siegel Andrew E. Sikora Saurabh Singh Kendrick M. Smith Ingrid Stairs Chia Min Tan S. P. Tendulkar Keith Vanderlinde Haochen Wang Dallas Wulf A. V. Zwaniga Department of Physics and Astronomy University of British Columbia 6224 Agricultural Road Vancouver BC V6T 1Z1 Canada Department of Physics McGill University 3600 rue University Montréal QC H3A 2T8 Canada McGill Space Institute McGill University 3550 rue University Montréal QC H3A 2A7 Canada Lane Department of Computer Science and Electrical Engineering 1220 Evansdale Drive PO Box 6109 Morgantown WV 26506 USA Center for Gravitational Waves and Cosmology West Virginia University Chestnut Ridge Research Building Morgantown WV 26505 USA Department of Physics and Astronomy University of Manitoba Winnipeg MB R3T 2N2 Canada Department of Physics University of Toronto 60 St. George Street Toronto ON M5S 1A7 Canada Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street Toronto ON M5S 3H4 Canada David A. Dunlap Department of Astronomy & Astrophysics University of Toronto 50 St. George Street Toronto ON M5S 3H4 Canada MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA Perimeter Institute for Theoretical Physics 31 Caroline Street N Waterloo ON N25 2YL Canada Dominion Radio Astrophysical Observatory Herzberg Research Centre for Astronomy and Astrophysics National Research Council Canada PO Box 248 Penticton BC V2A 6J9 Canada Department of Physics and Astronomy University of Waterloo Waterloo ON N2L 3G1 Canada Department of Computer Science Math Physics & Statistics University of British Columbia Kelowna BC V1V 1V7 Canada Department of Physics and Astronomy West Virginia University PO Box 6315 Morgantown WV 26506 USA Department of Physics Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA kshin@mit.edu Canadian Institute for Theoretical Astrophysics 60 St. George Street Toronto ON M5S 3H8 Canada Department of Physics University of Wisconsin–Madison 1150 University Ave. Madison WI 53706

Modeling Fast Radio Burst Dispersion and Scattering Properties in the First CHIME/FRB Catalog

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arXiv 2021年

作者： Chawla, Pragya Kaspi, V.M. Ransom, S.M. Bhardwaj, M. Boyle, P.J. Breitman, D. Cassanelli, T. Cubranic, D. Dong, F.Q. Fonseca, E. Gaensler, B.M. Giri, U. Josephy, A. Kaczmarek, J.F. Leung, C. Masui, K.W. Mena-Parra, J. Merryfield, M. Michilli, D. Münchmeyer, M. Ng, C. Patel, C. Pearlman, A.B. Petroff, E. Pleunis, Z. Rahman, M. Sanghavi, P. Shin, K. Smith, K.M. Stairs, I. Tendulkar, S.P. Department of Physics McGill University 3600 rue University MontréalQCH3A 2T8 Canada McGill Space Institute McGill University 3550 rue University MontréalQCH3A 2A7 Canada Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands National Radio Astronomy Observatory 520 Edgemont Rd CharlottesvilleVA22903 United States Department of Physics University of Toronto 60 St. George Street TorontoONM5S 1A7 Canada Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Department of Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Department of Physics and Astronomy University of British Columbia 6224 Agricultural Road VancouverBCV6T 1Z1 Canada Perimeter Institute for Theoretical Physics 31 Caroline Street N WaterlooONN25 2YL Canada Department of Physics and Astronomy University of Waterloo WaterlooONN2L 3G1 Canada Dominion Radio Astrophysical Observatory Herzberg Research Centre for Astronomy and Astrophysics National Research Council Canada PO Box 248 PentictonBCV2A 6J9 Canada MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Department of Physics Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Department of Physics University of Wisconsin-Madison 1150 University Ave MadisonWI53706 United States Sidrat Research PO Box 73527 RPO Wychwood TorontoONM6C 4A7 Canada Lane Department of Computer Science and Electrical Engineering 1220 Evansdale Drive PO Box 6109 MorgantownWV26506 United States Center for Gravitational Waves and Cosmology West Virginia University Chestnut Ridge Research Building MorgantownWV26505 United States Department of Astronomy and Astrophysics Tata Institute of Fundamental Research Mumbai400005 India National Centre for R

We present a Monte Carlo-based population synthesis study of fast radio burst (FRB) dispersion and scattering focusing on the first catalog of sources detected with the Canadian Hydrogen Intensity Mapping Experiment Fast Radio Burst (CHIME/FRB) project. We simulate intrinsic properties and propagation effects for a variety of FRB population models and compare the simulated distributions of dispersion measures (DMs) and scattering timescales with the corresponding distributions from the CHIME/FRB catalog. Our simulations confirm the results of previous population studies, which suggested that the interstellar medium of the host galaxy alone (simulated based on the NE2001 model) cannot explain the observed scattering timescales of FRBs. We therefore consider additional sources of scattering, namely, the circumgalactic medium (CGM) of intervening galaxies and the circumburst medium whose properties are modeled based on typical Galactic plane environments. We find that a population of FRBs with scattering contributed by these media is marginally consistent with the CHIME/FRB catalog. In this scenario, our simulations favor a population of FRBs offset from their galaxy centers over a population which is distributed along the spiral arms. However, if the models proposing the CGM as a source of intense scattering are incorrect, then we conclude that FRBs may inhabit environments with more extreme properties than those inferred for pulsars in the Milky Way. Copyright © 2021, The Authors. All rights reserved.

关键词： Galaxies

Shape-independent hardness estimation using deep learning and a GelSight tactile sensor

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arXiv 2017年

作者： Yuan, Wenzhen Zhu, Chenzhuo Owens, Andrew Srinivasan, Mandayam A. Adelson, Edward H. Department of Mechanical Engineering Computer Science and Artificial Intelligence Laboratory CambridgeMA02139 United States CSAIL MIT CambridgeMA United States Department of Electronical Engineering Tsinghua University Beijing100084 China Electrical Engineering and Computer Science Department U.C. Berkeley CambridgeMA02139 United States Research Laboratory of Electronics Department of Mechanical Engineering MIT CambridgeMA02139 United States UCL TouchLab Computer Science Department UCL London United Kingdom Department of Brain and Cognitive Sciences CSAIL MIT CambridgeMA02139 United States

Hardness is among the most important attributes of an object that humans learn about through touch. However, approaches for robots to estimate hardness are limited, due to the lack of information provided by current tactile sensors. In this work, we address these limitations by introducing a novel method for hardness estimation, based on the GelSight tactile sensor, and the method does not require accurate control of contact conditions or the shape of objects. A GelSight has a soft contact interface, and provides high resolution tactile images of contact geometry, as well as contact force and slip conditions. In this paper, we try to use the sensor to measure hardness of objects with multiple shapes, under a loosely controlled contact condition. The contact is made manually or by a robot hand, while the force and trajectory are unknown and uneven. We analyze the data using a deep constitutional (and recurrent) neural network. Experiments show that the neural net model can estimate the hardness of objects with different shapes and hardness ranging from 8 to 87 in Shore 00 scale. Copyright © 2017, The Authors. All rights reserved.

关键词： Hardness

Examining the effects of anisotropy on longitudinally propagating waves on isolated tectorial membranes

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AIP Conference Proceedings 2018年第1期1965卷

作者： Charlsie Lemons Jonathan B. Sellon Dennis M. Freeman Julien Meaud 1G.W.W. Woodruff School of Mechanical Engineering Georgia Institute of Technology Atlanta GA USA 2Research Laboratory of Electronics MIT Cambridge MA USA 3Department of Electrical Engineering and Computer Science MIT Cambridge MA USA

Knowledge of the mechanical properties of the tectorial membrane (TM) would improve the understanding of TM function in hearing mechanics. In recent years, several groups have used measurements of wave propagation on isolated TMs to estimate the mechanical properties of the TM at acoustic frequencies. However, these studies have ignored the curvature, finite dimensions and anisotropy of the TM. In this study, optical images of an isolated wild-type basal TM segment in response to harmonic radial excitation are used to determine the amplitude and phase of the motion at acoustic frequencies. Wave propagation on the TM segment is modeled using a finite element model that takes into account the geometry, anisotropy and viscoelasticity of the TM. An automated least-square fitting algorithm is used to find material parameters of the TM. The resulting material properties are compared to previous estimates.

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