Yujie Li, Su Xu, Xue Wang, Nilüfer Ertekin-Taner, Duan Chen
{"title":"An augmented GSNMF model for complete deconvolution of bulk RNA-seq data.","authors":"Yujie Li, Su Xu, Xue Wang, Nilüfer Ertekin-Taner, Duan Chen","doi":"10.3934/mbe.2025036","DOIUrl":"https://doi.org/10.3934/mbe.2025036","url":null,"abstract":"<p><p>Performing complete deconvolution analysis for bulk RNA-seq data to obtain both cell type specific gene expression profiles (GEP) and relative cell abundances is a challenging task. One of the fundamental models used, the nonnegative matrix factorization (NMF), is mathematically ill-posed. Although several complete deconvolution methods have been developed, and their estimates compared to ground truth for some datasets appear promising, a comprehensive understanding of how to circumvent the ill-posedness and improve solution accuracy is lacking. In this paper, we first investigated the necessary requirements for a given dataset to satisfy the solvability conditions in NMF theory. Even with solvability conditions, the \"unique\" solutions of NMF are subject to a rescaling matrix. Therefore, we provide estimates of the converged local minima and the possible rescaling matrix, based on informative initial conditions. Using these strategies, we developed a new pipeline of pseudo-bulk tissue data augmented, geometric structure guided NMF model (GSNMF+). In our approach, pseudo-bulk tissue data was generated, by statistical distribution simulated pseudo cellular compositions and single-cell RNA-seq (scRNA-seq) data, and then mixed with the original dataset. The constituent matrices of the hybrid dataset then satisfy the weak solvability conditions of NMF. Furthermore, an estimated rescaling matrix was used to adjust the minimizer of the NMF, which was expected to reduce mean square root errors of solutions. Our algorithms are tested on several realistic bulk-tissue datasets and showed significant improvements in scenarios with singular cellular compositions.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"988-1018"},"PeriodicalIF":2.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring brain dysfunction in IBD: A study of EEG-fMRI source imaging based on empirical mode diagram decomposition.","authors":"Yujie Kang, Wenjie Li, Jidong Lv, Ling Zou, Haifeng Shi, Wenjia Liu","doi":"10.3934/mbe.2025035","DOIUrl":"https://doi.org/10.3934/mbe.2025035","url":null,"abstract":"<p><p>Patients with inflammatory bowel disease (IBD) often suffer from mood disorders and cognitive decline, which has prompted research into abnormalities in emotional brain regions and their functional analysis. However, most IBD studies only focus on single-modality neuroimaging technologies. Due to a limited spatiotemporal resolution, it is unfeasible to fully explore deep brain source activities and accurately evaluate the brain functional connectivity. Therefore, we propose an electroencephalography (EEG)-functional magnetic resonance imaging (fMRI)source imaging method based on an empirical mode diagram decomposition (EMDD) and performed a synchronous EEG-fMRI source imaging analysis on 21 IBD patients and 11 healthy subjects. The high-frequency spatial components of the fMRI were extracted through EMDD as prior constraints and compared with the EEG source imaging based on the entire fMRI spatial prior. Then, the cortical source time series were reconstructed according to the Desikan-Killiany atlas for an effective connectivity analysis. The results showed that the EEG-fMRI source imaging based on EMDD had a better performance, with the average log model evidence increased by 29.60% and the average explained variance increased by 19.12%. There were significant differences in the activation intensity of a series of abnormal brain regions between IBD patients and healthy controls, some of which were newly discovered: the uncus, claustrum, lentiform nucleus, and lingual gyrus. Moreover, the findings from the effective connectivity analysis of cortical source signals revealed that IBD patients had information flow loss in the frontal lobes, central areas, left parietal lobe, and right temporal lobe, and the information flow intensity of the right lingual gyrus was enhanced.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"962-987"},"PeriodicalIF":2.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nariyuki Nakagiri, Hiroki Yokoi, Yukio Sakisaka, Kei-Ichi Tainaka, Kazunori Sato
{"title":"Influence of network structure on infectious disease control.","authors":"Nariyuki Nakagiri, Hiroki Yokoi, Yukio Sakisaka, Kei-Ichi Tainaka, Kazunori Sato","doi":"10.3934/mbe.2025034","DOIUrl":"https://doi.org/10.3934/mbe.2025034","url":null,"abstract":"<p><p>Control of infectious disease is very hard but important for the life of human beings. We study the susceptible-infected-susceptible (SIS) model of three-city networks. The SIS model simply contains both infection and recovery processes. We assume that human beings (\"agents\") live in three spatially separated cities, and they randomly migrate between cities. Two methods are applied: one is a computer simulation of an agent-based model, and the other is the theory of metapopulation dynamics. Both the simulation and theory reveal that the \"hub city\" plays an important role for disease control. It was found that we can eliminate the entire infection by disease control measures on the hub city only. Moreover, we found a paradoxical result: increased agent interaction does not necessarily lead to the spread of infection.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"943-961"},"PeriodicalIF":2.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rhiannon Loster, Sarah Smook, Lia Humphrey, David Lyver, Zahra Mohammadi, Edward W Thommes, Monica G Cojocaru
{"title":"Behaviour quantification of public health policy adoption - the case of non-pharmaceutical measures during COVID-19.","authors":"Rhiannon Loster, Sarah Smook, Lia Humphrey, David Lyver, Zahra Mohammadi, Edward W Thommes, Monica G Cojocaru","doi":"10.3934/mbe.2025033","DOIUrl":"https://doi.org/10.3934/mbe.2025033","url":null,"abstract":"<p><p>In this work, we provide estimates of non-pharmaceutical interventions (NPIs) adoption and its effects on the COVID-19 disease transmission across the province of Ontario, Canada, in 2020. Using freely available data, we estimate perceived risks of infection and a personal discomfort with complying with NPIs for Ontarians across 34 public health units. With the use of game theory, we model a time series of decision making processes in each public health region to extract an estimate of the adoption level of NPIs from March to December 2020. In conjunction with a susceptible-exposed-recovered-isolated compartmental model for Ontario, we are able to estimate a province-wide effectiveness level of NPIs. Last but not least, we show the model's versatility by applying it to Pennsylvania and Georgia in the United States.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"920-942"},"PeriodicalIF":2.6,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Event-triggered impulsive control for input-to-state stability of nonlinear time-delay system with delayed impulse.","authors":"Yilin Tu, Jin-E Zhang","doi":"10.3934/mbe.2025031","DOIUrl":"https://doi.org/10.3934/mbe.2025031","url":null,"abstract":"<p><p>The problem of input-to-state stability (ISS) was studied in this paper for a class of nonlinear time-delay systems with delayed impulses under event-triggered impulsive control (ETIC), where delays were flexible and external inputs in continuous and impulse dynamics were different. To avoid Zeno behavior, an event-triggered mechanism (ETM) that used the information of the system state and external disturbances was proposed, and the feasibility was enhanced by introducing a forced impulse sequence. Furthermore, some sufficient conditions were formulated to enable ISS for the considered system by using Lyapunov-Razumikhin-like methods. For a class of nonlinear impulse control systems, an application was introduced that utilizes linear matrix inequalities (LMIs) to design an ETM and control gain. Finally, two numerical examples were given to validate the theoretical results.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"876-896"},"PeriodicalIF":2.6,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bayesian inference and impact of parameter prior specification in flexible multilevel nonlinear models in the context of infectious disease modeling.","authors":"Olaiya Mathilde Adéoti, Aliou Diop, Romain Glèlè Kakaï","doi":"10.3934/mbe.2025032","DOIUrl":"https://doi.org/10.3934/mbe.2025032","url":null,"abstract":"<p><p>Bayesian flexible multilevel nonlinear models (FMNLMs) are powerful tools to analyze infectious disease data with asymmetric and unbalanced structures, such as varying epidemic stages across countries. However, the robustness of these models can be undermined by poorly designed estimation methods, particularly due to uncertainties in prior distributions and initial values. This study investigates how varying levels of prior informativeness can influence the model convergence, parameter estimation, and computation time in a Bayesian flexible multilevel nonlinear model (FMNLM). A simulation study was conducted to evaluate the impact of modifying prior assumptions on posterior estimates and their subsequent effects on the interpretations. The framework was applied to COVID-19 data from Francophone West Africa. The results indicate that accurate, informative priors enhance the prediction performance with minimal impact on the computation time. Conversely, non-informative or inaccurate priors for nonlinear parameters led to lower convergence rates and a reduced recovery accuracy, although they may remain viable in standard multilevel nonlinear models.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"897-919"},"PeriodicalIF":2.6,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144010856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Predator-prey dynamics with refuge, alternate food, and harvesting strategies in a patchy habitat.","authors":"Rajalakshmi Manoharan, Reenu Rani, Ali Moussaoui","doi":"10.3934/mbe.2025029","DOIUrl":"https://doi.org/10.3934/mbe.2025029","url":null,"abstract":"<p><p>A predator-prey dynamic reaction model is investigated in a two-layered water body where only the prey is subjected to harvesting. The surface layer (Layer-1) provides food for both species, while the prey migrates to deeper layer (Layer-2) as a refuge from predation. Although the prey is the preferred food for the predator, the predator can also consume alternative food resources that are abundantly available. The availability of alternative food resources plays a crucial role in species' coexistence by mitigating the risk of extinction. The main objective of the work was to explore the effect of different harvesting strategies (nonlinear and linear harvesting) on a predator-prey model with effort dynamics in a heterogeneous habitat. The analysis incorporates a dual timescale approach: the prey species migrate between the layers on a fast timescale, whereas the growth of resource biomass, prey-predator interactions, and harvesting dynamics evolve on a slow timescale. The complete model involving both slow and fast timescales has been investigated by using aggregated model. The reduced aggregated model is analyzed analytically as well as numerically. Moreover, it is demonstrated that the reduced system exhibits the bifurcations (transcritical and Hopf point) by setting the additional food parameter as a bifurcation parameter. A comparative study using different harvesting strategies found that there is chaos in the system when using linear harvesting in the predator-prey model. However, nonlinear harvesting gives only stable or periodic solutions. This concludes that nonlinear harvesting can control the chaos in the system. Additionally, a one-dimensional parametric bifurcation, phase portraits, and time series plots are also explored in the numerical simulation.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"810-845"},"PeriodicalIF":2.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Persistence and extinction of infection in stochastic population model with horizontal and imperfect vertical disease transmissions.","authors":"Abhijit Majumder, Debadatta Adak, Adeline Samson, Nandadulal Bairagi","doi":"10.3934/mbe.2025030","DOIUrl":"https://doi.org/10.3934/mbe.2025030","url":null,"abstract":"<p><p>Epidemic models are used to understand the dynamics of disease transmission and explore the possible measures for preventing the spread of infection in the population. Disease transmission is intrinsically random and severely affected by environmental factors. We investigated a stochastic population model of the susceptible-infected-susceptible (SIS) type, in which infection spreads via both vertical and horizontal transmission routes. To incorporate stochasticity to the system, white multiplicative noise was taken into account in the horizontal disease transmission term. We proved that noise intensity, disease transmission, and recovery rates are potential routes for eradicating the disease. Furthermore, the parasite population reduces its fitness for some fixed noise if the relative fecundity of infected hosts and the disease transmission are low. However, if either of these is increased, it observes enhanced fitness. A simulation study illustrated the system's analytically dynamic properties and provided different insights. A case study for the imperfect vertical and horizontal infection transmission is also presented, supporting some of our observed theoretical results.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"846-875"},"PeriodicalIF":2.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bistable dynamics of TAN-NK cells in tumor growth and control of radiotherapy-induced neutropenia in lung cancer treatment.","authors":"Donggu Lee, Sunju Oh, Sean Lawler, Yangjin Kim","doi":"10.3934/mbe.2025028","DOIUrl":"https://doi.org/10.3934/mbe.2025028","url":null,"abstract":"<p><p>Neutrophils play a crucial role in the innate immune response as a first line of defense in many diseases, including cancer. Tumor-associated neutrophils (TANs) can either promote or inhibit tumor growth in various steps of cancer progression via mutual interactions with cancer cells in a complex tumor microenvironment (TME). In this study, we developed and analyzed mathematical models to investigate the role of natural killer cells (NK cells) and the dynamic transition between N1 and N2 TAN phenotypes in killing cancer cells through key signaling networks and how adjuvant therapy with radiation can be used in combination to increase anti-tumor efficacy. We examined the complex immune-tumor dynamics among N1/N2 TANs, NK cells, and tumor cells, communicating through key extracellular mediators (Transforming growth factor (TGF-$ beta $), Interferon gamma (IFN-$ gamma $)) and intracellular regulation in the apoptosis signaling network. We developed several tumor prevention strategies to eradicate tumors, including combination (IFN-$ gamma $, exogenous NK, TGF-$ beta $ inhibitor) therapy and optimally-controlled ionizing radiation in a complex TME. Using this model, we investigated the fundamental mechanism of radiation-induced changes in the TME and the impact of internal and external immune composition on the tumor cell fate and their response to different treatment schedules.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 4","pages":"744-809"},"PeriodicalIF":2.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Determining the best mathematical model for implementation of non-pharmaceutical interventions.","authors":"Gabriel McCarthy, Hana M Dobrovolny","doi":"10.3934/mbe.2025026","DOIUrl":"10.3934/mbe.2025026","url":null,"abstract":"<p><p>At the onset of the SARS-CoV-2 pandemic in early 2020, only non-pharmaceutical interventions (NPIs) were available to stem the spread of the infection. Much of the early interventions in the US were applied at a state level, with varying levels of strictness and compliance. While NPIs clearly slowed the rate of transmission, it is not clear how these changes are best incorporated into epidemiological models. In order to characterize the effects of early preventative measures, we use a Susceptible-Exposed-Infected-Recovered (SEIR) model and cumulative case counts from US states to analyze the effect of lockdown measures. We test four transition models to simulate the change in transmission rate: instantaneous, linear, exponential, and logarithmic. We find that of the four models examined here, the exponential transition best represents the change in the transmission rate due to implementation of NPIs in the most states, followed by the logistic transition model. The instantaneous and linear models generally lead to poor fits and are the best transition models for the fewest states.</p>","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":"22 3","pages":"700-724"},"PeriodicalIF":2.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}