803 results match your criteria Acta Biotheoretica[Journal]


Bridging Theories for Ecosystem Stability Through Structural Sensitivity Analysis of Ecological Models in Equilibrium.

Acta Biotheor 2022 Jun 23;70(3):18. Epub 2022 Jun 23.

Department of Aquatic Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands.

Ecologists are challenged by the need to bridge and synthesize different approaches and theories to obtain a coherent understanding of ecosystems in a changing world. Both food web theory and regime shift theory shine light on mechanisms that confer stability to ecosystems, but from different angles. Empirical food web models are developed to analyze how equilibria in real multi-trophic ecosystems are shaped by species interactions, and often include linear functional response terms for simple estimation of interaction strengths from observations. Read More

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Limited Cognitive Abilities and Dominance Hierarchies.

Acta Biotheor 2022 Jun 17;70(3):17. Epub 2022 Jun 17.

Department of Economics, University of Oregon, Eugene, USA.

We propose a novel model to explain the mechanisms underlying dominance hierarchical structures. Guided by a predetermined social convention, agents with limited cognitive abilities optimize their strategies in a Hawk-Dove game. We find that several commonly observed hierarchical structures in nature such as linear hierarchy and despotism, emerge as the total fitness-maximizing social structures given different levels of cognitive abilities. Read More

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Optimal Drug Regimen and Combined Drug Therapy and Its Efficacy in the Treatment of COVID-19: A Within-Host Modeling Study.

Acta Biotheor 2022 May 19;70(2):16. Epub 2022 May 19.

Sri Sathya Sai Institute of Higher Learning - SSSIHL, Anantapur, India.

The COVID-19 pandemic has resulted in more than 524 million cases and 6 million deaths worldwide. Various drug interventions targeting multiple stages of COVID-19 pathogenesis can significantly reduce infection-related mortality. The current within-host mathematical modeling study addresses the optimal drug regimen and efficacy of combination therapies in the treatment of COVID-19. Read More

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Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges.

Acta Biotheor 2022 May 16;70(2):15. Epub 2022 May 16.

Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria, 04510, Coyoacán, DF, Mexico.

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. Read More

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Finding or Creating a Living Organism? Past and Future Thought Experiments in Astrobiology Applied to Artificial Intelligence.

Authors:
Daniel S Helman

Acta Biotheor 2022 Apr 28;70(2):13. Epub 2022 Apr 28.

Education Division, College of Micronesia-FSM, Yap Campus, Federated States of Micronesia.

This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms-definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution-to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. Read More

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Mathematical Analysis of Membrane Transporters Dynamics: A Calcium Fluxes Case Study.

Acta Biotheor 2022 Apr 28;70(2):14. Epub 2022 Apr 28.

Université de Poitiers, Laboratoire Signalisation et Transports Ioniques Membranaires, ERL CNRS 7003, Equipe 4CS, Bâtiment B36 - TSA 51106, 1 Rue Georges Bonnet, Poitiers Cedex 9, 86073, France.

A tight control of intracellular [Ca[Formula: see text]] is essential for the survival and normal function of cells. In this study we investigate key mechanistic steps by which calcium is regulated and calcium oscillations could occur using in silico modeling of membrane transporters. To do so we give a deterministic description of intracellular Ca[Formula: see text] dynamics using nonlinear dynamics in order to understand Ca[Formula: see text] signaling. Read More

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Nonlocal Reaction-Diffusion Equations in Biomedical Applications.

Acta Biotheor 2022 Mar 17;70(2):12. Epub 2022 Mar 17.

Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, Russia, 117198.

Nonlocal reaction-diffusion equations describe various biological and biomedical applications. Their mathematical properties are essentially different in comparison with the local equations, and this difference can lead to important biological implications. This review will present the state of the art in the investigation of nonlocal reaction-diffusion models in biomedical applications. Read More

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Qualitative and Dynamical Analysis of a Bionomic Fishery Model with Prey Refuge.

Authors:
S N Raw B P Sarangi

Acta Biotheor 2022 Feb 4;70(1):11. Epub 2022 Feb 4.

Department of Mathematics, National Institute of Technology Raipur, Raipur, CG, 492010, India.

Predation and escaping from predation through hiding are two fundamental phenomena in ecology. The most common approach to reducing the chance of predation is to use a refuge. Here, we consider a three species fishery model system with prey refuge induced by a Holling type-II functional response. Read More

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February 2022

The Hybrid Incidence Susceptible-Transmissible-Removed Model for Pandemics : Scaling Time to Predict an Epidemic's Population Density Dependent Temporal Propagation.

Acta Biotheor 2022 Jan 29;70(1):10. Epub 2022 Jan 29.

Lancet Laboratories, Johannesburg, South Africa.

The susceptible-transmissible-removed (STR) model is a deterministic compartment model, based on the susceptible-infected-removed (SIR) prototype. The STR replaces 2 SIR assumptions. SIR assumes that the emigration rate (due to death or recovery) is directly proportional to the infected compartment's size. Read More

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January 2022

A Mathematical Model of the Transmission Dynamics of Bovine Schistosomiasis with Contaminated Environment.

Acta Biotheor 2022 Jan 12;70(1). Epub 2022 Jan 12.

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

Schistosomiasis, a vector-borne chronically debilitating infectious disease, is a serious public health concern for humans and animals in the affected tropical and sub-tropical regions. We formulate and theoretically analyze a deterministic mathematical model with snail and bovine hosts. The basic reproduction number [Formula: see text] is computed and used to investigate the local stability of the model's steady states. Read More

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January 2022

Modeling the Waves of Covid-19.

Authors:
Ivan Cherednik

Acta Biotheor 2021 Dec 27;70(1). Epub 2021 Dec 27.

University of North Carolina at Chapel Hill, Chapel Hill, USA.

The challenges with modeling the spread of Covid-19 are its power-type growth during the middle stages of the waves with the exponents depending on time, and that the saturation of the waves is mainly due to the protective measures and other restriction mechanisms working in the same direction. The two-phase solution we propose for modeling the total number of detected cases of Covid-19 describes the actual curves for many its waves and in many countries almost with the accuracy of physics laws. Bessel functions play the key role in our approach. Read More

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December 2021

Average and Standard Deviation of the Error Function for Random Genetic Codes with Standard Stop Codons.

Authors:
Dino G Salinas

Acta Biotheor 2021 Dec 17;70(1). Epub 2021 Dec 17.

Centro de Investigación Biomédica, Facultad de Medicina, Universidad Diego Portales, Santiago, Chile.

The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick's hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code. Read More

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December 2021

A Partition Theorem for a Randomly Selected Large Population.

Acta Biotheor 2021 Dec 16;70(1). Epub 2021 Dec 16.

Laboratory for Theory and Mathematical Modeling, Division of Infectious Diseases, Department of Medicine, Medical College of Georgia, Augusta, USA.

A theorem on the partitioning of a randomly selected large population into stationary and non-stationary components by using a property of the stationary population identity is stated and proved. The methods of partitioning demonstrated are original and these are helpful in real-world situations where age-wise data is available. Applications of this theorem for practical purposes are summarized at the end. Read More

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December 2021

Achieving Minimum-Time Biological Conservation and Pest Management for Additional Food provided Predator-Prey Systems involving Inhibitory Effect: A Qualitative Investigation.

Acta Biotheor 2021 Dec 14;70(1). Epub 2021 Dec 14.

Department of Mathematics and Computer Science, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur District, Puttaparthi, Andhra Pradesh, 515134, India.

Theoretical and experimental studies on prey-predator systems where predator is supplied with alternate sources of food have received significant attention over the years due to their relevance in achieving biological conservation and biological control. Some of the outcomes of these studies suggest that with appropriate quality and quantity of additional food, the system can be steered towards any desired state eventually with time. One of the limitations of previous studies is that the desired state is reached asymptotically, which makes the outcomes not easily applicable in practical scenarios. Read More

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December 2021

Host Manipulation Mechanisms of SARS-CoV-2.

Authors:
Steven E Massey

Acta Biotheor 2021 Dec 13;70(1). Epub 2021 Dec 13.

Biology Department, University of Puerto Rico - Rio Piedras, San Juan, PR, USA.

Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to bind to the host receptor neuropilin-1 in order to gain entry into the cell. To do this, the virus utilizes its spike protein polybasic cleavage site (PCS), which mimics the CendR motif of neuropilin-1's endogenous ligands. Read More

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December 2021

The Concept of Evenness/Unevenness: Less Evenness or More Unevenness?

Acta Biotheor 2021 Dec 10;70(1). Epub 2021 Dec 10.

Forstgenetik und Forstpflanzenzüchtung, Fakultät Forstwissenschaften und Waldökologie, Universität Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.

While evenness is understood to be maximal if all types (species, genotypes, alleles, etc.) are represented equally (via abundance, biomass, area, etc.), its opposite, maximal unevenness, either remains conceptually in the dark or is conceived as the type distribution that minimizes the applied evenness index. Read More

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December 2021

The [Formula: see text]-Wave of the Electroretinogram and Iron-Induced Oxidative Stress: A Model.

Acta Biotheor 2021 Dec 6;70(1). Epub 2021 Dec 6.

Siksha 'O' Anusandhan University, Bhubaneswar, 751030, India.

In photoreceptors of a dark adapted eye, the inward flux of sodium and calcium ions in the outer segment is balanced by the outward flux of potassium ions. But in the presence of light the creation of cyclic guanosine monophosphate in the outer segment decreases. Due to low concentration of cG (cyclic GMP) the channels in the outer segment open relatively less and thus the influx of calcium ion decreases, leading finally to hyperpolarization of the photoreceptors. Read More

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December 2021

The Indeterminacy Bottleneck: Implications for Habitable Worlds.

Authors:
Ian von Hegner

Acta Biotheor 2021 Dec 4;70(1). Epub 2021 Dec 4.

Future Foundation Assoc., Karlslunde, Denmark.

It is often assumed that the transition between chemical evolution and biological evolution undergoes a smooth process; that once life has arisen, it will automatically 'flood' a solar system body. However, there is no a priori reason to assume that a link between them is a given. The fact that both chemical evolution and biological evolution meet in a single point can be critical. Read More

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December 2021

Toward a More General Understanding of Bohr's Complementarity: Insights from Modeling of Ion Channels.

Authors:
Srdjan Kesić

Acta Biotheor 2021 Dec 28;69(4):723-744. Epub 2021 Sep 28.

Department of Neurophysiology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Despot Stefan Blvd., 142, 11060, Belgrade, Serbia.

Some contemporary theorists such as Mazzocchi, Theise and Kafatos are convinced that the reformed complementarity may redefine how we might exploit the complexity theory in 21st-century life sciences research. However, the motives behind the profound re-invention of "biological complementarity" need to be substantiated with concrete shreds of evidence about this principle's applicability in real-life science experimentation, which we found missing in the literature. This paper discusses such pieces of evidence by confronting Bohr's complementarity and ion channel modeling practice. Read More

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December 2021

Strong Emergence in Biological Systems: Is It Open to Mathematical Reasoning?

Acta Biotheor 2021 Dec 31;69(4):841-856. Epub 2021 Aug 31.

International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, People's Republic of China.

Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54-61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n 'constitutive' proteins at concentrations exceeding individual threshold values (strong emergence). The latter algorithm is modified here to take account of protein redundancy with respect to a complex trait ('full redundancy'). Read More

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December 2021

Organic Codes: A Unifying Concept for Life.

Acta Biotheor 2021 Dec 30;69(4):769-782. Epub 2021 Jul 30.

Departamento de Filosofia, Universidade Federal de Santa Catarina, Florianopolis, Brazil.

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Read More

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December 2021

Optimal Control Strategies and Sensitivity Analysis of an HIV/AIDS-Resistant Model with Behavior Change.

Acta Biotheor 2021 Dec 30;69(4):543-589. Epub 2021 Jul 30.

School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa.

Despite several research on HIV/AIDS, it is still incumbent to investigate more effective control measures to mitigate its infection level. Therefore, we introduce an HIV/AIDS-resistant model with behavior change and study its basic properties. In order to determine the most sensitive parameters that are responsible for disease transmission with respect to the basic reproduction number and those responsible for disease prevalence with respect to the endemic equilibrium, the sensitivity analysis was established and it was confirmed that the influx rate of people into the infected population and total abstinence from all risk practices and endemic areas are some of the most sensitive parameters for disease spread and disease eradication, respectively. Read More

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December 2021

Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code.

Acta Biotheor 2021 Dec 20;69(4):745-767. Epub 2021 Jul 20.

Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, Perm, Russia, 614081.

Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature T, the T:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single -C=C bond and two nitrogen atoms in each heterocycle involved in C-N and C=N bonds. Read More

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December 2021

What is Causal Specificity About, and What is it Good for in Philosophy of Biology?

Acta Biotheor 2021 Dec 12;69(4):821-839. Epub 2021 Jul 12.

Department of Philosophy, Universitat Bielefeld, Bielefeld, Nordrhein-Westfalen, Germany.

The concept of causal specificity is drawing considerable attention from philosophers of biology. It became the rationale for rejecting (and occasionally, accepting) a thesis of causal parity of developmental factors. This literature assumes that attributing specificity to causal relations is at least in principle a straightforward (if not systematic) task. Read More

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December 2021

A Human-Bovine Schistosomiasis Mathematical Model with Treatment and Mollusciciding.

Acta Biotheor 2021 Dec 30;69(4):511-541. Epub 2021 Jun 30.

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

To mitigate the spread of schistosomiasis, a deterministic human-bovine mathematical model of its transmission dynamics accounting for contaminated water reservoirs, including treatment of bovines and humans and mollusciciding is formulated and theoretically analyzed. The disease-free equilibrium is locally and globally asymptotically stable whenever the basic reproduction number [Formula: see text], while global stability of the endemic equilibrium is investigated by constructing a suitable Lyapunov function. To support the analytical results, parameter values from published literature are used for numerical simulations and where applicable, uncertainty analysis on the non-dimensional system parameters is performed using the Latin Hypercube Sampling and Partial Rank Correlation Coefficient techniques. Read More

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December 2021

How Do Trees Grow in Girth? Controversy on the Role of Cellular Events in the Vascular Cambium.

Acta Biotheor 2021 Dec 21;69(4):643-670. Epub 2021 Jun 21.

Department of Botany, Hamdard University, Tughlaqabad, New Delhi, 110 062, India.

Radial growth has long been a subject of interest in tree biology research. Recent studies have brought a significant change in the understanding of some basic processes characteristic to the vascular cambium, a meristem that produces secondary vascular tissues (phloem and xylem) in woody plants. A new hypothesis regarding the mechanism of intrusive growth of the cambial initials, which has been ratified by studies of the arrangement of cambial cells, negates the influence of this apical cell growth on the expansion of the cambial circumference. Read More

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December 2021

The Effect of Mitochondrial DNA Half-Life on Deletion Mutation Proliferation in Long Lived Cells.

Acta Biotheor 2021 Dec 15;69(4):671-695. Epub 2021 Jun 15.

, Shrewsbury, Shropshire, UK.

The proliferation of mitochondrial DNA (mtDNA) with deletion mutations has been linked to aging and age related neurodegenerative conditions. In this study we model the effect of mtDNA half-life on mtDNA competition and selection. It has been proposed that mutation deletions ([Formula: see text]) have a replicative advantage over wild-type ([Formula: see text]) and that this is detrimental to the host cell, especially in post-mitotic cells. Read More

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December 2021

Memory in Ion Channel Kinetics.

Acta Biotheor 2021 Dec 27;69(4):697-722. Epub 2021 May 27.

Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil.

Ion channels are transport proteins present in the lipid bilayers of biological membranes. They are involved in many physiological processes, such as the generation of nerve impulses, hormonal secretion, and heartbeat. Conformational changes in the ion channel-forming protein allow the opening or closing of pores to control the ionic flux through the cell membranes. Read More

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December 2021

On Predation-Commensalism Processes as Models of Bi-stability and Constructive Role of Systemic Extinctions.

Acta Biotheor 2021 Dec 13;69(4):497-510. Epub 2021 May 13.

Sorbonne Université, UPMC Univ Paris 06, and CNRS, UMR 7598, Laboratoire Jacques-louis Lions, 75005, Paris, France.

We propose a mathematical model for a class of predator-prey systems more complex than the usual one, involving a commensalism effect consisting in an influence of the predator on the sustainability of the prey. This effect induces interesting new features, including bi-stability (two attractors with disjoint attraction basins). The question of the possibility of reaching a certain attractor starting from initial conditions with a small population of predators, which presents an interest from the vewpoint of the onset of the predator in evolution, is addressed. Read More

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December 2021

Phylogenetic Inference and the Misplaced Premise of Substitution Rates.

Authors:
Kirk Fitzhugh

Acta Biotheor 2021 Dec 6;69(4):799-819. Epub 2021 May 6.

Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA, 90007, USA.

Three competing 'methods' have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. Read More

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December 2021