UPSpace
Institutional Repository
Faculty Research Collections
UP Research Output Collections
Featured
Recent Submissions
Attribute based spatial segmentation for optimising POI placement
(Elsevier, 2025-08) De Klerk, Michelle; Fabris-Rotelli, Inger Nicolette
Effective spatial planning and resource optimisation require precise demarcation of potential spatial accessible areas and optimal placement of points of interest (POIs). Our approach introduces a novel attribute based spatial segmentation methodology that utilises an iterative clustering approach to create unique macro-regions, each associated with key structural and attribute specific properties. By integrating a probabilistic attribute based structure with k-means clustering, we adaptively segment spatial regions to balance area based attributes and topological characteristics. The full geographical network is segmented into attribute based macro-regions for all spatially accessible and spatially disjoint regions. Attribute based spatial segmentation offers insights into why certain areas may be spatially disjoint and if it is identified as potential spatially accessible areas to determine which POIs can be placed to maximise accessibility. This approach transforms city planning and resource allocation by aligning POI placement with regional needs and characteristics.
Pathogenicity of Pythium myriotylum on Acacia crassicarpa and Acacia mangium x Acacia auriculiformis clones in Indonesia
(Taylor and Francis, 2025) Tarigan, Marthin; Wingfield, Michael J.; Jami, Fahimeh; Oliveira, Leonardo S.S.; Saha, Muhammad A.; Duran, Alvaro; Pham, Nam Q.; nam.pham@fabi.up.ac.za
The oomycete Pythium myriotylum is an important pathogen of several crops, causing wilt and damping-off during nursery propagation. The pathogen was recently reported as the causal agent of wilt and damping-off on Acacia crassicarpa plants in nurseries located in Riau, Indonesia. The aim of this study was to evaluate the relative pathogenicity of P. myriotylum on different clones of A. crassicarpa and Acacia mangium × Acacia auriculiformis hybrids. Based on the results, greater tolerance was found on the A. mangium × A. auriculiformis hybrid clones than on those of pure A. crassicarpa. The different Acacia clones also displayed different levels of tolerance of infection. Overall the results showed that screening for tolerance to infection by P. myriotylum will be important in the Acacia breeding programme and make it possible to produce sufficient nursery stock for plantation establishment.
Analytical and quality control validation of a novel symmetric dimethylarginine assay in dogs and cats
(Wiley, 2025-09) Mashego, Portia Tshidi; Hooijberg, Emma Henriette
BACKGROUND : An immunoturbidometric assay for symmetric dimethylarginine (SDMA) measurement on automated chemistry analyzers has recently become available.
OBJECTIVE : To perform analytical validation of the EUROLyser SDMA assay in dogs and cats.
METHODS : Method validation experiments were performed using stored canine and feline serum. Quality control validation was performed according to Westgard. Performance goals were derived from SDMA biological variation data for both species.
RESULTS : Imprecision ranged from 3.7%-7.8% (dogs) to 6.0%-11.8% (cats) with a dispersion of ±35% for dogs and ±44% for cats. The assay showed linearity (up to 85 μg/dL [dogs], 75 μg/dL [cats]); the preliminary LoQ was 9.5 and 6.9 μg/dL, respectively. Recovery was 19.7% and 6.5%, respectively. Severe hemolysis resulted in a significant bias in both species. The EUROLyser method showed a significant negative proportional and constant bias in dogs and a significant positive proportional and negative constant bias in cats, compared to the comparative method. In dogs, the mean bias (-19.5%) and the bias at clinical decision limits exceeded the desirable bias; in cats, the mean bias (-4.0%) and the bias at clinical decision limits was < 8%. Because of high imprecision, the TEA that could be controlled for was 35%, with a 1-2.5 s rule using patient pools as quality control material.
CONCLUSIONS : The novel SDMA assay showed acceptable analytical performance, but high dispersion has consequences for the interpretation of results at reference limits and serial measurements. Method-specific reference intervals and decision limits should be generated for both species, particularly for dogs, given the significant bias vs. the comparative method.
An evaluation of alternative treatment strategies in mitigating colistin resistance : targeting plasmid transfer through the use of Bambermycin or the protein coded by the Mcr-1 gene with antibodies and Streptomycin
(Wiley, 2025-09) Hassan, Ibrahim Zubairu; Qekwana, Daniel Nenene; Naidoo, Vinny; hassan.ibrahim@up.ac.za
BACKGROUND : Plasmid mediated antimicrobial resistance continues to be a source of global concern, especially given the limited pipeline of novel antibiotics. The horizontal transfer of the plasmid mediated colistin resistance gene (mcr-1) between microorganisms confer resistance to previously susceptible bacterial strains and renders colistin and polymyxin B antimicrobials ineffective.
OBJECTIVE : To mitigate plasmid mediated colistin resistance using bambermycin and streptomycin on mcr-1 positive field strains of Escherichia coli. Furthermore, to assess if a commercial MCR-1 polyclonal antibody would have any synergistic effect on colistin in killing mcr-1 gene associated colistin-resistant E. coli in vitro.
METHODS : Colistin-resistant E. coli strains recovered from clinical cases were subjected to checkerboard assays and conjugation assays using varying drug combinations viz colistin, bambermycin, streptomycin, MCR-1 antibody and human complement serum, to mitigate drug resistance.
RESULTS : Following conjugation assay, the plasmid bound resistance gene was successfully transferred to J53 E. coli strain with colistin minimum inhibitory concentration (MIC) rising from ≤0.125 to >2 µg/mL conferring resistance to the former organism. The combination of bambermycin and colistin in a checkerboard assay proved to be synergistic in killing mcr-1 associated colistin-resistant strains. The combination of streptomycin, colistin and MCR-1 polyclonal antibody showed additive lethal effect on mcr-1 associated colistin-resistant strains. Bambermycin did not interfere with the transfer of mcr-1 bound plasmid from donors to recipient organism.
CONCLUSION : Further studies on bambermycin's mechanism of action are required, as both inhibiting and enhancing effects have been documented. Similarly, the addition of MCR-1 polyclonal antibody in a checkerboard assay did not enhance colistin's lethal effect on mcr-1 carrying E. coli strains, thus highlighting the need for further research.
Seroprevalence and risk factors associated with Brucellosis in goats in Nyagatare District, Rwanda
(Wiley, 2025-08) Habimana, Jean Paul; Ntivuguruzwa, Jean Bosco; Uwimana, Aime Lambert; Ugirabe, Marie Aurore; Gasana, Eric; Van Heerden, Henriette
Given the endemic nature of bovine brucellosis in Rwanda, caprine brucellosis, primarily caused by Brucella melitensis in goats, may also be prevalent. However, no data exist on the disease’s prevalence and associated risk factors in goats, particularly in Nyagatare district. A cross-sectional study was therefore conducted to determine the seroprevalence of brucellosis and to identify herd-level risk factors associated with the disease among goat herds (n = 102) across six sectors of Nyagatare district. Serum samples from 612 goats were tested using both the indirect enzyme-linked immunosorbent assay (i-ELISA) and the Rose Bengal Test (RBT), applied in parallel. A systematic questionnaire, pretested for reliability, was used to gather data on potential risk factors for caprine brucellosis. The study found a brucellosis true adjusted seroprevalence of 6.08% and 10.7% using RBT and i-ELISA, respectively. When combining the results from both tests, the overall seroprevalence was 6.08% at the animal level and 16.6% at the herd level. The most significant risk factors for Brucella seropositivity were mixing of cattle and goats within the same herd and a history of abortions in the herd (p < 0.05). This study confirms that caprine brucellosis is endemic in Nyagatare district, highlighting the need for a One Health approach to control and prevent the disease in both livestock and humans. The study recommends implementing awareness campaigns to educate livestock farmers about brucellosis and calls for further research to characterize Brucella spp. in small ruminants in Rwanda and to establish appropriate control measures.