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Item Data Series : Teacher Choices in Action(2022-02-28) Rusznyak, LeeThe data is in its raw state and is subject to ethics restrictions. The data will be made accessible to via an application to the Teacher Choices in Action Project data access committee ( see https://forms.gle/QYhmfpMdcJct9dRN8) . Data access is granted to researchers who are employed by participating institutions and the post-graduate students they supervise. Applications to use the dataset must be accompanied by a full research proposal that shows how the proposed study aligns with the Project aims and comply with the ethical protocols. and will be subject to peer review by a committee appointed by the Project Governance Steering Committee. A data sharing agreement needs to be completed, signed and lodged with the Research Office.Item Data Set : Prevalence, characterization and response to chronic kidney disease in an urban and rural setting in South Africa(2016-11-18) Naicker, Saraladevi; Fabian, June; Jaya A George; Harriet R Etheredge; Manuel van Deventer; Robert Kalyesubula; Alisha N Wade; Laurie A Tomlinson; Stephen TollmanGlobally, chronic kidney disease (CKD) is an emerging public health challenge but accurate data on its true prevalence are scarce, particularly in poorly resourced regions such as sub-Saharan Africa (SSA). Limited funding for population-based studies, poor laboratory infrastructure and the absence of a validated estimating equation for kidney function in Africans are contributing factors. Consequently, most available studies used to estimate population prevalence are hospital-based, with small samples of participants who are at high risk for kidney disease. While serum creatinine is most commonly used to estimate glomerular filtration, there is considerable potential bias in the measurement of creatinine that might lead to inaccurate estimates of kidney disease at individual and population level. To address this, the Laboratory Working Group of the National Kidney Disease Education Program published recommendations in 2006 to standardize the laboratory measurement of creatinine. The primary objective of this review was to appraise implementation of these recommendations in studies conducted in SSA after 2006. Secondary objectives were to assess bias relating to choice of estimating equations for assessing glomerular function in Africans and to evaluate use of recommended diagnostic criteria for CKD. This study was registered with Prospero (CRD42017068151), and using PubMed, African Journals Online and Web of Science, 5845 abstracts were reviewed and 252 full-text articles included for narrative analysis. Overall, two-thirds of studies did not report laboratory methods for creatinine measurement and just over 80% did not report whether their creatinine measurement was isotope dilution mass spectroscopy (IDMS) traceable. For those reporting a method, Jaffe was the most common (93%). The four-variable Modification of Diet in Renal Disease (4-v MDRD) equation was most frequently used (42%), followed by the CKD Epidemiology Collaboration (CKD-EPI) equation for creatinine (26%). For the 4-v MDRD equation and CKD-EPI equations, respectively, one-third to one half of studies clarified use of the coefficient for African-American (AA) ethnicity. When reporting CKD prevalence, <15% of studies fulfilled Kidney Disease: Improving Global Outcomes criteria and even fewer used a population-based sample. Six studies compared performance of estimating equations to measured glomerular filtration rate (GFR) demonstrating that coefficients for AA ethnicity used in the 4-v MDRD and the CKD-EPI equations overestimated GFR in Africans. To improve on reporting in future studies, we propose an 'easy to use' checklist that will standardize reporting of kidney function and improve the quality of studies in the region. This research contributes some understanding of the factors requiring attention to ensure accurate assessment of the burden of kidney disease in SSA. Many of these factors are difficult to address and extend beyond individual researchers to health systems and governmental policy, but understanding the burden of kidney disease is a critical first step to informing an integrated public health response that would provide appropriate screening, prevention and management of kidney disease in countries from SSA. This is particularly relevant as CKD is a common pathway in both infectious and non-communicable diseases, and multimorbidity is now commonplace, and even more so when those living with severe kidney disease have limited or no access to renal replacement therapy.Item Dataset : metadata extration tables of femicide reported in News Media(Faculty of Humanities, University of the Witwatersrand, Johannesburg,, 2019-03-15) Brodie, Nechama RachelSouth Africa has a femicide rate that is six times the world average. Over 2,500 women aged 14 years or older are murdered every year, the majority of these women killed by an intimate partner. Despite the prevalence of femicide, less than 20% of these murders are ever reported in South African news media. Studies on news-media coverage of femicide reveal a subjective and obscure process of media selection and exclusion, which contribute to an archive of crime reporting that is not reflective of actual crime rates and which actively distort the nature and frequency of certain types of crime. This influences public perceptions and fear of violent crime, including notions of who is a suspect and who is most at risk. This study uses mixed-method approaches to document and analyse the content and extent of commercial news media coverage of femicides that took place in South Africa during the 2012/2013 crime reporting year, through an original media database listing 408 femicide victims associated with 5,778 press articles. Victim and incident information is compared with epidemiological and statistical data, including mortuary-based studies and police crime statistics. Media data is explored through various media effects models, including a mixed methods framing analysis, and is also examined by title, and by language. These analyses reveal how media constructs and depicts particular notions of gender, violence, race, and crime in South Africa. contact Nechama.Brodie@wits.ac.zaItem Dataset for AJIC Issue 22 (2018) article entitled "Evolution of Africa’s Intellectual Property Treaty Ratification Landscape"(LINK Centre, University of the Witwatersrand (Wits), Johannesburg, 2018-12-07) De Beer, Jeremy; Baarbé, Jeremiah; Ncube,Caroline; Open African Innovation Research (Open AIR) networkThis open access dataset is described and analysed in the following article: De Beer, J., Baarbé, J., & Ncube, C. (2018). Evolution of Africa’s intellectual property treaty ratification landscape. The African Journal of Information and Communication (AJIC), 22, 53-82. https://doi.org/10.23962/10539/26173 . The data is a subset of the Open AIR network’s research project data holding via a working paper entitled The Intellectual Property Treaty Landscape in Africa, 1885 to 2015 by Jeremy de Beer, Jeremiah Baarbé, Caroline Ncube, working paper 4, published online 5 May 2017, http://www.openair.org.za/publications/the-intellectual-property-treaty-landscape-in-africa-1885-to-2015/ . Open Air is a network of African researchers in the University of Ottawa in Canada, the University of Cape Town in South Africa, Strathmore University in Kenya, the Nigerian Institute for Advanced Legal Studies, and the American University in Cairo, Egypt. Its purpose is to answer two major research questions in order to ensure that African knowledge and innovation is not lost in the knowledge economy. The major research questions are: 1 How can open collaborative innovation help businesses scale up and seize the new opportunities of a global knowledge economy? And 2. Which knowledge governance policies will best ensure that the social and economic benefits of innovation are shared inclusively? (Openair Network , 10 Dec 11:12 am http://www.openair.org.za/about-us/ ) Under this overarching framework: the specific research question is whether it is correct that local Intellectual policy making was “constrained to some extent by the powerful global IP governance schemata.”( De Beer, J., Baarbé, J., & Ncube, C. 2018) To answer this question a historical systematic review of IP treaties along with the extents and dates of ratification via electronic scraping. Specifically, researchers wished to explore whether the tension that they saw between countries who’s “International commitments harmonized in intellectual property treaties exist in tension with local needs for flexibility”. (De Beer et al., 2018) could be supported quantitatively. This project created simple quantitative data out of qualitative lists of policies along with the presence or absence of ratification by African countries. The source of the data is the UN Convention on World Intellectual Property Organization( WIPO) database which has tables listing parties to the treaty, as well as the date of signature, filling of legal instrument used to ratify the treaty and entry into force. These terms are defined in the Glossary attached. Data collected by hand is from the Nagoya Protocol, the International Treaty on Plant Genetic Resources, and International Convention for the Protection of New Varieties of Plants (UPOV). UPOV data is defined in the explanatory note attached. The data contains Six major variables: Country name, Treaty name, Date of Treaty, ratification by country, IP Regime defined in legal terms i.e. copyright, Colonising state. The minor variables is the Official Language. The main independent variable was 36 treaties of which two were excluded as not yet being in force at the time of data collection. The major dependent variable was the date of ratification by country present in WIPO database. Total data was 485 ratifications by the 34 countries thus creating 16 490 geographical- time data points.Item Dataset From " Factors affecting students’ eLearning at one South African medical school: A cross-sectional survey(Open Science Framework osf.io/8n3ys, 2019-01-29) Ingratta, Argentina Maria; George, Ann; Lionel, Green-ThompsonItem Dataset from : Browsing is a strong filter for savanna tree seedlings in their first growing season(ARCHIBALD ECOLOGY LAB, 2021-06-15) Archibald, Sally; Twine, Wayne; Mthabini, Craddock; Stevens, Nicola1: Newly germinated seedlings are vulnerable to biomass removal but usually have at least six months to grow before they are exposed to dry-season fires, a major disturbance in savannas. In contrast, plants are exposed to browsers from the time they germinate, making browsing potentially a very powerful bottleneck for establishing seedlings. 2: Here we assess the resilience of seedlings of 10 savanna tree species to top-kill during the first 6 months of growth. Newly-germinated seeds from four dominant African genera from across the rainfall gradient were planted in a common garden experiment at the Wits Rural Facility and clipped at 1 cm when they were ~2, 3, 4, and 5 months old. Survival, growth, and key plant traits were monitored for the following 2.5 years. 3: Seedlings from environments with high herbivory pressure survived top-kill at a younger age than those from low-herbivore environments, and more palatable genera had higher herbivore-tolerance. Most individuals that survived were able to recover lost biomass within 12 months, but the clipping treatment affected root mass fraction and branching patterns. 4: Synthesis: The impact of early browsing as a demographic bottleneck can be predicted by integrating information on the probability of being browsed and the probability of surviving a browse event. Establishment limitation through early-browsing is an under-recognised constraint on savanna tree species distributions. Data may be used without requesting permission after the J Ecology paper is published and in the public domain (estimated after October 2021).Item Dataset from : The lateral semicircular canal and head posture in “ungulate” mammals: implications on diet, behavior and paleobiological reconstructions(2020-07-07) Benoit, Julien; Legendre, Lucas; Farke, Andrew; Neenan, James M; Mennecart, Bastien; Costeur, Loic; Merigeaud, Samuel; Manger, PaulFor over a century, it has been assumed that the plane of the lateral semicircular canal of the inner ear is parallel to the earth horizontal when the head is at rest. This has long been used by paleontologists to reconstruct head posture in extinct species. Thought this hypothesis has been repeatedly questioned, it has never been tested on a large sample size and at a broad taxonomic scale in mammals. This study presents a comprehensive test of this hypothesis in more than a hundred “ungulate” species. Using CT scanning and manual segmentation, the orientation of the skull was reconstructed as if the lateral semicircular canal of the bony labyrinth was aligned with the earth's horizontal plane. This reconstructed cranial orientation was statistically compared to the actual head posture of the corresponding animals using a dataset of 10,000 photographs and phylogenetic regressions. A statistically significant correlation between the reconstructed cranial orientation and head posture is found, although the plane of the lateral semicircular canal significantly departs from the earth's horizontal plane. We thus caution against the use of the lateral semicircular canal as a proxy to infer the horizontal plane on dry skulls and in extinct species. Diet (browsing or grazing) and head-butting behavior are significantly correlated to the orientation of the lateral semicircular canal, but not to the actual head posture. Head posture and the orientation of the lateral semicircular canal are both strongly predetermined by phylogenyItem Dataset from Ark Consortium - Understanding kidney disease in rural central Uganda - Findings from a qualitative study.(2016-11-09) Saraladevi, Naicker; June, Fabian; Working group ARK Consortium,; Seeley, Janet; Kabunga, Elizabeth; Laurie, Tomlinson; Liam, Smeeth; Moffat, Nyirenda; Robert, Newton; Robert, Kalyesubula; Dominic, Bukenya; Joseph SsembatyaItem Dataset from: Chronic kidney disease (CKD) and associated risk in rural South Africa: a population-based cohort study(2022-07-13) Fabian, June; Gondwe, Mwawi; Mayindi, Nokthula; Khoza, Bongekile; Gaylard, Petra; Wade, Alisha N.; Gómez‑Olivé, F. Xavier; Tomlinson, Laurie A.; Ramsay, Michele; Tollman, Stephen Meir; Winkler, Cheryl; George, Jaya Anna; Naicker, Saraladevi; Study data were collected and managed using opensource REDCap electronic data capture tools hosted at the University of the WitwatersrandStudy Methods This longitudinal cohort study was conducted from November 2017 to September 2018 in the Medical Research Council (MRC)/Wits Rural Public Health and Health Transitions Research Unit (otherwise referred to as "Agincourt") in Bushbuckridge, a rural subdistrict of the Mpumalanga province in north-eastern South Africa. Agincourt is a Health and Socio-Demographic Surveillance System (HDSS) site that includes approximately 115,000 people. For this study, a minimum sample size of 1800 was required to provide at least 80% power to determine CKD prevalence of at least 5%, provided the true prevalence was equal to or more than 6.5%. Proportional allocation of Black African adults aged 20 to 79 years ensured a representative sample based on the most recent annual population census. Sample size was increased proportionately to 2759 individuals to accommodate a 25% non-participation rate. Dataset is 2022 cases Variables are: 1. age 2. Gender 3. Years of Education (refers to completed years of schooling) 4. Height (cm) (one decimal place) 5. weight (kg) (one decimal place) 6. BMI (body mass index) 7. POC random cholesterol (mmol/L) (2 decimal places) 8. POC random glucose (mmol/L) (1 decimal place) 9. HIV status is: Based on (i) prior HIV testing history OR (ii) HIV PCR testing for ARK 10. Using the urine pregnancy test, is this participant pregnant? ( 11. ERY (erythrocytes, blood) 12. Hb (haemoglobin, blood) LEU (leucocytes) 13. NIT (nitrites) 14. PRO (protein) 15. hepatitis B surface antigen 16. Serum creatinine (umol/L) 17. Systolic BP(1) 18. Diastolic BP (1) 19. Systolic BP(2) 20. Diastolic BP (2) 21. Systolic BP(3) 22. Diastolic BP (3) 23. Serum creatinine (umol/L) 24. Urine microalbumin (mg/L) 25. Urine creatinine (mmol/L) 26. Urine microalbumin (mg/L) 27. Urine creatinine (mmol/L) 28. APOL1 haplotypeItem Dataset from: Clinicopathological correlation of kidney disease in HIV infection pre- and post- ART rollout: VERSION 2(2022-04-14) Diana, Nina Elisabeth; Davies, Malcolm; Mosiane, Pulane; Vermeulen, Alda; Naicker, SaraladeviData note Methods Ethics approval for this study was granted in writing by the Human Research Ethics Committee (Medical) of the University of the Witwatersrand, Johannesburg, South Africa (clearance certificate numbers M1511104, M121184, M120874). This approval permitted a record review of all HIV-positive patients who underwent a kidney biopsy at two tertiary hospitals in Johannesburg within the defined study period. Informed consent for this retrospective record review was waived. Data from included patients was anonymised prior to statistical analysis. Renal biopsies performed at these two tertiary hospitals, on HIV-positive individuals, from January 1989 to December 2014 were retrospectively analysed. Demographic data (age, sex and race), clinical parameters (CD4 count, HIV viral load, serum creatinine and urine protein creatinine ratio), indication for biopsy and renal histological pattern was recorded at time of kidney biopsy. The estimated glomerular filtration rate (eGFR) was calculated according to the CKD-EPI creatinine equation without ethnicity correction. ART rollout began in April 2004 in South Africa. Patients were divided into 2 groups - those who were biopsied pre-ART rollout and those biopsied post-ART rollout. These two groups were compared with respect to the above parameters. In a subgroup of the patients biopsied between 2004 and 2014, additional data laboratory parameters (serum haemoglobin, serum albumin, serial serum creatinine and eGFR) and ART use (at time of biopsy) were recorded. All renal biopsies were processed according to standard techniques for light microscopy, immunofluorescence and electron microscopy. All biopsies were reviewed by the National Health Laboratory Service histopathology team who were aware of the HIV status of the patient at time of biopsy. Histological diagnoses were tabulated using the 2018 Kidney Disease Improving Global Outcomes (KDIGO) Controversies Conference guidelines. As per this guideline FSGS (NOS) in the setting of HIV describes all non-collapsing forms of FSGS. Those ICGN with no identifiable comparative etiology other than HIV were categorized as uncharacterized ICGN with no etiology other than HIV. The biopsies with multiple diagnoses were assigned its major clinical-pathological diagnosis for the purposes of analysis. All data was collected by Dr Nina Diana and Dr Alda Vermeulen from paper based patient hospital records and the electronic hospital laboratory system. All data was checked twice to ensure accuracy. Each patient was allocated a study number and data anonymised prior to entry into Microsoft Excel. Shapiro Wilk W testing and visual inspection of the histogram plot indicated non-parametric distribution of baseline characteristics of the cohort; accordingly, central and dispersal measurements were described using the median and interquartile range (IQR), and the Kruskal Wallis ANOVA and Mann-Whitney U tests were used for comparative analyses. Kidney survival, defined by an eGFR above threshold for consideration for dialysis initiation in these institutions (15mL/min/1.73m²), censored for patient default with preserved function, was fitted for patients in the subgroup using the Kaplan Meyer method; histological diagnoses were compared using Log-rank testing.Item Dataset From: Evaluation of potential kidney donors and outcomes post-donation at Charlotte Maxeke Johannesburg Academic Hospital (1983-2015)(Division of Nephrology, Charlotte Maxeke Johannesburg Academic Hospital, 2022-03-23) Dayal, Chandni; Davies, Malcolm; Diana, Nina Elisabeth; Meyers, Anthony M.Data was collected from existing clinical records of the Living Donor Clinic held by the Division of Nephrology at Charlotte Maxeke Johannesburg Academic Hospital. This was performed by the primary investigator / first author in a pseudo-anonymized fashion and stored securely in an Excel database to which only the primary investigator had access along with the data key. Procedures pertaining to original data capturing to clinical records by the data manager (Sister Nancy Makoe), were in accordance with the standard operating procedure set out by the Transplant Unit at Charlotte Maxeke Johannesburg Academic Hospital. Objectives of research Primary Objective • To determine donor morbidity and mortality after donation. • Analysis of morbidity will focus on the development of - New onset hypertension following donation (BP ≥140/90) - Chronic kidney disease following donation, defined as the development of either of the following - New onset proteinuria (AER >300mg/day) - An eGFR <60 ml/min/1.73 m² (using the CKD-EPI formula) Secondary Objectives • To determine the reasons for exclusion of potential donors from living kidney donation • To determine the prevalence of ESKD following donation (eGFR <15 ml/min/1.73 m² using the CKD-EPI formula) • To determine potential risk factors associated with proteinuria and/or a reduced eGFR post kidney donation, by evaluating a. donor demographics b. the presence of isolated medical abnormalities prior to donation, defined by: - a borderline pre-donation 51Cr-EDTA GFR (<80 ml/min/1.73 m²) - pre-existing hypertension (well controlled on a single agent with no end-organ damage) - class I obesity (BMI 30-35 kg/m²) • To determine the proportion of patients lost to follow-up post donation 5.2 Study design A single centre retrospective observational study was conducted of all patients attending the Living Donor Clinic in the Renal Unit at CMJAH over a 32-year period between 01 January 1983 and 31 July 2015. The closing date for sampling reflects the period of protocol submission for this study. The cohort comprised of 1208 potential living donors, of which: • 910 are failed living donors, assessed between 01 January 1990 and 31 July 2015 • 298 are accepted living donors, assessed between 01 January 1983 and 31 July 2015 5.3 Data collection 5.2.1 Data collection for failed living donors Data collection for failed living donors comprised the following parameters: • Demographic data – age at assessment, gender and ethnicity • Family history of the donor • Relation to the intended recipient – whether related, unrelated or altruistic • The outcome of eligibility evaluation • If excluded from living donation, reasons for non-donation will be documented, which were categorised as: - donor-recipient related, - donor-related, - recipient-related, or - miscellaneous. • The indications and findings of any renal biopsy undertaken on a donor was recorded 5.2.2 Data collection for accepted living donors Data collection for accepted living donors comprised the following parameters: • Demographic information – gender, ethnicity, age at donation (as well as age at each follow-up point) • Family history of the accepted donor • Details pertaining to the donation, specifically: - relation to the recipient, as well as cause of renal failure in the recipient - the date of donation - the graft outcome (if known) • The last follow-up date at the Living Donor Clinic and the approximate number of post-donation follow-up visits • Domicile in relation to the Living Donor Clinic (in kilometres from transplant centre) • The reason for lost to follow-up (if known) • Baseline characteristics at donation, including: - Body mass index - Urine albumin: creatinine ratio - Systolic blood pressure - Diastolic blood pressure - Baseline serum creatinine - eGFR as defined by an isotope study, the chromium-51-ethylene-diamine-tetra-aceticacid scan (51Cr EDTA scan) as well as the CKD-EPI formula - Habits, including smoking status and history of alcohol consumption - History of pre-existing medical condition(s) • Characteristics at follow-up (correlated with time after donation), including: - Body mass index - Urine albumin: creatinine ratio - Systolic blood pressure - Diastolic blood pressure - Serum creatinine - eGFR as defined by the CKD-EPI formula - Habits, including smoking status and alcohol consumption - Development of co-morbid disease - History of nephrotoxic drug intake The above variables were retrospectively collected from data recorded at the patients’ first follow-up visit post-donation, one-year post-donation visit, and at the most recent follow-up visit. • Mortality data was collected in accepted living donors that demised during the study period, and will include: - age at death - the time from donation to mortality - cause of death, whether related to renal disease, a cardiovascular event or other cause 5.3 Definition of variables 5.3.1 Classification of donors • Potential living donors (PLDs) – refer to all donors assessed at the CMJAH Living Donor Clinic • Failed living donors (FLDs) – refer to the sub-group of PLDs excluded from living kidney donation • Accepted living donors (ALDs) – refer to the subgroup of PLDs that ultimately donated a kidney 5.3.2 Hypertension Defined as per the Eighth Joint National Committee (JNC8) guidelines for blood pressure targets: • For donors with a current age of more than sixty years: - a systolic blood pressure of more than 150mmHg, with - a diastolic blood pressure of more than 90mmHg • For donors with a current age of less than sixty years: - a systolic blood pressure of more than 140mmHg, with - a diastolic blood pressure of more than 90mmHg 5.3.2 Albuminuria Quantified as per the revised Kidney Disease Improving Global Outcomes (KDIGO) chronic kidney disease classification into three stages of albuminuria based on the albumin excretion rate (AER) in milligrams per day (mg/day): • A1: Normal or mildly increased (AER <30 mg/day) • A2: Moderately increased (AER between 30 - 300 mg/day) • A3: Severely increased (AER >300 mg/day, with nephrotic range proteinuria defined as >3500 mg/day) 5.3.3 Glomerular filtration rate • Pre-donation GFR will be defined: - as per isotope study: 51Cr EDTA scan - as calculated by the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) formula, expressed as: GFR = 141 × min (Scr /κ, 1) α × max (Scr /κ, 1)-1.209 × 0.993Age × 1.018 [if female] × 1.159 [if black] where: GFR = glomerular filtration rate in ml/min/1,73m2 Scr = serum creatinine in mg/dL κ = 0.7 for females and 0.9 for males α = -0.329 for females and -0.411 for males min indicates the minimum of Scr /κ or 1, and max indicates the maximum of Scr /κ or 1. • Post-donation GFR will be calculated by the CKD-EPI formula, as expressed above. 5.3.4 Chronic kidney disease Defined as per the revised Kidney Disease Outcomes Quality Initiative (KDOQI) as either kidney damage or GFR<60 ml/min/1.73 m² for ≥ 3 months. Kidney damage encompasses pathological abnormalities or markers of damage, including biochemical or radiological abnormalities. GFR is further classified into stages (table 1.1). Table 1.1 | Revised KDOQI classification for chronic kidney disease GFR Stages GFR (ml/min/1.73 m2) Classification 1 >90 Normal 2 60 – 89 Mildly decreased 3a 45 – 59 Mildly to moderately decreased 3b 30 – 44 Moderately to severely decreased 4 15 – 29 Severely decreased 5 <15 ESKD 5.3.5 Body mass index • BMI will be calculated as weight (in kilograms) divided by height (in meters) squared. • It will then be sub-classified as per the World Health Organisation (WHO) international BMI classification (table 1.2). Table 1.2 | WHO international classification of BMI Classification BMI (kg/m2) Underweight < 18.5 Normal Range 18.5 to 24.99 Overweight Pre-obese Obese - Obese Class I - Obese Class II - Obese Class III ≥ 25 25 to 29.99 ≥ 30 30 to 34.99 35 to 39.99 ≥ 40 5.3.6 Isolated medical abnormalities Refers to donors with any of the following characteristics prior to donation: • A borderline 51Cr-EDTA GFR <80 ml/min/1.73 m2 • Pre-existing hypertension well-controlled on a single agent with no end- organ damage • Class I obesity (BMI 30 - 35 kg/m2 )Item Dataset From: Forgotten but not gone in rural South Africa: Urinary schistosomiasis and implications for chronic kidney disease screening in endemic countries(2022-12-11) Craik,Alison; Mayindi,Nokthula; Chipungu,Shingirai; Khoza,Bongekile; Gómez-Olivé, Xavier F; Tomlinson, Laurie AlexandraStudy information The African Research on Kidney Disease (ARK) Study aimed to determine chronic kidney disease (CKD) prevalence and identify associated risk factors in rural South Africa. The study took place from November 2017 to September 2018 and included a population-based sample (N=2759) of adults aged 20-79 years from the Agincourt Health and Socio-Demographic Surveillance System (HDSS) site in rural Bushbuckridge, Mpumalanga Province. Institutional review board approval was obtained from the University of Witwatersrand (clearance number M170583) Written informed consent was obtained from individual participants prior to enrolment. This is a secondary data analysis nested within the ARK study. In this population-based cohort study, we aimed to characterise the burden of urinary schistosomiasis in rural South Africa and evaluate its relationship with markers of kidney dysfunction with implications for CKD screening. We recruited 2021 adults aged 20-79 years in the Mpumalanga Province, South Africa. Sociodemographic and anthropometric data were recorded, urinalysis performed, and serum and urine samples collected. We measured serum creatinine and urine albumin/creatinine. Kidney dysfunction was defined as an estimated glomerular filtration rate (eGFR) <60ml/min/1.73m2 and/or urine albumin-creatinine ratio >3.0mg/mmol. S.haematobium infection was determined by urine microscopy. Multivariable analyses were performed to determine relationships between S.haematobium and kidney dysfunction. The methodology for this sub-study is dependent on the larger ARK study processes. Data quality and ethics processes have previously been validated by the ARK consortium . Institutional review board approval was obtained from the University of Witwatersrand (clearance number M170583) Written informed consent was obtained from individual participants prior to enrolment. Additional approval for this sub-study from the London School of Hygiene and Tropical Medicine (reference number 22152). Kalyesubula R, Fabian J, Nakanga W, Newton R, Ssebunnya B, Prynn J, et al. How to estimate glomerular filtration rate in sub-Saharan Africa: design and methods of the African Research into Kidney Diseases (ARK) study. BMC Nephrol. 2020 Jan 15;21(1):20.Item Dataset from: The effect of TNF-α inhibitor treatment on microRNAs and endothelial function in collagen induced arthritis(2022-01-13) Gunter, Sulè; Michel, Frederic S.; Fourie, Serena; Singh, Mikayra; Le Roux, Regina; Manilall, Ashmeetha; Mokotedi, Lebogang.Palesa; Millen, Aletta M.E.; Millen, Aletta M.E.The dataset consists of 129 datapoints. The data is taken across two-time points. The dataset comprises two components. A subset from a previous study (Le Roux R, Mokotedi L, Fourie S, Manilall A, Gunter S, Millen AME. TNF-α inhibitors reduce inflammation-induced concentric remodelling but not diastolic dysfunction in collagen-induced arthritis. Clin Exp Rheumatol. 2021. Epub Jan 2021.) and additional data were collected for this study. The codebook details 58 variables, with ranges, definitions and protocols. However, only complete data is available for only 7 variables: number, group, sex, time in weeks, bodyweight in grams, Systolic and diastolic blood pressure. Rats were randomly divided into the control (n=24, 9 females and 15 males), CIA (n=24, 12 females and 12 males) and CIA+etanercept (n=16, 8 females and 8 males) groups. Systemic inflammation was induced in the CIA and CIA+etanercept groups using bovine type II collagen dissolved in incomplete Freund’s adjuvant, as previously reported (Le Roux et al., 2021). Upon the first signs of inflammation, approximately 3-4 weeks after CIA was first induced. Rats in the CIA+etanercept group received intraperitoneal injections of etanercept (Enbrel) and a 10 mg/kg dose of TNF-α inhibitor (Roche, Basel, Switzerland) every three days for six weeks. The data reports on the experiment and its resulting markers of inflammation and responses in mesenteric arteries.Item Dataset from:Combination antiretroviral therapy (Atripla) in diabetes exacerbates diabetogenic effects on hippocampal microstructure, neurogenesis, and cytokines levels in male Sprague Dawley rats(2021-11-25) Johnson, Jaclyn Asouzu; Ndou, Robert; Mbajiorgu, Ejikeme F; Our appreciation goes to our co-workers, Dr Eguavoen Idemudia and Vaughan Perry for excellent collaborative efforts. And special appreciation goes to Mrs Hasina Ali for her technical and laboratory assistance.Combination antiretroviral therapy (cART) has effectively reduced the scourge of HIV infection. However, with the increasing incidence of diabetes, HIV/AIDS-diabetes co-morbidity has become prevalent in society with chronic cART therapy in diabetes. Therefore, this study investigated the neuronal effects of cART and type two diabetes (T2D) on the levels of cytokines, lipid peroxidation, histomorphology and neurogenesis in the hippocampus. Adult male Sprague Dawley rats were divided into 4 groups: DB (diabetic rats), DAV (diabetic rats treated with cART (efavirenz, emtricitabine, and tenofovir), AV (normal rats treated with cART) and NC group (with no treatment). Following ninety days treatment, the rats were terminated, and the brains excised. Immunoassay (IL-1α, IL-6, TNFα and MDA), immunohistochemical (Ki67 and DCX) and Cresyl violet histomorphology analysis were carried out on brain homogenate and sections, respectively. In comparison to the control, the results show that cART significantly elevated IL-1α, IL-6, TNFα and MDA levels but had no effect on FBG, NFBG and glucose tolerance. While DB and DAV significantly reduced body weight ,glucose tolerance, IL-1α, IL-6, TNFα and MDA levels. Hippocampal neuronal density was reduced in cART (in DG), diabetes group (in CA1 and DG only) and in cART therapy in diabetes (in all hippocampal regions). Also, the expression of Ki67 and DCX were reduced in diabetic both the DB and DAV groups. Furthermore, increase in DG neuronal nuclei of DB and DAV is significantly corelated to FBG, NFBG, AUC, and inversely corelated to neuronal density and neurogenesis. These findings indicate that cART treatment in diabetes maintains diabetic effects of impairing cytokine and inducing oxidative stress, but it cumulates in exacerbated neurotoxicity by significantly reducing DCX compared to DB and reduction in the density and nuclei size of CA3 hippocampal neurons, unlike cART or diabetes independently.Item Institutionalizing research capacity strengthening in LMICs: A systematic review and meta-synthesis(2020) Vicente-Crespo, M; Agunbiade, M.O; Eyers, J.; Thorogood, M; Fonn, SItem Moringa Study (20151151B)(2020-12-15) Muhammad, Nasiru; Ibrahim, Kasimu Ghandi; Ndhlala, Ashwell; Erlwanger, Kennedy; Erlwanger, KennedyCleaned data from the experiement conducted with 21-day old male Sprague-Dawley rats . These rats(n=50) were randomized to six treatment groups (n=8-9) with unlimited access to commercial rat feed. Either plain water (C) or 20% fructose solution (Fr) were provided to drink. 400 mg.kg-1 M. oleifera methanolic leaf extract (Mo) or 100 mg.kg-1 fenofibrate were also administered daily for ten weeks. Growth, circulating metabolites, visceral and epididymal fat pads mass, hepatic lipids and general health markers were assessed. Liver samples were histologically examined using H&E stain. Analysis of the data was done with GraphPad Prism 5.0v for windows (GraphPad Software, Inc. CA), and the data were expressed as mean ± standard deviation and analysed by means of a one-way analysis of variance (ANOVA). Statistical significance was considered at P < 0.05.Item Sterkfontein Member 4 fabric data(2022) Stratford, DominicItem Survey of the perceptions of key stakeholders on the attributes of the South African Notifiable Diseases Surveillance System: data documentation(2016-10-25) Benson, Frew; Supervisor: Rispel LC; Project over sight Blumberg L,An original and uniquely created electronic semi-structured questionnaire was piloted and then sent out using the secure, web-based Research Electronic Data Capture (REDCap), programme hosted at the University of Witwatersrand. In addition to socio- demographic information, the questionnaire elicited information on participants’ perceptions of the NDSS( Notifiable Diseases Surveillance System) attributes of acceptability (the willingness of providers to participate in the NDSS), flexibility (adaptability to changing circumstances and needs), simplicity (ease of understanding of NDSS forms and processes), timeliness (the speed at which the provider takes the appropriate steps after an event came to her/his attention) and usefulness (whether the data contributes to outbreak response, or the prevention and control of communicable diseases or improved public health knowledge).Item WDGMC Paediatric Liver Transplant Research Database(REDcap, 2019-12-09) Fabian, June; Botha, Jean; Van der Schyff, Francisca.; Terblanche, Alberta JBiliary atresia (BA) is a progressive fibrosing cholangiopathy of infancy, the most common cause of cholestatic jaundice in infants and the top indication for liver transplantation in children. Kasai portoenterostomy (KPE) when successful may delay the requirement for liver transplantation, which in the majority offers the only cure. Good outcomes demand early surgical intervention, appropriate management of liver cirrhosis, and in most cases, liver transplantation. These parameters were audited of children with BA treated at the Steve Biko Academic Hospital (SBAH) in Pretoria, South Africa.Item Wits Face Database(2020-11-02) Bacci, Nicholas; Davimes, Joshua; Steyn, Maryna; Briers, Nanette; Data Manager: N Bacci,The human face is important in social, cultural and recognition contexts. Many research fields make use of faces to understand human interaction and identify individuals. Studies relying on facial image data often make use of ad hoc datasets specifically created for those studies as there is a dearth of large scale controlled and matching facial image databases. Actualistic (taken in a real life, natural setting) and standardised databases of facial images can be of extreme value to many research areas, such as facial identification and recognition. While multiple face databases are available, the majority, if not all, are developed in order to address very specific questions and hypotheses with limited standardisation, severely limiting their potential applicability. The Wits Face Database was developed as a generic, yet actualistic dataset of facial images obtained from consenting young adult South African male individuals. This database consists of high resolution standardised facial photographs (3264 x 4080 pixels) and corresponding closed-circuit television (CCTV) recordings of male South Africans under different camera conditions. A total of 6220 standardised (clothing and background controlled) and natural (visible clothing and out of focus background) facial photographs of 622 matching individuals in five different views are included. Corresponding CCTV footage of 334 of these individuals is also included. Across both the CCTV recordings and the photographs, the faces were captured in five different views: anterior, left 45-degree, left lateral, right 45-degree, and right lateral. The CCTV recordings were grouped under the following actualistic conditions: a standard internet protocol (IP) CCTV set-up, a low-resolution analogue CCTV set-up, an eye-level IP CCTV system, and the standard IP CCTV set-up with the addition of sunglasses and caps for target individuals. A detailed description of the composition and acquisition process of the database will be made available in a database descriptor publication format. The database is available strictly for non-commercial scientific research following approval of a formal application, assessed by the School of Anatomical Sciences’ Collections Committee within the University of the Witwatersrand.