Thesis (Ph.D.(Public Health))--University of the Witwatersrand, Faculty of Health Sciences, 2012. / Measuring HIV incidence has proved challenging over the years. A number of serological HIV assays have been proposed, and among these, the BED Capture Enzyme Immunoassay (CEIA) is one of the more widely used. Although the assay performs well among known seroconverting panels, it has been shown to classify some long term infected patients as being recently infected. Information on the performance of the BED assay among low CD4 cell count patients and those on antiretroviral therapy is limited. The risk of onwards transmission of HIV has been reported to be elevated around the seroconversion period compared to the chronic stage of infection. RNA viral load has been reported as the strongest predictor of HIV transmission compared to other HIV markers. Understanding how these markers influence the relationship between the likelihood of being recently infected and the BED assay might help in understanding some of the shortcomings of the BED assay. The main aim of this study was to understand the properties of the BED assay. The performance of the BED assay among advanced HIV disease patients and the influence of ART on BED levels once patients started treatment was investigated. The BED assay and CD4 cell count were used to quantify the risk of in utero and intrapartum transmission to their infants among women believed to have seroconverted during pregnancy. The influence of viral load, haemoglobin and mid-upper arm circumference was investigated on the relationship between the probability of being recently infected and BED ODn levels. Methods Cryopreserved plasma samples from HIV patients on the national antiretroviral treatment (ART) rollout programme at Tygerberg Hospital HIV clinic, South Africa, iv were used to investigate the effect of ART on BED ODn levels once patients commenced treatment. Mixed effect logistic regression models accounting for multiple readings per patient were used. To investigate the risk associated with seroconversion during pregnancy HIV seropositive women who had just given birth were classified into mutually exclusive groups according to their likelihood of having recently seroconverted using BED and CD4 cell count levels. Multinomial logistic regression models adjusting for other factors were used to assess the risk of MTCT in utero and intra-partum infection comparing these groups. To investigate the relationship between BED ODn levels and the probability of being recently infected, BED data from known HIV infected women and women who seroconverted over a 2 year period was used. Fractional polynomial regression models that allow for non-linear functions to be fitted were used, and the influence of viral load, haemoglobin and mid-upper arm circumference was assessed through multi-variable models. Data from the Zimbabwe Vitamin A for Mothers and Babies (ZVITAMBO) project, a double blinded treatment-placebo trial was used for these last two objectives. Results Patients with very low CD4 cell counts were more likely to test false recently infected according to the BED assay than other patients. ART changed BED ODn kinetics among HIV patients on treatment. Over half of advanced disease stage patients were likely to be classified as being recently infected according to the BED assay 2 years into ART treatment. v Women who seemed to have seroconverted during pregnancy had elevated risk of transmitting HIV in-utero compared to chronic HIV patients. BED and CD4 cell count were not predictive of risk of intra-partum infections attributed to seroconversion during pregnancy. The relationship between the probability of being recently infected with HIV and BED ODn levels was described better using Fractional Polynomial regression models than using a linear model in BED ODn or a model in which the BED ODn was categorised. Viral load and haemoglobin were important independent predictors of incident infections. Conclusions If the BED assay is to be used for HIV incidence estimations patients on ART should be accounted for. The BED assay together with other HIV serological markers can be used as prognostic tools to assess the risk of HIV transmission. The risk of in-utero transmission of HIV is higher among women who seroconvert during pregnancy. Repeat HIV testing among pregnant women may help in identifying women who seroconvert during pregnancy, and these women will benefit from Prevention of Mother-to-Child transmission (PMTCT) programmes. It was found that additional markers such as viral load and haemoglobin did not alter the relationship between the probability of having been recently infected and BED ODn.

Geographic research on the Corn Belt and other regional landscapes of the central U.S. has not to date identified quantitatively the climatic, edaphic, topographic, and economic characteristics that determine rural land cover, and that therefore govern land cover change. Using the USDA/NASS Cropland Data Layer, this study identifies these characteristics using Multivariable Fractional Polynomials within a logistic regression framework. It maps the suitability distribution for corn, soybeans, spring and winter wheat, cotton, grassland, and forest land covers that dominate the central U.S., at a 56m resolution across 16 central U.S. states. The non-linear logistic regression models are successful in identifying determinants of land cover with relative operating characteristic (ROC) scores that range from 0.769 for soybeans to 0.888 for forest, with a combined corn/soybean model achieving an ROC of 0.871. For corn and soybean models, when prior land cover of a pixel is added, predictability and ROC scores increase substantially (0.07-0.10), indicating a strong temporal feedback in land cover dynamics. This process also aids in the delineation of fields from pixels. Adding neighboring land covers, however, improves predictability and ROC scores only slightly (0.014-0.019), indicating a weak spatial feedback mechanism. By including annual crop prices within the logit models, economically marginal cropland that comes into crop production only when prices are high is identified in a spatially-explicit manner. This capacity improves further analyses of economic and environmental impacts of policies that affect crop prices. The sustainability of current rural land use trends in the central U.S. is highly dependent on the ability to adapt to changing climatic conditions of the 21st century. As the climate begins to shift towards longer growing seasons, more erratic rainfall patterns, and overall warmer temperatures, there is potential for major impacts on seven major land covers of the central U.S. Suitability landscapes of individual land covers (corn, soybeans, spring and winter wheat, cotton, grasslands, and forests) were utilized to determine the influence of climate change on these landscapes. Twenty-seven climate change projection scenarios based on three global climate models, three representative concentration pathways, and three time periods were applied to the land cover suitability maps utilizing raster regression. The area now identified as the Corn Belt is projected to see a dramatic shift in the suitable climate with a potential for a 30 percent increase in summer growing degree days. While the area where conditions are suitable for corn, soybeans and spring wheat are all expected to decrease, winter wheat has the potential to increase in suitable area. In order to maintain current geographic patterns of crop production, corn would need to be adapted to higher temperatures.