Collection D

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The architecture of antagonistic networks : node degree distribution, compartmentalization and nestedness
(International Academy of Ecology and Environmental Sciences, 2015-12-01) Nuwagaba, Savannah; Hui, Cang
Describing complex ecosystems as networks of interacting components has proved fruitful – revealing many distinctive patterns and dynamics of ecological systems. Of these patterns, three have often been brought up in literature, including species degree distribution, compartmentalization and nestedness, due largely to their implications for the functionality and stability of communities. Here, using 61 empirical antagonistic networks, we aim to settle the inconsistency in literature by (i) fitting their node degree distributions to five different parametric models and identifying the one fits the best, (ii) measuring the levels of nestedness and compartmentalization of these 61 networks and testing their significance using different null models, and (iii) exploring how network connectance affects these three network architecture metrics. This research showed that most antagonistic networks do not display power law degree distributions and that resource species are generally uniformly distributed. We also clearly showed that the conclusion of whether a network is significantly compartmentalized or nested depends largely on the null model used.
Binding of deoxy-thymidine-5'-triphosphate and deoxyadenosine-5'-triphosphate to chrysotile asbestos
(Academy of Science for South Africa, 2003) Hawtrey, A.; Pieterse, A.; Van Zyl, J. M.; Bester, A. J.; Harington, J. S.
Tritiated deoxythymidine-5'-triphosphate ([3H]dTTP) and deoxyadenosine- 5'-triphosphate ([3H]dATP) were found to bind strongly to fibres of chrysotile asbestos. Binding of both triphosphates to amosite and crocidolite, however, was much less than that to chrysotile. Further work with chrysotile showed that the binding appears to be electrostatic in nature, with the negative phosphate groups of the nucleotides attaching to the positively charged groups on the mineral fibre. Attachment of the triphosphates to the mineral surface was found to be concentration dependent. Time curves of binding indicated that, for both nucleoside triphosphates, binding was rapid at 20oC and 37oC. Strong binding was also observed at 55oC. Binding at the higher temperatures depended on the type of buffer used and pH. Bound [3H]dTTP and [3H]dATP could be partially removed from chrysotile by 0.1 M sodium pyrophosphate after a short incubation at 20oC. Various chemical reagents that affected binding were studied and are discussed. The possible use of chrysotile asbestos as a solid phase material for the polymerization of dTTP and dATP or activated 5'-phosphorimidazolide of adenosine is also discussed.
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.
Deep Learning-Enabled Temperature Simulation of a Greenhouse Tunnel
(IWACP, 2023) Jogunola, O.; Hull. K.J.; Mabitsela, M. M.; Phiri, E.E; Adebisi, B.; Booysen, MJ
Agriculture is poised to suffer greatly from the effects of climate change. Prediction models, using deep learning, have been developed that can simulate and predict conditions in open field farming to combat the climate variability from climate change. However, deep learning used in precision agriculture, specifically greenhouse tunnels, is under-researched despite also being affected by this variability. Utilising tunnel data collected over 42 days, two hybrid deep learning models were designed. Specifically, a hybrid of convolutional neural network (CNN) and Long Short-Term Memory (LSTM), and a hybrid of CNN and Bidirectional LSTM (BLSTM). The models are designed to forecast the internal temperature of the tunnel to support its management. The cooling wet wall state, solar irradiance, inside and outside temperature of the tunnel are input variables to the developed deep-learning models. Two scenarios are discussed with the results, the first scenario includes all the external variables as input, while the second scenario only considers the internal temperature as input. Results show a performance improvement of 48% and 14% computation time for the CNN-LSTM compared to the CNN-BLSTM model for the two scenarios, respectively. In terms of the measured loss metrics, both models had varied performance and model fitness, with an average mean square error of 0.025 across the models and scenarios.
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.
Huwelikstevredenheid en vryetydsbesteding
(Faculty of the Humanities, University of the Free State, 2002) Viljoen, Hendrik; Greeff, Abraham
The aim of this study was to investigate patterns in leisure activities and their relation to marital satisfaction. A biographical questionnaire, a leisure activity questionnaire and two sub-scales of the Enriching and Nurturing Relationship Issues, Communication and Happiness (ENRICH) scale were completed independently by 35 married couples with adolescent children. The results indicated a significant positive relationship between marital satisfaction and contentment with the use of leisure time in both joint and individual-and-joint leisure activities. These results have important implications for premarital guidance, the enrichment of married life and marriage counselling.
INH preventive therapy (IPT) in HIV-infected south African children
(AOSIS, 2011) Cotton, Mark F.
HIV-infected children have a high risk of acquiring tuberculosis. The World Health Organization (WHO) has released isoniazid preventive therapy (IPT) recommendations for adults and children living with HIV, based on efficacy studies, mainly in adults. Data from children appear conflicting. IPT guidelines for children were developed in response to WHO guidelines at a local meeting, followed by discussions. IPT should be given to all HIV-infected children after exposure to a source case if treatment for active disease is not required. For children whose mothers' HIV status was known antentally, when tuberculosis has been actively excluded in mothers and at infant follow-up, and when infants have commenced antiretroviral therapy in the first 3 months of life, IPT is not required. Otherwise, all infants and children should be given IPT for 6 months once active tuberculosis has been excluded.
A novel method (FotoMaster) of documenting endosocopic surgical procedures
(Elsevier, 2000) Kruger, Thinus F.; Van der Merwe, Jacobus P.; Marino, Horacio; Hoogendijk, Christiaan F.; Du Toit, Thomas C.
Optimal design of intermittently operated subsonic-supersonic ejectors
(South African Institution of Mechanical Engineers, 2002) Pienaar, D. v V.
The optimal design for maximum run duration of intermittently operated subsonic-supersonic air-air ejector pumps of fixed geometry was investigated using an inviscid one-dimensional model of the mixing chamber. The study was confined to the case of matched static pressures of the primary and secondary air streams. An empirical correction factor was applied to the ID results in order to take approximate account of the two-dimensional velocity distributions at the inlet and outlet of the mixing chamber and of viscous shear forces. Optimisation of both the primary and secondary Mach numbers was found to yield significantly longer run durations than when the secondary is flow is sonic and just the primary Mach number is optimised. The most pronounced advantages of optimising both the primary and secondary Mach numbers were obtained in the range of high ejector performance. The main advantage is that an optimised ejector is physically smaller, and requires a smaller storage vessel than one that is not optimised.
Pathology-supported genetic testing presents opportunities for improved disability outcomes in multiple sclerosis
(2023-05-17) Johannes, Clint; Moremi, Kelebogile E.; Kemp, Merlisa C.; Whati, Lindiwe; Engel- Hills, Penelope; Kidd, Martin; van Toorn, Ronald; Jaftha, Mariaan; Janse van Rensburg, Susan; Kotze, Maritha J.
Background: Lipid metabolism may impact disability in people with multiple sclerosis (pwMS). Methods: Fifty-one pwMS entered an ultrasound and MRI study, of whom 19 had followed a pathology- supported genetic testing program for more than 10 years (pwMS-ON). Genetic variation, blood biochemistry, vascular blood flow velocities, diet and exercise were investigated. Results: PwMS-ON had significantly lower (p < 0.01) disability (Expanded Disability Status Scale) than pwMS not on the program (1.91 ± 0.75 vs 3.87 ± 2.32). A genetic variant in the lipid transporter FABP2 gene (rs1799883; 2445G>A, A54T) was significantly associated (p < 0.01) with disability in pwMS not on the program, but not in pwMS-ON (p = 0.88). Vascular blood flow velocities were lower in the presence of the A-allele. Conclusion: Pathology-supported genetic testing may provide guidance for lifestyle interventions with a significant impact on improved disability in pwMS. Plain Language Summary This study investigated the role of a genetic variant that increases saturated fat absorption and may make people with multiple sclerosis (MS) more susceptible to disability progression. Of 51 people with MS, 19 had followed a program which includes normalization of blood test results and daily intake of unsaturated fatty acids for more than 10 years, while the others had not. The latter group had significantly greater disability than the people who had followed the program, suggesting that the unsaturated fatty acids modulated the effect of the genetic variant. Six MS cases are presented as examples, including a marathon athlete (Case 1) and a patient who showed a dramatic decrease in disability from being wheelchair-bound for 15 years to walking freely (Case 2). Executive Summary: • In order to investigate the conundrum of why some people with multiple sclerosis (pwMS) become disabled while others do not, a cross-sectional interdisciplinary study was initiated from 1996 to the present at Stellenbosch University, to record data into a database regarding genetic variations, blood biochemistry, diet and exercise. Pathology-supported genetic testing (PSGT), a practical method to apply personalized medicine, was implemented to elucidate potential modulation of genetic variations through lifestyle interventions toward prevention of disability in pwMS. • The Gknowmix.org database is used to translate information obtained from a comprehensive study into personalized reports containing guidelines for treatment of pwMS by clinicians and supporting healthcare professionals, which enables P4 medicine: participatory (patient), personalized (scientist), predictive (clinician) and preventive (dietitian). • In the present case–control sub-study, 51 pwMS and 25 controls volunteered for an ultrasound and MRI study. Of these pwMS, 19 had followed the PSGT lifestyle program for more than 10 years, which included normalization of blood biochemistry, dietary intervention and exercise, as well as daily intake of specific supplements (the Rapha Regimen) [3], including unsaturated fatty acids (omega-3 and evening primrose oil). • The 19 pwMS who had followed the program had significantly less disability (p < 0.01), as assessed with the Expanded disability status scale (EDSS), than those who had not followed the program (1.91 ± 0.75 vs 3.87 ± 2.32). Furthermore, in the pwMS who had not followed the program, a genetic variant of a lipid transporter which favors increased absorption of saturated fatty acids, FABP2 rs1799883 (2445G>A, A54T), was associated significantly (p < 0.01) with the EDSS, while in the pwMS who had followed the program there was no association (p = 0.88). There was no difference in allele frequency between pwMS and controls. • Ultrasound assessments showed that higher blood flow velocities in the right common carotid arteries and vertebral arteries were significantly associated with improved EDSS, while the FABP2 rs1799883 variant was associated with decreased blood flow. • In the pwMS, homocysteine was significantly inversely associated with folate intake (p < 0.01). In the controls, saturated/trans fat intake was significantly associated with BMI (p < 0.01). • Six MS cases selected randomly are presented to demonstrate how data integration was instrumental in elucidating how dietary unsaturated fat intake may modulate the effect of FABP2 rs1799883 toward prevention of disability in pwMS who followed the PSGT protocol over more than 10 years. Of these, Case 1 is a marathon athlete, and Case 2 showed a dramatic decrease in EDSS from 7.5 to 2.0 over more than 10 years.
Performance of rotor-only axial fans designed for minimum exit kinetic energy
(South African Institution of Mechanical Engineers, 2002) Van der Spuy, S. J.; Von Backstrom, T. W.
The major loss source in rotor-only axial fans is the kinetic energy associated with the axial and circumferential components of the exit flow. This paper investigated the aerodynamic and acoustic performance of two fans designed to produce minimum exit kinetic energy. The first was a general application fan and the second a low-noise fan with large-chord forward-swept blades. The fans were tested for fan noise and performance in accordance with BS 848. The low-noise fan was the quieter and more efficient of the two fans, whilst both fans were quieter and more efficient than an existing typical general application fan, of unknown design. The results underlined the importance of following a well-defined design methodology when designing rotor-only axial flow fans.
Quantifying the role of personal management style in the success of investment portfolios
(Operations Research Society of South Africa, 2002) Wagenaar, E. A.; Van Vuuren, J. H.
It is extremely difficult to quantify the effect of different management styles of portfolio managers upon the success of their portfolios. Various mathematical models in the literature attempt to predict the risk and returns of portfolios according to changes in the economic arena, but these models usually do not take into account the personal styles of portfolio managers. The aim of this paper is a modest attempt at quantifying the effect of different managerial styles upon decisions regarding portfolios. This is accomplished by the formulation of a mathematical performance index that portrays the influence of a portfolio manager's personal and managerial characteristics on the success of his portfolio.
Rehabilitation and primary care treatment guidelines, South Africa
(World Health Organization, 2022-08-22) Conradie, Thandi; Charumbira, Maria; Bezuidenhout, Maryke; Leong, Trudy; Louw, Quinette
The World Health Organization recognizes rehabilitation as an essential component of universal health coverage (UHC). In many countries, UHC builds on a standard benefits package of services that is informed by the country’s essential medicines list, standard treatment guidelines and primary health care essential laboratory list. In South Africa, primary health care is largely provided and managed by primary health-care nurses and medical officers in accordance with primary health care standard treatment guidelines. However, rehabilitation is mostly excluded from these guidelines. This paper describes the 10-year process that led to rehabilitation referral recommendations being considered for inclusion in South Africa’s primary health care standard treatment guidelines. There were five key events: (i) a breakthrough moment; (ii) producing a scientific evidence synthesis and formulating recommendations; (iii) presenting recommendations to the national essential medicines list committee; (iv) mapping rehabilitation recommendations onto relevant treatment guideline sections; and (v) submitting revised recommendations to the committee for final consideration. The main lesson learnt is that, by working together, rehabilitation professionals can be of sufficient number to make a difference, improve service delivery and increase referrals to rehabilitation from primary health care. A remaining challenge is the lack of a rehabilitation representative on the national essential medicines list committee, which could hamper understanding of rehabilitation and of the complexities of the supporting evidence.
Simulating The Driving and Charging of Electric Minibus Taxis: A Case Study for Stellenbosch
(IWACP, 2023) Pretorius, B. G.; Strauss, J. M.; Booysen, M. J.
The Global North is increasing the drive for the electrification of the mobility industry. In sub-Saharan Africa, however, the adoption is yet to pick up steam due to various other challenges in the region. The viability of converting the paratransit fleet (which consists mostly of minibus taxis) to electric vehicles (EVs) with current combustion-based operations is investigated by making use of simulation software, and EV-Fleet-Sim. This developed software simulates the driving and charging of operationally tracked taxis in the Stellenbosch area. A charging algorithm, as well as a simple battery model, was included in the simulation to provide a more accurate representation of the scenario. Most of the taxis were found to still complete their required trips with the specified battery size of 70 kWh. However, new methods would need to be found, such as including a mixed fleet with some petrol or diesel taxis, to assure a 100% trip completion rate. The grid impact per vehicle was found with an expected maximum load appearing between the hours of 08h00 and 10h00 of 22 kW per vehicle, which corresponds to the time after the morning peak traffic of getting people to work. Furthermore, a minimum number of chargers can be implemented which will not affect the trip completion rate of the taxis. This was found to be for 4 chargers per 17 taxis. Future work is left to the testing of various parameters to find optimal solutions as well as including home charging and failed trip classification.
A survey dataset to evaluate the changes in mobility and transportation due to COVID-19 travel restrictions in Australia, Brazil, China, Ghana, India, Iran, Italy, Norway, South Africa, United States
(Elsevier, 2020) Barbieri, Diego Maria; Lou, Baowen; Passavanti, Marco; Hui, Cang; Lessa, Daniela Antunes; Maharaj, Brij; Banerjee, Arunabha; Wang, Fusong; Chang, Kevin; Naik, Bhaven; Yu, Lei; Liu, Zhuangzhuang; Sikka, Gaurav; Tucker, Andrew; Mirhosseini, Gaurav; Naseri, Sahra; Qiao, Yaning; Gupta, Akshay; Abbas, Montasir; Fang, Kevin; Ghasemi, Navid; Peprah, Prince; Goswami, Shubham; Hessami, Amir; Agarwal, Nithin; Lam, Louisa; Adomako, Solomon
COVID-19 pandemic has heavily impacted the global community. To curb the viral transmission, travel restrictions have been enforced across the world. The dataset documents the mobility disruptions and the modal shifts that have occurred as a consequence of the restrictive measures implemented in ten countries: Australia, Brazil, China, Ghana, India, Iran, Italy, Norway, South Africa and the United States. An online questionnaire was distributed during the period from the 11st to the 31st of May 2020, with a total of 9 394 respondents. The first part of the survey has characterized the frequency of use of all transport modes before and during the enforcement of the restrictions, while the second part of the survey has dealt with perceived risks of contracting COVID-19 from different transport modes and perceived effectiveness of travel mitigation measures. Overall, the dataset (stored in a repository publicly available) can be conveniently used to quantify and understand the modal shifts and people's cognitive behavior towards travel due to COVID-19. The collected responses can be further analysed by considering other demographic and socioeconomic covariates.
The effect of a post‑anaesthesia high‑care unit (PAHCU) admission on mobilization, length of stay and in‑hospital mortality post‑surgery in low energy neck of femur fracture patients
(Springer Link, 2024-01-09) Essa, S.; Venter, S.; Jordaan, J. D.
Purpose/aim: With an ageing population and an increase in fragility fractures of the hip (FFH), the role of an anaesthetist is evolving to include more peri-operative care. A post-anaesthesia high-care unit (PAHCU) should enhance care in postoperative patients. To our knowledge, there are no studies that have investigated the effect of a PAHCU admission on postoperative outcomes after FFH. This study aimed to compare post-operative outcomes of FFH patients admitted to PAHCU versus a standard post-operative orthopaedic ward (POOW). Methodology: A retrospective cohort study was conducted on adult patients with FFH who underwent surgery between January 2019 and December 2020 at our institution. Data were sourced from electronic medical records. SPSS version 28 was used to analyse data. Results: A total of 231 patients were included. The PAHCU group (n = 35) displayed a higher burden of chronic illness and higher peri-operative risk scores as compared to the POOW group (n = 196). Median time to mobilize (TTM) in PAHCU was 84 h vs. 45 h in POOW group (p = 0.013). Median length of stay (LOS) in PAHCU was 133 h vs. 94 h in POOW (p = 0.001). The in-hospital mortality was 2.9% (n = 1) for PAHCU and 3.6% (n = 7) for POOW (p = 1). The 30-day mortality was 11.8% (n = 4) for PAHCU and 10.1% (n = 19) in POOW. Conclusion: PAHCU admission resulted in delayed time to surgery and TTM, together with prolonged LOS, compared to those managed in POOW. However, these mortality rates remained comparable in both groups. This study contributes valuable insights into post-operative care of FFH patients in a resource-poor setting.
Thermofluid analysis of an axial flux permanent magnet (AFPM) generator
(South African Institution of Mechanical Engineers, 2001) Wang, R.; Dobson, R. T.; Kamper, M. J.
In this article a lumped-parameter heat transfer model and an air flow model of a typical Axial Flux Permanent Magnet (AFPM) machine is presented. The application of the proposed models to an AFPM generator is described in detail. The calculated results are compared with the measurements taken from a prototype AFPM machine. The advantages and disadvantages of the approach are then outlined and conclusions drawn. The developed thermofluid model is shown to perform thermal analyses with reasonable accuracy.
Thermogravimetric study of the pyrolysis characteristics and kinetics of coal blends with corn and sugarcane residues
(Elsevier, 2013) Aboyade, Akinwale O.; Gorgens, Johann F.; Carrier, Marion; Meyer, Edson L.; Knoetze, Johannes H.
This paper investigates the non-isothermal thermokinetics of the co-pyrolysis of sugarcane bagasse and corn residue blended with coal. The individual devolatilization behaviour of each of the fuels obtained separately was compared with the behaviour of the biomass blends with coal at various mix ratios. Possible synergistic behaviour that points to the existence of chemical interactions during pyrolysis between the coal and biomass fractions of the blends could thus be quantified. Synergistic interactions in the blends resulted in higher than expected volatile yields. The interactions occurred between 300 °C and 500 °C, corresponding to the end of biomass devolatilization and the start of coal decomposition. Isoconversional kinetic analysis revealed that apparent activation energy values varied between 165–180, 162–190, 160–175, and 225–260 kJ mol− 1 for sugarcane bagasse, corn cobs, corn stover, and coal in the 0.1 to 0.8 conversion range. A comparison of E(α) for single fuels and coal-biomass blends gave further evidence of synergistic behaviour as demonstrated by larger variation in E(α) during the decomposition of the blends, compared to the individual fuels.
Towards a Cleaner Production of an Underutilised Legume, Bambara Groundnut
(IWACP, 2023) Mabitsela, M. MA; Hull, K.JA; Mavengahama, SB.; Phiri, E.E.; Booysen, M.J
Soilless cultivation systems such as aeroponics provide a more efficient, and clean food production of in areas where there is limited access to arable land for agricultural practices and drought-prone countries. The objective of this study was to evaluate the yield performance of seventy Bambara groundnut (BGN) landraces cultivated in aeroponics and compared with a traditional drip-irrigated hydroponic system with sawdust as a growing medium. The result showed that BGN landraces cultivated in aeroponics accumulated a high number of seeds, as compared to those landraces cultivated in hydroponics. However, BGN landraces cultivated in hydroponics recorded a high shoot dry weight and one hundred seed weight. The root length that could only be measured in BGN landraces cultivated in the aeroponics systems, showed that BGN root length can extend beyond one meter. Soilless cultivation systems with their high-water use efficiency have the potential of reducing production costs, thus making them accessible to farmers in countries where drought is a reality.

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