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Acta Biotheoretica

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https://www.readbyqxmd.com/read/30182354/from-biological-determination-to-entangled-causation
#1
Davide Vecchi, Paul-Antoine Miquel, Isaac Hernández
Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion of developmental determinant is causal...
September 4, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29846858/an-inverse-problem-trappers-drove-hares-to-eat-lynx
#2
Bo Deng
The Canadian lynx and snowshoe hare pelt data by the Hudson Bay Company did not fit the classical predator-prey theory. Rather than following the peak density of the hare, that of the lynx leads it, creating the hares-eat-lynx (HEL) paradox. Although trappers were suspected to play a role, no mathematical model has ever demonstrated the HEL effect. Here we show that the long-held assumption that the pelt number is a proxy of the wild populations is false and that when the data are modeled by the harvest rates by the trappers, the problem is finally resolved: both the HEL paradox and the classical theory are unified in our mechanistic hare-lynx-competitor-trapper (HLCT) model where competitor stands for all predators of the hares other than the lynx...
September 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29797159/descriptive-modeling-of-the-dynamical-systems-and-determination-of-feedback-homeostasis-at-different-levels-of-life-organization
#3
G N Zholtkevych, K V Nosov, Yu G Bespalov, L I Rak, M Abhishek, E V Vysotskaya
The state-of-art research in the field of life's organization confronts the need to investigate a number of interacting components, their properties and conditions of sustainable behaviour within a natural system. In biology, ecology and life sciences, the performance of such stable system is usually related to homeostasis, a property of the system to actively regulate its state within a certain allowable limits. In our previous work, we proposed a deterministic model for systems' homeostasis. The model was based on dynamical system's theory and pairwise relationships of competition, amensalism and antagonism taken from theoretical biology and ecology...
September 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/30121875/design-methodologies-and-the-limits-of-the-engineering-dominated-conception-of-synthetic-biology
#4
Tero Ijäs
Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational design and directed evolution...
August 18, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/30097799/proceedings-of-the-first-vietnamese-french-joint-conference-on-applications-of-mathematics-to-ecology-bio-economics-epidemiology-and-health-care-hanoi-and-tuanchau-vietnam-december-12-15-2016
#5
EDITORIAL
https://www.readbyqxmd.com/read/29971669/mathematical-assessment-of-the-role-of-early-latent-infections-and-targeted-control-strategies-on-syphilis-transmission-dynamics
#6
D Okuonghae, A B Gumel, B O Ikhimwin, E Iboi
A new multi-stage deterministic model for the transmission dynamics of syphilis, which incorporates disease transmission by individuals in the early latent stage of syphilis infection and the reversions of early latent syphilis to the primary and secondary stages, is formulated and rigorously analysed. The model is used to assess the population-level impact of preventive (condom use) and therapeutic measures (treatment using antibiotics) against the spread of the disease in a community. It is shown that the disease-free equilibrium of the model is globally-asymptotically stable whenever the associated control reproduction number (denoted by [Formula: see text]) is less than unity...
July 3, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29948413/study-of-the-population-dynamics-of-busseola-fusca-maize-pest
#7
Janvier Pesser Ntahomvukiye, Anatole Temgoua, Samuel Bowong
Busseola fusca is a maize and sorghum pest that can cause significant damage to both crops. Given that maize is one of the main cereals grown in the worldwide, this pest is a major challenge for maize production and therefore for the economies of several countries . In this paper , based on the life cycle of B. fusca, we propose a mathematical model to study the population dynamics of this insect pest . A sensitivity analysis using the eFast method was performed to show the most important parameters of the model...
June 14, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29872936/correction-to-graphical-representation-and-similarity-analysis-of-dna-sequences-based-on-trigonometric-functions
#8
Guo-Sen Xie, Xiao-Bo Jin, Chunlei Yang, Jiexin Pu, Zhongxi Mo
In the original publication of the article, the y axis labels present in Figs. 1a and 2a are incorrect. The correct Figs. 1a and 2a are provided here.
June 5, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29700659/mathematical-basis-of-predicting-dominant-function-in-protein-sequences-by-a-generic-hmm-ann-algorithm
#9
Siddhartha Kundu
The accurate annotation of an unknown protein sequence depends on extant data of template sequences. This could be empirical or sets of reference sequences, and provides an exhaustive pool of probable functions. Individual methods of predicting dominant function possess shortcomings such as varying degrees of inter-sequence redundancy, arbitrary domain inclusion thresholds, heterogeneous parameterization protocols, and ill-conditioned input channels. Here, I present a rigorous theoretical derivation of various steps of a generic algorithm that integrates and utilizes several statistical methods to predict the dominant function in unknown protein sequences...
June 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29675730/graphical-representation-and-similarity-analysis-of-dna-sequences-based-on-trigonometric-functions
#10
Guo-Sen Xie, Xiao-Bo Jin, Chunlei Yang, Jiexin Pu, Zhongxi Mo
In this paper, we propose two four-base related 2D curves of DNA primary sequences (termed as F-B curves) and their corresponding single-base related 2D curves (termed as A-related, G-related, T-related and C-related curves). The constructions of these graphical curves are based on the assignments of individual base to four different sinusoidal (or tangent) functions; then by connecting all these points on these four sinusoidal (tangent) functions, we can get the F-B curves; similarly, by connecting the points on each of the four sinusoidal (tangent) functions, we get the single-base related 2D curves...
June 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29616380/culture-and-the-trajectories-of-developmental-pathology-insights-from-control-and-information-theories
#11
Rodrick Wallace
Cognition in living entities-and their social groupings or institutional artifacts-is necessarily as complicated as their embedding environments, which, for humans, includes a particularly rich cultural milieu. The asymptotic limit theorems of information and control theories permit construction of a new class of empirical 'regression-like' statistical models for cognitive developmental processes, their dynamics, and modes of dysfunction. Such models may, as have their simpler analogs, prove useful in the study and re-mediation of cognitive failure at and across the scales and levels of organization that constitute and drive the phenomena of life...
June 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29808449/permanence-and-extinction-of-a-diffusive-predator-prey-model-with-robin-boundary-conditions
#12
M A Aziz-Alaoui, M Daher Okiye, A Moussaoui
The main concern of this paper is to study the dynamic of a predator-prey system with diffusion. It incorporates the Holling-type-II and a modified Leslie-Gower functional responses under Robin boundary conditions. More concretely, we study the dissipativeness of the system by using the comparison principle, and we derive a criteria for permanence and for predator extinction.
May 28, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29761301/importance-of-initial-concentration-of-factor-viii-in-a-mechanistic-model-of-in-vitro-coagulation
#13
M Susree, M Anand
This computational study generates a hypothesis for the coagulation protein whose initial concentration greatly influences the course of coagulation. Many clinical malignancies of blood coagulation arise due to abnormal initial concentrations of coagulation factors. Sensitivity analysis of mechanistic models of blood coagulation is a convenient method to assess the effect of such abnormalities. Accordingly, the study presents sensitivity analysis, with respect to initial concentrations, of a recently developed mechanistic model of blood coagulation...
May 14, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29761300/natural-selection-and-drift-as-individual-level-causes-of-evolution
#14
Pierrick Bourrat
In this paper I critically evaluate Reisman and Forber's (Philos Sci 72(5):1113-1123, 2005) arguments that drift and natural selection are population-level causes of evolution based on what they call the manipulation condition. Although I agree that this condition is an important step for identifying causes for evolutionary change, it is insufficient. Following Woodward, I argue that the invariance of a relationship is another crucial parameter to take into consideration for causal explanations. Starting from Reisman and Forber's example on drift and after having briefly presented the criterion of invariance, I show that once both the manipulation condition and the criterion of invariance are taken into account, drift, in this example, should better be understood as an individual-level rather than a population-level cause...
May 14, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29744615/systems-biology-systems-medicine-systems-pharmacology-the-what-and-the-why
#15
Angélique Stéphanou, Eric Fanchon, Pasquale F Innominato, Annabelle Ballesta
Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop...
May 9, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29728954/theoretical-assessment-of-the-impact-of-climatic-factors-in-a-vibrio-cholerae-model
#16
G Kolaye, I Damakoa, S Bowong, R Houe, D Békollè
A mathematical model for Vibrio Cholerae (V. Cholerae) in a closed environment is considered, with the aim of investigating the impact of climatic factors which exerts a direct influence on the bacterial metabolism and on the bacterial reservoir capacity. We first propose a V. Cholerae mathematical model in a closed environment. A sensitivity analysis using the eFast method was performed to show the most important parameters of the model. After, we extend this V. cholerae model by taking account climatic factors that influence the bacterial reservoir capacity...
May 4, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29713844/the-origin-of-species-by-means-of-mathematical-modelling
#17
Nikolai Bessonov, Natalia Reinberg, Malay Banerjee, Vitaly Volpert
Darwin described biological species as groups of morphologically similar individuals. These groups of individuals can split into several subgroups due to natural selection, resulting in the emergence of new species. Some species can stay stable without the appearance of a new species, some others can disappear or evolve. Some of these evolutionary patterns were described in our previous works independently of each other. In this work we have developed a single model which allows us to reproduce the principal patterns in Darwin's diagram...
April 30, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29700660/drug-repositioning-by-integrating-known-disease-gene-and-drug-target-associations-in-a-semi-supervised-learning-model
#18
Duc-Hau Le, Doanh Nguyen-Ngoc
Computational drug repositioning has been proven as a promising and efficient strategy for discovering new uses from existing drugs. To achieve this goal, a number of computational methods have been proposed, which are based on different data sources of drugs and diseases. These methods approach the problem using either machine learning- or network-based models with an assumption that similar drugs can be used for similar diseases to identify new indications of drugs. Therefore, similarities between drugs and between diseases are usually used as inputs...
April 26, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29687203/adaptive-control-based-harvesting-strategy-for-a-predator-prey-dynamical-system
#19
Moitri Sen, Ashutosh Simha, Soumyendu Raha
This paper deals with designing a harvesting control strategy for a predator-prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical block strict feedback structure of the dynamics is exploited in designing a backstepping control law, based on Lyapunov theory...
April 23, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29546657/a-3d-individual-based-model-to-study-effects-of-chemotaxis-competition-and-diffusion-on-the-motile-phytoplankton-aggregation
#20
Ilhem Bouderbala, Nadjia El Saadi, Alassane Bah, Pierre Auger
In this paper, we develop a 3D-individual-based model (IBM) to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities (chemotaxis), a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells...
March 15, 2018: Acta Biotheoretica
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