Cape Town Science Centre

Despite being rich in natural resources and scientific talent, Africa continues to bear a staggering infectious disease burden. Historically, health innovation on the continent has relied on international funding and has been constrained by limited infrastructure and the emigration of skilled professionals. Data science tools offer a promising alternative, typically requiring fewer costly resources than traditional empirical research, with the potential to empower African scientists to generate tangible and impactful health solutions for the continent. Rapid progress in data science is expected to transform infectious disease research; thus, it is encouraging that numerous African initiatives are already applying data science tools to tackling pressing unmet medical needs, particularly in drug discovery. These efforts include identifying novel therapeutic targets, predicting drug-like molecules and their synthesis, enhancing clinical trial success rates and preparing for future disease threats. This review examines the current landscape of data science in infectious disease drug discovery across Africa.

Adolescents living with HIV (ALHIV) are a priority population for achieving global HIV prevention and treatment targets but experience poorer outcomes than adults. Long-term follow-up is essential to understand their transition into adulthood. By linking self-reported survey data with routine laboratory records, we established a social science clinical cohort of ALHIV South Africa's Eastern Cape to explore factors shaping their long-term health and well-being. Eligible participants were adolescents who were part of a three-wave quantitative cohort of ALHIV and not living with HIV (2014-2018) and had consented (adolescent and caregiver) to having their self-reported interviews linked with routine health records (n=1563). Adolescents were recruited into the existing three-wave cohort through clinic and community-based methods (97% enrolment, >90% retention over three waves). Between 2019 and 2022, we abstracted laboratory test records from the National Health Laboratory Services database for all eligible participants, with matching based on demographic variables. Individuals with at least one HIV-related record form our 'lifelong social science cohort', a total of 956 ALHIV (852 of 1107 ALHIV and 104 of 456 HIV-uninfected). A total of 32 886 laboratory test records from 2004 to 2023 were matched through three rounds of data extraction, using iteratively refined record-linking searches. Most records were viral load (8864) and CD4 count (6801) results, with a median of 10 (IQR: 7-14) and 8 (IQR: 5-11) tests per matched adolescent, respectively. Overall, 956 of 1563 adolescents (61%) were successfully linked to laboratory data, including 852 of 1107 (77%) ALHIV. Analysis of the matched cohort survey-laboratory data provided several insights. Self-reported antiretroviral therapy adherence was strongly associated with viral suppression, even after adjusting for covariates. The strongest predictors of suppression were not reporting missed doses in the past 3 days, past week and not missing clinic appointments in the past year. Among adolescent girls and young women living with HIV, access to safe and affordable facilities, and kind and respectful staff were associated with a higher likelihood of multiple improved HIV-related outcomes, including viral suppression. Exposure to sexual and intimate partner violence predicted worse viral load outcomes among adolescents. This integrated prospective cohort provides an opportunity to characterise long-term HIV treatment outcomes among ALHIV in Africa. We will investigate how individual, familial, community and healthcare experiences in childhood, and adolescence shape these outcomes. Since the COVID-19 pandemic happened during the period of matched data, we will also investigate the potential effect of the COVID-19 pandemic on adolescent HIV treatment outcomes, with potential subgroup analyses for individuals with available COVID-19-related results.

Platinum group minerals (PGMs) are critical for the green energy transition, playing key roles as catalysts in fuel cells and catalytic converters. Their limited global supply as well as geopolitical challenges further elevate their strategic importance. Southern Africa continues to dominate the global supply of PGMs, but mining operations face increasing challenges as ore bodies become deeper and more mineralogically complex. These complexities include a higher prevalence of slower-floating PGM species, such as platinum arsenides, and problematic gangue minerals like talc and serpentine. This paper addresses these challenges by ranking the major PGM species in order of floatability and provides critical insights for optimizing flotation processes. Additionally, the importance of effective gangue management in mineralogically complex ores is illustrated through the decoupling of gangue recovered by entrainment or true flotation and, further, by mineral species. The findings offer broader implications for addressing mineralogical barriers to flotation, providing solutions applicable not only to PGM ores but also to other complex ore systems. These advancements aim to enhance the efficiency and sustainability of mineral processing in the face of evolving global resource challenges.

Fetal alcohol spectrum disorders (FASD) include a range of neurocognitive and behavioral impairments resulting from prenatal alcohol exposure (PAE). Among the PAE-related cognitive deficits, number processing is particularly affected. This study examines alterations in number processing networks and whether changes in functional connectivity mediate the adverse effects of PAE on arithmetic performance. Magnetic resonance imaging (MRI) was acquired in 57 children (mean (SD) age = 11.3 (+0.9) yr), 38 with FASD (19 fetal alcohol syndrome (FAS) or partial FAS (PFAS), 19 heavily exposed (HE)) and 19 controls. Whole-brain correlation analyses were performed from five seeds located in regions involved in number processing. Children with FAS/PFAS showed dose-dependent reductions in resting state functional connectivity between the seed in the right (R) posterior superior parietal lobule and a cluster in the left (L) inferior frontal gyrus, and between a seed in the R horizontal intraparietal sulcus and clusters in the R precentral gyrus and L cerebellar lobule VI. HE children showed lower resting state functional connectivity in a subset of these regions. Lower functional connectivity in the two fronto-parietal connections partially mediated the adverse effects of PAE on arithmetic performance. This study demonstrates PAE-related functional connectivity impairments in functional networks involved in number processing. The weaker connectivity between the R posterior superior parietal lobule and the L inferior frontal gyrus suggests that impaired verbal processing and visuospatial working memory may play a role in number processing deficits, while weaker connectivity between the R intraparietal sulcus and the R precentral gyrus points to poorer finger-based numerical representation, which has been linked to arithmetic computational skills.

The Ecological Reserve (environmental flows) as defined under the South African National Water Act 36 of 1998 was designed to equitably manage water for river sustainability while maximizing economic and social welfare. We investigated the climate change impacts on the Ecological Reserve targets for a seasonal river in an agricultural catchment in the Western Cape region using the Habitat Flow Stressor Response method (which integrates hydrology, hydraulics, water quality, and ecological data) under projected climate scenarios (2041–2070). Current Ecological Reserve model outcomes for 3 sites on the Doring River were compared with the future hydrology using Global Circulation Models associated with four Representative Concentration Pathways (RCP 2.6–8.5). Climate predictions reflected reduced future flows, but the uncertainty band of predicted future flows overlapped with present day flows. Flood flashiness following heavy rains and the increased length of dry periods that are predicted would both contribute to increased erosion and geomorphological degradation, and further compromise biodiversity including the endangered fish populations and threaten both freshwater and estuarine ecosystems downstream. Salinity variation is predicted to increase in future leading to increased seasonal salinity stress and reduced use of abstracted water. We interrogate various options for mitigating the impacts including augmenting dry season flows, developing on-farm, catchment-scale, and strategic water resources management, and removing alien vegetation.

Prenatal alcohol exposure (PAE) is associated with smaller regional and global brain volumes. In rats, gestational choline supplementation mitigates adverse developmental effects of ethanol exposure. Our recent randomized, double-blind, placebo-controlled maternal choline supplementation trial showed improved somatic and functional outcomes in infants at 6.5 and 12months postpartum. Here, we examined whether maternal choline supplementation protected the newborn brain from PAE-related volume reductions and, if so, whether these volume changes were associated with improved infant recognition memory. Fifty-two infants born to heavy-drinking women who had participated in a choline supplementation trial during pregnancy underwent structural magnetic resonance imaging with a multi-echo FLASH protocol on a 3T Siemens Allegra MRI (median age=2.8weeks postpartum). Subcortical regions were manually segmented. Recognition memory was assessed at 12months on the Fagan Test of Infant Intelligence (FTII). We examined the effects of choline on regional brain volumes, whether choline-related volume increases were associated with higher FTII scores, and the degree to which the regional volume increases mediated the effects of choline on the FTII. Usable MRI data were acquired in 50 infants (choline: n=27; placebo: n=23). Normalized volumes were larger in six of 12 regions in the choline than placebo arm (t≥2.05, p≤0.05) and were correlated with the degree of maternal choline adherence (β≥0.28, p≤0.04). Larger right putamen and corpus callosum were related to higher FTII scores (r=0.36, p=0.02) with a trend toward partial mediation of the choline effect on recognition memory. High-dose choline supplementation during pregnancy mitigated PAE-related regional volume reductions, with larger volumes associated with improved 12-month recognition memory. These results provide the first evidence that choline may be neuroprotective against PAE-related brain structural deficits in humans.