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QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm

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Science China(Life Sciences) 2019年第7期62卷 937-946页

作者： xiangjun ji Weida Tong Baitang Ning Christopher E. Mason David P. Kreil Pawel P. Labaj Geng Chen Tieliu Shi The Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National Center for Toxicological Research U.S. Food and Drug Administration3900 NCTR RDJefferson AR 72079USA Department of Physiology and Biophysics Weill Cornell MedicineNew York 10065USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10021USA Feil Family Brain & Mind Research Institute New York 10065USA Chair of Bioinformatics Research Group Boku UniversityVienna A-1190Austria Malopolska Centre of Biotechnology Jagiellonian UniversityKrakow 30-387Poland APART Fellow Austrian Academy of ScienceVienna A-1190Austria National Center for International Research of Biological Targeting Diagnosis and Therapy Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy ResearchCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNanning 530021China

RNA sequencing(RNA-seq) has greatly facilitated the exploring of transcriptome landscape for diverse organisms.However,transcriptome reconstruction is still challenging due to various limitations of current tools and sequencing technologies.Here,we introduce an efficient tool,QuaPra(Quadratic Programming combined with Apriori),for accurate transcriptome assembly and quantification.QuaPra could detect at least 26.5% more low abundance(0.1–1 FPKM) transcripts with over 2.7% increase of sensitivity and precision on simulated data compared to other currently popular tools.Moreover,around one-quarter more known transcripts were correctly assembled by QuaPra than other assemblers on real sequencing data.QuaPra is freely available at http://***/QuaPra/.

关键词： RNA-Seq transcriptome reconstruction transcript assembly transcript quantification

Interplay of transcription factors and microRNAs during embryonic hematopoiesis

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Science China(Life Sciences) 2017年第2期60卷 168-177页

作者： Xueping Gong Ruihua Chao Pengxiang Wang Xiaoli Huang jingjing Zhang Xiaozhou Zhu Yanyang Zhang Xue Yang Chao Hou xiangjun ji Tieliu Shi Yuan Wang Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai 200241 China

Hematopoietic stem cells (HSCs), which are localized in the bone marrow of adult mammals, come from hematopoietic endothelium during embryonic stages. Although the basic processes of HSC generation and differentiation have been described in the past, the epigenetic regulation of embryonic hematopoiesis remains to be fully described. Here, by utilizing an in vitro differentiation system of mouse embryonic stem cells (ESCs), we identified more than 20 microRNAs that were highly enriched in embryonic hematopoietic cells, including some (e.g. miR-10b, miR-15b, and miR-27a) with previously unknown functions in blood formation. Luciferase and gene expression assays further revealed combinational binding and regulation of these microRNAs by key transcription factors in blood cells. Finally, bioinformatics and functional analyses supported an interactive regulatory control between transcription factors and microRNAs in hematopoiesis.

关键词： microRNA 造血干细胞转录因子胚胎期相互作用小鼠胚胎干细胞遗传调控成年哺乳动物

基于OCO-2遥感数据的新疆维吾尔自治区大气XCO_(2)空间化研究

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生态环境学报 2024年第2期33卷 231-241页

作者：张杨徐永明卢响军莫亚萍吉蒙祝善友南京信息工程大学遥感与测绘工程学院江苏南京210044 新疆生产建设兵团生态环境第一监测站新疆乌鲁木齐830011

二氧化碳(CO_(2))是导致全球变暖最主要的温室气体,掌握准确的CO_(2)空间分布信息可以有效评估碳减排成效,对于推进碳达峰、碳中和工作具有重要意义。相比站点观测,碳卫星能够获取大尺度的CO_(2)分布信息,但是由于其幅宽较窄以及云覆盖... 详细信息

二氧化碳(CO_(2))是导致全球变暖最主要的温室气体,掌握准确的CO_(2)空间分布信息可以有效评估碳减排成效,对于推进碳达峰、碳中和工作具有重要意义。相比站点观测,碳卫星能够获取大尺度的CO_(2)分布信息,但是由于其幅宽较窄以及云覆盖的影响,大气CO_(2)卫星遥感数据存在大量缺值区域,不能获得空间连续的大气CO_(2)分布。以新疆维吾尔自治区为研究区,基于2019年OCO-2卫星大气二氧化碳柱平均干空气混合比(XCO_(2))数据,结合气温、地形、植被、大气NO_(2)浓度等相关变量,综合对比了多元线性回归(MLR)、地理加权回归(GWR)、支持向量机(SVR)、随机森林(RF)、极端梯度提升树(XGBoost)和极端随机树(ERT)等方法在生成大气XCO_(2)空间连续数据中的表现。交叉验证结果表明,RF、XGBoost和ERT这3种集成学习模型精度明显优于SVR、GWR和MLR模型,其中ERT模型精度最高,决定系数R^(2)为0.748,平均绝对误差σ_(MAE)为0.489×10^(-6)。基于ERT模型生成了新疆2019年逐月大气XCO_(2)空间连续数据,该地区大气XCO_(2)空间差异和季节变化都很明显。在空间分布格局上总体呈现与地形“三山夹两盆”相似的空间分布特征,裸地XCO_(2)年均值最高,林地和草原的XCO_(2)年均值最低;季节变化特征与植被生长周期相似,春冬季浓度较高,夏秋季浓度较低,最高值出现在4月,最低值出现在8月,不同土地覆盖类型的大气XCO_(2)季节变化与全区域类似,其中草原和林地的季节差异最大,裸地季节差异最小。该研究为基于碳卫星遥感数据生成时空连续的大尺度XCO_(2)数据提供了参考和借鉴。

关键词： OCO-2 XCO_(2) 卫星遥感集成学习模型空间化时空分布新疆维吾尔自治区

基于BIM的施工进度管理虚拟仿真实验教学研究

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现代信息科技 2024年第3期8卷 191-194页

作者：纪凡荣李祥军南云泉山东建筑大学管理工程学院山东济南250101 山东建筑大学测绘地理信息学院山东济南250101

虚拟仿真实验教学是国家教育改革的重要内容。为解决由于建筑物庞大、施工工期长、过程不可逆等特点造成的无法在实验室实施进度实验问题,基于BIM开发了施工进度管理虚拟仿真实验教学系统,实现了进度管理实验的三维可视化、模型轻量化... 详细信息

虚拟仿真实验教学是国家教育改革的重要内容。为解决由于建筑物庞大、施工工期长、过程不可逆等特点造成的无法在实验室实施进度实验问题,基于BIM开发了施工进度管理虚拟仿真实验教学系统,实现了进度管理实验的三维可视化、模型轻量化、进度专业化、检测智能化、教学规模化及过程协同化。文章围绕虚拟仿真实验进度问题,分析了传统教学存在的问题、仿真实验系统架构、功能设计与实施过程,总结了实验系统在管理类知识评价、大规模并行实验及多课程联动机制等方面的成效。研究成果可为工程管理领域的实验开发及进度管理实验教学提供借鉴。

关键词：建筑信息模型施工进度实验仿真实验开发实验教学

Analysis of the Activation of the Nrf2-ARE Pathway Following Optic Nerve Injury in Mice

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Eye Science 2012年第4期27卷 161-164页

作者： Feng Yan Suihua Chen xiangjun ji Chuang Nie Hainan Xie Department of Ophthalmology Jinling Hospital Department of Neurosurgery Jinling HospitalSchool of MedicineNanjing University

Purpose:The Nrf2-ARE pathway plays a cytoprotective role in many tissues,but its protective function in the optic nerve is unclear. The purpose of the study is to investigate the changes in activation of the Nrf2-ARE pathway following optic nerve injury (ONI) in mice. Methods:Using ONI mice models,the expression levels of Nrf2 in optic nerves were determined by real-time PCR at various time points. Results:The expression of Nrf2mRNA was significantly up-regulated at 1 d after ONI, peaking at 30 min after ONI. Conclusion:The Nrf2-ARE pathway was activated after ONI, providing evidence for the study of the protection and underlying mechanism of Nrf2-ARE pathway on optic nerves.

关键词：视神经损伤小鼠模型通路激活保护作用实时PCR 保护功能时间点

基于数据挖掘分析邵荣世使用中药配方颗粒治疗慢性胃炎用药规律

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临床合理用药杂志 2024年第1期17卷 7-12页

作者：季恋苑姜晓燕倪红辉蔡艳廖湘君严玮江苏省南通市中医院 226001

目的基于数据挖掘分析邵荣世使用中药配方颗粒治疗慢性胃炎的用药规律。方法收集整理邵荣世2021年1—12月治疗慢性胃炎的中药配方颗粒处方,筛选整理后建立数据库,应用Microsoft Excel 2019进行药物频数及性味归经分析,采用IBM SPSS Mo... 详细信息

目的基于数据挖掘分析邵荣世使用中药配方颗粒治疗慢性胃炎的用药规律。方法收集整理邵荣世2021年1—12月治疗慢性胃炎的中药配方颗粒处方,筛选整理后建立数据库,应用Microsoft Excel 2019进行药物频数及性味归经分析,采用IBM SPSS Modeler 18对中药进行关联规则分析,使用SPSS 25.0软件对高频药物进行因子分析和系统聚类分析。结果纳入中药处方530张,使用配方颗粒207味,中药使用总频次9 951次。高频中药有陈皮、半夏、白术、豆蔻、甘草、厚朴等;中药功效以理气、补虚、化湿为主;药性以温为主,药味多为苦、辛、甘,归经主要在脾经、胃经;药物关联规则分析表明白术—半夏、白术—陈皮、白术—豆蔻、半夏—陈皮、半夏—豆蔻、陈皮—豆蔻关联紧密;因子分析共提取公因子8个;系统聚类分析得到新处方5首。结论邵荣世使用中药配方颗粒治疗慢性胃炎,多从辨证分型、辨病治疗、脏腑论治着手治疗,以健脾化湿、理气疏肝为基本大法,随症加用清热、活血、利水渗湿等药。

关键词：慢性胃炎数据挖掘中药配方颗粒用药规律

PSO-LSSVM-based Online SOC Estimation for Simulation Substation Battery

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Structural Durability & Health Monitoring 2022年第1期16卷 37-51页

作者： Qiang Zhang Xianguang Zha Jun Wu Liang Zhang Wei Dai Gang Ren Shiqian Li Ning ji xiangjun Zhu Fengwei Tian State Grid jiangsu Electric Power Co. Ltd.Nanjing210024China State Grid jiangsu Electric Power Company Research Institute Nanjing211103China Technican Training Center of State Grid jiangsu Electric Power Co. Ltd.Suzhou215004China

As the emergency power supply for a simulation substation,lead-acid batteries have a work pattern featuring noncontinuous operation,which leads to capacity regeneration.However,the accurate estimation of battery state of charge(SOC),a measurement of the amount of energy available in a battery,remains a hard nut to crack because of the non-stationarity and randomness of battery capacity change.This paper has proposed a comprehensive method for lead-acid battery SOC estimation,which may aid in maintaining a reasonable charging schedule in a simulation substation and improving battery’s durability.Based on the battery work pattern,an improved Ampere-hour method is used to calculate the SOC during constant current and constant voltage(CC/CV)charging and discharging.In addition,the combined Particle Swarm Optimization(PSO)and Least Squares Support Vector Machine(LSSVM)model is used to estimate the SOC during non-CC discharging.Experimental results show that this method is workable in online SOC estimation of working batteries in a simulation substaion,with the maximum relative error standing at only 2.1%during the non-training period,indicating a high precision and wide applicability.

关键词： Simulation substation lead-acid batteries SOC PSO LSSVM

KXT-CG-1型超高温钻孔轨迹测量仪的应用研究

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地质装备 2024年第2期25卷 27-33页

作者：彭新明季伟峰李忠邓启江孔祥军沈鹏飞北京市生态地质研究所北京100120 中国地质科学院探矿工艺研究所成都610081 云南地质工程勘察设计研究院有限公司昆明650041 北京市地热调查研究所北京102206

KXT-CG-1型超高温钻孔轨迹测量仪在北京、云南、黑龙江、青海等地区地热井、科学钻探井等的应用解决了高温环境钻探施工轨迹测量问题,形成了超高温钻孔轨迹野外测量解决方案和工艺规程。该仪器在满足测斜的基础上增加了井温的测量,适用... 详细信息

KXT-CG-1型超高温钻孔轨迹测量仪在北京、云南、黑龙江、青海等地区地热井、科学钻探井等的应用解决了高温环境钻探施工轨迹测量问题,形成了超高温钻孔轨迹野外测量解决方案和工艺规程。该仪器在满足测斜的基础上增加了井温的测量,适用于高温地热井、干热岩钻探等高温环境下的测温需求,在地表模拟270℃条件下可以连续工作4 h,这对于高温环境下的钻孔轨迹测量是有力的技术支撑。本文通过对比分析不同钻井现场的试验测量数据,可知KXT-CG-1型超高温钻孔轨迹测量仪具有集成度高、技术先进、测量精度高、辅助器具少以及结构轻便的特征,其中顶角测量精度0.15°,方位角测量精度1.5°。

关键词：超高温钻孔轨迹测量井温测量

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Single-cell analysis reveals an Angpt4-initiated EPDC-EC-CM cellular coordination cascade during heart regeneration

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Protein & Cell 2023年第5期14卷 350-368页

作者： Zekai Wu Yuan Shi Yueli Cui Xin Xing Liya Zhang Da Liu Yutian Zhang ji Dong Li jin Meijun Pang Rui-Ping Xiao Zuoyan Zhu jing-Wei Xiong xiangjun Tong Yan Zhang Shiqiang Wang Fuchou Tang Bo Zhang Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education Peking University Genome Editing Research CenterCollege of Life SciencesPeking UniversityBeijing 100871China Beijing Advanced Innovation Center for Genomics(ICG) College of Life SciencesPeking UniversityBeijing 100871China State Key Laboratory of Membrane Biology Institute of Molecular MedicineCollege of Future TechnologyPeking UniversityBeijing 100871China State Key Laboratory of Membrane Biology College of Life SciencesPeking UniversityBeijing 100871China Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences School of Basic Medical SciencesMinistry of EducationPeking University Health Science CenterBeijing 100191China Institute of Molecular Medicine College of Future TechnologyPeking UniversityBeijing 100871China

Mammals exhibit limited heart regeneration ability,which can lead to heart failure after myocardial infarction.In contrast,zebrafish exhibit remarkable cardiac regeneration capacity.Several cell types and signaling pathways have been reported to participate in this process.However,a comprehensive analysis of how different cells and signals interact and coordinate to regulate cardiac regeneration is unavailable.We collected major cardiac cell types from zebrafish and performed high-precision single-cell transcriptome analyses during both development and post-injury regeneration.We revealed the cellular heterogeneity as well as the molecular progress of cardiomyocytes during these processes,and identified a subtype of atrial cardiomyocyte exhibiting a stem-like state which may transdifferentiate into ventricular cardiomyocytes during regeneration.Furthermore,we identified a regeneration-induced cell(RIC)population in the epicardium-derived cells(EPDC),and demonstrated Angiopoietin 4(Angpt4)as a specific regulator of heart regeneration.angpt4 expression is specifically and transiently activated in RIC,which initiates a signaling cascade from EPDC to endocardium through the Tie2-MAPK pathway,and further induces activation of cathepsin K in cardiomyocytes through RA signaling.Loss of angpt4 leads to defects in scar tissue resolution and cardiomyocyte proliferation,while overexpression of angpt4 accelerates regeneration.Furthermore,we found that ANGPT4 could enhance proliferation of neonatal rat cardiomyocytes,and promote cardiac repair in mice after myocardial infarction,indicating that the function of Angpt4 is conserved in mammals.Our study provides a mechanistic understanding of heart regeneration at single-cell precision,identifies Angpt4 as a key regulator of cardiomyocyte proliferation and regeneration,and offers a novel therapeutic target for improved recovery after human heart injuries.

关键词： scRNA-seq zebrafish heart regeneration Angpt4 EPDC