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Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

Military Medical Research 2023年第4期10卷 529-553页

作者： Min Su Tao Pan qiu‑zhen chen Wei‑Wei Zhou Yi Gong Gang Xu Huan‑Yu Yan Si Li Qiao‑zhen Shi Ya Zhang Xiao He Chun‑Jie Jiang Shi‑Cai Fan Xia Li Murray J.Cairns Xi Wang Yong‑Sheng Li State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineering the First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081HeilongjiangChina Department of Immunology Nanjing Medical UniversityNanjing 211166China Department of Laboratory Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of Medicine HoustonTX 77030USA Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and Pharmacy Faculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research Program Hunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic *** the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this ***,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

关键词： Single-cell RNA-sequencing(scRNA-seq) Data analysis Biomedical research Clinical applications

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不确定经济环境下基于EVA的鲁棒供应链网络设计模型

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控制与决策 2017年第2期32卷 203-212页

作者：邱若臻陈瑞颍关志民黄小原东北大学工商管理学院沈阳110004

针对由制造商、仓库、分销中心和客户组成的四级供应链网络设计问题,考虑以产品需求、短期利率、长期利率、无风险利率、预期市场回报、证券承销费用和市场流动性等因素描述的经济环境不确定性,建立以供应链经济增加值绩效为目标,网络... 详细信息

针对由制造商、仓库、分销中心和客户组成的四级供应链网络设计问题,考虑以产品需求、短期利率、长期利率、无风险利率、预期市场回报、证券承销费用和市场流动性等因素描述的经济环境不确定性,建立以供应链经济增加值绩效为目标,网络设计、物流和财务运作为约束条件,设施选择、连接路径等为网络要素,生产、运输等物流量和负债、保理、应收账款等财务项为决策变量的多产品、多周期供应链网络鲁棒设计模型.数值结果表明,基于经济增加值的鲁棒供应链网络能够有效应对经济不确定性的影响.特别地,与传统随机优化方法相比,鲁棒优化能够确保供应链网络具有更好的鲁棒性和财务状况.

关键词：供应链经济增加值鲁棒优化经济不确定网络设计

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Brain region-specific roles of brain-derived neurotrophic factor in social stress-induced depressive-like behavior

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Neural Regeneration Research 2025年第1期20卷 159-173页

作者： Man Han Deyang Zeng Wei Tan Xingxing chen Shuyuan Bai Qiong Wu Yushan chen zhen Wei Yufei Mei Yan Zeng Brain Science and Advanced Technology Institute Wuhan University of Science and TechnologyWuhanHubei ProvinceChina Geriatric Hospital Affiliated to Wuhan University of Science and Technology WuhanHubei ProvinceChina School of Public Health Wuhan University of Science and TechnologyWuhanHubei ProvinceChina

Brain-derived neurotrophic factor is a key factor in stress adaptation and avoidance of a social stress behavioral *** studies have shown that brain-derived neurotrophic factor expression in stressed mice is brain region–specific,particularly involving the corticolimbic system,including the ventral tegmental area,nucleus accumbens,prefrontal cortex,amygdala,and *** how brain-derived neurotrophic factor participates in stress processing in different brain regions will deepen our understanding of social stress *** this review,we discuss the expression and regulation of brain-derived neurotrophic factor in stress-sensitive brain regions closely related to the pathophysiology of *** focused on associated molecular pathways and neural circuits,with special attention to the brain-derived neurotrophic factor–tropomyosin receptor kinase B signaling pathway and the ventral tegmental area–nucleus accumbens dopamine *** determined that stress-induced alterations in brain-derived neurotrophic factor levels are likely related to the nature,severity,and duration of stress,especially in the above-mentioned brain regions of the corticolimbic ***,BDNF might be a biological indicator regulating stress-related processes in various brain regions.

关键词： amygdala chronic mild stress chronic social defeat stress corticolimbic system depression hippocampus medial prefrontal cortex nucleus accumbens social stress models ventral tegmental area

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雌激素缺乏型人骨髓间充质干细胞肾虚表型的验证

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中国组织工程研究 2017年第5期21卷 669-675页

作者：魏秋实何伟陈镇秋陈达洪郭驹陈建发杨鹏广州中医药大学第一附属医院骨科广东省广州市510407 广州中医药大学国家重点学科中医骨伤科学实验室广东省广州市510405

背景:因雌激素缺乏导致绝经后骨质疏松症患者骨髓间充质干细胞增殖和成骨分化能力下降,从雌激素及其受体角度研究该病的发病机制和治疗策略具有重要意义。目的:观察雌激素缺乏型骨髓间充质干细胞的肾虚表型特点。方法:第3代骨髓间充质... 详细信息

背景:因雌激素缺乏导致绝经后骨质疏松症患者骨髓间充质干细胞增殖和成骨分化能力下降,从雌激素及其受体角度研究该病的发病机制和治疗策略具有重要意义。目的:观察雌激素缺乏型骨髓间充质干细胞的肾虚表型特点。方法:第3代骨髓间充质干细胞在成骨诱导条件下培养,用不同浓度(0,10-10,10^(-9),10^(-8),10^(-7)mol/L)芳香化酶抑制剂来曲唑干预细胞,未诱导的骨髓间充质干细胞作空白对照组。q PCR和Western Blot检测AROM mR NA和蛋白表达,MTT检测细胞增殖能力,碱性磷酸酶活性检测细胞成骨能力,ELISA检测细胞上清液中雌二醇水平,qP CR检测肾虚标志物cAMP mRNA表达。结果与结论:(1)10^(-8) mol/L来曲唑对骨髓间充质干细胞内AROM mR NA和蛋白的抑制效果最好;(2)培养72 h,10^(-8) mol/L来曲唑组细胞增殖能力最低;(3)培养第14天,10^(-8)mol/L来曲唑组细胞碱性磷酸酶活性低于其他组;(4)10^(-8) mol/L来曲唑组细胞上清液中雌二醇水平低于其他组;(5)10^(-8) mol/L组细胞cAMP mRNA表达低于其他组;(6)结果表明,10^(-8) mol/L来曲唑在成骨诱导环境中能明显抑制骨髓间充质干细胞增殖及向成骨分化,同时降低骨髓间充质干细胞内cAMP表达及合成和分泌雌二醇的能力,说明适宜浓度来曲唑作为AROM抑制剂建立的雌激素缺乏型骨髓间充质干细胞模型具有肾虚表型特征。

关键词：骨髓间质干细胞雌激素拮抗剂组织工程干细胞骨髓干细胞雌激素骨髓间充质干细胞芳香化酶肾虚表型骨代谢疾病国家自然科学基金

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Characteristic changes in astrocyte properties during astrocyte-to-neuron conversion induced by NeuroD1/Ascl1/Dlx2

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Neural Regeneration Research 2025年第6期20卷 1801-1815页

作者： Qing He zhen Wang Yuchen Wang Mengjie Zhu Zhile Liang Kanghong Zhang Yuge Xu Gong chen GHM Institute of CNS Regeneration Jinan UniversityGuangzhouGuangdong ProvinceChina

Direct in vivo conversion of astrocytes into functional new neurons induced by neural transcription factors has been recognized as a potential new therapeutic intervention for neural injury and degenerative disorders. However, a few recent studies have claimed that neural transcription factors cannot convert astrocytes into neurons, attributing the converted neurons to pre-existing neurons mis-expressing transgenes. In this study, we overexpressed three distinct neural transcription factors––NeuroD1, Ascl1, and Dlx2––in reactive astrocytes in mouse cortices subjected to stab injury, resulting in a series of significant changes in astrocyte properties. Initially, the three neural transcription factors were exclusively expressed in the nuclei of astrocytes. Over time, however, these astrocytes gradually adopted neuronal morphology, and the neural transcription factors was gradually observed in the nuclei of neuron-like cells instead of astrocytes. Furthermore,we noted that transcription factor-infected astrocytes showed a progressive decrease in the expression of astrocytic markers AQP4(astrocyte endfeet signal), CX43(gap junction signal), and S100β. Importantly, none of these changes could be attributed to transgene leakage into preexisting neurons. Therefore, our findings suggest that neural transcription factors such as NeuroD1, Ascl1, and Dlx2 can effectively convert reactive astrocytes into neurons in the adult mammalian brain.

关键词： aquaporin-4 Ascl1 astrocyte cortex Dlx2 gap junction glia-to-neuron conversion neural regeneration NeuroD1 reprogramming

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Enzymological characterization of Flla,a fibrinolytic enzyme from Agkistrodon acutus venom

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Acta Pharmacologica Sinica 2005年第12期26卷 1474-1478页

作者： Xiu-xia LIANG Ying-na ZHOU Jia-shu chen~2 Peng-xin qiu Hui-zhen chen Huan-huan SUN Yu-ping WU Guang-mei YAN Department of Pharmacology,Zhongshan Medical College,Sun Yat-Sen University,Guangzhou 510080,China DepartmentofPharmacology ZhongshanMedicalCollegeSunYat-SenUniversityGuangzhou510080China

Aim:To study the enzymological characterization of a fibrinolytic enzyme(FⅡa)from Agkistrodon acutus ***:The fibrinogenolytic effect and theinfluences of several protease inhibitors,chelating agents,and metal ions onfibrinogenolytic activity were visualized by sodium dodecyl sulfate-polyacryla-mide gel *** metal content of FⅡawas determined by atomicabsorption ***:After incubation with FⅡa(0.25 g/L),Aα-,Bβ-and γ-chains of fibrinogen disappeared within 5 min,30 min,and 8 h,*** molecular weights of major degradation products were 45 000 and 41 000,which were different from those bands produced by *** fibrinogenolyticactivity of FⅡawas strongly inhibited by ethylenediamine tetraacetic acid(EDTA),ethyleneglycol tetraacetic acid(EGTA),dithiothreitol and cysteine,but not byphenyhnethyl-sulfonyl fluoride and soybean trypsin ***(3171±25rag&g),potassium(489±17 mg/kg)and calcium(319±13 mg/kg)were found in FⅡ***2+,Ca2+and Mg2+could recover the fibrinogenolytic activity of FⅡa,which wasinhibited by *** Ca2+ could recover the fibrinogenolytic activity inhibitedby ***:FⅡacan degrade the Aα-,Bβ-and γ-chains of fibrinogen.FⅡais a metalloproteinase,and Zn2+,Ca2+,and disulfide bonds are necessary forits fibrinogenolytic activity.

关键词： snake venoms Agkistrodon acutus fibrinolysis metalloproteinase

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Insufficient MIRO1 contributes to declined oocyte quality during reproductive aging

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Science China Life Sciences 2025年

作者： zhen-Nan Pan Hao-Lin Zhang Kun-Huan Zhang Jia-Qian Ju Jing-Cai Liu Shao-chen Sun College of Animal Science and Technology Nanjing Agricultural University Reproductive Medicine Centre The Affiliated Yantai Yuhuangding Hospital of Qingdao University

Mitochondrial Rho-GTPase 1 (MIRO1) is an outer mitochondrial membrane protein which regulates mitochondrial transport and mitophagy in mitosis. In present study, we reported the crucial roles of MIRO1 in mammalian oocyte meiosis and its potential relationship with aging. We found that MIRO1 expressed in mouse and porcine oocytes, and its expression decreased in aged mice. MIRO1 deficiency caused the failure of meiotic resumption and polar body extrusion in both mouse and porcine oocytes, which could be rescued by exogenous MIRO1supplementation. Mass spectrometry data indicated that MIRO1 associated with several cytoskeleton and cell cycle-related proteins, and MIRO1 regulated motor protein Dynein for microtubule-organizing centers (MTOCs) dynamics at germinal vesicle (GV) stage, which determined meiotic resumption. Furthermore, we found that MIRO1 regulated Aurora A and kinesin family member 11 (KIF11) for meiotic spindle assembly in oocytes. Besides, MIRO1 associated with several mitochondria-related proteins dynamic-related protein 1 (DRP1),Parkin and lysosomal-associated membrane protein 2 (LAMP2) for mitochondrial dynamics and mitophagy during oocyte meiosis. Taken together, our results suggested that MIRO1 played pivotal roles in meiotic resumption, spindle assembly and mitochondrial function in mouse and porcine oocytes, and its insufficiency might contribute to the oocyte maturation defects during aging.

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新疆柴窝堡盆地南缘晚新生代陆源沉积物岩石磁学特征及其古环境意义

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沉积学报 2017年第3期35卷 516-526页

作者：王振邱思静陈一凡程璐吕红华郑祥民华东师范大学地理科学学院上海200241

亚洲内陆晚新生代干旱化历史及其驱动机制是非常重要的科学问题。选择天山北麓柴窝堡盆地南缘乌鲁木齐河剖面为研究对象,基于磁性地层年代学研究建立的时间标尺,分析了该剖面碎屑沉积物岩石磁学特征及其控制因素,进一步探讨了柴窝堡盆... 详细信息

亚洲内陆晚新生代干旱化历史及其驱动机制是非常重要的科学问题。选择天山北麓柴窝堡盆地南缘乌鲁木齐河剖面为研究对象,基于磁性地层年代学研究建立的时间标尺,分析了该剖面碎屑沉积物岩石磁学特征及其控制因素,进一步探讨了柴窝堡盆地晚新生代古气候特征。磁性地层年代学研究约束乌鲁木齐河剖面底界年龄为~6.8 Ma,顶界年龄为~3.3 Ma。详细的岩石磁学测量及漫反射光谱分析结果表明,乌鲁木齐河剖面沉积物中磁性矿物主要包括磁铁矿、赤铁矿等,磁学参数X_(lf)、X_(ARM)、SIRM、S_(-100m T)、S_(-300m T)、X_(ARM)/SIRM等在~6.3 Ma、~5.2 Ma存在明显变化,揭示磁性矿物粒度、含量等存在相应变化,如在"6.3 Ma前后,磁性矿物颗粒逐渐变粗、含量降低;在"5.2 Ma前后,磁性矿物颗粒逐渐变细后趋于稳定、含量逐渐增多。基于稀土元素分析、沉积粒度与磁学参数相关性分析,认为沉积物源与沉积物粒度不是导致乌鲁木齐河剖面磁学性质变化的主要因素,自~6.8Ma以来逐步干旱化的气候条件可能是导致该剖面磁学特征变化的重要原因。基于漫反射光谱分析得到的红度与亮度数据结果也揭示了同样的古气候特征。

关键词：岩石磁学干旱化晚新生代柴窝堡盆地天山北麓

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Nitrogen-rich hierarchically porous carbon foams as high-performance electrodes for lithium-based dual-ion capacitor

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Journal of Energy Chemistry 2020年第9期29卷 187-194,I0006页

作者： Yue chen Xiaoming qiu Li-zhen Fan Beijing Advanced Innovation Center for Materials Genome Engineering Institute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing 100083China Shanxi Key Laboratory of New Energy Materials and Devices Taiyuan University of TechnologyTaiyuan 030024ShanxiChina

Nitrogen-rich porous carbonaceous materials have shown great potential in energy storage and conversion applications due to their facile fabrication,high electronic conductivity,and improved hydrophilic ***,three-dimensional porous N-rich carbon foams are fabricated through a one-step carbonization-activation method of the commercial melamine foam,and displaying hierarchically porous structure(macro-,meso-,and micro-pores),large surface area(1686.5 m2 g^-1),high N-containing level(3.3 at%),and excellent *** as-prepared carbon foams as electrodes for quasi-solid-state supercapacitors exhibit enhanced energy storage ability with 210 F g^-1 and 2.48c at 0.1 A g^-1,and150 F g^-1 and 1.77 F cm^-2 at 1 A g^-1,***,as an electrode for lithium-based dual-ion capacitor,this distinctive porous carbon also delivers remarkable specific capacitance with 143.6 F g^-1 at0.1 A g^-1 and 116.2 F g^-1 at 1 A g^-*** simple preparation method and the fascinating electrochemical performance endow the N-rich porous carbon foams great prospects as high-performance electrodes for electrochemical energy storage.

关键词： Nitrogen-rich Carbon foam Hierarchically porous structure Dual-ion capacitor

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马铃薯立枯丝核菌AG-3毒素诱导的幼苗细胞膜病理反应

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甘肃农业大学学报 2017年第4期52卷 82-89页

作者：贾蕊鸿邱慧珍陈转成张春红张文明赵婧甘肃农业大学资源与环境学院甘肃省干旱生境作物学重点实验室甘肃兰州730070 甘肃农业大学农学院甘肃兰州730070

【目的】为明确马铃薯立枯丝核菌融合群AG-3毒素诱导的幼苗细胞膜病理反应,以及AG-3毒素对马铃薯幼苗茎和叶组织的细胞膜透性、膜质过氧化及活性氧代谢的影响.【方法】用AG-3毒素处理马铃薯组培苗,比较处理和对照间各项指标的差异.【结... 详细信息

【目的】为明确马铃薯立枯丝核菌融合群AG-3毒素诱导的幼苗细胞膜病理反应,以及AG-3毒素对马铃薯幼苗茎和叶组织的细胞膜透性、膜质过氧化及活性氧代谢的影响.【方法】用AG-3毒素处理马铃薯组培苗,比较处理和对照间各项指标的差异.【结果】病原菌AG-3毒素处理显著增大了马铃薯幼苗茎和叶细胞的膜透性,且叶细胞对毒素处理的反应敏感性大于茎细胞;病原菌AG-3毒素处理加速了马铃薯幼苗细胞膜的膜质过氧化,茎和叶细胞的红墨水吸收量、细胞浸提液的相对电导率以及细胞丙二醛(MDA)的含量均显著高于对照,其中叶片的变化幅度大于茎部;在处理96h时,茎部相对电导率较对照处理增加了75.47%,而叶片的增加高达136.99%;在处理144h时,与对照处理MDA含量相比,茎部组织MDA含量较对照处理增加了92.58%,而叶片则增加了96.65%;立枯丝核菌毒素处理改变了马铃薯幼苗的活性氧代谢,茎部和叶片过氧化氢(H2O2)含量和超氧阴离子(O2-)的产生速率均显著高于对照处理,茎部达到最大值的时间比叶片提前24h.【结论】马铃薯立枯丝核菌AG-3毒素使寄主植物细胞膜系统受到破坏,使其结构和功能发生改变,严重影响植物的代谢过程.

关键词：马铃薯立枯丝核菌毒素细胞膜透性丙二醛活性氧

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