arXiv - QuanBio - Populations and Evolution最新文献_第10页

Smectic-like bundle formation of planktonic bacteria upon nutrient starvation 浮游细菌在营养匮乏时形成的胶状菌束

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-06 DOI: arxiv-2407.05031

Takuro Shimaya, Kazumasa A. Takeuchi

引用次数: 0

Speed and shape of population fronts with density-dependent diffusion 依赖密度扩散的人口前沿的速度和形状

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-05 DOI: arxiv-2407.07915

Beth M. Stokes, Tim Rogers, Richard James

引用次数: 0

Predictability of viral load kinetics in the early phases of SARS-CoV-2 through a model-based approach 通过基于模型的方法预测 SARS-CoV-2 早期阶段的病毒载量动力学

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-03 DOI: arxiv-2407.03158

Andrea Bondesan, Antonio Piralla, Elena Ballante, Antonino Maria Guglielmo Pitrolo, Silvia Figini, Fausto Baldanti, Mattia Zanella

{"title":"Predictability of viral load kinetics in the early phases of SARS-CoV-2 through a model-based approach","authors":"Andrea Bondesan, Antonio Piralla, Elena Ballante, Antonino Maria Guglielmo Pitrolo, Silvia Figini, Fausto Baldanti, Mattia Zanella","doi":"arxiv-2407.03158","DOIUrl":"https://doi.org/arxiv-2407.03158","url":null,"abstract":"A pipeline to evaluate the evolution of viral dynamics based on a new\u0000model-driven approach has been developed in the present study. The proposed\u0000methods exploit real data and the multiscale structure of the infection\u0000dynamics to provide robust predictions of the epidemic dynamics. We focus on\u0000viral load kinetics whose dynamical features are typically available in the\u0000symptomatic stage of the infection. Hence, the epidemiological evolution is\u0000obtained by relying on a compartmental approach characterized by a varying\u0000infection rate to estimate early-stage viral load dynamics, of which few data\u0000are available. We test the proposed approach with real data of SARS-CoV-2 viral\u0000load kinetics collected from patients living in an Italian province. The\u0000considered database refers to early-phase infections, whose viral load kinetics\u0000are not affected by mass vaccination policies in Italy. Our contribution is\u0000devoted to provide an effective computational pipeline to evaluate in real time\u0000the evolution of infectivity. Comprehending the factors influencing the in-host\u0000viral dynamics represents a fundamental tool to provide robust public health\u0000strategies. This pilot study could be implemented in further investigations\u0000involving other respiratory viruses, to better clarify the process of viral\u0000dynamics as a preparatory action for future pandemics.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548796","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

Parameter estimation of epidemic spread in two-layer random graphs by classical and machine learning methods 用经典方法和机器学习方法估计双层随机图中流行病传播的参数

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-03 DOI: arxiv-2407.07118

Ágnes Backhausz, Edit Bognár, Villő Csiszár, Damján Tárkányi, András Zempléni

引用次数: 0

Inconsistency of parsimony under the multispecies coalescent 多物种聚合下的解析不一致性

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-02 DOI: arxiv-2407.02634

Daniel Rickert, Wai-Tong Fan, Matthew Hahn

{"title":"Inconsistency of parsimony under the multispecies coalescent","authors":"Daniel Rickert, Wai-Tong Fan, Matthew Hahn","doi":"arxiv-2407.02634","DOIUrl":"https://doi.org/arxiv-2407.02634","url":null,"abstract":"While it is known that parsimony can be statistically inconsistent under\u0000certain models of evolution due to high levels of homoplasy, the consistency of\u0000parsimony under the multispecies coalescent (MSC) is less well studied.\u0000Previous studies have shown the consistency of concatenated parsimony\u0000(parsimony applied to concatenated alignments) under the MSC for the rooted\u00004-taxa case under an infinite-sites model of mutation; on the other hand, other\u0000work has also established the inconsistency of concatenated parsimony for the\u0000unrooted 6-taxa case. These seemingly contradictory results suggest that\u0000concatenated parsimony may fail to be consistent for trees with more than 5\u0000taxa, for all unrooted trees, or for some combination of the two. Here, we\u0000present a technique for computing the expected internal branch lengths of gene\u0000trees under the MSC. This technique allows us to determine the regions of the\u0000parameter space of the species tree under which concatenated parsimony fails\u0000for different numbers of taxa, for rooted or unrooted trees. We use our new\u0000approach to demonstrate that there are always regions of statistical\u0000inconsistency for concatenated parsimony for the 5- and 6-taxa cases,\u0000regardless of rooting. Our results therefore suggest that parsimony is not\u0000generally dependable under the MSC.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141552635","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

The Accumulation of Beneficial Mutations and Convergence to a Poisson Process 有益突变的积累和向泊松过程的收敛

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-02 DOI: arxiv-2407.01999

Nantawat Udomchatpitak, Jason Schweinsberg

引用次数: 0

The Complex Interplay Between Risk Tolerance and the Spread of Infectious Diseases 风险容忍度与传染病传播之间的复杂相互作用

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-01 DOI: arxiv-2407.03376

Maximilian Nguyen, Ari Freedman, Matthew Cheung, Chadi Saad-Roy, Baltazar Espinoza, Bryan Grenfell, Simon Levin

{"title":"The Complex Interplay Between Risk Tolerance and the Spread of Infectious Diseases","authors":"Maximilian Nguyen, Ari Freedman, Matthew Cheung, Chadi Saad-Roy, Baltazar Espinoza, Bryan Grenfell, Simon Levin","doi":"arxiv-2407.03376","DOIUrl":"https://doi.org/arxiv-2407.03376","url":null,"abstract":"Risk-driven behavior provides a feedback mechanism through which individuals\u0000both shape and are collectively affected by an epidemic. We introduce a general\u0000and flexible compartmental model to study the effect of heterogeneity in the\u0000population with regards to risk tolerance. The interplay between behavior and\u0000epidemiology leads to a rich set of possible epidemic dynamics. Depending on\u0000the behavioral composition of the population, we find that increasing\u0000heterogeneity in risk tolerance can either increase or decrease the epidemic\u0000size. We find that multiple waves of infection can arise due to the interplay\u0000between transmission and behavior, even without the replenishment of\u0000susceptibles. We find that increasing protective mechanisms such as the\u0000effectiveness of interventions, the number of risk-averse people in the\u0000population, and the duration of intervention usage reduces the epidemic\u0000overshoot. When the protection is pushed past a critical threshold, the\u0000epidemic dynamics enter an underdamped regime where the epidemic size exactly\u0000equals the herd immunity threshold. Lastly, we can find regimes where epidemic\u0000size does not monotonically decrease with a population that becomes\u0000increasingly risk-averse.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141568182","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

Bernstein duality revisited: frequency-dependent selection, coordinated mutation and opposing environments 伯恩斯坦二元论再探：频率依赖性选择、协调突变和对立环境

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-07-01 DOI: arxiv-2407.01242

Fernando Cordero, Sebastian Hummel, Grégoire Véchambre

{"title":"Bernstein duality revisited: frequency-dependent selection, coordinated mutation and opposing environments","authors":"Fernando Cordero, Sebastian Hummel, Grégoire Véchambre","doi":"arxiv-2407.01242","DOIUrl":"https://doi.org/arxiv-2407.01242","url":null,"abstract":"Population models usually come in pairs; one process describes forward\u0000evolution (e.g. type composition) and the other describes backward evolution\u0000(e.g. lines of descent). These processes are often linked by a formal\u0000relationship known as duality. Ideally, one of the two processes is easier to\u0000analyze, and the duality relation is so simple that properties of the more\u0000involved process can be inferred from the simpler one. This is the case when\u0000the forward process admits a moment dual. Unfortunately, moment duality seems\u0000to be the exception rather than the rule. Various approaches have been used to\u0000analyze models in the absence of a moment dual, one of them is based on\u0000Bernstein duality and another one on Siegmund duality. As a rule of thumb, the\u0000first approach seems to work well whenever the ancestral processes are positive\u0000recurrent; the second one, in contrast, works well in situations where the\u0000ancestral structures can grow to infinity (in size). The second approach was\u0000recently used to provide a full characterization of the long-term behavior of a\u0000broad class of $Lambda$-Wright--Fisher processes subject to\u0000frequency-dependent selection and opposing environments. In this paper, we use\u0000the first approach to complete the picture, i.e. we describe the long-term\u0000behavior of a different class of $Lambda$-Wright--Fisher processes, which\u0000covers many of the cases that were not covered by the aforementioned result\u0000(the two classes intersect, but none is a proper subset of the other one).\u0000Moreover, we extend the notion of Bernstein duality to cases with (single and\u0000coordinated) mutations {and environmental selection}, and we use it to show\u0000ergodic properties of the process.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141511192","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

Stability of a Delayed Predator-Prey Model for Puma Concolor 美洲狮延迟捕食者-猎物模型的稳定性

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-06-28 DOI: arxiv-2407.07904

Wilson Mejías, Daniel Sepúlveda

引用次数: 0

The impact of fear and behaviour response to established and novel diseases 恐惧和行为反应对既定疾病和新型疾病的影响

arXiv - QuanBio - Populations and Evolution Pub Date : 2024-06-21 DOI: arxiv-2406.15595

Avneet Kaur, Rebecca Tyson, Iain Moyles

{"title":"The impact of fear and behaviour response to established and novel diseases","authors":"Avneet Kaur, Rebecca Tyson, Iain Moyles","doi":"arxiv-2406.15595","DOIUrl":"https://doi.org/arxiv-2406.15595","url":null,"abstract":"We analyze a disease transmission model that allows individuals to acquire\u0000fear and change their behaviour to reduce transmission. Fear is acquired\u0000through contact with infected individuals and through the influence of fearful\u0000individuals. We analyze the model in two limits: First, an Established Disease\u0000Limit (EDL), where the spread of the disease is much faster than the spread of\u0000fear, and second, a Novel Disease Limit (NDL), where the spread of the disease\u0000is comparable to that of fear. For the EDL, we show that the relative rate of\u0000fear acquisition to disease transmission controls the size of the fearful\u0000population at the end of a disease outbreak, and that the fear-induced contact\u0000reduction behaviour has very little impact on disease burden. Conversely, we\u0000show that in the NDL, disease burden can be controlled by fear-induced\u0000behaviour depending on the rate of fear loss. Specifically, fear-induced\u0000behaviour introduces a contact parameter $p$, which if too large prevents the\u0000contact reduction from effectively managing the epidemic. We analytically\u0000identify a critical prophylactic behaviour parameter $p=p_c$ where this happens\u0000leading to a discontinuity in epidemic prevalence. We show that this change in\u0000disease burden introduces multiple epidemic waves.","PeriodicalId":501044,"journal":{"name":"arXiv - QuanBio - Populations and Evolution","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141511195","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