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Identification of gene expression signatures for psoriasis classification using machine learning techniques

Medicine in Omics 2021年 1卷

作者： Nguyen Quoc Khanh Le duyen Thi do Trinh-Trung-duong Nguyen Ngan Thi Kim Nguyen Truong Nguyen Khanh Hung Nguyen Thi Thu Trang Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei City 106 Taiwan Research Center for Artificial Intelligence in Medicine Taipei Medical University Taipei City 106 Taiwan Graduate Institute of Biomedical Informatics Taipei Medical University Taipei City 106 Taiwan Department of Computer Science and Engineering Yuan Ze University Chung-Li 32003 Taiwan School of Nutrition and Health Sciences Taipei Medical University Taipei City 110 Taiwan International Master/Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei City 110 Taiwan Orthopedic and Trauma Department Cho Ray Hospital Ho Chi Minh City Viet Nam International PhD Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei City 110 Taiwan

Psoriasis classification requires the accurate identification of the lesional types for the early and effective diagnosis and it is worth interesting that the normal and psoriasis cell tissues exhibit different gene expression. Therefore, gene expression data is an effective source for psoriasis classification and there is a challenge regarding the selection of suitable gene signatures for its purpose. In this present study, the gene expression-based microarray data were used and 35 expression features linked with psoriasis were utilized to feed into our machine learning model. Overall, the performance of our model based on 35 mentioned-above features surpassed that of other state-of-the-art classifiers with an average accuracy of 98.3%, recall of 98.6%, and precision of 98% in 5-fold cross-validation tests. We also validate our model on two different sets of psoriasis and the performance results are significant. These results have suggested that our 35 expression signatures have been identified as key features for classifying samples between lesion and non-lesion. More specifically, the expression levels of few genes i.e., FABP5 , TGM1 , or BCAR3 are discovered as newly potential biomarkers for psoriasis classification and treatment with high confidence. This study, therefore, could shed light on developing the prediction models for psoriasis classification and treatment using gene expression profiles.

关键词： Psoriasis classification Random forest Gene expression Feature selection Machine learning FABP5 dermatology

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Anti-Inflammatory Glycosides from Gomphandra mollis Merr.: Structural Elucidation and Mechanistic Insights

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phytochemistry 2025年 114583页

作者： Quoc-dung Tran Huynh Thuy-Tien Thi phan Man-Hsiu Chu Thanh-Vu Nguyen Truc-Ly Thi duong Su-Jung Hsu Yun-Han Wang Ngoc-Thac pham Bien-Thuy Nguyen Bui dang-Khoa Nguyen Thanh-Hoa Vo Ta-Wei Liu Ching-Kuo Lee Ph.D. Program in Clinical Drug Development of Herbal Medicine College of Pharmacy Taipei Medical University Taipei 11031 Taiwan Institute of Pharmaceutical Education and Research Binh Duong University Thu Dau Mot 820000 Binh Duong Vietnam Graduate Institute of Biomedical Materials and Tissue Engineering College of Biomedical Engineering Taipei Medical University Taipei 11031 Taiwan School of Pharmacy College of Pharmacy Taipei Medical University Taipei 11042 Taiwan Biotechnology Center Of Ho Chi Minh City Ho Chi Minh 700000 Vietnam Faculty of Traditional medicine Can Tho University of Medicine and Pharmacy Can Tho 900000 Vietnam Faculty of Pharmacy Can Tho University of Medicine and Pharmacy Can Tho 900000 Vietnam Institute of Fisheries Science National Taiwan University Taipei 106 Taiwan National Research Institute of Chinese Medicine Ministry of Health and Welfare Taipei 11221 Taiwan University of Health Sciences Vietnam National University Ho Chi Minh City Ho Chi Minh 700000 Vietnam School of Pharmacy University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City 700000 Vietnam Center for Discovery and Development of Healthcare Product Vietnam National University Ho Chi Minh City Ho Chi Minh 700000 Vietnam Institute of Pharmaceutical Sciences Department of Pharmacognosy University of Graz Universitätsplatz 4 8010 Graz Austria Graduate Institute of Pharmacognosy College of Pharmacy Taipei Medical University Taipei 11042 Taiwan Department of Chemistry Chung Yuan Christian University Zhongli District Taoyuan 32023 Taiwan

Eight previously unreported glycosides, designated gomphandranosides I–VIII, along with nine known compounds, were isolated from the roots of Gomphandra mollis Merr. Their structures were elucidated through comprehensive spectroscopic analyses, including NMR, HR-ESI-MS, Cd, dP4+ probability, and ECd calculations. The anti-inflammatory activities of the isolated compounds were assessed using nitric oxide inhibition assays in LPS-stimulated RAW264.7 macrophages. Compounds 5 , 10 , and 16 exhibited significant anti-inflammatory activity with IC 50 values of 7.56 ± 0.9, 15.0 ± 1.2, and 14.2 ± 0.9 μM, respectively. Network pharmacology, gene ontology, Kyoto Encyclopedia of Genes and Genomes analysis, and molecular docking studies identified IL-6, TNF-α, MMP9, PTGS2, and HIF1A as key targets, with potentially involved in the NF- κ B and IL-17 signaling pathways. These findings highlight G. mollis as a promising candidate for the treatment of inflammation-related diseases.

关键词： Gomphandra mollis Stemonuraceae anti-inflammatory activity molecular docking network pharmacology

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Proton Radiation Studies on Conjugated Polymer Thin Films

Proton Radiation Studies on Conjugated Polymer Thin Films

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MRS Advances

作者： Lee, Harold O. Hasib, Muhammed Sun, Sam-Shajing Center for Materials Research Ph.D. Program in Materials Science and Engineering Norfolk State University NorfolkVA23504 United States Department of Chemistry Norfolk State University NorfolkVA23504 United States

Polymeric thin film based electronic and optoelectronic materials and devices are attractive for potential space and certain radiation related applications due to their inherent features such as being light weight, flexible, biocompatible and environmental friendly, etc. Proton radiation is a major form of ionizing radiation in space, yet very few literature and data are available on proton radiation effects on conjugated polymer systems. In this study, UV-Vis absorption spectra of several conjugated polymers and/or their composite thin films were measured and compared right before and after a 200 MeV proton beam irradiation at different dosages, and the results revealed that proton radiation has very little or negligible impact up to 800 Rads on the optoelectronic properties of several polymers and their composite thin films. Copyright © materials Research Society 2017.

关键词： Conjugated polymers

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Mediation analysis for TNF-α as a mediator between multiple metal exposure and kidney function

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Ecotoxicology and environmental safety 2024年 283卷 116837页

作者： Kuei-Hau Luo Hung-Pin Tu Huang-Chih Chang Chen-Cheng Yang Wei-Chun Weng Tzu-Hua Chen Cheng-Hong Yang Hung-Yi Chuang Graduate Institute of Medicine College of Medicine Kaohsiung Medicine University Kaohsiung City 807 Taiwan. Department of Public Health and Environmental Medicine School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung 807 Taiwan. Divisions of Pulmonary & Critical Care Medicine Department of Internal Medicine Kaohsiung Chang Gung Memorial Hospital Chang Gung University College of Medicine Kaohsiung Taiwan. Graduate Institute of Medicine College of Medicine Kaohsiung Medicine University Kaohsiung City 807 Taiwan Department of Occupational Medicine Kaohsiung Municipal Siaogang Hospital Kaohsiung Medical University Kaohsiung 812 Taiwan. Division of Gastroenterology Department of Internal Medicine Kaohsiung Armed Forces General Hospital Kaohsiung 802 Taiwan. Department of Family Medicine Kaohsiung Municipal Ta-Tung Hospital Kaohsiung 801 Taiwan. Department of Information Management Tainan University of Technology Tainan 71002 Taiwan Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung 80778 Taiwan. Department of Public Health and Environmental Medicine School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung 807 Taiwan Department of Occupational and Environmental Medicine Kaohsiung Medicine University Hospital Kaohsiung Medicine University Kaohsiung 807 Taiwan Ph.D. Program in Environmental and Occupational Medicine College of Medicine and Research Center for Precision Environmental Medicine Kaohsiung Medical University Kaohsiung 807 Taiwan. Electronic address: ericch@kmu.edu.tw.

The association between metal mixtures and kidney function has been reported. However, reports on the mechanism of metal toxicity were limited. Oxidative stress was reported as a possible cause. This study aimed to determine the association between of kidney function and metals, such as arsenic (As), cadmium (Cd), cobalt (Co), copper (Cu), lead (Pb), selenium (Se), and zinc (Zn), and to explore the possible mediating role of tumor necrosis factor alpha (TNF-α) between metal toxicity and kidney function. In this study, we recruited 421 adults from a health examination. The concentration of blood metals was analyzed using inductively coupled plasma mass spectrometry. We used linear regression models to assess the association between metals and TNF-α. Then, mediation analysis was applied to investigate the relationship between metal exposure, TNF-α, and kidney function. In univariate linear regression, blood As, Cd, Co, Cu, Pb, and Zn levels significantly increased TNF-α and decreased kidney function. Higher blood As and Pb levels significantly increased TNF-α in multivariable linear regressions after adjusting for covariates. We found that blood levels of As (coefficients = -0.021, p = 0.011), Pb (coefficients = -0.060, p < 0.001), and Zn (coefficients = -0.230, p < 0.001) showed a significant negative association with eGFR in the multiple-metal model. Furthermore, mediation analysis showed that TNF-α mediated 41.7 %, 38.8 %, and 20.8 % of blood Cd, As and Pb, respectively. Among the essential elements, TNF-α mediated 24.5 %, 21.5 % and 19.9 % in the effects of blood Co, Cu, and Zn on kidney function, respectively. TNF-α, acting as a mediator, accounted for 20.1 % of the contribution between the WQS score of metal mixtures and the eGFR (p < 0.001). This study suggested that TNF-α may be a persuasive pathway mediating the association between metals and kidney function. Inflammation and kidney injury could be the underlying mechanisms of metal exposure. However, there i

关键词： Kidney function Mediation analysis Metals Pb TNF-α

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Technology dictates algorithms: Recent developments in read alignment

arXiv

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arXiv 2020年

作者： Alser, Mohammed Rotman, Jeremy Taraszka, Kodi Shi, Huwenbo Baykal, Pelin Icer Yang, Harry Taegyun Xue, Victor Knyazev, Sergey Singer, Benjamin d. Balliu, Brunilda Koslicki, david Skums, Pavel Zelikovsky, Alex Alkan, Can Mutlu, Onur Mangul, Serghei Computer Science Department ETH Zürich Zürich8092 Switzerland Computer Engineering Department Bilkent University Bilkent Ankara 06800 Turkey Department of Computer Science University of California Los Angeles Los AngelesCA90095 United States Department of Epidemiology Harvard T.H. Chan School of Public Health MA02115 United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA02142 United States Department of Computer Science Georgia State University AtlantaGA30302 United States Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles Los AngelesCA90095 United States Division of Pulmonary and Critical Care Medicine Northwestern University Feinberg School of Medicine ChicagoIL60611 United States Department of Biochemistry & Molecular Genetics Northwestern University Feinberg School of Medicine United States Simpson Querrey Center for Epigenetics Northwestern University Feinberg School of Medicine ChicagoIL60611 United States Department of Computational Medicine University of California Los Angeles Los AngelesCA90095 United States Computer Science and Engineering Pennsylvania State University University ParkPA16801 United States Biology Department Pennsylvania State University University ParkPA16801 United States The Huck Institutes of the Life Sciences Pennsylvania State University University ParkPA16801 United States The Laboratory of Bioinformatics I.M. Sechenov First Moscow State Medical University Moscow119991 Russia Bilkent-Hacettepe Health Sciences and Technologies Program Ankara Turkey Department of Clinical Pharmacy School of Pharmacy University of Southern California Los AngelesCA90089 United States

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of genomic data in the form of nucleotide sequences or reads. Aligning reads onto reference genomes enables the identification of individual-specific genetic variants and is an essential step of the majority of genomic analysis pipelines. Aligned reads are essential for answering important biological questions, such as detecting mutations driving various human diseases and complex traits as well as identifying species present in metagenomic samples. The read alignment problem is extremely challenging due to the large size of analyzed datasets and numerous technological limitations of sequencing platforms, and researchers have developed novel bioinformatics algorithms to tackle these difficulties. Importantly, computational algorithms have evolved and diversified in accordance with technological advances, leading to today’s diverse array of bioinformatics tools. Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads. We provide rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read aligners. We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques. We also discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology, including whole transcriptome, adaptive immune repertoire, and human microbiome studies. Copyright © 2020, The Authors. All rights reserved.

关键词： Bioinformatics

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Corrigendum to “Application of an optically induced dielectrophoresis (OdEP)-based microfluidic system for the detection and isolation of bacteria with heterogeneity of antibiotic susceptibility” [Sens. Actuators B: Chem. 307 (15 March) (2020) 127540]

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Sensors and Actuators B: Chemical 2020年 323卷

作者： Hsin-Yao Wang Chih-Yu Chen Po-Yu Chu Yu-Xian Zhu Chia-Hsun Hsieh Jang-Jih Lu Min-Hsien Wu Department of Laboratory Medicine Chang Gung Memorial Hospital at Linkou Taoyuan City Taiwan ROC Ph.D. Program in Biomedical Engineering Chang Gung University Taoyuan City Taiwan Graduate Institute of Biomedical Engineering Chang Gung University Taoyuan City Taiwan ROC Division of Haematology/Oncology Department of Internal Medicine Chang Gung Memorial Hospital at Linkou Taoyuan City Taiwan ROC School of Medicine Chang Gung University Taoyuan City Taiwan ROC Department of Medical Biotechnology and Laboratory Science Chang Gung University Taoyuan City Taiwan ROC

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Ovatodiolide and antrocin synergistically inhibit the stemness and metastatic potential of hepatocellular carcinoma via impairing ribosome biogenesis and modulating ERK/Akt-mTOR signaling axis

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phytomedicine : international journal of phytotherapy and phytopharmacology 2023年 108卷 154478页

作者： Ming-Yao Chen Chia-Hung Hsu Syahru Agung Setiawan david T W Tzeng Hon-Ping Ma Jiann Ruey Ong Yi Cheng Chu Ming-Shou Hsieh Alexander T H Wu Yew-Min Tzeng Chi-Tai Yeh Division of Gastroenterology and Hepatology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei City 110 Taiwan Division of Gastroenterology and Hepatology Department of Internal Medicine Taipei Medical University-Shuang Ho Hospital New Taipei City 235 Taiwan. Department of Emergency Medicine Taipei Medical University-Shuang Ho Hospital New Taipei City 235 Taiwan Graduate Institute of Injury Prevention and Control College of Public Health Taipei Medical University Taipei City 110 Taiwan Department of Emergency Medicine School of Medicine Taipei Medical University Taipei City 110 Taiwan. International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei City 110 Taiwan Department of Medical Research & Education Taipei Medical University - Shuang-Ho Hospital New Taipei City 235 Taiwan. School of Life Sciences The Chinese University of Hong Kong Hong Kong SAR 999077 China Lifebit Mindspace Shoreditch London England EC2A 2AP UK. Department of Medicine St. George's University School of Medicine St. George Grenada. Department of Applied Science National Taitung University Taitung 95092 Taiwan. Electronic address: ymtzeng@nttu.edu.tw. Department of Medical Research & Education Taipei Medical University - Shuang-Ho Hospital New Taipei City 235 Taiwan Continuing Education Program of Food Biotechnology Applications College of Science and Engineering National Taitung University Taitung 95092 Taiwan. Electronic address: ctyeh@s.tmu.edu.tw.

Activation of mitogen-activated protein kinase (MAPK) and PI3K signaling confers resistance against sorafenib, a mainstay treatment for advanced hepatocellular carcinoma (HCC). Antrocin and ovatodiolide constitute as the most potent secondary metabolites isolated from Antrodia camphorata and Anisomeles indica, respectively. Both natural compounds have recently gained a lot of attention due to their putative inhibition of MAPK and PI3K signaling in various solid cancers. However, whether their combination is effective in HCC remains unknown. Here, we investigated their effect, alone or in various combinations, on MAPK and PI3K signaling pathways in HCC cells. An array of in vitro study were used to investigate anticancer and stemness effects to treat HCC, such as cytotoxicity, drug combination index, migration, invasion, colony formation, and tumor sphere formation. drug effect in vivo was evaluated using mouse xenograft models. In this study, antrocin and ovatodiolide synergistically inhibited the SNU387, Hep3B, Mahlavu, and Huh7 cell lines. Sequential combination treatment of Huh7 and Mahlavu with ovatodiolide followed by antrocin resulted stronger cytotoxic effect than did treatment with antrocin followed by ovatodiolide, their simultaneous administration, antrocin alone, or ovatodiolide alone. In the Huh7 and Mahlavu cell lines, ovatodiolide→antrocin significantly suppressed colony formation and proliferation as well as markedly downregulated ERK1/2, Akt, and mTOR expression. Inhibition of ERK1/2 and Akt/mTOR signaling by ovatodiolide→antrocin suppressed ribosomal biogenesis, autophagy, and cancer stem cell-like phenotypes and promoted apoptosis in Huh7 and Mahlavu cells. The sorafenib-resistant clone of Huh7 was effectively inhibited by synergistic combination of both compound in vitro. Eventually, the ovatodiolide→antrocin combination synergistically suppressed the growth of HCC xenografts. Taken together, our findings suggested that ovatodiolide→antrocin combi

关键词： Advanced HCC Antrocin (ANC) MAPK Ovatodiolide (OVA) PI3K

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Simulation of a 3d Turbulent Wavy Channel based on the High-order WENO Scheme

引用

IOP Conference Series: materials science and engineering 2018年第1期307卷

作者： Bor-Jang Tsai Chung-Chyi Chou Yeong-Pei Tsai Ying Hung Chuang Ph.D. Program in Engineering Science Chung Hua University Department of Fire and Safety Da-Yeh University

Passive interest turbulent drag reduction, effective means to improve air vehicle fuel consumption costs. Most turbulent problems happening to the nature and engineering applications were exactly the turbulence problem frequently caused by one or more turbulent shear flows. This study was operated with incompressible 3-d channels with cyclic wavy boundary to explore the physical properties of turbulence flow. This research measures the distribution of average velocity, instant flowing field shapes, turbulence and pressure distribution, etc. Furthermore, the systematic computation and analysis for the 3-d flow field was also implemented. It was aimed to clearly understand the turbulence fields formed by wavy boundary of tube flow. The purpose of this research is to obtain systematic structural information about the turbulent flow field and features of the turbulence structure are discussed.

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Unsupervised extraction of phenotypes from cancer clinical notes for association studies

arXiv

引用

arXiv 2019年

作者： Stark, Stefan G. Hyland, Stephanie L. Pradier, Melanie F. Lehmann, Kjong-Van Wicki, Andreas Perez-Cruz, Fernando Vogt, Julia E. Rätsch, Gunnar Computational Biology Program Memorial Sloan Kettering Cancer Center New York United States Tri-Institutional Ph.D. Program in Computational Biology and Medicine Weill Cornell Medicine New York United States Department of Computer Science ETH Zürich Zürich Switzerland Medical Informatics Group University Hospital Zürich Zürich Switzerland Swiss Institute for Bioinformatics Zurich Switzerland Department of Biology ETH Zürich Zürich Switzerland Department of Signal Processing and Information Theory University Carlos III in Madrid Leganés Spain School of Engineering and Applied Sciences Harvard University CambridgeMA United States Department of Biomedicine University of Basel Basel Switzerland Tumorzentrum University Hospital Basel Basel Switzerland Swiss Data Science Center ETH Zürich and EPFL Lausanne Switzerland Department of Mathematics and Computer Science University of Basel Basel Switzerland

The recent adoption of Electronic Health Records (EHRs) by healthcare providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opportunities for research and clinical care. However, many methods require the patient representations to be in structured formats, while the information in the EHR is often locked in unstructured text designed for human readability. In this work, we develop the methodology to automatically extract clinical features from clinical narratives from large EHR corpora without the need for prior knowledge. We consider medical terms and sentences appearing in clinical narratives as atomic information units. We propose an efficient clustering strategy suitable for the analysis of large text corpora and utilize the clusters to represent information about the patient compactly. Additionally, we define the sentences on ontologic and natural language vocabularies to automatically detect pertinent combinations of concepts present in the corpus, even when an ontology is not available. To demonstrate the utility of our approach, we perform an association study of clinical features with somatic mutation profiles from 4,007 cancer patients and their tumors. We apply the proposed algorithm to a dataset consisting of .65 thousand documents with a total of .3.2 million sentences. After correcting for cancer type and other confounding factors, we identify a total of 340 significant statistical associations between the presence of somatic mutations and clinical features. We annotated these associations according to their novelty and we report several known associations. We also propose 37 plausible, testable hypothesis for associations where the underlying biological mechanism does not appear to be known. These results illustrate that the automated discovery of clinical features

关键词： diseases

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Molecular modelling of broccoli myrosinase and its interaction with different ligands

引用

Chemical engineering Transactions 2018年 64卷 373-378页

作者： Roman, Juan Castillo, Antonio Cottet, Luis Mahn, Andrea Ph.D. Program in Food Science and Technology University of Santiago of Chile Obispo Manuel Umaña 050 Estación Central Santiago Chile Department of Biology University of Santiago of Chile Estación Central Avenida Libertador Bernardo O'Higgins 3363 Santiago9170019 Chile Department of Chemical Engineering University of Santiago of Chile Avenida Libertador Bernardo O'Higgins 3363 Santiago9170019 Chile

ISBN: (纸本)9788895608563

Myrosinase (ß-thioglucosidase glucohydrolase (EC 3.2.3.1)) is a glycoprotein responsible for the hydrolysis of glucosinolates, a group of sulfur-containing secondary metabolites present in Brassicaceae plants. Sulforaphane, a powerful anti-cancer compound, comes from the hydrolysis of glucoraphanin, the main glucosinolate found in broccoli. The aim of this work was to investigate the interaction between broccoli myrosinase and different substrates through molecular modelling. Currently the amino acid sequence and the molecular structure of broccoli myrosinase are unknown. The amino acid sequence was deduced from the nucleotide sequence, which in turn was obtained experimentally. The primary sequence of broccoli myrosinase used for modelling consisted of 548 amino acids. The three-dimensional model was generated by an ab initio/threading method using the crystal structure of 1MYR_A and 1dWF_M of Sinapis alba, 1CBG_A of Trifolium repens L, 3PTK_A of Oryza sativa and 3WQ4_A of Camellia sinensis as templates, employing the I-TASSER server. The interaction with glucoraphanin (GRA), sinigrin (SIN), glucoiberin (GIB) and N-acetylglucosamine (NAG) was investigated through molecular docking. The binding energy of GRA, SIN, GIB and NAG to myrosinase were -3.80;-4.71;-4.77 and -5.55 (Kcal/mol), respectively. The simulations of the interaction between GRA and myrosinase suggested that the residues of the active site responsible for substrate stabilization by hydrogen bonding were Gln207, Gly431, Ser433 and Trp 477. The residue involved in the hydrolysis of the ß-d-thioglucose binding was Tyr352. NAG interacts with the active site, as inhibitor. Our results will allow further studies about molecular mechanisms of broccoli myrosinase. Copyright © 2018, AIdIC Servizi S.r.l.

关键词： Hydrolysis

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