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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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Investigating the Head Impact Force-Induced Evolution of Hyperphosphorylated Tau Proteins in Brain Tissue Through Mechanical Mesoscale Finite Element Simulation

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Acta Mechanica Solida Sinica 2022年第4期35卷 705-715页

作者： Ge He lei.fan Shanghai Key Laboratory of Mechanics in Energy Enginering Shanghai Institute of Applied Mathematics and MechanicsSchool of Mechanics and Engineering ScienceShanghai UniversityShanghai 200444China Department of Mechanical Engineering Michigan State UniversityEast LansingMI 48824USA

For human heads that experienced repetitive subconcussive impacts,abnormal accumulation of hyperphosphorylated tau(p-tau)proteins was found in the postmortem brain *** numerically understand the cause–effect relationship between the external force and the microscopic volume change of the p-tau protein,we created a mesoscale finite element model of the multilayer brain tissue containing microscopic voids representing the p-tau *** model was applied under the loading boundary conditions obtained from a larger length scale simulation.A formerly developed internal state variable elastoplasticity model was implemented to describe the constitutive behaviors of gray and white matters,while the cerebrospinal fluid was assumed to be purely *** effects of the initial sizes and distances of p-tau proteins located at four different brain regions(frontal,parietal,temporal and occipital lobes)on their volumetric evolutions were *** is concluded that both the initial sizes and distances of the proteins have more or less(depending on the specific brain region)influential effects on the growth or contraction rate of the p-tau *** p-tau proteins located within the brain tissue at the frontal and occipital lobes are more heavily affected by the frontal impact load compared with those at the parietal and temporal *** summary,the modeling approach presented in this paper provides a strategy for mechanically studying the evolution of p-tau proteins in the brain tissue and gives insight into understanding the correlation between macroscopic force and microstructure change of the brain tissue.

关键词： Traumatic head injury Hyperphosphorylated tau(p-tau)protein Internal state variable Brain tissue

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JWST Observations Constrain the Time Evolution of Fine Structure Constants and Dark Energy-electromagnetic Coupling

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Research in Astronomy and Astrophysics 2024年第12期24卷 118-126页

作者： Ze-fan Wang lei lei lei Feng Yi-Zhong fan Key Laboratory of Dark Matter and Space Astronomy Purple Mountain Observatory Chinese Academy of Sciences School of Astronomy and Space Science University of Science and Technology of China

It was hypothesized in the literature that some physical parameters may be time-evolving and the astrophysical data can serve as a ***,the James Webb Space Telescope (JWST) released its early *** this work,we select the JWST spectroscopic observations of the high redshift (z>7.1) galaxies with strong[O III](λ=4959?and 5007?in the rest frame) emission lines to constraint the evolution of the fine structure constant(α).With the spectra from two galaxies at redshifts of 7.19 and 8.47,the deviation of α from its fiducial value is found to be as small as ■respectively (the first error is statistical and the latter is systematic).The combination of our results with the previous data reveals that ■Clearly,there is no evidence for a cosmic evolution of α.The prospect of further constraining the time evolution of α is also *** scalar field of dark energy is hypothesized to drive the acceleration of the universe’s expansion through an interaction with the electromagnetic *** integrating the observational data of the fine-structure constant variation,■,we have established a stringent upper limit on the coupling strength between dark energy and *** analysis yields ■at the 95%confidence level,representing the most stringent bound to date.

关键词： (cosmology:) dark energy cosmology: observations galaxies: high-redshift

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黄土边坡微生物矿化加固及植被恢复试验

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水土保持研究 2025年第1期32卷 227-234+242页

作者：雷磊王良樊成虎刘子瑞宋洋薛倩楠田堪良段金贵国网陕西省电力有限公司电力科学研究院国网(西安)环保技术中心有限公司国网陕西省电力有限公司国网陕西省电力有限公司安康水力发电公司国网陕西省电力有限公司西安供电公司西北农林科技大学水土保持研究所中国科学院水利部水土保持研究所黄河水利委员会西峰水土保持科学试验站

[目的]研究黄土边坡微生物矿化加固及植被恢复，为黄土边坡的加固及坡面土壤侵蚀防治提供新方法和新技术。[方法]采用微生物诱导碳酸钙沉淀(Microbially Induced Calcite Precipitation, MICP)技术对黄土边坡进行矿化加固处理，并在固... 详细信息

[目的]研究黄土边坡微生物矿化加固及植被恢复，为黄土边坡的加固及坡面土壤侵蚀防治提供新方法和新技术。[方法]采用微生物诱导碳酸钙沉淀(Microbially Induced Calcite Precipitation, MICP)技术对黄土边坡进行矿化加固处理，并在固化黄土边坡上进行植被恢复，利用扫描电子显微镜(SEM)和光学显微镜，从微观角度探究MICP技术对黄土边坡矿化加固的作用机制，并统计分析了固化黄土边坡的植被恢复效果。[结果]采用MICP技术对黄土边坡进行固化处理后，在坡面上生成的固化层将松散且相邻的土壤颗粒胶结在一起，使黄土坡面形成一个整体，固化层最大厚度为0.23 cm,平均厚度为0.21 cm;固化黄土边坡恢复植被后第60天，A1,A2,B1,B2,A1B1,A2B2各区域内植被成活率比A0,B0,A0B0各区域分别显著提高26.66%,20%,37.5%,25%,33.33%,25%(p<0.05),第60天后，各区域内植被的成活率均差异显著，而且固化后加保水剂的A1,B1,A1B1各区域内植被的成活率最高；固化后加保水剂的B1和A1B1区域内紫穗槐高度和地径的生长变化量最大，且固化后加保水剂的A1,B1,A1B1各区域内麦冬草和紫穗槐的生长状况最好。[结论]采用MIC技术可以有效固化黄土坡面，与植被恢复技术相结合，既能防治土壤侵蚀，又能恢复生态环境。这种综合防治措施为黄土边坡水土流失防治与生态修复提供了良好的技术支持。

关键词：黄土边坡微生物矿化加固技术植被恢复边坡防护

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Bounded Tiles in ■_p are Compact Open Sets

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Acta Mathematica Sinica,English Series 2020年第2期36卷 189-195页

作者： Ai Hua fan Shi lei.fan LA MFA UMR 7352 CNRSUniversity of Picardie33 rue Saint Leu80039 AmiensFrance School of Mathematics and Statistics&Hubei Key Laboratory of Mathematical Sciences Central China Normal UniversityWuhan430079P.R.China

Any bounded tile of the field Qp of p-adic numbers is a compact open set up to a set of zero Haar *** this note,we present two simple and direct proofs of this fact.

关键词： p-adic field tile bounded compact open

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Antibacterial hydrogel with pH-responsive microcarriers of slow-release VEGF for bacterial infected wounds repair

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Journal of Materials Science & Technology 2023年第13期144卷 198-212页

作者： Xiaofei Xie Huan lei Daidi fan Shaanxi Key Laboratory of Degradable Biomedical Materials School of Chemical EngineeringNorthwest UniversityXi’an 710069China Shaanxi R&D Center of Biomaterials and Fermentation Engineering School of Chemical EngineeringNorthwest UniversityXi’an 710069China Biotech.&Biomed.Research Institute Northwest UniversityXi’an 710069China

Bacterial infection causes wound inflammation and makes angiogenesis *** is urgent to develop effectively antibacterial and pro-vascularizing dressings for wound *** hydrogel is developed with pH-responsive drug-releasing microcarriers which were loaded with vascular endothelial growth factor(VEGF)that promotes angiogenesis and actively respond to wound pH for control and prolong VEGF *** surfaces of the microcarriers were coated with polydopamine which can reduce the silver nanoparticles(AgNPs)in situ,and dynamically crosslink with the polyacrylamide,which forms a stable slow-release system with different release behavior for the VEGF and *** hydrogel inhib-ited bacterial formation and accelerated wound *** the hydrogel dressing,83.3%±4.29%of the wound heals at day 7,which is 40.9%±8.5%higher than the non-treatment group in defect infected *** antibacterial properties of hydrogel down-regulate early inflammation-related cytokines,and the release of VEGF in the middle and late phases of wound healing in response to pH changes pro-motes angiogenesis and up-regulate the expression of angiogenesis-associated *** sequential release of antibacterial agents and pro-vascularizing agents in response to the change in wound microen-vironmental cues facilitate temporally controlled therapy that suites the need of different wound healing ***,the hydrogel loaded with multifunctional microcarriers that enable controlled release of AgNPs and VEGF is an effective system for treating infected wounds.

关键词： Antibacterial pH-responsive microcarriers Slow-release Infected wound repair

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A Rapid and Automatic Optimal Design Method for Six-Stage Axial-Flow Industry Compressor

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Journal of Thermal Science 2021年第5期30卷 1658-1673页

作者： lei.fan JU Yaping ZHANG Chuhua School of Energy and Power Engineering Xi’an Jiaotong UniversityXi’an710049China

Existing aerodynamic design systems for multi-stage axial-flow compressor suffer from several limitations,such as experience dependent models and time costly *** attempts,however,have been devoted to the rapid and automatic optimization of aerodynamic performance at the preliminary design phase,which plays a crucial role in the final aerodynamic *** this work,a rapid and automatic aerodynamic optimal design method is developed for the multi-stage axial-flow compressor based on one-dimensional meanline design method,radial-equilibrium equation and genetic *** one-dimensional performance prediction model includes some popular empirical correlations to calculate the flow loss,incidence angle,deviation angle and flow *** radial-equilibrium equation is solved to obtain the spanwise distribution of aerodynamic and thermodynamic parameters at the inlet and outlet of each blade *** genetic algorithm is used for an automatic search of the global optimal compressor configuration aiming at maximizing the design *** developed method is illustrated with the aerodynamic optimal design of a 6-stage axial-flow industry compressor and verified by computational fluid dynamics *** results show that the developed method is capable of improving effectively the design efficiency and predicting accurately the aerodynamic performance of the 6-stage axial-flow industry compressor in a few *** work is of scientific significance to improve the axial-flow compressor design system and of engineering importance to release the designers from the heavy experience dependence especially at the preliminary design phase.

关键词： one-dimensional meanline design two-dimensional throughflow design three-dimensional CFD simulation optimal design genetic algorithm multi-stage axial-flow compressor

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Three‑Dimensional Numerical Study on the Metal Rotating Spray Transfer Process of High‑Current GMAW

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Chinese Journal of Mechanical Engineering 2022年第6期35卷 234-246页

作者： lei Xiao Ding fan Jiankang Huang School of Materials Science and Engineering Lanzhou Jiaotong UniversityLanzhou 730070China State Key Laboratory of Advanced Processing and Recycling of Non‑ferrous Metals Lanzhou University of TechnologyLanzhou 730050China School of Materials Science and Engineering Lanzhou University of TechnologyLanzhou 730050China

A three-dimensional numerical model based on the volume-of-fluid(VOF)method is typically preferred for studying high-current gas metal arc welding(GMAW)metal transfer mechanism and then controlling *** is informed that the rotating spray transfer is extremely complicated,and some researchers have focused on simplified models without considering the energy conservation to make analysis manageable for the unstable metal transfer *** our created numerical model,the metal transfer of high-current GMAW with shielding gas of different conductivities has been studied by analyzing acting forces and fluid flows in the metal liquid column,especially for the contributions of the self-induced electromagnetic force,equivalent volume force of the capillary pressure of the surface tension(Named surface tension force in this work),static arc *** is found that the unbalanced electromagnetic force greatly promotes the metal rotating motion in 500 A metal inert gas(MIG)welding with pure argon shielding gas and it pushes the metal liquid column to *** the arc constricting effect in active shielding gas by simply changing the arc conductivity,it is found that the metal liquid column no longer rotates,it turns to swing since the unbalanced electromagnetic force is large enough to break the rotating *** calculated results of the metal liquid column deflected angle and rotating/swing frequency agree well with the experiment of high-speed camera observations.

关键词： Gas metal arc welding Rotating spray transfer Three-dimensional model Electromagnetic force Surface tension

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Multi-factor high-order intuitionistic fuzzy timeseries forecasting model

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Journal of Systems Engineering and Electronics 2016年第5期27卷 1054-1062页

作者： Ya'nan Wang Yingjie lei Yang lei Xiaoshi fan Air and Missile Defense College Air Force Engineering UniversityXi'an 710051China Department of Electronics Technology Engineering University of Armed Police ForceXi'an 710051China

Fuzzy sets theory cannot describe the neutrality degreeof data, which has largely limited the objectivity of fuzzy time seriesin uncertain data forecasting. With this regard, a multi-factor highorderintuitionistic fuzzy time series forecasting model is built. Inthe new model, a fuzzy clustering algorithm is used to get unequalintervals, and a more objective technique for ascertaining membershipand non-membership functions of the intuitionistic fuzzy setis proposed. On these bases, forecast rules based on multidimensionalintuitionistic fuzzy modus ponens inference are ***, contrast experiments on the daily mean temperature ofBeijing are carried out, which show that the novel model has aclear advantage of improving the forecast accuracy.

关键词： multi-factor high-order intuitionistic fuzzy time series,forecasting model intuitionistic fuzzy inference.

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The nanohertz stochastic gravitational wave background from cosmic string loops and the abundant high redshift massive galaxies

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Science China(Physics,Mechanics & Astronomy) 2023年第12期66卷 11-19页

作者： Ziwei Wang lei lei Hao Jiao lei Feng Yi-Zhong fan Key Laboratory of Dark Matter and Space Astronomy Purple Mountain ObservatoryChinese Academy of SciencesNanjing 210023China School of Astronomy and Space Science University of Science and Technology of ChinaHefei 230026China Department of Physics McGill UniversityMontreal H3A 2T8Canada

Recently,pulsar timing array(PTA)experiments have provided compelling evidence for the existence of the nanohertz stochastic gravitational wave background(SGWB).In this work,we demonstrated that cosmic string loops generated from cosmic global strings offer a viable explanation for the observed nanohertz SGWB data,requiring a cosmic string tension parameter of log(Gμ)~-12 and a loop number density of log N~***,we revisited the impact of cosmic string loops on the abundance of massive galaxies at high ***,our analysis revealed challenges in identifying a consistent parameter space that can concurrently explain both the SGWB data and observations from the James Webb Space *** indicates the necessity for either extending the existing model employed in this research or acknowledging distinct physical origins for these two phenomena.

关键词： nanohertz stochastic gravitational-wave background cosmic string loop JamesWebb Space Telescope galaxy formation

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