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World Congress on Engineering 2016, WCE 2016

作者： Gebreyesus, Kidane Desta Chang, Chuan-Hsiung Institute of Information Science Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan Center for Systems and Synthetic Biology Institute of Biomedical Informatics National Yang-Ming University Taipei 112 Taiwan

ISBN: (纸本)9789881925305

SIR (susceptible, infectious, removed) epidemic models are commonly used in infectious disease study. These models use systems of differential equations to estimate epidemiological parameters. However, differential equations often suffer from numerical challenges. Here, we proposed simple, effective and robust innovative methods for estimating key infectious disease parameters. Our methods are reformed from the SIR models, by adjusting components of model compartments. We illustrated the methods using the recent large disease outbreaks, Ebola virus disease and Middle East respiratory syndrome Coronavirus.

关键词： Coronavirus

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CHITOSAN-COLLAGEN COMPOSITE SCAFFOLDS FOR GROWTH DIRECTION GUIDANCE OF PC12 AXONS

CHITOSAN-COLLAGEN COMPOSITE SCAFFOLDS FOR GROWTH DIRECTION G...

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ASME 2024 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC-CIE 2024

作者： Tsai, Po-Yu Lin, Ying-Ting Wang, Gou-Jen Graduate Institute of Biomedical Engineering National Chung-Hsing University Taichung Taiwan PhD Program in Tissue Engineering and Regenerative Medicine National Chung-Hsing University Taichung Taiwan Department of Mechanical Engineering Graduate Institute of Biomedical Engineering National Chung-Hsing University Taichung Taiwan

ISBN: (纸本)9780791888421

In this study, nerve conduits of chitosan and collagen composites with biocompatibility and biodegradability were fabricated. The effects of material composition and surface morphology on the axonal growth and directionality of rat epinephric pheochromocytoma PC12 were investigated. The cells were separated by a PDMS structure to simulate nerve injury, and the growth of axons of PC12 cells was observed under the separation of large gaps. At the same time, mitochondria extracted from osteosarcoma cybrid cells (C2-GFP) were added to the culture to investigate the effect of healthy mitochondria on axon differentiation and growth. The experimental results showed that the chitosan-collagen composite film can promote the growth of PC12 axons more effectively than the pure chitosan film. Cell culture results at different groove widths also showed that smaller grooves resulted in more axon numbers and longer axon lengths. Nerve injury simulation experiments showed that the nerve repair could be almost completed after 12 days of culture. Copyright © 2024 by ASME.

关键词： Mitochondria

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Chemical-Induced Disease Detection Using Invariance-based Pattern Learning Model 1

Chemical-Induced Disease Detection Using Invariance-based Pa...

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1st International Workshop on Digital Disease Detection using Social Media, DDDSM 2017, co-located with the 8th International Joint Conference on Natural Language Processing, IJCNLP 2017

作者： Warikoo, Neha Chang, Yung-Chun Hsu, Wen-Lian Institute of Biomedical Informatics National Yang-Ming University Taipei112 Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Information Science Academia Sinica Taipei115 Taiwan Institute of Information Science Academia Sinica Taipei115 Taiwan Graduate Institute of Data Science Taipei Medical University Taipei106 Taiwan

ISBN: (纸本)9781948087070

In this work, we introduce a novel feature engineering approach named "algebraic invariance" to identify discriminative patterns for learning relation pair features for the chemical-disease relation (CDR) task of BioCreative V. Our method exploits the existing structural similarity of the key concepts of relation descriptions from the CDR corpus to generate robust linguistic patterns for SVM tree kernel-based learning. Preprocessing of the training data classifies the entity pairs as either related or unrelated to build instance types for both inter-sentential and intra-sentential scenarios. An invariant function is proposed to process and optimally cluster similar patterns for both positive and negative instances. The learning model for CDR pairs is based on the SVM tree kernel approach, which generates feature trees and vectors and is modeled on suitable invariance based patterns, bringing brevity, precision and context to the identifier features. Results demonstrate that our method outperformed compared approaches, achieved a high recall rate of 85.08%, and averaged an F1-score of 54.34% without the use of any additional knowledge bases. © 2017 AFNLP

关键词： Forestry

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A keratinocyte-adipocyte signaling loop is reprogrammed by loss of BTG3 to augment skin carcinogenesis

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Cell Death and Differentiation 2024年第8期31卷 970-982页

作者： Cheng, Yu-Che Acedera, Jack Dalit Li, Yi-Ju Shieh, Sheau-Yann Institute of Biomedical Sciences Academia Sinica Taipei Taiwan Taiwan International Graduate Program in Molecular Medicine National Yang Ming Chiao Tung University and Academia Sinica Taipei Taiwan

Obesity is endemic to many developed countries. Overweight or obesity is associated with an increased risk of developing cancer. Dysfunctional adipose tissue alters cancer cell proliferation and migration;however, whether and how neoplastic epithelial cells communicate with adipose tissue and the underlying mechanism are less clear. BTG3 is a member of the anti-proliferative BTG/Tob family and functions as a tumor suppressor. Here, we demonstrated that BTG3 levels are downregulated in basal cell carcinoma and squamous cell carcinoma compared to normal skin tissue, and Btg3 knockout in mice augmented the development of papilloma in a mouse model of DMBA/TPA-induced skin carcinogenesis. Mechanistically, BTG3-knockout keratinocytes promoted adipocyte differentiation mainly through the release of IL1α, IL10, and CCL4, as a result of elevated NF-κB activity. These adipocytes produced CCL20 and FGF7 in a feedback loop to promote keratinocyte migration. Thus, our findings showcased the role of BTG3 in guarding the interplay between keratinocytes and adjacent adipocytes, and identified the underlying neoplastic molecular mediators that may serve as possible targets in the treatment of skin cancer. (Figure presented.). © The Author(s) 2024.

关键词： Cancer microenvironment Tumour-suppressor proteins

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Picrasidine I Regulates Apoptosis in Melanoma Cell Lines by Activating ERK and JNK Pathways and Suppressing AKT Signaling

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Environmental Toxicology 2024年第12期39卷 5309-5320页

作者： Shieu, Mu-Kuei Lin, Chia-Chieh Ho, Hsin-Yu Lo, Yu-Sheng Chuang, Yi-Ching Hsieh, Ming-Ju Department of Dermatology Changhua Christian Hospital Changhua Taiwan Oral Cancer Research Center Changhua Christian Hospital Changhua Taiwan Graduate Institute of Clinical Medicine College of Medicine National Chung Hsing University Taichung Taiwan Doctoral Program in Tissue Engineering and Regenerative Medicine College of Medicine National Chung Hsing University Taichung Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan

World Health Organization data indicate a continuous increase in melanoma incidence, with metastatic melanoma characterized by poor prognosis and drug resistance. The exploration of therapeutics derived from natural products remains an active area of in vitro research. The aim of this study was to determine the antitumor effects of picrasidine I, a natural compound extracted from Picrasma quassioides, against two melanoma cell lines. We selected two metastatic melanoma cell lines, HMY-1 and A2058, for molecular studies, including Western blotting, 4′,6-diamidino-2-phenylindole staining, and flow cytometry. Picrasidine I demonstrated cytotoxic effects against the HMY-1 and A2058 melanoma cell lines. It induced cell cycle arrest in the sub-G1 phase and downregulated cell cycle–related proteins (e.g., cyclin A2, D1, cyclin-dependent kinases 4, and 6). In the intrinsic apoptosis pathway, picrasidine I activated proapoptotic proteins (e.g., Bax, Bak, t-Bid, BimL/S) and suppressed the expression of antiapoptotic proteins (e.g., Bcl-2, Bcl-xL), with an observed increase in the quantity of depolarized cells. In addition, the apoptotic effects of picrasidine I were linked to the activation of the c-Jun N-terminal kinase and extracellular signal-regulated kinase pathways and the inhibition of the protein kinase B signaling pathway. A human apoptosis array indicated claspin inhibition upon picrasidine I treatment, suggesting the potential involvement of picrasidine I in apoptosis and cell cycle regulation. Our findings suggest that picrasidine I has potential as a candidate for treating advanced melanoma, and thus these findings warrant further investigation. The modulation of claspin expression by picrasidine I could be investigated further as a potential biomarker to predict its efficacy in related to advanced stages of melanoma. © 2024 The Author(s). Environmental Toxicology published by Wiley Periodicals LLC.

关键词： Dermatology

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Transdermally administered nanozymes-infused F127/methylcellulose hydrogel for osteoarthritis relief via immunomodulatory pathways

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International journal of biological macromolecules 2025年 314卷 144114页

作者： Chih-Kuang Chen Hui-Wen Chiu Hieu Trung Nguyen Hsien-Tsung Lu Andrew E-Y Chuang Graduate Institute of Clinical Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan Department of Physical Medicine and Rehabilitation Chang Gung Memorial Hospital at Linkou Taoyuan Taiwan School of Medicine Chang Gung University Taoyuan Taiwan. Graduate Institute of Clinical Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan. Department of Orthopedics and Trauma Faculty of Medicine University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City 700000 Viet Nam. Department of Orthopedics School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan International Ph.D. Program in Cell Therapy and Regenerative Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan Department of Orthopedic Taipei Medical University Hospital Taipei City 11031 Taiwan. Electronic address: lu7788@tmu.edu.tw. Cell Physiology and Molecular Image Research Center Taipei Medical University-Wan Fang Hospital Taipei 11696 Taiwan Graduate Institute of Biomedical Materials and Tissue Engineering International Ph.D. Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University New Taipei City 235603 Taiwan. Electronic address: eychuang@tmu.edu.tw.

Osteoarthritis (OA) is a debilitating condition characterized by chronic inflammation, oxidative stress, hypoxia, angiogenesis-driven pain, and cartilage degradation, thus presenting significant therapeutic challenges. Herein, we introduce a wearable percutaneous hydrogel (Pluronic F127/methylcellulose) encapsulation platform, designed to address the multifaceted pathology of OA through a synergistic integration of multifunctional components. This nanomedicine-hydrogel system incorporates platelet-derived extracellular vesicles (pEVs) for inflammation delivery, phototherapeutic molybdenum disulfide (MoS2), capsaicin (CAP) and diferuloylmethane (DIF) for potent anti-inflammatory and antioxidative effects and hydrogen-bonded organic frameworks (HOFs) to enhance drug encapsulation and conductivity. Experimental findings demonstrated the pEV/MoS2/DIF/CAP NZHOF@F127/MC's ability to mitigate inflammation by promoting macrophage polarization from the M1 to the M2 phenotype, alleviate oxidative stress, inhibit angiogenesis, and modulate hypoxic microenvironments through the percutaneous phototherapeutic pEV/MoS2/DIF/CAP NZ-HOF@F127/MC. In vivo studies in a rat model of OA revealed substantial reductions in joint inflammation, enhanced cartilage regeneration, and improved mobility following near-infrared (NIR)-triggered phototherapy. The pEV/MoS2/DIF/CAP NZ-HOF@F127/MC's multifaceted mechanisms, including precise drug delivery, controlled release, and on-demand photo-responsiveness, underscore its transformative potential for OA management. These findings present a promising therapeutic strategy for OA, addressing inflammation, oxidative stress, and joint lesion mitigation, with strong potential for clinical translation.

关键词： Anti-inflammation Immunomodulation Modulation of hypoxic microenvironment Osteoarthritis alleviation Percutaneous phototherapeutic pEV/MoS2/DIF/CAP NZ-HOF@F127/MC

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Protein Folding as a Jamming Transition

PRX Life

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PRX Life 2025年第1期3卷 013018-013018页

作者： Alex T. Grigas Zhuoyi Liu Jack A. Logan Mark D. Shattuck Corey S. O'Hern Graduate Program in Computational Biology and Biomedical Informatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

Proteins fold to a specific functional conformation with a densely packed core that controls their stability. Despite their importance, we lack a quantitative explanation for why all protein cores, regardless of their overall fold, possess the same average packing fraction 〈ϕ〉≈0.55. However, important developments in the physics of jamming in particulate systems can shed light on the packing of protein cores. Here, we extend the framework of jamming to describe core packing in collapsed polymers, as well as in all-atom models of folded proteins. First, we show in a spherical bead-spring polymer model (with and without bond-angle constraints) that as the hydrophobic interactions increase relative to thermal fluctuations, a jamming-like transition occurs when the core packing fraction exceeds ϕc with the same power-law scaling behavior for the potential energy Vr, excess contact number ΔN, and characteristic frequency of the vibrational density of states ω* versus Δϕ=ϕ−ϕc as that for jammed particulate systems. Then, we develop an all-atom model for proteins and find that, above ϕc∼0.55, protein cores undergo a jamming-like transition, but with anomalous power-law scaling for Vr, ΔN, and ω* versus Δϕ. The all-atom protein model remains close to the native protein structure during jamming and accurately refolds from partially unfolded states.

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Wireless, self‑powered phototrophic algaerobot‑infused nanotherapeutic hydrogels for enhanced diabetic wound healing

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Chemical Engineering Journal 2025年 515卷

作者： Wei-Yung Huang Jiunn-Horng Kang Yan-Ting Chen Jia-Wei Liang Lan Pham Hoai Hoang Hieu Trung Nguyen Andrew E.-Y. Chuang Graduate Institute of Biomedical Materials and Tissue Engineering International Ph.D. Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University New Taipei City 23561 Taiwan International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei 110 Taiwan Department of Physical Medicine and Rehabilitation School of Medicine College of Medicine Taipei Medical University No.250 Wuxing Street Xinyi District Taipei 110 Taiwan Department of Physical Medicine and Rehabilitation Taipei Medical University Hospital Taipei 110 Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei 110 Taiwan Department of Orthopedics and Trauma Faculty of Medicine University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City 700000 Viet Nam Cell Physiology and Molecular Image Research Center Taipei Medical University-Wan Fang Hospital Taipei 11696 Taiwan Precision Medicine and Translational Cancer Research Center Taipei Medical University Hospital Taipei 11031 Taiwan

Diabetic wounds present a significant clinical challenge due to impaired immunity, hypoxia, poor neovascularization, and chronic inflammation, often resulting in severe complications such as amputation. Conventional therapies, including hyperbaric oxygen, antioxidants, and electrical stimulation, face limitations in delivering sustained and safe oxygen, hydrogen, and electrical stimulation to the wound site. This study introduces a groundbreaking approach by integrating phototrophic algae robots (AR) into a methylcellulose (MC) hydrogel, combined with platelet-derived extracellular vesicles (pEVs) and conductive glycol chitosan-polypyrrole nanoparticles (GCS-PPy NPs), forming a multifunctional composite system (MC-pEV-AR-GCS-PPy NPs). This advanced composite addresses the limitations of traditional treatments by integrating continuous, self-powered hydrogen and oxygen generation, electrical stimulation, and hyperthermia, all triggered by light-activated, electromagnetically driven mechanisms. Photosynthetic algae robots offer a sustainable solution for the generation of hydrogen and oxygen, effectively targeting the prevalent issues of hypoxia and the deficit frequently encountered in diabetic wounds. This innovative approach improves therapeutic outcomes through the integration of electrochemical processes and nanophototherapeutics, creating a multimodal platform. This platform not only promotes tissue regeneration and angiogenesis but also alleviates hypoxic conditions, modulates immune responses, and addresses key challenges associated with chronic wound healing. Incorporating pEVs amplifies the regenerative potential of the system, accelerating wound healing and promoting tissue regeneration. This self-powered platform not only reduces inflammation and suppresses M1 macrophage bioactivity but also regulates immune responses, creating an optimized healing environment. The MC-pEV-AR-GCS-PPy NPs composite represents a promising translational approach to diabetic wo

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O63: Leveraging global and local genomic data to guide equitable carrier screening: From Genome Aggregation Database (gnomAD) to Qatar Genome

Genetics in Medicine Open

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Genetics in medicine Open 2025年 3卷 102632-102632页

作者： Aarabi, Mahmoud Mbarek, Hamdi Bashar, Aryan Soman, Vishal Al-Mulla, Hajer Nkrumah, Esther Schmitz, Matthew Darabi, Helia Wang, John Kiehl, Paris Sethi, Rahil Saad, Chadi Rajkovic, Aleksandar Yatsenko, Svetlana Chandran, Uma Departments of Pathology and Obstetrics Gynecology and Reproductive Sciences University of Pittsburgh School of Medicine； Medical Genetics and Genomics Laboratories University of Pittsburgh Medical Center (UPMC) Pittsburgh PA Qatar Genome Program Qatar Foundation； Qatar Precision Health Institute Doha Qatar Data Science Graduate Program University of Colorado Boulder Boulder CO Department of Biomedical Informatics University of Pittsburgh School of Medicine Pittsburgh PA Joan H. Marks Graduate Program in Human Genetics Sarah Lawrence College New York NY Temerty Faculty of Medicine University of Toronto Toronto ON Canada Medical Genetics and Genomics Laboratories University of Pittsburgh Medical Center (UPMC) Department of Pediatrics University of Pittsburgh School of Medicine Pittsburgh PA Department of Microbiology Immunology and Pathology Colorado State University Fort Collins CO Department of Pathology and Institute of Human Genetics University of California San Francisco San Francisco CA Department of Pathology Stanford University School of Medicine Stanford CA

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Targeted tumor coating with antigenic, CTL-recognizable peptides via Annexin A5 chimeric constructs following chemotherapy redirects adaptive CD8+ T cell immunity for tumor clearance

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Cellular & Molecular Immunology 2021年第6期18卷 1578-1580页

作者： Tae Heung Kang Andrew Yang Yachea Tsai Louise Ferrall Chien-Fu Hung Institute of Biomedical Science and Technology Konkuk UniversitySeoulSouth Korea Genetics and Genomics Graduate Program Baylor College of MedicineHoustonTXUSA Medical Scientist Training Program Baylor College of MedicineHoustonTXUSA Department of Pathology Johns Hopkins UniversityBaltimoreMDUSA Department of Oncology Johns Hopkins UniversityBaltimoreMDUSA

A common drawback of many cancer immunotherapies,including immune checkpoint blockade,is their reliance on the expression of immunogenic tumor antigens by cancer cells for immune recognition and clearance,which limits their efficacy against cancers with weak antigenicity.1 To overcome this obstacle,we and others have explored strategies to harness the immune responses against nontumor antigens and redirect those immune responses to target tumor cells.2,3,4,5 In particular,we have pioneered a therapeutic strategy fusing tumor-targeting proteins with known antigenic peptide epitopes not naturally expressed by tumor cells,which are flanked by peptide sequences that can be recognized and cleaved by proteases overexpressed in most cancers.2,3 This strategy facilitates the targeted delivery of immunogenic peptides into tumor foci,the release of immunogenic peptides into the tumor microenvironment(TME)via tumor protease cleavage,and subsequent loading of these peptides onto major histocompatibility complex class 1(MHC-I)on the tumor cell surface,allowing the recognition of coated tumor cells by the respective peptide-specific cytotoxic CD8+T lymphocytes(CTLs)for elimination.

关键词： immunity overcome coating

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