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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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Optimizing the key parameter to accelerate the recovery of AMOC under a rapid increase of greenhouse gas forcing

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Atmospheric and Oceanic science Letters 2025年第1期18卷 39-45页

作者： Haolan Ren Fei Zheng Tingwei Cao Qiang Wang International center for Climate and Environment science(ICCES) Institute of Atmospheric PhysicsChinese Academy of SciencesBeijingChina University of Chinese Academy of sciences BeijingChina College of Oceanography Hohai UniversityNanjingChina CAS Key Laboratory of Ocean Circulation and Waves Institute of OceanologyChinese Academy of Sciences and Pilot National Laboratory for Marine Science and Technology(Qingdao)QingdaoChina

Atlantic Meridional Overturning Circulation(AMOC)plays a central role in long-term climate variations through its heat and freshwater transports,which can collapse under a rapid increase of greenhouse gas forcing in climate *** studies have suggested that the deviation of model parameters is one of the major factors in inducing inaccurate AMOC *** this work,with a low-resolution earth system model,the authors try to explore whether a reasonable adjustment of the key model parameter can help to re-establish the AMOC after its *** a new optimization strategy,the extra freshwater flux(FWF)parameter is determined to be the dominant one affecting the AMOC’s *** traditional ensemble optimal interpolation(EnOI)data assimilation and new machine learning methods are adopted to optimize the FWF parameter in an abrupt 4×CO_(2) forcing experiment to improve the adaptability of model parameters and accelerate the recovery of *** results show that,under an abrupt 4×CO_(2) forcing in millennial simulations,the AMOC will first collapse and then re-establish by the default FWF parameter ***,during the parameter adjustment process,the saltier and colder sea water over the North Atlantic region are the dominant factors in usefully improving the adaptability of the FWF parameter and accelerating the recovery of AMOC,according to their physical relationship with FWF on the interdecadal timescale.

关键词： Recovery of AMOC 4×CO_(2)forcing Key parameter Parameter estimation Data assimilation Machine learning

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Toward understanding the role of genomic repeat elements in neurodegenerative diseases

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Neural Regeneration Research 2025年第3期20卷 646-659页

作者： Zhengyu An Aidi Jiang Jingqi Chen institute of science and Technology for Brain-Inspired Intelligence Fudan UniversityShanghaiChina MOE Frontiers center for Brain science Fudan UniversityShanghaiChina MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan UniversityShanghaiChina Zhangjiang Fudan International Innovation center ShanghaiChina

Neurodegenerative diseases cause great medical and economic burdens for both patients and society;however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.

关键词： Alzheimer's disease ataxia deep learning long-read sequencing neurodegeneration neurodegenerative diseases Parkinson's disease repeat element structural variant

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Influence of introducing Zr,Ti,Nb and Ce elements on externally solidified crystals and mechanical properties of high-pressure die-casting Al–Si alloy

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International Journal of Minerals,Metallurgy and Materials 2025年第1期32卷 147-153页

作者： Junjie Li Wenbo Yu Zhenyu Sun Weichen Zheng Liangwei Zhang Yanling Xue Wenning Liu Shoumei Xiong center of Materials science and Engineering School of Mechanical and Electronic Control EngineeringBeijing Jiaotong UniversityBeijing 100044China Traffic&Transportation Engineering Central South UniversityChangsha 410075China Shanghai Synchrotron Radiation Facility Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai 201204China School of Materials science and Engineering Tsinghua UniversityBeijing 100084China

High pressure die casting(HPDC)AlSi10Mn Mg alloy castings are widely used in the automobile *** can optimize the mechanical properties of castings through heat treatment,while the release of thermal stress arouses the deformation of large integrated ***,the development of non-heat treatment Al alloys is becoming the hot *** addition,HPDC contains externally solidified crystals(ESCs),which are detrimental to the mechanical properties of *** achieve high strength and toughness of non-heat treatment die-casting Al-Si alloy,we used AlSi9Mn alloy as matrix with the introduction of Zr,Ti,Nb,and *** influences on ESCs and mechanical properties were systematically investigated through three-dimensional reconstruction and thermodynamic *** results reveal that the addition of Ti increased ESCs'size and porosity,while the introduction of Nb refined ESCs and decreased ***,large-sized Al_3(Zr,Ti)phases formed and degraded the mechanical *** introduction of Ce resulted in the poisoning effect and reduced mechanical properties.

关键词： aluminium alloy high-pressure die-casting externally solidified crystals non-heat treatment

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Role of the Greenland Sea ice anomaly in the late-spring drought over Northwest china

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Atmospheric and Oceanic science Letters 2025年第1期18卷 1-5页

作者： Yang Liu Huopo Chen Nansen-Zhu International Research Centre Institute of Atmospheric Physics Chinese Academy of SciencesBeijingChina Collaborative Innovation center on Forecast and Evaluation of Meteorological Disasters Nanjing University for Information Science and TechnologyNanjingChina

Drought across Northwest china in late spring has exerted a vital effect on the local climate and agricultural production,and has been alleviated during the past *** study explored the influence of the preceding Arctic sea ice on the May drought in Northwest china caused by the precipitation *** analysis indicated that when the Greenland Sea ice concentration is abnormally high during February to April,the dry conditions in Northwest china tend to be *** increase of sea ice in the Greenland Sea can excite a meridional circulation,which causes sea surface temperature(SST)anomalies in the North Atlantic via the sea-air interaction,manifested as significant warm SST anomalies over the south of Greenland and the subtropical North Atlantic,but negative SST anomalies over the west of the *** abnormal SST pattern maintains to May and triggers a zonal wave train from the North Atlantic through Scandinavia and Central Asia to Northwest china,leading to abnormal cyclones in Northwest ***,Northwest china experiences a more humid climate than usual.

关键词： Arctic sea ice Greenland Sea North Atlantic SST Drought Northwest china

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Movement analysis in the diagnosis and management of Parkinson’s disease

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Neural Regeneration Research 2025年第2期20卷 485-486页

作者： Johannes Burtscher Nicolas Bourdillon Jules MJanssen Daalen Aurélien Patoz Julien FBally Martin Kopp Davide Malatesta Bastiaan RBloem institute of sport sciences University of LausanneLausanneSwitzerland Radboud University Medical center Department of NeurologyDonders Institute for BrainCognition and BehaviorCenter of Expertise for Parkinson and Movement DisordersNijmegenThe Netherlands Radboud University Medical center Department of Medical BioSciencesNijmegenThe Netherlands Research and Development Department Volodalen Swiss Sport LabAigleSwitzerland Service of Neurology Department of Clinical NeurosciencesLausanne University Hospital(CHUV)and University of Lausanne(UNIL)LausanneSwitzerland Department of sport science University of InnsbruckInnsbruckAustria

Challenges in the diagnosis and treatment of Parkinson’s disease:Parkinson’s disease(PD)is an increasingly prevalent neurodegenerative disease,at first sight primarily characterized by motor symptoms,although non-motor symptoms also constitute a major part of the overall ***,this disease cannot be diagnosed reliably until a large part of the vulnerable dopaminergic neurons has been irretrievably lost,and the disease progresses *** biological criteria for PD have been proposed recently and might eventually improve early diagnosis,but they require further validation,and their use will initially be restricted to a research environment(Darweesh et al.,2024).

关键词： diagnosis Clinical eventually

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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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Unraveling brain aging through the lens of oral microbiota

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Neural Regeneration Research 2025年第7期20卷 1930-1943页

作者： Qinchao Hu Si Wang Weiqi Zhang Jing Qu Guang-Hui Liu State Key Laboratory of Membrane biology Institute of ZoologyChinese Academy of SciencesBeijingChina Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhouGuangdong ProvinceChina Advanced Innovation center for Human Brain Protection and National Clinical Research center for Geriatric Disorders Xuanwu HospitalCapital Medical UniversityBeijingChina Aging Translational Medicine center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijingChina CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina University of Chinese Academy of sciences BeijingChina institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijingChina Aging Biomarker Consortium BeijingChina State Key Laboratory of Stem Cell and Reproductive biology Institute of ZoologyChinese Academy of SciencesBeijingChina Beijing institute for Stem Cell and Regenerative Medicine BeijingChina

The oral cavity is a complex physiological community encompassing a wide range of *** of oral microbiota can lead to various oral infectious diseases,such as periodontitis and tooth decay,and even affect systemic health,including brain aging and neurodegenerative *** studies have highlighted how oral microbes might be involved in brain aging and neurodegeneration,indicating potential avenues for intervention *** this review,we summarize clinical evidence demonstrating a link between oral microbes/oral infectious diseases and brain aging/neurodegenerative diseases,and dissect potential mechanisms by which oral microbes contribute to brain aging and *** also highlight advances in therapeutic development grounded in the realm of oral microbes,with the goal of advancing brain health and promoting healthy aging.

关键词： Alzheimer's disease brain aging multiple sclerosis neurodegeneration neurodegenerative diseases oral microbiota Parkinson's disease periodontitis bacteria Porphyromonas gingivalis

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A cellulose-based lithium-ion battery separator with regulated ionic transport and high thermal stability for extreme environments

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Nano Research 2025年第1期18卷 315-322页

作者： Kun-Peng Yang Song Xie Zi-Meng Han Hao-Cheng Liu Chong-Han Yin Wen-Bin Sun Zhang-Chi Ling Huai-Bin Yang De-Han Li Qing-Fang Guan Shu-Hong Yu Department of Chemistry New Cornerstone Science LaboratoryInstitute of Biomimetic Materials&ChemistryAnhui Engineering Laboratory of Biomimetic MaterialsDivision of Nanomaterials&ChemistryHefei National Research Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefei 230026China institute of Innovative Materials Department of Materials Science and EngineeringDepartment of ChemistrySouthern University of Science and TechnologyShenzhen 518055China

Separators play a critical role in lithium-ion ***,the restrictions of thermal stability and inferior electrical performance in commercial polyolefin separators significantly limit their applications under harsh ***,we report a cellulose-assisted self-assembly strategy to construct a cellulose-based separator massively and *** an ultrahigh ionic conductivity in electrolytes of 3.7 mS·cm^(-1) and the ability to regulate ion transport,the obtained separator is a promising alternative for high-performance lithium-ion *** addition,integrated with high thermal stability,the cellulose-based separator endows batteries with high safety at high temperatures,greatly expanding the application scenarios of energy storage devices in extreme environments.

关键词： lithium-ion batteries bio-inspired materials battery separators cellulose nanofiber ultrahigh ionic conductivity high safety

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Passive activity enhances residual control ability in patients with complete spinal cord injury

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Neural Regeneration Research 2025年第8期20卷 2337-2347页

作者： Yanqing Xiao Mingming Gao Zejia He Jia Zheng Hongming Bai Jia-Sheng Rao Guiyun Song Wei Song Xiaoguang Li Beijing Key Laboratory for Biomaterials and Neural Regeneration Beijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina Department of Rehabilitation Evaluation China Rehabilitation Research CenterBeijingChina Cardiac center Beijing Children’s HospitalCapital Medical UniversityBeijingChina The State Key Laboratory of Virtual Reality Technology and Systems Beihang UniversityBeijingChina Department of Rehabilitation Engineering China Rehabilitation Science InstituteBeijingChina

Patients with complete spinal cord injury retain the potential for volitional muscle activity in muscles located below the spinal injury ***,because of prolonged inactivity,initial attempts to activate these muscles may not effectively engage any of the remaining neurons in the descending pathway.A previous study unexpectedly found that a brief clinical round of passive activity significantly increased volitional muscle activation,as measured by surface *** this study,we further explored the effect of passive activity on surface electromyographic signals during volitional control tasks among individuals with complete spinal cord *** patients with chronic complete thoracic spinal cord injury were *** electromyography data from eight major leg muscles were acquired and compared before and after the passive activity *** results indicated that the passive activity led to an increased number of activated volitional muscles and an increased frequency of *** the cumulative root mean square of surface electromyography amplitude for volitional control of movement showed a slight increase after passive activity,the difference was not statistically *** findings suggest that brief passive activity may enhance the ability to initiate volitional muscle activity during surface electromyography tasks and underscore the potential of passive activity for improving residual motor control among patients with motor complete spinal cord injury.

关键词： complete spinal cord injury cycle training epidural electrical stimulation motor training passive activity physiological state spinal cord circuit surface electromyography volitional control task

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