This thesis describes the work of three research projects, the background research that motivated the work, and the resultant project findings. The three projects concerned: (i) Geometric stochastic resonance in a double cavity, (ii) Synchronisation of geometric stochastic resonance by a bi-harmonic drive, and (iii) Rectification of Brownian particles with oscillating radii in asymmetric corrugated channels. In the project 'Geometric stochastic resonance in a double cavity', we investigated synchronisation processes for the geometric stochastic resonance of particles diffusing across a porous membrane and subject to a periodic driving force. Non-interacting particle currents were driven through a symmetric membrane pore either parallel or perpendicular to the membrane. Then, harmonic mixing spectral current components were generated by the combined action of parallel and perpendicular drives. The role of the repulsive interaction of particles as a controlling factor with potential applications to the transport of colloids and biological molecules through narrow pores was also investigated. In 'Synchronisation of geometric stochastic resonance by a bi-harmonic drive', we simulated the stochastic dynamics of an elliptical particle using the Langevin equation. The particle was simultaneously driven by low and high frequency harmonic drives across a porous inter-cavity membrane. It was observed that the particle oscillated out of phase with the low frequency drive. This effect was due to the absolute negative mobility the particle would have exhibited if the low frequency drive had been replaced by a dc static force. It was also observed that the magnitude of this out-of-phase stochastic resonance depends on how the combined action of the driving forces and noise fluctuations affect the particle orientation, and as such was shown to be sensitive to the particle shape. This emphasises the importance of particle geometry, in addition to chamber geometry, to the realisation and optimisation of geometric stochastic resonance. In the project 'Rectification of Brownian particles with oscillating radii in asymmetric corrugated channels', we simulated the transport of a Brownian particle with an oscillating radius freely diffusing in an asymmetric corrugated channel over a range of driving forces for a series of temperatures and angular frequencies of radial oscillation. It was observed that there was a strong influence of self-oscillation frequency upon the average particle velocity. This effect can be used to control rectification of biologically active particles as well as for their separation according to their activity, for instance in the separation of living and dead cells. The background research is described in Chapter One and the research findings are described along with their related projects in Chapters Two and Three.

Context. Over the past few years, on several occasions, large, continuous rotations of the electric vector position angle (EVPA) of linearly polarized optical emission from blazars have been reported. These events are often coincident with high energy gamma-ray flares and they have attracted considerable attention, since they could allow us to probe the magnetic field structure in the gamma-ray emitting region of the jet. The flat-spectrum radio quasar 3C 279 is one of the most prominent examples showing this behaviour. Aims. Our goal is to study the observed EVPA rotations and to distinguish between a stochastic and a deterministic origin of the polarization variability. Methods. We have combined multiple data sets of R-band photometry and optical polarimetry measurements of 3C 279, yielding exceptionally well-sampled flux density and polarization curves that cover a period of 2008-2012. Several large EVPA rotations are identified in the data. We introduce a quantitative measure for the EVPA curve smoothness, which is then used to test a set of simple random walk polarization variability models against the data. Results. 3C 279 shows different polarization variation characteristics during an optical low-flux state and a flaring state. The polarization variation during the flaring state, especially the smooth similar to 360 degrees rotation of the EVPA in mid-2011, is not consistent with the tested stochastic processes. Conclusions. We conclude that, during the two different optical flux states, two different processes govern polarization variation, which is possibly a stochastic process during the low-brightness state and a deterministic process during the flaring activity.

We present the discovery of nine quasars at z similar to 6 identified in the Sloan Digital Sky Survey (SDSS) imaging data. This completes our survey of z similar to 6 quasars in the SDSS footprint. Our final sample consists of 52 quasars at 5.7 < z << 6.4, including 29 quasars with z(AB) <= 20 mag selected from 11,240 deg(2) of the SDSS single-epoch imaging survey (the main survey), 10 quasars with 20 <= z(AB) <= 20.5 selected from 4223 deg2 of the SDSS overlap regions (regions with two or more imaging scans), and 13 quasars down to z(AB) approximate to 22 mag from the 277 deg2 in Stripe 82. They span a wide luminosity range of -29.0 <= M-1450 <= -24.5. This well-defined sample is used to derive the quasar luminosity function (QLF) at z similar to 6. After combining our SDSS sample with two faint (M-1450 >= -23 mag) quasars from the literature, we obtain the parameters for a double power-law fit to the QLF. The bright-end slope beta of the QLF is well constrained to be beta = -2.8 +/- 0.2. Due to the small number of low-luminosity quasars, the faint-end slope a and the characteristic magnitude M*(1450) are less well constrained, with alpha = -1.90(-0.44)(+0.58) and M* = -25.2(-3.8)(+1.2) mag. The spatial density of luminous quasars, parametrized as rho(M-1450 < -26, z) = rho(z = 6)10(k(z-6)), drops rapidly from z similar to 5 to 6, with k = -0.72 +/- 0.11. Based on our fitted QLF and assuming an intergalactic medium (IGM) clumping factor of C = 3, we find that the observed quasar population cannot provide enough photons to ionize the z similar to 6 IGM at similar to 90% confidence. Quasars may still provide a significant fraction of the required photons, although much larger samples of faint quasars are needed for more stringent constraints on the quasar contribution to reionization.

Master of Regional and Community Planning / Department of Landscape Architecture/Regional and Community Planning / Hyung Jin Kim / In the past 20 years, the promotion of bicycle-friendly environments in the United States has become a major topic for city planners, engineers, landscape architects, and concerned citizens. The City of Manhattan, Kansas, and Kansas State University (KSU) are following the trend by creating more bicycle infrastructure. As an example, the Campus Planning and Facilities Management Department at KSU recently installed new signs on the pavement that support existing bicycle rules around campus. The rules require cyclists to dismount and walk their bicycles on the main campus sidewalk and yield to pedestrians when crossing Bosco Plaza. While signs are important, these markers should be part of a bigger plan that includes infrastructure, education and enforcement working together to create a safe, active transportation system. This project explores bicycling culture at KSU campus and uses three key concepts of infrastructure, education, and enforcement to discover what improvements are needed and what improvements can be made. The video-based observation method consists of recording the activity of cyclists entering the campus core and analyzing the behavior of cyclists and pedestrians. The survey was conducted via social media in order to understand safety perceptions and behaviors of bicyclists and pedestrian as daily commuters to campus. The results from both methods show a lack of involvement with infrastructure, education, and enforcement for cycling at Kansas State which creates areas that are not safe for pedestrians. Bicycling (15.4%) and walking (46.7%) represent 62.1% of commuters to campus; therefore, a safer approach to campus infrastructure needs to be addressed for these users. Results indicate that the dismount signs are ignored 82.9% of the time, and collisions between cyclists and pedestrians do happen on campus. An absence of enforcement is shown in the data, which is compounded by a non-existing bicycling education program, making for a less than optimal active transportation system on campus.

Philosophiae Doctor - PhD / Background: Tuberculosis (TB) is a major cause of morbidity and mortality among children (<15 years) in resource-limited countries. The World Health Organization (WHO) identified active contact screening and isoniazid preventive therapy (IPT) as essential actions for detecting and preventing childhood TB. Despite their benefits and inclusion in the policy of most National TB Programme (NTP) guidelines of the resource-limited countries, there is still a wide gap between policy and implementation. The implementation of contact screening for active case finding might be improved by the decentralised use of the Xpert MTB/RIF test in gastric lavage (GL) specimens, but this has not been previously assessed. Furthermore, although the provision of IPT to eligible child contacts has been a focus for implementation by the NTP of Rwanda since 2005, implementation has not previously been evaluated. The assessment of IPT uptake and adherence as well as associated factors could be informative for the programme. Therefore, we aimed to assess the diagnostic yield of Xpert MTB/RIF in GL among child contacts with suspected pulmonary tuberculosis (PTB) and the uptake of and adherence to IPT by eligible child contacts to make recommendations towards strengthening TB diagnostic and prevention in children in Kigali, Rwanda. Methods: The proposed study setting Kigali, the capital city of Rwanda, was the location for 30% of the national PTB case notifications in 2013-14.A conceptual framework based on ecological theory was used in this study. Quantitative, qualitative and mixed (using both quantitative and qualitative research methods in one study) research methods were applied, and various research designs were used depending on the research questions. The study involved a cross-sectional analysis of the diagnostic yield of Xpert MTB/RIF in GL among all child contacts with suspected TB. Across-sectional and prospective cohort study design was used to assess the uptake and adherence of IPT among eligible child contacts.

MSc, Paediatrics and Child Health, Faculty of Health Sciences,University of the Witwatersrand / Background To investigate whether in-utero exposure to highly active antiretroviral treatment (HAART) is associated with low birth weight and/or preterm birth in a population of South African women with advanced HIV infection. Methods A retrospective observational study was performed on women with CD4 cell counts ≤250 cells/mm3 attending antenatal antiretroviral clinics at two clinics in Johannesburg between October 2004 and March 2007. Low birth weight (<2.5kg) and preterm birth rates (<37 weeks) were compared in those exposed versus unexposed to HAART during pregnancy. Effects of different HAART regimen and duration (<28 weeks or ≥ 28 weeks) were assessed. Results Among HAART-unexposed infants 27% (60/224) were low birth weight (LBW) compared to 23% (90/388) of early HAART-exposed and 19% (76/407) of late HAART-exposed infants (P=0.05). In the early HAART group, older maternal age was associated with LBW and higher CD4 cell count protective against LBW (AOR 1.06, 95% CI 1.00- 1.12 and AOR 0.58, 95% CI 0.46-0.73, P<0.001, respectively). HAART-exposed infants had an increased risk of preterm birth vii (<37 weeks) (15% [138/946] versus 5% [7/147], p=0.001), with early (<28 weeks) nevirapine and efavirenz having the strongest associations with preterm birth (AOR 5.4, 95%CI 2.1-13.7, P<0.001 and AOR 5.6, 95%CI 2.1-15.2, P=0.001, respectively). Conclusion Among infants born to women with CD4 cell counts <250 cells/mm3, HAART exposure was associated with preterm birth, but not with low birth weight. More advanced immunosuppression was a significant risk factor for both LBW and preterm birth, highlighting the importance of earlier HAART initiation in pregnant women, both to optimize maternal health and to improve infant outcomes

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in partial fulfilment of the requirements for the degree of Master of Medicine in Family Medicine. / Introduction South Africa has more people living with HIV than any other country in the world.1 Women infected with HIV have a high risk in the development of cervical dysplasia and cancer of the cervix more so than women who are not infected.2,3 Methods A cross-sectional descriptive study was carried out by reviewing cervical smears of HIV positive women in a district hospital. Three hundred and ninety cervical Pap smears were classified according to the Bethesda system. Adherence was measured by the patient’s report and viral load. Data was collected through the use of self administered questionaire and data capture sheet. Results The prevalence of abnormal Pap smears was 57 per cent and LSIL was the commonest abnormality seen (142/390, 36%). Eighty-four per cent (328/390) had stage 1 WHO-HIV classification. WHO stage 3 participants seemed to be three times more likely to have abnormal Pap smears than those with WHO stage 1 (OD 3.3, STD. error 1.70, p=0.018, 95% CI 1.23-9.04). Abnormal pap smears were seen more in participants with CD4 cell count ≤ 350 cells/μL as compared to participants with CD4 cell count ≥ 500 cells/μL { 122/172, (71.00 %) vs 48/117, (41.03%), p-0.000, 95% CI : 0.09-0.37}. Similarly, participants who did not use HAART had more abnormal results as compared to those who used HAART {42/60(70.00%) vs 180/330 (55.00%), p-0.028, 95% CI 0.28-0.93}.Adherence to HAART did not show any link with abnormal smears. Conclusion The more immune-suppressed a woman is, the higher the risk of developing cervical cancer precursors. The high risk group in this study was found to be the participants with the CD4 cell count of ≤ 350 cells/μL and the viral load ≥1000 copies/mm3. The self-reported adherence level did not show any impact.

This research investigated the ethical and legal issues that impact on the urgent implementation of Nurse Initiated and Managed Anti-Retroviral Treatment (NIMART) in South Africa, which is part of the task-shifting strategy recommended by the World Health Organization (WHO) to deal with the human resource shortage that has negatively impacted access to Anti-Retroviral Treatment (ART) in developing countries (WHO;2006). The objectives were to review and analyse the existing legal framework and provisions for NIMART in South Africa; and to identify ethical issues and implications of NIMART within the current legal framework. It analysed the legal issues that impact on the implementation of NIMART within the public health service in South Africa, as well as the ethical basis and implications of NIMART on the practice of nurses in the scale-up of Anti-Retroviral Treatment in Primary Health Care (PHC). A comparative analysis was done with case studies of task-shifting in other developing countries and evidence-based recommendations for an enabling and long-term sustainable ethico-legal approach to task-shifting were established. The research concluded that despite the existing legal framework for NIMART in South Africa being firmly founded in the Constitution and further enabled by health policy, challenges exist in implementation of certain critical aspects of the enabling legislation relating to nurse training and accreditation required for full authorization to practice NIMART and that these technical challenges if not attended to could threaten the long-term sustainability of NIMART.

In Malawi, the new Biology curriculum draws from constructivist approaches. The Biology teaching syllabus emphasises the use of students’ experiences as a resource and the use of active student involvement strategies when teaching the curriculum to enhance conceptual understanding. However, inspection reports show that students are less actively involved in the lessons and the teachers rarely draw from their students’ prior experiences to enhance conceptual understanding. In this study, I investigated some factors affecting four teachers’ use of constructivist approaches when teaching the new biology curriculum in Malawi. Information was collected on the four teachers’ understandings of active student involvement in lessons and students’ experiences, the extent to which the four teachers involved students and built on students’ experiences to enable comprehension of science concepts in the Biology lessons and the factors that promoted/ hindered the use of these practices. Data was collected through lesson observations and interviews with teachers using an observation guide and an interview schedule respectively. Four Biology teachers, two from community secondary schools and two from conventional secondary schools were observed and interviewed. I found that all the four teachers understood students’ experiences as prior knowledge from previous school learning. The teachers understood active student involvement in relation to the type of schools they were teaching. For the teachers in community schools, involving students meant engaging them in group discussion while to the teachers in conventional schools it meant students doing experiments / practical work. Their teaching focused on giving information and little was done to develop students’ metacognitive abilities. According to the four teachers, pressure to cover the syllabus before the national examinations; lack of text books and laboratory equipment; lack of motivation among students; students’ backgrounds; and inadequate students’ fluency in the English language are some of the factors that affect their implementation of the constructivist approaches. Based on the lessons I observed, the teachers’ knowledge of subject matter and teachers’ understandings of the constructivism concept also affect the use of constructivist approaches when teaching Biology in Malawi.

MPH, Faculty of Health Sciences, University of the Witwatersrand / Background: The increase use of highly active antiretroviral therapy (HAART) among patients with HIV infection and AIDS has led to increasing reports of metabolic abnormalities such as diabetes mellitus, hypertension, dyslipidaemia and obesity. Therefore, it is important to explore the burden of these diseases among HIV infected patients. Objectives: To determine the burden of metabolic diseases (hypertension, diabetes, obesity and dyslipidaemia) in patients attending HIV clinic at the Charlotte Maxeke Johannesburg Academic Hospital (JHBH). Methodology: It was a cross-sectional study. The study population included patients attending JHBH HIV clinic and on HAART for more than one year. A sample size of 304 patients, including 237 females and 67 males partook in this study. Anthropometric measurements were taken from patients and blood samples of these patients were sent to laboratory for lipograms, HbA1c, random glucose, CD4 lymphocytes counts as well as HIV viral load testing. The data was analysed with standard statistical software Epi-info version 6.0. Both descriptive and analytical statistics was used. Results: The prevalence of metabolic syndrome according to the IDF was 20.4 %; obesity (BMI 30 kg/m2) was 16.8% and patients that were overweight (BMI > 25 kg/m2 and BMI < 29.9 kg/m2) was 28.6%; hypercholesterolemia (TC 5.0 mmol/l) = 35.5%; HDL< 1.29 mmol\L in females was 58% and HDL <1.04 mmol/l in males was 36%; elevated triglycerides 1.7 mmol/l was 30% and only 16% was classified as being hypertensive (BP 140/90 mmHg and / or on Hypertensive medication). The majority of the patients (86.2%) had a CD4 lymphocyte count 200 X 106 cells/l and 84% of patients had less than detectable limits for viral loads (VL< 40 copies / μl), which has been reported as optimum levels for metabolic diseases in HAART recipients. Conclusion: These results clearly indicate that there is a growing burden of metabolic diseases among HIV patients on HAART attending the Johannesburg hospital HIV clinic. The current study also indicates that the metabolic disturbances are more frequent in women than in men, except for hypertension.