VictorJuiz/thesis huggingface dataset:
Exploring the Role of Attentional Bias in Tobacco Dependence
Keywords: Addiction
Attentional Bias
Imaging
Smoking Cessation
Tobacco Use Disorder

Attentional bias to smoking-related stimuli is an important behavioural feature of tobacco dependence. The overall aim for this thesis is to investigate if attentional bias can serve as a potential phenotypic biomarker to assist in understanding treatment effectiveness, as well as predicting treatment response.First, a comprehensive systematic review was conducted to examine the association between attentional bias to smoking-related cues using eye-tracking indices in smokers and to identify gaps in the literature. Following a thorough literature search, 18 unique articles were identified. It was determined that smokers have increased attentional bias to smoking-related cues in comparison to non-smokers. Second, we aimed to investigate differences in attentional bias to smoking, affective, and sensation-seeking cues in smokers and non-smokers using novel, free-viewing, eye- tracking technology. Smokers (n=50) spent over 2 times longer looking at smoking-related images than non-smokers (n=50; F=25.50, p<0.001). As well, greater impulsivity was significantly associated with increased attentional bias to sensation-seeking cues (R2=0.059, F=2.98, p=0.04) in smokers but not non-smokers. Finally, we investigated whether smoking cessation treatment combining varenicline and transcranial direct current stimulation applied on the left and right dorsolateral prefrontal cortex altered attentional bias to smoking cues, and whether eye-tracking can serve as a proxy measure for changes in neural responses. Preliminary findings show a decrease (coeff=-0.007, p=0.004) in attentional bias to smoking-related cues from baseline to end of treatment across treatment conditions. A positive correlation was found between attentional bias to smoking cues outside the scanner and BOLD signal during smoking cue presentation in the anterior cingulate cortex (rs=0.36, p=0.03) at baseline. This finding was reduced to a trend when number of cigarettes smoked per day was accounted for in the model. No significant stimulation type-by-time or quit status-by-time interaction effects were found. Findings of this thesis suggest that smoking-related attentional bias is an important characteristic of tobacco dependence and can reflect treatment-related changes. As well, findings support the use of eye-tracking as a non-invasive and affordable proxy for assessing brain reactivity to drug-related cues. Findings offer insights on underlying mechanisms influencing treatment-related changes and has the potential to inform new and effective cessation interventions.
Keeping Countries Safe from Refugees – How the Canadian Courts Interpret International Law to Place Sovereign Rights Above Individual Rights
Keywords: externalization
immigration
Refugee Convention
sovereignty
STCA
TWAIL

This thesis examines the Safe Third Country Agreement between Canada and the United States, and the ongoing litigation contesting its compliance with the Canadian Charter of Rights and Freedoms. Drawing from the work of Third World Approaches to International Law (TWAIL) scholars, the thesis traces the development and creation of racially motivated but facially neutral laws and procedures in the late nineteenth and early twentieth century to present-day immigration control measures. The thesis argues that the architecture of international law elevates sovereign rights over those of the individual, and this structural imbalance has encouraged and facilitated the widespread diffusion of “safe country” agreements between states. Building upon the work of private international law scholars, the thesis contends that the Canadian Supreme Court has interpreted the concept of comity to require an unnecessarily deferential posture to the interests of foreign sovereigns.
Structural Characterization of Novel Microbial Rhodopsins by X-ray Crystallography
Keywords: Crystallography
Membrane protein
Microbial rhodopsin
Retinal-binding protein
Structural biology
X-ray diffraction

X-ray crystallography has revolutionized science by unveiling the atomic structures of thousands of molecules, ultimately exposing how the building blocks of the universe fit together. However, there are millions of undetermined chemical and biological structures that would expand our understanding of nature and medicine. One such group of biomolecules with hundreds of undetermined structures comprise microbial rhodopsins, whose numbers are rapidly increasing with the yearly discovery of new members with different functions. Microbial rhodopsins are membrane proteins that convert light into chemical energy to drive a range of functions from ion pumps, ion channels, sensors, and enzymes. Despite recycling a similar architecture of seven-transmembrane alpha-helices bundled around a light-harvesting retinal chromophore, microbial rhodopsins perform vastly different functions by fine-tuning their structures including side chains, loops, internal water, and ions. This necessitates the acquisition of high-resolution structures to understand their complex structure-function relationships. This thesis employed X-ray crystallography to expand the structural database of the family of microbial rhodopsins, whose biomolecular structures provide valuable insight into their functional diversity and can potentially be applied in optogenetics to modulate brain neurons with light. To begin, I present the crystal structure of Mastigocladopsis repens rhodopsin (MastR), a representative of a new clade of cyanobacterial chloride ion pumps that was discovered in 2016. I further solved the structure of the MastR-T74D mutant, to provide a structural rationale explaining how a single threonine (‘T’)-to-aspartate (‘D’) mutation in a conserved motif can convert the natively inward chloride pump into an outward proton pump. Secondly, I present a high-resolution structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR). Discovered in 2018, the functions of heliorhodopsins are largely unknown. However, this low pH TaHeR structure helped elucidate a chloride binding site and a putative intramolecular signaling pathway. Finally, I reveal the structure of Antarctic Rhodopsin (AntR), a member of the Schizorhodopsins class discovered in 2019. AntR pumps protons inward, in stark contrast to previously discovered outward proton-pumping rhodopsins. The structure of AntR helped illuminate the mechanism of inverted proton transport and revealed a unique, elongated bent helix at the C-terminus that is required for efficient proton transport.
Understanding Rural-urban Disparities in Alcohol-related Health Service Use in Ontario, Canada
Keywords: Alcohol use
Alcohol use disorder
Health geography
Mental health
Public health

Introduction: Rural, relative to urban, communities in Ontario, Canada experience disproportionately high rates of alcohol-related emergency department (ED) visits and hospitalizations; however, we have a limited understanding of why this disparity exists. The purpose of this thesis was to better understand rural-urban disparities in alcohol-related health service use to inform the development of evidence-based public health strategies that address high rates of alcohol-related harm in rural Ontario. Methods: This thesis was composed of three separate but related projects. The first was a scoping review of the international literature on rural-urban disparities in hazardous alcohol use and alcohol-related harm. The second was a geospatial analysis of regional rates of alcohol-related ED visits and hospitalizations across rural and urban Ontario health regions. The third was a retrospective cohort study evaluating rural-urban differences in clinical outcomes following alcohol-related hospitalizations. The latter two projects made use of Ontario health administrative data. Results: All three projects demonstrated that increasing rurality is associated with higher rates of alcohol-related harm. The retrospective cohort study also indicated that limited access to mental health and addiction services partially mediates the increased risk of alcohol-related harm in rural Ontario. Despite this general trend, each study also revealed important complexities to this association that merit consideration in future policy development. For example, the scoping review found that rural-urban disparities in alcohol-related harm vary based on the type of harm being evaluated and the sociodemographic characteristics of the study population. The spatial analysis found that the association between rurality and alcohol-related health service use differed between Northern and Southern Ontario. Finally, the retrospective cohort study indicated that the associations between rurality and clinical outcomes following alcohol-related hospitalizations are non-linear and vary substantially between outcome types. Conclusions: The results of thesis corroborate previous evidence that rural, relative to urban, communities in Ontario experience higher rates of alcohol-related harm but indicate that this association is not simple or linear. Rural communities should be prioritized for public health interventions aimed at reducing alcohol-related harm; however, more research is required to understand how these policies can be tailored to meet regional needs in an evidence-based manner.
Medicine at the Bar: Medical Experts, Lawyers, and the Making of Malpractice in the Courtroom
Keywords: Evidence
Expert witnesses
Medical malpractice
Science studies
Tort
Trial practice

This dissertation shows, via a detailed analysis of trial proceedings, how medical malpractice is made in the courtroom. To show this I build on insights from work in the fields of philosophy, history, and sociology of medicine and science. I draw these insights together into a general, rhetorical perspective on the evidentiary process that takes place at trial. This perspective is then deployed in a case study of a single trial. Throughout the dissertation I focus on knowledge of the medical standard of care: the norm against which the conduct of physician–defendants is compared to determine whether or not malpractice occurred. Knowledge of the standard is of a particular kind. In many cases, this knowledge cannot be separated from the argumentative work that takes place during the trial. Furthermore, knowledge of the past events themselves—i.e. physician–defendants’ past actions in the situations in which they found themselves—cannot be separated from said argumentative work. The purview of this argumentative work is extensive, since it also includes authorizing certain people—medical expert witnesses—to opine regarding the events. The case study allows me to underscore the extent to which the trial is not only an argumentative practice, but also a highly disciplined and particularized inquiry into past events. Thus the standard of care is a product of the trial qua argumentative, disciplined, and particularized inquiry. This challenges prevailing conceptions of the standard of care in the doctrine and jurisprudence. Following these, the standard of care is akin to a fact that exists independently of the trial, and the trial is merely a means to make this fact accessible to the judge or jury with the least amount of distortion. I argue, contra these conceptions, that the trial has value in itself because it yields knowledge that cannot be gained any other way. In the case of the medical standard of care, it is knowledge made up of heterogeneous considerations—technical, scientific, moral, and legal—brought to bear on specific actions in specific situations.
(Re)conceptualizing Integration: An Arts-Informed Study of Kurdish-Turkish Asylum Claimants’ Post-Migration Experiences in Canada
Keywords: arts-informed research
integration
language education
language policy
refugees
resettlement

The number of Turkish and Kurdish refugee claimants to Canada has been increasing significantly over the last six years. Despite this increase, there are limited studies that focus on the post-migration experiences of Turkish and Kurdish individuals from refugee backgrounds in Canada. Although policies highlight that knowledge of the host society's language(s) is a key indicator of successful integration, little attention has been paid to the role of power relations, opportunities for social interaction, language practice and marginalization experiences in shaping the language learning experiences of migrants. Thus, my study aims to answer the following research questions: (a) How do individuals from refugee backgrounds perceive and experience “integration?” (b) What are the challenges of learning languages in Canada as an individual from a refugee background? (c) What opportunities or successes do individuals from refugee backgrounds experience while learning languages in Canada?Within the context of a participatory arts-informed multiple case study, I worked with ten Kurdish and Turkish youth between the ages of 18-30 who participated in semi-structured interviews and online focus groups. During the focus groups, participants produced and shared different (art)ifacts, such as music performance, sculptures, poems, photographs, etc. on diverse topics such as identity, language learning experiences, and involvement in community programs. Engaging in critical group dialogues, participants identified their needs, concerns, and opportunities and proposed solutions for stakeholders in the resettlement and education sectors. Findings revealed that participants’ intersecting identities and their marginalization experiences resulting from different forms of systemic oppression shaped their language learning and “integration” experiences in Canada. Their language learning trajectories were shaped by multilevel structural factors, ideologies and their own perceptions of their languages and position in Canada. Findings also revealed participants’ resilience and resistance to being understood as “lacking agency” as they created and sought opportunities for personal, academic, and language development to move towards a pathway to post-secondary education. I describe implications for language programs for newcomers and policies related to resettlement and language education and, in particular, the need to shift from measuring settlement success by considering integration to making inclusion a priority.
Thoroughbass Reductive Analysis Applied to Arranging Bach’s Solo Violin Sonata BWV 1003 for Guitar
Keywords: Analysis
Arrangement
Bach
Guitar
Reductive
Thoroughbass

Thoroughbass was not only a performance practice, but also a way J.S. Bach and his circle conceived of music. Since the beginning of the 20th century, guitar arrangements of Bach’s music have expanded the repertoire of the instrument. None of the existing guitar arrangements of the second solo violin sonata BWV 1003 have been developed from a thoroughbass-oriented perspective. Commonly, harmonic perspectives derived from Rameau have been employed in analyzing and arranging Bach’s music – mainly his ‘unaccompanied’ works. However, Rameau’s first harmonic treatise was not published until 1722, two years after Bach’s Sonatas and Partitas for solo violin were finished in 1720. Bach’s conviction was that thoroughbass was ‘the most perfect foundation ofmusic.1 Consequently, this thesis presents a tool called thoroughbass reductive analysis which not only unveil the underlying harmonic structure and voice-leading procedures of BWV 1003, but also address the implied polyphony of this solo work and potentially inform interpretive decisions such as phrasing, articulation, dynamics, and ornamentation. By utilizing thoroughbass reductive analysis, as well as becoming familiar with prototypical thoroughbass patterns, an arrangement can be developed that takes advantage of the idiomatic resources of the guitar while at the same time referencing the foundations upon which Bach’s music was largely conceived in his time. 1 Johann Sebastian Bach, Precepts and principles for playing the thorough bass or accompanying in fourparts Trans. Pamela L. Poulin ( 1738. New York: Clarendon Press, 1994), 10.
Knowledge Translation
Keywords: Data Exchange
Data Translation
Knowledge bases
Knowledge Translation
Ontologies
Schema mapping

Knowledge-rich applications can see significant performance improvementsby using domain-specific Knowledge bases (KBs). Populating and enriching these KBs has, thus, become an important challenge. In this thesis, we examine a powerful approach for KB population that is based on knowledge exchange, the process of translating knowledge from one KB to another, even when these KBs use very different concepts, properties, and graph structure to represent their knowledge. We introduce Kensho. A tool for generating mapping rules between two Knowledge Bases. In the data exchange problem, data that is structured under a source schema is transformed into an instance of a target schema. This is accomplished using a set of rules (called mapping rules) that specify the relationship between the source and target schemas. Kensho can produce mapping rules even in the presence of cycles, incompleteness in the source, and in settings with missing or unknown correspondences between properties or property paths. In addition, Kensho performs knowledge translation using value invention to preserve the proper grouping of data in the target KB. We also introduce two tools (Vizcurator and Sassho) that we have created to help domain experts in the task of knowledge translation. Vizcurator aims to help a domain expert understand and curate the source of exchange. Sassho aims to help a domain expert compare and understand mapping rules which are automatically created using a mapping generation tool such as Kensho. Sassho enables a domain expert to create examples that can be used to understand subtle differences among alternative mapping rules and explore the affect of those differences on the data being exchanged. As interest in supporting data exchange between heterogeneous knowledge bases (KBs) has increased, so has interest in benchmarking KB exchange systems. We introduce a set of new requirements for a KB exchange benchmark based on unique characteristics of KBs and based on important lessons learned from other data exchange systems. The field of exchanging information among KBs is relatively new. We outline an extensive research agenda for Knowledge Exchange based our experience in bringing data exchange to knowledge graphs.
Statistical Inference for Tail Dependence Structures
Keywords: Asymptotic independence
Concentration inequality
Extreme value theory
Graphical models

In multivariate extreme value theory, the study of tail dependence seeks to understand the dependence structure of multivariate data among those observations that are considered extreme, typically by having at least one of their components take a large value. This thesis offers solutions to two inferential problems concerning tail dependence. Existing work often assumes that observed variables are tail dependent, i.e., that observing multiple extreme values simultaneously is roughly as likely as observing at least one extreme. Real data, however, suggests that this is a restrictive assumption even in the bivariate case; the probability of simultaneous extremes can often be significantly smaller than the probability of a single extreme, while being non-negligible. In the first part of this thesis, a novel method is introduced to construct parametric models for bivariate tails that can be agnostic to the presence or absence of tail dependence. A class of M-estimators is constructed for the models and is theoretically justified. The model construction, inference methodology and asymptotic theory are then extended to the case where the tails of a spatial process are of interest. The conditional tail dependence structure of a moderate- to high-dimensional random vector can be encoded in the edges of an extremal graph, where each vertex represents an observed variable. Learning general extremal graphs in a fully data-driven way is an important open problem. In the second part of this thesis, a family of algorithms is introduced to solve this task by borrowing tools from Gaussian graphical model selection. For two such algorithms which are based on L1 regularization, consistency of the estimated graph is established in a general setting. No assumptions are made on the structure of the underlying graph, other than connectedness, and the number of variables is allowed to be exponentially larger than the effective sample size. Along the way, a general concentration result is proved for the empirical extremal variogram, which has widespread applicability in multivariate extreme value theory.
Asymptotics for High-dimensional Problems
Keywords: High-Dimensional Statistics
Higher-Order Asymptotics
Laplace Approximation
Likelihood Asymptotics
Modified Likelihood Root
Saddlepoint Approximation

We examine several classical inferential methods in the higher-order asymptotics literature and derive guarantees for their behaviour in high dimensions. In particular, we consider the accuracy and breaking points of the modified likelihood root, Laplace approximation and the saddlepoint approximation. Throughout this work, our objective is to obtain high-dimensional guarantees for these methods without sparsity assumptions on the underlying model. For the modified likelihood root, r*, we obtain the point at which its asymptotic distributional limit would differ from that of its unmodified version in high dimensions. We show that the modified likelihood root mostly adjusts for the influence of the nuisance parameters, confirming a long-held conjecture. We also characterize a measure of deviation from exponentiality through the modified likelihood root. We then examine the modified likelihood root via standard techniques used in higher-order asymptotics for general location-scale and linear exponential families. For these two families, we show that r* can be viewed as a location and scale adjustment to the likelihood root. We then derive error rates for the Laplace and saddlepoint approximations in the high-dimensional setting under general assumptions and then discuss ways by which these rates can be improved upon. Specific applications of the Laplace and saddlepoint approximations are described and a general discussion of their roles in high-dimensional inference is provided. We conclude with remarks on future research directions, including a discussion of other higher order methods and their applicability in high dimensions, higher order theory for infinite dimensional models, analytical approximations for complex Bayesian models and the role of sparsity in high-dimensional inference.