68 research outputs found
Revisiting the stability of spatially heterogeneous predator-prey systems under eutrophication
We employ partial integro-differential equations to model trophic interaction
in a spatially extended heterogeneous environment. Compared to classical
reaction-diffusion models, this framework allows us to more realistically
describe the situation where movement of individuals occurs on a faster time
scale than the demographic (population) time scale, and we cannot determine
population growth based on local density. However, most of the results reported
so far for such systems have only been verified numerically and for a
particular choice of model functions, which obviously casts doubts about these
findings. In this paper, we analyse a class of integro-differential
predator-prey models with a highly mobile predator in a heterogeneous
environment, and we reveal the main factors stabilizing such systems. In
particular, we explore an ecologically relevant case of interactions in a
highly eutrophic environment, where the prey carrying capacity can be formally
set to 'infinity'. We investigate two main scenarios: (i) the spatial gradient
of the growth rate is due to abiotic factors only, and (ii) the local growth
rate depends on the global density distribution across the environment (e.g.
due to non-local self-shading). For an arbitrary spatial gradient of the prey
growth rate, we analytically investigate the possibility of the predator-prey
equilibrium in such systems and we explore the conditions of stability of this
equilibrium. In particular, we demonstrate that for a Holling type I (linear)
functional response, the predator can stabilize the system at low prey density
even for an 'unlimited' carrying capacity. We conclude that the interplay
between spatial heterogeneity in the prey growth and fast displacement of the
predator across the habitat works as an efficient stabilizing mechanism.Comment: 2 figures; appendices available on request. To appear in the Bulletin
of Mathematical Biolog
Modelling Evolution of Virulence in Populations with a Distributed Parasite Load
Modelling evolution of virulence in host-parasite systems is an actively developing area of research with ever-growing literature. However, most of the existing studies overlook the fact that individuals within an infected population may have a variable infection load, i.e. infected populations are naturally structured with respect to the parasite burden. Empirical data suggests that the mortality and infectiousness of individuals can strongly depend on their infection load; moreover, the shape of distribution of infection load may vary on ecological and evolutionary time scales. Here we show that distributed infection load may have important consequences for the eventual evolution of virulence as compared to a similar model without structuring. Mathematically, we consider an SI model, where the dynamics of the infected subpopulation is described by a von Förster-type model, in which the infection load plays the role of age. We implement the adaptive dynamics framework to predict evolutionary outcomes in this model. We demonstrate that for simple trade-off functions between virulence, disease transmission and parasite growth rates, multiple evolutionary attractors are possible. Interestingly, unlike in the case of unstructured models, achieving an evolutionary stable strategy becomes possible even for a variation of a single ecological parameter (the parasite growth rate) and keeping the other parameters constant. We conclude that evolution in disease-structured populations is strongly mediated by alterations in the overall shape of the parasite load distribution
US Cosmic Visions: New Ideas in Dark Matter 2017: Community Report
This white paper summarizes the workshop "U.S. Cosmic Visions: New Ideas in
Dark Matter" held at University of Maryland on March 23-25, 2017.Comment: 102 pages + reference
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe
Identifying the sources of structural sensitivity in partially specified biological models
Biological systems are characterised by a high degree of uncertainty and complexity, which implies
that exact mathematical equations to describe biological processes cannot generally be justified.
Moreover, models can exhibit sensitivity to the precise formulations of their component functions—a
property known as structural sensitivity. Structural sensitivity can be revealed and quantified by
considering partially specified models with uncertain functions, but this goes beyond well-established,
parameter-based sensitivity analysis, and currently presents a mathematical challenge. Here we build
upon previous work in this direction by addressing the crucial question of identifying the processes
which act as the major sources of model uncertainty and those which are less influential. To achieve
this goal, we introduce two related concepts: (1) the gradient of structural sensitivity, accounting for
errors made in specifying unknown functions, and (2) the partial degree of sensitivity with respect to
each function, a global measure of the uncertainty due to possible variation of the given function while
the others are kept fixed. We propose an iterative framework of experiments and analysis to inform a
heuristic reduction of structural sensitivity in a model. To demonstrate the framework introduced, we
investigate the sources of structural sensitivity in a tritrophic food chain model
Modelling the spatiotemporal complexity of interactions between pathogenic bacteria and a phage with a temperature-dependent life cycle switch
Abstract We apply mathematical modelling to explore bacteria-phage interaction mediated by condition-dependent lysogeny, where the type of the phage infection cycle (lytic or lysogenic) is determined by the ambient temperature. In a natural environment, daily and seasonal variations of the temperature cause a frequent switch between the two infection scenarios, making the bacteria-phage interaction with condition-dependent lysogeny highly complex. As a case study, we explore the natural control of the pathogenic bacteria Burkholderia pseudomallei by its dominant phage. B. pseudomallei is the causative agent of melioidosis, which is among the most fatal diseases in Southeast Asia and across the world. We assess the spatial aspect of B. pseudomallei-phage interactions in soil, which has been so far overlooked in the literature, using the reaction-diffusion PDE-based framework with external forcing through daily and seasonal parameter variation. Through extensive computer simulations for realistic biological parameters, we obtain results suggesting that phages may regulate B. pseudomallei numbers across seasons in endemic areas, and that the abundance of highly pathogenic phage-free bacteria shows a clear annual cycle. The model predicts particularly dangerous soil layers characterised by high pathogen densities. Our findings can potentially help refine melioidosis prevention and monitoring practices
Varied Movement Strategies Employed by Triple Gene Block-Encoding Viruses
International audienc
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