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Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations

Quantitative Biology 2020年第4期8卷 336-346页

作者： Olha Kholod chi-ren shyu Jonathan Mitchem Jussuf Kaifi Dmitriy Shin MU Institute for Data Science and Informatics University of MissouriColumbiaMO 65201USA Department Pathology and Anatomical Sciences School of MedicineUniversity of MissouriColumbiaMO 65212USA Department of Surgery School of MedicineUniversity of MissouriColumbiaMO 65212USA Harry S.Truman Memorial Veterans'Hospital ColumbiaMO 65201USA Department of Electrical Engineering&Computer Science University of MissouriColumbiaMO 65212USA

Background:Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations is critical for improving patient outcomes in cancer ***,accurate estimation of mutational effects at the pathway level for such patients remains an open *** probabilistic pathway topology methods are gaining interest among the scientific community,the overwhelming majority do not account for network perturbation effects from multiple single-nucleotide ***:Here we present an improvement of the mutational forks formalism to infer the patient-specific flow of signal transduction based on multiple single-nucleotide alterations,including non-synonymous and synonymous *** lung adenocarcinoma and skin cutaneous melanoma datasets from TCGA Pan-Cancer Atlas have been employed to show the utility of the proposed ***:We have comprehensively characterized six mutational *** number of mutated nodes ranged from one to four depending on the topological characteristics of a *** confidences(TCs)have been computed for every possible combination of single-nucleotide alterations in the *** performed analysis demonstrated the capacity of the mutational forks formalism to follow a biologically explainable logic in the identification of high-likelihood signaling routes in lung adenocarcinoma and skin cutaneous melanoma *** findings have been largely supported by the evidence from the biomedical ***:We conclude that the formalism has a great chance to enable an assessment of patient-specific flow by leveraging information from multiple single-nucleotide alterations to adjust the transitional likelihoods that are solely based on the canonical view of a disease.

关键词： mutational forks signaling pathways cancer single-nucleotide alterations

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The role of tazarotene-induced gene 1 in carcinogenesis:is it a tumor suppressor gene or an oncogene?

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BIOCELL 2024年第9期48卷 1285-1297页

作者： CHUN-HUA WANG LU-KAI WANG RONG-YAUN shyu FU-MING TSAI Department of Dermatology Taipei Tzu Chi HospitalBuddhist Tzu Chi Medical FoundationNew Taipei City231TaiwanChina School of Medicine Tzu Chi UniversityHualien970TaiwanChina Department of Life Sciences Ministry of Science and TechnologyTaipei106TaiwanChina Department of Internal Medicine Taipei Tzu Chi HospitalThe Buddhist Tzu Chi Medical FoundationNew Taipei City231TaiwanChina Department of Research Taipei Tzu Chi HospitalBuddhist Tzu Chi Medical FoundationNew Taipei City231TaiwanChina

Tazarotene-induced gene 1(TIG1)is induced by a derivative of vitamin A and is known to regulate many important biological processes and control the development of ***1 is widely expressed in various tissues;yet in many cancer tissues,it is not expressed because of the methylation of its ***,the expression of TIG1 in cancer cells inhibits their growth and invasion,suggesting that TIG1 acts as a tumor suppressor ***,in some cancers,poor prognosis is associated with TIG1 expression,indicating its protumor growth characteristics,especially in promoting the invasion of inflammatory breast cancer *** review comprehensively summarizes the roles of the TIG1 gene in cancer development and details the mechanisms through which TIG1 regulates cancer development,with the aim of understanding its various roles in cancer development.

关键词： Tazarotene-induced gene 1 Retinoic acid receptor responder protein 1 Tumor suppressor gene Oncogene

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Effects of the Process Parameters on Austenitic Stainless Steel by TIG-Flux Welding

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Journal of Materials Science & Technology 2006年第3期22卷 367-374页

作者： Heryueh HUANG Shengwen shyu Kuanghung TSENG Changpin GHOU Department of Mechanical Engineering National Chiao Tung University Hsinchu 300 Taiwan China ARITEX Products Co. Ltd. Kaohsiung County 831 Taiwan China

The effects of the process parameters of TIG （tungsten inset gas）-flux welding on the welds morphology, angular distortion, ferrite content and hot cracking in austenitic stainless steel were investigated. Autogenous TIG welding process was applied to the type 304 stainless steel through a thin layer of activating flux to produce a bead on plate welded joint. TiO2, SiO2, Fe2O3, Cr2O3, ZnO and MnO2 were used as the activating fluxes. The experimental results indicated that the TIG-flux welding can increase the weld depth/width ratio and reduce the HAZ （heat affected zone） range, and therefore the angular distortion of the weldment can be reduced. It was also found that the retained ferrite content within the TIG-flux welds is increased, and has a beneficial effect in reducing hot cracking tendency for stainless steels of the austenitic type weld metals. A plasma column constriction increases the current density at the anode spot and then a substantial increase in penetration of the TIG-flux welds can be obtained.

关键词： TIG-flux welding Welds morphology Angular distortion Hot cracking

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Development of the Polymeric Grating -Waveguide for OADM Components

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光学学报 2003年第S1期23卷 225-226页

作者： Ruey Fang shyu Hsiharng Yang Wei-Chung Chuang Feng-Tsai Weng chi-Ting Ho Department of Mechanical Manufacturing Engineering Huwei Institute of Technology Yunlin Taiwan 632Institute of Precision Engineering Chung Hsing University Taichung Taiwan 402Department of Optoelectronics Huwei Institute of Technology Yunlin Taiwan 632Institute of Precision Engineering Chung Hsing University Taichung Taiwan 402Department of Mechanical Design Engineering Huwei Institute of Technology Yunlin Taiwan 632

The paper presents the design and simulation of a new polymeric grating-waveguide for the optical add-drop multiplexer (OADM) by using two pairs of grating-frustrated directional couplers. Design theory and simulation... 详细信息

关键词： OADM on Development of the Polymeric Grating for Waveguide for OADM Components Figure of

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Antitumor activity of a novel bis-aziridinylnaphthoquinone (AZ4) mediating cell cycle arrest and apoptosis in non-small cell lung cancer cell line NCl-H460

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Acta Pharmacologica Sinica 2007年第4期28卷 559-566页

作者： Kou-gea shyu Hsien-shou KUO Yuh-ling LIN Division of Cardiac Shin Kong Wu Ho-Su Memorial HospitalTaipei 106TaiwanChina Department of Biochemistry Taipei Medical UniversityTaipei City 110TaiwanChina Department of Medicine Fu-Jen Catholic UniversityHsin-ChuangTaipei Hsien 242TaiwanChina

Aim:The cytotoxic activities of a series of bis-aziridinylnaphthoquinone,AZ1 toAZ4,on human lung carcinoma cell lines,H460,and normal lung cells fibroblastcell line,MRC-5,and the mechanisms of H460 cells induced by AZ4 ***:The MTT assay was used to determine the *** cycle was analysed by *** activity of caspase 3,8 and 9was determined by cell-permeable fluorogenic detection *** blotassay was used to evaluate the regulation of cyclin B,Cdc-2,p53,p21,and the Bcl-2 ***:AZ1 to AZ4 displayed various cytotoxicity activities againstH460 and MRC-5 *** to those compounds,AZ4 was with the mosteffective agent among the 5 tested analogues at reducing H460 cell viability with anIC50value of 1.23 μmol/L;it also exhibited weak cytotoxicity against MRC-5 cells withan IC50value of 12.7 μmol/*** results show that growth arrest on the G2-M phaseof H460 cells induced by AZ4 for 24 h was discovered,and this might be alteredwith the reduced Cdc-2 protein expression of 47% at 2.0 μmol/L AZ4,but not withcyclin B protein *** AZ4 treated cells were then led to apoptosis after48 *** was associated with the activation of apoptotic enzyme caspase 3 andmediated by caspase 8,but not caspase 9 at various concentrations of AZ4 afterbeing cultured for 48 h and 30 h,*** anti-apoptotic protein （Bcl-2）expression in H460 cells altered by 39% with downregulation,and the p53 proteinby 25% with upregulation after being cultured with 2.0 μmol/L AZ4 for 48 *** atime-dependent wanrer,the expression of the p53 and p21 proteins were increasedto the maximum at 24 h,and then decreased at ***:AZ4 represents anovel antitumor aziridinylnaphthoquinone with therapeutic potential against thenon-small cell lung cancer cells.

关键词： cell cycle apoptosis Bcl-2 protein aziridinylnaphthoquinone

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A Novel Web Video Event Mining Framework with the Integration of Correlation and Co-Occurrence Information

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Journal of Computer Science & Technology 2013年第5期28卷 788-796页

作者：张承德吴晓 Mei-Ling shyu 彭强 School of Information Science and Technology Southwest Jiaotong University Department of Electrical and Computer Engineering University of Miami

The massive web videos prompt an imperative demand on efficiently grasping the major events. However, the distinct characteristics of web videos, such as the limited number of features, the noisy text information, and the unavoidable error in near-duplicate keyframes （NDKs） detection, make web video event mining a challenging task. In this paper, we propose a novel four-stage framework to improve the performance of web video event mining. Data preprocessing is the first stage. Multiple Correspondence Analysis （MCA） is then applied to explore the correlation between terms and classes, targeting for bridging the gap between NDKs and high-level semantic concepts. Next, co-occurrence information is used to detect the similarity between NDKs and classes using the NDK-within-video information. Finally, both of them are integrated for web video event mining through negative NDK pruning and positive NDK enhancement. Moreover, both NDKs and terms with relatively low frequencies are treated as useful information in our experiments. Experimental results on large-scale web videos from YouTube demonstrate that the proposed framework outperforms several existing mining methods and obtains good results for web video event mining.

关键词： web video event mining multiple correspondence analysis co-occurrence near-duplicate keyframe

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DDA与FEM耦合法在分缝重力坝非线性分析中的应用

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计算力学学报 2004年第5期21卷 585-591页

作者：刘君孔宪京 shyu Kuokai 大连理工大学土木水利学院工程抗震研究所辽宁大连116024 美国北卡罗莱纳州立大学土木工程系北卡罗莱纳州格林斯博罗27411

混凝土重力坝一般设有数条纵缝。纵缝使坝体的连续性遭到破坏,一般的有限单元法很难处理这样的不连续变形问题。本文首先阐述了DDA(DiscontinuousDeformationAnalysis)与FEM(FiniteElementMethod)耦合算法的原理,然后采用作者自行研制的... 详细信息

混凝土重力坝一般设有数条纵缝。纵缝使坝体的连续性遭到破坏,一般的有限单元法很难处理这样的不连续变形问题。本文首先阐述了DDA(DiscontinuousDeformationAnalysis)与FEM(FiniteElementMethod)耦合算法的原理,然后采用作者自行研制的DDA与FEM耦合法程序对一实际重力坝进行了详细的计算分析。重点讨论了纵缝的不同设置形式和缝宽大小对坝体变形和应力分布、坝底面接触应力分布以及坝基面应力分布的影响,为工程设计提供依据。

关键词：非连续变形分析有限元耦合纵缝重力坝接触

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Helicobacter pylori infection in relation to E-cadherin gene promoter polymorphism and hypermethylation in sporadic gastric carcinomas

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World Journal of Gastroenterology 2005年第33期11卷 5174-5179页

作者： Yao-chi Liu Chen-Yang Shen Hurng-Sheng Wu De-Chuan Chan Cheng-Jueng Chen Jyh-Cherng Yu Cheng-Ping Yu Horng-Jyh Harn Rong-Yaun shyu Yu-Lueng Shih Chung-Bao Hsieh Huan-Mieng Hsu Division of General Surgery Department of Surgery Tri-Service General HospitalNational Defense Medical Center Taipei Taiwan China Division of Gastroenterology Department of Internal Medicine Tri-Service General HospitalNational Defense Medical Center Taipei Taiwan China Department of Pathology Tri-Service GeneralHospital National Defense Medical Center Taipei Taiwan China Department of Pathology Buddhist Tzu-Chi General Hospital Hualien Taiwan China Department of Surgery Show Chwan Memorial Hospital Changhua Taiwan China Institute of Biomedical Sciences Academia Sinica Taipei Taiwan China

AIM: To study Helicobacter pylori (H pylori) infection in relation to E-cadherin (E-cad) promoter polymorphism and hypermethylation in ***: Specimens were taken from representative cancerous lesions and adjacent non-cancerous epithelia of 67 resected GCs. Hpyloriwas detected by real-time PCR of the cagA gene from non-neoplastic epithelium.E-cad promoter polymorphism and hypermethylation were determined by restriction fragment length polymorphism analysis and methylation-specific PCR, respectively. Expression of E-cad protein was determined by ***: Hpyloriwas found in 57% of patients with GC.H pylori infection was more frequently found in tumors with the -160C/C genotype than those with the -160C/A and -160A/A genotypes (74% vs47%, P = 0.02). Hpylori infection was associated with E-cad methylation in nonneoplastic epithelium; however, no significant difference in H pylori was observed between methylated and unmethylated cancerous ***: Patients with the -160C/C genotype might require Hpyloriinfection to promote the inactivation of CDH1, suggesting that Hpylori infection might affect GC in an initial stage because polymorphism is germ *** of hypermethylation of CDH1 promoter in GC is complex, and Hpyloriinfection might affect it in an initial stage.

关键词： H pylort E-cadherirr -160 C→A polymorphism Hypermethylation Gastric carcinoma

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Manufacturing of micro tungsten carbide electrode using supersonic aided electrolysis process

Manufacturing of micro tungsten carbide electrode using supe...

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2007年上海市电子电镀学术年会

作者： Feng-Tsai Weng Ray-fang shyu chi-Ting Ho Institute of Mechanical and Electrical-mechanical Engineering National Formosa University 64 Wen-Hua Road Huwei YunlinTaiwan Institute of Mechanical and Electrical-mechanical Engineering National Formosa University 64 Wen-Hua Road Huwei YunlinTaiwan Institute of Mechanical and Electrical-mechanical Engineering National Formosa University 64 Wen-Hua Road Huwei YunlinTaiwan

＜正＞A noble micromachining technology was developed for the fabrication of micro parts using a nontraditional machining process in this *** carbide rods were selected as *** original diameter of tungsten carbide rod was 3mm,it was processed to 50μm using precision grinding process in first step,and then the rod could be machined to the final desired diameter on the anode in supersonic aided ***-aspect-ratio of micro tungsten carbide rod was easily obtained by this *** roughness of the sample with supersonic aided agitation was compared with that with no agitation in *** machined surface of the sample is very smooth due to ionized particles of anode could be removed by supersonic aided agitation during *** with a tip of about 1/am could be obtained by this process.

关键词： Micromachining Tungsten carbide Electrode Electrolysis Supersonic

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Comparison between the therapeutic effects of differentiated and undifferentiated Wharton’s jelly mesenchymal stem cells in rats with streptozotocin-induced diabetes

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World Journal of Stem Cells 2020年第2期12卷 139-151页

作者： Chen-Yuan Hsiao Tien-Hua Chen Ben-Shian Huang Po-Han Chen Cheng-Hsi Su Jia-Fwu shyu Pei-Jiun Tsai Graduate Institute of Medical Sciences National Defense Medical CenterTaipei 114Taiwan Department of Surgery Landseed International HospitalTaoyuan 324Taiwan Institute of Anatomy and Cell Biology School of MedicineNational Yang Ming UniversityTaipei 112Taiwan Trauma Center Department of SurgeryVeterans General HospitalTaipei 112Taiwan Division of General Surgery Department of SurgeryVeterans General HospitalTaipei 112Taiwan Department of Obstetrics and Gynecology Veterans General HospitalTaipei 112Taiwan Department of Surgery Cheng Hsin General HospitalTaipei 112Taiwan Department of Biology and Anatomy National Defense Medical CenterTaipei 114Taiwan Department of Critical Care Medicine Veterans General HospitalTaipei 112Taiwan

BACKGROUND Despite the availability of current therapies,including oral antidiabetic drugs and insulin,for controlling the symptoms caused by high blood glucose,it is difficult to cure diabetes mellitus,especially type 1 diabetes *** Cell therapies using mesenchymal stem cells(MSCs)may be a promising ***,the therapeutic mechanisms by which MSCs exert their effects,such as whether they can differentiate into insulin-producing cells (IPCs) beforetransplantation, are *** this study, we used three types of differentiation media over 10 d to generateIPCs from human Wharton’s jelly MSCs (hWJ-MSCs). We further transplantedthe undifferentiated hWJ-MSCs and differentiated IPCs derived from them intothe portal vein of rats with streptozotocin-induced diabetes, and recorded thephysiological and pathological *** fluorescent staining and C-peptide enzyme-linked immunoassay, we wereable to successfully induce the differentiation of hWJ-MSCs into *** of both IPCs derived from hWJ-MSCs and undifferentiated hWJMSCshad the therapeutic effect of ameliorating blood glucose levels andimproving intraperitoneal glucose tolerance tests. The transplanted IPCs homedto the pancreas and functionally survived for at least 8 wk after transplantation,whereas the undifferentiated hWJ-MSCs were able to improve the insulitis andameliorate the serum inflammatory cytokine in streptozotocin-induced *** IPCs can significantly improve blood glucose levels in diabetic ratsdue to the continuous secretion of insulin by transplanted cells that survive in theislets of diabetic rats. Transplantation of undifferentiated hWJ-MSCs cansignificantly improve insulitis and re-balance the inflammatory condition indiabetic rats with only a slight improvement in blood glucose levels.

关键词： Human Wharton’s jelly mesenchymal stem cell Insulin-producing cells Diabetes mellitus Differentiation Regeneration therapy Anti-inflammatory

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