HIV-1 genetic diversity is a major obstacle for developing an effective vaccine. My hypothesis is that HIV-1 genetic diversity can be characterized and that cross-clade immunogens can be predicted at the population level. I systematically investigated positive selection (PS) pressures on HIV-1 Env and Gag proteins based on the analysis of the sequences collected from the Los Alamos Sequence Database. I identified PS sites, investigated PS patterns, correlated PS with the known functional sites of the two proteins, calculated frequencies of HLA alleles targeting CTL epitopes, and compared PS patterns among major subtypes. The results showed that PS pressure was widely dispersed across the entire regions of both HIV-1 Env and Gag proteins, suggesting the conserved regions are under host immune response pressure. The neutralizing antibody, non-neutralizing antibody, and CTL responses were found to be the major forces driving genetic diversity of HIV-1 env and gag genes at population level. However, PS pressures on both Env and Gag proteins remain stable over time, suggesting genetic diversity of HIV-1 driven by host immune responses changed very little over the last 29 years. Furthermore, the results also demonstrated that up to 70% PS sites were shared among the major HIV-1 clades, implying the existence of cross-clade immunogenicity. A number of potential cross-clades immunogens were predicted to elicit CTL or neutralizing antibody responses from Env and Gag proteins. I also detected a significant correlation between HLA allele frequencies and host CTL responses elicited by Accessory/Regulator’s proteins at population level. Moreover, I detected an association between the frequency of HLA-B7 supertype and the number of identified optimal CTL epitopes. The results suggest HLA class I allele frequencies in a population influence the evolution of HIV-1. I also systematically evaluated the utility of ultra-deep pyrosequencing to characterize genetic diversity of HIV-1 gag genes within quasispecies. The results showed that ultra-deep pyrosequencing of amplified HIV genes is a better method than the traditional Sanger-clone-based method in the comprehensive characterization of genetic diversity of HIV-1 quasispecies, especially in detecting low frequency variations. In conclusion, my thesis provides important information for rational design of an effective HIV-1 vaccine.

Aroma is one of the most important quality attributes of bread or any food. It will determine whether the product will be tasted and eaten in the first instance and is a major factor in establishing acceptability and preference. The dominant preference by consumers of bread made from refined flour in contrast to whole wheat flour is at least in part due to the strong and different aroma of whole wheat bread. White wheats may have an advantage over red wheat in this regard according to some industry reports, but the science is extremely limited. The goal of this research was to add more science-based knowledge to this topic via the use of machine olfaction technology, specifically electronic (E) nose and gas chromatography combined with mass spectrometry (GC-MS). A state-of-the-art E-nose system (AlphaMOS FOX 3000) with metal oxide sensors (MOS) was used to capture aroma volatiles from crumb, crust and whole slices of breads made from sound Canadian Western Red Spring (CWRS) wheat as well as representative samples of two hard white wheats, viz. Snowbird, a cultivar belonging to the Canada Western Hard White Spring (CWHWS) class of wheat, and Platte, a U.S. Hard White Winter (HWW) wheat. The same CWRS wheat provided the base flour for all the breads. A commercial formula and size format was used to produce breads from four flours for the study, i.e. refined CWRS wheat, and three whole wheat flours comprising blends of 85% CWRS flour and 15% bran from CWRS wheat, Snowbird and Platte. As there was no established protocol in the literature to evaluate bread aroma by E-nose, one was developed. Five temperatures (35, 40, 45, 50 and 60°C) were tested along with two incubation times (5 and 10 min) and four sample sizes (0.05, 0.1, 0.25 and 0.50 g) of ground bread crumbs. Through optimization using E-nose software including principal component analysis, a procedure was adopted using 40 °C, 5 min incubation time and 0.05 g of sample to acquire MOS data from 12 sensors for crust, crumb and whole slices of refined and whole wheat breads. Multivariate analysis methods were used to evaluate the capabilities of the E-nose system to discriminate and correctly classify samples according to bread type. Data for analysis comprised approximately 24 samples each of crust, crumb and whole slices randomly selected from three loaves each of refined and the three whole wheat breads. Results varied according to the nature of the sample, i.e. crust, crumb or whole slices. For crusts, the greatest distinction in aroma was found between refined and whole wheat breads. Refined bread crust was correctly classified 67% of the time. When refined bread crust was misclassified, samples were confused with whole white wheat crust predominantly from Platte bread. For whole wheat bread crusts, the pattern of classification depended mainly on bran colour. Whole wheat bread crust samples had correct classification scores in the range 54-58%. When misclassified, whole wheat CWRS crust was equally confused with the aroma of crust of the white whole wheat breads, Platte and Snowbird. Whole wheat Platte crust tended to be misclassified with the counterpart white whole wheat Snowbird or refined bread crust. In contrast, Snowbird whole wheat crust tended to be misclassified as either its counterpart HW wheat Platte or whole CWRS wheat. Accordingly, Platte bread crust appeared to possess an aroma more in line with refined wheat bread as opposed to whole wheat bread. For bread crumb, the pattern of E-nose differentiation of samples was different. In this case, CWRS whole wheat bread aroma was clearly and perfectly distinguished from the crumb aroma of all the other breads, either whole white wheat or refined CWRS. The latter tended to cluster on its own, as might be expected, and had a correct classification score of 75%, with the balance of samples largely misclassified as Snowbird crumb. Whole wheat Platte and Snowbird bread crumb had identical correct classification scores of 42%, and were similarly confused with the other’s aroma (average 3 4% classified) or the aroma of refined wheat bread (average 21% classified). E-nose results for crumb indicated a clear distinction in aroma between the hard red and white wheats in this study. E-nose analysis of bread samples representing whole slices produced results that provided unsatisfactory discrimination among bread types likely due to the blending of the different aromas of constituent crust and crumb. For whole slices, discrimination between refined and whole wheat breads was substantially lower than that for either crust and crumb samples. Based on this result, analysis of samples that combine both crust and crumb is not recommended for sensory analysis of bread, whether by instruments or human sensory panel. Further understanding of the differences between different types of bread made from refined wheat flour and whole wheat, and how the inclusion of bran from red and white-grained wheats modifies the composition and content of volatile and non-volatile compounds in crust and crumb was determined by gas chromatography-mass spectrometry (GC-MS). In total, 50 compounds were found, the greater majority of which have been previously reported in bread. Major Maillard reaction compounds like furfural, 2-furanmethanol, pyranone, maltol and 5-hydroxymethyl- 2-furancarboxaldehyde were present in highest concentration in whole CWRS bread. Significantly fewer compounds were found in the crust and crumb of CWRS refined wheat bread compared to the other whole wheat breads. In contrast, whole CWRS bread crumb and crust had the highest number of compounds, and in considerably higher total concentration compared to the other two whole white wheat breads, Snowbird and Platte. The higher concentration and number of compounds in whole CWRS bread was attributed to the wheat bran fraction. White whole wheat breads, Snowbird and Platte, had a total number of compounds in crust and crumb approximately intermediate between refined and whole CWRS bread, although Platte whole wheat bread crust was closer to refined bread crust in compound numbers. In terms of total compound concentrations, crust and crumb samples of the whole white breads were clearly more similar to refined CWRS bread, and in the case of whole wheat Platte bread crust, compound concentrations were much lower. On the whole, these aggregate totals of compound numbers and concentrations by GC-MS mirrored the discrimination and classification results obtained by E-nose, and supported the contention that whole wheat bread made with white wheat bran was milder in aroma compared to bread formulated using red wheat bran. While the number of samples of red and white wheats were very few in this study, results support the contention that different wheat genotypes and specifically, the bran tissue of these genotypes, contain differences in compound composition and/or concentration which when processed by breadmaking, manifest volatiles characteristic of those genotypes even between genotypes possessing the same colour of bran. E-nose instrumentation appears to be very capable of accommodating these sorts of complex tasks on fresh bread. It would be highly beneficial in future research to carry out similar studies in parallel with a human sensory panel, and ideally with many more genotypes of red and white grained wheat with an aim to firmly establish the relative superiority of particular genotypes to produce whole wheat bread with aroma profiles more similar to those of white pan bread. The long term goal of such studies would be to foster increased consumption of whole wheat products and constituent bioactive compounds which confer favourable health benefits in the general population.

ABSTRACT Background: Agriculture is identified as being one of the most hazardous industries in Canada. The different types of injuries that Canadian farmers experience have been addressed by other academic researchers. However, Canada does not have any national database that captures the overall prevalence of disability among farmers, regardless of the cause of their disability. Henceforth, this study provides a profile of Canadian farmers with disabilities in 2001 and in 2006. Purpose: The overall purpose of this study was to determine and compare the prevalence of disability among the adult Canadian farming population in two time periods, 2001 and 2006. Specific, objectives were to analyze the differences in age, gender, type of disability, severity of disability, and accessibility to health and social services among farmers with disabilities. Methods: This cross-sectional secondary data analysis focused on the prevalence of disability within the Canadian farming population. Adult data were retrieved from two Statistics Canada national surveys known as the Participation and Activity Limitations Survey (PALS) 2001 and PALS 2006. Microdata from the PALS 2001 and PALS 2006 were accessed through the Research Data Centre at the University of Manitoba. Results: Approximately 10% of Canadian farmers self-reported one or more activity limitation in 2001 and this figure increased to 20.3% in 2006. On the provincial level, the greatest proportion of farmers living with disabilities is situated in Ontario (27.92% in 2001; 27.04% in 2006), Alberta (17.14% in 2001; 26.12% in 2006), Manitoba (7.9% in 2001; 10.43% in 2006), and Quebec (7.52% in 2001; 10.16% in 2006). This study also reveals the prevalence of disability in both 2001 and 2006. The prevalence of disability is greatest among the senior farmers, i.e., those 65 years of age or older. Of all the Canadian farmers aged 65 and older, 28.1% reported experiencing a disability in 2001 and this prevalence increased to 47.2% in 2006. Of all reported disabilities in the Canadian farming community, physical disabilities accounted for 78.08% in 2001 and 59.04% in 2006. “Mild degree of severity” was the leading degree of severity in 2001 (56.98%) and 2006 (39.09%). Conclusion: One of the most significant findings suggests that there has been a significant increase in disability among Canadian farmers over five years’ time, especially among those over 65 years of age or older. The results from this study raise awareness of specific issues such as aging among Canadian farmers with disability, increasing prevalence of disability, and accessibility to health care and social services. This study concludes that future research should be directed toward the impact of disabilities in the agricultural community to guide health professionals and policy makers in designing cost-effective programs suited to Canadian farmers with disabilities.

Researchers have hypothesized that for people with autism, the deficits in learning certain tasks may be a function of deficits in learning the prerequisite auditory, visual and motor discriminations. The Assessment of Basic Learning Abilities (ABLA) Test is a useful tool by which these discriminations are assessed. This study investigated whether performance on ABLA Level 6, an auditory-visual discrimination, predicts performance on a receptive language task with children with autism. Participants included five children who passed ABLA Level 6, four children who passed ABLA Level 4 but failed ABLA Level 6, and one child who passed ABLA Level 3 but failed ABLA Level 4. Standardized prompting and reinforcement procedures were used to attempt to teach each participant to respond correctly on ten name-recognition tasks. During a task pictures of two objects were placed in randomly alternated left-right positions, and a child was required to point to the picture that was named. Training on a task continued until either a pass or a fail criterion was met, whichever came first. Three of the Level 4 participants passed all ten of the picture name recognition tasks, and one passed eight of the ten tasks. The Level 3 participant passed two of the ten tasks. All five of the Level 6 participants passed all picture name recognition tasks. The difference in performance between children at ABLA Level 4 and Level 6 was not significant at the .05 level. These results suggest that children with autism at ABLA Level 4 or 6 are approximately equally capable of learning receptive name recognition tasks.

Soil moisture plays a major role in the hydrologic water balance and is the basis for most hydrological models. It influences the partitioning of energy and moisture inputs at the land surface. Because of its importance, it has been used as a key variable for many hydrological studies such as flood forecasting, drought studies and the determination of groundwater recharge. Therefore, spatially distributed soil moisture with reasonable temporal resolution is considered a valuable source of information for hydrological model parameterization and validation. Unfortunately, soil moisture is difficult to measure and remains essentially unmeasured over spatial and temporal scales needed for a number of hydrological model applications. In 2002, the Gravity Recovery And Climate Experiment (GRACE) satellite platform was launched to measure, among other things, the gravitational field of the earth. Over its life span, these orbiting satellites have produced time series of mass changes of the earth-atmosphere system. The subsequent outcome of this, after integration over a number of years, is a time series of highly refined images of the earth's mass distribution. In addition to quantifying the static distribution of mass, the month-to-month variation in the earth's gravitational field are indicative of the integrated value of the subsurface total water storage for specific catchments. Utilization of these natural changes in the earth's gravitational field entails the transformation of the derived GRACE geopotential spherical harmonic coefficients into spatially varying time series estimates of total water storage. These remotely sensed basin total water storage estimates can be routinely validated against independent estimates of total water storage from an atmospheric-based water balance approach or from well calibrated macroscale hydrologic models. The hydrological relevance and implications of remotely estimated GRACE total water storage over poorly gauged, wetland-dominated watershed as well as over a deltaic region underlain by a thick sand aquifer in Western Canada are the focus of this thesis. The domain of the first case study was the Mackenzie River Basin wherein the GRACE total water storage estimates were successfully inter-compared and validated with the atmospheric based water balance. These were then used to assess the WATCLASS hydrological model estimates of total water storage. The outcome of this inter-comparison revealed the potential application of the GRACE-based approach for the closure of the hydrological water balance of the Mackenzie River Basin as well as a dependable source of data for the calibration of traditional hydrological models. The Mackenzie River Basin result led to a second case study where the GRACE-based total water storage was validated using storage estimated from the atmospheric-based water balance P-E computations in conjunction with the measured streamflow records for the Saskatchewan River Basin at its Grand Rapids outlet in Manitoba. The fallout from this comparison was then applied to the characterization of the Prairie-wide 2002/2003 drought enabling the development of a new drought index now known as the Total Storage Deficit Index (TSDI). This study demonstrated the potential application of the GRACE-based technique as a tool for drought characterization in the Canadian Prairies. Finally, the hydroinformatic approach based on the artificial neural network (ANN) enabled the downscaling of the groundwater component from the total water storage estimate from the remote sensing satellite, GRACE. This was subsequently explored as an alternate source of calibration and validation for a hydrological modeling application over the Assiniboine Delta Aquifer in Manitoba. Interestingly, a high correlation exists between the simulated groundwater storage from the coupled hydrological model, CLM-PF and the downscaled groundwater time series storage from the remote sensing satellite GRACE over this 4,000 km2 deltaic basin in Canada.

Immunopathological disorders are no longer defined by dysregulated T-helper (Th) type 1/ Th2 responses but account for modulatory cell types such as regulatory and Th17 cells. The newly defined Th17 subset is an effector memory subtype which regulates mucosal host defense responses. A distinctive feature of interleukin (IL)-17 is its ability to invoke neutrophilic responses and to synergize cytokine responses in proximal structural cells. This effect is most evident for proinflammatory cytokines and neutrophil-mobilizing chemokines which are under the regulatory control of the canonical, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. The uniqueness of the IL-17A receptor (IL-17RA) signal transduction pathway however has been a limiting factor in uncovering IL-17-mediated effector functions since the receptor bears little homology to other known receptors and contains a unique cytoplasmic consensus binding motif. Hence, the composition, dynamics and subunit interactions of the IL-17R complex have become an emerging area of research where novel recruitment motifs and adaptor proteins are actively being explored. Our study sought to uncover the signal transduction and molecular mechanisms mediating the initiation and amplification responses induced by IL-17. We hypothesize that (i) IL-17 represents a key cytokine which initiates inflammatory responses by acting on proximal structural cells to rapidly release neutrophil-mobilizing chemokines and myeloid growth factors and that (ii) IL-17 directly promotes survival responses of immune effector cells. Genomic analysis of stimulated human airway smooth muscle cells support the proinflammatory nature of IL-17 as NF-κB associated genes and chemokines were most significantly upregulated within 2 hours. However, IL-17 induced a modest fold increase in gene expression levels whereby only 4 genes achieved greater than 2 fold increases. This, along with the observation that IL-17 enhanced IL-1β-mediated CXCL8 expression via transcriptional promoter activation levels and post-transcriptional mRNA stabilization mechanisms suggests that IL-17 cooperatively functions with secondary cytokines to mediate inflammatory responses. Despite activating the p38-mitogen-activated protein kinase (MAPK) signaling pathway in peripheral blood neutrophils, IL-17 did not directly affect the apoptotic capacity of these cells but unexpectedly antagonized the survival response mediated by the granulocyte-macrophage colony stimulating factor (GM-CSF). Collectively, our results suggest that IL-17 is a potent synergistic cytokine which signals via the MAPK-NF-κB pathway to indirectly recruit neutrophils via CXC-chemokines produced by non-hematopoietic cells and that IL-17 may potentially dampen inflammatory responses by directly antagonizing inflammatory effector cells.

This thesis reports on research undertaken in the area of microwave tomography (MWT) where the goal is to find the dielectric profile of an object of interest using microwave measurements collected outside the object. The main focus of this research is on the development of inversion algorithms which solve the electromagnetic inverse scattering problem associated with MWT. Various regularization techniques for the Gauss-Newton inversion algorithm are studied and classified. It is shown that these regularization techniques can be viewed from within a single consistent framework after applying some modifications. Within the framework of the two-dimensional MWT problem, the inversion of transverse magnetic and transverse electric data sets are considered and compared in terms of computational complexity, image quality and convergence rate. A new solution to the contrast source inversion formulation of the microwave tomography problem for the case where the MWT chamber consists of a circular conductive enclosure is introduced. This solution is based on expressing the unknowns of the problem as truncated eigenfunction expansions corresponding to the Helmholtz operator for a homogeneous background medium with appropriate boundary conditions imposed at the chamber walls. The MWT problem is also formulated for MWT chambers made of conducting cylinders of arbitrary shapes. It is shown that collecting microwave scattered-field data inside MWT setups with different boundary conditions can provide a robust set of useful information for the reconstruction of the dielectric profile. This leads to a novel MWT setup wherein a rotatable conductive triangular enclosure is used to generate scattered-field data. Antenna arrays, with as few as only four elements, that are fixed with respect to the object of interest can provide sufficient data to give good reconstructions, if the triangular enclosure is rotated a sufficient number of times. Preliminary results of using the algorithms presented herein on data collected using two different MWT prototypes currently under development at the University of Manitoba are reported. Using the open-region MWT prototype, a resolution study using the Gauss-Newton inversion method was performed using various cylindrical targets.

Stephens Lake, Manitoba is an example of a peatland reservoir that has undergone physical changes related to mineral erosion and peatland disintegration processes since its initial impoundment. In this thesis I focused on the processes of peatland upheaval, transport, and disintegration as the primary drivers of dynamic change within the reservoir. The changes related to these processes are most frequent after initial reservoir impoundment and decline over time. They continue to occur over 35 years after initial flooding. I developed a remote sensing approach that employs both optical and microwave sensors for discriminating land (i.e. floating peatlands, forested land, and barren land) from open water within the reservoir. High spatial resolution visible and near-infrared (VNIR) optical data obtained from the QuickBird satellite, and synthetic aperture radar (SAR) microwave data obtained from the RADARSAT-1 satellite were implemented. The approach was facilitated with a Geographic Information System (GIS) based validation map for the extraction of optical and SAR pixel data. Each sensor’s extracted data set was first analyzed separately using univariate and multivariate statistical methods to determine the discriminant ability of each sensor. The initial analyses were followed by an integrated sensor approach; the development of an image classification model; and a change detection analysis. Results showed excellent (> 95%) classification accuracy using QuickBird satellite image data. Discrimination and classification of studied land cover classes using SAR image texture data resulted in lower overall classification accuracies (~ 60%). SAR data classification accuracy improved to > 90% when classifying only land and water, demonstrating SAR’s utility as a land and water mapping tool. An integrated sensor data approach showed no considerable improvement over the use of optical satellite image data alone. An image classification model was developed that could be used to map both detailed land cover classes and the land and water interface within the reservoir. Change detection analysis over a seven year period indicated that physical changes related to mineral erosion, peatland upheaval, transport, and disintegration, and operational water level variation continue to take place in the reservoir some 35 years after initial flooding. This thesis demonstrates the ability of optical and SAR satellite image remote sensing data sets to be used in an operational context for the routine discrimination of the land and water boundaries within a dynamic peatland reservoir. Future monitoring programs would benefit most from a complementary image acquisition program in which SAR images, known for their acquisition reliability under cloud cover, are acquired along with optical images given their ability to discriminate land cover classes in greater detail.

This thesis research examined the implementation of the Ktunaxa Nation network and explored its ongoing use and development. The Ktunaxa Nation is comprised of four Aboriginal communities in south-eastern British Columbia, Canada. The Nation established internet infrastructure throughout the communities primarily to enable the dissemination of the Ktunaxa language of which there are only 24 speakers remaining. The purpose of this research was to examine the various uses of the Ktunaxa internet network related to land and language, at both a community and organizational level. Methods included Nvivo-based content analysis and restorying which enables a number of individual experiences to be refashioned into one comprehensive set of events. Final recommendations are provided.

I compared understorey communities under Alnus viridis ssp. crispa (Ait.) Pursh (green alder) and Corylus cornuta Marsh. (beaked hazel) in two boreal jack pine forests. There was no difference in inorganic soil nitrogen, but alder plots had lower species richness at Star Lake and higher evenness in the Sandilands. I incubated chopsticks and litterbags containing natural litter assemblages underneath A. crispa and C. cornuta in the field, and litterbags containing artificial litter mixes in a dark growth chamber. There was no significant difference between treatments for litterbags or chopsticks in the field, nor between mixes with or without alder in the growth chamber.