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.

Bee Communities in Restored Landfill Sites of Niagara Region

This study examined the impact of habitat restoration on bee communities (Hymenoptera: Apidae) of the Niagara Region, Ontario, Canada. Bee abundance and diversity was studied in three restored landfill sites: the Glenridge Quarry Naturalization Site (GQNS) in St. Catharines, Elm Street Naturalization Site in Port Colborne, and Station Road Naturalization Site in Wainfleet during 2011 and 2012. GQNS represented older sites restored from 2001-2003. Elm and Station sites represented newly restored landfills as of 2011. These sites were compared to control sites at Brock University where bee communities are well established and again to other landfills where no stable habitat was available before restoration. The objective of this study is to investigate the impact of restoration level on bee abundance and diversity in restored landfill sites of the Niagara Region. Based on the increased disturbance hypothesis (InDH) and the intermediate disturbance hypothesis (IDH), I hypothesized that bee abundance and diversity will follow two patterns. First pattern according to InDH suggest that as the disturbance decrease the bee abundance and diversity will increased. Second pattern according to the IDH bee abundance and diversity will be the highest at the intermediate level of disturbance. A total of 7 173 bees were collected using pan traps and flower collections, from May to October 2011 and 2012. Bees were classified to five families, 21 genera and sub-genera, containing at least 78 species. In 2011 bee abundance was not significantly different among restoration levels while in 2012 bee abundance was significant difference among restoration level. According to family there were no significant difference in Halictidae and Apidae abundance among restoration level while Colletidae and Megachilidae abundance were varied among restoration levels. The bee species richness was highest in the newly restored sites followed by restored control sites, and then the control site. The current study demonstrates that habitat restoration results in rapid increases in bee abundance and diversity for newly restored sites, and, further, that it takes only 2-3 years for bee assemblages in newly restored sites to arrive at the same levels of abundance and diversity as in nearby control sites where bee communities are well established.

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.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

KAIRON PROJECT : assessing the role of expressive arts in community-based breast cancer support systems in the Niagara Region

Research Report Written for the Canadian Breast Cancer Foundation.

Development of a bovine adenovirus type 2-based gene delivery vector /

ABSTRACT Recombinant adenoviruses are currently under intense investigation as potential gene delivery and gene expression vectors with applications in human and veterinary medicine. As part of our efforts to develop a bovine adenovirus type 2 (BAV2) based vector system, the nucleotide sequence of BAV2 was determined. Sixty-six open reading frames (ORFs) were found with the potential to encode polypeptides that were at least 50 amino acid (aa) residue long. Thirty-one of the BAV2 polypeptide sequences were found to share homology to already identified adenovirus proteins. The arrangement of the genes revealed that the BAV2 genomic organization closely resembles that of well-characterized human adenoviruses. In the course of this study, continuous propagation of BAV2 over many generations in cell culture resulted in the isolation of a BAV2 spontaneous mutant in which the E3 region was deleted. Restriction enzyme, sequencing and PCR analyses produced concordant results that precisely located the deletion and revealed that its size was exactly 1299 bp. The E3-deleted virus was plaque-purified and further propagated in cell culture. It appeared that the replication of such a virus lacking a portion of the E3 region was not affected, at least in cell culture. Attempts to rescue a recombinant BAV2 virus with the bacterial kanamycin resistance gene in the E3 region yielded a candidate as verified with extensive Southern blotting and PCR analyses. Attempts to purify the recombinant virus were not successful, suggesting that such recombinant BAV2 was helper-dependent. Ten clones containing full-length BAV2 genomes in a pWE15 cosmid vector were constructed. The infectivity of these constructs was tested by using different transfection methods. The BAV2 genomic clones did appear to be infectious only after extended incubation period. This may be due to limitations of various transfection methods tested, or biological differences between virus- and E. co//-derived BAV2 DNA.

Irrigation scheduling for Sovereign Coronation grapevine based upon evapotranspiration calculations and crop coefficients /

Several irrigation treatments were evaluated on Sovereign Coronation table grapes at two sites over a 3-year period in the cool humid Niagara Peninsula of Ontario. Trials were conducted in the Hippie (Beamsville, ON) and the Lambert Vineyards (Niagara-on-the-Lake, ON) in 2003 to 2005 with the objective of assessing the usefulness of the modified Penman-Monteith equation to accurately schedule vine irrigation needs. Data (relative humidity, windspeed, solar radiation, and temperature) required to precisely calculate evapotranspiration (ETq) were downloaded from the Ontario Weather Network. One of two ETq values (either 100 or 150%) were used in combination with one of two crop coefficients (Kc; either fixed at 0.75 or 0.2 to 0.8 based upon increasing canopy volume) to calculate the amount of irrigation water required. Five irrigation treatments were: un irrigated control; (lOOET) X Kc =0.75; 150ET X Kc =0.75; lOOET X Kc =0.2-0.8; 150ET X Kc =0.2-0.8. Transpiration, water potential (v|/), and soil moisture data were collected each growing seasons. Yield component data was collected and berries from each treatment were analyzed for soluble solids (Brix), pH, titratable acidity (TA), anthocyanins, methyl anthranilate (MA), and total volatile esters (TVE). Irrigation showed a substantial positive effect on transpiration rate and soil moisture; the control treatment showed consistently lower transpiration and soil moisture over the 3 seasons. Transpiration appeared accurately reflect Sovereign Coronation grapevines water status. Soil moisture also accurately reflected level of irrigation. Moreover, irrigation showed impact of leaf \|/, which was more negative throughout the 3 seasons for vines that were not irrigated. Irrigation had a substantial positive effect on yield (kg/vine) and its various components (clusters/vine, cluster weight, and berries/cluster) in 2003 and 2005. Berry weights were higher under the irrigated treatments at both sites. Berry weight consistently appeared to be the main factor leading to these increased yields, as inconsistent responses were noted for some yield variables. Soluble solids was highest under the ET150 and ET100 treatments both with Kc at 0.75. Both pH and TA were highest under control treatments in 2003 and 2004, but highest under irrigated treatments in 2005. Anthocyanins and phenols were highest under the control treatments in 2003 and 2004, but highest under irrigated treatments in 2005. MA and TVE were highest under the ET150 treatments. Vine and soil water status measurements (soil moisture, leaf \|/, and transpiration) confirmed that irrigation was required for the summers of 2003 and 2005 due to dry weather in those years. They also partially supported the hypothesis that the Penman-Monteith equation is useful for calculating vineyard water needs. Both ET treatments gave clear evidence that irrigation could be effective in reducing water stress and for improving vine performance, yield and fruit composition. Use of properly scheduled irrigation was beneficial for Sovereign Coronation table grapes in the Niagara region. Findings herein should give growers some strong guidehnes on when, how and how much to irrigate their vineyards.

Development of techniques for testing the effect of the E1 region on adenovirus integration /

Adenoviral vectors are currently the most widely used gene therapeutic vectors, but their inability to integrate into host chromosomal DNA shortened their transgene expression and limited their use in clinical trials. In this project, we initially planned to develop a technique to test the effect of the early region 1 (E1) on adenovirus integration by comparing the integration efficiencies between an E1-deleted adenoviral vector (SubE1) and an Elcontaining vector (SubE3). However, we did not harvest any SubE3 virus, even if we repeated the transfection and successfully rescued the SubE1 virus (2/4 transfections generated viruses) and positive control virus (6/6). The failure of rescuing SubE3 could be caused by the instability of the genomic plasmid pFG173, as it had frequent intemal deletions when we were purifying It. Therefore, we developed techniques to test the effect of E1 on homologous recombination (HR) since literature suggested that adenovirus integration is initiated by HR. We attempted to silence the E1 in 293 cells by transfecting E1A/B-specific small interfering RNA (siRNA). However, no silenced phenotype was observed, even if we varied the concentrations of E1A/B siRNA (from 30 nM to 270 nM) and checked the silencing effects at different time points (48, 72, 96 h). One possible explanation would be that the E1A/B siRNA sequences are not potent enough to Induce the silenced phenotype. For evaluating HR efficiencies, an HR assay system based on bacterial transfonmatJon was designed. We constmcted two plasmids ( designated as pUC19-dl1 and pUC19-dl2) containing different defective lacZa cassettes (forming white colonies after transformation) that can generate a functional lacZa cassette (forming blue colonies) through HR after transfecting into 293 cells. The HR efficiencies would be expressed as the percentages of the blue colonies among all the colonies. Unfortunately, after transfonnation of plasmid isolated from 293 cells, no colony was found, even at a transformation efficiency of 1.8x10^ colonies/pg pUC19, suggesting the sensitivity of this system was low. To enhance the sensitivity, PCR was used. We designed a set of primers that can only amplify the recombinant plasmid fomied through HR. Therefore, the HR efficiencies among different treatments can be evaluated by the amplification results, and this system could be used to test the effect of E1 region on adenovirus integration. In addition, to our knowledge there was no previous studies using PCR/ Realtime PCR to evaluate HR efficiency, so this system also provides a PCR-based method to carry out the HR assays.

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.

Manipulation of adenovirus early region 1 rescue plasmids by homologous recombination in Saccharomyces cerevisiae

The manipulation of large (>10 kb) plasmid systems amplifies problems common to traditional cloning strategies. Unique or rare restriction enzyme recognition sequences are uncommon and very rarely located in opportunistic locations. Making site-specific deletions and insertions in larger plasmids consequently leads to multiple step cloning strategies that are often limited by time-consuming, low efficiency linker insertions or blunt-end cloning strategies. Manipulation ofthe adenovirus genome and the genomes ofother viruses as bacterial plasmids are systems that typify such situations. Recombinational cloning techniques based on homologous recombination in Saccharomyces cerevisiae that circumvent many ofthese common problems have been developed. However, these techniques are rarely realistic options for such large plasmid systems due to the above mentioned difficulties associated with the addition ofrequired yeast DNA replication, partitioning and selectable marker sequences. To determine ifrecombinational cloning techniques could be modified to simplify the manipulation of such a large plasmid system, a recombinational cloning system for the creation of human adenovirus EI-deletion rescue plasmids was developed. Here we report for the first time that the 1,456 bp TRP1/ARS fragment ofYRp7 is alone sufficient to foster successful recombinational cloning without additional partitioning sequences, using only slight modifications of existing protocols. In addition, we describe conditions for efficient recombinational cloning involving simultaneous deletion of large segments ofDNA (>4.2 kb) and insertion of donor fragment DNA using only a single non-unique restriction site. The discovery that recombinational cloning can foster large deletions has been used to develop a novel recombiliational cloillng technique, selectable inarker 'kilockouf" recombinational cloning, that uses deletion of a yeast selectable marker coupled with simultaneous negative and positive selection to reduce background transformants to undetectable levels. The modification of existing protocols as described in this report facilitates the use of recombinational cloning strategies that are otherwise difficult or impractical for use with large plasmid systems. Improvement of general recombinational cloning strategies and strategies specific to the manipulation ofthe adenovirus genome are considered in light of data presented herein.

Psychographic characteristics of weekend wine tourists : a multiple case study of four wineries in the Niagara Region

The purpose of this study is to examine the psychographic (product attributes, motivation opinions, interest, lifestyle, values) characteristics of wine tourists along the Niagara wine r,~ute, located in Ontario, Canada, using a multiple case study method. Four wineries were selected, two wineries each on the East, and West sides of the wine route during the shoulder-season (January, February, 2004). Using a computer generated survey technique, tourists were approached to fill out a questionnaire on one of the available laptop computers, where a sample ofN=321 was obtained. The study findings revealed that there are three distinct wine tourist segments in the Niagara region. The segments were determined using an exploratory factor analysis (EFA) and a K-means cluster analysis: Wine Lovers, Wine Interested, and Wine Curious wine tourists. These three segments displayed significant differences in their, motivation for visiting a winery, lifestyles, values, and wine purchasing behaviour. This study also examined differences between winery locations, on the East and West sides of the Niagara wine route, with respect to the aforementioned variables. The results indicated that there were significant differences between the regions with respect to these variables. The findings suggest that these differences present opportunities for more effective marketing strategies based on the uniqueness of each region. The results of this study provide insight for academia into a method of psychographic market segmentation of wine tourists and consumer behaviour. This study also contributes to the literature on wine tourism, and the identification of psychographic characteristics of wine tourists, an area where little research has taken place.

Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

Adenovirus-based exogenous gene expression in mammalian cells

Thesis (Ph.D.)--Brock University, 2010.

Using genetic algorithms for the single allocation hub location problem

Hub location problem is an NP-hard problem that frequently arises in the design of transportation and distribution systems, postal delivery networks, and airline passenger flow. This work focuses on the Single Allocation Hub Location Problem (SAHLP). Genetic Algorithms (GAs) for the capacitated and uncapacitated variants of the SAHLP based on new chromosome representations and crossover operators are explored. The GAs is tested on two well-known sets of real-world problems with up to 200 nodes. The obtained results are very promising. For most of the test problems the GA obtains improved or best-known solutions and the computational time remains low. The proposed GAs can easily be extended to other variants of location problems arising in network design planning in transportation systems.

A Comparative Analysis of Community-Based Service Providers for "Extreme" Case ASD: Exploring Activity Program Options

The purpose of my research was to examine how community-based organizations in the Niagara region provide programs for children with Autism Spectrum Disorder (ASD), who are considered to represent “extreme” or “severe” cases. A qualitative, comparative case study was conducted that focused on three organizations who provide summer recreation and activity programs, in order to examine the issues these organizations face when determining program structure and staff training; and to understand what the threshold for physical activity is in this type of setting, and how the unique needs surrounding these “severe” cases are met while attending the program. Purposeful sampling was employed to select a supervisor and senior staff member from each organization to discuss the training process, program development and implementation, and the resources and strategies used within their organization’s community-based program. A confirming comparative analysis was comparative analysis of a parents survey with six mothers whose children are considered “severe” indicated that camp staffs’ expectations are unrealistic where as the parents and supervisors have more realistic expectations within the “real world” of camp. There is no definition of “severe” or “extreme” and therefore severity is dependent upon the context.