矩阵奇异值分解(SVD)的应用

奇异值是矩阵的一个良好特征。本文通过对矩阵奇异值分解的分析,在主成分分析、图像压缩、数字水 印和文章分类等方面的应用方法进行了描述,同时提供了部分应用例子。     

基于非负矩阵分解的流程工业过程监控方法

提出了一种新的基于非负矩阵分解（NMF）的过程监控方法。考虑到数据的某些局部特征能够包含许多重要信息,有助于对异常情况进行检测,将NMF引入工业过程监控领域,并详述了基于NMF的过程监控方法。基于TE过程的仿真实验验证了该方法的有效性。     

非负矩阵分解算法在胃癌基因表达数据分类中的应用

依据基因表达数据,利用计算机技术对其样本进行分类并找到在肿瘤组织中特异表达的基因,使之能够对疾病的治疗和生物医学研究起到有益的参考和借鉴作用.本文采用非负矩阵分解算法,对基因表达数据进行分析,然后对分解后得到的基矩阵中各集合基因进行比较,找出在肿瘤组织中有特异表达的基因,并做出生物解释.以胃癌基因表达数据为例进行实验,结果表明了该方法的可行性和有效性.     

运用非相关文献知识发现方法挖掘疾病的潜在相关基因

基于非相关文献的知识发现有开放式挖掘和闭合式验证两个过程.先应用开放式的非相关文献知识发现方法寻找与先天性全身多毛症(CGH)相关的潜在候选基因,再应用闭合式方法进行验证和初筛,最后使用Gene、OMIM及PubMed数据库对初筛后保留的基因进一步分析研究,发现CGH可能与位于常染色体17q的潜在MAP2K6基因相关.实践证明,应用非相关文献知识发现方法可用于挖掘疾病的潜在基因.     

非负矩阵因子分解算法解析手性药物重叠峰的HPLC-DAD数据

目的:研究非负矩阵因子分解算法(NMF)用于手性药物HPLC-DAD二维数据解析的可行性及其影响因素。方法:根据化学波谱的基本特征如色谱的单峰性改进NMF算法。考查组分之间色谱分离度、光谱相似程度以及迭代次数对模拟重叠峰解析结果的影响,并将NMF算法应用于实测体系盐酸舍曲林对映异构体体(cis-1R,4R;cis-1S,4S)重叠峰解析。结果:解析结果表明,在色谱严重重叠,光谱相似甚至完全相同时,在合适的迭代次数下,NMF能解析出重叠峰中各单组分的光谱和相应色谱。结论该种二维数据的解析方法,将为混合样本特别是手性药物混合体系的分析提供新途径。     

利用生物信息学分析鉴定与骨关节炎相关的潜在核心基因

目的:初步探索骨关节炎病理进程中可能涉及的信号通路,筛选与骨关节炎发生相关的关键基因,从而揭示骨关节炎的发病机制.方法:从公共基因芯片数据库(Gene Expression Omnibus,GEO)下载骨关节炎相关芯片数据(GSE19060),利用GEO2R工具筛选骨关节炎(osteoarthritis,OA)和正常组...     

归并奇异值分解:一种快速更新隐含语义索引的方法

隐含语义索引（LSI）是一种解决信息检索中二义性问题和大规模文档分类的文档索引方法。为了提高LSI效率,应对大数据场景下文档量爆发式增长的问题,提出了一种通过归并奇异值分解来实现LSI快速更新的方法。该方法利用p-边宽单边对角矩阵和箭头矩阵分解技术来加快中间矩阵的奇异值分解过程,并通过将新增文档矩阵的薄奇异值分解（PSVD）归并进主文档矩阵的PSVD以避免重复计算,加快LSI更新速度。通过数学证明论证了该方法的有效性,并讨论了该算法扩展到词条更新场景中的情形。在多个测试数据集上的实验验证了该方法可以在保证检索准确率的前提下有效提高LSI的更新效率。     

利用基因表达谱提取乳腺癌细胞分化相关特征基因

目的 利用基因芯片数据挖掘识别与乳腺癌组织学分级相关的特征基因,对乳腺癌的临床诊断和生物医学研究起到借鉴和参考作用.方法 从公共基因芯片数据库GEO(gene expression omnibus)获得乳腺癌芯片表达数据,利用支持向量机提取获得不同组织学分级的肿瘤样本的特征基因,并对这些基因进行生物学功能分析.结果 获得了64个特征基因,分类正确率达到100%,这些基因与癌症有较大的相关性,主要集中在转录调控、离子运输、器官发生发育等多个生物学途径中.结论 通过对基因芯片数据的挖掘,可以从全局上了解肿瘤的表达情况,加深对乳腺癌细胞分化分子机制的认识.     

基于Gammachirp耳蜗能量谱特征提取的音频指纹算法

提出了基于Gammachirp耳蜗能量谱的音频时频域特征表示方法,并在此基础上进一步构造了一种音频指纹算法。首先利用非负矩阵分解(Non-negative Matrix Factorization, NMF)提取Gammachirp耳蜗能量谱的局部特征,然后对该局部特征进行差分和量化,以提高算法的鲁棒性,并降低检索的计算复杂度。实验结果表明:在经受音频编辑软件多种攻击和实际环境中录音检索时,本文算法都具有很好的鲁棒性和识别率。     

Identification of Prognostic Related Hub Genes in Clear-Cell Renal Cell Carcinoma via Bioinformatical Analysis

Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma (ccRCC) via bioinformatics analysis. Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database: GSE12606, GSE36895 and GSE66272. The differentially expressed genes were screened with GEO2R and J Venn online tools. Functional annotation including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was applied to identify the possible function of the hub genes involved in prognosis of ccRCC. In protein protein interaction network (PPI network), the STRING online tool was used to visualize the network of the differentially expressed genes, and the core gene was selected by MCODE App in Cytoscape software. Finally, GEPIA Survival Plot was performed to assess genes associated with worse survival. Results We totally found 648 differentially expressed genes, including 222 up-regulated genes and 426 down-regulated genes. PPI network showed that in 28 up-regulated genes 7 (CCNE2, CDK1, CDC6, CCNB2, BUB1, TTK and PTTG1) enriched in cell cycle and 4 genes (CCNE2, CDK1, CCNB2 and RRM2) enriched in p53 signaling pathway. GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1, CCNB2, RRM2, BUB1, and PTTG1 had a worse survival. GEPIA Box Plot showed that BUB1, CCNB2, PTTG1, and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues (P<0.05). Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1, CCNB2, PTTG1, and RRM2 might manifest a poor prognosis.     

对中国生物医学光盘文献的计量分析

利用《中目》(医药卫生)光盘数据库对1982～1997年收录的16年文献进行计量分析，通过统计分析发现，该数据库每年收录文献量呈增长趋势，平均发展速度为113.7％，平均增长速度为13.7％。     

Isoflavone Regulates Lipid Metabolism via Expression of Related Genes in OVX Rats Fed on a High-fat Diet

Objective To investigate the effects of isoflavone on body weight, fat mass, and gene expression in relation to lipid metabolism. Methods Thirty-six female SD rats were ovariectomized or sham-operated and fed on a high-fat diet. Two months later, abdominal incision was made, blood was collected to separate serum, and the liver and adipose tissue were immediately collected and weighed. Some portions of these tissues were frozen in liquid nitrogen and stored at -80℃. Results Ovariectomy （OVX） with a high-fat diet could induce obesity in rats, while treatment with isoflavone significantly inhibited the increase in body weight and fat mass in abdomen. Serum total cholesterol and leptin were significantly decreased in isoflavone group, compared with the OVX group. The mRNA expression of liver fatty acid synthase （FAS） in the OVX group was significantly higher than that in sham-operated group, while this difference was not observed in the isoflavone group. The mRNA expression of liver hormone-sensitive lipase （HSL） in the OVX rats tended to be lower than that in the sham-operated rats. Furthermore, a large amount of isoflavone maintained the mRNA expression at a sham level. Conclusion Isoflavone may prevent obesity induced by ovariectomy with a high-fat diet, in part by modulating gene expression related to lipid metabolism.     

瘢痕疙瘩相关基因的最新研究进展

在一定程度上,瘢痕疙瘩在临床表现和组织学上具有肿瘤的生物学特性,有学者借鉴肿瘤的研究成果将其引入瘢痕疙瘩的研究中。现已发现许多肿瘤相关基因及细胞因子在瘢痕疙瘩的发生、发展中起着重要作用。这些基因或者细胞因子能影响瘢痕疙瘩成纤维细胞增殖、凋亡或细胞外沉积、降解,从而对瘢痕疙瘩的发病机制产生影响。     

多囊卵巢综合征基因多态性研究新进展

多囊卵巢综合征(PCOS)是育龄妇女中一种常见的异质性内分泌疾病,患者临床表现及并发症复杂多样。PCOS的病因至今尚未阐明,高雄激素血症和胰岛素抵抗是PCOS患者主要的病理生理改变,雄激素和胰岛素生物合成和代谢相关基因的多态性可能与PCOS的发病机制相关。该综述概括了近年来相关基因多态性与PCOS关系的研究进展,进一步探讨PCOS的发病机制。     

瞬时感受器电位离子通道4相关的离子通道病

瞬时感受器电位离子通道4(TRPV4)是瞬时感受器电位离子通道家族香草素受体亚家族的成员之一,也是瞬时感受器电位离子通道家族中被阐述最多、最特别的一个。它具有使其编码的Ca~(2+)通道失活的多种突变倾向,侵袭骨骼系统、神经系统、呼吸系统等,且临床表型多样。目前,研究较多的是骨骼发育不良和周围神经病,但均只能推测TRPV4基因突变引起各种临床表现(骨骼、运动和感觉症状)的(病理)生理学机制。因此,明确此类疾病的发病机制、病因、分类、开发药理学的潜能,对TRPV4相关疾病的预防和治疗有重要意义。     

变应性鼻炎发病相关基因及基因敲除在其研究中的应用

变应性鼻炎(AR)是发生在鼻黏膜的慢性炎症性疾病,是多基因控制的变态反应性疾病。目前关于AR发病机制基因水平的研究,比较明确的主要集中在Toll样受体相关基因、细胞因子以及转录因子等。基因敲除技术作为研究基因功能的一种重要方法,已广泛应用于各领域疾病的基因研究。利用基因敲除技术,研究Toll样受体相关基因、细胞因子以及转录因子等AR易患基因,可能为治疗AR找到新的方法。     

常用国外全文数据库生物医学文献保障率评价分析

采用PubMed作为参照数据库，应用科技查新和文献检索实例，对Elsevier SDOS、EBSCO、SpringerLink、UMI ProQuest、Ovid等常用国外全文数据库生物医学文献收录情况进行小样本抽样统计、对比、分析和评价，并计算出文献保障率，旨在为医学科研人员快速、准确获取生物医学文献和图书馆选购国外全文数据库提供参考。     

The Prevalence and Inaccessibility of Internet References in the Biomedical Literature at the Time of Publication

Objectives

To determine the prevalence and inaccessibility of Internet references in the bibliography of biomedical publications when first released in PubMed®.

Methods

During a one-month observational study period (Feb 21 to Mar 21, 2006) the Internet citations from a 20% random sample of all forthcoming publications released in PubMed during the previous day were identified. Attempts to access the referenced Internet citations were completed within one day and inaccessible Internet citations were recorded.

Results

The study included 4,699 publications from 844 different journals. Among the 141,845 references there were 840 (0.6%) Internet citations. One or more Internet references were cited in 403 (8.6%) articles. From the 840 Internet references, 11.9% were already inaccessible within two days after an article’s release to the public.

Conclusion

The prevalence of Internet citations in journals included in PubMed is small (<1%); however, the inaccessibility rate at the time of publication is considered substantial. Authors, editors, and publishers need to take responsibility for providing accurate and accessible Internet references.     

大肠杆菌莽草酸生物合成途径的基因操作

为了调查大肠杆菌中相关基因的遗传操作对莽草酸途径和莽草酸积累的影响,利用温度敏感型质粒敲除了大肠杆菌JM83染色体DNA上编码莽草酸激酶的aroL基因,获得了该基因缺陷株JDL02;同时从大肠杆菌JM83染色体中分别克隆了aroG、ppsA和tktA 3个基因,构建了多个表达质粒导入JDL02,得到了一系列重组菌。摇瓶发酵显示aroG基因的作用最为明显,各重组菌莽草酸产量均有不同程度的提高;在等生物量情况下,JDL02/pTrc-aroG-tktA的莽草酸产量是JM83的18.35倍,其摇瓶产量为94.33 mg/L。