Steffen Lange, Jannik Schmied, Paul Willam, Anja Voss-Böhme
Regulation of cell proliferation is a crucial aspect of tissue development and homeostasis and plays a major role in morphogenesis, wound healing, and tumor invasion. A phenomenon of such regulation is contact inhibition, which describes the dramatic slowing of proliferation, cell migration and individual cell growth when multiple cells are in contact with each other. While many physiological, molecular and genetic factors are known, the mechanism of contact inhibition is still not fully understood. In particular, the relevance of cellular signaling due to interfacial contact for contact inhibition is still debated. Cellular automata (CA) have been employed in the past as numerically efficient mathematical models to study the dynamics of cell ensembles, but they are not suitable to explore the origins of contact inhibition as such agent-based models assume fixed cell sizes. We develop a minimal, data-driven model to simulate the dynamics of planar cell cultures by extending a probabilistic CA to incorporate size changes of individual cells during growth and cell division. We successfully apply this model to previous in-vitro experiments on contact inhibition in epithelial tissue: After a systematic calibration of the model parameters to measurements of single-cell dynamics, our CA model quantitatively reproduces independent measurements of emergent, culture-wide features, like colony size, cell density and collective cell migration. In particular, the dynamics of the CA model also exhibit the transition from a low-density confluent regime to a stationary postconfluent regime with a rapid decrease in cell size and motion. This implies that the volume exclusion principle, a mechanical constraint which is the only inter-cellular interaction incorporated in the model, paired with a size-dependent proliferation rate is sufficient to generate the observed contact inhibition.
细胞增殖调控是组织发育和稳态的一个重要方面，在形态发生、伤口愈合和肿瘤侵袭中发挥着重要作用。这种调控的一种现象是接触抑制，它描述了当多个细胞相互接触时，细胞增殖、细胞迁移和单个细胞生长的速度急剧减慢。虽然许多生理、分子和遗传因素已经为人所知，但接触抑制的机制仍未完全明了。尤其是界面接触导致的细胞信号传导与接触抑制的相关性仍存在争议。细胞自动机（CA）过去曾被用作研究细胞团动态的高效数学模型，但它们并不适合探索接触抑制的起源，因为这种基于代理的模型假定细胞大小是固定的。我们通过扩展概率 CA，将单个细胞在生长和细胞分裂过程中的大小变化纳入其中，开发了一个最小的、数据驱动的模型来模拟平面细胞培养的动态。我们成功地将这一模型应用于之前的上皮组织接触抑制体外实验：在根据单细胞动力学测量结果对模型参数进行系统校准后，我们的 CA 模型定量地再现了对菌落大小、细胞密度和细胞集体迁移等整个培养物特征的独立测量结果。特别是，CA 模型的动力学还表现出从低密度汇合状态到静止的后汇合状态的过渡，细胞体积和运动迅速减小。这意味着体积排斥原理--模型中唯一包含的细胞间相互作用的机械约束--与依赖于细胞大小的增殖率配对，足以产生观察到的接触抑制。
{"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":"16 1","pages":""},"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}
Jin-Can Liu, Li-Ya Tang, Xiao-Ying Sun, Qi-Rui Qu, Qiong Liu, Lu Zhou, Hong Zhang, Bruce Song, Ming Xu, Kun Ai
Purpose The aim of this study was to explore whether electroacupuncture regulates phenotypic transformation of smooth muscle cells by inhibiting ferroptosis and inhibiting fibrosis, thereby improving bladder urination function after suprasacral spinal cord injury (SSCI). Methods The experiment was divided into sham, model, and electroacupuncture group. After 10 days of electroacupuncture intervention, urodynamic examination was performed, and bladder neck was taken for HE staining, tandem mass tag (TMT)-based quantitative proteomics analysis, Western blot(WB) detection, ferrous ion concentration detection and Masson staining. Conclusion Electroacupuncture may prevent the phenotype of bladder neck smooth muscle cells from transforming from contraction type to synthesis type by inhibiting ferroptosis, inhibit bladder neck fibrosis, improve bladder neck compliance, and thus improve bladder urination function after SSCI.
{"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":"56 1","pages":""},"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}
In biology, arborized structures are well represented and typically complex for visualization and analysis. In order to have a profound understanding of the topology of arborized 3D biological model, higher level abstraction is needed. We aim at constructing an abstraction of arborized 3D biological model to an L-system that provides a generalized formalization in a grammar to represent complex structures. The focus of this paper is to combine 3D visualization, analysis and L-system abstraction into a single web application. We designed a front-end user interface and a back-end. In the front-end, we used A-Frame and defined algorithms to generate and visualize L-systems. In the back-end, we utilized the Vascular Modelling Toolkit's (VMTK) centerline analysis methods to extract important features from the arborized 3D models, which can be applied to L-system generation. In addition, two 3D biological models: lactiferous duct and artery are used as two case studies to verify the functionality of this web application. In conclusion, our web application is able to visualize, analyse and create L-system abstractions of arborized 3D models. This in turn provides workflow-improving benefits, easy accessibility and extensibility.
在生物学中，树枝状结构有很好的表现形式，通常可用于可视化和分析。为了深刻理解树枝状三维生物模型的拓扑结构，需要更高层次的抽象。我们的目标是将树枝化三维生物模型抽象为一个 L 系统，用语法提供一个通用的形式化来表示复杂的结构。本文的重点是将三维可视化、分析和 L 系统抽象结合到一个单一的网络应用程序中。在前端，我们使用了 A-Frame，并定义了生成和可视化 L 系统的算法。在后端，我们利用血管建模工具包（VMTK）的中心线分析方法从树枝化三维模型中提取重要特征，并将其应用于 L 系统的生成。此外，我们还使用了两个三维生物模型：乳腺导管和动脉作为案例研究，以验证该网络应用程序的功能。总之，我们的网络应用程序能够可视化、分析和创建树枝化三维模型的 L 系统抽象。这反过来又提供了改进工作流程的好处、易访问性和可扩展性。
{"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":"23 1","pages":""},"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}
Ricardo Omar Ramirez Flores, Philipp Sven Lars Schäfer, Leonie Küchenhoff, Julio Saez-Rodriguez
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of single-cell dynamics upon shared external queues and spatial organizations. However, little is known about the relationship between single cell heterogeneity and the emergence and maintenance of robust multicellular processes in developed tissues and its role in (patho)physiology. Here, we present emerging computational modeling strategies that use increasingly available large-scale cross-condition single cell and spatial datasets, to study multicellular organization in tissues and complement cell taxonomies. This perspective should enable us to better understand how cells within tissues collectively process information and adapt synchronized responses in disease contexts and to bridge the gap between structural changes and functions in tissues.
{"title":"Complementing cell taxonomies with a multicellular functional analysis of tissues","authors":"Ricardo Omar Ramirez Flores, Philipp Sven Lars Schäfer, Leonie Küchenhoff, Julio Saez-Rodriguez","doi":"arxiv-2403.06753","DOIUrl":"https://doi.org/arxiv-2403.06753","url":null,"abstract":"The application of single-cell molecular profiling coupled with spatial\u0000technologies has enabled charting cellular heterogeneity in reference tissues\u0000and in disease. This new wave of molecular data has highlighted the expected\u0000diversity of single-cell dynamics upon shared external queues and spatial\u0000organizations. However, little is known about the relationship between single\u0000cell heterogeneity and the emergence and maintenance of robust multicellular\u0000processes in developed tissues and its role in (patho)physiology. Here, we\u0000present emerging computational modeling strategies that use increasingly\u0000available large-scale cross-condition single cell and spatial datasets, to\u0000study multicellular organization in tissues and complement cell taxonomies.\u0000This perspective should enable us to better understand how cells within tissues\u0000collectively process information and adapt synchronized responses in disease\u0000contexts and to bridge the gap between structural changes and functions in\u0000tissues.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140105551","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}
Samuel Schmidgall, Ji Woong Kim, Jeffery Jopling, Axel Krieger
The absence of openly accessible data and specialized foundation models is a major barrier for computational research in surgery. Toward this, (i) we open-source the largest dataset of general surgery videos to-date, consisting of 680 hours of surgical videos, including data from robotic and laparoscopic techniques across 28 procedures; (ii) we propose a technique for video pre-training a general surgery vision transformer (GSViT) on surgical videos based on forward video prediction that can run in real-time for surgical applications, toward which we open-source the code and weights of GSViT; (iii) we also release code and weights for procedure-specific fine-tuned versions of GSViT across 10 procedures; (iv) we demonstrate the performance of GSViT on the Cholec80 phase annotation task, displaying improved performance over state-of-the-art single frame predictors.
{"title":"General surgery vision transformer: A video pre-trained foundation model for general surgery","authors":"Samuel Schmidgall, Ji Woong Kim, Jeffery Jopling, Axel Krieger","doi":"arxiv-2403.05949","DOIUrl":"https://doi.org/arxiv-2403.05949","url":null,"abstract":"The absence of openly accessible data and specialized foundation models is a\u0000major barrier for computational research in surgery. Toward this, (i) we\u0000open-source the largest dataset of general surgery videos to-date, consisting\u0000of 680 hours of surgical videos, including data from robotic and laparoscopic\u0000techniques across 28 procedures; (ii) we propose a technique for video\u0000pre-training a general surgery vision transformer (GSViT) on surgical videos\u0000based on forward video prediction that can run in real-time for surgical\u0000applications, toward which we open-source the code and weights of GSViT; (iii)\u0000we also release code and weights for procedure-specific fine-tuned versions of\u0000GSViT across 10 procedures; (iv) we demonstrate the performance of GSViT on the\u0000Cholec80 phase annotation task, displaying improved performance over\u0000state-of-the-art single frame predictors.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140105392","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}
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
We develop a model the dynamics of human mesenchymal stem cells (hMSCs) and chondrocytes evolving in a nonwoven polyethylene terephtalate (PET) scaffold impregnated with hyaluron and supplied with a differentiation medium. The scaffold and the cells are assumed to be contained in a bioreactor with fluid perfusion. The differentiation of hMSCs into chondrocytes favors the production of extracellular matrix (ECM) and is influenced by fluid stress. The model takes deformations of ECM and PET scaffold into account. The scaffold structure is explicitly included by statistical assessment of the fibre distribution from CT images. The effective macroscopic equations are obtained by appropriate upscaling from dynamics on lower (microscopic and mesoscopic) scales and feature in the motility terms an explicit cell diffusion tensor encoding the assessed anisotropic scaffold structure. Numerical simulations show its influence on the overall cell and tissue dynamics.
我们建立了一个人类间充质干细胞（hMSCs）和软骨细胞在用透明质酸浸渍并提供分化培养基的无纺布聚对苯二甲酸乙二醇酯（PET）支架中进化的动力学模型。假定支架和细胞都包含在有液体灌注的生物反应器中。hMSCs 向软骨细胞的分化有利于细胞外基质（ECM）的生成，并受到流体应力的影响。该模型考虑了 ECM 和 PET 支架的变形。通过对 CT 图像中纤维分布的统计评估，支架结构被明确包括在内。通过对较低（微观和中观）尺度的动力学进行适当的放大，得到了有效的宏观方程，并在运动项中加入了一个明确的细胞扩散张量，该张量对评估的各向异性支架结构进行了编码。数值模拟显示了它对整个细胞和组织动力学的影响。
{"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":"5 1","pages":""},"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}
Lucas Farndale, Chris Walsh, Robert Insall, Ke Yuan
Multimodal self-supervised representation learning has consistently proven to be a highly effective method in medical image analysis, offering strong task performance and producing biologically informed insights. However, these methods heavily rely on large, paired datasets, which is prohibitive for their use in scenarios where paired data does not exist, or there is only a small amount available. In contrast, image generation methods can work well on very small datasets, and can find mappings between unpaired datasets, meaning an effectively unlimited amount of paired synthetic data can be generated. In this work, we demonstrate that representation learning can be significantly improved by synthetically generating paired information, both compared to training on either single-modality (up to 4.4x error reduction) or authentic multi-modal paired datasets (up to 5.6x error reduction).
{"title":"Synthetic Privileged Information Enhances Medical Image Representation Learning","authors":"Lucas Farndale, Chris Walsh, Robert Insall, Ke Yuan","doi":"arxiv-2403.05220","DOIUrl":"https://doi.org/arxiv-2403.05220","url":null,"abstract":"Multimodal self-supervised representation learning has consistently proven to\u0000be a highly effective method in medical image analysis, offering strong task\u0000performance and producing biologically informed insights. However, these\u0000methods heavily rely on large, paired datasets, which is prohibitive for their\u0000use in scenarios where paired data does not exist, or there is only a small\u0000amount available. In contrast, image generation methods can work well on very\u0000small datasets, and can find mappings between unpaired datasets, meaning an\u0000effectively unlimited amount of paired synthetic data can be generated. In this\u0000work, we demonstrate that representation learning can be significantly improved\u0000by synthetically generating paired information, both compared to training on\u0000either single-modality (up to 4.4x error reduction) or authentic multi-modal\u0000paired datasets (up to 5.6x error reduction).","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140098466","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}
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
This report relates to a study group hosted by the EPSRC funded network, Integrating data-driven BIOphysical models into REspiratory MEdicine (BIOREME), and supported by The Insigneo Institute and The Knowledge Transfer Network. The BIOREME network hosts events, including this study group, to bring together multi-disciplinary researchers, clinicians, companies and charities to catalyse research in the applications of mathematical modelling for respiratory medicine. The goal of this study group was to provide an interface between companies, clinicians, and mathematicians to develop mathematical tools to the problems presented. The study group was held at The University of Sheffield on the 17 - 20 April 2023 and was attended by 24 researchers from 13 different institutions. This report relates to a challenge presented by Arete Medical Technologies relating to impulse oscillometry (IOS), whereby a short pressure oscillation is imposed at a person's mouth during normal breathing, usually by a loudspeaker. The resulting pressure and flow rate changes can be used to the impedance of the airways, which in turn can provide proxy measurements for (patho)physiological changes in the small airways. Disentangling the signal so that airway mechanics can be measured accurately (and device properties/environmental effects can be accounted for) remains an open challenge that has the potential to significantly improve the device and its translation to clinic. In this report, several approaches to this problem, and the wider problem of interpreting oscillometry resuts are explored.
{"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":"5 1","pages":""},"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}
Quantification of lymphoid aggregates including tertiary lymphoid structures with germinal centers in histology images of cancer is a promising approach for developing prognostic and predictive tissue biomarkers. In this article, we provide recommendations for identifying lymphoid aggregates in tissue sections from routine pathology workflows such as hematoxylin and eosin staining. To overcome the intrinsic variability associated with manual image analysis (such as subjective decision making, attention span), we recently developed a deep learning-based algorithm called HookNet-TLS to detect lymphoid aggregates and germinal centers in various tissues. Here, we additionally provide a guideline for using manually annotated images for training and implementing HookNet-TLS for automated and objective quantification of lymphoid aggregates in various cancer types.
{"title":"Hitchhiker's guide to cancer-associated lymphoid aggregates in histology images: manual and deep learning-based quantification approaches","authors":"Karina Silina, Francesco Ciompi","doi":"arxiv-2403.04142","DOIUrl":"https://doi.org/arxiv-2403.04142","url":null,"abstract":"Quantification of lymphoid aggregates including tertiary lymphoid structures\u0000with germinal centers in histology images of cancer is a promising approach for\u0000developing prognostic and predictive tissue biomarkers. In this article, we\u0000provide recommendations for identifying lymphoid aggregates in tissue sections\u0000from routine pathology workflows such as hematoxylin and eosin staining. To\u0000overcome the intrinsic variability associated with manual image analysis (such\u0000as subjective decision making, attention span), we recently developed a deep\u0000learning-based algorithm called HookNet-TLS to detect lymphoid aggregates and\u0000germinal centers in various tissues. Here, we additionally provide a guideline\u0000for using manually annotated images for training and implementing HookNet-TLS\u0000for automated and objective quantification of lymphoid aggregates in various\u0000cancer types.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140072285","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}
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
Background: To date, no standardized protocols nor a quantitative assessment of the near-infrared fluorescence angiography with indocyanine green (NIR-ICG) are available. The aim of this study was to evaluate the timing of fluorescence as a reproducible parameter and its efficacy in predicting anastomotic leakage (AL) in colorectal surgery. Methods: A consecutive cohort of 108 patients undergoing minimally invasive elective procedures for colorectal cancer was prospectively enrolled. The difference between macro and microperfusion DeltaT was obtained by calculating the timing of fluorescence at the level of iliac artery division and colonic wall, respectively. Results: Subjects with a DeltaT higher 15.5 s had a higher tendency to develop an AL (p lower 0.01). The DeltaT/heart rate interaction was found to predict AL with an odds ratio of 1.02 (p lower 0.01); a cut-off threshold of 832 was identified (sensitivity 0.86, specificity 0.77). Perfusion parameters were also associated with a faster bowel motility resumption and a reduced length of hospital stay. Conclusions: The analysis of the timing of fluorescence provides a quantitative, easy evaluation of tissue perfusion. A DeltaT/HR interaction higher 832 may be used as a real-time parameter to guide surgical decision making in colorectal surgery.
{"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":"48 1","pages":""},"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}
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