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Search Results: 1 - 10 of 91304 matches for " Yen-Chun Chen "
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Intelligent Systems Developed for the Early Detection of Chronic Kidney Disease
Ruey Kei Chiu,Renee Y. Chen,Shin-An Wang,Yen-Chun Chang
Advances in Artificial Neural Systems , 2013, DOI: 10.1155/2013/539570
Abstract:
Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly
Yen-Chun Chen, Tsunglin Liu, Chun-Hui Yu, Tzen-Yuh Chiang, Chi-Chuan Hwang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062856
Abstract: Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.
Intelligent Systems Developed for the Early Detection of Chronic Kidney Disease
Ruey Kei Chiu,Renee Y. Chen,Shin-An Wang,Yen-Chun Chang,Li-Chien Chen
Advances in Artificial Neural Systems , 2013, DOI: 10.1155/2013/539570
Abstract: This paper aims to construct intelligence models by applying the technologies of artificial neural networks including back-propagation network (BPN), generalized feedforward neural networks (GRNN), and modular neural network (MNN) that are developed, respectively, for the early detection of chronic kidney disease (CKD). The comparison of accuracy, sensitivity, and specificity among three models is subsequently performed. The model of best performance is chosen. By leveraging the aid of this system, CKD physicians can have an alternative way to detect chronic kidney diseases in early stage of a patient. Meanwhile, it may also be used by the public for self-detecting the risk of contracting CKD. 1. Introduction According to the statistical data announced by the Department of Health of Taiwan’s government in 2010 [1], the mortality caused by kidney disease has been ranked in the 10th place in all causes of death in Taiwan and thousands of others are at increased risk. The mortality caused from kidney disease is estimated as 12.5 in every 100,000 people. As a result, it costs as high as 35 percent of health insurance budget to treat the chronic kidney disease (CKD) patients with the age over 65 years old and end-stage kidney disease patients in all ages. It occupies a huge amount of expenditures in national insurance budget. Regarding the measurement of serious levels of CKD, presently glomerular filtration rate (GFR) is the most commonly measuring indicator used in health institutions to estimate kidney health function. The physician in the health institution can calculate GFR from patient’s blood creatinine, age, race, gender, and other factors depending upon the type of formal-recognized computation formulas [2, 3] employed. The GFR may indicate the health of a patent’s kidney and can also be taken to determine the stage of severity of a patient with or without kidney disease. In this paper, we aim to develop a feasible intelligent model for detecting CKD for evaluating the severity of a patient with or without CKD. The input data for model development and testing is collected from the health examination which is periodically carried out by the collaborative teaching hospital of this research. 2. The Major Methods for Measuring Chronic Kidney Disease As it is mentioned in prior section, the GFR is the most common method used to measure kidney health function. It refers to the water filterability of glomerular of people’s kidney. The normal value should be between 90 and 120?mL/min/1.73?m2 (i.e., measured by mL per minute per 1.73?m2). There are three
Few-Photon All-Optical π Phase modulation Based on a Double-Λ System
Yen-Chun Chen,Hao-Chung Chen,Hsiang-Yu Lo,Bing-Ru Tsai,Ite A. Yu,Ying-Cheng Chen,Yong-Fan Chen
Physics , 2013,
Abstract: We propose an efficient all-optical phase modulation based on a double-{\Lambda} system and demonstrate a {\pi} phase shift of a few-photon pulse induced by another few-photon pulse in cold rubidium atoms with this scheme. By changing the phases of the applied laser fields, one can control the property of the double-{\Lambda} medium. This phase-dependent mechanism makes the double-{\Lambda} system different form the conventional cross-Kerr-based system which only depends on the applied laser intensities. The proposed scheme provides a new route to generate strong nonlinear interactions between photons, and may have potential for applications in quantum information technologies.
Low-light-level four-wave mixing by quantum interference
Chang-Kai Chiu,Yi-Hsin Chen,Yen-Chun Chen,Ite A. Yu,Ying-Cheng Chen,Yong-Fan Chen
Physics , 2013, DOI: 10.1103/PhysRevA.89.023839
Abstract: We observed electromagnetically-induced-transparency-based four-wave mixing (FWM) in the pulsed regime at low light levels. The FWM conversion efficiency of 3.8(9)% was observed in a four-level system of cold 87Rb atoms using a driving laser pulse with a peak intensity of approximately 80 {\mu}W/cm^2, corresponding to an energy of approximately 60 photons per atomic cross section. Comparison between the experimental data and the theoretical predictions proposed by Harris and Hau [Phys. Rev. Lett. 82, 4611 (1999)] showed good agreement. Additionally, a high conversion efficiency of 46(2)% was demonstrated when applying this scheme using a driving laser intensity of approximately 1.8 mW/cm^2. According to our theoretical predictions, this FWM scheme can achieve a conversion efficiency of nearly 100% when using a dense medium with an optical depth of 500.
Interferon-Based Therapy Decreases Risks of Hepatocellular Carcinoma and Complications of Cirrhosis in Chronic Hepatitis C Patients
Ching-Sheng Hsu, Chun-Jen Huang, Jia-Horng Kao, Hans Hsienhong Lin, You-Chen Chao, Yen-Chun Fan, Pei-Shan Tsai
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0070458
Abstract: Background Interferon-based therapy (IBT) has been the standard of care for hepatitis C virus (HCV) infection. However, conflicting results exist regarding the effects of IBT on risk of developing hepatocellular carcinoma (HCC) and cirrhosis-associated complications, and most included highly selected patients. Methods This 8-year cohort study was based on the Longitudinal Health Insurance Database 2000 (LHID 2000) consisting of 1,000,000 beneficiaries randomly selected from all Taiwan National Health Insurance enrollees in 2000 (>23.7 million). Patients with newly detected HCV infections (n = 11,264) were classified based on treatment and clinical outcomes. IBTs were defined as regimens that included interferon- alfa, pegylated interferon- alfa -2a, or pegylated interferon- alfa -2b for at least 3 months. The Cox proportional hazards models were used to estimate the hazard ratio (HR) and associated confidence interval (CI) of HCC and cirrhosis-associated complications for IBT. Results The 8-year incidence rate for HCC was 3.9% among patients who received IBT and 5.6% among those who did not. The HCC-free survival rate was significantly higher among patients receiving IBT during the 8-year period than their counterpart (adjusted HR, 0.50; 95% CI, 0.31–0.81; P = .004). Similarly, the event-free survival rates for esophageal variceal bleeding (adjusted HR, 0.45; 95% CI, 0.22–0.91; P = .026), hepatic encephalopathy (adjusted HR, 0.38; 95% CI, 0.21–0.69; P = .001), ascites (adjusted HR, 0.28; 95% CI, 0.14–0.57; P<.001), and cirrhosis (adjusted HR, 0.63; 95% CI, 0.44–0.91; P = .013) were significantly higher among patients who received IBT than those who did not, after adjustment for associated factors. Conclusion Treatment with interferon may reduce the 8-year risk of HCC and cirrhosis-associated complications in patients with chronic HCV infection.
Spatiotemporal Dynamics and Epistatic Interaction Sites in Dengue Virus Type 1: A Comprehensive Sequence-Based Analysis
Pei-Yu Chu, Guan-Ming Ke, Po-Chih Chen, Li-Teh Liu, Yen-Chun Tsai, Jih-Jin Tsai
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0074165
Abstract: The continuing threat of dengue fever necessitates a comprehensive characterisation of its epidemiological trends. Phylogenetic and recombination events were reconstructed based on 100 worldwide dengue virus (DENV) type 1 genome sequences with an outgroup (prototypes of DENV2-4). The phylodynamic characteristics and site-specific variation were then analysed using data without the outgroup. Five genotypes (GI-GV) and a ladder-like structure with short terminal branch topology were observed in this study. Apparently, the transmission of DENV1 was geographically random before gradual localising with human activity as GI-GIII in South Asia, GIV in the South Pacific, and GV in the Americas. Genotypes IV and V have recently shown higher population densities compared to older genotypes. All codon regions and all tree branches were skewed toward a negative selection, which indicated that their variation was restricted by protein function. Notably, multi-epistatic interaction sites were found in both PrM 221 and NS3 1730. Recombination events accumulated in regions E, NS3-NS4A, and particularly in region NS5. The estimated coevolution pattern also highlights the need for further study of the biological role of protein PrM 221 and NS3 1730. The recent transmission of emergent GV sublineages into Central America and Europe mandates closely monitoring of genotype interaction and succession.
Potential Risk of Malposition of Nasogastric Tube Using Nose-Ear-Xiphoid Measurement
Yen-Chun Chen, Lien-Yen Wang, Yu-Jun Chang, Chao-Pin Yang, Tsung-Ju Wu, Fung-Ru Lin, Sen-Yung Liu, Ta-Sen Wei
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088046
Abstract: Background Correct placement of nasogastric tubes provide proper functionality and maximize benefit and minimize risk. The Nose-Ear-Xiphoid (NEX) body surface estimate method is a long-lasting technique, and this study was conducted to evaluate the correlation between NEX method and the secure insertion depth of nasogastric tube. Materials and Methods Thirty patients with nasogastric tube insertion who received whole body positron emission tomography with computerized tomography scan (PET-CT) were recruited. All data were gathered in the image center, which included Nose-Ear (NE), Ear-Xiphoid (EX), Nose-Ear-Xiphoid (NEX), glabella-xiphoid (GX) and glabella-umbilicus (GU) lengths. The distances of the inserted portion of the nasogastric tube between the cardiac and the nostril were measured by multiplanar reconstruction algorithm. Results Only one patient successfully placed all side-holes into the stomach while using NEX method to estimate inserting depth. Twenty-nine patients (96.7%) failed to place correctly. Fourteen participants had one or more side-holes in both the esophagus and the stomach sides. Fifteen patients could not pass through any side-hole across the gastroesophageal junction. They had shorter EX distances (p = 0.02), but no difference among the NE distances. Body height had the highest statistical correlation with nasogastric tube length (adjusted R2 = 0.459), as compared with the NEX, GX and GU body surface methods. Conclusion This study suggests that NEX method is inappropriate for adult patients to estimate the ideal inserting length of nasogastric tube. Physicians should realize these underinsertions with any side-hole above the gastroesophageal junctions may increase the potential risk of complications.
Up-Regulation of MicroRNA-190b Plays a Role for Decreased IGF-1 That Induces Insulin Resistance in Human Hepatocellular Carcinoma
Tzu-Min Hung, Cheng-Maw Ho, Yen-Chun Liu, Jia-Ling Lee, Yow-Rong Liao, Yao-Ming Wu, Ming-Chih Ho, Chien-Hung Chen, Hong-Shiee Lai, Po-Huang Lee
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0089446
Abstract: Background & Aims Insulin-like growth factor, (IGF)-1, is produced mainly by the liver and plays important roles in promoting growth and regulating metabolism. Previous study reported that development of hepatocellular carcinoma (HCC) was accompanied by a significant reduction in serum IGF-1 levels. Here, we hypothesized that dysregulation of microRNAs (miRNA) in HCC can modulate IGF-1 expression post-transcriptionally. Methods The miRNAs expression profiles in a dataset of 29 HCC patients were examined using illumina BeadArray. Specific miRNA (miR)-190b, which was significantly up-regulated in HCC tumor tissues when compared with paired non-tumor tissues, was among those predicted to interact with 3′-untranslated region (UTR) of IGF-1. In order to explore the regulatory effects of miR-190b on IGF-1 expression, luciferase reporter assay, quantitative real-time PCR, western blotting and immunofluorecence analysis were performed in HCC cells. Results Overexpression of miR-190b in Huh7 cells attenuated the expression of IGF-1, whereas inhibition of miR-190b resulted in up-regulation of IGF-1. Restoration of IGF-1 expression reversed miR-190b-mediated impaired insulin signaling in Huh7 cells, supporting that IGF-1 was a direct and functional target of miR-190b. Additionally, low serum IGF-1 level was associated with insulin resistance and poor overall survival in HCC patients. Conclusions Increased expression of miR-190 may cause decreased IGF-1 in HCC development. Insulin resistance appears to be a part of the physiopathologic significance of decreased IGF-1 levels in HCC progression. This study provides a novel miRNA-mediated regulatory mechanism for controlling IGF-1 expression in HCC and elucidates the biological relevance of this interaction in HCC.
Current Rectification and Seebeck Coefficient of Serially Coupled Double Quantum Dots
Yen-Chun Tseng,David M. -T. Kuo
Physics , 2012, DOI: 10.7567/JJAP.52.014002
Abstract: The transport properties of serially coupled quantum dots (SCQDs) embedded in a matrix connected to metallic electrodes are theoretically studied in the linear and nonlinear regimes. The current rectification and negative differential conductance of SCQDs under the Pauli spin blockade condition are attributed to the combination of bias-direction dependent probability weight and off-resonant energy levels yielded by the applied bias across the junctions. We observe the spin-polarization current rectification under the Zeeman effect. The maximum spin-polarization current occurs in the forward bias regime. Such behavior is different from the charge current rectification. Finally, the Seebeck coefficient ($S$)of SCQDs is calculated and analyzed in the cases without and with electron phonon interactions. The application of SCQDs as a temperature detector is discussed on the basis of the nonlinear behavior of $S$ with respect to temperature difference across the junction.
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