Acta Biotheoretica最新文献_第5页

Inferential Pluralism in Causal Reasoning from Randomized Experiments 随机实验因果推理中的多元推理

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-08-13 DOI: 10.1007/s10441-022-09446-2

Tudor M. Baetu

引用次数: 2

Stem Cells and the Microenvironment: Reciprocity with Asymmetry in Regenerative Medicine 干细胞与微环境:再生医学中的互惠与不对称

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-08-13 DOI: 10.1007/s10441-022-09448-0

Guglielmo Militello, Marta Bertolaso

{"title":"Stem Cells and the Microenvironment: Reciprocity with Asymmetry in Regenerative Medicine","authors":"Guglielmo Militello, Marta Bertolaso","doi":"10.1007/s10441-022-09448-0","DOIUrl":"10.1007/s10441-022-09448-0","url":null,"abstract":"<div><p>Much of the current research in regenerative medicine concentrates on stem-cell therapy that exploits the regenerative capacities of stem cells when injected into different types of human tissues. Although new therapeutic paths have been opened up by induced pluripotent cells and human mesenchymal cells, the rate of success is still low and mainly due to the difficulties of managing cell proliferation and differentiation, giving rise to non-controlled stem cell differentiation that ultimately leads to cancer. Despite being still far from becoming a reality, these studies highlight the role of physical and biological constraints (e.g., cues and morphogenetic fields) placed by tissue microenvironment on stem cell fate. This asks for a clarification of the coupling of stem cells and microenvironmental factors in regenerative medicine. We argue that extracellular matrix and stem cells have a causal reciprocal and asymmetric relationship in that the 3D organization and composition of the extracellular matrix establish a spatial, temporal, and mechanical control over the fate of stem cells, which enable them to interact and control (as well as be controlled by) the cellular components and soluble factors of microenvironment. Such an account clarifies the notions of stemness and stem cell regeneration consistently with that of microenvironment.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-022-09448-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10739563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 3

COVID-19 Adaptive Humoral Immunity Models: Weakly Neutralizing Versus Antibody-Disease Enhancement Scenarios COVID-19适应性体液免疫模型:弱中和与抗体疾病增强方案

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-08-13 DOI: 10.1007/s10441-022-09447-1

Antoine Danchin, Oriane Pagani-Azizi, Gabriel Turinici, Ghozlane Yahiaoui

引用次数: 9

An Epidemic Model with Pro and Anti-vaccine Groups 具有支持和反疫苗组的流行病模型

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-07-08 DOI: 10.1007/s10441-022-09443-5

G. S. Harari, L. H. A. Monteiro

引用次数: 5

Modelling the Influence of Climatic Factors on the Population Dynamics of Radopholus Similis: Banana-Plantain Pest 气候因子对香蕉-芭蕉害虫相似瓢虫种群动态影响的模拟

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-07-08 DOI: 10.1007/s10441-022-09444-4

S. Fotso, G. Kolaye, J. Ntahomvukiye, S. Bowong, V. Taffouo

{"title":"Modelling the Influence of Climatic Factors on the Population Dynamics of Radopholus Similis: Banana-Plantain Pest","authors":"S. Fotso, G. Kolaye, J. Ntahomvukiye, S. Bowong, V. Taffouo","doi":"10.1007/s10441-022-09444-4","DOIUrl":"10.1007/s10441-022-09444-4","url":null,"abstract":"<div><p><i>Radopholus Similis</i> (<i>R. Similis</i>) or burrowing nematode, is one of the most damaging and widespread nematodes attacking bananas, causing toppling or blackhead disease. A mathematical model for the population dynamics of <i>R. Similis</i> is considered, with the aim of investigating the impact of climatic factors on the growth of <i>R. Similis</i>. In this paper, based on the life cycle of <i>R. Similis</i>, we first propose a mathematical model to study and control the population dynamics of this banana pest. We show also how control terms based on biological and chemical controls can be integrated to reduce the population of <i>R. Similis</i> within banana-plantain roots. Sensitivity analysis was performed to show the most important parameters of the model. We present the theoretical analysis of the model. More precisely, we derive a threshold parameter <span>({mathcal{N}}_0)</span>, called the basic offspring number and show that the trivial equilibrium is globally asymptotically stable whenever <span>({mathcal{N}}_0le 1)</span>, while when <span>({mathcal{N}}_0> 1)</span>, the non trivial equilibrium is globally asymptotically stable. After, we extend the proposed model by taking account climatic factors that influence the growth of this pest. Biological and chemical controls are now introduced through impulsive equations. Threshold and equilibria are obtained and global stabilities have been studied. The theoretical results are supported by numerical simulations. Numerical results of model with biological and chemical controls reveal that biological methods are more effective than chemical methods. We also found that the month February is the best time to apply these controls.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40494193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1

Integration of Heterogeneous Biological Data in Multiscale Mechanistic Model Calibration: Application to Lung Adenocarcinoma 多尺度机械模型校准中异构生物学数据的整合：在肺腺癌中的应用。

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-07-07 DOI: 10.1007/s10441-022-09445-3

Jean-Louis Palgen, Angélique Perrillat-Mercerot, Nicoletta Ceres, Emmanuel Peyronnet, Matthieu Coudron, Eliott Tixier, Ben M. W. Illigens, Jim Bosley, Adèle L’Hostis, Claudio Monteiro

{"title":"Integration of Heterogeneous Biological Data in Multiscale Mechanistic Model Calibration: Application to Lung Adenocarcinoma","authors":"Jean-Louis Palgen, Angélique Perrillat-Mercerot, Nicoletta Ceres, Emmanuel Peyronnet, Matthieu Coudron, Eliott Tixier, Ben M. W. Illigens, Jim Bosley, Adèle L’Hostis, Claudio Monteiro","doi":"10.1007/s10441-022-09445-3","DOIUrl":"10.1007/s10441-022-09445-3","url":null,"abstract":"<div><p>Mechanistic models are built using knowledge as the primary information source, with well-established biological and physical laws determining the causal relationships within the model. Once the causal structure of the model is determined, parameters must be defined in order to accurately reproduce relevant data. Determining parameters and their values is particularly challenging in the case of models of pathophysiology, for which data for calibration is sparse. Multiple data sources might be required, and data may not be in a uniform or desirable format. We describe a calibration strategy to address the challenges of scarcity and heterogeneity of calibration data. Our strategy focuses on parameters whose initial values cannot be easily derived from the literature, and our goal is to determine the values of these parameters via calibration with constraints set by relevant data. When combined with a covariance matrix adaptation evolution strategy (CMA-ES), this step-by-step approach can be applied to a wide range of biological models. We describe a stepwise, integrative and iterative approach to multiscale mechanistic model calibration, and provide an example of calibrating a pathophysiological lung adenocarcinoma model. Using the approach described here we illustrate the successful calibration of a complex knowledge-based mechanistic model using only the limited heterogeneous datasets publicly available in the literature.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-022-09445-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40567039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Bridging Theories for Ecosystem Stability Through Structural Sensitivity Analysis of Ecological Models in Equilibrium 从平衡状态下生态模型的结构敏感性分析探讨生态系统稳定性的桥梁理论

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-06-23 DOI: 10.1007/s10441-022-09441-7

Jan J. Kuiper, Bob W. Kooi, Garry D. Peterson, Wolf M. Mooij

{"title":"Bridging Theories for Ecosystem Stability Through Structural Sensitivity Analysis of Ecological Models in Equilibrium","authors":"Jan J. Kuiper, Bob W. Kooi, Garry D. Peterson, Wolf M. Mooij","doi":"10.1007/s10441-022-09441-7","DOIUrl":"10.1007/s10441-022-09441-7","url":null,"abstract":"<div><p>Ecologists are challenged by the need to bridge and synthesize different approaches and theories to obtain a coherent understanding of ecosystems in a changing world. Both food web theory and regime shift theory shine light on mechanisms that confer stability to ecosystems, but from different angles. Empirical food web models are developed to analyze how equilibria in real multi-trophic ecosystems are shaped by species interactions, and often include linear functional response terms for simple estimation of interaction strengths from observations. Models of regime shifts focus on qualitative changes of equilibrium points in a slowly changing environment, and typically include non-linear functional response terms. Currently, it is unclear how the stability of an empirical food web model, expressed as the rate of system recovery after a small perturbation, relates to the vulnerability of the ecosystem to collapse. Here, we conduct structural sensitivity analyses of classical consumer-resource models in equilibrium along an environmental gradient. Specifically, we change non-proportional interaction terms into proportional ones, while maintaining the equilibrium biomass densities and material flux rates, to analyze how alternative model formulations shape the stability properties of the equilibria. The results reveal no consistent relationship between the stability of the original models and the proportionalized versions, even though they describe the same biomass values and material flows. We use these findings to critically discuss whether stability analysis of observed equilibria by empirical food web models can provide insight into regime shift dynamics, and highlight the challenge of bridging alternative modelling approaches in ecology and beyond.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10441-022-09441-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40269329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 2

Limited Cognitive Abilities and Dominance Hierarchies 有限的认知能力和统治等级

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-06-17 DOI: 10.1007/s10441-022-09442-6

Hanyuan Huang, Jiabin Wu

引用次数: 1

Optimal Drug Regimen and Combined Drug Therapy and Its Efficacy in the Treatment of COVID-19: A Within-Host Modeling Study 新型冠状病毒肺炎的最佳药物方案和联合药物治疗及其疗效:宿主内模型研究

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-05-19 DOI: 10.1007/s10441-022-09440-8

Bishal Chhetri, Vijay M. Bhagat, D. K. K. Vamsi, V. S. Ananth, Bhanu Prakash, Swapna Muthusamy, Pradeep Deshmukh, Carani B. Sanjeevi

{"title":"Optimal Drug Regimen and Combined Drug Therapy and Its Efficacy in the Treatment of COVID-19: A Within-Host Modeling Study","authors":"Bishal Chhetri, Vijay M. Bhagat, D. K. K. Vamsi, V. S. Ananth, Bhanu Prakash, Swapna Muthusamy, Pradeep Deshmukh, Carani B. Sanjeevi","doi":"10.1007/s10441-022-09440-8","DOIUrl":"10.1007/s10441-022-09440-8","url":null,"abstract":"<div><p>The COVID-19 pandemic has resulted in more than 524 million cases and 6 million deaths worldwide. Various drug interventions targeting multiple stages of COVID-19 pathogenesis can significantly reduce infection-related mortality. The current within-host mathematical modeling study addresses the optimal drug regimen and efficacy of combination therapies in the treatment of COVID-19. The drugs/interventions considered include Arbidol, Remdesivir, Interferon (INF) and Lopinavir/Ritonavir. It is concluded that these drugs, when administered singly or in combination, reduce the number of infected cells and viral load. Four scenarios dealing with the administration of a single drug, two drugs, three drugs and all four are discussed. In all these scenarios, the optimal drug regimen is proposed based on two methods. In the first method, these medical interventions are modeled as control interventions and a corresponding objective function and optimal control problem are formulated. In this framework, the optimal drug regimen is derived. Later, using the comparative effectiveness method, the optimal drug regimen is derived based on the basic reproduction number and viral load. The average number of infected cells and viral load decreased the most when all four drugs were used together. On the other hand, the average number of susceptible cells decreased the most when Arbidol was administered alone. The basic reproduction number and viral load decreased the most when all four interventions were used together, confirming the previously obtained finding of the optimal control problem. The results of this study can help physicians make decisions about the treatment of the life-threatening COVID-19 infection.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41577563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges 重建最后的共同祖先:认识论和经验的挑战

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-05-16 DOI: 10.1007/s10441-022-09439-1

Amadeo Estrada, Edna Suárez-Díaz, Arturo Becerra

{"title":"Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges","authors":"Amadeo Estrada, Edna Suárez-Díaz, Arturo Becerra","doi":"10.1007/s10441-022-09439-1","DOIUrl":"10.1007/s10441-022-09439-1","url":null,"abstract":"<div><p>Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a <i>slim LCA</i> based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50031579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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