VictorJuiz/thesis huggingface dataset:
Gluten-Related Disorders in a Population of Canadian Adults

Background: The prevalence of celiac disease (CD) in Canadian adults is unknown, and the extent of adverse health effects associated with undiagnosed CD remains unclear. Gluten sensitivity in the absence of CD is also thought to exist; however, the physiological effects of gluten intake in those without CD remain poorly understood. Objectives: To determine the prevalence of CD seropositivity in Canadian adults, investigate whether undiagnosed CD is associated with altered biomarkers of health, and examine associations of gluten intake with proteomic biomarkers and genetic variants in those without CD using a multi-omics approach. Methods: Subjects were 2,832 men and women from the Toronto Nutrigenomics and Health and Toronto Healthy Diet studies. Fasting blood samples were collected for CD screening, biomarker assessment and DNA isolation. CD was assessed using self-reported diagnoses and positive tissue transglutaminase (tTG) serology. Dietary gluten intake was estimated using a 196-item food-frequency questionnaire. Results: The prevalence of CD seropositivity was 1 in 114 (0.88%; 95% CI, 0.57-1.30%), with the majority of cases being undiagnosed (87%). The prevalence of CD seropositivity, predisposing human leukocyte antigen risk variants, and average gluten intake was highest in Caucasians. Undiagnosed CD was associated with lower circulating HDL-cholesterol (p=0.008), apolipoprotein-AI (p=0.02), and retinol (p=0.006), but not widespread nutrient deficiencies. In individuals without CD, gluten intake was positively associated with plasma Îą2-macroglobulin (p=0.004), a protein with various immune-related functions. Îą2-Macroglobulin was associated with variation in ICOSLG (p=1.67x10-7), a T-cell stimulatory gene involved in cytokine release and gastrointestinal immune-related disorders; however, there was no significant interaction between ICOSLG and gluten intake on Îą2-macroglobulin. Conclusions: Approximately 1% of Canadian adults likely have CD. Undiagnosed CD is associated with less favourable lipid profiles and lower concentrations of certain fat-soluble vitamins. In individuals without CD, gluten intake may be associated with plasma proteomic biomarkers of immune function.

Keywords: Celiac disease
Genetics
Gluten-related disorders
Nutrition
Advisor: El-Sohemy, Ahmed
Tools for Probing and Perturbing Mitochondrial Biology

Mitochondria are organelles with critical roles in key processes within eukaryotic cells, and their dysfunction is linked with numerous diseases including neurodegenerative disorders and cancer. Pharmacological manipulation of mitochondrial function is therefore important both for basic science research and eventually, clinical medicine. However, in comparison to other organelles, mitochondria are difficult to access due to their hydrophobic and dense double membrane system as well as their negative membrane potential. To tackle the challenge of targeting these important subcellular compartments, we have developed peptide-based vectors in order to deliver therapeutic agents and probes to mitochondria. Interestingly, mitochondria-targeted DNA damaging agents demonstrate high potency and the ability to evade resistance mechanisms and off-target effects. In this thesis, we demonstrated that we can control the biological activity of these mitochondria-targeted DNA damaging agents via structural modification. In a related study, a mitochondria-targeted anticancer drug has been used to probe and eliminate secondary effects of the untargeted parent compound in healthy and disease-relevant cellular and animal models. Interestingly, analysis of the targeted drugâ s activity in healthy and xenograft mice revealed that mitochondria-targeting can served as a promising approach to enhancing the therapeutic window. Moreover, a combination of these mitochondria-targeted DNA damaging agents was applied to an siRNA screen for the elucidation of poorly understood mitochondrial DNA repair and replication pathways. Significantly, multiple proteins were identified that are essential for the maintenance of mitochondrial nucleic acids including a new DNA polymerase (POLÎ¸). This thesis outlines the various ways to probe and manipulate mitochondrial biology for basic scientific studies and clinical applications. Nevertheless, the mitochondrial targeting field is quite nascent and many exciting applications of organelle-specific conjugates remain to be explored.

Advisor: Kelley, Shana O
Inquiry-Based Learning: A Case Study of an Experienced Elementary Mathematics Teacher in Action

Currently, Inquiry-Based Learning (IBL) has become the central focus and method of delivery to support mathematics learning, especially within elementary schools in Ontario. Through undertaking a single case study of my colleague who teaches Grade 5, I investigated the Inquiry-Based Learning strategies she uses in her classroom to increase student understanding and proficiency in mathematics. Additionally, I explored the challenges teachers of Grades 4 to 6 may confront when seeking to implement IBL methods in their mathematics classroom. My participant is a former math coach and instructional leader of mathematics. My data was collected from interviews with my colleague, interviews with her students, classroom observations, and through student questionnaires, journals and classwork. My findings indicate that various IBL related strategies and techniques should be implemented to promote students’ mathematical understanding and proficiency. Eight major findings have been summarized, which point to how my case study practices/exhibits the following: (1) she constructs/implements rich, open-ended inquiry-based tasks that permit multiple-entry points; (2) she asks deliberate and intentional questions to elicit students’ mathematical thinking and develop their conceptual understanding; (3) she makes students’ invisible thinking become visible through the process of questioning and recording students’ thinking; (4) she provides learning experiences where students must struggle with their mathematical understanding; (5) she provides students will ample opportunities to experience repeated practice of procedural knowledge; (6) she promotes ongoing and active student mathematical discourse; (7) she possesses deep mathematical content knowledge to effectively implement IBL practices; and (8) she incorporates all five dimensions of mathematical proficiency into her IBL mathematics lessons (Kilpatrick, Swafford Findell, 2001). Implications from this study suggest that teachers as well as educational policy-makers need to consider a variety of measures to help deepen teachers’ mathematical content knowledge. Whether it occurs at the individual, pre-service or in-service level, literature as well as the findings from this study indicate the dire need for teachers to possess sufficient mathematical background knowledge and ability in order to promote mathematical proficiency among their students. Acquiring this deep mathematical content knowledge by teachers must then be married with the implementation of various key IBL strategies/techniques. Suggestions for areas of further research are included at the end of the study.

Keywords: elementary teacher
Inquiry-based learning
mathematics
pedagogy
teaching
Advisor: McDougall, Douglass
Improving Communication in Chip Multiprocessors Using Emerging Technologies and Machine Learning

Technology scaling along with power and thermal limitations ushers the industry to the many-core system era. Thread level parallelism and complex applications demand a communication architecture that can provide high bandwidth communication and facilitate efficient usage of the computational units. Therefore, the communication architecture plays a major role in the performance of applications and the energy expended on data movements. The communication framework can be viewed at: 1) the interconnect infrastructure (physical) level and, 2) the inter-thread communication (logical) level. This thesis offers three different approaches to address the communication issues in many-core systems at the physical and the logical levels. First, we propose a novel low-power all-optical Networks-on-Chip (NoC) with a deterministic wavelength routing algorithm. This routing algorithm is based on wavelength division multiplexing that allows us to reduce the number of wavelengths and optimize micro-ring resonators in optical switches. The key advantages of our optical network are simplicity and lower power consumption. Second, to improve performance of on-chip interconnect infrastructure, we em- ploy three-dimensional (3D) integration technology. To tackle the temperature issues in 3D NoCs, we model the mapping problem as an Integer Linear Programing (ILP) problem and propose three static ILP-based thermal-aware mapping algorithms. We then investigate the thermal constraints and their effects on temperature and performance. Third, we propose a new scheme to dynamically predict the critical path of a multi-threaded application. We formulate the cache statistics and the barrier arrival times as a machine learning problem to predict critical threads. We propagate criticality of these critical threads to the other threads using lock contention information. This dissertation demonstrates how opportunities at the physical and logical levels can be used to improve the communication framework.

Keywords: Critical path of multi-threaded application
Machine learning
Networks-on-chip
On-chip communication
Silicon Photonics
Thermal management
Advisor: Enright Jerger, Natalie
Development and clinical application of a novel ex vivo assay to assess genital HIV susceptibility

A better understanding of the biological factors that promote heterosexual HIV acquisition in the female genital tract (FGT) may inform HIV prevention efforts. The mucosal cellular targets of HIV are not well defined and proposed cellular and molecular correlates include the HIV co-receptor CCR5 and markers of immune activation, including CD69. I established a novel ex vivo HIV entry assay for mucosal studies to enable assessment of ex vivo HIV infection in freshly isolated and unstimulated endocervical CD4+ T cells. HIV susceptibility was enhanced in cervix-derived CD4+ T cells compared to blood. Cervical CCR5+, CD69+, α4β7+ or α4β1+ CD4+ T cells were preferential HIV targets, however, the homing integrins α4β7 or α4β1 did not mediate direct binding to the HIV env or HIV entry into CD4+ T cells, suggesting that α4β7 and α4β1 are unlikely to be HIV entry receptors. Next, I tested whether ex vivo HIV entry predicts subsequent heterosexual HIV acquisition. Ideally, this would be done using fresh genital samples, but these are usually not available. Hence, I performed a nested, retrospective, blinded, case-control study in blood CD4+ T cells obtained from HIV-uninfected South African female participants enrolled in the CAPRISA 004 clinical trial. Virus entry into blood CD4+ T cell subsets did not predict subsequent HIV acquisition, possibly due to the compartmentalization of immune factors in the genital mucosa. One such compartmentalized factor in the FGT is the bacterial microbiota, which is dominated in the majority of women by lactobacilli, while a shift towards diverse gram-negative anaerobic species, defined (based on Gram stain) as bacterial vaginosis (BV), is associated with increased HIV acquisition in women. To investigate underlying biological mechanisms that may increase HIV acquisition risk in women with BV, I assessed the impact of BV treatment using the current standard of care, oral metronidazole, on genital immunology and HIV susceptibility. BV treatment reduced endocervical CD4+ T cell susceptibility to HIV and genital IL-1 levels; however, an unexpected increase in several chemokines previously associated with increased HIV risk suggests that more studies are needed before the treatment and/or prevention of asymptomatic BV can be recommended for HIV prevention.

Keywords: bacterial vaginosis
female genital tract
HIV
HIV infection assay
integrins
mucosal immunology
Advisor: Kaul, Rupert
PERFORMING “THE OTHER” AND BECOMING DIFFERENT: AFFECTS OF YOUTH AND SCHOOLING IN JAPAN

This dissertation explores how Japanese youth experience their senses of self through looking into drama/theatre classes in secondary school. To consider the issue of “multicultural coexistence” in Japan with the idea of multiple belongings and the liberation of youth, I explore the ways, if any, in which young people are involved in a radical repositioning or internal qualitative transformation in a productive and affirmative manner, as well as what factors prevent those transformations from occurring. Applying Deleuze and Guattari’s concepts such as “becoming” and “affects,” I especially examine the experiences of acting or performance, in particular the practices of “mimesis,” which refers to embodying the image of “the other” through imagination. The analysis is based on one year and five months of ethnographic research with high school students at a school in a cosmopolitan but relatively economically deprived area of Tokyo. The narratives emerged from observation in drama classes and in-depth interviews with journal writing and assignments, utilizing a methodology of postqualitative research. As seen through repeated patterns of being stuck, the analysis reveals how the identity category of ethnicity/nationality as well as the notions of “Japaneseness,” “kyara,” and “school caste” rigidly function to territorialize youth, blocking possibilities for them to become otherwise. Reconstructing the gender hierarchy, silencing of the girls’ desire for masculinity, and normalization of the boys’ rejections of femininities formed other patterns. Affects fluctuate with different constellations of possibilities and constraints. The assemblages of femininities and masculinities, and particularly the respective positions within those, form a significant component of the affective experiences of youth at school. Considering pedagogical aspects, which might have restricted those experiences, I also sketch several points for drama pedagogy to deepen role-playing or acting as a testing ground where new relationality with other bodies is tried out. This study contributes to the educational research that sheds light on the complexities of the affective experiences of youth at school.

Keywords: affect
Deleuze and Guattari
drama/theatre education
ethnography
Japanese youth
schooling
Advisor: McDougall, Doug
The Impact of Sexual Behaviours, Risk Perceptions and the Criminalization of HIV Non-Disclosure on HIV Transmission among HIV-Negative and HIV-Positive Men Who Have Sex With Men in Toronto

Background: Men who have sex with men (MSM) continue to have disproportionately high rates of human immunodeficiency virus (HIV), even though risk factors for HIV acquisition are known and antiretroviral treatment has reduced transmission. Objectives: To characterize the sexual behaviours and risk perceptions of HIV transmission among HIV-negative and HIV-positive MSM. Methods: 150 HIV-negative and 292 HIV-positive MSM participated in the STI/HIV Co-Infection Study between September 2010 and June 2012. Participants were recruited from the Maple Leaf Medical Clinic, a primary and HIV-related care centre in Toronto. Multivariable logistic regression (MLR) models quantified the relationships between actualsexual HIV risk, HIV incidence risk index for MSM (HIRI-MSM), perceived HIV risk and willingness to take pre-exposure prophylaxis (PrEP) among HIV-negative MSM. MLR and flow chart models were used to estimate the potential impact of HIV non-disclosure laws on HIV testing rates and transmission among HIV-negative MSM, and on condom use, HIV status disclosure and proportion at risk for criminal prosecutions among HIV-positive MSM. Results: As condom use frequency with HIV-positive regular partners decreased, perceived HIV risk (Odds Ratio (OR):18.33, 95% Confidence Interval (CI):1.65-203.45) and willingness to take PrEP (OR:27.11, 95% CI:1.33-554.43) increased. Condom use frequency with casual or HIV-unknown status regular partners and the HIRI-MSM index were not associated with perceived HIV risk or PrEP willingness. The 7% (9/124) reduction in HIV testing due to fear of prosecution found in this study could increase community HIV transmission by 18.5%; the majority of transmission being driven by the unmet needs of undiagnosed HIV-positive MSM. Almost half of HIV-positive MSM were more likely to use condoms and/or disclose their HIV-positive status due to fear of prosecution and 8.6% (25/292) could be at risk for non-disclosure prosecutions given their condom use, viral load and disclosure rates. Conclusions: HIV-negative MSM using condoms less frequently with HIV-positive partners but not with HIV-unknown status or casual partners accurately gauged their sexual risk behaviour and were willing to take PrEP. HIV non-disclosure laws may incentivize safer sex practices among HIV-positive MSM; however, they may also deter HIV testing which impedes HIV prevention efforts and increases community HIV transmission .

Keywords: Criminalization of HIV Non-Disclosure
Epidemiology/Public Health
Gay
Bisexual and Other Men Who Have Sex With Men
HIV
Perceived HIV Risk
Sexual Behaviour
Advisor: Gesink, Dionne
Remis, Robert S
The Relationship between Immigration and Crime in Canada, 1976-2011

This dissertation examines whether changes in immigration are associated with changes in crime rates at the macro-level over time in Canada. Specifically, I analyze this relationship in Canadian census metropolitan areas (CMAs) and provinces for the period 1976-2011. In general, the research on the relationship between immigration and crime has shown that they are either negatively associated or not related at all. However, most of this work has been conducted in the United States using cross-sectional designs and has focused on one type of crime, namely homicide. Differences between Canada and the United States in the extent and nature of both immigration and crime warrant a study of their relationship and its generalizability beyond the US. My dissertation adds to the literature by using a longitudinal design â which treats immigration as a process that unfolds over time â and extending the analysis beyond homicide to include violent, property, and crime rates. My findings show that, controlling for demographic and socioeconomic covariates, changes in immigration are either not significantly associated or negatively associated with changes in crime rates. These results lend support to the generalizability of the findings from studies of US cities to Canadian cities, to larger units of aggregation (i.e., provinces),and across different types of crime.

Keywords: crime
immigration
Advisor: Gartner, Rosemary
Customizing Information Delivery for Citizens in Transportation Infrastructure Projects: Towards Active Community Participation in Decision-Making

The communities living and working within many of today's high density urban cores are pushing for greater transparency in planning and governance, and a higher level of public involvement in the identification of impacts of construction activities and mitigating them. Lately, the integration of Information and Communication Technologies (ICTs) has enabled the use of electronic community engagement, which provides greater accessibility and wider reach. However, these technologies have exhibited a deficiency partially due to a lack of an automated semantic platform for knowledge exchange. To engage the public, the process needs to extend beyond simple, one-way communication into a realm where relevant knowledge is more easily shared between the public and project teams. Thus, this research proposes a social, semantic, customized knowledge exchange framework to address this gap. The main purpose of this research is to extend the scope of construction management research that is typically limited to a number of stakeholders such as the designer, builder, owner and regulatory authority. The proposed framework is intended to complement the current process rather than completely replace it. To successfully create this partnership between project teams (planners and designers) and the public, this research uses ontologies as a formal form of knowledge representation. The social web and other social networking tools are also proposed as the best available technologies to maintain public engagement. Finally, as a way to enhance the user experience on the web implementation of this social-semantic framework, a wayfinding and recommender system is integrated. The eSocOnto ontology and decision support framework were evaluated with the aid of domain experts. The ontology and framework were also further validated through the development of a web software platform as a proof of concept to showcase a variety of features enabled by the framework and the knowledge base.

Advisor: El-Diraby, Tamer
Consuming Global Language and Culture: South Korean Youth in English Study Abroad

In globalizing South Korea, it is a prevalent belief that English competence and global awareness are key qualifications for successful employment. This belief has led South Korean young adults to pursue transnational experiences to improve their employability in the neoliberal job market. This thesis examines how the ideology of English as a global language produces the necessity of learning the language abroad and governs students’ overseas learning and life, through the case of Korean youth studying English in Toronto. Drawing on 13-month ethnographic fieldwork in Toronto, two research trips to South Korea, and various types of relevant documents, this thesis analyzes sociolinguistic trajectories of a group of Korean students attending a private language school. Especially, from a political economic perspective of language and culture, the thesis focuses on the ways in which the Korean students consume and negotiate desired types of English and English speakers. This study shows that the majority of students accessing the English study abroad market were students from non-elite universities who had no legitimate global experiences and low levels of oral proficiency in English. Recognizing the necessity of linguistic and cultural capital, the Korean youth decided to study English abroad, as their parents agreed to financially support their overseas education. In the private language teaching industry, such social, linguistic, and economic positions of the Korean youth led them to be strategic, calculative, and consumerist in terms of their English learning. In multilingual Toronto, the Korean students stratified English speakers according to the latter’s authenticity, proficiency, and intimacy. They constantly navigated “good” English programs and teachers in their language school. However, their status in the Western society, which remained as temporary visitors, non-native English speakers, and (East) Asians, posed challenges to immersing themselves in local cultures. Furthermore, this thesis demonstrates that the Korean students’ attitudes toward life and learning emphasizing accountability and effectiveness caused emotional burn-out and intercultural fatigue. Subsequently, the Korean students temporarily suspended the normative ways for success in English study abroad and pursued an alternative way of life. They enjoyed leisure activities such as travels and everyday mingling, thus constructing their version of cosmopolitanism.

Keywords: English
Neoliberalism
South Korea
Study abroad
Youth
Advisor: Heller, Monica