Theory in Biosciences最新文献

{"title":"Optimal allocation in annual plants with density-dependent fitness.","authors":"Sergiy Koshkin,&nbsp;Zachary Zalles,&nbsp;Michael F Tobin,&nbsp;Nicolas Toumbacaris,&nbsp;Cameron Spiess","doi":"10.1007/s12064-021-00343-9","DOIUrl":"https://doi.org/10.1007/s12064-021-00343-9","url":null,"abstract":"<p><p>We study optimal two-sector (vegetative and reproductive) allocation models of annual plants in temporally variable environments that incorporate effects of density-dependent lifetime variability and juvenile mortality in a fitness function whose expected value is maximized. Only special cases of arithmetic and geometric mean maximizers have previously been considered in the literature, and we also allow a wider range of production functions with diminishing returns. The model predicts that the time of maturity is pushed to an earlier date as the correlation between individual lifetimes increases, and while optimal schedules are bang-bang at the extremes, the transition is mediated by schedules where vegetative growth is mixed with reproduction for a wide intermediate range. The mixed growth lasts longer when the production function is less concave allowing for better leveraging of plant size when generating seeds. Analytic estimates are obtained for the power means that interpolate between arithmetic and geometric mean and correspond to partially correlated lifetime distributions.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"177-196"},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00343-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25584593","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}

{"title":"Role of integrated noise in pathway-specific signal propagation in feed-forward loops.","authors":"Mintu Nandi","doi":"10.1007/s12064-021-00338-6","DOIUrl":"https://doi.org/10.1007/s12064-021-00338-6","url":null,"abstract":"<p><p>Cells impose optimal noise control mechanism in diverse situations to cope with distinct environmental cues. Sometimes, it is desirable for the cell to utilize fluctuations for noise-driven processes. In other cases, noise can be harmful to the cell to show optimal fitness. It is, therefore, important to unravel the noise propagation mechanism inside the cell. Such noise controlling mechanism is accomplished by using gene transcription regulatory networks. One such gene regulatory network is feed-forward loop, having three regulatory nodes S, X and Y. Here, we consider the most abundant type 1 of coherent and incoherent feed-forward loops with both OR and AND logic functions, forming four different architectures. In OR logic function, the functions representing S and X act additively for the regulation of Y, while in AND logic function, the same functions (S and X) act multiplicatively for the regulation of Y. Measurement of susceptibility of the signal at output Y is done using elasticity of each regulation in FFLs. Using susceptibility, we demonstrate the nature of pathway integration by which one-step and two-step pathways get overlapped. The integration type is competitive for motifs having OR gate, while it is noncompetitive for the same with AND gate. The pathway integration property explains the output noise behavior of the motifs properly but cannot infer about the mechanism by which the upstream noise propagates to output. To account this, the total output noise is decomposed, which results in integrated noise as an additional noise source along with pathway-specific noise components. The integrated noise is found to appear as a consequence of integration between the pathways and has different functional characteristics explaining noise amplification and noise attenuation property of coherent and incoherent feed-forward loops, respectively. The noise decomposition also quantifies the contribution of different noise sources toward total noise. Finally, the noise propagation is being tuned as a function of input signal noise and its time scale of fluctuations, which shows considerable intrinsic noise strength and relatively slow relaxation time scale causes a higher degree of noise propagation in FFLs.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"139-155"},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00338-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25504545","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}

{"title":"Effects of water currents on fish migration through a Feynman-type path integral approach under [Formula: see text] Liouville-like quantum gravity surfaces.","authors":"Paramahansa Pramanik","doi":"10.1007/s12064-021-00345-7","DOIUrl":"https://doi.org/10.1007/s12064-021-00345-7","url":null,"abstract":"<p><p>A stochastic differential game theoretic model has been proposed to determine optimal behavior of a fish while migrating against water currents both in rivers and oceans. Then, a dynamic objective function is maximized subject to two stochastic dynamics, one represents its location and another its relative velocity against water currents. In relative velocity stochastic dynamics, a Cucker-Smale type stochastic differential equation is introduced under white noise. As the information regarding hydrodynamic environment is incomplete and imperfect, a Feynman type path integral under [Formula: see text] Liouville-like quantum gravity surface has been introduced to obtain a Wick-rotated Schrödinger type equation to determine an optimal strategy of a fish during its migration. The advantage of having Feynman type path integral is that, it can be used in more generalized nonlinear stochastic differential equations where constructing a Hamiltonian-Jacobi-Bellman (HJB) equation is impossible. The mathematical analytic results show exact expression of an optimal strategy of a fish under imperfect information and uncertainty.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"205-223"},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00345-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39001856","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}

{"title":"Optimal harvesting and stability of a predator-prey model for fish populations with schooling behavior.","authors":"Mohamed El Mahdi Hacini,&nbsp;Djammel Hammoudi,&nbsp;Salih Djilali,&nbsp;Soufiane Bentout","doi":"10.1007/s12064-021-00347-5","DOIUrl":"https://doi.org/10.1007/s12064-021-00347-5","url":null,"abstract":"<p><p>In this paper, the schooling behavior of prey fish population in a predator-prey interaction is investigated. By taking an economical interest which can be elaborated by the presence of nonselective harvesting into consideration, we studied the dynamical behavior. The existence, positivity and boundedness of solution have been established. The analysis of the equilibrium states is presented by studying the local and the global stability. The possible types of local bifurcation that the system can undergoes are discussed. The effect of fishing effort on the evolution of the species is examined. Further, by using Pontryagin's maximum principle a proper management strategy has been used for avoiding the extinction of the considered species and maximizing the benefits. For the validation of the theoretical result, several of graphical representations have been used.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"225-239"},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00347-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39014965","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}

{"title":"A reaction norm perspective on reproducibility.","authors":"Bernhard Voelkl, Hanno Würbel","doi":"10.1007/s12064-021-00340-y","DOIUrl":"10.1007/s12064-021-00340-y","url":null,"abstract":"<p><p>Reproducibility in biomedical research, and more specifically in preclinical animal research, has been seriously questioned. Several cases of spectacular failures to replicate findings published in the primary scientific literature have led to a perceived reproducibility crisis. Diverse threats to reproducibility have been proposed, including lack of scientific rigour, low statistical power, publication bias, analytical flexibility and fraud. An important aspect that is generally overlooked is the lack of external validity caused by rigorous standardization of both the animals and the environment. Here, we argue that a reaction norm approach to phenotypic variation, acknowledging gene-by-environment interactions, can help us seeing reproducibility of animal experiments in a new light. We illustrate how dominating environmental effects can affect inference and effect size estimates of studies and how elimination of dominant factors through standardization affects the nature of the expected phenotype variation through the reaction norms of small effect. Finally, we discuss the consequences of reaction norms of small effect for statistical analysis, specifically for random effect latent variable models and the random lab model.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"169-176"},"PeriodicalIF":1.3,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8175247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25531423","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}

{"title":"Mathematical computations on epidemiology: a case study of the novel coronavirus (SARS-CoV-2).","authors":"Saikat Batabyal, Arthita Batabyal","doi":"10.1007/s12064-021-00339-5","DOIUrl":"10.1007/s12064-021-00339-5","url":null,"abstract":"<p><p>The outbreak of coronavirus COVID-19 is spreading at an unprecedented rate to the human populations and taking several thousands of life all over the world. Scientists are trying to map the pattern of the transmission of coronavirus (SARS-CoV-2). Many countries are in the phase of lockdown in the globe. In this paper we predict about the effect of coronavirus COVID-19 and give a sneak peak when it will reduce the transmission rate in the world via mathematical modelling. In this research work our study is based on extensions of the well-known susceptible-exposed-infected-recovered (SEIR) family of compartmental models and later we observe the new model changes into (SEIR) without changing its physical meanings. The stability analysis of the coronavirus depends on changing of its basic reproductive ratio. The progress rate of the virus in the critically infected cases and the recovery rate have major roles to control this epidemic. The impact of social distancing, lockdown of the country, self-isolation, home quarantine and the wariness of global public health system have significant influence on the parameters of the model system that can alter the effect of recovery rates, mortality rates and active contaminated cases with the progression of time in the real world. The prognostic ability of mathematical model is circumscribed as of the accuracy of the available data and its application to the problem.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"123-138"},"PeriodicalIF":1.3,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7937432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25455706","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}

{"title":"On the historical roots of creationism and intelligent design: German Allmacht and Darwinian evolution in context.","authors":"Elizabeth Watts,&nbsp;Ulrich Kutschera","doi":"10.1007/s12064-021-00341-x","DOIUrl":"https://doi.org/10.1007/s12064-021-00341-x","url":null,"abstract":"<p><p>As detailed in a Letter published in Science in 2017, the adherents of creationism and intelligent design are still active in promoting their biblical-literalist views of the origin and evolution of life on Earth. In this contribution, we take a look at this ideological phenomenon in the USA and analyze the philosophical roots of this ongoing movement. Specifically, we discuss Vernon Kellogg's book entitled Headquarters Nights (1917) with reference to the German 'Allmacht' (English-omnipotence) and Darwinian evolution to demonstrate how this publication bolstered the development of active anti-evolutionism in the USA among American fundamentalist Christians, inclusive of the Intelligent Design (ID)-agenda. The current activities of creationist associations in the USA and Germany are summarized, with reference to a new pro-ID-group established in Austria in 2019 that is sponsored by the Discovery Institute in Seattle, Washington (USA).</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 2","pages":"157-168"},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00341-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25512317","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}

{"title":"Modelling and optimal control for Chikungunya disease.","authors":"Miled El Hajji","doi":"10.1007/s12064-020-00324-4","DOIUrl":"https://doi.org/10.1007/s12064-020-00324-4","url":null,"abstract":"<p><p>A generalized model of intra-host CHIKV infection with two routes of infection has been proposed. In a first step, the basic reproduction number [Formula: see text] was calculated using the next-generation matrix method and the local and global stability analyses of the steady states are carried out using the Lyapunov method. It is proven that the CHIKV-free steady state [Formula: see text] is globally asymptotically stable when [Formula: see text] and the infected steady state [Formula: see text] is globally asymptotically stable when [Formula: see text]. In a second step, we applied an optimal strategy via the antibodies' flow rate in order to optimize infected compartment and to maximize the uninfected one. For this, we formulated a nonlinear optimal control problem. Existence of the optimal solution was discussed and characterized using an adjoint variables. Thus, an algorithm based on competitive Gauss-Seidel-like implicit difference method was applied in order to resolve the optimality system. The theoretical results are confirmed by some numerical simulations.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 1","pages":"27-44"},"PeriodicalIF":1.1,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00324-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38551241","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}

{"title":"\"Cladus\" and clade: a taxonomic odyssey.","authors":"P Tassy,&nbsp;M S Fischer","doi":"10.1007/s12064-020-00326-2","DOIUrl":"https://doi.org/10.1007/s12064-020-00326-2","url":null,"abstract":"<p><p>The fate of \"clade,\" both as concept and word, is reconstructed here beginning with its first appearance in 1866 as \"Cladus,\" in Haeckel's Generelle Morphologie, continuing up to the present. Although central to phylogenetics, the concept of clade is paradoxical since it has been ambiguously understood or even misunderstood by its own promoters. Writings by Ernst Haeckel, Lucien Cuénot, and Julian Huxley, the three authors who discussed the notion of clade at length, are analyzed here in detail as a means of exploring this paradox. First conceived as a rank for a higher-level category, and later as a taxon, the clade is understood today in connection with Hennig's definition of a monophyletic group rather than through Huxley's successful but somehow ambiguous formalization. The inability of these authors to formulate a clear-cut exposition of the concept is considered here within three contexts: firstly, the burden of pre-Darwinian classifications based on similarity; secondly, the underestimation of Darwin's description of a genealogical group; and thirdly, the predominance of thinking in process (vs thinking in pattern), which was the basis of evolutionary systematics in the mid-twentieth century.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 1","pages":"77-85"},"PeriodicalIF":1.1,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00326-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38522349","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}

{"title":"Hypothesis: nucleoid-associated proteins segregate with a parental DNA strand to generate coherent phenotypic diversity.","authors":"Yoan Konto-Ghiorghi,&nbsp;Vic Norris","doi":"10.1007/s12064-020-00323-5","DOIUrl":"https://doi.org/10.1007/s12064-020-00323-5","url":null,"abstract":"<p><p>The generation of a phenotypic diversity that is coherent across a bacterial population is a fundamental problem. We propose here that the DNA strand-specific segregation of certain nucleoid-associated proteins or NAPs results in these proteins being asymmetrically distributed to the daughter cells. We invoke a variety of mechanisms as responsible for this asymmetrical segregation including those based on differences between the leading and lagging strands, post-translational modifications, oligomerisation and association with membrane domains.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"140 1","pages":"17-25"},"PeriodicalIF":1.1,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-020-00323-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38522350","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}