Introduction: The impact of HIV on the one-month perioperative morbidity and mortality in patients undergoing cardiac surgery in sub-Saharan Africa (SSA) in the AntiRetroviral Therapy (ART) era is not known. Pre ART era data from South Africa suggested that patients with a CD4 count less than 400 should be selected with caution. European and North American information suggest that short and long-term outcomes of cardiac surgery in patients with HIV on ART are acceptable, but this experience cannot be generalized to the SSA where demographic profiles, co-morbidities and underlying cardiac pathology requiring surgery is significantly different. Methods: We set out to conduct a retrospective review of the Groote Schuur Hospital and Chris Barnard Division of Cardiothoracic Surgery patient records between 2003 and 2013, to evaluate the perioperative and one month outcomes of HIV positive patients undergoing cardiac surgery at our tertiary care institution. Eighty-one patients met all our study inclusion criteria. Findings: The patient cohort were young, (mean age 34), female (73%) and predominantly black (83%), 41% were on ART, 28% had previous tuberculosis and the average CD4 count was 426.5 cells/μL. Of the 81 patients 54 (67%) underwent valve surgery, 5 (6%) underwent CABG and 3 (4%) had both. Five (6%) patients died in hospital prior to discharge. Bleeding requiring transfusion was the most common complication (n=14; 17.3%) with 2 (2.5%) requiring relook. Other complications included wound sepsis in 9 (11%), complete heart block in 5 (6%), acute kidney injury in 4 (5%), hospital-acquired pneumonia in 3 (4%), cardiac tamponade in 3 (4%) and only one (1%) needlestick injury was reported. The predictors of death included the need for aortic root replacement and prolonged cardiopulmonary bypass time (OR 25 [p=0.006] and OR 1.02 [p= 0.01] respectively) Conclusion: HIV positive patients had cardiac surgical outcomes with low mortality rates comparable to international trends which were independent of CD4 counts. Perioperative complications rates were slightly higher than anticipated.

Aims: The first aim was to describe the characteristics and demands of the Torpedo SwimRun Cape 2019 race. The second aim was to determine predictors of race performance, by using entry, result and questionnaire data. Objectives: The first objective was to explore distributions of age (y), sex, 1km pool swimming time (mm:ss), 5km road running time (mm:ss), competency level (Likert scale), estimated race finishing time (hh:mm), training habits (min/week and sessions/week), background sport (type), equipment used (type), wave selection (athletes select if they want to start in a slow, medium or fast wave)(type), total and segment race times (mm:ss) and questionnaire scores of race participants. The second objective was to analyze segment and race result times, 5km run times, 1km swim times and ocean knowledge questionnaire results. Results: In total, there were 99 participants (288 athletes took part in the race) of which 36% were female and 64% were male. Each team in the Torpedo SwimRun Cape must consist of two athletes. Of the athletes, 53% were entered in male teams, 30% in mixed teams (a male and a female per team) and 17% entered in female teams. The median age was 41 years with an interquartile range (IQR) of 19 years. The mean race time was 174:15 mm:ss (± 29:51 mm:ss). Athletes trained on average 7 sessions/week (IQR 7 sessions/week), and 435 min/week (IQR 345 min/week). The median ocean knowledge score (OKQ) was 9 (IQR 4). Athletes' self-reported current 5km road running time was on average 25:00 mm:ss (IQR 07:41 mm:ss) and their current 1km pool swimming time was 18:00 mm:ss (IQR 07:02 mm:ss). Total race time was significantly associated with current 5km road running time ( = 0.488, p = 0.001), current 1km pool swimming time ( = 0.607, p = 0.001) and OKQ score ( = -0.349, p = 0.003). These three variables were also used to predict total race time. The over-all linear regression model was found to be significant (R2 = 0.514, p = 0.001). Conclusion: The athletes that participated in the Torpedo SwimRun Cape 2019 display a large variance in their training habits, particularly their training loads. It was found that the performance in this SwimRun race was not only dependent on how trained athletes were, but 4 also their ocean knowledge. Ocean knowledge is a learned skill and not necessarily attained by swimming in the ocean more (training open-water swimming was not associated with OKQ score). The OKQ questionnaire showed that better scores were associated with faster total racing time. The model used to predict performance accounted for approximately half of the variation seen in total race time. There is a clear need to further understand how performance is affected in SwimRun races. Repeat studies should be done to investigate different training strategies (also taking an athlete's team partner into account), the effect of various environmental exposures and how different equipment influence racing.

Irritable Bowel Syndrome (IBS) is the most prevalent functional gastrointestinal (GI) disease in the western world today. There are multiple subtypes of IBS and the symptoms of the disease vary drastically. The main types of IBS are IBS with constipation (IBS-C), IBS with diarrhea (IBS-D) and mixed IBS (IBS-M). Because of the commonality of this disease, there are a wide array of treatments that have been used and are currently being used to treat patients suffering with IBS symptoms. These treatments vary in their efficacy, with some being much more effective than others for the specific subtypes of the disease. However, as technological advances increase and the root cause and pathophysiology of IBS is discovered, more efficacious treatments are also being discovered. The most common treatments used today include but are not limited to probiotic supplements, limited diets such as the FODMAP diet, antibiotics and antidepressants, and psychological interventions such as Cognitive Behavioral Therapy (CBT) and hypnosis. New promising treatments include Fecal Microbiota Transplants (FMT) and individualized medicine. The pathophysiology of IBS has not yet been completely elucidated but the literature is clear on the fact that there are microbiome changes in patients with IBS. Many of the treatments that have high rates of success address the microbiome changes. The future of IBS treatments may depend on the gut microbiota and establishing a new gut environment through a variety of methods. Moreover, many of the current treatments treat this aspect of IBS as well. IBS is not a disease exclusive to the gut and is thought to influence and be influenced by outside stress and neurotransmitters such as serotonin. The research on IBS treatments indicates that there is no one treatment that is the most effective but rather that individuals need to work with health professionals to find a unique treatment that will work for their particular symptoms.

BACKGROUND: Malignant gliomas are a fatal disease that despite extensive research in the field, are still poorly understood. The primary form of treatment has been tumor reduction using a combination of radiotherapy, chemotherapy and surgery, but median survival of adult and pediatric patients is about 2 years. Thus, it is imperative to understand this disease and develop therapies that can eradicate these infiltrative tumor cells without having significant toxicity to the normal functioning of the brain. CRISPR-interference (Clustered Regularly Interspaced Short Palindromic Repeats; CRISPRi) screens have identified long noncoding RNAs (lncRNAs) that may potentiate the effects of radiation in gliomas. lncRNAs exhibit highly cell type-specific expression and function, making these attractive targets for potential cancer therapies. This class of transcript is poorly studied thus far as a potential therapeutic target. Current models of human glioma fall short of recapitulating the tumor microenvironment, and therefore, make testing potential therapies difficult. For example, because CTC338M12.4 (lncGRS-1), a potential glioma therapeutic target, is only expressed in primates, it would be time-consuming and expensive to perform studies on genetically-engineered mouse models. OBJECTIVES: 1) To explore the role of lncGRS-1 as a glioma-specific therapeutic target and in the p53-mediated DNA damage response, 2) To build upon a new experimental model system that can better represent the characteristics of human glioma. METHODS: Project One: I performed knockdown assays of lncGRS-1 and analyzed levels p53 and p21 levels by Western Blot analysis. I also identified presence of phospho-53 binding protein (P53BP1) and γ H2AX by immunohistochemistry. Finally, I performed double knockdowns of lncGRS-1 and p53 to study the effect on cell proliferation. Project Two: I generated mature brain organoids (MBOs) of 10,000 cells comprised of astrocytes, neurons, and pediatric glioma cells. Tumor burden of glioma cells growing in the MBOs was assessed over a period of 10 days and quantified with ImageJ. I generated MBOs of 60,000 cells comprised of astrocytes, neurons, pediatric glioma cells, and two different types of endothelial cells labeled with calcein. Organoids were placed in three different media compositions and combinations of epithelial growth factor and basic fibroblast growth factor and followed for 8 days. RESULTS: Project One: lncGRS-1 knockdown reduced both p53 and p21 levels. P53BP1 levels increased in the presence of radiation and lncGRS-1 knockdown, as well as with knockdown alone. γ-H2AX levels were not impacted significantly by lncGRS-1 knockdown. U87 glioma cells had decreased proliferation with p53 and lncGRS-1 double knockdown than with lnGRS-1 knockdown alone. Project Two: Introducing EGF/FGF-2 at 10 ng/mL concentration produced MBOs with tumors that did not overtake the organoid within 10 days. Cortical organoid media appeared to be the best media composition to support MBOs comprised of endothelial cells, astrocytes, neurons, and glioma cells. CONCLUSIONS: Project One: Our results suggest that lncGRS-1 plays a role in the DNA damage response by modifying a cell’s ability to pass cell cycle checkpoints. Project Two: I generated mature brain organoids comprised of 4 different cell types – astrocytes, neurons, endothelial cells, and glioma cells. Furthermore, I identified a media composition (cortical organoid media) that allowed for all cell types to survive for at least a one week.

For HIV-infected patients undergoing antiretroviral treatment (ART), the latent reservoir is a major barrier to cure. Formed in the acute stages of infection, the latent reservoir consists of cells in the host’s body where HIV can hide from the immune system and remain in a quiescent state. When a patient stops ART, the virus quickly rebounds, proliferates, and begins infecting more cells. The majority of assays available to measure the latent HIV reservoir measure HIV DNA and RNA using polymerase chain reaction (PCR). However, these methods can overestimate the reservoir size, because unintegrated and replication-incompetent DNA comprise a larger proportion of HIV nucleic acids than does replication competent HIV provirus. To measure integrated HIV DNA from infected donor samples provided by the HIV Reservoir Assay Validation and Evaluation Network (RAVEN) and The University of Texas Health Sciences Center at Houston (UTHealth), I applied pulsed-field gel electrophoresis (PFGE) to reduce the amount of unintegrated HIV DNA such as episomal 2-long-terminal-repeat (2-LTR) circles before quantitation with droplet digital PCR (ddPCR). This assay could prove useful to measure changes in the latent HIV reservoir, especially in clinical trials that aim to reduce its size through a variety of compounds.

Tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) is an inflammatory disorder which affects up to 54% of TB-HIV co-infected patients. Its pathogenesis remains unclear, and although treatment with the corticosteroid prednisone has shown some benefits, there is no specific treatment currently available for TB-IRIS. N-3 polyunsaturated fatty acids (PUFA) have safely and successfully been used in the treatment of other inflammatory diseases, and we hypothesized that they will have beneficial anti-inflammatory effects on TB-IRIS patient-derived immune cells. To investigate this hypothesis, we used mass spectrometry (MS)-based proteomic methods to probe the secretome of peripheral blood mononuclear cells (PBMCs) re-stimulated ex vivo with Mycobacterium tuberculosis (Mtb) whole cell lysate (WCL), and treated with n-3 PUFA. Optimization experiments were performed on cells obtained from eight healthy donors to assess the secretome changes induced by re-stimulation with Mtb WCL and treatment with n-3 PUFA. In addition, experiments were repeated using PBMCs obtained from five non-IRIS and five TB-IRIS patients. The secretome was prepared via chloroform/methanol precipitation and overnight Trypsin digestion, and investigated via MS-based shotgun proteomics. MaxQuant was used for protein identification and Perseus for statistical analysis. Stimulation with Mtb WCL shifted the secretome of healthy PBMCs towards an inflammatory state, and this was altered by treatment with EPA/DHA via changes in the regulation of several proteins. Preliminary results from TB-IRIS patient-derived PBMCs show the same trend. These promising early results suggest the potential benefits of n-3 PUFA dietary supplementation for patients with TB-IRIS, and warrant further studies with increased sample size to confirm findings, and the possible inclusion of n-3 PUFA in a future clinical trial on patients with TBIRIS.

Background Efavirenz (EFV), a non-nucleoside reverse transcriptase inhibitor (NNRTI), has been a component of first line antiretroviral treatment in the South African HIV/AIDS programme since 2004. Similarly, it is extensively used in ART programmes in other low and middle incomes countries. The natural history of the previously reported EFV drug induced liver injury (DILI), is unknown. Objectives To establish causality assessment for the drug-induced liver injury and elucidate the natural history of EFV DILI by observing a cohort of patients through documenting all the factors influencing the patterns of clinical and histological injury, the time to clinical and biochemical recovery, the associated mortality rate and to establish if any demographic or clinical factors predict poor outcomes. Methods Patients were prospectively included after establishing causality criteria for EFV DILI. Clinical, demographic and histological features were carefully documented from the time of presentation and through follow up. Prednisone at 0.25-0.5mg/kg was initiated at the discretion of the treating hepatologist. Risk factors for severe injury or death and time to event (full clinical recovery and full biochemical recovery) were analyzed. Results 50 patients were included in the analysis, median age 34 (IQR 29-39) years, men significantly older than women, p=0.014. Most (92%) were female gender, and of black African ethnicity (86%). The median duration on ART at time of presentation was 6.5 months with half of the women initiating ART during pregnancy at a median gestation of 24 weeks (IQR 11 – 36). Median CD4 nadir at ART treatment initiation was 517 cells/mm3, with no significant difference (p=NS) in CD4 nadir in those pregnant or not. Median RUCAM score was 7 and of the 66% of patients who had liver biopsies, 3 histological patterns were identified: submassive necrosis (57,5%), nonspecific hepatitis (36%) and mixed cholestatic hepatitis (6%). Multivariate analysis suggested predictors for the development of submassive necrosis included age >30 years [OR 0.86 (0.15-0.97), p=0.02], pregnancy [OR 6.9 (1.34 – 35.6), p=0.02]; CD4 >350 [OR, 7.1 (1.5-31.9), p=0.02] but not alcohol use [OR 1.17 (0.72-1.18); p=0.07]. For the non-specific hepatitis group, only pregnancy predicted [OR 8.7 (1.3- 58.2), p=0.03]. The mortality rate was 14%, median time from admission to death was 15 days with the median duration to initial hospital discharge 33 (IQR 24 -52) days. Biochemical recovery was prolonged necessitating a follow up period of more than a year at an outpatient specialist clinic. 86% initiated protease inhibitor based ART successfully. Conclusion EFV DILI is a severe injury with significant inpatient mortality and morbidity requiring prolonged hospitalization and outpatient follow up.

Introduction. Interstitial lung disease (ILD) is prevalent in patients with autoimmune rheumatic diseases (ARD), leads to significant morbidity and mortality and is poorly characterized in South Africa (SA). We undertook this study to describe the clinical, serological and radiological features of ILD associated with ARD in a tertiary referral hospital. Methods. A cross-sectional study of patients with ILD attending the rheumatology and respiratory outpatient clinics of Groote Schuur Hospital between October 2018 and September 2019. Clinical, serological and radiological features were documented. We compared features of 3 groups of patients: rheumatoid arthritis (RA), systemic sclerosis (SSc) and other autoimmune connective tissue diseases (OCTD) which included idiopathic inflammatory myopathies, mixed connective tissue disease, systemic lupus erythematosus, primary Sjogren's syndrome and overlap syndromes. Factors associated with usual interstitial pneumonia (UIP) subtype were assessed. Results. Of 124 patients, 37 (29.8%) had RA, 32 (25,8%) SSc and 55 (44.4%) OCTD. Most patients were female (86.3%), of mixed racial ancestry (75.0%), and the median (IQR) age was 55 (46-66). Over one-third were smokers, emphysema was diagnosed in 22.6%, and one-third had previous pulmonary tuberculosis (PTB) infection. Smoking, emphysema, and previous PTB were higher in RA group but the difference was not statistically significant. All SSc patients and more than two-thirds of RA and OCTD patients had gastroesophageal reflux disease (GORD). Nonspecific interstitial pneumonia (NSIP) was the commonest pattern of ILD (63.7%), followed by usual interstitial pneumonia (UIP) (26.6%) and other patterns (9.7%). RA patients had similar frequencies of NSIP and UIP. Patients with RA were significantly older (median (IQR)) at ILD onset (62 (55-68) years), compared to SSc (49 (38-56)) and OCTD (42 (33-56)) (p < 0.001). Pulmonary function tests (PFTs) were significantly worse in SSc and OCTD groups. Regarding MTX exposure, 37.1% patients has MTX prescribed before ILD diagnosis, 33.9% continued, started or restarted after ILD diagnosis. No case of acute pneumonitis was documented. Pulmonary function tests and high-resolution computer tomography severity correlated poorly, with PFTs underestimating the severity. In the analysis comparing patients with and without UIP, RA diagnosis (OR 3.8, 95% CI 1.5-9.5), older age (0R 1.1, 95% CI 1.0-1.1), COPD (OR 3.2, 95% CI 1.4-8.0), longer ARD-ILD interval, and higher FVC (OR 1.0, 95% CI 1.0-1.1) were significantly associated with UIP. Conclusions: ILD was most commonly diagnosed in RA and SSc patients, with NSIP seen most frequently overall. Smoking, GORD, and PTB were frequent comorbidities. Amongst RA patients, we observed older age of onset and, interestingly, similar frequencies of NSIP and UIP patterns. The use of MTX was not associated with the development of acute pneumonitis in patients with ILD.

Background: Habitual levels of moderate to vigorous levels of physical activity (MVPA) levels are associated with positive health outcomes and improvement in cognitive function. A challenge facing optimal health outcomes is determining optimal levels of physical activity levels; people can engage in extreme sedentary or high levels of physical activity. For example, levels of low physical activity and participation in ultra-endurance events are increasing. However, the impact of extreme physical activity levels on brain matter volume and working memory is not well understood. This thesis thus investigated the relationship between different levels of MVPA, brain structure, and working memory. The aim of the thesis was to understand the relationship between large volumes of physical activity with global and regional brain matter volumes using brain imaging, and the impact of physical activity on cognitive function using the N-back task. The first part of the thesis examined how habitually high or low levels of MVPA differently impacted brain matter volume in healthy individuals. Whilst, the second part of the thesis investigated the differences in working memory between the low active and high active groups. Methods: Participants aged 20-59 years, were split into a High Activity (HA) group (N = 12, 27.9 ± 26.6 years) that exercised for > 9 hours of per week (MVPA > 540 minutes) and a Low Activity (LA) group (N = 9, 28.33 ± 11.192 years) that exercised < 2 hours (MVPA < 120 minutes). Total and regional brain matter volumes were measured using Magnetic Resonance Imaging (MRI) and analysed using Voxel-Based Morphometry (VBM). Habitual levels of physical activity were measured using the Global Physical Activity Questionnaire (GPAQ). For the second part of this thesis, we tested participants aged 20-59 years. Participants were split into a High Activity (HA) group (N = 6, 24.86 ± 4.67 years) that exercised for > 9 hours of per week (MVPA > 540 minutes) and a Low Activity (LA) group (N = 6, 30.14 ± 15.31 years) that exercised < 2 hours (MVPA < 120 minutes). Working memory was compared between the two groups using a PC-based N-back task. Results: The HA group had greater total brain matter and total white matter volumes vs. the LA group, and brain matter volumes were positively associated with increasing physical activity levels. However, the HA group had reduced regional brain volumes in the postcentral gyrus, middle frontal lobe, and the sub-lobar thalamus. HA and LA groups did not differ in working memory performance on the N-back task. Conclusion: Larger than normal amounts of weekly PA was associated with increased total brain matter and total white matter volumes, however, the volume of three regional brain areas were reduced.

Includes bibliographical references. / The work presented in this thesis investigated virulence in Helicobacter pylori isolates of the Western Cape and related this virulent fingerprint to alterations in gastric cell physiology and cell cycle events. Initially, the "virulence profile" of 109 isolates from 86 patients with a spectrum of clinically significant gastroduodenal diseases was investigated.