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arXiv 2019年

作者： Chen, Muyuan Bell, James M. Shi, Xiaodong Sun, Stella Y. Wang, Zhao Ludtke, Steven J. Verna Marrs and McLean Department of Biochemistry and Molecular Biology Baylor College of Medicine HoustonTX United States Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine HoustonTX United States Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Xuzhou Medical University Xuzhou Jiangsu China Department of Bioengineering Stanford University StanfordCA United States CryoEM Core at Baylor College of Medicine HoustonTX77030 United States

Electron cryotomography (CryoET) is currently the only method capable of visualizing cells in 3D at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, the data processing is very labor intensive and results are often limited by the skills of the personnel rather than the data. We present an integrated workflow that covers the entire tomography data processing pipeline, from automated tilt series alignment to subnanometer resolution subtomogram averaging. This workflow greatly reduces human effort and increases throughput, and is capable of determining protein structures at state-of-the-art resolutions for both purified macromolecules and cells. Copyright © 2019, The Authors. All rights reserved.

关键词： Tomography

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Correction to: Toward Automatic Detection of Radiation-Induced Cerebral Microbleeds Using a 3D Deep Residual Network

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Journal of digital imaging 2019年第5期32卷 898页

作者： Yicheng Chen Javier E Villanueva-Meyer Melanie A Morrison Janine M Lupo UCSF-UC Berkeley Graduate Program in Bioengineering San Francisco USA. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA. UCSF-UC Berkeley Graduate Program in Bioengineering San Francisco USA. Janine.Lupo@ucsf.edu. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA. Janine.Lupo@ucsf.edu.

This paper was published inadvertently as open access. It has been corrected online.

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Engineered extracellular vesicles carrying let-7a-5p for alleviating inflammation in acute lung injury

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Journal of Biomedical Science 2024年第1期31卷 1页

作者： Chen, Sin-Yu Chen, Yi-Ling Li, Po-Chen Cheng, Tai-Shan Chu, Yeh-Shiu Shen, Yi-Shan Chen, Hsin-Tung Tsai, Wei-Ni Huang, Chien-Ling Sieber, Martin Yeh, Yuan-Chieh Liu, Hsiao-Sheng Chiang, Chi-Ling Chang, Chih-Hung Lee, Andrew S. Tseng, Yen-Han Lee, Ly James Liao, Hsiu-Jung Yip, Hon-Kan Huang, Chi-Ying F. Institute of Biopharmaceutical Sciences College of Pharmaceutical Sciences National Yang Ming Chiao Tung University Taipei 112304 Taiwan Division of Cardiology Department of Internal Medicine Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung 833401 Taiwan Institute for Translational Research in Biomedicine Kaohsiung Chang Gung Memorial Hospital Kaohsiung 833401 Taiwan Department of Orthopedic Surgery Far Eastern Memorial Hospital New Taipei City 220216 Taiwan Brain Research Center National Yang Ming Chiao Tung University Taipei 112304 Taiwan Department of Biomedical Engineering National Taiwan University Taipei 106319 Taiwan Bionet Therapeutics Taipei 114065 Taiwan Department of Traditional Chinese Medicine Chang Gung Memorial Hospital Keelung 204201 Taiwan Program in Molecular Medicine College of Life Sciences National Yang Ming Chiao Tung University Taipei 112304 Taiwan Department of Microbiology and Immunology College of Medicine National Cheng Kung University Tainan 701401 Taiwan Center for Cancer Research College of Medicine Kaohsiung Medical University Kaohsiung 807378 Taiwan Teaching and Research Center Kaohsiung Municipal Siaogang Hospital Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung 812015 Taiwan Department of Chemical and Biomolecular Engineering The Ohio State University Columbus 43210 OH United States Comprehensive Cancer Center College of Medicine The Ohio State University Columbus 43210 OH United States Graduate School of Biotechnology and Bioengineering Yuan Ze University Taoyuan 320315 Taiwan Spot Biosystems Ltd. Palo Alto 94305 CA United States Department of Chest Medicine Taipei Veterans General Hospital Taipei 112201 Taiwan Department of Medical Research Far Eastern Memorial Hospital New Taipei City 220216 Taiwan Center for Shockwave Medicine and Tissue Engineering Kaohsiung Chang Gung Memorial Hospital Kaohsiung 833401 Taiwan Departme

Background: Acute lung injury (ALI) is a life-threatening respiratory condition characterized by severe inflammation and lung tissue damage, frequently causing rapid respiratory failure and long-term complications. The microRNA let-7a-5p is involved in the progression of lung injury, inflammation, and fibrosis by regulating immune cell activation and cytokine production. This study aims to use an innovative cellular electroporation platform to generate extracellular vesicles (EVs) carring let-7a-5p (EV-let-7a-5p) derived from transfected Wharton’s jelly-mesenchymal stem cells (WJ-MSCs) as a potential gene therapy for ALI. Methods: A cellular nanoporation (CNP) method was used to induce the production and release of EV-let-7a-5p from WJ-MSCs transfected with the relevant plasmid DNA. EV-let-7a-5p in the conditioned medium were isolated using a tangential flow filtration (TFF) system. EV characterization followed the minimal consensus guidelines outlined by the International Society for Extracellular Vesicles. We conducted a thorough set of therapeutic assessments, including the antifibrotic effects using a transforming growth factor beta (TGF-β)-induced cell model, the modulation effects on macrophage polarization, and the influence of EV-let-7a-5p in a rat model of hyperoxia-induced ALI. Results: The CNP platform significantly increased EV secretion from transfected WJ-MSCs, and the encapsulated let-7a-5p in engineered EVs was markedly higher than that in untreated WJ-MSCs. These EV-let-7a-5p did not influence cell proliferation and effectively mitigated the TGF-β-induced fibrotic phenotype by downregulating SMAD2/3 phosphorylation in LL29 cells. Furthermore, EV-let-7a-5p regulated M2-like macrophage activation in an inflammatory microenvironment and significantly induced interleukin (IL)-10 secretion, demonstrating their modulatory effect on inflammation. Administering EVs from untreated WJ-MSCs slightly improved lung function and increased let-7a-5p expression in

关键词： Acute lung injury Anti-inflammation Cellular nanoporation Extracellular vesicles Let-7a-5p Mesenchymal stem cells

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Self-packaged stretchable printed circuits with ligand-bound liquid metal particles in elastomer

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Nature communications 2025年第1期16卷 4944页

作者： Hyeonyeob Seo Gun-Hee Lee Jiwoo Park Dong-Yeong Kim Yeonzu Son Semin Kim Kum Seok Nam Congqi Yang Joonhee Won Jae-Young Bae Hyunjun Kim Seung-Kyun Kang Steve Park Jiheong Kang Seongjun Park Department of Bio and Brain Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea. Departments of Cogno-Mechatronics Engineering Pusan National University Busan Republic of Korea. Departments of Optics and Mechatronics Engineering Pusan National University Busan Republic of Korea. School of Electrical Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea. Program of Brain and Cognitive Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon South Korea. Graduate School of Semiconductor Technology Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea. Medical Research Center Seoul National University Seoul Republic of Korea. Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea. Department of Materials Science and Engineering Seoul National University Seoul Republic of Korea. KAIST Institute for NanoCentury Daejeon Republic of Korea. Department of Chemistry Seoul National University Seoul Republic of Korea. jiheongkang@snu.ac.kr. Medical Research Center Seoul National University Seoul Republic of Korea. seongjunpark@snu.ac.kr. Department of Biomedical Sciences College of Medicine Seoul National University Seoul Republic of Korea. seongjunpark@snu.ac.kr. School of Transdisciplinary Innovations Seoul National University Seoul Republic of Korea. seongjunpark@snu.ac.kr. Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Seoul Republic of Korea. seongjunpark@snu.ac.kr. Department of Transdisciplinary Medicine Seoul National University Hospital Seoul South Korea. seongjunpark@snu.ac.kr.

Packaging in stretchable electronics is crucial to protect components from environmental damage while preserving mechanical flexibility and providing electrical insulation. The conventional packaging process involves multiple steps that increase in complexity as the number of circuit layers multiply. In this study, we introduce a self-packaged stretchable printed circuit board enabled by the in situ phase separation of liquid metal particles (LMPs) within various polymer matrices during solution-based printing processes. The ligand-bound LMPs (LB-LMPs), engineered to inhibit oxide growth, undergo in situ sintering, prompting vertical phase separation. This synthesis strategy not only achieves high initial conductivity of the LMPs but also encapsulates them within the polymer matrix, preventing leakage and providing electrical insulation. Our method enables multi-layer circuit printing, eliminating the need for additional activation and packaging processes. Furthermore, by integrating conductive materials into packaging layers for selective electrical conductivity, vertical interconnect accesses and conductive pads can be formed, enabling large-scale, stretchable, and leakage-free multi-layer electrical circuits and bio-interfaces.

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Author Correction: Generation of accurate, expandable phylogenomic trees with uDance

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Nature biotechnology 2024年第5期42卷 814页

作者： Metin Balaban Yueyu Jiang Qiyun Zhu Daniel McDonald Rob Knight Siavash Mirarab Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. Biodesign Center for Fundamental and Applied Microbiomics Arizona State University Tempe AZ USA. School of Life Sciences Arizona State University Tempe AZ USA. Department of Pediatrics University of California San Diego La Jolla CA USA. Department of Computer Science and Engineering Jacobs School of Engineering University of California San Diego La Jolla CA USA. Department of Bioengineering University of California San Diego La Jolla CA USA. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu. Department of Computer Science and Engineering Jacobs School of Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu.

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Benchmark problems for transcranial ultrasound simulation: Intercomparison of compressional wave models

arXiv

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arXiv 2022年

作者： Aubry, Jean-Francois Bates, Oscar Boehm, Christian Pauly, Kim Butts Christensen, Douglas Cueto, Carlos Gélat, Pierre Guasch, Lluis Jaros, Jiri Jing, Yun Jones, Rebecca Li, Ningrui Marty, Patrick Montanaro, Hazael Neufeld, Esra Pichardo, Samuel Pinton, Gianmarco Pulkkinen, Aki Stanziola, Antonio Thielscher, Axel Treeby, Bradley Van't Wout, Elwin Physics for Medicine Paris INSERM U1273 ESPCI Paris PSL University CNRS UMR 8063 France Department of Bioengineering Imperial College London Exhibition Road LondonSW7 2AZ United Kingdom Institute of Geophysics ETH Zürich Sonneggstrasse 5 Zürich8092 Switzerland Department of Radiology Stanford University StanfordCA United States Department of Biomedical Engineering Department of Electrical and Computer Engineering University of Utah United States Department of Surgical Biotechnology Division of Surgery and Interventional Science University College London LondonNW3 2PF United Kingdom Earth Science and Engineering Department Imperial College London London United Kingdom Centre of Excellence IT4Innovations Faculty of Information Technology Brno University of Technology Bozetechova 2 Brno612 00 Czech Republic Graduate Program in Acoustics The Pennsylvania State University University Park PA16802 United States Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill North Carolina State University NC United States Department of Electrical Engineering Stanford University StanfordCA United States Zurich Switzerland Laboratory for Acoustics / Noise control Empa Swiss Federal Laboratories for Materials Science and Technology Dubendorf Switzerland Zurich Switzerland Radiology and Clinical Neurosciences Departments Cumming School of Medicine University of Calgary Canada Department of Applied Physics University of Eastern Finland Kuopio70211 Finland Department of Medical Physics and Biomedical Engineering University College London Gower Street LondonWC1E 6BT United Kingdom Technical University of Denmark Denmark Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre Denmark Institute for Mathematical and Computational Engineering School of Engineering and Faculty of Mathematics Pontificia Universidad Catolica de Chile Santiago Chile

Computational models of acoustic wave propagation are frequently used in transcranial ultrasound therapy, for example, to calculate the intracranial pressure field or to calculate phase delays to correct for skull distortions. To allow intercomparison between the different modeling tools and techniques used by the community, an international working group was convened to formulate a set of numerical benchmarks. Here, these benchmarks are presented, along with intercomparison results. Nine different benchmarks of increasing geometric complexity are defined. These include a single-layer planar bone immersed in water, a multi-layer bone, and a whole skull. Two transducer configurations are considered (a focused bowl and a plane piston), giving a total of 18 permutations of the benchmarks. Eleven different modeling tools are used to compute the benchmark results. The models span a wide range of numerical techniques, including the finite-difference time-domain method, angular-spectrum method, pseudospectral method, boundary-element method, and spectral-element method. Good agreement is found between the models, particularly for the position, size, and magnitude of the acoustic focus within the skull. When comparing results for each model with every other model in a cross comparison, the median values for each benchmark for the difference in focal pressure and position are less than 10% and 1 mm, respectively. The benchmark definitions, model results, and intercomparison codes are freely available to facilitate further comparisons. Copyright © 2022, The Authors. All rights reserved.

关键词： Bone

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Generative Adversarial Networks Enable Cross-Modality Super-Resolution in Fluorescence Microscopy

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Microscopy and Microanalysis 2019年第S2期25卷 1228-1229页

作者： Hongda Wang Yair Rivenson Yiyin Jin Zhensong Wei Ronald Gao Harun Günaydın Laurent A. Bentolila Comert Kural Aydogan Ozcan Electrical & Computer Engineering Department University of California Los Angeles Los Angeles USA Bioengineering Department University of California Los Angeles Los Angeles USA California NanoSystems Institute University of California Los Angeles Los Angeles USA Computer Science Department University of California Los Angeles Los Angeles USA Department of Chemistry and Biochemistry University of California Los Angeles Los Angeles USA Department of Physics Ohio State University Columbus USA Biophysics Graduate Program Ohio State University Columbus USA Department of Surgery David Geffen School of Medicine University of California Los Angeles Los Angeles USA.

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Structuring stress for active materials control

arXiv

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arXiv 2019年

作者： Zhang, Rui Redford, Steven A. Ruijgrok, Paul V. Kumar, Nitin Mozaffari, Ali Zemsky, Sasha Dinner, Aaron R. Vitelli, Vincenzo Bryant, Zev Gardel, Margaret L. de Pablo, Juan J. Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States The graduate program in Biophysical Sciences University of Chicago ChicagoIL60637 United States James Franck Institute University of Chicago ChicagoIL60637 United States Department of Bioengineering Stanford University StanfordCA94305 United States Program in Biophysics Stanford University StanfordCA94305 United States Department of Chemistry University of Chicago ChicagoIL60637 United States Department of Physics University of Chicago ChicagoIL60637 United States Department of Structural Biology Stanford University Medical Center StanfordCA94305 United States Center for Molecular Engineering Argonne National Laboratory LemontIL60439 United States

Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to demonstrate that topological defects can be generated at will, and then constrained to move along specified trajectories, by inducing local stresses in an otherwise passive material. These results provide a foundation for design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light. Copyright © 2019, The Authors. All rights reserved.

关键词： Nematic liquid crystals

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Drug Delivery: Injectable Drug‐Releasing Microporous Annealed Particle Scaffolds for Treating Myocardial Infarction (Adv. Funct. Mater. 43/2020)

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Advanced Functional Materials 2020年第43期30卷

作者： Jun Fang Jaekyung Koh Qizhi Fang Huiliang Qiu Maani M. Archang Mohammad Mahdi Hasani‐Sadrabadi Hiromi Miwa Xintong Zhong Richard Sievers Dong‐Wei Gao Randall Lee Dino Di Carlo Song Li Department of Bioengineering University of California Los Angeles CA 90095 USA Department of Medicine University of California Los Angeles CA 90095 USA Department of Medicine Cardiovascular Research Institute and Institute for Regeneration Medicine University of California San Francisco CA 94143 USA California NanoSystems Institute (CNSI) University of California Los Angeles CA 90095 USA UC Berkeley‐UCSF Graduate Program in Bioengineering University of California San Francisco San Francisco CA 94158 USA Department of Mechanical and Aerospace Engineering University of California Los Angeles CA 90095 USA Jonsson Comprehensive Cancer Centre University of California Los Angeles CA 90024 USA

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Utility of plasma GFAP as a secondary endpoint for clinical trials in Alzheimer's disease

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The journal of prevention of Alzheimer's disease 2025年 100205页

作者： Sarah Abbas Pamela C L Ferreira Bruna Bellaver Guilherme Povala Francieli Rohden Cristiano Schaffer Aguzzoli Hussein Zalzale João Pedro Ferrari-Souza Douglas T Leffa Firoza Z Lussier Carolina Soares Guilherme Bauer-Negrini Markley Silva Oliveira-Junior Matheus Scarpatto Rodrigues Pampa Saha Emma Ruppert Marina Scop Medeiros Cécile Tissot Joseph Therriault Nesrine Rahmouni Stijn Servaes Andrea L Benedet Nicholas J Ashton Dana L Tudorascu Serge Gauthier Helmet Karim Chang Hyung Hong Hyun Woong Roh Eduardo R Zimmer Thomas K Karikari Henrik Zetterberg Kaj Blennow Anum Saeed Sang Joon Son Pedro Rosa-Neto Tharick Pascoal Department of Psychiatry School of Medicine University of Pittsburgh Pittsburgh PA USA. Department of Psychiatry School of Medicine University of Pittsburgh Pittsburgh PA USA Graduate Program in Biological Sciences: Biochemistry Universidade Federal do Rio Grande do Sul Porto Alegre RS Brazil. Brain Institute of Rio Grande do Sul PUCRS 6690 Ipiranga Avenue 90610-000 Porto Alegre RS Brazil. Translational Neuroimaging Laboratory McGill University Research Centre for Studies in Aging Alzheimer's Disease Research Unit Douglas Research Institute Le Centre intégré universitaire de santé et de services sociaux (CIUSSS) de l'Ouest-de-l'Île-de-Montréal Canada Department of Neurology and Neurosurgery Psychiatry and Pharmacology and Therapeutics McGill University Montreal QC Canada Department of Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Neurology and Neurosurgery Psychiatry and Pharmacology and Therapeutics McGill University Montreal QC Canada. Translational Neuroimaging Laboratory McGill University Research Centre for Studies in Aging Alzheimer's Disease Research Unit Douglas Research Institute Le Centre intégré universitaire de santé et de services sociaux (CIUSSS) de l'Ouest-de-l'Île-de-Montréal Canada. Department of Psychiatry and Neurochemistry The Sahlgrenska Academy at the University of Gothenburg Mölndal Sweden Clinical Neurochemistry Laboratory Sahlgrenska University Hospital Gothenburg Sweden. Clinical Neurochemistry Laboratory Sahlgrenska University Hospital Gothenburg Sweden Wallenberg Centre for Molecular and Translational Medicine University of Gothenburg Gothenburg Sweden Department of Old Age Psychiatry Institute of Psychiatry Psychology & Neuroscience King's College London London UK. Department of Bioengineering University of Pittsburgh Pittsburgh PA USA. Department of Psychiatry Ajou University School of Medicine Suwon Republic of Korea South Korea. Graduate Program

BACKGROUND:Clinical trials have recently incorporated plasma glial fibrillary acidic protein (GFAP) as an exploratory endpoint. To include plasma GFAP as a secondary endpoint, it is essential to characterize its longitudinal progression in target populations. OBJECTIVE:To evaluate the potential use of plasma GFAP changes as a secondary endpoint in Alzheimer's disease trials. METHODS:We longitudinally evaluated plasma GFAP in individuals with amyloid-beta (Aβ)-PET scans at baseline in three well-characterized cohorts. Cox proportional hazards regression tested the association between changes in plasma GFAP and cognitive function. Analysis of the 95 % confidence interval of annualized change in plasma GFAP provided statistical inference for a significant longitudinal change. Effect size was calculated as the group mean divided by the standard deviation (SD). We estimated the sample size needed to test a 25% drug effect with 80% power on reducing changes in GFAP. RESULTS:We assessed 487 individuals [176 cognitively unimpaired (CU; 29% Aβ positive) and 311 cognitively impaired (CI; 51% Aβ positive)] with some degree of cerebrovascular disease (Fazekas 1-3), over a mean (SD) follow-up of 1.84 (0.46) years. Changes in plasma GFAP were significantly associated with worsening in Clinical Dementia Rating sum of boxes (CDR-SB) score across the population (p < 0.0001). In CU, only Aβ positive individuals showed significant changes in GFAP (p < 0.001). On the other hand, both CI Aβ positive and negative individuals showed longitudinal progression in GFAP levels (p < 0.0001). The effect size of changes in plasma GFAP was higher in CU Aβ positive (0.44), followed by CI Aβ positive (0.42) and CI Aβ negative (0.38). Clinical trials focusing on CU Aβ positive would require 1320 individuals per study arm, while focusing on CI Aβ positive would require 1440 individuals per study arm. CONCLUSION:Plasma GFAP increased in parallel with cognitive decline, making it a candidate for monitor

关键词： Biomarker Clinical trial Plasma GFAP

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