Bulletin of Mathematical Biology最新文献_第5页

Multi-layer Bundling as a New Approach for Determining Multi-scale Correlations Within a High-Dimensional Dataset. 多层捆绑是确定高维数据集内多尺度相关性的新方法

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-12 DOI: 10.1007/s11538-024-01335-8

Mehran Fazli, Richard Bertram, Deborah A Striegel

{"title":"Multi-layer Bundling as a New Approach for Determining Multi-scale Correlations Within a High-Dimensional Dataset.","authors":"Mehran Fazli, Richard Bertram, Deborah A Striegel","doi":"10.1007/s11538-024-01335-8","DOIUrl":"10.1007/s11538-024-01335-8","url":null,"abstract":"The growing complexity of biological data has spurred the development of innovative computational techniques to extract meaningful information and uncover hidden patterns within vast datasets. Biological networks, such as gene regulatory networks and protein-protein interaction networks, hold critical insights into biological features' connections and functions. Integrating and analyzing high-dimensional data, particularly in gene expression studies, stands prominent among the challenges in deciphering these networks. Clustering methods play a crucial role in addressing these challenges, with spectral clustering emerging as a potent unsupervised technique considering intrinsic geometric structures. However, spectral clustering's user-defined cluster number can lead to inconsistent and sometimes orthogonal clustering regimes. We propose the Multi-layer Bundling (MLB) method to address this limitation, combining multiple prominent clustering regimes to offer a comprehensive data view. We call the outcome clusters \"bundles\". This approach refines clustering outcomes, unravels hierarchical organization, and identifies bridge elements mediating communication between network components. By layering clustering results, MLB provides a global-to-local view of biological feature clusters enabling insights into intricate biological systems. Furthermore, the method enhances bundle network predictions by integrating the bundle co-cluster matrix with the affinity matrix. The versatility of MLB extends beyond biological networks, making it applicable to various domains where understanding complex relationships and patterns is needed.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11245441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589644","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

Phylogenetic Diversity Indices from an Affine and Projective Viewpoint. 从仿射和投影角度看系统发育多样性指数

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-09 DOI: 10.1007/s11538-024-01332-x

V Moulton, A Spillner, K Wicke

{"title":"Phylogenetic Diversity Indices from an Affine and Projective Viewpoint.","authors":"V Moulton, A Spillner, K Wicke","doi":"10.1007/s11538-024-01332-x","DOIUrl":"10.1007/s11538-024-01332-x","url":null,"abstract":"Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the evolutionary history of the species in question, which is often given in terms of a phylogenetic tree. Both rooted and unrooted phylogenetic trees can be employed, and there are close connections between the indices that are derived in these two different ways. In this paper, we introduce more general phylogenetic diversity indices that can be derived from collections of subsets (clusters) and collections of bipartitions (splits) of the given set of species. Such indices could be useful, for example, in case there is some uncertainty in the topology of the tree being used to derive a phylogenetic diversity index. As well as characterizing some of the indices that we introduce in terms of their special properties, we provide a link between cluster-based and split-based phylogenetic diversity indices that uses a discrete analogue of the classical link between affine and projective geometry. This provides a unified framework for many of the various phylogenetic diversity indices used in the literature based on rooted and unrooted phylogenetic trees, generalizations and new proofs for previous results concerning tree-based indices, and a way to define some new phylogenetic diversity indices that naturally arise as affine or projective variants of each other or as generalizations of tree-based indices.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11233365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558122","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 Lipid-Structured Model of Atherosclerosis with Macrophage Proliferation. 具有巨噬细胞增殖的动脉粥样硬化脂质结构模型

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-09 DOI: 10.1007/s11538-024-01333-w

Keith L Chambers, Michael G Watson, Mary R Myerscough

{"title":"A Lipid-Structured Model of Atherosclerosis with Macrophage Proliferation.","authors":"Keith L Chambers, Michael G Watson, Mary R Myerscough","doi":"10.1007/s11538-024-01333-w","DOIUrl":"10.1007/s11538-024-01333-w","url":null,"abstract":"Atherosclerotic plaques are fatty deposits that form in the walls of major arteries and are one of the major causes of heart attacks and strokes. Macrophages are the main immune cells in plaques and macrophage dynamics influence whether plaques grow or regress. Macrophage proliferation is a key process in atherosclerosis, particularly in the development of mid-stage plaques, but very few mathematical models include proliferation. In this paper we reframe the lipid-structured model of Ford et al. (J Theor Biol 479:48-63, 2019. https://doi.org/10.1016/j.jtbi.2019.07.003 ) to account for macrophage proliferation. Proliferation is modelled as a non-local decrease in the lipid structural variable. Steady state analysis indicates that proliferation assists in reducing eventual necrotic core lipid content and spreads the lipid load of the macrophage population amongst the cells. The contribution of plaque macrophages from proliferation relative to recruitment from the bloodstream is also examined. The model suggests that a more proliferative plaque differs from an equivalent (defined as having the same lipid content and cell numbers) recruitment-dominant plaque in the way lipid is distributed amongst the macrophages. The macrophage lipid distribution of an equivalent proliferation-dominant plaque is less skewed and exhibits a local maximum near the endogenous lipid content.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11233351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558121","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

Source-Sink Dynamics in a Two-Patch SI Epidemic Model with Life Stages and No Recovery from Infection. 具有生命阶段和感染后无恢复期的双斑 SI 流行病模型中的源-汇动态。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-08 DOI: 10.1007/s11538-024-01328-7

Jimmy Calvo-Monge, Jorge Arroyo-Esquivel, Alyssa Gehman, Fabio Sanchez

{"title":"Source-Sink Dynamics in a Two-Patch SI Epidemic Model with Life Stages and No Recovery from Infection.","authors":"Jimmy Calvo-Monge, Jorge Arroyo-Esquivel, Alyssa Gehman, Fabio Sanchez","doi":"10.1007/s11538-024-01328-7","DOIUrl":"10.1007/s11538-024-01328-7","url":null,"abstract":"This study presents a comprehensive analysis of a two-patch, two-life stage SI model without recovery from infection, focusing on the dynamics of disease spread and host population viability in natural populations. The model, inspired by real-world ecological crises like the decline of amphibian populations due to chytridiomycosis and sea star populations due to Sea Star Wasting Disease, aims to understand the conditions under which a sink host population can present ecological rescue from a healthier, source population. Mathematical and numerical analyses reveal the critical roles of the basic reproductive numbers of the source and sink populations, the maturation rate, and the dispersal rate of juveniles in determining population outcomes. The study identifies basic reproduction numbers <math><msub><mi>R</mi> <mn>0</mn></msub> </math> for each of the patches, and conditions for the basic reproduction numbers to produce a receiving patch under which its population. These findings provide insights into managing natural populations affected by disease, with implications for conservation strategies, such as the importance of maintaining reproductively viable refuge populations and considering the effects of dispersal and maturation rates on population recovery. The research underscores the complexity of host-pathogen dynamics in spatially structured environments and highlights the need for multi-faceted approaches to biodiversity conservation in the face of emerging diseases.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141554208","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 Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics. 一种基于扩散的方法，用于模拟前向时间状态依赖性物种和灭绝动态。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-06 DOI: 10.1007/s11538-024-01337-6

Albert C Soewongsono, Michael J Landis

引用次数: 0

Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics. 非线性动态生物网络完美适应的设计原则

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-03 DOI: 10.1007/s11538-024-01318-9

Priyan Bhattacharya, Karthik Raman, Arun K Tangirala

{"title":"Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics.","authors":"Priyan Bhattacharya, Karthik Raman, Arun K Tangirala","doi":"10.1007/s11538-024-01318-9","DOIUrl":"10.1007/s11538-024-01318-9","url":null,"abstract":"Establishing a mapping between the emergent biological properties and the repository of network structures has been of great relevance in systems and synthetic biology. Adaptation is one such biological property of paramount importance that promotes regulation in the presence of environmental disturbances. This paper presents a nonlinear systems theory-driven framework to identify the design principles for perfect adaptation with respect to external disturbances of arbitrary magnitude. Based on the prior information about the network, we frame precise mathematical conditions for adaptation using nonlinear systems theory. We first deduce the mathematical conditions for perfect adaptation for constant input disturbances. Subsequently, we translate these conditions to specific necessary structural requirements for adaptation in networks of small size and then extend to argue that there exist only two classes of architectures for a network of any size that can provide local adaptation in the entire state space, namely, incoherent feed-forward (IFF) structure and negative feedback loop with buffer node (NFB). The additional positiveness constraints further narrow the admissible set of network structures. This also aids in establishing the global asymptotic stability for the steady state given a constant input disturbance. The proposed method does not assume any explicit knowledge of the underlying rate kinetics, barring some minimal assumptions. Finally, we also discuss the infeasibility of certain IFF networks in providing adaptation in the presence of downstream connections. Moreover, we propose a generic and novel algorithm based on non-linear systems theory to unravel the design principles for global adaptation. Detailed and extensive simulation studies corroborate the theoretical findings.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490958","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

Tropical Logistic Regression Model on Space of Phylogenetic Trees. 系统发生树空间上的热带逻辑回归模型

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-02 DOI: 10.1007/s11538-024-01327-8

Georgios Aliatimis, Ruriko Yoshida, Burak Boyacı, James A Grant

{"title":"Tropical Logistic Regression Model on Space of Phylogenetic Trees.","authors":"Georgios Aliatimis, Ruriko Yoshida, Burak Boyacı, James A Grant","doi":"10.1007/s11538-024-01327-8","DOIUrl":"10.1007/s11538-024-01327-8","url":null,"abstract":"Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The logistic regression model is one of the most popular classification models in statistical learning, thanks to its computational speed and interpretability. However, it is not appropriate to directly apply the standard logistic regression model to a set of phylogenetic trees, as the space of phylogenetic trees is non-Euclidean and thus contradicts the standard assumptions on covariates. It is well-known in tropical geometry and phylogenetics that the space of phylogenetic trees is a tropical linear space in terms of the max-plus algebra. Therefore, in this paper, we propose an analogue approach of the logistic regression model in the setting of tropical geometry. Our proposed method outperforms classical logistic regression in terms of Area under the ROC Curve in numerical examples, including with data generated by the multi-species coalescent model. Theoretical properties such as statistical consistency have been proved and generalization error rates have been derived. Finally, our classification algorithm is proposed as an MCMC convergence criterion for Mr Bayes. Unlike the convergence metric used by Mr Bayes which is only dependent on tree topologies, our method is sensitive to branch lengths and therefore provides a more robust metric for convergence. In a test case, it is illustrated that the tropical logistic regression can differentiate between two independently run MCMC chains, even when the standard metric cannot.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11219468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490959","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 Theoretical Comparison of Alternative Male Mating Strategies in Cephalopods and Fishes. 头足类和鱼类雄性交配策略的理论比较

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-06-28 DOI: 10.1007/s11538-024-01330-z

Joseph A Landsittel, G Bard Ermentrout, Klaus M Stiefel

引用次数: 0

A New Method for Low Density Distribution Modeling and Near Threatened Species: The Study Case of Plectrohyla Guatemalensis. 低密度分布建模和近危物种的新方法：Plectrohyla Guatemalensis 的研究案例。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-06-27 DOI: 10.1007/s11538-024-01315-y

Miguel Ballesteros, Carlos Díaz-Avalos, Omar Hernández, Guillermo Garro

{"title":"A New Method for Low Density Distribution Modeling and Near Threatened Species: The Study Case of Plectrohyla Guatemalensis.","authors":"Miguel Ballesteros, Carlos Díaz-Avalos, Omar Hernández, Guillermo Garro","doi":"10.1007/s11538-024-01315-y","DOIUrl":"10.1007/s11538-024-01315-y","url":null,"abstract":"We introduce a model that can be used for the description of the distribution of species when there is scarcity of data, based on our previous work (Ballesteros et al. J Math Biol 85(4):31, 2022). We address challenges in modeling species that are seldom observed in nature, for example species included in The International Union for Conservation of Nature's Red List of Threatened Species (IUCN 2023). We introduce a general method and test it using a case study of a near threatened species of amphibians called Plectrohyla Guatemalensis (see IUCN 2023) in a region of the UNESCO natural reserve \"Tacaná Volcano\", in the border between Mexico and Guatemala. Since threatened species are difficult to find in nature, collected data can be extremely reduced. This produces a mathematical problem in the sense that the usual modeling in terms of Markov random fields representing individuals associated to locations in a grid generates artificial clusters around the observations, which are unreasonable. We propose a different approach in which our random variables describe yearly averages of expectation values of the number of individuals instead of individuals (and they take values on a compact interval). Our approach takes advantage of intuitive insights from environmental properties: in nature individuals are attracted or repulsed by specific features (Ballesteros et al. J Math Biol 85(4):31, 2022). Drawing inspiration from quantum mechanics, we incorporate quantum Hamiltonians into classical statistical mechanics (i.e. Gibbs measures or Markov random fields). The equilibrium between spreading and attractive/repulsive forces governs the behavior of the species, expressed through a global control problem involving an energy operator.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141455421","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

Modeling the Growth and Size Distribution of Human Pluripotent Stem Cell Clusters in Culture. 模拟培养过程中人类多能干细胞集群的生长和大小分布。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-06-25 DOI: 10.1007/s11538-024-01325-w

Tharana Yosprakob, Alexandra Shyntar, Diepiriye G Iworima, Leah Edelstein-Keshet

引用次数: 0