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Decomposing mechanisms of COVID-19 mortality in empirical datasets: A modeling study J. Theor. Biol. (IF 2.0) Pub Date : 2024-03-05 Tong Zhang, Jiaying Qiao, Katsuma Hayashi, Hiroshi Nishiura
Our objective was to decompose mortality mechanisms during the coronavirus disease 2019 (COVID-19) pandemic to estimate direct, indirect, and associated deaths from COVID-19. Given the confirmatory diagnosis of COVID-19, a death event that was not necessarily caused by respiratory complications but stemmed from other complications was categorized as an indirect death from COVID-19. Associated deaths
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Revisiting the Modularity-Disease transmission Link: Uncovering the importance of intra-modular structure J. Theor. Biol. (IF 2.0) Pub Date : 2024-03-03 Yan Song, Qian Yang
Studies have shown that the internal structure of modules is hardly important for the spread of epidemics. However, most of these studies have assumed that intra-module connectivity and inter-module connectivity do not affect each other. In reality, changes in the internal structure of modules may affect inter-module links and thus change the modularity of the entire network. Therefore, we have developed
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Tumor growth for remodeling process: A 2D approach J. Theor. Biol. (IF 2.0) Pub Date : 2024-03-02 Juan Felipe Sánchez, Salah Ramtani, Abdelkader Boucetta, Marco Antonio Velasco, Juan Jairo Vaca-González, Carlos A. Duque. D., Diego A. Garzón-Alvarado
This paper aims to present a comprehensive framework for coupling tumor-bone remodeling processes in a 2-dimensional geometry. This is achieved by introducing a bio-inspired damage that represents the growing tumor, which subsequently affects the main populations involved in the remodeling process, namely, osteoclasts, osteoblasts, and bone tissue. The model is constructed using a set of differential
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Biomechanics of transduction by mechanosensory cilia for prey detection in aquatic organisms J. Theor. Biol. (IF 2.0) Pub Date : 2024-03-01 Faye Piephoff, Brian K. Taylor, Catherine E. Kehl, Bruno Mota, Cynthia M. Harley
Surface-feeding aquatic animals navigate towards the source of water disturbances and must differentiate prey from other environmental stimuli. Medicinal leeches locate prey, in part, using a distribution of mechanosensory hairs along their body that deflect under fluid flow. Leech’s behavioral responses to surface wave temporal frequency are well documented. However, a surface wave’s temporal frequency
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Discrete-state models identify pathway specific B cell states across diseases and infections at single-cell resolution J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-28 George Kassis, Mukta G. Palshikar, Shannon P. Hilchey, Martin S. Zand, Juilee Thakar
Oxygen (O) regulated pathways modulate B cell activation, migration and proliferation during infection, vaccination, and other diseases. Modeling these pathways in health and disease is critical to understand B cell states and ways to mediate them. To characterize B cells by their activation of O regulated pathways we develop pathway specific discrete state models using previously published single-cell
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The unreasonable effectiveness of the total quasi-steady state approximation, and its limitations J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-27 Justin Eilertsen, Santiago Schnell, Sebastian Walcher
In this note, we discuss the range of parameters for which the total quasi-steady-state approximation of the Michaelis–Menten reaction mechanism holds validity. We challenge the prevalent notion that total quasi-steady-state approximation is “roughly valid” across all parameters, showing that its validity cannot be assumed, even roughly, across the entire parameter space — when the initial substrate
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Investigating the synergistic effects of immunotherapy and normalization treatment in modulating tumor microenvironment and enhancing treatment efficacy J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-23 Constantinos Harkos, Triantafyllos Stylianopoulos
We developed a comprehensive mathematical model of cancer immunotherapy that takes into account: i) Immune checkpoint blockers (ICBs) and the interactions between cancer cells and the immune system, ii) characteristics of the tumor microenvironment, such as the tumor hydraulic conductivity, interstitial fluid pressure, and vascular permeability, iii) spatial and temporal variations of the modeled components
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Viral rebound occurrence immediately after drug discontinuation involving neither drug resistance nor latent reservoir J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-21 Rena Hayashi, Akane Hara, Yoh Iwasa
Some viruses exhibit “rebound” when the administration of antiviral drugs is discontinued. Viral rebound caused by resistance mutations or latent reservoirs has been studied mathematically. In this study, we investigated the viral rebound due to other causes. Since immunity is weaker during antiviral treatment than without the treatment, drug discontinuation may lead to an increase in the viral load
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Generalized synchronization in a tritrophic food web metacommunity J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-15 Dweepabiswa Bagchi, Ramesh Arumugam, V.K. Chandrasekar, D.V. Senthilkumar
Complete synchronization among the metacommunity is known to elevate the risk of their extinction due to stochasticity and other environmental perturbations. Owing to the inherent heterogeneous nature of the metacommunity, we demonstrate the emergence of generalized synchronization among the patches of dispersally connected tritrophic food web using the framework of an auxiliary system approach and
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Pólya-splitting distributions as stationary solutions of multivariate birth–death processes under extended neutral theory J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-12 Jean Peyhardi, Fabien Laroche, Frédéric Mortier
Multivariate count distributions are crucial for the inference of ecological processes underpinning biodiversity. In particular, neutral theory provides useful null distributions allowing the evaluation of adaptation or natural selection. In this paper, we build a broader family of multivariate distributions: the Polya-splitting distributions. We show that they emerge naturally as stationary distributions
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Modelling of the in-stent thrombus formation by dissipative particle dynamics J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-07 Jiashuai Liu, Zhenmin Fan, Xia Ye, Yingying Zhang, Mingyuan Liu, Xiaoyan Deng
Stent implantation is a highly efficacious intervention for the treatment of coronary atherosclerosis. Nevertheless, stent thrombosis and other post-operative complications persist, and the underlying mechanism of adverse event remains elusive. In the present study, a dissipative particle dynamics model was formulated to simulate the motion, adhesion, activation, and aggregation of platelets, with
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Kill rates by immune cells: Ratio-dependent, or mass action? J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-07 Ami Radunskaya, Joshua Sack
We describe a cell-based fixed-lattice model to simulate immune cell and tumor cell interaction involving MHC recognition, and FasL vs perforin lysis. We are motivated by open questions about the mechanisms behind observed kill rates of tumor cells by different types of effector cells. These mechanisms play a big role in the effectiveness of many cancer immunotherapies. The model is a stochastic cellular
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Kinetics and regulation of coagulation factor X activation by intrinsic tenase on phospholipid membranes J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-07 Anastasia N. Sveshnikova, Alexey M. Shibeko, Tatiana A. Kovalenko, Mikhail A. Panteleev
Factor X activation by the phospholipid-bound intrinsic tenase complex is a critical membrane-dependent reaction of blood coagulation. Its regulation mechanisms are unclear, and a number of questions regarding diffusional limitation, pathways of assembly and substrate delivery remain open. We develop and analyze here a detailed mechanism-driven computer model of intrinsic tenase on phospholipid surfaces
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Many-to-many mapping: A simulation study of how the number of traits and tasks affect the evolution of form and function J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-27 Philip J. Bergmann, Isabel Tonelli-Sippel
Many-to-many mapping of form-to-function posits that multiple morphological and physiological traits affect the performance of multiple tasks in an organism, and that redundancy and multitasking occur simultaneously to shape the evolution of an organism’s phenotype. Many-to-many mapping is expected to be ubiquitous in nature, yet little is known about how it influences the evolution of organismal phenotype
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A novel multiscale framework for delineating cancer evolution from subclonal compositions J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-01 Zhihao Yao, Suoqin Jin, Fuling Zhou, Junbai Wang, Kai Wang, Xiufen Zou
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A mathematical model of obesity-induced type 2 diabetes and efficacy of anti-diabetic weight reducing drug J. Theor. Biol. (IF 2.0) Pub Date : 2024-02-01 Nourridine Siewe, Avner Friedman
The dominant paradigm for modeling the obesity-induced T2DM (type 2 diabetes mellitus) today focuses on glucose and insulin regulatory systems, diabetes pathways, and diagnostic test evaluations. The problem with this approach is that it is not possible to explicitly account for the glucose transport mechanism from the blood to the liver, where the glucose is stored, and from the liver to the blood
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A mixture-like model for tumor-immune system interactions J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-24 Christian Tayou Fotso, Simon Girel, Fabienne Anjuère, Véronique M. Braud, Florence Hubert, Thierry Goudon
We introduce a mathematical model based on mixture theory intended to describe the tumor-immune system interactions within the tumor microenvironment. The equations account for the geometry of the tumor expansion, and the displacement of the immune cells, driven by diffusion and chemotactic mechanisms. They also take into account the constraints in terms of nutrient and oxygen supply. The numerical
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Corrigendum to “Multiscale numerical workflow describing microalgae motion and light pattern incidence towards population growth in a photobioreactor” [J. Theoret. Biol. 498 (2020) 110293] J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-26 Victor Pozzobon, Patrick Perré
Abstract not available
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A model about regulation on three division modes of stem cell J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-26 Qingxin Xie, Han Zhang, Maoxiang Wang, Kexun Yan, Fenglan Hu, Meng Xu
We construct a multi-stage cell lineage model for cell division, apoptosis and movement. Cells are assumed to secrete and respond to negative feedback molecules which act as a control on the stem cell divisions (including self-renewal, asymmetrical cell division (ACD) and differentiation). The densities of cells and molecules are described by coupled reaction–diffusion partial differential equations
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The evolutionary dynamics of hyperparasites J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-26 Graham R. Northrup, Andy White, Steven R. Parratt, Carly Rozins, Anna-Liisa Laine, Mike Boots
Evolutionary theory has typically focused on pairwise interactions, such as those between hosts and parasites, with relatively little work having been carried out on more complex interactions including hyperparasites: parasites of parasites. Hyperparasites are common in nature, with the chestnut blight fungus virus CHV-1 a well-known natural example, but also notably include the phages of important
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Oscillations of algal cell quota: Considering two-stage phosphate uptake kinetics J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-26 Anglu Shen, Shufei Gao, Jie Jiang, Qingjing Hu, Hao Wang, Sanling Yuan
Elucidating the mechanism of effect of phosphate (PO43−) uptake on the growth of algal cells helps understand the frequent outbreaks of algal blooms caused by eutrophication. In this study, we develop a comprehensive mathematical model that incorporates two stages of PO43− uptake and accounts for transport time delay. The model parameter values are determined by fitting experimental data of Prorocentrum
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Mathematical modeling of adipocyte size distributions: Identifiability and parameter estimation from rat data J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-24 Anne-Sophie Giacobbi, Leo Meyer, Magali Ribot, Romain Yvinec, Hedi Soula, Chloe Audebert
Fat cells, called adipocytes, are designed to regulate energy homeostasis by storing energy in the form of lipids. Adipocyte size distribution is assumed to play a role in the development of obesity-related diseases. This population of cells that do not have a characteristic size, indeed a bimodal size distribution is observed in adipose tissue. We propose a model based on a partial differential equation
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Emergence of broad cytosolic Ca2+ oscillations in the absence of CRAC channels: A model for CRAC-mediated negative feedback on PLC and Ca2+ oscillations through PKC J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-20 Lloyd Lee, Ryan Yoast, Scott Emrich, Mohamed Trebak, Vivien Kirk, James Sneyd
The role of Ca2+ release-activated Ca2+ (CRAC) channels mediated by ORAI isoforms in calcium signalling has been extensively investigated. It has been shown that the presence or absence of different isoforms has a significant effect on store-operated calcium entry (SOCE). Yoast et al. (2020) showed that, in addition to the reported narrow-spike oscillations (whereby cytosolic calcium decreases quickly
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A mathematical model of biofilm growth and spread within plant xylem: Case study of Xylella fastidiosa in olive trees J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-25 N.C. Walker, S.M. White, S.A. Ruiz, D. McKay Fletcher, M. Saponari, T. Roose
Xylem-limited bacterial pathogens cause some of the most destructive plant diseases. Though imposed measures to control these pathogens are generally ineffective, even among susceptible taxa, some hosts can limit bacterial loads and symptom expression. Mechanisms by which this resistance is achieved are poorly understood. In particular, it is still unknown how differences in vascular structure may
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A stochastic model for topographically influenced cell migration J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-23 A.J. Mitchinson, M. Pogson, G. Czanner, D. Conway, R.R. Wilkinson, M.F. Murphy, I. Siekmann, S.D. Webb
Migrating cells traverse a range of topographic configurations presented by the native extracellular environment to conduct their physiologic functions. It is well documented cells can modulate their behaviour in response to different topographic features, finding promising applications in biomaterial and bioimplant design. It is useful, in these areas of research, to be able to predict which topographic
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Lewy body radius growth: The hypothesis of the cube root of time dependency J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-20 Andrey V. Kuznetsov
This paper presents a model for the growth of Lewy bodies (LBs), which are pathological hallmarks of Parkinson's disease (PD). The model simulates the growth of classical LBs, consisting of a core and a halo. The core is assumed to comprise lipid membrane fragments and damaged organelles, while the halo consists of radiating alpha-synuclein (α-syn) fibrils. The Finke-Watzky model is employed to simulate
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The mechanism of pattern transitions between formation and dispersion J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-19 Shin Nishihara, Toru Ohira
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Crozier’s paradox and kin recognition: Insights from simplified models J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-19 Thomas W. Scott
Crozier’s paradox suggests that genetic kin recognition will not be evolutionarily stable. The problem is that more common tags (markers) are more likely to be recognised and helped. This causes common tags to increase in frequency, eliminating the genetic variability that is required for genetic kin recognition. In recent years, theoretical models have resolved Crozier’s paradox in different ways
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Stoichiometric microplastics models in natural and laboratory environments J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-14 Tianxu Wang, Hao Wang
Microplastics pose a severe threat to marine ecosystems; however, relevant mathematical modeling and analysis are lacking. This paper formulates two stoichiometric producer-grazer models to investigate the interactive effects of microplastics, nutrients, and light on population dynamics under different settings. One model incorporates optimal microplastic uptake and foraging behavior based on nutrient
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Who acquires infection from whom? A sensitivity analysis of transmission dynamics during the early phase of the COVID-19 pandemic in Belgium J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-11 Leonardo Angeli, Constantino Pereira Caetano, Nicolas Franco, Steven Abrams, Pietro Coletti, Inneke Van Nieuwenhuyse, Sorin Pop, Niel Hens
Age-related heterogeneity in a host population, whether due to how individuals mix and contact each other, the nature of host–pathogen interactions defining epidemiological parameters, or demographics, is crucial in studying infectious disease dynamics. Compartmental models represent a popular approach to address the problem, dividing the population of interest into a discrete and finite number of
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Modelling count data with partial differential equation models in biology J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-11 Matthew J. Simpson, Ryan J. Murphy, Oliver J. Maclaren
Partial differential equation (PDE) models are often used to study biological phenomena involving movement-birth–death processes, including ecological population dynamics and the invasion of populations of biological cells. Count data, by definition, is non-negative, and count data relating to biological populations is often bounded above by some carrying capacity that arises through biological competition
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Towards a qualitative theory of the interruption of eating behavior change J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-09 Philippe Dague, Laurent Muller, Loïc Paulevé, Marc Irigoin-Guichandut
The poor maintenance of eating behavior change is one of the main obstacles to minimizing weight regain after weight loss during diets for non-surgical care of obese or overweight patients. We start with a known informal explanation of interruption in eating behavior change during severe restriction and formalize it as a causal network involving psychological variables, which we extend with energetic
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Quantifying robustness of the gap gene network J. Theor. Biol. (IF 2.0) Pub Date : 2024-01-09 Elizabeth Andreas, Breschine Cummins, Tomáš Gedeon
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Antigenic cooperation in viral populations: Transformation of functions of intra-host viral variants J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-27 Leonid Bunimovich, Athulya Ram, Pavel Skums
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by continuous genomic diversification and allows to explain a number of experimental observations associated with the establishment of chronic infections by highly mutable viruses. Within this mechanism, the topology of a cross-immunoreactivity
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Using registry data to identify individual dairy cows with abnormal patterns in routinely recorded somatic cell counts J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-22 Maj Beldring Henningsen, Mossa Merhi Reimert, Matt Denwood, Maya Katrin Gussmann, Carsten Thure Kirkeby, Søren Saxmose Nielsen
Data from the Danish milk recording system routinely enter the Danish Cattle Database, including somatic cell counts (SCC) for individual animals. Elevated SCC can signal intramammary inflammation, suggesting subclinical mastitis. Detecting mastitis is pivotal to limit severity, prevent pathogen spread, and target treatment or culling. This study aimed to differentiate normal and abnormal SCC patterns
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Indirect reciprocity with abductive reasoning J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-27 Neel Pandula, Erol Akçay, Bryce Morsky
Indirect reciprocity is a reputational mechanism through which cooperative behavior can be promoted amongst a group of individuals. However, in order for this mechanism to effectively do so, cheating must be appropriately punished and cooperating appropriately rewarded. Errors in assessments and actions can hinder this process. In such a setting, individuals might try to reason about evidence to assign
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On the exclusion of exponential autocatalysts by sub-exponential autocatalysts J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-19 Yann Sakref, Olivier Rivoire
Selection among autocatalytic species fundamentally depends on their growth law: exponential species, whose number of copies grows exponentially, are mutually exclusive, while sub-exponential ones, whose number of copies grows polynomially, can coexist. Here we consider competitions between autocatalytic species with different growth laws and make the simple yet counterintuitive observation that sub-exponential
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On minimising tumoural growth under treatment resistance J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-20 Matthias M. Fischer, Nils Blüthgen
Drug resistance is a major challenge for curative cancer treatment, representing the main reason of death in patients. Evolutionary biology suggests pauses between treatment rounds as a way to delay or even avoid resistance emergence. Indeed, this approach has already shown promising preclinical and early clinical results, and stimulated the development of mathematical models for finding optimal treatment
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Exponential dynamics of DNA methylation with age J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-21 Grant Dufek, Guy Katriel, Sagi Snir, Matteo Pellegrini
The association of DNA methylation with age has been extensively studied. Previous work has investigated the trajectories of methylation with age, and developed predictive biomarkers of age. However, we still have a limited understanding of the functional form of methylation-age dynamics. To address this we present a theoretical framework to model the dynamics of DNA methylation at single sites. We
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IL-27 in combination with anti-PD-1 can be anti-cancer or pro-cancer J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-15 Kang-Ling Liao, Xue-Feng Bai, Avner Friedman
Interleukin-27 (IL-27) is known to play opposing roles in immunology. The present paper considers, specifically, the role IL-27 plays in cancer immunotherapy when combined with immune checkpoint inhibitor anti-PD-1. We first develop a mathematical model for this combination therapy, by a system of Partial Differential Equations, and show agreement with experimental results in mice injected with melanoma
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Modeling transposable elements dynamics during polyploidization in plants J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-19 Esteban Meca, Concepción M. Díez, Brandon S. Gaut
In this work we study the proliferation of transposable elements (TEs) and the epigenetic response of plants during the process of polyploidization. Through a deterministic model, expanding on our previous work on TE proliferation under epigenetic regulation, we study the long-term TE distribution and TE stability in the subgenomes of both autopolyploids and allopolyploids. We also explore different
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The Ideal Free Distribution with travel costs J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-19 Vlastimil Křivan, Ross Cressman
This article studies the effect of travel costs on population distribution in a patchy environment. The Ideal Free Distribution with travel costs is defined in the article as the distribution under which it is not profitable for individuals to move, i.e., the movement between patches ceases. It is shown that depending on the travel costs between patches, the Ideal Free Distribution may be unique, there
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The impacts of spatial–temporal heterogeneity of human-to-human contacts on the extinction probability of infectious disease from branching process model J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-12 Wuqiong Zhao, Xia Wang, Biao Tang
In this study, we focus on the impacts of spatial–temporal heterogeneity of human-to-human contacts on the spread of infectious diseases and develop a multi-type branching process model by introducing random human-to-human contact mode into a structured population. We provide the general formulas of the generation size, extinction probability, and basic reproduction number of the proposed branching
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Spatially-dependent model for rods and cones in the retina J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-14 Daniel M. Anderson, Danielle C. Brager, Anthony J. Kearsley
We develop a mathematical model for photoreceptors in the retina. We focus on rod and cone outer segment dynamics and interactions with a nutrient source associated with the retinal pigment epithelium cells. Rod and cone densities (number per unit area of retinal surface) are known to have significant spatial dependence in the retina with cones located primarily near the fovea and the rods located
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Separation of evolutionary timescales in coevolving species J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-13 Lydia J. Buckingham, Ben Ashby
Many coevolutionary processes, including host-parasite and host-symbiont interactions, involve one species or trait which evolves much faster than the other. Whether or not a coevolutionary trajectory converges depends on the relative rates of evolutionary change in the two species, and so current adaptive dynamics approaches generally either determine convergence stability by considering arbitrary
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Multisolitons-like patterns in a one-dimensional MARCKS protein cyclic model J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-12 Chenceline Fouedji, Armand Sylvin Etémé, Conrad Bertrand Tabi, Henri Paul Ekobena Fouda, Timoléon Crépin Kofané
In this paper, we study the nonlinear dynamics of the MARCKS protein between cytosol and cytoplasmic membrane through the modulational instability phenomenon. The reaction–diffusion generic model used here is firstly transformed into a cubic complex Ginzburg–Landau equation. Then, modulational instability (MI) is carried out in order to derive the MI criteria. We find the domains of some parameter
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Effect of small molecular crowders on dynamics of kinesin molecular motors J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-05 Ping Xie
Kinesin is a motor protein that can convert chemical energy of ATP hydrolysis into mechanical energy of moving processively on microtubules. Apart from the load and ATP concentration affecting the dynamics of the motor such as velocity, run length, dissociation rate, etc., the increase of solution viscosity by supplementing crowding agents of low molecular weight into the buffer can also affect the
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A Josephson junction-coupled neuron with double capacitive membranes J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-06 Feifei Yang, Jun Ma, Guodong Ren
The channel currents have distinct magnetic field effect and any changes of the electromagnetic field or electirc stimulus will change the membrane potential effectively. A feasible neuron model considers the distinct physical characteristic is more suitable to mimic the neural activities accompanying with shift in energy level. A Josephson junction (JJ) is connected to a neural circuit for estimating
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Capturing diversity: Split systems and circular approximations for conservation J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-06 Niloufar Abhari, Caroline Colijn, Arne Mooers, Paul Tupper
We investigated the implications of employing a circular approximation of split systems in the calculation of maximum diversity subsets of a set of taxa in a conservation biology context where diversity is measured using Split System Diversity (SSD). We conducted a comparative analysis between the maximum SSD score and the maximum SSD set(s) of size k, efficiently determined using a circular approximation
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Predicting pathways for old and new metabolites through clustering J. Theor. Biol. (IF 2.0) Pub Date : 2023-12-03 Thiru Siddharth, Nathan E. Lewis
The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While the discovery of new metabolites and pathways continues, the prediction of pathways for new metabolites can be challenging. It can take vast amounts of time to elucidate pathways for new metabolites;
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The eco-evolutionary dynamics of Batesian mimicry J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-24 Haruto Tomizuka, Yuuya Tachiki
Batesian mimicry is a strategy in which palatable prey species (mimic-species) resemble unpalatable prey species with aposematism (model-species). Theoretical studies on Batesian mimicry have been conducted in terms of their evolutionary significance and ecological consequences. However, despite the importance of eco-evolutionary feedback, the evolution and population dynamics of mimicry complex have
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Pillars of biology: Boolean modeling of gene-regulatory networks J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-25 Juilee Thakar
Boolean modeling is a mathematical modeling framework used for defining and studying gene-regulatory networks (GRNs). It serves as a means to develop mechanistic models, offering insights into the trajectories and dynamic properties of GRNs. In this review, I delve into seminal papers published in the Journal of Theoretical Biology that have spearheaded this field. Additionally, I explore the application
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On the limits to invasion prediction using coexistence outcomes J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-24 Jie Deng, Washington Taylor, Simon A. Levin, Serguei Saavedra
The dynamics of ecological communities in nature are typically characterized by probabilistic processes involving invasion dynamics. Because of technical challenges, however, the majority of theoretical and experimental studies have focused on coexistence dynamics. Therefore, it has become central to understand the extent to which coexistence outcomes can be used to predict analogous invasion outcomes
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Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-19 Qing Hu, Min Luo, Ruiqi Wang
One of the most significant challenges in biology is to elucidate the roles of various regulatory interactions in cell fate decision and transition. However, it remains to be fully clarified how they cooperate and determine fate transition. Here, a general framework based on statistical analysis and bifurcation theory is proposed to identify crucial regulatory interactions and how they play decisive
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Cellular communication among smooth muscle cells: The role of membrane potential via connexins J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-17 Chun Xiao, Yishui Sun, Huaxiong Huang, Xingye Yue, Zilong Song, Tim David, Shixin Xu
Communication via action potentials among neurons has been extensively studied. However, effective communication without action potentials is ubiquitous in biological systems, yet it has received much less attention in comparison. Multi-cellular communication among smooth muscles is crucial for regulating blood flow, for example. Understanding the mechanism of this non-action potential communication
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Modeling long COVID dynamics: Impact of underlying health conditions J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-15 Jie Bai, Jin Wang
We propose a new mathematical model to investigate the population dynamics of long COVID, with a focus on the impact of chronic health conditions. Our model connects long COVID with the transmission of COVID-19 so as to accurately predict the prevalence of long COVID from the progression of the infection in the host population. The model additionally incorporates the effects of COVID-19 vaccination
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Comparative analysis of kinetic realizations of insulin signaling J. Theor. Biol. (IF 2.0) Pub Date : 2023-11-19 Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Several studies have developed dynamical models to understand the underlying mechanisms of insulin signaling, a signaling cascade that leads to the translocation of glucose, the human body’s main source of energy. Fortunately, reaction network analysis allows us to extract properties of dynamical systems without depending on their model parameter values. This study focuses on the comparison of insulin