SA-MRC/Wits Agincourt Unit (Research Outputs/Publications)
Permanent URI for this collectionhttps://hdl.handle.net/10539/37309
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Item Performance of four computer-coded verbal autopsy methods for cause of death assignment compared with physician coding on 24,000 deaths in low- and middle-income countries(2014) Nikita Desai; Lukasz Aleksandrowicz; Pierre Miasnikof; Ying Lu; Jordana Leitao; Peter Byass; Stephen Tollman; Paul Mee; Dewan Alam; Suresh Kumar Rathi; Abhishek Singh; Rajesh Kumar; Faujdar Ram; Prabhat JhaBackground: Physician-coded verbal autopsy (PCVA) is the most widely used method to determine causes of death (CODs) in countries where medical certification of death is uncommon. Computer-coded verbal autopsy (CCVA) methods have been proposed as a faster and cheaper alternative to PCVA, though they have not been widely compared to PCVA or to each other. Methods: We compared the performance of open-source random forest, open-source tariff method, InterVA-4, and the King-Lu method to PCVA on five datasets comprising over 24,000 verbal autopsies from low- and middle-income countries. Metrics to assess performance were positive predictive value and partial chance-corrected concordance at the individual level, and cause-specific mortality fraction accuracy and cause-specific mortality fraction error at the population level. Results: The positive predictive value for the most probable COD predicted by the four CCVA methods averaged about 43% to 44% across the datasets. The average positive predictive value improved for the top three most probable CODs, with greater improvements for open-source random forest (69%) and open-source tariff method (68%) than for InterVA-4 (62%). The average partial chance-corrected concordance for the most probable COD predicted by the open-source random forest, open-source tariff method and InterVA-4 were 41%, 40% and 41%, respectively, with better results for the top three most probable CODs. Performance generally improved with larger datasets. At the population level, the King-Lu method had the highest average cause-specific mortality fraction accuracy across all five datasets (91%), followed by InterVA-4 (72% across three datasets), open-source random forest (71%) and open-source tariff method (54%). Conclusions: On an individual level, no single method was able to replicate the physician assignment of COD more than about half the time. At the population level, the King-Lu method was the best method to estimate cause-specific mortality fractions, though it does not assign individual CODs. Future testing should focus on combining different computer-coded verbal autopsy tools, paired with PCVA strengths. This includes using open-source tools applied to larger and varied datasets (especially those including a random sample of deaths drawn from the population), so as to establish the performance for age- and sex-specific CODsItem Dimensions of internal migration and their relationship to blood pressure in South Africa(2019-11) Chantel F. Pheiffer; Stephen T. McGarvey; Carren Ginsburg; Mark Collinson; F. Xavier Gómez-Olivé; Stephen Tollman; Michael J. WhiteHypertension prevalence is on the rise in low and middle income countries like South Africa, and migration and concomitant urbanization are often considered to be associated with this rise. However, relatively little is known about the relationship between blood pressure (BP) and internal migration - a highly prevalent population process in LMICs. This study employs data for a group of 194 adult men and women from an original pilot dataset drawn from the Agincourt Health and Demographic Surveillance System in northeast South Africa. Migrants in the sample are identified, tracked, and interviewed. The relationship between BP and migration distance and the number of months an individual spends away from his/her home village is estimated using robust OLS regression, controlling for a series of socioeconomic, health, and behavioral characteristics. This study finds migrants who move further distances and for longer durations to have significantly higher systolic and diastolic BP compared with shorter-term migrants and those who remain nearby or in their home village. These associations remain robust and statistically significant when adjusting for measures of socioeconomic conditions, as well as body mass index (BMI), and the number of meals consumed per day. Migration, both in terms of distance and time away, explains significant variation in BP among migrants in a typical South African context. This finding suggests the need for further studies of nutritional and psychosocial factors associated with geographic mobility that may be important factors for understanding rising hypertension in LMICs.Item Genomic and environmental risk factors for cardiometabolic diseases in Africa: methods used for Phase 1 of the AWI-Gen population cross-sectional study(2018-07-12) Stuart A. Al; Cassandra Soo; Godfred Agongo; Marianne Alberts; Lucas Amenga-Etego; Romuald P. Boua; Ananyo Choudhury; Nigel J. Crowther; Cornelius Depuur; F. Xavier GómezOlivé; Issa Guiraud; Tilahun N. Haregu; Scott Hazelhurst; Kathleen Kahn; Christopher Khayeka-Wandabwa; Catherine Kyobutung; Zané Lombard; Felistas Mashinya; Lisa Micklesfield; Shukri F. Mohamed; Freedom Mukomana; Seydou Nakanabo-Diallo; Hamtandi M. Natama; Nicholas Ngomi; Engelbert A. Nonterah; Shane A. Norris; Abraham R. Oduro; Athanase M. Somé; Hermann Sorgho; Paulina Tindana; Halidou Tinto; Stephen Tollman; Rhian Twine; Alisha Wade; Osman Sankoh; Michèle RamsayThere is an alarming tide of cardiovascular and metabolic disease (CMD) sweeping across Africa. This may be a result of an increasingly urbanized lifestyle characterized by the growing consumption of processed and calorie-dense food, combined with physical inactivity and more sedentary behaviour. While the link between lifestyle and public health has been extensively studied in Caucasian and African American populations, few studies have been conducted in Africa. This paper describes the detailed methods for Phase 1 of the AWI-Gen study that were used to capture phenotype data and assess the associated risk factors and end points for CMD in persons over the age of 40 years in sub-Saharan Africa (SSA). We developed a population-based cross-sectional study of disease burden and phenotype in Africans, across six centres in SSA. These centres are in West Africa (Nanoro, Burkina Faso, and Navrongo, Ghana), in East Africa (Nairobi, Kenya) and in South Africa (Agincourt, Dikgale and Soweto). A total of 10,702 individuals between the ages of 40 and 60 years were recruited into the study across the six centres, plus an additional 1021 participants over the age of 60 years from the Agincourt centre. We collected socio-demographic, anthropometric, medical history, diet, physical activity, fat distribution and alcohol/tobacco consumption data from participants. Blood samples were collected for disease-related biomarker assays, and genomic DNA extraction for genome-wide association studies. Urine samples were collected to assess kidney function. The study provides base-line data for the development of a series of cohorts with a second wave of data collection in Phase 2 of the study. These data will provide valuable insights into the genetic and environmental influences on CMD on the African continentItem Body composition and physical activity as mediators in the relationship between socioeconomic status and blood pressure in young South African women: a structural equation model analysis(2018-11-11) Richard J Munthali; Mercy Manyema; Rihlat Said-Mohamed; Juliana Kagura; Stephen Tollman; Kathleen Kahn; F Xavier Gómez-Olivé; Lisa K Micklesfield; David Dunger; Shane A NorrisObjectives Varying hypertension prevalence across different socioeconomic strata within a population has been well reported. However, the causal factors and pathways across different settings are less clear, especially in sub-Saharan Africa. Therefore, this study aimed to compare blood pressure (BP) levels and investigate the extent to which socioeconomic status (SES) is associated with BP, in rural and urban South Africa women. Setting Rural and urban South Africa. Design Cross-sectional. Participants Cross-sectional data on SES, total moderate and vigorous physical activity (MVPA), anthropometric and BP were collected on rural (n=509) and urban (n=510) young black women (18–23 years age). Pregnant and mentally or physically disabled women were excluded from the study. Results The prevalence of combined overweight and obesity (46.5% vs 38.8%) and elevated BP (27.0% vs 9.3%) was higher in urban than rural women, respectively. Results from the structural equation modelling showed significant direct positive effects of body mass index (BMI) on systolic BP (SBP) in rural, urban and pooled datasets. Negative direct effects of SES on SBP and positive total effects of SES on SBP were observed in the rural and pooled datasets, respectively. In rural young women, SES had direct positive effects on BMI and was negatively associated with MVPA in urban and pooled analyses. BMI mediated the positive total effects association between SES and SBP in pooled analyses (ß 0.46; 95% CI 0.15 to 0.76). Conclusions Though South Africa is undergoing nutritional and epidemiological transitions, the prevalence of elevated BP still varies between rural and urban young women. The association between SES and SBP varies considerably in economically diverse populations with BMI being the most significant mediator. There is a need to tailor prevention strategies to take into account optimizing BMI when designing strategies to reduce future risk of hypertension in young women. This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the license is given, and indication of whether changes were made.Item Executive function associated with sexual risk in young South African women: Findings from the HPTN 068 cohort(2018-04-02) Molly Rosenberg; Audrey Pettifor; Mihaela Duta; Nele Demeyere; Ryan G. Wagner; Amanda Selin; Catherine MacPhail; Oliver Laeyendecker; James P. Hughes; Alan Stein; Stephen Tollman; Kathleen KahnPurpose Heightened sexual risk in adolescence and young adulthood may be partially explained by deficits in executive functioning, the set of cognitive processes used to make reasoned decisions. However, the association between executive function and sexual risk is understudied among adolescent girls and young women, particularly in low- and middle-income countries. Methods In a cohort of 853 young women age 18–25 in rural Mpumalanga province, South Africa, we evaluated executive function with three non-verbal cognitive tests: I. a rule-finding test, II. a trail-making test, and III. a figure drawing test. Using log-binomial regression models, we estimated the association between lower executive function test scores and indicators of sexual risk (unprotected sex acts, concurrent partnerships, transactional sex, and recent HSV-2 infection). Results In general, young women with lower executive function scores reported higher frequencies of sexual risk outcomes, though associations tended to be small with wide confidence intervals. Testing in the lowest quintile of Test I was associated with more unprotected sex [aPR (95% CI): 1.4 (1.0, 1.8)]. Testing in the lowest quintile of Test II was associated with more concurrent relationships and transactional sex [aPR (95% CI): 1.6 (1.1, 2.5) and 1.7 (1.3, 2.4), respectively], and testing in the lowest four quintiles of Test III was associated with more concurrent relationships [aPR (95% CI): 1.7 (1.0, 2.7)]. Conclusions These results demonstrate an association between low executive function and sexual risk in South African young women. Future work should seek to understand the nature of this association and whether there is promise in developing interventions to enhance executive function to reduce sexual risk.Item Multilevel measures of education and pathways to incident HSV-2 in adolescent girls and young women in South Africa (HPTN 068)(2019-12) Marie C.D. Stoner, PhD; Torsten B. Neilands, PhD; Kathleen Kahn, PhD; James P. Hughes, PhD; F. Xavier Gómez-Olivé, PhD; Rhian Twine, MPH; Stephen Tollman; Oliver Laeyendecker, PhD; Catherine MacPhail, PhD; Jennifer Ahern, PhD; Sheri A. Lippman; Audrey Pettifor, PhDPurpose: Schooling is associated with a lower risk of Herpes simplex virus type 2 (HSV-2) in adolescent girls and young women, but there is little understanding of the pathways underlying this relationship. Methods: We used data from adolescent girls and young women in South Africa enrolled in the HIV Prevention Trials Network 068 study. We tested a structural equation model where individual household and community education measures were associated directly and indirectly with incident HSV-2 through HIV knowledge, future aspirations, age-disparate partnerships, sex in the last 12 months, and condomless sex. Results: Community, household, and individual measures of schooling were all associated with incident HSV-2 infection through mediated pathways that increased the likelihood of having sex. Low school attendance (<80% of school days) increased the likelihood of having sex through increased age-disparate partnerships and reduced future aspirations. Fewer community years of education increased the likelihood of having sex through increased age-disparate partnerships. Parental education level was indirectly associated with HSV-2 overall, although we could not identify the individual pathways that were responsible for this association. Conclusions: Community and individual schooling interventions may reduce the risk of HSV-2 infection by influencing the likelihood of having sex, partner age, and future aspirations. Keywords: Adolescent girls and young women; Education; HSV-2; Mediation; Multilevel; Sexual behaviors.