VictorJuiz/thesis huggingface dataset:
Semantic Web Based Multi-agent Framework for Real-time Freeway Traffic Incident Management System

Recurring traffic congestion is attributable to steadily increasing travel demand coupled with constrained space and financial resources for infrastructure expansion. Another major source of congestion is non-recurrent incidents that disrupt the normal operation of the infrastructure. Aiming to optimize the utilization of the transportation infrastructure, innovative infrastructure management techniques that incorporate on edge technological equipment and information systems need to be adopted to manage recurrent and non-recurrent congestion and reduce their adverse externalities. The framework presented in this thesis lays the foundation for multi-disciplinary semantic web based incident management. During traffic incident response, involved stakeholders will share their knowledge and resources, forming an ad-hoc framework within which each party will focus on its core competencies and cooperate to achieve a coherent incident management process. Negotiation between various response agencies operators is performed using intelligent software agents, alleviating the coordination and synchronization burden of the massive information flow during the incident response. The software agents provide a decision support to human operators based on the reasoning provided from the underlying system knowledge models. Ontological engineering is used to lay the foundation of the knowledge models, which are coded in a web based ontology language, allowing a decentralized access to various elements of the system. The whole system communication infrastructure is based on the Semantic Web technologies. The semantic web facilitates the use of, in an enhanced manner, the already existing web technologies as the communication infrastructure of the proposed system. Its semantic capabilities help to resolve the information and data interoperability issues among various parties. The web services concepts combined with the semantic web allow the direct exploration and access of knowledge models, resources, and data repertories held by various parties. The developed ontology along with the developed software system were tested and evaluated by domain experts and targeted system users. Based on the conducted evaluation, both the ontology and the software system were found to be promising tools in developing pervasive, collaborative and multi-disciplinary traffic incident management systems

Keywords: Traffic
Multi-agent
Advisor: Abdulhai, Baher
Modernist Curiosities: Desire, Knowledge and Literature in Gustave Flaubert's "Bouvard et Pécuchet", Elias Canetti's "Die Blendung" and Jorge Luis Borges's "El Aleph"

In modernity, probably more than ever, “knowledge” has become the object of an intense desire. The tensions underwriting this modern desire for knowledge are inscribed in the very term, curiosity, which is at the centre of this dissertation. A venerable motif, curiosity anchors the specifically modern desire to know within a longstanding philosophical, theological and literary tradition. By the 19th century, “curiosity” is certainly an anachronistic paradigm. Yet, inscribed in curiosity, there are two conflicting dialectics which can be found at the heart of modernity’s unquenchable thirst for knowledge: one the one hand, the dialectic between curiosity as a disenchanting desire to see through into the innermost secrets of things, and curiosity as a “thing”, the product of a fetishist desire arrested on the glittering surface of things. On the other hand, curiosity is beset by the dialectic between the desire for a “totalizing”, meaningful vision and the compulsive drive of an increasingly specialized, meaningless pursuit of knowledge. This dissertation examines a series of Modernist narratives which expose this double dialectic. The protagonists of Gustave Flaubert’s Bouvard et Pécuchet, Elias Canetti’s Die Blendung and Jorge Luis Borges’ El Aleph are all caricatural, anachronistic, curieux ultimately seeking an “absolute knowledge” that cannot be embodied. The moment it seems to have been attained, it is reified, “objectified” into a fetish, a “curiosity”. Yet, these narratives are not only about curiosity; they are in fact true vortexes of curiosity: that of the protagonists of the narratives as well as that of the authors and the readers themselves. As a result, these narratives also speak to the paradoxical location of literature within culture: literature appears simultaneously as the privileged site of all – ultimately phantasmic – totalizing, meaningful visions of the world, as well as a marginal locus, a monstrous cultural residue.

Keywords: modernism
curiosity
desire
knowledge and literature
epistemology of literature
Advisor: Kushner, Eva
Zilcosky, John
Identification and Validation of Candidate Breast Cancer Biomarkers: A Mass Spectrometric Approach

One of the best ways to diagnose breast cancer early or to predict therapeutic response is to use serum biomarkers. Unfortunately, for breast cancer, we do not have effective serological biomarkers. We hypothesized that novel candidate tumor markers for breast cancer may be secreted or shed proteins that can be detected in tissue culture supernatants of human breast cancer cell lines. A two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) strategy was utilized to identify and compare levels of extracellular and membrane-bound proteins in the conditioned media. Proteomic analysis of the media identified in excess of 600, 500 and 700 proteins in MCF-10A, BT474 and MDA-MB-468, respectively. We successfully identified the internal control proteins, kallikreins 5, 6 and 10 (ranging in concentration from 2-50 µg/L), as validated by ELISA and confidently identified HER-2/neu in BT474 cells. Sub-cellular localization was determined based on Genome Ontology (GO) for the 1,139 proteins, of which 34% were classified as extracellular and membrane-bound. Tissue specificity, functional classifications and label-free quantification were performed. The levels of eleven promising molecules were measured in biological samples to determine its discriminatory ability for control versus cases. This screen yielded activated leukocyte cell adhesion molecule (ALCAM) as a promising candidate. The levels of ALCAM, in addition to the classical breast cancer tumor markers carbohydrate antigen 15-3 (CA 15-3) and carcinoembryonic antigen (CEA) were examined in 300 serum samples by quantitative ELISA. All three biomarkers effectively separated cancer from non-cancer groups. ALCAM, with area under the curve (AUC) of 0.78 [95% CI: 0.73, 0.84] outperformed CA15-3 (AUC= 0.70 [95% CI: 0.64, 0.76]) and CEA (AUC= 0.63 [95% CI: 0.56, 0.70]). The incremental values of AUC for ALCAM over that for CA15-3 were statistically significant (Delong test, p <0.05). Serum ALCAM appears to be a new biomarker for breast cancer and may have value for disease diagnosis.

Keywords: proteomics
mass spectrometry
breast cancer
diagnostics
Advisor: Diamandis, Eleftherios P.
Predictors of Hospitalization Among Cystic Fibrosis Patients in Ontario

This dissertation involved linking a clinical cystic fibrosis (CF) data registry with administrative databases to evaluate clinical, demographic, and geographical predictors of hospitalization in CF patients living in Ontario over a 10 year period. In addition, this work assessed the ability of administrative data to identify individuals with CF using the clinical registry as the reference standard. Sex was an independent predictor of hospitalization rates for individuals with CF. Females had a significantly higher hospitalization rate compared to males even after adjusting for important clinical factors suggesting that this finding is not simply due to worse CF disease. In those between 7 and 19 years of age, the adjusted hospitalization rate was 38% higher in females (rate ratio[RR] 1.38, 95% confidence interval [CI] 1.11-1.73). Similarly in those over the age of 19, females had a 30% higher hospitalization rate compared to males (RR 1.30, 95% CI 1.06-1.59). Other significant predictors associated with higher hospitalization rates in both age groups were lower lung function, worse nutritional status, pancreatic insufficiency, and the presence of CF-related diabetes. The presence of Burkholderia cepacia complex in the sputum was a significant predictor in those over the age of 19 years (RR 1.54, 95% CI 1.26-1.89). Distance to CF centre, community size and socioeconomic status were not significant predictors of hospitalization rates in either age group. There was no significant trend in hospitalization rates over time once rates were adjusted for markers of disease severity (p=0.08). Comparing administrative data with the CF registry data, administrative data captured hospitalizations more comprehensively. Despite CF being a specific diagnosis, health administrative databases alone were insufficient to reliably and accurately identify individuals with CF unless they had been hospitalized. The reason for the gender disparity seen within this dissertation is likely multifactorial. There may be differences in outpatient management between the sexes, hormonal influences may modulate disease severity causing higher hospitalization rates, and patient and provider-level influences may affect the decision to hospitalize a patient. Further research is needed in this area to elucidate the factors contributing to this gender gap.

Keywords: cystic fibrosis
Hospitalization
epidemiology
health services utilization
gender
Advisor: Hux, Janet
Corey, Mary
National Fate and Empire: George Grant and Canadian Foreign Policy

This study examines the foreign policy views of the Canadian thinker, George Grant. It focuses on the years between Mackenzie King’s re-election in 1935 and the Liberal party’s return to power under Lester Pearson in 1963. During this period, Grant argued, Canada was transformed from a British dependent to a satellite of the United States, a process that he believed had been accelerated by the continentalist economic and security policies of successive Liberal governments. As a young man during World War II, Grant admired the United States of F. D. Roosevelt. But as he began to contemplate the threat that a postwar Pax Americana posed to the societies of the Old World, and, ultimately, to Canada, his misgivings grew. His attempts to understand the emerging order led him to a critical study of modern liberalism, which he believed provided the chief philosophical justification for America’s expansion. Unlike Marxists who saw liberalism as simply an ideology of individual greed, Grant claimed that it succeeded largely by appealing to our hopes for social progress. These hopes found their loftiest expression in the belief that liberalism’s internationalization would produce the conditions for the overcoming of war within and between nations. Grant feared that this ideal could only be achieved through the annihilation of all real cultural diversity—the realization of what he called the universal and homogeneous state. One of his unique claims was that the Liberal policy of rapprochement with the United States after 1935 signaled the growing dominance of this ideal within Canada. This dominance was fed during the Cold War by “realists” like Pearson who decried the utopianism of communism, while failing to reckon with the utopian aspirations of his own society. Fearful of Marxist one-worldism, Pearson committed himself to a single-minded defence of a liberal order that tended to produce even greater homogeneity around the world. Grant’s own practical aim in writing about foreign policy, I argue, was neither to defend liberalism against its “utopian” critics, nor to reject it for an alternative like Marxism, but to highlight the utopian aspirations of liberal society, and thereby subject it to the moderating influence of doubt.

Keywords: Canadian Foreign Policy
Political Thought
Advisor: Forbes, Hugh Donald
Electromagnetically Induced Exciton Dynamics and Bose-Einstein Condensation near a Photonic Band Gap

We demonstrate electromagnetically-induced anomalous quantum dynamics of an exciton in a photonic band gap (PBG) - quantum well (QW) hetero-structure. Within the engineered electromagnetic vacuum of the PBG material, the exciton can propagate through the QW by the emission and re-absorption of virtual photons in addition to the conventional electronic hopping mechanism. When the exciton wavevector and recombination energy coincide nearly with a photonic band edge, the exciton kinetic energy is lowered by 1-10meV through coherent radiative hopping. This capture of the exciton by the photonic band edge is accompanied by strong electromagnetic dressing in which the exciton's renormalized effective mass is 4-5 orders of magnitude smaller than in the absence of the PBG environment. This dressed exciton exhibits a long radiative lifetime characteristic of a photon-atom bound state and is robust to phonon-assisted, re-combinative decay. By inheriting properties of the PBG electromagnetic vacuum, the bound electron-hole pair becomes a stable, ultra-mobile quantum excitation. Unlike traditional exciton-polariton modes created by placing a QW in a one-dimensional optical cavity, our PBG-QW excitons exhibit strong coupling to optical modes and retain a long lifetime. This is crucial for unambiguous observation of quantum coherence effects such as Bose-Einstein condensation. We present a model for the equilibrium quantum statistics of a condensate of repulsively interacting bosons in a two-dimensional trap. Particle correlations in the ground state are treated exactly, whereas interactions with excited particles are treated in a generalized Bogoliubov mean-field theory. This leads to a fundamental physical picture for condensation of interacting bosons through an anharmonic oscillator ground state coupled to excited Bogoliubov quasiparticles in which the quantum number statistics of condensate particles emerges self-consistently. Our anharmonic oscillator model for the exciton ground state manifold goes beyond the conceptual framework of traditional Bogoliubov theory. Below the Bose-Einstein condensation temperature, our model exhibits a crossover from particle bunching to Poissonian statistics and finally antibunching as temperature is lowered or as the trapping area is decreased. When applied to Bose condensation of long-lived dressed excitons in a photonic band gap material, our model suggests that this system may serve as a novel tunable source for non-classical states of light.

Keywords: Quantum Well Exciton
Photonic Band Gap
Bose-Einstein Condensation
Antibunching
Advisor: John, Sajeev
Molecular Evolution of Visual System Genes in Fishes

For many species, vision contributes to a number of fitness-related tasks, including mating and the detection of prey and predators. Selection on the visual system should therefore be strong, especially when ecological or genomic changes open new avenues for evolutionary changes. Visual system proteins are thus attractive systems for molecular evolutionary analyses. This thesis presents a collection of evolutionary studies on two gene families, opsins and crystallins. Opsin proteins determine the wavelengths of light detected by the retina, while crystallin proteins contribute to lens transparency and refractory power. My studies focus on teleost fishes, because teleost visual ecology is exceptionally diverse and because gene duplication is common in this group. In Chapter One, I outline the relevance of protein variation to organismal evolution and describe the analytical methods employed throughout this thesis. Chapter Two considers the long-wavelength sensitive (LWS) opsins of the guppy (Poecilia reticulata). The guppy is shown to possess multiple LWS opsins that have accumulated differences at functionally important amino acid sites since duplicating. Chapter Three focuses on the guppy’s main predator, the pike cichlid Crenicichla frenata, which is shown to have a greater capacity for short-wavelength vision than previously believed. However, this cichlid possesses three fewer opsins than closely-related African cichlids, a difference partly due to duplication of a green-sensitive (RH2) opsin in African cichlids. In Chapter Four, this RH2 duplication event is studied in greater depth; variation in selective constraint is documented following gene duplication and between species from different lakes. Some of the analytical methods employed in Chapter Four were newly developed, as detailed in Chapter Five, where a test for functional divergence among clades is evaluated and then improved upon through the presentation of a new null model that better accommodates among-site variation in selection. In Chapter Six, phylogenetic relationships within the βγ lens crystallin superfamily are clarified, and the functionally distinct γN family is shown to have evolved conservatively compared to other crystallin families. The thesis concludes with suggestions for future directions for evolutionary research on opsins and crystallins, and summarizes recent work that has built on these studies.

Keywords: Molecular Evolution
Opsins
Crystallins
Fishes
Advisor: Chang, Belinda
Rodd, F. Helen
Danger Signal in a Rat Model of Nevirapine-induced Skin Rash

Nevirapine (NVP) can cause serious skin rashes and hepatotoxicity. It also causes an immune-mediated skin rash in rats but not hepatotoxicity. There is strong evidence that the rash is due to 12-hydroxynevirapine (12-OH-NVP), which is further metabolized to a reactive benzylic sulfate in the skin. This could both act as a hapten and induce a danger signal. In contrast, most of the covalent binding in the liver appears to involve oxidation of the methyl group leading to a reactive quinone methide. In this study we examined the effects of NVP and 12-OH-NVP on gene expression in the liver and skin. Both NVP and 12-OH-NVP induced changes in the liver, but the list of genes was different, presumably reflecting different bioactivation pathways. In contrast, many more genes were up-regulated in the skin by 12-OH-NVP than by NVP, which is consistent with the hypothesis that the 12-hydroxylation pathway is involved in causing the rash. Some genes up-regulated by 12-OH-NVP were Trim63, S100a7a, and IL22ra2, etc. Up-regulation of genes such as S100a7a, which is considered a danger signal, supports the danger hypothesis. Up-regulation of genes such as the ubiquitin ligase and Trim63 are consistent with protein-adduct formation. Up-regulation of IL-22ra2 gene suggests an immune response. These results provide important clues to how NVP causes induction of an immune response, in some cases leading to an idiosyncratic drug reaction.

Keywords: pharmaceutical science, toxicology
nevirapine, reactive metabolites, skin rash, immune response, danger signals
Advisor: Uetrecht, Jack
Leading Diverse Schools: Tempering Accountability Policy with Social Justice

This qualitative research examines how school principals perceive social justice and accountability, the actions they take, and the reasoning process they use in their attempt to satisfy accountability mandates while simultaneously tackling the various causes of social injustices in their schools. This constructive study aims to gain an in-depth understanding of the world from the subjects’ points of view, to unfold the meaning of their experiences, and to uncover their lived world. It employs semi-structured interviews with open-ended questions guided by the conceptual framework developed from review of literature on social justice, educational leadership, and accountability policy. Twenty-two school principals and vice-principals from the Greater Toronto Area (GTA) were interviewed. The findings show that some participants define social justice as equity, which goes from the economic and political dimensions of resource distribution and equality of opportunity and access, to the cultural aspect of social representation and inclusion. Some view public education as a social justice endeavour with a particular reference to the purpose of public education. Others construe social justice by focusing on its end goal – the academic and social outcomes of students and the impact on their lives. Study participants implement their social justice beliefs and values in praxis by engaging all stakeholders and catalyzing them to be the new force for the social justice movement. Evident in this study is that participants enacted their social justice practices by putting students at the centre, positioning themselves as social justice leaders, developing people for social justice, building school climate through justice, and fostering positive relationship with families and communities. Under current accountability context, principals in this study responded to the current reform by going beyond its narrow focus through instilling a sense of moral responsibility in their perceptions of accountability itself. As social justice activists, they are proactively engaged in expanding its parameters by encompassing the moral, social, and professional aspects of their accountability. Leading for social justice thus becomes a process of constantly confronting and tearing down such obstacles and barriers by leveraging the politics of accountability and social justice to move towards what is best for students.

Keywords: leadership
social justice
accountability policy
equity
Advisor: Ryan, James
Talker Discrimination, Emotion Identification, and Melody Recognition by Young Children with Bilateral Cochlear Implants

Users of cochlear implants typically have difficulty differentiating talkers, identifying vocal expressions of emotion, and recognizing familiar melodies because of the degraded spectral cues provided by conventional implants. This thesis examined these abilities in a small, relatively privileged sample of young bilateral implant users. In Study 1 child implant users and a control sample of hearing children were required to judge whether various utterances were produced by a man, woman, or girl (Experiment 1) and to identify the voices of cartoon characters from familiar television programs (Experiment 2). Child implant users’ performance on talker classification was comparable to that of hearing children. Their identification of cartoon characters’ voices was less accurate than that of hearing children but well above chance levels. These findings challenge conventional wisdom about the talker identification difficulties of implant users. In Study 2 the children were required to indicate whether semantically neutral utterances (Experiment 1) or classical piano excerpts (Experiment 2) sounded “happy” or “sad”. In both cases, implant users performed less accurately than hearing children but well above chance levels. Although the findings on emotion recognition in music are in line with those of previous research, the findings on emotion in speech are at odds with claims that young implant users are insensitive to vocal affect. In Study 3 the children were required to identify the theme songs from familiar television programs on the basis of combined timing and pitch cues as well as timing or pitch cues alone. Implant users’ performance was comparable to that of hearing children except when the cues were restricted to pitch relations, which resulted in performance at chance levels. The findings suggest that the musical representations of young implanted listeners include precise information about timing and coarser information about pitch. They also demonstrate, for the first time, that children, both implant users and those with normal hearing, can identify familiar music on the basis of timing cues alone. Overall, the findings highlight the importance of timing cues for implant users, the range of individual differences, and habilitation possibilities for the recognition of talkers, emotion, and music.

Keywords: cochlear implants
talker discrimination
emotion identification
music recognition
Advisor: Trehub, Sandra E.
Schellenberg, E. Glenn