Correcting for measurement error in fractional polynomial models using Bayesian modelling and regression calibration,with an application to alcohol and mortality

Exposure measurement error can result in a biased estimate of the association between an exposure and outcome. When the exposure–outcome relationship is linear on the appropriate scale (e.g. linear, logistic) and the measurement error is classical, that is the result of random noise, the result is attenuation of the effect. When the relationship is non‐linear, measurement error distorts the true shape of the association. Regression calibration is a commonly used method for correcting for measurement error, in which each individual's unknown true exposure in the outcome regression model is replaced by its expectation conditional on the error‐prone measure and any fully measured covariates. Regression calibration is simple to execute when the exposure is untransformed in the linear predictor of the outcome regression model, but less straightforward when non‐linear transformations of the exposure are used. We describe a method for applying regression calibration in models in which a non‐linear association is modelled by transforming the exposure using a fractional polynomial model. It is shown that taking a Bayesian estimation approach is advantageous. By use of Markov chain Monte Carlo algorithms, one can sample from the distribution of the true exposure for each individual. Transformations of the sampled values can then be performed directly and used to find the expectation of the transformed exposure required for regression calibration. A simulation study shows that the proposed approach performs well. We apply the method to investigate the relationship between usual alcohol intake and subsequent all‐cause mortality using an error model that adjusts for the episodic nature of alcohol consumption.     

Proliferation of Submesothelial Mesenchymal Cells during Early Phase of Serosal Thickening in the Rabbit Bladder Is Accompanied by Transient Keratin 18 Expression

Partial outlet obstruction of the rabbit bladder induces serosal thickening and smooth muscle (SM) hypertrophy. Within thickened serosa, submesothelial (mesenchymal) cells differentiate into SM cells after 30 days of obstruction [S. Buoroet al. Lab. Invest.69, 589–602, 1993]. Here, we show that submesothelial cells transiently express keratin (K) 18 but not K8 soon after obstruction. We investigated a possible relationship between keratin expression and cell proliferation/differentiationin vivoandin vitro.The results of this study indicate that expression of K18 is spatiotemporally related to the pattern of cell proliferation with respect to the localization of an elastic membrane which divides the thickened serosa into an “extrinsic” and an “intrinsic” region. Moreover, K18 is not present in bladder mesenchyma during early development, indicating that its expression in the adult is not attributable to a dedifferentiation process. However, simultaneous K18, K8, and desmoplakin (DP) expression can be induced in normal and thickened serosa upon treatment with bromo-deoxyuridine. Our results indicate that K18 is a marker of proliferating mesenchymal cells in rabbit serosa, whereas the combined expression of K18, K8, and DP might be related to the hypothesized alterations in the stability of gene expression. A model is proposed in which keratin-containing submesothelial cells can act as a “transit” cell phenotype involved in both regenerating mesothelial cells and formation of SM cells.     

Individual adherence to mass drug administration in neglected tropical disease control: A probability model conditional on past behaviour

We present a general framework which describes the systematic (binary) scenario of individuals either taking treatment or not for any reason, over the course of mass drug administration (MDA)—which we refer to as ‘adherence’ and ‘non-adherence’. The probability models developed can be informed by observed adherence behaviour as well as employed to explore how different patterns influence the impact of MDA programmes, by the use of mathematical models of transmission and control. We demonstrate the interpretative value of the developed probability model employing a dataset collected in the TUMIKIA project, a randomised trial of deworming strategies to control soil-transmitted helminths (STH) by MDA conducted in coastal Kenya. We stratify our analysis by age and sex, although the framework which we introduce here may be readily adapted to accommodate other stratifications. Our findings include the detection of specific patterns of non-adherence in all age groups to varying extents. This is particularly apparent in men of ages 30+. We then demonstrate the use of the probability model in stochastic individual-based simulations by running two example forecasts for the elimination of STH transmission employing MDA within the TUMIKIA trial setting with different adherence patterns. This suggested a substantial reduction in the probability of elimination (between 23-43%) when comparing observed adherence patterns with an assumption of independence, with important implications for programmes. The results here demonstrate the considerable impact and utility of considering non-adherence on the success of MDA programmes to control neglected tropical diseases (NTDs).     

Model-Based Investigations of Different Vector-Related Intervention Strategies to Eliminate Visceral Leishmaniasis on the Indian Subcontinent

The elimination of infectious diseases requires reducing transmission below a certain threshold. The Visceral Leishmaniasis (VL) Elimination Initiative in Southeast Asia aims to reduce the annual VL incidence rate below 1 case per 10,000 inhabitants in endemic areas by 2015 via a combination of case management and vector control. Using a previously developed VL transmission model, we investigated transmission thresholds dependent on measures reducing the sand fly density either by killing sand flies (e.g., indoor residual spraying and long-lasting insecticidal nets) or by destroying breeding sites (e.g., environmental management).Model simulations suggest that elimination of VL is possible if the sand fly density can be reduced by 67% through killing sand flies, or if the number of breeding sites can be reduced by more than 79% through measures of environmental management.These results were compared to data from two recent cluster randomised controlled trials conducted in India, Nepal and Bangladesh showing a 72% reduction in sand fly density after indoor residual spraying, a 44% and 25% reduction through the use of long-lasting insecticidal nets and a 42% reduction after environmental management.Based on model predictions, we identified the parameters within the transmission cycle of VL that predominantly determine the prospects of intervention success. We suggest further research to refine model-based predictions into the elimination of VL.     

QuantiFERON-TB GOLD ELISA assay for the detection of Mycobacterium tuberculosis-specific antigens in blood specimens of HIV-positive patients in a high-burden country

Tuberculosis is a life-threatening infection worldwide. Despite improvements in therapy, it results in 2 million deaths and 9 million new cases annually. This study evaluated the use of the QuantiFERON-TB GOLD enzyme-linked immunosorbent assay in a high HIV/TB burden setting in an ARV clinic at the Tshwane District Hospital, South Africa. The sensitivity and specificity of the QF assay in the clinic were 30% (9/30) and 63% (19/30), respectively, when compared with the gold standard culture results. Analysis also suggested that the sensitivity of the QuantiFERON assay is determined by a limiting patient CD4 value between 150 and 200.     

Motherhood and the “Madness of Hunger”: <Emphasis Type="Italic">“…Want Almal Vra vir My vir ‘n Stukkie Brood”</Emphasis> (“…Because Everyone Asks Me for a Little Piece of Bread”)

It is widely assumed that the social and economic conditions of poverty can be linked to common mental disorders in low-, middle- and high-income countries. Despite the considerable increase in quantitative studies investigating the link between poverty and mental health, the nature of the connection between poverty and emotional well-being/distress is still not fully comprehended. In this qualitative study, exploring how one group of Coloured South African women, diagnosed with depression and residing in a semi-rural low-income South African community, subjectively understand and experience their emotional distress, data was collected by means of in-depth semi-structured interviews and social constructionist grounded theory was used to analyse the data. We will attempt to show (1) that the depressed women in this group of respondents frequently refer to the emotional distress caused by hungry children and (2) that the emotional distress described by the respondents included emotions typically associated with depression (such as sadness, hopelessness and guilt), but also included emotions not necessarily associated with depression (such as anxiety, anger and anomie). In our attempt to understand (both psychologically and politically) the complex emotional response of mothers to their children’s hunger, we argue that powerful gender and neo-liberal discourses within which mothers are interpellated to care for children, and more specifically, to make sure that children are not hungry, mean that the mothers of hungry children felt that they were not fulfilling their responsibilities and thus felt guilty and ashamed. This shame seemed, in turn, to lead to anger and/or anomie, informing acting out behaviours ranging from verbal and physical aggression to passive withdrawal. A vicious cycle of hunger, sadness and anxiety, shame, anger and anomie, aggression and withdrawal, negative judgement, and more shame, are thus maintained. As such, the unbearable rebukes of hungry children can be thought of as evoking a kind of “madness” in low-income mothers.     

Identification of Novel Candidate Genes for Early-Onset Colorectal Cancer Susceptibility

Approximately 25–30% of colorectal cancer (CRC) cases are expected to result from a genetic predisposition, but in only 5–10% of these cases highly penetrant germline mutations are found. The remaining CRC heritability is still unexplained, and may be caused by a hitherto-undefined set of rare variants with a moderately penetrant risk. Here we aimed to identify novel risk factors for early-onset CRC using whole-exome sequencing, which was performed on a cohort of CRC individuals (n = 55) with a disease onset before 45 years of age. We searched for genes that were recurrently affected by rare variants (minor allele frequency ≤0.001) with potentially damaging effects and, subsequently, re-sequenced the candidate genes in a replication cohort of 174 early-onset or familial CRC individuals. Two functionally relevant genes with low frequency variants with potentially damaging effects, PTPN12 and LRP6, were found in at least three individuals. The protein tyrosine phosphatase PTP-PEST, encoded by PTPN12, is a regulator of cell motility and LRP6 is a component of the WNT-FZD-LRP5-LRP6 complex that triggers WNT signaling. All variants in LRP6 were identified in individuals with an extremely early-onset of the disease (≤30 years of age), and two of the three variants showed increased WNT signaling activity in vitro. In conclusion, we present PTPN12 and LRP6 as novel candidates contributing to the heterogeneous susceptibility to CRC.     

Detection of blaSHV, blaTEM and blaCTX-M antibiotic resistance genes in randomly selected bacterial pathogens from the Steve Biko Academic Hospital

Extended-spectrum β-lactamases (ESBLs) are considered to be one of the most important antibiotic resistance mechanisms. This study reported the ESBL-producing genes in 53 randomly selected clinical bacterial isolates from the Steve Biko Academic Hospital. The presence of the bla _SHV, bla _TEM and bla _CTX-M genes was determined, and the overall prevalence of these genes detected in this study was 87% (46/53) in comparison with the literature; these results were higher when compared with 33% for Escherichia coli in Europe and 0.8% in Denmark for similar pathogens. These research findings indicated that it is crucial to routinely monitor the prevalence of these resistance genes.