Insights into the timing of repeated testing after treatment for Chlamydia trachomatis: data and modelling study

The objective of this study was to determine the optimal time interval for a repeated Chlamydia trachomatis (chlamydia) test.

Modelling zero-inflated count data when exposure varies: with an application to tumor counts)

This paper is concerned with the analysis of zero-inflated count data when time of exposure varies. It proposes a modified zero-inflated count data model where the probability of an extra zero is derived from an underlying duration model with Weibull hazard rate. The new model is compared to the standard Poisson model with logit zero inflation in an application to the effect of treatment with thiotepa on the number of new bladder tumors.

Comparing CFSR and conventional weather data for discharge and soil loss modelling with SWAT in small catchments in the Ethiopian Highlands

Accurate rainfall data are the key input parameter for modelling river discharge and soil loss. Remote areas of Ethiopia often lack adequate precipitation data and where these data are available, there might be substantial temporal or spatial gaps. To counter this challenge, the Climate Forecast System Reanalysis (CFSR) of the National Centers for Environmental Prediction (NCEP) readily provides weather data for any geographic location on earth between 1979 and 2014. This study assesses the applicability of CFSR weather data to three watersheds in the Blue Nile Basin in Ethiopia. To this end, the Soil and Water Assessment Tool (SWAT) was set up to simulate discharge and soil loss, using CFSR and conventional weather data, in three small-scale watersheds ranging from 112 to 477 ha. Calibrated simulation results were compared to observed river discharge and observed soil loss over a period of 32 years. The conventional weather data resulted in very good discharge outputs for all three watersheds, while the CFSR weather data resulted in unsatisfactory discharge outputs for all of the three gauging stations. Soil loss simulation with conventional weather inputs yielded satisfactory outputs for two of three watersheds, while the CFSR weather input resulted in three unsatisfactory results. Overall, the simulations with the conventional data resulted in far better results for discharge and soil loss than simulations with CFSR data. The simulations with CFSR data were unable to adequately represent the specific regional climate for the three watersheds, performing even worse in climatic areas with two rainy seasons. Hence, CFSR data should not be used lightly in remote areas with no conventional weather data where no prior analysis is possible.

Misleading Population Estimates: Biases and Consistency of Visual Surveys and Matrix Modelling in the Endangered Bearded Vulture

Conservation strategies for long-lived vertebrates require accurate estimates of parameters relative to the populations' size, numbers of non-breeding individuals (the “cryptic” fraction of the population) and the age structure. Frequently, visual survey techniques are used to make these estimates but the accuracy of these approaches is questionable, mainly because of the existence of numerous potential biases. Here we compare data on population trends and age structure in a bearded vulture (Gypaetus barbatus) population from visual surveys performed at supplementary feeding stations with data derived from population matrix-modelling approximations. Our results suggest that visual surveys overestimate the number of immature (<2 years old) birds, whereas subadults (3–5 y.o.) and adults (>6 y.o.) were underestimated in comparison with the predictions of a population model using a stable-age distribution. In addition, we found that visual surveys did not provide conclusive information on true variations in the size of the focal population. Our results suggest that although long-term studies (i.e. population matrix modelling based on capture-recapture procedures) are a more time-consuming method, they provide more reliable and robust estimates of population parameters needed in designing and applying conservation strategies. The findings shown here are likely transferable to the management and conservation of other long-lived vertebrate populations that share similar life-history traits and ecological requirements.

Biogeochemical processes in a clay formation in situ experiment: Part F - Reactive transport modelling

Reactive transport modelling was used to simulate solute transport, thermodynamic reactions, ion exchange and biodegradation in the Porewater Chemistry (PC) experiment at the Mont Terri Rock Laboratory. Simulations show that the most important chemical processes controlling the fluid composition within the borehole and the surrounding formation during the experiment are ion exchange, biodegradation and dissolution/precipitation reactions involving pyrite and carbonate minerals. In contrast, thermodynamic mineral dissolution/precipitation reactions involving alumo-silicate minerals have little impact on the fluid composition on the time-scale of the experiment. With the accurate description of the initial chemical condition in the formation in combination with kinetic formulations describing the different stages of bacterial activities, it has been possible to reproduce the evolution of important system parameters, such as the pH, redox potential, total organic C. dissolved inorganic C and SO(4) concentration. Leaching of glycerol from the pH-electrode may be the primary source of organic material that initiated bacterial growth, which caused the chemical perturbation in the borehole. Results from these simulations are consistent with data from the over-coring and demonstrate that the Opalinus Clay has a high buffering capacity in terms of chemical perturbations caused by bacterial activity. This buffering capacity can be attributed to the carbonate system as well as to the reactivity of clay surfaces.

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

Background 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.

Risk attribution of Campylobacter infection by age group using exposure modelling

Knowledge on the relative importance of alternative sources of human campylobacteriosis is important in order to implement effective disease prevention measures. The objective of this study was to assess the relative importance of three key exposure pathways (travelling abroad, poultry meat, pet contact) for different patient age groups in Switzerland. With a stochastic exposure model data on Campylobacter incidence for the years 2002-2007 were linked with data for the three exposure pathways and the results of a case-control study. Mean values for the population attributable fractions (PAF) over all age groups and years were 27% (95% CI 17-39) for poultry consumption, 27% (95% CI 22-32) for travelling abroad, 8% (95% CI 6-9) for pet contact and 39% (95% CI 25-50) for other risk factors. This model provided robust results when using data available for Switzerland, but the uncertainties remained high. The output of the model could be improved if more accurate input data are available to estimate the infection rate per exposure. In particular, the relatively high proportion of cases attributed to 'other risk factors' requires further attention.