检索结果-内蒙古大学图书馆

Efficient and Stereoselective Synthesis of α(2→9) Oligosialic Acids: From Monomers to Dodecamers†

Angewandte Chemie 2011年第40期123卷

作者： Kuo‐Ching Chu Chien‐Tai Ren Chun‐Ping Lu Che‐Hsiung Hsu Tsung‐Hsien Sun Jeng‐Liang Han Bikash Pal Tsung‐An Chao Yung‐Feng Lin Shih‐Hsiung Wu Chi‐Huey Wong Chung‐Yi Wu Genomics Research Center Academia Sinica 128 Academia Road Section 2 Nankang Taipei 115 (Taiwan) Institute of Biological Chemistry Academia Sinica (Taiwan) Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica 128 Academia Road Section 2 Nankang Taipei 115 (Taiwan) Institute of Bioinformatics and Structural Biology National Tsing‐Hua University Hsin‐Chu (Taiwan)

来源：评论

学校读者我要写书评

暂无评论

Auf dem Weg zur automatisierten Oligosaccharid‐ Synthese

引用

Angewandte Chemie 2011年第50期123卷

作者： Che‐Hsiung Hsu Shang‐Cheng Hung Chung‐Yi Wu Chi‐Huey Wong The Genomics Research Center Academia Sinica Taiwan 128 Academia Road Section 2 Nankang Taipei 115 (Taiwan) Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica (Taiwan) Institute of Bioinformatics and Structural Biology National Tsing‐Hua University Hsin‐Chu (Taiwan) Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 (USA)

Kohlenhydrate spielen eine wichtige Rolle bei biologischen Vorgängen. Das Fortschrittstempo der Kohlenhydratforschung ist jedoch relativ langsam, was unter anderem mit der Komplexität der Kohlenhydratstrukturen und dem Fehlen allgemein anwendbarer Synthesemethoden und Verfahren zur Untersuchung dieser Klasse von Biomolekülen zusammenhängt. Jüngste Fortschritte in der Synthese haben ergeben, dass viele dieser Probleme umgangen werden können. In diesem Aufsatz beschreiben wir die Methoden, die entwickelt wurden, um mit den Herausforderungen kohlenhydratvermittelter biologischer Vorgänge umzugehen. Besonderes Augenmerk wird dabei auf die Entwicklung der automatisierten Synthese von Oligosacchariden gerichtet. Darüber hinaus werden auch Kohlenhydrat‐Mikroarrays und Impfstoffe auf Kohlenhydratbasis behandelt.

关键词： Eintopfreaktionen Festphasensynthese Impfstoffe Kohlenhydrate Mikroarrays

来源：评论

学校读者我要写书评

暂无评论

The keyword-based and semantic-driven data matching approach for assisting structuralizing the textual clinical documents

The keyword-based and semantic-driven data matching approach...

引用

international Conference on BioMedical Engineering and Informatics (BMEI)

作者： Chi-Huang Chen Xiao-Ou Ping Zi-Jun Wang Sheau-Ling Hsieh Li-Chin Chen Yi-Ju Tseng Ching-Wei Hsu Feipei Lai Department of Electrical Engineering National Taiwan University Taipei Taiwan Graduate Institute of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronic and Bioinformatics National Taiwan University Taipei Taiwan EECS International Graduate Program Institute IT Center National Chiao Tung University Hsinchu Taiwan

The clinical data stored in the health information system can be categorized as two types including structuralized data and non-structuralized ones. In the paper, a data extraction system is developed to assist data retrieval from the non-structuralized textual clinical documents such as radiology reports, pathology reports, etc. The system provides keyword-based and semantic-driven data matching methodology to extract the specific information from the textual clinical documents. The matching methodology provides the capabilities to recognize the selected keywords and the related semantics in the documents. Through the extraction verification interface, clinicians can extract and verify the matched information semi-automatically. The extracted data can be filled into predefined case-oriented templates. The structuralized data can be stored back into the clinical data warehouse for further analyzing. Moreover, the case-oriented templates can support collecting corresponding extracted data for various researches.

关键词： Data mining Semantics Pattern matching Tumors Radiology Pathology Cancer

来源：评论

学校读者我要写书评

暂无评论

Web-based healthcare Hand Drawing Management System

Web-based healthcare Hand Drawing Management System

引用

Annual international Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Sheau-Ling Hsieh Yung-Ching Weng Chi-Huang Chen Kai-Ping Hsu Jeng-Wei Lin Feipei Lai EECS International Graduate Program Institute IT Center National Chiao Tung University Hsinchu Taiwan Taiwan University Taipei Taiwan Department of Electrical Engineering National Taiwan University Taipei Taiwan Computer and Information Networking Center National Taiwan University Taipei Taiwan Department of Information Management Tunghai University Taichung Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan

The paper addresses Medical Hand Drawing Management System architecture and implementation. In the system, we developed four modules: hand drawing management module; patient medical records query module; hand drawing editing and upload module; hand drawing query module. The system adapts windows-based applications and encompasses web pages by *** hosting mechanism under web services platforms. The hand drawings implemented as files are stored in a FTP server. The file names with associated data, e.g. patient identification, drawing physician, access rights, etc. are reposited in a database. The modules can be conveniently embedded, integrated into any system. Therefore, the system possesses the hand drawing features to support daily medical operations, effectively improve healthcare qualities as well. Moreover, the system includes the printing capability to achieve a complete, computerized medical document process. In summary, the system allows web-based applications to facilitate the graphic processes for healthcare operations.

关键词： Medical services Biomedical imaging Printing Conferences Web services Graphics Databases

来源：评论

学校读者我要写书评

暂无评论

引用

Annual international Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Chi-Huang Chen Sheau-Ling Hsieh Yung-Ching Weng Wen-Yung Chang Feipei Lai Department of Electrical Engineering National Taiwan University Taipei Taiwan EECS International Graduate Program Institute IT Center National Chiao Tung University Hsinchu Taiwan Department of Computer Science and Engineering National Taiwan University Taiwan Institute of Computer Science and Engineering College of Computer Science National Chiao Tung University Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan

Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

关键词： Semantics Biomedical measurements Correlation Kernel Training Medical services Support vector machine classification

来源：评论

学校读者我要写书评

暂无评论

Protein subcellular localization prediction of eukaryotes using a knowledge-based approach

引用

BMC bioinformatics 2009年第SUPPL. 15期10卷 1-13页

作者： Lin, Hsin-Nan Chen, Ching-Tai Sung, Ting-Yi Ho, Shinn-Ying Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Bioinformatics Lab. Institute of Information Science Academia Sinica Taipei Taiwan Institute of Bioinformatics National Chiao Tung University Hsinchu Taiwan

Background: The study of protein subcellular localization (PSL) is important for elucidating protein functions involved in various cellular processes. However, determining the localization sites of a protein through wet-lab experiments can be time-consuming and labor-intensive. Thus, computational approaches become highly desirable. Most of the PSL prediction systems are established for single-localized proteins. However, a significant number of eukaryotic proteins are known to be localized into multiple subcellular organelles. Many studies have shown that proteins may simultaneously locate or move between different cellular compartments and be involved in different biological processes with different roles. Results: In this study, we propose a knowledge based method, called KnowPredsite, to predict the localization site(s) of both single-localized and multi-localized proteins. Based on the local similarity, we can identify the "related sequences" for prediction. We construct a knowledge base to record the possible sequence variations for protein sequences. When predicting the localization annotation of a query protein, we search against the knowledge base and used a scoring mechanism to determine the predicted sites. We downloaded the dataset from ngLOC, which consisted of ten distinct subcellular organelles from 1923 species, and performed ten-fold cross validation experiments to evaluate KnowPredsite's performance. The experiment results show that KnowPredsite achieves higher prediction accuracy than ngLOC and Blast-hit method. For single-localized proteins, the overall accuracy of KnowPredsite is 91.7%. For multi-localized proteins, the overall accuracy of KnowPredsite is 72.1%, which is significantly higher than that of ngLOC by 12.4%. Notably, half of the proteins in the dataset that cannot find any Blast hit sequence above a specified threshold can still be correctly predicted by KnowPredsite. Conclusion: KnowPredsite demonstrates the power of identifying rel

关键词： Proteins

来源：评论

学校读者我要写书评

暂无评论

The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA

引用

Nucleic Acids Research 2009年第3期37卷 804-814页

作者： Lo, Yu-Hua Tsai, Kuang-Lei Sun, Yuh-Ju Chen, Wei-Ti Huang, Cheng-Yang Hsiao, Chwan-Deng Institute of Molecular Biology Academia Sinica Taipei 115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu 300 Taiwan Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan

DNA helicases are motor proteins that play essential roles in DNA replication, repair and recombination. In the replicative hexameric helicase, the fundamental reaction is the unwinding of duplex DNA;however, our understanding of this function remains vague due to insufficient structural information. Here, we report two crystal structures of the DnaB-family replicative helicase from Geobacillus kaustophilus HTA426 (Gk DnaC) in the apo-form and bound to single-stranded DNA (ssDNA). The Gk DnaC-ssDNA complex structure reveals that three symmetrical basic grooves on the interior surface of the hexamer individually encircle ssDNA. The ssDNA-binding pockets in this structure are directed toward the N-terminal domain collar of the hexameric ring, thus orienting the ssDNA toward the DnaG primase to facilitate the synthesis of short RNA primers. These findings provide insight into the mechanism of ssDNA binding and provide a working model to establish a novel mechanism for DNA translocation at the replication fork. © 2008 The Author(s).

关键词：

来源：评论

学校读者我要写书评

暂无评论

Structural insights into TDP-43 in nucleic-acid binding and domain interactions

引用

Nucleic Acids Research 2009年第6期37卷 1799-1808页

作者： Kuo, Pan-Hsien Doudeva, Lyudmila G. Wang, Yi-Ting Shen, Che-Kun James Yuan, Hanna S. Institute of Bioinformatics and Structural Biology National Tsing Hua University Taipei Taiwan Institute of Molecular Biology National Taiwan University Taipei Taiwan Taiwan International Graduate Program Chemical Biology and Molecular Biophysics National Taiwan University Taipei Taiwan Graduate Institute of Biochemistry and Molecular Biology National Taiwan University Taipei Taiwan

TDP-43 is a pathogenic protein: its normal function in binding to UG-rich RNA is related to cystic fibrosis, and inclusion of its C-terminal fragments in brain cells is directly linked to frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Here we report the 1.65 Å crystal structure of the C-terminal RRM2 domain of TDP-43 in complex with a single-stranded DNA. We show that TDP-43 is a dimeric protein with two RRM domains, both involved in DNA and RNA binding. The crystal structure reveals the basis of TDP-43's TG/ UG preference in nucleic acids binding. It also reveals that RRM2 domain has an atypical RRM-fold with an additional β-strand involved in making protein-protein interactions. This self association of RRM2 domains produced thermal-stable RRM2 assemblies with a melting point greater than 85°C as monitored by circular dichroism at physiological conditions. These studies thus characterize the recognition between TDP-43 and nucleic acids and the mode of RRM2 self association, and provide molecular models for understanding the role of TDP-43 in cystic fibrosis and the neurodegenerative diseases related to TDP-43 proteinopathy. © 2009 The Author(s).

关键词：

来源：评论

学校读者我要写书评

暂无评论

Impact of DNA-binding position variants on yeast gene expression

引用

Nucleic Acids Research 2009年第21期37卷 6991-7001页

作者： Swamy, Krishna B.S. Cho, Chung-Yi Chiang, Sufeng Tsai, Zing Tsung-Yeh Tsai, Huai-Kuang Institute of Information Science National Yang-Ming University Taiwan Bioinformatics Program Taiwan International Graduate Program National Yang-Ming University Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Research Center for Information Technology Innovation Academia Sinica Taipei 115 Taiwan

Transcription factors (TFs) regulate gene expression by binding to specific binding sites (TFBSs) in gene promoters. TFBS motifs may contain one or more variable positions. Although the prevailing assumption is that nucleotide variants at such positions are functionally equivalent, there is increasing evidence that such variants play a role in regulation of gene expression. In this article, we propose a method for studying the relationship between the expression of target genes and nucleotide variants in TFBS motifs at a genome-wide scale in Saccharomyces cerevisiae, especially the combinatorial effects of variants at two positions. Our analysis shows that nucleotide variations in more than one-third of variable positions and in 20% of dependent position pairs are highly correlated to gene expression. We define such positions as 'functional'. However, some positions are only functional as dependent pairs, but not individually. In addition, a significant proportion of the functional positions have been well conserved across all yeast-related species studied. We also find that some positions require the presence of co-occurring TFs, while others maintain their functionality in the absence of a co-occurring TF. Our analysis supports the importance of nucleotide variants at variable positions of TFBSs in gene regulation. © The Author(s) 2009. Published by Oxford University Press.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Predicting helix-helix interactions from residue contacts in membrane proteins

引用

bioinformatics 2009年第8期25卷 996-1003页

作者： Lo, Allan Chiu, Yi-Yuan Rødland, Einar Andreas Lyu, Ping-Chiang Sung, Ting-Yi Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Institute of Bioinformatics and Structural Biology Department of Life Sciences National Tsing Hua University Hsinchu Taiwan Bioinformatics Laboratory Institute of Information Science Academia Sinica Taipei Taiwan Centre for Cancer Biomedicine University of Oslo NO-0027 Oslo Norway SAMBA Norwegian Computing Center Blindern NO-0314 Oslo P.O. Box 114 Norway

Motivation: Helix-helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or more residue contacts. Although previous studies focused on helix-packing patterns and sequence motifs, few of them developed methods specifically for contact prediction. Results: We present a new hierarchical framework for contact prediction, with an application in membrane proteins. The hierarchical scheme consists of two levels: in the first level, contact residues are predicted from the sequence and their pairing relationships are further predicted in the second level. Statistical analyses on contact propensities are combined with other sequence and structural information for training the support vector machine classifiers. Evaluated on 52 protein chains using leave-one-out cross validation (LOOCV) and an independent test set of 14 protein chains, the two-level approach consistently improves the conventional direct approach in prediction accuracy, with 80% reduction of input for prediction. Furthermore, the predicted contacts are then used to infer interactions between pairs of helices. When at least three predicted contacts are required for an inferred interaction, the accuracy, sensitivity and specificity are 56%, 40% and 89%, respectively. Our results demonstrate that a hierarchical framework can be applied to eliminate false positives (FP) while reducing computational complexity in predicting contacts. Together with the estimated contact propensities, this method can be used to gain insights into helix-packing in membrane proteins. © 2009 The Author(s).

关键词：

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：