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Biomedical subjects

Lewi Stone

Publications and source records attributed to Lewi Stone.

At least 19 recordsLinked to original sources
PubMed2005

Generating uniformly distributed random networks.

The analysis of real networks taken from the biological, social, and physical sciences often requires a carefully posed statistical null-hypothesis approach. One common method requires comparing real networks to an ensemble of random matrices that satisfy realistic constraints in which each different matrix member is equiprobable. We discuss existing methods for generating uniformly distributed (constrained) random matrices, describe their shortcomings, and present an efficient technique that should have many practical applications.

Journal Article↗
PubMed2005

A model for seasonal phytoplankton blooms.

We analyse a generic bottom-up nutrient phytoplankton model to help understand the dynamics of seasonally recurring algae blooms. The deterministic model displays a wide spectrum of dynamical behaviours, from simple cyclical blooms which trigger annually, to irregular chaotic blooms in which both the time between outbreaks and their magnitudes are erratic. Unusually, despite the persistent seasonal forcing, it is extremely difficult to generate blooms that are both annually recurring and also chaotic or irregular (i.e. in amplitude) even though this characterizes many real time-series. Instead the model has a tendency to 'skip' with outbreaks often being suppressed from 1 year to the next. This behaviour is studied in detail and we develop analytical expressions to describe the model's flow in phase space, yielding insights into the mechanism of the bloom recurrence. We also discuss how modifications to the equations through the inclusion of appropriate functional forms can generate more realistic dynamics.

Ecosystem↗
PubMed2005

Trade up polygyny and breeding synchrony in avian populations.

The advent of the molecular techniques used to assign paternity has focused attention on the differences between the social and the genetic mating systems of sexual species. In particular, the interrelations between breeding synchrony-the degree to which the fertility periods of individual females in a population overlap and the degree of extra pair paternity (EPP) in that population, has became a subject of a lively debate. Investigation of the subject can be facilitated by examining the criteria that females use in choosing extra pair partners. These preferences constitute a continuum ranging between two extremes. At one end, there are situations wherein all the females in a population exhibit a preference for males with particular phenotypic markers, and females mated to males lacking such "quality" markers seek extra pair fertilizations from males that do -trade up polygyny. At the other extreme, there are situations wherein females seek to maximize the total number of male partners, rather than secure fertilization by males of particular type -indiscriminate polygyny. Previously, we used game theoretical methods to model the interrelations between breeding synchrony and EPP in the context of indiscriminate polygyny. Here we present an analogous investigation in the context of trade up polygyny. Our results for the two cases, which delimit the range of the possible behavior, are similar. That is, we see that it is the pursuit of extra pair fertilizations opportunities that determines breeding synchrony of populations, rather than the vice versa as has been previously suggested.

Animals↗
PubMed2005

Modeling polio as a disease of development.

Poliomyelitis is a disease which began to appear in epidemic proportions in the late 19th century, paradoxically, just at the time when living conditions and developments in health were transforming enormously for the better. We present a simple age-class model that explains this "disease of development" as a threshold phenomenon. Epidemics arise when improved conditions in hygiene are able to reduce disease transmission of polio amongst children below a critical threshold level. This generates a large susceptible adult population in which, under appropriate conditions, epidemics can propagate. The polio model is analysed in terms of its bifurcation properties and in terms of its non-equilibrium outbreak dynamics.

Adolescent↗
PubMed2005

GC composition of the human genome: in search of isochores.

The isochore theory, proposed nearly three decades ago, depicts the mammalian genome as a mosaic of long, fairly homogeneous genomic regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five distinct isochore families: L1, L2, H1, H2, and H3, with GC contents of <37%, 37%-42%, 42%-47%, 47%-52%, and >52%, respectively. In this paper, we address the question of the validity of the isochore theory through a rigorous sequence-based analysis of the human genome. Toward this end, we adopt a set of six attributes that are generally claimed to characterize isochores and statistically test their veracity against the available draft sequence of the complete human genome. By the selection criteria used in this study: distinctiveness, homogeneity, and minimal length of 300 kb, we identify 1,857 genomic segments that warrant the label "isochore." These putative isochores are nonuniformly scattered throughout the genome and cover about 41% of the human genome. We found that a four-family model of putative isochores is the most parsimonious multi-Gaussian model that can be fitted to the empirical data. These families, however, are GC poor, with mean GC contents of 35%, 38%, 41%, and 48% and do not resemble the five isochore families in the literature. Moreover, due to large overlaps among the families, it is impossible to classify genomic segments into isochore families reliably, according to compositional properties alone. These findings undermine the utility of the isochore theory and seem to indicate that the theory may have reached the limits of its usefulness as a description of genomic compositional structures.

Base Composition↗
PubMed2005

Fertility assurance and breeding synchrony.

Extrapair fertilizations are an important factor in reproduction of many bird species. It has been suggested that pursuit of extrapair fertilizations provides a selective pressure capable of affecting the "ecological" attributes of some bird species. It is known that in some cases the pursuit of extrapair copulations is motivated by fertility assurance. That is, there are populations in which (i) some males and females cannot produce viable offspring, and (ii) there is no pre-copulatory way to choose a compatible mate. In such situations individuals mate for "economic" reasons and attempt to secure reproduction by copulating with multiple partners. Here we formulate and analyze a simple game theoretical model addressing the interplay between environmental constraints and the pursuit of fertility assurance via extrapair copulations in determining breeding synchrony. Our results indicate that breeding synchrony in such cases is determined by the magnitude of the costs (due to environmental constraints) of breeding asynchronously versus the worth of the attendant increase in extrapair opportunities.

Animals↗
PubMed2004

Unexpected epidemic thresholds in heterogeneous networks: the role of disease transmission.

We reformulate several recent analyses of infection processes on highly heterogeneous networks (e.g., scale-free networks) which conclude that diseases will spread and persist even for vanishingly small transmission probabilities. The results of these latter studies contrast with conventional epidemiological models where there are clear threshold effects, namely, should the transmission probability fall below a critical threshold level the disease is expected to die out. Here we show that epidemic propagation depends equally on the infection scheme as well as the network structure. Connectivity-dependent infection schemes can yield threshold effects even in scale-free networks where they would otherwise be unexpected.

Animals↗
PubMed2004

Advantageous indirect interactions in systems of competition.

Ecological foodwebs display complex networks of species interactions. Here we discuss how two species, whether directly interacting or not, can crucially affect each other 'indirectly' through their mutual associations with intermediary species. A technique is presented for quantifying these "indirect effects", so that a simple measure emerges for the degree of overall harm or advantage that a particular species encounters from another in the context of a given foodweb. If the system is one of pure competition, the "direct" interaction between any two species is of course harmful to both. But when the method is applied to such systems it predicts that, if all interactions are allowed for including the indirect, in a large proportion of pair interactions at least one species will be deriving benefit from the other. Computer-generated samples confirm that this proportion is accurately predicted. The many pathways for indirect interaction can thus often reverse the direct connection, so that competing species achieve an interaction here called 'Advantageous in A Community Context' (ACC).

Animals↗
PubMed2004

The effects of interaction compartments on stability for competitive systems.

The interactions between species are unlikely to be randomly arranged, and there is increasing evidence that most interactions occur within small species sub-groups, or compartments, that do not strongly interact with one another. We examine whether arranging the interactions of a competitive system into compartments influences the system properties of linear stability, feasibility, reactivity, and biomass stability, thereby altering the likelihood of species persistence. Model Lotka-Volterra systems of diffuse competition were analysed with interactions arranged randomly and in compartments. It was found, using a variety of dynamical measures, that arranging interactions into compartments enhances the likelihood of species persistence. Since many natural competitive systems appear to have interactions arranged within compartments, this may be an outcome of the positive attributes that this form of organization offers.

Competitive Behavior↗
PubMed2004

Bottom-up excitable models of phytoplankton blooms.

A simple nutrient-phytoplankton model is used to explore the dynamics of phytoplankton blooms. The model exhibits excitable behaviour in the sense that a large scale outbreak can only be triggered when a critical nutrient threshold is exceeded. The model takes into account several features often neglected but whose combined effect proves very important: (i) rapid nutrient recycling associated with the microbial loop and patch formation; (ii) self-shading; and (iii) a bottom-up approach, whereby nutrient levels are responsible for both the triggering and the demise of the bloom. Although the literature is replete with studies of 'top-down' models in which zooplankton grazing control the triggering and demise of the bloom, bottom-up models are nevertheless appropriate in many circumstances. We provide a full mathematical investigation of the effects of these three different features in an excitable system framework.

Models, Biological↗
PubMed2004

Indiscriminate polyandry and male parental effort.

Extrapair paternity involves cooperation between mated females and extrapair males. On the other hand, mated males exhibit a spectrum of anti-cuckolding strategies. Hence, extrapair attributes of diverse species and populations reported in the literature are particular solutions of evolutionary games involving gender-specific cuckolding/anti-cuckolding strategies. Here we use game theoretical methods to study the effect of male paternal effort conserving strategies in situations where females seek extrapair fertilizations (EPF) for reasons of genetic compatibility and/or in pursuit of genetic diversity for their offspring. In such cases, females cannot make a pre-copulatory selection of the optimal genetic partners, and therefore combine promiscuous copulation with the use of in copula and/or post-copulatory selection mechanisms to optimize the genetic endowment of their offspring-indiscriminate polyandry. Our results indicate that, when indiscriminate polygamy is constrained by the availability of extrapair male partners, there are three possible (parameter regime wise) evolutionary stable strategy solutions. (1). All females seek EPF, while all males restrict parental care. (2). All females seek EPF, while all males are unconditionally parental. (3). Females use a combination strategy where pursuit of EPF is mixed-on either a population, or an individual level-with genetic monogamy, while all males use a conditional paternal care strategy, which involves adjusting their parental efforts according to their certainty of paternity.

Animals↗
PubMed2003

Unexpected correspondence between noise-induced and master-slave complete synchronizations.

A comparison between noise-induced synchronization and master-slave (Pecora-Carroll) synchronization is investigated in this paper. We find an interesting correspondence between the effective driving variables of these two kinds of synchronizations in three-dimensional chaotic systems, when the systems have nonlinear terms in more than one equation. A study of the Lorenz model, the Hindmarsh-Rose neuron model, and the Hastings-Powell foodweb model is given to support this claim. It is a somewhat surprising result since these two kinds of synchronizations arise through different mechanisms. We also examine an exceptional case, where the nonlinear term of the system appears in a single equation, as in the Pikovsky-Rabinovich circuit model, and explain why the correspondence fails.

Journal Article↗
PubMed2003

Spatio-temporal synchronization of recurrent epidemics.

Long-term spatio-temporal datasets of disease incidences have made it clear that many recurring epidemics, especially childhood infections, tend to synchronize in-phase across suburbs. In some special cases, epidemics between suburbs have been found to oscillate in an out-of-phase ('antiphase') relationship for lengthy periods. Here, we use modelling techniques to help explain the presence of in-phase and antiphase synchronization. The nonlinearity of the epidemic dynamics is often such that the intensity of the outbreak influences the phase of the oscillation thereby introducing 'shear', a factor that is found to be important for generating antiphase synchronization. By contrast, the coupling between suburbs via the immigration of infectives tends to enhance in-phase synchronization. The emerging synchronization depends delicately on these opposite factors. We use theoretical results from continuous time models to provide a framework for understanding the relationship between synchronization patterns for different model structures.

Computer Simulation↗
PubMed2003

Fertility assurance through extrapair fertilizations and male paternity defense.

Extrapair paternity has been observed in many formally monogamous species. Male pursuit of extrapair fertilizations is explained by the advantages of having offspring that receive essential paternal care from other males. Since females are capable of exercising a degree of control over the post-copulatory sperm competition, extrapair paternity cannot persist unless it confers fitness benefits on cuckolding females. Thus, extrapair paternity involves cooperation between mated females and extrapair males. On the other hand, paired males frequently exhibit strategies that minimize their loss of paternity and/or conserve paternal investment if paternity is lost. Hence, extrapair attributes of diverse species and populations reported in the literature are particular solutions of evolutionary games involving gender-specific cuckolding/anti-cuckolding strategies. Here we use methods of evolutionary game theory to study the role of male paternity guarding strategies in situations where females seek extrapair fertilizations for reasons of genetic compatibility and/or in pursuit of genetic diversity for their offspring. Our results indicate that in these circumstances pursuit of extrapair fertilizations is the only evolutionary stable female strategy. Males, on the other hand, have two, mutually exclusive, evolutionary stable strategies: full time pursuit of extrapair fertilizations and a compromise strategy wherein they protect in-pair paternity during their mate's fertile periods and pursue extrapair paternity the rest of the time. The relative merits of these two strategies are determined by the efficiency of male in-pair paternity defense, breeding synchrony, fitness advantages of extrapair over in-pair offspring, and the intensity of competition for extrapair fertilizations from floater males.

Animals↗
PubMed2003

Detecting generalized synchrony: an improved approach.

We examine some of the difficulties involved in detecting generalized synchrony (GS) in systems that exhibit noninvertibility and/or wrinkling. These latter features severely hinder identification of GS by conventional techniques. It is shown that it is possible to greatly improve detection by reducing the pseudofalse neighbors effects. Here we propose the delta(p)-neighbor method to overcome the noninvertibility effect and the delta(p,q) method to detect GS in systems with wrinkled structures.

Journal Article↗
PubMed2003

Noise-induced synchronization in realistic models.

Noise-induced synchronization is studied numerically in two realistic models--the Pikovsky-Rabinovich circuit model and the Hindmarsh-Rose neuron model. A different feature, single-variable-Jacobian matrix, is found in these two models and conditions are found by which two noncoupled identical systems can been synchronized by forcing with a common Gaussian noise term.

Journal Article↗