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Prediction of human microRNA hairpins using only positive sample learning

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Journal of Biomedical Science and Engineering 2008年第2期1卷 141-146页

作者： Dang Hung tran Tho Hoan Pham Kenji Satou Tu bao Ho Hanoi National University of Education Japan Advanced Institute of Science and Technology

MicroRNAs(miRNA) are small molecular non-coding RNAs that have important roles in the post-transcriptional mechanism of animal and plant. They are commonly 21-25 nucleotides (nt) long and derived from 60-90 nt RNA hairpin structures, called miRNA hairpins. A larger num-ber of sequence segments in the human genome have been computationally identified with such 60-90 nt hairpins, however a majority of them are not miRNA hairpins. Most computational meth-ods so far for predicting miRNA hairpins were based on a two-class classifier to distinguish between miRNA hairpins and other sequence segments with hairpin structures. The difficulty of these methods is how to select hairpins as negative examples of miRNA hairpins in the classifier-training datasets, since only a few miRNA hairpins are available. Therefore, their classifier may be mis-trained due to some false negative examples of the training dataset. In this paper, we introduce a one-class support vector machine (SVM) method to predict miRNA hair-pins among the hairpin structures. Different from existing methods for predicting miRNA hairpins, the one-class SVM model is trained only on the information of the miRNA class. We also illus-trate some examples of predicting miRNA hair-pins in human chromosomes 10, 15, and 21, where our method overcomes the above disad-vantages of existing two-class methods.

关键词： MicroRNA Hairpin One-class SVM

基于转录组测序的花斑裸鲤SSR、SNP和InDel位点特征分析

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大连海洋大学学报 2024年第1期39卷 48-56页

作者：贺彩霞李长忠金文杰保长虹简生龙李昭楠王丽楠严青春王振吉王国杰陈艳霞青海大学生态环境工程学院青海西宁810016 青海省渔业环境监测站青海西宁810012

为利用分子标记规模化开发与辅助花斑裸鲤(Gymnocypris eckloni)良种选育,以花斑裸鲤(2+龄)的鳃、肾脏和肝脏组织为材料,经总RNA提取和cDNA文库构建后采用Illumina Novaseq 2000平台进行转录组测序,并采用MISA和GATK3软件分析转录组的SS... 详细信息

为利用分子标记规模化开发与辅助花斑裸鲤(Gymnocypris eckloni)良种选育,以花斑裸鲤(2+龄)的鳃、肾脏和肝脏组织为材料,经总RNA提取和cDNA文库构建后采用Illumina Novaseq 2000平台进行转录组测序,并采用MISA和GATK3软件分析转录组的SSR、SNP和插入缺失标记(InDel)位点特征。结果表明:在486221条Unigenes序列中共发现了128727个SSR,出现频率为26.47%,平均每3.76 kb出现1个SSR;花斑裸鲤SSR包括6个重复类型,以单碱基和二碱基重复基元类型为主,分别占总SSR位点数的46.53%和42.45%,重复基元类型共77种,其中,A/T和AC/GT两种基元的出现频率最高,是花斑裸鲤SSR的优势重复基元;所有重复次数中出现次数最多的为5~15次,占所有SSR位点的87.52%;通过GATK3软件搜索得到399080个SNP位点,转换类型多于颠换类型,分别占总SNP的56.29%和43.71%,转换类型中A/G发生频率略高于C/T,而颠换类型中A/T发生频率最高,C/G发生频率最低;InDel分析显示,从花斑裸鲤转录组Unigenes中共筛选出254065个InDel位点,平均每1903 bp出现1个InDel位点,且SNP位点和InDel位点均以含1个位点的Unigenes数最多。研究表明,花斑裸鲤转录组中SSR、SNP和InDel位点非常丰富,这些位点对花斑裸鲤种质资源鉴定、种群遗传学研究及保护管理具有重要价值。

关键词：花斑裸鲤转录组分子标记 SSR SNP InDel

Biventricular pulsus alternans: An echocardiographic finding in patient with pulmonary embolism

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World Journal of Clinical Cases 2013年第5期1卷 162-165页

作者： Tin Nguyen Long-bao Cao Minh tran Assad Movahed Department of Cardiovascular Sciences East Carolina UniversityBrody School of Medicine East Carolina Heart Institute Greenville NC 27834 United States

Pulsus alternans is characterized by regular rhythm with beat-to-beat alternation of systolic pressures. Left ventricular alternans is usually found in severe left ventricular dysfunction due to cardiomyopathy, coronary artery disease, systemic hypertension, and aortic stenosis. Right ventricular alternans is usually associated with left ventricular alternans, right ventricular dysfunction, pulmonary embolism, and pulmonary hypertension. Biventricular alternans is rare and associated with severe left ventricular dysfunction and left anterior descending coronary artery disease. The exact mechanism of pulsus alternans has not been clearly delineated, and it has been remained a subject of investigation and conjecture since the nineteenth century. Two fundamental mechanisms have been proposed to explain ventricular alteration. The first, based on the Frank-Starling mechanism, proposes beat-to-beat alteration in end-diastolic volume accounted for the alternating contractile force. The second proposed mechanism which explains the physiology of pulsus alternans involves the abnormal calcium handling by cardiac myocytes. To the best of our knowledge, biventricular alternans in pulmonaryembolism has not been previously reported in the medical literature. We present and discuss the mechanisms of pulsus alternans and its clinical implications.

关键词： Pulsus alternans Biventricular alternans Pulmonary embolism

Spatial relationship of high-speed transportation construction and land-use efficiency and its mechanism:Case study of Shandong Peninsula urban agglomeration

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Journal of Geographical Sciences 2019年第4期29卷 549-562页

作者： CUI Xuegang FANG Chuanglin WANG Zhenbo bao Chao Institute of Geographic Sciences and Natural Resources Research CASBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Land-use efficiency is low for the urban agglomeration of ***-speed transportation construction has been an important factor driving land use *** is criti?cally importa nt to explore the spatial relati on ship between the high-speed transportation su?periority degree and land-use efficie *** built a model to evaluate the ben efits of con?venient high-speed transportation using the relative density of highways and the distanee from high-speed rail stations and airports as a *** used 42 coun ties of the Shan dong Peninsula urban agglomeration as an ***?use efficiency was calculated by a DEA model with capital,labor,economic ben efits and envir on mental ben efits as input and output *** examined the spatial relati on ships betwee n high-speed tran sport superiority degree and land-use efficiency and obtained the following ***,there are significant spatial differe nces in the relati on ships betwee n the high-speed transportati on superiority degree and land-use *** the two major cities of Jinan and Qingdao as the hubs,the core surrounding counties show significant spatial relationship between land-use efficiency and the high-speed transportation superiority *** correlation declines as the distance from the hubs in ***-use efficiency is less tha n high-speed tran sportation convenience in areas along the transportation trunks that are distant from the hub *** is low in areas that are away from both hub cities and transportation trunk ***,high-speed transportation has a positive relationship with land?use efficiency due to the mechanism of element agglomeration exogenous ***,high-speed transportation facilitates the flow of goods,services and tech no logies between core cities and peripheral cities as space spillover(the hub effect).This alters the spatial pattern of regional land-use *** ally,the short-board effect caused by decreased high-spee

关键词： high-speed transportation superiority degree DEA land-use efficiency spatial relationship Shandong Peninsula urban agglomeration

RANBP17在胶质母细胞瘤中的生物学功能研究

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解剖学研究 2024年第3期46卷 248-256页

作者：唐海周令麒刘雪梅刘群娣温宝莹敬美莲黄华聪广东江门中医药职业学院基础医学院广东江门529000 中山大学中山医学院遗传学与生物医学信息学系广东广州510080 广州市妇女儿童医疗中心儿科研究所广东广州510623 南方医科大学顺德医院(顺德第一人民医院)妇科广东佛山528308 广东江门中医药职业学院南药学院广东江门529000 广东江门中医药职业学院中医学院广东江门529000

目的探讨RAN结合蛋白17(RANBP17)基因在胶质母细胞瘤(GBM)中的生物学功能。方法采用UALCAN和CGGA数据库分析RANBP17在GBM中的表达及预后价值。采用LinkedOmics数据库筛选与RANBP17表达相关的基因并通过DAVID数据库进行基因功能富集分析... 详细信息

目的探讨RAN结合蛋白17(RANBP17)基因在胶质母细胞瘤(GBM)中的生物学功能。方法采用UALCAN和CGGA数据库分析RANBP17在GBM中的表达及预后价值。采用LinkedOmics数据库筛选与RANBP17表达相关的基因并通过DAVID数据库进行基因功能富集分析。采用荧光定量PCR(RT-qPCR)检测RANBP17在GBM和正常胶质细胞(HEB)中的表达水平。采用CCK8、流式细胞术、tran-swell方法检测过表达RANBP17对GBM U251细胞增殖、凋亡、迁移和侵袭的影响;采用ENCORI、miRWalk和miRDB数据库预测RANBP17的上游miRNA。结果RANBP17在GBM中的表达水平低于正常组织(P<0.05);RANBP17在41岁以下、继发性GBM、IDH突变型、MGMT启动子甲基化和1p19q联合缺失的GBM患者中高表达(均P<0.01);500个RANBP17表达相关的基因富集分析显示RANBP17表达相关基因能参与炎症反应、细胞粘附、凋亡过程的负向调控、紧密连接和亚油酸代谢等过程和信号通路;过表达RANBP17降低GBM U251细胞的增殖、迁移、侵袭并促进细胞凋亡(均P<0.05);ENCORI、miRWalk和miRDB数据库中有8个共同的miRNAs(hsa-miR-650、hsa-miR-361-5p、hsa-miR-421、hsa-miR-9-5p、hsa-miR-3612、hsa-miR-299-5p、hsa-miR-2115-3p和hsa-miR-19b-3p)调控RANBP17。结论RANBP17可能作为一种抑癌基因参与GBM的发生发展,是GBM潜在的预后生物标志物和治疗靶点。

关键词：胶质母细胞瘤 RAN结合蛋白17 表达预后生物学功能生物信息学

越南中级汉语综合课语法教学模式个案研究 ——以胡志明市人文社科大学中文系为例

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越南中级汉语综合课语法教学模式个案研究 ——以胡志明市人文社...

作者：陈皇宝珠（tran HOANG bao CHAU）中央民族大学

学位级别：硕士

汉语教学在越南已有悠久的历史。据记载,早在公元5世纪,越南就开始了汉语教学。近十几年中国经济的崛起,带动了全世界学习汉语的热潮。与此同时越南经济也迅猛发展,中国、台湾及新加坡等国家和地区踊跃地在越南投资,这无疑给汉语传播带... 详细信息

汉语教学在越南已有悠久的历史。据记载,早在公元5世纪,越南就开始了汉语教学。近十几年中国经济的崛起,带动了全世界学习汉语的热潮。与此同时越南经济也迅猛发展,中国、台湾及新加坡等国家和地区踊跃地在越南投资,这无疑给汉语传播带来了新的活力,汉语的需求量大大提升,学习汉语已成为当务之急。现在在越南汉语已经成为了外语教学的热门语种之一。在越南,关于汉语教学已有大量的研究,如语音、词汇、汉字等语言要素方面的研究,三教问题的研究,文化方面的研究等等都十分丰富。但汉语教学模式研究还是一个全新的领域。根据笔者所查阅的文献来看,现在在越南似乎没有关于汉语教学模式研究类的文章,这方面的研究还有很大的研究空间与价值。因此,根据越南的实际情况,总结归纳出越南本土的汉语教学模式非常有必要。本研究主要针对越南胡志明市人文社科大学中级汉语综合课的语法教学,运用案例分析、课堂观察、问卷调查及口头与书面访谈等研究方法,调查、分析、总结出越南胡志明市人文社科大学的中级汉语综合课的语法教学模式,并通过分析其教学任务、目的及特点较为系统地论述了此模式的合理性及局限性。本研究为越南汉语教学模式提供了一个有价值的个案研究,本文的研究成果将为提高越南汉语教学水平、进行教学改革提供一些参考,对教师教学方法的改善有所启示与帮助。同时也希望本文能引起越南汉语教学界对教学模式研究的关注。本文主要包括五个部分的研究内容：第一章绪论阐述了本研究的选题缘起、研究意义、研究思路、研究方法及国内外的相关研究。第二章主要介绍研究背景,包括越南汉语教学的基本情况、越南胡志明市人文社科大学与中国语文系的简介以及越南人文社科大学中级汉语综合课教学的概述。第三章对胡志明市人文社科大学中级汉语综合课的语法教学模式进行全面描述。首先阐述了该校语法教学模式的理念、语法教学的任务、目的及特点,然后描述该模式的教学设计及实施情况,最后对该校语法教学模式的实施条件进行了分析。第四章通过对胡志明市人文社科大学中级汉语综合课语法教学中的典型案例分析展现该校中级汉语综合课语法教学的具体步骤。第五章通过分析学生调查问卷的统计结果及教师访谈,总结出该校语法教学模式的特点,并指出其合理性与局限性,并为胡志明市人文社科大学中级汉语综合课语法教学提供了教学建议。

关键词：越南胡志明市人文社科大学综合课语法教学教学模式

Deepwater gas kick simulation with consideration of the gas hydrate phase transition

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Journal of Hydrodynamics 2014年第1期26卷 94-103页

作者：王志远孙宝江 School of Petroleum Engineering China University of Petroleum (East China)

The hydrate phase transition presents new problems and challenges for the deepwater well control in the drilling processes. A simulation model is built for deepwater gas kicks with consideration of the hydrate phase transition. The model is based on the multiphase flow governing equations and the hydrate phase transition calculation equations. The influence of the hydrate phase tran-sition on the gas kick hydraulics is investigated through numerical simulations. It is shown that the diameter of the gas bubbles can significantly influence the hydrate phase transition effect. The influence of the hydrate phase transition on the gas kick hydraulics in-creases with the decrease of the average gas bubble diameter. The hydrate phase transition adds a＂hidden＂nature for the well kick in deepwater and hinders the early detection of the gas kick. The influence of the hydrate phase transition on the gas kick hydraulics is also studied in the case when the hydrate inhibitor is added to the drilling fluid.

关键词： deepwater gas kick simulation gas hydrate phase transition

transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing

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Journal of Integrative Plant Biology 2016年第2期58卷 150-164页

作者： Ying Wu Yue Sun Xutong Wang Xiuyun Lin Shuai Sun Kun Shen Jie Wang Tingting Jiang Silin Zhong Chunming Xu bao Liu Key Laboratory of Molecular Epigenetics of the Ministry of Education(MOE) Northeast Normal UniversityChangchun 130024China Jilin Academy of Agricultural Sciences Changchun 130032China State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina

Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed ＂transcriptome shock＂. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica （2n=2x=24, genome AA） and the tetraploid form of O. punctata （2n=4x =48, genome, BBCC）, and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico ＂hybrids＂（parental mixtures）. We found that approximately 16% （2,541） of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the tran- scriptome response to interspecific hybridization and heterosis.

关键词： Cis- and trans-regulation homeolog expression rewiring interspecific hybrid Oryza promoter divergence transcriptome shock

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整体涡对跨声速单转子性能和稳定性影响

航空动力学报 2016年第9期31卷 2233-2238页

作者：屠宝锋胡骏张凯南京航空航天大学能源与动力学院江苏省航空动力系统重点实验室南京210016 先进航空发动机协同创新中心北京100191

为研究整体涡影响轴流压气机性能和稳定性的机理,设计了一种叶片式旋流发生器,并对旋流发生器和跨声速单转子进行了联合数值模拟研究.计算结果表明:反向整体涡导致堵塞点流量、进口攻角和总压比增加,效率和稳定工作范围降低;同向整体涡... 详细信息

为研究整体涡影响轴流压气机性能和稳定性的机理,设计了一种叶片式旋流发生器,并对旋流发生器和跨声速单转子进行了联合数值模拟研究.计算结果表明:反向整体涡导致堵塞点流量、进口攻角和总压比增加,效率和稳定工作范围降低;同向整体涡导致堵塞点流量、进口攻角、总压比和稳定工作范围减小,效率增加;反向整体涡导致50%叶高以上吸力面附面层分离以及叶尖泄漏流堵塞加剧是压气机失稳的主要原因.

关键词：压气机跨声速整体涡旋转发生器稳定性