752 results match your criteria Acta Biotheoretica[Journal]


Assessing the Effects of Holling Type-II Treatment Rate on HIV-TB Co-infection.

Acta Biotheor 2020 Jun 16. Epub 2020 Jun 16.

Postdoctoral Researcher at ELTE, Institute for Theoretical Physics, Eotvos University, Budapest, Hungary.

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. Read More

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http://dx.doi.org/10.1007/s10441-020-09385-wDOI Listing

Correction to: Mathematical Basis of Predicting Dominant Function in Protein Sequences by a Generic HMM-ANN Algorithm.

Authors:
Siddhartha Kundu

Acta Biotheor 2020 May 8. Epub 2020 May 8.

Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College and Hospital, Government of NCT of Delhi, Sector - 6, Rohini, Delhi, 110085, India.

An amendment to this paper has been published and can be accessed via the original article. Read More

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http://dx.doi.org/10.1007/s10441-020-09383-yDOI Listing
May 2020
0.704 Impact Factor

How Could This Happen? : Narrowing Down the Contagion of COVID-19 and Preventing Acute Respiratory Distress Syndrome (ARDS).

Acta Biotheor 2020 Apr 25. Epub 2020 Apr 25.

Biological Publishing A&O and Immunology Department, Erasmus MC, Rotterdam, The Netherlands.

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 understanding the present pandemic outbreak. However, important questions remain unanswered about the underlying mechanism causing the very high case fatality ratios (CFR) and mechanisms regarding severe reactions like ARDS, fatal cardiac and renal failures, associated with a number of important comorbidity factors. Read More

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http://dx.doi.org/10.1007/s10441-020-09382-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7183256PMC

What's Wrong with Evolutionary Causation?

Authors:
Jan Baedke

Acta Biotheor 2020 Apr 13. Epub 2020 Apr 13.

Department of Philosophy I, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.

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 Uller's and Kevin Laland's volume Evolutionary Causation as well as recent reviews of it as a starting point to reflect on the causal role of agency, individuality, and the environment in evolution. Read More

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http://dx.doi.org/10.1007/s10441-020-09381-0DOI Listing

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.

Authors:
Philippe Huneman

Acta Biotheor 2020 Apr 1. Epub 2020 Apr 1.

Institut d'Histoire et de Philosophie des Sciences et des Techniques, CNRS/Université Paris I Panthéon Sorbonne), Paris, France.

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, even when they seem unadaptive (such as sterility). The link between selection and adaptation through which selection or organisms can be seen as agents, as well as the scope and nature of Hamiltonian conceptions of social evolution, stimulated many formal elaborations (such as, initially, Fisher's "Fundamental theorem of natural selection"), but also raise major philosophical issues about causation and statistics, and about rationality and adaptation or selection. Read More

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http://dx.doi.org/10.1007/s10441-020-09380-1DOI Listing

The Goodwin Oscillator and its Legacy.

Acta Biotheor 2020 Mar 25. Epub 2020 Mar 25.

Centre for Organelle Research, University of Stavanger, Richard Johnsens gate 4, 4021, Stavanger, Norway.

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 aiming at identifying minimal mechanisms to generate limit cycle oscillations and deciphering design principles of biological oscillators. Read More

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http://dx.doi.org/10.1007/s10441-020-09379-8DOI Listing

Retraction Note to: Robust Model Selection and Estimation for Censored Survival Data with High Dimensional Genomic Covariates.

Acta Biotheor 2020 06;68(2):295

Department of Finance, Beijing Forestry University, Beijing, China.

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. Read More

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http://dx.doi.org/10.1007/s10441-020-09377-wDOI Listing

Proceedings of the XXXVIIIth Seminar of the French-Speaking Society for Theoretical Biology; Saint-Flour (Cantal), France, 11-13 June, 2018.

Acta Biotheor 2020 03 24;68(1):1-3. Epub 2020 Feb 24.

IBISC Laboratory, Evry Val d'Essonne University, Evry, France.

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http://dx.doi.org/10.1007/s10441-020-09378-9DOI Listing

Measuring Infection Transmission in a Stochastic SIV Model with Infection Reintroduction and Imperfect Vaccine.

Acta Biotheor 2020 Jan 8. Epub 2020 Jan 8.

Faculty of Statistical Studies, Complutense University of Madrid, Madrid , Spain.

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 [Formula: see text], which determines the herd immunity threshold or the critical proportion of immune individuals required to stop the spread of a disease when a vaccine offers a complete protection. Read More

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http://dx.doi.org/10.1007/s10441-019-09373-9DOI Listing
January 2020

On the Variety of Cognitive Temperatures and Their Symmetry-Breaking Dynamics.

Authors:
Rodrick Wallace

Acta Biotheor 2020 Jan 7. Epub 2020 Jan 7.

NYSPI 1051 Riverside Dr., New York, NY, USA.

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 characterize life at every scale and level of organization. Theories of cognition may be confronted by canonical conundrums similar to those plaguing the study of consciousness and its regulation. Read More

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http://dx.doi.org/10.1007/s10441-019-09375-7DOI Listing
January 2020

Clustering of Thrombin Generation Test Data Using a Reduced Mathematical Model of Blood Coagulation.

Acta Biotheor 2020 Mar 18;68(1):21-43. Epub 2019 Dec 18.

Institute Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622, Villeurbanne, France.

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 HA/HB patients with in vitro added tissue factor pathway inhibitor (TFPI) antibody. Read More

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http://dx.doi.org/10.1007/s10441-019-09372-wDOI Listing

Additional Food Supplements as a Tool for Biological Conservation of Biosystems in the Presence of Inhibitory Effect of the Prey.

Acta Biotheor 2019 Nov 26. Epub 2019 Nov 26.

Sri Sathya Sai Institute of Higher Learning, Puttaparthi, India.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09371-xDOI Listing
November 2019

A Mathematical Model for the Transmission Dynamics of Lymphatic Filariasis with Intervention Strategies.

Acta Biotheor 2019 Nov 22. Epub 2019 Nov 22.

School of Computer Science and Applied Mathematics, University of the Witwatersrand, Johannesburg, Private Bag 3, Wits, 2050, South Africa.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09370-yDOI Listing
November 2019

Optimality Models and the Propensity Interpretation of Fitness.

Acta Biotheor 2019 Nov 2. Epub 2019 Nov 2.

Centro de Estudios de Filosofía e Historia de la Ciencia (CEFHIC-UNQ-CONICET), Universidad de Buenos Aires (UBA), Universidad Tres de Febrero (UNTREF), Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.

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 values through optimality models. Read More

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http://dx.doi.org/10.1007/s10441-019-09369-5DOI Listing
November 2019

Synapomorphies Behind Shared Derived Characters: Examples from the Great Apes' Genomic Data.

Acta Biotheor 2019 Oct 3. Epub 2019 Oct 3.

University of Florida, Florida Museum of Natural History, Museum Road and Newell Drive, Dickinson Hall, 301, Gainesville, FL, 32611, USA.

Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. Read More

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http://dx.doi.org/10.1007/s10441-019-09368-6DOI Listing
October 2019

Expansion Speed as a Generic Measure of Spread for Alien Species.

Authors:
Hanno Sandvik

Acta Biotheor 2020 Jun 28;68(2):227-252. Epub 2019 Sep 28.

Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09366-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188734PMC

The Cultural Evolution of Human Nature.

Authors:
Mark Stanford

Acta Biotheor 2020 Jun 28;68(2):275-285. Epub 2019 Sep 28.

Institute of Cognitive and Evolutionary Anthropology, University of Oxford, Oxford, UK.

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 framework. Read More

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http://dx.doi.org/10.1007/s10441-019-09367-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188694PMC

Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes.

Acta Biotheor 2020 Mar 20;68(1):171-199. Epub 2019 Sep 20.

INSERM, Immunology, Immunopathology, Immunotherapies, UMRS959, Sorbonne Université, 83, Boulevard de l'Hôpital, 75013, Paris, France.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09364-wDOI Listing

The Objectivity of Organizational Functions.

Acta Biotheor 2020 Jun 13;68(2):253-269. Epub 2019 Sep 13.

School of Life Sciences, Arizona State University, Tempe, USA.

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 candle flames can realize closure on a more thorough analysis of the case, contradicting the claim that these "simple" systems lack functional organization. Read More

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http://link.springer.com/10.1007/s10441-019-09365-9
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http://dx.doi.org/10.1007/s10441-019-09365-9DOI Listing
June 2020
8 Reads

Sensitivity Analysis of a Left Ventricle Model in the Context of Intraventricular Dyssynchrony.

Acta Biotheor 2020 Mar 10;68(1):45-59. Epub 2019 Sep 10.

Univ Rennes, CHU Rennes, Inserm, LTSI-UMR 1099, 35000, Rennes, France.

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 the importance of propagation parameters associated with septal and lateral segments activation. Read More

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http://dx.doi.org/10.1007/s10441-019-09362-yDOI Listing
March 2020
1 Read

A Global-Scale Mid-Domain Effect Cannot Explain the Latitudinal Gradient in Species Richness.

Acta Biotheor 2020 Jun 31;68(2):271-274. Epub 2019 Aug 31.

Department of Biological Sciences, Florida International University, Miami, FL, USA.

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 given great circle-usually the Equator-can constitute the geometric "mid-domain" of the Earth's surface, and (2) that geophysical or bioclimatic boundaries are of geometric relevance in the context of a global-scale mid-domain effect. This article gives a brief overview of the relevant literature and history of thought on the subject, and describes in clear and simple terms why a global-scale mid-domain effect cannot arise, and thus cannot possibly represent a mechanistic basis for the latitudinal gradient in species richness. Read More

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http://dx.doi.org/10.1007/s10441-019-09361-zDOI Listing

A Host-Parasite System with Multiple Parasite Strains and Superinfection Revisited: The Global Dynamics.

Acta Biotheor 2020 Jun 30;68(2):201-225. Epub 2019 Aug 30.

Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Mathematics and Statistics, Southwest University, Chongqing, 400715, China.

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 [Formula: see text] is the threshold condition for parasite extinction and the invasion reproduction number [Formula: see text] is the subthreshold condition for coexistence of two parasite strains. As for system with three parasite strains, we are surprised to discover the global stability of parasite-free and coexistence equilibrium, which is distinct from the previous result. Read More

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http://dx.doi.org/10.1007/s10441-019-09359-7DOI Listing

A GPU Algorithm for Agent-Based Models to Simulate the Integration of Cell Membrane Signals.

Acta Biotheor 2020 Mar 29;68(1):61-71. Epub 2019 Aug 29.

Laboratory of Medical Data Processing, Inserm UMR 1101, University of Brest, 20 avenue Le Gorgeu, 29238, Brest, France.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09360-0DOI Listing
March 2020
1 Read

On Computing Structural and Behavioral Complexities of Threshold Boolean Networks : Application to Biological Networks.

Acta Biotheor 2020 Mar 24;68(1):119-138. Epub 2019 Aug 24.

CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Univ. Grenoble Alpes, 38000, Grenoble, France.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09358-8DOI Listing
March 2020
2 Reads

Investigating Macrophages Plasticity Following Tumour-Immune Interactions During Oncolytic Therapies.

Authors:
R Eftimie G Eftimie

Acta Biotheor 2019 Dec 13;67(4):321-359. Epub 2019 Aug 13.

Hopital Privé de La Miotte, 90002, Belfort, France.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09357-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825040PMC
December 2019

A Combinatorial Exploration of Boolean Dynamics Generated by Isolated and Chorded Circuits.

Authors:
B Mossé É Remy

Acta Biotheor 2020 Mar 12;68(1):87-117. Epub 2019 Aug 12.

Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09355-xDOI Listing

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 2019 Dec 6;67(4):273-297. Epub 2019 Aug 6.

The National Natural History Collections, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.

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. Read More

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http://dx.doi.org/10.1007/s10441-019-09356-wDOI Listing
December 2019

On the Effect of Age-Dependent Mortality on the Stability of a System of Delay-Differential Equations Modeling Erythropoiesis.

Acta Biotheor 2020 Mar 26;68(1):5-19. Epub 2019 Jul 26.

Département de mathématiques et de statistique and Centre de recherches mathématiques, Université de Montréal, CP 6128 Succ. centre-ville, Montréal, QC, H3C 3J7, Canada.

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 bifurcations are described for a number of probability distributions. Read More

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http://dx.doi.org/10.1007/s10441-019-09351-1DOI Listing

Formalizing Metabolic-Regulatory Networks by Hybrid Automata.

Acta Biotheor 2020 Mar 24;68(1):73-85. Epub 2019 Jul 24.

Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany.

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 events. Read More

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http://dx.doi.org/10.1007/s10441-019-09354-yDOI Listing
March 2020
1 Read

Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase.

Acta Biotheor 2020 Mar 16;68(1):139-156. Epub 2019 Jul 16.

Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France.

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 evolutionary trajectories of proteins in the sequence space. Read More

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http://dx.doi.org/10.1007/s10441-019-09352-0DOI Listing

New Schemes of Dynamic Preservation of Diversity: Remarks on Stability and Topology.

Acta Biotheor 2020 Mar 15;68(1):157-169. Epub 2019 Jul 15.

Sorbonne-Université, CNRS, Université de Paris, Laboratoire Jacques-Louis Lions (LJLL), 75005, Paris, France.

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 topology, which implies the presence of exceptional heteroclinic connections binding equilibria on the boundary. Read More

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http://dx.doi.org/10.1007/s10441-019-09353-zDOI Listing
March 2020
1 Read

Genotype Components as Predictors of Phenotype in Model Gene Regulatory Networks.

Authors:
S Garte A Albert

Acta Biotheor 2019 Dec 8;67(4):299-320. Epub 2019 Jul 8.

Natural Philosophy Institute, 516 Calvin Lane, Rockville, MD, USA.

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 parameters such as number of network genes, interaction density, and initial condition could be derived depending on the strength of the topological (positional) genotype on specific phenotypes. Read More

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http://dx.doi.org/10.1007/s10441-019-09350-2DOI Listing
December 2019

Robust Model Selection and Estimation for Censored Survival Data with High Dimensional Genomic Covariates.

Acta Biotheor 2019 Sep 28;67(3):225-251. Epub 2019 May 28.

Department of Finance, Beijing Forestry University, Beijing, China.

When relating genomic data to survival outcomes, there are three main challenges that are the censored survival outcomes, the high-dimensionality of the genomic data, and the non-normality of data. We propose a method to tackle these challenges simultaneously and obtain a robust estimation of detecting significant genes related to survival outcomes based on Accelerated Failure Time (AFT) model. Specifically, we include a general loss function to the AFT model, adopt model regularization and shrinkage technique, cope with parameters tuning and model selection, and develop an algorithm based on unified Expectation-Maximization approach for easy implementation. Read More

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http://dx.doi.org/10.1007/s10441-019-09349-9DOI Listing
September 2019
1 Read

Causally Modeling Adaptation to the Environment.

Authors:
Wes Anderson

Acta Biotheor 2019 Sep 26;67(3):201-224. Epub 2019 Apr 26.

Western New England University, Springfield, USA.

Brandon claims that to explain adaptation one must specify fitnesses in each selective environment and specify the distribution of individuals across selective environments. Glymour claims, using an example of the adaptive evolution of costly plasticity in a symmetric environment, that there are some predictive or explanatory tasks for which Brandon's claim is limited. In this paper, I provide necessary conditions for carrying out Brandon's task, produce a new version of the argument for his claim, and show that Glymour's reasons for making his claim are problematic. Read More

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http://dx.doi.org/10.1007/s10441-019-09345-zDOI Listing
September 2019
2 Reads

Control by Viability in a Chemotherapy Cancer Model.

Acta Biotheor 2019 Sep 4;67(3):177-200. Epub 2019 Apr 4.

TSI Team, Faculty of Sciences, University Moulay Ismail, Meknes, Morocco.

The aim of this study is to provide a feedback control, called the Chemotherapy Protocol Law, with the purpose to keep the density of tumor cells that are treated by chemotherapy below a "tolerance level" [Formula: see text], while retaining the density of normal cells above a "healthy level" [Formula: see text]. The mathematical model is a controlled dynamical system involving three nonlinear differential equations, based on a Gompertzian law of cell growth. By evoking viability and set-valued theories, we derive sufficient conditions for the existence of a Chemotherapy Protocol Law. Read More

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http://dx.doi.org/10.1007/s10441-019-09344-0DOI Listing
September 2019
3 Reads

Mathematical Modeling of Substrates Fluxes and Tumor Growth in the Brain.

Acta Biotheor 2019 Jun 13;67(2):149-175. Epub 2019 Mar 13.

Laboratoire de Mathématiques et Applications, UMR CNRS 7348, SP2MI, Equipe DACTIM-MIS, Université de Poitiers, Boulevard Marie et Pierre Curie - Téléport 2, 86962, Chasseneuil Futuroscope Cedex, France.

The aim of this article is to show how a tumor can modify energy substrates fluxes in the brain to support its own growth. To address this question we use a modeling approach to explain brain nutrient kinetics. In particular we set up a system of 17 equations for oxygen, lactate, glucose concentrations and cells number in the brain. Read More

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http://dx.doi.org/10.1007/s10441-019-09343-1DOI Listing
June 2019
2 Reads

An Organisational Approach to Biological Communication.

Acta Biotheor 2019 Jun 2;67(2):103-128. Epub 2019 Feb 2.

Department of Logic and Philosophy of Science, IAS-Research Centre for Life, Mind and Society, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, 20018, Donostia-San Sebastian, Spain.

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted by a sender triggers a change in the behaviour of the receiver that is functional for the sender itself. Read More

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http://dx.doi.org/10.1007/s10441-019-09342-2DOI Listing
June 2019
3 Reads

The Coherence of Evolutionary Theory with Its Neighboring Theories.

Authors:
Seungbae Park

Acta Biotheor 2019 Jun 24;67(2):87-102. Epub 2019 Jan 24.

Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.

Evolutionary theory coheres with its neighboring theories, such as the theory of plate tectonics, molecular biology, electromagnetic theory, and the germ theory of disease. These neighboring theories were previously unconceived, but they were later conceived, and then they cohered with evolutionary theory. Since evolutionary theory has been strengthened by its several neighboring theories that were previously unconceived, it will be strengthened by infinitely many hitherto unconceived neighboring theories. Read More

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http://dx.doi.org/10.1007/s10441-019-09341-3DOI Listing
June 2019
2 Reads

Multidrug Therapy for HIV Infection: Dynamics of Immune System.

Acta Biotheor 2019 Jun 4;67(2):129-147. Epub 2018 Dec 4.

Department of Mathematics, Kurukshetra University, Kurukshetra, Haryana, India.

A mathematical model of the dynamics of the immune system is considered to illustrate the effect of its response to HIV infection, i.e. on viral growth and on T-cell dynamics. Read More

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http://dx.doi.org/10.1007/s10441-018-9340-0DOI Listing
June 2019
2 Reads

From Biological Determination to Entangled Causation.

Acta Biotheor 2019 Mar 4;67(1):19-46. Epub 2018 Sep 4.

Laboratoire ERRAPHIS, PhSciVi, Université Toulouse Jean Jaurès, Maison de la Recherche 5 allée Antonio-Machado, 31058, Toulouse Cedex 9, France.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9339-6DOI Listing
March 2019
3 Reads

Design Methodologies and the Limits of the Engineering-Dominated Conception of Synthetic Biology.

Authors:
Tero Ijäs

Acta Biotheor 2019 Mar 18;67(1):1-18. Epub 2018 Aug 18.

Practical Philosophy, University of Helsinki, Unioninkatu 40, P.O. Box 24, 00014, Helsinki, Finland.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9338-7DOI Listing
March 2019
5 Reads

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 2018 Dec 10;66(4):255-256. Epub 2018 Aug 10.

IRD, Sorbonne Universités, UPMC Univ Paris 06, Unité Mixte Internationale de Modélisation Mathématique et Informatique des Systèmes Complexes (UMMISCO), 32 Avenue Henri Varagnat, 93143, Bondy Cedex, France.

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http://dx.doi.org/10.1007/s10441-018-9337-8DOI Listing
December 2018
9 Reads

Mathematical Assessment of the Role of Early Latent Infections and Targeted Control Strategies on Syphilis Transmission Dynamics.

Acta Biotheor 2019 Mar 3;67(1):47-84. Epub 2018 Jul 3.

School of Mathematical and Statistical Sciences, Arizona State University, Arizona, USA.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9336-9DOI Listing
March 2019
3 Reads

Study of the Population Dynamics of Busseola fusca, Maize Pest.

Acta Biotheor 2018 Dec 14;66(4):379-397. Epub 2018 Jun 14.

Laboratory of Mathematics, Department of Mathematics and Computer Science, Faculty of Science, University of Douala, PO Box 24157, Douala, Cameroon.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9335-xDOI Listing
December 2018
22 Reads

Correction to: Graphical Representation and Similarity Analysis of DNA Sequences Based on Trigonometric Functions.

Acta Biotheor 2018 09;66(3):251-253

School of Mathematics and Statistics, Wuhan University, Wuhan, 430072, China.

In the original publication of the article, the y axis labels present in Figs. 1a and 2a are incorrect. The correct Figs. Read More

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http://dx.doi.org/10.1007/s10441-018-9334-yDOI Listing
September 2018
2 Reads

An Inverse Problem: Trappers Drove Hares to Eat Lynx.

Authors:
Bo Deng

Acta Biotheor 2018 Sep 30;66(3):213-242. Epub 2018 May 30.

Mathematics and Science College, Shanghai Normal University, Shanghai, 200234, China.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9333-zDOI Listing
September 2018
3 Reads

Permanence and Extinction of a Diffusive Predator-Prey Model with Robin Boundary Conditions.

Acta Biotheor 2018 Dec 28;66(4):367-378. Epub 2018 May 28.

Department of Mathematics, Faculty of Sciences, University of Tlemcen, B.P. 119, 13000, Tlemcen, Algeria.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9332-0DOI Listing
December 2018
3 Reads

Descriptive Modeling of the Dynamical Systems and Determination of Feedback Homeostasis at Different Levels of Life Organization.

Acta Biotheor 2018 Sep 24;66(3):177-199. Epub 2018 May 24.

Kharkiv National University of Radio Electronics, Nauky ave., 14, Kharkiv, 61166, Ukraine.

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. Read More

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http://dx.doi.org/10.1007/s10441-018-9321-3DOI Listing
September 2018
2 Reads