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Frontiers of physics 2021年第6期16卷 1-78页

作者： Daniele PAnderle Valerio Bertone Xu Cao Lei Chang Ningbo Chang Gu Chen Xurong Chen Zhuojun Chen Zhufang Cui Lingyun Dai Weitian Deng Minghui Ding Xu Feng Chang Gong Longcheng Gui Feng-Kun Guo Chengdong Han Jun He Tie-Jiun Hou Hongxia Huang Yin Huang KrešImir KumeričKi LPKaptari Demin Li Hengne Li Minxiang Li Xueqian Li Yutie Liang Zuotang Liang Chen Liu Chuan Liu Guoming Liu Jie Liu Liuming Liu Xiang Liu Tianbo Liu Xiaofeng Luo Zhun Lyu Boqiang Ma Fu Ma Jianping Ma Yugang Ma Lijun Mao Cédric Mezrag HervéMoutarde Jialun Ping Sixue Qin Hang Ren Craig DRoberts Juan Rojo Guodong Shen Chao Shi Qintao Song Hao Sun PawełSznajder Enke Wang Fan Wang Qian Wang Rong Wang Ruiru Wang Taofeng Wang Wei Wang Xiaoyu Wang Xiaoyun Wang Jiajun Wu Xinggang Wu Lei Xia Bowen Xiao Guoqing Xiao Ju-Jun Xie Yaping Xie Hongxi Xing Hushan Xu Nu Xu Shusheng Xu Mengshi Yan Wenbiao Yan Wencheng Yan Xinhu Yan Jiancheng Yang Yi-Bo Yang Zhi Yang Deliang Yao Zhihong Ye Peilin Yin C-PYuan Wenlong Zhan Jianhui Zhang Jinlong Zhang Pengming Zhang Yifei Zhang Chao-Hsi Chang Zhenyu Zhang Hongwei Zhao Kuang-Ta Chao Qiang Zhao Yuxiang Zhao Zhengguo Zhao Liang Zheng Jian Zhou Xiang Zhou Xiaorong Zhou Bingsong Zou Liping Zou Guangdong Provincial Key Laboratory of Nuclear Science Institute of Quantum MatterSouth China Normal UniversityGuangzhou 510006China IRFU CEAUniversitéParis-SaclayF-91191 Gif-sur-YvetteFrance Institute of Modern Physics Chinese Academy of SciencesLanzhou 730000China University of Chinese Academy of Sciences Beijing 100049China Nankai University Tianjin 300071China Xinyang Normal University Xinyang 464000China School of Physics and Materials Science Guangzhou UniversityGuangzhou 510006China Hunan University Changsha 410082China Nanjing University Nanjing 210093China Huazhong University of Science and Technology Wuhan 430074China European Centre for Theoretical Studies in Nuclear Physics and Related Areas(ECT*)and Fondazione Bruno Kessler Villa TambosiStrada delle Tabarelle 286I-38123 Villazzano(TN)Italy School of Physics Peking UniversityBeijing 100871China Hunan Normal University Changsha 410081China Institute of Theoretical Physics Chinese Academy of SciencesBeijing 100190China Nanjing Normal University Nanjing 210023China Department of Physics College of SciencesNortheastern UniversityShenyang 110819China Southwest Jiaotong University Chengdu 610000China Department of Physics Faculty of ScienceUniversity of ZagrebBijenička c.3210000 ZagrebCroatia Bogoliubov Laboratory of Theoretical Physics Joint Institute for Nuclear ResearchDubna 141980Russia School of Physics and Microelectronics Zhengzhou UniversityZhengzhou 450001China Lanzhou University Lanzhou 730000China Key Laboratory of Particle Physics and Particle Irradiation(MOE) Shandong UniversityQingdao 266237China Key Laboratory of Quark and Lepton Physics(MOE)and Institute of Particle Physics Central China Normal UniversityWuhan 430079China School of Physics Southeast UniversityNanjing 211189China Key Laboratory of Nuclear Physics and Ion-beam Application(MOE) Institute of Modern PhysicsFudan UniversityShanghai 200433China Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China Depa

Lepton scattering is an established ideal tool for studying inner structure of small particles such as nucleons as well as *** a future high energy nuclear physics project,an Electron-ion collider in China(EicC)has been *** will be constructed based on an upgraded heavy-ion accelerator,High Intensity heavy-ion Accelerator Facility(HIAF)which is currently under construction,together with a new electron *** proposed collider will provide highly polarized electrons(with a po-larization of 80%)and protons(with a polarization of 70%)with variable center of mass energies from 15 to 20 GeV and the luminosity of(2–3)×1033 cm^(−2)·s^(−1).Polarized deuterons and Helium-3,as well as unpolarized ion beams from Carbon to Uranium,will be also available at the *** main foci of the EicC will be precision measurements of the structure of the nucleon in the sea quark region,including 3D tomography of nucleon;the partonic structure of nuclei and the parton interaction with the nuclear environment;the exotic states,especially those with heavy flavor quark *** addition,issues fundamental to understanding the origin of mass could be addressed by measurements of heavy quarkonia near-threshold production at the *** order to achieve the above-mentioned physics goals,a hermetical detector system will be constructed with cutting-edge *** document is the result of collective contributions and valuable inputs from experts across the *** EicC physics program complements the ongoing scientific programs at the Jefferson laboratory and the future EIC project in the United *** success of this project will also advance both nuclear and particle physics as well as accelerator and detector technology in China.

关键词： electron ion collider nucleon structure nucleon mass exotic hadronic states quantum chromodynamics 3D-tomography helicity transverse momentum dependent parton distribution generalized parton distribution energy recovery linac polarization spin rotator

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Measuring holographic entanglement entropy on a quantum simulator

arXiv

引用

arXiv 2017年

作者： Li, Keren Han, Muxin Qu, Dongxue Huang, Zichang Long, Guilu Wan, Yidun Lu, Dawei Zeng, Bei Laflamme, Raymond Shenzhen Institute for Quantum Science and Engineering Department of Physics Southern University of Science and Technology Shenzhen518055 China Center for Quantum Computing Peng Cheng Laboratory Shenzhen518055 China Institute for Quantum Computing and Department of Physics and Astronomy University of Waterloo WaterlooONN2L 3G1 Canada State Key Laboratory of Low-Dimensional Quantum Physics and Department of Physics Tsinghua University Beijing100084 China Department of Physics Florida Atlantic University 777 Glades Road Boca RatonFL33431 United States Institut für Quantengravitation Universität Erlangen-Nürnberg Staudtstr. 7/B2 Erlangen91058 Germany State Key Laboratory of Surface Physics Fudan University Shanghai200433 China Department of Physics and Center for Field Theory and Particle Physics Fudan University Shanghai200433 China Institute for Nanoelectronic devices and Quantum computing Fudan University Shanghai200433 China Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing210093 China Shenzhen Key Laboratory of Quantum Science and Engineering Shenzhen518055 China Department of Mathematics and Statistics University of Guelph GuelphONN1G 2W1 Canada Perimeter Institute for Theoretical Physics WaterlooONN2L 2Y5 Canada

Quantum simulation promises to have wide applications in many fields where problems are hard to model with classical computers. Various quantum devices of different platforms have been built to tackle the problems in, say, quantum chemistry, condensed matter physics, and high-energy physics. Here, we report an experiment towards the simulation of quantum gravity by simulating the holographic entanglement entropy. On a six-qubit nuclear magnetic resonance quantum simulator, we demonstrate a key result of Anti-de Sitter/conformal field theory(AdS/CFT ) correspondence-the Ryu-Takayanagi formula is demonstrated by measuring the relevant entanglement entropies on the perfect tensor state. The fidelity of our experimentally prepared the six-qubit state is 85.0% via full state tomography and reaches 93.7%if the signal-decay due to decoherence is taken into account. Our experiment serves as the basic module of simulating more complex tensor network states that exploring AdS/CFT correspondence. As the initial experimental attempt to study AdS/CFT via quantum information processing, our work opens up new avenues exploring quantum gravity phenomena on quantum simulators. Copyright © 2017, The Authors. All rights reserved.

关键词： Quantum chemistry

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Correction to: A method of VR‑EEG scene cognitive rehabilitation training

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Health information science and systems 2021年第1期9卷 7页

作者： Wenjun Tan Yang Xu Pan Liu Chunyan Liu Yujin Li Yanrui Du Chao Chen Yuping Wang Yanchun Zhang Key Laboratory of Intelligent Computing in Medical Image Ministry of Education Northeastern University Shenyang 110189 China. Cyberspace Institute of Advanced Technology Guangzhou University Guangzhou 510006 China. Department of Neurology Xuanwu Hospital Capital Medical University Beijing 100053 China. Key Laboratory of Complex System Control Theory and Application Tianjin University of Technology Tianjin 300384 China. Institute for Sustainable Industries and Liveable Cities Victoria University Melbourne VIC 8001 Australia.

[This corrects the article DOI: 10.1007/s13755-020-00132-6.].

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Quantum spacetime on a quantum simulator

arXiv

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arXiv 2017年

作者： Li, Keren Li, Youning Han, Muxin Lu, Sirui Zhou, Jie Ruan, Dong Long, Guilu Wan, Yidun Lu, Dawei Zeng, Bei Laflamme, Raymond State Key Laboratory of Low-Dimensional Quantum Physics and Department of Physics Tsinghua University Beijing100084 China Institute for Quantum Computing Department of Physics and Astronomy University of Waterloo WaterlooONN2L 3G1 Canada Department of Physics Florida Atlantic University 777 Glades Road Boca RatonFL33431 United States Institut für Quantengravitation Universität Erlangen-Nürnberg Staudtstr. 7/B2 Erlangen91058 Germany Perimeter Institute for Theoretical Physics WaterlooONN2L 2Y5 Canada Department of Physics Center for Field Theory and Particle Physics Fudan University Shanghai200433 China Collaborative Innovation Center of Advanced Microstructures Nanjing210093 China Department of Physics and Institute for Quantum Science and Engineering Southern University of Science and Technology Shenzhen518055 China Department of Mathematics and Statistics University of Guelph GuelphONN1G 2W1 Canada Canadian Institute for Advanced Research TorontoONM5G 1Z8 Canada

We experimentally simulate the spin networks—a fundamental description of quantum spacetime at the Planck level. We achieve this by simulating quantum tetrahedra and their interactions. The tensor product of these quantum tetrahedra comprises spin networks. In this initial attempt to study quantum spacetime by quantum information processing, on a four-qubit nuclear magnetic resonance quantum simulator, we simulate the basic module—comprising five quantum tetrahedra—of the interactions of quantum spacetime. By measuring the geometric properties on the corresponding quantum tetrahedra and simulate their interactions, our experiment serves as the basic module that represents the Feynman diagram vertex in the spin-network formulation of quantum spacetime. Copyright © 2017, The Authors. All rights reserved.

关键词： Geometry

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Electronic structure of pristine and Ni-substituted LaFeO3 from near edge x-ray absorption fine structure experiments and first-principles simulations

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Physical Review Research 2020年第3期2卷 033265-033265页

作者： Iurii Timrov Piyush Agrawal Xinyu Zhang Selma Erat Riping Liu Artur Braun Matteo Cococcioni Matteo Calandra Nicola Marzari Daniele Passerone Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL) École Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland nanotech@surfaces Laboratory and National Centre for Computational Design and Discovery of Novel Materials (MARVEL) Empa–Swiss Federal Laboratories for Materials Science and Technology CH-8600 Dübendorf Switzerland Electron Microscopy Center Empa–Swiss Federal Laboratories for Materials Science and Technology CH-8600 Dübendorf Switzerland nanotech@surfaces Laboratory Empa–Swiss Federal Laboratories for Materials Science and Technology CH-8600 Dübendorf Switzerland State Key Laboratory of Metastable Material Science and Technology Yanshan University CN-066004 Qinhuangdao China High Performance Ceramics Laboratory Empa–Swiss Federal Laboratories for Materials Science and Technology CH-8600 Dubendorf Switzerland Department for Materials Nonmetallic Inorganic Materials ETH Zurich Swiss Federal Institute of Technology CH-8037 Zurich Switzerland Vocational School of Technical Sciences Department of Medical Services and Techniques Program of Opticianry Mersin University TR-33343 Yenisehir Mersin Turkey Advanced Technology Education Research and Application Center Mersin University TR-33343 Yenisehir Mersin Turkey Department of Physics University of Pavia Via Bassi 6 I-27100 Pavia Italy Dipartmento di Fisica Università di Trento Via Sommarive 14 38123 Povo Italy Sorbonne Université CNRS Institut des Nanosciences de Paris UMR7588 F-75252 Paris France

We present a joint theoretical and experimental study of the oxygen K-edge spectra for LaFeO3 and homovalent Ni-substituted LaFeO3 (LaFe0.75Ni0.25O3), using first-principles simulations based on density-functional theory with extended Hubbard functionals and x-ray absorption near edge structure (XANES) measurements. Ground-state and excited-state XANES calculations employ Hubbard onsite U and intersite V parameters determined from first principles and the Lanczos recursive method to obtain absorption cross sections, which allows for a reliable description of XANES spectra in transition-metal compounds in a very broad energy range, with an accuracy comparable to that of hybrid functionals but at a substantially lower cost. We show that standard gradient-corrected exchange-correlation functionals fail in capturing accurately the electronic properties of both materials. In particular, for LaFe0.75Ni0.25O3 they do not reproduce its semiconducting behavior and provide a poor description of the pre-edge features at the O K edge. The inclusion of Hubbard interactions leads to a drastic improvement, accounting for the semiconducting ground state of LaFe0.75Ni0.25O3 and for good agreement between calculated and measured XANES spectra. We show that the partial substitution of Ni for Fe affects the conduction-band bottom by generating a strongly hybridized O(2p)−Ni(3d) minority-spin empty electronic state. The present work, based on a consistent correction of self-interaction errors, outlines the crucial role of extended Hubbard functionals to describe the electronic structure of complex transition-metal oxides such as LaFeO3 and LaFe0.75Ni0.25O3 and paves the way to future studies on similar systems.

关键词： Density of states Electronic structure Transition-metal rare-earth alloys DFT+U Density functional calculations Density functional theory X-ray absorption near-edge spectroscopy

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Comparison of heavy-ion transport simulations: Mean-field dynamics in a box

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Physical Review C 2021年第2期104卷 024603-024603页

作者： Maria Colonna Ying-Xun Zhang Yong-Jia Wang Dan Cozma Pawel Danielewicz Che Ming Ko Akira Ono Manyee Betty Tsang Rui Wang Hermann Wolter Jun Xu Zhen Zhang Lie-Wen Chen Hui-Gan Cheng Hannah Elfner Zhao-Qing Feng Myungkuk Kim Youngman Kim Sangyong Jeon Chang-Hwan Lee Bao-An Li Qing-Feng Li Zhu-Xia Li Swagata Mallik Dmytro Oliinychenko Jun Su Taesoo Song Agnieszka Sorensen Feng-Shou Zhang INFN-LNS Laboratori Nazionali del Sud 95123 Catania Italy China Institute of Atomic Energy Beijing 102413 China Guangxi Key Laboratory Breeding Base of Nuclear Physics and Technology Guilin 541004 China School of Science Huzhou University Huzhou 313000 China IFIN-HH 077125 Măgurele-Bucharest Romania National Superconducting Cyclotron Laboratory and Department of Physics and Astronomy Michigan State University East Lansing Michigan 48824 USA Cyclotron Institute and Department of Physics and Astronomy Texas A&M University College Station Texas 77843 USA Department of Physics Tohoku University Sendai 980-8578 Japan Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) Institute of Modern Physics Fudan University Shanghai 200433 China Physics Department University of Munich D-85748 Garching Germany Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China Sino-French Institute of Nuclear Engineering & Technology Sun Yat-sen University Zhuhai 519082 China School of Physics and Astronomy Shanghai Key Laboratory for Particle Physics and Cosmology and Key Laboratory for Particle Astrophysics and Cosmology (MOE) Shanghai Jiao Tong University Shanghai 200240 China School of Physics and Optoelectronic Technology South China University of Technology Guangzhou 510641 China Frankfurt Institute for Advanced Studies Johann Wolfgang Goethe University Ruth-Moufang-Strasse 1 60438 Frankfurt am Main Germany Institute for Theoretical Physics Goethe University Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany GSI Helmholtzzentrum für Schwerionenforschung Planckstrasse 1 64291 Darmstadt Germany Department of Physics Ulsan National Institute of Science and Technology Ulsan 44919 Korea Rare Isotope Science Project Institute for Basic Science Daejeon 34000 Korea Department of Physics McGill University Montreal Quebec H3A2T8 Canada Department

Within the transport model evaluation project (TMEP) of simulations for heavy-ion collisions, the mean-field response is examined here. Specifically, zero-sound propagation is considered for neutron-proton symmetric matter enclosed in a periodic box, at zero temperature and around normal density. The results of several transport codes belonging to two families (BUU-like and QMD-like) are compared among each other and to exact calculations. For BUU-like codes, employing the test particle method, the results depend on the combination of the number of test particles and the spread of the profile functions that weight integration over space. These parameters can be properly adapted to give a good reproduction of the analytical zero-sound features. QMD-like codes, using molecular dynamics methods, are characterized by large damping effects, attributable to the fluctuations inherent in their phase-space representation. Moreover, for a given nuclear effective interaction, they generally lead to slower density oscillations, as compared to BUU-like codes. The latter problem is mitigated in the more recent lattice formulation of some of the QMD codes. The significance of these results for the description of real heavy-ion collisions is discussed.

关键词： Low & intermediate energy heavy-ion reactions Models & methods for nuclear reactions Nuclear reactions

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Titelbild: Single‐Atom Iron Catalysts on Overhang‐Eave Carbon Cages for High‐Performance Oxygen Reduction Reaction (Angew. Chem. 19/2020)

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Angewandte Chemie 2020年第19期132卷

作者： Chun‐Chao Hou Lianli Zou Liming Sun Kexin Zhang Zheng Liu Yinwei Li Caixia Li Ruqiang Zou Jihong Yu Qiang Xu AIST-Kyoto University Chemical Energy Materials Open Innovation Laboratory (ChEM-OIL) National Institute of Advanced Industrial Science and Technology (AIST) Sakyo-ku Kyoto 606-8501 Japan Graduate School of Engineering Kobe University Nada Ku Kobe Hyogo 657-8501 Japan Laboratory of Quantum Materials Design and Application School of Physics and Electronic Engineering Jiangsu Normal University Xuzhou 221116 P. R. China Beijing Key laboratory for Theory and Technology of Advanced Battery Materials Department of Materials Science and Engineering College of Engineering Peking University Beijing 100871 P. R. China Inorganic Functional Materials Research Institute National Institute of Advanced Industrial Science and Technology (AIST) 2266-98 Anagahora Shimoshidami Moriyamaku Nagoya Aichi 463-8560 Japan State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry International Center of Future Science Jilin University Changchun 130012 P. R. China

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Cover Picture: Single-Atom Iron Catalysts on Overhang-Eave Carbon Cages for High-Performance Oxygen Reduction Reaction (Angew. Chem. Int. Ed. 19/2020)

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Angewandte Chemie International Edition 2020年第19期59卷

作者： Dr. Chun-Chao Hou Dr. Lianli Zou Dr. Liming Sun Dr. Kexin Zhang Dr. Zheng Liu Prof. Yinwei Li Dr. Caixia Li Prof. Ruqiang Zou Prof. Jihong Yu Prof. Qiang Xu AIST-Kyoto University Chemical Energy Materials Open Innovation Laboratory (ChEM-OIL) National Institute of Advanced Industrial Science and Technology (AIST) Sakyo-ku Kyoto 606-8501 Japan Graduate School of Engineering Kobe University Nada Ku Kobe Hyogo 657-8501 Japan Laboratory of Quantum Materials Design and Application School of Physics and Electronic Engineering Jiangsu Normal University Xuzhou 221116 P. R. China Beijing Key laboratory for Theory and Technology of Advanced Battery Materials Department of Materials Science and Engineering College of Engineering Peking University Beijing 100871 P. R. China Inorganic Functional Materials Research Institute National Institute of Advanced Industrial Science and Technology (AIST) 2266-98 Anagahora Shimoshidami Moriyamaku Nagoya Aichi 463-8560 Japan State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry International Center of Future Science Jilin University Changchun 130012 P. R. China

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The environmental dependence of Spitzer dusty Supernovae

arXiv

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arXiv 2023年

作者： Xiao, Lin Szalai, Tamás Galbany, Lluís Fox, Ori Hu, Lei Hu, Maokai Yang, Yi Moriya, Takashi J. Pessi, Thallis Han, Zhanwen Wang, Xiaofeng Yan, Shengyu Department of Physics Hebei University Baoding071002 China Hebei Key Laboratory of High-precision Computation and Application of Quantum Field Theory Baoding071002 China Hebei Research Center of the Basic Discipline for Computational Physics Baoding071002 China Department of Experimental Physics Institute of Physics University of Szeged Dóm tér 9 SzegedH-6720 Hungary HUN-REN–SZTE Stellar Astrophysics Research Group H-6500 BajaSzegedi út Kt. 766 Hungary Campus UAB Carrer de Can Magrans s/n BarcelonaE-08193 Spain BarcelonaE-08034 Spain Space Telescope Science Institute 3700 San Martin Drive BaltimoreMD21218 United States McWilliams Center for Cosmology Department of Physics Carnegie Mellon University 5000 Forbes Ave PittsburghPA15213 United States Purple Mountain Observatory Chinese Academy of Sciences Nanjing210023 China Tsinghua University Beijing100084 China Department of Astronomy University of California BerkeleyCA94720-3411 United States National Astronomical Observatory of Japan National Institutes of Natural Sciences 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan School of Physics and Astronomy Monash University ClaytonVIC3800 Australia Instituto de Estudios Astrofísicos Facultad de Ingeniería y Ciencias Universidad Diego Portales Av. Ejército Libertador 441 Santiago Chile Yunnan Observatories Chinese Academy of Sciences Kunming650216 China Key Laboratory for the Structure and Evolution of Celestial Objects Yunnan Observatories CAS Kunming650216 China International Centre of Supernovae Yunnan Key Laboratory Kunming650216 China Beijing Planetarium Beijing Academy of Science and Technology Beijing100044 China

Thanks to the mid-infrared capability offered by Spitzer, systematic searches of dust in SNe have been carried out over the past decade. Studies have revealed the presence of a substantial amount of dust over a broad range of SN subtypes. How normal SNe present mid-IR excess at later time and turn out to be dusty SNe can be affected by several factors, such as mass-loss history and envelope structure of progenitors and their explosion environment. All these can be combined and related to their environmental properties. A systematic analysis of SNe that exploded under a dusty environment could be of critical importance to measure the properties of the dust-veiled exploding stars, and whether such an intense dust production process is associated with the local environment. In this work, we firstly use the IFS data to study the environmental properties of dusty SNe compared to those of normal ones, and analyze correlations between the environmental properties and their dust parameters. We find that dusty SNe have a larger proportion located at higher SFR regions compared to the normal types. The occurrence of dusty SNe is less dependent on metallicity, with the oxygen abundance spanning from subsolar to oversolar metallicity. We also find the host extinction of dusty SNe scatters a lot, with about 40% of dusty SN located at extremely low extinction environments, and another 30% of them with considerably high host extinction of E(B-V)>0.6 mag. Copyright © 2023, The Authors. All rights reserved.

关键词： Supernovae

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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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