Region Connection Calculus: Composition Tables and Constraint Satisfaction Problems

Qualitative spatial reasoning (QSR) is an important field of AI that deals with qualitative aspects of spatial entities. Regions and their relationships are described in qualitative terms instead of numerical values. This approach models human based reasoning about such entities closer than other approaches. Any relationships between regions that we encounter in our daily life situations are normally formulated in natural language. For example, one can outline one's room plan to an expert by indicating which rooms should be connected to each other. Mereotopology as an area of QSR combines mereology, topology and algebraic methods. As mereotopology plays an important role in region based theories of space, our focus is on one of the most widely referenced formalisms for QSR, the region connection calculus (RCC). RCC is a first order theory based on a primitive connectedness relation, which is a binary symmetric relation satisfying some additional properties. By using this relation we can define a set of basic binary relations which have the property of being jointly exhaustive and pairwise disjoint (JEPD), which means that between any two spatial entities exactly one of the basic relations hold. Basic reasoning can now be done by using the composition operation on relations whose results are stored in a composition table. Relation algebras (RAs) have become a main entity for spatial reasoning in the area of QSR. These algebras are based on equational reasoning which can be used to derive further relations between regions in a certain situation. Any of those algebras describe the relation between regions up to a certain degree of detail. In this thesis we will use the method of splitting atoms in a RA in order to reproduce known algebras such as RCC15 and RCC25 systematically and to generate new algebras, and hence a more detailed description of regions, beyond RCC25.

Development of packaging cell lines for rescuing BAV2 viral vectors

The construction of adenovirus vectors for cloning and foreign gene expression requires packaging cell lines that can complement missing viral functions caused by sequence deletions and/or replacement with foreign DNA sequences. In this study, packaging cell lines were designed to provide in trans the missing bovine adenovirus functions, so that recombinant viruses could be generated. Fetal bovine kidney and lUng cells, acquired at the trimester term from a pregnant cow, were tranfected with both digested wild type BAV2 genomic DNA and pCMV-EI. The plasmid pCMV-EI was specifically constructed to express El of BAV2 under the control of the cytomegalovirus enhancer/promoter (CMV). Selection for "true" transformants by continuous passaging showed no success in isolating immortalised cells, since the cells underwent crisis resulting in complete cell death. Moreover, selection for G418 resistance, using the same cells, also did not result in the isolation of an immortalised cell line and the same culture-collapse event was observed. The lack of success in establishing an immortalised cell line from fetal tissue prompted us to transfect a pre-established cell line. We began by transfecting MDBK (Mardin-Dardy bovine kidney) cells with pCMV-El-neo, which contain the bacterial selectable marker neo gene. A series of MDBK-derived cell lines, that constitutively express bovine adenoviral (BAV) early region 1 (El), were then isolated. Cells selected for resistance to the drug G418 were isolated collectively for full characterisation to assess their suitability as packaging cell lines. Individual colonies were isolated by limiting dilution and further tested for El expression and efficiency of DNA uptake. Two cell lines, L-23 and L-24, out of 48 generated foci tested positive for £1 expression using Northern Blot analysis. DNA uptake studies, using both lipofectamine and calcium phosphate methods, were performed to compare these cells, their parental MDBK cells, 8 and the unrelated human 293 cells as a benchmark. The results revealed that the new MDBKderived clones were no more efficient than MDBK cells in the transient expression of transfected DNA and that they were inferior to 293 cells, when using lacZ as the reporter gene. In view of the inherently poor transfection efficiency of MDBK cells and their derivatives, a number of other bovine cells were investigated for their potential as packaging cells. The cell line CCL40 was chosen for its high efficiency in DNA uptake and subsequently transfected with the plasmid vector pCMV El-neo. By selection with the drug G418, two cell lines were isolated, ProCell 1 and ProCell 2. These cell lines were tested for El expression, permissivity to BAV2 and DNA uptake efficiency, revealing a DNA uptake efficiency of 37 % , comparable to that of CCL40. Attempts to rescue BAV2 mutants carrying the lacZ gene in place of £1 or £3 were carried out by co-transfecting wild type viral DNA with either the plasmid pdlElE-Z (which contains BAV2 sequences from 0% to 40.4% with the lacZ gene in place of the £1 region from 1.1% to 8.25%) or with the plasmid pdlE3-5-Z (which contains BAV2 sequences from 64.8% to 100% with the lacZ gene in place of the E3 region from 75.8% to 81.4%). These cotransfections did not result in the generation of a viral mutant. The lack of mutant generation was thought to be caused by the relative inefficiency ofDNA uptake. Consequently, cosBAV2, a cosmid vector carrying the BAV2 genome, was modified to carry the neo reporter gene in place of the £3 region from 75.8% to 81.4%. The use of a single cosmid vector earring the whole genome would eliminate the need for homologous recombination in order to generate a viral vector. Unfortunately, the transfection of cosBAV2- neo also did not result in the generation of a viral mutant. This may have been caused by the size of the £3 deletion, where excess sequences that are essential to the virus' survival might have been deleted. As an extension to this study, the spontaneous E3 deletion, accidently discovered in our viral stock, could be used as site of foreign gene insertion.

Generating Relation Algebras for Qualitative Spatial Reasoning

Basic relationships between certain regions of space are formulated in natural language in everyday situations. For example, a customer specifies the outline of his future home to the architect by indicating which rooms should be close to each other. Qualitative spatial reasoning as an area of artificial intelligence tries to develop a theory of space based on similar notions. In formal ontology and in ontological computer science, mereotopology is a first-order theory, embodying mereological and topological concepts, of the relations among wholes, parts, parts of parts, and the boundaries between parts. We shall introduce abstract relation algebras and present their structural properties as well as their connection to algebras of binary relations. This will be followed by details of the expressiveness of algebras of relations for region based models. Mereotopology has been the main basis for most region based theories of space. Since its earliest inception many theories have been proposed for mereotopology in artificial intelligence among which Region Connection Calculus is most prominent. The expressiveness of the region connection calculus in relational logic is far greater than its original eight base relations might suggest. In the thesis we formulate ways to automatically generate representable relation algebras using spatial data based on region connection calculus. The generation of new algebras is a two pronged approach involving splitting of existing relations to form new algebras and refinement of such newly generated algebras. We present an implementation of a system for automating aforementioned steps and provide an effective and convenient interface to define new spatial relations and generate representable relational algebras.

Preliminary epidemiological study of latent tuberculosis in Mexican agricultural workers in the Niagara region, Canada

It is well documented that the majority of Tuberculosis (TB) cases diagnosed in Canada are related to foreign-bom persons from TB high-burden countries. The Canadian seasonal agricultural workers program (SAWP) operating with Mexico allows migrant workers to enter the country with a temporary work permit for up to 8 months. Preiimnigration screening of these workers by both clinical examination and chest X-ray (CXR) reduces the risk of introducing cases of active pulmonary TB to Canada, but screening for latent TB (LTBI) is not routinely done. Studies carried out in industrialized nations with high immigration from TBendemic countries provide data of lifetime LTBI reactivation of around 10% but little is known about reactivation rates within TB-endemic countries where new infections (or reinfections) may be impossible to distinguish from reactivation. Migrant populations like the SAWP workers who spend considerable amounts of time in both Canada and TBendemic rural areas in Mexico are a unique population in terms of TB epidemiology. However, to our knowledge no studies have been undertaken to explore either the existence of LTBI among Mexican workers, the probability of reactivation or the workers' exposure to TB cases while back in their communities before returning the following season. Being aware of their LTBI status may help workers to exercise healthy behaviours to avoid TB reactivation and therefore continue to access the SAWP. In order to assess the prevalence of LTBI and associated risk factors among Mexican migrant workers a preliminary cross sectional study was designed to involve a convenience sample of the Niagara Region's Mexican workers in 2007. Research ethics clearance was granted by Brock University. Individual questionnaires were administered to collect socio-demographic and TB-related epidemiological data as well as TB knowledge and awareness levels. Cellular immunity to M tuberculosis was assessed by both an Interferon-y release assay (lGRA), QuantiFERON -TB Gold In-Tube (QFf™) and by the tuberculin skin test (TSn using Mantoux. A total of 82 Mexican workers (out of 125 invited) completed the study. Most participants were male (80%) and their age ranged from 22 to 65 years (mean 38.5). The prevalence of LTBI was 34% using TST and 18% using QFTTM. As previously reported, TST (using ~lOmm cut-off) showed a sensitivity of 93.3% and a specificity of 79.1 %. These findings at the moment cannot predict the probability of progression to active TB; only longitudinal cohort studies of this population can ascertain this outcome. However, based on recent publications, lORA positive individuals may have up to 14% probability of reactivation within the next two years. Although according to the SA WP guidelines, all workers undergo TB screening before entering or re-entering Canada, CXR examination requirements showed to be inconsistent for this population: whereas 100% of the workers coming to Canada for the first time reported having the procedure done, only 31 % of returning participants reported having had a CXR in the past year. None of the participants reported ever having a CXR compatible with TB which was consistent with the fact that none had ever been diagnosed with active pulmonary TB and with only 3.6% reporting close contact with a person with active TB in their lifetime. Although Mexico reports that 99% of popUlation is fully immunized against TB within the first year of age, only 85.3% of participants reported receiving BOC vaccine in childhood. Conversely, even when TST is not part of the routine TB screening in endemic countries, a suqDrisingly high 25.6% reported receiving a TST in the past. In regards to TB knowledge and awareness, 74% of the studied population had previous knowledge about (active) TB, 42% correctly identified active TB symptomatology, 4.8% identified the correct route of transmission, 4.8% knew about the existence of LTBI, 3.6% knew that latent TB could reactivate and 48% recognized TB as treatable and curable. Of all variables explored as potential risk factors for LTBI, age was the only one which showed statistical significance. Significant associations could not be proven for other known variables (such as sex, TB contact, history of TB) probably because of the small sample size and the homogeneity of the sample. Screening for LTBI by TST (high sensitivity) followed by confirmation with QFT''"'^ (high specificity) suggests to be a good strategy especially for immigrants from TB high-burden countries. After educational sessions, workers positive for LTBI gained greater knowledge about the signs and symptoms of TB reactivation as well as the risk factors commonly associated with reactivation. Additionally, they were more likely to attend their annual health check up and request a CXR exam to monitor for TB reactivation.