SUNScholar

SUNScholar is a leading digital archive for the preservation and promotion of the research output of Stellenbosch University.

 

Recent Submissions

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Bovine tuberculosis in African buffalo (Syncerus caffer): Progression of pathology during infection
(PLOS, 2022-11-11) Lakin, Hilary Ann; Tavalire, Hannah; Sakamoto, Kaori; Buss, Peter; Miller, Michele; Budischak, Sarah A.; Raum, Kristina; Ezenwa, Vanessa O.; Beechler, Brianna; Jolles, Anna
Background Bovine tuberculosis (BTB) is a zoonotic disease of global importance endemic in African buffalo (Syncerus caffer) in sub-Saharan Africa. Zoonotic tuberculosis is a disease of global importance, accounting for over 12,000 deaths annually. Cattle affected with BTB have been proposed as a model for the study of human tuberculosis, more closely resembling the localization and progression of lesions in controlled studies than murine models. If disease in African buffalo progresses similarly to experimentally infected cattle, they may serve as a model, both for human tuberculosis and cattle BTB, in a natural environment. Methodology/Principal findings We utilized a herd of African buffalo that were captured, fitted with radio collars, and tested for BTB twice annually during a 4-year-cohort study. At the end of the project, BTB positive buffalo were culled, and necropsies performed. Here we describe the pathologic progression of BTB over time in African buffalo, utilizing gross and histological methods. We found that BTB in buffalo follows a pattern of infection like that seen in experimental studies of cattle. BTB localizes to the lymph nodes of the respiratory tract first, beginning with the retropharyngeal and tracheobronchial lymph nodes, gradually increasing in lymph nodes affected over time. At 36 months, rate of spread to additional lymph nodes sharply increases. The lung lesions follow a similar pattern, progressing slowly, then accelerating their progression at 36 months post infection. Lastly, a genetic marker that correlated to risk of M. bovis infection in previous studies was marginally associated with BTB progression. Buffalo with at least one risk allele at this locus tended to progress faster, with more lung necrosis. Conclusions/Significance The progression of disease in the African buffalo mirrors the progression found in experimental cattle models, offering insight into BTB and the interaction with its host in the context of naturally varying environments, host, and pathogen populations.
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Scientific selection: A century of increasing crop varietal diversity in US wheat
(National Academy of Science, 2022-12-13) Chaia, Yuan; Pardey, Philip G.; Silverstein, Kevin A. T.
A prevalent and persistent biodiversity concern is that modern cropping systems lead to an erosion in crop genetic diversity. Although certain trait uniformity provides advantages in crop management and marketing, farmers facing risks from change in climate, pests, and markets are also incentivized to adopt new varieties to address complex and spatially variable genetics, environment, and crop management interactions to optimize crop performance. In this study, we applied phylogenetically blind and phylogenetically informed diversity metrics to reveal significant increases in both the spatial and temporal diversity of the US wheat crop over the past century. Contrary to commonly held perceptions on the negative impact of modern cropping systems on crop genetic diversity, our results demonstrated a win-win outcome where the widespread uptake of scientifically selected varieties increased both crop production and crop diversity.
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Analysing the changes in the bathymetry of Saldanha Bay between the years 1977 and 2021
(CONSAS Conference, 2022-12) Du Toit, Louis; Henrico, Ivan; Bezuidenhout, Jacques; Mtshawu, Babalwa
The construction of the Saldanha Port has been the reason for the major changes in the bathymetry and sediment dynamics observed in Saldanha Bay in the last decades. In this paper, newly acquired soundings from the National Hydrographer were used to analyse the changes between 1977 and 2021 - over a 44-year period - in the bathymetry of Saldanha Bay. The Ordinary Kriging (OK) interpolation method, available through the Geostatistical Wizard in ArcGIS Pro, was used for creating surface models to conduct comparisons with the bathymetry of Saldanha Bay. The results indicate a general increase in depth since 1977 of between 0.395 and 3.203 m, and an average increase in depth within the Big Bay of 1.799 m. Between 1977 and 2021, a total volume loss of 49 364 560.0 m3 in sediment was calculated - an indication of how the sedimentation process in Saldanha Bay has changed subsequent to the construction of the harbour.
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Looking closely at what they say and what it tells us: experiences in a digital learning space
(Higher Education Learning and Teaching Association of South African (HELTASA) , 2022) Khoza, L. M.; Van der Merwe, K.
This study explores lecturer and student experiences of using the Learning Management System (LMS) within a Faculty at a South African University. The results of the study highlight the extent to which lecturers and students engage with the LMS. This article aims to determine the following: 1) the value that lecturers and students place on using the LMS as a platform to facilitate learning and teaching, 2) the typical resources, activities and assessments that lecturers and students place value on and why, and 3) to compare lecturer and student perspectives on the best utilization of the LMS. Quantitative data were collected from the LMS and qualitative data collected from lecturers and undergraduate students through questionnaires and focus groups. A Social Constructivist framework was adopted as a lens for analysis of collected data. The results show resources are valued the most by both lecturers and students but the majority of students only access, on average, just more than half of the postings. In terms of the constructs of the Social Constructivist framework, Learning and Connectedness showed positive responses, while improvement is necessary for Making Meaning and Agency.
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Flood frequency analysis – Part 2: Development of a modified plotting position
(South African Water Research Commission., 2022-04-27) Van der Spuy D; Du Plessis JA
The original plotting position concept was suggested more than a century ago. Since then, many alternative plotting position approaches have been developed. Despite a general lack of agreement around which plotting position is theoretically ‘correct’ and the ‘best’ to use, all plotting positions fail to adequately address outliers and data of similar magnitude. Hydrologists generally fail to acknowledge that the plotting position primarily offers an informative display of data, against which distributions can be compared, rather than an absolute measure of probability. This paper does not intend to challenge any of the many lengthy theoretical mathematical arguments, utilised to ‘prove’ why one plotting position is superior to the others. These theoretical arguments may very well be valid for a ‘population’ of flood peaks – the reality, however, is that hydrologists are confronted with the challenge of analysing very limited ‘samples’ of the population. Consequently, the plotting position issue demands a more pragmatic approach, rather than a purely theoretical approach. This paper illustrates various problems with existing plotting position techniques in use and offers an alternative approach and a more sensible plotting position technique, using Z-scores and referred to as the Z-set PP, against which distributions can be checked. The study further illustrates how effectively the Z‑set PP deals with outliers and its robustness with various record lengths. Although derived from a study of flood peak data obtained from South African flow-gauging sites, it is deemed that it will be universally applicable.