Moving from discourse to Praxis: Situating academics at the centre of decolonisation struggle:

As part of contributing to the decolonisation debate to reclaim and re-purpose the universities as public good institutions, drawing from Freire’s notion of praxis we argue that there is a need to move from theorisation of concepts or what we refer to as discourses to praxis, and academics must drive the decolonisation project. Unlike students, academics have immense power to influence choices of pedagogical approaches, processes of curriculum design, and knowledge production. Academics enjoy academic freedom. This implies that they have the freedom to teach and conduct research without external control in their area of expertise, which gives them special protection within the classroom and the parameters of their field of expert knowledge. Thus, we argue that the freedom that academics enjoy puts them in a good position to be drivers of the project of decolonising higher education. As key role players on processes of teaching and learning as well as knowledge production in higher education, they have some degree of power that they are better positioned to drive the decolonial project. They can use their roles as teachers and researchers to advance the decolonisation agenda

Utilising the Healy and Jenkin’s Research Teaching and Curriculum Design Nexus to transform undergraduate nursing research communities of practice

In science, research is known to be a diligent systematic inquiry into nature and society or both. It assists in validating and refining existing knowledge and generating new knowledge. Lecturers and scholars have embraced the integration of evidence-based practice into the nursing education curriculum in numerous ways. Although the learning competencies necessary for research competencies amongst undergraduate nurses include an understanding of the basic concepts and processes of research methods, it does not adequately support student preparedness for the attainment of postgraduate research competencies. The design of this study adopted a qualitative, exploratory and descriptive course of enquiry that explored current pedagogical research practices amongst lecturers and supervisors. A case study approach utilising, specifically, a cross-case analysis helped provide a clear picture of institutional pedagogical practices related to the topic of inquiry and its implementation thereof. The cases from approved local, national and international higher education institutions formed the setting for the study. Lecturers facilitating and supervising undergraduate and postgraduate research studies comprised the target population of a purposive sampling selection. In this study, the authors utilised the Healey and Jenkins Teaching Nexus to show that the research engagement of students and nursing research communities of practice can be strengthened if embraced by sound pedagogical practices. The Nexus outlines four concepts that guide the pedagogical practice of the research module that promotes undergraduate students as researchers. The authors of this article concluded that it was necessary to engage students as producers and not merely as consumers of knowledge. In this study, the researchers also utilised the Nexus to show students’ engagement in fostering different teaching approaches to research knowledge acquisition

Development and Application of Solid Phase Extraction Method for Polycyclic Aromatic Hydrocarbons in Water Samples in Johannesburg Area, South Africa

A solid phase extraction (SPE) technique has been developed for the quantitative determination of polyaromatic hydrocarbons (PAHs) in aqueous samples. The SPE technique involved extraction of PAHs froma 100 mL sample containing 10 % methanol as a modifier onto C18 cartridges. 40 % methanol in water was used as conditioning solvent, and 3 mL acetone:THF (1:1) as eluting solvent. After eluting, the extract was reduced to 1 mL under nitrogen and then analyzed by GC-MS. The extraction was optimized for the addition of organic modifier, sample load volume, conditioning solvent, washing solvent and eluting solvent. In order to evaluate the practical applicability of SPE technique, water samples were spiked with the PAHs to give final sample concentrationsbetween 3 and 7 μg L–1. Enrichment factors of 81–135 were achieved with relative standard deviations (RSDs) of less than 6 %. Recoveries obtained ranged from 81 to 135 %. Detection limits ranged from 20.0–52.0 ng L–1. The optimized method was validated by analyzing certified reference materials. The optimized method was then applied to spiked real river samples in and around the Johannesburg area, South Africa. The concentrations obtained varied from 22.0 to 1040.0 ng L–1. The RSDs were between 2.3 and 13 %. The overall order of PAHs levels was: phenanthrene > acenaphthene > naphthalene > fluoranthene > pyrene.Keywords: Solid phase extraction, polycyclic aromatic hydrocarbons, water samples, Johannesburg, South Afric

Assessments and improvement of filter media cleanliness in rapid gravity sand filters

Introduction: Rapid sand filtration is an essential unit process in the water purification process. It captures and removes coagulated and flocculated material and other suspended matter not removed during the preceding treatment processes. The pores in the filter bed gradually become clogged and the media progressively collects deposit through the continuous use and life of the filter. During normal operations cleaning is initiated by excessive head loss, deterioration in filtrate quality or when the predetermined time for a filter run has elapsed. Air scour, to remove deposit from filter media by vigorous agitation, and wash water, to remove this deposit from the filter bed, are applied. The combined action of air and water should quickly return the media to its original perfectly clean state for the cycle to continue. However, on inspection it is often found that filter sand on purification plants is unacceptably dirty and backwash systems are clearly incapable of cleaning the media to its initial state of cleanliness. It is at times possible to relate the dirty filter media to faulty designs or poor operating procedures, but often the reasons for the media deterioration remain elusive and the media becomes dirtier the longer it is in use. As there was an almost complete lack of published or agreed upon procedures to measure the cleanliness of filter media, rudimentary methods for measuring filter media cleanliness and backwash efficiency were developed. Thereafter filter media from full-scale treatment plants was analyzed with these methods at regular intervals to establish some benchmarks for these determinants. These methods were also applied during the laboratory and pilot plant phases of the project

Air quality indicators from the Environmental Performance Index: potential use and limitations in South Africa

In responding to deteriorating air quality, many countries, including South Africa, have implemented national programmes that aim to manage and regulate ambient air quality, and the emissions of air pollutants. One aspect within these management strategies is effective communication to stakeholders, including the general public, with regard to the state and trend of ambient air quality in South Africa. Currently, information on ambient air quality is communicated through ambient mass concentration values, as well as number of exceedances of South African National Ambient Standards. However, these do not directly communicate the potential impact on human health and the ecosystem. To this end, the use of air quality indicators is seen as a potential way to achieve communication to stakeholders in a simplified, yet scientifically defensible manner. Air quality indicators and their source data from the Environmental Performance Index (EPI) were interrogated to understand their potential use in South Africa. An assessment of four air quality indicators, together with their source data, showed improvements in air quality over the time period studied, though the input data do have uncertainties. The source data for the PM indicators, which came from a global dataset, underestimated the annual PM2.5 concentrations in the Highveld Priority Area and Vaal Triangle Airshed Priority Area over the time period studied (2009-2014) by ~3.7 times. This highlights a key limitation of national-scale indicators and input data, that while the data used by the EPI are a well-thought out estimate of a country’s air quality profile, they remain a generalised estimate. The assumptions and uncertainty inherent in such an ambitious global-wide attempt make the estimates inaccurate for countries without proper emissions tracking and accounting and few monitoring stations, such as South Africa. Thus, the inputs and resultant indicators should be used with caution until such a timethat local and ground-truthed data and inputs can be utilised

Assessment of genetic diversity of rice based on SNP markers for selection of parents for sheath rot (Sarocladium oryzae) resistance breeding

Sheath rot of rice, caused by Sarocladium oryzae, is an important emerging rice disease not only in Rwanda, but also in other rice-growing countries. Given that cultivar resistance is a sustainable management strategy for small-scale farmers, the aim of this study was to identify genetically distant parental materials for sheath rot resistance breeding. Ten resistant and fifteen susceptible accessions were analysed using 94 single nucleotide polymorphism (SNP) markers. The number of alleles amplified per locus ranged from 1 to 4 with a mean of 2.01 and a total of 189 alleles detected from the 25 genotypes. The number of observations per marker locus ranged from 11 to 25 with an average of 23. The mean major allele frequency was 76.2%, whereas the mean polymorphic information content was 0.263, and gene diversity was estimated at 0.325. Consequently, the markers were highly informative and revealed good estimates of genetic diversity among the studied accessions. Genetic distances ranged from 0 to 0.63 and a UPGMA dendrogram distinguished resistant and susceptible genotypes. This study revealed the possibility of improving resistance to sheath rot with minimum risk of genetic depression or reduced variability among progenies through hybridisation of locally adapted germplasm

Genetic analysis of mechanisms associated with inheritance of resistance to sheath rot of rice

Understanding genetic mechanisms controlling inheritance of disease resistance traits is essential in breeding investigations targeting development of resistant genotypes. Using North Carolina design II, 32 F1 hybrids were generated by crossing eight susceptible to four resistant parents and submitted for field evaluation. The analysis of general and specific combining ability (GCA and SCA) indicated involvement of additive and non-additive gene action controlling inheritance of horizontal resistance to sheath rot of rice. High GCA/SCA ratio and high heritability estimates revealed additive effects and were more predominant than none additive ones. The level of dominance indicated dominant genes was more important than recessive genes. Estimates of GCA and SCA analysis suggested that crop improvement programmes should be directed towards selection of superior parents or good combiners, emphasizing on GCA. As far as source of resistance is concerned, most promising genotypes were Cyicaro, Yunertian and Yunkeng. The predominance of additive genetic effects together with the relevance of dominant genes suggested possibilities of improving the resistance by introgression of resistance genes through recurrent selection coupled with phenotypic selection

Xpert Ultra testing of blood in severe HIV-associated tuberculosis to detect and measure Mycobacterium tuberculosis blood stream infection: a diagnostic and disease biomarker cohort study

BACKGROUND: Mycobacterium tuberculosis bloodstream infection is a leading cause of death in people living with HIV and disseminated bacillary load might be a key driver of disease severity. We aimed to assess Xpert MTB/RIF Ultra (Xpert Ultra) testing of blood as a diagnostic for M tuberculosis bloodstream infection and investigate cycle threshold as a quantitative disease biomarker. METHODS: In this cohort study, we obtained biobanked blood samples from a large and well characterised cohort of adult patients admitted to hospital in Western Cape, South Africa with suspected HIV-associated tuberculosis and a CD4 count less than 350 cells per μL. Patients already receiving antituberculosis therapy were excluded. Samples were obtained on recruitment within 72 h of admission to hospital, and patients were followed up for 12 weeks to determine survival. We tested the biobanked blood samples using the Xpert Ultra platform after lysis and wash processing of the blood. We assessed diagnostic yield (proportion of cases detected, with unavailable test results coded as negative) against a microbiological reference, both as a function of markers of critical-illness and compared with other rapid diagnostics (urine lipoarabinomannan and sputum Xpert). Quantitative blood Xpert Ultra results were evaluated as a disease biomarker by assessing association with disease phenotype defined by principal component analysis of 32 host-response markers. Prognostic value compared to other tuberculosis biomarkers was assessed using likelihood ratio testing of nested models predicting 12-week mortality. FINDINGS: Between Jan 16, 2014, and Oct 19, 2016, of the 659 participants recruited to the parent study, 582 had an available biobanked blood sample. 447 (77%) of 582 met the microbiological reference standard for tuberculosis diagnosis. Median CD4 count was 62 (IQR 221-33) cells per μL, and 123 (21%) of participants died by 12-weeks follow-up. Blood Xpert Ultra was positive in 165 (37%) of 447 participants with confirmed tuberculosis by the microbiological reference standard, with a diagnostic yield of 0·37 (95% CI 0·32-0·42). Diagnostic yield increased with lower CD4 count or haemoglobin, and outperformed urine lipoarabinomannan testing in participants with elevated venous lactate. Quantitative blood Xpert Ultra results were more closely associated with mortality than other tuberculosis biomarkers including blood culture, and urine lipoarabinomannan, or urine Xpert (all p<0·05). A principal component of clinical phenotype capturing markers of inflammation, tissue damage, and organ dysfunction was strongly associated with both blood Xpert-Ultra positivity (associated with a SD increase of 1·1 in PC score, p<0·0001) and cycle threshold (r= -0·5; p<0·0001). INTERPRETATION: Xpert Ultra testing of pre-processed blood could be used as a rapid diagnostic test in critically ill patients with suspected HIV-associated tuberculosis, while also giving additional prognostic information compared with other available markers. A dose-response relationship between quantitative blood Xpert Ultra results, host-response phenotype, and mortality risk adds to evidence that suggests M tuberculosis bloodstream infection bacillary load is causally related to outcomes. FUNDING: Wellcome Trust, National Institute of Health Fogarty International Center, South African MRC, UK National Institute of Health Research, National Research Foundation of South Africa. TRANSLATIONS: For the Xhosa and Afrikaans translations of the abstract see Supplementary Materials section

Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs

The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits

Phenotypic correlation, path coefficient and multivariate analysis for yield and yield-associated traits in groundnut accessions

Yield is a complex quantitative trait largely influenced by the environment. Direct selection for grain yield is less efficient in improving groundnut productivity. The selection efficiency can be enhanced by exploiting the relationship between yield and its related traits. Moreover, the use of genetically diverse parents is essential to generate genetic variation for successful selection of genotypes in a breeding program. Therefore, the study aimed at analysing the relationship between grain yield and its related traits and determining the morphological diversity among selected groundnut genotypes under natural rosette disease (GRD) infestation. The genotypes were evaluated in a 7 × 4 alpha lattice design with three replications. Data were collected on yield and yield-related traits. Correlation, path coefficient and multivariate analyses were done. The results revealed that yield was directly associated with plant height, number of pods per plant, hundred seed weight, GRD incidence and number of secondary branches. Therefore, these traits should be considered in selection when improving groundnut for yield. Cluster analysis revealed existence of diversity among the evaluated groundnut genotypes with no influence of geographical origin to the clustering pattern. The Principal Components Analysis (PCA) biplot was effective in showing the genetic distance among the genotypes and the results were comparable with those of the cluster analysis. Moreover, Shannon-Weaver diversity indices revealed existence of high diversity among the genotypes, an implication that groundnut improvement for yield is possible through selection in breeding