Journal of Theoretical Biology最新文献

Contact data and SARS-CoV-2: Retrospective analysis of the estimated impact of the first UK lockdown 接触数据与SARS-CoV-2：对英国首次封锁估计影响的回顾性分析

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-24 DOI: 10.1016/j.jtbi.2025.112158

Joel Kandiah , Edwin van Leeuwen , Paul J. Birrell , Daniela De Angelis

{"title":"Contact data and SARS-CoV-2: Retrospective analysis of the estimated impact of the first UK lockdown","authors":"Joel Kandiah , Edwin van Leeuwen , Paul J. Birrell , Daniela De Angelis","doi":"10.1016/j.jtbi.2025.112158","DOIUrl":"10.1016/j.jtbi.2025.112158","url":null,"abstract":"<div><div>To combat the spread of SARS-CoV-2 in March 2020 the United Kingdom (UK) announced a series of restrictions on social interaction, culminating with the introduction of lockdown measures. Estimation of lockdown effectiveness using pandemic models relied on the availability of contact data and choices on how to structure models accordingly.</div><div>We revisit the Cambridge/Public Health England real-time model (RTM), which was routinely implemented during the pandemic to monitor its development and produce short-term projections. To derive contact matrices, Google Mobility weekly contact data and school attendance data from the Department for Education were combined with information from the POLYMOD study and the UK Time Use Survey. These matrices were combined with susceptibility and transmissibility parameters to estimate effective reproduction numbers, which were taken as indicators of transmission trends.</div><div>We explore alternative formulations of the RTM, which make fuller use of the available contact data, and assess the impact of each formulation on the conclusions of lockdown effectiveness. Results show that the estimated impact of the lockdown remains unchanged, but also uncover previously uncaptured early epidemic dynamics. This highlights the importance of the timely availability of contact data in understanding transmission dynamics during the early stages of an epidemic and assessing the effectiveness of interventions.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"610 ","pages":"Article 112158"},"PeriodicalIF":1.9,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151804","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

Heat delivery accompanying pulsed field ablation 伴随脉冲场烧蚀的热传递。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-22 DOI: 10.1016/j.jtbi.2025.112145

Angiolo Farina , Antonio Fasano , Massimo Grimaldi , Fabio Rosso

引用次数: 0

Hybrid of glioma growth model and deformable image registration for longitudinal brain MRIs synthesis. 脑胶质瘤生长模型与形变图像配准的混合合成。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-17 DOI: 10.1016/j.jtbi.2025.112147

Fulian Zhong, Yujian Liu, Jianquan Zhong, Ling He, Zhonglan Tang, Jing Zhang

{"title":"Hybrid of glioma growth model and deformable image registration for longitudinal brain MRIs synthesis.","authors":"Fulian Zhong, Yujian Liu, Jianquan Zhong, Ling He, Zhonglan Tang, Jing Zhang","doi":"10.1016/j.jtbi.2025.112147","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112147","url":null,"abstract":"<p><p>Modeling and visualization of glioma growth could assist in cancer diagnosis, tumor progression prediction, and clinical treatment outcome improvement. However, most studies either failed to make patient-specific predictions or could only display information about tumor size and shape, lacking the capability to characterize the impact of tumor growth on surrounding tissues. In this study, a method (HybrSyn) combining tumor growth model and deformable image registration technique for synthesizing MRIs at arbitrary time point after the detection time has been proposed. Through the tumor growth model, tumor growth process for consecutive time point has been predicted according to the characteristics of tumor cell diffusion and proliferation within the brain. The glioma deformable image registration model was employed to obtain the deformation fields between the tumors at detection time and simulations at subsequent time points. These fields were then mapped to the patient's initial MRI scans to generate the synthetic MRIs corresponding to that time points. To validate the HybrSyn, various experiments were conducted on the BraTS19 and the internal dataset collected from Zigong First People's Hospital. The quantitative results demonstrated a structural similarity of 80.93% between the synthesized MRIs and the patients' MRI scans. The qualitative results indicated that the HybrSyn could effectively capture changes during tumor progression and provide a global view. From the clinical point of view, synthesized longitudinal brain MRIs could potentially aid in presenting the impact of glioma growth on surrounding functional areas, and identifying target regions for personalized treatment planning.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112147"},"PeriodicalIF":1.9,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103245","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

Crick’s “Frozen accident theory” of the genetic code explored by Ising models 克里克的“冻结事故理论”的遗传密码探索了伊辛模型。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-17 DOI: 10.1016/j.jtbi.2025.112146

Reijer Lenstra , Antonia Claudio Lenstra , Marco V. José

引用次数: 0

Optimal targeted therapy for multiple cancers based on contrastive Notch signaling networks. 基于对比Notch信号网络的多种癌症的最佳靶向治疗。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-13 DOI: 10.1016/j.jtbi.2025.112143

Tamaki Wakamoto, Sungrim Seirin-Lee

{"title":"Optimal targeted therapy for multiple cancers based on contrastive Notch signaling networks.","authors":"Tamaki Wakamoto, Sungrim Seirin-Lee","doi":"10.1016/j.jtbi.2025.112143","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112143","url":null,"abstract":"<p><p>Over decades, cancer understanding has advanced significantly at molecular and cellular levels, leading to various therapies based on intra-/inter-cellular networks. Despite this, cancer still remains a leading cause of death globally. The Notch signaling pathway, a crucial intercellular network in many cancers, has been extensively studied and therapies targeting the Notch pathway also have been well-studied based on inhibiting various stages of Notch activation. Nonetheless, the unclear pathophysiological mechanisms of metastasis, responsible for about 90% of cancer deaths, complicate treatment development. For example, the role of Notch signaling varies between cancers; in non-small cell lung cancer, Notch1 and Notch2 exhibit opposing effects compared to their roles in embryonal brain tumors. This suggests that a single targeted therapy to Notch signaling could produce opposing effects in the metastatic state, necessitating a more careful selection of therapies. To address this, we considered a scenario involving multiple cancers with contrasting Notch signaling pathways. We developed two mathematical models and explored optimal targeted therapies for reducing cancer cells in the metastatic state of two types of cancers with these contrasting pathways. From the in silico tests of existing Notch-targeted therapies and newly suggested therapies in this study, we found that multiple cancers with contrasting Notch networks can be controlled by one common targeted signal network. Furthermore, combination therapies enhancing Notch production may be most effective in early-stage cancer, whereas cleavage therapies may prove more effective in late-stage cancer. We also found that the order of multiple targeted therapies significantly affects treatment effectiveness and should be a key consideration. Our study proposes that optimal treatment should take into account the cancer stage, with careful selection and sequencing of medication therapies.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112143"},"PeriodicalIF":1.9,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082089","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

Synchronization transition in networks of Fractional-Order memristive Hindmarsh-Rose neurons 分数阶记忆Hindmarsh-Rose神经元网络的同步转换。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-13 DOI: 10.1016/j.jtbi.2025.112144

Sheida Ansarinasab , Fahimeh Nazarimehr , Farnaz Ghassemi , Sajad Jafari

引用次数: 0

Pillars of theoretical biology: ‘Mathematical models for cellular interaction in development, I and II’ 理论生物学的支柱：“发育过程中细胞相互作用的数学模型，I和II”

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-12 DOI: 10.1016/j.jtbi.2025.112142

Przemyslaw Prusinkiewicz

引用次数: 0

Network modeling of the different SARS-CoV-2 spike protein infection points within the human hematopoietic network 人造血网络中不同SARS-CoV-2刺突蛋白感染点的网络建模

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-09 DOI: 10.1016/j.jtbi.2025.112139

Marni E. Cueno , Noa Shintaku , Noe Hayasaki , Yuna Migita , Kenichi Imai

{"title":"Network modeling of the different SARS-CoV-2 spike protein infection points within the human hematopoietic network","authors":"Marni E. Cueno , Noa Shintaku , Noe Hayasaki , Yuna Migita , Kenichi Imai","doi":"10.1016/j.jtbi.2025.112139","DOIUrl":"10.1016/j.jtbi.2025.112139","url":null,"abstract":"<div><div>Hematopoiesis is a physiological process that mainly functions in both the formation and replenishment of varying types of blood cells. SARS-CoV-2 has been reported to affect the human hematopoietic system at multiple infection points leading to multiple types of blood disorders. However, the possible effects of the different SARS-CoV-2 infection points within the hematopoietic system were never fully understood. In this study, we designed and generated multiple human hematopoietic network models representing the varying known SARS-CoV-2 infection points within the human hematopoietic system. Subsequently, centrality measurement analyses were performed to identify significant nodes and edges within the models. We putatively generated human hematopoietic network models to represent the distinct, synergistic, and integrated SARS-CoV-2 spike protein infection points within the human hematopoietic system. Additionally, we potentially established that neither the discrete nor the synergistic network models showed any changes in the human hematopoietic network, which we attributed to the conserved nature of the hematopoietic system. Furthermore, we presumably demonstrated that the integrated network model indicated that erythropoiesis and thrombopoiesis were primarily affected. Overall, we propose that an integrated network model is putatively the more accurate representation of the human hematopoietic system in the presence of SARS-CoV-2 infection involving the spike protein.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"609 ","pages":"Article 112139"},"PeriodicalIF":1.9,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143941643","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

Extinctions as a vestige of instability: The geometry of stability and feasibility 作为不稳定遗迹的灭绝：稳定性和可行性的几何学

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-08 DOI: 10.1016/j.jtbi.2025.112141

Stav Marcus, Ari M. Turner, Guy Bunin

{"title":"Extinctions as a vestige of instability: The geometry of stability and feasibility","authors":"Stav Marcus, Ari M. Turner, Guy Bunin","doi":"10.1016/j.jtbi.2025.112141","DOIUrl":"10.1016/j.jtbi.2025.112141","url":null,"abstract":"<div><div>Species coexistence is a complex, multifaceted problem. At an equilibrium, coexistence requires two conditions: stability under small perturbations; and feasibility, meaning all species abundances are positive. Which of these two conditions is more restrictive has been debated for many years, with many works focusing on statistical arguments for systems with many species. Within the framework of the Lotka-Volterra equations, we examine the geometry of the region of coexistence in the space of interaction strengths, for symmetric competitive interactions and any finite number of species. We consider what happens when starting at a point within the coexistence region, and changing the interaction strengths continuously until one of the two conditions breaks. We find that coexistence generically breaks through the loss of feasibility, as the abundance of one species reaches zero. An exception to this rule - where stability breaks before feasibility - happens only at isolated points, or more generally on a lower dimensional subset of the boundary.</div><div>The reason behind this is that as a stability boundary is approached, some of the abundances generally diverge towards minus infinity, and so go extinct at some earlier point, breaking the feasibility condition first. These results define a new sense in which feasibility is a more restrictive condition than stability, and show that these two requirements are closely interrelated. We then show how our results affect the changes in the set of coexisting species when interaction strengths are changed: a system of coexisting species loses a species by its abundance continuously going to zero, and this new fixed point is unique. As parameters are further changed, multiple alternative equilibria may be found. Finally, we discuss the extent to which our results apply to asymmetric interactions.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112141"},"PeriodicalIF":1.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143949023","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

Effect of inosine on recurrence of tumor after radiation therapy: A mathematical investigation 肌苷对放射治疗后肿瘤复发的影响：一个数学研究。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2025-05-08 DOI: 10.1016/j.jtbi.2025.112138

K.S. Yadav , Gopinath Sadhu

{"title":"Effect of inosine on recurrence of tumor after radiation therapy: A mathematical investigation","authors":"K.S. Yadav , Gopinath Sadhu","doi":"10.1016/j.jtbi.2025.112138","DOIUrl":"10.1016/j.jtbi.2025.112138","url":null,"abstract":"<div><div>Tumor invasion that marks the transition from localized growth to aggressive spread is critical in cancer biology. It involves the breakdown of surrounding tissues through matrix degradation enzymes, such as urokinase plasminogen activator and matrix metalloproteinases, to promote cancer cells migration. Understanding invasion pathways is crucial for developing effective therapies and improving patient outcomes. There is a significant progress in cancer treatments; however, the treatments such as radiotherapy and chemotherapy are ineffective many times in the sense that some cancer cells survive, leading to tumor recurrence. It has been observed that dead cells play a key role in cancer recurrence. The dead cells, particularly due to treatments like radiation or chemotherapy, release signals and cellular components, including nucleotides like inosine, cytokines, and growth factors. These factors influence the tumor microenvironment and promote the survival and proliferation of nearby cancer cells. In this article, a novel mathematical model is proposed to investigate the effects of inosine on tumor recurrence and invasion. The simulated results are in very good agreement with the experimental and numerical results of the literature. The model simulated the inosine generation after some time of radiotherapy treatment withdrawal, and it achieves a log-normal profile. In line of experimental observations, it is obtained that the cancer cells proliferate with usual proliferation but once inosine gets generated from the dead cells, the proliferation intensity of cancer cells is enhanced significantly.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"609 ","pages":"Article 112138"},"PeriodicalIF":1.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144000022","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