PLoS Computational Biology最新文献_第10页

A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers. 纤溶蛋白介导单纤维蛋白纤维蛋白溶解的数学模型。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-20 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012684

Roukayatou R Ouedraogo, Hannah K Sowers, Spencer R Lynch, Nathan E Hudson, Brittany E Bannish

{"title":"A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers.","authors":"Roukayatou R Ouedraogo, Hannah K Sowers, Spencer R Lynch, Nathan E Hudson, Brittany E Bannish","doi":"10.1371/journal.pcbi.1012684","DOIUrl":"10.1371/journal.pcbi.1012684","url":null,"abstract":"Fibrinolysis, the plasmin-mediated degradation of the fibrin mesh that stabilizes blood clots, is an important physiological process, and understanding mechanisms underlying lysis is critical for improved stroke treatment. Experimentalists are now able to study lysis on the scale of single fibrin fibers, but mathematical models of lysis continue to focus mostly on fibrin network degradation. Experiments have shown that while some degradation occurs along the length of a fiber, ultimately the fiber is cleaved at a single location. We built a 2-dimensional stochastic model of a fibrin fiber cross-section that uses the Gillespie algorithm to study single fiber lysis initiated by plasmin. We simulated the model over a range of parameter values to learn about patterns and rates of single fiber lysis in various physiological conditions. We also used epifluorescent microscopy to measure the cleavage times of fibrin fibers with different apparent diameters. By comparing our model results to the laboratory experiments, we were able to: 1) suggest value ranges for unknown rate constants(namely that the degradation rate of fibrin by plasmin should be ≤ 10 s-1 and that if plasmin crawls, the rate of crawling should be between 10 s-1 and 60 s-1); 2) estimate the fraction of fibrin within a fiber cross-section that must be degraded for the fiber to cleave in two; and 3) propose that that fraction is higher in thinner fibers and lower in thicker fibers. Collectively, this information provides more details about how fibrin fibers degrade, which can be leveraged in the future for a better understanding of why fibrinolysis is impaired in certain disease states, and could inform intervention strategies.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"20 12","pages":"e1012684"},"PeriodicalIF":3.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A computational model for angular velocity integration in a locust heading circuit. 蝗虫航向回路中角速度积分的计算模型。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-20 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012155

Kathrin Pabst, Evripidis Gkanias, Barbara Webb, Uwe Homberg, Dominik Endres

{"title":"A computational model for angular velocity integration in a locust heading circuit.","authors":"Kathrin Pabst, Evripidis Gkanias, Barbara Webb, Uwe Homberg, Dominik Endres","doi":"10.1371/journal.pcbi.1012155","DOIUrl":"10.1371/journal.pcbi.1012155","url":null,"abstract":"Accurate navigation often requires the maintenance of a robust internal estimate of heading relative to external surroundings. We present a model for angular velocity integration in a desert locust heading circuit, applying concepts from early theoretical work on heading circuits in mammals to a novel biological context in insects. In contrast to similar models proposed for the fruit fly, this circuit model uses a single 360° heading direction representation and is updated by neuromodulatory angular velocity inputs. Our computational model was implemented using steady-state firing rate neurons with dynamical synapses. The circuit connectivity was constrained by biological data, and remaining degrees of freedom were optimised with a machine learning approach to yield physiologically plausible neuron activities. We demonstrate that the integration of heading and angular velocity in this circuit is robust to noise. The heading signal can be effectively used as input to an existing insect goal-directed steering circuit, adapted for outbound locomotion in a steady direction that resembles locust migration. Our study supports the possibility that similar computations for orientation may be implemented differently in the neural hardware of the fruit fly and the locust.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"20 12","pages":"e1012155"},"PeriodicalIF":3.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimisation strategies for directed evolution without sequencing. 无序列定向进化的优化策略。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-19 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012695

Jessica James, Sebastian Towers, Jakob Foerster, Harrison Steel

{"title":"Optimisation strategies for directed evolution without sequencing.","authors":"Jessica James, Sebastian Towers, Jakob Foerster, Harrison Steel","doi":"10.1371/journal.pcbi.1012695","DOIUrl":"10.1371/journal.pcbi.1012695","url":null,"abstract":"Directed evolution can enable engineering of biological systems with minimal knowledge of their underlying sequence-to-function relationships. A typical directed evolution process consists of iterative rounds of mutagenesis and selection that are designed to steer changes in a biological system (e.g. a protein) towards some functional goal. Much work has been done, particularly leveraging advancements in machine learning, to optimise the process of directed evolution. Many of these methods, however, require DNA sequencing and synthesis, making them resource-intensive and incompatible with developments in targeted in vivo mutagenesis. Operating within the experimental constraints of established sorting-based directed evolution techniques (e.g. Fluorescence-Activated Cell Sorting, FACS), we explore approaches for optimisation of directed evolution that could in future be implemented without sequencing information. We then expand our methods to the context of emerging experimental techniques in directed evolution, which allow for single-cell selection based on fitness objectives defined from any combination of measurable traits. Finally, we explore these alternative strategies on the GB1 and TrpB empirical landscapes, demonstrating that they could lead to up to 19-fold and 7-fold increases respectively in the probability of attaining the global fitness peak.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"20 12","pages":"e1012695"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution of cooperation in multichannel games on multiplex networks. 多路网络中多通道博弈的合作演化。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-19 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012678

Amit Basak, Supratim Sengupta

{"title":"Evolution of cooperation in multichannel games on multiplex networks.","authors":"Amit Basak, Supratim Sengupta","doi":"10.1371/journal.pcbi.1012678","DOIUrl":"10.1371/journal.pcbi.1012678","url":null,"abstract":"Humans navigate diverse social relationships and concurrently interact across multiple social contexts. An individual's behavior in one context can influence behavior in other contexts. Different payoffs associated with interactions in the different domains have motivated recent studies of the evolution of cooperation through the analysis of multichannel games where each individual is simultaneously engaged in multiple repeated games. However, previous investigations have ignored the potential role of network structure in each domain and the effect of playing against distinct interacting partners in different domains. Multiplex networks provide a useful framework to represent social interactions between the same set of agents across different social contexts. We investigate the role of multiplex network structure and strategy linking in multichannel games on the spread of cooperative behavior in all layers of the multiplex. We find that multiplex structure along with strategy linking enhances the cooperation rate in all layers of the multiplex compared to a well-mixed population in Prisoners' Dilemma games, provided the network structure is identical across layers. The effectiveness of strategy linking in enhancing cooperation depends on the degree of similarity of the network structure across the layers and perception errors due to imperfect memory. Higher cooperation rates are achieved when the degree of structural overlap of the different layers is sufficiently large, and the probability of perception error is relatively low. Our work reveals how the social network structure in different layers of a multiplex can affect the spread of cooperation by limiting the ability of individuals to link strategies across different social domains.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"20 12","pages":"e1012678"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A framework for modelling desert locust population dynamics and large-scale dispersal. 模拟沙漠蝗虫种群动态和大规模扩散的框架。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-19 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012562

Renata Retkute, William Thurston, Keith Cressman, Christopher A Gilligan

{"title":"A framework for modelling desert locust population dynamics and large-scale dispersal.","authors":"Renata Retkute, William Thurston, Keith Cressman, Christopher A Gilligan","doi":"10.1371/journal.pcbi.1012562","DOIUrl":"10.1371/journal.pcbi.1012562","url":null,"abstract":"There is an urgent need for mathematical models that can be used to inform the deployment of surveillance, early warning and management systems for transboundary pest invasions. This is especially important for desert locust, one of the most dangerous migratory pests for smallholder farmers. During periods of desert locust upsurges and plagues, gregarious adult locusts form into swarms that are capable of long-range dispersal. Here we introduce a novel integrated modelling framework for use in predicting gregarious locust populations. The framework integrates the selection of breeding sites, maturation through egg, hopper and adult stages and swarm dispersal in search of areas suitable for feeding and breeding. Using a combination of concepts from epidemiological modelling, weather and environment data, together with an atmospheric transport model for swarm movement we provide a tool to forecast short- and long-term swarm movements. A principal aim of the framework is to provide a practical starting point for use in the next upsurge.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"20 12","pages":"e1012562"},"PeriodicalIF":3.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11658591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Predicting lung aging using scRNA-Seq data. 使用scRNA-Seq数据预测肺老化。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-19 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012632

Qi Song, Alex Singh, John E McDonough, Taylor S Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J Ceulemans, Bart M Vanaudenaerde, Wim A Wuyts, Xiting Yan, Jonas Schupp, James S Hagood, Naftali Kaminski, Ziv Bar-Joseph

引用次数: 0

Comment on: Toward an optimal contraception dosing strategy. 点评：迈向最佳避孕剂量策略。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-18 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012398

Giuseppe Benagiano, Andrea R Genazzani, Giovanni Grandi, Sun-Wei Guo, Marwan Habiba

引用次数: 0

scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis. scMoMtF：用于单细胞多组学数据分析的可解释多任务学习框架。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-18 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012679

Wei Lan, Tongsheng Ling, Qingfeng Chen, Ruiqing Zheng, Min Li, Yi Pan

引用次数: 0

Hands-on training about data clustering with orange data mining toolbox. 使用橙色数据挖掘工具箱进行数据聚类的实践培训。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-18 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012574

Janez Demšar, Blaž Zupan

{"title":"Hands-on training about data clustering with orange data mining toolbox.","authors":"Janez Demšar, Blaž Zupan","doi":"10.1371/journal.pcbi.1012574","DOIUrl":"10.1371/journal.pcbi.1012574","url":null,"abstract":"Data clustering is a core data science approach widely used and referenced in the scientific literature. Its algorithms are often intuitive and can lead to exciting, insightful results that are easy to interpret. For these reasons, data clustering techniques could be the first method encountered in data science training. This paper proposes a hands-on approach to data clustering training suitable for introductory courses. The education approach features problem-based training that starts with the data and gradually introduces various data processing and analysis methods, illustrating them through visual representations of data and models. The proposed training is suitable for a general audience, does not require a background in statistics, mathematics, or computer science, and aims to engage the audience through practical examples, an exploratory approach to data analysis with visual analysis, experimentation, and a gentle learning curve. The manuscript details the pedagogical units of the training, motivates them through the sequence of methods introduced, and proposes data sets and data analysis workflows to be explored in the class.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"20 12","pages":"e1012574"},"PeriodicalIF":3.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11654965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Response to comment on: Toward an optimal contraception dosing strategy. 对关于最佳避孕剂量策略的评论的回应。

IF 3.8 2区生物学

PLoS Computational Biology Pub Date : 2024-12-18 eCollection Date: 2024-12-01 DOI: 10.1371/journal.pcbi.1012649

Brenda Lyn A Gavina, Aurelio A de Los Reyes V, Mette S Olufsen, Suzanne Lenhart, Johnny T Ottesen

引用次数: 0