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International Conference on Machine Learning and Cybernetics (ICMLC)

作者： Jen-Chien Yu Chun-Chieh Yang John Reuben Gilbert Rou-Jun Liu Yen-Jen Oyang Meng-Han Yang Department of Computer Science and Information Engineering National Kaohsiung University of Science and Technology Kaohsiung City Taiwan ROC Master Program in Statistics National Taiwan University Taipei Taiwan ROC Department of Computer Science & Information Engineering National Taiwan University Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University

A vast number of spatiotemporal datasets collected from a wide range of sources has motivated scientists to develop effective approaches to identify interesting patterns hidden in these datasets. In this respect, kernel density estimators, which belong to a class of non-parametric estimators in statistics, have been widely exploited in recent years. With this background, we have developed a novel kernel density estimator aiming to provide accurate analysis results. According to the evaluation with a real spatiotemporal dataset, which collected emergency medical service records in a county in the United States, the proposed kernel density estimator can approximate the probability density function significantly more accurately than a conventional kernel density estimator. Furthermore, we have exploited the proposed kernel density estimator to identify interesting patterns hidden in the real spatiotemporal dataset.

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Exercise-induced CLCF1 attenuates age-related muscle and bone decline in mice

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Nature Communications 2025年第1期16卷 1-20页

作者： Jae Sook Kang Min Ju Kim Seung-Min Lee Ga-Yeon Go Ji-Won Kim Seongwan Kim Ju Yeon Kwak Chuna Kim Kwang-Pyo Lee Eun-Soo Kwon Ki-Sun Kwon Yong Ryoul Yang Jung Ha Kim Nacksung Kim Byungkuk Min Sung-Wook Chun Wook Song Hyo Youl Moon Sun Gun Chung Dong-Ho Park Ji Hoon Park Aging Convergence Research Center Korea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea Department of Biomolecular Science KRIBB School of Bioscience Korea University of Science and Technology (UST) Daejeon Republic of Korea Department of Bioinformatics KRIBB School of Bioscience Korea University of Science and Technology (UST) Daejeon Republic of Korea Aventi Inc. Daejeon Republic of Korea Department of Pharmacology Chonnam National University Medical School Gwangju Republic of Korea Stem Cell Research Center Korea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea Research Institute of Physical Education & Sports Science Pusan National University Pusan Republic of Korea Department of Physical Education Seoul National University Seoul Republic of Korea Institute on Aging Seoul National University Seoul Republic of Korea Department of Rehabilitation Medicine Seoul National University College of Medicine Seoul Republic of Korea Department of Kinesiology Inha University Incheon Republic of Korea Program in Biomedical Science and Engineering Inha University Incheon Republic of Korea New Drug Development Center Osong Medical Innovation Foundation (KBioHealth) ChungJu Republic of Korea

Skeletal muscle undergoes many alterations with aging. However, the impact of aging on muscle’s ability to secrete myokines and its subsequent effects on the body remain largely unexplored. Here, we identify myokines that have the potential to ameliorate age-related muscle and bone decline. Notably, circulating levels of cardiotrophin-like cytokine factor 1 (CLCF1) decrease with age, while exercise significantly upregulates CLCF1 levels in both humans and rodents. Restoring CLCF1 levels in aged male mice improves their physical performance, glucose tolerance, and mitochondrial activity. Furthermore, CLCF1 protects against age-induced bone loss by inhibiting osteoclastogenesis and promoting osteoblast differentiation in aged male mice. These improvements mirror some of the effects of exercise training. Conversely, blocking CLCF1 activity significantly abolishes these beneficial effects, confirming the crucial role of CLCF1 in mediating the positive effects of exercise on muscle and bone health in male mice. These findings collectively suggest that CLCF1 may contribute to the regulation of age-associated musculoskeletal deterioration, and warrant further investigation into its potential role as a modulator of musculoskeletal health during aging.

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The keyword-based and semantic-driven data matching approach for assisting structuralizing the textual clinical documents

The keyword-based and semantic-driven data matching approach...

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International Conference on biomedical engineering and Informatics (BMEI)

作者： Chi-Huang Chen Xiao-Ou Ping Zi-Jun Wang Sheau-Ling Hsieh Li-Chin Chen Yi-Ju Tseng Ching-Wei Hsu Feipei Lai Department of Electrical Engineering National Taiwan University Taipei Taiwan Graduate Institute of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronic and Bioinformatics National Taiwan University Taipei Taiwan EECS International Graduate Program Institute IT Center National Chiao Tung University Hsinchu Taiwan

The clinical data stored in the health information system can be categorized as two types including structuralized data and non-structuralized ones. In the paper, a data extraction system is developed to assist data retrieval from the non-structuralized textual clinical documents such as radiology reports, pathology reports, etc. The system provides keyword-based and semantic-driven data matching methodology to extract the specific information from the textual clinical documents. The matching methodology provides the capabilities to recognize the selected keywords and the related semantics in the documents. Through the extraction verification interface, clinicians can extract and verify the matched information semi-automatically. The extracted data can be filled into predefined case-oriented templates. The structuralized data can be stored back into the clinical data warehouse for further analyzing. Moreover, the case-oriented templates can support collecting corresponding extracted data for various researches.

关键词： Data mining Semantics Pattern matching Tumors Radiology Pathology Cancer

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Chi-Huang Chen Sheau-Ling Hsieh Yung-Ching Weng Wen-Yung Chang Feipei Lai Department of Electrical Engineering National Taiwan University Taipei Taiwan EECS International Graduate Program Institute IT Center National Chiao Tung University Hsinchu Taiwan Department of Computer Science and Engineering National Taiwan University Taiwan Institute of Computer Science and Engineering College of Computer Science National Chiao Tung University Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan

Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

关键词： Semantics biomedical measurements Correlation Kernel Training Medical services Support vector machine classification

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Development of label-free triboelectric nanosensors as screening platforms for anti-tumor drugs

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Nano Energy 2024年 125卷

作者： Cheng, Yu-Ying Ganguly, Anindita Cheng, Yi-Yun Ortiz, Christopher Llynard D. Pal, Arnab Shah, Pramod Kaswan, Kuldeep Yang, Lee-Wei Lin, Zong-Hong Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan Internet of Senses Research Center National Tsing Hua University Hsinchu30013 Taiwan Praexisio Taiwan Inc. New Taipei221425 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300044 Taiwan Chemical Biology and Molecular Biophysics Program Taiwan International Graduate Program Institute of Biological Chemistry Academia Sinica Taipei115 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300044 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu300044 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu300044 Taiwan Biomedical Artificial Intelligence PhD Program National Tsing Hua University Hsinchu300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei Taiwan

This study introduces a general label-free drug screening platform with potential to support high-throughput drug screening for any protein target. Its innovation lies in quantifying the affinity of molecule-molecule interactions via voltage output variation, which achieves unprecedented selectivity and sensitivity. It combines computational analysis complemented by experimental substantiation with a solid-liquid triboelectric nanosensor. Owing to its high binding affinity, FKBP-rapamycin is used as a model system to demonstrate the platform's sensitivity. Subsequently, the research is extended to study drug interactions with an oncogenic protein ATG4B. The findings unveil the binding of S130 and Tioconazole to ATG4B, a critical cysteine protease involved in autophagy, while revealing that Dexamethasone does not bind ATG4B. This binding exerts a specific inhibitory effect on autophagic flux and triggers cancer cell apoptosis. The results support the previously verified inhibitory effects of these drugs and the effectiveness of a newly developed self-powered drug screening platform, leveraging the principles of solid-liquid contact electrification. This approach adeptly confronts enduring challenges in traditional drug development methods where biochemical assays need to be designed for each individual protein target or only time-consuming and concentration-demanding molecular interaction measurements were made available. © 2024 Elsevier Ltd

关键词： Nanosensors

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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter

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Scientific Reports 2023年第1期13卷 1-10页

作者： Kuo, Tzu-Yun Wang, Jen-Hung Huang, Yung-Wen Sung, Ting-Yi Chen, Ching-Tai Department of Biochemical Science and Technology National Taiwan University Taipei 10617 Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Statistical Science Academia Sinica Taipei 11529 Taiwan Institute of Information Science Academia Sinica Taipei 11529 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 11221 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan Department of Bioinformatics and Biomedical Engineering Asia University Taichung 41354 Taiwan Center for Precision Health Research Asia University Taichung 41354 Taiwan

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms;its executable files, user manual, and sample data sets are freely available at https://***/comics/Software_*** . Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline. © 2023, Springer Nature Limited.

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Comparative analyses for plant virus-based cancer immunotherapy drug development

Cell Biomaterials

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Cell Biomaterials 2025年

作者： Anthony O. Omole Hannah S. Newton Edward Cedrone Kimia Nematpour Shaojun Xie Yongmei Zhao Bao Tran Marina A. Dobrovolskaia Nicole F. Steinmetz Aiiso Yufeng Li Family Department of Chemical and Nano Engineering University of California San Diego La Jolla San Diego CA 92093 USA Shu and K.C. Chien and Peter Farrell Collaboratory University of California San Diego La Jolla San Diego CA 92093 USA Center for Nano-ImmunoEngineering University of California San Diego La Jolla San Diego CA 92093 USA Moores Cancer Center University of California San Diego La Jolla San Diego CA 92093 USA Nanotechnology Characterization Lab Cancer Research Technology Program Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute Frederick MD 21702 USA Sequencing Facility Bioinformatics Group Biomedical Informatics and Data Science Directorate Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute Frederick MD 21702 USA CCR Sequencing Facility Cancer Research Technology Program Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute Frederick MD 21702 USA Department of Bioengineering University of California San Diego La Jolla San Diego CA 92093 USA Department of Radiology University of California San Diego La Jolla San Diego CA USA Institute for Materials Discovery and Design University of California San Diego La Jolla San Diego CA 92093 USA Center for Engineering in Cancer Institute of Engineering Medicine University of California San Diego La Jolla San Diego CA 92093 USA

Cowpea mosaic virus (CPMV) is a plant virus with potent anti-tumor efficacy. Intratumoral CPMV, but not cowpea chlorotic mottle virus (CCMV), reprograms the tumor microenvironment priming durable, systemic anti-tumor immunity. Here, we performed a side-by-side mechanism of action comparison between CPMV and CCMV. Through immune-multiplexing and trafficking studies we observed that CPMV and CCMV are taken up by innate immune cells at similar rates but are processed differently. While CCMV induces proinflammatory interleukins 22, 23, and 27, CPMV is a strong inducer of type I, II, and III interferons, which contribute to the activation and enhancement of immune cell function. We observed that CPMV RNAs activate Toll-like receptor (TLR) 7 upon delivery—and not CCMV RNAs; CPMV RNAs persist longer within cells compared with CCMV. Taken together, this work identifies determinants for CPMV’s unique mechanism for intratumoral immunotherapy. It also broadens our understanding of the utility of plant viruses for biomedical applications.

关键词： plant viruses intratumoral immunotherapy cowpea mosaic virus cowpea chlorotic mottle virus cancer nanotechnology

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The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges

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BioDesign Research 2020年第1期2020卷 1-8页

作者： Charles DeLisi Aristides Patrinos Michael MacCracken Dan Drell George Annas Adam Arkin George Church Robert Cook-Deegan Henry Jacoby Mary Lidstrom Jerry Melillo Ron Milo Keith Paustian John Reilly Richard J.Roberts Daniel Segrè Susan Solomon Dominic Woolf Stan D.Wullschleger Xiaohan Yang Department of Biomedical Engineering and Program in Bioinformatics College of EngineeringBoston UniversityBoston MA 02215USA The NOVIM Group Kohn HallUC Santa BarbaraCA 93106USA Climate Institute WashingtonDCUSA Department of Energy WashingtonDCUSA Center for Health Law Ethics&Human Rights at the Boston University School of Public HealthSchool of MedicineBoston UniversityUSA Department of Bioengineering University of CaliforniaBerkeley CAUSA Department of Genetics Harvard Medical SchoolCambridge MAUSA School for the Future of Innovation in Society Arizona State UniversityBarrett&O’Connor Washington Center1800 I StreetNWWashingtonDC 20006USA Sloan School of Management MITCambridge MAUSA Department of Chemical Engineering University of WashingtonSeattle WashingtonUSA The Ecosystems Center of the Marine Biological Laboratory in Woods Hole MAUSA Department of Plant and Environmental Sciences Weizmann Institute of ScienceRehovotIsrael Department of Soil and Crop Sciences Colorado State UniversityFort Collins CO 80523USA MIT Joint Program on the Science and Policy of Global Change MITCambridge MAUSA New England Biolabs Beverly MAUSA Department of Biology and Program in Bioinformatics Boston UniversityBoston MA 02215USA Department of Earth Atmospheric and Planetary SciencesMITCambridge MAUSA Soil and Crop Sciences Section School of Integrated Plant SciencesCornell UniversityIthaca NYUSA Environmental Sciences Division Oak Ridge National LaboratoryOak Ridge TNUSA Biosciences Division Oak Ridge National LaboratoryOak RidgeTNUSA

The long atmospheric residence time of CO2 creates an urgent need to add atmospheric carbon drawdown to CO2 regulatory *** and systems biology(SSB),which enables manipulation of cellular phenotypes,offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric *** participants(in attendance:Christina Agapakis,George Annas,Adam Arkin,George Church,Robert Cook-Deegan,Charles DeLisi,Dan Drell,Sheldon Glashow,Steve Hamburg,Henry Jacoby,Henry Kelly,Mark Kon,Todd Kuiken,Mary Lidstrom,Mike MacCracken,June Medford,Jerry Melillo,Ron Milo,Pilar Ossorio,Ari Patrinos,Keith Paustian,Kristala Jones Prather,Kent Redford,David Resnik,John Reilly,Richard ***,Daniel Segre,Susan Solomon,Elizabeth Strychalski,Chris Voigt,Dominic Woolf,Stan Wullschleger,and Xiaohan Yang)identified a range of possibilities by which SSB might help reduce greenhouse gas concentrations and which might also contribute to environmental sustainability and *** include,among other possibilities,engineering plants to convert CO2 produced by respiration into a stable carbonate,designing plants with an increased root-to-shoot ratio,and creating plants with the ability to self-fertilize.A number of serious ecological and societal challenges must,however,be confronted and resolved before any such application can be fully assessed,realized,and deployed.

关键词： Synthetic Roberts enable

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Mechanistic Insights into CLNS1A-Mediated Chemoresistance and Tumor Progression in Non-small Cell Lung Cancer

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Cancer letters 2025年 626卷 217783页

作者： Tong-You Wade Wei Jiun-Yi Hsia Tsung-Ying Yang Yu-Xu Huang Guo-Zhi Wang Yi-Chung Liu Yi-Wun Wang Fangzhou He Jo-Mei Maureen Chen Guo-Jun Zhao Ping-Chiang Lyu Li-Jen Su Shao-Chih Chiu Chang-Tze Ricky Yu Department of Applied Chemistry National Chi Nan University Nantou Taiwan Division of Cardiology Department of Medicine University of California San Diego La Jolla California USA. Electronic address: t1wei@health.ucsd.edu. Division of Thoracic Surgery Chung Shan Medical University Hospital Taichung Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan. Department of Chest Medicine Taichung Veterans General Hospital Taichung Taiwan Doctoral Program in Translational Medicine National Chung Hsing University Taichung Taiwan. Department of Medicine JingGangShan University Ji'an China. Division of Thoracic Surgery Chung Shan Medical University Hospital Taichung Taiwan. Department of Life Sciences National Tsing Hua University Hsinchu Taiwan. Cardiovascular Research Center School of Basic Medical Sciences Xi'an Jiaotong University Health Science Center Xi'an China. Department of Applied Chemistry National Chi Nan University Nantou Taiwan. Department of Cardiology The First Affiliated Hospital of Zhengzhou University Zhengzhou China. Institute of Bioinformatics and Structural Biology Department of Life Science National Tsing Hua University Hsinchu Taiwan. Department of Biomedical Sciences and Engineering Education and Research Center for Technology Assisted Substance Abuse Prevention and Management and Core Facilities for High Throughput Experimental Analysis National Central University Taoyuan Taiwan. Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Translational Cell Therapy Center Department of Medical Research China Medical University Hospital Taichung Taiwan. Electronic address: scchiu@mail.cmu.edu.tw. Department of Applied Chemistry National Chi Nan University Nantou Taiwan. Electronic address: ctyu@ncnu.edu.tw.

CLNS1A is a chloride channel protein and an essential component of the methylosome complex, which additionally comprises PRMT5 and MEP50. In this study, we investigated its contribution to lung cancer and its potential as a therapeutic target. Analysis of transcriptomic datasets and western blotting revealed that CLNS1A, PRMT5, and MEP50 were overexpressed in lung cancer tissues, with elevated CLNS1A expression correlating with poor patient survival. CLNS1A overexpression enhanced platinum clearance from cells, increased the IC values for chemotherapy, and improved cell survival. Conversely, the knockdown of CLNS1A increased drug accumulation, reduced survival, and increased sensitivity to chemotherapy. The 3W mutant, a chloride channel-defective variant with steric hindrance at key bottleneck residues, impaired chloride ion transport, thereby reducing drug resistance, migration, and anchorage-independent growth. Mechanistically, CLNS1A promotes drug efflux through its chloride channel activity and activates the FAK-SRC-RAC1 pathway to enhance motility and clonogenicity. It also facilitates PRMT5-mediated RUVBL1 methylation to support anti-apoptotic DNA damage response signaling. In vivo, CLNS1A overexpression accelerated tumor growth and reduced survival, whereas CLNS1A knockdown sensitized tumors to cisplatin, enhancing therapeutic efficacy. These findings suggest that CLNS1A is a potential biomarker and therapeutic target, and its inhibition offers a strategy to overcome drug resistance and limit the metastatic progression of lung cancer.

关键词： Chemoresistance Chloride channel DNA damage response Lung cancer Metastasis

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Study on the immobilization of Ni-NTA and NTA on PMMA substrate base

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Key engineering Materials 2008年 381-382卷 357-360页

作者： Chong, W.S. Kim, G.B. Hong, C.U. Department of Biomedical Engineering Graduate School Chonbuk National University Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of Education Program for 21st Century Chonbuk National University Research Institute of Clinical Medicine Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of Division of Bionics and Bioinformatics Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of

In this study, we attempts to develop a sensing method to detect mismatched DNA in order to diagnose cancer. The sensing method will be developed to use for early diagnosis of cancer. Thus, protein immobilization was applied on the surface of the sensor in order to facilitate the detection of mismatched DNA. This method was designed to achieve the Ni-His-Tag to selectively bond with MutS, which has a covalent bond with the His-Tag, by using Ni-NTA. This method is troublesome because it involves a number of repeated composition processes. This method need gold surface to immobilize NTA (nitrotriamino acid). But this process is very complicated and expensive cost. Therefore, we try to immobilize NTA using PMMA (poly methyl methacrylate) polymer in this research to improve this method. In this study revealed that we could directly immobilize the NTA to the PMMA substrate not used Gold substrate. Also, we could directly immobilize the MutS to the NTA using the EDC solution. In addition, we can expect that the mismatched DNA can be detected from the results.

关键词： Proteins

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