Region-based and pathway-based QTL mapping using a p-value combination method

Quantitative trait locus (QTL) mapping using deep DNA sequencing data is a challenging task. In this study we performed region-based and pathway-based QTL mappings using a p-value combination method to analyze the simulated quantitative traits Q1 and Q4 and the exome sequencing data. The aims were to evaluate the performance of the QTL mapping approaches that were used and to suggest plausible strategies for QTL mapping of DNA sequencing data. We conducted single-locus QTL mappings using a linear regression model with adjustments for age and smoking status, and we also conducted region-based and pathway-based QTL mappings using a truncated product method for combining p-values from the single-locus QTL mapping. To account for the features of rare variants and common single-nucleotide polymorphisms (SNPs), we considered independently rare-variant-only, common-SNP-only, and combined analyses. An analysis of 200 simulated replications showed that the three region-based methods reasonably controlled type I error, whereas the combined analysis yielded the greatest statistical power. Rare-variant-only, common-SNP-only, and combined analyses were also applied to pathway-based QTL mappings. We found that pathway-based QTL mappings had a power of approximately 100% when the significance of the vascular endothelial growth factor pathway was evaluated, but type I errors were slightly inflated. Our approach complements single-locus QTL mapping. An integrated approach using single-locus, combined region-based, and combined pathway-based analyses should yield promising results for QTL mapping of DNA sequencing data

Comparison of the degradations of diphenamid by homogeneous photolysis and heterogeneous photocatalysis in aqueous solution

2009-2010 > Academic research: refereed > Publication in refereed journalAccepted ManuscriptPublishe

Effects of dissolved oxygen, pH, and anions on the 2,3-dichlorophenol degradation by photocatalytic reaction with anodic TiO?nanotube films

2008-2009 > Academic research: refereed > Publication in refereed journalAccepted ManuscriptPublishe

What is required in terms of mass drug administration to interrupt the transmission of schistosome parasites in regions of endemic infection?

Supplementary information. (PDF 445 kb

Sample entropy analysis of EEG signals via artificial neural networks to model patients' consciousness level based on anesthesiologists experience.

Electroencephalogram (EEG) signals, as it can express the human brain's activities and reflect awareness, have been widely used in many research and medical equipment to build a noninvasive monitoring index to the depth of anesthesia (DOA). Bispectral (BIS) index monitor is one of the famous and important indicators for anesthesiologists primarily using EEG signals when assessing the DOA. In this study, an attempt is made to build a new indicator using EEG signals to provide a more valuable reference to the DOA for clinical researchers. The EEG signals are collected from patients under anesthetic surgery which are filtered using multivariate empirical mode decomposition (MEMD) method and analyzed using sample entropy (SampEn) analysis. The calculated signals from SampEn are utilized to train an artificial neural network (ANN) model through using expert assessment of consciousness level (EACL) which is assessed by experienced anesthesiologists as the target to train, validate, and test the ANN. The results that are achieved using the proposed system are compared to BIS index. The proposed system results show that it is not only having similar characteristic to BIS index but also more close to experienced anesthesiologists which illustrates the consciousness level and reflects the DOA successfully.This research is supported by the Center forDynamical Biomarkers and Translational Medicine, National Central University, Taiwan, which is sponsored by Ministry of Science and Technology (Grant no. MOST103-2911-I-008-001). Also, it is supported by National Chung-Shan Institute of Science & Technology in Taiwan (Grant nos. CSIST-095-V301 and CSIST-095-V302)

Proteomic approach to study the cytotoxicity of dioscin (saponin)

Dioscin, extracted from the root of Polygonatum zanlanscianense pamp, exhibits cytotoxicity towards human myeloblast leukemia HL-60 cells. Proteomic analysis revealed that the expression of mitochondrial associated proteins was substantially altered in HL-60 cells corresponding to the dioscin treatment, suggesting that mitochondria are the major cellular target of dioscin. Mitochondrial functional studies validated that mitochondrial apoptotic pathway was initiated by dioscin treatment. Changes in proteome other than mitochondrial related proteins implicate that other mechanisms were also involved in dioscin-induced apoptosis in HL-60 cells, including the activity impairment in protein synthesis, alterations of phosphatases in cell signaling, and deregulation of oxidative stress and cell proliferation. Current study of protein alterations in dioscin-treated HL-60 cells suggested that dioscin exerts cytotoxicity through multiple apoptosis-inducing pathways. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.postprin

An efficient approach to generating location-sensitive recommendations in ad-hoc social network environments

Social recommendation has been popular and successful in various urban sustainable applications such as online sharing, products recommendation and shopping services. These applications allow users to form several implicit social networks through their daily social interactions. The users in such social networks can rate some interesting items and give comments. The majority of the existing studies have investigated the rating prediction and recommendation of items based on user-item bipartite graph and user-user social graph, so called social recommendation. However, the spatial factor was not considered in their recommendation mechanisms. With the rapid development of the service of location-based social networks, the spatial information gradually affects the quality and correlation of rating and recommendation of items. This paper proposes spatial social union (SSU), an approach of similarity measurement between two users that integrates the interconnection among users, items and locations. The SSU-aware location-sensitive recommendation algorithm is then devised. We evaluate and compare the proposed approach with the existing rating prediction and item recommendation algorithms subject to a real-life data set. Experimental results show that the proposed SSU-aware recommendation algorithm is more effective in recommending items with the better consideration of user's preference and location.This work was supported by the National Natural Science Foundation of China under Grant 61372187. G. Min’s work was partly supported by the EU FP7 CLIMBER project under Grant Agreement No. PIRSES-GA-2012-318939. L. T. Yang is the corresponding author

Intelligent spider for Internet searching

As World Wide Web (WWW) based Internet services become more popular, information overload also becomes a pressing research problem. Difficulties with searching on the Internet get worse as the amount of information that is available increases. A scalable approach to support Internet search is critical to the success of Internet services and other current or future national information infrastructure (NII) applications. A new approach to build an intelligent personal spider (agent), which is based on automatic textual analysis of Internet documents, is proposed. Best first search and genetic algorithm have been tested to develop the intelligent spider. These personal spiders are able to dynamically and intelligently analyze the contents of the users' selected homepages as the starting point to search for the most relevant homepages based on the links and indexing. An intelligent spider must have the capability to make adjustments according to progress of searching in order to be an intelligent agent. However, the current searching engines do not have communication between the users and the robots. The spider presented in the paper uses Java to develop the user interface such that the users can adjust the control parameters according to the progress and observe the intermediate results. The performances of the genetic algorithm based and best first search based spiders are also reported.published_or_final_versio

Late spontaneous rupture of the extensor pollicis longus tendon after corticosteroid injection for flexor tenosynovitis

INTRODUCTION: Spontaneous rupture of the extensor pollicis longus (EPL) tendon has been reported after trauma, rheumatoid arthritis and sports. Rupture may also occur as a consequence of the use of anabolic steroids for recreational purposes, or systemic steroids for the treatment of a variety of medical conditions. CASE REPORT: We present a case report of a woman affected with a spontaneous EPL tendon rupture resulted 14 months after a corticosteroid injection for flexor tenosynovitis, "trigger finger," of the thumb. The edges of the tendon were debrided and sutured using figure of eight stitch and a running locked stitch. In addition multiple specimens were sent to Pathology. DISCUSSION: Duplay in 1876 described spontaneous rupture as a problem of mechanical and pressure phenomena. Another cause of EPL rupture is related to the development and persistence of inflammatory processes seen in patients with medical illnesses such as rheumatoid arthritis. There have been no reports in the literature to date of spontaneous EPL tendon rupture in the late period after steroid injection. Tendon ruptures in the hand usually occur one or two weeks after a corticosteroid injection, and the affected tendons are usually in neighbouring areas