Vaccination against Foot-and-mouth disease : do initial conditions affect its benefit?

When facing incursion of a major livestock infectious disease, the decision to implement a vaccination programme is made at the national level. To make this decision, governments must consider whether the benefits of vaccination are sufficient to outweigh potential additional costs, including further trade restrictions that may be imposed due to the implementation of vaccination. However, little consensus exists on the factors triggering its implementation on the field. This work explores the effect of several triggers in the implementation of a reactive vaccination-to-live policy when facing epidemics of foot-and-mouth disease. In particular, we tested whether changes in the location of the incursion and the delay of implementation would affect the epidemiological benefit of such a policy in the context of Scotland. To reach this goal, we used a spatial, premises-based model that has been extensively used to investigate the effectiveness of mitigation procedures in Great Britain. The results show that the decision to vaccinate, or not, is not straightforward and strongly depends on the underlying local structure of the population-at-risk. With regards to disease incursion preparedness, simply identifying areas of highest population density may not capture all complexities that may influence the spread of disease as well as the benefit of implementing vaccination. However, if a decision to vaccinate is made, we show that delaying its implementation in the field may markedly reduce its benefit. This work provides guidelines to support policy makers in their decision to implement, or not, a vaccination-to-live policy when facing epidemics of infectious livestock disease

Converging and diverging convection around axisymmetric magnetic flux tubes

A numerical model of idealized sunspots and pores is presented, where axisymmetric cylindrical domains are used with aspect ratios (radius versus depth) up to 4. The model contains a compressible plasma with density and temperature gradients simulating the upper layer of the Sun's convection zone. Non-linear magnetohydrodynamic equations are solved numerically and time-dependent solutions are obtained where the magnetic field is pushed to the centre of the domain by convection cells. This central magnetic flux bundle is maintained by an inner convection cell, situated next to it and with a flow such that there is an inflow at the top of the numerical domain towards the flux bundle. For aspect ratio 4, a large inner cell persists in time, but for lower aspect ratios it becomes highly time dependent. For aspect ratios 2 and 3 this inner convection cell is smaller, tends to be situated towards the top of the domain next to the flux bundle, and appears and disappears with time. When it is gone, the neighbouring cell (with an opposite sense of rotation, i.e. outflow at the top) pulls the magnetic field away from the central axis. As this happens a new inner cell forms with an inflow which pushes the magnetic field towards the centre. This suggests that to maintain their form, both pores and sunspots need a neighbouring convection cell with inflow at the top towards the magnetic flux bundle. This convection cell does not have to be at the top of the convection zone and could be underneath the penumbral structure around sunspots. For an aspect ratio of 1, there is not enough space in the numerical domain for magnetic flux and convection to separate. In this case the solution oscillates between two steady states: two dominant convection cells threaded by magnetic field and one dominant cell that pushes magnetic flux towards the central axis

Effects of regional differences and demography in modelling foot-and-mouth disease in cattle at the national scale

Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costly outbreaks in livestock populations. Transmission occurs at multiple spatial scales, as can the actions used to control outbreaks. The US cattle industry is spatially expansive, with heterogeneous distributions of animals and infrastructure. We have developed a model that incorporates the effects of scale for both disease transmission and control actions, applied here in simulating FMD outbreaks in US cattle. We simulated infection initiating in each of the 3049 counties in the contiguous US, 100 times per county. When initial infection was located in specific regions, large outbreaks were more likely to occur, driven by infrastructure and other demographic attributes such as premises clustering and number of cattle on premises. Sensitivity analyses suggest these attributes had more impact on outbreak metrics than the ranges of estimated disease parameter values. Additionally, although shipping accounted for a small percentage of overall transmission, areas receiving the most animal shipments tended to have other attributes that increase the probability of large outbreaks. The importance of including spatial and demographic heterogeneity in modelling outbreak trajectories and control actions is illustrated by specific regions consistently producing larger outbreaks than others

Striation and convection in penumbral filaments

Observations with the 1-m Swedish Solar Telescope of the flows seen in penumbral filaments are presented. Time sequences of bright filaments show overturning motions strikingly similar to those seen along the walls of small isolated structures in the active regions. The filaments show outward propagating striations with inclination angles suggesting that they are aligned with the local magnetic field. We interpret it as the equivalent of the striations seen in the walls of small isolated magnetic structures. Their origin is then a corrugation of the boundary between an overturning convective flow inside the filament and the magnetic field wrapping around it. The outward propagation is a combination of a pattern motion due to the downflow observed along the sides of bright filaments, and the Evershed flow. The observed short wavelength of the striation argues against the existence of a dynamically significant horizontal field inside the bright filaments. Its intensity contrast is explained by the same physical effect that causes the dark cores of filaments, light bridges and `canals'. In this way striation represents an important clue to the physics of penumbral structure and its relation with other magnetic structures on the solar surface. We put this in perspective with results from the recent 3-D radiative hydrodynamic simulations.Comment: Accepted for publication in A&

Angle of Repose and Angle of Marginal Stability: Molecular Dyanmics of Granular Particles

We present an implementation of realistic static friction in molecular dynamics (MD) simulations of granular particles. In our model, to break contacts between two particles, one has to apply a finite amount of force, determined by the Coulomb criterion. Using a two dimensional model, we show that piles generated by avalanches have a {\it finite} angle of repose $\theta_R$ (finite slopes). Furthermore, these piles are stable under tilting by an angle smaller than a non-zero tilting angle $\theta_T$, showing that $\theta_R$ is different from the angle of marginal stability $\theta_{MS}$, which is the maximum angle of stable piles. These measured angles are compared to a theoretical approximation. We also measure $\theta_{MS}$ by continuously adding particles on the top of a stable pile.Comment: 14 pages, Plain Te

Modelling H5N1 in Bangladesh across spatial scales : model complexity and zoonotic transmission risk

Highly pathogenic avian influenza H5N1 remains a persistent public health threat, capable of causing infection in humans with a high mortality rate while simultaneously negatively impacting the livestock industry. A central question is to determine regions that are likely sources of newly emerging influenza strains with pandemic causing potential. A suitable candidate is Bangladesh, being one of the most densely populated countries in the world and having an intensifying farming system. It is therefore vital to establish the key factors, specific to Bangladesh, that enable both continued transmission within poultry and spillover across the human–animal interface. We apply a modelling framework to H5N1 epidemics in the Dhaka region of Bangladesh, occurring from 2007 onwards, that resulted in large outbreaks in the poultry sector and a limited number of confirmed human cases. This model consisted of separate poultry transmission and zoonotic transmission components. Utilising poultry farm spatial and population information a set of competing nested models of varying complexity were fitted to the observed case data, with parameter inference carried out using Bayesian methodology and goodness-of-fit verified by stochastic simulations. For the poultry transmission component, successfully identifying a model of minimal complexity, which enabled the accurate prediction of the size and spatial distribution of cases in H5N1 outbreaks, was found to be dependent on the administration level being analysed. A consistent outcome of non-optimal reporting of infected premises materialised in each poultry epidemic of interest, though across the outbreaks analysed there were substantial differences in the estimated transmission parameters. The zoonotic transmission component found the main contributor to spillover transmission of H5N1 in Bangladesh was found to differ from one poultry epidemic to another. We conclude by discussing possible explanations for these discrepancies in transmission behaviour between epidemics, such as changes in surveillance sensitivity and biosecurity practices

Beyond clustering: mean-field dynamics on networks with arbitrary subgraph composition

Clustering is the propensity of nodes that share a common neighbour to be connected. It is ubiquitous in many networks but poses many modelling challenges. Clustering typically manifests itself by a higher than expected frequency of triangles, and this has led to the principle of constructing networks from such building blocks. This approach has been generalised to networks being constructed from a set of more exotic subgraphs. As long as these are fully connected, it is then possible to derive mean-field models that approximate epidemic dynamics well. However, there are virtually no results for non-fully connected subgraphs. In this paper, we provide a general and automated approach to deriving a set of ordinary differential equations, or mean-field model, that describes, to a high degree of accuracy, the expected values of system-level quantities, such as the prevalence of infection. Our approach offers a previously unattainable degree of control over the arrangement of subgraphs and network characteristics such as classical node degree, variance and clustering. The combination of these features makes it possible to generate families of networks with different subgraph compositions while keeping classical network metrics constant. Using our approach, we show that higher-order structure realised either through the introduction of loops of different sizes or by generating networks based on different subgraphs but with identical degree distribution and clustering, leads to non-negligible differences in epidemic dynamics

Yukawa potentials in systems with partial periodic boundary conditions I : Ewald sums for quasi-two dimensional systems

Yukawa potentials are often used as effective potentials for systems as colloids, plasmas, etc. When the Debye screening length is large, the Yukawa potential tends to the non-screened Coulomb potential ; in this small screening limit, or Coulomb limit, the potential is long ranged. As it is well known in computer simulation, a simple truncation of the long ranged potential and the minimum image convention are insufficient to obtain accurate numerical data on systems. The Ewald method for bulk systems, i.e. with periodic boundary conditions in all three directions of the space, has already been derived for Yukawa potential [cf. Y., Rosenfeld, {\it Mol. Phys.}, \bm{88}, 1357, (1996) and G., Salin and J.-M., Caillol, {\it J. Chem. Phys.}, \bm{113}, 10459, (2000)], but for systems with partial periodic boundary conditions, the Ewald sums have only recently been obtained [M., Mazars, {\it J. Chem. Phys.}, {\bf 126}, 056101 (2007)]. In this paper, we provide a closed derivation of the Ewald sums for Yukawa potentials in systems with periodic boundary conditions in only two directions and for any value of the Debye length. A special attention is paid to the Coulomb limit and its relation with the electroneutrality of systems.Comment: 40 pages, 5 figures and 4 table

The impact of contact tracing in clustered populations

The tracing of potentially infectious contacts has become an important part of the control strategy for many infectious diseases, from early cases of novel infections to endemic sexually transmitted infections. Here, we make use of mathematical models to consider the case of partner notification for sexually transmitted infection, however these models are sufficiently simple to allow more general conclusions to be drawn. We show that, when contact network structure is considered in addition to contact tracing, standard “mass action” models are generally inadequate. To consider the impact of mutual contacts (specifically clustering) we develop an improvement to existing pairwise network models, which we use to demonstrate that ceteris paribus, clustering improves the efficacy of contact tracing for a large region of parameter space. This result is sometimes reversed, however, for the case of highly effective contact tracing. We also develop stochastic simulations for comparison, using simple re-wiring methods that allow the generation of appropriate comparator networks. In this way we contribute to the general theory of network-based interventions against infectious disease

Molecular-dynamics simulations of the dynamical excitations in commensurate submonolayer films of nitrogen molecules on graphite

URL:http://link.aps.org/doi/10.1103/PhysRevB.54.14077 DOI:10.1103/PhysRevB.54.14077The dynamics of commensurate submonolayer solids of N2 molecules adsorbed on the basal planes of graphite have been studied using molecular-dynamics simulations. The calculations yielded the temperature dependence of the Brillouin-zone-center gap in the acoustic-phonon branches, for comparison with inelastic neutron-scattering experiments on the submonolayer solid. The calculated frequency gap was the same in submonolayer and monolayer films at low temperatures. At intermediate temperatures, the diffusive molecular motion associated with the presence of vacancies caused the gap mode to be less clearly defined in the coherent scattering function. Diffusion constants are calculated at submonolayer coverages, and temperatures up to 40 K for a population of molecules identified as mobile.This work was partially supported by the National Science Foundation under Grant No. DMR-9314235 (H.T.) and Nos. DMR-9120199 and DMR-9423307 (L.W.B.) and by The Danish Natural Science Foundation (F.Y.H.). L.W.B. thanks the Fysisk-Kemisk Institut and the Technical University of Denmark for hospitality during the period this work was completed