Mathematical Biosciences and Engineering最新文献_第2页

An augmented GSNMF model for complete deconvolution of bulk RNA-seq data. 一种用于大量RNA-seq数据完全反卷积的增强GSNMF模型。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-14 DOI: 10.3934/mbe.2025036

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":"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.","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}

引用次数: 0

Exploring brain dysfunction in IBD: A study of EEG-fMRI source imaging based on empirical mode diagram decomposition. 探讨IBD脑功能障碍：基于经验模态图分解的EEG-fMRI源成像研究。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-14 DOI: 10.3934/mbe.2025035

Yujie Kang, Wenjie Li, Jidong Lv, Ling Zou, Haifeng Shi, Wenjia Liu

{"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":"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.","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}

引用次数: 0

Influence of network structure on infectious disease control. 网络结构对传染病控制的影响。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-12 DOI: 10.3934/mbe.2025034

Nariyuki Nakagiri, Hiroki Yokoi, Yukio Sakisaka, Kei-Ichi Tainaka, Kazunori Sato

引用次数: 0

Behaviour quantification of public health policy adoption - the case of non-pharmaceutical measures during COVID-19. 公共卫生政策采纳的行为量化——以COVID-19期间非药物措施为例

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-10 DOI: 10.3934/mbe.2025033

Rhiannon Loster, Sarah Smook, Lia Humphrey, David Lyver, Zahra Mohammadi, Edward W Thommes, Monica G Cojocaru

引用次数: 0

Event-triggered impulsive control for input-to-state stability of nonlinear time-delay system with delayed impulse. 时滞非线性时滞系统输入状态稳定性的事件触发脉冲控制。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-07 DOI: 10.3934/mbe.2025031

Yilin Tu, Jin-E Zhang

引用次数: 0

Bayesian inference and impact of parameter prior specification in flexible multilevel nonlinear models in the context of infectious disease modeling. 传染病建模中柔性多层非线性模型贝叶斯推理及参数先验规范的影响

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-07 DOI: 10.3934/mbe.2025032

Olaiya Mathilde Adéoti, Aliou Diop, Romain Glèlè Kakaï

{"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":"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.","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}

引用次数: 0

Predator-prey dynamics with refuge, alternate food, and harvesting strategies in a patchy habitat. 在斑驳的栖息地中，捕食者-猎物动态与避难所、替代食物和收获策略。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-05 DOI: 10.3934/mbe.2025029

Rajalakshmi Manoharan, Reenu Rani, Ali Moussaoui

{"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":"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.","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}

引用次数: 0

Persistence and extinction of infection in stochastic population model with horizontal and imperfect vertical disease transmissions. 具有水平和不完全垂直疾病传播的随机种群模型中感染的持续和消失。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-05 DOI: 10.3934/mbe.2025030

Abhijit Majumder, Debadatta Adak, Adeline Samson, Nandadulal Bairagi

{"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":"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.","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}

引用次数: 0

Bistable dynamics of TAN-NK cells in tumor growth and control of radiotherapy-induced neutropenia in lung cancer treatment. TAN-NK细胞在肿瘤生长中的双稳态动力学和肺癌治疗中放疗诱导的中性粒细胞减少的控制。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-04 DOI: 10.3934/mbe.2025028

Donggu Lee, Sunju Oh, Sean Lawler, Yangjin Kim

{"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":"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.","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}

引用次数: 0

Determining the best mathematical model for implementation of non-pharmaceutical interventions. 确定实施非药物干预措施的最佳数学模型。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2025-03-03 DOI: 10.3934/mbe.2025026

Gabriel McCarthy, Hana M Dobrovolny

引用次数: 0