VictorJuiz/thesis huggingface dataset:
A Comparison of the Academic Attitudes, Behaviours and Attainments of Three Groups of First-generation Students at an Ontario College

This quantitative study focused on first generation students (FGS) entering diploma programs at a large urban college in Toronto, Canada. The FGS were divided into three groups based on their birthplaces and/or parental birthplaces: those born in Canada to at least one Canadian-born parent ("domestic" FGS), those born in Canada to foreign-born parents ("established immigrant" FGS), and those born outside of Canada ("recent immigrant" FGS). The intent of the study was to identify any significant differences among the groups in their academic attitudes, behaviours, and attainments. The choice of dependent variables was informed by Bourdieu's social reproduction theory, especially the concept of habitus, and by prior American and Canadian FGS research. The data was obtained from a 2008 survey of all entering students, and from academic transcripts in May 2012, the four-year graduation time limit. Of the 549 students included in the study, 259 were "domestic," 203 were "established immigrant," and 87 were "recent immigrant." No significant differences were found in high school GPAs or academic behaviours, levels of academic confidence, value placed on PSE, retention and graduation rates, time needed to complete programs, status at the time of withdrawing, or college GPAs. However, significance differences did occur among the three groups in the time spent studying in high school, time spent exploring vocational outcomes, intent to persist, and intent to pursue degree-level studies, with small to medium effect sizes. Many of these findings are consistent with prior research; however, others may indicate traditional models used to predict student retention and graduation rates, such as incoming GPAs, levels of academic confidence, and intent to persist, do not appear to have the same predictive power for FGS entering diploma programs that they may have for those entering degree programs; in other words, for FGS, these variables may be more relevant in predicting who accesses PSE, and not persistence. In addition, the established and recent immigrant FGS in this study appear to be using the college system as a gateway to degree-level studies, which has implications for the types of programming, services and supports the colleges provide for FGS.

Keywords: college
first generation students
habitus
immigrant students
Advisor: Joshee, Reva
Very Nonlinear Quantum Optics

This thesis presents a study of photon generation and conversion processes in nonlinear optics. Our results extend beyond the first order perturbative regime, in which only pairs of photons are generated in spontaneous parametric down-conversion or four wave mixing. They also allow us to identify the limiting factors for achieving unit efficiency frequency conversion, and to correctly account for the propagation of bright nonclassical photon states generated in the nonlinear material. This is done using the Magnus expansion, which allows us to incorporate corrections due to time-ordering effects in the time evolution of the state, while also respecting the quantum statistics associated with squeezed states (in photon generation) and single photons or coherent states (in photon conversion). We show more generally that this expansion should be the preferred strategy when dealing with any type of time-dependent Hamiltonian that is a quadratic form in the creation and annihilation operators of the fields involved. Using the Magnus expansion, simple figures of merit to estimate the relevance of these time-ordering corrections are obtained. These quantities depend on the group velocities of the modes involved in the nonlinear process and provide a very simple physical picture of the interactions between the photons at different times. These time-ordering effects are shown to be important only when the photons and pump beam overlap within the nonlinear material for a significant amount of time. We also discuss the possibility of preparing Fock states with many photons using parametric down-conversion sources and realistic photon-number-resolving detectors. After discussing photon generation processes, we study photon conversion processes in which a nonlinear material and a classical strong pump field are used modify the frequency of a second incoming low-intensity field. We show that time-ordering effects limit the efficiency of this conversion process, re-examine strategies to get around this problem, and show that it should be possible to have a clear observation of modified upconversion probabilities due to these effects, and thus have an experimental demonstration of time-ordering effects in nonlinear optics.

Keywords: Frequency Conversion (FC)
Magnus Expansion
Photon Generation
Spontaneous Four Wave Mixing (SFWM)
Spontaneous Parametric Down-Conversion (SPDC)
Squeezing
Advisor: James, Daniel F.V.
Sipe, John E.
"He is almost a normal child": An Ethnography of Malawi's National Pediatric HIV Treatment Program

My dissertation is an ethnographic exploration of what it means to raise a child with HIV in one of the poorest countries in the world. Throughout I follow a small number of children and their caregivers as they engage with a new Global Health Initiative (GHI) to provide free universal access to antiretroviral therapy (ART), or anti-AIDS treatment, for infected children at a government run hospital in rural Northern Malawi. To date very little is known about how the roll-out of pediatric ART in decentralized health settings is progressing. The few studies that exist tend to emaphasize access to medicines as the key barrier to treatment, which decontextualizes patients from their social milieu. My project focuses on the clinic-household nexus in order to better understand how historically emdedded social relations impact treatment pathways for young children living with HIV. Specifically, I trace how gendered norms within marriage, disease etiologies, the clinical encounter, land tenancy and migration affect diagnosis and long term treatment adherence. My findings indicate that access to and the long term benefits of ART for children are mediated along socioeconomic fault lines. Although ART is an essential component of any HIV/AIDS care and treatment programme, I argue thoughout that the distribution of medicines alone is ineffective in the absence of loving caregivers, good living conditions, sustainable food sources or a robust public health care system. My research contributes to academic debates about the mechanisms behind embodied inequalities and calls for a broadened scope beyond the individual patient in the development and implementation of HIV care and treatment services for children living with HIV.

Keywords: ART
Childhood
Global Health
Health disparities
HIV/AIDS
Pharmaceuticals
Advisor: Wardlow, Holly
Overprotective and Overcontrolling Parenting of Emerging Adult Survivors of Childhood Cancer: Links to Coping Styles, Anxiety, and Depression

The goals of this study were, in a sample of emerging adult survivors of childhood cancer, 1) to compare levels of psychological distress with general population norms, 2) to examine the association between overprotective parenting and psychological distress, 2) to differentiate between maternal overprotection and maternal overcontrol, and 3) to uncover mechanisms linking overprotective parenting to psychological distress, including the assessment of emerging adults’ coping styles and perceptions of their mothers’ overprotective parenting. Participants were 109 emerging adult survivors of childhood cancer, ranging in age from 18 to 30 years (M = 23 years; 60% female). Ninety of the emerging adults’ mothers also participated in this research. Survivors were recruited from the waiting room of The Pediatric Cancer AfterCare Clinic at Princess Margaret Cancer Centre in Toronto, Canada. Emerging adults and their mothers provided ratings of mothers’ overprotective and overcontrolling parenting practices on the Overparenting of Emerging Adults Scale (OPEAS), a measure designed for this study. Emerging adults’ coping styles and symptoms of anxiety and depression were also assessed. Factor analysis of the OPEAS revealed seven overparenting subscales; four subscales conceptually similar to the construct of overprotection: infantilization, medical management, parenting anxiety, and harm reduction, and three subscales conceptually similar to the construct of overcontrol: problem solving intervention, intrusive decision making, and discounting of opinions/ideas. Nearly half of the sample reported clinically significant levels of anxiety symptoms, although levels of clinically significant depression symptoms did not differ from general population norms. Further analyses revealed that mother-reported overprotective practices of infantilization and parenting anxiety were indirectly related to emerging adults’ anxiety and depression symptoms through serial multiple mediation, and that the mother-reported overcontrolling practice of intrusive decision making was indirectly related to depression symptoms through serial multiple mediation. Specifically, the mediators were emerging adults’ perceptions of the overparenting and emerging adults’ nonproductive coping style. The theoretical and practical implications of these findings are discussed in terms of the relations of overprotective and overcontrolling parenting to emerging adults’ mental health, and importance of the socialization of coping.

Keywords: Anxiety
Coping
Depression
Emerging adulthood
Maternal overprotection
Survivors of childhood cancer
Advisor: Grusec, Joan E
The Atypical Cadherin Fat Directly Regulates Mitochondrial Function and Metabolic State

The atypical cadherin Fat plays essential roles during development to regulate tissue growth and patterning. It has also been implicated in a number of human diseases including polycystic kidney disease and some forms of cancer. Ft has been established as an input into the Hippo tumour suppressive pathway; however, the direct connections between Ft and its downstream effectors are not well understood. In this work, I have identified components of the ETC and mitochondrial import machinery as novel physical and genetic interactors of Ft. I found that mitochondrial complex I component, Ndufv2, can act in planar cell polarity and Hpo pathways. We have also carefully examined ft mutants and uncovered defects in mitochondrial morphology and complex I levels and activity that result in changes in metabolism. We outline a mechanism whereby Ft is cleaved at the cell surface, releasing a cytosolic fragment that is imported into the mitochondrial matrix to directly modulate mitochondrial function by assisting in the assembly or stability of mitochondrial complex I and V. This novel Ft function allows it to coordinate tissue growth and patterning with changing energy requirements during development, and may contribute to metabolic shifts observed in tumour progression.

Keywords: Drosophila
Fat cadherin
Growth control
Hippo
Mitochondria
Planar cell polarity
Advisor: McNeill, Helen
Modular Multilevel Converters with Integrated Energy Storage

Battery energy storage (BES) integration into the grid is typically achieved using a 2- or 3- level dc/ac converter with BES interfaced directly to the inverter’s dc link or through a dc/dc converter. In both cases, long series connected strings of batteries are required to efficiently maintain the necessary dc link voltage. Such configurations are susceptible to reliability issues as failure or shutdown of an individual battery cells results in loss of a large fraction of BES capacity. This thesis addresses the aforementioned issue by subdividing the BES into units and integrating each unit into the submodules of a modular multilevel converter (MMC). This reduces conduction losses within the MMC submodules and provides a mechanism for electronically protecting BES units from both ac and dc side fault events. However, integrating BES units into the submodules disrupts the power flow of the MMC. Therefore, this thesis analyzes the power flow of the MMC to identify the different power transfer mechanisms, which enables energy balance between BES units. To easily understand the analysis, a graphical user interface tool was developed to assess the impact of integrating BES units into a select number of submodules, and identify alternate BES distributions within the MMC. From the power flow analysis, a control method is developed to maintain energy balance across all submodule capacitors and BES units in the MMC. Validation of the analysis is performed through simulation and experimental work. As part of this work, a 600V/100kVA MMC was developed with 4MJ of supercapacitor energy storage, which is used to represent the distributed BES. The results from both simulation and experiment verified the analytic conclusions, which found that the integration of BES into the submodules of a MMC increases reliability by using short series strings of batteries and reduces conduction losses. This is achieved without impacting the terminal characteristics of the MMC as state of charge balance between BES units can be achieved through internally circulating currents. Finally, the MMC is found to be capable of operating with BES integrated into a select number of submodules, which can reduce BES installation costs and increase reliability.

Keywords: AC-DC power conversion
energy storage
modular systems
multilevel systems
renewable energy sources
Advisor: Lehn, Peter W
Molecular Classification and Clinical Genomics of Medulloblastoma

Background: Children with medulloblastoma have a 72% chance of surviving more than 5 years under current treatment, and those who survive suffer long-term developmental and neurocognitive deficits due to treatment-associated toxicity. We believe that refining the classification of medulloblastoma will facilitate the optimization of treatment intensity and the discovery of novel therapeutics. Recent studies have identified four molecular subgroups of medulloblastoma with distinct expression patterns: WNT, SHH, Group3, and Group4. These subgroups represent different molecular entities that arise through and rely on different oncogenic processes. Accordingly, we aim to improve prediction of patient survival by identifying prognostic markers for each subgroup, and we hope to abrogate non-specific cytotoxic treatments by discovering candidates for targeted intervention against each subgroup. Methods: We proposed and validated a new classification method for medulloblastoma based on molecular patterns. Using this method, tumours were classified into molecular subgroups. Their DNA copy-number profiles (n = 1087) were analyzed to identify somatic copy-number aberrations (SCNAs) and recurrently disrupted genes and pathways. Prognostic SCNAs were identified by Kaplan-Meier survival analyses on a discovery set (n = 673), and the candidates were validated by FISH on a tissue microarray of validation samples (n = 453). Results: Tumours of each subgroup harbour recurrent SCNAs disrupting different pathways. WNT medulloblastoma is characterized by CTNNB1 mutation, SHH medulloblastoma by activated Gli signaling, Group3 medulloblastoma by MYC activation, and Group4 medulloblastoma by SNCAIP duplication. Further, patients of different subgroups exhibit differential response to standard treatments. Incorporating subgroup data into survival models significantly improved predictive performance. Using six FISH biomarkers on FFPE tissues, we reproducibly stratified patients into risk groups with distinct survivorships. Conclusion: The stark differences in genetic alterations among molecular subgroups of medulloblastoma suggest that each subgroup arises through different biological mechanisms. The molecular classification of medulloblastoma not only improved survival prediction but also revealed pathways for therapeutic intervention. We have identified a panel of prognostic markers that can be used to select patients for therapy de-escalation in future trials, and we have also discovered candidates for targeted therapy.

Keywords: brain tumour
classification
genomics
pediatric cancer
prognostication
Advisor: Taylor, Michael D
Bader, Gary
Resource Allocation and Risk Analysis of Dialysis Centres

The number of hemodialysis patients is growing every year. The majority of these patients visit centres at least three times a week for their treatment. Two types of nurses perform general dialysis procedures on the patients. These are registered nurses (RNs) and registered practical nurses (RPNs). Hemodialysis patients may experience complications during their treatment. When complications occur, patients need the assistance of RNs. The time RNs spend with patients increases the duration of their treatment. It is essential for all centres to hire enough nurses to maintain the quality of service for the growing number of patients while minimizing nursing cost. However, facilities have different nurse-to-patient ratio because they are unique in terms of the combination of patients and the workload policies regulating their nurses. Moreover, since there are no generally accepted guidelines, the staffing decisions at each centre are highly subjective. As a result, it is very difficult for the decision makers to create consistent guidelines to determine the number of nurses required in each centre. In this research, we assume that the centre has a given list of specific patients, each of which is defined by patient type. Two approaches are used to help dialysis units schedule their patients and minimize nursing cost while having enough nurses to maintain quality of service. In the first approach, an MIP model and a heuristic algorithm are developed separately to minimize the number of nurses (RPNs or RNs) to set up, monitor, and disconnect patients from dialysis machines. The methods find the start time of the dialysis session for each patient. An M/M/s queuing equation is then used to find the number of RNs needed to attend to any potential complications of scheduled patients. In the second approach, the methodologies are merged into a non-linear model to find patient schedules that minimize the number of RNs and RPNs. Tabu Search is used to solve the non-linear model. Further, the models and results presented in this study can be treated as benchmarks for decision makers to find the approximate number of nurses needed for each unit as well as a forecasting tool to estimate the average number of nurses needed for any patient size population based on their historical data.

Keywords: Heuristic
Mixed Integer Programming
Optimization
Risk Analysis
Scheduling
Tabu Search
Advisor: Carter, Michael W.
Scaling Macro- and microevolutionary Dynamics in the Caesar’s Mushrooms (Amanita sect. Caesareae)

Biological diversity is the product of evolutionary and ecological factors that operate at different spatial, temporal, and genomic scales. Phylogenies and genomes have the potential to uncover the mechanisms leading to such diversity, with clues imprinted throughout the evolution of DNA sequences. There are several challenges to study fungal evolution, some of which include inaccurate species delimitations, unknown distributions, sampling biases, and a poor fossil record. However, most fungi have small genomes, making them practical for studying evolutionary genomics. This thesis includes four Chapters that use phylogenetic and genomic approaches to answer questions related to the ecology and evolution of the Caesar’s mushrooms (Amanita sect. Caesareae). Chapters 2 and 3 show how diversification and historical biogeogaphical models explain the distribution, geographic disjunctions, and diversity of temperate and tropical taxa worldwide. Results indicate that land-mediated dispersal and high diversification rates in the New World and in the temperate region have played important roles, which explain, in part, “shifted” latitudinal diversity gradients within the group. Chapter 4 describes new genomic data from A. jacksonii, and comparing it with that of other species. Chapters 5 and 6 deal with the interrelationships between past climate change, regional geography, species richness, genomic variation, selection, and historical demography. Gene genealogies and coalescent-based multi-locus species delimitations reveal high levels of cryptic diversity in North America (NA). Higher speciation rate in climatically stable areas and recent population expansions highlight the importance of Pleistocene glacial dynamics in shaping diversity patterns within NA Caesar’s mushrooms. Finally, both natural selection on coding DNA and demography explain genome-wide diversity across 500 single-copy genes within eight species from a recently diverged species complex. This work evidences the spatial dynamics of populations and species of a gastronomically and culturally important group of mushrooms over millions of years, adding significant insights onto the evolution of symbiotic fungi.

Keywords: Biogeorgaphy
Diversification
Ectomycorrhizal fungi
Genomics
Population genetics
Speciation
Advisor: Moncalvo, Jean-Marc
Chronicling the Relationships, Attitudes, and Sexual Encounters of Men who have Sex with Men in Shanghai, China: A Web-administered Sexual Events Diary

Background: Unprotected anal intercourse (UAI) remains the primary mode of HIV infection among MSM in China. As no sexual events studies have been conducted to date, little is known about how characteristics of a sexual event influence sexual behaviour. Objectives: Utilizing a conceptual framework to situate the quantitative analyses within the community, cultural, and social structures that affect the lives of MSM, this dissertation describes attitudes towards homophobia and masculinity; characterizes community involvement and social support; describes egocentric sexual networks; and investigates individual- and event level variables associated with UAI during sexual events (UAIevents). Methods: Data were collected using a cross-sectional questionnaire and a 28-day event-based, web-administered diary. Bivariable and multivariable logistic regression models with GEE were used to investigate associations between individual- and event- level variables and UAIevents. Results: During 4,172 days of follow-up, 149 diary participants reported 854 sexual events with 389 unique partners. Individual-level variables associated with UAIevents included the end of a close relationship; number of social contacts; uncertain filial intentions; masculinity (selfreliance); internalized homophobia (failings and heteronormativity); perceived community homophobia (acceptance), sexual history; and attachment to the Tongzhi circle. Event-level variables associated with UAIevents included: the discussion of personal matters during the sexual event; partner dynamics (confidence), partnership duration; and participant intoxication. Conclusions: The novel diary method allowed an in-depth exploration of partners and partnerships which revealed that the duration of the partnership and the discussion of personal matters (but not partner type) were associated with UAIevents. This suggests that the former two should be considered as alternatives to the traditional measure of partner type. Childrearing is important to many Shanghainese MSM. Uncertainty about one’s filial intentions increases the odds of UAIevents. Failure to acknowledge the socio-cultural and political context in which men live can affect the collection, interpretation and utility of epidemiologic findings.

Keywords: Men who have sex with men
Sexual Behavior
Sexual events
Sexual Partners
Socio-cultural
Unsafe Sex
Advisor: Myers, Ted