HLA typing: Conventional techniques v. next-generation sequencing

Background. The large number of population-specific polymorphisms present in the HLA complex in the South African (SA) population reduces the probability of finding an adequate HLA-matched donor for individuals in need of an unrelated haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) has numerous advantages compared with conventional typing techniques.Objective. To evaluate whether NGS can provide any additional value over conventional techniques in the SA context for the purpose of HSCT and cord blood banking.Methods. HLA genotyping was performed using NGS on 20 samples that had previously been HLA typed by conventional methods to evaluate whether NGS might provide any additional value over conventional HLA determination techniques.Results. NGS of routinely sequenced loci and exons yielded accurate genotypes for 98.5% of the five loci of interest, compared with 98% when additional exons were included.Conclusion. The study shows that the additional value of NGS over conventional techniques is limited, and unless done on a large scale to reduce cost may not be appropriate in SA at this stage in the context of HSCT and cord blood banking

Use of the Bayesian family of methods to correct for effects of exposure measurement error in polynomial regression models

Measurement error in a continuous exposure, if ignored, may cause bias in the estimation of the relationship between exposure and outcome. This presents a significant challenge for understanding exposure-outcome associations in many areas of research, including economic, social, medical and epidemiological research. The presence of classical, i.e. random, measurement error in a continuous exposure has been shown to lead to underestimation of a simple linear relationship. When the functional form of the exposure within a regression model is not linear, i.e. when transformations of the exposure are included, measurement error obscures the true shape of the relationship by making the association appear more linear. Bias in this case will be unknown in direction and vary by exposure level. The most commonly used method for measurement error correction is regression calibration, but this requires an approximation for logistic and survival regression models and does not extend easily to more complex error models. This work investigates three methods for measurement error correction from the Bayesian family of methods: Bayesian analysis using Markov chain Monte Carlo (MCMC), integrated nested Laplace approximations (INLA), and multiple imputation (MI). These have been proposed for measurement error correction but have not been extensively compared, extended for use in several important scenarios, or applied to flexible parametric models. The focus on Bayesian methods was motivated by their flexibility to accommodate complex measurement error models and non-linear exposure-outcome associations. Polynomial regression models are widely used and are often the most interpretable models. In order for measurement error correction methods to be widely implemented, they should be able to accommodate known polynomial transformations as well as model selection procedures when the functional form of the error-prone exposure is unknown. Therefore, in this thesis, correction methods are integrated with the fractional polynomial method, a flexible polynomial model-building procedure for positive continuous variables. In this thesis, I perform a large simulation study comparing proposed methods for measurement error correction from the Bayesian family (i.e. MCMC, INLA, and MI) to the most common method of measurement error correction. Extensions of INLA and MI are presented in order to accommodate both a validation study setting wherein the error-free exposure is measured in a subgroup as well as a replicate study setting wherein there are multiple measures of the error-prone exposure. In order to accommodate unknown polynomial transformations of the error-prone variable, two approaches not used before in this context are proposed and explored in simulation studies alongside more standard methods. The first approach uses Bayesian posterior means in lieu of maximum likelihood estimates within regression calibration. The second approach adapts methods of Bayesian variable selection to the selection of the best polynomial transformation of the error-prone exposure while accommodating measurement error. Successful methods are applied to a motivating example, fitting the non-linear association between alcohol intake and all-cause mortality. By combining measurement error correction adaptable to complex error models with polynomial regression inclusive of model-selection, this work fills a niche which will facilitate wider use of measurement error correction techniques

Immunology for Clinicians: A ‘Trojan Horse’ approach

A South African website imparts basic immunology information to clinicians and other health care workers

Explaining the social patterning of lung function in adulthood at different ages: the roles of childhood precursors, health behaviours and environmental factors

Background: Lung function successfully predicts subsequent health. Although lung function is known to decline over age, little is known about changes in association with socioeconomic status (SES) throughout life, and whether explanatory factors for association vary with age or patterns for non smokers. Methods: Analyses were based on data on 24 500 participants aged ≥ 18 years from the 1995, 1998 and 2003 Scottish Health Surveys who were invited to provide 1 s forced expiratory volume (FEV1) and forced vital capacity (FVC) lung measurements. Sex-stratified multiple linear regression assessed lung function-SES (occupational social class) associations and attenuation by covariates in three age groups (2003 data (n=7928)). Results: The FEV1-SES patterns were clear ( p<0.001) and constant over time. Relative to the least disadvantaged, FEV1 in the most disadvantaged was lower by 0.28 L in men and 0.20 L in women under 40 years compared with differences of 0.51 L in men and 0.25 L in women over 64 years (pinteraction<0.001 men, pinteraction=0.004 women). The greatest attenuation of these results was seen by height, parental social class and smoking, especially among the under 65s. Secondhand smoke exposure and urban/rural residence had some impact among older groups. Adjusting for physical activity and weight had little effect generally. Similar patterns were seen for FVC and among never smokers. Conclusions: We found cross-sectional evidence that SES disparity in lung function increases with age, especially for men. Our findings indicate that early-life factors may predict inequity during younger adulthood, with environmental factors becoming more important at older ages

A gender-sensitised weight loss and healthy living programme for overweight and obese men delivered by Scottish Premier League football clubs (FFIT): a pragmatic randomised controlled trial.

BACKGROUND: The prevalence of male obesity is increasing but few men take part in weight loss programmes. We assessed the effect of a weight loss and healthy living programme on weight loss in football (soccer) fans. METHODS: We did a two-group, pragmatic, randomised controlled trial of 747 male football fans aged 35-65 years with a body-mass index (BMI) of 28 kg/m(2) or higher from 13 Scottish professional football clubs. Participants were randomly assigned with SAS (version 9·2, block size 2-9) in a 1:1 ratio, stratified by club, to a weight loss programme delivered by community coaching staff in 12 sessions held every week. The intervention group started a weight loss programme within 3 weeks, and the comparison group were put on a 12 month waiting list. All participants received a weight management booklet. Primary outcome was mean difference in weight loss between groups at 12 months, expressed as absolute weight and a percentage of their baseline weight. Primary outcome assessment was masked. Analyses were based on intention to treat. The trial is registered with Current Controlled Trials, number ISRCTN32677491. FINDINGS: 374 men were allocated to the intervention group and 374 to the comparison group. 333 (89%) of the intervention group and 355 (95%) of the comparison group completed 12 month assessments. At 12 months the mean difference in weight loss between groups, adjusted for baseline weight and club, was 4·94 kg (95% CI 3·95-5·94) and percentage weight loss, similarly adjusted, was 4·36% (3·64-5·08), both in favour of the intervention (p<0·0001). Eight serious adverse events were reported, five in the intervention group (lost consciousness due to drugs for pre-existing angina, gallbladder removal, hospital admission with suspected heart attack, ruptured gut, and ruptured Achilles tendon) and three in the comparison group (transient ischaemic attack, and two deaths). Of these, two adverse events were reported as related to participation in the programme (gallbladder removal and ruptured Achilles tendon). INTERPRETATION: The FFIT programme can help a large proportion of men to lose a clinically important amount of weight; it offers one effective strategy to challenge male obesity. FUNDING: Scottish Government and The UK Football Pools funded delivery of the programme through a grant to the Scottish Premier League Trust. The National Institute for Health Research Public Health Research Programme funded the assessment (09/3010/06)

Football fans in training: the development and optimization of an intervention delivered through professional sports clubs to help men lose weight, become more active and adopt healthier eating habits

&lt;p&gt;Background: The prevalence of obesity in men is rising, but they are less likely than women to engage in existing weight management programmes. The potential of professional sports club settings to engage men in health promotion activities is being increasingly recognised. This paper describes the development and optimization of the Football Fans in Training (FFIT) programme, which aims to help overweight men (many of them football supporters) lose weight through becoming more active and adopting healthier eating habits.&lt;/p&gt; &lt;p&gt;Methods: The MRC Framework for the design and evaluation of complex interventions was used to guide programme development in two phases. In Phase 1, a multidisciplinary working group developed the pilot programme (p-FFIT) and used a scoping review to summarize previous research and identify the target population. Phase 2 involved a process evaluation of p-FFIT in 11 Scottish Premier League (SPL) clubs. Participant and coach feedback, focus group discussions and interviews explored the utility/acceptability of programme components and suggestions for changes. Programme session observations identified examples of good practice and problems/issues with delivery. Together, these findings informed redevelopment of the optimized programme (FFIT), whose components were mapped onto specific behaviour change techniques using an evidence-based taxonomy.&lt;/p&gt; &lt;p&gt;Results: p-FFIT comprised 12, weekly, gender-sensitised, group-based weight management classroom and ‘pitch-side’ physical activity sessions. These in-stadia sessions were complemented by an incremental, pedometer-based walking programme. p-FFIT was targeted at men aged 35-65 years with body mass index ≥ 27 kg/m2. Phase 2 demonstrated that participants in p-FFIT were enthusiastic about both the classroom and physical activity components, and valued the camaraderie and peer-support offered by the programme. Coaches appreciated the simplicity of the key healthy eating and physical activity messages. Suggestions for improvements that were incorporated into the optimized FFIT programme included: more varied in-stadia physical activity with football-related components; post-programme weight management support (emails and a reunion session); and additional training for coaches in SMART goal setting and the pedometer-based walking programme.&lt;/p&gt; &lt;p&gt;Conclusions: The Football Fans in Training programme is highly acceptable to participants and SPL coaches, and is appropriate for evaluation in a randomised controlled trial.&lt;/p&gt

Charting the landscape of N=4 flux compactifications

We analyse the vacuum structure of isotropic Z_2 x Z_2 flux compactifications, allowing for a single set of sources. Combining algebraic geometry with supergravity techniques, we are able to classify all vacua for both type IIA and IIB backgrounds with arbitrary gauge and geometric fluxes. Surprisingly, geometric IIA compactifications lead to a unique theory with four different vacua. In this case we also perform the general analysis allowing for sources compatible with minimal supersymmetry. Moreover, some relevant examples of type IIB non-geometric compactifications are studied. The computation of the full N=4 mass spectrum reveals the presence of a number of non-supersymmetric and nevertheless stable AdS_4 vacua. In addition we find a novel dS_4 solution based on a non-semisimple gauging.Comment: Minor corrections and references added. Version published in JHE

Increased differentiation associates with decreased polyfunctionality for HIV but not CMV-specific CD8+ T cell responses

The generation of polyfunctional CD8+ T cells, in response to vaccination or natural infection, has been associated with improved protective immunity. However, it remains unclear whether the maintenance of polyfunctionality is linked to particular phenotypic characteristics of the cell, such as the differentiation stage of memory T cells. The goal of this study was to investigate the relationship between the memory maturation stage and polyfunctional profiles of antigen-specific CD8+ T cells

Diagnostic performance of tuberculosis-specific IgG antibody profiles in patients with presumptive tuberculosis from two continents

Background. Development of rapid diagnostic tests for tuberculosis is a global priority. A  whole proteome screen identified Mycobacterium tuberculosis antigens associated with serological responses in tuberculosis patients. We used World Health Organization (WHO) target product profile (TPP) criteria for a detection test and triage test to evaluate these antigens. Methods. Consecutive patients presenting to microscopy centers and district hospitals in Peru and to outpatient clinics at a tuberculosis reference center in Vietnam were recruited. We tested blood samples from 755 HIV–uninfected adults with presumptive pulmonary tuberculosis to measure IgG antibody responses to 57 M. tuberculosis antigens using a field-based multiplexed serological assay and a 132-antigen bead-based reference assay. We evaluated single antigen performance and models of all possible 3-antigen combinations and multiantigen combinations. Results. Three-antigen and multiantigen models performed similarly and were superior to single antigens. With specificity set at 90% for a detection test, the best sensitivity of a 3-antigen model was 35% (95% confidence interval [CI], 31–40). With sensitivity set at 85% for a triage test, the specificity of the best 3-antigen model was 34% (95% CI, 29–40). The reference assay also did not meet study targets. Antigen performance differed significantly between the study sites for 7/22 of the best-performing antigens. Conclusions. Although M. tuberculosis antigens were recognized by the IgG response during tuberculosis, no single antigen or multiantigen set performance approached WHO TPP criteria for clinical utility among HIV-uninfected adults with presumed tuberculosis in high-volume, urban settings in tuberculosis-endemic countries