arXiv - QuanBio - Tissues and Organs最新文献_第8页

Minimal cellular automaton model with heterogeneous cell sizes predicts epithelial colony growth 具有异质细胞大小的最小细胞自动机模型可预测上皮细胞集落的生长

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-12 DOI: arxiv-2403.07612

Steffen Lange, Jannik Schmied, Paul Willam, Anja Voss-Böhme

{"title":"Minimal cellular automaton model with heterogeneous cell sizes predicts epithelial colony growth","authors":"Steffen Lange, Jannik Schmied, Paul Willam, Anja Voss-Böhme","doi":"arxiv-2403.07612","DOIUrl":"https://doi.org/arxiv-2403.07612","url":null,"abstract":"Regulation of cell proliferation is a crucial aspect of tissue development\u0000and homeostasis and plays a major role in morphogenesis, wound healing, and\u0000tumor invasion. A phenomenon of such regulation is contact inhibition, which\u0000describes the dramatic slowing of proliferation, cell migration and individual\u0000cell growth when multiple cells are in contact with each other. While many\u0000physiological, molecular and genetic factors are known, the mechanism of\u0000contact inhibition is still not fully understood. In particular, the relevance\u0000of cellular signaling due to interfacial contact for contact inhibition is\u0000still debated. Cellular automata (CA) have been employed in the past as\u0000numerically efficient mathematical models to study the dynamics of cell\u0000ensembles, but they are not suitable to explore the origins of contact\u0000inhibition as such agent-based models assume fixed cell sizes. We develop a\u0000minimal, data-driven model to simulate the dynamics of planar cell cultures by\u0000extending a probabilistic CA to incorporate size changes of individual cells\u0000during growth and cell division. We successfully apply this model to previous\u0000in-vitro experiments on contact inhibition in epithelial tissue: After a\u0000systematic calibration of the model parameters to measurements of single-cell\u0000dynamics, our CA model quantitatively reproduces independent measurements of\u0000emergent, culture-wide features, like colony size, cell density and collective\u0000cell migration. In particular, the dynamics of the CA model also exhibit the\u0000transition from a low-density confluent regime to a stationary postconfluent\u0000regime with a rapid decrease in cell size and motion. This implies that the\u0000volume exclusion principle, a mechanical constraint which is the only\u0000inter-cellular interaction incorporated in the model, paired with a\u0000size-dependent proliferation rate is sufficient to generate the observed\u0000contact inhibition.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140129010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Study of the mechanism of electroacupuncture regulating ferroptosis, inhibiting bladder neck fibrosis, and improving bladder urination function after suprasacral spinal cord injury using proteomics 利用蛋白质组学研究电针调节铁蛋白沉积、抑制膀胱颈纤维化、改善骶骨上脊髓损伤后膀胱排尿功能的机制

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-11 DOI: arxiv-2403.06792

Jin-Can Liu, Li-Ya Tang, Xiao-Ying Sun, Qi-Rui Qu, Qiong Liu, Lu Zhou, Hong Zhang, Bruce Song, Ming Xu, Kun Ai

{"title":"Study of the mechanism of electroacupuncture regulating ferroptosis, inhibiting bladder neck fibrosis, and improving bladder urination function after suprasacral spinal cord injury using proteomics","authors":"Jin-Can Liu, Li-Ya Tang, Xiao-Ying Sun, Qi-Rui Qu, Qiong Liu, Lu Zhou, Hong Zhang, Bruce Song, Ming Xu, Kun Ai","doi":"arxiv-2403.06792","DOIUrl":"https://doi.org/arxiv-2403.06792","url":null,"abstract":"Purpose The aim of this study was to explore whether electroacupuncture\u0000regulates phenotypic transformation of smooth muscle cells by inhibiting\u0000ferroptosis and inhibiting fibrosis, thereby improving bladder urination\u0000function after suprasacral spinal cord injury (SSCI). Methods The experiment\u0000was divided into sham, model, and electroacupuncture group. After 10 days of\u0000electroacupuncture intervention, urodynamic examination was performed, and\u0000bladder neck was taken for HE staining, tandem mass tag (TMT)-based\u0000quantitative proteomics analysis, Western blot(WB) detection, ferrous ion\u0000concentration detection and Masson staining. Conclusion Electroacupuncture may\u0000prevent the phenotype of bladder neck smooth muscle cells from transforming\u0000from contraction type to synthesis type by inhibiting ferroptosis, inhibit\u0000bladder neck fibrosis, improve bladder neck compliance, and thus improve\u0000bladder urination function after SSCI.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140105561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Visualizing, Analyzing and Constructing L-System from Arborized 3D Model Using a Web Application 使用网络应用程序，从 Arborized 3D 模型可视化、分析和构建 L 系统

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-11 DOI: arxiv-2403.06638

Nick van Nielen, Fons Verbeek, Lu Cao

{"title":"Visualizing, Analyzing and Constructing L-System from Arborized 3D Model Using a Web Application","authors":"Nick van Nielen, Fons Verbeek, Lu Cao","doi":"arxiv-2403.06638","DOIUrl":"https://doi.org/arxiv-2403.06638","url":null,"abstract":"In biology, arborized structures are well represented and typically complex\u0000for visualization and analysis. In order to have a profound understanding of\u0000the topology of arborized 3D biological model, higher level abstraction is\u0000needed. We aim at constructing an abstraction of arborized 3D biological model\u0000to an L-system that provides a generalized formalization in a grammar to\u0000represent complex structures. The focus of this paper is to combine 3D\u0000visualization, analysis and L-system abstraction into a single web application.\u0000We designed a front-end user interface and a back-end. In the front-end, we\u0000used A-Frame and defined algorithms to generate and visualize L-systems. In the\u0000back-end, we utilized the Vascular Modelling Toolkit's (VMTK) centerline\u0000analysis methods to extract important features from the arborized 3D models,\u0000which can be applied to L-system generation. In addition, two 3D biological\u0000models: lactiferous duct and artery are used as two case studies to verify the\u0000functionality of this web application. In conclusion, our web application is\u0000able to visualize, analyse and create L-system abstractions of arborized 3D\u0000models. This in turn provides workflow-improving benefits, easy accessibility\u0000and extensibility.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140105554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Complementing cell taxonomies with a multicellular functional analysis of tissues 用组织的多细胞功能分析补充细胞分类法

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-11 DOI: arxiv-2403.06753

Ricardo Omar Ramirez Flores, Philipp Sven Lars Schäfer, Leonie Küchenhoff, Julio Saez-Rodriguez

引用次数: 0

General surgery vision transformer: A video pre-trained foundation model for general surgery 普外科视觉转换器：用于普外科手术的视频预训练基础模型

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-09 DOI: arxiv-2403.05949

Samuel Schmidgall, Ji Woong Kim, Jeffery Jopling, Axel Krieger

引用次数: 0

An in-silico approach to meniscus tissue regeneration: Modeling, numerical simulation, and experimental analysis 半月板组织再生的模拟方法：建模、数值模拟和实验分析

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-09 DOI: arxiv-2403.05909

Elise Grosjean, Alex Keilmann, Henry Jäger, Shimi Mohanan, Claudia Redenbach, Bernd Simeon, Christina Surulescu, Luisa de Roy, Andreas Seitz, Graciosa Teixeira, Martin Dauner, Carsten Linti, Günter Schmidt

{"title":"An in-silico approach to meniscus tissue regeneration: Modeling, numerical simulation, and experimental analysis","authors":"Elise Grosjean, Alex Keilmann, Henry Jäger, Shimi Mohanan, Claudia Redenbach, Bernd Simeon, Christina Surulescu, Luisa de Roy, Andreas Seitz, Graciosa Teixeira, Martin Dauner, Carsten Linti, Günter Schmidt","doi":"arxiv-2403.05909","DOIUrl":"https://doi.org/arxiv-2403.05909","url":null,"abstract":"We develop a model the dynamics of human mesenchymal stem cells (hMSCs) and\u0000chondrocytes evolving in a nonwoven polyethylene terephtalate (PET) scaffold\u0000impregnated with hyaluron and supplied with a differentiation medium. The\u0000scaffold and the cells are assumed to be contained in a bioreactor with fluid\u0000perfusion. The differentiation of hMSCs into chondrocytes favors the production\u0000of extracellular matrix (ECM) and is influenced by fluid stress. The model\u0000takes deformations of ECM and PET scaffold into account. The scaffold structure\u0000is explicitly included by statistical assessment of the fibre distribution from\u0000CT images. The effective macroscopic equations are obtained by appropriate\u0000upscaling from dynamics on lower (microscopic and mesoscopic) scales and\u0000feature in the motility terms an explicit cell diffusion tensor encoding the\u0000assessed anisotropic scaffold structure. Numerical simulations show its\u0000influence on the overall cell and tissue dynamics.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140105553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthetic Privileged Information Enhances Medical Image Representation Learning 合成特权信息加强医学图像表征学习

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-08 DOI: arxiv-2403.05220

Lucas Farndale, Chris Walsh, Robert Insall, Ke Yuan

引用次数: 0

Correction and standardisation of lung oscillometry techniques using parameter inference: A study group report 利用参数推理对肺振荡测量技术进行校正和标准化：研究小组报告

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-07 DOI: arxiv-2403.04621

Bindi S. Brook, Graeham R. Douglas, Oliver E. Jensen, Sonal Mistry, Sujit Kumar Nath, Matthew J. Russell, Sina Saffaran, James Shemilt, Liam Weaver, Carl A. Whitfield

{"title":"Correction and standardisation of lung oscillometry techniques using parameter inference: A study group report","authors":"Bindi S. Brook, Graeham R. Douglas, Oliver E. Jensen, Sonal Mistry, Sujit Kumar Nath, Matthew J. Russell, Sina Saffaran, James Shemilt, Liam Weaver, Carl A. Whitfield","doi":"arxiv-2403.04621","DOIUrl":"https://doi.org/arxiv-2403.04621","url":null,"abstract":"This report relates to a study group hosted by the EPSRC funded network,\u0000Integrating data-driven BIOphysical models into REspiratory MEdicine (BIOREME),\u0000and supported by The Insigneo Institute and The Knowledge Transfer Network. The\u0000BIOREME network hosts events, including this study group, to bring together\u0000multi-disciplinary researchers, clinicians, companies and charities to catalyse\u0000research in the applications of mathematical modelling for respiratory\u0000medicine. The goal of this study group was to provide an interface between\u0000companies, clinicians, and mathematicians to develop mathematical tools to the\u0000problems presented. The study group was held at The University of Sheffield on\u0000the 17 - 20 April 2023 and was attended by 24 researchers from 13 different\u0000institutions. This report relates to a challenge presented by Arete Medical Technologies\u0000relating to impulse oscillometry (IOS), whereby a short pressure oscillation is\u0000imposed at a person's mouth during normal breathing, usually by a loudspeaker.\u0000The resulting pressure and flow rate changes can be used to the impedance of\u0000the airways, which in turn can provide proxy measurements for\u0000(patho)physiological changes in the small airways. Disentangling the signal so\u0000that airway mechanics can be measured accurately (and device\u0000properties/environmental effects can be accounted for) remains an open\u0000challenge that has the potential to significantly improve the device and its\u0000translation to clinic. In this report, several approaches to this problem, and\u0000the wider problem of interpreting oscillometry resuts are explored.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140072192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hitchhiker's guide to cancer-associated lymphoid aggregates in histology images: manual and deep learning-based quantification approaches 组织学图像中癌症相关淋巴聚集体的 "搭便车指南"：手动和基于深度学习的量化方法

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-06 DOI: arxiv-2403.04142

Karina Silina, Francesco Ciompi

引用次数: 0

NIR ICG-Enhanced Fluorescence: A Quantitative Evaluation of Bowel Microperfusion and Its Relation to Central Perfusion in Colorectal Surgery 近红外 ICG 增强荧光：定量评估结肠直肠手术中的肠道微灌注及其与中心灌注的关系

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-03-04 DOI: arxiv-2403.01844

N. Depalma, S. D Ugo, F. Manoochehri, A. Libia, W. Sergi, T. R. L. Marchese, S. Forciniti, L. L. del Mercato, P. Piscitelli, S. Garritano, F. Castellana, R. Zupo, M. G. Spampinato

{"title":"NIR ICG-Enhanced Fluorescence: A Quantitative Evaluation of Bowel Microperfusion and Its Relation to Central Perfusion in Colorectal Surgery","authors":"N. Depalma, S. D Ugo, F. Manoochehri, A. Libia, W. Sergi, T. R. L. Marchese, S. Forciniti, L. L. del Mercato, P. Piscitelli, S. Garritano, F. Castellana, R. Zupo, M. G. Spampinato","doi":"arxiv-2403.01844","DOIUrl":"https://doi.org/arxiv-2403.01844","url":null,"abstract":"Background: To date, no standardized protocols nor a quantitative assessment\u0000of the near-infrared fluorescence angiography with indocyanine green (NIR-ICG)\u0000are available. The aim of this study was to evaluate the timing of fluorescence\u0000as a reproducible parameter and its efficacy in predicting anastomotic leakage\u0000(AL) in colorectal surgery. Methods: A consecutive cohort of 108 patients\u0000undergoing minimally invasive elective procedures for colorectal cancer was\u0000prospectively enrolled. The difference between macro and microperfusion DeltaT\u0000was obtained by calculating the timing of fluorescence at the level of iliac\u0000artery division and colonic wall, respectively. Results: Subjects with a DeltaT\u0000higher 15.5 s had a higher tendency to develop an AL (p lower 0.01). The\u0000DeltaT/heart rate interaction was found to predict AL with an odds ratio of\u00001.02 (p lower 0.01); a cut-off threshold of 832 was identified (sensitivity\u00000.86, specificity 0.77). Perfusion parameters were also associated with a\u0000faster bowel motility resumption and a reduced length of hospital stay.\u0000Conclusions: The analysis of the timing of fluorescence provides a\u0000quantitative, easy evaluation of tissue perfusion. A DeltaT/HR interaction\u0000higher 832 may be used as a real-time parameter to guide surgical decision\u0000making in colorectal surgery.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140035401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0