174 Works

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: Evolutionary rates of mid-Permian tetrapods from South Africa and the role of temporal resolution in turnover reconstruction

Michael O. Day, Roger B.J. Benson, Christian F. Kammerer & Bruce S. Rubidge
The Main Karoo Basin of South Africa contains a near-continuous sequence of continental deposition spanning 45 million years from the middle Permian to the Early Jurassic. The terrestrial vertebrates of this sequence provide a high-resolution stratigraphic record of regional origination and extinction, especially for the middle–late Permian. Until now, data have only been surveyed at coarse stratigraphic resolution using methods that are biased by non-uniform sampling rates, limiting our understanding of the dynamics of diversification...

Data from: Foraging mode, relative prey size and diet breadth: a phylogenetically-explicit analysis of snake feeding ecology

Xavier Glaudas, Kelsey L. Glennon, Marcio Martins, Luca Luiselli, Simon Fearn, Dane F. Trembath, Dusan Jelic & Graham J. Alexander
1. Foraging modes (ambush vs. active foraging) are often correlated with a suite of morphological, physiological, behavioral and ecological traits known as the adaptive syndrome or syndrome hypothesis. In snakes, an ecological correlate often reported in the literature is that ambush-hunting snakes have a higher relative meal size compared to actively foraging snakes which feed on smaller prey items. This “large meal vs. small meal” feeding hypothesis between ambush and active foragers has become a...

Factors associated with COVID-19 infections and mortality in Africa: A cross-sectional study using publicly available data

Kennedy Otwombe
Introduction The current COVID-19 pandemic is a global threat. This elicits questions on the level of preparedness and capacity of health systems to respond to emergencies. Relative to other parts of the world, Africa has poorly developed health systems with limited capacity to respond to health crises. Africa is particularly disadvantaged. Methods This cross-sectional study uses publicly available core health data for 53 African countries, to determine risk factors for cumulative COVID-19 deaths and cases...

Association of chronic inflammation and accelerated atherosclerosis among an indigenous black population with chronic kidney disease

Muzamil Olamide Hassan, Therese Dix-Peek, Raquel Duarte, Caroline Dickens, Sagren Naidoo, Ahmed Vachiat, Sacha Grinter, Pravin Manga & Saraladevi Naicker
Introduction: Inflammation plays a major role in the development of atherosclerosis and cardiovascular morbidity and mortality in chronic kidney disease (CKD) patients. Toll-like receptor-4 (TLR4) is a major receptor for lipopolysaccharides (endotoxin) and other ligands involved in the pathogenesis of inflammation. We determined whether endotoxin levels and the presence of TLR4 polymorphisms are associated with markers of inflammation and atherosclerosis among South African CKD patients. Materials and methods: Endotoxin, lipopolysaccharide binding protein (LBP), serum CD14...

Data from: Glucocorticoid levels predict subsequent social tactic in females of a facultatively social mammal

Davina Hill, Neville Pillay & Carsten Schradin
Facultatively social species, in which individuals can switch between group- and solitary-living tactics, offer an opportunity to shed light on proximate mechanisms underlying alternative life histories. Promising hormonal mediators of social tactic include glucocorticoids, which control energy allocation and are negatively related to body condition, and testosterone which regulates numerous social behaviours. Here, we investigated hormonal profiles associated with social tactic in eight generations of free-living female striped mice (Rhabdomys pumilio). Females are group living...

Data from: Initiating Antiretroviral Therapy for HIV at a Patient’s First Clinic Visit: The RapIT Randomized Controlled Trial

Mhairi Maskew, Sydney Rose, Matthew Fox, Cynthia Nyoni, Constance Mongwenyana, Given Malete, Ian Sanne, Dorah Bokaba, Celeste Sauls, Julia Rohr & Lawrence Long
Background: High rates of patient attrition from care between HIV testing and antiretroviral therapy (ART) initiation have been documented in sub-Saharan Africa, contributing to persistently low CD4 cell counts at treatment initiation. One reason for this is that starting ART in many countries is a lengthy and burdensome process, imposing long waits and multiple clinic visits on patients. We estimated the effect on uptake of ART and viral suppression of an accelerated initiation algorithm that...

Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

Marc Bennedbæk, Anna Zhukova, Man-Hung Eric Tang, Jaclyn Bennet, Paula Munderi, Kiat Ruxrungtham, Magnus Gisslen, Michael Worobey, Jens D Lundgren & Rasmus L Marvig
Understanding of pandemics depends on characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, HIV-1 has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to inform on the origin and distribution of subtypes. We sequenced two 3.6 kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and...

Seismograms and snapshot files for dynamic models (crack and shear sources)

Lindsay Linzer, Mark Hildyard & Johan Wesseloo
This paper presents a numerical investigation on the influence of the mining environment on seismic sources with a focus of pillar failure mechanisms in tabular mining. We investigate the influence of the stope on seismic inversions for the scalar moment, corner frequency, source radius, stress drop and moment tensor through dynamic numerical modelling using elastodynamic modelling software, WAVE3D. The main objective is to determine whether the source parameters calculated from the recorded waveforms are due...

Hierarchy of fear: experimentally testing ungulate reactions to lion, African wild dog and cheetah

Liana Zanette, Noa Rigoudy, Michael Clinchy, Mike Peel, Sarah Huebner & Craig Packer
Experiments have begun demonstrating that the fear (antipredator responses) large carnivores inspire in ungulates can shape ecosystem structure and function. Most such experiments have focused on the impacts of either just one large carnivore, or all as a whole, rather than the different impacts different large carnivores may have in intact multi-predator-prey systems. Experimentally testing the relative fearfulness ungulates demonstrate toward different large carnivores is a necessary first step in addressing these likely differing impacts....

Additional file 1 of Postnatal clubs for integrated postnatal care in Johannesburg, South Africa: a qualitative assessment of implementation

Ndinda Makina-Zimalirana, Jackie Dunlop, Anele Jiyane, Sophia Marie Bartels, Helen Struthers, James McIntyre & Kate Rees
Additional file 1. Supplementary Material for: Postnatal clubs for integrated postnatal care in Johannesburg, South Africa: a qualitative assessment of implementation. Interview Guide.

Additional file 5 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 5: Figure S4. Two stage individual participant data meta-analysis on the association between malaria in pregnancy (MIP) and small for gestational age (SGA) using the STOPPAM (SGASTOPPAM) vs. the Intergrowth-21 reference (SGAIG21). uOR: unadjusted odds ratio in panels A and B, aOR: adjusted odds ratio in panels C and D controlling for body mass index, gravidity, gestational age at enrolment, HIV, and hemoglobin level at enrolment. In addition, adjusted for gestational age at...

Additional file 6 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 6: Figure S5. Funnel plots for meta-analysis. The closed dots indicate the observed studies, panel A indicate the trim and fill funnel plot for STOPPAM (P = 0.10) and panel B for Intergrowth-21 reference (P = 0.35). The contour enhanced funnel plot for STOPPAM (panel C) and Intergrowth-21 (panel D) show the distribution of studies in both the small and large p-values contours, hence no publication bias.

The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Abstract Background The prevalence of small for gestational age (SGA) may vary depending on the chosen weight-for-gestational-age reference chart. An individual participant data meta-analysis was conducted to assess the implications of using a local reference (STOPPAM) instead of a universal reference (Intergrowth-21) on the association between malaria in pregnancy and SGA. Methods Individual participant data of 6,236 newborns were pooled from seven conveniently identified studies conducted in Tanzania and Malawi from 2003–2018 with data on...

Additional file 1 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 1: Table S1. Comparison of the Intergrowth-21 and STOPPAM standard charts. Table S2. Quality of studies using Cochrane’s Risk of Bias 2 tool (ROB-2) for randomized trials. Table S3. Risk of Bias assessment by Newcastle scale for cohort studies. Table S4. Prevalence of small for gestational age by gestational age and birthweight. Table S5. Prevalence of small for gestational age when applying the inclusion criteria for each reference chart. Table S6. Sensitivity analysis...

Additional file 3 of Factors associated with men’s health facility attendance as clients and caregivers in Malawi: a community-representative survey

Marguerite Thorp, Kelvin T. Balakasi, Misheck Mphande, Isabella Robson, Shaukat Khan, Christian Stillson, Naoko Doi, Brooke E. Nichols & Kathryn Dovel
Supplementary Material 3

Additional file 1 of Malaria attributable fractions with changing transmission intensity: Bayesian latent class vs logistic models

Kennedy Mwai, Irene Nkumama, Amos Thairu, James Mburu, Dennis Odera, Rinter Kimathi, Lydia Nyamako, James Tuju, Samson Kinyanjui, Eustasius Musenge & Faith Osier
Additional file 1: Table S1. Parasites/µL cut off using Logistic regression. Fig S1. Distribution of predicted probabilities. Fig S2. Comparison of probabilities for Bayesian and Logistic, Junju 2008. Table S2. Anova test for Figure 2B. Fig S3. Comparison of probability of febrile and non-febrile. Fig S4. Predicted probabilities over age groups. Fig S5. Sensitivity and specificity of the different years. Fig S6. Posterior estimates of AF.

Malaria attributable fractions with changing transmission intensity: Bayesian latent class vs logistic models

Kennedy Mwai, Irene Nkumama, Amos Thairu, James Mburu, Dennis Odera, Rinter Kimathi, Lydia Nyamako, James Tuju, Samson Kinyanjui, Eustasius Musenge & Faith Osier
Abstract Background Asymptomatic carriage of malaria parasites is common in high transmission intensity areas and confounds clinical case definitions for research studies. This is important for investigations that aim to identify immune correlates of protection from clinical malaria. The proportion of fevers attributable to malaria parasites is widely used to define different thresholds of parasite density associated with febrile episodes. The varying intensity of malaria transmission was investigated to check whether it had a significant...

Additional file 2 of Communication Skills (CS) training of physicians in China and its role in actual challenges of patient-physician relationship: a cross-sectional survey

Junfeng Du, Gwendolyn Mayer, Elisabetta Posenato, Svenja Hummel, Ali Zafar, Till Bärnighausen & Jobst-Hendrik Schultz
Additional file 2: Appendix II. Results of the Communication Skills Attitudes Scale: Items, direction of scale, means, standard deviations, and 95% confidence intervals (N = 772).

An STI test and treat programme for adolescents in Cape Town (STAX Study) - Annoymised dataset (Youth Centre)

Carey Pike, Linda- Gail Bekker, Rebecca Marcus, Philip Smith, Katherine Gill, Gesine Meyer-Rath, Naomi Lince-Deroche & Jackie Roseleur
Dataset from the STAX Study, which investigated the acceptability, feasibility and cost of point of care testing for sexually transmitted infections among South African adolescents from a youth centre health facility and an adolescent mobile health service.
This dataset looks at enrollment data, STI testing data, and acceptability feedback from participants recruited from the Desmond Tutu Health Foundation Youth Centre.

Melt inclusions in zircon are powerful petrogenetic indicators and improve zircon thermometry

Dominik Gudelius , Armin Zeh , Renat R. Almeev , Allan H. Wilson , Lennart A. Fischer & Axel K. Schmitt
Melt inclusions in zircon (MIZ) directly reflect the physicochemical state of the magma during zircon growth. However, their potential as geothermometers and petrogenetic indicators is still poorly explored. Therefore, we investigated MIZ from well-characterized mafic and felsic rocks of the Bushveld Complex (South Africa) and acquired a novel dataset of major, trace and volatile element contents. Re-homogenized MIZ of all rock types display rhyolitic compositions (65-78 wt% SiO2) and similar H2O contents (1.6-4.0 wt%). Liquidus...

Participatory development of practical, affordable, insecticide-treated mosquito proofing for a range of housing designs in rural southern Tanzania

Rogath Msoffe, Matilda Hewitt, John P. Masalu, Marcelina Finda, Deogratius R. Kavishe, Fredros O. Okumu, Emmanuel A. Mpolya, Emmanuel W. Kaindoa & Gerry F. Killeen
Abstract Background Insecticidal mosquito-proof netting screens could combine the best features of insecticide-treated nets (ITNs) and indoor residual spraying (IRS), the two most important front line vector control interventions in Africa today, and also overcome the most important limitations of these methods. This study engaged members of a rural Tanzanian community in developing and evaluating simple, affordable and scalable procedures for installing readily available screening materials on eave gaps and windows of their own houses,...

Lp(a), oxidized phospholipids and oxidation-specific epitopes are increased in subjects with keloid formation

Sundeep Ruder, Brett Mansfield, Andrew Ronald Immelman, Nissi Varki, Phuong Miu, Frederick Raal & Sotirios Tsimikas
Abstract Background Keloid formation following trauma or surgery is common among darkly pigmented individuals. Since lipoprotein(a) [Lp(a)] has been postulated to have a putative role in wound healing, and also mediates atherosclerotic cardiovascular disease, it was assessed whether Lp(a), its associated oxidized phospholipids and other oxidation-specific biomarkers were associated with keloid formation. Methods This case-control study included darkly pigmented individuals of African ancestry, 100 with keloid scarring and 100 non-keloid controls. The lipid panel, hsCRP,...

Twin epidemics: the effects of HIV and systolic blood pressure on mortality risk in rural South Africa 2010-2019

Nicole Angotti, Samuel Clark, F. Xavier Gómez-Olivé, Brian Houle, Chodziwadziwa Kabudula Whiteson, Jane Menken, Sanyu Mojola , Enid Schatz , Andrea Tilstra , Jill Williams, Vusi Dlamini & Erin Ice

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