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SSRN 2022年

作者： Kim, Yonghwan Lee, Dongtak Seo, Youngjun Jung, Hyo Gi Jang, Jae Won Park, Dongsung Kim, Insu Lee, Gyudo Hwang, Kyo Seon Kim, Seung-Hyun Lee, Sang Won Lee, Jeong Hoon Yoon, Dae Sung School of Biomedical Engineering Korea University Seoul02841 Korea Republic of Interdisciplinary Program in Precision Public Health Korea University Seoul02841 Korea Republic of Department of Clinical Pharmacology and Therapeutics College of Medicine Kyung Hee University Seoul02447 Korea Republic of Department of Biotechnology and Bioinformatics Korea University Sejong30019 Korea Republic of Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology Korea University Sejong30019 Korea Republic of School of Engineering Brown University ProvidenceRI02912 United States Department of Electrical Engineering and Computer Science University of California IrvineCA92697 United States Department of Electrical Engineering Kwangwoon University Seoul01897 Korea Republic of Astrion Inc Seoul02841 Korea Republic of

Cholera is a highly contagious and lethal waterborne disease induced by an infection with Vibrio cholerae (V. cholerae) secreting cholera toxin (CTx). Cholera toxin subunit B (CTxB) from the CTx specifically binds with monosialo-tetra-hexosyl-ganglioside (GM1) found on the exterior cell membrane of an enterocyte. Owing to the pathological process of CTx, a biomimetic electrochemical biosensor (CCB) was developed by applying GM1-expressing Caco-2 cell membrane (CCM) on the electrode surface of the biosensor for CTx detection. Briefly, the electrode surface was functionalized with CCM using the vesicle fusion method. The specific binding between GM1 and CTxB on the electrode surface was verified using confocal laser scanning microscopy and atomic force microscopy. The CTxB detection performances of the CCB, including sensitivity, selectivity, and long-term stability, were determined using electrochemical impedance spectroscopy (EIS). Based on the results, the CCB had an excellent limit of detection of ~11.46 nM and a detection range spanning 100 ng/mL - 1 mg/mL. Further, the CCB had high selectivity for the CTxB compared to different interfering molecules, which are abundant constituents of intestinal fluid and fecal matter in the human body. The long-term stability of the CCBs was also verified for 3 weeks using EIS. Overall, the CCB was found to have an excellent potential for application to point-of-care and cost-effective testing for CTxB detection in developing countries. © 2022, The Authors. All rights reserved.

关键词： Electrochemical impedance spectroscopy

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High-temperature strain-mediated oxidation of 2D MoS2

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Materials and Design 2023年 236卷

作者： Rouhan, Mehdi Hobley, Jonathan Lin, Kuang-I Hofmann, Mario Yao, Yu-Chi Chang, Yung-Huang Carpick, Robert William Schall, J. David Jeng, Yeau-Ren Department of Biomedical Engineering National Cheng Kung University 1 University Road Tainan City70101 Taiwan Core Facility Center National Cheng Kung University 1 University Road Tainan City70101 Taiwan Department of Physics National Taiwan University Taipei106 Taiwan Bachelor Program in Interdisciplinary Studies National Yunlin University of Science and Technology 123 University Road Yunlin64002 Taiwan Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania 220 S. 33rd St. PhiladelphiaPA19104-6315 United States Department of Mechanical Engineering North Carolina Agricultural and Technical State University GreensboroNC27411 United States Tainan70101 Taiwan

MoS2 is 2D material applicable for electronics, photo-detectors, light-emitting diodes, and solar cells. Since these applications operate at elevated temperatures, determining and controlling the environmental stability of MoS2 is essential. This study uses Raman spectroscopic experiments at elevated temperatures to observe reversible and irreversible changes in 2D MoS2 films with varying thickness, morphology, and substrate to explore the limits of its thermal stability. Molecular dynamics simulations and in-situ X-ray diffraction confirm that thermal expansion causes the Raman reversible spectral shifts. Further analysis reveals irreversible spectral shifts associated with oxidation and strain effects caused by oxidation with two distinct modes. The former is due to the general homogenous thinning of layers from the top layer down through randomly spaced sulfur vacancies. The latter is due to inhomogeneous oxidation, which known to occur as localized pitting at grain boundaries, void formation from nucleation centers, or stress corrosion cracking starting from edges under strain. Segregation of doping and strain contributions confirms higher strain in the edges. Annealing increases the spread of the strain distribution. These results highlight the critical role of strain, resulting from thermal expansion coefficient mismatch between substrates and 2D MoS2 films, on their environmental stability. © 2023 The Authors

关键词： Raman spectroscopy

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Extracellular Matrix Protein Composition Dynamically Changes During Murine Forelimb Development

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SSRN 2023年

作者： Jacobson, Kathryn R. Saleh, Aya M. Lipp, Sarah N. Tian, Chengzhe Watson, Audrey R. Luetkemeyer, Callan M. Ocken, Alexander R. Spencer, Sabrina L. Kinzer-Ursem, Tamara L. Calve, Sarah Purdue University Interdisciplinary Life Science Program Purdue University West LafayetteIN47907 United States Weldon School of Biomedical Engineering Purdue University West LafayetteIN47907 United States The Indiana University School of Medicine IndianapolisIN46202 United States Department of Biochemistry University of Colorado Boulder BoulderCO80303 United States BioFrontiers Institute University of Colorado Boulder BoulderCO80303 United States Austrian Academy of Sciences Vienna Austria Paul M. Rady Department of Mechanical Engineering University of Colorado Boulder BoulderCO80309 United States Paul M. Rady Department of Mechanical Engineering United States

The extracellular matrix (ECM) is an integral part of multicellular organisms, connecting different cell layers and tissue types. During morphogenesis and growth, tissues undergo substantial reorganization. While it is intuitive that the ECM remodels in concert, little is known regarding how matrix composition and organization change during development. Here, we quantified ECM protein dynamics in the murine forelimb during appendicular musculoskeletal morphogenesis (embryonic days 11.5-14.5) using tissue fractionation, bioorthogonal non-canonical amino acid tagging, and mass spectrometry. Our analyses indicated that ECM protein (matrisome) composition in the embryonic forelimb changed as a function of development and growth, was distinct from other developing organs (brain), and was altered in a model of disease (osteogenesis imperfecta murine). Additionally, the tissue distribution for select matrisome were assessed via immunohistochemistry in the wild-type embryonic and postnatal musculoskeletal system, which did not directly correlate with single-cell transcriptomic expression profiles, indicating the importance for investigating the proteome in addition to the transcriptome. This resource will guide future research investigating the role of the matrisome during complex tissue development. © 2023, The Authors. All rights reserved.

关键词： Mass spectrometry

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Development of novel gene carrier using modified nano hydroxyapatite derived from equine bone for osteogenic differentiation of dental pulp stem cells

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Bioactive Materials 2021年第9期6卷 2742-2751页

作者： Myung Chul Lee Hoon Seonwoo Kyoung Je Jang Shambhavi Pandey Jaewoon Lim Sangbae Park Jae Eun Kim Yun-Hoon Choung Pankaj Garg Jong Hoon Chung Department of Biosystems&Biomaterials Science and Engineering Seoul National UniversitySeoul08826Republic of Korea Department of Biosystems Engineering Seoul National UniversitySeoul08826Republic of Korea Department of Industrial Machinery Engineering Sunchon National University315 Maegok-dongSunchon57922Republic of Korea Interdisciplinary Program in IT-Bio Convergence System Sunchon National UniversitySuncheon57922Republic of Korea Division of Agro-system Engineering Gyeongsang National University501 Jinju-daeroJinju52828Republic of Korea Institute of Agriculture&Life Science Gyeongsang National UniversityJinju52828Republic of Korea Research Institute for Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Department of Otolaryngology Ajou University School of MedicineSuwon16499Republic of Korea Ajou University Graduate School of Medicine Bk21 Plus Research Center for Biomedical SciencesSuwon16499Republic of Korea BK21 Global Smart Farm Educational Research Center Seoul National UniversitySeoul08826Republic of Korea

Hydroxyapatite(HA)is a representative substance that induces bone *** research team extracted nanohydroxyapatite(EH)from natural resources,especially equine bones,and developed it as a molecular biological ***(PEI)was used to coat the EH to develop a gene *** verify that PEI is well coated in the EH,we first observed the morphology and dispersity of PEI-coated EH(pEH)by electron *** pEH particles were well distributed,while only the EH particles were not distributed and ***,the existence of nitrogen elements of PEI on the surface of the pEH was confirmed by EDS,calcium concentration measurement and fourier transform infrared spectroscopy(FT-IR).Additionally,the pEH was confirmed to have a more positive charge than the 25 kD PEI by comparing the zeta *** a result of pGL3 transfection,pEH was better able to transport genes to cells than 25 kD *** verification as a gene carrier for pEH,we induced osteogenic differentiation of DPSCs by loading the BMP-2 gene in pEH(BMP-2/pEH)and delivering it to the *** a result,it was confirmed that osteogenic differentiation was promoted by showing that the expression of osteopontin(OPN),osteocalcin(OCN),and runt-related transcription factor 2(RUNX2)was significantly increased in the group treated with BMP-2/*** conclusion,we have not only developed a novel nonviral gene carrier that is better performing and less toxic than 25 kD PEI by modifying natural HA(the agricultural byproduct)but also proved that bone differentiation can be effectively promoted by delivering BMP-2 with pEH to stem cells.

关键词： Nanocomposites biomedical applications Hydroxyapatite Polyethyleneimine Gene carrier Osteogenic differentiation

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Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

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Nucleic acids research 2023年第13期51卷 6578-6592页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Bo-Jia Chen Yu-Te Lin Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Program in Integrative & Complex Diseases Department of Nutrition Texas A&M University College Station TX 77843 USA. Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

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Recent Advancements in engineering Strategies for Manipulating Neural Stem Cell Behavior

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Current tissue microenvironment reports 2020年第2期1卷 41-47页

作者： Brian J O'Grady Ethan S Lippmann Department of Chemical and Biomolecular Engineering Vanderbilt University Nashville TN USA. Department of Biomedical Engineering Vanderbilt University Nashville TN USA. Vanderbilt Brain Institute Vanderbilt University Nashville TN USA. Interdisciplinary Materials Science Program Vanderbilt University Nashville TN USA.

PURPOSE OF REVIEW:Stem cells are exquisitely sensitive to biophysical and biochemical cues within the native microenvironment. This review focuses on emerging strategies to manipulate neural cell behavior using these influences in three-dimensional (3D) culture systems. RECENT FINDINGS:Traditional systems for neural cell differentiation typically produce heterogeneous populations with limited diversity rather than the complex, organized tissue structures observed . Advancements in developing engineering tools to direct neural cell fates can enable new applications in basic research, disease modeling, and regenerative medicine. SUMMARY:This review article highlights engineering strategies that facilitate controlled presentation of biophysical and biochemical cues to guide differentiation and impart desired phenotypes on neural cell populations. Specific highlighted examples include engineered biomaterials and microfluidic platforms for spatiotemporal control over the presentation of morphogen gradients.

关键词： biomaterial morphogen gradient neural stem cell stem cell differentiation

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Plasma-Derived Nanoclusters for Site-Specific Multimodality Photo/Magnetic Thrombus Theranostics

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Advanced Healthcare Materials 2023年第28期12卷 e2301504页

作者： Liu, Chia-Hung Liu, Ming-Che Jheng, Pei-Ru Yu, Jiashing Fan, Yu-Jui Liang, Jia-Wei Hsiao, Yu-Cheng Chiang, Chih-Wei Bolouki, Nima Lee, Jyh-Wei Hsieh, Jang-Hsing Mansel, Bradley W Chen, Yan-Ting Nguyen, Hieu Trung Chuang, Er-Yuan Department of Urology School of Medicine College of Medicine Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan TMU Research Center of Urology and Kidney Taipei Medical University 250 Wu-Hsing Street Taipei11031 Taiwan Department of Urology Shuang Ho Hospital Taipei Medical University 291 Zhongzheng Road Zhonghe District New Taipei City23561 Taiwan Clinical Research Center Taipei Medical University Hospital Taipei11031 Taiwan School of Dental Technology College of Oral Medicine Taipei Medical University Taipei11031 Taiwan Graduate Institute of Biomedical Materials and Tissue Engineering International Ph.D. Program in Biomedical Engineering Graduate Institute of Biomedical Optomechatronics School of Biomedical Engineering Research Center of Biomedical Device Innovation Entrepreneurship Education Center College of Interdisciplinary Studies Taipei Medical University Taipei11031 Taiwan Department of Chemical Engineering College of Engineering National Taiwan University Taipei106 Taiwan Department of Orthopedics Taipei Medical University Taipei11031 Taiwan Department of Orthopedics Taipei Medical University Hospital Taipei11031 Taiwan Department of Physical Electronics Faculty of Science Masaryk University Brno60177 Czech Republic Department of Materials Engineering Ming Chi University of Technology New Taipei City24301 Taiwan Center for Plasma and Thin Film Technologies Ming Chi University of Technology New Taipei City24301 Taiwan National Synchrotron Radiation Research Center Hsinchu Science Park Hsinchu30076 Taiwan Department of Orthopedics and Trauma Faculty of Medicine University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City700000 Viet Nam Cell Physiology and Molecular Image Research Center Taipei Medical University Wan Fang Hospital Taipei11696 Taiwan Precision Medicine and Translational Cancer Research Center Taipei Medical University Hospital Taipei11031 Taiwan

Traditional thrombolytic therapeutics for vascular blockage are affected by their limited penetration into thrombi, associated off-target side effects, and low bioavailability, leading to insufficient thrombolytic efficacy. It is hypothesized that these limitations can be overcome by the precisely controlled and targeted delivery of thrombolytic therapeutics. A theranostic platform is developed that is biocompatible, fluorescent, magnetic, and well-characterized, with multiple targeting modes. This multimodal theranostic system can be remotely visualized and magnetically guided toward thrombi, noninvasively irradiated by near-infrared (NIR) phototherapies, and remotely activated by actuated magnets for additional mechanical therapy. Magnetic guidance can also improve the penetration of nanomedicines into thrombi. In a mouse model of thrombosis, the thrombosis residues are reduced by ≈80% and with no risk of side effects or of secondary embolization. This strategy not only enables the progression of thrombolysis but also accelerates the lysis rate, thereby facilitating its prospective use in time-critical thrombolytic treatment. © 2023 Wiley-VCH GmbH.

关键词： Diseases

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Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors

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Biophysical Reviews 2020年第2期12卷 323-332页

作者： Murata, Takeshi Yasuda, Satoshi Hayashi, Tomohiko Kinoshita, Masahiro Graduate School of Science Chiba University 1-33 Yayoi-cho Inage Chiba 263-8522 Japan Molecular Chirality Research Center Chiba University 1-33 Yayoi-cho Inage Chiba 263-8522 Japan Institute of Advanced Energy Kyoto University Uji Kyoto 611-0011 Japan Present address: Interdisciplinary Program of Biomedical Engineering Assistive Technology and Art and Sports Sciences Faculty of Engineering Niigata University 8050 Ikarashi 2-no-cho Nishi-ku Niigata 950-2181 Japan

Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor;a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen;and all the possible mutations can be examined with moderate computational effort. It was shown that mutating the residue at a position of N_BW = 3.39 (N_BW is the Ballesteros-Weinstein number) to Arg or Lys leads to the stabilization of significantly many different GPCRs of class A in the inactive state. Up to now, we have been successful in stabilizing several GPCRs and newly solving three-dimensional structures for the muscarinic acetylcholine receptor 2 (M2R), prostaglandin E receptor 4 (EP4), and serotonin 2A receptor (5-HT_2AR) using X-ray crystallography. The subjects to be pursued in future studies are also discussed. © 2020, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： G-protein-coupled receptor Integral equation theory Lipid bilayer Membrane protein Morphometric approach Protein folding Solvation thermodynamics Thermostabilizing mutation

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The mitochondrial genome data of the Capsicum annuum cv. Dempsey (Solanaceae)

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Data in Brief 2025年 60卷

作者： Seona Yun Junseong Bae Jeongbin Park Hyeran Kim Institute of Life Sciences Kangwon National University Chuncheon Republic of Korea Interdisciplinary Program of Genomic Data Science Pusan National University Yangsan Republic of Korea Graduate School of Medical AI Pusan National University Yangsan Republic of Korea School of Biomedical Convergence Engineering Pusan National University Yangsan Republic of Korea Department of Biological Sciences Kangwon National University Chuncheon Republic of Korea

Capsicum annuum L. (1753), commonly known as pepper, holds significant economic value as one of the globally cultivated horticultural crops. This study presents the mitochondrial genome of the sweet pepper C. annuum cv. Dempsey, assembled using Illumina NovaSeq data. The circular mitogenome is 577,453 base pairs (bp) in length and includes 36 protein-coding genes, three ribosomal RNA genes, and 43 transfer RNA genes. Phylogenetic analysis reveals that C. annuum is not monophyletic, with C. annuum cv. Dempsey identified as a sister to the hot pepper C. annuum cv. Jeju. This study provides as a valuable resource for comparative analyses of pepper mitogenomes, enhancing our understanding of the evolution and adaptive mechanisms of pepper species.

关键词： Capsicum annuum Sweet pepper Cultivar dempsey Mitogenome Phylogeny

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A Mechanized Pediatric Elbow Joint Powered by a De-Based Artificial Skeletal Muscle*

A Mechanized Pediatric Elbow Joint Powered by a De-Based Art...

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

作者： A. Behboodi C. DeSantis J. Lubsen S.C.K. Lee Venture Development Center University of Delaware Newark DE USA Mechanical Engineering Department University of Delaware Newark DE USA Departments of Physical Therapy Biomedical Engineering and Interdisciplinary Graduate Program in Biomechanics and Movement Science University of Delaware Newark DE USA

ISBN: (数字)9781728119908

ISBN: (纸本)9781728119915

To increase the acceptability of exoskeletons, there is growing attention toward finding an alternative soft actuator that can safely perform at close vicinity of the human body. In this study, we investigated the capability of the dielectric elastomer actuators (DEAs), for muscle-like actuation of rehabilitation robots. First, an artificial skeletal muscle was configured using commercially available stacked DEAs arranged in a 3×4 array of three parallel fibers consisting of four DEAs connected in series. The shortening and force generation capabilities of this artificial muscle were then measured. An alternate 3×5 version of this muscle was mounted on the forearm of an upper extremity phantom model to actuate its elbow joint. The actuation capability of this muscle was then tested under various tensile loads, 1 N to 4 N, placed at the center of mass of the forearm+hand of the phantom model. The active range of motion and angular velocity of the phantom model's tip of the hand were measured using a motion capture system. The 3×4 artificial muscle produced 30.47 N of force and 5.3 mm of maximum shortening. The 3×5 artificial muscle was capable of actuating the elbow flexion 19.5 o with 16.2 o /s angular velocity in the sagittal plane, under a 1 N tensile load. The active range of motion was substantially reduced as the tensile loads increased, which limits the capability of these muscles in the current upper extremity exoskeleton design.

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