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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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deep learning-based air pollution analysis on carbon monoxide in Taiwan

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Ecological Informatics 2024年 80卷

作者： Cheng-Hong Yang Po-Hung Chen Chih-Hsien Wu Cheng-San Yang Li-Yeh Chuang Department of Information Management Tainan University of Technology Tainan Taiwan Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung Taiwan Ph. D. Program in Biomedical Engineering Kaohsiung Medical University Kaohsiung Taiwan School of Dentistry Kaohsiung Medical University Kaohsiung Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung Taiwan Division of Plastic and Reconstruction Surgery Department of Surgery Ditmanson Medical Foundation Chia-Yi Christian Hospital Chia-Yi Taiwan Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering I-Shou University Kaohsiung Taiwan

Global air pollution poses a threat to humanity. Specifically, CO directly affects cardiovascular and other organ tissues and leads to numerous chronic diseases and major public health problems. The effective implementation of a deep learning model for predicting variations in CO levels would enable the early formulation of policies for controlling air pollution. In this study, a seasonal gated recurrent unit (SGRU) model, which is a deep learning time-series prediction model, was developed to predict the levels of CO in Taiwan. Atmospheric CO measurements from 2005 to 2021 were collected from the Environmental Protection Administration of Taiwan and preprocessed using the Kalman filter to achieve accurate forecasting. The performance of the proposed SGRU model was compared with that of the autoregressive integrated moving average (ARIMA), seasonal ARIMA, exponential smoothing (ETS), Holt–Winters ETS, support vector regression, and seasonal long short-term memory models in terms of mean absolute percentage error (MAPE) and root mean square error. The SGRU model achieved the lowest MAPE value of 0.94, which demonstrated its superior performance. The construction of an accurate air pollution prediction model can assist government entities in formulating health and social care strategies and in planning future air pollution control measures.

关键词： Air pollution Carbon Monoxide (CO) deep learning Seasonal gated recurrent unit (SGRU)

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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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RAdT-33. GAMMA KNIFE RAdIOSURGERY FOR ORBITAL CAVERNOUS HEMANGIOMA: A SYSTEMATIC REVIEW ANd SINGLE-ARM META-ANALYSIS

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Neuro-Oncology 2024年第SUPPLEMENT_8期26卷 viii79–viii80页

作者： Chen, Hsien-Chung Franklin, Brodus Punukollu, Anurraag Pineda, Felipe Palavani, Lucca Department of Neurosurgery Shuang Ho Hospital Taipei Medical University Taipei Taiwan Ph.D. Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University and National Health Research Institutes Taipei Taiwan Global Health Texas Children’s Hospital Houston USA Andhra Medical College Visakhapatnam India Department of Neurosurgery University of Antioquia School of Medicine Medellin Colombia Department of Neurosurgery Colombian Neurological Institute Medellin Colombia Faculty of Medicine Universidade Federal do Rio de Janeiro (UFRJ) Rio de Janeiro Brazil

Gamma knife radiosurgery (GKRS) for orbital cavernous hemangioma (OCH) has emerged as a promising method due to its significant clinical improvement and low incidence of complications. This study aimed to evaluate the safety and efficacy of GKRS for the treatment of OCH. Following the PRISMA framework, we searched PubMed, Cochrane Central, and Embase for studies reporting outcomes of GKRS for OCH, including complications, visual improvement, proptosis, tumor reduction rate, and tumor progression rate. From 1856 search results, six studies with 100 patients were included. Only five minor complications related to GKRS were reported, including three with orbital pain and two with periorbital chemosis, resulting in a complication rate of 13% (95% CI: 7% - 25%). Visual acuity and visual field improvement rates after GKRS were 80% (95% CI: 63% - 96%) and 71% (95% CI: 47% - 95%), respectively. Proptosis improved in 94% of cases (95% CI: 83% - 100%). The tumor reduction rate was 77% after GKRS (95% CI: 69% - 85%). In conclusion, GKRS for OCH appears to be a safe technique, as evidenced by the rate of clinical improvement and radiological improvement. However, studies are limited by the absence of a control group, and additional studies are needed to evaluate the relative efficacy of GKRS compared with alternative surgical modalities for OCH.

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Model Target of Food Production and Farmers’ Incomes in Banten Province, Indonesia

SSRN

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SSRN 2023年

作者： Siagian, Viktor Siregar, Hermanto Fariyanti, Anna Nainggolan, Kaman Haloho, Lermansius Hutapea, Ronald Suratman Salim, Zamroni Wamaer, demas da Silva, Helena Ekaswati, Rini Rusdiana, Supardi Marwati, Tri Toha, Mohammad Sondakh, Joula Marpaung, Imelda Research Center for Macro Economic and Finance Research Organization for Governance Economy and Community Welfare National Research and Innovation Agency Jakarta12710 Indonesia IPB University Faculty of Economics and Management Bogor16680 Indonesia College of Management and Computer Science Nusa Mandiri Jakarta12540 Indonesia Research Center for Cooperative Corporation and People's Economy National Research and Innovation Agency Jakarta12710 Indonesia Universitas Islam Malang Indonesia Research Center for Behavioral and Circular Economics National Research and Innovation Agency Jakarta12710 Indonesia Research Center for Animal Research Organization for Agriculture and Food National Research and Innovation Agency Cibinong-Bogor 16128 Indonesia Research Center for Food and Technology Processing Research Organization for Agriculture and Food National Research and Innovation Agency Serpong15314 Indonesia Ph.D. Study Program Natural Resources and Environmental Management Graduate School of IPB University Campus IPB Baranangsiang Bogor16144 Indonesia National Research and Innovation Agency Indonesia

The area of the rice harvest in Banten Province in 2021 was 319,558 ha with a production of 1,63 million tons of unhusked rice or with a productivity of 5.1 tons/ha (CBS,2022). The objectives of this study were: 1) to optimize the target of rice and corn production in Banten Province, and 2) to optimize the target farmers' income in Banten Province. The study method used was a survey, with purposive sampling at the farmer level. data were analyzed qualitatively (uses descriptive tabulation) and quantitatively (uses goal programming). The results of this study were:1) The target of rice production in the Banten Province of 2.1 million tons of unhusked rice can be achieved with the optimal area of irrigated paddy of 299,755.7 ha and the optimal area of field/dry land of 87,750.9 ha. The target for maize production of 1.75 million tonnes in Banten Province can be achieved with an optimal planting area of 342.211.7 ha of dry land. 2) The optimal area of food crops to achieve the farmer's income target in Banten Province in 2018 is IdR. 8.79 trillion comes from the planting area of lowland rice covering an area of 391,222.1 ha, the corn planting area of 169,059.9 ha, soybean planting area of 23,074.82 ha and cassava planting area of 2,832.77 ha. © 2023, The Authors. All rights reserved.

关键词： Agriculture

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Two dimensional solvothermal synthesis via ultrasound (2d-STSUS) of fluorescent tungsten-doped hBN nanosheets for the selective detection of cancer markers

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Microchemical Journal 2024年 200卷

作者： deepak dabur Muhammad Arshad Sanwal Piracha Hui-Fen Wu Department of Chemistry National Sun Yat-Sen University Kaohsiung 70 Lien-Hai Road Kaohsiung 80424 Taiwan International Ph.D. Program for Science National Sun Yat-Sen University Kaohsiung 80424 Taiwan Institute of Medical Science and Technology National Sun Yat-Sen University Kaohsiung 80424 Taiwan Institute of Precision Medicine College of Medicine National Sun Yat-Sen University Kaohsiung 80424 Taiwan School of Pharmacy College of Pharmacy Kaohsiung Medical University Kaohsiung 80708 Taiwan School of Medicine College of Medicine National Sun Yat-Sen University Kaohsiung 80424 Taiwan

We propose an ultrasensitive and cost-effective novel fluorometric approach for effective detection of cysteamine/cancer marker. The synthesis of the 2d nanomaterial is accomplished via the solvothermal process using the ultrasound system which is termed as the two dimensional solvothermal synthesis of ultrasound (2d-STSUS). 2d Hexagonal boron nitride (hBN) has emerged as a promising material for sensing applications due to its exceptional properties like broad bandgap and high thermal stability makes it ideal for application in a wide range of sensors and biosensors. Since hBN cannot effectively absorb or emit light because of broad band gap, it cannot produce fluorescence. On the contrary, using W-doped hexagonal boron nitride nanosheets (hBNW), we were able to successfully increase the method's selectivity, sensitivity, and easy usage by fusing the unique properties of W metal with hBN. For the first time, hBNW nanosheets exhibited a clear blue color transition and were effectively employed to detect varied levels of cysteamine in human urine and aqueous samples. When combined with hBNW nanosheets, cysteamine has excellent outcomes among other drugs and neurotransmitters. The linearity value R 2 = 0.9991 for aqueous was observed in the range of 1 nM to 28 nM and the detection limit was 0.0936 nM under ideal conditions. Additionally, quantification tests were conducted on human serum and urine samples for real sample analysis, yielding R 2 values of 0.9961 and 0.9958, respectively.

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Uncovering the conformational dynamics of dengue virus and its virus-like particles as novel vaccine candidates

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Biophysical Journal 2023年第3期122卷 508a-509a页

作者： Jan K. Marzinek Venkata Raghuvamsi Palur Gielenny Salem Fan-Chi Chen Shang-Rung Wu Peter J. Bond day-Yu Chao Bioinformatics Institute Agency for Science Technology and Research Singapore Republic of Singapore Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung City Taiwan Microbial Genomics Ph.D. Program National Chung Hsing University Taichung City Taiwan Academia Sinica Taipei Taiwan Department of Dentistry Institute of Oral Medicine National Cheng Kung University Tainan Taiwan Department of Biological Sciences National University of Singapore Singapore Republic of Singapore

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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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Creatine and l-carnitine attenuate muscular laminopathy in the LMNA mutation transgenic zebrafish

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Scientific Reports 2024年第1期14卷 1-19页

作者： Pan, Shao-Wei Wang, Horng-dar Hsiao, He-Yun Hsu, Po-Jui Tseng, Yung-Che Liang, Wen-Chen Jong, Yuh-Jyh Yuh, Chiou-Hwa Institute of Molecular and Genomic Medicine National Health Research Institutes Miaoli Zhunan Taiwan Institute of Biotechnology National Tsing Hua University Hsinchu Taiwan Department of Laboratory Medicine Mackay Memorial Hospital Taipei Taiwan Department of Medical Laboratory Science and Biotechnology Yuanpei University of Medical Technology Hsinchu Taiwan Department of Nursing MacKay Medical College Taipei Taiwan Marine Research Station Institute of Cellular and Organism Biology Academia Sinica I-Lan Taiwan Department of Pediatrics School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Clinical Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Pediatrics Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Translational Research Center of Neuromuscular Diseases Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Laboratory Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu Taiwan Ph.D. Program in Environmental and Occupational Medicine Kaohsiung Medical University Kaohsiung Taiwan

Lamin A/C gene (LMNA) mutations contribute to severe striated muscle laminopathies, affecting cardiac and skeletal muscles, with limited treatment options. In this study, we delve into the investigations of five distinct LMNA mutations, including three novel variants and two pathogenic variants identified in patients with muscular laminopathy. Our approach employs zebrafish models to comprehensively study these variants. Transgenic zebrafish expressing wild-type LMNA and each mutation undergo extensive morphological profiling, swimming behavior assessments, muscle endurance evaluations, heartbeat measurement, and histopathological analysis of skeletal muscles. Additionally, these models serve as platform for focused drug screening. We explore the transcriptomic landscape through qPCR and RNAseq to unveil altered gene expression profiles in muscle tissues. Larvae of LMNA(L35P), LMNA(E358K), and LMNA(R453W) transgenic fish exhibit reduced swim speed compared to LMNA(WT) measured by danioVision. All LMNA transgenic adult fish exhibit reduced swim speed compared to LMNA(WT) in T-maze. Moreover, all LMNA transgenic adult fish, except LMNA(E358K), display weaker muscle endurance than LMNA(WT) measured by swimming tunnel. Histochemical staining reveals decreased fiber size in all LMNA mutations transgenic fish, excluding LMNA(WT) fish. Interestingly, LMNA(A539V) and LMNA(E358K) exhibited elevated heartbeats. We recognize potential limitations with transgene overexpression and conducted association calculations to explore its effects on zebrafish phenotypes. Our results suggest lamin A/C overexpression may not directly impact mutant phenotypes, such as impaired swim speed, increased heart rates, or decreased muscle fiber diameter. Utilizing LMNA zebrafish models for drug screening, we identify l-carnitine treatment rescuing muscle endurance in LMNA(L35P) and creatine treatment reversing muscle endurance in LMNA(R453W) zebrafish models. Creatine activates AMPK and mTOR pathw

关键词： Creatine l-Carnitine LMNA Striated muscle laminopathy Zebrafish

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Crosstalk between GBM cells and mesenchymal stemlike cells promotes the invasiveness of GBM through the C5a/p38/ZEB1 axis (vol 22, pg 1452, 2020)

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NEURO-ONCOLOGY 2020年第8期22卷 1229-1229页

作者： Lim, Eun-Jung Kim, Seungmo Oh, Yoonjee Suh, Yongjoon Kaushik, Neha Lee, Ji-Hyun Lee, Hae-June Kim, Min-Jung Park, Myung-Jin Kim, Rae-Kwon Cha, Junghwa Kim, Se Hoon Shim, Jin-Kyoung Choi, Junjeong Chang, Jong Hee Hong, Yong Kil Huh, Yong Min Kim, Pilnam Kang, Seok-Gu Lee, Su-Jae Department of Life Science Research Institute for Natural Sciences Hanyang University Seoul Korea Memorial Sloan Kettering Cancer Center New York New York USA Department of Life Science Research Institute for Natural Sciences Hanyang University Seoul Korea Department of Bio and Brain Engineering Korea Advanced Institute of Science and Technology Daejeon Korea Department of Life Science Research Institute for Natural Sciences Hanyang University Seoul Korea Department of Life Science Research Institute for Natural Sciences Hanyang University Seoul Korea Department of Neurosurgery Brain Tumor Center Severance Hospital Yonsei University College of Medicine Seoul Korea Division of Radiation Effect Korea Institute of Radiological & Medical Sciences Seoul Korea Laboratory of Radiation Exposure & Therapeutics National Radiation Emergency Medical Center Korea Institute of Radiological and Medical Sciences Seoul Korea Division of Radiation Cancer Biology Korea Institute of Radiological and Medical Sciences Seoul Korea Department of Radiation Biology Environmental Radiation Research Group Korea Atomic Energy Research Institute Daejeon Korea College of Pharmacy Yonsei Institute of Pharmaceutical Science Yonsei University Incheon Korea Department of Pathology Severance Hospital Yonsei University College of Medicine Seoul Korea Department of Life Science Research Institute for Natural Sciences Hanyang University Seoul Korea College of Pharmacy Yonsei Institute of Pharmaceutical Science Yonsei University Incheon Korea KAIST Institute for Health Science and Technology Daejeon Korea Department of Neurosurgery Brain Tumor Center Severance Hospital Yonsei University College of Medicine Seoul Korea Department of Neurosurgery Seoul St Mary’s Hospital The Catholic University of Korea College of Medicine Seoul Korea Department of Radiology Severance Hospital Yonsei University College of Medicine Seoul Korea Department of Life Science Research Institute for Natu

BackgroundMesenchymal stemlike cells (MSLCs) have been detected in many types of cancer including brain tumors and have received attention as stromal cells in the tumor microenvironment. However, the cellular mechanisms underlying their participation in cancer progression remain largely unexplored. The aim of this study was to determine whether MSLCs have a tumorigenic role in brain *** figure out molecular and cellular mechanisms in glioma invasion, we have cultured glioma with MSLCs in a co-culture ***, we show that MSLCs in human glioblastoma (GBM) secrete complement component C5a, which is known for its role as a complement factor. MSLC-secreted C5a increases expression of zinc finger E-box-binding homeobox 1 (ZEB1) via activation of p38 mitogen-activated protein kinase (MAPK) in GBM cells, thereby enhancing the invasion of GBM cells into parenchymal brain *** results reveal a mechanism by which MSLCs undergo crosstalk with GBM cells through the C5a/p38 MAPK/ZEB1 signaling loop and act as a booster in GBM *** Points1. MSLCs activate p38 MAPK-ZEB1 signaling in GBM cells through C5a in a paracrine manner, thereby boosting the invasiveness of GBM cells in the tumor microenvironment.2. Neutralizing of C5a could be a potential therapeutic target for GBM by inhibition of mesenchymal phenotype.

关键词： C5a glioblastoma invasiveness mesenchymal stem-like cells tumor microenvironment

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