Two-dimensional stability analysis in a HIV model with quadratic logistic growth term

We consider a Human Immunodeficiency Virus (HIV) model with a logistic growth term and continue the analysis of the previous article [6]. We now take the viral diffusion in a two-dimensional environment. The model consists of two ODEs for the concentrations of the target T cells, the infected cells, and a parabolic PDE for the virus particles. We study the stability of the uninfected and infected equilibria, the occurrence of Hopf bifurcation and the stability of the periodic solutions.Comment: To appear on Commun. Pure Appl. Ana

Regression-based heterogeneity analysis to identify overlapping subgroup structure in high-dimensional data

Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the underlying subgroup structure and estimates the subgroup-specific regression coefficients. However, most of the existing regression-based heterogeneity analyses can only address disjoint subgroups; that is, each sample is assigned to only one subgroup. In reality, some samples have multiple labels, for example, many genes have several biological functions, and some cells of pure cell types transition into other types over time, which suggest that their outcome-feature relationships (regression coefficients) can be a mixture of relationships in more than one subgroups, and as a result, the disjoint subgrouping results can be unsatisfactory. To this end, we develop a novel approach to regression-based heterogeneity analysis, which takes into account possible overlaps between subgroups and high data dimensions. A subgroup membership vector is introduced for each sample, which is combined with a loss function. Considering the lack of information arising from small sample sizes, an $l_2$ norm penalty is developed for each membership vector to encourage similarity in its elements. A sparse penalization is also applied for regularized estimation and feature selection. Extensive simulations demonstrate its superiority over direct competitors. The analysis of Cancer Cell Line Encyclopedia data and lung cancer data from The Cancer Genome Atlas shows that the proposed approach can identify an overlapping subgroup structure with favorable performance in prediction and stability.Comment: 33 pages, 16 figure

Research on the coordinated development of resource-based cities in Sichuan Province: from the perspective of industrial structure and ecological environment

During their journey of developing, resource-based cities gradually deplete the resources on which they rely for survival. Scientific and reasonable research on the industrial and ecological aspects of resource-based cities is conducive to the coordinated development of cities. In order to further analyze the industrial structure of resource-based cities systematically and analyze the comprehensive level of resource-based cities from multi-dimensional perspective. This paper took 8 resource-based cities in Sichuan Province as the research object, and constructed the index system from two systems: industrial structure and ecological environment, then the shift-share analysis, entropy weight method and capacity coupling coefficient model were used to analyze their level of industrial structure, ecological environment and the coupling relationship respectively. According to the results of the study, it can be concluded that the main influencing factor in the development of industrial structure is the industrialmix effect, while the ecological level presents a decreasing level due to the lack of control of total industrial solid waste and energy consumption. The coupling degree between industrial structure and ecological environment in resource-based cities in Sichuan Province is relatively stable, and the coupling coordination degree also gradually tends to a stable state. In the subsequent development, the focus should be on the coal mining and dressing industry and the power, heat production and supply industry. Starting with the actual industrial structure of resource-based cities and specific indicators that affected the ecological environment, this paper hereby analyzed the development momentum and unified and coordinated development status of resource-based cities. The main purpose of this paper is providing some technical support for resource-based cities to improve their coordinated urban development, and giving policy suggestions for the coordinated development of resource-based cities

Efficient Cavity Searching for Gene Network of Influenza A Virus

High order structures (cavities and cliques) of the gene network of influenza A virus reveal tight associations among viruses during evolution and are key signals that indicate viral cross-species infection and cause pandemics. As indicators for sensing the dynamic changes of viral genes, these higher order structures have been the focus of attention in the field of virology. However, the size of the viral gene network is usually huge, and searching these structures in the networks introduces unacceptable delay. To mitigate this issue, in this paper, we propose a simple-yet-effective model named HyperSearch based on deep learning to search cavities in a computable complex network for influenza virus genetics. Extensive experiments conducted on a public influenza virus dataset demonstrate the effectiveness of HyperSearch over other advanced deep-learning methods without any elaborated model crafting. Moreover, HyperSearch can finish the search works in minutes while 0-1 programming takes days. Since the proposed method is simple and easy to be transferred to other complex networks, HyperSearch has the potential to facilitate the monitoring of dynamic changes in viral genes and help humans keep up with the pace of virus mutations.Comment: work in progres

Analysis of research trends (2014-2023) on oxidative stress and male fertility based on bibliometrics and knowledge graphs

BackgroundOxidative stress (OS) is considered one of the major factors affecting male fertility, and research in this field has seen constant growth year by year. Currently, around 700 relevant papers are published each year, with a trend of further growth. Therefore, this study systematically summarizes the literature published in the last decade from a bibliometric perspective, revealing the dynamic development of the field, identifying research hotspots, analyzing future trends, and providing reference for further research.MethodsRelevant literature on oxidative stress and male fertility was retrieved from the Web of Science Core Collection (WoSCC) database, covering the timespan from 2014 to 2023 and including two types, articles and reviews. CiteSpace and VOSviewer were used for bibliometric analysis, including cluster analysis, co-occurrence analysis, co-citation analysis, and burst analysis of countries/regions, institutions, journals, authors, references, and keywords.ResultsThis paper studied a total of 5,301 papers involving 107 countries/regions, with China having the highest number of publications (898 papers) and the United States having the highest centrality (0.62). Burst analysis of journal citations revealed the emergence of many new journals (e.g., Antioxidants-Basel, Front Endocrinol) after 2021, indicating continuous expansion and development in this field. Cluster analysis of co-cited references and co-occurring keywords divided the research into areas such as oxidative stress and male infertility, oxidative stress level detection, and antioxidants. The keywords associated with research hotspots shifted from oxidative stress detection, sperm DNA damage, apoptosis, and redox potential to DNA methylation, embryonic development, infection, polyunsaturated fatty acids, and antioxidants.ConclusionBibliometric methods provide an intuitive reflection of the development process in the field of oxidative stress and male fertility, as well as the analysis of research hotspots in different periods. Research on oxidative stress and embryonic development, as well as antioxidant health management, may become hotspots in future research

Ambient PM Toxicity is Correlated with Expression Levels of Specific MicroRNAs

Uncertainties regarding optimized air pollution control remain as the underlying mechanisms of city-specific ambient particulate matter (PM)-induced health effects are unknown. Here, water-soluble extracts of PMs collected from four global cities via automobile air-conditioning filters were consecutively injected three times by an amount of 1, 2, and 2 mg into the blood circulation of Wistar rats after filtration by a 0.45 μm pore size membrane. Acute health effects, such as immune and inflammatory responses and hemorrhage in alveoli, were observed right after the PM extraction injection. Significant differences between cities in biomarker tumor necrosis factor-α (TNF-α) and monocyte chemoattractant protein-1 (MCP-1) levels were detected following the second and third PM injections. Rats’ inflammatory responses varied substantially with the injections of city-specific PMs. Repeated PM extract exposure rendered the rats more vulnerable to subsequent challenges, and downregulation of certain microRNAs was observed in rats. Among the studied miRNAs, miR-125b, and miR-21 were most sensitive to the PM exposure, exhibiting a negative dose–response-type relationship with a source-specific PM (oxidative potential) toxicity (r² = 0.63 and 0.57; p-values < 0.05). The results indicated that city-specific PMs could induce different health effects by selectively regulating different miRNAs, and that certain microRNAs, e.g., miR-125b and miR-21, may be externally mediated to neutralize PM-related health damages

Ambient PM Toxicity is Correlated with Expression Levels of Specific MicroRNAs

Uncertainties regarding optimized air pollution control remain as the underlying mechanisms of city-specific ambient particulate matter (PM)-induced health effects are unknown. Here, water-soluble extracts of PMs collected from four global cities via automobile air-conditioning filters were consecutively injected three times by an amount of 1, 2, and 2 mg into the blood circulation of Wistar rats after filtration by a 0.45 μm pore size membrane. Acute health effects, such as immune and inflammatory responses and hemorrhage in alveoli, were observed right after the PM extraction injection. Significant differences between cities in biomarker tumor necrosis factor-α (TNF-α) and monocyte chemoattractant protein-1 (MCP-1) levels were detected following the second and third PM injections. Rats’ inflammatory responses varied substantially with the injections of city-specific PMs. Repeated PM extract exposure rendered the rats more vulnerable to subsequent challenges, and downregulation of certain microRNAs was observed in rats. Among the studied miRNAs, miR-125b, and miR-21 were most sensitive to the PM exposure, exhibiting a negative dose–response-type relationship with a source-specific PM (oxidative potential) toxicity (r² = 0.63 and 0.57; p-values < 0.05). The results indicated that city-specific PMs could induce different health effects by selectively regulating different miRNAs, and that certain microRNAs, e.g., miR-125b and miR-21, may be externally mediated to neutralize PM-related health damages