Browsing by Author "Mohapi, Lerato"

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    Development and testing of the RHINO host streamed data acquisition framework
    (2017) Boleme, Mpati; Winberg, Simon; Mohapi, Lerato
    This project focuses on developing a supporting framework for integrating the Reconfigurable Hardware INterface for computing and radiO (RHINO) with a Personal Computer (PC) host in order to facilitate the development of Software Defined Radio (SDR) applications built using a hybrid RHINO/multicore PC system. The supporting framework that is the focus of this dissertation is designed around two main parts: a) resources for integrating the GNU Radio framework with the RHINO platform to allow data streams to be sent from RHINO to be processed by GNU Radio, and b) a concise and highly efficient C code module with accompanying Application Program Interface (API) that will receive streamed data from RHINO and provide data marshalling facilities to gather and dispatch blocks of data for further processing using C/C++ routines. The methodology followed in this research project involves investigating real-time streaming techniques using User Datagram Protocol (UDP) packets, furthermore, investigating how GNU Radio high-level SDR development framework can be integrated into the real-time data acquisition systems such as in the case of this project with RHINO. The literature for real-time processing requirements for the streamer framework was reviewed. The guidelines to implement a high performance, low latency and maximum throughput for streaming will consequently be presented and the proposed design motivated. The results achieved demonstrate an efficient data streaming system. The objectives of implementing RHINO data acquisition system through integration with standard C/C++ code and GNU Radio were satisfactorily met. The system was tested with real-time Radio Frequency (RF) demodulation. The system captures a pair of an In-phase/Quadrature signal (I/Q) sample at a time, which is one packet. The results show that data can be streamed from the RHINO board to GNU Radio over GbE with a minimum capturing latency of 10.2μs for 2 0 packet size and an average data capturing throughput of 0.54 Mega Bytes per second (MBps). The capturing latency, in this case, is the time taken from the time of the request to receiving the data. The FM receiver case study successfully demonstrated results of a demodulated FM signal of a 94.5 Mega Hetz (MHz) radio station. Further recommendations include making use of the 10GbE port on RHINO for data streaming purposes. 10GbE port on RHINO can be used together with GNU Radio to improve the speed of the RHINO streamer.
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    Liver toxicity associated with tuberculosis chemotherapy in the REMoxTB study
    (BioMed Central, 2018-03-28) Tweed, Conor D; Wills, Genevieve H; Crook, Angela M; Dawson, Rodney; Diacon, Andreas H; Louw, Cheryl E; McHugh, Timothy D; Mendel, Carl; Meredith, Sarah; Mohapi, Lerato; Murphy, Michael E; Murray, Stephen; Murthy, Sara; Nunn, Andrew J; Phillips, Patrick P J; Singh, Kasha; Spigelman, M; Gillespie, S H
    Background Drug-induced liver injury (DILI) is a common complication of tuberculosis treatment. We utilised data from the REMoxTB clinical trial to describe the incidence of predisposing factors and the natural history in patients with liver enzyme levels elevated in response to tuberculosis treatment. Methods Patients received either standard tuberculosis treatment (2EHRZ/4HR), or a 4-month regimen in which moxifloxacin replaced either ethambutol (isoniazid arm, 2MHRZ/2MHR) or isoniazid (ethambutol arm, 2EMRZ/2MR). Hepatic enzymes were measured at 0, 2, 4, 8, 12 and 17 weeks and as clinically indicated during reported adverse events. Patients included were those receiving at least one dose of drug and with two or more hepatic enzyme measurements. Results A total of 1928 patients were included (639 2EHRZ/4HR, 654 2MHRZ/2MHR and 635 2EMRZ/2MR). DILI was defined as peak alanine aminotransferase (ALT) ≥ 5 times the upper limit of normal (5 × ULN) or ALT ≥ 3 × ULN with total bilirubin > 2 × ULN. DILI was identified in 58 of the 1928 (3.0%) patients at a median time of 28 days (interquartile range IQR 14–56). Of 639 (6.4%) patients taking standard tuberculosis therapy, 41 experienced clinically significant enzyme elevations (peak ALT ≥ 3 × ULN). On standard therapy, 21.1% of patients aged >55 years developed a peak ALT/aspartate aminotransferase (AST) ≥ 3 × ULN (p = 0.01) and 15% of HIV-positive patients experienced a peak ALT/AST ≥ 3 × ULN compared to 9% of HIV-negative patients (p = 0.160). The median peak ALT/AST was higher in isoniazid-containing regimens vs no-isoniazid regimens (p < 0.05), and lower in moxifloxacin-containing arms vs no-moxifloxacin arms (p < 0.05). Patients receiving isoniazid reached a peak ALT ≥ 3 × ULN 9.5 days earlier than those on the ethambutol arm (median time of 28 days vs 18.5 days). Of the 67 Asian patients with a peak ALT/AST ≥ 3 × ULN, 57 (85.1%) were on an isoniazid-containing regimen (p = 0.008). Conclusions Our results provide evidence of the risk of DILI in tuberculosis patients on standard treatment. Older patients on standard therapy, HIV-positive patients, Asian patients and those receiving isoniazid were at higher risk of elevated enzyme levels. Monitoring hepatic enzymes during the first 2 months of standard therapy detected approximately 75% of patients with a peak enzyme elevation ≥3 × ULN, suggesting this should be a standard of care. These results provide evidence for the potential of moxifloxacin in hepatic sparing.
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    Monitoring the South African National Antireteoviral Treatment Programme, 2003-2007: The IeDEA Southern Africa Collaboration
    (2009) Cornell, Morna; Technau, Karl; Fairall, Lara; Wood, Robin; Moultrie, Harry; Van Cutsem, Gilles; Giddy, Janet; Mohapi, Lerato; Eley, Brian; MacPhail, Patrick; Prozesky, Hans; Rabie, Helena; Davies, Mary-Ann; Maxwell, Nicola; Boulle, Andrew
    Objectives: To introduce the combined South African cohorts of the International Epidemiologic Databases to Evaluate AIDS-Southern Africa (IeDEA-SA) collaboration as reflecting the South African national antiretroviral treatment (ART) programme; to characterize patients accessing these services; and to describe changes in services and patients 2003-2007. Design & setting Multi-cohort study of 11 ART programmes in Gauteng, Western Cape, Free State and KwaZulu-Natal. Subjects ART-naïve adults and children (<16 years old) who initiated ART with ≥3 antiretroviral drugs before 2008. Results: Most sites were offering free treatment to adults and children in the public sector, ranging from 264 to 17,835 patients per site. Among 45,383 adults and 6,198 children combined, median (IQR) range was 35.0 years (29.8-41.4) and 42.5 months (14.7-82.5) respectively. Of adults, 68% were female. Median CD4 cell count was 102 cells/µL (44-164) and was lower among males than females (86, 34-150 vs 110, 50-169, p<0.001). Median CD4% among children was 12% (7-17.7). Between 2003 and 2007, enrolment increased 11-fold in adults and 3-fold in children. Median CD4 count at enrolment increased for all adults (67-111 cells/µL, p<0.001) and for those in Stage IV (39-89 cells/µL, p<0.001). Among children <5 years, baseline CD4% increased over time (11.5%-16.0%, p<0.001). Conclusions: IeDEA-SA provides a unique opportunity to report on the national ART programme. The study describes dramatically increasing enrolment. Late presentation, especially of men and children, remains a concern. Investment in sentinel sites ensures good individual-level data while freeing most sites to continue with simplified reporting.
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    Toxicity related to standard TB therapy for pulmonary tuberculosis and treatment outcomes in the REMoxTB study according to HIV status
    (2019-08-14) Tweed, Conor D; Crook, Angela M; Dawson, Rodney; Diacon, Andreas H; McHugh, Timothy D; Mendel, Carl M; Meredith, Sarah K; Mohapi, Lerato; Murphy, Michael E; Nunn, Andrew J; Phillips, Patrick P J; Singh, Kasha P; Spigelman, Melvin; Gillespie, Stephen H
    Abstract Background The phase III REMoxTB study prospectively enrolled HIV-positive (with CD4+ count > 250 cells, not on anti-retroviral therapy) and HIV-negative patients. We investigated the incidence of adverse events and cure rates according to HIV status for patients receiving standard TB therapy in the trial. Methods Forty-two HIV-positive cases were matched to 220 HIV-negative controls by age, gender, ethnicity, and trial site using coarsened exact matching. Grade 3 and 4 adverse events (AEs) were summarised by MedDRA System Organ Class. Kaplan-Meier curves for time to first grade 3 or 4 AE were constructed according to HIV status with hazard ratios calculated. Patients were considered cured if they were culture negative 18 months after commencing therapy with ≥2 consecutive negative culture results. Results Twenty of 42 (47.6%) HIV-positive and 34 of 220 (15.5%) HIV-negative patients experienced ≥1 grade 3 or 4 AE, respectively. The majority of these were hepatobiliary disorders that accounted for 12 of 40 (30.0%) events occurring in 6 of 42 (14.3%) HIV-positive patients and for 15 of 60 (25.0%) events occurring in 9 of 220 (4.1%) HIV-negative patients. The median time to first grade 3 or 4 AE was 54 days (IQR 15.5–59.0) for HIV-positive and 29.5 days (IQR 9.0–119.0) for HIV-negative patients, respectively. The hazard ratio for experiencing a grade 3 or 4 AE among HIV-positive patients was 3.25 (95% CI 1.87–5.66, p < 0.01). Cure rates were similar, with 38 of 42 (90.5%) HIV-positive and 195 of 220 (88.6%) HIV-negative patients (p = 0.73) cured at 18 months. Conclusions HIV-positive patients receiving standard TB therapy in the REMoxTB study were at greater risk of adverse events during treatment but cure rates were similar when compared to a matched sample of HIV-negative patients.