Research Articles (University of Pretoria)

Permanent URI for this collectionhttp://hdl.handle.net/2263/121

This collection offers open access to the full text of research articles published by staff, students and affiliates of the University of Pretoria. These items are identical in content to their published counterparts. It is linked to the Research Information System and complements the Annual Research Report.

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Sub-Saharan Africa's oldest shipwreck : historical-archaeological research of an early modern-era Portuguese merchantman on the Namibian coast
Werz, Bruno E.J.S. (Routledge, 2010)
No abstract available.
Wind direction and strength determine the genetic structure of an insect-pollinated plant across heterogeneous landscape
Deng, Jun-Yin; Fu, Rong-Hua; Compton, Stephen G.; Yuan, Chuan; Kling, Matthew M.; Chen, Xiao-Yong; Song, Yao-Bin; Jiang, Kai; Liu, Mei; Greeff, Jacobus Maree; Chen, Yan (Wiley, 2025-06)
AIM : Dispersal of plant propagules and their genes is crucial for plant responses to landscape heterogeneities, yet the mechanisms behind this dispersal remain unclear. Ficus species depend on wind-borne fig wasps for pollination, but research on airflow effects on Ficus genetic structure has produced conflicting results. Our study aims to clarify the role of wind in shaping the genetic structure of such plants with wind-borne insect pollinators by examining how geomorphological complexity interacts with air movements to influence genetic structures. LOCATION : Southwest China: Sichuan, Yunnan, Guangxi and Guizhou provinces. TAXON : Ficus tikoua Bur., Ficus, Moraceae. METHODS : We sampled 56 F. tikoua sites across southwest China, characterised by high geomorphologic complexity. River basins and predominant winds were visualised across the sampled regions. Wind connectivity between sampled sites during the main pollination season was modelled based on hourly daily wind data. The maternal and biparental genetic structure of sites were reconstructed using chloroplast DNA (cpDNA) and nuclear SSR (nuSSR) markers. Links between genetic structure, location, and wind parameters were estimated by Mantel or partial Mantel tests. RESULTS : The plant's maternal genetic structure was defined by river systems, with two distinct cpDNA groups located in the Yangtze and Pearl River basins, respectively. The boundaries for nuclear variation were less clearly delimited geographically. Sites with mixtures of nuSSR groups were concentrated where prevailing winds arrived from several directions. Stronger between-site air flows increased nuSSR geneflow and genetic similarities, while populations receiving more wind flow were also more genetically variable. MAIN CONCLUSIONS : Our study reveals how plant gene dispersal reflects air and water movements that in turn respond to geomorphologic complexity, thereby directly demonstrating the effects of wind on gene flow of plants with wind-borne insect pollinators. Wind data matching pollinator flight times and large sample sizes are crucial for testing wind effects.
In silico and in vitro evaluation of flavonoid derivatives for diabetes management : molecular dynamics, and enzyme kinetics for pancreatic alpha-amylase and alpha-glucosidase
McMillan, Jamie; Bester, Megan Jean; Apostolides, Zeno (Springer, 2025-11)
Please read abstract in the article.
Maxi Schoeman - an appreciation
Vale, Peter Christopher Julius (Vale, Peter Christopher Julius, 2026)
More than anything else – and certainly, more than anyone else – Maxi Schoeman, who passed away on 14 September 2025 has ensured the longevity of the academic discipline of International Relations in South Africa. This is because Professor Schoeman encouraged scholars to build trust with those who practice the diplomatic craft. She also championed rigorous academic standards, a deep commitment to public service, and called on scholars to frame policies relevant to their work. This is the principal message of this Appreciation of a friend, a colleague, and a confidant, not only of this writer, but of many in the ‘political science’ community beyond African shores.
A public sector reputation management framework for South Africa’s Eastern Cape Provincial Government
Msiya, Mgwebi; De Beer, Estelle (University of the Free State, 2025-12)
Reputation management was synonymous with the private sector until recently when public sector organisations, particularly in Europe and America, adopted the concept. This study's aim is to contribute to the scant body of knowledge on public sector reputation management, specifically in South Africa's Eastern Cape province. The study adopted a qualitative approach to gain an understanding of the public perceptions of the Eastern Cape Provincial Government's reputation. The findings were based on two participant observations and a purposively selected sample of 15 participants who were recruited from non-governmental organisations (NGOs), media institutions, government departments, youth structures, and business organisations. The study utilised semi-structured interviews and participant observations as data collection techniques. The collected data was analysed thematically through categorisation and Leximancer software analysis. The results of the study show that the Eastern Cape Provincial Government lacks the capacity to manage its reputation strategically, resulting in increasingly discontented communities. Furthermore, the findings reveal that the public held negative views of the Eastern Cape Provincial Government's reputation. The Public Sector Reputation Management Framework, which was developed in this study, provides an understanding of how the Eastern Cape Provincial Government's reputation could be strategically and sustainably managed.
An epigenetic perspective on neonatal encephalopathy with suspected hypoxic ischaemic encephalopathy
Mistry, Priyal; Mellet, Juanita; Durandt, Chrisna; Smuts, Izelle; Pepper, Michael Sean (BioMed Central, 2025-12-08)
Neonatal encephalopathy with suspected hypoxic ischaemic encephalopathy (NESHIE) is a neurological disorder caused by oxygen deprivation and limited blood flow to a neonate's brain. Although various antenatal and perinatal factors have been identified, their precise role in NESHIE pathogenesis remains unclear. The pathophysiology involves multiple molecular pathways that can be explored using a multi-omics approach, including epigenetics. Epigenetics involves heritable changes in gene expression without altering the DNA sequence, encompassing chemical modifications to DNA and histone proteins, as well as changes mediated by non-coding RNAs (ncRNAs). These epigenetic changes regulate gene expression and can be influenced by environmental factors, offering crucial insights into gene regulation and disease mechanisms. This review examines the role of epigenetic mechanisms in NESHIE, focusing on the modulation of hypoxia-inducible factor-1 alpha (HIF-1α) and ncRNA during hypoxic conditions. Additionally, epigenetic-mediated foetal programming may shed light on how maternal and antenatal risk factors contribute to NESHIE susceptibility. Understanding these epigenetic signatures could advance biomarker discovery and the development of novel therapeutic strategies for NESHIE.
Light sensitivity and diel activity rhythms in the Angoni vlei rat (Otomys angoniensis) under natural and artificial conditions
Oosthuizen, Tasha; Pillay, Neville; Oosthuizen, Maria Kathleen (Taylor and Francis, 2025-10-16)
Artificial light at night (ALAN) can disrupt daily rhythms of wildlife, yet little is known about its effects on African rodents. We investigated the diel activity rhythms of the Angoni vlei rat (Otomys angoniensis), a species with an inconclusive temporal niche. We exposed wild-caught vlei rats to three treatments: (1) standard laboratory light–dark cycle; (2) laboratory light–dark cycle with low-intensity ALAN (2 Lux); and (3) natural ambient light and temperature fluctuations. Activity was recorded via infrared sensors, and the activity rhythm was quantified using Cosinor analysis. Activity was predominantly nocturnal across all treatments. However, rhythm amplitude, MESOR and robustness were nearly three-times higher under natural conditions than in both laboratory treatments. ALAN did not significantly suppress activity, suggesting minimal masking effects (unlike strictly nocturnal animals) and possible flexibility in the temporal niche. In nature, O. angoniensis occupies dense grass habitats, and therefore, its predominantly nocturnal activity in captivity could be due to the lack of adequate cover during experiments. Moreover, the greater activity under natural conditions could be a consequence of brighter daytime light and natural temperature cycles. We suggest that although O. angoniensis displays nocturnal activity in the laboratory, it may be more diurnal in its natural habitat. Our findings demonstrate that the temporal activity of O. angoniensis is shaped by environmental context, with implications for contextualising circadian flexibility in species inhabiting human-altered landscapes.
Reflections on editorial leadership : looking back…moving forward
Den Hond, Frank; Painter, Mollie (Cambridge University Press, 2025-10)
We take the opportunity in this editorial that marks the end of our tenure, to offer some reflections on our experiences. It is an occasion for looking back, for reflection on the scholarship and practice of business ethics, and for celebrating some of the outstanding work that is being done in and for the journal.
Spectral modelling of Cygnus A between 110 and 250 MHz : impact on the LOFAR 21-cm signal power spectrum
Ceccotti, E.; Offringa, A.R.; Koopmans, L.V.E.; Mertens, F.G.; Mevius, M.; Acharya, A.; Brackenho, S.A.; Ciardi, B.; Gehlot, B.K.; Ghara, R.; Chege, J.K.; Ghosh, S.; Höfer, C.; Hothi, I.; Iliev, I.T.; McKean, J.P.; Munshi, S.; Zaroubi, S. (EDP Sciences, 2025-04)
Studying the redshifted 21-cm signal from the neutral hydrogen during the Epoch of Reionisation and Cosmic Dawn is fundamental for understanding the physics of the early universe. One of the challenges that 21-cm experiments face is the contamination by bright foreground sources, such as Cygnus A, for which accurate spatial and spectral models are needed to minimise the residual contamination after their removal. In this work, we develop a new, high-resolution model of Cygnus A using Low Frequency Array (LOFAR) observations in the 110–250 MHz range, improving upon previous models by incorporating physical spectral information through the forced-spectrum method during multi-frequency deconvolution. This approach addresses the limitations of earlier models by providing a more accurate representation of the complex structure and spectral behaviour of Cygnus A, including the spectral turnover in its brightest hotspots. The impact of this new model on the LOFAR 21-cm signal power spectrum is assessed by comparing it with both simulated and observed North Celestial Pole datasets. Significant improvements are observed in the cylindrical power spectrum along the Cygnus A direction, highlighting the importance of having spectrally accurate models of the brightest foreground sources. However, this improvement is washed out in the spherical power spectrum, where we measure differences of a few hundred mK at k < 0.63 h cMpc−1, but not statistically significant. The results suggest that other systematic effects must be mitigated before a substantial impact on 21-cm power spectrum can be achieved.
Investigation of mass substructure in gravitational lens system SDP 81 with ALMA long-baseline observations
Stacey, H.R.; Powell, D.M.; Vegetti, S.; McKean, J.P.; Wen, D. (EDP Sciences, 2025-11)
The prevalence and properties of low-mass dark matter haloes serve as a crucial test for understanding the nature of dark matter, and may be constrained through the gravitational deflection of strongly lensed arcs. Previous studies found evidence for the presence of low-mass dark matter haloes in observations of the gravitationally lensed, dusty star-forming galaxy SDP.81, using the Atacama Large Millimetre/sub-millimetre Array (ALMA). In this work, we analyse these observations to assess the robustness of these reported results. While our analysis indicates that the data support additional angular structure in the lensing mass distribution beyond an elliptical power-law density profile, we do not find evidence for two previously reported sub-halo detections. However, we verify with realistic mock data that we could have found evidence in favour of a previously reported sub-halo with a log Bayes factor of 29, should it exist in the real data. After testing various systematics, we find that this previous sub-halo inference was most likely spurious and resulted from an inadequate smooth model, specifically, poorly fitting multipoles. While we do not find evidence in favour of any individual sub-halo, we find evidence for similarity in the lensing signatures of multipoles () and single massive sub-haloes, consistent with other recent work. We suggest that future searches for low-mass haloes in lensed arcs include lens angular structure in the form of multipoles up to 4th order and require a good-fitting smooth model as a prerequisite. Overall, our findings demonstrate the suitability of ALMA data of this quality to simultaneously constrain the abundance of low-mass haloes and lens angular structure.
Stochastic analysis of a system of two interconnected inventories
Yadavalli, Venkata S. Sarma; Tshinangi, Kapya; Adetunji, Olufemi (MDPI, 2025-12-05)
This paper considers a continuous review inventory system for two interconnected product types, 1 and 2. Product type 1 is purchased from an external agency, whereas type 2 is manufactured in-house through a sequential batching process. The maximum stock position attainable by type 1 is 𝑆1 and that of type 2 is 𝑆2 . Unit demands arise independently for the two products, where type 1 demand arrives following a Poisson process with rate 𝜆1 and that for product B also follows a Poisson process with rate 𝜆2. At the instance of the stock level of type 1 dropping to zero, it is replenished instantaneously to the maximum level 𝑆1 , such that the stock level is never zero, and hence all demands for type 1 product are satisfied. The production machine attached to type 2 stops manufacturing immediately when its stock level reaches 𝑆2, and resumes immediately when the stock level drops to 𝑆2−1. In the event of the type 2 product not being available when demand arrives, it is substituted with the type 1 product with probability p. The production time for a single unit of type 2 is exponentially distributed with mean 1𝛾. We identify the underlying Markov process and analyse the performance of the interconnected inventory system.
An inventory model for growing items with imperfect quality, deterioration, and freshness- and inventory level-dependent demand under carbon emissions
Tshinangi, Kapya; Adetunji, Olufemi; Yadavalli, Venkata S. Sarma (MDPI, 2025-12-12)
Inventory models have evolved to incorporate a wide range of realistic factors, including growing items, imperfect quality, deterioration, and sustainability concerns. While these areas have received significant individual attention, no model has yet integrated the complexities of growing items, imperfect quality, deterioration, and carbon emissions. This study addresses this gap by introducing an economic order quantity (EOQ) model for growing items that simultaneously accounts for imperfect quality, deterioration, carbon emissions, and a demand rate that is influenced by both stock levels and the freshness condition. The goal is to determine the replenishment cycle and the optimal order quantity that will maximise profit. A numerical example is presented to illustrate the model’s feasibility. A sensitivity analysis on key parameters is also conducted to provide critical managerial insights. The results reveal that the shelf life of items and the scaling parameter of demand are among the most influential factors of profit, causing up to 150% and 112% increase in profit, respectively. The findings also indicate that deterioration significantly impacts system profitability by up to −45%. Another critical insight is that profit decreases by up to 80% when the weight of the growing items increases. Furthermore, emissions can be most effectively reduced by focusing on the feeding process, which represents the most impactful factor for improving sustainability, whereas emissions from the screening process, purchasing, deterioration, and storage hold minimal financial consequence.
Spectral indices and principal component analysis for lithological mapping in the Erongo region, Namibia
Benade, Ryan Theodore; Ajayi, Oluibukun Gbenga (MDPI, 2025-12-18)
The mineral deposits in Namibia’s Erongo region are renowned and frequently associated with complex geological environments, including calcrete-hosted paleochannels and hydrothermal alteration zones. Mineral extraction is hindered by high operational costs, restricted accessibility and stringent environmental regulations. To address these challenges, this study proposes an integrated approach that combines satellite remote sensing and machine learning to map and identify mineralisation-indicative zones. Sentinel 2 Multispectral Instrument (MSI) and Landsat 8 Operational Land Imager (OLI) multispectral data were employed due to their global coverage, spectral fidelity and suitability for geological investigations. Normalized Difference Vegetation Index (NDVI) masking was applied to minimise vegetation interference. Spectral indices—the Clay Index, Carbonate Index, Iron Oxide Index and Ferrous Iron Index—were developed and enhanced using false-colour composites. Principal Component Analysis (PCA) was used to reduce redundancy and extract significant spectral patterns. Supervised classification was performed using Support Vector Machine (SVM), Random Forest (RF) and Maximum Likelihood Classification (MLC), with validation through confusion matrices and metrics such as Overall Accuracy, User’s Accuracy, Producer’s Accuracy and the Kappa coefficient. The results showed that RF achieved the highest accuracy on Landsat 8 and MLC outperformed others on Sentinel 2, while SVM showed balanced performance. Sentinel 2’s higher spatial resolution enabled improved delineation of alteration zones. This approach supports efficient and low-impact mineral prospecting in remote environments.
Biochemical and haemostatic variables associated with metastasis in dogs with carcinoma or sarcoma
Pazzi, Paolo; Fosgate, Geoffrey Theodore; Kristensen, Annemarie T.; Goddard, Amelia (Wiley, 2026-01)
OBJECTIVES : Identify alterations in biochemical and haemostatic variables between tumour-bearing dogs with and without metastasis that can be used to predict the presence of metastasis. MATERIALS AND METHODS : Thirty dogs with sarcoma and 29 with carcinoma were included in the analysis. Serum biochemistry profiles and haemostatic variables (haematocrit value, platelet count, thromboelastography (TEG), fibrinogen, Factor X, VII, antithrombin activity and D-dimer concentration) were measured for all dogs. All dogs underwent complete post-mortem and histopathological evaluations. For tumour-bearing dogs without intracavitary haemorrhage, measured variables were compared between dogs with and without metastasis, and univariate and multivariable analysis were performed to identify predictors of metastasis. RESULTS : Metastasis was identified in 31 of 59 (53%) dogs, of which 5 of 31 (16%) had metastasis to the regional lymph node only and 26 of 31 (84%) had distant metastasis. Sodium, ionised calcium, TEG lysis % at 30 and 60 minutes (Ly60) were significantly lower in tumour-bearing dogs without intracavitary haemorrhage with metastasis compared to dogs without metastasis. Multivariable analysis identified sodium <142.5 mmol/L as 64% sensitive (CI95%:45% to 82%) and 63% specific (CI95%:44% to 81%); and Ly60 < 1.0% as 68% sensitive (CI95%: 49% to 88%) and 78% specific (CI95%:61% to 95%) for prediction of the presence of metastasis. Parallel interpretation of lower sodium and decreased Ly60 resulted in high sensitivity (96%) for the presence of metastasis. CLINICAL SIGNIFICANCE : Sodium and TEG-based decreased fibrinolysis were associated with metastasis in tumour-bearing dogs without haemorrhage; when identified, they should prompt further diagnostics to detect possible metastasis of a primary carcinoma or sarcoma.
Identification of sources of Fusarium head blight and deoxynivalenol resistance in Ethiopian wheat cultivars
Mawcha, Kahsay Tadesse; Yang, Wenxiang; Ndolo, Dennis (Springer, 2026-02)
Fusarium head blight (FHB), caused by Fusarium graminearum, poses a significant threat to wheat production in Ethiopia, causing yield losses of up to 30–70% in severe epidemics and contaminating grain with deoxynivalenol (DON). This study aimed to identify sources of FHB and DON toxin resistance among selected Ethiopian wheat cultivars. Forty-three cultivars were evaluated for FHB resistance under greenhouse and field conditions, using the spawn inoculation method. Disease index (DI), Fusarium-damaged kernels (FDK), and DON content were quantified. The mean DI across cultivars ranged from 2.33% to 56.8%, FDK from 1.2% to 48.5%, and DON from 0.12 to 8.64 mg kg⁻¹. Cultivar “Sulla” exhibited the highest level of FHB resistance with a stable DI of 2.33%, FDK of 1.8%, and DON content of 0.16 mg kg⁻¹—the first such finding reported in Ethiopian germplasm. Notably, cultivars “Menze”, “Shorima”, and “Lemu” displayed strong resistance to DON contamination, with toxin levels ≤ 0.25 mg kg⁻¹, exceeding previously reported resistance thresholds. Eleven cultivars, including “Sulla”, exhibited significantly reduced yield losses (< 10%) compared to controls, whereas cultivars such as “Abola”, “Alidoro”, “Kakaba”, “Kingbird”, and “Simba” accumulated the highest DON levels (≥ 6.5 mg kg⁻¹) and showed high susceptibility. Based on the specific molecular marker Xumn10, the Fhb1 resistance gene was detected in 23 cultivars and the resistant control, “Sumai-3”. These findings significantly expand the pool of resources for FHB and DON resistance in Ethiopian wheat breeding, with the potential to improve yields by up to 20% and reduce mycotoxin contamination by more than 80% in FHB hotspots.
Draft genome sequences of Rahnella perminowiae, R. aceris, and R. aquatilis isolated from onion bulbs (Allium cepa L.) displaying symptoms of bacterial rot
Mnguni, Fanele Cabangile; Shin, Gi Yoon; Aegerter, Brenna J.; Du Toit, Lindsey J.; Derie, Michael L.; Coutinho, Teresa A. (Springer, 2026-02)
Onions (Allium cepa L.) are among the most widely produced vegetables globally, and their cultivation plays an important role in food security (Schwartz et al. 2007). However, the emergence of opportunistic bacterial plant pathogens, such as Rahnella species, which are not fully understood yet, poses a threat to onion production (Asselin et al. 2019; Brady et al. 2022). Rahnella species are Gram-negative, facultative anaerobes within the Yersiniaceae family, part of the order Enterobacteriales (Adeolu et al. 2016). According to the List of Prokaryotic Names with Standing in Nomenclature (LPSN), the genus consists of 15 described species that are isolated from various environments and are considered validly characterised (Guo et al. 2012; Brady et al. 2014; Lee et al. 2019; Liang et al. 2020).
Multi-disciplinary initiatives to rendering services to women survivors of human trafficking in South Africa
Sambo, Juliet Patience; Sibanda, Sipho (Routledge, 2026)
The women survivors of human trafficking suffer diverse consequences that require service providers to be creative, well-coordinated, and to render services in a multi-disciplinary manner. For social services to be relevant to the needs of women, they should be conducted from an ecological systems approach. Based on a qualitative study conducted at five organizations in South Africa, this paper highlights the multi-disciplinary initiatives to rendering services to women survivors of human trafficking. Employing a phenomenological research design, data was collected from 14 social service providers through one-on-one interviews and analyzed using a thematic analysis. The findings indicate that social service providers make use of a multi-disciplinary approach in rendering services and that this has contributed toward building the resilience of the women, who now seem to have a hope to heal and restart a new life. However, there are challenges in working from a multi-disciplinary approach due to some stakeholders not delivering on their mandates. The conclusion is that social service providers are fully aware of the opportunities presented by the multi-disciplinary approach to rendering services. Future research should be conducted on designing programmes and interventions aimed at addressing the needs of women survivors of human trafficking.
Bridging gaps in mitochondrial disease diagnosis : the role of advanced biomarker discovery
Makwikwi, Tendai; Schoonen, Maryke; Smuts, Izelle; Van der Westhuizen, Francois H. (Springer, 2026-01)
Mitochondrial disease (MD) is associated with dysfunction of the oxidative phosphorylation (OXPHOS) system and represents one of the most frequently occurring inherited neuromuscular diseases. Like many rare diseases, MD is characterised by striking clinical heterogeneity, resulting from its unique bi-genomic aetiology and multi-system involvement of energy-dependent tissues. Despite four decades of genetic discoveries and the advent of omics-driven insights into genes, mutations, and phenotypes, achieving an early and accurate diagnosis remains challenging—even within advanced diagnostic settings. A reliable genetic diagnosis for MD requires specialised clinical expertise capable of recognising population-specific phenotypes, providing access to genomic diagnostic services, and interpreting local genotype–phenotype correlations. However, these resources remain unevenly distributed, limiting diagnostic yield and equity. Research output and diagnostic infrastructure for MD are disproportionately concentrated in high-income countries. This imbalance persists even though ~ 84% of the global population resides in low- and middle-income countries (LMICs), where access to MD diagnostics, research infrastructure, and specialised care remains limited. Recent World Health Organisation (WHO) and International Classification of Diseases (ICD-11) initiatives have acknowledged these disparities, emphasising the need for improved diagnostic access, laboratory capacity, and data-sharing mechanisms [4,5,6,7]. Nevertheless, the diagnostic capacity divide remains substantial. A major contributor to the diagnostic gap in MD is the absence of reliable biomarkers that enable early detection, disease monitoring, and assessment of therapeutic efficacy. The lack of validated biomarkers restricts both diagnostic precision and therapeutic development.
Type I multivariate Pólya-Aeppli distributions with applications
Geldenhuys, Claire; Ehlers, Rene; Bekker, Andriette, 1958- (Elsevier, 2026-03)
An extensive body of literature exists that specifically addresses the univariate case of zero-inflated count models. In contrast, research pertaining to multivariate models is notably less developed. We propose two new parsimonious multivariate models that can be used to model correlated multivariate overdispersed count data. Furthermore, for different parameter settings and sample sizes, various simulations are performed. In conclusion, we demonstrate the performance of the newly proposed multivariate candidates on two benchmark datasets, which surpasses that of several alternative approaches.
An international interdisciplinary commentary on the revised guidelines for music-based interventions checklist, elaboration guide and validation study
Magee, Wendy L.; Bhana-Pema, Varshika; Carr, Catherine E.; Ettenberger, Mark; Fancourt, Daisy; Garrido, Sandra; Kwan, Melanie; Lichtensztejn, Marcela; Marinho, Valeska; Sarkamo, Teppo; Sundar, Sumathy; Yoo, Ga Eul; Zhang, Jingwen (Oxford University Press, 2026-02)
No abstract available.

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