Simulation-based Bayesian inference for epidemic models

This is the author pre-print version. The final version is available from the publisher via the DOI in this record.A powerful and flexible method for fitting dynamic models to missing and censored data is to use the Bayesian paradigm via data-augmented Markov chain Monte Carlo (DA-MCMC). This samples from the joint posterior for the parameters and missing data, but requires high memory overheads for large-scale systems. In addition, designing efficient proposal distributions for the missing data is typically challenging. Pseudo-marginal methods instead integrate across the missing data using a Monte Carlo estimate for the likelihood, generated from multiple independent simulations from the model. These techniques can avoid the high memory requirements of DA-MCMC, and under certain conditions produce the exact marginal posterior distribution for parameters. A novel method is presented for implementing importance sampling for dynamic epidemic models, by conditioning the simulations on sets of validity criteria (based on the model structure) as well as the observed data. The flexibility of these techniques is illustrated using both removal time and final size data from an outbreak of smallpox. It is shown that these approaches can circumvent the need for reversible-jump MCMC, and can allow inference in situations where DA-MCMC is impossible due to computationally infeasible likelihoods. © 2013 Elsevier B.V. All rights reserved.T. J. M. was in part supported by Department for the Environment, Food and Rural Affairs/Higher Education Funding Council of England, grant number VT0105 and BBSRC grant (BB/I012192/1). J. V. R was in part supported by Australian Research Council’s Discovery Projects funding scheme (project number DP110102893). R. D. was in part supported by Natural Sciences and Engineering Research Council (NSERC) of Canada’s Discovery Grants Program. A. R. C. was in part supported by National Medical Research Council (NMRC/HINIR/005/2009) and NUS Initiative to Improve Health in Asia. The authors would like to thank Andrew Conlan and Theo Kypraios for useful discussions

The influence of föhn winds on annual and seasonal surface melt on the Larsen C Ice Shelf, Antarctica

Abstract. Warm, dry föhn winds are observed over the Larsen C Ice Shelf year-round and are thought to contribute to the continuing weakening and collapse of ice shelves on the eastern Antarctic Peninsula (AP). We use a surface energy balance (SEB) model, driven by observations from two locations on the Larsen C Ice Shelf and one on the remnants of Larsen B, in combination with output from the Antarctic Mesoscale Prediction System (AMPS), to investigate the year-round impact of föhn winds on the SEB and melt from 2009 to 2012. Föhn winds have an impact on the individual components of the surface energy balance in all seasons and lead to an increase in surface melt in spring, summer and autumn up to 100 km away from the foot of the AP. When föhn winds occur in spring they increase surface melt, extend the melt season and increase the number of melt days within a year. Whilst AMPS is able to simulate the percentage of melt days associated with föhn with high skill, it overestimates the total amount of melting during föhn events and non-föhn events. This study extends previous attempts to quantify the impact of föhn on the Larsen C Ice Shelf by including a 4-year study period and a wider area of interest and provides evidence for föhn-related melting on both the Larsen C and Larsen B ice shelves. </jats:p

Extinction times in the subcritical stochastic SIS logistic epidemic

Many real epidemics of an infectious disease are not straightforwardly super- or sub-critical, and the understanding of epidemic models that exhibit such complexity has been identified as a priority for theoretical work. We provide insights into the near-critical regime by considering the stochastic SIS logistic epidemic, a well-known birth-and-death chain used to model the spread of an epidemic within a population of a given size $N$. We study the behaviour of the process as the population size $N$ tends to infinity. Our results cover the entire subcritical regime, including the "barely subcritical" regime, where the recovery rate exceeds the infection rate by an amount that tends to 0 as $N \to \infty$ but more slowly than $N^{-1/2}$. We derive precise asymptotics for the distribution of the extinction time and the total number of cases throughout the subcritical regime, give a detailed description of the course of the epidemic, and compare to numerical results for a range of parameter values. We hypothesise that features of the course of the epidemic will be seen in a wide class of other epidemic models, and we use real data to provide some tentative and preliminary support for this theory.Comment: Revised; 34 pages; 6 figure

Reduced haemodynamic response in the ageing visual cortex measured by absolute fNIRS

The effect of healthy ageing on visual cortical activation is still to be fully explored. This study aimed to elucidate whether the haemodynamic response (HDR) of the visual cortex altered as a result of ageing. Visually normal (healthy) participants were presented with a simple visual stimulus (reversing checkerboard). Full optometric screening was implemented to identify two age groups: younger adults (n = 12, mean age 21) and older adults (n = 13, mean age 71). Frequency-domain Multi-distance (FD-MD) functional Near-Infrared Spectroscopy (fNIRS) was used to measure absolute changes in oxygenated [HbO] and deoxygenated [HbR] haemoglobin concentrations in the occipital cortices. Utilising a slow event-related design, subjects viewed a full field reversing checkerboard with contrast and check size manipulations (15 and 30 minutes of arc, 50% and 100% contrast). Both groups showed the characteristic response of increased [HbO] and decreased [HbR] during stimulus presentation. However, older adults produced a more varied HDR and often had comparable levels of [HbO] and [HbR] during both stimulus presentation and baseline resting state. Younger adults had significantly greater concentrations of both [HbO] and [HbR] in every investigation regardless of the type of stimulus displayed (p<0.05). The average variance associated with this age-related effect for [HbO] was 88% and [HbR] 91%. Passive viewing of a visual stimulus, without any cognitive input, showed a marked age-related decline in the cortical HDR. Moreover, regardless of stimulus parameters such as check size, the HDR was characterised by age. In concurrence with present neuroimaging literature, we conclude that the visual HDR decreases as healthy ageing proceeds

The aging Canadian population and hospitalizations for acute myocardial infarction: projection to 2020

<p>Abstract</p> <p>Background</p> <p>The risk of experiencing an acute myocardial infarction (AMI) increases with age and Canada's population is aging. The objective of this analysis was to examine trends in the AMI hospitalization rate in Canada between 2002 and 2009 and to estimate the potential increase in the number of AMI hospitalizations over the next decade.</p> <p>Methods</p> <p>Aggregated data on annual AMI hospitalizations were obtained from the Canadian Institute for Health Information for all provinces and territories, except Quebec, for 2002/03 and 2009/10. Using these data in a Poisson regression model to control for age, gender and year, the rate of AMI hospitalizations was extrapolated between 2010 and 2020. The extrapolated rate and Statistics Canada population projections were used to estimate the number of AMI hospitalizations in 2020.</p> <p>Results</p> <p>The rates of AMI hospitalizations by gender and age group showed a decrease between 2002 and 2009 in patients aged ≥ 65 years and relatively stable rates in those aged < 64 years in both males and females. However, the total number of AMI hospitalizations in Canada (excluding Quebec) is projected to increase by 4667 from 51847 in 2009 to 56514 in 2020, a 9.0% increase. Inflating this number to account for the unavailable Quebec data results in an increase of approximately 6200 for the whole of Canada. This would amount to an additional cost of between $46 and$54 million and sensitivity analyses indicate that it could be between $36 and$65 million.</p> <p>Conclusions</p> <p>Despite projected decreasing or stable rates of AMI hospitalization, the number of hospitalizations is expected to increase substantially as a result of the aging of the Canadian population. The cost of these hospitalizations will be substantial. An increase of this extent in the number of AMI hospitalizations and the ensuing costs would significantly impact the already over-stretched Canadian healthcare system.</p

U-Pb memory behavior in Chicxulub's peak ring - Applying U-Pb depth profiling to shocked zircon

The zircon U-Pb system is one of the most robust geochronometers, but during an impact event individual crystals can be affected differently by the passage of the shock wave and impact generated heat. Unraveling the potentially complex thermal history recorded by zircon crystals that experienced variable levels of shock and heating, as well as additioanl pre- and post-impact thermal events, has been difficult using classical geochronological methods. The existing high-precision 40Ar/39Ar age constraints for the K-Pg Chicxulub event, and the previous U-Pb dating of the basement rocks from the impact site, make Chicxulub an ideal location to study impact-induced effects on the zircon U-Pb systematics and to evaluate potential 'memory effects' of pre-impact U-Pb signatures preserved within those individual zircon crystals. Recent IODP-ICDP drilling of the Chicxulub impact structure recovered 580 m of uplifted shocked granitoid and 130 m of melt and suevite, providing an unprecedented opportunity to study zircon crystals subjected to a range of shock pressures, thermal, and deformational histories. Zircon morphologies were classified using scanning electron microscopy (SEM) imaging and then samples were depth profiled using laser ablation inductively coupled plasma mass-spectrometry (LA-ICP-MS) to document the range of preserved age domains from rim-to-center within individual crystals. The results show U-Pb ages range from 66 to 472 Ma, which are consistent with both inherited Carboniferous and Late Paleozoic basement ages as well as Pb loss ages in response to the K-Pg impact event. While the bulk of the zircon grains preserve Paleozoic ages, high U (metamict) zones within fractured zircon crystals exhibited an age within uncertainty (66 ± 6.2 Ma) of the impact age (66.038 ± 0.049 Ma), indicating that inherited intragrain U-Pb kinetics and/or hydrothermal fluid flow may have controlled age resetting those zircon crystals rather than impact-induced shock and heating alone. Moreover, the calculated α-decay doses suggest that the zircon crystals experienced Stage 1 or early Stage 2 radiation damage accumulation. Therefore, we suggest that the lowered crystal annealing temperature in crystals that previoulsy experienced radiation damage make the zircon U-Pb clock either more susceptible to the relatively short heat pulse of the impact event, the moderate pressure and temperature conditions in the peak ring, and/or to hot-fluid flow in the long-lasting post impact hydrothermal system

Thyroid function tests in patients taking thyroid medication in Germany: Results from the population-based Study of Health in Pomerania (SHIP)

<p>Abstract</p> <p>Background</p> <p>Studies from iodine-sufficient areas have shown that a high proportion of patients taking medication for thyroid diseases have thyroid stimulating hormone (TSH) levels outside the reference range. Next to patient compliance, inadequate dosing adjustment resulting in under- and over-treatment of thyroid disease is a major cause of poor therapy outcomes. Using thyroid function tests, we aim to measure the proportions of subjects, who are under- or over-treated with thyroid medication in a previously iodine-deficient area.</p> <p>Findings</p> <p>Data from 266 subjects participating in the population-based Study of Health in Pomerania (SHIP) were analysed. All subjects were taking thyroid medication. Serum TSH levels were measured using immunochemiluminescent procedures. TSH levels of < 0.27 or > 2.15 mIU/L in subjects younger than 50 years and < 0.19 or > 2.09 mIU/L in subjects 50 years and older, were defined as decreased or elevated, according to the established reference range for the specific study area. Our analysis revealed that 56 of 190 (29.5%) subjects treated with thyroxine had TSH levels outside the reference range (10.0% elevated, 19.5% decreased). Of the 31 subjects taking antithyroid drugs, 12 (38.7%) had TSH levels outside the reference range (9.7% elevated, 29.0% decreased). These proportions were lower in the 45 subjects receiving iodine supplementation (2.2% elevated, 8.9% decreased). Among the 3,974 SHIP participants not taking thyroid medication, TSH levels outside the reference range (2.8% elevated, 5.9% decreased) were less frequent.</p> <p>Conclusion</p> <p>In concordance with previous studies in iodine-sufficient areas, our results indicate that a considerable number of patients taking thyroid medication are either under- or over-treated. Improved monitoring of these patients' TSH levels, compared to the local reference range, is recommended.</p