Acta Biotheoretica最新文献_第6页

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, E. Suárez-Díaz, A. Becerra

引用次数: 0

Mathematical Analysis of Membrane Transporters Dynamics: A Calcium Fluxes Case Study 膜转运体动力学的数学分析:钙通量案例研究

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-04-28 DOI: 10.1007/s10441-022-09437-3

A. Perrillat-Mercerot, N. Deliot, A. Miranville, R. Guillevin, B. Constantin

引用次数: 0

Finding or Creating a Living Organism? Past and Future Thought Experiments in Astrobiology Applied to Artificial Intelligence 寻找或创造一个有生命的有机体？天体生物学应用于人工智能的过去和未来思想实验

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-04-28 DOI: 10.1007/s10441-022-09438-2

Daniel S. Helman Ph.D.

{"title":"Finding or Creating a Living Organism? Past and Future Thought Experiments in Astrobiology Applied to Artificial Intelligence","authors":"Daniel S. Helman Ph.D.","doi":"10.1007/s10441-022-09438-2","DOIUrl":"10.1007/s10441-022-09438-2","url":null,"abstract":"<div><p>This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms—definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution—to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. A novel definition of consciousness is developed which describes mental objects both with and without communicable properties, and this helps to clarify how consciousness in machines may be studied as an emergent process related to choice functions in systems. A perspective on how quantization, acting on nucleic acids, sets up natural limits to system behavior is offered as a partial address to the problem of biogenesis.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43970209","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

Nonlocal Reaction–Diffusion Equations in Biomedical Applications 非局部反应扩散方程在生物医学中的应用

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-03-17 DOI: 10.1007/s10441-022-09436-4

M. Banerjee, M. Kuznetsov, O. Udovenko, V. Volpert

引用次数: 5

Qualitative and Dynamical Analysis of a Bionomic Fishery Model with Prey Refuge 具有猎物庇护的生物渔业模型的定性和动力学分析

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-02-04 DOI: 10.1007/s10441-022-09435-5

S. N. Raw, B. P. Sarangi

{"title":"Qualitative and Dynamical Analysis of a Bionomic Fishery Model with Prey Refuge","authors":"S. N. Raw, B. P. Sarangi","doi":"10.1007/s10441-022-09435-5","DOIUrl":"10.1007/s10441-022-09435-5","url":null,"abstract":"<div><p>Predation and escaping from predation through hiding are two fundamental phenomena in ecology. The most common approach to reducing the chance of predation is to use a refuge. Here, we consider a three species fishery model system with prey refuge induced by a Holling type-II functional response. These three species of fish populations are named prey, middle predator, and top predator. Harvesting is employed in most fishery models to achieve both ecological and commercial benefits. Research proves that non-linear harvesting (Michaelis–Menten type) returns more realistic outcomes. So, we have combined the Michaelis–Menten type of harvesting efforts for all populations. Uniform boundedness conditions for the solutions of the model are discussed. The existence conditions for possible equilibrium points with stability are presented. We explain the dynamical behavior at each equilibrium point through bifurcation analysis. The persistent criteria of the system are examined. Bionomic equilibrium and optimal harvesting control using Pontryagin’s maximum principle are calculated. For validation of the model in the real world, we have implemented this in the freshwater ecosystem of Lake Victoria. Extraction of native fish species and ecological balances are the foremost solicitude of Lake Victoria. We may resolve this concern partially by implementing prey refuge, since it may sustain the ecology of Lake Victoria, and therefore also its economical importance. Lake Victoria is acclaimed worldwide for the trade of fishing. Also, it provides the largest employment in east-central Africa and is beneficial to fishing equipment manufacturers. So, the bionomic equilibrium and harvesting control have significant applications in the fisheries. All the analytical studies are verified by numerical simulations. We have plotted phase portraits, bifurcation diagrams, Lyapunov exponents to explore the dynamics of the proposed model.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39889033","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: 3

The Hybrid Incidence Susceptible-Transmissible-Removed Model for Pandemics 流行病的混合发生率-易感-传播-去除模型

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-01-29 DOI: 10.1007/s10441-021-09431-1

Ryan Lester Benjamin

{"title":"The Hybrid Incidence Susceptible-Transmissible-Removed Model for Pandemics","authors":"Ryan Lester Benjamin","doi":"10.1007/s10441-021-09431-1","DOIUrl":"10.1007/s10441-021-09431-1","url":null,"abstract":"<div><p>The susceptible-transmissible-removed (STR) model is a deterministic compartment model, based on the susceptible-infected-removed (SIR) prototype. The STR replaces 2 SIR assumptions. SIR assumes that the emigration rate (due to death or recovery) is directly proportional to the infected compartment’s size. The STR replaces this assumption with the biologically appropriate assumption that the emigration rate is the same as the immigration rate one infected period ago. This results in a unique delay differential equation epidemic model with the delay equal to the infected period. Hamer’s mass action law for epidemiology is modified to resemble its chemistry precursor—the law of mass action. Constructing the model for an isolated population that exists on a surface bounded by the extent of the population’s movements permits compartment density to replace compartment size. The STR reduces to a SIR model in a timescale that negates the delay—the transmissible timescale. This establishes that the SIR model applies to an isolated population in the disease’s transmissible timescale. Cyclical social interactions will define a rhythmic timescale. It is demonstrated that the geometric mean maps transmissible timescale properties to their rhythmic timescale equivalents. This mapping defines the hybrid incidence (HI). The model validation demonstrates that the HI-STR can be constructed directly from the disease’s transmission dynamics. The basic reproduction number (<span>({mathcal{R}}_0)</span>) is an epidemic impact property. The HI-STR model predicts that <span>({mathcal{R}}_0 propto root mathfrak{B} of {rho_n})</span> where <span>(rho_n)</span> is the population density, and <span>({mathfrak{B}})</span> is the ratio of time increments in the transmissible- and rhythmic timescales. The model is validated by experimentally verifying the relationship. <span>({mathcal{R}}_0)</span>’s dependence on <span>(rho_n)</span> is demonstrated for droplet-spread SARS in Asian cities, aerosol-spread measles in Europe and non-airborne Ebola in Africa.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50053128","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: 2

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

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-01-20 DOI: 10.1101/2022.01.17.476676

J. Palgen, A. Perrillat-Mercerot, N. Ceres, E. Peyronnet, Matthieu Coudron, Eliott Tixier, B. Illigens, J. Bosley, A. L’Hostis, C. Monteiro

{"title":"Integration of Heterogeneous Biological Data in Multiscale Mechanistic Model Calibration: Application to Lung Adenocarcinoma","authors":"J. Palgen, A. Perrillat-Mercerot, N. Ceres, E. Peyronnet, Matthieu Coudron, Eliott Tixier, B. Illigens, J. Bosley, A. L’Hostis, C. Monteiro","doi":"10.1101/2022.01.17.476676","DOIUrl":"https://doi.org/10.1101/2022.01.17.476676","url":null,"abstract":"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.","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45053425","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: 6

A Mathematical Model of the Transmission Dynamics of Bovine Schistosomiasis with Contaminated Environment 牛血吸虫病受污染环境传播动力学的数学模型

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2022-01-12 DOI: 10.1007/s10441-021-09434-y

Solomon Kadaleka, Shirley Abelman, Jean M. Tchuenche

{"title":"A Mathematical Model of the Transmission Dynamics of Bovine Schistosomiasis with Contaminated Environment","authors":"Solomon Kadaleka, Shirley Abelman, Jean M. Tchuenche","doi":"10.1007/s10441-021-09434-y","DOIUrl":"10.1007/s10441-021-09434-y","url":null,"abstract":"<div><p>Schistosomiasis, a vector-borne chronically debilitating infectious disease, is a serious public health concern for humans and animals in the affected tropical and sub-tropical regions. We formulate and theoretically analyze a deterministic mathematical model with snail and bovine hosts. The basic reproduction number <span>(R_0)</span> is computed and used to investigate the local stability of the model’s steady states. Global stability of the endemic equilibrium is carried out by constructing a suitable Lyapunov function. Sensitivity analysis shows that the basic reproduction number is most sensitive to the model parameters related to the contaminated environment, namely: shedding rate of cercariae by snails, cercariae to miracidia survival probability, snails-miracidia effective contact rate and natural death rate of miracidia and cercariae. Numerical results show that when no intervention measures are implemented, there is an increase of the infected classes, and a rapid decline of the number of susceptible and exposed bovines and snails. Effects of the variation of some of the key sensitive model parameters on the schistosomiasis dynamics as well as on the initial disease transmission threshold parameter <span>(R_0)</span> are graphically depicted.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2022-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39690432","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: 2

Modeling the Waves of Covid-19 模拟Covid-19的波动

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-12-27 DOI: 10.1007/s10441-021-09428-w

Ivan Cherednik

引用次数: 10

Average and Standard Deviation of the Error Function for Random Genetic Codes with Standard Stop Codons 具有标准终止密码子的随机遗传密码误差函数的平均值和标准差

IF 1.3 4区生物学

Acta Biotheoretica Pub Date : 2021-12-17 DOI: 10.1007/s10441-021-09427-x

Dino G. Salinas

{"title":"Average and Standard Deviation of the Error Function for Random Genetic Codes with Standard Stop Codons","authors":"Dino G. Salinas","doi":"10.1007/s10441-021-09427-x","DOIUrl":"10.1007/s10441-021-09427-x","url":null,"abstract":"<div><p>The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick’s hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code. This work aims to contribute in this regard, that is, it provides a theoretical framework in which statistical parameters of error functions are calculated. Given a genetic code and an amino acid property, the functional code robustness is estimated by means of a known error function. In this work, using analytical calculations, general expressions for the average and standard deviation of the error function distributions of completely random codes with standard stop codons were obtained. As a possible biological application of these results, any set of amino acids and any pure or mixed amino acid properties can be used in the calculations, such that, in case of having to select a set of amino acids to create a genetic code, possible advantages of natural selection of the genetic codes could be discussed.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39734508","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: 2