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driverdBv4:ã multi-omics integration database for cancer driv er g ene resear c h

Nucleic Acids Research 2024年第D1期52卷 D1246-D1252页

作者： Liu, Chia-Hsin Lai, Yo-Liang Shen, Pei-Chun Liu, Hsiu-Cheng Tsai, Meng-Hsin Wang, Yu-de Lin, Wen-Jen Chen, Fang-Hsin Li, Chia-Yang Wang, Shu-Chi Hung, Mien-Chie Cheng, Wei-Chung Cancer Biologyãnd Precision Therapeutics Center China Medical University Taichung 404328 Taiwan Department of Radiation Oncology China Medical University Taichung 404328 Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung 404328 Taiwan Department of Urology China Medical University Taichung 404328 Taiwan School of Medicine China Medical University Taichung 404328 Taiwan Institute of Nuclear Engineeringãnd Science National Tsing Hua University Hsinchu 300044 Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung 80708 Taiwan Department of Medical Laboratory Scienceãnd Biotechnology Kaohsiung Medical University Kaohsiung 80708 Taiwan Institute of Biochemistryãnd Molecular Biology China Medical University Taichung 404328 Taiwan Molecular Medicine Center China Medical University Hospital China Medical University Taichung 404328 Taiwan Department of Biotechnology Asia University Taichung 413305 Taiwan The Ph.D. program for Cancer Biologyãnd Drug Discovery China Medical Universityãnd Academia Sinica Taichung 404328 Taiwan

A dvãncements in high-throughput technology offer researchersãn e xtensiv e range of multi-omics data that provide deep insights into the complex landscape of cancer biology . However , traditional statistical modelsãnd databasesãre inadequate to interpret these high-dimensional data withinã multi-omics frame w ork. Toãddress this limitation, we introduce driverdBv4,ãn updated iteration of the driverdB cancer driver gene database ( http://driv *** ***/). T his updated v ersion offers se v eral significant enhancements: (i)ãn increase in the number of cohorts from 33 to 70, encompassingãpproximately 24 0 0 0 samples;(ii) inclusion of proteomics data,ãugmenting the existing types of omics dataãnd thus expanding theãnalytical scope;(iii) implementation of multiple multi-omicsãlgorithms for identification of cancer drivers;(iv) new visualization features designed to succinctly summarize high-context dataãnd redesigned existing sections toãccommodate the increased volume of datasetsãnd (v) two new functions in Customized Analysis, specifically designed for multi-omics driver identificationãnd subgroup e xpressionãnaly sis. driv erdBv4 fãcilitates comprehensiv e interpretãtion of multi-omics datããcross diverse cancer types, thereby enriching the understanding of cancer heterogeneityãndãiding in the de v elopment of personalized clinicalãpproaches. The database is designed to fosterã more nuanced understanding of the multi-faceted nature of cancer. © The Author(s) 2023.

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Activation of PI3K/Akt mediates the protective effect of diallyl trisulfide on doxorubicin induced cardiac apoptosis

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Current Research in Toxicology 2023年 5卷 100136页

作者： Wen, Su-Ying Ng, Shang-Chuan Ho, Wen-Kun Huang, Han-Zhe Huang, Chih-Yang Kuo, Wei-Wen Department of Dermatology Taipei City Hospital Renai Branch Taipei Taiwan Department of Cosmetic Applications and Management Mackay Junior College of Medicine Nursing and Management Taipei Taiwan Department of Health Care Management National Taipei University of Nursing and Health Sciences Taipei Taiwan Department of Biological Science and Technology College of Life Sciences China Medical University Taichung Taiwan Ph.D. Program for Biotechnology Industry China Medical University Taichung Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Cardiovascular and Mitochondrial Related Disease Research Center Hualien Tzu Chi Hospital Buddhist Tzu Chi Medical Foundation Hualien Taiwan Center of General Education Buddhist Tzu Chi Medical Foundation Tzu Chi University of Science and Technology Hualien Taiwan Department of Medical Research China Medical University Hospital China Medical University Taichung Taiwan Department of Biotechnology Asia University Taichung Taiwan

diallyl trisulfide (dATS), an organosulfide compound derived from garlic, is renowned for its potent antioxidant properties, particularly in countering the generation of reactive oxygen species (ROS). It has also gained recognition as a potential agent for preventing heart-related conditions. doxorubicin (dox), a commonly used chemotherapeutic drug, is known to induce severe cardiac complications by promoting ROS production. Therefore, it was imperative to investigate whether dATS possesses cardioprotective capabilities against dox-induced cardiac apoptosis and elucidate the underlying mechanisms. In this study, we observed that the intracellular ROS levels and cardiac apoptosis were heightened in H9c2 cells exposed to dox (1 μM). However, treatment with 10 μM dATS effectively mitigated the dox-induced ROS generation and apoptotic signaling, concurrently activating the PI3K/Akt pathway. Notably, the anti-apoptotic effects of dATS were attenuated when PI3K siRNA and the LY294002 PI3K inhibitor were employed. Furthermore, the TUNEL assay results demonstrated a significant reduction in dox-induced apoptosis with dATS treatment. In summary, our findings indicate that dATS can activate the PI3K/Akt pathway, reducing ROS production in cardiac cells exposed to dox, and subsequently rescue cardiac cells from apoptosis. © 2023 The Authors

关键词： Cardiac apoptosis dially trisulfide doxorubicin Reactive oxygen species

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Improvement of extracellular polysaccharides production from Cordyceps militaris immobilized alginate beads in repeated-batch fermentation

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LWT 2024年 193卷

作者： Hou, Shi-Jing Cheng, Kuan-Chen Lin, Shyh-Hsiang Hsiao, I-Lun Santoso, Shella Permatasari Singajaya, Stephanie Chou, Yu-Chieh Lin, Shin-Ping Master Program in Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Institute of Biotechnology National Taiwan University 1 Roosevelt Rd. Sec. 4 Taipei10617 Taiwan Graduate Institute of Food Science and Technology National Taiwan University 1 Roosevelt Rd. Sec. 4 Taipei10617 Taiwan Department of Medical Research China Medical University Hospital China Medical University 91 Hsueh-Shih Rd. Taichung40402 Taiwan Department of Optometry Asia University 500 Lioufeng Rd. Wufeng Taichung41354 Taiwan School of Nutrition and Health Sciences Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan School of Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Department of Chemical Engineering Widya Mandala Surabaya Catholic University Kalijudan 37 East Java Surabaya60114 Indonesia Collaborative Research Center for Sustainable and Zero Waste Industries Kalijudan 37 East Java Surabaya60114 Indonesia Ph.D. Program in Drug Discovery and Development Industry Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Research Center of Biomedical Device Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan TMU Research Center for Digestive Medicine Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan

Cordyceps militaris (C. militaris) is a unique medicinal fungus of the genus Cordyceps. It has high economic value due to various biological functions from the extracellular polysaccharides (EPSs) it produces. The aim of this study was to establish a mycelium-immobilization system for EPS production in a bubble column system. First, EPS production was optimized by 90.2% (from 0.72 to 1.37 g/L) using response surface methodology under an alginate-immobilized mycelium system with 6 days of cultivation. The highest EPS production was obtained (5.3 g/L) in a flask system through elongation to 15 days of cultivation. EPS production subsequently further increased to 10.42 g/L utilizing a bubble column reactor. Furthermore, the system can be reused for at least three rounds. In the EPS characteristics analysis, the produced EPSs were mainly composed of glucose and galactose. They presented strong antibacterial activity against Staphylococcus aureus. In terms of antioxidant activity, respective the EPS concentration that caused 50% scavenging of dPph and ABTS free radicals values (IC50) were 4.65 and 7.92 mg/mL. In summary, these findings should be helpful for establishing a suitable industrial fermentation system for C. militaris and can be studied in the food and medical industries in future work. © 2024 The Authors

关键词： Mycelium

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P12.03.A MULTIMOdAL ANALYSIS OF GLIOBLASTOMA REVEALS THE POTENTIAL OF CXCR7-CXCL12 IN GBM CELLS SENSITIZES GBM TO IMMUNE CHECKPOINT BLOCKAdE THERAPY

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Neuro-Oncology 2023年第SUPPLEMENT_2期25卷 ii96–ii97页

作者： Liu, C Chien, C Yang, W Chuang, J Chang, K National Health Research Institutes Tainan City Taiwan School of Medicine I-Shou University Kaohsiung Taiwan TMU Research Center of Neuroscience Taipei Medical University Taipei City Taiwan The Ph.D. Program for Neural Regenerative Medicine College of Medical Science and Technology Taipei Medical University Taipei City Taiwan Department of Oncology National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan City Taiwan

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Correction: A network-based approach to overcome BCR::ABL1-independent resistance in chronic myeloid leukemia

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Cell communication and signaling : CCS 2025年第1期23卷 205页

作者： Valeria Bica Veronica Venafra Giorgia Massacci Simone Graziosi Sara Gualdi Gessica Minnella Federica Sorà Patrizia Chiusolo Maria Elsa Brunetti Gennaro Napolitano Massimo Breccia dimitrios Mougiakakos Martin Böttcher Thomas Fischer Livia Perfetto Francesca Sacco Ph.D. Program in Cellular and Molecular Biology Department of Biology University of Rome 'Tor Vergata' Rome Italy. Department of Biology and Biotechnologies "C. Darwin" University of Rome La Sapienza Rome Italy. Department of Biology University of Rome Tor Vergata Rome Italy. Sezione di Ematologia Dipartimento di Scienze Radiologiche ed Ematologiche Università Cattolica del Sacro Cuore Roma Italy. Dipartimento di Scienze di laboratorio ed Ematologiche Fondazione Policlinico A. Gemelli IRCCS Roma Italy. Telethon Institute of Genetics and Medicine (TIGEM) Naples Italy. Department of Medical and Translational Science Federico II University Naples Italy. Scuola Superiore Meridionale (SSM) School for Advanced Studies Genomics and Experimental Medicine program Naples Italy. Department of Translational and Precision Medicine Azienda Policlinico Umberto I Sapienza University of Rome Rome Italy. Health campus for Inflammation Immunity and Infection (GCI3) University of Magdeburg Magdeburg Germany. Department of Hematology Oncology and Cell Therapy University of Magdeburg Magdeburg Germany. Department of Biology and Biotechnologies "C. Darwin" University of Rome La Sapienza Rome Italy. livia.perfetto@uniroma1.it. Department of Biology University of Rome Tor Vergata Rome Italy. francesca.sacco@uniroma2.it. Telethon Institute of Genetics and Medicine (TIGEM) Naples Italy. francesca.sacco@uniroma2.it.

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Graph Generation with a Focusing Lexicon

Graph Generation with a Focusing Lexicon

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IEEE International Conference on Big data

作者： Mayanka Chandra Shekar Joseph A. Cottam University of Missouri-Kansas City Computer Science (Ph.D. Candidate) Kansas City Missouri USA Pacific Northwest National Laboratory Richland WA USA

ISBN: (数字)9781728108582

ISBN: (纸本)9781728108599

The major part of graph generation is deriving connections (links) between entities (nodes). In this paper, a novel technique RAKE-IdF is introduced for key-phrase extraction across multiple documents. There are two main parts to this work: First is a Contextual Lexicon Generation generation step (in this case, White Collar Crime Lexicon) and second is a text-to-graph generation process. The text-graph generation is an ensemble model of state of the art semantic role labeling models with our key-phrase extraction technique: RAKE-IdF. These two parts are combined by augmenting standard graph with lexicon-generation derived elements to ensure interesting components are represented.

关键词： Graph theory Semantics Labeling Feature extraction Natural language processing Text analysis

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SRT1720 as an SIRT1 Activator for Alleviating Paraquat-Induced Models of Parkinson's disease

SSRN

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SSRN 2022年

作者： Chao, Chih-Chang Huang, Chuen-Lin Cheng, Jing-Jy Chiou, Chun-Tang Lee, I-Jung Yang, Ying-Chen Hsu, Ting-Huang Yei, Chan Lin, Pei-Yin Cheng, Jih-Jung Huang, Nai-Kuei Institute of Neuroscience National Chengchi University Taipei Taiwan Medical Research Center Cardinal Tien Hospital Hsintien New Taipei City Taiwan Graduate Institute of Physiology Department of Physiology and Biophysics National Defense Medical Center Taipei114 Taiwan National Research Institute of Chinese Medicine Ministry of Health and Welfare Taipei112 Taiwan Institute of Biophotonics National Yang-Ming University Taipei112 Taiwan Herbal Medicine Department Yokohama University of Pharmacy Yokohama Japan Department of Biotechnology and Animal Science National Ilan University Ilan Taiwan School of Pharmaceutical Sciences National Yang-Ming Chiao Tung University Taipei Taiwan Ph.D. Program for Neural Regenerative Medicine College of Medical Science and Technology Taipei Medical University Taipei11031 Taiwan Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei11031 Taiwan

Epidemiological studies have linked herbicides and Parkinson’s disease (Pd), with the strongest associations resulting from long exposure durations. Paraquat (PQ), an herbicide, induces Pd-like syndromes and has widely been accepted as a Pd mimetic. Currently, there is still no cure to prevent the progression of Pd, and the search for effective therapeutic ways is urgent. Recently, the impairing activity of sirtuins (SIRTs), such as SIRT1, may correlate with Pd etiology. However, the nonspecificity of SIRT1 agonists has made the protective mechanisms against Pd unclear and hampered the therapeutic application of SIRT1. Thus, this study investigated the protective mechanism and therapeutic potential of SRT1720, a more specific agonist for SIRT1, in alleviating the toxicity of PQ-induced cellular and animal models of Pd. Here we show that SRT1720 alleviates PQ-induced toxicity in cell and animal models. Genetic silencing and pharmacological inhibition of SIRT1 attenuated SRT1720’s protection against PQ-induced toxicity. Moreover, SRT1720 not only attenuated PQ-induced increased oxidative stress and mitochondrial free radical formations but also decreased mitochondrial membrane potential. Furthermore, SRT1720 reversed PQ-induced decreased PGC-1α levels and mitochondrial biogenesis. Although PQ and SRT1720 elevated NRF2 and antioxidative enzyme levels, only PQ decreased antioxidative enzyme activity but not SRT1720. NRF2 and PGC-1α silencing attenuated SRT1720 protection against PQ-induced toxicity. SRT1720 targeted SIRT1 and activated downstream PGC-1a and NRF2 signalings to prevent PQ-induced toxicity involving oxidative stress and mitochondrial dysfunction. Thus, SRT1720 might have therapeutic potential in preventing Pd. © 2022, The Authors. All rights reserved.

关键词： Mitochondria

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Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

arXiv

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arXiv 2023年

作者： Takaba, Kenichiro Pulido, Iván Behara, Pavan Kumar Cavender, Chapin E. Friedman, Anika J. Henry, Michael M. Macdermott-Opeskin, Hugo Iacovella, Christopher R. Nagle, Arnav M. Payne, Alexander Matthew Shirts, Michael R. Mobley, david L. Chodera, John d. Wang, Yuanqing Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Pharmaceuticals Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Center for Neurotherapeutics Department of Pathology and Laboratory Medicine University of California IrvineCA92697 United States Skaggs School of Pharmacy and Pharmaceutical Sciences University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States Department of Chemical and Biological Engineering University of Colorado Boulder BoulderCO80309 United States Open Molecular Software Foundation DavisCA95618 United States Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Department of Pharmaceutical Sciences University of California IrvineCA92697 United States Tri-Institutional Ph.D. Program in Chemical Biology Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University New YorkNY10004 United States

The development of reliable and extensible molecular mechanics (MM) force fields—fast, empirical models characterizing the potential energy surface of molecular systems—is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest. © 2023, CC BY.

关键词： Quantum chemistry

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Targeting the Neuropilin-1 receptor with Ovatodiolide and progress in using periodontal ligament organoids for COVId-19 research and therapy

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Life sciences 2024年 351卷 122764页

作者： Hsieh, Ming-Shou Chen, Ming-Yao Chang, Yu-Sheng Huang, Chin-Sheng Hsu, Tung-Nien Huang, Mao-Suan Yeh, Chi-Tai Tzeng, Yew-Min Department of Otolaryngology School of Medicine College of Medicine Taipei Medical University Taipei City 11031 Taiwan Department of Otolaryngology-Head and Neck Surgery Shuang Ho Hospital Taipei Medical University New Taipei City 23561 Taiwan 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 Division of Allergy Immunology and Rheumatology Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei City 23561 Taiwan Division of Allergy Immunology and Rheumatology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan Department of Medical Research & Education Taipei Medical University-Shuang Ho Hospital New Taipei City 23561 Taiwan International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei City 11031 Taiwan Continuing Education Program of Food Biotechnology Applications College of Science and Engineering National Taitung University Taitung 95092 Taiwan Department of Applied Science National Taitung University Taitung 95092 Taiwan TMU Research Center for Digestive Medicine Taipei Medical University Taipei 110 Taiwan

The discovery of SARS-CoV-2 RNA in the periodontal tissues of patients who tested positive for COVId-19, 24 days post the initial symptom onset, indicates the oral cavity could serve as a viral reservoir. This research aims to investigate the antiviral capabilities of Ovatodiolide, introducing a novel periodontal ligament organoid model for the study of SARS-CoV-2. We have successfully established a reliable and expandable organoid culture from the human periodontal ligament, showcasing characteristics typical of epithelial stem cells. This organoid model enables us to delve into the lesser-known aspects of dental epithelial stem cell biology and their interactions with viruses and oral tissues. We conducted a series of in vitro and ex vivo studies to examine the inhibitory impacts of Ova on SARS-CoV-2. Our findings indicate that Ovatodiolide molecules can bind effectively to the NRP1 active domain. Our study identifies potential interaction sites for Ovatodiolide (OVA) within the b1 domain of the NRP1 receptor. We generated point mutations at this site, resulting in three variants: Y25A, T44A, and a double mutation Y25A/T44A. While these mutations did not alter the binding activity of the spike protein, they did impact the concentration of OVA required for inhibition. The inhibitory concentrations for these variants are 15 μM for Y25A, 15.2 μM for T44A, and 25 μM for the double mutant Y25A/T44A. In addition, in vitro inhibition experiments demonstrate that the EC50 of Ova against the main protease (Mpro) of the SARS-CoV-2 virus is 7.316 μM. Our in vitro studies and the use of the periodontal ligament organoid model highlight Ovatodiolide's potential as a small molecule therapeutic agent that impedes the virus's ability to bind to the Neuropilin-1 receptor on host cells. The research uncovers various pathways and biochemical strategies through which Ovatodiolide may function as an effective antiviral small molecule drug. © 2024 Elsevier Inc.

关键词： Human Neuropilin-1 Main protease Ovatodiolide Periodontal ligament organoids SARS-CoV-2

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Constructing a Smart Home Control System with the Internet of Things 7

Constructing a Smart Home Control System with the Internet o...

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7th IEEE Asia-Pacific Conference on Antennas and Propagation, APCAP 2018

作者： Hsu, Huan-Po Yu, Kun-Ming Ouyang, Wen Cheng Jie, X. Ph.D. Program in Engineering Science Chung Hua University Hsinchu Taiwan Dept. of Computer Science Information Engineering Chung-Hua University Hsinchu Taiwan Faculty of Computer and Software Engineering Huaiyin Institute of Technology Jiangsu China

ISBN: (纸本)9781538656488

The development of Internet of Things (IoT) makes the application of smart homes grow rapidly. It is very popular to install smart appliances in the house. However, building a smart control system at home not only costs a lot but also has many limitations. For this reason, this study proposes a smart homes control system to easily integrate IoT, WSN, smart robot and single-board computer to implement smart home applications. We use wireless technology and automatic equipment to avoid excessive communication cable and to make the house more intelligent to keep in-house movement unimpeded and indoor space tidy and to let appliance adjust appropriate environment settings automatically. This system brings intelligence and convenience to home, making living environment more comfortable. © 2018 IEEE.

关键词： Wireless sensor networks

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