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Single-cell omics: experimental workflow, data analyses and applications

Science China life sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab shanghai Research Institute for Intelligent Autonomous Systems center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of life Science Chinese Academy of Sciences Peking-Tsinghua center for life sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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A new horizon for neuroscience:terahertz biotechnology in brain research

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Neural Regeneration Research 2025年第2期20卷 309-325页

作者： Zhengping Pu Yu Wu Zhongjie Zhu Hongwei Zhao Donghong Cui shanghai Key Laboratory of Psychotic Disorders Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina department of Psychiatry Kangci Hospital of JiaxingTongxiangZhejiang ProvinceChina shanghai Synchrotron Radiation Facility Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina Key Laboratory of Interfacial physics and Technology Shanghai Institute of Applied PhysicsChinese Academy of ScienceShanghaiChina National Facility for Protein Science in shanghai Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina

Terahertz biotechnology has been increasingly applied in various biomedical fields and has especially shown great potential for application in brain *** this article,we review the development of terahertz biotechnology and its applications in the field of *** evidence indicates promising prospects for the use of terahertz spectroscopy and terahertz imaging techniques in the diagnosis of amyloid disease,cerebrovascular disease,glioma,psychiatric disease,traumatic brain injury,and myelin *** vitro and animal experiments have also demonstrated the potential therapeutic value of terahertz technology in some neuropsychiatric *** the precise underlying mechanism of the interactions between terahertz electromagnetic waves and the biosystem is not yet fully understood,the research progress in this field shows great potential for biomedical noninvasive diagnostic and therapeutic ***,the biosafety of terahertz radiation requires further exploration regarding its two-sided efficacy in practical *** review demonstrates that terahertz biotechnology has the potential to be a promising method in the field of neuropsychiatry based on its unique advantages.

关键词： biological effect brain neuron neuropsychiatry neuroscience non-thermal effect terahertz imaging terahertz radiation terahertz spectroscopy terahertz technology

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Einstein Probe discovery of EP240408a: A peculiar X-ray transient with an intermediate timescale

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Science China(physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 222-240页

作者： Wenda Zhang Weimin Yuan Zhixing Ling Yong Chen Nanda Rea Arne Rau Zhiming Cai Huaqing Cheng Francesco Coti Zelati Lixin Dai Jingwei Hu Shumei Jia Chichuan Jin Dongyue Li Paul O’Brien Rongfeng Shen Xinwen Shu Shengli Sun Xiaojin Sun Xiaofeng Wang Lei Yang Bing Zhang Chen Zhang Shuang-Nan Zhang Yonghe Zhang Jie An David Buckley Alexis Coleiro Bertrand Cordier Liming Dou Rob Eyles-Ferris Zhou Fan Hua Feng Shaoyu Fu Johan P.U.Fynbo Lluis Galbany Saurabh W.Jha Shuaiqing Jiang Albert Kong Erik Kuulkers Weihua Lei Wenxiong Li Bifang Liu Mingjun Liu Xing Liu Yuan Liu Zhu Liu Chandreyee Maitra Alessio Marino Itumeleng Monageng Kirpal Nandra Jeremy Sanders Roberto Soria Lian Tao Junfeng Wang Song Wang Tinggui Wang Zhongxiang Wang Qingwen Wu Xuefeng Wu Dong Xu Yanjun Xu Suijian Xue Yongquan Xue Zijian Zhang Zipei Zhu Hu Zou Congying Bao Fansheng Chen Houlei Chen Tianxiang Chen Wei Chen Yehai Chen Yifan Chen Chenzhou Cui Weiwei Cui Yanfeng Dai Dongwei Fan Ju Guan Dawei Han Dongjie Hou Haibo Hu Maohai Huang Jia Huo Zhenqing Jia Bowen Jiang Ge Jin Chengkui Li Junfei Li Longhui Li Maoshun Li Wei Li Zhengda Li Tianying Lian Congzhan Liu Heyang Liu Huaqiu Liu Fangjun Lu Laidan Luo Jia Ma Xuan Mao Haiwu Pan Xin Pan Liming Song Hui Sun Yunyin Tan Qingjun Tang Yihan Tao Hao Wang Juan Wang Lei Wang Wenxin Wang Yilong Wang Yusa Wang Qinyu Wu Haitao Xu Jingjing Xu Xinpeng Xu Yunfei Xu Zhao Xu Changbin Xue Yulong Xue Ailiang Yan Haonan Yang Xiongtao Yang Yanji Yang Juan Zhang Mo Zhang Wenjie Zhang Zhen Zhang Zhen Zhang Ziliang Zhang Donghua Zhao Haisheng Zhao Xiaofan Zhao Zijian Zhao Hongyan Zhou Yilin Zhou Yuxuan Zhu Zhencai Zhu National Astronomical Observatories Chinese Academy of sciences School of Astronomy and Space sciences University of Chinese Academy of sciences Key Laboratory of Particle Astrophysics Institute of High Energy physics Chinese Academy of sciences Institute of Space sciences (ICE) CSIC Institut d’Estudis Espacials de Catalunya (IEEC) Max Planck Institute for Extraterrestrial physics Innovation Academy for Microsatellites Chinese Academy of sciences department of physics University of Hong Kong School of physics and Astronomy University of Leicester School of physics and Astronomy Sun Yat-sen University department of physics Anhui Normal University shanghai Institute of Technical physics Chinese Academy of sciences physics department Tsinghua University Nevada center for Astrophysics University of Nevada Las Vegas department of physics and Astronomy University of Nevada Las Vegas South African Astronomical Observatory department of Astronomy University of Cape Town department of physics University of the Free State Université Paris Cité CNRS Astroparticule et Cosmologie Université Paris Cité CEA Paris-Saclay IRFU/DAp-AIM department of Astronomy Guangzhou University Cosmic Dawn center (DAWN) Niels Bohr Institute University of Copenhagen department of physics and Astronomy Rutgers the State University of New Jersey Institute for Cosmic Ray Research The University of Tokyo ESA/ESTEC department of Astronomy School of physics Huazhong University of Science and Technology INAF-Osservatorio Astrofisico di Torino Sydney Institute for Astronomy School of physics The University of Sydney department of Astronomy Xiamen University Institute for Frontiers in Astronomy and Astrophysics Beijing Normal University department of Astronomy University of Science and Technology School of Astronomy and Space sciences University of Science and Technology of China Institute of Deep Space sciences Deep Space Exploration Laboratory department of Astronomy School of physics and Astronomy Yunnan University shanghai Astronomical Observatory Chi

We report the discovery of a peculiar X-ray transient,EP240408a,by Einstein Probe （EP） and follow-up studies made with EP,Swift,NICER,GROND,ATCA and other ground-based multiwavelength *** new transient was first detected with Wide-field X-ray Telescope （WXT） on board EP on April 8th,2024,manifested in an intense yet brief X-ray flare lasting for *** flare reached a peak flux of 3.9×10-9erg cm-2s-1in 0.5-4 ke V,～300 times brighter than the underlying X-ray emission detected throughout the *** and more precise follow-up observations by EP/FXT,Swift and NICER confirmed the finding of this new *** X-ray spectrum is non-thermal in 0.5-10 ke V,with a power-law photon index varying *** X-ray light curve shows a plateau lasting for ～4 d,followed by a steep decay till becoming undetectable ～10 d after the initial *** on its temporal property and constraints from previous EP observations,an unusual timescale in the range of 7-23 d is found for EP240408a,which is intermediate between the commonly found fast and long-term *** counterparts have been found in optical and near-infrared,with the earliest observation at 17 h after the initial X-ray detection,suggestive of intrinsically weak emission in these *** demonstrate that the remarkable properties of EP240408a are inconsistent with any of the transient types known so far,by comparison with,in particular,jetted tidal disruption events,gamma-ray bursts,X-ray binaries and fast blue optical *** nature of EP240408a thus remains an *** suggest that EP240408a may represent a new type of transients with intermediate timescales of the order of～10 *** detection and follow-ups of more of such objects are essential for revealing their origin.

关键词： X-ray transients ${\bm~{Einstein~~Probe}}$

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Is philosophy of any use for scientists？

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Science Bulletin 2018年第16期63卷 1017-1018页

作者： Ping Ao shanghai center for quantitative life sciences and department of physics Shanghai University.Shanghai 200444 China

This is a question which would certainly divide physicists in particular and scientists in *** aware of that,here I would like to take the successful career path of an excellent physicist as a positive example,supplemented by my own humble and negligible experience.I do hope that a bit of such discussion would be useful in the current rash state of scientific research in China.

关键词：科学家哲学物理学家科学研究

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Efficient transfer of metallophosphor excitons via confined polaritons in organic nanocrystals

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Chinese physics B 2023年第10期32卷 503-508页

作者：芦文斌陈永聪杨旭云敖平 shanghai center for quantitative life sciences&physics department Shanghai UniversityShanghai 200444China College of Biomedical Engineering Sichuan UniversitySichuan 610064China

We investigate the transfer of phosphorescent energy between co-assembled metallophosphors in crystalline nanostructures [Angew. Chem. Int. Ed. 57 7820(2018) and J. Am. Chem. Soc. 140 4269(2018)]. Neither Dexter's nor Forster's mechanism of resonance energy transfer(RET) could account fully for the observed rates, which exceed 85% with significant temperature dependence. But there exists an alternative pathway on RET mediated by intermediate states of resonantly confined exciton–polaritons. Such a mechanism was used to analyze artificial photosynthesis in organic fluorescents [***. Lett. 122 257402(2019)]. For metallophosphors, the confined modes act as extended states lying between the molecular S_(1) and T_(1) states, offering a bridge for the long-lived T_(1) excitons to migrate from donors to acceptors. Population dynamics with parameters taken entirely based on experiments fits the observed lifetimes of phosphorescence across a broad range of doping and temperature.

关键词： organic nanocrystals phosphorescent emission resonance energy transfer exciton–polariton

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Solution‑Processed Thin Film Transparent Photovoltaics:Present Challenges and Future Development

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Nano-Micro Letters 2025年第2期17卷 566-600页

作者： Tianle Liu Munerah M.S.Almutairi Jie Ma Aisling Stewart Zhaohui Xing Mengxia Liu Bo Hou Yuljae Cho UM-SJTU Joint Institute Shanghai Jiao Tong UniversityShanghai 200240People’s Republic of China School of physics and Astronomy Cardiff UniversityCardiff CF243AAWalesUK department of Electrical and Computer Engineering Yale UniversityNew HavenCT 06511USA Energy sciences Institute Yale UniversityWest HavenCT 06516USA Future Photovoltaics Research center Global Institute of Future TechnologyShanghai Jiao Tong UniversityShanghai 200240People’s Republic of China

Electrical energy is essential for modern society to sustain economic *** soaring demand for the electrical energy,together with an awareness of the environmental impact of fossil fuels,has been driving a shift towards the utilization of solar ***,traditional solar energy solutions often require extensive spaces for a panel installation,limiting their practicality in a dense urban *** overcome the spatial constraint,researchers have developed transparent photovoltaics(TPV),enabling windows and facades in vehicles and buildings to generate electric *** TPV advancements are focused on improving both transparency and power output to rival commercially available silicon solar *** this review,we first briefly introduce wavelength-and non-wavelengthselective strategies to achieve *** of merit and theoretical limits of TPVs are discussed to comprehensively understand the status of current TPV *** we highlight recent progress in different types of TPVs,with a particular focus on solution-processed thin-film photovoltaics(PVs),including colloidal quantum dot PVs,metal halide perovskite PVs and organic *** applications of TPVs are also reviewed,with emphasis on agrivoltaics,smart windows and ***,current challenges and future opportunities in TPV research are pointed out.

关键词： Transparent semiconductors Solution-processable transparent solar cell Emerging solar cell materials Buildingintegrated photovoltaics

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Stochastic Gradient Descent and Anomaly of Variance-Flatness Relation in Artificial Neural Networks

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Chinese physics Letters 2023年第8期40卷 6-10页

作者：熊霞陈永聪石春晓敖平 shanghai center for quantitative life sciences and physics department Shanghai UniversityShanghai 200444China Colloge of Biomedical Engineering Sichuan UniversityChengdu 610065China

Stochastic gradient descent(SGD),a widely used algorithm in deep-learning neural networks,has attracted continuing research interests for the theoretical principles behind its success.A recent work reported an anomaly(inverse)relation between the variance of neural weights and the landscape flatness of the loss function driven under SGD[Feng Y and Tu Y *** 118 e2015617118(2021)].To investigate this seeming violation of statistical physics principle,the properties of SGD near fixed points are analyzed with a dynamic decomposition *** approach recovers the true“energy”function under which the universal Boltzmann distribution *** differs from the cost function in general and resolves the paradox raised by the the *** study bridges the gap between the classical statistical mechanics and the emerging discipline of artificial intelligence,with potential for better algorithms to the latter.

关键词： neural bridges holds

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Cryo-EM Data Statistics and Theoretical Analysis of KaiC Hexamer

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Chinese physics Letters 2022年第7期39卷 24-29页

作者： Xu Han Zhaolong Wu Tian Yang Qi Ouyang department of physics Peking UniversityBeijing 100871China center for quantitative Biology and Peking-Tsinghua center for life sciences AAICPeking UniversityBeijing 100871China

Cryo-electron microscopy(cryo-EM) provides a powerful tool to resolve the structure of biological macromolecules in natural state. One advantage of cryo-EM technology is that different conformation states of a protein complex structure can be simultaneously built, and the distribution of different states can be measured. This provides a tool to push cryo-EM technology beyond just to resolve protein structures, but to obtain the thermodynamic properties of protein machines. Here, we used a deep manifold learning framework to get the conformational landscape of Kai C proteins, and further obtained the thermodynamic properties of this central oscillator component in the circadian clock by means of statistical physics.

关键词： Cryo-EM Data Statistics and Theoretical Analysis of KaiC Hexamer

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High density gas state at water/graphite interface studied by molecular dynamics simulation

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Chinese physics B 2008年第7期17卷 2646-2654页

作者：王春雷李朝霞李敬源修鹏胡钧方海平 shanghai Institute of Applied physics Chinese Academy of Sciences Graduate School of the Chinese Academy of sciences department of physics Zhejiang University School of physics and Microelectronics Shandong University Bio-X life sciences Research center College of Life Science and TechnologyShanghai Jiaotong University

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.

关键词： nanobubbles and gas film hydrophobic interface molecular dynamics simulations high density

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Humidity Effects on Imaging and Nanomanipulation of Individual DNA Molecules on HOPG Surface

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Chinese physics Letters 2007年第9期24卷 2692-2695页

作者：周星飞张益王化斌牛冬校王培卿胡钧 department of physics College of Sciences Ningbo University Ningbo 315211 shanghai Institute of Applied physics Chinese Academy of Sciences Shanghai 201800 Bio-X life Science Research center Shanghai Jiao Tong University Shanghai 200240

Single DNA molecules are aligned on highly ordered pyrolytic graphite （HOPG） surface in ambient air. It is shown that environmental humidity has a remarkable influence on the measured height of DNA by atomic force microscopy （AFM）, probably due to the conformation transition of DNA. We also demonstrate that DNA molecules deposited on HOPG surface can be ＇pushed＇ much more easily by AFM tip at high humidity than at 10W one.

关键词： coated conductor buffer layer self-epitaxy CeO2

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