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arXiv 2023年

作者： Jeon, Hyeongseon Xie, Juan Jeon, Yeseul Jung, Kyeong Joo Gupta, Arkobrato Chang, Won Chung, Dongjun Department of Biomedical Informatics The Ohio State University ColumbusOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH43210 United States The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Department of Statistics and Data Science Yonsei University Seoul Korea Republic of Department of Applied Statistics Yonsei University Seoul Korea Republic of Department of Computer Science and Engineering The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct characteristics. In order to guarantee biologically meaningful findings using transcriptomic experiments, it is important to consider various experimental factors in a systematic way through statistical power analysis. In this paper, we review and discuss the power analysis for three types of gene expression profiling technologies from a practical standpoint, including bulk RNA-seq, single-cell RNA-seq, and high-throughput spatial transcriptomics. Specifically, we describe the existing power analysis tools for each research objective for each of the bulk RNA-seq and scRNA-seq experiments, along with recommendations. On the other hand, since there are no power analysis tools for high-throughput spatial transcriptomics at this point, we instead investigate the factors that can influence power analysis. © 2023, CC BY-NC-ND.

关键词： RNA

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Author Correction: SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs

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EXPERIMENTAL AND MOLECULAR MEDICINE 2023年第12期55卷 2609-2609页

作者： Kim, Junsoo Youn, Daehwa Choi, Seunghoon Lee, Youn Woo Sumberzul, Dulguun Yoon, Jeongeun Lee, Hanju Bae, Jong Woo Noh, Hyuna On, Dain Hong, Seung-Min An, Se-Hee Jang, Hui Jeong Kim, Seo Yeon Kim, Young Been Hwang, Ji-Yeon Lee, Hyo-Jung Kim, Hong Bin Park, Jun Won Yun, Jun-Won Shin, Jeon-Soo Seo, Jun-Young Nam, Ki Taek Choi, Kang-Seuk Lee, Ho-Young Chang, Hyeshik Seong, Je Kyung Cho, Jun Center for RNA Research Institute for Basic Science (IBS) Seoul National University Seoul Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea Department of Biomedical Science and Engineering Gwangju Institute of Science and Technology (GIST) Gwangju Republic of Korea Korea Mouse Phenotyping Center (KMPC) Seoul National University Seoul Republic of Korea Laboratory of Developmental Biology and Genomics Research Institute for Veterinary Science and BK 21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul Republic of Korea Department of Nuclear Medicine Seoul National University Bundang Hospital Seongnam Republic of Korea School of Biological Sciences Seoul National University Seoul Republic of Korea Laboratory of Avian Diseases Research Institute for Veterinary Science and BK 21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul Republic of Korea Preclinical Research Center Seoul National University Bundang Hospital Seongnam Republic of Korea Department of Periodontology Section of Dentistry Seoul National University Bundang Hospital Seongnam Republic of Korea Department of Internal Medicine Seoul National University Bundang Hospital Seoul National University College of Medicine Seongnam Republic of Korea Division of Biomedical Convergence College of Biomedical Science Kangwon National University ChunCheon Republic of Korea Laboratory of Veterinary Toxicology College of Veterinary Medicine Seoul National University Seoul Republic of Korea Severance Biomedical Science Institute Graduate School of Medical Science Brain Korea 21 Project Yonsei University College of Medicine Seoul Republic of Korea Department of Nuclear Medicine Seoul National University College of Medicine Seoul Republic of Korea Interdisciplinary Program and BIO MAX Institute Seoul National University

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Electron Tomography Finds Three-Dimensional Chromatin Packing Domain Structure in Single Cell Different from Topological Associated Domains

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Li, Wing Shun Carter, Lucas Almassalha, Luay Pujadas, Emily Carignano, Marcelo Bleher, Reiner dos Reis, Roberto Backman, Vadim Dravid, Vinayak Applied Physics Program Northwestern University Evanston IL USA Department of Biomedical Engineering Northwestern University Evanston IL USA IBIS Interdisciplinary Biological Sciences Graduate Program Northwestern University Evanston IL USA Department of Materials Sciences and Engineering Northwestern University Evanston IL USA Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center Northwestern University Evanston IL USA International Institute of Nanotechnology Northwestern University Evanston IL USA

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Cross-modal attention for MRI and ultrasound volume registration

arXiv

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arXiv 2021年

作者： Song, Xinrui Guo, Hengtao Xu, Xuanang Chao, Hanqing Xu, Sheng Turkbey, Baris Wood, Bradford J. Wang, Ge Yan, Pingkun Department of Biomedical Engineering Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute TroyNY12180 United States Center for Interventional Oncology Radiology and Imaging Sciences National Institutes of Health BethesdaMD20892 United States Molecular Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20892 United States

Prostate cancer biopsy benefits from accurate fusion of transrectal ultrasound (TRUS) and magnetic resonance (MR) images. In the past few years, convolutional neural networks (CNNs) have been proved powerful in extracting image features crucial for image registration. However, challenging applications and recent advances in computer vision suggest that CNNs are quite limited in its ability to understand spatial correspondence between features, a task in which the self-attention mechanism excels. This paper aims to develop a self-attention mechanism specifically for cross-modal image registration. Our proposed crossmodal attention block effectively maps each of the features in one volume to all features in the corresponding volume. Our experimental results demonstrate that a CNN network designed with the cross-modal attention block embedded outperforms an advanced CNN network 10 times of its size. We also incorporated visualization techniques to improve the interpretability of our network. The source code of our work is available at https://***/DIAL-RPI/Attention-Reg. Copyright © 2021, The Authors. All rights reserved.

关键词： Urology

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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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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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Correction: Analysis of Photoplethysmography-Based Surgical Pain Severity Assessment Markers

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Journal of Electrical engineering & Technology 2024年第8期19卷 5439-5439页

作者： Ryu, Gayeon Choi, Jae Moon Lee, Jaehyung Seok, Hyeon Seok Shin, Hangsik Choi, Byung-Moon Department of Digital Medicine Brain Korea 21 Project Asan Medical Center University of Ulsan College of Medicine Seoul Republic of Korea Department of Anesthesiology and Pain Medicine Asan Medical Center University of Ulsan College of Medicine Seoul Republic of Korea Interdisciplinary Program of Biomedical Engineering Graduate School Chonnam National University Yeosu Republic of Korea

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An immersed peridynamics model of fluid-structure interaction accounting for material damage and failure

arXiv

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arXiv 2022年

作者： Kim, Keon Ho Bhalla, Amneet P.S. Griffith, Boyce E. Department of Mathematics University of North Carolina Chapel HillNC United States Department of Mechanical Engineering San Diego State University San DiegoCA United States Departments of Mathematics Applied Physical Sciences and Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina Chapel HillNC United States McAllister Heart Institute University of North Carolina Chapel HillNC United States

This paper develops and benchmarks an immersed peridynamics method to simulate the deformation, damage, and failure of hyperelastic materials within a fluid-structure interaction framework. The immersed peridynamics method describes an incompressible structure immersed in a viscous incompressible fluid. It expresses the momentum equation and incompressibility constraint in Eulerian form, and it describes the structural motion and resultant forces in Lagrangian form. Coupling between Eulerian and Lagrangian variables is achieved by integral transforms with Dirac delta function kernels, as in standard immersed boundary methods. The major difference between our approach and conventional immersed boundary methods is that we use peridynamics, instead of classical continuum mechanics, to determine the structural forces. We focus on non-ordinary state-based peridynamic material descriptions that allow us to use a constitutive correspondence framework that can leverage well-characterized nonlinear constitutive models of soft materials. The convergence and accuracy of our approach are compared to both conventional and immersed finite element methods using widely used benchmark problems of nonlinear incompressible elasticity. We demonstrate that the immersed peridynamics method yields comparable accuracy with similar numbers of structural degrees of freedom for several choices of the size of the peridynamic horizon. We also demonstrate that the method can generate grid-converged simulations of fluid-driven material damage growth, crack formation and propagation, and rupture under large deformations. © 2022, CC BY-SA.

关键词： Continuum mechanics

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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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Laryngeal Hypersensitivity From the Perspective of Pain Science: An Integrative Review of Empirical Studies on Associated Factors and Processes

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Journal of Voice 2025年

作者： Saint-Jules, William Massé-Alarie, Hugo Li-Jessen, Nicole Y.K. Desjardins, Maude Faculty of Medicine Université Laval Quebec City QC Canada Faculty of Medicine and Health Sciences University of Sherbrooke Sherbrooke QC Canada Center for Interdisciplinary Research in Rehabilitation and Social Inclusion Quebec City QC Canada School of Rehabilitation Sciences Université Laval Quebec City QC Canada School of Communication Sciences and Disorders McGill University Montreal QC Canada Department of Biomedical Engineering McGill University Montreal QC Canada The Centre for Research on Brain Language and Music McGill University Montreal QC Canada Department of Otolaryngology - Head and Neck Surgery McGill University Montreal QC Canada Translational Research in Respiratory Diseases Program Research Institute of McGill University Health Center Montreal QC Canada

Objective: Laryngeal hypersensitivity (LHS) is a state of heightened sensorimotor response to stimuli in the upper airway. Although its clinical picture is becoming progressively clearer with recent research progress, specificities about its associated factors and processes remain to be clarified. The aim of this integrative review was to synthesize published empirical data from human studies on LHS, focusing on related factors and pathophysiology. Study Design and Data Sources: Integrative review of the literature;Pubmed, EMBASE, and Web of Science. Methods: Keywords associated with the following three main concepts were used to query databases: (1) manifestations potentially associated with an irritable larynx (dysphonia, inducible laryngeal obstruction (ILO), chronic cough, and globus);(2) hypersensitivity;and (3) pathophysiology. Peer-reviewed studies in English providing empirical original research data on the pathophysiology of LHS were included, with no restriction based on study design. Results: In total, 54 papers met the inclusion criteria. Factors potentially associated with LHS were identified, namely (1) psychological and lifestyle factors, (2) upper airway inflammation and injuries from exogenous/endogenous irritants, infections, or mucosal atrophy, (3) sex hormones, (4) metabolic abnormalities, and (5) aberrant respiratory behavior. Given the parallels between pain-related mechanisms and suggested LHS mechanisms, processes identified as putatively contributing to LHS were categorized in light of the current pain literature. Findings suggest that LHS may stem from a peripheral tissue insult, a neuropathic insult, and/or maladaptive neuroplasticity. Gaps in the literature were identified, in part driven by an uneven repartition of research across the various alleged manifestations of LHS. In fact, a large majority of studies pertained to chronic cough, with very few addressing muscle tension dysphonia, ILO, and globus. Conclusion: Future research can fo

关键词： Hypersensitivity—Chronic cough—Dysphonia—Inducible laryngeal obstruction—Irritable larynx

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