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

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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

Dissecting the cell microenvironment of ovarian endometrioma through single-cell RNA sequencing

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Science China life Sciences 2025年第1期68卷 116-129页

作者： Jiangpeng Wu Siyu Xia Wenting Ye Yan Sun jing Cai Fubing Yu Haiping Wen Xiuwei Yi Taikang li Mingwei Chen Jiayun Chen Ge Song Chuanbin Yang Yali Song Jigang Wang Department of Reproductive Medicine Dongguan Maternal and Child Health Care Hospital Department of Urology and Shenzhen Clinical Research Centre for GeriatricsShenzhen People's HospitalSouthern University of Science and Technology State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical Sciences Reproductive Medicine Center Foshan Women and Children Hospital State Key Laboratory of Antiviral Drugs School of PharmacyHenan University

Ovarian endometrioma（OE）, also known as “chocolate cysts,” is a cystic mass that develops in the ovaries due to endometriosis and is a common gynecological condition characterized by the growth of endometrial tissue outside the uterus, leading to symptoms such as dysmenorrhea, pelvic pain, and infertility. However, the precise molecular and cellular mechanisms driving this pathophysiology remain largely unknown, posing challenges for diagnosis and treatment. Here, we employed integrated single-cell transcriptomic profiling of over 52,000 individual cells from endometrial tissues of OE patients and healthy donors and identified twelve major cell populations. We identified notable alterations in cell type-specific proportions and molecular signatures associated with OE. Notably, the activation of IGFBP5+macrophages with pro-inflammatory properties, NK cell exhaustion, and aberrant proliferation of IQCG+and KLF2+epithelium are key features and may be the potential mechanisms underlying the pathogenesis of OE. Collectively, our data contribute to a better understanding of OE at the single cell level and may pave the way for the development of novel therapeutic strategies.

关键词： ovary high-throughput sequencing transcriptomics gene expression analysis ligand-receptor analysis

Interpretable Machine Learning Method for Compressive Strength Prediction and Analysis of Pure Fly Ash-based Geopolymer Concrete

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Journal of Wuhan University of Technology(Materials Science) 2025年第1期40卷 65-78页

作者： SHI Yuqiong li jingyi ZHANG Yang li li Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education Northwest A&F Uni-versityYangling 712100China College of Water Resources and Architectural Engineering Northwest A&F UniversityYangling 712100China Chongqing Key Laboratory of Public Big Data Security Technology Chongqing 401420China Chongqing College of Mobile Communication Chongqing 401520China Department of Civil and Environmental Engineering The Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina National Rail Transit Electrification and Automation Engineering Technology Research Center(Hong Kong Branch) The Hong Kong Polytechnic UniversityKowloonHung HomHong KongChina

In order to study the characteristics of pure fly ash-based geopolymer concrete(PFGC)conveniently,we used a machine learning method that can quantify the perception of characteristics to predict its compressive *** this study,505 groups of data were collected,and a new database of compressive strength of PFGC was *** order to establish an accurate prediction model of compressive strength,five different types of machine learning networks were used for comparative *** five machine learning models all showed good compressive strength prediction performance on *** them,R2,MSE,RMSE and MAE of decision tree model(DT)are 0.99,1.58,1.25,and 0.25,*** R2,MSE,RMSE and MAE of random forest model(RF)are 0.97,5.17,2.27 and 1.38,*** two models have high prediction accuracy and outstanding generalization *** order to enhance the interpretability of model decision-making,we used importance ranking to obtain the perception of machine learning model to 13 *** 13 variables include chemical composition of fly ash(SiO_(2)/Al_(2)O_(3),Si/Al),the ratio of alkaline liquid to the binder,curing temperature,curing durations inside oven,fly ash dosage,fine aggregate dosage,coarse aggregate dosage,extra water dosage and sodium hydroxide *** temperature,specimen ages and curing durations inside oven have the greatest influence on the prediction results,indicating that curing conditions have more prominent influence on the compressive strength of PFGC than ordinary Portland cement *** importance of curing conditions of PFGC even exceeds that of the concrete mix proportion,due to the low reactivity of pure fly ash.

关键词： machine learning pure fly ash geopolymer compressive strength feature perception

Prevalence and evolution of drug resistance HIV-1 variants in Henan, China

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Cell Research 2005年第Z1期 843-849页

作者： jing yun li1,, Han Ping li1, lin li1, Hong li2, Zhe WANG2, Kun YANG1, Zuo Yi BAO1, Dao Min ZHUANG1, Si Yang liU1, Yong Jian liU1, Hui XING3, Yi Ming SHAO3 1AIDS Research Department, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing 100071, China 2Center of Disease Prevention and Control, Henan Province,China 3National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China

To understand the prevalence and evolution of drug resistant HIV strains in Henan China after the implementation of free antiretroviral therapy for AIDS patients. 45 drug nave AIDS patients, 118 AIDS patients who received three months antiretroviral therapy and 124 AIDS patients who received six months antiretroviral treatment were recruited in the southern part of Henan province. Information on general condition, antiretroviral medicines, adherence and clinical syndromes were collected by face to face interview. Meanwhile, 14ml EDTA anticoagulant blood was drawn. CD4/CD8 T cell count, viral load and genotypic drug resistance were tested. The rates of clinical improvement were 55.1% and 50.8% respectively three months and six months after antiretroviral therapy. The mean CD4 cell count after antiretroviral therapy was significantly higher than in drug nave patients. The prevalence rate of drug resistant HIV strains were 13. 9%, 45.4% and 62.7% in drug nave patients, three month treatment patients and six month treatment patients, respectively. The number of resistance mutation codons and the frequency of mutations increased significantly with continued antiretroviral therapy. The mutation sites were primarily at the 103, 106 and 215 codons in the three-month treatment group and they increased to 15 codon mutations in the six-month treatment group. From this result, the evolution of drug resistant strains was inferred to begin with the high level NNRTI resistant strain, and then develop low level resistant strains to NRTIs. The HIV strains with high level resistance to NVP and low level resistance to AZT and DDI were highly prevalent because of the AZT+DDI+NVP combination therapy. These HIV strains were also cross resistant to DLV, EFV, DDC and D4T. Poor adherence to therapy was believed to be the main reason for the emergence and prevalence of drug resistant HIV strains. The prevalence of drug resistant HIV strains was increased with the continu- ation of antiretrov

关键词： AIDS drug resistance adherence antiretroviral therapy.

地缘政治风险与中资企业债券融资成本——情绪传递与避险效应

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东北师大学报（哲学社会科学版） 2025年第1期 19-31页

作者：李婧李博渝首都经济贸易大学经济学院北京100070

中国作为全球系统重要性国家,外部环境变化必然冲击国内债券市场,投资者情绪起落传递金融风险.本文选取2007—2022年中国非金融上市公司发行债券数据验证地缘政治风险对企业融资成本的影响.研究发现,此类风险带来的冲击扩大企业债券信... 详细信息

中国作为全球系统重要性国家,外部环境变化必然冲击国内债券市场,投资者情绪起落传递金融风险.本文选取2007—2022年中国非金融上市公司发行债券数据验证地缘政治风险对企业融资成本的影响.研究发现,此类风险带来的冲击扩大企业债券信用利差,投资者乐观情绪与低违约避险效应缓解了冲击,国有企业债券违约强化负面信息传递,并且企业应对措施因其特性和货币金融环境不同而异,良好的经济基本面是应对地缘政治冲击最有效的平滑器.为增加企业财务韧性,建议宏观上应健全风险预警机制,完善资本市场体系,合理引导预期,同时要加强企业信息披露机制,建立信誉累积的长效机制.

关键词：地缘政治风险企业融资成本债券市场投资者情绪

维普期刊数据库博看期刊评论

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不同进展期圆锥角膜生物力学研究

国际眼科杂志 2017年第8期17卷 1540-1544页

作者：董晶张振华高晓唯胡裕坤李晓虹李文静郭云林解放军第四七四医院眼科

目的:探讨可视化角膜生物力学分析仪(Corvis ST)测量正常角膜、顿挫期圆锥角膜、亚临床期圆锥角膜、临床期圆锥角膜的生物力学变化,分析不同进展期圆锥角膜生物力学特征,为更早期地诊断圆锥角膜提供临床依据。方法:病例对照研究。选取... 详细信息

目的:探讨可视化角膜生物力学分析仪(Corvis ST)测量正常角膜、顿挫期圆锥角膜、亚临床期圆锥角膜、临床期圆锥角膜的生物力学变化,分析不同进展期圆锥角膜生物力学特征,为更早期地诊断圆锥角膜提供临床依据。方法:病例对照研究。选取顿挫期圆锥角膜15眼为顿挫组,亚临床期圆锥角膜23眼为亚临床期组,临床期圆锥角膜40眼为圆锥角膜组,欲行近视激光手术和正常角膜志愿者40眼为正常组(对照组),应用Corvis ST测定各组的生物力学参数,并进行比较分析,绘制受试者工作曲线(ROC)。结果:正常角膜与顿挫期圆锥角膜生物力学各参数差异均无统计学意义(P>0.05)。正常角膜与亚临床期组第二压平长度(AL2)、第一压平速率(AV1)、最大压陷曲率半径(HC-radius)、最大压陷深度(DA)间的差异有统计学意义(P<0.05)。正常角膜与圆锥角膜组除第二压平速度(AV2)、最大压陷时间(HC-time)、最大压陷屈膝峰间距(PD)差异无统计学意义外,其余生物力学数据差异均有统计学意义(P<0.05),ROC曲线分析DA对于圆锥角膜诊断效率最高(曲线下面积0.891±0.028)。结论:顿挫期圆锥角膜生物力学较正常角膜无改变,亚临床期圆锥角膜生物力学较正常角膜部分参数有改变,但其参数单独诊断圆锥角膜特异性和敏感性均较差。临床期圆锥角膜生物力学较正常角膜明显改变,DA诊断效率最高。

关键词：可视化角膜生物力学分析仪圆锥角膜角膜生物力学

Manufacture the conducting polymer with light

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Science China Chemistry 2025年第1期68卷 8-9页

作者： Yang li Tianyu li Yan Ji Baoguang liu College of Electronic and Optical Engineering & College of Flexible Electronics (Future Technology) Nanjing University of Posts & Telecommunications

Poly(3,4-ethylenedioxythiophene) (PEDOT), heralded as the “king” of conducting polymers, is esteemed in bioelectronics for its mixed electronic and ionic conductivity, mechanical properties compatible with biological tissues, tunable healing ability and stability in diverse environments [1]. Based on additive manufacturing of three-dimensional structures,PEDOT realizes the implementation in the efficient production of flexible bioelectronics, the construction of intricate electrode-neural implantations, and the development of smart brain-computer-interfaces [2].

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Increase in the variability of terrestrial carbon uptake in response to enhanced future ENSO modulation

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 32-38页

作者： Younong li li Dan jing Peng Qidong Yang Fuqiang Yang Key Laboratory of Regional Climate-Environment for Temperate East Asia Institute of Atmospheric PhysicsChinese Academy of SciencesBeijingChina Key Laboratory of Atmospheric Environment and Processes in the Boundary Layer over the Low-Latitude Plateau Region Department of Atmospheric ScienceYunnan UniversityKunmingChina

El Niño-Southern Oscillation(ENSO)is a major driver of climate change in middle and low latitudes and thus strongly influences the terrestrial carbon cycle through land-air *** the ENSO modulation and carbon flux variability are projected to increase in the future,but their connection still needs further *** investigate the impact of future ENSO modulation on carbon flux variability,this study used 10 CMIP6 earth system models to analyze ENSO modulation and carbon flux variability in middle and low latitudes,and their relationship,under different scenarios simulated by CMIP6 *** results show a high consistency in the simulations,with both ENSO modulation and carbon flux variability showing an increasing trend in the *** higher the emissions scenario,especially SSP5-8.5 compared to SSP2-4.5,the greater the increase in *** flux variability in the middle and low latitudes under SSP2-4.5 increases by 30.9%compared to historical levels during 1951-2000,while under SSP5-8.5 it increases by 58.2%.Further analysis suggests that ENSO influences mid-and low-latitude carbon flux variability primarily through *** occurrence may potentially be attributed to the increased responsiveness of gross primary productivity towards regional temperature fluctuations,combined with the intensified influence of ENSO on land surface temperatures.

关键词： Carbon variability ENSO modulation CMIP6 models

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针灸治疗无先兆性偏头痛研究现状

中医药临床杂志 2017年第7期29卷 1119-1122页

作者：袁静邢运李应昆成都中医药大学四川成都610075 成都中医药大学附属医院四川成都610072

偏头痛（Migraine）是一种病因较为复杂的临床综合征,是一组反复发作的头痛疾病。根据临床表现偏头痛可分多个型,其中无先兆性偏头痛（Migraine without aura）是临床上最为常见的类型,约占80%,其头痛典型特征为偏侧分布、搏动性性质、... 详细信息

偏头痛（Migraine）是一种病因较为复杂的临床综合征,是一组反复发作的头痛疾病。根据临床表现偏头痛可分多个型,其中无先兆性偏头痛（Migraine without aura）是临床上最为常见的类型,约占80%,其头痛典型特征为偏侧分布、搏动性性质、中或重度程度、日常活动加重头痛,伴随恶心和（或）畏光、畏声。反复发生的头痛,每次持续4~72 h[1]。目前偏头痛的发病机制至今仍未有统一的理论解释,各国学者研究重点主要集中在神经血管假说、皮层扩散抑制假说、生化因素、遗传因素等方面[2]。

关键词：无先兆性偏头痛偏头痛针灸研究进展