1. Academic Wits Research Outputs/Journal articles
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Item Introducing a secondary segmentation to construct a radiomics model for pulmonary tuberculosis cavities(Springer, 2023) du Plessis, Tamarisk; Ramkilawon, Gopika; Duncombe Rae, William Ian; Botha, Tanita; Martinson, Neil Alexander; Dixon, Sarah Alice Parry; Kyme, Andre; Sathekge, Mike MichaelPurpose: Accurate segmentation (separating diseased portions of the lung from normal appearing lung) is a challenge in radiomic studies of non-neoplastic diseases, such as pulmonary tuberculosis (PTB). In this study, we developed a segmentation method, applicable to chest X-rays (CXR), that can eliminate the need for precise disease delineation, and that is effective for constructing radiomic models for automatic PTB cavity classification. Methods: This retrospective study used a dataset of 266 posteroanterior CXR of patients diagnosed with laboratory confirmed PTB. The lungs were segmented using a U-net-based in-house automatic segmentation model. A secondary segmentation was developed using a sliding window, superimposed on the primary lung segmentation. Pyradiomics was used for feature extraction from every window which increased the dimensionality of the data, but this allowed us to accurately capture the spread of the features across the lung. Two separate measures (standard-deviation and variance) were used to consolidate the features. Pearson’s correlation analysis (with a 0.8 cut-off value) was then applied for dimensionality reduction followed by the construction of Random Forest radiomic models. Results: Two almost identical radiomic signatures consisting of 10 texture features each (9 were the same plus 1 other feature) were identified using the two separate consolidation measures. Two well performing random forest models were constructed from these signatures. The standard-deviation model (AUC = 0.9444 (95% CI, 0.8762; 0.9814)) performed marginally better than the variance model (AUC = 0.9288 (95% CI, 0.9046; 0.9843)). Conclusion: The introduction of the secondary sliding window segmentation on CXR could eliminate the need for disease delineation in pulmonary radiomic studies, and it could improve the accuracy of CXR reporting currently regaining prominence as a high-volume screening tool as the developed radiomic models correctly classify cavities from normal CXR.Item Female condom color and scent preference in Durban, South Africa(Elsevier, 2023-06) Beksinska, Mags; Smit, Jenni; Mona, Amanda; Maphumulo, Virginia; Mphili, Nonhlanhla; Manzini-Matebula, Nontsikelelo; Chidarikire, ThatoObjectives: To assess preferences for female condom (FC) colors and scents. Study design: Women aged 18–40 years were randomized to one of three FCs (FC2, Cupid1, Cupid2) two of which offered a choice of color and scent (red/strawberry, purple/vanilla, natural/unscented). Women could choose any variety within condom types while participating in an FC contraceptive efficacy study in South Africa. Results: One hundred and thirty-three women were allocated to each FC type. Strawberry was the most popular variety for both FC2 and Cupid1 (60.9%, 78.3% respectively). Some women chose more than one variety but few chose the natural. Conclusions: Data support a clear preference for colored and scented FCs. Implications: These data can inform FC programme managers to predict demand for different varieties of FC and can adjust supply of FCs accordinglyItem The stability of C-peptide and insulin in plasma and serum samples under different storage conditions(De Gruyter, 2023-07) Nkuna, Delhia X.; Khoza, Siyabonga P.; George, Jaya A.; Maphayi, Mpho R.Objectives: C-peptide and insulin are peptide hormones and their stability is affected by a number of pre-analytical factors. The study aimed to investigate the impact of sample type, storage temperature and time delays before centrifugation and analysis on the stability of C-peptide and insulin. Methods: Ten healthy non-diabetic adults in fasting and non-fasting state were enrolled. 40 mL of blood was collected from each participant into SST and dipotassium EDTA tubes. Samples were centrifuged immediately or at timed intervals (8, 12, 48 and 72 h). After baseline measurements on the Roche Cobas e602 analyzer using electrochemiluminescence immunoassays, aliquots were stored at room temperature (RT), 2–8 and −20 °C for 4 h to 30 days. The percentage deviation (PD) from baseline was calculated and a change greater than desirable biological variation total error was considered clinically significant. Results: C-peptide was more stable in separated serum than plasma (PD of −5 vs. −13 %) samples stored at 2–8 °C for 7 days and was most unstable at RT when centrifugation was delayed (PD −46 % in plasma and −74 % in serum after 48 h). Insulin was more stable in plasma than in serum under the different storage conditions with a minimum PD of −1% when stored at −20 °C for 30 days. When samples were kept unspun at RT for 72 h, PD was −23 and −80 % in plasma and serum, respectively. Conclusions: C-peptide was more stable in serum provided the sample was centrifuged immediately and stored in the fridge or freezer while insulin was found to be more stable in EDTA plasma.Item Spectrum of ascending aortic aneurysms at a peri-urban tertiary hospital: an echocardiography-based study(Oxford University Press, 2023-07) Meel, Ruchika; Hasenkam, Michael; Goncalves, Ricardo; Goncalvev, Ricardo; Mogaladi, ShunguIntroduction: Thoracic ascending aortic (TAA) aneurysms are an important cause of disability and death and require early detection for effective management. Currently, there is a paucity of data from Africa pertaining to TAA aneurysms. This study describes the spectrum of TAA aneurysms at a peri-urban tertiary hospital. Methods: A descriptive retrospective study based on clinical and echocardiographic imaging data of patients with TAA aneurysms from October 2017–October 2022. Advanced strain imaging was performed to measure left ventricular (LV) basal, apical, and global longitudinal strain as well as circumferential strain (CS) of the ascending aorta as a proxy measurement of aortic compliance. Results: The study comprised 139 cases of TAA aneurysms (52.5% females) with a mean age of 50 ± 14.8 years with 45 age and gender matched controls. Most cases (95%) were of African ethnicity. The main etiologies were hypertension (41.7%), HIV (36.6%), connective tissue disease (10.7%), congenital (2.2%) and mixed pathologies (8.6%). Two-thirds of patients (69.7%) presented in heart failure, 10% presented with aortic dissection. Thirty percent of the patients were classified as New York Heart Association (NYHA) class I, 59.7% NYHA II, 8.6% NYHA III and two patients NYHA class IV. Echocardiography revealed enlarged aortic dimensions compared to controls (P < 0.001). TAA aneurysms were complicated by severe aortic regurgitation (AR) in half (50.3%) of patients, moderate AR in 25.8%, and mild AR in 14.3%. The mean LV ejection fraction (46.9 ± 12.7%) was reduced compared to controls (P < 0.001). Aortic CS was reduced compared to controls [4.4 (3.2–6.2) % vs. 9.0 (7.1–13.4) %, P < 0.001]. Aortic stiffness was higher in the aortic aneurysm group compared to controls (15.39 ± 20.65 vs. 5.04 ± 2.09, P = 0.001). LV longitudinal strain (−13.9 ± 3.9% vs. 18.1 ± 6.7%), basal CS (−13.9 ± 5.6% vs. −17.9 ± 5.8%) and apical CS (−8.7 ± 8.5% vs. −30.6 ± 3.8%) were reduced compared to controls (P < 0.001). Most patients were on diuretic and anti-remodeling therapy. Surgery was performed in 29.4% and overall mortality was 7.9%. Mortality for acute aortic dissection was 40%. Conclusion: TAA aneurysms associated with hypertension and HIV are common in this predominantly African female population and are associated with considerable morbidity and mortality. Two-dimensional echocardiography and advanced strain imaging are potential tools for detecting and risk stratifying TAA aneurysms.Item Causes and predictors of mortality in South Africans with systemic sclerosis(Wiley, 2023-05) Dire, Zodwa; Ickinger, Claudia; Tikly, MohammedBackground: There is a dearth of mortality data on systemic sclerosis (SSc) in sub‐Saharan Africa. We undertook a retrospective study of causes and predictors of death in low‐income indigent South Africans with SSc. Methods: A retrospective records review of clinicodemographic, laboratory, and outcome data of SSc patients attending a state‐funded tertiary Rheumatology service in South Africa. Results: Most of the 164 patients were Black (92.7%) and female (87.8%). The mean (SD) age at diagnosis and follow‐up duration were 42.6 (12.9) and 5.5 (5.6) years, respectively. The majority (75.6%) had diffuse cutaneous SSc (dcSSc); and digital pits/ulcers, interstitial lung disease (ILD), and pulmonary hypertension (PH) were documented in 73.6%, 55.0%, and 38.3%, respectively. There were 56 known deaths and an equal number of patients were lost to follow‐up. Deaths resulted from ILD complicated by PH (42.9%), infections (8.9%), cardiac disease (7.1%), and malignancies (3.6%). Estimated 5‐ and 10‐year survival rates for patients with known outcomes were 58% and 42%, respectively. Independent predictors of death were renal dysfunction and cor pulmonale. Conclusion: Most patients in this study of South Africans had dcSSc and poor outcomes. Known deaths resulted from cardiorespiratory complications of ILD complicated by PH. Cor pulmonale and renal dysfunction were independent predictors of death.Item Association of close-range contact patterns with SARS-CoV-2: a household transmission study(eLife Sciences Publications, 2023-07) Kleynhans, Jackie; Dall'Amico, Lorenzo; Gauvin, Laetitia; Tizzoni, Michele; Maloma, Lucia; Walaza, Sibongile; Martinson, Neil A.; von Gottberg, Anne; Wolter, Nicole; Makhasi, Mvuyo; Cohen, Cheryl; Cattuto, Ciro; Tempia, StefanoBackground: Households are an important location for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, especially during periods when travel and work was restricted to essential services. We aimed to assess the association of close-range contact patterns with SARS-CoV-2 transmission. Methods: We deployed proximity sensors for two weeks to measure face-to-face interactions between household members after SARS-CoV-2 was identified in the household, in South Africa, 2020-2021. We calculated the duration, frequency, and average duration of close-range proximity events with SARS-CoV-2 index cases. We assessed the association of contact parameters with SARS-CoV-2 transmission using mixed effects logistic regression accounting for index and household member characteristics. Results: We included 340 individuals (88 SARS-CoV-2 index cases and 252 household members). On multivariable analysis, factors associated with SARS-CoV-2 acquisition were index cases with minimum Ct value <30 (aOR 16.8 95% CI 3.1-93.1) vs >35, and female contacts (aOR 2.5 95% CI 1.3-5.0). No contact parameters were associated with acquisition (aOR 1.0-1.1) for any of the duration, frequency, cumulative time in contact, or average duration parameters. Conclusions: We did not find an association between close-range proximity events and SARS-CoV-2 household transmission. Our findings may be due to study limitations, that droplet-mediated transmission during close-proximity contacts plays a smaller role than airborne transmission of SARS-CoV-2 in the household, or due to high contact rates in households.Item Adsorptive removal of BTEX compounds from wastewater using activated carbon derived from macadamia nut shells(IWA Publishing, 2023-01) Melaphi, Kedibone; Sadare, Olawumi O.; Simate, Geoffrey S.; Wagenaar, Stephan; Moothi, KapilIn this study, adsorptive removal of benzene, toluene, ethylbenzene and xylenes (BTEX) from synthetic water using activated carbon adsorbent derived from macadamia nut shells was investigated. The surface functional groups of the synthesized adsorbents were assessed by Fourier transform infrared spectra. The specific surface area, pore size and pore volume at 77 K nitrogen adsorption, surface morphology, and the crystalline structure of the adsorbents were determined using Brunauer-Emmett-Teller, scanning electron microscopy and x-ray diffraction, respectively. Batch adsorption mode was used to evaluate the performance of the activated carbon. The stock solutions of synthetic wastewater were prepared by dissolving 100 mg/L of each of the BTEX compound into distilled water in a 250 mL volumetric flask. Effect of initial concentration of BTEX compounds, contact time, and mass of adsorbent on the removal of BTEX compounds from the synthetic wastewater was investigated. The macadamia nut shell–derived activated carbon (MAC) proved to be an effective adsorbent for BTEX compounds, with a large surface area of 405.56 m2 /g. The exposure time to reach equilibrium for maximum removal of BTEX was observed to be 20 min. The adsorption capacity of the BTEX compounds by MAC followed the following adsorption order: benzene > toluene > ethylbenzene > xylene.Item A qualitative study to explore strategies to improve the Road to Health Application for maternal and child health outcomes in South Africa(Frontiers Media, 2023-03) Dietrich, Janan Janine; Tsotetsi, Lerato; Dubazane, Thenjiwe; Tshabalala, Gugulethu; Maimela, Boitumelo; Weiss, Martin; Mulaudzi, MamakiriBackground: The Road to Health Application (RTHA) is essentially a digitalized version of the National Department of Health’s Road to Health book, and a hand-printed booklet given to mothers at the birth of each baby. The RTHA, like the booklet, provides guidelines for maternal and child health outcomes, with the goal of creating a database of children and caregivers in South Africa and teaching them how to raise a healthy child. This paper explored potential barriers and enablers to using the RTHA in the South African context based on user experiences. Methods: Using a qualitative design, we conducted 50 serial interviews (two separate interviews, 1 month apart). Through convenience, sampling eligible participants were 18 years or older women who were pregnant and/or had a child under the age of 5 years. Participants included 25 existing users and 25 new users of the RTHA, who owned android smart phones at enrollment. Existing users were recruited telephonically through the National Department of Health database, and new users were approached at the antenatal care unit and wellness baby clinic (women with children under 5 years) at the Chris Hani Baragwaneth Academic Hospital. Upon enrollment, participants completed a brief survey on sociodemographics and mobile phone use, and thereafter, they had a baseline interview followed by a telephonic interview 1 month later. A semistructured interview guide was used to explore barriers, enablers, and the usability of the RTHA. Using thematic data analysis, we identified enablers and barriers to the use of the RTHA. Results: A third (33%) of all participants reported IsiZulu as their main language of communication, and 6% of the participants reported English as their main language of communication. The RTHA was an important addition to the booklet that helped keep new mothers informed about child immunization and provided important information about healthy child rearing practices. However, multiple barriers were cited to using the RTHA; these included the fact that the app was only available in two languages, high data costs, lack of access to smart phones, and app functionalities. The enablers to using the RTHA included the accessibility of important information regarding prenatal and postnatal childcare. Conclusion: This study gives insight into the barriers and enablers from the end-user perspective to improve the RTHA for future use in South Africa and offers guidance on how to improve the RTHA to be more user-friendly, which could increase its usability among mothers. It further emphasizes the need to consider the challenges experienced by users in South Africa when developing future mobile health interventions to increase uptake.Item CSPG4 as a target for the specific killing of triple-negative breast cancer cells by a recombinant SNAP-tag-based antibody-auristatin F drug conjugate(Springer, 2023-07) Mungra, Neelakshi; Bitegh, Fleury A. N.; Malindi, Zaria; Huysamen, Allan M.; Karaan, Maryam; Hardcastle, Natasha S.; Bunjun, Rubina; Chetty, Shivan; Naran, Krupa; Lang, Dirk; Richter, Wolfgang; Hunter, Roger; Barth, StefanPurpose: Triple-negative breast cancer (TNBC) is phenotypic of breast tumors lacking expression of the estrogen receptor (ER), the progesterone receptor (PgR), and the human epidermal growth factor receptor 2 (HER2). The paucity of well-defined molecular targets in TNBC, coupled with the increasing burden of breast cancer-related mortality, emphasizes the need to develop targeted diagnostics and therapeutics. While antibody-drug conjugates (ADCs) have emerged as revolutionary tools in the selective delivery of drugs to malignant cells, their widespread clinical use has been hampered by traditional strategies which often give rise to heterogeneous mixtures of ADC products. Methods: Utilizing SNAP-tag technology as a cutting-edge site-specific conjugation method, a chondroitin sulfate proteoglycan 4 (CSPG4)-targeting ADC was engineered, encompassing a single-chain antibody fragment (scFv) conjugated to auristatin F (AURIF) via a click chemistry strategy. Results: After showcasing the self-labeling potential of the SNAP-tag component, surface binding and internalization of the fluorescently labeled product were demonstrated on CSPG4-positive TNBC cell lines through confocal microscopy and flow cytometry. The cell-killing ability of the novel AURIF-based recombinant ADC was illustrated by the induction of a 50% reduction in cell viability at nanomolar to micromolar concentrations on target cell lines. Conclusion: This research underscores the applicability of SNAP-tag in the unambiguous generation of homogeneous and pharmaceutically relevant immunoconjugates that could potentially be instrumental in the management of a daunting disease like TNBC.Item Accuracy of CT angiography for detecting ruptured intracranial aneurysms(AOSIS Publishing, 2023-05) Mkhize, Nomasonto N.; Mngomezulu, Victor; Thandi E. ButheleziBackground: Digital subtraction angiography (DSA) is invasive, costly and unavailable in many South African hospitals; however, it remains the gold standard for imaging intracranial aneurysms. CT angiography (CTA) is a non-invasive and readily available screening tool prior to DSA. Objectives: This study aimed to evaluate the diagnostic performance of CTA in detecting ruptured intracranial aneurysms using DSA as the reference standard and to determine the effect of aneurysm size and location on CTA sensitivity. Method: A retrospective analysis of CTA and DSA data from reports of patients suspected to have aneurysmal subarachnoid haemorrhage (SAH) at Chris Hani Baragwanath Academic Hospital between January 2017 and June 2020. Results: Conventional DSA detected aneurysms in 94 out of 115 patients; while of these, CTA detected 75 and missed 19. The CTA sensitivity, specificity and accuracy was 80%, 43% and 73%, respectively. The CTA sensitivity for aneurysms < 3 mm and 3 mm – 5 mm in size was 30% and 81.5%, respectively (p = 0.024). Sensitivity of CTA for posterior communicating artery (PComm) aneurysms was 56% and lower than other major anterior circulation locations (83% – 91%) (p = 0.045). Conclusion: The CTA diagnostic efficiency was lower than previously reported, with even lower sensitivity for aneurysms < 3 mm and for those arising from the PComm. Thus, CTA should remain a screening tool prior to DSA in all local patients suspected to have aneurysmal SAH.