arXiv - QuanBio - Tissues and Organs最新文献_第4页

A reaction-diffusion model for relapsing-remitting multiple sclerosis with a treatment term 带有治疗项的复发缓解型多发性硬化症反应扩散模型

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-07-09 DOI: arxiv-2407.06802

Romina Travaglini

引用次数: 0

Src Kinase Slows Collective Rotation of Confined Epithelial Cell Monolayers Src 激酶减缓封闭上皮细胞单层的集体旋转

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-07-09 DOI: arxiv-2407.06920

Nastassia Pricoupenko, Flavia Marsigliesi, Philippe Marcq, Carles Blanch-Mercader, Isabelle Bonnet

{"title":"Src Kinase Slows Collective Rotation of Confined Epithelial Cell Monolayers","authors":"Nastassia Pricoupenko, Flavia Marsigliesi, Philippe Marcq, Carles Blanch-Mercader, Isabelle Bonnet","doi":"arxiv-2407.06920","DOIUrl":"https://doi.org/arxiv-2407.06920","url":null,"abstract":"Collective cell migration is key during development, wound healing and\u0000metastasis and relies on coordinated cell behaviors at the group level. Src\u0000kinase is a signalling enzyme regulating many cellular processes including\u0000adhesion and motility and its deregulated activation has been associated to\u0000aggressiveness of different cancers. Here, we take advantage of optogenetics to\u0000precisely control Src activation in time to study the effect of its over\u0000activation on collective rotation of confined monolayers. We show that Src\u0000activation slows down collective rotation of epithelial cells confined into\u0000circular adhesive patches. We interpret velocity, force and stress data during\u0000period of non-activation and period of activation of Src thanks to an\u0000hydrodynamic description of the cell assembly as a polar active fluid. Src\u0000activation leads to a 2-fold decrease in the ratio of polar angle to friction,\u0000which could result from increased adhesive bonds at the cell-substrate\u0000interface. Our work reveals the importance of fine-tuning the level of Src\u0000activity for coordinated collective behaviors.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141572058","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

Disk-stacking models are consistent with Fibonacci and non-Fibonacci structure in sunflowers 圆盘堆积模型与向日葵的斐波纳契和非斐波纳契结构一致

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-07-08 DOI: arxiv-2407.05857

Jonathan Swinton

{"title":"Disk-stacking models are consistent with Fibonacci and non-Fibonacci structure in sunflowers","authors":"Jonathan Swinton","doi":"arxiv-2407.05857","DOIUrl":"https://doi.org/arxiv-2407.05857","url":null,"abstract":"This paper investigates a model of plant organ placement motivated by the\u0000appearance of large Fibonacci numbers in phyllotaxis, and provides the first\u0000large-scale empirical validation of this model. Specifically it evaluates the\u0000ability of Schwendener disk-stacking models to generate parastichy patterns\u0000seen in a large dataset of sunflower seedheads. We find that features of this\u0000data that the models can account for include a predominance of Fibonacci\u0000counts, usually in a pair of left and right counts on a single seedhead, a\u0000smaller but detectable frequency of Lucas and double Fibonacci numbers, a\u0000comparable frequency of Fibonacci numbers plus or minus one, and occurrences of\u0000pairs of roughly equal but non-Fibonacci counts in a `columnar' structure. A\u0000further observation in the dataset was an occasional lack of rotational\u0000symmetry in the parastichy spirals, and this paper demonstrates those in the\u0000model for the first time. Schwendener disk-stacking models allow Fibonacci structure by ensuring that a\u0000parameter of the model corresponding to the speed of plant growth is kept small\u0000enough. While many other models can exhibit Fibonacci structure, usually by\u0000specifying a rotation parameter to an extremely high precision, no other model\u0000has accounted for further, non-Fibonacci, features in the observed data. The\u0000Schwendener model produces these naturally in the region of parameter space\u0000just beyond where the Fibonacci structure breaks down, without any further\u0000parameter fitting. We also introduce stochasticity into the model and show that\u0000it while it can be responsible for the appearance of columnar structure, the\u0000disordered dynamics of the deterministic system near the critical region can\u0000also generate this structure.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141572056","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

Ultra-low-energy defibrillation through adjoint optimization 通过邻接优化实现超低能量除颤

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-07-06 DOI: arxiv-2407.05115

Alejandro GarzonUniversidad Sergio Arboleda, Roman O. GrigorievGeorgia Institute of Technology

引用次数: 0

Automatic motion estimation with applicationsto hiPSC-CMs 自动运动估计并应用于 hiPSC-CMs

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-06-30 DOI: arxiv-2407.00799

Henrik Finsberg, Verena Charwat, Kevin Healy, Samuel Wall

引用次数: 0

Mechanical cell interactions on curved interfaces 弯曲界面上的机械细胞相互作用

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-06-27 DOI: arxiv-2406.19197

Pascal R. Buenzli, Shahak Kuba, Ryan J. Murphy, Matthew J. Simpson

{"title":"Mechanical cell interactions on curved interfaces","authors":"Pascal R. Buenzli, Shahak Kuba, Ryan J. Murphy, Matthew J. Simpson","doi":"arxiv-2406.19197","DOIUrl":"https://doi.org/arxiv-2406.19197","url":null,"abstract":"We propose a simple mathematical model to describe the mechanical relaxation\u0000of cells within a curved epithelial tissue layer represented by an arbitrary\u0000curve in two-dimensional space. The model represents the mechanics of the cell\u0000body either by straight springs between points of the curve, or by curved\u0000springs whose shape follows the curve. To understand the collective behaviour\u0000of these discrete models of cells at the broader tissue scale, we devise an\u0000appropriate continuum limit in which the number of cells is constant but the\u0000number of springs tends to infinity. The continuum limit shows that (i)~the\u0000straight spring model and the curved spring model converge to the same\u0000dynamics; and (ii)~the density of cells becomes governed by a diffusion\u0000equation in arc length space with second-order accuracy, where diffusion may be\u0000linear or nonlinear depending on the choice of the spring restoring force law.\u0000Our derivation of the continuum limit justifies that to reach consistent\u0000dynamics as the number of springs increases, the spring restoring force laws\u0000must be rescaled appropriately. Despite mechanical relaxation occurring within\u0000a curved tissue layer, we find that the curvature of the tissue does not affect\u0000tangential stress nor the mechanics-induced redistribution of cells within the\u0000layer in the continuum limit. However, the cell's normal stress does depend on\u0000curvature due to surface tension induced by the tangential forces. By\u0000characterising the full stress state of a cell, these models provide a basis to\u0000represent further mechanobiological processes.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510778","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

Building multiscale models with PhysiBoSS, an agent-based modeling tool 利用基于代理的建模工具 PhysiBoSS 建立多尺度模型

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-06-26 DOI: arxiv-2406.18371

Marco Ruscone, Andrea Checcoli, Randy Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël

{"title":"Building multiscale models with PhysiBoSS, an agent-based modeling tool","authors":"Marco Ruscone, Andrea Checcoli, Randy Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël","doi":"arxiv-2406.18371","DOIUrl":"https://doi.org/arxiv-2406.18371","url":null,"abstract":"Multiscale models provide a unique tool for studying complex processes that\u0000study events occurring at different scales across space and time. In the\u0000context of biological systems, such models can simulate mechanisms happening at\u0000the intracellular level such as signaling, and at the extracellular level where\u0000cells communicate and coordinate with other cells. They aim to understand the\u0000impact of genetic or environmental deregulation observed in complex diseases,\u0000describe the interplay between a pathological tissue and the immune system, and\u0000suggest strategies to revert the diseased phenotypes. The construction of these\u0000multiscale models remains a very complex task, including the choice of the\u0000components to consider, the level of details of the processes to simulate, or\u0000the fitting of the parameters to the data. One additional difficulty is the\u0000expert knowledge needed to program these models in languages such as C++ or\u0000Python, which may discourage the participation of non-experts. Simplifying this\u0000process through structured description formalisms -- coupled with a graphical\u0000interface -- is crucial in making modeling more accessible to the broader\u0000scientific community, as well as streamlining the process for advanced users.\u0000This article introduces three examples of multiscale models which rely on the\u0000framework PhysiBoSS, an add-on of PhysiCell that includes intracellular\u0000descriptions as continuous time Boolean models to the agent-based approach. The\u0000article demonstrates how to easily construct such models, relying on PhysiCell\u0000Studio, the PhysiCell Graphical User Interface. A step-by-step tutorial is\u0000provided as a Supplementary Material and all models are provided at:\u0000https://physiboss.github.io/tutorial/.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510780","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

Implant-to-Wearable Communication through the Human Body: Exploring the Effects of Encapsulated Capacitive and Galvanic Transmitters 通过人体进行植入式可穿戴通信：探索封装电容式和电加热式发射器的效果

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-06-19 DOI: arxiv-2406.13141

Anyu Jiang, Cassandra Acebal, Brook Heyd, Trustin White, Gurleen Kainth, Arunashish Datta, Shreyas Sen, Adam Khalifa, Baibhab Chatterjee

{"title":"Implant-to-Wearable Communication through the Human Body: Exploring the Effects of Encapsulated Capacitive and Galvanic Transmitters","authors":"Anyu Jiang, Cassandra Acebal, Brook Heyd, Trustin White, Gurleen Kainth, Arunashish Datta, Shreyas Sen, Adam Khalifa, Baibhab Chatterjee","doi":"arxiv-2406.13141","DOIUrl":"https://doi.org/arxiv-2406.13141","url":null,"abstract":"Data transfer using human-body communication (HBC) represents an actively\u0000explored alternative solution to address the challenges related to\u0000energy-efficiency, tissue absorption, and security of conventional wireless.\u0000Although the use of HBC for wearable-to-wearable communication has been\u0000well-explored, different configurations for the transmitter (Tx) and receiver\u0000(Rx) for implant-to-wearable HBC needs further studies. This paper\u0000substantiates the hypothesis that a fully implanted galvanic Tx is more\u0000efficient than a capacitive Tx for interaction with a wearable Rx. Given the\u0000practical limitations of implanting an ideal capacitive device, we choose a\u0000galvanic device with one electrode encapsulated to model the capacitive\u0000scenario. We analyze the lumped circuit model for in-body to out-of-body\u0000communication, and perform Circuit-based as well as Finite Element Method (FEM)\u0000simulations to explore how the encapsulation thickness affects the received\u0000signal levels. We demonstrate in-vivo experimental results on live Sprague\u0000Dawley rats to validate the hypothesis, and show that compared to the galvanic\u0000Tx, the channel loss will be $approx$ 20 dB higher with each additional mm\u0000thickness of capacitive encapsulation, eventually going below the noise floor\u0000for ideal capacitive Tx.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510779","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

Thrombogenic Risk Assessment of Transcatheter Prosthetic Heart Valves Using a Fluid-Structure Interaction Approach 采用流体-结构相互作用方法评估经导管人工心脏瓣膜的血栓形成风险

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-06-18 DOI: arxiv-2406.12156

Kyle Baylous, Brandon Kovarovic, Salwa Anam, Ryan Helbock, Marvin Slepian, Danny Bluestein

{"title":"Thrombogenic Risk Assessment of Transcatheter Prosthetic Heart Valves Using a Fluid-Structure Interaction Approach","authors":"Kyle Baylous, Brandon Kovarovic, Salwa Anam, Ryan Helbock, Marvin Slepian, Danny Bluestein","doi":"arxiv-2406.12156","DOIUrl":"https://doi.org/arxiv-2406.12156","url":null,"abstract":"Prosthetic heart valve interventions such as TAVR have surged over the past\u0000decade, but the associated complication of long-term, life-threatening\u0000thrombotic events continues to undermine patient outcomes. Thus, improving\u0000thrombogenic risk analysis of TAVR devices is crucial. In vitro studies for\u0000thrombogenicity are typically difficult to perform. However, revised ISO\u0000testing standards include computational testing for thrombogenic risk\u0000assessment of cardiovascular implants. We present a fluid-structure interaction\u0000(FSI) approach for assessing thrombogenic risk of prosthetic heart valves. An FSI framework was implemented via the incompressible computational fluid\u0000dynamics multi-physics solver of the Ansys LS-DYNA software. The numerical\u0000modeling approach for flow analysis was validated by comparing the derived flow\u0000rate of the 29-mm CoreValve device from benchtop testing and orifice areas of\u0000commercial TAVR valves in the literature to in silico results. Thrombogenic\u0000risk was analyzed by computing stress accumulation (SA) on virtual platelets\u0000seeded in the flow fields via Ansys EnSight. The integrated FSI-thrombogenicity\u0000methodology was subsequently employed to examine hemodynamics and thrombogenic\u0000risk of TAVR devices with two approaches: 1) engineering optimization and 2)\u0000clinical assessment. Our methodology can be used to improve the thromboresistance of prosthetic\u0000valves from the initial design stage to the clinic. It allows for unparalleled\u0000optimization of devices, uncovering key TAVR leaflet design parameters that can\u0000be used to mitigate thrombogenic risk, in addition to patient-specific modeling\u0000to evaluate device performance. This work demonstrates the utility of advanced\u0000in silico analysis of TAVR devices that can be utilized for thrombogenic risk\u0000assessment of other blood recirculating devices.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530188","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

Graph Neural Networks in Histopathology: Emerging Trends and Future Directions 组织病理学中的图神经网络：新趋势和未来方向

arXiv - QuanBio - Tissues and Organs Pub Date : 2024-06-18 DOI: arxiv-2406.12808

Siemen Brussee, Giorgio Buzzanca, Anne M. R. Schrader, Jesper Kers

{"title":"Graph Neural Networks in Histopathology: Emerging Trends and Future Directions","authors":"Siemen Brussee, Giorgio Buzzanca, Anne M. R. Schrader, Jesper Kers","doi":"arxiv-2406.12808","DOIUrl":"https://doi.org/arxiv-2406.12808","url":null,"abstract":"Histopathological analysis of Whole Slide Images (WSIs) has seen a surge in\u0000the utilization of deep learning methods, particularly Convolutional Neural\u0000Networks (CNNs). However, CNNs often fall short in capturing the intricate\u0000spatial dependencies inherent in WSIs. Graph Neural Networks (GNNs) present a\u0000promising alternative, adept at directly modeling pairwise interactions and\u0000effectively discerning the topological tissue and cellular structures within\u0000WSIs. Recognizing the pressing need for deep learning techniques that harness\u0000the topological structure of WSIs, the application of GNNs in histopathology\u0000has experienced rapid growth. In this comprehensive review, we survey GNNs in\u0000histopathology, discuss their applications, and exploring emerging trends that\u0000pave the way for future advancements in the field. We begin by elucidating the\u0000fundamentals of GNNs and their potential applications in histopathology.\u0000Leveraging quantitative literature analysis, we identify four emerging trends:\u0000Hierarchical GNNs, Adaptive Graph Structure Learning, Multimodal GNNs, and\u0000Higher-order GNNs. Through an in-depth exploration of these trends, we offer\u0000insights into the evolving landscape of GNNs in histopathological analysis.\u0000Based on our findings, we propose future directions to propel the field\u0000forward. Our analysis serves to guide researchers and practitioners towards\u0000innovative approaches and methodologies, fostering advancements in\u0000histopathological analysis through the lens of graph neural networks.","PeriodicalId":501572,"journal":{"name":"arXiv - QuanBio - Tissues and Organs","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530189","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