75 Works

Data from: A quantitative method for inferring locomotory shifts in amniotes during ontogeny, its application to dinosaurs, and its bearing on the evolution of posture

Kimberley E. J. Chapelle, Roger B. J. Benson, Josef Stiegler, Alejandro Otero, Qi Zhao & Jonah N. Choiniere
Evolutionary transitions between quadrupedal and bipedal postures are pivotal to the diversification of amniotes on land, including in our own lineage (Hominini). Heterochrony is suggested as a macroevolutionary mechanism for postural transitions, but understanding postural evolution in deep time is hindered by a lack of methods for inferring posture in extinct species. Dinosaurs are an excellent natural laboratory for understanding postural transitions, because their lineage contains at least four instances of quadrupedality evolving from bipedality,...

Data from: Programmed death in a unicellular organism has species-specific fitness effects

Pierre M. Durand, Rajdeep Choudhury, Armin Rashidi & Richard E. Michod
Programmed cell death (PCD) is an ancient phenomenon and its origin and maintenance in unicellular life is unclear. We report that programmed death provides differential fitness effects that are species specific in the model organism Chlamydomonas reinhardtii. Remarkably, PCD in this organism not only benefits others of the same species, but also has an inhibitory effect on the growth of other species. These data reveal that the fitness effects of PCD can depend upon genetic...

A reassessment of the enigmatic diapsid Paliguana whitei and the early history of Lepidosauromorpha

David Paul Ford, Susan Evans, Jonah Choiniere, Vincent Fernandez & Roger Benson
Lepidosaurs include lizards, snakes, amphisbaenians and the tuatara, comprising a highly speciose evolutionary radiation with widely varying anatomical traits. Their stem-lineage originated by the late middle Permian 259 million years ago, but its early fossil record is poorly documented, obscuring the origins of key anatomical and functional traits of the group. Paliguana whitei, from the Early Triassic of South Africa, is an enigmatic fossil species with potential to provide information on this. However, its anatomy...

Data from: Functional MRI in the Nile crocodile: a new avenue for evolutionary neurobiology

Mehdi Behroozi, Brendon K. Billings, Xavier Helluy, Paul R. Manger, Onur Güntürkün & Felix Ströckens
Crocodilians are important for understanding the evolutionary history of amniote neural systems as they are the nearest extant relatives of modern birds and share a stem amniote ancestor with mammals. Although the crocodilian brain has been investigated anatomically, functional studies are rare. Here we employed fMRI, never tested in poikilotherms, to investigate crocodilian telencephalic sensory processing. Juvenile Crocodylus niloticus were placed in a 7T MRI scanner to record BOLD signal changes during presentation of visual...

Data from: Alternative reproductive tactics in female striped mice: heavier females are more likely to breed solitary than communally

Davina L. Hill, Neville Pillay & Carsten Schradin
1. Alternative reproductive tactics (ARTs) are discrete reproductive phenotypes governed by decision rules called strategies. ARTs are fixed for life in species with alternative strategies, while tactic expression is plastic in species with a single strategy. ARTs have been investigated in males of many species, but few studies have tested whether the same theoretical framework applies in females. 2. Female striped mice (Rhabdomys pumilio) employ three ARTs: communal breeders give birth in a nest shared...

Data from: Lifestyle and socio-economic inequalities in diabetes prevalence in South Africa: a decomposition analysis

Chipo Mutyambizi, Frederik Booysen, Andrew Stokes, Milena Pavlova & Wim Groot
Background: Inequalities in diabetes are widespread and are exacerbated by differences in lifestyle. Many studies that have estimated inequalities in diabetes make use of self-reported diabetes which is often biased by differences in access to health care and diabetes awareness. This study adds to this literature by making use of a more objective standardised measure of diabetes in South Africa. The study estimates socio-economic inequalities in undiagnosed diabetes, diagnosed diabetes (self-reported), as well as total...

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: Pneumococcal colonisation density: a new marker for disease severity in HIV-infected adults with pneumonia

Werner C. Albrich, Shabir A. Madhi, Peter V. Adrian, Nadia Van Niekerk, Jean-Noel Telles, Naseem Ebrahim, Melina Messaoudi, Glaucia Paranhos-Baccalà, Sven Giersdorf, Guy Vernet, Beat Mueller & Keith P. Klugman
Objective: A high genomic load of Pneumococcus from blood or cerebrospinal fluid has been associated with increased mortality. We aimed to analyse whether nasopharyngeal colonisation density in HIV-infected patients with community-acquired pneumonia (CAP) is associated with markers of disease severity or poor outcome. Methods: Quantitative lytA real-time PCR was performed on nasopharyngeal swabs in HIV-infected South African adults hospitalised for acute CAP at Chris Hani Baragwanath Hospital, Soweto, South Africa. Pneumonia aetiology was considered pneumococcal...

Data from: Seasonal patterns of hormones, macroparasites, and microparasites in wild African ungulates: the interplay between stress, reproduction, and disease

Carrie A. Cizauskas, Wendy C. Turner, Neville I. Pitts, Wayne M. Getz & Neville Pitts
Sex hormones, reproductive status, and pathogen load all affect stress. Together with stress, these factors can modulate the immune system and affect disease incidence. Thus, it is important to concurrently measure these factors, along with their seasonal fluctuations, to better understand their complex interactions. Using steroid hormone metabolites from fecal samples, we examined seasonal correlations among zebra and springbok stress, reproduction, gastrointestinal (GI) parasite infections, and anthrax infection signatures in zebra and springbok in Etosha...

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: 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: 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: 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...

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...

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...

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...

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...

Quality of Life Survey I 2009

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: Interactive effects of exogenous and endogenous factors on demographic rates of an African rodent

Chloé R. Nater, Cindy I. Canale, Koen J. Van Benthem, Chi-Hang Yuen, Ivana Schoepf, Neville Pillay, Arpat Ozgul & Carsten Schradin
Exogenous and endogenous environmental factors can have simultaneous additive as well as interacting effects on life-history traits. Ignoring such interactions can lead to a biased understanding of variability in demographic rates and consequently population dynamics. These interactions have been the focus of decades-long debates on the mechanisms underlying small mammal population fluctuations. They have often been studied indirectly through seasonal effects, but studies considering them directly and more mechanistically are rare. We investigated the joint...

Data from: Fire frequency drives habitat selection by a diverse herbivore guild impacting top–down control of plant communities in an African savanna

Deron E. Burkepile, Dave I. Thompson, Richard W. S. Fynn, Sally E. Koerner, Stephanie Eby, Navashni Govender, Nicole Hagenah, Nathan P. Lemoine, Katherine J. Matchett, Kevin R. Wilcox, Scott L. Collins, Kevin P. Kirkman, Alan K. Knapp & Melinda D. Smith
In areas with diverse herbivore communities such as African savannas, the frequency of disturbance by fire may alter the top–down role of different herbivore species on plant community dynamics. In a seven year experiment in the Kruger National Park, South Africa, we examined the habitat use of nine common herbivore species across annually burned, triennially burned and unburned areas. We also used two types of exclosures (plus open access controls) to examine the impacts of...

Data from: Fuelwood sustainability revisited: integrating size structure and resprouting into a spatially realistic fuelshed model

Wayne C. Twine & Ricardo M. Holdo
Much concern has been expressed about the sustainability of fuelwood harvesting in Africa. Most models predict that demand will outstrip supply within a few decades, resulting in severe deforestation. However, despite substantial impacts of harvesting on woody vegetation structure, the ‘fuelwood crisis’ predicted since the 1970s has not materialized. We propose that this is at least partially because regeneration through coppicing has been poorly accounted for in most models. We developed a local fuelwood model...

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