The accessibility of high-throughput biology data brought a great deal of attention to disease association studies. High density maps of single nucleotide polymorphism (SNP's) as well as massive genotype data with large number of individuals and number of SNP's become publicly available. By now most analysis of the new data is undertaken by the statistics community. In this dissertation, we pursue a different line of attack on genetic susceptibility to complex disease that adheres to the computer science community with an emphasis on design rather than analytical methodology. The main goal of disease association analysis is to identify gene variations contributing to the risk of and/or susceptibility to a particular disease. There are basically two main steps in susceptibility: (i) haplotyping of the population and (ii) predicting the genetic susceptibility to diseases. Although there exist many phasing methods for step (i), phasing and missing data recovery for data representing family trios is lagging behind, and most disease association studies are based on family trios. This study is devoted to the problem of assessing accumulated information targeting to predict genotype susceptibility to complex diseases with significantly high accuracy and statistical power. The dissertation proposes two new greedy and integer linear programming based solution methods for step (i). We also proposed several universal and ad hoc methods for step (ii). The quality of susceptibility prediction algorithm has been assessed using leave-one-out and leave-many-out tests and shown to be statistically significant based on randomization tests. The prediction of disease status can also be viewed as an integrated risk factor. A combinatorial prediction complexity measure has been proposed for case/control studies. The best prediction rate achieved by the proposed algorithms is 69.5% for Crohn's disease and 61.3% for autoimmune disorder, respectively, which are significantly higher than those achieved by universal prediction methods such as Support Vector Machine (SVM) and known statistic methods.

All matter has a specific magnetic signal , due to their magnetic properties. These range from a high susceptibility to become magnetised (ferrimagnetic) to a low ability to be magnetised (diamagnetic). Magnetic susceptibility measures the degree to which a substance can be magnetised, and this can be used to identi fy minerals within material and used as an indicator for processes Le., erosion. Therefore magnetic susceptibility has been widely used to investigate soil related research as the values obtained correspond with the types of magnetic mineral s in the soil, mainly the iron oxides such as magnetite and maghaemite (higher MS), and haematite and goethite (lower MS). Thus MS acts as a signature for different types of soils allowing them to be categorised. The amount of magnetic minerals present in the soil is largely dependent on soil processes active in the profile and external factors, such as parent material. Soil processes influence the type or amount of magnetic mineral in the soil, or the strength of the magnetic signal. Lower MS values are associated with horizons that have undergone gleying, eluviation, leaching and reductive weathering. Higher MS values are found in horizons that have undergone illuviation, and hydrolytic and oxidative weathering. Diamagnetic materials, such as calcium carbonate, decrease the magnetic susceptibility by diluting the magnetic signal. The relationship between MS and iron in soil is influenced by both external factors such as parent material ; climate; topography; land use history of the area and time. Similarly these factors significantly contribute to soil genesis and are highly interactive. Parent materials that are igneous are found to form soil with higher magnetic susceptibility, and sedimentary and metamorphic rocks form less magnetic soils. However, it has also been found that materials such as slate are related to soil with high susceptibility, which is argued to result from more rapid weathering and the release of iron in the ionic form. Climate has a direct affect on the soil processes that drive magnetic susceptibility, thus in warm tropical climates magnetic susceptibility is expected to have higher values . Topography has been shown to alter magnetic susceptibility values , and generall y the top and foot of the slope have higher values than the slopes. Land-use history influences magnetic susceptibility as cultivation is likely to disturb the soil causing magnetic susceptibility values to be lower due to mixing of the upper and lower soil layers. Time relates to the age of the soil and older soil either has large magnetic susceptibility values due to more prolonged pedogenesis, or the magnetic particles have weathered out of the profile and magnetic susceptibility is lowered. Past research has found topsoil to have higher frequency dependent magnetic susceptibility than lower soil horizons. Frequency dependent magnetic susceptibility measures fine-grained ferrimagnetic particles with grain sizes between 0.013 and O.027f.lm. Two measurements at low and high frequency (0.46 and 46 kHz respectively) are used to calculate frequency dependent magnetic susceptibility. These are measured using a Bartington MS2B sensor and certain measures need to be taken in order to obtain an accurate measurements of magnetic susceptibility. Frequency dependent magnetic susceptibility values are influenced by factors including burning, organic matter and pedogenesis. However, the nature of contribution of these is still highly debated. Many South African soils are considered to be old soils and the amount of magnetic minerals in these is unknown. It has been found that magnetic minerals such as maghaemite have been depleted due to erosion cycles. Very little research has been undertaken regarding the applicability of magnetic susceptibility for South African soils as most of the research on magnetic susceptibility in soils has been carried out in countries of the northern hemisphere, where soil materials are much younger than in South Africa. The ability of frequency dependent magnetic susceptibility to differentiate between topsoil and subsoil allows it to be used as a method of assessing topsoil erosion. Topsoil erosion has a detrimental effect on the environment and it is vital a rapid field indicator is developed to assess erosion in order to curb the process. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2002.

Thesis (M.S.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 34 pages. Includes Vita. Includes bibliographical references.

Hypnotic susceptibility, often regarded as a relatively stable individual characteristic, has been found to be related to the personality dimension of absorption. To test the hypothesis that this relationship is a function of the nature of the sensory response to stimulus events and the development of cognitive models pursuant to the processing of that information, a group of hospitalized, chronic pain patients were assessed on the following dimensions: absorption, clinical hypnotic responsiveness, cognitive resistance to interference, and visual automatization.

Pleistocene loess-palaeosol sequences provide a unique proxy-record enabling detailed reconstruction of Quaternary palaeoenvironments. Environmental magnetic methods are often used to read the natural archives. The loess-palaeosol sequences exposed in two sections located in southern Moravia and a sequence from central Bohemia were studied in a frame of this Diploma Thesis. Variations of bulk magnetic susceptibility, measured in the sediments, show similar pattern as in the Chinese loess-palaeosol bodies - i.e. palaeosols reveal higher magnetic susceptibility in comparison with loess due to magnetic enhancement. The magnetic enhancement is driven by weathering during pedogenic processes related to the formation of ultra-fine magnetite particles. The magnetite content is controlling the sediment magnetic behavior. The magnetic enhancement rate indicates more intense pedogenic processes in the Moravia in comparison with Bohemia. Magnetic fabric in studied loess, represented by space orientation of anisotropy of magnetic susceptibility ellipsoid, indicates dominating glacial wind palaeocurrents across the southern Moravia blowing from W or SW, respectively. The magnetic fabric in the central Bohemian sequence has revealed a dominant control of running water and re-deposition of the loess material...

Salmonella species is the etiologic agent of salmonellosis, which is a zoonotic infection that is characterized by diarrhea and systemic infection. Contaminated foods are usually the vehicles of Salmonella transmission along the food supply chain. Asymptomatic food production animals and effluents also contribute to contamination of meat. Antimicrobials have contributed significantly to treatment of salmonellosis. However, uncontrolled antimicrobial use is among the causes of antibiotic resistance, which results in treatment failure. The aim of this research study was to determine the extent of Salmonella spp contamination during the cattle slaughtering process in South African rural abattoirs (n = 23), water and cattle feaces. In addition, the aim was to determine antimicrobial resistance profiles of the Salmonella spp isolates. The specific objectives were: i) to establish the occurrence and distribution of Salmonella spp on cattle carcasses, hides, and intestinal contents and environmental samples using classical microbiology and molecular techniques; ii) to determine the Salmonella serovars using serotyping; and iii) to determine antimicrobial resistance patterns and multidrug resistance among the Salmonella isolates using the Kirby-Bauer disc diffusion method. Materials and Classical microbiology techniques were used to analyze cattle faeces (n = 400), hides (n = 67), intestinal contents (n = 62), carcass sponges (n = 100), and water from the abattoirs (n = 75) for the presence of Salmonella spp. Further confirmation of the Salmonella isolates was done using Polymerase Chain Reaction whereby the invA gene was targeted. A total of 92 Salmonella spp isolates were recuperated. The 92 Salmonella were serotyped as described in the White-Kauffmann-Le Minor scheme. The 92 Salmonella spp isolates were further subjected to antimicrobial susceptibility examination towards the following antimicrobials: ampicillin (10μg), cefotaxine (30μg), kanamycin (30μg), oxytetracycline (30μg), and enrofloxacin (5μg) by using the Kirby-Bauer disk diffusion procedure. All the isolates carried the invA genes. The average Salmonella spp occurrence on carcasses, hides, and intestinal contents was 35.37% (n = 81). Eleven of the faecal samples (2.75%) tested positive for Salmonella spp. The Salmonella serovar that occurred more frequently was S. Enteritidis. Different serovars that were recognized on carcasses were not automatically found on the hides and intestinal contents. The incompatible frequency of the different Salmonella serovars on carcasses, intestinal contents and hides means that in addition to carriage on hides and in intestinal contents, new external causes that did not form part of this study also play a vital role concerning carcass contamination. Most Salmonella spp (n = 66; 71.7%) isolates were resistant to a minimum of one antimicrobial with main resistance detected towards oxytetracycline (51.90%). This emphasizes on the call for wise antimicrobial use at some stage in animal production and strict sanitation for the duration of slaughtering. Briefly, cattle slaughtered in South African rural abattoirs harboured different types of Salmonella serovars that were resistant to antimicrobials, which could be a public health risk and danger. The outcome should support policymakers with determining the effectiveness of existing sanitary measures during cattle slaughtering in rural abattoirs, which is vital from socio-economic, public health, and epidemiological perspectives. / College of Agriculture and Environmental Sciences

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Susceptibility Weighted Imaging (SWI) utilizes the susceptibility difference between tissues to create a new type of imaging contrast in MRI that is different from conventional spin density, T1-, or T2-weighted imaging. The SWI sequence is a high resolution, fully flow compensated gradient echo sequence. High resolution reduces the signal loss caused by local field inhomogeneities yet with relatively long echo time sufficient contrast can be generated between tissues with a susceptibility difference. Contrast between tissues in the phase image is directly proportional to the susceptibility difference and can be used to enhance the contrast in the magnitude image. In this thesis, we optimize the contrast to noise ratio (CNR) in the magnitude image as a function of the multiplication of the phase mask generated from the phase image. We find that a shorter echo time has the advantage of achieving higher CNR efficiency compared with longer echo times. SWI has found numerous clinical applications due to its sensitivity to blood products. Partial volume effects occur when a voxel contains both venous blood and brain parenchyma. We studied the apparent phase of a voxel as a function of imaging resolution and predict what the best imaging parameters for a specific clinical application should be. Currently, a long acquisition time is the bottleneck for SWI to be used as a routine protocol in the clinical environment. This thesis evaluates segmented echo planar imaging (SEPI) as an alternative to speed up the acquisition while reducing the artifacts usually associated with other fast imaging methods. / Thesis / Doctor of Philosophy (PhD)

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<p>Quantitatively measuring oxygen saturation is important to characterize the physiological or pathological state of tissue function. In this thesis, we demonstrate the possibility of using susceptibility mapping to noninvasively estimate the venous blood oxygen saturation level. Accurate susceptibility quantification is the key to oxygen saturation quantification. Two approaches are presented in this thesis to generate accurate and artifact free susceptibility maps (SM): a regularized inverse filter and a k-space iterative method. Using the regularized inverse filter, with sufficient resolution, major veins in the brain can be visualized. We found that different sized vessels show a different level of contrast depending on their partial volume effects; larger vessels show a bias toward a reduced susceptibility approaching 90% of the expected value. Also, streaking artifacts associated with high susceptibility structures such as veins are obvious in the reconstructed SM. To further improve susceptibility quantification and reduce the streaking artifacts in the SMs, we proposed a threshold-based k-space iterative approach that used geometric information from the SM itself as a constraint to overcome the ill-posed nature of the inverse filter. Both simulations and in vivo results show that most streaking artifacts inside the SM were suppressed by the iterative approach. In simulated data, the bias toward lower mean susceptibility values inside vessels has been shown to decrease from around 10% to 2% when choosing an appropriate threshold value for the proposed iterative method, which brings us one step closer to a practical means to map out oxygen saturation in the brain.</p> / Doctor of Philosophy (PhD)