VictorJuiz/thesis huggingface dataset:
Hyperpolarized 129Xe Diffusion-weighted MRI for Lung Morphometry of Bronchopulmonary Dysplasia

Bronchopulmonary dysplasia (BPD) is a disease that affects very prematurely born infants requiring ventilatory support and supplemental oxygen from birth. Despite advances in neonatal critical care, about 40% of very preterm infants develop BPD, characterized by alveolar simplification and microvascular stunting. Chronic sequelae of the disease persist into adulthood, reducing quality of life and exacting a significant toll on the healthcare system. Hyperoxia exposure followed by intermittent hypoxia in newborn rats mimics features of human BPD, specifically alveolar simplification. Alveolar simplification is morphometrically quantified by the mean linear intercept (MLI) that is based on hand-counting of intercepts from a limited number of representative histological sections and fields. With the advent of hyperpolarized (HP) gas magnetic resonance (MR) imaging, non-invasive imaging of terminal airway structure and function is achievable in vivo. HP 129Xe MR morphometric imaging exploits diffusion weighting along with a theoretical cylinder model of the terminal airways, to characterize the microstructure (eg. the terminal airway chord length, Lm) of the terminal airways. In this thesis, hyperpolarized 129Xe MR morphometric imaging was applied to characterize the microstructural changes associated with an O2 exposure rat model of BPD. Hyperoxia exposures consisted of either 60% or 85% O2 from post-natal day (PND) 1 – 7, followed by 60% O2 from PND 8-14. MR morphometry was performed and microstructural changes were compared with histology obtained from the same rats post-imaging. Lm and MLI were moderately correlated (r2 = 0.34, p = 0.0028), and MLI was increased by 11.3 ± 4.6µm in the 85% O2 exposed group compared to the control group, while Lm showed similar trends. Regional compliance was also estimated, assessing lung microstructural elasticity by performing morphometry at multiple peak-inspiratory-pressures. On average, alveolar compliance values scaled to a whole lung (19.1±15.1mL/cmH2O) were two orders of magnitude larger than conventional whole lung compliance obtained in the same animals (0.36±0.08mL/cmH2O) in a cohort of healthy rats. The two quantities were moderately correlated (r2 = 0.63, p = 0.019). HP 129Xe MR morphometric imaging affords non-invasive regional characterization of the lung microstructure and may be useful for the long term tracking of BPD in the clinic.

Advisor: Santyr, Giles
Mid-infrared Photophysics of Boron Nitride Nanotubes

Boron nitride nanotubes (BNNTs) represent ideal substrates for first principles understanding of phonon polaritons (PhPs) due to their one-dimensional nature, tunable sizes and ready synthetic techniques. Herein, we present work towards a comprehensive understanding of their photophysical properties within the Upper Reststrahlhan Band (~1360 – 1530 cm-1). Synthetic methods towards chemical vapor deposition (CVD) growth of BNNTs and hierarchical 2D BNNT structures are presented. The ability to characterize BNNTs using a novel broadband infrared source is addressed as well as computational modeling for the reflection of a polariton wave at a strong, internal dielectric barrier. Work showing the modification of the dielectric function and subsequent polariton dispersion by the internal void within BNNTs is demonstrated, culminating in understanding of the large geometry-mediated scattering enhancement at the ε = −1 crossing of the dielectric function. Conditions that result in strongly resonant PhPs are examined in tubes which support Fabry-Perot behavior. Finally, next steps are discussed in the field of BNNT polaritonics including perspectives on future devices.

Keywords: Boron Nitride
Hyperbolic
Nanotube
Photophysics
Polariton
s-SNOM
Advisor: Walker, Gilber C
Les Professionnelles et Les Professionnels Formes a L'etranger et Leur Insertion au Travail dans le Contexte Francophone Minoritaire en Ontario: Le Cas des Enseignantes et des Enseignants Originaires de L'Afrique Subsaharienne

La présente étude vise un double objectif, d’une part, appréhender la réalité de l’insertion professionnelle des Africaines et des Africains francophones en milieu minoritaire au Canada et d’autre part connaitre leur vécu dans les écoles de langue française de l’Ontario. Devant les enjeux comme ceux liés à l’accès à l’emploi, ces professionnelles et professionnels imaginent différentes stratégies, incluant celle de devenir enseignantes ou enseignants, ce qui m’a poussée à me poser les questions suivantes : Premièrement, comment les professionnelles et les professionnels originaires de l’Afrique subsaharienne formés à l’étranger dans un domaine autre que l’éducation vivent-elles ou vivent-ils leur réorientation vers la profession enseignante une fois embauchés dans le système d’éducation de langue française de l’Ontario? Deuxièmement, à partir de leurs différentes expériences sociales et professionnelles précédentes comment ces enseignantes et ces enseignants se perçoivent-elles et se perçoivent-ils après leur passage à une autre profession? Troisièmement, cette nouvelle expérience peut-elle être considérée comme une reconstruction potentielle de leur identité professionnelle dans leur trajectoire migratoire? Et, enfin, en quoi leur participation à la communauté de pratique les lie-t-elle à une carrière en enseignement? Cette stratégie nous semble attrayante en raison du contexte actuel de la pénurie d’enseignantes et d’enseignants dans les écoles de langue française de l’Ontario. La présente recherche s’articule autour de deux théories clés, à savoir l’insertion sous l’angle de la socialisation professionnelle et la construction des identités sociales et professionnelles (Dubar, 1991 cité dans Trottier, 2001, p 9) ainsi que celle de la communauté de pratique (Wenger, 2005). Pour bien appréhender la manière dont les identités sociales se perpétuent et changent, il importe de comprendre par quel mécanisme de socialisation elles se constituent et se recomposent. À cette fin, j’ai analysé les parcours migratoires diversifiés qui ont amené ces personnes à une insertion professionnelle dans l’enseignement. Mais, aussi, j’ai abordé la manière dont elles ont construit leur identité professionnelle comme produit d’une histoire à la fois singulière et collective. Et cela, dans trois communautés de pratique différentes. Cette étude m’a donné l’occasion de comprendre les parcours variés d’insertion professionnelle des immigrantes et immigrants ainsi que les stratégies utilisées.

Keywords: diversité
Éducation
francophonie
migration
minoritaire
professionnels formés à l'étranger
Advisor: Farmer, Diane
Labrie, Normand
Vibrant Stone: Ground Stone Celt Biographies Among the Ancestral and Historic Wendat in Southern Ontario from the 14th to mid-17th Centuries

Ground stone celts are an understudied artifact category in Ontario archaeology despite their essential contribution to the intensification of sedentarism and horticulture in northern Iroquoian communities. This dissertation studies 2660 ground stone celt artifacts – including blanks, roughouts, debitage, complete celts, recycled and unrecycled celt fragments — from 20 legacy collections of ancestral and historic Wendat sites dating between the 14th and mid-17th centuries in southern Ontario to better understand their comprehensive roles in northern Iroquoian lifeways before and at the onset of European contact.I integrate the chaîne opératoire and New Materialism to reconstruct ground stone celt biographies from a relational perspective. Viewing stones as a vibrant agent, my investigation begins with geological histories, which preshaped celts at the source and affected morphological changes in later stages of their biographies. Metamorphic stones predominantly used to make the documented celts originate from the Canadian Shield, a powerful and geologically complex landscape with a long history of human and non-human relations. Regional longue durée shows that Indigenous peoples made and used ground stone celts since the Middle Archaic period. Thousands of years of relations to stones and the landscape carried through the biographies of ancestral and historic ground stone celts during the Late Woodland period. Ethnohistoric and ethnographic accounts indicate that ground stone celts came to mediate transformative relations between the Wendat and various non-human beings including trees, soil, animals, and plants. The chaînes opératoires of the documented celts reveal that stone selection processes and celt morphologies resulted from reciprocal and co-creative engagements assembling humans, non-humans, and historical contexts, which preserved and transformed geologically formed surfaces, morphologies, and functions. Throughout changing social, economic, political, and territorial contexts of the American Northeast between ca. 1300 and 1650 CE, Wendat communities reoriented procurement strategies while maintaining shared ways of relating to ground stone celt properties and biographies. The ever-changing ground stone celts thus escape typological classification, and cannot be used as cultural, temporal, or functional markers. Their persistence alongside copper and iron cutting tools of European origin on early to mid-17th-century sites further indicates the strong connections that the Wendat developed with these vibrant stones.

Keywords: 14th to mid-17th century
American Northeast
Chaîne opératoire
Ground stone celts
Southern Ontario
Wendat
Advisor: Xie, Liye
Docile Minds: Discursive Implications of Mental Health Policies Related to Young People in Ontario

This study investigated how administrative interests impact understandings of youth mental health in Ontario’s public education system. Drawing on Michel Foucault’s model of Administrative Control as a theoretical framework and Norman Fairclough’s five-stage method of Critical Discourse Analysis (CDA) as a research methodology, this report examined seven (7) policy documents released between 2011 and 2015. These documents include the Ontario secondary school Health and Physical Education curriculum document, two provincial policy documents, a report commissioned by an independent charitable organization, an online resource hosted by a children’s mental health centre, a report commissioned by a national non-profit organization, and a public school board implementation plan. Results of the study revealed a powerful underlying interest in Administrative Control that presents systemic barriers to the development of positive student mental health outcomes. Discursive constructions of youth mental health in Ontario were found to associate mental health with a set of adverse clinical outcomes to be monitored and reported. More specifically, existing discourses were found to (a) prioritize clinical approaches to addressing adverse individual outcomes over developmental approaches to promoting psychological resilience, (b) call for sweeping normalization, to promote simplistic notions of risk and protection, (c) discursively appropriate the concept of mental health through collectivization, and to exclude the role of challenge as a developmental tool. Instead, this study suggests that mental health should be reframed within the context of public education policies as an ongoing developmental process of adjustment to a range of environmental factors. Finally, this study recommends the application of psychological resilience, academic resilience, and academic buoyancy as underlying constructs in the development of future school mental health policies. This study contributes to ongoing discussions about the role of discourse in both reflecting and shaping mental health outcomes among young people in Ontario.

Keywords: Academic Buoyancy
Challenge
Critical Discourse Analysis
Foucault
Mental Health
Psychological Resilience
Advisor: Flessa, Joseph
Peter Comestor’s Lectures on the Gospel of Luke and its Glosses (c. 1163-8): A Partial Critical Edition and Study

This dissertation studies the Latin biblical lectures of Peter Comestor — a Paris-based scholar who lived and taught in the middle of the twelfth century — through the preparation of a critical edition of his lectures on the Gospel of Luke. Comestor’s corpus of writings formed part of a larger tradition of twelfth-century Latin biblical commentaries that were composed in the cathedral schools of Laon and Paris from roughly 1100 until the University of Paris superseded them around 1215. In recent decades, recognition that the medieval study of the liberal arts and sacred scriptures shared much in terms of didactic approach has led scholarship to revisit a once- common distinction made by modern historians between biblical commentaries and systematic, theological treatises. Emerging research has begun to emphasize the importance of the liberal arts for understanding medieval theology, in whatever literary form, in terms of the generic expectations of classical philology. In order to bolster these efforts to recontextualize the study of the Bible within the broader educational programs of the Latin Middle Ages, I explore Peter Comestor’s lectures on the Gospel of Luke according to one of the informative structures of education that provided continuity across medieval northern France: the methods of literary exposition originally taught in the Roman grammar schools and handed on throughout the Middle Ages in the ‘liberal’ study of the ars grammatica (the art of grammar).My study of Comestor’s Luke lectures, which is enabled by my preliminary work editing the manuscripts containing the writings of Comestor and some of his contemporaries, demonstrates how the lecturers at the cathedral schools of northern France conceived of Christian theology, especially biblical exegesis, as a work of textual criticism. The fact that this scholarly endeavor had as its object the totality of all intelligible reality thus afforded the exegete the right to use the biblical text as an opportunity to teach everything from geometry to canon law. Thus, my research illustrates how liberal arts pedagogies in turn influenced scholars’ conception of Christian theology as sacra pagina (philological exegesis of the Bible) in the decades before the advent of the first European universities.

Keywords: Critical Edition
Gospel of Luke
Latin palaeography
Peter Comestor
Study of the Bible
Twelfth-Century Renaissance
Advisor: Andreé, Alexander
Understanding Pathways Underlying Inpatient Mortality of Children with Complicated Severe Malnutrition

Children admitted to hospitals with severe malnutrition are exceptionally vulnerable to death and account for a large proportion of early childhood mortality globally. In low- and middle- income countries, inpatient mortality rates of severely malnourished children remain high, despite implementation of the empirical management guidelines developed by the World Health Organization. Upon hospital admission, this group of children often present with a wide range of life-threatening illnesses and complications, making risk stratification and identification of underlying causes challenging. Severe malnutrition is also associated with concurrences of subclinical conditions, such as metabolic defects and enteric dysfunctions, that may not be clinically addressed but contribute to mortality. However, very few studies have investigated the pathophysiological pathways involved in the mortality of these children.Using medical records and biological samples among children hospitalized with severe malnutrition in African countries, Malawi and Kenya, the present research aimed to (1) identify clinical warning signs associated with inpatient mortality and evaluate their values in monitoring risks over the course of hospitalization, (2) define systemic pathways associated with mortality employing a multi-omic approach, and (3) evaluate the role of intestinal disturbances in mortality. It was found that monitoring the clinical warning signs: hypoglycemia, reduced consciousness, chest indrawing, not able to complete feeds, nutritional edema, diarrhea, and fever, can serve as a valuable tool for assessing children’s mortality risks during hospitalization. Compared to children who were discharged alive, children who died had distinct biomolecular profiles at admission, indicating that altered energy metabolism and systemic inflammation are associated with inpatient death. Furthermore, enteropathy was found to have a partial contributory role in the mortality of severely malnourished children. These findings alter our thinking around management of children hospitalized with severe malnutrition with important implications in providing novel evidence for guideline optimization to ultimately improve survival outcome of vulnerable children.

Keywords: Childhood Malnutrition
Enteropathy
Metabolomics
Proteomics
Statistical Learning
Survival Prediction
Advisor: Bandsma, Robert HJ
A Phenomenological Study of Gratitude-based Educational Assessment

Although recent studies confirm the benefits of gratitude practices in professional settings, relatively few have explored benefits of gratitude practices for teachers (Griffith, 2016; Howells, 2012). Gratitude practices can conceivably be of value in areas where teachers experience difficult or conflicted emotions, such as assessing and evaluating students’ written work. This study explores the effect of a gratitude practice on assessment of student written work, through a visualization practice in which student writing is imagined as a gift. Specifically, the study explores what teachers experience when they assess student writing alongside a visualization designed by the researcher which metaphorically positions student writing as a gift to teachers. The research question guiding this study is: How do teachers experience the practice of assessment when student writing is metaphorically reimagined as the process of ‘receiving a gift’? In posing this question, the study explores both the teachers’ experiences of the visualization and how it affected their assessment practices and orientations. The methodological framework for this study is transcendental phenomenology (Hycner, 1985) while conceptual metaphor theory (Lakoff Johnson, 1980) forms the guiding theoretical framework. Data was drawn from questionnaires and reflective journals of ten secondary and post-secondary teachers. The teachers assessed two separate pieces of student writing, both before and after the guided visualization, for a total of four periods of assessment, and wrote reflections on what they experienced when they reframed assessment as a process of receiving a gift. The study findings indicate that the gift visualization enriched the teachers’ experiences of assessment by fostering a more relaxed approach to assessment; an attitude of discovery and surprise; a growing trust in the student’s inner truths; greater attentiveness to the meaning of the student writing; an enhanced empathy for the students’ intentions and efforts; and, finally, a desire to reciprocate on students’ efforts through extensive feedback. Over time, the guided visualization tended to orient teachers toward a more expressivist approach to assessing student texts, with an enhanced perception of writing as the revealing and expression of a student’s unique voice, rather than an exercise in conformity to established forms and genre.

Keywords: Assessment
Gift Phenomenology
Gratitude
Holistic Education
Metaphor
Visualization
Advisor: Miller, John P
Life in a Mixed Neighbourhood: Three Essays on Tenure Mix and Sociality in the Redeveloped Regent Park

This dissertation comprises three chapters of original empirical research concerning the mixed-tenure redevelopment of Toronto’s Regent Park public housing community. These chapters use survey data from 517 unique respondents in two different surveys to provide the first systematic account of attitudes towards the mixed community among both residents and users of Regent Park’s public spaces. It provides a quantitative complement to the large body of qualitative research that has so far been produced on the redevelopment and contributes to our understanding about how programs of mixed-tenure redevelopment may impact individuals on a range of social, health-related, and economic dimensions. Two chapters are based on data collected in a survey of residents of the redeveloped portions of the neighbourhood and investigate perceptions of stigma and collective efficacy. Another chapter uses data from a street-intercept survey to assess more general attitudes towards the redeveloped neighbourhood among all users of its public spaces. In general, responses to the various survey measures employed are broadly positive, although differences between tenure groups and along certain demographic lines are also apparent. An important contribution of this research is the explicit measurement of variation between individuals and the treatment of this variation as a phenomenon of fundamental interest. It is uniformly the case across chapters in this dissertation that variation between individuals explains vastly more of the observed variation in outcomes than do any other variables considered, helping to contextualize the diversity of experience reported in other research. The findings of this dissertation are broadly consistent with expectations that mixed-tenure redevelopment primarily tend to improve ‘placed-based’ outcomes and provides support for the policy, if expectations are limited to the provision of improved housing and public amenities with relative comity between neighbours rather than meaningful interaction between residents of different tenures.

Keywords: Housing policy
Social mix
Tenure mix
Urban redevelopment
Advisor: Hess, Paul
Characterization and Reconstruction of the RNA-guided Cascade Complex from Escherichia coli

CRISPR immunity utilizes a wide range of effector complexes in order to target and destroy invading nucleic acids. CRISPR Type I systems employ a multi-subunit protein-RNA complex (termed Cascade), with varying protein composition and activity. They have already been harnessed to regulate cellular metabolism, silence genes, and edit genomes in bacterial and human cells. The E. coli Cascade complex (Type I-E) includes 11-subunits (CasA (Cas8), CasB2 (Cas112), CasC6 (Cas76), CasD (Cas5), and CasE (Cas6)) and 61nt crRNA guide making it a versatile tool for bacteria to safeguard against invading generic elements throughout CRISPR immunity. Cascade shows functional flexibility, with its main function as an effector complex through Protospacer Adjacent Motif (PAM)-specific dsDNA targeting, R-loop formation and Cas3 nuclease recruitment for DNA cleaving. Here I describe the characterization of the minimal E. coli Cascade components required for specific RNA binding, dsDNA targeting, R-loop formation and Cas3 recruitment. I show that all eight nucleotides of the crRNA 5-handle are critical for binding to Cascade and target DNA recognition, whereas most of the 21 nucleotides of the 3-handle (up to 20 nt) were dispensable for Cascade activities. Furthermore, the E. coli Cascade tolerates significant alterations in the crRNA spacer length (32 nt) being able to form functional effector complexes (though with altered stoichiometry) with crRNAs containing either elongated (+ 6 nt) or reduced (-12 nt) spacers. I also show that CasCD (Cas7-5) is the minimal Cascade preparation that can specifically bind Type I-E crRNA at efficiency analogous to full Cascade. Moreover, CasCD (Cas7-5) can be programmed using the crRNA sequence to specifically target dsDNA in a PAM-less manner, with both spacer sequence and repeat handles contributing to DNA targeting specificity, with the former having a greater effect. Cascade reconstitution experiments using purified proteins revealed that both CasA (Cas8) and CasB (Cas11) are needed to achieve the downstream functions of R-loop formation and subsequent Cas3 nuclease recruitment. Together, these results highlight the plasticity of the Cascade-crRNA system and indicate that the E. coli Cascade represents a viable alternative to single-protein effector complexes in developing novel genome editing tools.

Keywords: CRISPR
E.coli Cascade
multi-protein effector complex
partial Cascade
Advisor: Yakunin, Alexander F