Modelling the impact of local reactive school closures on critical care provision during an influenza pandemic

Despite the fact that the 2009 H1N1 pandemic influenza strain was less severe than had been feared, both seasonal epidemics of influenza-like-illness and future influenza pandemics have the potential to place a serious burden on health services. The closure of schools has been postulated as a means of reducing transmission between children and hence reducing the number of cases at the peak of an epidemic; this is supported by the marked reduction in cases during school holidays observed across the world during the 2009 pandemic. However, a national policy of long-duration school closures could have severe economic costs. Reactive short-duration closure of schools in regions where health services are close to capacity offers a potential compromise, but it is unclear over what spatial scale and time frame closures would need to be made to be effective. Here, using detailed geographical information for England, we assess how localized school closures could alleviate the burden on hospital intensive care units (ICUs) that are reaching capacity. We show that, for a range of epidemiologically plausible assumptions, considerable local coordination of school closures is needed to achieve a substantial reduction in the number of hospitals where capacity is exceeded at the peak of the epidemic. The heterogeneity in demand per hospital ICU bed means that even widespread school closures are unlikely to have an impact on whether demand will exceed capacity for many hospitals. These results support the UK decision not to use localized school closures as a control mechanism, but have far wider international public-health implications. The spatial heterogeneities in both population density and hospital capacity that give rise to our results exist in many developed countries, while our model assumptions are sufficiently general to cover a wide range of pathogens. This leads us to believe that when a pandemic has severe implications for ICU capacity, only widespread school closures (with their associated costs and organizational challenges) are sufficient to mitigate the burden on the worst-affected hospitals

Resurgence of HIV infection among men who have sex with men in Switzerland : mathematical modelling study

New HIV infections in men who have sex with men (MSM) have increased in Switzerland since 2000 despite combination antiretroviral therapy (cART). The objectives of this mathematical modelling study were: to describe the dynamics of the HIV epidemic in MSM in Switzerland using national data; to explore the effects of hypothetical prevention scenarios; and to conduct a multivariate sensitivity analysis. METHODOLOGY/PRINCIPAL FINDINGS: The model describes HIV transmission, progression and the effects of cART using differential equations. The model was fitted to Swiss HIV and AIDS surveillance data and twelve unknown parameters were estimated. Predicted numbers of diagnosed HIV infections and AIDS cases fitted the observed data well. By the end of 2010, an estimated 13.5% (95% CI 12.5, 14.6%) of all HIV-infected MSM were undiagnosed and accounted for 81.8% (95% CI 81.1, 82.4%) of new HIV infections. The transmission rate was at its lowest from 1995-1999, with a nadir of 46 incident HIV infections in 1999, but increased from 2000. The estimated number of new infections continued to increase to more than 250 in 2010, although the reproduction number was still below the epidemic threshold. Prevention scenarios included temporary reductions in risk behaviour, annual test and treat, and reduction in risk behaviour to levels observed earlier in the epidemic. These led to predicted reductions in new infections from 2 to 26% by 2020. Parameters related to disease progression and relative infectiousness at different HIV stages had the greatest influence on estimates of the net transmission rate. CONCLUSIONS/SIGNIFICANCE: The model outputs suggest that the increase in HIV transmission amongst MSM in Switzerland is the result of continuing risky sexual behaviour, particularly by those unaware of their infection status. Long term reductions in the incidence of HIV infection in MSM in Switzerland will require increased and sustained uptake of effective interventions

The effect of competition on the control of invading plant pathogens

1. New invading pathogen strains must compete with endemic pathogen strains to emerge and spread. As disease control measures are often non-specific, i.e. they do not distinguish between strains, applying control not only affects the invading pathogen strain but the endemic as well. We hypothesise that the control of the invasive strain could be compromised due to the non-specific nature of the control. 2. A spatially-explicit model, describing the East African cassava mosaic virus-Uganda strain (EACMV-UG) outbreak, is used to evaluate methods of controlling both disease incidence and spread of invading pathogen strains in pathosystems with and without an endemic pathogen strain present. 3. We find that while many newly introduced or intensified control measures (such as resistant cultivars or roguing) decrease the expected incidence, they have the unintended consequence of increasing, or at least not reducing, the speed with which the invasive pathogen spreads geographically. We identify which controls cause this effect and methods in which these controls may be applied to prevent it. 4. We found that the spatial spread of the invading strain is chiefly governed by the incidence at the wave front. Control can therefore be applied, or intensified, once the wave front has passed without increasing the pathogen’s rate of spread. 5. When trade of planting material occurs, it is possible that the planting material is already infected. The only forms of control in this study that reduces the speed of geographic spread, regardless of the presence of an endemic strain, are those that reduce the amount of trade and the distance over which trade takes place. 6. Synthesis and applications. Imposing trade restrictions before the epidemic has reached a given area and increasing other control methods only once the wave front has passed is the most effective way of both slowing down spread and controlling incidence when the presence of an endemic strain is unknow

Seals at sea: modelling seal distribution in the German bight based on aerial survey data

The Wadden Sea is an important habitat for harbour seals and grey seals. They regularly haul-out on sandbanks and islands along the coast. Comparably little is known about the time seals spend at sea and how they use the remainder of the North Sea. Yet, human activity in offshore waters is increasing and information on seal distribution in the North Sea is crucial for conservation and management. Aerial line transect surveys were conducted in the German bight from 2002 to 2007 to investigate the distribution and abundance of marine mammals. Distance sampling methodology was combined with density surface modelling for a spatially explicit analysis of seal distribution in the German North Sea. Depth and distance to coast were found to be relevant predictor variables for seal density. Density surface modelling allowed for a depiction of seal distribution in the study area as well as an abundance estimate. This is the first study to use aerial survey data to develop a density surface model (DSM) for a spatially explicit distribution estimate of seals at se

Capturing the time-varying drivers of an epidemic using stochastic dynamical systems

Epidemics are often modelled using non-linear dynamical systems observed through partial and noisy data. In this paper, we consider stochastic extensions in order to capture unknown influences (changing behaviors, public interventions, seasonal effects etc). These models assign diffusion processes to the time-varying parameters, and our inferential procedure is based on a suitably adjusted adaptive particle MCMC algorithm. The performance of the proposed computational methods is validated on simulated data and the adopted model is applied to the 2009 H1N1 pandemic in England. In addition to estimating the effective contact rate trajectories, the methodology is applied in real time to provide evidence in related public health decisions. Diffusion driven SEIR-type models with age structure are also introduced.Comment: 21 pages, 5 figure

Overdiagnosis due to screening mammography for women aged 40 years and over

This is a protocol for a Cochrane Review. The objective was to assess the effect of screening mammography for breast cancer on overdiagnosis in women aged 40 years and older at average risk of breast cancer

SimpactCyan 1.0 : an open-source simulator for individual-based models in HIV epidemiology with R and Python interfaces

SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework

Observations of magnetic fields in hot stars

The presence of magnetic fields at the surfaces of many massive stars has been suspected for decades, to explain the observed properties and activity of OB stars. However, very few genuine high-mass stars had been identified as magnetic before the advent of a new generation of powerful spectropolarimeters that has resulted in a rapid burst of precise information about the magnetic properties of massive stars. During this talk, I will briefly review modern methods used to diagnose magnetic fields of higher-mass stars, and summarize our current understanding of the magnetic properties of OB stars.Comment: Proceedings of IAUS272: Active OB stars, review talk (11 pages

The unavoidable costs of ethnicity : a review of evidence on health costs

This report was commissioned by the Advisory Committee on Resource Allocation (ACRA), and prepared by the Centre for Health Services Studies (CHESS) and the Centre for Research in Ethnic Relations (CRER) at the University of Warwick. The NHS Executive does not necessarily assent to the factual accuracy of the report, nor necessarily share the opinions and recommendations of the authors. The study reviews the evidence concerning the degree to which the presence of populations of minority ethnic origin was associated with ‘unavoidable additional costs’ in health service delivery. While local health authorities retail full autonomy in their use of funds allocated to them under the Hospital and Community Health Services formula, the size of that budget is governed by a set of weightings applied to their population, to allow for factors known to influence levels of need, and the costs of providing services. The study began by considering the definitions used in describing ‘ethnicity’ and ethnic groups in relevant medical and social policy literature. It is clear that no fixed set of terms can be adopted, and that flexibility is required to respond to social changes. The terms used in the 1991 Census, with additions to allow for local and contemporary developments, provide a suitable baseline but require additional information on religion language and migration history for clinical and health service delivery planning. There have been notable developments in health service strategy to meet the needs of black and minority ethnic groups which have been encouraged by good practice guidelines and local initiatives. Together with research into epidemiology and ethnic monitoring of services, these have enlarged understanding of the impact of diversity. A conceptual model is developed which explores the potential for such diversity to lead to variations in the cost of providing health services to a multi-ethnic population. The research team reviewed the existing published evidence relating to ethnic health and disease treatment in medical, social science, academic and practitioner literature, using conventional techniques. Additional evidence was located through trawls of ‘grey’ literature in specialist collections, and through contacting all English health districts with a request for information. A number of authorities and trusts provided written and oral evidence, and a bibliography of key materials is provided. Key issues considered include the need for and use of, interpreter and translation services, the incidence of ‘ethnically-specific’ disease, and variations in the prevalence and cost of treating ‘common’ conditions in minority ethnic populations. Sources of variation are discussed, and a ‘scoping’ approach adopted to explore the extent to which these variations could be adequately modelled. It is clear that while some additional costs can be identified, and seen to be unavoidable, there are other areas where the presence of minority populations may lead to lessened pressures on budgets, or where provision of ‘ethnic-specific’ facilities may be alternative to existing needs. The literature provides a range of estimates which can be used in a modelling exercise, but is deficient in many respects, particularly in terms of precise costs associated with procedure and conditions, or in associating precise and consistent categories of ethnic group with epidemiological and operational service provision data. Certain other activities require funding to set them up, and may not be directly related to population size. There is considerable variation in the approaches adopted by different health authorities, and many services are provided by agencies not funded by NHS budgets. The study was completed before the announcement of proposed changes in health service commissioning which may have other implications for ethnic diversity. The presence of minorities is associated with the need to provide additional services in respect of interpreting and translation, and the media of communication. In order to achieve clinical effectiveness, a range of advocacy support facilities or alternative models of provision seem to be desirable. Ethnic diversity requires adaptation and additional evidence in order to inform processes of consultation and commissioning. Minority populations do create demands for certain additional specific clinical services not required by the bulk of the majority population: it is not yet clear to what extent the reverse can be stated since research on ‘under-use’ is less well developed. Some variations in levels of need, particularly those relating to established clinical difference in susceptibility or deprivation, are already incorporated in funding formulae although it is not clear how far the indicators adequately reflect these factors. Costs are not necessarily simply related to the size of minority populations. The provision of services to meet minority needs is not always a reflection of their presence, but has frequently depended upon the provision of additional specific funds. There is a consensus that the NHS research and development strategy should accept the need for more work to establish the actual levels of need and usage of service by ethnic minority groups, and that effort should be made to use and improve the growing collection of relevant information through ethnic monitoring activities. A variety of modelling techniques are suggested, and can be shown to have the potential to provide practical guidance to future policy in the field. Current data availability at a national or regional scale is inadequate to provide estimates of the ‘additional costs of ethnicity’ but locally collected data and the existence of relevant policy initiatives suggest that a focused study in selected districts would provide sufficiently robust information to provide reliable estimates. The review has demonstrated that there are costs associated with the presence of minority ethnic groups in the population which can be shown to be unavoidable and additional, but that others are either ‘desirable’ or ‘alternative’. It would be wrong to assume that all cost pressures of this nature are in the same direction. Our study has drawn attention to deficiencies in data collection and budgeting which may hinder investigation of the effectiveness of the service in general. The process of drawing attention to ethnic minority needs itself leads to developments in services which are functional and desirable for the majority population