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arXiv 2025年

作者： Park, Junseok Maury, Eduardo A. Oh, Changhoon Shin, Donghoon Denisko, Danielle Lee, Eunjung Alice Division of Genetics and Genomics Boston Children’s Hospital 3 Blackfan Circle BostonMA United States Department of Pediatrics Harvard Medical School 25 Shattuck St BostonMA United States Bioinformatics Integrative Genomics Program Harvard/MIT MD-PHD Program Harvard Medical School BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Graduate School of Information Yonsei University 50 Yonsei-ro Seodaemun-gu Seoul Korea Republic of Department of Human Centered Design and Engineering University of Washington SeattleWA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States

Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing of such large-scale genomic sequence data in distributed processing environments with a significant reduction in analysis time. However, parallel processing on cloud computing platforms presents many challenges to researchers, even skillful bioinformaticians. In particular, it is difficult to design a computing architecture optimized to reduce the cost of computing and disk storage as genomic data analysis pipelines often employ many heterogeneous tools with different resource requirements. To address these issues, we developed GenomeFlow, a tool for automated development of computing architecture and resource optimization on Google Cloud Platform, which allows users to process a large number of samples at minimal cost. We outline multiple use cases of GenomeFlow demonstrating its utility to significantly reduce computing time and cost associated with analyzing genomic and transcriptomic data from hundreds to tens of thousands of samples from several consortia. Here, we describe a step-by-step protocol on how to use GenomeFlow for a common genomic data processing task. We introduce this example protocol geared toward a bioinformatician with little experience in cloud computing. © 2025, CC BY.

关键词： Cloud platforms

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Correction: Ubiquitin carboxyl-terminal hydrolase 11 promotes autophagy by de-ubiquitinating and stabilizing Beclin-1

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Genome Instability & Disease 2023年第5期4卷 303-303页

作者： Li, Zheng Rao, Shaohong Song, Chunwei Zhu, Min Zhao, Hongchang Yuan, Shuping Peng, Bin Xu, Xingzhi Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center Marshall Laboratory of Biomedical Engineering Shenzhen University School of Medicine Shenzhen China Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering Shenzhen University Medical School Shenzhen China College of Life Sciences Capital Normal University Beijing China Institute of Translational Medicine College of Medicine Qingdao University Qingdao China Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences Shenzhen University School of Medicine Shenzhen China

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Effect of Implant Scan Body type, Intraoral scanner and Scan Strategy on the accuracy and scanning time of a maxillary complete arch implant scans: an in vitro study

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Journal of Dentistry 2025年 159卷

作者： Francesco Grande Alessandro Mosca Balma Federico Mussano Santo Catapano PhD student Department of Mechanical and aerospace engineering Polytechnic University of Turin Turin Italy Biomedical Engineer Department of Surgical Sciences CIR Dental School University of Turin Turin Italy Associate Professor Department of Surgical Sciences CIR Dental School University of Turin Turin Italy Associate Professor and Department Head Department of Prosthodontics University of Ferrara Ferrara Italy

Objectives This study aimed to investigate the influence of three Implant Scan Bodies (ISBs), four intraoral scanners (IOSs), and two scan strategies on the trueness of complete arch implant scans. Methods A reference digital cast of an all-on-six maxillary rehabilitation was obtained using a coordinate measuring machine. Three ISBs - AQ (ISB-AQ), One-shot, Elos (ISB-PEEK) - four IOSs - Trios3POD (TRIOS), Medit i700 (MED), iTero Element 5D (iTe), Primescan (PRIME) - and two scan strategies - Zig-zag (ZZ), One-shot (OS) - were used for evaluation. For each group created by the combination of the different variables, 10 digital scans were taken by one operator ( n = 240) under controlled temperature and lighting conditions. The positions of the ISB connections were compared to the standard tessellation language reference file by using the nurbs-to-nurbs method. The overall 3D linear and angular deviations of the ISBs connections between reference and test scans were evaluated by computing the Euler distances (α=0.05). Interimplant distance discrepancies were calculated at the ISB connection level. Scanning times were recorded. Results Regarding linear and angular deviations, AQ had significantly higher trueness than the other ISBs ( p < 0.01). TRIOS showed significantly higher trueness ( p < 0.01). No significant differences for scan strategies were found ( p > 0.05). ISB-OneSh, Primescan and ZZ method resulted in significant shortest scanning times ( p <<0.01). Conclusions ISB-AQ demonstrated higher trueness than One-Shot and PEEK. TRIOS performed better than the other IOSs. Scan strategy didn’t influence the trueness. ISB-OneSh, Primescan, and ZZ strategy allowed the fastest scans. Clinical Significance The choice of ISB and IOS significantly affects the accuracy of complete-arch implant scans. The scan strategy did not impact trueness but influenced the efficiency. As an in vitro study, results observed need confirmation in the clinical settings.

关键词： Intraoral scanner Implant scan body Accuracy Scanning strategy Interimplant discrepancy Angular deviation Scanning time

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Microfluidic nanodevices for drug sensing and screening applications

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Biosensors and Bioelectronics 2023年 219卷 114783页

作者： Pal, Arnab Kaswan, Kuldeep Barman, Snigdha Roy Lin, Yu-Zih Chung, Jun-Hsuan Sharma, Manish Kumar Liu, Kuei-Lin Chen, Bo-Huan Wu, Chih-Cheng Lee, Sangmin Choi, Dongwhi Lin, Zong-Hong Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu30013 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu30013 Taiwan Department of Materials Science and Engineering National Tsing Hua University Hsinchu30013 Taiwan Department of Chemistry National Tsing Hua University Hsinchu30013 Taiwan Frontier Research Center on Fundamental and Applied Sciences of Matters National Tsing Hua University Hsinchu30013 Taiwan Department of Gastroenterology and Hepatology Chang Gung Memorial Hospital Linkou Medical Center Taoyuan333 Taiwan Center of Quality Management National Taiwan University Hospital Hsinchu Branch Hsinchu30059 Taiwan College of Medicine National Taiwan University Taipei10051 Taiwan Institute of Cellular and System Medicine National Health Research Institute Zhunan 35053 Taiwan School of Mechanical Engineering Chung-Ang University Seoul06974 Korea Republic of Kyung Hee University Gyeonggi 17104 Korea Republic of

The outbreak of pandemics (e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 in 2019), influenza A viruses (H1N1 in 2009), etc.), and worldwide spike in the aging population have created unprecedented urgency for developing new drugs to improve disease treatment. As a result, extensive efforts have been made to design novel techniques for efficient drug monitoring and screening, which form the backbone of drug development. Compared to traditional techniques, microfluidics-based platforms have emerged as promising alternatives for high-throughput drug screening due to their inherent miniaturization characteristics, low sample consumption, integration, and compatibility with diverse analytical strategies. Moreover, the microfluidic-based models utilizing human cells to produce in-vitro biomimetics of the human body pave new ways to predict more accurate drug effects in humans. This review provides a comprehensive summary of different microfluidics-based drug sensing and screening strategies and briefly discusses their advantages. Most importantly, an in-depth outlook of the commonly used detection techniques integrated with microfluidic chips for highly sensitive drug screening is provided. Then, the influence of critical parameters such as sensing materials and microfluidic platform geometries on screening performance is summarized. This review also outlines the recent applications of microfluidic approaches for screening therapeutic and illicit drugs. Moreover, the current challenges and the future perspective of this research field is elaborately highlighted, which we believe will contribute immensely towards significant achievements in all aspects of drug development. © 2022 Elsevier B.V.

关键词： Microfluidics

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CCL5 Protects Cortical Neuron Function by Regulating M2 Microglia Activation After Mild Traumatic Brain Injury

SSRN

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SSRN 2022年

作者： Tsai, Yih-Jeng Ho, Man-Hau Yen, Chia-Hung Wang, Jia-Yi Burnouf, Thierry Chen, Chia-Yen Wang, Yun Chiang, Yung-Hsiao Hoffer, Barry J. Chou, Szu-Yi Department of Otolaryngology Head and Neck Surgery Shin Kong Wu HoSu Memorial Hospital Taipei Taiwan School of Medicine Fu Jen Catholic University New Taipei City Taiwan Ph.D. Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University National Health Research Institute Taiwan Graduate Institute of Neural Regenerative Medicine College of Medical Science and Technology Taipei Medical University Taipei Taiwan Department of Biological Science and Technology National Pingtung University of Science and Technology Neipu Pingtung91201 Taiwan Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei11031 Taiwan Department of Neurosurgery Taipei Medical University Hospital Taipei11031 Taiwan Neuroscience Research Center Taipei Medical University Taipei11031 Taiwan International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei Taiwan Graduate Institute of Biomedical Materials and Tissue Engineering College of Biomedical Engineering Taipei Medical University Taipei Taiwan NeuroTMULille International Laboratory Taipei Medical University Taipei Taiwan International PhD Program in Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei Taiwan Brain and Consciousness Research Centre TMU Shuang Ho Hospital New Taipei City Taiwan Center for Neuropsychiatric Research National Health Research Institutes Zhunan Miaoli County Taiwan Department of Surgery School of Medicine College of Medicine Taipei Medical University 11031 Taiwan Department of Neurosurgery Case Western Reserve University School of Medicine ClevelandOH United States Scientist Emeritus National Institutes of Health United States International Master Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University Taipei Taiwan

Cytokines and chemokines play important roles in inflammation and repair following brain injury. M1 microglia are pro-inflammatory which produce cytokines and lead to neural injury;in contrast, M2 microglia are anti-inflammatory, release neurotrophic factors, and promote neural repair processes. Chemokine CCL5, increased after TBI, shows a neuroprotective function by reducing oxidative stress. CCL5 may contribute to the balance between oxidative stress and immune responses after brain injury. Herein, we investigated the role of CCL5 in microglial polarization after mild traumatic brain injury, focusing on the cerebral cortex.C57BL/6 and CCL5 knockout (CCL5-KO) mice were given a mild traumatic brain injury (TBI) using weight-drop. Neurological parameters such as motor and sensory functions were analyzed by mNSS score, accelerating rotarod, beam walking, and adhesive removal tests. Oxidative stress and neuron damage were measured by NADPH oxidase activity, hypoxyloprobe staining and FJC. Performance of motor and sensory functions in both WT and CCL5-KO mice were impaired after brain injury which recovered after 7 days-post-injury (dpi) in the WT group but only after 14 days in the CCL5-KO mouse group. RT-qPCR analysis revealed that pro-inflammation cytokines - IL-1β, TNF-α, and IL-6 were higher in CCL5-KO mice compared to WT mice at 4 and 14 dpi. In contrast, M2-like microglia markers - IL-10 and Agr-1 were increased in WT mouse cortical tissue at 4 dpi. Oxidative stress increased both M1 and M2- related cytokine expression in BV2 cells treated with H 2 O 2;CCL5 treatment increased M2- but suppressed M1- related cytokine gene activation. Intranasal delivery of CCL5 reduced neuronal oxidative stress, increased IL-10 expression and improved motor and sensory functions in CCL5-KO mice after brain *** summary, CCL5, which alters immune responses and protects neurons from TBI damage, has an important function in regulating M2-like microglial polarization during post-

关键词： Polarization

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Comparative analysis of the retention force and deformation of PEEK and PEKK removable partial denture clasps with different thicknesses and undercut depths

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Journal of Prosthetic Dentistry 2024年第2期131卷 291-291.e9页

作者： Lee, Wei-Fang Chen, May-Show Peng, Tzu-Yu Huang, Peng-Chien Nikawa, Hiroki Peng, Pei-Wen Associate Professor School of Dental Technology Taipei Medical University Taipei Taiwan ROC and PhD student School of Dentistry Taipei Medical University Taipei Taiwan Associate Professor School of Dentistry Taipei Medical University Taipei Taiwan ROC and Visiting Doctor Division of Prosthodontics Department of Dentistry Taipei Medical University Hospital Taipei Taiwan School of Dentistry Taipei Medical University Taipei Taiwan Dental Technician School of Dental Technology Taipei Medical University Taipei Taiwan Department of Oral Biology & Engineering Graduate School of Biomedical and Health Sciences Hiroshima University Hiroshima Hiroshima City Japan School of Dental Technology Taipei Medical University Taipei Taiwan

Statement of problem: The retentive force and deformation of milled polyetheretherketone (PEEK) and polyetherketoneketone (PEKK) removable partial denture (RPD) frameworks are not well understood. Purpose: The purpose of this in vitro study was to assess the retentive force and deformation of PEEK and PEKK Akers clasps with different designs and undercut depths. Material and methods: A master model containing the first and second molar abutments was used to design Akers clasps of different cross-sectional dimensions, undercut depths (0.5 and 0.75 mm), and materials. The components of the removable partial denture framework also included an occlusal rest and were manufactured using a milling machine (n=5). The fatigue resistance of the Akers clasps was measured before and after deformation regarding the retentive forces. Results: The PEEK2-U50 clasp had the largest retentive force with no significant difference among all groups before and after the insertion and removal cycle. In addition, the increased cross-sectional dimensions of the design resulted in significant differences in retentive forces between the PEEK1 and PEEK2 groups and between the PEEK and PEKK materials. Conclusions: Increasing the clasp's cross-sectional dimensions significantly impacted retentive forces, especially between different PEEK groups and between PEEK and PEKK materials. © 2024 Editorial Council for The Journal of Prosthetic Dentistry

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Artificial intelligence applications in histopathology

Nature Reviews Electrical Engineering

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Nature Reviews Electrical engineering 2024年第2期1卷 93-108页

作者： Cagla Deniz Bahadir Mohamed Omar Luigi Marchionni Benjamin Liechty David J. Pisapia Jacob Rosenthal Mert R. Sabuncu Biomedical Engineering Cornell University and Cornell Tech New York NY USA Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program New York NY USA Radiology Weill Cornell Medicine New York NY USA Electrical and Computer Engineering Cornell University and Cornell Tech New York NY USA

Histopathology is a vital diagnostic discipline in medicine, fundamental to our understanding, detection, assessment and treatment of conditions such as cancer, dementia and heart disease. Traditionally, the standard workflow in histopathology has primarily relied on the visual interpretation of tissue samples carried out by human experts under a light microscope. Since the 2000s, thanks to advances in scanning technologies such as whole-slide imaging, histopathology is undergoing a digital transformation. The rapid increase in digital data is fuelling the development and application of artificial intelligence (AI) methods. In this Review, we delve into the latest progress in AI methods for histopathology, which promise to yield accurate, scalable, useful and affordable support tools for clinical decision. We examine the challenges and opportunities in this domain, exploring historically important approaches and problems that have shaped the field, while also highlighting recent technological breakthroughs that are poised to redefine its future. Furthermore, we offer an overview of publicly available datasets that have been instrumental in propelling the development of AI methods in histopathology.

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Sustainable flower-like Cu-Ni metal-organic frameworks catalyst for enhanced electrochemical sensing and photocatalytic degradation of antibiotic pollutants

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Microchemical Journal 2025年 214卷

作者： N.S.K. Gowthaman Ameer Farithkhan E. Narayanamoorthi Ponnusamy Arul Chinnathambi Nandhini Vellaichamy Balakumar S. Selvarajan School of Engineering Monash University Bandar Sunway Selangor 47500 Malaysia Center for Advanced Energy Materials SRM TRP Engineering College Tiruchirapalli 621 105 Tamil Nadu India Center for Research Easwari Engineering College Chennai 600 089 Tamil Nadu India School of Materials Science and Engineering Pusan National University Busan 46241 Republic of Korea International PhD Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City 243303 Taiwan Institute of Biochemical and Biomedical Engineering Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei 106 Taiwan Department of Materials Engineering Ming Chi University of Technology New Taipei City 24303 Taiwan Department of Chemistry Sri Ramakrishna College of Arts & Science Coimbatore 641 006 Tamil Nadu India Department of Chemistry Theni Kammavar Sangam College of Arts & Science Theni 625 531 Tamil Nadu India

Massive usage of antibiotics harms the environment through animals’ excrement and squeezes open-wellbeing issues. Enrofloxacin (EF), an antimicrobial agent, treats bacterial diseases and infections in cattle, poultry and exotic animals and exhibits harmful side effects. The present work proposed a sensitive and rapid electrochemical scaffold based on the Cu-Ni bimetallic-organic framework (Cu-Ni-MOF) for the detection of harmful EF in real-time applications. The Cu-Ni-MOF was synthesized through solvothermal approach with the support of a multifunctional organic ligand, 4,4-biphenyldicarboxylicacid and characterized through various analytical tools. The electrochemical sensor for EF detection was constructed by drop-casting the Cu-Ni-MOF on a glassy carbon electrode and the fabricated sensor exhibited higher catalytic activity when compared to the parental counterparts by exhibiting 1.7-fold higher current for EF oxidation. Further, the fabricated sensor is highly active in the linear range response of 200 nM–2 mM with a limit of detection of 15.17 nM and sensitivity of 638.71 µA mM cm −2 under optimized environments. The higher electrocatalytic activity of the Cu-Ni-MOF electrode synergistically stems from the strong interaction between Cu 2+ of the MOF and pyridone and carboxylate moieties of the EF and facile electron transition facilitated by Ni 2+ . The practicability of the sensor was evaluated in milk, egg and river water samples and the obtained results were validated with Liquid Chromatography-Mass Spectrometric technique. Furthermore, the prepared catalyst was utilized for the photochemical decontamination of EF and the present Cu-Ni-MOF catalyst delivered excellent photocatalytic activity in the decontamination of EF under visible light at ambient temperature.

关键词： Cu-Ni-MOF Electrochemical sensor Enrofloxacin Environmental pollutants Metal-organic framework Photocatalytic degradation

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Corrigendum to “Metal ratio and bimetal nanoarchitectonics of ammonia-based fluoride complex induced nickel hydroxide and manganese oxide composites as active materials of an energy storage device” [J. Energy Storage 80 (2024) 110316]

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Journal of Energy Storage 2025年 108卷

作者： Chuan-Chih Hsu You Zher Yu Chung-Hsien Wu Pin-Yan Lee Hung-Ming Chen Sadang Husain Chutima Kongvarhodom Yu-Cheng Hsiao Lu-Yin Lin Division of Cardiovascular Surgery Department of Surgery School of Medicine College of Medicine Taipei Medical University Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Medical University Hospital Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Gingen Technology Co. LTD. Rm. 7 10F. No.189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei 11054 Taiwan Department of Physics Faculty of Mathematics and Natural Science Lambung Mangkurat University Banjarmasin 70124 Indonesia Department of Chemical Engineering King Mongkut's University of Technology Thonburi 126 Pracha-u-thit Toong-kru Bangkok 10140 Thailand Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei 11696 Taiwan International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei 11031 Taiwan Stanford Byers Center for Biodesign Stanford University CA 94305-5428 USA Graduate Institute of Biomedical Optomechatronics College of Biomedical Engineering Taipei Medical University Taipei 11031 Taiwan

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Dual-Targeting EGCG/NO-Supplying protein assembled nanoparticles with Multi-Synergistic effects against atherosclerosis

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Chemical engineering Journal 2024年 493卷

作者： Lin, Chi Cheng, Tsai-Mu Liu, Yun-Chun Hsu, Fang-Yu Shih, Chun-Ming Tsai, Min-Lang Shih, Chun-Che Mi, Fwu-Long Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei11031 Taiwan The PhD Program for Translational Medicine College of Medical Science and Technology Taipei Medical University Taipei11031 Taiwan Taipei Heart Institute Taipei Medical University Taipei11031 Taiwan Department of Food Science National Taiwan Ocean University Keelung20224 Taiwan Department of Biochemistry and Molecular Cell Biology School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Division of Cardiology and Cardiovascular Research Center Taipei Medical University Hospital Taipei11031 Taiwan Division of Cardiovascular Surgery Department of Surgery Wan Fang Hospital Taipei Medical University Taipei11031 Taiwan Institute of Clinical Medicine School of Medicine National Yang-Ming Chiao Tung University Taipei Taiwan Department of Surgery School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan International Ph.D. Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei Taiwan

Limited therapeutic options are available to effectively preventing atherosclerosis. Inflammatory endothelial cells, foamy macrophages, and high protease levels contribute to atherosclerotic plaque formation. Studies have shown that catechins effectively scavenge reactive oxygen species (ROS), inhibit monocyte adhesion and reduce cholesterol levels, while nitric oxide (NO) enhances endothelial function. However, due to the poor stability and bioavailability of catechins and the toxicity from the burst release of current synthetic small molecules NO donor, effective delivery of these bioactive compounds to treat atherosclerosis is still a challenge. Herein, a catechin/protein-based NO donor co-delivery nanosystem was designed for combinatorial anti-atherosclerotic therapy. We engineered a (−)-epigallocatechin-3-gallate (EGCG)/NO-releasing protein co-assembled nanocomplex based on specific catechin-protein interactions. Furthermore, the nanocomplex was surface modified with fucoidan (Fu), a sulfated polysaccharide with anti-inflammatory activity. This nanocomplex exhibits sensitivity to ROS, pH, and enzymes. The Fu-functionalized nanoparticles specifically accumulates in atherosclerotic plaques mediated by P-selectin on inflamed endothelial cells and scavenger receptor A (SR-A) on foamy macrophages. Under environmental stimuli that simulate the condition of plaque, the nanoparticles are readily activated to release EGCG and NO in response to excess ROS and high protease levels, exerting the multi-synergistic anti-atherosclerosic effects on reducing monocyte adhesion, promoting NO production to proliferate endothelial cells, lowering ROS levels, and decreasing the foam cell formation in vitro, and reducing lipid accumulation, plaque size, and inflammatory cytokines release in high-fat diet-induced atherosclerosis model in ApoE−/− mice. The integration of plaques targeting ability and multiple therapeutic functions can provide an advanced therapeutic strategy for athero

关键词： Nitric oxide

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