Bulletin of Mathematical Biology最新文献

{"title":"Harnessing Flex Point Symmetry to Estimate Logistic Tumor Population Growth.","authors":"Stefano Pasetto, Isha Harshe, Renee Brady-Nicholls, Robert A Gatenby, Heiko Enderling","doi":"10.1007/s11538-024-01361-6","DOIUrl":"10.1007/s11538-024-01361-6","url":null,"abstract":"<p><p>The observed time evolution of a population is well approximated by a logistic growth function in many research fields, including oncology, ecology, chemistry, demography, economy, linguistics, and artificial neural networks. Initial growth is exponential, then decelerates as the population approaches its limit size, i.e., the carrying capacity. In mathematical oncology, the tumor carrying capacity has been postulated to be dynamically evolving as the tumor overcomes several evolutionary bottlenecks and, thus, to be patient specific. As the relative tumor-over-carrying capacity ratio may be predictive and prognostic for tumor growth and treatment response dynamics, it is paramount to estimate it from limited clinical data. We show that exploiting the logistic function's rotation symmetry can help estimate the population's growth rate and carry capacity from fewer data points than conventional regression approaches. We test this novel approach against published pan-cancer animal and human breast cancer data, achieving a 30% to 40% reduction in the time at which subsequent data collection is necessary to estimate the logistic growth rate and carrying capacity correctly. These results could improve tumor dynamics forecasting and augment the clinical decision-making process.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142388257","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}

{"title":"Modelling Mucus Clearance in Sinuses: Thin-Film Flow Inside a Fluid-Producing Cavity Lined with an Active Surface.","authors":"Nikhil Desai, Eric Lauga","doi":"10.1007/s11538-024-01360-7","DOIUrl":"10.1007/s11538-024-01360-7","url":null,"abstract":"<p><p>The paranasal sinuses are a group of hollow spaces within the human skull, surrounding the nose. They are lined with an epithelium that contains mucus-producing cells and tiny hairlike active appendages called cilia. The cilia beat constantly to sweep mucus out of the sinus into the nasal cavity, thus maintaining a clean mucus layer within the sinuses. This process, called mucociliary clearance, is essential for a healthy nasal environment and disruption in mucus clearance leads to diseases such as chronic rhinosinusitis, specifically in the maxillary sinuses, which are the largest of the paranasal sinuses. We present here a continuum mathematical model of mucociliary clearance inside the human maxillary sinus. Using a combination of analysis and computations, we study the flow of a thin fluid film inside a fluid-producing cavity lined with an active surface: fluid is continuously produced by a wall-normal flux in the cavity and then is swept out, against gravity, due to an effective tangential flow induced by the cilia. We show that a steady layer of mucus develops over the cavity surface only when the rate of ciliary clearance exceeds a threshold, which itself depends on the rate of mucus production. We then use a scaling analysis, which highlights the competition between gravitational retention and cilia-driven drainage of mucus, to rationalise our computational results. We discuss the biological relevance of our findings, noting that measurements of mucus production and clearance rates in healthy sinuses fall within our predicted regime of steady-state mucus layer development.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11455677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379124","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}

{"title":"A Coupled Spatial-Network Model: A Mathematical Framework for Applications in Epidemiology.","authors":"Hannah Kravitz, Christina Durón, Moysey Brio","doi":"10.1007/s11538-024-01364-3","DOIUrl":"10.1007/s11538-024-01364-3","url":null,"abstract":"<p><p>There is extensive evidence that network structure (e.g., air transport, rivers, or roads) may significantly enhance the spread of epidemics into the surrounding geographical area. A new compartmental modeling framework is proposed which couples well-mixed (ODE in time) population centers at the vertices, 1D travel routes on the graph's edges, and a 2D continuum containing the rest of the population to simulate how an infection spreads through a population. The edge equations are coupled to the vertex ODEs through junction conditions, while the domain equations are coupled to the edges through boundary conditions. A numerical method based on spatial finite differences for the edges and finite elements in the 2D domain is described to approximate the model, and numerical verification of the method is provided. The model is illustrated on two simple and one complex example geometries, and a parameter study example is performed. The observed solutions exhibit exponential decay after a certain time has passed, and the cumulative infected population over the vertices, edges, and domain tends to a constant in time but varying in space, i.e., a steady state solution.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142342128","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}

{"title":"A Pressure-Based Model of IV Fluid Therapy Kinetics.","authors":"Sarah Abel, Xiu Ting Yiew, Shane Bateman, Allan R Willms","doi":"10.1007/s11538-024-01362-5","DOIUrl":"10.1007/s11538-024-01362-5","url":null,"abstract":"<p><p>The kinetics of intravenous (IV) fluid therapy and how it affects the movement of fluids within humans and animals is an ongoing research topic. Clinical researchers have in the past used a mathematical model adopted from pharmacokinetics that attempts to mimic these kinetics. This linear model is based on the ideas that the body tries to maintain fluid levels in various compartments at some baseline targets and that fluid movement between compartments is driven by differences between the actual volumes and the targets. Here a nonlinear pressure-based model is introduced, where the driving force of fluid movement out of the blood stream is the pressure differences, both hydrostatic and oncotic, between the capillaries and the interstitial space. This model is, like the linear model, a coarse representation of fluid movement on the whole body scale, but, unlike the linear model, it is based on some of the body's biophysical processes. The abilities of both models to fit data from experiments on both awake and anesthetized cats was analyzed. The pressure-based model fit the data better than the linear model in all but one case, and was deemed statistically significantly better in a third of the cases.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364495","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}

{"title":"Forecasting and Predicting Stochastic Agent-Based Model Data with Biologically-Informed Neural Networks.","authors":"John T Nardini","doi":"10.1007/s11538-024-01357-2","DOIUrl":"10.1007/s11538-024-01357-2","url":null,"abstract":"<p><p>Collective migration is an important component of many biological processes, including wound healing, tumorigenesis, and embryo development. Spatial agent-based models (ABMs) are often used to model collective migration, but it is challenging to thoroughly predict these models' behavior throughout parameter space due to their random and computationally intensive nature. Modelers often coarse-grain ABM rules into mean-field differential equation (DE) models. While these DE models are fast to simulate, they suffer from poor (or even ill-posed) ABM predictions in some regions of parameter space. In this work, we describe how biologically-informed neural networks (BINNs) can be trained to learn interpretable BINN-guided DE models capable of accurately predicting ABM behavior. In particular, we show that BINN-guided partial DE (PDE) simulations can (1) forecast future spatial ABM data not seen during model training, and (2) predict ABM data at previously-unexplored parameter values. This latter task is achieved by combining BINN-guided PDE simulations with multivariate interpolation. We demonstrate our approach using three case study ABMs of collective migration that imitate cell biology experiments and find that BINN-guided PDEs accurately forecast and predict ABM data with a one-compartment PDE when the mean-field PDE is ill-posed or requires two compartments. This work suggests that BINN-guided PDEs allow modelers to efficiently explore parameter space, which may enable data-driven tasks for ABMs, such as estimating parameters from experimental data. All code and data from our study is available at https://github.com/johnnardini/Forecasting_predicting_ABMs .</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280562","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}

{"title":"Mathematical Modeling of Mating Probability and Fertile Egg Production in Helminth Parasites.","authors":"Gonzalo Maximiliano Lopez, Juan Pablo Aparicio","doi":"10.1007/s11538-024-01356-3","DOIUrl":"10.1007/s11538-024-01356-3","url":null,"abstract":"<p><p>In this work, we obtained a general formulation for the mating probability and fertile egg production in helminth parasites, focusing on the reproductive behavior of polygamous parasites and its implications for transmission dynamics. By exploring various reproductive variables in parasites with density-dependent fecundity, such as helminth parasites, we departed from the traditional assumptions of Poisson and negative binomial distributions to adopt an arbitrary distribution model. Our analysis considered critical factors such as mating probability, fertile egg production, and the distribution of female and male parasites among hosts, whether they are distributed together or separately. We show that the distribution of parasites within hosts significantly influences transmission dynamics, with implications for parasite persistence and, therefore, with implications in parasite control. Using statistical models and empirical data from Monte Carlo simulations, we provide insights into the complex interplay of reproductive variables in helminth parasites, enhancing our understanding of parasite dynamics and the transmission of parasitic diseases.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280564","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}

{"title":"How Cells Stay Together: A Mechanism for Maintenance of a Robust Cluster Explored by Local and Non-local Continuum Models.","authors":"Andreas Buttenschön, Shona Sinclair, Leah Edelstein-Keshet","doi":"10.1007/s11538-024-01355-4","DOIUrl":"10.1007/s11538-024-01355-4","url":null,"abstract":"<p><p>Formation of organs and specialized tissues in embryonic development requires migration of cells to specific targets. In some instances, such cells migrate as a robust cluster. We here explore a recent local approximation of non-local continuum models by Falcó et al. (SIAM J Appl Math 84:17-42, 2023). We apply their theoretical results by specifying biologically-based cell-cell interactions, showing how such cell communication results in an effective attraction-repulsion Morse potential. We then explore the clustering instability, the existence and size of the cluster, and its stability. For attractant-repellent chemotaxis, we derive an explicit condition on cell and chemical properties that guarantee the existence of robust clusters. We also extend their work by investigating the accuracy of the local approximation relative to the full non-local model.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142280563","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}

{"title":"Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment","authors":"Bernadette J. Stolz, Jagdeep Dhesi, Joshua A. Bull, Heather A. Harrington, Helen M. Byrne, Iris H. R. Yoon","doi":"10.1007/s11538-024-01353-6","DOIUrl":"https://doi.org/10.1007/s11538-024-01353-6","url":null,"abstract":"<p>Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259014","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}

{"title":"Revisiting Fishery Sustainability Targets","authors":"Vincent Cattoni, Leah F. South, David J. Warne, Carl Boettiger, Bhavya Thakran, Matthew H. Holden","doi":"10.1007/s11538-024-01352-7","DOIUrl":"https://doi.org/10.1007/s11538-024-01352-7","url":null,"abstract":"<p>Density-dependent population dynamic models strongly influence many of the world’s most important harvest policies. Nearly all classic models (e.g. Beverton-Holt and Ricker) recommend that managers maintain a population size of roughly 40–50 percent of carrying capacity to maximize sustainable harvest, no matter the species’ population growth rate. Such insights are the foundational logic behind most sustainability targets and biomass reference points for fisheries. However, a simple, less-commonly used model, called the Hockey-Stick model, yields very different recommendations. We show that the optimal population size to maintain in this model, as a proportion of carrying capacity, is one over the population growth rate. This leads to more conservative optimal harvest policies for slow-growing species, compared to other models, if all models use the same growth rate and carrying capacity values. However, parameters typically are not fixed; they are estimated after model-fitting. If the Hockey-Stick model leads to lower estimates of carrying capacity than other models, then the Hockey-Stick policy could yield lower absolute population size targets in practice. Therefore, to better understand the population size targets that may be recommended across real fisheries, we fit the Hockey-Stick, Ricker and Beverton-Holt models to population time series data across 284 fished species from the RAM Stock Assessment database. We found that the Hockey-Stick model usually recommended fisheries maintain population sizes higher than all other models (in 69–81% of the data sets). Furthermore, in 77% of the datasets, the Hockey-Stick model recommended an optimal population target even higher than 60% of carrying capacity (a widely used target, thought to be conservative). However, there was considerable uncertainty in the model fitting. While Beverton-Holt fit several of the data sets best, Hockey-Stick also frequently fit similarly well. In general, the best-fitting model rarely had overwhelming support (a model probability of greater than 95% was achieved in less than five percent of the datasets). A computational experiment, where time series data were simulated from all three models, revealed that Beverton-Holt often fit best even when it was not the true model, suggesting that fisheries data are likely too small and too noisy to resolve uncertainties in the functional forms of density-dependent growth. Therefore, sustainability targets may warrant revisiting, especially for slow-growing species.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259325","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}

{"title":"An Approximate Bayesian Computation Approach for Embryonic Astrocyte Migration Model Reduction","authors":"Tracy L. Stepien","doi":"10.1007/s11538-024-01354-5","DOIUrl":"https://doi.org/10.1007/s11538-024-01354-5","url":null,"abstract":"<p>During embryonic development of the retina of the eye, astrocytes, a type of glial cell, migrate over the retinal surface and form a dynamic mesh. This mesh then serves as scaffolding for blood vessels to form the retinal vasculature network that supplies oxygen and nutrients to the inner portion of the retina. Astrocyte spreading proceeds in a radially symmetric manner over the retinal surface. Additionally, astrocytes mature from astrocyte precursor cells (APCs) to immature perinatal astrocytes (IPAs) during this embryonic stage. We extend a previously-developed continuum model that describes tension-driven migration and oxygen and growth factor influenced proliferation and differentiation. Comparing numerical simulations to experimental data, we identify model equation components that can be removed via model reduction using approximate Bayesian computation (ABC). Our results verify experimental studies indicating that the choroid oxygen supply plays a negligible role in promoting differentiation of APCs into IPAs and in promoting IPA proliferation, and the hyaloid artery oxygen supply and APC apoptosis play negligible roles in astrocyte spreading and differentiation.</p>","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217420","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}