Journal of Theoretical Biology最新文献_第3页

Cooperative SIR dynamics as a model for spontaneous blood clot initiation 作为自发血凝块形成模型的合作 SIR 动力学。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-17 DOI: 10.1016/j.jtbi.2024.111991

Philip Greulich

{"title":"Cooperative SIR dynamics as a model for spontaneous blood clot initiation","authors":"Philip Greulich","doi":"10.1016/j.jtbi.2024.111991","DOIUrl":"10.1016/j.jtbi.2024.111991","url":null,"abstract":"<div><div>Blood clotting is an important physiological process to suppress bleeding upon injury, but when it occurs inadvertently, it can cause thrombosis, which can lead to life threatening conditions. Hence, understanding the microscopic mechanistic factors for inadvertent, spontaneous blood clotting, in absence of a vessel breach, can help in predicting and averting such conditions. Here, we present a minimal model – reminiscent of the SIR model – for the initiating stage of spontaneous blood clotting, the collective activation of blood platelets. This model predicts that in the presence of very small initial activation signals, collective activation of the platelet population is possible, but requires a sufficient degree of heterogeneity of platelet sensitivity. To propagate the activation signal and achieve collective activation of the bulk platelet population, it requires the presence of, possibly only few, hyper-sensitive platelets, but also a sufficient proportion of platelets with intermediate, yet higher-than-average sensitivity. A comparison with experimental results demonstrates a qualitative agreement for high platelet signalling activity.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"598 ","pages":"Article 111991"},"PeriodicalIF":1.9,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enlightening the blind spot of the Michaelis–Menten rate law: The role of relaxation dynamics in molecular complex formation 揭示迈克尔-门顿速率定律的盲点：弛豫动力学在分子复合物形成中的作用。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-16 DOI: 10.1016/j.jtbi.2024.111989

Junghun Chae , Roktaek Lim , Thomas L.P. Martin , Cheol-Min Ghim , Pan-Jun Kim

{"title":"Enlightening the blind spot of the Michaelis–Menten rate law: The role of relaxation dynamics in molecular complex formation","authors":"Junghun Chae , Roktaek Lim , Thomas L.P. Martin , Cheol-Min Ghim , Pan-Jun Kim","doi":"10.1016/j.jtbi.2024.111989","DOIUrl":"10.1016/j.jtbi.2024.111989","url":null,"abstract":"<div><div>The century-long Michaelis–Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an equilibrium (quasi-steady state) compared to the pace of molecular concentration changes. Yet, in the case of actively time-varying molecular concentrations with transient or oscillatory dynamics, the deviation of the complex profile from the quasi-steady state becomes relevant. A recent theoretical approach, known as the effective time-delay scheme (ETS), suggests that the delay from the relaxation time of molecular complex formation contributes to the substantial breakdown of the quasi-steady state assumption. Here, we systematically expand this ETS and inquire into the comprehensive roles of relaxation dynamics in complex formation. Through the modeling of rhythmic protein–protein and protein–DNA interactions and the mammalian circadian clock, our analysis reveals the effect of the relaxation dynamics beyond the time delay, which extends to the dampening of changes in the complex concentration with a reduction in the oscillation amplitude compared to the quasi-steady state. Interestingly, the combined effect of the time delay and amplitude reduction shapes both qualitative and quantitative oscillatory patterns such as the emergence and variability of the mammalian circadian rhythms. These findings highlight the downside of the routine assumption of quasi-steady states and enhance the mechanistic understanding of rich time-varying biomolecular processes.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"597 ","pages":"Article 111989"},"PeriodicalIF":1.9,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach 人类乳头瘤病毒感染配对形成模型中的疫苗接种策略：最佳控制方法。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-16 DOI: 10.1016/j.jtbi.2024.111994

Fernando Saldaña

{"title":"Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach","authors":"Fernando Saldaña","doi":"10.1016/j.jtbi.2024.111994","DOIUrl":"10.1016/j.jtbi.2024.111994","url":null,"abstract":"<div><div>Human papillomavirus (HPV) infection is a widespread sexually transmitted infection responsible for several cancers including anal, oropharyngeal, penile, vaginal, and cervical cancer. Despite HPV vaccines have been available for almost 20 years and are incredibly effective in preventing infection, the scale-up of vaccination has been slow in many low and middle-income countries. This analysis uses a pair model that explicitly accounts for sexual partnership formation to investigate HPV immunization programs. The optimality of vaccine interventions is analyzed using optimal control theory. We give formal proof of the existence of optimal control solutions and obtain first-order optimality conditions via Pontryagin’s Maximum Principle. Extensive numerical simulations are used to investigate plausible what-if scenarios to understand under which conditions the inclusion of males should be recommended in addition to female vaccination. The results suggest that a gender-neutral vaccination program should be recommended in regions where vaccination uptake in women is still low whereas for an already existing female-only program with high uptake, it is more effective to keep increasing coverage in females.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"597 ","pages":"Article 111994"},"PeriodicalIF":1.9,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142669413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Peripheral straightness leads to shape diversification during formations of entire leaves 外围平直度导致整个叶片形成过程中的形状多样化。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-15 DOI: 10.1016/j.jtbi.2024.111990

Akiko M. Nakamasu

{"title":"Peripheral straightness leads to shape diversification during formations of entire leaves","authors":"Akiko M. Nakamasu","doi":"10.1016/j.jtbi.2024.111990","DOIUrl":"10.1016/j.jtbi.2024.111990","url":null,"abstract":"<div><div>The ways to read out positional information are essential to determine final shapes in developmental processes. Relative shaping to different sizes of positional information enables robust morphogenesis; however, the same difference sometimes causes diversity. Different responses to a positional information will enable such switching of identical/diverse shapes, though detail mechanisms remain unknown.</div><div>In this paper, we describe growing forms by constructing the contour of a two-dimensional object using propagating points and segments connecting them. In plant morphogenesis that lacks almost cell movements, tissue growth accompanied by cell divisions is central. We focused on peripheral cell composition in leaf formation as a frame. The growth with or without cell division on the periphery was analyzed with simple algorithms. We calculated the shapes of entire leaves with different ovality using combined growth algorithms as a model. Responces of the respective algorithms to simple positional information were explored to seek the origin of the shape diversification.</div><div>The algorithm for “growth with cell divisions” maintained identical shapes; however, diverse shapes were generated by the algorithm “growth without cell division” with gradients. The simplified model allowed us to interpret the oval shape diversity due to slants on edges. We concluded that peripheral straightness can generate shape diversity, at least in leaf morphogenesis.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"597 ","pages":"Article 111990"},"PeriodicalIF":1.9,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A comprehensive study on tuberculosis prediction models: Integrating machine learning into epidemiological analysis 结核病预测模型综合研究：将机器学习融入流行病学分析。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-13 DOI: 10.1016/j.jtbi.2024.111988

Hamna Mariyam K.B. , Sayooj Aby Jose , Anuwat Jirawattanapanit , Karuna Mathew

{"title":"A comprehensive study on tuberculosis prediction models: Integrating machine learning into epidemiological analysis","authors":"Hamna Mariyam K.B. , Sayooj Aby Jose , Anuwat Jirawattanapanit , Karuna Mathew","doi":"10.1016/j.jtbi.2024.111988","DOIUrl":"10.1016/j.jtbi.2024.111988","url":null,"abstract":"<div><div>Tuberculosis (TB), the second leading infectious killer globally, claimed the lives of 1.3 million individuals in 2022, after COVID-19, surpassing the toll of HIV and AIDS. With an estimated 10.6 million new TB cases worldwide in 2022, the gravity of the disease persists, necessitating urgent attention. Tuberculosis remains a critical public health crisis, and efforts to combat this infectious disease demand intensified global commitment and resources. This study utilizes predictive modeling techniques to forecast the incidence of Tuberculosis (TB), employing a range of machine learning models. Additionally, the research incorporates impactful visualizations for comprehensive data exploration, analysis and comparison. Various machine learning models are developed to anticipate TB incidence, with the optimal performing model to customize a user-defined function. This research provides valuable insights into the potential determinants influencing TB incidence, contributing to the identification of strategies for preventing the spread of Tuberculosis.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"597 ","pages":"Article 111988"},"PeriodicalIF":1.9,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note 关于滥用进化论为智能设计 "科学 "辩护：警言。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-09 DOI: 10.1016/j.jtbi.2024.111985

Arne Traulsen , Mikkel Nif Rasmussen , Joachim Krug , Andreas Beyer

引用次数: 0

Statistical inference and neural network training based on stochastic difference model for air pollution and associated disease transmission 基于随机差分模型的空气污染及相关疾病传播的统计推理和神经网络训练。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-08 DOI: 10.1016/j.jtbi.2024.111987

Sha He, Mengqi He, Sanyi Tang

{"title":"Statistical inference and neural network training based on stochastic difference model for air pollution and associated disease transmission","authors":"Sha He, Mengqi He, Sanyi Tang","doi":"10.1016/j.jtbi.2024.111987","DOIUrl":"10.1016/j.jtbi.2024.111987","url":null,"abstract":"<div><div>A polluted air environment can potentially provoke infections of diverse respiratory diseases. The development of mathematical models can study the mechanism of air pollution and its effect on the spread of diseases. The key is to characterize the intrinsic correlation between the disease infection and the change in air pollutant concentration. In this paper, we establish a coupled discrete susceptible–exposed–infectious–susceptible (SEIS) model with demography to characterize the transmission of disease, and the change in the concentration of air pollutants is described in the form of the Beverton–Holt (BH) model with a time-varying inflow rate of air pollutants. Considering the periodic variation characteristics of data, time-varying parameters are defined as specific functional forms. We estimate the change point at which the parameters switch and the parameter values within the switching interval based on Bayesian statistical theory. The data fitting of the model can reflect the seasonal peaks and annual growth trends of values of air quality index (AQI) and the number of influenza-like illnesses (ILI) cases. However, the bias in data fitting indicates a more complex correlation pattern between disease and pollutant concentration changes. To explore unknown mechanisms, we propose the extended transmission-dynamics-informed neural network (TDINN) algorithm by combining deep learning with difference equations and obtain the curves of the transmission rate and inflow rate functions over time. The results show that neural network models can help us determine time-varying parameters in the model, thereby better reflecting the trend of data changes.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111987"},"PeriodicalIF":1.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimal seasonal schedule for producing biogenic volatile organic compounds for tree defense 生产用于树木防御的生物挥发性有机化合物的最佳季节安排。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-08 DOI: 10.1016/j.jtbi.2024.111986

Yoh Iwasa, Rena Hayashi, Akiko Satake

{"title":"Optimal seasonal schedule for producing biogenic volatile organic compounds for tree defense","authors":"Yoh Iwasa, Rena Hayashi, Akiko Satake","doi":"10.1016/j.jtbi.2024.111986","DOIUrl":"10.1016/j.jtbi.2024.111986","url":null,"abstract":"<div><div>The leaves of many trees emit biogenic volatile organic compounds (BVOCs) that protect them from various threats, including herbivory, pathogens, and heat stress. In a previous study, we analyzed the optimal seasonal schedule for producing isoprene, a highly volatile BVOC, in leaves to mitigate heat damage and maximize net carbon gain. In this paper, we investigate the seasonal production schedule of BVOCs stored in leaves, such as monoterpenes and sesquiterpenes, which decay slowly. When the leaves are bitten, these chemicals are emitted and help to prevent further herbivory. The optimal seasonal schedule, analyzed using Pontryagin’s maximum principle, includes a period of singular control. Producing BVOCs for defense is advantageous if their decay rate is slow and the photosynthetic rate is fast. The amount of BVOCs produced increases with slower decay rate and faster photosynthetic rate. But it does not increase monotonically with the magnitude of the threat. BVOCs are produced earlier than the peak period of the threat for which the chemicals are intended. Based on the results of the model, we discuss the reported variations in BVOC production among different chemical species and tree species, as well as the seasonal patterns of gene expression in different pathways for BVOC production.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111986"},"PeriodicalIF":1.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Implementation of actin polymerization and depolymerization in a two-dimensional cell migration model and its implications on mammalian cell morphology and velocity 二维细胞迁移模型中肌动蛋白聚合和解聚的实现及其对哺乳动物细胞形态和速度的影响。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-11-05 DOI: 10.1016/j.jtbi.2024.111977

Lingxing Yao , Yizeng Li

{"title":"Implementation of actin polymerization and depolymerization in a two-dimensional cell migration model and its implications on mammalian cell morphology and velocity","authors":"Lingxing Yao , Yizeng Li","doi":"10.1016/j.jtbi.2024.111977","DOIUrl":"10.1016/j.jtbi.2024.111977","url":null,"abstract":"<div><div>Cell migration, a pivotal process in wound healing, immune response, and even cancer metastasis, manifests through intricate interplay between morphology, speed, and cytoskeletal dynamics. Mathematical modeling emerges as a powerful tool to dissect these complex interactions. This work presents a two-dimensional immersed boundary model for mammalian cell migration, incorporating both filamentous actin (F-actin) and monomeric actin (G-actin) to explicitly capture polymerization and depolymerization. This model builds upon our previous one-dimensional efforts, now enabling us to explore the impact of G-actin on not just cell velocity but also morphology. We compare predictions from both models, revealing that while the one-dimensional model captures core dynamics along the cell’s axis, the two-dimensional model excels in portraying cell shape evolution and transverse variations in actin concentration and velocity. Our findings highlight the crucial role of including G-actin in shaping cell morphology. Actin velocity aligned with migration direction elongates the cell, while velocity normal to the membrane promotes spreading. Importantly, the model establishes a link between these microscopic aspects and macroscopic observables like cell shape, offering a deeper understanding of cell migration dynamics. This work not only provides a more comprehensive picture of cell migration but also paves the way for future studies exploring the interplay of actin dynamics, cell morphology, and biophysical parameters in diverse biological contexts.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111977"},"PeriodicalIF":1.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Event-based biological pest control: An LMI approach 基于事件的生物害虫控制：LMI 方法

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-10-28 DOI: 10.1016/j.jtbi.2024.111975

M. Sathishkumar , Maya Joby , Srimanta Santra , Yong-Ki Ma , S. Marshal Anthoni

引用次数: 0