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Search Results: 1 - 10 of 7556 matches for " Jung-Hsien Chiang "
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Modeling human cancer-related regulatory modules by GA-RNN hybrid algorithms
Jung-Hsien Chiang, Shih-Yi Chao
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-91
Abstract: In this study, we introduce a Genetic Algorithm-Recurrent Neural Network (GA-RNN) hybrid method for finding feed-forward regulated genes when given some transcription factors to construct cancer-related regulatory modules in human cancer microarray data. This hybrid approach focuses on the construction of various kinds of regulatory modules, that is, Recurrent Neural Network has the capability of controlling feed-forward and feedback loops in regulatory modules and Genetic Algorithms provide the ability of global searching of common regulated genes. This approach unravels new feed-forward connections in regulatory models by modified multi-layer RNN architectures. We also validate our approach by demonstrating that the connections in our cancer-related regulatory modules have been most identified and verified by previously-published biological documents.The major contribution provided by this approach is regarding the chain influences upon a set of genes sequentially. In addition, this inverse modeling correctly identifies known oncogenes and their interaction genes in a purely data-driven way.A regulatory module is a set of genes that is regulated or co-regulated by one or more common transcription factors (TFs). A TF is a protein that binds to a cis-regulatory element (e.g. an enhancer, a TATA box) and thereby, directly or indirectly, positively or negatively affects the initiation of transcription of regulated genes. A cancer-related regulatory module is a set of genes (oncogenes or tumor suppressor genes) that is regulated by one ore more common TFs. Modeling the cancer-related regulatory modules of the cell division cycle in human cells is a critical and fundamental step toward understanding cancers. The aim of this paper is not only to drive cancer-related regulatory modules, but also to identify the relationships of regulations between genes that fit the feed-forward or feedback influences. A feed-forward regulatory module, contains a TF that controls a second
GeneLibrarian: an effective gene-information summarization and visualization system
Jung-Hsien Chiang, Jyh-Wei Shin, Heng-Hui Liu, Chong-Liang Chin
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-392
Abstract: We have developed a novel method for semantic measurement of annotation and integrated it with a biomedical literature summarization system to establish a platform, GeneLibrarian, to provide users well-organized information about any specific group of genes (e.g. one cluster of genes from a microarray chip) they might be interested in. The GeneLibrarian generates a summarized viewgraph of candidate genes for a user based on his/her preference and delivers the desired background information effectively to the user. The summarization technique involves optimizing the text mining algorithm and Gene Ontology-based clustering method to enable the discovery of gene relations.GeneLibrarian is a Java-based web application that automates the process of retrieving critical information from the literature and expanding the number of potential genes for further analysis. This study concentrates on providing well organized information to users and we believe that will be useful in their researches. GeneLibrarian is available on http://gen.csie.ncku.edu.tw/GeneLibrarian/ webciteImagine the following situation. Your search engine at the NCBI site finds out that in addition to the 400 medical documents that match your query, another 400 are also relevant, but they are just one of the 44,000 genes at your favorite microarray chip. Imagine now that you have a sophisticated software that will automatically extract the most useful information from all the documents and summarize it for you in sentences so that you don't have to read the entire documents!Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes. A growing number of researchers have attempted to annotate gene products via controlled vocabularies in Gene Ontology (GO), given that gene ontologies are centra
An integrative approach to identifying cancer chemoresistance-associated pathways
Shih-Yi Chao, Jung-Hsien Chiang, A-Mei Huang, Woan-Shan Chang
BMC Medical Genomics , 2011, DOI: 10.1186/1755-8794-4-23
Abstract: An integrated network was constructed by collecting multiple metabolic interactions from public databases and the k-shortest path algorithm was implemented to identify chemoresistant related pathways. The identified pathways were then scored using differential expression values from microarray data in chemosensitive and chemoresistant ovarian and lung cancers. Finally, another pathway database, Reactome, was used to evaluate the significance of genes within each filtered pathway based on topological characteristics.By this method, we discovered pathways specific to chemoresistance. Many of these pathways were consistent with or supported by known involvement in chemotherapy. Experimental results also indicated that integration of pathway structure information with gene differential expression analysis can identify dissimilar modes of gene reactions between chemosensitivity and chemoresistance. Several identified pathways can increase the development of chemotherapeutic resistance and the predicted signature genes are involved in drug resistant during chemotherapy. In particular, we observed that some genes were key factors for joining two or more metabolic pathways and passing down signals, which may be potential key targets for treatment.This study is expected to identify targets for chemoresistant issues and highlights the interconnectivity of chemoresistant mechanisms. The experimental results not only offer insights into the mode of biological action of drug resistance but also provide information on potential key targets (new biological hypothesis) for further drug-development efforts.The development of chemotherapy resistance is of tremendous significance to patients, researchers, and care providers who rely on conventional cytotoxic agents for the treatment of cancer. Still, the mechanisms and related biological pathways that contribute to chemotherapy resistance are relatively poorly understood. Numerous attempts have been made to mitigate or eliminate chemo
Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly
Tsunglin Liu, Cheng-Hung Tsai, Wen-Bin Lee, Jung-Hsien Chiang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069503
Abstract: Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/.
Visual Feedback Balance Control of a Robot Manipulator and Ball-Beam System  [PDF]
Ching-Long Shih, Jung-Hsien Hsu, Chi-Jen Chang
Journal of Computer and Communications (JCC) , 2017, DOI: 10.4236/jcc.2017.59002
Abstract: In this paper, we present a vision guided robotic ball-beam balancing control system, consisting of a robot manipulator (actuator), a ball-beam system (plant) and a machine vision system (feedback). The machine vision system feedbacks real-time beam angle and ball position data at a speed of 50 frames per second. Based on feedback data, the end-effector of a robot manipulator is driven to control the ball position by maneuvering of the inclination angle of the ball-beam system. The overall control system is implemented with two FPGA chips, one for machine vision processing, and one for robot joints servo PID controllers as well as ball position PD controller. Experiments are performed on a 5-axes robot manipulator to validate the proposed ball beam balancing control system.
Transcriptional activation of the Axl and PDGFR-α by c-Met through a ras- and Src-independent mechanism in human bladder cancer
Chen-Yun Yeh, Shin-Mei Shin, Hsuan-Heng Yeh, Tsung-Jung Wu, Jyh-Wei Shin, Tsuey-Yu Chang, Giri Raghavaraju, Chung-Ta Lee, Jung-Hsien Chiang, Vincent S Tseng, Yuan-Chii G Lee, Cheng-Huang Shen, Nan-Haw Chow, Hsiao-Sheng Liu
BMC Cancer , 2011, DOI: 10.1186/1471-2407-11-139
Abstract: Both NIH-Met5 and T24-Met3 cell lines harboring an inducible human c-Met gene were established. C-Met-related RTKs were screened by RTK microarray analysis. The cross-talk of RTKs was demonstrated by Western blotting and confirmed by small interfering RNA (siRNA) silencing, followed by elucidation of the underlying mechanism. The impact of this cross-talk on biological function was demonstrated by Trans-well migration assay. Finally, the potential clinical importance was examined in a cohort of 65 cases of locally advanced and metastatic bladder cancer patients.A positive association of Axl or platelet-derived growth factor receptor-alpha (PDGFR-α) with c-Met expression was demonstrated at translational level, and confirmed by specific siRNA knock-down. The transactivation of c-Met on Axl or PDGFR-α in vitro was through a ras- and Src-independent activation of mitogen-activated protein kinase/extracellular signal-regulated kinase (MEK/ERK) pathway. In human bladder cancer, co-expression of these RTKs was associated with poor patient survival (p < 0.05), and overexpression of c-Met/Axl/PDGFR-α or c-Met alone showed the most significant correlation with poor survival (p < 0.01).In addition to c-Met, the cross-talk with Axl and/or PDGFR-α also contributes to the progression of human bladder cancer. Evaluation of Axl and PDGFR-α expression status may identify a subset of c-Met-positive bladder cancer patients who may require co-targeting therapy.The RTK c-Met is expressed during normal development and plays a crucial role in many cell regulatory processes [1]. After binding to its cognate ligand-hepatocyte growth factor (HGF), activated c-Met transmits signals implicated in the cell proliferation, motility, survival, and morphogenesis [2-4]. C-Met is over-expressed and usually associated with metastatic progression of a variety of human malignant tumors, including bladder cancer [1,5]. We have reported that c-Met is over-expressed in 32.3%, 63.2%, and 65.2% of superfici
Antioxidant Sol-Gel Improves Cutaneous Wound Healing in Streptozotocin-Induced Diabetic Rats
Yen-Hsien Lee,Jung-Jhih Chang,Chiang-Ting Chien,Ming-Chien Yang,Hsiung-Fei Chien
Experimental Diabetes Research , 2012, DOI: 10.1155/2012/504693
Abstract: We examined the effects of vitamin C in Pluronic F127 on diabetic wound healing. Full-thickness excision skin wounds were made in normal and diabetic Wistar rats to evaluate the effect of saline, saline plus vitamin C (antioxidant sol), Pluronic F127, or Pluronic F127 plus vitamin C (antioxidant sol-gel). The rate of wound contraction, the levels of epidermal and dermal maturation, collagen synthesis, and apoptosis production in the wound tissue were determined. In vitro data showed that after 6 hours of air exposure, the order of the scavenging abilities for HOCl, H2O2, and O2? was antioxidant sol-gel > antioxidant saline > Pluronic F127 = saline. After 7 and 14 days of wound injury, the antioxidant sol-gel improved wound healing significantly by accelerated epidermal and dermal maturation, an increase in collagen content, and a decrease in apoptosis formation. However, the wounds of all treatments healed mostly at 3 weeks. Vitamin C in Pluronic F127 hastened cutaneous wound healing by its antioxidant and antiapoptotic mechanisms through a good drug delivery system. This study showed that Pluronic F127 plus vitamin C could potentially be employed as a novel wound-healing enhancer.
Antioxidant Sol-Gel Improves Cutaneous Wound Healing in Streptozotocin-Induced Diabetic Rats
Yen-Hsien Lee,Jung-Jhih Chang,Chiang-Ting Chien,Ming-Chien Yang,Hsiung-Fei Chien
Journal of Diabetes Research , 2012, DOI: 10.1155/2012/504693
Abstract: We examined the effects of vitamin C in Pluronic F127 on diabetic wound healing. Full-thickness excision skin wounds were made in normal and diabetic Wistar rats to evaluate the effect of saline, saline plus vitamin C (antioxidant sol), Pluronic F127, or Pluronic F127 plus vitamin C (antioxidant sol-gel). The rate of wound contraction, the levels of epidermal and dermal maturation, collagen synthesis, and apoptosis production in the wound tissue were determined. In vitro data showed that after 6 hours of air exposure, the order of the scavenging abilities for HOCl, , and was antioxidant sol-gel > antioxidant saline > Pluronic F127 = saline. After 7 and 14 days of wound injury, the antioxidant sol-gel improved wound healing significantly by accelerated epidermal and dermal maturation, an increase in collagen content, and a decrease in apoptosis formation. However, the wounds of all treatments healed mostly at 3 weeks. Vitamin C in Pluronic F127 hastened cutaneous wound healing by its antioxidant and antiapoptotic mechanisms through a good drug delivery system. This study showed that Pluronic F127 plus vitamin C could potentially be employed as a novel wound-healing enhancer. 1. Introduction Wound healing represents a well-orchestrated reparative response that occurs after all surgical procedures or traumatic injury. Wound healing is a complex multifactorial process, involving inflammation, migration of different cell types, fibroplasia, collagen deposition, and wound contraction. During the inflammation phase, inflammatory cells significantly increased in the wound site [1] and produced burst amounts of reactive oxygen species (ROS) formation in the wound tissue [2] affecting wound healing. Diabetes mellitus is one of the major contributors to chronic wound-healing problems, because minor skin wounds can lead to chronic, nonhealing ulcers and ultimately result in infection, gangrene, or even amputation. In critical ill diabetic patients, the antioxidant vitamin C in plasma was reported lower than nondiabetic critical ill patients [3]. In streptozotocin-induced and gene-induced diabetic mice, increased oxidative stress in the wounds has been noted [2]. Besides, increased oxidative stress promoted apoptosis formation in the damaged tissue and the increased apoptosis signaling also delayed the wound-healing process [4]. In addition, the diabetic rat skin was underhydroxylated in nascent collagen alpha chains (types I and III) [5]. Compromised collagen production associated with vitamin C deficiency results in impaired wound healing [6]. Vitamin C is an
Antioxidant Activity of Ixora parviflora in a Cell/Cell-Free System and in UV-Exposed Human Fibroblasts
Kuo-Ching Wen,Hua-Hsien Chiu,Pei-Ching Fan,Chien-Wen Chen,Shih-Mei Wu,Jung-Hsiang Chang,Hsiu-Mei Chiang
Molecules , 2011, DOI: 10.3390/molecules16075735
Abstract: Polyphenols and flavonoids possess a variety of biological activities including antioxidant and anti-tumor activities. Ixora parviflora is a member of the flavonoid-rich Rubiaceae family of flowering plants and used as folk medicine in India. The aim of this study was to investigate the antioxidant activity of Ixora parviflora extract (IPE) in a cell-free system and erythrocytes, and the ability of IPE to inhibit reactive oxygen species (ROS) generation in human fibroblasts (Hs68) after ultraviolet (UV) exposure. Various in vitro antioxidant assays were employed in this study. The extraction yield of IPE was 17.4 ± 3.9%, the total phenolic content of IPE was 26.2 μg gallic acid equivalent (GAE)/mg leaves dry weight and the total flavonoids content was 54.2 ± 4.4 μg quercetin equvalent (QE)/mg extract. The content of chlorogenic acid was 9.7 ± 1.2 mg/g extract. IPE at 1000 μg/mL exhibited a reducing capacity of 90.5 ± 0.6%, a 1,1-diphenyl-2-picrylhydrazy (DPPH) radical scavenging activity of 96.0 ± 0.4%, a ferrous chelating activity of 72.2 ± 3.5%, a hydroxyl radical scavenging activity of 96.8 ± 1.4%, and a hydrogen peroxide scavenging activity of 99.5 ± 3.3%. IPE at 500 μg/mL also possessed inhibitory activity against 2,2'-azobis (2-methylpropionamidine) dihydrochloride (AAPH)-induced hemolysis of erythrocytes (89.4 ± 1.8%) and resulted in a 52.9% reduction in ROS generation in UV-exposed fibroblasts. According to our findings, IPE is a potent antioxidant and a potential anti-photoaging agent.
An Adaptive Video-on-Demand Framework for Multimedia Cross-Platform Cloud Services  [PDF]
Chao-Hsien Hsieh, Chih-Horng Ke, Chiang Lee
Journal of Software Engineering and Applications (JSEA) , 2016, DOI: 10.4236/jsea.2016.95013
Abstract: Although Video-On-Demand (VOD) has been in existence for years, its cross-platform applicability in cloud service environments is still in increasing need. In this paper, an Adaptive Video-On-Demand (AVOD) framework that is suitable for private cloud environments is proposed. Private cloud has the key advantage of satisfying the real need of both consumers and providers. Hence, demands such as reasonable benefits for provider and high quality for consumers are essential design considerations in this framework. The difficulty is that these two factors are always high in one end and low in the other, and hard to find a delicate balance. Cloud service could be an opportunity for the multimedia providers to obtain higher benefits and cost less for the consumers but with an even better quality in service. An adaptive framework for such a cloud service environment is proposed to resolve this problem. Some interesting phenomena are observed from the experimental results including CPU utilization, data reading and writing speed, memory usage, port configuration execution time, and bandwidth.
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