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Nitrogen cycling in the South Atlantic and South Indian Oceans investigated using nitrate isotopes: implications for nutrient supply, ocean fertility, carbon export, and climate
(2023) Marshall, Tanya; Fawcett, Sarah
Bioavailable nitrogen (N) limits phytoplankton growth across much of the (sub)tropical ocean, thereby modulating ocean fertility and climate. Dinitrogen (N2) fixation is the dominant source of new N to the ocean and is thought to occur mainly in well-lit, warm, oligotrophic waters. The under-sampled South Atlantic and South Indian Ocean basins are predicted by models to host widespread N2 fixation; for the South Atlantic, this predication contradicts the limited available observations and for the South Indian, is yet to be confirmed by measurements. In this thesis, four new nitrate isotope datasets from the South Atlantic and South Indian Oceans are presented alongside coincident nutrient and hydrographic data, and other published nitrate isotope datasets. Combined, these data provide a means of quantifying the rate and distribution of N2 fixation, along with characterizing additional co-occurring N cycle processes, mechanisms of subsurface nutrient supply, and water mass circulation. Measurements of nitrate N isotope ratios (15N) and nutrient stoichiometry (i.e., nitrate to phosphate ratios; N:P) from a zonal transect of the tropical South Atlantic (at ~12S) and a meridional transect along the Angola margin (at ~12E) reveal an N2 fixation hotspot in the eastern tropical Angola Gyre. Here, thermocline nitrate 15N is low and N:P is high relative to the underlying source water and the western tropical basin thermocline. The N2 fixation rate estimated from the Angola Gyre nitrate 15N data of 1.4-5.4 Tg N.a-1 accounts for 28-108% of the rate predicted for the South Atlantic basin. These findings contradict recent model diagnoses of N2 fixation, which predict high rates in the western tropical basin and none to the east. The overlapping biogeography of a basin-wide P excess relative to N and bioavailable iron supplied locally from the Angola margin likely control N2 fixation in the Angola Gyre. Analogous conditions elsewhere in the ocean, such as in other eastern boundary shadow zones and retentive near-coast subtropical systems, should also favour N2 fixation. The western boundary current of the South Indian Ocean, the Agulhas Current, is the strongest boundary current on Earth, yet nutrient cycling in this subtropical system remains largely uncharacterized. Measurements of the dual isotope ratios (N and oxygen) of nitrate from within and upstream of the greater Agulhas region provide insights into regional circulation and N cycle dynamics. The nitrate isotopes reveal both local and remote signals of Indian Ocean N cycling such as denitrification in the Arabian Sea and partial nitrate assimilation in Southern Ocean surface waters, as well as evidence of local N2 fixation and coupled partial nitrate assimilation and nitrification. Using a one-box model to simulate the newly-fixed nitrate flux, the local N2 fixation rate for the greater Agulhas region is estimated to Thesis abstract be 7-25 Tg N.a-1; this value is the first observation-based N2 fixation rate estimate for the South Indian Ocean. Local N cycling imprints an isotopic signal on Indian Ocean nitrate that can be tracked beyond the Indian Ocean because it persists in Agulhas eddies that “leak” into the South Atlantic at the Agulhas Retroflection. If this signal is retained in plankton that sink to the seafloor, it could be used to reconstruct past Agulhas leakage, yielding quantitative insights into the strength of the Atlantic Meridional Overturning Circulation in the past. The Agulhas Current system, like other western boundary current systems, is characterised by high energy and turbulence. A novel application of the dual isotopes of nitrate reveals the occurrence of three (sub)mesoscale mechanisms of upward nitrate supply; entrainment at the edges of a mesoscale anticyclonic eddy, inshore upwelling likely driven by a frontal eddy, and overturning at the offshore edge of the current core likely driven by coupled mesoscalesubmesoscale instabilities. The intensity and (sub)surface expression of these nutrient supply events are not always apparent in the hydrographic data, highlighting the utility of the nitrate isotopes for exploring physical ocean processes. The conditions driving the nitrate supply mechanisms in the Agulhas region are common to western boundary currents, implying that the (sub)mesoscale vertical nitrate supply is quantitatively significant at the global scale. Additionally, these events of upward nitrate supply likely increase regional fertility in all western boundary current systems, with implications for the sustenance of higher trophic levels. Finally, increasing turbulence observed along mid-latitude western boundaries may enhance the upward nutrient supply to subtropical surface waters, and possibly compensate for the diminished productivity predicted as a result of increasing subtropical gyre stratification. Collectively, the work detailed in this thesis reveals the strong regionality of N cycling in the historically under-studied South Atlantic and South Indian Oceans, as well as the importance of interpreting biogeochemical data in the context of ocean dynamics across various scales. Improved predictions of N fluxes at the basin- and global scale, which are critical for estimating the ocean's CO2 sink and fertility, will require careful consideration of these southern basins so as not to mischaracterise their functioning, as has occurred in the past.
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Open Access
Optimizing learning & teaching on paediatric ward rounds
(2023) Mantzor, Savarra; Cilliers, Francois
Bandura's Social Cognitive Theory asserts that an individual's perceptions of his/her self-efficacy influence not only their ability to learn knowledge and skill, but more importantly, influences their ability to act utilizing that knowledge or skill. In the context of health professional education, it is not enough to know the facts of medicine, but learners must also have a positive perception of their selfefficacy in order to practice medicine as a competent physician. The aim of this study was to improve the quality of ward round learning and teaching for University of Botswana medical trainees working in the Department of Paediatrics at Princess Maria Hospital in order to enhance their self-efficacy beliefs regarding their ability to provide paediatric patient care. Specifically, we utilized a threepronged approach to 1) improve trainees' participation in, and sense of belonging to, a local community of clinical practice, 2) introduce a structured bedside teaching model, and 3) promote a favourable clinical learning environment, all of which we postulated could improve trainees' selfefficacy beliefs. In this research I assert that four educational elements, (i) the method of teaching (i.e. bedside teaching), (ii) the environment in which learning occurs (i.e. the clinical learning environment), (iii) the epistemological value of social participation (i.e. communities of practice), and (iv) an individual's ability to both acquire and utilize their knowledge (i.e. perceived self-efficacy), are not distinct phenomena, but are interrelated, dynamic forces that influence each other in meaningful ways. This study was conducted as an action research (AR) project using mixed methods evaluation for data capture and analysis. Following the iterative Plan-Act-Observe-Reflect cycles of action research, a total of three phases occurred. In Phase 1, we developed an in-depth understanding of trainees' and faculty's perceptions of the prevailing paediatric ward rounds. In Phase 2, through ongoing departmental collaboration and review of the literature, we conceptually analysed the findings from Phase 1 to determine specific interventions for Phase 3. In Phase 3, we implemented the Phase 2 generated solutions, including the introduction of a structured bedside teaching model, SNAPPS (Summarize-Narrow-Analyse-Probe-Plan-Select); this was subsequently adapted to provide local and contextual relevance. Throughout all Phases, we conducted serial measurements of trainees' perceptions of (i) the clinical learning environment (CLE) on ward rounds, (ii) their sense of participation in, and belonging to, the community of practice on ward rounds (COP); and (iii) their perceived self-efficacy (PSE) to provide paediatric patient care. The types of study instruments and data sources included focus group discussions, interviews, debriefs, my action research journal, and questionnaires. Four consecutive types of data analysis occurred throughout the project: qualitative data analysis, quantitative data analysis, mixed methods integration, and critical reflection. Over the 28-month study period, there was a total of 208 participants, including representation from faculty, senior residents, junior residents, and medical students. There were three primary outcomes of this action research project. 1) Trainee use of SNAPPS was associated with (i) a CLE that was more favourable to respecting uncertainty; (ii) an increase in trainees' participation in and, sense of belonging to, a paediatric ward round; and (iii) positive influences on their perceived self-efficacy to manage patients. 2) We identified several non-traditional uses of SNAPPS that created opportunities for trainees to learn and faculty to teach beyond the primary diagnosis. 3) In contrast to the literature, we were unsuccessful at introducing SNAPPS at a department-wide level. Note, when I first set out to do this research, I postulated that bedside teaching, the clinical learning environment, and participation in a community of practice all had the potential to influence an individual's perceived self-efficacy. I assumed that while bedside teaching models (BTM) provide a structured approach to student engagement to enhance the content of bedside teaching, they do not, in and of themselves, regulate the clinical learning environment in which they occur. I did not consider the influence of a BTM on a learner's sense of belonging to a community of clinical practice. Through the findings of this project, I discovered the power of the BTM itself, which shifted the foci of influence, that not only does it have the potential to positively influence learner's PSE, but indeed has direct influential effects on the CLE and elements of COP. These findings compliment and broaden my original assumptions that the educational dimensions involved are not isolated elements, but together simultaneously impact learning and teaching. Note, during the course of this project, my positionality as the researcher underwent considerable shifts from “outsider” conducting “participatory action research” to “insider” conducting “practitioner research”. In turn, an unexpected secondary aim and outcome developed – to explore, understand and articulate the influences of SNAPPS on my own practice as a physician and clinical teacher. Limitations included: over utilization of traditional research instruments and analysis; lack of quality control of the implemented intervention; difficulty in interpreting results; delays in important critical reflections during the project; inability to achieve full collaboration with other department members; and unsuccessful attempt to introduce SNAPPS department-wide. Based on the findings from this study, a structured bedside teaching model, specifically SNAPPS, offers a holistic approach to maximize learning and teaching, addressing several learner and environmental needs concurrently. That said, when clinical teachers set out to introduce SNAPPS, they ought to be prepared to offer ongoing support for the successful implementation beyond a brief SNAPPS sensitization. The flexibility and potential advantages of SNAPPS promotes its use, especially in clinically challenging teaching environments.
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Open Access
A stepwise Study on the characterisation and processing of South African Platinum Group Tailings
(2023) Manenzhe, Re?oket?we; Corin, Kirsten
The endurance of the mining industry has led to the near-depletion of some of the most processible ore types. This has resulted in a unique challenge that necessitates unique innovation for the industry. Firstly, existing technologies are increasingly geared towards improved efficiency in processing lower grade ores. Secondly, ores that were previously processed with older, and in some cases, inefficient technologies, have emerged as potentially viable solutions that would help maintain concentrator capacities. On the other hand, as the industry has endured, so has its waste accumulation. Tailings dumps continue to grow, and continue to pose various environmental issues. But although they are a waste product, tailings also have several merits to them. They are already mined and readily available, and reprocessing them immediately addresses two conundrums i.e. how can the industry source alternative ores, and how can it deal with the steady accumulation of waste? It is expected that as a result of their initial processing from so-called fresh ores, and their stay in their respective dumps, the tailings will be altered or tarnished. The surface properties of their compositional minerals will be oxidised and layered with other compounds that might hinder their interaction with flotation reagents such as collectors and hence, hinder their flotation response, presenting a challenge for their proposed reprocessing. More obviously, as they are a waste product, their grades will be far lower than the fresh ores that produced them. Numerous studies aim to elucidate the viability of the metallurgical reprocessing of tailings. However, this flurry of innovation thus far extends to the vast stretches of the Witwatersrand dumps, and thus, to gold. The issue with processing other tailings types then becomes threefold. Is there enough value in the dumps to justify tailings beneficiation? What beneficiation method would be suitable? Would the method yield economically viable results? This study acquired three bulks of PGM tailings to investigate these questions. The first bulk was Merensky, the second was UG2, and the third was a deslimed version of UG2 in which a portion of denser minerals were separated out. For the sake of convenience, the bulks are referred to by their shorthands throughout the thesis. Merensky became MER, the normal or raw UG2 became UG2R, and the deslimed UG2 became UG2D. The study conducted the investigations along two lines: first, by characterising the tailings, and secondly, by floating them. The first characterisation step was a full elemental and mineralogical analysis that quantified the amount of valuables as well as gangue minerals; this was done via XRD and QEMSCAN. The second step was to determine the degree of oxidation by using qualitative, in-situ experimental methods; these are EDTA extraction and oxygen reactivity. It was hypothesised that EDTA extraction would measure the concentration of secondary and oxidised materials on the mineral surfaces; and oxygen reactivity would measure the demand of oxygen in each tailings, and therefore the tailings' capacity to react with species in the pulp phase. The qualitative methods have only ever been used for fresh ores, and have shown to be reliable in predicting and/or explaining the flotation behaviour of those ores. They have never been used to predict an/or explain the flotation behaviour of an ore material that has already been processed, and is therefore very low grade, and oxidised. If they are as viable for tailings as they are for fresh ores, they would determine different EDTA extraction indices and oxygen demand constants. QEMSCAN and XRD provided the different concentrations of the different minerals across the tailings, and showed that some minerals were present in one tailings but not the other. For instance, MER contained the highest fraction of chalcopyrite, as well as the highest fraction of sulphides. UG2R and UG2D each had more than ten times the fraction of chromite seen in MER. MER, on the other hand, had more pyroxenes, plagioclase and amphibole. It was expected that these differences in composition would be the cause of the different extraction indices and oxygen demand constants. The robustness of both methods thus had to be tested. This was done by altering each of the tailings and testing whether the extraction indices and oxygen demand constants would change. The surface and composition alteration was induced with ultrasonication and desliming. The study thus answered the question: can the EDTA extraction and oxygen reactivity methods detect when a change has occurred on the mineral surfaces of the same tailings? The tailings were then floated, and it was here that the question of economic viability was assessed. For the concentrators from which MER, UG2R and UG2D were collected, a reprocessing venture would be deemed economically viable if 30% of the copper present in the tailings was recovered. The flotation performance was thus analysed with copper recovery as the primary positive indicator. Nickel behaviour was also tracked in case of any supporting elucidations, and also because pentlandite is the primary PGE-carrier for Merensky and UG2. The tailings were floated with DOW200 as the frother, SIBX as the collector, and CMC as the depressant. The results showed that the presence of the depressant resulted in very low solid quantities being recovered to the concentrate. In fact, less than 2% of each tailings was recovered, and less than 10% of the present copper (and therefore chalcopyrite) was extracted. When the depressant was removed from the reagent scheme, recovery of the solids improved to 10%, but the copper yield was still below 30%. So, the collector dosage was increased under the fundamental assumption that the hydrophobicity of the valuables would be improved, and in this way, the efficiency of separating the hydrophilic gangue from the valuables would also improve. The plan worked, and UG2R finally achieved the industrial objective of recovering 30% of the present copper. While MER and UG2D failed to do the same, their performance was also at its best under these conditions, with each tailings yielding roughly 23% copper recovery. In an effort to improve floatation, the tailings were cleaned via ultrasonication and desliming. These cleaning methods both had a detrimental effect on copper recovery. However, nickel (and therefore pentlandite) behaviour improved, showing that while the methods were disadvantageous to one mineral, they were favourable to another, and they might be useful for a study that uses a different metal as its positive performance indicator. The study also showed that MER, UG2R and UG2D have different copper EDTA extraction indices. UG2D had the highest index, followed by UG2R, and then MER. The copper minerals associated with UG2D can therefore be concluded to be more oxidised than those associated with UG2R and MER. Moreover, UG2D was the least reactive to oxygen, having an oxygen consumption rate constant of 0.113 min-1 when compared to 0.198 and 0.152 min-1 for UG2R and MER, respectively. Ultrasonication and desliming decreased each of these constants, indicating that when cleaned with the chosen methods, the mineral surfaces became less reactive to oxygen. And so, it was concluded that of the investigated tailings, UG2D was more oxidised than the other two, reacted the least with oxygen, and yielded the lowest copper recoveries. When UG2R achieved the highest reactivity with oxygen, it also yielded the lowest copper extraction index and the highest copper recovery. Overall, nickel behaved contrary to copper.
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Open Access
Proposing a context-sensitive model of family supportive supervision for breastfeeding at work from the global South
(2023) Mabaso, Prudence Bongekile; Jaga, Ameeta
Managing breastfeeding and employment remains a major challenge for working mothers and for the advancement of gender equality across the world. Despite global public health organisations' attempts to encourage workplace support for breastfeeding, progress remains slow particularly in countries with limited state resources. The small but growing body of research on combining breastfeeding and employment typically originates from high-income countries in the global North. Findings and theories from this literature cannot be uncritically imposed on low and middle-income countries (LMICs) in the global South which have distinct sociocultural, economic, and historic contexts. This study advances understanding and theorising of context-sensitive workplace support for breastfeeding by focusing on a specific form of informal support, family supportive supervisor behaviours (FSSB), in the public education sector in South Africa, a middle-income country in the global South. A qualitative research approach was adopted and enabled grounding of the research in the lived realities and material circumstances of working women in the local context. The contribution of the thesis is shown through three papers. The first paper is an exploratory qualitative study to understand practices and challenges related to breastfeeding at work in a public sector context. Thematic analysis of interview data from working mothers (n = 8) and senior managers (n = 4) in two provincial government departments in the Western Cape provided a context-sensitive understanding of breastfeeding at work. The study findings underscored the key role of supervisors in offering relatively low-cost informal support for mothers to better combine breastfeeding and employment. The second paper builds on the concept of informal support from supervisors as key catalysts to advance support for breastfeeding at work among a specific group of public sector employees, teachers. Interview data from teachers who are mothers (n = 13) and principals as their supervisors (n = 14) yielded findings that presented a critical understanding of FSSB for breastfeeding at work in a global South context. The findings from this study extend knowledge by emphasising the importance of contextual factors which affect supervisors' demonstration of, and mothers' accessing FSSB, cautioning against universalising the FSSB construct across diverse contexts. The final conceptual paper contributes to theory building by proposing a context-sensitive model of FSSB for breastfeeding at work from the global South. Sociocultural, economic, and historicalpolitical factors are proposed as important antecedents of FSSB, and interpersonal trust with one's supervisor as a potential moderator of the relationship between the contextual factors and FSSB. Implications for management and workplace policies in LMICs in the global South are presented and recommendations for future research that opens space for diverse ways of knowing are offered. Keywords: Breastfeeding at work, Blended work and family, Family supportive supervisor behaviours, Low and middle-income country context, Global South, Public education sector
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Open Access
The genetics of non-syndromic hearing impairment in South Africa
(2023) Manyisa, Noluthando; Wonkam, Ambroise; Chimusa Emile
Hearing impairment (HI) is a sensory disorder resulting in the partial or complete disability to perceive sound in the better-hearing ear. It is defined as the inability to hear better than 25dB in the better-hearing ear. Subsequently, it is considered disabling when a child cannot perceive sound better the 30dB, in the better hearing ear, and an adult cannot perceive sound better than 40dB, in the better hearing ear. Hearing impairment may result from genetic, environmental, or unknown factors. The connexin gene, GJB2, is the prevalent gene resulting in congenital HI in most children with European, North American, and East Asian ancestry. Apart from the founder mutations present in GJB2 in Morocco, Ghana and Senegal, the prevalent causative genes resulting in congenital HI in African populations are yet to be fully elucidated. Congenital Hearing impairment in South Africa (RSA), has been estimated to have an incidence rate of 5.5 per 1000 live births, which is 5 times higher than the birth incidence in high-income countries (approximately 1 to 2 per 1000 live births). Patients are generally diagnosed late with HI, at approximately 3 years old, and the most prevalent environmental factors associated with HI in RSA are middle ear infections, with several reports implicating ototoxicity as a cause of HI. Variants in connexin genes i.e. GJB2 associated with HI have been shown to be irrelevant in the Black South African populations, and the limited genetic studies have identified private mutations in selected families. However, the full extent of prevalent genes associated with HI in the South African populations is still to be investigated. Methods and results Through a systematic review, we investigated the state of HI research in South Africa was established. Though studies have been performed since the 1960s, the results showed that genetics of HI in South Africa was not well explored. Universal new-born hearing screening is ideal in detecting congenital HI, but it is currently not standard practice in the country. However, with the advent of modern technology, HI screening may be more accessible to patients through community health workers. Patients who fail the repeated screenings may then be referred for further audiometry testing. This may positively impact the identification of patients with HI and assist with the necessary interventions. We also collaboratively worked to establish the first disease ontology for HI to further allow standardised and harmonised language surrounding HI. This provides the scalability and interoperability of research going forward. It will allow for all stakeholders in HI research to use the same terminology when discussing HI. In order to address the dearth of genetics research regarding non-syndromic HI, patients presenting with putative genetic HI were recruited from schools of the deaf across South Africa and two hospitals in Cape Town. The patients were recruited along with their family members, both with and without HI, and their DNA was extracted from whole blood. Twenty-seven families segregating non-syndromic HI, consisting of 65 affected and 35 unaffected individuals were subjected to whole exome sequencing (WES). The HI was resolved in 20 families (74%), and pathogenic variants were identified in the genes: WFS1 (c.A2141), MITF (cT918A), ADGRV1(c.G564T, c.A17450G, c.A11298C), PDSS1(c.C641T, NEU1(c.C1069T, c.G754C), c.G727A), TBC1D24(c.G1514A), MYO15A(c.C1378T, TMPRSS3(c.205+6t>A), c.9303+5G>A, c.G6634A), USH2A(c.T9437A, c.G2990T, c.G101A), STRC(c.G225A, c.C4057T, c.G4655C, c.C4351T, c.G4403A), P2RX2(c.G1064A, c.C1187G), OTOG(c.C2525A, c.G3143A, c.G916A), LHFPL5(c.621delC), TRIOBP(c.C3133T, c.C4298T), SLC26A4(c.T94C, c.T716A), GJB2(c.35delG), REST(c.G1244C), CRYM(c.*6_*2delACAAA), CDH23(c.T1585C, c.G8230A), FGFR2(c.1297+10G>C), MYO7A(c.6255delC). The pathogenic variants presented 8 autosomal dominant alleles and 12 autosomal recessive alleles Five families presented with pathogenic or likely pathogenic variations associated with Usher Syndrome and the remaining 14 families presented with pathogenic variations associated with non-syndromic HI. One family presented with putative pathogenic variations in NEU1, which is a gene associated with Sialidosis. We specifically investigated, in greater detail, a dominant novel variation in REST, present in one family, which encodes a transcription factor, that was identified using whole exome sequencing. This gene was previously suspected to be associated with hearing impairment only once, in an American family. The variation was absent in the unaffected South African family members, unrelated patients, and unaffected controls. In vitro cell-based studies indicated that the variation results in the loss of nuclear exclusivity of REST. Luciferase assays indicated that the mutant was unable to repress the expression of one of its target genes, whereas the wild-type effectively inhibited the expression of the target. Conclusions This thesis successfully performed the following investigations: 1) development of the first Hearing Impairment Ontology worldwide, 2) review the genetic profile of HI in South Africa, 3) used WES to find known and novel variants in established HI genes, and 4) confirmed REST as a novel HI gene. Future work will focus on sequencing all the remaining samples and identifying their putative causative mutations. Further work includes feedbacking the results of the genetic testing to the patients and their families. The data will contribute to improving the HI-genes pairs' curation in Africa, and globally.