Clustering South African households based on their asset status using latent variable models

The Agincourt Health and Demographic Surveillance System has since 2001 conducted a biannual household asset survey in order to quantify household socio-economic status (SES) in a rural population living in northeast South Africa. The survey contains binary, ordinal and nominal items. In the absence of income or expenditure data, the SES landscape in the study population is explored and described by clustering the households into homogeneous groups based on their asset status. A model-based approach to clustering the Agincourt households, based on latent variable models, is proposed. In the case of modeling binary or ordinal items, item response theory models are employed. For nominal survey items, a factor analysis model, similar in nature to a multinomial probit model, is used. Both model types have an underlying latent variable structure - this similarity is exploited and the models are combined to produce a hybrid model capable of handling mixed data types. Further, a mixture of the hybrid models is considered to provide clustering capabilities within the context of mixed binary, ordinal and nominal response data. The proposed model is termed a mixture of factor analyzers for mixed data (MFA-MD). The MFA-MD model is applied to the survey data to cluster the Agincourt households into homogeneous groups. The model is estimated within the Bayesian paradigm, using a Markov chain Monte Carlo algorithm. Intuitive groupings result, providing insight to the different socio-economic strata within the Agincourt region.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS726 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The stall in fertility decline in rural, northeast, South Africa: the contribution of a self-settled, Mozambican, refugee sub-population

Using longitudinal data from the Agincourt Health and socio-Demographic Surveillance System (HDSS) in rural South Africa, this paper examines the role of the fertility of self-settled, former Mozambican refugee sub-population on the stall in fertility decline in the Agincourt HDSS from 1993 to 2009. The Agincourt HDSS fertility trend is decomposed to quantify the relative contribution of the Mozambicans to fertility changes. Results show that fertility level declined by about 1.5 children per woman over the period and the level remain around 2.5 children per woman in the last eight years of the period examined suggesting a stall in fertility decline in the sub-district population covered by the HDSS. However, while the fertility of the Mozambicans fell consistently over the period, there was a reversal in the fertility decline of South African women residing in the area suggesting that the overall stalls are attributable to stalls in fertility decline among South African women.

Ubiquitous burden: the contribution of migration to AIDS and Tuberculosis mortality in rural South Africa

The paper aims to estimate the extent to which migrants are contributing to AIDS or tuberculosis (TB) mortality among rural sub-district populations. The Agincourt (South Africa) health and socio-demographic surveillance system provided comprehensive data on vital and migration events between 1994 and 2006. AIDS and TB cause-deleted life expectancy, and crude death rates by gender, migration status and period were computed. The annualised crude death rate almost tripled from 5∙39 [95% CI 5∙13–5∙65] to 15∙10 [95% CI 14∙62–15∙59] per 1000 over the years 1994-2006. The contribution of AIDS and TB in returned migrants to the increase in crude death rate was 78∙7% [95% CI 77∙4–80∙1] for males and 44∙4% [95% CI 43∙2–46∙1] for females. So, in a typical South African setting dependent on labour migration for rural livelihoods, the contribution of returned migrants, many infected with AIDS and TB, to the burden of disease is high.

Evidence for localised HIV related micro-epidemics associated with the decentralised provision of antiretroviral treatment in rural South Africa: a spatio-temporal analysis of changing mortality patterns (2007-2010).

BACKGROUND: In this study we analysed the spatial and temporal changes in patterns of mortality over a period when antiretroviral therapy (ART) was rolled out in a rural region of north-eastern South Africa. Previous studies have identified localised concentrated HIV related sub-epidemics and recommended that micro-level analyses be carried out in order to direct focused interventions. METHODS: Data from an ongoing health and socio-demographic surveillance study was used in the analysis. The follow-up was divided into two periods, 2007-2008 and 2009-2010, representing the times immediately before and after the effects on mortality of the decentralised ART provision from a newly established local health centre would be expected to be evident. The study population at the start of the analysis was approximately 73 000 individuals. Data were aggregated by village and also using a 2 × 2 km grid. We identified villages, grid squares and regions in the site where mortality rates within each time period or rate ratios between the periods differed significantly from the overall trends. We used clustering techniques to identify cause-specific mortality hotspots. FINDINGS: Comparing the two periods, there was a 30% decrease in age and gender standardised adult HIV-related and TB (HIV/TB) mortality with no change in mortality due to other causes. There was considerable spatial heterogeneity in the mortality patterns. Areas separated by 2 to 4 km with very different epidemic trajectories were identified. There was evidence that the impact of ART in reducing HIV/TB mortality was greatest in communities with higher mortality rates in the earlier period. CONCLUSIONS: This study shows the value of conducting high resolution spatial analyses in order to understand how local micro-epidemics contribute to changes seen over a wider area. Such analyses can support targeted interventions

The employment environment for youth in rural South Africa: A mixed-methods study

South Africa has high youth unemployment. This paper examines the predictors of youth employment in rural Agincourt, Mpumalanga Province. A survey of 187 out-of-school 18–24 year olds found only 12% of women and 38% of men were currently employed. Men with skills/training were significantly more likely to report employment, mostly physical labour (aOR: 4.5; CI: 1.3, 15.3). In-depth interviews with 14 of the youth revealed women are perceived more suitable for formal employment, which is scarce informing why women were more likely to pursue further education and yet less likely to be employed. Ten key informants from local organisations highlighted numerous local youth employment resources while, in contrast, all youth in the sample said no resources were available, highlighting a need for the organisations to extend their services into rural areas. As these services are focused on entrepreneurship, programs to increase financial literacy and formal employment opportunities are also needed

Composition and activity of the non-canonical Gram-positive SecY2 complex

The accessory Sec system in Streptococcus gordonii DL1 is a specialized export system that transports a large serine-rich repeat protein, Hsa, to the bacterial surface. The system is composed of core proteins SecA2 and SecY2 and accessory Sec proteins Asp1–Asp5. Similar to canonical SecYEG, SecY2 forms a channel for translocation of the Hsa adhesin across the cytoplasmic membrane. Accessory Sec proteins Asp4 and Asp5 have been suggested to work alongside SecY2 to form the translocon, similar to the associated SecY, SecE, and SecG of the canonical system (SecYEG). To test this theory, S. gordonii secY2, asp4, and asp5 were co-expressed in Escherichia coli. The resultant complex was subsequently purified, and its composition was confirmed by mass spectrometry to be SecY2-Asp4-Asp5. Like SecYEG, the non-canonical complex activates the ATPase activity of the SecA motor (SecA2). This study also shows that Asp4 and Asp5 are necessary for optimal adhesion of S. gordonii to glycoproteins gp340 and fibronectin, known Hsa binding partners, as well as for early stage biofilm formation. This work opens new avenues for understanding the structure and function of the accessory Sec system

Socioeconomic differences in mortality in the antiretroviral therapy era in Agincourt, rural South Africa, 2001–13: a population surveillance analysis

Background Understanding the effects of socioeconomic disparities in health outcomes is important to implement specific preventive actions. We assessed socioeconomic disparities in mortality indicators in a rural South African population over the period 2001–13. Methods We used data from 21 villages of the Agincourt Health and socio-Demographic Surveillance System (HDSS). We calculated the probabilities of death from birth to age 5 years and from age 15 to 60 years, life expectancy at birth, and cause-specific and age-specific mortality by sex (not in children <5 years), time period, and socioeconomic status (household wealth) quintile for HIV/AIDS and tuberculosis, other communicable diseases (excluding HIV/AIDS and tuberculosis) and maternal, perinatal, and nutritional causes, non-communicable diseases, and injury. We also quantified differences with relative risk ratios and relative and slope indices of inequality. Findings Between 2001 and 2013, 10 414 deaths were registered over 1 058 538 person-years of follow-up, meaning the overall crude mortality was 9·8 deaths per 1000 person-years. We found significant socioecomonic status gradients for mortality and life expectancy at birth, with outcomes improving with increasing socioeconomic status. An inverse relation was seen for HIV/AIDS and tuberculosis mortality and socioeconomic status that persisted from 2001 to 2013. Deaths from non-communicable diseases increased over time in both sexes, and injury was an important cause of death in men and boys. Neither of these causes of death, however, showed consistent significant associations with household socioeconomic status. Interpretation The poorest people in the population continue to bear a high burden of HIV/AIDS and tuberculosis mortality, despite free antiretroviral therapy being made available from public health facilities. Associations between socioeconomic status and increasing burden of mortality from non-communicable diseases is likely to become prominent. Integrated strategies are needed to improve access to and uptake of HIV testing, care, and treatment, and management of non-communicable diseases in the poorest populations

Assessing Changes in Household Socioeconomic Status in Rural South Africa, 2001-2013: A Distributional Analysis Using Household Asset Indicators.

Understanding the distribution of socioeconomic status (SES) and its temporal dynamics within a population is critical to ensure that policies and interventions adequately and equitably contribute to the well-being and life chances of all individuals. This study assesses the dynamics of SES in a typical rural South African setting over the period 2001-2013 using data on household assets from the Agincourt Health and Demographic Surveillance System. Three SES indices, an absolute index, principal component analysis index and multiple correspondence analysis index, are constructed from the household asset indicators. Relative distribution methods are then applied to the indices to assess changes over time in the distribution of SES with special focus on location and shape shifts. Results show that the proportion of households that own assets associated with greater modern wealth has substantially increased over time. In addition, relative distributions in all three indices show that the median SES index value has shifted up and the distribution has become less polarized and is converging towards the middle. However, the convergence is larger from the upper tail than from the lower tail, which suggests that the improvement in SES has been slower for poorer households. The results also show persistent ethnic differences in SES with households of former Mozambican refugees being at a disadvantage. From a methodological perspective, the study findings demonstrate the comparability of the easy-to-compute absolute index to other SES indices constructed using more advanced statistical techniques in assessing household SES

Prevalence and risk factors for active convulsive epilepsy in rural northeast South Africa

Rationale: Epilepsy is among the most common neurological disorders worldwide. However,there are few large, population-based studies of the prevalence and risk factors for epilepsy in southern Africa. Methods: From August 2008 to February 2009, as part of a multi-site study, we undertook a three-stage, population-based study, embedded within the Agincourt health and socio-demographic surveillance system, to estimate the prevalence and identify risk factors of active convulsiveepilepsy (ACE) in a rural South African population. Results: The crude prevalence of ACE, after adjusting for non-response and the sensitivity of the screening method, was 7.0/1,000 individuals (95%CI 6.4—7.6) with significant geographic hetero-geneity across the study area. Being male (OR = 2.3; 95%CI 1.6—3.2), family history of seizures(OR = 4.0; 95%CI 2.0—8.1), a sibling with seizures (OR = 7.0; 95%CI 1.6—31.7), problems after deliv-ery (OR = 5.9; 95%CI 1.2—24.6), and history of snoring (OR = 6.5; 95%CI 4.5—9.5) were significantlyassociated with ACE. For children, their mother’s exposure to some formal schooling was pro-tective (OR = 0.30; 95%CI 0.11—0.84) after controlling for age and sex. Human immunodeficiencyvirus was not found to be associated with ACE. Conclusions: ACE is less frequent in this part of rural South Africa than other parts of sub-SaharanAfrica. Improving obstetric services could prevent epilepsy. The relationship between snoring and ACE requires further investigation, as does the relative contribution of genetic and environmental factors to examine the increased risk in those with a family history of epilepsy

A Successful Failure: Missing the MDG4 Target for Under-Five Mortality in South Africa.

Reflecting on under-five mortality, Peter Byass and colleagues consider how some countries may fail to meet millennium development goal targets despite making considerable advances