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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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HER2 amplification in colorectal cancer with brain metastasis: A propensity score matching study

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European journal of cancer (Oxford, England : 1990) 2023年 181卷 62-69页

作者： Po-Chuan Chen Yu-Min Yeh Chun-Ting Chu Pei-Fang Su Pin-Hsuan Chiu Bo-Wen Lin Shang-Hung Chen Peng-Chan Lin Chung-Ta Lee Helen H W Chen Chien-Chin Chen Division of Colorectal Surgery Department of Surgery National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 704 Taiwan. Department of Oncology National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 704 Taiwan. Division of Colorectal Surgery Department of Surgery Ditmanson Medical Foundation Chia-Yi Christian Hospital Chiayi 600 Taiwan. Department of Statistics National Cheng Kung University Tainan 701 Taiwan. The Center of Quantitative Sciences Clinical Medicine Research Center National Cheng Kung University Hospital Tainan 704 Taiwan. Department of Oncology National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 704 Taiwan National Institute of Cancer Research National Health Research Institute Tainan 704 Taiwan. Department of Genomic Medicine National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 704 Taiwan Department of Computer Science and Information Engineering College of Electrical Engineering and Computer Science National Cheng Kung University Tainan 704 Taiwan. Department of Pathology National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 704 Taiwan. Department of Oncology National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 704 Taiwan. Electronic address: helen@mail.ncku.edu.tw. Department of Pathology Ditmanson Medical Foundation Chia-Yi Christian Hospital Chiayi 600 Taiwan Department of Cosmetic Science Chia Nan University of Pharmacy and Science Tainan 717 Taiwan Department of Biotechnology and Bioindustry Sciences College of Bioscience and Biotechnology National Cheng Kung University Tainan 701 Taiwan Ph.D. Program in Translational Medicine Rong Hsing Research Center for Translational Medicine National Chung Hsing University Taichung 40227 Taiwan. Electronic address: hlmarkc@gmail.c

BACKGROUNd:The association between human epidermal growth factor receptor-2 (HER2) amplification and brain metastasis (BM) in patients having colorectal cancer (CRC) has been suggested but not yet established. This study investigated the expression patterns of HER2, its association with BM, and its prognostic value in patients having CRC. METHOdS:We retrospectively identified 99 patients having metastatic CRC (mCRC) and BM (the BM cohort) and compared them with a cohort of 249 patients having mCRC and without BM (the stage IV cohort) by propensity score matching. Immunohistochemical studies of HER2 on all available paraffin-embedded tumour samples, either from the primary tumour, the metastasis (brain and/or extracranial sites) or both, were performed and analysed. HER2 fluorescent in situ hybridisation was applied when necessary. The expression of HER2 was compared and correlated with survival. RESULTS:HER2 amplifications were detected in 16 (18.4%) of 87 and 9 (3.6%) of 249 patients who had specimens available in the BM and stage IV cohorts, respectively (P < .001). After propensity score matching, HER2 amplification was significantly associated with BM (odds ratio: 5.38, P = .003). HER2 heterogeneity was frequently observed not only at the single tumour level but also in paired tumour samples. A marginally significant longer survival since BM was found in patients having HER2-amplified mCRC than in those without (P = .07). CONCLUSIONS:HER2 amplification was significantly associated with BM in patients having mCRC and might have prognostic value for survival since BM. Given the heterogeneity of HER2 expression, the testing of HER2 status on available tissues from both primary and metastatic tumours should be encouraged.

关键词： Brain metastasis Colorectal cancer HER2 amplification Heterogeneity Propensity score matching

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Surface modification of alginate sponge using tannic acid and dodecanethiol for diesel oil spill separation from water

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International Journal of Biological Macromolecules 2025年 317卷 144453页

作者： Wijaya, Ronald Cheng, Kuan-Chen Santoso, Shella Permatasari Lin, Shin-Ping Putro, Jindrayani Nyoo Lie, Jenni Hsieh, Chang-Wei Hsu, Hsien-Yi Go, Alchris Woo Angkawijaya, Artik Elisa Chemical Engineering Department National Taiwan University of Science and Technology Taipei10607 Taiwan Institute of Food Science and Technology National Taiwan University Daan District Taipei City10617 Taiwan Institute of Biotechnology National Taiwan University No. 1 Sec. 4 Roosevelt Rd. Taipei Taiwan Department of Optometry Asia University 500 Lioufeng Rd. Wufeng Taichung Taiwan Department of Medical Research China Medical University Hospital China Medical University 91 Hsueh-Shih Rd. Taichung Taiwan Department of Food Science Fu Jen Catholic University No. 510 Zhongzheng Rd. Xinzhuang Dist. New Taipei City242062 Taiwan Chemical Engineering Department Faculty of Engineering Universitas Katolik Widya Mandala Surabaya Jl. Kalijudan No. 37 East Java Surabaya60114 Indonesia Chemical Engineering Master Program Faculty of Engineering Universitas Katolik Widya Mandala Surabaya Jl. Kalijudan No. 37 East Java Surabaya60114 Indonesia Collaborative Research Center for Zero Waste and Sustainability Universitas Katolik Widya Mandala Surabaya Jl. Kalijudan No. 37 East Java Surabaya60114 Indonesia School of Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Ph.D. Program in Drug Discovery and Development Industry College of Pharmacy Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Research Center of Biomedical Device Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Department of Food Science and Biotechnology National Chung Hsing University South Dist Taichung City402202 Taiwan Department of Food Science National Ilan University Shennong Road Yilan City260007 Taiwan Department of Medical Research China Medical University Hospital Taichung City404333 Taiwan City University of Hong Kong Kowloon Tong Hong Kong Shenzhen Research Institute of City University of Hong Kong Shenzhen518057 China School of Engineering University of San Carlos - Talamban Campus Gov. M. Cuenco Cebu City

An environmentally friendly absorbent sponge was successfully developed for diesel spill remediation via alginate polymer crosslinking followed by surface modification using tannic acid and dodecanethiol (TA/do). The optimal sponge was obtained with a 3 h crosslinking duration, achieving a balance between absorption performance and structural durability, while longer crosslinking times led to increased density and reduced efficiency. Surface modification imparted hydrophobicity to the alginate sponge, confirmed by a water contact angle of 120.2°, and the successful incorporation of TA/do was confirmed from FTIR and XPS analysis. The modified sponge (AA-3-TA/do) exhibited a diesel absorption capacity of 17.54 g/g—a 36 % increase over the unmodified form—and retained ∼90 % of this capacity after 34 absorption–desorption cycles. Kinetic modeling showed that diesel was rapidly absorbed during early contact, with faster uptake than water. A cytotoxicity assay confirmed its non-toxic nature, indicating environmental compatibility. This study demonstrates that a simple, scalable modification using accessible materials can significantly enhance oil sorbent performance without requiring complex techniques or hazardous reagents. © 2025 Elsevier B.V.

关键词： Toxicity

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A Global Genome-wide Scan with Optimal Cutoff Mining for Emerging Biomarkers in Head and Neck Squamous Cell Carcinoma

Research Square

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Research Square 2020年

作者： Chi, Li-Hsing Wu, Alexander T.H. Hsiao, Michael Li, Yu-Chuan The Ph.D. Program for Translational Medicine College of Medical Science and Technology Taipei Medical University Academia Sinica Taipei Taiwan Division of Oral and Maxillofacial Surgery Department of Dentistry Taipei Medical University Hospital Taipei Taiwan Genomics Research Center Academia Sinica Taipei Taiwan Graduate Institute of Biomedical Informatics College of Medical Science and Technology Taipei Medical University Taipei Taiwan

Background: The survival analysis of the Cancer Genome Atlas (TCGA) dataset is a well-known method to discover the gene expression-based prognostic biomarkers of head and neck squamous cell carcinoma (HNSCC). In order to utilize a continuous gene expression for survival analysis, it is necessary to determine a cutoff point by the dichotomization of the patients. There is some optimization software for cutoff determination. However, those predetermined cutoffs by software usually set at the median, 1/4 quantile, or 3/4 quantile of RNA sequencing (RNA-Seq) value to find a significant P-value of the Kaplan-Meier curve. There are few clinicopathological features available on their pre-processed data sets. Methods: We developed a comprehensive workflow by R script, running on the Rstudio platform. It includes data retrieving and pre-processing, feature selection, cutoff mining engine, Kaplan-Meier survival analysis, Cox proportional hazard modeling, and biomarker discovery. Results: Using this workflow on the TCGA HNSCC cohort, we scanned human protein-coding genes (20,500) programmatically. After adjustment with other confounders, we found that the clinical tumor stage and the surgical margin involvement are independent risk factors in patient survival. According to the resulting tables with Bonferroni adjusted P-value under optimal cutoff as well as hazard ratio (>= 1.5), there were ten candidate biomarkers, named as dKK1, CAMK2N1, STC2, PGK1, SURF4, USP10, NdFIP1, FOXA2, STIP1, and dKC1, which are significantly associated with the poor prognosis of overall survival (OS). At the same time, the other ten genes were over-expressed in the better survival patients (with hazard ratio © 2020, CC BY.

关键词： Tumors

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