Nutritional, immune, micronutrient and health status of HIV-infected children in care centres in Mangaung

Aim: To assess the nutritional, immune, micronutrient and health status of antiretroviral-naïve HIV-infected children.Method: A cross-sectional descriptive study was undertaken between September 2004 and March 2006 amongst HIV-infected children of which none received antiretroviral therapy, in care centres in Mangaung, Free State.Results: The study included 37 clinically stable and food-secure HIV-infected children. Their median age was 5.4 years (range 1.2–10.2 years). Fifteen children (41%) were underweight, 30 (81%) were stunted and one (3%) was wasted. The most commonly observed clinical features were lymphadenopathy (84%), skin rashes (51%), hepatomegaly (32%) and pallor (41%). Eight per cent of children had features of TB, while 19% had a lower respiratory tract infection. The median viral load of the group (n = 35) was 117 000 copies/ml, the median CD4+ cell count was 477 cells/mm3 and the median CD4 percentage was 22.5%. A significant negative correlation could be demonstrated between viral load and nutritional indicators. Children had deficient serum levels relative to normal reference values for glutathione (91% of children), albumin (78%), vitamin A (63%), vitamin D (44%), zinc (38%) and vitamin E (13%). Sixty per cent of the children were anaemic and 30% were iron deficient.Conclusion: A high prevalence of acute and chronic malnutrition and micronutrient deficiencies occurred among HIV-infected children residing in care centres. The study highlights the need to investigate early initiation of antiretroviral therapy and nutrition interventions, including aggressive supplementation, in order to improve the prognosis of these children

Mechanical and hydraulic properties of residual dolomite and wad

The properties of residual dolomite, sometimes termed wad, are variable and uncertain. It represents the insoluble residue after dissolution of dolomite and is commonly found in the Neoarchaean Malmani Subgroup of the Chuniespoort Group (South Africa). This study comprised triaxial tests, crumb tests, X-Ray diffraction and fluorescence spectroscopy, foundation indicators, stereo-microscope imagery and permeability testing of the represented formations outcropping in the northeastern portions of South Africa. Results concur that residual dolomite is not typically dispersive, has low density that can be below that of water, mostly grades in the silt fraction, has high plasticity indices with low to high liquid limits, and has hydraulic conductivities in the order of 1x10-6 m/s. This new knowledge database contributes to our understanding of the flow through these systems and to how ingress scenario subsidences and sinkholes can possibly occur.The South African Water Research Commissionhttp://www.gssa.org.zapm2020Geolog

Cretaceous fossils from the Orapa Diamond Mine

Main articleThe Orapa kimberlite pipe, situated in north-central Botswana, is well-known for its rich reserves of diamonds. It is indeed one of the largest and richest diamond mines in the world. The kimberlite magma transporting the diamonds from the upper mantle erupted through a sequence ofKaroo-aged rocks before the deposition ofthe Kalahari Sands. This eruption has been radiometrically dated at early Late Cretaceous (Cenomanian-Coniacian). When volcanism ceased, a succession of epiclastic crater lake sediments was deposited above the kimberlite plug. Analysis of these sediments, which mostly comprise the results of mudflows and debris flows and fmer sediments during quiescenttimes, suggests that most of the sediments within the crater were deposited rapidly as mass flows, and were therefore mobilised soon after the volcanic eruption. Buried within the fine-grained sediments is a unique assemblage of fossils including flowering plants and many whole-bodied insects. The fossils are commonly exquisitely preserved in extremely fine-grained mudstone. Interpretation of the sedimentary facies and fossils is that the mid-Cretaceous climate of central Botswana was temperate, seasonal and wet, and the area surrounding the crater was forested. The fossils represent the recovery of the biota of the area after the violent eruptions of Orapa and other nearby kimberlite fissures and pipes. The fossils have contributed considerably to our understanding of mid-Cretaceous insects and flowering plants and suggest intimate relationships between the two at an early stage in the radiation of flowering plants. It seems that southern Gondwana (including southern Africa) was a centre of diversification for both insects and angiosperms in the mid-Cretaceous.Friends of the Museum, Gaborone; Debswana (Orapa); University of the Witwatersrand; South African Foundation for Research Developmen

Assessing geotechnical centrifuge modelling in addressing variably saturated flow in soil and fractured rock

The vadose zone typically comprises soil underlain by fractured rock. Often, surface water and groundwater parameters are readily available, but variably saturated flow through soil and rock are oversimplified or estimated as input for hydrological models. In this paper, a series of geotechnical centrifuge experiments are conducted to contribute to the knowledge gaps in: (i) variably saturated flow and dispersion in soil and (ii) variably saturated flow in discrete vertical and horizontal fractures. Findings from the research show that the hydraulic gradient, and not the hydraulic conductivity, is scaled for seepage flow in the geotechnical centrifuge. Furthermore, geotechnical centrifuge modelling has been proven as a viable experimental tool for the modelling of hydrodynamic dispersion as well as the replication of similar flow mechanisms for unsaturated fracture flow, as previously observed in literature. Despite the imminent challenges of modelling variable saturation in the vadose zone, the geotechnical centrifuge offers a powerful experimental tool to physically model and observe variably saturated flow. This can be used to give valuable insight into mechanisms associated with solid–fluid interaction problems under these conditions. Findings from future research can be used to validate current numerical modelling techniques and address the subsequent influence on aquifer recharge and vulnerability, contaminant transport, waste disposal, dam construction, slope stability and seepage into subsurface excavations.The Water Research Commission of South Africahttp://link.springer.com/journal/113562018-05-31hb2017Geolog

Diagnostic performance of dobutamine stress echocardiography: A South African experience

Background. Dobutamine stress echocardiography (DSE) is a well-established modality for the diagnosis of coronary artery disease, but there are no reported diagnostic data in southern Africa. Objectives. To compare the safety, sensitivity and specificity of a South African (SA) DSE programme with larger, international series. Methods. All patients undergoing DSE from 2019 to 2021 at a single SA centre were included. A new wall motion abnormality (≥2 segments) signified inducible ischaemia. Results. A total of 106 patients (mean (standard deviation) age 61 (11) years, 68% male) were analysed. Six patients (6%) experienced chest pain during DSE and 4 (4%) developed an atrial arrhythmia. The sensitivity and specificity for epicardial coronary stenosis were 77% and 74%, respectively, changing to 82% and 72% when excluding those who had previous coronary artery bypass surgery. Conclusion. The sensitivity, specificity and safety of an SA DSE programme were comparable to international series. A DSE programme is feasible in a resource-constrained environment

An epidemiological study of a patient population, triage category allocations and principal diagnosis within the emergency centres of a private healthcare group in the Emirate of Dubai, United Arab Emirates

Aim: To describe, compare and correlate the number of patients seen, their demographics, triage category allocations and principal diagnosis in four emergency centres; to better understand the patient population and triage practices in this setting. Design: An observational, cross-sectional, epidemiological study. Methods: Electronic medical records were retrospectively evaluated from patients triaged in each of the four emergency centres over six months. Descriptive statistics were used to describe the patient demographics and variance between triage category allocations. Results: A total of 56,984 patient records were captured, with an equal gender split and the workforce being the largest patient population (20–50 years). Acute upper respiratory infection was the most prolific diagnosis, and lower acuity triage categories were allocated the most. There were inconsistencies in the application of triage systems between the emergency centres, the most obvious being the variance in triage system selection and application

Evaluation of nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis

BACKGROUND: Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. For both applications, Illumina technology is used by most public health laboratories; however, Nanopore technology developed by Oxford Nanopore Technologies has not been thoroughly evaluated. The aim of this study was to determine whether Nanopore sequencing data can provide equivalent information to Illumina for transmission clustering and genotypic DST for M tuberculosis. METHODS: In this genomic analysis, we analysed 151 M tuberculosis isolates from Madagascar, South Africa, and England, which were collected between 2011 and 2018, using phenotypic DST and matched Illumina and Nanopore data. Illumina sequencing was done with the MiSeq, HiSeq 2500, or NextSeq500 platforms and Nanopore sequencing was done on the MinION or GridION platforms. Using highly reliable PacBio sequencing assemblies and pairwise distance correlation between Nanopore and Illumina data, we optimise Nanopore variant filters for detecting single-nucleotide polymorphisms (SNPs; using BCFtools software). We then used those SNPs to compare transmission clusters identified by Nanopore with the currently used UK Health Security Agency Illumina pipeline (COMPASS). We compared Illumina and Nanopore WGS-based DST predictions using the Mykrobe software and mutation catalogue. FINDINGS: The Nanopore BCFtools pipeline identified SNPs with a median precision of 99.3% (IQR 99.1-99.6) and recall of 90.2% (88.1-94.2) compared with a precision of 99.6% (99.4-99.7) and recall of 91.9% (87.6-98.6) using the Illumina COMPASS pipeline. Using a threshold of 12 SNPs for putative transmission clusters, Illumina identified 98 isolates as unrelated and 53 as belonging to 19 distinct clusters (size range 2-7). Nanopore reproduced 15 out of 19 clusters perfectly; two clusters were merged into one cluster, one cluster had a single sample missing, and one cluster had an additional sample adjoined. Illumina-based clusters were also closely replicated using a five SNP threshold and clustering accuracy was maintained using mixed Illumina and Nanopore datasets. Genotyping resistance variants with Nanopore was highly concordant with Illumina, having zero discordant SNPs across more than 3000 SNPs and four insertions or deletions (indels), across 60 000 indels. INTERPRETATION: Illumina and Nanopore technologies can be used independently or together by public health laboratories performing M tuberculosis genotypic DST and outbreak investigations. As a result, clinical and public health institutions making decisions on which sequencing technology to adopt for tuberculosis can base the choice on cost (which varies by country), batching, and turnaround time. FUNDING: Academy for Medical Sciences, Oxford Wellcome Institutional Strategic Support Fund, and the Swiss South Africa Joint Research Award (Swiss National Science Foundation and South African National Research Foundation)