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Jackknife and Bootstrap Tests of the Composition Vector Trees

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genomics, Proteomics & Bioinformatics 2010年第4期8卷 262-267页

作者： Guanghong Zuo1,2, Zhao Xu1,3, Hongjie Yu1,4, and Bailin Hao1,5,6 1T-Life Research center & Department of Physics, Fudan University, shanghai 200433, china 2shanghai Institute of Applied Physics, chinese Acadamy of Sciences, shanghai 201800, china 3Applied Biosystems, Inc., Beijing 100027, china 4Fudan-VARI center for Genetic Epidemiology, Fudan University, shanghai 200433, china 5Institute of Theoretical Physics, chinese Acadamy of Sciences, Beijing 100190, china 6Santa Fe Institute, Santa Fe, NM 87505, USA. [a] T-Life Research center & Department of Physics Fudan University shanghai 200433 china [b] shanghai Institute of Applied Physics chinese Acadamy of Sciences shanghai 201800 china [c] Applied Biosystems Inc. Beijing 100027 china [d] Fudan-VARI center for Genetic Epidemiology Fudan University shanghai 200433 china [e] Institute of Theoretical Physics chinese Acadamy of Sciences Beijing 100190 china [f] Santa Fe Institute Santa Fe NM 87505 USA

Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.

关键词： composition vector phylogeny topological distance bootstrap jackknife CVTree

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中国百日咳诊疗与预防指南(2024版)

中华医学杂志 2024年第15期104卷 1258-1279页

作者：中华医学会感染病学分会儿科感染学组国家卫生健康委能力建设和继续教育儿科专委会感染组中国临床实践指南联盟方法学专委会国家儿童医学中心(上海) 国家传染病医学中心曾玫邵祝军张文宏夏君蔡洁皓陈明亮冯天行姚开虎不详复旦大学附属儿科医院感染传染科国家儿童医学中心(上海)上海200032 中国疾病预防控制中心传染病预防控制所北京102206 复旦大学附属华山医院感染科国家传染病医学中心上海200040 宁波诺丁汉大学GRADE中心宁波315100 复旦大学附属儿科医院感染传染科复旦大学附属闵行医院检验科上海临床研究中心儿科首都医科大学附属北京儿童医院北京市儿科研究所感染与微生物研究室国家儿童医学中心(北京)

百日咳再现是全球性的公共卫生问题,2018—2022年我国国内百日咳报告发病率接近20世纪80年代末的报告水平。实际上,我国的百日咳发病率被严重低估,主要因为国内尚未全面建立百日咳主动监测工作,不典型百日咳病例在临床上容易被漏诊,许... 详细信息

百日咳再现是全球性的公共卫生问题,2018—2022年我国国内百日咳报告发病率接近20世纪80年代末的报告水平。实际上,我国的百日咳发病率被严重低估,主要因为国内尚未全面建立百日咳主动监测工作,不典型百日咳病例在临床上容易被漏诊,许多医疗机构未开展百日咳的实验室诊断;同时,我国还面临百日咳鲍特菌对一线抗菌药物大环内酯类高度耐药的临床问题。为了更好地指导和规范我国百日咳病例的临床诊疗、监测和防控工作,由感染病学、流行病学、免疫规划及指南方法学专家组成指南制订小组,从实践角度提出有关百日咳诊断、治疗、预防,尤其是疫苗免疫策略的12个临床问题,经过研究问题构建、证据检索和综合、证据评价以及证据到推荐意见讨论,制订推荐意见和实施建议,为从事百日咳诊疗和防控的临床医师、微生物实验室专业人员、医院感染控制专业人员以及公共卫生领域从事传染病防控和免疫规划的专业人员提供参考。

关键词：百日咳诊断治疗预防疫苗接种

Construction of a full bacterial artificial chromosome(BAC) library of Oryza sativa genome

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Cell Research 1994年第2期4卷 127-133页

作者： TAO QUANZHOU HAIYING ZHAO LONGFANG QIU GUOFAN HONG.(national center for Gene Researsh, Chincse Academy of Sciences, shanghai 200233, china）（shanghai Institute of Biochemistry, Chinesc Academyof Scienccs, shanghai 200031, china) shanghai Institute of Biochemistry Chinese Academy of Sciences Shanghai 200031 China.

We have constructed a full BAC library for the superior eaxly indica variety of OryZa sativa, Guang Lu Ai4. The MAX Efficiency DHlOB with increased stabilltyof inserts was used as BAC host cells. The potent pBelo BACII with double selection markers was used as cloning vector. The cloning efficiency we have reached was as high as 98%, and the transformation efficiency was raised up to 1Oo transformants / pg of large fragment DNA. The BAC recombinant transformants were picked at random and analyzed for the size of inserts, which turned out to be of 120 kb in length on average. We have obtained more than 20,000 such BAC clones. According to conventional probabillty equation, they covered the entire rice genome of 420,000 kb in length. The entire length of inserts of the library obtained has the 5- to 6- fold coverage of the genome. To our knowledge, this is the first reported full BAC library for a complex genome.

关键词： bacterial artificial chromosome indica Oryza sativa library

人类成体干细胞临床试验和应用的伦理准则(建议稿)

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中国医学伦理学 2014年第2期27卷 191-194页

作者： Department of Ethics,chinese national human genome center in shanghai 国家人类基因组南方研究中心伦理学部

第一章总则第一条为了使我国生物医学领域人类成体干细胞研究切实遵守我国的相关法规，使干细胞技术更好地为治疗人类疾病、增进人民健康服务，并切实保护患者和受试者的权益，根据我国《执业医师法》、《人体器官移植条例》、《人胚... 详细信息

第一章总则第一条为了使我国生物医学领域人类成体干细胞研究切实遵守我国的相关法规，使干细胞技术更好地为治疗人类疾病、增进人民健康服务，并切实保护患者和受试者的权益，根据我国《执业医师法》、《人体器官移植条例》、《人胚胎干细胞研究伦理指导原则》、《医疗技术临床应用管理办法》、《药品临床试验管理规范》、《药物临床试验伦理审查工作指导原则》及《涉及人的生物医学研究伦理审查办法（试则）》，参考国际干细胞研究协会（ISSCR）《干细胞临床转化（应用）指导原则》，特制定本伦理准则。

关键词：《药品临床试验管理规范》成体干细胞人类疾病临床应用伦理准则《人胚胎干细胞研究伦理指导原则》伦理审查工作《执业医师法》

genome size and sequence composition of moso bamboo: A comparative study

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Science china(Life Sciences) 2007年第5期50卷 700-705页

作者： GUI YiJie1, WANG Sheng1, QUAN LiYan1, ZHOU ChangPing2, LONG ShiBao2, ZHENG HuaJun3, JIN Liang1, ZHANG XianYin 1, MA NaiXun 4 & FAN LongJiang1 1 Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, china 2 Zhejiang Anji Bamboo Exposition Garden, Anji 313300, china 3 chinese national human genome center at shanghai, shanghai 2.12.3, china 4 The Research Institute of Subtropical Forestry, chinese Academy of Forestry, Fuyang 311400, china 1. Institute of Crop Science/Institute of Bioinformatics Zhejiang University Hangzhou 310029 China 2. Zhejiang Anji Bamboo Exposition Garden Anji 313300 China 3. chinese national human genome center at shanghai Shanghai 201203 China 4. The Research Institute of Subtropical Forestry Chinese Academy of Forestry Fuyang 311400 China

Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo―over two-thirds of the total bamboo forest area―and the highest economic value in china. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize ge-nome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotrans-posons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to con-firm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.

关键词： flow cytometry (FCM), genome size, GSS, Phyllostachys pubescens, repeat elements

Construction of Oryza sativa genome contigs by fingerprint strategy

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Cell Research 1995年第2期5卷 263-271页

作者： TAO QUANZHOU YUEMIN QIAN HAIYING ZHAO SHULIANG YU LONGFANG QIU BOQIAN WU JIA ZHU DI YU XIAOHUI LIU GUOFAN HONG(national center for Gene Research, chinese Academy of Sciences, shanghai 200233, china.)(shanghai Institute of Biochemistry, chinese Acad shanghai Institute of Biochemistry Chinese Academy of Sciences Shanghai 200031 China.

We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa, Guang Lu Ai *** entire representative (sixfold coverage of rice chromosomes) and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. And all the images thus obtained were subject to image-processing, which consisted of preliminary location of bands, cooperative tracking of lanesby correlation of adjacent bands, a precise densitometric pass, alignment at the marker bands with the standard,optional interactive editing, and normalization of the accepted bands. The contigs were generated based on the Computer Software specially designed for genome map ping. The number of contigs with 600 kb in length on average was 464; of contigs with 1000 kb in length on average was 107; of contigs with 1500 kb in length on average was 23. Therefore, all the contigs we have obtained amounted up to 420 megabases in length. Considering the size of rice genome (430 megabased), the contigs generated in this lab have covered nearly 98% of the rice genome. We are now in the process of mapping the contigs to chromosomes.

关键词： Contig genome indica oryza sativa BAC

Transcriptome profiling analysis reveals multiple modulatory effects of Ginkgo biloba extract in the liver of rats on a high-fat diet

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Transcriptome profiling analysis reveals multiple modulatory...

中国自身免疫性胰腺炎诊治指南(上海,2023)

中药药效提高与中药饮片质量控制交流研讨会

作者： Xiaomei Gu~(1,*),Zuoquan Xie~(2,*),Qi Wang~(1,*),Gang Liu~1,Yi Qu~1,Lu Zhang~(1,2),Jiahu Pan~3,Guoping Zhao~(1,4) and Qinghua Zhang~(1,2,4) 1 national Engineering center for Biochip at shanghai,china 2 State Key laboratory of Medical genomics and shanghai Institute of Hematology,Ruijin Hospital,shanghai Jiaotong University School of Medicine,china 3 School of Pharmacy,Fudan University,shanghai,china 4 MOST-shanghai Key laboratory of disease and health Related genomics,china

Leaf extract of Ginkgo biloba(GBE) is increasingly used as a herbal medicine for the treatment of neurodegenerative,cardiovascular and cerebrovascular *** studies have demonstrated many protective effects of GBE in neurons,the endothelium and *** this study,we investigated the molecular mechanisms underlying the effects of GBE in disorders induced by long-term exposure to a high-fat diet(HFD).Rats were fed an HFD with or without the GBE product GBE50 for 19 *** found that GBE50 reduced the development of fatty liver induced by an HFD and inhibited the commonly observed elevation of serum cholesterol and lactate dehydrogenase *** profiling analysis showed that several genes were modulated by GBE50 in liver,including those involved in lipid metabolism,carbohydrate metabolism,vascular constriction,ion transportation,neuronal systems and drug ***,a number of genes coding for proteins involved in cholesterol metabolism were repressed,and some were *** acid biosynthesis appeared to be repressed,whereas fatty acid metabolism appeared to be *** conclusion,using transcriptome profiling analysis,we demonstrated the molecular basis for the pleiotropic effects of GBE50,particularly those involved in lipid *** study provided new clues for further pharmacological study of GBEs.

关键词： Ginkgo biloba extract high-fat diet rat liver regulation transcriptome

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临床肝胆病杂志 2024年第7期40卷 1312-1320页

作者：国家消化系统疾病临床医学研究中心(上海) 免疫与炎症全国重点实验室中国医师协会胰腺病学专业委员会中华医学会消化病学分会胰腺疾病学组《中华胰腺病杂志》编辑委员会李兆申李汛郭晓钟廖专辛磊蔡亦李胡良皞李宏宇吴东不详海军军医大学第一附属医院消化内科上海200433 兰州大学第一医院普外科兰州730000 北部战区总医院消化内科沈阳110840 海军军医大学第一附属医院海军特色医学中心北部战区总医院北京协和医院

自身免疫性胰腺炎(AIP)是一种由免疫介导的、特殊类型的慢性胰腺炎,可合并全身多器官的损害,临床表现复杂多样,诊治仍具有一定困难。本指南结合国内外AIP最新指南和研究进展,针对AIP的诊断、治疗、随访和预后4个方面,共提出20条推荐意见... 详细信息

自身免疫性胰腺炎(AIP)是一种由免疫介导的、特殊类型的慢性胰腺炎,可合并全身多器官的损害,临床表现复杂多样,诊治仍具有一定困难。本指南结合国内外AIP最新指南和研究进展,针对AIP的诊断、治疗、随访和预后4个方面,共提出20条推荐意见,旨在规范和提高我国AIP的诊治水平,改善患者预后。

关键词：自身免疫性胰腺炎 IgG4相关性疾病指南多学科诊治

The Biomarkers for Metastasis and Recurrence of Hepatocellular Carcinoma

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The Biomarkers for Metastasis and Recurrence of Hepatocellul...