Age differences between sexual partners, behavioural and demographic correlates, and HIV infection on Likoma Island, Malawi

Patterns of age differences between sexual partners-"age-mixing"-may partially explain the magnitude of HIV epidemics in Sub-Saharan Africa. However, evidence of age-disparity as a risk factor for HIV remains mixed. We used data from a socio-centric study of sexual behaviour in Malawi to quantify the age-mixing pattern and to find associations between relationship characteristics and age differences for 1,922 participants. Three age difference measures were explored as predictors of prevalent HIV infection. We found that for each year increase in male participant age, the average age difference with their partners increased by 0.26 years, while among women it remained approximately constant around 5 years. Women in the study had larger within-individual variation in partner ages compared to men. Spousal partnerships and never using a condom during sex were associated with larger age differences in relationships of both men and women. Men who were more than five years younger than their partners had 5.39 times higher odds ( 95% CI: 0.93-31.24) of being HIV-infected than men 0-4 years older. The relationship between HIV-infection and age-asymmetry may be more complex than previously described. The role that women play in HIV transmission should not be underestimated, particularly in populations with large within-individual variation in partner ages

Laplacian P-splines for Bayesian inference in the mixture cure model

The mixture cure model for analyzing survival data is characterized by the assumption that the population under study is divided into a group of subjects who will experience the event of interest over some finite time horizon and another group of cured subjects who will never experience the event irrespective of the duration of follow-up. When using the Bayesian paradigm for inference in survival models with a cure fraction, it is common practice to rely on Markov chain Monte Carlo (MCMC) methods to sample from posterior distributions. Although computationally feasible, the iterative nature of MCMC often implies long sampling times to explore the target space with chains that may suffer from slow convergence and poor mixing. Furthermore, extra efforts have to be invested in diagnostic checks to monitor the reliability of the generated posterior samples. An alternative strategy for fast and flexible sampling-free Bayesian inference in the mixture cure model is suggested in this paper by combining Laplace approximations and penalized B-splines. A logistic regression model is assumed for the cure proportion and a Cox proportional hazards model with a P-spline approximated baseline hazard is used to specify the conditional survival function of susceptible subjects. Laplace approximations to the conditional latent vector are based on analytical formulas for the gradient and Hessian of the log-likelihood, resulting in a substantial speed-up in approximating posterior distributions. Results show that LPSMC is an appealing alternative to classic MCMC for approximate Bayesian inference in standard mixture cure models.Comment: 34 pages, 6 figures, 5 table

Model Selection in Regression Based on Presmoothing

In this paper we investigate the effect of presmoothing on model selection. Christobal Christobal et al. (1987) showed the beneficial effect of presmoothing for estimating the parameters in a linear regression model. Here, in a regression setting, we show that smoothing the response data prior to model selection by Akaike's Information Criterion can lead to an improved selection procedure. The bootstrap is used to control the magnitude of the random error structure in the smoothed data. The effect of presmoothing on model selection is shown in simulations. The method is illustrated in a variety of settings, including the selection of the best fractional polynomial in a generalized linear model.Statistics Working Papers Serie

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

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

On A Model For The Cross Protection Of Two Infectious Diseases

This paper studies the effects of the spread of two similarly transmitted infectious diseases with cross protection in an unvaccinated population using a basic SEIR model with vital dynamics (births and deaths). A basic Mathematical model is built-up to study the joint transmission dynamics of diseases in the population. The equilibriums of these models as well as their stabilities are studied. Specifically, the stability results for disease-free and endemic steady states are proven. Finally, numerical simulations of the models are carried out with Matlab / Mathematica to study the behavior of the solutions in different regions of the parameter space. Keywords: cross protection, infectious diseases, disease-free and endemic equilibria, numerical simulations, joint modelin

The Belgian policy of funding antimicrobial stewardship in hospitals and trends of selected quality indicators for antimicrobial use, 1999-2010: a longitudinal study

Objectives: In order to improve antimicrobial (AM) use, a policy of providing technical and financial support to AM management teams (AMTs) was rolled out in all Belgian hospitals between 2002 and 2008. We aimed to analyse the association of this policy with AM use for the two indications accounting for the largest number of patients receiving AM: prophylaxis for major lower limb orthopaedic surgery and pneumonia. Design, setting, participants: We used patient-level data routinely collected in all Belgian acute care hospitals between 1999 and 2010. We modelled trends for selected quality indicators (QIs) using the year of AMT implementation in each hospital as the main 'change point', with fine-tuned case-mix adjustment. Of all admissions for lower limb orthopaedic surgery, and pneumonia between 1999 and 2010, 90% (325 094) and 95% (327 635), respectively, were found eligible for analyses. Outcomes: The surgery QI was defined as: cefazolin, dose in the expected range, and no use of other AM. For pneumonia, QIs were: ratio of oral/parenteral defined daily doses (DDD, O/P QI), and mean number of DDD minus penicillin, per 100 days of hospitalisation (DDD QI). Results: Between 1999 and 2010, the surgery QI improved from 59% to 71%, the O/P QI from 0.72 to 0.97, and the DDD QI from 96 to 64. Heterogeneity between hospitals was high. Overall, no association was found with the year of implementation of the AMT. Conclusions: Improvements have been observed but could not be related at the national level to the policy under study. However, these results cannot be extrapolated to other QIs for AM use in hospitals. Our findings do not question the need for AMT, nor the need for continuation of AMT funding. Several recommendations can be made in order to make the best of Belgium's unique political and financial commitments in that field

EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.

In infectious disease epidemiology, the instantaneous reproduction number [Formula: see text] is a time-varying parameter defined as the average number of secondary infections generated by an infected individual at time t. It is therefore a crucial epidemiological statistic that assists public health decision makers in the management of an epidemic. We present a new Bayesian tool (EpiLPS) for robust estimation of the time-varying reproduction number. The proposed methodology smooths the epidemic curve and allows to obtain (approximate) point estimates and credible intervals of [Formula: see text] by employing the renewal equation, using Bayesian P-splines coupled with Laplace approximations of the conditional posterior of the spline vector. Two alternative approaches for inference are presented: (1) an approach based on a maximum a posteriori argument for the model hyperparameters, delivering estimates of [Formula: see text] in only a few seconds; and (2) an approach based on a Markov chain Monte Carlo (MCMC) scheme with underlying Langevin dynamics for efficient sampling of the posterior target distribution. Case counts per unit of time are assumed to follow a negative binomial distribution to account for potential overdispersion in the data that would not be captured by a classic Poisson model. Furthermore, after smoothing the epidemic curve, a "plug-in'' estimate of the reproduction number can be obtained from the renewal equation yielding a closed form expression of [Formula: see text] as a function of the spline parameters. The approach is extremely fast and free of arbitrary smoothing assumptions. EpiLPS is applied on data of SARS-CoV-1 in Hong-Kong (2003), influenza A H1N1 (2009) in the USA and on the SARS-CoV-2 pandemic (2020-2021) for Belgium, Portugal, Denmark and France