检索结果-南通市图书馆

Science China(Life Sciences) 2013年第2期56卷 119-124页

作者： GUO YongLi SHI LeMing hong huixiao SU ZhenQiang FUSCOE James NING BaiTang Division of Systems Biology National Center for Toxicological Researchthe US Food and Drug Administration Division of Bioinformatics and Biostatistics National Center for Toxicological Researchthe US Food and Drug Administration

Abacavir is an effective nucleoside analog reverse transcriptase inhibitor used to treat human immunodeficiency virus(HIV) infected *** main side effect is hypersensitivity reaction(HSR).The incidence of the HSR is associated with ethnicity among patients exposed to abacavir,and retrospective and prospective studies show a significantly increased risk of abacavir-induced HSR in human leukocyte antigen(HLA)-B*57:01-carrying *** studies indicated that abacavir interacts specifically with HLA-B*57:01 and changed the binding specificity between the HLA molecule and the HLA-presented endogenous peptide repertoire,leading to a systemic autoimmune ***-B*57:01 screening,combined with patch testing,had clinically predictive value and cost-effective impact in reducing the incidence of abacavir-induced HSR regardless of the HLA-B*57:01 prevalence in the ***,the US Food and Drug Administration(FDA) and international HIV treatment guidelines recommend a routine HLA-B*57:01 screening prior to abacavir treatment to decrease false positive diagnosis and prevent abacavir-induced *** studies of abacavir-induced HSR and the implementation of the HLA-B*57:01 screening in the clinic represent a successful example of the use of pharmacogenetics for personalized diagnosis and therapy.

关键词：过敏性反应药理学个性化药物 HLA-B 人类免疫缺陷病毒人类白细胞抗原翻译

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

在线全文

学校读者我要写书评

暂无评论

Science China(Life Sciences) 2013年第2期56卷 110-118页

作者： hong huixiao ZHANG WenQian SHEN Jie SU ZhenQiang NING BaiTang HAN Tao PERKINS Roger SHI LeMing TONG WeiDa Division of Bioinformatics and Biostatistics National Center for Toxicological ResearchUS Food and Drug Administration Beijing Genomic Institute Beishan Industrial Zone Division of Systems Biology National Center for Toxicological ResearchUS Food and Drug Administration

Realizing personalized medicine requires integrating diverse data types with *** most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at *** technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the *** prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work *** is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized *** review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers.

关键词：生物信息学个性化数据转换测序 IT基础设施医药基因组信息生物标志物

Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine

在线全文

学校读者我要写书评

暂无评论

Science China(Life Sciences) 2019年第7期62卷 895-904页

作者： Yaqiong Jin Geng Chen Wenming Xiao huixiao hong Joshua Xu Yongli Guo Wenzhong Xiao Tieliu Shi Leming Shi Weida Tong Baitang Ning Beijing Key Laboratory for Pediatric Diseases of Otolaryngology Head and Neck SurgeryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijing 100045China Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesShanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National Center for Toxicological Research U.S. Food and Drug AdministrationJefferson AR 72079USA Department of Surgery Massachusetts General HospitalHarvard Medical SchoolBoston MA 02114USA State Key Laboratory of Genetic Engineering School of Life Sciences and Cancer CenterCollaborative Innovation Center for Genetics and DevelopmentFudan UniversityShanghai 200433China

High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference *** technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of ***,due to the limitations of sequencing-based chemistry,length of sequencing reads and the complexity of genes,it is difficult to determine the sequences of some portions of the human genome,leaving gaps in genomic data that frustrate further ***,some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions,and complicated pseudogenes,such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs).The genetic variants in XMET genes are critical to predicate interindividual variability in drug efficacy,drug safety and susceptibility to environmental *** summarized and discussed challenges,wet-lab methods,and bioinformatics algorithms in sequencing "complex" XMET genes,which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics.

关键词： next generation sequencing precision medicine xenobiotic metabolizing enzymes and transporters toxicogenomics pharmacogenomics

Application of genome analysis strategies in the clinical testing for pediatric diseases

在线全文

学校读者我要写书评

暂无评论

Pediatric Investigation 2018年第2期2卷 72-81页

作者： Yaqiong Jin Li Zhang Baitang Ning huixiao hong Wenming Xiao Weida Tong Yiran Tao Xin Ni Tieliu Shi Yongli Guo Beijing Key Laboratory for Pediatric Diseases of Otolaryngology Head and Neck Surgery MOE Key Laboratory of Major Diseases in Children Beijing Pediatric Research Institute Beijing Children's Hospital Capital Medical University National Center for Children's Health Beijing China Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai China National Center for Toxicological Research U.S.Food and Drug Administration Jefferson AR USA

Next-generation sequencing (NGS) is being used in clinical *** authorities in both China and the United States are overseeing the clinical application of NGS instruments and *** addition,the US Association for Molecular Pathology and the College of American Pathologists have jointly released a guidance to standardize the analysis and interpretation of NGS data involved in clinical *** present,the analysis strategies and pipelines for NGS data related to the clinical detection of pediatric disease are similar to those used for adult ***,for rare pediatric diseases without linkage to known genetic variants,it is currently difficult to detect the relevant pathogenic genes using NGS ***,it is challenging to identify novel pathogenic genes of familial pediatric ***,characterization of the pathogenic genes associated with above diseases is important for the diagnosis and treatment of rare diseases in *** article introduces the general pipelines for NGS data analyses of diseases and elucidates data analysis strategies for the pathogenic genes of rare pediatric diseases and familial pediatric tumors.

关键词： Familial pediatric tumors Next-generation sequencing Rare pediatric diseases

Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development

在线全文

学校读者我要写书评

暂无评论

Journal of Biomedical Science and Engineering 2011年第10期4卷 666-676页

作者： Jie Liu Steven F. Jennings Weida Tong huixiao hong University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Bioinformatics Graduate Program Little Rock USA.

miRNAs are non-coding RNAs that play a regulatory role in expression of genes and are associated with diseases. Quantitatively measuring expression levels of miRNAs can help understanding the mechanisms of human diseases and discovering new drug targets. There are three major methods that have been used to measure the expression levels of miRNAs: real-time reverse transcription PCR (qRT-PCR), microarray, and the newly introduced next-generation sequencing (NGS). NGS is not only suitable for profiling of known miRNAs that qRT-PCR and microarray can do too but also able to detect unknown miRNAs that the other two methods are incapable. Profiling of miRNAs by NGS has been progressed rapidly and is a promising field for applications in drug development. This paper will review the technical advancement of NGS for profiling miRNAs, including comparative analyses between different platforms and software packages for analyzing NGS data. Examples and future perspectives of applications of NGS profiling miRNAs in drug development will be discussed.

关键词： MiRNAs Next-Generation Sequencing Expression Data Analysis Drug Development

Pitfall of genome-wide association studies: Sources of inconsistency in genotypes and their effects

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Biomedical Science and Engineering 2012年第10期5卷 557-573页

作者： huixiao hong Lei Xu Zhenqiang Su Jie Liu Weigong Ge Jie Shen hong Fang Roger Perkins Leming Shi Weida Tong Bioinformatics Graduate Program University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Little Rock AR 72079 USA Division of Bioinformatics and Biostatistics National Center for Toxicological Research US Food and Drug Administration Jefferson AR 72079 USA ICF International at National Center for Toxicological Research US Food and Drug Administration Jefferson AR 72079 USA School of Materials Science and Engineering Chang’an University Xi’an China

Personalized medicine will improve heath outcomes and patient satisfaction. However, implementing personalized medicine based on individuals’ biological information is far from simple, requiring genetic biomarkers that are mainly developed and used by the pharmaceutical companies for selecting those patients who benefit more, or have less risk of adverse drug reactions, from a particular drug. Genome-wide Association Studies (GWAS) aim to identify genetic variants across the human genome that might be utilized as genetic biomarkers for diagnosis and prognosis. During the last several years, high-density genotyping SNP arrays have facilitated GWAS that successfully identified common genetic variants associated with a variety of phenotypes. However, each of the identified genetic variants only explains a very small fraction of the underlying genetic contribution to the studied phenotypic trait. The replication studies demonstrated that only a small portion of associated loci in the initial GWAS can be replicated, even within the same populations. Given the complexity of GWAS, multiple sources of Type I (false positive) and Type II (false negative) errors exist. The inconsistency in genotypes that caused either by the genotypeing experiment or by genotype calling process is a major source of the false GWAS findings. Accurate and reproducible genotypes are paramount as inconsistency in genotypes can lead to an inflation of false associations. This article will review the sources of inconsistency in genotypes and discuss its effect in GWAS findings.

关键词： Genotype Association Reproducibility Inconsistency Batch Effect Genotyping Platform

Homology Model and Ligand Binding Interactions of the Extracellular Domain of the Human α4β2 Nicotinic Acetylcholine Receptor

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Biomedical Science and Engineering 2016年第1期9卷 41-100页

作者： Shu Mao Hui Wen Ng Michael Orr Heng Luo Hao Ye Weigong Ge Weida Tong huixiao hong Division of Bioinformatics and Biostatistics National Center for Toxicological Research U.S. Food and Drug Administration Jefferson AR USA School of Pharmacy and Bioengineering Chongqing University of Technology Chongqing China Division of Nonclinical Science Office of Science Center for Tobacco Products U.S. Food and Drug Administration Silver Spring MD USA Division of Systems Biology National Center for Toxicological Research U.S. Food and Drug Administration Jefferson AR USA

Addiction to nicotine, and possibly other tobacco constituents, is a major factor that contributes to the difficulties smokers face when attempting to quit smoking. Amongst the various subtypes of nicotinic acetylcholine receptors (nAChRs), the α4β2 subtype plays an important role in mediating the addiction process. The characterization of human α4β2-ligand binding interactions provides a molecular framework for understanding ligand-receptor interactions, rendering insights into mechanisms of nicotine addiction and may furnish a tool for efficiently identifying ligands that can bind the nicotine receptor. Therefore, we constructed a homology model of human α4β2 nAChR and performed molecular docking and molecular dynamics (MD) simulations to elucidate the potential human α4β2-ligand binding modes for eleven compounds known to bind to this receptor. Residues V96, L97 and F151 of the α4 subunit and L111, F119 and F121 of the β2 subunit were found to be involved in hydrophobic interactions while residues S153 and W154 of the α4 subunit were involved in the formation of hydrogen bonds between the receptor and respective ligands. The homology model and its eleven ligand-bound structures will be used to develop a virtual screening program for identifying tobacco constituents that are potentially addictive.

关键词： Nicotinic Acetylcholine Receptors Homology Model Ligand-Receptor Interactions

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

X射线荧光谱仪模拟系统

南京大学学报（自然科学版） 1989年第1期25卷 68-73页

作者：洪汇孝忻新泉南京大学化学系

本文介绍SXRFS(x射线荧光谱仪模拟)系统的设计思想和实现方法。SXRFS是在AppleⅡ机上开发的计算机软件,采用浮点BASIC语言实现。系统由五个部分组成:XRFS(x射线荧光谱仪)简介、基本原理、仪器结构、样品制备和操作模拟。系统具有较强的... 详细信息

本文介绍SXRFS(x射线荧光谱仪模拟)系统的设计思想和实现方法。SXRFS是在AppleⅡ机上开发的计算机软件,采用浮点BASIC语言实现。系统由五个部分组成:XRFS(x射线荧光谱仪)简介、基本原理、仪器结构、样品制备和操作模拟。系统具有较强的交互功能,操作方便、灵治。SXRFS采用了计算机图形显示技术,特别是动画技术,使系统形象,逼真地模拟XRFS的全过程。

关键词：模拟荧光光谱仪软件 SXRFS

江汉平原养殖水面结构转型路径及驱动机制研究

在线全文

学校读者我要写书评

暂无评论

地理科学进展 2024年第5期43卷 921-935页

作者：刘文卉宋小青徐惠孝高厚兴中国地质大学(武汉)地理与信息工程学院区域生态过程与环境演变湖北省重点实验室武汉430074 自然资源部国土碳汇智能监测与空间调控工程技术创新中心武汉430074

深入理解淡水养殖水面结构转型是贯彻落实新发展理念和大食物观的必然要求,对促进全球可持续发展具有重要意义。然而,有关淡水养殖水面结构变化的研究还十分不足。论文在认识到淡水产品市场需求和河湖长制等水域管控政策对淡水养殖的影... 详细信息

深入理解淡水养殖水面结构转型是贯彻落实新发展理念和大食物观的必然要求,对促进全球可持续发展具有重要意义。然而,有关淡水养殖水面结构变化的研究还十分不足。论文在认识到淡水产品市场需求和河湖长制等水域管控政策对淡水养殖的影响基础上,综合运用Simpson多样性指数、地理要素重心模型和面板回归模型,从类型结构和空间结构两方面研究揭示江汉平原养殖水面的转型特征,着重探索市场诱致和政策管控共同作用下养殖水面结构转型的驱动机制。结果表明:①2001—2020年,江汉平原养殖水面从快速扩张转为扩张减缓,类型结构发生了“大水转小水、小水精养化、综合种养化主导”的转型,空间结构出现了“大水爬坡、小水向江”的转型趋势;②市场诱致性类型替代叠加政策强制性结构调整共同驱动了江汉平原养殖水面结构转型。其中,前者即以追求劳动生产力最大化为养殖目标的自下而上市场诱致性类型替代,后者即以河湖长制为代表的自上而下的水域管控政策实施导致的结构调整。此外,论文提出了加强江汉平原养殖水面结构转型调控的政策建议。研究结果有助于土地利用转型研究对象向养殖水面拓展,同时能够为从结构演化视角开展土地利用转型研究提供案例支撑。

关键词：养殖水面结构土地利用转型市场诱致江汉平原

在线全文

学校读者我要写书评

暂无评论

基于深度学习的大地电磁二维反演方法

地质科技通报 2024年第2期43卷 344-354页

作者：王方熊杰田慧潇李思平康佳帅长江大学电子信息学院湖北荆州434023

如何通过大地电磁测深反演方法来提高数据解释的精度一直都是大地电磁测深研究领域的重要课题。针对大地电磁传统反演方法存在的初始模型依赖、易陷入局部最优的问题,提出了一种基于深度学习的大地电磁二维反演方法。该方法首先设计Goog... 详细信息

如何通过大地电磁测深反演方法来提高数据解释的精度一直都是大地电磁测深研究领域的重要课题。针对大地电磁传统反演方法存在的初始模型依赖、易陷入局部最优的问题,提出了一种基于深度学习的大地电磁二维反演方法。该方法首先设计GoogLeNetINV神经网络;接着构造多种地电模型,在TM模式下通过正演得到视电阻率数据,组成训练数据集;然后用训练数据集训练该神经网络并调整网络参数;最后,将视电阻率数据输入已训练好的GoogLeNetINV神经网络直接得到反演结果。实验结果表明,该方法能快速、准确地反演出“未学习”过地电模型的位置和电阻率数据,具有较好的泛化能力;使用噪声数据测试仍能取得良好的反演结果,有一定的抗噪声能力。将该神经网络应用于Bendigo Zone实际数据资料处理中,反演得到的电阻率模型与地震解释一致,因此基于深度学习的大地电磁反演方法能有效解决大地电磁反演问题。

关键词：深度学习大地电磁反演神经网络 GoogLeNetINV