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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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Lipid droplets in the nervous system:involvement in cell metabolic homeostasis

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Neural Regeneration Research 2025年第3期20卷 740-750页

作者： Yuchen Zhang Yiqing Chen Cheng Zhuang Jingxuan Qi Robert Chunhua Zhao Jiao Wang school of Life sciences Shanghai UniversityShanghaiChina school of Medicine Shanghai UniversityShanghaiChina Institute of Basic Medical sciences Chinese Academy of Medical sciences School of Basic MedicinePeking Union Medical CollegeBeijingChina Center of Excellence in Tissue Engineering Chinese Academy of Medical SciencesBeijingChina Beijing key laboratory of New Drug Development and Clinical Trial of Stem Cell Therapy BeijingChina

Lipid droplets serve as primary storage organelles for neutral lipids in neurons,glial cells,and other cells in the nervous *** droplet formation begins with the synthesis of neutral lipids in the endoplasmic ***,lipid droplets were recognized for their role in maintaining lipid metabolism and energy homeostasis;however,recent research has shown that lipid droplets are highly adaptive organelles with diverse functions in the nervous *** addition to their role in regulating cell metabolism,lipid droplets play a protective role in various cellular stress ***,lipid droplets exhibit specific functions in neurons and glial *** of lipid droplet formation leads to cellular dysfunction,metabolic abnormalities,and nervous system *** review aims to provide an overview of the role of lipid droplets in the nervous system,covering topics such as biogenesis,cellular specificity,and ***,it will explore the association between lipid droplets and neurodegenerative *** the involvement of lipid droplets in cell metabolic homeostasis related to the nervous system is crucial to determine the underlying causes and in exploring potential therapeutic approaches for these diseases.

关键词： Alzheimer's disease lipid droplet biogenesis lipid droplets lipid metabolism nervous system neurodegenerative disorders oxidative stress Parkinson's disease

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Potential role of tanycyte-derived neurogenesis in Alzheimer's disease

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Neural Regeneration Research 2025年第6期20卷 1599-1612页

作者： Guibo Qi Han Tang Jianian Hu Siying Kang Song Qin Department of Anatomy Histologyand EmbryologySchool of Basic Medical SciencesFudan UniversityShanghaiChina State key laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Fudan UniversityShanghaiChina

Tanycytes, specialized ependymal cells located in the hypothalamus, play a crucial role in the generation of new neurons that contribute to the neural circuits responsible for regulating the systemic energy balance. The precise coordination of the gene networks controlling neurogenesis in naive and mature tanycytes is essential for maintaining homeostasis in adulthood. However, our understanding of the molecular mechanisms and signaling pathways that govern the proliferation and differentiation of tanycytes into neurons remains limited. This article aims to review the recent advancements in research into the mechanisms and functions of tanycyte-derived neurogenesis. Studies employing lineage-tracing techniques have revealed that the neurogenesis specifically originating from tanycytes in the hypothalamus has a compensatory role in neuronal loss and helps maintain energy homeostasis during metabolic diseases. Intriguingly,metabolic disorders are considered early biomarkers of Alzheimer's disease. Furthermore,the neurogenic potential of tanycytes and the state of newborn neurons derived from tanycytes heavily depend on the maintenance of mild microenvironments, which may be disrupted in Alzheimer's disease due to the impaired blood–brain barrier ***, the specific alterations and regulatory mechanisms governing tanycyte-derived neurogenesis in Alzheimer's disease remain unclear. Accumulating evidence suggests that tanycyte-derived neurogenesis might be impaired in Alzheimer's disease, exacerbating neurodegeneration. Confirming this hypothesis, however, poses a challenge because of the lack of long-term tracing and nucleus-specific analyses of newborn neurons in the hypothalamus of patients with Alzheimer's disease. Further research into the molecular mechanisms underlying tanycyte-derived neurogenesis holds promise for identifying small molecules capable of restoring tanycyte proliferation in neurodegenerative diseases. This line of investigation could pro

关键词： Alzheimer's disease blood–brain barrier ependymoglial cells hypothalamus metabolic diseases neural stem cells neurogenesis neuroinflammatory diseases neurons tanycyte

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The detection, extraction and parameter estimation of extreme-mass-ratio inspirals with deep learning

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 86-96页

作者： Qianyun Yun Wen-Biao Han Yi-Yang Guo He Wang Minghui Du Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences shanghai Astronomical Observatory Chinese Academy of Sciences school of Physics and Astronomy Shanghai Jiao Tong University school of Astronomy and Space Science University of Chinese Academy of Sciences Taiji laboratory for Gravitational Wave Universe (Beijing/Hangzhou) University of Chinese Academy of Sciences Lanzhou Center for Theoretical Physics Key Laboratory of Theoretical Physics of Gansu Province Key Laboratory of Quantum Theory and Applications of MoE Lanzhou University Institute of Theoretical Physics & Research Center of Gravitation Lanzhou University International Centre for Theoretical Physics Asia-Pacific (ICTP-AP) University of Chinese Academy of Sciences (UCAS) Center for Gravitational Wave Experiment National Microgravity Laboratory Institute of Mechanics Chinese Academy of Sciences

One of the primary goals of space-borne gravitational wave detectors is to detect and analyze extreme-mass-ratio inspirals(EMRIs). This task is particularly challenging because EMRI signals are complex, lengthy, and faint. In this work, we introduce a2-layer convolutional neural network(CNN) approach to detect EMRI signals for space-borne detectors, achieving a true positive rate(TPR) of 96.9% at a 1% false positive rate(FPR) for signal-to-noise ratio(SNR) from 50 to 100. Especially, the key intrinsic parameters of EMRIs such as the mass, spin of the supermassive black hole(SMBH) and the initial eccentricity of the orbit can also be inferred directly by employing a neural network. The mass and spin of the SMBH can be determined at 99% and 92% respectively. This will greatly reduce the parameter spaces and computing cost for the following Bayesian parameter *** model also has a low dependency on the accuracy of the waveform model. This study underscores the potential of deep learning methods in EMRI data analysis, enabling the rapid detection of EMRI signals and efficient parameter estimation.

关键词： gravitational wave EMRIs deep-learing

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Graphene Aerogel Composites with Self‑Organized Nanowires‑Packed Honeycomb Structure for Highly Efficient Electromagnetic Wave Absorption

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Nano-Micro Letters 2025年第2期17卷 533-547页

作者： Xiao You Huiying Ouyang Ruixiang Deng Qiuqi Zhang Zhenzhong Xing Xiaowu Chen Qingliang Shan Jinshan Yang Shaoming Dong State key laboratory of High Performance Ceramics and Superfine Microstructure Shanghai Institute of CeramicsChinese Academy of SciencesShanghai 200050People’s Republic of China key laboratory of Inorganic Coating Materials CAS Shanghai Institute of CeramicsChinese Academy of SciencesShanghai 200050People’s Republic of China Structural Ceramics and Composites Engineering Research Center Shanghai Institute of CeramicsChinese Academy of SciencesShanghai 200050People’s Republic of China Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBeijing 100049People’s Republic of China school of Physical Science and Technology ShanghaiTech UniversityShanghai 201210People’s Republic of China school of Materials Science and Engineering Zhejiang Sci-Tech UniversityHangzhou 310018People’s Republic of China University of Chinese Academy of sciences Beijing 100039People’s Republic of China

With vigorous developments in nanotechnology,the elaborate regulation of microstructure shows attractive potential in the design of electromagnetic wave ***,a hierarchical porous structure and composite heterogeneous interface are constructed successfully to optimize the electromagnetic loss *** macro–micro-synergistic graphene aerogel formed by the ice template‑assisted 3D printing strategy is cut by silicon carbide nanowires(SiC_(nws))grown in situ,while boron nitride(BN)interfacial structure is introduced on graphene *** unique composite structure forces multiple scattering of incident EMWs,ensuring the combined effects of interfacial polarization,conduction networks,and magnetic-dielectric ***,the as-prepared composites present a minimum reflection loss value of−37.8 dB and a wide effective absorption bandwidth(EAB)of 9.2 GHz(from 8.8 to 18.0 GHz)at 2.5 ***,relying on the intrinsic high-temperature resistance of SiC_(nws) and BN,the EAB also remains above 5.0 GHz after annealing in air environment at 600℃ for 10 h.

关键词： Hierarchical porous structure Interface High-temperature resistance Graphene aerogel composites Electromagnetic wave absorption

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Equivariant eta forms and equivariant differential K-theory

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Science China Mathematics 2021年第10期64卷 2159-2206页

作者： Bo Liu school of mathematical sciences Shanghai Key Laboratory of PMMPEast China Normal UniversityShanghai 200241China

In this paper,we propose a new numerical scheme for the coupled Stokes-Darcy model with the Beavers-Joseph-Saffman interface *** use the weak Galerkin method to discretize the Stokes equation and the mixed finite element method to discretize the Darcy equation.A discrete inf-sup condition is proved and the optimal error estimates are also *** experiments validate the theoretical analysis.

关键词： equivariant eta form equivariant differential K-theory equivariant spectral section equivariant higher spectral flow orbifold

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SOME RESULTS ON HEEGAARD SPLITTING

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Acta Mathematica Scientia 2022年第6期42卷 2437-2449页

作者： Ruifeng QIU Yanqing ZOU school of mathematical sciences&shanghai key laboratory of pmmp East China Normal University Shanghai 200241China

A Heegaard splitting is a type of combinatorial structure on an orientable compact *** will give a survey on Heegaard spliting and its applications,including those pertaining to the classification and stabilization pr... 详细信息

关键词： stabilization Heegaard genus Heegaard distance

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Approximate Controllability of Second-order Semilinear Evolution Systems with Finite Delay

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Acta Mathematicae Applicatae Sinica 2021年第3期37卷 573-589页

作者： Xiao-feng SU Xian-long FU school of mathematical sciences Fudan UniversityShanghai 200433China school of mathematical sciences Shanghai Key Laboratory of PMMPEast China Normal UniversityShanghai200241China

In this work,we study the approximate controllability for a class of semilinear second-order control systems with finite *** conditions for approximate controllability are established by constructing fundamental solutions and using the resolvent condition and techniques on cosine family of linear *** illustrate the applications of the obtained results,an example is provided in the end.

关键词： approximate controllability second-order evolution equation fundamental solution cosine operator

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A MULTIPLE q-EXPONENTIAL DIFFERENTIAL OPERATIONAL IDENTITY

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Acta Mathematica Scientia 2023年第6期43卷 2449-2470页

作者：刘治国 school of mathematical sciences Key Laboratory of MEA(Ministry of Education)&Shanghai Key Laboratory of PMMPEast China Normal UniversityShanghai 200241China

Using Hartogs’fundamental theorem for analytic functions in several complex variables and q-partial differential equations,we establish a multiple q-exponential differential formula for analytic functions in several *** this identity,we give new proofs of a variety of important classical formulas including Bailey’s 6ψ6 series summation formula and the Atakishiyev integral.A new transformation formula for a double q-series with several interesting special cases is given.A new transformation formula for a 3ψ3 series is proved.

关键词： q-hypergeometric series q-exponential differential operator Bailey's 6b6 summation double q-hypergeometric series q-partial differential equation

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