-
Mathematical Analysis of an Industrial HIV/AIDS Model that Incorporates Carefree Attitude Towards Sex Acta Biotheor. (IF 0.719) Pub Date : 2021-01-27 Baba Seidu, O. D. Makinde, Christopher S. Bornaa
A nonlinear differential equation model is proposed to study the dynamics of HIV/AIDS and its effects on workforce productivity. The disease-free equilibrium point of the model is shown to be locally asymptotically stable when the associated basic reproduction number \(\mathcal{{R}}_{0}\) is less than unity. The model is also shown to exhibit multiple endemic states for some parameter values when
-
The Structure of Causal Explanations in Population Biology Acta Biotheor. (IF 0.719) Pub Date : 2021-01-14 Erik Weber, Roxan Degeyter
The scope of this paper can be clarified by means of a well-known phenomenon that is usually called ‘industrial melanism’: the fact that the melanic form of the peppered moth became dominant in industrial areas in England in the second half of the nineteenth century. Such changes in relative phenotype frequencies are important explananda for population biologists. Apart from trying to explain such
-
Optimal Control and Cost-Effectiveness Analysis of an HPV– Chlamydia trachomatis Co-infection Model Acta Biotheor. (IF 0.719) Pub Date : 2021-01-03 A. Omame, C. U. Nnanna, S. C. Inyama
In this work, a co-infection model for human papillomavirus (HPV) and Chlamydia trachomatis with cost-effectiveness optimal control analysis is developed and analyzed. The disease-free equilibrium of the co-infection model is shown not to be globally asymptotically stable, when the associated reproduction number is less unity. It is proven that the model undergoes the phenomenon of backward bifurcation
-
Photosynthetic Systems Suggest an Evolutionary Pathway to Diderms Acta Biotheor. (IF 0.719) Pub Date : 2020-12-07 Scott O. Rogers
Bacteria are divided primarily into monoderms (with one cell membrane, and usually Gram-positive, due to a thick peptidoglycan layer) and diderms (with two cell membranes, and mostly Gram-negative, due to a thin peptidoglycan layer sandwiched between the two membranes). Photosynthetic species are spread among the taxonomic groups, some having type I reaction centers (RCI in monoderm phylum Firmicutes;
-
The Continuity Principle and the Evolution of Replication Fidelity Acta Biotheor. (IF 0.719) Pub Date : 2020-11-29 Seymour Garte
Evolution in modern life requires high replication fidelity to allow for natural selection. A simulation model utilizing simulated phenotype data on cellular probability of survival was developed to determine how self-replication fidelity could evolve in early life. The results indicate that initial survivability and replication fidelity both contribute to overall fitness as measured by growth rates
-
Fitness Beats Truth in the Evolution of Perception Acta Biotheor. (IF 0.719) Pub Date : 2020-11-24 Chetan Prakash, Kyle D. Stephens, Donald D. Hoffman, Manish Singh, Chris Fields
Does natural selection favor veridical percepts—those that accurately (if not exhaustively) depict objective reality? Perceptual and cognitive scientists standardly claim that it does. Here we formalize this claim using the tools of evolutionary game theory and Bayesian decision theory. We state and prove the “Fitness-Beats-Truth (FBT) Theorem” which shows that the claim is false: If one starts with
-
Mechanical Properties of Long Leaves: Experiment and Theory Acta Biotheor. (IF 0.719) Pub Date : 2020-10-31 A. Jakubska-Busse, M. W. Janowicz, L. Ochnio, B. Jackowska-Zduniak, J. M. A. Ashbourn
The static properties of leaves with parallel venation from terrestrial orchids of the genus Epipactis were modelled as coupled elastic rods using the geometrically exact Cosserat theory and the resulting boundary-value problem was solved numerically using a method from Shampine, Muir and Xu. The response of the leaf structure to the applied force was obtained from preliminary measurements. These measurements
-
The Metaphysics of Causation in Biological Mechanisms: A Case of the Genetic Switch in Lambda Phage Acta Biotheor. (IF 0.719) Pub Date : 2020-10-27 Zvonimir Anić
The emphasis on the organization of entities and their activities and interactions has been labeled one of the most distinct contributions of mechanistic philosophy. In this paper I discuss the manner in which the organization of entities and their activities and interactions participates in bringing about phenomena. I present a well-known example from molecular biology—the functioning of the genetic
-
Inheritance as Evolved and Evolving Physiological Processes Acta Biotheor. (IF 0.719) Pub Date : 2020-10-21 Francesca Merlin, Livio Riboli-Sasco
In this paper, we adopt a physiological perspective in order to produce an intelligible overview of biological transmission in all its diversity. This allows us to put forward the analysis of transmission mechanisms, with the aim of complementing the usual focus on transmitted factors. We underline the importance of the structural, dynamical, and functional features of transmission mechanisms throughout
-
Different Mechanisms of Cigarette Smoking-Induced Lung Cancer. Acta Biotheor. (IF 0.719) Pub Date : 2020-09-26 Ahmed Nagah,Asmaa Amer
The risk of cigarette smoking plays a pivotal role in increasing the incidence rates of lung cancer. This paper sheds new light on modeling the impact of cigarette smoking on lung cancer evolution, especially genetic instability and the number of gene mutations in the genome of stem cells. To handle this issue, we have set up stochastic multi-stage models to fit the data set of the probabilities of
-
Probability of Disease Extinction or Outbreak in a Stochastic Epidemic Model for West Nile Virus Dynamics in Birds. Acta Biotheor. (IF 0.719) Pub Date : 2020-09-05 Milliward Maliyoni
Thresholds for disease extinction provide essential information for the prevention and control of diseases. In this paper, a stochastic epidemic model, a continuous-time Markov chain, for the transmission dynamics of West Nile virus in birds is developed based on the assumptions of its analogous deterministic model. The branching process is applied to derive the extinction threshold for the stochastic
-
The Epistemology of a Positive SARS-CoV-2 Test. Acta Biotheor. (IF 0.719) Pub Date : 2020-09-04 Rainer Johannes Klement,Prasanta S Bandyopadhyay
We investigate the epistemological consequences of a positive polymerase chain reaction SARS-CoV test for two relevant hypotheses: (i) V is the hypothesis that an individual has been infected with SARS-CoV-2; (ii) C is the hypothesis that SARS-CoV-2 is the cause of flu-like symptoms in a given patient. We ask two fundamental epistemological questions regarding each hypothesis: First, how much confirmation
-
Computational and Theoretical Analysis of the Association Between Gender and HSV-2 Treatment Adherence. Acta Biotheor. (IF 0.719) Pub Date : 2020-09-03 A Mhlanga,S Mushayabasa
Herpes simplex virus type 2 (HSV-2) is the most prevalent sexually transmitted infection in the world, despite the availability of effective anti-viral treatments. A mathematical model to explore the association between gender and HSV-2 treatment adherence is developed. Threshold parameters are determined and stabilities analyzed. Sensitivity analysis of the reproduction number and the numerical simulations
-
Wolf Howling and Emergency Sirens: A Hypothesis of Natural and Technical Convergence of Aposematic Signals. Acta Biotheor. (IF 0.719) Pub Date : 2020-09-02 Diana Kořanová,Lucie Němcová,Richard Policht,Vlastimil Hart,Sabine Begall,Hynek Burda
Acoustic signals serving intraspecific communication by predators are perceived by potential prey as warning signals. We analysed the acoustic characteristics of howling of wolves and found a striking similarity to the warning sounds of technical sirens. We hypothesize that the effectivity of sirens as warning signals has been enhanced by natural sensory predisposition of humans to get alerted by howling
-
Functional Integration and Individuality in Prokaryotic Collective Organisations. Acta Biotheor. (IF 0.719) Pub Date : 2020-08-20 Guglielmo Militello,Leonardo Bich,Alvaro Moreno
Both physiological and evolutionary criteria of biological individuality are underpinned by the idea that an individual is a functionally integrated whole. However, a precise account of functional integration has not been provided so far, and current notions are not developed in the details, especially in the case of composite systems. To address this issue, this paper focuses on the organisational
-
The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems (Origin of Life). Acta Biotheor. (IF 0.719) Pub Date : 2020-08-11 Francisco Prosdocimi,Marco V José,Sávio Torres de Farias
The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. This folding catalyzed the formation
-
Fractured Symmetries: Information and Control Theory Perspectives on Mitochondrial Dysfunction. Acta Biotheor. (IF 0.719) Pub Date : 2020-07-28 Rodrick Wallace
Mitochondrial dysfunction underlies a vast array of chronic disorders across the life span. The asymptotic limit theorems of information and control theories, supplemented by symmetry-breaking phase transition arguments adapted from physical theory, give deep insight into canonical mechanisms of cognition and regulation associated with such dysfunction. The probability models studied here can provide
-
A Note Against the Use of "Belonging To" Properties in Multilevel Selection Theory. Acta Biotheor. (IF 0.719) Pub Date : 2020-07-13 Ciprian Jeler
In this short paper, I argue against what I call the “belonging to” interpretation of group selection in scenarios in which a group’s fitness is defined as the per capita reproductive output of the individuals of the group. According to this interpretation, group selection acts on “belonging to” properties of individuals, i.e. on relational or contextual properties that all the individuals of a group
-
Assessing the Effects of Holling Type-II Treatment Rate on HIV-TB Co-infection. Acta Biotheor. (IF 0.719) Pub Date : 2020-06-16 Tanvi,Rajiv Aggarwal,Tamas Kovacs
In this paper, a HIV-TB co-infection model is explored which incorporates a non-linear treatment rate for TB. We begin with presenting a HIV-TB co-infection model and analyze both HIV and TB sub-models separately. The basic reproduction numbers corresponding to HIV-only, TB-only and the HIV-TB full model are computed. The disease-free equilibrium point of the HIV sub-model is shown to be locally as
-
Evolution, Cultural Evolution, and Epistemic Optimism : Alberto Acerbi. Cultural Evolution in the Digital Age. Oxford: Oxford University Press. 272pp. ISBN: 9780198835943. Hugo Mercier. Not Born Yesterday: The Science of Who We Trust and What We Believe. Princeton: Princeton University Press. 384pp. ISBN: 9780691178707. Acta Biotheor. (IF 0.719) Pub Date : 2020-05-24 Andrew Buskell
-
Correction to: Mathematical Basis of Predicting Dominant Function in Protein Sequences by a Generic HMM-ANN Algorithm. Acta Biotheor. (IF 0.719) Pub Date : 2020-05-08 Siddhartha Kundu
An amendment to this paper has been published and can be accessed via the original article.
-
How Could This Happen? : Narrowing Down the Contagion of COVID-19 and Preventing Acute Respiratory Distress Syndrome (ARDS). Acta Biotheor. (IF 0.719) Pub Date : 2020-04-25 Wilfried Allaerts
In this rapid commentary, a mini-review is given of the present state-of-knowledge regarding the etiology and epidemiology of the new coronavirus 2019-nCoV and the risks for developing Acute respiratory distress syndrome (ARDS). The available knowledge on the viral genomics, molecular biology and pathogenicity of viruses of the Coronaviridae family and other Nidovirales, forms a helpful template for
-
What’s Wrong with Evolutionary Causation? Acta Biotheor. (IF 0.719) Pub Date : 2020-04-13 Jan Baedke
This review essay reflects on recent discussions in evolutionary biology and philosophy of science on the central causes of evolution and the structure of causal explanations in evolutionary theory. In this debate, it has been argued that our view of evolutionary causation should be rethought by including more seriously developmental causes and causes of the individual acting organism. I use Tobias
-
Essay Review: Exploring the Conceptual Foundations of Post-Hamiltonian Evolutionary Biology-Rationality and Evolution of Social Agents : Samir Okasha. Agents and Goals in Evolution. Oxford: Oxford University Press, 2018. 254p. $40. Jonathan Birch. The Philosophy of Social Evolution. Oxford: Oxford University Press, 2017. 266p. $19,74. Acta Biotheor. (IF 0.719) Pub Date : 2020-04-01 Philippe Huneman
Evolutionary theorists often talk as if natural selection were choosing the most adapted traits, or if organisms were deciding to do the most adaptive strategy. Moreover, the payoff of those decisions often depend on what others are doing, and since Hamilton (1964), biologists possess conceptual tools such as kin selection and inclusive fitness to make sense of outcomes of evolution in these contexts
-
The Goodwin Oscillator and its Legacy Acta Biotheor. (IF 0.719) Pub Date : 2020-03-25 Didier Gonze, Peter Ruoff
In the 1960’s Brian Goodwin published a couple of mathematical models showing how feedback inhibition can lead to oscillations and discussed possible implications of this behaviour for the physiology of the cell. He also presented key ideas about the rich dynamics that may result from the coupling between such biochemical oscillators. Goodwin’s work motivated a series of theoretical investigations
-
Retraction Note to: Robust Model Selection and Estimation for Censored Survival Data with High Dimensional Genomic Covariates. Acta Biotheor. (IF 0.719) Pub Date : 2020-02-27 Guorong Chen,Sijian Wang,Guannan Sun,Huanxue Pan
The authors have retracted this article [1] because they found a fundamental mistake in the methodology that is not correctable at this time. This mistake is found in the methodology and the derivation of the model with Tukey and Huber's losses. Because of the error, the findings in the article are not reliable. All authors agree to this retraction.
-
Proceedings of the XXXVIIIth Seminar of the French-Speaking Society for Theoretical Biology; Saint-Flour (Cantal), France, 11-13 June, 2018. Acta Biotheor. (IF 0.719) Pub Date : 2020-02-24 Nicolas Glade,Ibrahim Cheddadi,Sergiu Ivanov
-
What is Paradoxical About 'Fermi's Paradox'? : Review of Milan Ćirković: The Great Silence, Oxford University Press, 2018. Acta Biotheor. (IF 0.719) Pub Date : 2020-02-11 Cansu Hepçağlayan,Aja Watkins,Russell Powell
In this review of Milan Ćirković’s The Great Silence: Science and Philosophy of Fermi’s Paradox, we attempt to reconstruct the logic of Fermi’s paradox as understood by the author, and we critically examine the reasoning that leads to the paradox. We show that there is no plausible solution to Fermi’s paradox that can satisfy all of Ćirković’s proposed desiderata, which in turn suggests that the author’s
-
Not by Memes Alone : Review of Alan C. Love and William C. Wimsatt (Eds.): Beyond the Meme: Development and Structure in Cultural Evolution (Minnesota Studies in the Philosophy of Science, 22). Minneapolis, MN: The University of Minnesota Press, 2019 (Paperback edition, pp. 542). Acta Biotheor. (IF 0.719) Pub Date : 2020-01-28 Lorenzo Baravalle
-
Measuring Infection Transmission in a Stochastic SIV Model with Infection Reintroduction and Imperfect Vaccine. Acta Biotheor. (IF 0.719) Pub Date : 2020-01-08 M Gamboa,M J Lopez-Herrero
An additional compartment of vaccinated individuals is considered in a SIS stochastic epidemic model with infection reintroduction. The quantification of the spread of the disease is modeled by a continuous time Markov chain. A well-known measure of the initial transmission potential is the basic reproduction number \(R_0\), which determines the herd immunity threshold or the critical proportion of
-
On the Variety of Cognitive Temperatures and Their Symmetry-Breaking Dynamics Acta Biotheor. (IF 0.719) Pub Date : 2020-01-07 Rodrick Wallace
The asymptotic limit theorems of information and control theories permit exploration of a surprising number of temperature-like measures and symmetry-breaking dynamics associated with cognition. Each of several markedly different perspectives produces a distinct temperature-analog, capturing a rich and highly-punctuated behavioral landscape across the complex, hierarchical cognitive phenomena that
-
Clustering of Thrombin Generation Test Data Using a Reduced Mathematical Model of Blood Coagulation Acta Biotheor. (IF 0.719) Pub Date : 2019-12-18 N. Ratto, A. Tokarev, P. Chelle, B. Tardy-Poncet, V. Volpert
Correct interpretation of the data from integral laboratory tests, including Thrombin Generation Test (TGT), requires biochemistry-based mathematical models of blood coagulation. The purpose of this study is to describe the experimental TGT data from healthy donors and hemophilia A (HA) and B (HB) patients. We derive a simplified ODE model and apply it to analyze the TGT data from healthy donors and
-
Additional Food Supplements as a Tool for Biological Conservation of Biosystems in the Presence of Inhibitory Effect of the Prey. Acta Biotheor. (IF 0.719) Pub Date : 2019-11-26 D K K Vamsi,Deva Siva Sai Murari Kanumoori,Bishal Chhetri
Provision of additional food supplements for the purpose of biological conservation has been widely researched both theoretically and experimentally. The study of these biosystems is usually done using predator–prey models. In this paper, we consider an additional food provided predator–prey system in the presence of the inhibitory effect of the prey. This model is analyzed in the control parameter
-
A Mathematical Model for the Transmission Dynamics of Lymphatic Filariasis with Intervention Strategies. Acta Biotheor. (IF 0.719) Pub Date : 2019-11-22 S M Simelane,P M Mwamtobe,S Abelman,J M Tchuenche
This manuscript considers the transmission dynamics of lymphatic filariasis with some intervention strategies in place. Unlike previously developed models, our model takes into account both the exposed and infected classes in both the human and mosquito populations, respectively. We also consider vaccinated, treated and recovered humans in the presented model. The global dynamics of the proposed model
-
Optimality Models and the Propensity Interpretation of Fitness. Acta Biotheor. (IF 0.719) Pub Date : 2019-11-02 Ariel Jonathan Roffé,Santiago Ginnobili
The propensity account of fitness intends to solve the classical tautologicity issue by identifying fitness with a disposition, the ability to survive and reproduce. As proponents recognized early on, this account requires operational independence from actual reproductive success to avoid circularity and vacuousness charges. They suggested that operational independence is achieved by measuring fitness
-
A Word of Welcome to Our New Editorial Board Members, and Presentation of the New Editorial Board. Acta Biotheor. (IF 0.719) Pub Date : 2019-06-01
-
Walking the Line: A Tempered View of Contingency and Convergence in Life's History : Review of Jonathan B. Losos: Improbable Destinies: Fate, Chance, and the Future of Evolution (2017). Acta Biotheor. (IF 0.719) Pub Date : 2019-05-16 Alison K McConwell
-
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. Acta Biotheor. (IF 0.719) Pub Date : 2018-08-12 Doanh Nguyen-Ngoc,Tri Nguyen-Huu
-
Correction to: Graphical Representation and Similarity Analysis of DNA Sequences Based on Trigonometric Functions. Acta Biotheor. (IF 0.719) Pub Date : 2018-06-07 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.
-
Preface. Acta Biotheor. (IF 0.719) Pub Date : 2016-10-23 Hermine Biermé,Jean-Pierre Françoise,Rémy Guillevin,Alain Miranville
-
-
Synapomorphies Behind Shared Derived Characters: Examples from the Great Apes' Genomic Data. Acta Biotheor. (IF 0.719) Pub Date : 2019-10-03 Evgeny V Mavrodiev
Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. It seems to be common knowledge that within phylogenetics, ‘groups’ must be defined based solely on the synapomorphies or on the “derived” characters that unite two or more taxa in a clade or monophyletic group. Thus, the idea of synapomorphy seems to be of fundamental influence and importance
-
Expansion Speed as a Generic Measure of Spread for Alien Species. Acta Biotheor. (IF 0.719) Pub Date : 2019-09-28 Hanno Sandvik
The ecological impact of alien species is a function of the area colonised. Impact assessments of alien species are thus incomplete unless they take the spatial component of invasion processes into account. This paper describes a measure, termed expansion speed, that quantifies the speed with which a species increases its spatial presence in an assessment area. It is based on the area of occupancy
-
The Cultural Evolution of Human Nature. Acta Biotheor. (IF 0.719) Pub Date : 2019-09-28 Mark Stanford
Recent years have seen the growing promise of cultural evolutionary theory as a new approach to bringing human behaviour fully within the broader evolutionary synthesis. This review of two recent seminal works on this topic argues that cultural evolution now holds the potential to bring together fields as disparate as neuroscience and social anthropology within a unified explanatory and ontological
-
In Search of the Origins of Consciousness : Simona Ginsburg and Eva Jablonka: The Evolution of the Sensitive Soul: Learning and the Origins of Consciousness. MIT Press, Cambridge, MA, 2019, 646pp, ISBN: 9780262039307. Acta Biotheor. (IF 0.719) Pub Date : 2019-09-26 Jonathan Birch
The Evolution of the Sensitive Soul is a landmark attempt to make progress on the problem of animal consciousness. Ginsburg and Jablonka propose a general cognitive marker of the presence of consciousness: Unlimited Associative Learning. They use this marker to defend a generous view about the distribution of consciousness in the natural world, on which a capacity for conscious experience is common
-
Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes. Acta Biotheor. (IF 0.719) Pub Date : 2019-09-20 Véronique Thomas-Vaslin
Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living “holon” displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as
-
The Objectivity of Organizational Functions. Acta Biotheor. (IF 0.719) Pub Date : 2019-09-13 Samuel Cusimano,Beckett Sterner
We critique the organizational account of biological functions by showing how its basis in the closure of constraints fails to be objective. While the account treats constraints as objective features of physical systems, the number and relationship of potential constraints are subject to potentially arbitrary redescription by investigators. For example, we show that self-maintaining systems such as
-
Sensitivity Analysis of a Left Ventricle Model in the Context of Intraventricular Dyssynchrony. Acta Biotheor. (IF 0.719) Pub Date : 2019-09-10 Virginie Le Rolle,Elena Galli,David Danan,Karim El Houari,Arnaud Hubert,Erwan Donal,Alfredo I Hernández
The objective of the current study was to propose a sensitivity analysis of a 3D left ventricle model in order to assess the influence of parameters on myocardial mechanical dispersion. A finite element model of LV electro-mechanical activity was proposed and a screening method was used to evaluate the sensitivity of model parameters on the standard deviation of time to peak strain. Results highlight
-
A Global-Scale Mid-Domain Effect Cannot Explain the Latitudinal Gradient in Species Richness. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-31 Thomas W Fieldsend
The latitudinal gradient in species richness is perhaps the most fundamental pattern of biodiversity, yet a satisfactory explanation for its existence remains elusive. A geometric “mid-domain effect” is often cited as having potential to help explain the latitudinal gradient in species richness, but the logic underpinning this hypothesis is apparently built on two incorrect assumptions: (1) that a
-
A Host-Parasite System with Multiple Parasite Strains and Superinfection Revisited: The Global Dynamics. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-30 Lili Liu,Xinzhi Ren,Xianning Liu
In this paper, we revisit a host–parasite system with multiple parasite strains and superinfection proposed by Nowak and May (Proc R Soc Lond B 255(1342):81–89, 1994), and study its global dynamics when we relax the two strict conditions assumed therein. As for system with two parasite strains, we derive that the basic reproduction number \(R_0\) is the threshold condition for parasite extinction and
-
A GPU Algorithm for Agent-Based Models to Simulate the Integration of Cell Membrane Signals. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-29 Arthur Douillet,Pascal Ballet
Simulation of complex biological systems with agent-based models is becoming more relevant with the increase in Graphics Processing Unit (GPU) power. In those simulations, up to millions of virtual cells are individually computed, involving daunting processing times. An important part of computational models is the algorithm that manages how agents perceive their surroundings. This can be particularly
-
On Computing Structural and Behavioral Complexities of Threshold Boolean Networks : Application to Biological Networks. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-24 Urvan Christen,Sergiu Ivanov,Rémi Segretain,Laurent Trilling,Nicolas Glade
Various threshold Boolean networks (TBNs), a formalism used to model different types of biological networks (genes notably), can produce similar dynamics, i.e. share same behaviors. Among them, some are complex (according to Kolmogorov complexity), others not. By computing both structural and behavioral complexities, we show that most TBNs are structurally complex, even those having simple behaviors
-
Investigating Macrophages Plasticity Following Tumour-Immune Interactions During Oncolytic Therapies. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-13 R Eftimie,G Eftimie
Over the last few years, oncolytic virus therapy has been recognised as a promising approach in cancer treatment, due to the potential of these viruses to induce systemic anti-tumour immunity and selectively killing tumour cells. However, the effectiveness of these viruses depends significantly on their interactions with the host immune responses, both innate (e.g., macrophages, which accumulate in
-
A Combinatorial Exploration of Boolean Dynamics Generated by Isolated and Chorded Circuits. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-12 B Mossé,É Remy
Most studies of motifs of biological regulatory networks focus on the analysis of asymptotical behaviours (attractors, and even often only stable states), but transient properties are rarely addressed. In the line of our previous study devoted to isolated circuits (Remy et al. in Bioinformatics (Oxford, England) 19(Suppl. 2):172–178, 2003), we consider chorded circuits, that are motifs made of an elementary
-
The Uroboros Theory of Life's Origin: 22-Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries. Acta Biotheor. (IF 0.719) Pub Date : 2019-08-06 Jacques Demongeot,Hervé Seligmann
Theoretical minimal RNA rings attempt to mimick life’s primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring’s 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs
-
On the Effect of Age-Dependent Mortality on the Stability of a System of Delay-Differential Equations Modeling Erythropoiesis. Acta Biotheor. (IF 0.719) Pub Date : 2019-07-26 Frédéric Paquin-Lefebvre,Jacques Bélair
We present an age-structured model for erythropoiesis in which the mortality of mature cells is described empirically by a physiologically realistic probability distribution of survival times. Under some assumptions, the model can be transformed into a system of delay differential equations with both constant and distributed delays. The stability of the equilibrium of this system and possible Hopf
-
Formalizing Metabolic-Regulatory Networks by Hybrid Automata. Acta Biotheor. (IF 0.719) Pub Date : 2019-07-24 Lin Liu,Alexander Bockmayr
Computational approaches in systems biology have become a powerful tool for understanding the fundamental mechanisms of cellular metabolism and regulation. However, the interplay between the regulatory and the metabolic system is still poorly understood. In particular, there is a need for formal mathematical frameworks that allow analyzing metabolism together with dynamic enzyme resources and regulatory
-
Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase. Acta Biotheor. (IF 0.719) Pub Date : 2019-07-16 Sylvain Lespinats,Olivier De Clerck,Benoît Colange,Vera Gorelova,Delphine Grando,Eric Maréchal,Dominique Van Der Straeten,Fabrice Rébeillé,Olivier Bastien
During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the
-
New Schemes of Dynamic Preservation of Diversity: Remarks on Stability and Topology. Acta Biotheor. (IF 0.719) Pub Date : 2019-07-15 Evariste Sanchez-Palencia,Jean-Pierre Françoise
We address the biological dynamics problem of the persistence of several species in conditions of non-existence of an equilibrium, including an example of stabilization by predation and the very controversial “competitive exclusion” (which depends on the precise definition of persistence). We give normal forms for various examples of such (essentially dynamical) persistence and comments on the involved
-
Genotype Components as Predictors of Phenotype in Model Gene Regulatory Networks. Acta Biotheor. (IF 0.719) Pub Date : 2019-07-08 S Garte,A Albert
Models of gene regulatory networks (GRN) have proven useful for understanding many aspects of the highly complex behavior of biological control networks. Randomly generated non-Boolean networks were used in experimental simulations to generate data on dynamic phenotypes as a function of several genotypic parameters. We found that predictive relationships between some phenotypes and quantitative genotypic
Contents have been reproduced by permission of the publishers.