Bulletin of Mathematical Biology最新文献_第3页

Statistical Mobility of Multicellular Colonies of Flagellated Swimming Cells. 鞭毛游动细胞多细胞群的统计流动性

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-30 DOI: 10.1007/s11538-024-01351-8

Yonatan Ashenafi, Peter R Kramer

引用次数: 0

p53 Orchestrates Cancer Metabolism: Unveiling Strategies to Reverse the Warburg Effect. p53 协调癌症代谢：揭示逆转沃伯格效应的策略。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-29 DOI: 10.1007/s11538-024-01346-5

Roba Abukwaik, Elias Vera-Siguenza, Daniel Tennant, Fabian Spill

{"title":"p53 Orchestrates Cancer Metabolism: Unveiling Strategies to Reverse the Warburg Effect.","authors":"Roba Abukwaik, Elias Vera-Siguenza, Daniel Tennant, Fabian Spill","doi":"10.1007/s11538-024-01346-5","DOIUrl":"10.1007/s11538-024-01346-5","url":null,"abstract":"Cancer cells exhibit significant alterations in their metabolism, characterised by a reduction in oxidative phosphorylation (OXPHOS) and an increased reliance on glycolysis, even in the presence of oxygen. This metabolic shift, known as the Warburg effect, is pivotal in fuelling cancer's uncontrolled growth, invasion, and therapeutic resistance. While dysregulation of many genes contributes to this metabolic shift, the tumour suppressor gene p53 emerges as a master player. Yet, the molecular mechanisms remain elusive. This study introduces a comprehensive mathematical model, integrating essential p53 targets, offering insights into how p53 orchestrates its targets to redirect cancer metabolism towards an OXPHOS-dominant state. Simulation outcomes align closely with experimental data comparing glucose metabolism in colon cancer cells with wild-type and mutated p53. Additionally, our findings reveal the dynamic capability of elevated p53 activation to fully reverse the Warburg effect, highlighting the significance of its activity levels not just in triggering apoptosis (programmed cell death) post-chemotherapy but also in modifying the metabolic pathways implicated in treatment resistance. In scenarios of p53 mutations, our analysis suggests targeting glycolysis-instigating signalling pathways as an alternative strategy, whereas targeting solely synthesis of cytochrome c oxidase 2 (SCO2) does support mitochondrial respiration but may not effectively suppress the glycolysis pathway, potentially boosting the energy production and cancer cell viability.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142104556","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

A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms. 光养混合种亚气态生物膜昼夜活动和长期存活的数学模型

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-28 DOI: 10.1007/s11538-024-01348-3

A Tenore, F Russo, J Jacob, J D Grattepanche, B Buttaro, I Klapper

{"title":"A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms.","authors":"A Tenore, F Russo, J Jacob, J D Grattepanche, B Buttaro, I Klapper","doi":"10.1007/s11538-024-01348-3","DOIUrl":"10.1007/s11538-024-01348-3","url":null,"abstract":"Subaerial biofilms (SAB) are intricate microbial communities living on terrestrial surfaces, of interest in a variety of contexts including cultural heritage preservation, microbial ecology, biogeochemical cycling, and biotechnology. Here we propose a mathematical model aimed at better understanding the interplay between cyanobacteria and heterotrophic bacteria, common microbial SAB constituents, and their mutual dependence on local environmental conditions. SABs are modeled as thin mixed biofilm-liquid water layers sitting on stone. A system of ordinary differential equations regulates the dynamics of key SAB components: cyanobacteria, heterotrophs, polysaccharides and decayed biomass, as well as cellular levels of organic carbon, nitrogen and energy. These components are interconnected through a network of energetically dominant metabolic pathways, modeled with limitation terms reflecting the impact of biotic and abiotic factors. Daily cylces of temperature, humidity, and light intensity are considered as input model variables that regulate microbial activity by influencing water availability and metabolic kinetics. Relevant physico-chemical processes, including pH regulation, further contribute to a description of the SAB ecology. Numerical simulations explore the dynamics of SABs in a real-world context, revealing distinct daily activity periods shaped by water activity and light availability, as well as longer time scale survivability conditions. Results also suggest that heterotrophs could play a substantial role in decomposing non-volatile carbon compounds and regulating pH, thus influencing the overall composition and stability of the biofilm.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11358337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142079215","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

Onset of Spontaneous Filling and Voiding Cycles in the Lower Urinary Tract: A Modeling Study. 下尿路自发充盈和排尿周期的开始：一项模型研究。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-24 DOI: 10.1007/s11538-024-01320-1

Roberto Nunez, Elie Alhajjar, Daniel Jaskowak, Zachary C Danziger, Giovanna Guidoboni

引用次数: 0

Bounding the Softwired Parsimony Score of a Phylogenetic Network. 确定系统发育网络的软连接解析得分的边界

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-22 DOI: 10.1007/s11538-024-01350-9

Janosch Döcker, Simone Linz, Kristina Wicke

{"title":"Bounding the Softwired Parsimony Score of a Phylogenetic Network.","authors":"Janosch Döcker, Simone Linz, Kristina Wicke","doi":"10.1007/s11538-024-01350-9","DOIUrl":"10.1007/s11538-024-01350-9","url":null,"abstract":"In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by <math><mrow><mi>k</mi> <mo>+</mo> <mn>1</mn></mrow> </math> times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11341636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035325","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

Make the Most of Your Society Journal. 充分利用你的学会期刊

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-20 DOI: 10.1007/s11538-024-01349-2

Matthew J Simpson, Reinhard C Laubenbacher, Ruth E Baker

引用次数: 0

Assessing the Role of Patient Generation Techniques in Virtual Clinical Trial Outcomes. 评估患者生成技术在虚拟临床试验结果中的作用。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-13 DOI: 10.1007/s11538-024-01345-6

Jana L Gevertz, Joanna R Wares

{"title":"Assessing the Role of Patient Generation Techniques in Virtual Clinical Trial Outcomes.","authors":"Jana L Gevertz, Joanna R Wares","doi":"10.1007/s11538-024-01345-6","DOIUrl":"10.1007/s11538-024-01345-6","url":null,"abstract":"Virtual clinical trials (VCTs) are growing in popularity as a tool for quantitatively predicting heterogeneous treatment responses across a population. In the context of a VCT, a plausible patient is an instance of a mathematical model with parameter (or attribute) values chosen to reflect features of the disease and response to treatment for that particular patient. A number of techniques have been introduced to determine the set of model parametrizations to include in a virtual patient cohort. These methodologies generally start with a prior distribution for each model parameter and utilize some criteria to determine whether a parameter set sampled from the priors should be included or excluded from the plausible population. No standard technique exists, however, for generating these prior distributions and choosing the inclusion/exclusion criteria. In this work, we rigorously quantify the impact that VCT design choices have on VCT predictions. Rather than use real data and a complex mathematical model, a spatial model of radiotherapy is used to generate simulated patient data and the mathematical model used to describe the patient data is a two-parameter ordinary differential equations model. This controlled setup allows us to isolate the impact of both the prior distribution and the inclusion/exclusion criteria on both the heterogeneity of plausible populations and on predicted treatment response. We find that the prior distribution, rather than the inclusion/exclusion criteria, has a larger impact on the heterogeneity of the plausible population. Yet, the percent of treatment responders in the plausible population was more sensitive to the inclusion/exclusion criteria utilized. This foundational understanding of the role of virtual clinical trial design should help inform the development of future VCTs that use more complex models and real data.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970668","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 Modeling Study on the Effect of Interstate Mobility Restrictions on the SARS-CoV-2 Pandemic. 州际流动限制对 SARS-CoV-2 大流行影响的模型研究。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-12 DOI: 10.1007/s11538-024-01347-4

Gustavo B Libotte, Lucas Dos Anjos, Regina C C de Almeida, Sandra M C Malta

{"title":"A Modeling Study on the Effect of Interstate Mobility Restrictions on the SARS-CoV-2 Pandemic.","authors":"Gustavo B Libotte, Lucas Dos Anjos, Regina C C de Almeida, Sandra M C Malta","doi":"10.1007/s11538-024-01347-4","DOIUrl":"10.1007/s11538-024-01347-4","url":null,"abstract":"Mobility is a crucial element in comprehending the possible expansion of the transmission chain in an epidemic. In the initial phases, strategies for containing cases can be directly linked to population mobility restrictions, especially when only non-pharmaceutical measures are available. During the pandemic of COVID-19 in Brazil, mobility limitation measures were strongly opposed by a large portion of the population. Hypothetically, if the population had supported such measures, the sharp rise in the number of cases could have been suppressed. In this context, computational modeling offers systematic methods for analyzing scenarios about the development of the epidemiological situation taking into account specific conditions. In this study, we examine the impacts of interstate mobility in Brazil. To do so, we develop a metapopulational model that considers both intra and intercompartmental dynamics, utilizing graph theory. We use a parameter estimation technique that allows us to infer the effective reproduction number in each state and estimate the time-varying transmission rate. This makes it possible to investigate scenarios related to mobility and quantify the effect of people moving between states and how certain measures to limit movement might reduce the impact of the pandemic. Our results demonstrate a clear association between the number of cases and mobility, which is heightened when states are closer to each other. This serves as a proof of concept and shows how reducing mobility in more heavily trafficked areas can be more effective.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970667","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

Mathematical Modeling of Tumor Immune Interactions: The Role of Anti-FGFR and Anti-PD-1 in the Combination Therapy. 肿瘤免疫相互作用的数学建模：抗表皮生长因子受体和抗 PD-1 在联合疗法中的作用。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-07 DOI: 10.1007/s11538-024-01329-6

Chenghang Li, Zonghang Ren, Guiyu Yang, Jinzhi Lei

{"title":"Mathematical Modeling of Tumor Immune Interactions: The Role of Anti-FGFR and Anti-PD-1 in the Combination Therapy.","authors":"Chenghang Li, Zonghang Ren, Guiyu Yang, Jinzhi Lei","doi":"10.1007/s11538-024-01329-6","DOIUrl":"10.1007/s11538-024-01329-6","url":null,"abstract":"Bladder cancer poses a significant global health burden with high incidence and recurrence rates. This study addresses the therapeutic challenges in advanced bladder cancer, focusing on the competitive mechanisms of ligand or drug binding to receptors. We developed a refined mathematical model that integrates the dynamics of tumor cells and immune responses, particularly targeting fibroblast growth factor receptor 3 (FGFR3) and immune checkpoint inhibitors (ICIs). This study contributes to understanding combination therapies by elucidating the competitive binding dynamics and quantifying the synergistic effects. The findings highlight the importance of personalized immunotherapeutic strategies, considering factors such as drug dosage, dosing schedules, and patient-specific parameters. Our model further reveals that ligand-independent activated-state receptors are the most essential drivers of tumor proliferation. Moreover, we found that PD-L1 expression rate was more important than PD-1 in driving the dynamic evolution of tumor and immune cells. The proposed mathematical model provides a comprehensive framework for unraveling the complexities of combination therapies in advanced bladder cancer. As research progresses, this multidisciplinary approach contributes valuable insights toward optimizing therapeutic strategies and advancing cancer treatment paradigms.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896771","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

Exploring Aeration Strategies for Enhanced Simultaneous Nitrification and Denitrification in Membrane Aerated Bioreactors: A Computational Approach. 探索膜充气生物反应器中强化同时硝化和反硝化的曝气策略：计算方法。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-07 DOI: 10.1007/s11538-024-01343-8

Maryam Ghasemi, Sheng Chang, Sivabal Sivaloganathan

{"title":"Exploring Aeration Strategies for Enhanced Simultaneous Nitrification and Denitrification in Membrane Aerated Bioreactors: A Computational Approach.","authors":"Maryam Ghasemi, Sheng Chang, Sivabal Sivaloganathan","doi":"10.1007/s11538-024-01343-8","DOIUrl":"10.1007/s11538-024-01343-8","url":null,"abstract":"In this study we employ computational methods to investigate the influence of aeration strategies on simultaneous nitrification-denitrification processes. Specifically, we explore the impact of periodic and intermittent aeration on denitrification rates, which typically lag behind nitrification rates under identical environmental conditions. A two-dimensional deterministic multi-scale model is employed to elucidate the fundamental processes governing the behavior of membrane aerated biofilm reactors (MABRs). We aim to identify key factors that promote denitrification under varying aeration strategies. Our findings indicate that the concentration of oxygen during the off phase and the duration of the off interval play crucial roles in controlling denitrification. Complete discontinuation of oxygen is not advisable, as it inhibits the formation of anaerobic heterotrophic bacteria, thereby impeding denitrification. Extending the length of the off interval, however, enhances denitrification. Furthermore, we demonstrate that the initial inoculation of the substratum (membrane in this study) influences substrate degradation under periodic aeration, with implications for both nitrification and denitrification. Comparison between continuous and periodic/intermittent aeration scenarios reveals that the latter can extend the operational cycle of MABRs. This extension is attributed to relatively low biofilm growth rates associated with non-continuous aeration strategies. Consequently, our study provides a comprehensive understanding of the intricate interplay between aeration strategies and simultaneous nitrification-denitrification in MABRs. The insights presented herein can contribute significantly to the optimization of MABR performance in wastewater treatment applications.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901021","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