12 Works

Data from: Factors associated with pulmonary impairment in HIV-infected South African adults

Akshay N. Gupte, Michelle L. Wong, Reginah Masandiwa, Grace L. Barnes, Jonathan Golub, Richard E. Chaisson, Christopher J. Hoffmann, Neil A. Martinson & Reginah Msandiwa
Background: HIV-infected individuals have increased risk of developing obstructive lung disease (OLD). Studies from developed countries report high viral load, low CD4 counts, and anti-retroviral therapy (ART) to be associated with OLD; but these findings may not be generalizable to populations in resource-limited settings. Methods: We conducted a prospective cohort study of lung function in 730 HIV-infected black South African adults. Pre-bronchodilator spirometry was performed at enrollment and repeated annually for three years. Logistic regression...

Data from: Empirical and theoretical investigation into the potential impacts of insecticide resistance on the effectiveness of insecticide-treated bed nets

Katey D. Glunt, Maureen Coetzee, Silvie Huijben, A. Alphonsine Koffi, Penelope A. Lynch, Raphael N'Guessan, Welbeck A. Oumbouke, Eleanore D. Sternberg & Matthew B. Thomas
In spite of widespread insecticide resistance in vector mosquitoes throughout Africa, there is limited evidence that long lasting insecticidal bed nets (LLINs) are failing to protect against malaria. Here, we showed that LLIN contact in the course of host-seeking resulted in higher mortality of resistant Anopheles spp. mosquitoes than predicted from standard laboratory exposures with the same net. We also found that sub-lethal contact with an LLIN caused a reduction in blood feeding and subsequent...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns

Zizipho Z.A. Mbulawa, Cari Van Schalkwyk, Nai-Chung Hu, Tracy L. Meiring, Shaun Barnabas, Smritee Dabee, Heather Jaspan, Jean-MAri Kriek, Shameem Z. Jaumdally, Etienne Muller, Linda-Gail Bekker, David A. Lewis, Janan Dietrich, Glenda Gray, Jo-Ann S. Passmore, Anna-Lise Williamson & Zizipho Z. A. Mbulawa
Objectives: To investigate prevalence of cervical human papillomavirus (HPV) genotypes to inform HPV vaccination strategy in South Africa and to study factors associated with HPV prevalence. Methods: Sexually active, HIV-negative women, aged 16-22 years recruited from Soweto (n=143) and Cape Town (n=148) were tested for cervical HPV and other genital infections. Results: Overall HPV prevalence was 66.7% (194/291) in young women. Cape Town women were more likely to have multiple HPV infections than the Soweto...

Data from: Continent-level drivers of African pyrodiversity

Gareth P. Hempson, Catherine L. Parr, Sally Archibald, T. Michael Anderson, Colin J. Courtney Mustaphi, Andrew P. Dobson, Jason E. Donaldson, Thomas A. Morrison, James Probert & Colin M. Beale
Pyrodiversity, which describes fire variability over space and time, is believed to increase habitat heterogeneity and thereby promote biodiversity. However, to date there is no standardised metric for quantifying pyrodiversity, and so broad geographic patterns and drivers of pyrodiversity remain unexplored. We present the first generalizable method to quantify pyrodiversity, and use it to address the fundamental questions of what drives pyrodiversity, which fire attributes constrain pyrodiversity under different conditions, and whether pyrodiversity is spatial...

Data from: Drought-induced starvation of aardvarks in the Kalahari: an indirect effect of climate change

Benjamin Rey, Andrea Fuller, Duncan Mitchell, Leith C.R. Meyer, Robyn S. Hetem & Leith C. R. Meyer
Aardvarks (Orycteropus afer) are elusive burrowing mammals, predominantly nocturnal and distributed widely throughout Africa except for arid deserts. Their survival may be threatened by climate change via direct and indirect effects of increasing heat and aridity. To measure their current physiological plasticity, we implanted biologgers into six adult aardvarks resident in the semi-arid Kalahari. Following a particularly dry and hot summer, five of the study aardvarks and 11 other aardvarks at the study site died....

Data from: Delays and loss to follow up before treatment of drug-resistant TB following implementation of Xpert MTB/RIF in South Africa: a retrospective cohort study

Helen Cox, Lindy Dickson-Hall, Norbert Ndjeka, Anja Van't Hoog, Alison Grant, Frank Cobelens, Wendy Stevens, Mark Nicol & Anja Van’t Hoog
Background: South Africa has a large burden of rifampicin-resistant tuberculosis (RR-TB), with 18,734 patients diagnosed in 2014. The number of diagnosed patients has increased substantially with the introduction of the Xpert MTB/RIF test, used for TB diagnosis for all patients with presumptive TB. Routine aggregate data suggest a large treatment gap (pre-treatment loss to follow up) between the numbers of laboratory confirmed RR-TB patients and those reported to have started second-line treatment. We aimed to...

Data from: The earliest bird-line archosaurs and the assembly of the dinosaur body plan

Sterling J. Nesbitt, Richard J. Butler, Martin D. Ezcurra, Paul M. Barrett, Michelle R. Stocker, Kenneth D. Angielczyk, Roger M. H. Smith, Christian A. Sidor, Grzegorz Niedźwiedzki, Andrey G. Sennikov & Alan J. Charig
The relationship between dinosaurs and other reptiles is well established, but the sequence of acquisition of dinosaurian features has been obscured by the scarcity of fossils with transitional morphologies. The closest extinct relatives of dinosaurs either have highly derived morphologies or are known from poorly preserved or incomplete material. Here we describe one of the stratigraphically lowest and phylogenetically earliest members of the avian stem lineage (Avemetatarsalia), Teleocrater rhadinus gen. et sp. nov., from the...

Data from: Prevalence and unmet need for diabetes care across the care continuum in a national sample of South African adults: evidence from the SANHANES-1, 2011-2012

Andrew Stokes, Kaitlyn M. Berry, Zandile Mchiza, Whadi-Ah Parker, Demetre Labadarios, Lumbwe Chola, Charles Hongoro, Khangelani Zuma, Alana T. Brennan, Peter C. Rockers & Sydney Rosen
South Africa faces an epidemic of chronic non-communicable diseases (NCDs), yet national surveillance is limited due to the lack of recent data. We used data from the first comprehensive national survey on NCDs—the South African National Health and Nutrition Examination Survey (SANHANES-1 (2011–2012))—to evaluate the prevalence of and health system response to diabetes through a diabetes care cascade. We defined diabetes as a Hemoglobin A1c equal to or above 6.5% or currently on treatment for...

Data from: Extreme precipitation variability, forage quality and large herbivore diet selection in arid environments

, Jay V. Gedir, Jason P. Marshal, Paul R. Krausman, Jamison D. Allen, Glenn C. Duff, Brian D. Jansen, John R. Morgart & James W. Cain
Nutritional ecology forms the interface between environmental variability and large herbivore behaviour, life history characteristics, and population dynamics. Forage conditions in arid and semi-arid regions are driven by unpredictable spatial and temporal patterns in rainfall. Diet selection by herbivores should be directed towards overcoming the most pressing nutritional limitation (i.e. energy, protein [nitrogen, N], moisture) within the constraints imposed by temporal and spatial variability in forage conditions. We investigated the influence of precipitation-induced shifts in...

Data from: Habitat attributes similarities reduce impacts of land-use conversion on seed removal

Ananza M. Rabello, Catherine L. Parr, Antônio C.M. Queiroz, Danielle L. Braga, Graziele S. Santiago & Carla R. Ribas
Changes in land use strongly influence habitat attributes (e.g., herbaceous ground cover and tree richness) and can consequently affect ecological functions. Most studies have focused on the response of these ecological functions to land-use changes within only a single vegetation type. These studies have often focused solely on agricultural conversion of forests, making it nearly impossible to draw general conclusions across other vegetation types or with other land use changes (e.g., afforestation). We examined the...

Data from: The Victoria West: earliest prepared core technology in the Acheulean at Canteen Kopje and implications for the cognitive evolution of early hominids

Hao Li, Kathleen Kuman, Matt G. Lotter, George M. Leader & Ryan J. Gibbon
Prepared core technology illustrates in-depth planning and the presence of a mental template during the core reduction process. This technology is, therefore, a significant indicator in studying the evolution of abstract thought and the cognitive abilities of hominids. Here, we report on Victoria West cores excavated from the Canteen Kopje site in central South Africa, with a preliminary age estimate of approximately 1 Ma (million years ago) for these cores. Technological analysis shows that the...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of the Witwatersrand
  • University of Pretoria
  • University of Cape Town
  • University of Washington
  • National Health Laboratory Service
  • University of KwaZulu-Natal
  • University of Liverpool
  • Institute of Vertebrate Paleontology and Paleoanthropology
  • Fred Hutchinson Cancer Research Center
  • London School of Hygiene & Tropical Medicine