We propose a compartmental mathematical model for the spread of the COVID-19 disease with special focus on the transmissibility of super-spreaders individuals. We compute the basic reproduction number threshold, we study the local stability of the disease free equilibrium in terms of the basic reproduction number, and we investigate the sensitivity of the model with respect to the variation of each one of its parameters. Numerical simulations show the suitability of the proposed COVID-19 model for the outbreak that occurred in Wuhan, China.
Biological systems like long-lived clonal organisms, holobionts and clades challenge traditional evolutionary thinking since they adapt without populations or reproduction. This paper aims to provide an overarching theoretical framework which encompasses standard Darwinian evolution as well as other processes of adaptation. This framework is cumulative selection and I provide a general `recipe' for it to occur. Lewontin's recipe for evolution by natural selection is shown to be a particular example of cumulative selection, but not the only one. Similarly, reproduction, inheritance and populations are just one way to perform cumulative selection. I discuss several other examples of cumulative selection including clonal organisms, dioecious populations, Gaia and neural networks.
We investigate an infection-age structured competitive epidemiological model involving multiple strains. While classical results establish competitive exclusion when a unique maximal basic reproduction number exists, we provide here a complete characterization of the asymptotic behavior for an arbitrary number of populations without assuming uniqueness of the maximal reproduction number. By means of integrated semigroups theory, persistence results, and Lyapunov functionals, we establish global asymptotic stability of equilibria and extend previous results obtained for simpler (ODE) models. A key contribution lies in overcoming technical difficulties related to the definition and differentiation of Lyapunov functionals, as well as in refining arguments based on the LaSalle invariance principle.
An epidemic Susceptible-Vaccinated-Infected-Removed-Susceptible (SVIRS) model is presented on a weighted-undirected network with graph Laplacian diffusion. Disease-free equilibrium always exists while the existence and uniqueness of endemic equilibrium have been shown. When the basic reproduction number is below unity, the disease-free equilibrium is asymptotically globally stable. The endemic equilibrium is asymptotically globally stable if the basic reproduction number is above unity. Numerical analysis is illustrated with a road graph of the state of Minnesota. The effect of all important model parameters has been discussed.
One of the fundamental questions in population dynamics is how biological populations respond to environmental perturbations. In population dynamics, the mean fitness and the fraction of a trait in the steady state are important because they indicate how well the trait and the population adapt to the environment. In this study, we examine the parallel mutation-reproduction model, which is one of the simplest models of an evolvable population. As an extension of the Markov chain tree theorem, we derive diagrammatic expressions for the static responses of mean fitness and the steady-state distribution of the population. For the parallel mutation-reproduction model, we consider self-loops, which represent trait reproduction and are excluded from the Markov chain tree theorem for the linear master equation. To generalize the theorem, we introduce the concept of rooted $0$/$1$ loop forests, which generalize spanning trees with loops. We demonstrate that the weights of rooted $0$/$1$ loop forests yield the static responses of mean fitness and the steady-state distribution. Our results provide exact expressions for the static responses and the steady-state distribution. Additionally, we discuss approximations of these expressions in cases where reproduction or mutation is dominant. We provide numerical examples to illustrate these approximations and exact expressions.
Recalling previously experienced movements is essential for a range of activities, including sports, music, and rehabilitation, yet little is known about the accuracy and decay of proprioceptive working memory. We examined how introducing a short-term memory component affected movement reproduction accuracy by comparing movement reproduction under two conditions: simultaneous reproduction (SimRep) and memorized reproduction (MemRep). In Experiment 1 (N = 191), participants felt a 5-s haptic trajectory with one hand and reproduced it with the other hand simultaneously or immediately after the template ended. Errors were greater in MemRep than SimRep (31.1 deg vs. 21.5 deg, p < 0.001). MemRep trajectories showed systematic temporal distortions: participants lagged fast movements and led slow ones (R = -0.32, p = 0.01), unlike the ~279 ms lag in SimRep. In Experiment 2 (N = 33), we varied template durations (2-8 s). Longer durations increased error for MemRep but not SimRep (p < 0.001). During MemRep, accuracy declined steadily, with replay-template correlations dropping from ~0.4 to ~0.1 over ~3 s, while SimRep correlations rose from ~0.25 to ~0.6. In ~10% of MemRep templates, participants moved in the wrong direction initially, especially for low-amplitude movements (p < 0.001). Templates with more than four movements showed element omission; after four movements had been reproduced participants ceased movement prematurely, affecting up to 40% of 8-s templates. These findings show that transferring proprioceptive experiences into working memory introduces systematic temporal and structural distortions. Accuracy decays within seconds, and memory span for movement trajectories was limited to four movements.
Mehil B Shah, Mohammad Masudur Rahman, Foutse Khomh
Despite their wide adoption in various domains (e.g., healthcare, finance, software engineering), Deep Learning (DL)-based applications suffer from many bugs, failures, and vulnerabilities. Reproducing these bugs is essential for their resolution, but it is extremely challenging due to the inherent nondeterminism of DL models and their tight coupling with hardware and software environments. According to recent studies, only about 3% of DL bugs can be reliably reproduced using manual approaches. To address these challenges, we present RepGen, a novel, automated, and intelligent approach for reproducing deep learning bugs. RepGen constructs a learning-enhanced context from a project, develops a comprehensive plan for bug reproduction, employs an iterative generate-validate-refine mechanism, and thus generates such code using an LLM that reproduces the bug at hand. We evaluate RepGen on 106 real-world deep learning bugs and achieve a reproduction rate of 80.19%, a 19.81% improvement over the state-of-the-art measure. A developer study involving 27 participants shows that RepGen improves the success rate of DL bug reproduction by 23.35%, reduces the time to reproduce by 56.8%, and lowers participants' cognitive load.
ABSTRACT Understanding the impact mechanism of inter‐basin water transfer projects (IBWTs) on fish assemblages is critical for conserving aquatic ecosystems and managing water transfer. However, direct evidence of the impact mechanism of IBWTs on fish assemblages is absent. Fish assemblages in newly built terminal reservoirs originate and assemble with diverted individuals through water transfer in IBWTs, providing a valuable model for mechanistic research. This study sampled fish quarterly using a combination net in three terminal reservoirs along the Eastern Route of the South‐to‐North Water Transfer Project (ER‐SNWTP) from July 2021 to May 2022. We investigated assemblage composition and structure, calculated alpha and beta diversity indices, and analyzed the effects of environmental factors on fish assemblages. A total of 35 species were collected and indicated which species could be diverted accompanying water transfers along the ER‐SNWTP. Fish assemblages were dominated by eurytopic species, but showed clear seasonal differences. The distance from Dongping Lake, operation time of the reservoirs, and water quality affected diversity indices, composition and structure of the fish assemblages in the reservoirs. Fish assemblages in the terminal reservoirs were unstable and periodically disturbed by the water transfers of the ER‐SNWTP. Our results indicate that fish diverted by water transfer are likely to be the main cause of the impact of IBWTs on fish assemblages, and the distance and number of water transfers, and nutrient loading of diverted water are crucial factors affecting the impact of IBWTs. Our study provides a theoretical understanding of the ecological impacts of IBWTs by introducing fish and periodically disturbing fish assemblage through water transfer and highlights the necessity of scheming transfer programs to avoid overlapping with the spawning peaks of some fish with special guilds, such as small‐sized fish. In terminal reservoirs, the fish assemblages are not and may have no possibility to reach a stability like a natural one, and then their management should be oriented toward water quality regulation, such as rational harvesting and replenishment of biomanipulation fish to enhance their capacity for water quality regulation.
This contribution introduces a dataset of 7th-order Ambisonic Room Impulse Responses (HOA-RIRs), created using the Image Source Method. By employing higher-order Ambisonics, our dataset enables precise spatial audio reproduction, a critical requirement for realistic immersive audio applications. Leveraging the virtual simulation, we present a unique microphone configuration, based on the superposition principle, designed to optimize sound field coverage while addressing the limitations of traditional microphone arrays. The presented 64-microphone configuration allows us to capture RIRs directly in the Spherical Harmonics domain. The dataset features a wide range of room configurations, encompassing variations in room geometry, acoustic absorption materials, and source-receiver distances. A detailed description of the simulation setup is provided alongside for an accurate reproduction. The dataset serves as a vital resource for researchers working on spatial audio, particularly in applications involving machine learning to improve room acoustics modeling and sound field synthesis. It further provides a very high level of spatial resolution and realism crucial for tasks such as source localization, reverberation prediction, and immersive sound reproduction.
Consider first a memoryless population model described by the usual branching process with a given mean reproduction matrix on a finite space of types. Motivated by the consequences of atavism in Evolutionary Biology, we are interested in a modification of the dynamics where individuals keep full memory of their forebears and procreation involves the reactivation of a gene picked at random on the ancestral lineage. By comparing the spectral radii of the two mean reproduction matrices (with and without memory), we observe that, on average, the model with memory always grows at least as fast as the model without memory. The proof relies on analyzing a biased Markov chain on the space of memories, and the existence of a unique ergodic law is demonstrated through asymptotic coupling.
ABSTRACT: Avian arthritis is a common disease in the poultry industry, and the etiology is complex. Bacterial arthritis is usually caused by Staphylococcus aureus (S. aureus) infection. This study explored the minimum inhibitory concentration (MIC) of different organic acids against S. aureus MRSA85 and found that vanillic acid, suberic acid, itaconic acid, salicylic acid, and other organic acids had significant inhibitory effects on this strain, especially cinnamic acid, which exhibited the best inhibitory effect. The Fractional Inhibitory Concentration Index (FICI) test further revealed the synergistic effect among some compound organic acids, which can significantly enhance the antibacterial efficiency against MRSA85 while reducing the risk of bacterial resistance. Under the low concentrations (1/2 or 1/4 MIC) conditions, the MIC of the compound organic acids against S. aureus remains unchanged, and it can even enhance the sensitivity of antibiotic-resistant S. aureus to Oxacillin. Furthermore, the compound organic acids could effectively promote the recovery of S. aureus-induced arthritis in broiler models, reduce inflammatory responses, and lower down bacterial loads and inflammatory cytokine levels in joints, which indicated that the effects of the Compound 2 is comparable to that of the trimethoprim-sulfamethoxazole group. These results support the potential and application value of organic acids and their compounds, including Compound 1 to 3, as novel antibacterial agents in the treatment of S. aureus infections.
In global water management, the winter-storage, summer-drainage reservoir mechanism effectively mitigates summer floods and winter droughts. However, this counter-seasonal operation poses complex challenges to riparian ecosystems. To explore Nature-based Solutions (NbS), a deep understanding of the spatial development mechanisms of dominant species is crucial. Taking the Longkaikou Reservoir on China’s Jinsha River as an example, we employed drone photogrammetry, quadrat surveys, and null model simulations to intuitively and quantitatively analyze the spatial patterns of dominant riparian species and the underlying ecological processes. Our results showed that a 40 m × 40 m area is the minimum sampling size for determining riparian plant communities. Habitat heterogeneity and dispersal limitation jointly influence population spatial patterns, modulated by spatial scale and species biology. At smaller scales, population aggregation is driven by reproduction and dispersal, while at larger scales, habitat filtering significantly impacts population distribution, leading to random or uniform patterns. Based on these findings, we propose an innovative NbS approach for riparian zones. Using the minimum sampling area as a unit, we suggest employing remote sensing and GIS for grid-based fine management. Within grids (at the community level), enhance habitat connectivity and prioritize native pioneer species with efficient dispersal mechanisms. Between grids (at the metapopulation and ecosystem levels), implement differentiated ecological strategies based on habitat heterogeneity. Additionally, fostering cross-regional and interdisciplinary collaboration will form an integrated research and application framework, supporting riparian ecosystem conservation.
Kathleen E. Hurwitz, Oluwaseyi O. Isehunwa, Kayla R. Hendrickson
et al.
BackgroundDaily, oral tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) as pre-exposure prophylaxis (PrEP) reduces HIV acquisition for African women. Adherence is key to efficacy and patterns of adherence can be highly variable in real-world settings. Using group-based trajectory modeling (GBTM), we sought to identify distinct patterns of periconception PrEP adherence and evaluate potential baseline predictors of such adherence trajectories.MethodsWe conducted a single-arm longitudinal study for women aged 18–35 years living in Durban, South Africa with personal or partner plans for pregnancy with a partner with HIV or of unknown serostatus. Participants were offered safer conception counseling, including daily oral PrEP; women who initiated PrEP were given a bottle with an electronic pillcap that recorded when device opens. Weekly adherence to daily PrEP was modeled using GBTM with a censored normal outcome distribution as a function of weeks since PrEP initiation. The number and functional form of the adherence trajectory groups were primarily selected based on Bayesian information criteria (BIC) and confirmed by mean estimated probabilities of group membership. A multivariable version of the selected model assessed baseline predictors of membership in adherence trajectory groups.ResultsOverall mean (95% CI) adherence to PrEP was 63% (60%, 67%). We identified four groups of women with distinct patterns of adherence: (1) high (i.e., ≥6 doses per week) steady adherence throughout follow-up (22% of PrEP initiators); (2) moderate (i.e., 4–5 doses per week), but steady adherence (31%); (3) initially high, but consistently declining adherence (21%); and (4) initially moderate adherence, followed by a rapid decline and subsequent rebound (26%). In multivariable-adjusted analyses, older age was associated with membership in the high, steady adherence group as compared to the group identified with an adherence trajectory of initially high, then decline, and finally a rebound.ConclusionsGBTM is useful for exploring potential heterogeneity in longitudinal patterns of medication adherence. Although a large proportion of women in this study achieved high levels of adherence by electronic pillcap initially, far fewer women maintained these levels consistently. Knowledge of different adherence trajectories could be used to develop targeted strategies for optimizing HIV prevention during periconception.
Abstract Enhanced early life nutrition accelerates sexual development in the bull calf through neuroendocrine-signalling mediated via the hypothalamic–pituitary–testicular axis. Our aim was to assess the impact of contrasting feeding regimes in bull calves during the first 12 weeks of life on the testes transcriptome and proteome. Holstein–Friesian bull calves were offered either a high (HI) or moderate (MOD) plane of nutrition, designed to support target growth rates of 1.0 and 0.5 kg/day, respectively. At 12 weeks of age all calves were euthanized, testicular parenchyma sampled, and global transcriptome (miRNAseq and mRNAseq) and proteome analyses undertaken. Bioinformatic analyses revealed 7 differentially expressed (DE) miRNA and 20 DE mRNA. There were no differentially abundant proteins between the two dietary groups. Integration of omics results highlighted a potential role for the cadherin gene, CDH13, in earlier reproductive development. Furthermore, co-regulatory network analysis of the proteomic data revealed CDH13 as a hub protein within a network enriched for processes related to insulin, IGF-1, androgen and Sertoli cell junction signalling pathways as well as cholesterol biosynthesis. Overall, results highlight a potential role for CDH13 in mediating earlier reproductive development as a consequence of enhanced early life nutrition in the bull calf.
Zooplankton provides bacteria with a complex microhabitat richen in organic and inorganic nutrients, and the bacteria community also changes the physiochemical conditions for zooplankton, where the symbiotic relationship between them plays an important role in the nutrient cycle. However, there are few studies on the effect of associated bacteria on the population dynamics of rotifers. In order to make clear their relationships, we reconstructed the associated bacterial community in Brachionus calyciflorus culture, and examined the life history and population growth parameters, and analyzed the diversity and community composition of the associated bacteria at different growth stages of B. calyciflorus. The results showed that the addition of bacteria from natural water can promote the population growth and asexual reproduction of B. calyciflorus, but has no significant effect on sexual reproduction, exhibited by the improvement of its life expectancy at hatching, net reproduction rates and intrinsic growth rate, no significant effects on the generation time and mixis ratio of offspring. It was found that the B. calyciflorus-associated bacterial community was mainly composed of Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria and Firmicutes. Through correlation network analysis, the members of Burkholderiales, Pseudomonadales, Micrococcales, Caulobacterales and Bifidobacteriales were the keystone taxa of B. calyciflorus-associated bacteria. In addition, the relative abundance of some specific bacteria strains increased as the population density of B. calyciflorus increased, such as Hydrogenophaga, Acidovorax, Flavobacterium, Rheinheimera, Novosphingobium and Limnobacter, and their relative abundance increased obviously during the slow and exponential phases of population growth. Meanwhile, the relative abundance of adverse taxa (such as Elizabethkingia and Rickettsiales) decreased significantly with the increase in rotifer population density. In conclusion, the closely associated bacteria are not sufficient for the best growth of B. calyciflorus, and external bacterioplankton is necessary. Furthermore, the function of keystone and rare taxa is necessary for further exploration. The investigation of the symbiotic relationship between zooplankton-associated bacterial and bacterioplankton communities will contribute to monitoring their roles in freshwater ecosystems, and regulate the population dynamics of the micro-food web.
Various fields of science face a reproducibility crisis. For quantum software engineering as an emerging field, it is therefore imminent to focus on proper reproducibility engineering from the start. Yet the provision of reproduction packages is almost universally lacking. Actionable advice on how to build such packages is rare, particularly unfortunate in a field with many contributions from researchers with backgrounds outside computer science. In this article, we argue how to rectify this deficiency by proposing a 1-2-3~approach to reproducibility engineering for quantum software experiments: Using a meta-generation mechanism, we generate DOI-safe, long-term functioning and dependency-free reproduction packages. They are designed to satisfy the requirements of professional and learned societies solely on the basis of project-specific research artefacts (source code, measurement and configuration data), and require little temporal investment by researchers. Our scheme ascertains long-term traceability even when the quantum processor itself is no longer accessible. By drastically lowering the technical bar, we foster the proliferation of reproduction packages in quantum software experiments and ease the inclusion of non-CS researchers entering the field.
This paper investigates two important analytical properties of hyperbolic-polynomial penalized splines, HP-splines for short. HP-splines, obtained by combining a special type of difference penalty with hyperbolic-polynomial B-splines (HB-splines), were recently introduced by the authors as a generalization of P-splines. HB-splines are bell-shaped basis functions consisting of segments made of real exponentials $e^{αx},\, e^{-αx}$ and linear functions multiplied by these exponentials, $xe^{+αx}$ and $xe^{-αx}$. Here, we show that these type of penalized splines reproduce function in the space $\{e^{-αx},\ x e^{-αx}\}$, that is they fit exponential data exactly. Moreover, we show that they conserve the first and second 'exponential' moments.