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Advanced Intelligent Systems 2025年第3期7卷

作者： Chen, Po-Yuan Ko, Tai-Ming Institute of Bioinformatics and Systems Biology College of Engineering Bioscience National Yang Ming Chiao Tung University Hsinchu300 Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei115 Taiwan Institute of Statistical Science Academia Sinica Taipei115 Taiwan Department of Biological Science and Technology College of Engineering Bioscience National Yang Ming Chiao Tung University Hsinchu300 Taiwan National Yang Ming Chiao Tung University Hsinchu300 Taiwan School of Pharmacy College of Pharmacy Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung807 Taiwan

Oxidative stress, characterized by an imbalance between reactive oxygen species (ROS) and antioxidants, plays a pivotal role in inflammatory responses associated with both chronic diseases and acute injuries. In this study, OXidative Stress PREDictor (OxSpred), a supervised learning model tailored to accurately annotate the oxidative stress state of innate immune cells at the single-cell level, is introduced. Compared to the traditional gene-set-variation-analysis-based enrichment method, OxSpred demonstrates superior accuracy with an area under the receiver operating characteristic curve of 0.89 and offers interpretable embeddings with significant biological relevance. Using the predicted ROS states, precise elucidation and interpretation of the roles of novel innate immune cell subtypes can be achieved. Overall, OxSpred enhances the utility of single-cell transcriptomic datasets by providing a robust in silico method for determining intracellular oxidative stress states, thereby enriching the understanding of innate immune cell functions during inflammation. © 2024 The Author(s). Advanced Intelligent Systems published by Wiley-VCH GmbH.

关键词： Cells

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Watermelons Talk: Predicting Ripeness through Tapping

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IEEE Internet of Things Magazine 2024年第4期7卷 154-161页

作者： Lin, Yun-Wei Lin, Yi-Bing Chen, Wen-Liang Chang, Chia-Hui Li, Han-Kuan College of Artificial Intelligence Yang Ming Chiao Tung University (NYCU) NYCU China Medical University Miin Wu School of Computing National Cheng Kung University Research Center for Information Technology Innovation Academia Sinica College of Biological Science and Technology NYCU Industrial Development Graduate Program of College of Biological Science and Technology

During the commercial production of watermelons, farmers must swiftly assess fruit ripeness post-harvest to minimize losses through sorting based on edibility time. This process enhances marketability and productivity but is often very tedious in traditional approaches. This article delves into the multifaceted realm of Internet of Things (IoT) based real-time watermelon ripeness evaluation. Watermelons, subject to diverse degrees of ripeness, significantly impact the fruit's taste and texture. Notably, watermelons cease to mature after detachment from the vine, underscoring the importance of selecting the ripest specimens at purchase. Prompt post-harvest fruit ripeness assessment is pivotal to mitigate losses, ensuring accurate sorting based on edibility timeline. Consequently, diligent watermelon ripeness assessment by farmers gains importance for enhanced marketability and productivity. While manual techniques like tapping, color examination, and day counting serve practical purposes, their accuracy relies on subjective judgment. Currently, the prevailing method for assessing watermelon ripeness is the sound test. This tapping technique surprisingly rests on logical grounds, as the resulting sounds offer an adequate ripeness indicator. However, personal interpretations of these sounds are influenced by subjective experiences and traditional wisdom. This article investigates non-destructive methodologies for evaluating watermelon ripeness. Then we propose WatermelonTalk, an IoT based real-time deep learning platform designed for acoustic watermelon testing. We also introduce the concept of the 'tapping ensemble,' not previously found in the literature, which significantly enhances prediction accuracy. The article's contributions encompass the most comprehensive categorization of watermelons in the literature, specifically categorizing 1698 watermelons across 343 varieties by ripeness. Previous studies have considered either the 2-level test (unripe and ripe) or th

关键词： Productivity Deep learning Accuracy Real-time systems Acoustics Crops Farming Agricultural products Commercialization Color Testing

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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IoT-Based Strawberry Disease Detection With Wall-Mounted Monitoring Cameras

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IEEE Internet of Things Journal 2024年第1期11卷 1439-1451页

作者： Lin, Yi-Bing Liu, Chun-You Chen, Wen-Liang Chang, Chia-Hui Ng, Fung-Ling Yang, Krista Hsung, Jerry Department of Computer Science National Yang Ming Chiao Tung University Hsinchu30010 Taiwan China Medical University College of Humanities and Sciences Taichung404 Taiwan National Cheng Kung University MiinWu School of Computing Tainan701 Taiwan Academia Sinica Research Center for Information Technology Innovation Taipei115 Taiwan National Yang Ming Chiao Tung University College of Biological Science and Technology Hsinchu30010 Taiwan National Yang Ming Chiao Tung University Industrial Development Graduate Program College of Biological Science and Technology Hsinchu30010 Taiwan Proto Solution System Company Ltd. Hsinchu302052 Taiwan

This article proposes StrawberryTalk, an Internet of Things (IoT) platform for image-based strawberry disease detection. StrawberryTalk reuses the wall-mounted monitoring cameras without extra hardware cost. The contributions of StrawberryTalk are the utilization of IoT for automatic photo shoot and the wind detection mechanism to eliminate the obscure photos due to the wind effects. Also, the data preprocessing and the infection detection models are manipulated as IoT devices to simplify the implementation of the multicascade artificial intelligence (AI) models. We derive the relationship between the camera zoom factor and the distance between the camera and the strawberries for optimal disease detection. Accuracy of detection may be affected by obscure photos. In terms of eliminating obscure photos due to wind effect, we analytically derive the relationship between the wind alert delay and the number of obscure photos that must be retaken. For the greenhouses in the Bao Mountain, we only need to retake one photo. Based on the experiments, the mean average precision (mAP) of StrawberryTalk (to detect exact spots in a leaf) can be up to 92.37%, which is better than the previous approaches. To detect if a pot has infected leaves, the accuracy of StrawberryTalk can be up to 97.92% at the zoom factor 30×. In commercial operation, it is important to detect all infected strawberry pots. StrawberryTalk is able to detect all infected pots (i.e., recall is 100%) with a camera of zoom factor of 12× . The accuracy is 96.88%. © 2014 IEEE.

关键词： Cameras

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TREATMENT OF A LANDFILL LEACHATE IN POWDERED ACTIVATED CARBON ENHANCED SEQUENCING BATCH BIOREACTORS

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ENVIRONMENTAL PROGRESS 1987年第1期6卷 1-8页

作者： YING, WC BONK, RR SOJKA, SA Occidental Chemical Corporation Grand Island Technology Center Grand Island NY 14072 Robert B. Bonk:is an associate chemist of Environmental Technology at the Grand Island Technology Center New York of Occidental Chemical Corporation. He has participated in a variety of environmental control research and development projects including biological chemical and physical processes for treating industrial wastewaters. He earned a B.S. in Chemistry from Rochester Institute of Technology and an M.B.A. from Canisius College. He is enrolled in the graduate Water Resources and Environmental Engineering program at State University of New York at Buffalo.

Addition of powdered activated carbon (PAC) significantly improved treatment of a chemical waste landfill leachate in sequencing batch bioreactors (SBRs). Concentrations for many of the monitored halogenated organic compounds in the effluent were below their respective detection limits. Excellent treatment efficiency was achieved under a variety of operating conditions: wastewater composition, feed rate, hydraulic retention time, organic loading, PAC dosages, biomass and PAC concentrations in the bioreactors. The PAC-SBR performance was unaffected when wastewater feeding was suspended during weekends and holidays. The PAC-SBR treatment cost is much lower than either that of the conventional granular activated carbon adsorption technology or the two-stage process of biodegradation and carbon treatment.

关键词： WASTEWATER

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Vitisin B, a resveratrol tetramer from Vitis thunbergii var. taiwaniana, ameliorates impaired glucose regulations in nicotinamide/streptozotocin-induced type 2 diabetic mice

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Journal of Traditional and Complementary Medicine 2023年第5期13卷 479-488页

作者： Liu, Yuh-Hwa Lin, Yin-Shiou Sie, Yi-Yan Wang, Ching-Chiung Chang, Chi-I Hou, Wen-Chi Department of General Medicine School of Medicine College of Medicine Taipei Medical University Taipei 110 Taiwan Division of Gastroenterology Shin Kong Wu Ho-Su Memorial Hospital Taipei 111 Taiwan Graduate Institute of Pharmacognosy Taipei Medical University Taipei 110 Taiwan Ph.D. Program in Clinical Drug Development of Herbal Medicine College of Pharmacy Taipei Medical University Taipei Taiwan School of Pharmacy College of Pharmacy Taipei Medical University Taipei 110 Taiwan Department of Biological Science and Technology National Pingtung University of Science and Technology Pingtung 912 Taiwan

Background and aim: In Taiwan, Vitis thunbergii var. taiwaniana (VTT) is used in traditional medicine and as a local tea. VTT rich in resveratrol and resveratrol oligomers have been reported to exhibit anti-obesity and anti-hypertensive activities in animal models;however, no studies have investigated type 2 diabetes mellitus (T2DM) treatments. This study aimed to investigate the anti-T2DM effects of resveratrol tetramers isolated from the VTT in nicotinamide/streptozotocin (STZ)-induced Institute of Cancer Research (ICR) mice. Experimental procedure: The oral glucose tolerance test (OGTT) was used to imitate postprandial blood glucose (BG) regulations in mice by pre-treatment with VTT extracts, resveratrol tetramers of vitisin A, vitisin B, and hopeaphenol 30 min before glucose loads. Vitisin B (50 mg/kg) was administered to treat T2DM-ICR mice once daily for 28 days to investigate its hypoglycemic activity. Results and conclusion: Mice pre-treated with VTT-S-95EE, or vitisin B (100 mg/kg) 30-min before glucose loading showed significant reductions (P < 0.001) in the area under the curve at 120-min (BG-AUC_0-120) than those without pre-treatment with VTT-S-95 E E or vitisin B. Vitisin B-treated T2DM mice showed hypoglycemic activities via a reduction in plasma dipeptidyl peptidase (DPP)-IV activities to maintain insulin actions and differed significantly than those of untreated T2DM mice (P < 0.05), and also reduced BG-AUC_0-120 and insulin-AUC_0-120 in the OGTT. These in vivo results showed that VTT containing vitisin B would be beneficial for developing nutraceuticals and/or functional foods for glycemic control in patients with T2DM, which should be investigated further. © 2023 Center for Food and Biomolecules, National Taiwan University

关键词： and hopeaphenol Nutraceuticals Resveratrol tetramers of vitisin a Type 2 diabetes mellitus (T2DM) Vitis thunbergii var. taiwaniana (VTT) Vitisin B

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Metabolomics and network biology for sensitive monitoring of how growth environment changes affect the physiology of industrial-scale perfusion cultures

Metabolomics and network biology for sensitive monitoring of...

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12th IFAC Symposium on Computer Applications in Biotechnology, CAB 2013

作者： Vernardis, S.I. Goudar, C.T. Klapa, M.I. Metabolic Engineering and Systems Biology Laboratory Institute of Chemical Engineering Foundation for Research and Technology-Hellas Patras GR-265 04 Greece Cell Culture Development Global Biological Development Bayer HealthCare 800 Dwight Way Berkeley CA 94710 United States Interdepartmental Graduate Program in Informatics in Life Sciences Medical School University of Patras Greece Cell Science and Technology AMGEN Inc. Thousand Oaks CA 91320 United States Depts. of Chemical and Biomolecular Eng. and Bioengineering University of Maryland College Park MD 20742 United States

ISBN: (纸本)9783902823588

Metabolomic analysis can indeed enhance the prime variable dataset for the monitoring of perfusion cultures by providing a higher resolution view of the metabolic state. Metabolic profiles can capture physiological state shifts over the course of the perfusion cultures and indicate a metabolic "signature" of the phase transitions, which is not observable from prime variable data. Notably, metabolomics provides orthogonal (to prime variables) evidence that all cultures follow this same metabolic state shift with cell age, independently of bioreactor scale. Additionally, this analysis can increase the information content of process development experiments by helping better understand the impact of changes in bioreactor operating conditions on cell physiology. In this context, metabolic profiling could be integrated into the monitoring of cell physiology in perfusion cultures. © IFAC.

关键词： Bioreactors

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Hepatitis B surface antigen loss in chronic hepatitis B patients with low-viral-load

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Journal of Gastroenterology and Hepatology (Australia) 2024年第11期39卷 2327-2331页

作者： Jang, Tyng-Yuan Batsaikhan, Batbold Chen, Yo-Chia Dai, Chia-Yen PhD Program of Environmental and Occupational Medicine and Graduate Institute of Clinical Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Internal Medicine Pingtung Hospital Ministry of Health and Welfare Ping-Tung Taiwan Department of Internal Medicine Institute of Medical Sciences Mongolian National University of Medical Sciences Ulaanbaatar Mongolia Department of Biological Science and Technology National Pingtung University of Science and Technology Pingtung Taiwan College of Professional Studies National Pingtung University of Science and Technology Pingtung Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung Taiwan

Background and Aim: Among low viral load (DNA of hepatitis B virus (HBV) was 10 IU/mL vs 2.3 log10 IU/mL;P = 0.003), and higher proportion of prior NAs-treated history. Logistic regression analysis revealed ... 详细信息

Background and Aim: Among low viral load (DNA of hepatitis B virus (HBV) was < 2000 IU/mL), the factor of the loss of hepatitis B surface antigen (HBsAg) remained elusive. Methods: The retrospective study recruited patients with chronic hepatitis B (CHB) who were negative low for hepatitis B e-antigen (HBeAg), had a low viral load, and experienced HBsAg loss during follow-up. CHB patients with low-viral load but without consequent HBsAg loss were also enrolled at the ratio of 1:4. The factors contributing to HBsAg loss were analyzed. Results: A total of 80 patients were recruited for the current study, with a mean age of 63.9 years and 61.3% being male. Among them, 62.5% patients (50/80) were treated with potent nucleoside/nucleotide analogues (NAs) during the follow-up period. Additionally, 12.5% patients (10/80) had a prior history of NAs treatment before enrolment. During the follow-up, HBsAg loss occurred in 17 patients (21.3%). Compared with patients without HBsAg loss, those with HBsAg loss were younger (57.9 years vs 65.5 years;P = 0.01), had lower HBV DNA levels (1.3 log₁₀ IU/mL vs 2.3 log₁₀ IU/mL;P = 0.003), and higher proportion of prior NAs-treated history. Logistic regression analysis revealed that the factors associated with factors associated with HBsAg loss were age < 60 years (OR/CI: 3.95/1.15–13.60, P = 0.03), prior NAs-treated history (OR/CI: 7.59/1.42–40.51, P = 0.01) and current NAs-treated (OR/CI: 0.19/0.05–0.71, P = 0.01). Conclusions: In the study, older age and prior NAs were positively associated with HBsAg loss, and current NAs was negatively associated with HBsAg loss. Additionally, some patients experienced HBsAg loss during the NAs therapy. © 2024 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

关键词： HBeAg HBsAg HBV NAs viral load

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Structure-guided identification and characterization of potent inhibitors targeting PhoP and MtrA to combat mycobacteria

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Computational and Structural Biotechnology Journal 2024年 23卷 1477-1488页

作者： Su, Han-Li Lai, Shu-Jung Tsai, Keng-Chang Fung, Kit-Man Lung, Tse-Lin Hsu, Hsing-Mien Wu, Yi-Chen Liu, Ching-Hui Lai, Hui-Xiang Lin, Jiun-Han Tseng, Tien-Sheng Department of Emergency Medicine Ditmanson Medical Foundation Chia-Yi Christian Hospital Chiayi City600 Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Research Center for Cancer Biology China Medical University Taichung Taiwan National Research Institute of Chinese Medicine Ministry of Health and Welfare Taipei Taiwan Ph.D. Program in Medical Biotechnology College of Medical Science and Technology Taipei Medical University Taipei Taiwan Academia Sinica Taipei11529 Taiwan Institute of Molecular Biology National Chung Hsing University Taichung Taiwan Department of Industrial Technology Ministry of Economic Affairs Taipei Taiwan Food Industry Research and Development Institute Hsinchu City Taiwan

Mycobacteria are causative agents of tuberculosis (TB), which is a global health concern. Drug-resistant TB strains are rapidly emerging, thereby necessitating the urgent development of new drugs. Two-component signal transduction systems (TCSs) are signaling pathways involved in the regulation of various bacterial behaviors and responses to environmental stimuli. Applying specific inhibitors of TCSs can disrupt bacterial signaling, growth, and virulence, and can help combat drug-resistant TB. We conducted a comprehensive pharmacophore-based inhibitor screening and biochemical and biophysical examinations to identify, characterize, and validate potential inhibitors targeting the response regulators PhoP and MtrA of mycobacteria. The constructed pharmacophore model Phar-PR-n4 identified effective inhibitors of formation of the PhoP–DNA complex: ST132 (IC50 = 29 ± 1.6 µM) and ST166 (IC50 = 18 ± 1.3 µM). ST166 (KD = 18.4 ± 4.3 μM) and ST132 (KD = 14.5 ± 0.1 μM) strongly targeted PhoP in a slow-on, slow-off manner. The inhibitory potency and binding affinity of ST166 and ST132 for MtrAC were comparable to those of PhoP. Structural analyses and molecular dynamics simulations revealed that ST166 and ST132 mainly interact with the α8-helix and C-terminal β-hairpin of PhoP, with functionally essential residue hotspots for structure-based inhibitor optimization. Moreover, ST166 has in vitro antibacterial activity against Macrobacterium marinum. Thus, ST166, with its characteristic 1,2,5,6-tetrathiocane and terminal sulphonic groups, has excellent potential as a candidate for the development of novel antimicrobial agents to combat pathogenic mycobacteria. © 2024 The Authors

关键词： Antimicrobial agents

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Improving iPSC Differentiation Using a Nanodot Platform

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ACS Applied Materials and Interfaces 2024年第28期16卷 36030-36046页

作者： Chiew, Men Yee Wang, Erick Lan, Kuan-Chun Lin, Yan-Ren Hsueh, Yu-Huan Tu, Yuan-Kun Liu, Chu-Feng Chen, Po-Chun Lu, Huai-En Chen, Wen Liang Center for Regenerative Medicine and Cellular Therapy National Yang Ming Chiao Tung University Hsinchu300 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu300 Taiwan College of Biological Science and Technology Industrial Ph. D. Program National Yang Ming Chiao Tung University Hsinchu300 Taiwan Kyoto University Kyoto606-8397 Japan Department of Emergency and Critical Care Medicine Changhua Christian Hospital Changhua500 Taiwan Department of Post Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung402 Taiwan School of Medicine Kaohsiung Medical University Kaohsiung807 Taiwan School of Medicine Chung Shan Medical University Taichung402 Taiwan College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu300 Taiwan Department of Orthopedic Surgery E-Da Hospital I-Shou University Kaohsiung824 Taiwan Emergency Medicine Department Kaohsiung Chang Gung Memorial Hospital Kaohsiung833 Taiwan Ph. D. Degree Program of Biomedical Science and Engineering National Yang Ming Chiao Tung University Hsinchu300 Taiwan Institute of Materials Science and Engineering National Taipei University of Technology Taipei106 Taiwan Institute of Biochemistry and Molecular Biology National Yang Ming Chiao Tung University Hsinchu300 Taiwan Bioresource Collection and Research Center Food Industry Research and Development Institute Hsinchu City300 Taiwan

Differentiation of induced pluripotent stem cells (iPSCs) is an extremely complex process that has proven difficult to study. In this research, we utilized nanotopography to elucidate details regarding iPSC differentiation by developing a nanodot platform consisting of nanodot arrays of increasing diameter. Subjecting iPSCs cultured on the nanodot platform to a cardiomyocyte (CM) differentiation protocol revealed several significant gene expression profiles that were associated with poor differentiation. The observed expression trends were used to select existing small-molecule drugs capable of modulating differentiation efficiency. BRD K98 was repurposed to inhibit CM differentiation, while iPSCs treated with NSC-663284, carmofur, and KPT-330 all exhibited significant increases in not only CM marker expression but also spontaneous beating, suggesting improved CM differentiation. In addition, quantitative polymerase chain reaction was performed to determine the gene regulation responsible for modulating differentiation efficiency. Multiple genes involved in extracellular matrix remodeling were correlated with a CM differentiation efficiency, while genes involved in the cell cycle exhibited contrasting expression trends that warrant further studies. The results suggest that expression profiles determined via short time-series expression miner analysis of nanodot-cultured iPSC differentiation can not only reveal drugs capable of enhancing differentiation efficiency but also highlight crucial sets of genes related to processes such as extracellular matrix remodeling and the cell cycle that can be targeted for further investigation. Our findings confirm that the nanodot platform can be used to reveal complex mechanisms behind iPSC differentiation and could be an indispensable tool for optimizing iPSC technology for clinical applications. © 2024 The Authors. Published by American Chemical Society.

关键词： Efficiency

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