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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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Constraints on holographic QCD phase transitions from PTA observations

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 71-78页

作者： Song He Li Li Sai Wang Shao-Jiang Wang Center for Theoretical Physics and College of Physics Jilin University School of Physical Science and Technology Ningbo University Max Planck institute for Gravitational Physics (Albert Einstein institute) CAS Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences School of Fundamental Physics and Mathematical sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences (UCAS) School of Physical sciences University of Chinese Academy of Sciences (UCAS) Theoretical Physics Division Institute of High Energy Physics Chinese Academy of Sciences

The underlying physics of QCD phase transition in the early Universe remains largely unknown due to its strong-coupling nature during the quark-gluon plasma/hadron gas transition, yet a holographic model has been proposed to quantitatively fit the lattice QCD data while with its duration of the first-order phase transition(FoPT) left undetermined. At specific baryon chemical potential, the first-order QCD phase transition agrees with the observational constraint of baryon asymmetry. It, therefore, provides a scenario for phase transition gravitational waves(GWs) within the standard model of particle physics. If these background GWs could contribute dominantly to the recently claimed common-spectrum red noise from pulsar timing array(PTA) observations, the duration of this FoPT can be well constrained, and the associated primordial black holes are still allowed by current observations.

关键词： pulsar timing array QCD phase transition gravitational waves primordial black holes

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Traffic safety helmet wear detection based on improved YOLOv5 network

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Optoelectronics Letters 2025年第1期21卷 35-42页

作者： GUI Dongdong SUN Bo College of Software Southeast University Quanzhou Equipment Research Centre Haixi Institute Chinese Academy of Sciences

Aiming at the problem that the current traffic safety helmet detection model can't balance the accuracy of detection with the size of the model and the poor generalization of the model, a method based on improving you only look once version 5(YOLOv5) is proposed. By incorporating the lightweight Ghost Net module into the YOLOv5 backbone network, we effectively reduce the model size. The addition of the receptive fields block(RFB) module enhances feature extraction and improves the feature acquisition capability of the lightweight model. Subsequently, the high-performance lightweight convolution, GSConv, is integrated into the neck structure for further model size compression. Moreover, the baseline model's loss function is substituted with efficient insertion over union(EIoU), accelerating network convergence and enhancing detection precision. Experimental results corroborate the effectiveness of this improved algorithm in real-world traffic scenarios.

关键词： Traffic control

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Highly conductive and stable iodine doped argyrodite electrolyte for all-solid-state lithium batteries

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Journal of Energy Chemistry 2025年第1期100卷 50-58页

作者： Gaozhan Liu Jing Zhang Jing Yang Jinghui Chen Xingyue Xiao Xiayin Yao Ningbo institute of Materials Technology and Engineering Chinese Academy of Sciences Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of Sciences

Lithium argyrodites with high ionic conductivity and low cost are considered as one of the most prospective solid electrolytes for all-solid-state lithium ***,the poor chemical stability and compatibility with lithium metal limit their ***,Li5.4PS4.4Cl1.4I0.2solid electrolyte with high ionic conductivity of 11.49 m S cm-1and improved chemical stability is synthesized by iodine *** ultra-thin Li5.4PS4.4Cl1.4I0.2membrane with thickness of 10μm can be obtained by wet coating process,exhibiting a high ionic conductivity of 2.09 mS cm-1and low areal resistance of 1.17Ω***,iodine doping could in-situ form LiI at the lithium/electrolyte interface and improve the critical current density of Li5.4PS4.4Cl1.6from 0.8 to 1.35 mA *** resultant LiCoO2/Li5.4PS4.4Cl1.4I0.2/Li battery shows excellent cycling stability at 1 C,with a reversible specific capacity of 110.1 mA h g-1and a retention of 80.5% after 1000 *** addition,the assembled LiCoO2/Li5.4PS4.4Cl1.4I0.2membrane/Li pouch cell delivers an initial discharge capacity of 110.4 mA h g-1and 80.5% capacity retention after 100 cycles.

关键词： Argyrodite electrolytes Iodine doping Ionic conductivity Stability All-solid-state lithium battery

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Apolipoprotein E elicits targetdirected miRNA degradation to maintain neuronal integrity

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Neural Regeneration Research 2025年第9期20卷 2577-2578页

作者： Jiazi Tan Chin-Tong Ong Temasek life sciences Laboratory National University of SingaporeSingapore Department of Biological sciences National University of SingaporeSingapore

Apolipoprotein E has diverse functions in neurons:Apolipoprotein E(ApoE)is a glycoprotein that primarily regulates lipid metabolism and transport in the central nervous *** are three predominant human ApoE protein isoforms with cysteine and arginine substitutions at amino acid positions 112 and 158 that impact their lipidation and related functions(Flowers and Rebeck,2020).ApoE2 is characterized by Cys112 and Cys158,ApoE3 by Cys112 and Arg158,whereas ApoE4 contains Arg112 and Arg158.

关键词： metabolism glycoprotein maintain

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Tuning beneficial calcineurin phosphatase activation to counterα-synuclein toxicity in a yeast model of Parkinson’s disease

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Neural Regeneration Research 2025年第1期20卷 199-200页

作者： Srishti Chawla Mikael Molin Thomas Nystrom institute for Biomedicine Sahlgrenska AcademyCentre for Ageing and Health-AgeCapUniversity of GothenburgGothenburgSweden Department of life sciences Chalmers University of TechnologyGothenburgSweden

Calcineurin(CN)is a calcium-and calmodulindependent serine/threonine that has been studied in many model organisms including yeast,filamentous fungi,plants,and *** biological functions range from ion homeostasis and virulence in lower eukaryotes to T-cell activation in humans by human nuclear factors of activated *** is a heterodimeric protein consisting of a catalytic subunit,calcineurin A(Cna1p),which contains an active site with a dinuclear metal center,and a regulatory Ca^(2+) binding subunit called calcineurin B(Cnb1p)required to activate *** calcineurin B subunit has been highly conserved through evolution:For example,the mammalian calcineurin B shows 54%identity with calcineurin B from Saccharomyces cerevisiae.

关键词： activation dinuclear conserved

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Harnessing therapeutic potential of induced pluripotent stem cell–derived endothelial cells for remyelination in the central nervous system

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Neural Regeneration Research 2025年第6期20卷 1715-1716页

作者： Dan Ma Nona Pop Aston Medical School College of Health and Life SciencesAston UniversityBirminghamUK

Myelin is the protective sheath surrounding nerve fibers, and its damage(demyelination) occurs in many central nervous system(CNS) diseases, including multiple sclerosis(MS), traumatic injury, neurodegenerative diseases such as Alzheimer's disease, and mental disorders such as schizophrenia(Barateiro et al., 2016). Repair of damaged myelin sheaths(remyelination) often fails in MS, leading to neuronal loss and irreversible functional deficits.

关键词： myelin protective diseases

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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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Unlocking the stable interface in aqueous zinc-ion battery with multifunctional xylose-based electrolyte additives

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Journal of Energy Chemistry 2025年第1期100卷 770-778页

作者： Xiaoqin Li Jian Xiang Lu Qiu Xiaohan Chen Yinkun Zhao Yujue Wang Qu Yue Taotao Gao Wenlong Liu Dan Xiao Zhaoyu Jin Panpan Li institute for Advanced Study Chengdu University School of Mechanical Engineering Chengdu University College of Food and Biological Engineering Chengdu University institute of Fundamental and Frontier sciences University of Electronic Science and Technology of China College of Materials Science and Engineering Sichuan University

The growth of dendrites and the side reactions occurring at the Zn anode pose significant challenges to the commercialization of aqueous Zn-ion batteries（AZIBs）. These challenges arise from the inherent conflict between mass transfer and electrochemical kinetics. In this study, we propose the use of a multifunctional electrolyte additive based on the xylose（Xylo） molecule to address these issues by modulating the solvation structure and electrode/electrolyte interface, thereby stabilizing the Zn anode. The introduction of the additive alters the solvation structure, creating steric hindrance that impedes charge transfer and then reduces electrochemical kinetics. Furthermore, in-situ analyses demonstrate that the reconstructed electrode/electrolyte interface facilitates stable and rapid Zn2+ion migration and suppresses corrosion and hydrogen evolution reactions. As a result, symmetric cells incorporating the Xylo additive exhibit significantly enhanced reversibility during the Zn plating/stripping process, with an impressively long lifespan of up to 1986 h, compared to cells using pure ZnSO4electrolyte. When combined with a polyaniline cathode, the full cells demonstrate improved capacity and long-term cyclic stability. This work offers an effective direction for improving the stability of Zn anode via electrolyte design, as well as highperformance AZIBs.

关键词： Solvation

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Sky location of massive black hole binaries in the foreground of Galactic white dwarf binaries

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 97-108页

作者： Pan Guo Hong-Bo Jin Cong-Feng Qiao Yue-Liang Wu The International Centre for Theoretical Physics Asia-Pacific University of Chinese Academy of Sciences The School of Physical sciences University of Chinese Academy of Sciences institute for Frontiers in Astronomy and Astrophysics Beijing Normal University National Astronomical Observatories Chinese Academy of Sciences institute of Theoretical Physics Chinese Academy of Sciences

For space-based gravitational wave （GW） detection,the main noise source for massive black hole binaries （MBHBs） is attributed to approximately 10～7double white dwarf binaries in the *** a GW source,the amplitude of the detector response,recorded by a space-based gravitational wave detector,exhibits a modulation effect with a year period when observing the source from various orbital *** the adverse conditions mentioned above,where there is a strong foreground noise and annual modulation in the signals,we employed the wavelet transform and the strong-amplitude relevant orbital position search methods,which allows the weak MBHB sources to achieve higher locating *** detail,for two MBHB sources of lower intensity,the precision of luminosity distance,represented by the ratio ?DL/DLat the 95%confidence level,is enhanced by factors of ～*** angular resolutions,denoted by??s,are enhanced by a factor of ～*** improvements increase the number of detectable GW sources,facilitate multi-messenger follow-up observations and provide constraints on the cosmological constant.

关键词： space-based gravitational wave detection gravitational waves massive black hole binaries

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