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The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Cell 2025年第12期188卷 3167-3183.e18页

作者： Pekar, Jonathan E. Lytras, Spyros Ghafari, Mahan Magee, Andrew F. Parker, Edyth Wang, Yu Ji, Xiang Havens, Jennifer L. Katzourakis, Aris Vasylyeva, Tetyana I. Suchard, Marc A. Hughes, Alice C. Hughes, Joseph Rambaut, Andrew Robertson, David L. Dellicour, Simon Worobey, Michael Wertheim, Joel O. Lemey, Philippe Institute of Ecology and Evolution University of Edinburgh Edinburgh United Kingdom Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla 92093 CA United States Department of Biomedical Informatics University of California San Diego La Jolla 92093 CA United States Department of Medicine University of California San Diego La Jolla 92093 CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Medical Research Council University of Glasgow Centre for Virus Research Glasgow United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States Department of Immunology and Microbiology The Scripps Research Institute La Jolla 92037 CA United States Institute of Genomics and Global Health Redeemer's University Osun State Ede Nigeria Department of Computer Science and Engineering University of California San Diego La Jolla 92093 CA United States Department of Mathematics School of Science and Engineering Tulane University New Orleans LA United States Department of Population Health and Disease Prevention University of California Irvine Irvine 92617 CA United States Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles 90095 CA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States School of Biological Sciences University of Hong Kong Hong Kong Hong Kong China Biodiversity Green Development Foundation Beijing China Spatial Epidemiology Lab (SpELL) Université Libre de Bruxelles CP160/12 50 av. FD Roosevelt Bruxelles 1050 Belgium Department of Microbiology Immunology and Transplantation Rega Institute

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses. © 2025 The Authors

关键词： molecular epidemiology phylogeography sarbecoviruses virus evolution

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Passive Acoustic Metasurface with Unitary Reflection Based on Nonlocality

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Physical Review Applied 2019年第5期11卷 054077-054077页

作者： Li Quan Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10026 USA Department of Electrical Engineering City College of New York New York New York 10031 USA

Metasurfaces have introduced large flexibility in manipulating the impinging wavefront for light and sound by locally engineering the reflection and transmission coefficients based on generalized Snell’s laws. Local phenomena in each unit cell, however, are fundamentally limited in the level of efficiency with which anomalous wavefront transformations can be achieved. Here, we explore acoustic metasurfaces with suitably engineered nonlocality, obtained by coupling neighboring cells. We demonstrate that nonlocal passive metastructures can overcome the limitations of local designs, and mimic balanced gain and loss distributions, enabling unitary efficiency for extreme beam steering.

关键词： Acoustic metamaterials Acoustic wave phenomena Beam control Beam optics Light propagation, transmission & absorption

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IoT-Based Architecture for Data Analytics of Arboviruses in Smart Cities

IoT-Based Architecture for Data Analytics of Arboviruses in ...

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IEEE Symposium on computers and Communications

作者： Priscylla da S. Tavares Emanuel B. Rodrigues Group of Computer Networks Software Engineering and Systems (GREat) Graduate Program in Computer Science (MDCC) Federal University of Ceará (UFC) Fortaleza Brazil

With the progress of sensor technologies, there has been an increase in the number of connected computing devices capable of collecting information and interacting with the environment in which they are inserted, forming the basis of the Internet of Things (IoT). Such devices enable the development of new applications capable of making cities more intelligent, providing improvements to society and urban infrastructure. As a result of the interaction between different applications, there is a large set of data, from which useful knowledge can be extracted. An important problem to be faced is the recurrent occurrence of arbovirus outbreaks in big cities with tropical climate. This research proposes an architecture capable of aggregating data from different types of IoT devices, and manipulating them using data analytics techniques to assist the surveillance of arbovirus outbreaks. As an example of case study, we present an exploratory analysis of climatology data and cases of arbovirus diseases in the city of Fortaleza, Ceara, Brazil, between the years of 2011 and 2017.

关键词： Internet of Things Data analytics Health care Smart city

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Rainfall forecasting using PSPline and rice production with ocean-atmosphere interaction 2

Rainfall forecasting using PSPline and rice production with ...

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2nd International Conference on Eco engineering Development 2018, ICEED 2018

作者： Caraka, Rezzy Eko Supatmanto, Budi Darmawan Tahmid, Muhammad Soebagyo, Joko Mauludin, M. Ali Iskandar, Akbar Pardamean, Bens Bina Nusantara University Jakarta11480 Indonesia Indonesia Indonesia Agency for Meteorology Climatology and Geophysics Indonesia College of Technology Wastukancana Purwakarta Indonesia Laboratory of Sociology and Extension Padjadjaran University Indonesia Informatics Engineering STMIK AKBA Makassar Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

The role of climate can be affected by plants. The weather can accelerate and multiply the existence of various plant pests and diseases, accelerate the growth and development of grass among plants, and encourage the emergence of infection and significant damage to plants. The elements of climate that affect the growth of plants are one of them is rainfall. In this paper, we performed the simulation using the non-parametric penalized spline (PSPLINE) method and studied the effect on rice production in Lampung. It can be concluded that the increasing fluctuation, frequency, and intensity of climate anomalies in the last decade caused by the ENSO phenomenon have an impact on changes in distribution patterns, intensity, and period of the wet season so that the start of the rainy season and the dry season becomes too late. As a result, there is a seasonal shift from normal average conditions that can ultimately have severe implications for food crops. In a nutshell penalized spline gives high accuracy with R 2 = 96.227% and MAPE = 1.62%. © 2018 Institute of Physics Publishing. All rights reserved.

关键词： Rain

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engineering chirality at wafer scale with ordered carbon nanotube architectures

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Nature communications 2023年第1期14卷 7380页

作者： Jacques Doumani Minhan Lou Oliver Dewey Nina Hong Jichao Fan Andrey Baydin Keshav Zahn Yohei Yomogida Kazuhiro Yanagi Matteo Pasquali Riichiro Saito Junichiro Kono Weilu Gao Department of Electrical and Computer Engineering Rice University Houston TX USA. Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston TX USA. Department of Electrical and Computer Engineering The University of Utah Salt Lake City UT USA. Carbon Hub Rice University Houston TX USA. Department of Chemical and Biomolecular Engineering Rice University Houston TX USA. J.A. Woollam Co. Inc. Lincoln NE USA. Smalley-Curl Institute Rice University Houston TX USA. Department of Physics Tokyo Metropolitan University Tokyo Japan. Department of Chemistry Rice University Houston TX USA. Department of Materials Science and NanoEngineering Rice University Houston TX USA. Department of Physics Tohoku University Sendai Japan. Department of Physics National Taiwan Normal University Taipei Taiwan. Department of Physics and Astronomy Rice University Houston TX USA. Department of Electrical and Computer Engineering The University of Utah Salt Lake City UT USA. weilu.gao@utah.edu. Carbon Hub Rice University Houston TX USA. weilu.gao@utah.edu.

Creating artificial matter with controllable chirality in a simple and scalable manner brings new opportunities to diverse areas. Here we show two such methods based on controlled vacuum filtration - twist stacking and mechanical rotation - for fabricating wafer-scale chiral architectures of ordered carbon nanotubes (CNTs) with tunable and large circular dichroism (CD). By controlling the stacking angle and handedness in the twist-stacking approach, we maximize the CD response and achieve a high deep-ultraviolet ellipticity of 40 ± 1 mdeg nm. Our theoretical simulations using the transfer matrix method reproduce the experimentally observed CD spectra and further predict that an optimized film of twist-stacked CNTs can exhibit an ellipticity as high as 150 mdeg nm, corresponding to a g factor of 0.22. Furthermore, the mechanical rotation method not only accelerates the fabrication of twisted structures but also produces both chiralities simultaneously in a single sample, in a single run, and in a controllable manner. The created wafer-scale objects represent an alternative type of synthetic chiral matter consisting of ordered quantum wires whose macroscopic properties are governed by nanoscopic electronic signatures and can be used to explore chiral phenomena and develop chiral photonic and optoelectronic devices.

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Erratum: “Two-dimensional porous graphitic carbon nitride C6N7 monolayer: First-principles calculations” [Appl. Phys. Lett. 119, 142102 (2021)]

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Applied Physics Letters 2022年第18期120卷

作者： A. Bafekry M. Faraji M. M. Fadlallah I. Abdolhosseini Sarsari H. R. Jappor S. Fazeli M. Ghergherehchi 1Department of Radiation Application Shahid Beheshti University Tehran Iran 2Micro and Nanotechnology Graduate Program TOBB University of Economics and Technology Sogutozu Caddesi No 43 Sogutozu 06560 Ankara Turkey 3Department of Physics Faculty of Science Benha University 13518 Benha Egypt 4Department of Physics Isfahan University of Technology Isfahan 84156-83111 Iran 5Department of Physics College of Education for Pure Sciences University of Babylon Hilla Iraq 6Department of Material Science and Engineering Sharif University of Technology PO Box 11155-9466 Tehran Iran 7Department of Electrical and Computer Engineering Sungkyunkwan University 16419 Suwon South Korea

The original article1 contains misprints in the values of the elastic parameters. The values of C11 = 258.6 GPa, C22 = 290.8 GPa, and C12 = 70.73 GPa and C13 =

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scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

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Cell systems 2023年第4期14卷 302-311.e4页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Yu-Te Lin Cristhian Roman-Vicharra Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Department of Nutrition and the Program in Integrative Nutrition & Complex Diseases Texas A&M University College Station TX 77843 USA. Electronic address: r-chapkin@tamu.edu. Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA. Electronic address: jcai@tamu.edu.

We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.

关键词： cell-cell interaction cellular communication gene regression network machine learning manifold alignment neural networks scRNA-seq single-cell RNA sequencing

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Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors

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Physical Review B 2020年第2期101卷 020504(R)-020504(R)页

作者： Areg Ghazaryan P. L. S. Lopes Pavan Hosur Matthew J. Gilbert Pouyan Ghaemi IST Austria (Institute of Science and Technology Austria) Am Campus 1 3400 Klosterneuburg Austria Stewart Blusson Quantum Matter Institute University of British Columbia Vancouver British Columbia Canada V6T 1Z4 Department of Physics University of Houston Houston Texas 77204 USA Micro and Nanotechnology Laboratory University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA Department of Electrical and Computer Engineering University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA Department of Electrical Engineering Stanford University Stanford California 94305 USA Physics Department City College of the City University of New York New York New York 10031 USA Physics Program Graduate Center of the City University of New York New York 10031 USA

In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.

关键词： Majorana bound states Topological superconductors Iron-based superconductors

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A potential neurophysiological correlate of electric-acoustic pitch matching in adult cochlear implant users: Pilot data

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Cochlear Implants International 2018年第4期19卷 198-209页

作者： Tan, Chin-Tuan Martin, Brett A. Svirsky, Mario A. Department of Electrical and Computer Engineering School of Behavioral and Brain Science (Callier Center for Communication Disorders) University of Texas at Dallas Richardson TX United States Program in Speech-Language-Hearing Sciences and Program in Audiology Graduate Center City University of New York New York NY United States Department of Otolaryngology New York University New York NY United States

The overall goal of this study was to identify an objective physiological correlate of electric-acoustic pitch matching in unilaterally implanted cochlear implant (CI) participants with residual hearing in the non-implanted ear. Electrical and acoustic stimuli were presented in a continuously alternating fashion across ears. The acoustic stimulus and the electrical stimulus were either matched or mismatched in pitch. Auditory evoked potentials were obtained from nine CI users. Results indicated that N1 latency was stimulus-dependent, decreasing when the acoustic frequency of the tone presented to the non-implanted ear was increased. More importantly, there was an additional decrease in N1 latency in the pitch-matched condition. These results indicate the potential utility of N1 latency as an index of pitch matching in CI users. © 2018 Informa UK Limited, trading as Taylor & Francis Group.

关键词： Auditory evoked potential Electric-acoustic pitch matching N1 latency

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Hypermedia Driven Application programming Interface for Learning Object Management

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Procedia computer science 2018年 135卷 120-127页

作者： Herru Darmadi Suryadiputra Liawatimena Bahtiar Saleh Abbas Agung Trisetyarso Computer Science Department School of Computer Science Bina Nusantara University Jl. Kebun Jeruk Raya No 27 Kemanggisan Jakarta 11480 Indonesia Computer Engineering Department Faculty of Engineering Bina Nusantara University Jl. Kebun Jeruk Raya No 27 Kemanggisan Jakarta 11480 Indonesia Industrial Engineering Department BINUS Graduate Program - Doctor Computer Science Bina Nusantara University Jl. Kebun Jeruk Raya No 27 Kemanggisan Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program - Doctor Computer Science Bina Nusantara University Jl. Kebun Jeruk Raya No 27 Kemanggisan Jakarta 11480 Indonesia

The research purpose is to create a hypermedia driven API for learning object management. The research focuses on conception, design, implementation and evaluation of the learning object management hypermedia API. The hypermedia API was designed based on learning object models, hypermedia concepts, and related studies. Learning object model can be represented and manipulated as a hypermedia resource. It contains page resources with text and links to multimedia elements. The hypermedia API was designed using UML and represented in HTML5 because of its rich affordance. The implementation and evaluation phase were conducted by testing the API using three different client’s software to prove the concept of hypermedia as the engine of application state for managing learning objects. The results show that the hypermedia API for learning object management is accessible, consistent, and discoverable by heterogonous client applications.

关键词： hypermedia API HTML5 learning object content management

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