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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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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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Integration of MRI and somatosensory evoked potentials facilitate diagnosis of spinal cord compression

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Scientific Reports 2023年第1期13卷 1-12页

作者： Sun, Shu-Pin phang, Chun-Ren Tzou, Shey-Cherng Chen, Chang-Mu Ko, Li-Wei International Ph.D. Program in Interdisciplinary Neuroscience (UST) College of Biological Science and Technology National Yang Ming Chiao Tung University 734 Engineering Bldg. 5 1001 Daxue Road Hsinchu 30010 Taiwan Department of Medical Research National Taiwan University Hospital Hsin-Chu Branch Hsinchu 300 Taiwan Institute of Molecular Medicine and Bioengineering National Yang Ming Chiao Tung University Hsinchu 300 Taiwan Department of Surgery College of Medicine and Hospital National Taiwan University No. 7 Zhongshan South Road Taipei 10002 Taiwan Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu 300 Taiwan Institute of Electrical and Control Engineering Department of Electronics and Electrical Engineering National Yang Ming Chiao Tung University Hsinchu 300 Taiwan Department of Biomedical Science and Environment Biology and the Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung 807 Taiwan

This study aimed to integrate magnetic resonance imaging (MRI) and related somatosensory evoked potential (SSEP) features to assist in the diagnosis of spinal cord compression (SCC). MRI scans were graded from 0 to 3 according to the changes in the subarachnoid space and scan signals to confirm differences in SCC levels. The amplitude, latency, and time–frequency analysis (TFA) power of preoperative SSEP features were extracted and the changes were used as standard judgments to detect neurological function changes. Then the patient distribution was quantified according to the SSEP feature changes under the same and different MRI compression grades. Significant differences were found in the amplitude and TFA power between MRI grades. We estimated three degrees of amplitude anomalies and power loss under each MRI grade and found the presence or absence of power loss occurs after abnormal changes in amplitude only. For SCC, few integrated approach combines the advantages of both MRI and evoked potentials. However, integrating the amplitude and TFA power changes of SSEP features with MRI grading can help in the diagnosis and speculate progression of SCC. © 2023, The Author(s).

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A New Architecture for Transformation of Binary to double Base Number System (dBNS) with Bases 2 and 5 using different Search Algorithms

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IOP Conference Series: Materials science and Engineering 2021年第1期1084卷

作者： Satrughna Singha Amitabha Sinha Ph.D. Scholar Department of Computer Science and Engineering MaulanaAbulKalam Azad University of Technology Haringhata NadiaWestBengal India UGC Adjunct Faculty and Director (Academic Reforms) MaulanaAbulKalam Azad University of Technology Haringhata NadiaWestBengal India

In this paper a new architecture for the transformation of binary to double base number system (dBNS) with bases 2 and 5 using different search algorithms has been presented. Nowadays the dBNS is becoming popular among the other non-binary number systems for their competences of carrying out multiplication operation proficiently. The dBNS has the major problem which is associated with this number system is the transformation from binary data to dBNS data despite the various advantages of the dBNS. A number of schemes are there to transform the binary number into the dBNS. By observing these matters a new transformation scheme has been presented for the transformation of binary data into a single index pair (i.e., singledigit) dBNS data with bases 2 and 5.

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The Limited Effect of Reduced Typhoon Frequency on Stream Hydrochemistry in a Subtropical Forest Watershed

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Earth's Future 2024年第6期12卷

作者： Chung-Te Chang Jr-Chuan Huang Lixin Wang Hsiang-Hua Wang Jun-Yi Lee Teng-Chiu Lin Taiwan International Graduate Program (TIGP) –Ph.D. Program on Biodiversity Tunghai University Taichung Taiwan Center for Ecology and Environment Tunghai University Taichung Taiwan Department of Geography National Taiwan University Taipei Taiwan Department of Earth Sciences Indiana University-Purdue University Indianapolis (IUPUI) Indianapolis IN USA Watershed Management Division Taiwan Forestry Research Institute Taipei Taiwan Department of Soil and Environmental Sciences National Chung Hsing University Taichung Taiwan Department of Life Science National Taiwan Normal University Taipei Taiwan Department of Natural Resources and Environmental Studies National Dong Hwa University Hualien Taiwan T.-C. Lin

Tropical cyclones are often accompanied by large amount of precipitation potentially impacting stream hydrochemistry. Global warming is altering typhoon disturbance regime. Little is known about how cyclone changes, especially cyclone-frequency reduction may affect stream hydrochemistry. In this study, we compared water and nutrient input via precipitation and output via streamflow between a frequent-typhoon period (2013–2017), with 1.2 typhoon yr −1 , and a no-typhoon period (2018–2022) at a long-term monitoring site, the Fushan Experimental Forest of Taiwan. Precipitation and streamflow quantities were not different between the two periods because typhoons increased the fluctuation but not the mean of monthly precipitation in the major typhoon months (July–September). Inputs of Mg 2+ , NO 3 − , and SO 4 2− via precipitation were greater in the frequent-typhoon period than the no-typhoon period while inputs of other ions were not different between the two periods. Only the output of Mg 2+ was different between the two periods, greater in the frequent-typhoon period. Output/input ratio of NO 3 − was greater in the no-typhoon period than the frequent-typhoon period despite the greater input in the frequent-typhoon period, while no differences were found for others. Increases in mineralization rates due to warming is suggested to be the cause of the greater NO 3 − output/input ratio during the no-typhoon period. Relationships between stream discharge and ion export were similar between the two periods both with and without removing typhoon events. The limited variation in hydrochemistry between periods of contrasting cyclone activities suggests high resilience of the undisturbed subtropical forests to changes in cyclone frequency at the decadal scale. A no-typhoon period (2018–2022) was observed in Taiwan despite an average of two typhoons per year in 1958–2017 Relationships between stream discharge and ion export were similar between the two periods Output/input rati

关键词： biogeochemistry Fushan Experimental Forest resilience tropical cyclone typhoon nutrient input and output

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3200 – dEVELOPMENTAL REGULATION OF ENdOTHELIAL-TO-HEMATOPOIETIC TRANSITION FROM INdUCEd PLURIPOTENT STEM CELLS

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Experimental Hematology 2024年 137卷 104520-104520页

作者： Rachel Wellington Xiaoyi Cheng Clyde Campbell Cole Trapnell Raquel Espin-Palazon Brandon Hadland Sergei doulatov Division of Hematology School of Medicine University of Washington Seattle WA Seattle United States Translational Science and Therapeutics Division Fred Hutchinson Cancer Center Seattle WA Seattle United States Molecular and Cellular Biology Ph.D. Program School of Medicine University of Washington Seattle WA Seattle United States Institute for Stem Cell and Regenerative Medicine University of Washington Seattle WA Seattle United States Iowa State University Ames United States University of Washington Seattle United States Fred Hutchinson Cancer Center Seattle United States

Hematopoietic stem cells (HSCs) arise in mid-gestation embryos from a specialized hemogenic endothelium (HE). In this process, HE cells undergo a unique fate change termed endothelial-to-hematopoietic transition, or EHT, leading to the production of hematopoietic cells. While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, the generation of bona fide HSCs from iPSCs remains a challenge. Here, we map the single cell transcriptomic dynamics of EHT during embryoid body differentiation from iPSCs and integrate this data with published human embryo datasets to identify key transcriptional differences between in vitro and in vivo cell states. We map ligand-receptor interactions associated with the differential expression of developmental programs in the iPSC system. We found that the expression of endothelial genes was incompletely repressed during in vitro EHT. Elevated FGF signaling by FGF23, an endothelial pathway ligand, was associated with the differential gene expression between in vitro and in vivo EHT. Chemical inhibition of FGF signaling during EHT increased HSPC generation in the zebrafish system, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hemogenic output from iPSCs. In summary, we map the dynamics of EHT from iPSCs at single cell resolution and identify ligand-receptor interactions that can be modulated to improve iPSC differentiation protocols. We show, as a proof of principle, that chemical inhibition of FGF signaling during EHT improves hematopoietic output in both the zebrafish and iPSC systems.

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phosphatidylethanolamine N-methyltransferase G175A Modifies Methyl donor Intake Requirements and Alzheimer’s-Related Biomarkers for Predicting Cognitive dysfunction

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Current developments in Nutrition 2025年 9卷

作者： Li-Chun Chen Chang-Sheng Kuo Yu-Chen Cheng Bei Wen Wang Shi Hui-Xuan Ya-Wen Hsueh Chao-Yun Wang Ming Lu Lin Ta-Fu Chen Rwei-Fen S Huang Fu Jen Catholic University Taiwan Republic of China Fu Jen University Hospital Department of Nutrition Taiwan Republic of China Fu Jen Catholic University College of Medicine School of Medicine Taiwan Republic of China； Fu Jen Catholic University Hospital Fu Jen Catholic University Department of Neurology Taiwan Republic of China Fu Jen University Hospital Department of Nutrition； Fu Jen Catholic University Department of Nutritional Science Taiwan Republic of China Fu Jen Catholic University Department of Nutritional Science Taiwan Republic of China National Taiwan University Hospital Department of Neurosurgery Taiwan Republic of China Fu Jen Catholic University Ph.D. Program of Nutrition and Food Science Taiwan Republic of China

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