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Yang K.-C.,National Yang Ming University | Lin C.-C.,National Yang Ming University | Lin C.-C.,Graduate Institute of Biomedical Electronics and Bioinformatics | Juan H.-F.,Graduate Institute of Biomedical Electronics and Bioinformatics | And 2 more authors.
Bioinformatics | Year: 2014

Summary: Exploring microRNA (miRNA) regulations and protein- protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein- protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein-protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users. Mirin has successfully uncovered oncomirs and their regulatory networks in various cancers, such as gastric and breast cancer. © The Author 2014. Published by Oxford University Press. All rights reserved.


Wu C.-K.,National Taiwan University Hospital | Wu C.-K.,National Taiwan University | Huang Y.-T.,Far Eastern Memorial Hospital | Lee J.-K.,National Taiwan University Hospital | And 10 more authors.
Atherosclerosis | Year: 2014

Objective: Anti-anxiety medication in patients with anxiety may lessen the stress and thereby lower their risk for myocardial infarction (MI). The aim of current study is to examine an association between the use of anti-anxiety medication and long-term mortality risk in patients following MI. Methods: A universal national health insurance (NHI) program has been implemented in Taiwan since 1995. We used system sampling database from 1997 to 2008 with a total of 1,000,000 subjects. We included subjects with first episode of MI and were above 30 years old. Sudden death, cardiovascular mortality, and heart failure hospitalization were assessed in all included subjects. Anti-anxiety as well as other medications and risk factors were obtained. Cox regression analysis was used to evaluate the adjusted hazard ratio (HR) for all patients and subgroups. Results: The adjusted HRs of sudden death were significantly associated with increased benzodiazepam (BZD) dosage (HRs=0.639, 1.003, 1.957 from Q2 to Q4 vs. Q1, p=.019 for trend) during approximately 4.8 years. For cardiac mortality and heart failure hospitalization, there was a J-curve dose-response relationship. The HRs for cardiac mortality were 0.255 (p<.001) and 0.385 (p<.001) for Q2 and Q3 vs. Q1, respectively. For patients receiving higher doses of daily BZDs (>5mg), protective effects for cardiac mortality and heart failure hospitalization decreased and a J-curve dose-response relationship was seen. Conclusion: Anti-anxiety medications are independent associated with a decreased risk of cardiac mortality and heart failure hospitalization in patients after a new MI. © 2014 Elsevier Ireland Ltd.


Chang Y.-H.,National Taiwan Ocean University | Chao K.-M.,Graduate Institute of Biomedical Electronics and Bioinformatics | Chao K.-M.,National Taiwan University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2013

As XML data nowadays are extensively used in the applications of data exchange and other fields, supporting efficient query processing on XML data, particularly in determining the structural relationships between two elements, is in great demand recently. To avoid the time-consuming tree traversal tasks, many labeling schemes have been proposed to assign each node a unique label, so that the structural relationships between nodes, such as the ancestor-descendant relationship, can be efficiently determined by comparing their labels. However, to the best of our knowledge, none of the existing labeling schemes can support all structural relationships in constant time and also require the least amount of space. In this paper, we propose a labeling scheme based on the concept of the complete tree, which is called the CT (complete-tree) labeling scheme. This labeling scheme is simple and the resultant labels are compact. We formally analyze its properties and perform an empirical evaluation between the CT labeling scheme and other state-of-the-art labeling schemes on different data sets. The experimental results show that the space requirement of our CT labeling scheme is superior to others in most cases. It is also demonstrated that this scheme can efficiently support all structural relationships and may perform even better than other labeling schemes. © Springer-Verlag 2013.


Lin X.-Y.,Graduate Institute of Biomedical Electronics and Bioinformatics | Ho T.-W.,Graduate Institute of Biomedical Electronics and Bioinformatics | Fang C.-C.,National Taiwan University Hospital | Yen Z.-S.,National Taiwan University Hospital | And 3 more authors.
Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS | Year: 2015

To increase the efficiency in the emergency room, the goal of this research is to implement a mobile-based indoor positioning system using mobile applications (APP) with the iBeacon solution based on the Bluetooth Low Energy (BLE) technology. We use the Received Signal Strength (RSS) based localization method to estimate the patients' locations. Our positioning algorithm achieves 97.22% (95% Confidence Interval = 95.90% - 98.55%) accuracy of classification. As the result, our mechanism is reliable enough to satisfy the need for medical staff to track the locations of their patients. © 2015 IEEE.


Chu H.-T.,Asia University, Taiwan | Hsiao W.W.L.,BCCDC Public Health Microbiology and Reference Laboratory | Hsiao W.W.L.,University of British Columbia | Chen J.-C.,Institute of Biotechnology | And 11 more authors.
Bioinformatics | Year: 2013

Motivation: High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.Results: EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases. © 2013 The Author.


Wu Z.-Y.,National Taiwan University | Chung Y.,Tunghai University | Lai F.,National Taiwan University | Lai F.,Graduate Institute of Biomedical Electronics and Bioinformatics | And 2 more authors.
International Journal of Innovative Computing, Information and Control | Year: 2011

Based upon Elliptic Curve Cryptosystem, a simple password user authentication scheme was proposed by Lu et al. for grid computing. In their scheme, Lu et al. not only kept the advantages of Yoon et al.'s scheme, but enhanced the efficiency of mutual authentication and at the same time avoided the stolen-verifier attacks as well. However, their scheme is proven to be unable to resist the off-line password guessing attacks. Apart from that, the problem of people masquerading as a server to communicate with the other users in their scheme is also inevitable. Therefore, an ameliorative password-based authentication scheme is proposed subsequently in this paper to achieve perfect forward secrecy and to resist replay attacks, server spoofing attacks, on-line and off-line password guessing attacks and impersonation attacks. The proposed scheme is shown to be more secure and practical than those previously proposed schemes. © 2011.


Luo C.-W.,National Taiwan University | Chen M.-C.,National Taiwan University | Chen Y.-C.,National Taiwan University | Yang R.W.L.,National Taiwan University | And 2 more authors.
IEEE/ACM Transactions on Computational Biology and Bioinformatics | Year: 2011

A fundamental problem arising in the evolutionary molecular biology is to discover the locations of gene duplications and multiple gene duplication episodes based on the phylogenetic information. The solutions to the MULTIPLE GENE DUPLICATION problems can provide useful clues to place the gene duplication events onto the locations of a species tree and to expose the multiple gene duplication episodes. In this paper, we study two variations of the MULTIPLE GENE DUPLICATION problems: the EPISODE-CLUSTERING (EC) problem and the MINIMUM EPISODES (ME) problem. For the EC problem, we improve the results of Burleigh et al. with an optimal linear-time algorithm. For the ME problem, on the basis of the algorithm presented by Bansal and Eulenstein, we propose an optimal linear-time algorithm. © 2011 IEEE.


Chang Y.-C.,Institute of Information Science | Chang Y.-C.,National Taiwan University | Su Y.-C.,National Taiwan University | Chang N.-W.,Institute of Information Science | And 2 more authors.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2014

Discovering the interactions between proteins mentioned in biomedical literature is one of the core topics of text mining in the life sciences. In this paper, we propose an interaction pattern generation approach to capture frequent PPI patterns in text. We also present an interaction pattern tree kernel method that integrates the PPI pattern with convolution tree kernel to extract protein-protein interactions. Empirical evaluations on LLL, IEPA, and HPRD50 corpora demonstrate that our method is effective and outperforms several wellknown PPI extraction methods. © Springer International Publishing Switzerland 2014.


Wu S.-Y.,Graduate Institute of Biomedical Electronics and Bioinformatics | Wang S.-L.I.,National Taiwan University | Li P.-C.,Graduate Institute of Biomedical Electronics and Bioinformatics | Li P.-C.,National Taiwan University
Ultrasonic Imaging | Year: 2010

Speckle tracking has been used for motion estimation in ultrasound imaging. Unlike conventional Doppler techniques, which are angle-dependent, speckle tracking can be utilized to estimate velocity vectors. However, the accuracy of speckle-tracking methods is limited by speckle decorrelation, which is related to the displacement between two consecutive images, and, hence, combining high-frame-rate imaging and speckle tracking could potentially increase the accuracy of motion estimation. However, the lack of transmit focusing may also affect the tracking results and the high computational requirement may be problematic. This study therefore assessed the performance of high-frame-rate speckle tracking and compared it with conventional focusing. The effects of the signal-to-noise ratio (SNR), bulk motion, and velocity gradients were investigated in both experiments and simulations. The results show that high-frame-rate speckle tracking can achieve high accuracy if the SNR is sufficiently high. In addition, its computational complexity is acceptable because smaller search windows can be used due to the displacements between frames generally being smaller during high-frame-rate imaging. Speckle decorrelation resulting from velocity gradients within a sample volume is also not as significant during high-frame-rate imaging. Copyright 2010 by Dynamedia, Inc.

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