VictorJuiz/thesis huggingface dataset:
Listening to Writers and Riders: Partial Contrast and the Perception of Canadian Raising

Listeners generally have a greater perceptual sensitivity to native contrasts compared to allophones (Whalen et al., 1997; Boomershine et al., 2008) or non-native contrasts (Goto, 1971; Sundara et al., 2006) in discrimination and other tasks. Recent research has emphasized the gradient nature of contrast, showing that many phonological relationships are intermediate or variable between contrast and allophony (Hall, 2009, 2013). This dissertation presents a series of experiments investigating the perception of what has been called marginal contrast or partial contrast using Canadian Raising as a testing ground. Experiment 1 tests discrimination of raised and non-raised diphthongs ([ʌj]~[aj] and [ʌw]~[aw]) in different phonological environments, finding better discrimination in the contrastive environment where they can create different words than in the allophonic environment where they cannot, but only for one of the two diphthongs (/aj/ but not /aw/). This diphthong difference was ambiguous—it could be a property of the diphthongs themselves, or it could have been a result of the stimuli used, specifically that [ʌj]~[aj] has more recognizable minimal pairs (e.g., writing/riding) than [ʌw]~[aw] (e.g., clouting/clouding). Experiments 2, 3, and 4 clarify this partial contrast effect and diphthong difference, finding support for an inherent diphthong difference (using non-words in Experiment 2) and for an additional effect of the minimal pairs (Experiments 3 and 4). Experiments 1b, 1c, 2b, 3b, and 4b are semi-replications of these initial four experiments. They lack an additional experimental condition that was present in the original experiments, and in each case the original partial contrast effect fails to replicate, suggesting that partial contrast effects depend on quality/quantity of linguistic exposure. Finally, Experiment 5 tests discrimination of Canadian Raising diphthongs by Canadians and Americans, finding generally faster and more accurate discrimination by Canadians, with differences between different American regions as well. Together, these experiments provide insight first and foremost into the effect of contrast—specifically partial contrast—on discrimination, as well as other topics such as cross-dialectal perception (and the effect of dialect stereotypes and dialect exposure on perception) and regional differences in the production of raising (and related phenomena) in Canada and the United States.

Keywords: Canadian English
dialect variation
psycholinguistics
speech perception
Advisor: Monahan, Philip J.
An Investigation into Relationships between Organizational Structure, Regulation and Quality in Ontario Nursing Homes

Ensuring the delivery of high quality nursing home (NH) care has proved complex to achieve. This complexity may stem in part from the uncertainty that exists around the determinants of quality and the effectiveness of policy tools that can be used to ensure quality across heterogeneous NH providers. Ontario has the highest proportion of for-profit, chain-owned NHs in Canada and witnessed significant change in its regulatory approach in 2010. Drawing on Ontario’s NH context, this thesis examines three research questions: 1. What is known about the effects of government regulation on NH quality? 2. Does NH organizational structure affect the production of quality and, if so, how? 3. What are the effects of government regulation on NH quality and do effects differ according to NH ownership type? These questions are examined as separate studies, including a systematic review and two empirical analyses. The systematic review revealed that the majority of the literature concerning the effects of regulation on NH quality comes from the US. The evidence suggests that quality tends to improve in dimensions explicitly targeted by the regulation, but that unintended consequences are not uncommon. The analysis of relationships between NH organizational structure and quality found that, with the exception of two quality indicators (QIs), statistically significant differences according to organizational structure were not observed. The seemingly unrelated regression (SUR) error correlation matrix revealed the presence of significant error correlations between different QIs, indicating complementary relationships and potential trade-offs in the pursuit of multidimensional quality. The analysis of the effects of regulation on NH quality revealed statistically significant improvements in three of seven QIs that were targeted by the regulation and improvements in four of the nine QIs that were not targeted. These results imply that quality improvements in targeted QIs did not come at the expense of declines in non-targeted QIs. By using a SUR framework, the empirical analyses modeled the production of quality in a manner consistent with the literature that recognizes quality as a multidimensional construct. In doing so, the model harnessed information on the correlations between objectives and the synergies and trade-offs NHs face when pursuing multiple goals.

Keywords: Econometrics
Nursing homes
Organizational structure
Ownership type
Quality of care
Regulation
Advisor: Laporte, Audrey
Anaerobic Biodegradation of Chlorinated Benzenes and Hexachlorocyclohexane by Mixed Microbial Cultures Derived from Contaminated Field Sites

Environmental contamination with toxic organohalides is of worldwide concern. Chlorinated ethenes, benzenes, and pesticides are organohalides frequently found in contaminated soil and groundwater. Bioaugmentation with mixed microbial cultures derived from contaminated sites has been successfully applied to remediate groundwater contaminated with chlorinated ethenes and ethanes, in which the halogenated compounds are electron acceptors in microbial respiration. On the other hand, in situ bioremediation of soil, sediment, and groundwater contaminated with chlorinated benzenes and the pesticide γ-hexachlorocyclohexane (lindane) has yet to be comprehensively explored. Hexachlorocyclohexane has been reported to dechlorinate into a mixture of chlorinated benzenes, so the bioremediation of these two types of organohalides is highly interrelated. In this thesis, the organohalide bioremediation potential of previously established and novel anaerobic mixed cultures was investigated using analytical and molecular omics techniques. In the commercial chlorinated ethene-to-ethene dechlorinating culture KB-1, cobalamin (vitamin B12), an essential corrinoid cofactor for the reductive dehalogenation of vinyl chloride, was determined to be supplied to organohalide-respiring Dehalococcoides by a growing Acetobacterium population. After switching the electron acceptor from trichloroethene to 1,2,4-trichlorobenzene, native KB-1 Dehalobacter populations that respire chlorinated benzenes were identified along with a KB-1 reductive dehalogenase enzyme that dechlorinates 1,2,4-trichlorobenzene to 1,3- and 1,4-dichlorobenzene. In addition, the metagenome-assembled genomes of three distinct KB-1 Dehalobacter spp. were shown to contain more than 70 reductive dehalogenase genes (rdh) which considerably increases the number of known KB-1 rdh genes and will allow for the examination of evolutionary relationships in Dehalobacter genomes. A Dehalobacter-containing culture (referred to as GT), enriched from soils and sediments contaminated with hexachlorocyclohexane, was shown to dechlorinate lindane to monochlorobenzene and benzene, and was found to contain a Dehalobacter population that use γ-hexachlorocyclohexane as terminal electron acceptor. A GT culture was combined with a KB-1 subculture that dechlorinates monochlorobenzene to benzene, and a benzene-degrading culture, to achieve complete biotransformation of lindane to non-toxic end products. Using metagenomics and proteomics data, a novel reductive dehalogenase enzyme, HchA, was for the first time identified. Altogether, this body of work demonstrates that the mixed cultures KB-1 and GT have bioremediation potential against the chlorinated benzenes and hexachlorocyclohexane, respectively.

Keywords: anaerobic
benzenes
chlorinated
cultures
dehalogenation
hexachlorocyclohexane
Advisor: Edwards, Elizabeth A
Investigation of CSF1-CSF1R Signaling in AML-Bone Marrow Stromal Cell Interactions

Acute myeloid leukemia (AML) is a highly heterogeneous and growth factor-dependent disease. Colony stimulating factor 1 (CSF1) is a cytokine produced by bone marrow (BM) stromal cells that directs the differentiation and growth of myeloid cell precursors into monocytes and macrophages. Human CSF1 (hCSF1) exists as a soluble/secreted (hCSF1-sol), and a transmembrane (hCSF1-mem) isoform. CSF1 acts on the CSF1 receptor (CSF1R), which is expressed on mononuclear phagocytic cells. In this study, the CSF1-CSF1R ligand-receptor pair was investigated in the context of AML-stromal cell interactions. Analysis of cell surface CSF1R protein levels revealed that a subset of AML patient samples express high levels of CSF1R (CSF1Rhigh), and that these patients have shorter overall survival (OS) times compared to patients with low CSF1R expression (CSF1Rlow). In examining the CSF1-CSF1R interaction experimentally, the long-term growth and survival of CSF1Rhigh AML cells was supported by MS-5 stromal cells expressing human CSF1 (hCSF1) in co-culture experiments. MS-5 cells expressing the membrane-bound form of CSF1 (hCSF1-mem) in particular led to significant increases in AML cell numbers and adhesion to stroma, compared to cells co-cultured with MS-5 empty vector (EV) or hCSF1-sol cells. Co-culture of AML cells with MS-5 hCSF1-mem cells led to activation of mTOR signaling in AML cells as observed through increases in pS6, increased expression of the hematopoietic stem cell markers CD34 and c-Kit on AML cells, and distinct changes in the cytokine profiles of both AML and stromal cells. Further to this, deletion of the PDZ domain binding motif (PDBM) at the C-terminal end of CSF1 ligand in MS-5 stromal cells led to decreased stromal support of AML cells, and reduced mTOR pathway activation. The interaction between CSF1 and CSF1R mediates supportive effects between AML and stromal cells by fostering bilateral intracellular and intercellular signaling changes. As such, targeting the CSF1-CSF1R interaction may prove to be an effective therapeutic strategy to overcome and compromise the protective and supportive role of the BM niche in AML disease pathogenesis.

Keywords: Acute Myeloid Leukemia
Bone Marrow Stroma
Cell Signaling
CSF1-CSF1R
Tumour microenvironment
Advisor: Minden, Mark D
Optimal Design of Multi-user Distributed Massive MIMO Systems

This thesis studies two fundamental challenges facing the optimal deployment of distributed massive multiple-input multiple-output (DM-MIMO) systems: (1) the need for the optimal design of the locations of the remote-radio-heads (RRHs) and (2) the issue of non-reciprocal uplink/downlink channels and their impact on the performance of DM-MIMO systems. The radio access network in a DM-MIMO system consists of several RRHs, each equipped with one or more antennas, scattered throughout the coverage area. To reap the potential benefits of DM-MIMO systems, the locations of these RRHs need to be carefully optimized. The majority of this thesis is dedicated to the optimal RRH placement for DM-MIMO systems, investigating this problem from different aspects. We first consider the RRH location optimization to maximize the average downlink rate. Two variants of the harmonic clustering algorithm (HCA) are proposed to obtain the locations of the RRHs in both homogeneous and non-homogeneous propagation settings. Afterwards, this thesis proposes a framework using signal-to-leakage-and-noise ratio (SLNR) for RRH placement. The SLNR-based RAN design approach demonstrates promising gains in the average throughput of the system, however, this comes at the cost of performance degradation at the cell-edge users. Alternatively, this thesis also considers the cell-edge rate maximization problem for RRH placement. An optimization framework based on an approximation of the probability distribution of the downlink rate is proposed. This approach is capable of outperforming the HCA placement in terms of the cell-edge rate. As a last step towards optimal RRH placement, this thesis considers a scenario where the positions of the RRHs are to be selected from a discrete set of possible locations. Two efficient solutions based on sequential decision making formulation and Monte-Carlo tree search are proposed to tackle the RRH location selection problem. The last part of this thesis investigates the impacts of non-reciprocal uplink/downlink channels on the performance of DM-MIMO systems operating in time-division-duplexing mode. Accurate expressions for downlink rate are obtained illustrating the degrading effects of the residual non-reciprocity on the achievable throughput. Finally, a robust downlink beamforming method is proposed which is capable of mitigating the impacts of the non-reciprocal channels.

Keywords: 5G
Distributed antenna systems
Massive MIMO
RAN design
Advisor: Adve, Raviraj S.
ShahbazPanahi, Shahram
Microfluidic and Nanofluidic Study of Solvent-based Unconventional Hydrocarbon Processes

Unconventional resources such as tight oil and bitumen do not yield to conventional production processes and are difficult to produce economically. The use of solvents to extract unconventional resources has shown promise and has potential to enable efficient production while overcoming the limitations of the current processes. However, adding a solvent phase adds further complexity to a physical system that is already poorly understood, with multicomponent mixtures within multiscale micro- and nano-confined geometries. While conventional laboratory testing methods can provide some insight, they do not resolve the critical physical/chemical mechanisms at the pore-scale. Over the past few years, microfluidic approaches have been increasingly applied in the energy sector, and particularly in oil and gas. In contrast to conventional methods, microfluidics can provide direct visualization of pore-scale dynamics during extraction processes and generate fast and accurate phase data for the fluids under reservoir-relevant temperatures, pressures, and scales. In this thesis, a new generation of high-temperature and high-pressure microfluidic and nanofluidic devices are developed for the study of solvent-based unconventional resources recovery methods. For bitumen extraction, both pure solvent and solvent-steam co-injection methods are studied using a glass-glass micromodel at reservoir relevant temperature and pressure. To investigate asphaltene precipitation and deposition resulting from solvent-bitumen interactions during solvent-based extraction processes, a silicon-glass microfluidic device is developed. To improve the practicality of silicon-glass microfluidic based methods for such applications, a new approach was developed whereby the device yield per wafer was increased by one to two orders of magnitude, rendering these otherwise expensive microfluidic systems effectively disposable. This new approach was tested in application to immiscible flooding for heavy oil production, and a CO2 capture fluid with successful tests at pressures up to 80 bar. Lastly, these methods were extended to the nanoscale and applied to measure the first contact miscibility pressure of CO2 and oil under nano-confinement for enhanced oil recovery implications in tight and shale oil reservoirs. Collectively, these contributions provide insight into solvent-based recovery methods for unconventional resources by levering the precision, robustness, and optical access provided by microfluidics and nanofluidics.

Keywords: Bitumen
Microfluidics
Nanofluidics
Shale oil
Solvent based EOR
Advisor: Sinton, David A.
Investing in “The Academic 1%”: Caring for South Korean Adolescence at the Junctures of Global Market Volatility, Obsolescence, and Play

This dissertation analyses the production of South Korea’s aspirant “1%.” Focusing on affluent adolescents, their parents, and private educators, I show how my interlocutors understand the world to be inherently volatile and uncertain under the current conditions of global capitalism. Understanding their current position to be fundamentally precarious, my interlocutors seek to create new circumstances from which value can be accumulated, invested, appreciated and generated. These orientations towards futurity position adolescents as sites of speculation and investment in the production of human capital. Based on fieldwork undertaken at “IHE Prep,” a private academy (hagwŏn) specializing in American college exam and application preparatory lessons, in addition to international schools (Kukchehakkyo) in the Seoul metropolitan area, I analyse how the South Korean economy, education, and class conflict fuel my interlocutors’ aspirations to embed themselves in global markets. Notably, international schools are vested with special powers by the Ministry of Education to implement their own curriculums in full foreign language immersion. I will argue that these processes rest on social obligations of kinship, intergenerational exchanges of reciprocity, and aspirational classed identity. By tracking the process leading up to admissions into elite American universities, I argue that adolescents’ pursuits are not effects of rational, calculating individuals. Rather, their aspirations are wrought from their status as debtors to their parents’ enormous investments. Intently focused on American education, the valuation of adolescents is further grounded in English acquisition and university branding, as markers of future leaders, entrepreneurs, philanthropists, and innovators. Moreover, adolescents as financialized subjects, constituted through care and capital, are further valued for their physical, emotional, and social well-being. Throughout my examination, I show how processes of investment become a lived reality, contingent not only on the global economy, but forms of embodiment where one should cultivate a creative, playful disposition, compassionate heart, indexing their status as the newly aspirant “1%.”

Advisor: Muehlebach, Andrea
Androgen Receptor and Histone Variant H2A.Z Interact to Regulate Fear Memory and Memory-related Gene Transcription

Sex hormones are potent regulators of memory, but the role of androgen receptors in males is poorly characterized compared to the role of estrogens in females. Thus, the goal of my thesis is to characterize the role of AR in fear memory and the mechanistic basis of this effect in male mice. In Chapter 2, I utilized transgenic male mice that overexpress the androgen receptor (AR) to elucidate its effects on fear memory. I showed that AR overexpression impairs fear memory and that this effect is regulated by circulating androgens. Moreover, I showed that AR regulates the expression of several memory-related genes, including the epigenetic memory suppressor, histone H2A.Z. Our lab previously identified the histone variant H2A.Z as a negative modulator of fear memory through its effects on transcription. Given that AR is a transcription factor that interacts with H2A.Z in prostate cancer, I next characterized the functional and mechanistic interaction between the two. In Chapters 4 and 5, I used inducible-conditional H2A.Z knockout mice to delete the two genes (H2afz and H2afv) that encode H2A.Z in excitatory neurons in adult mice. I showed that simultaneous deletion of both H2A.Z-encoding genes enhanced fear memory, which extends our prior findings that virally-mediated depletion of H2afz alone enhances memory. Next, I showed that H2A.Z deletion blocked the effects of androgen receptor manipulation on fear memory, suggesting that AR and H2A.Z interact at a functional level. To test the mechanistic basis of this interaction, I utilized cultured hippocampal neurons to show that manipulating AR activation alters H2A.Z binding to DNA, suggesting that AR regulates behaviour through H2A.Z. Given its interaction with AR, I next investigated whether H2A.Z deletion produces unique effects in males and females. In contrast to males, H2A.Z deletion did not enhance fear memory in females, but it did serve as a protective factor against stress-enhanced fear memory (a PTSD-modeling paradigm). Overall, these data suggest that AR and H2A.Z interact at the chromatin level to regulate fear memory and that interactions with sex hormones may produce sex-specific effects of H2A.Z on fear memory.

Keywords: Androgen receptor
Epigenetics
Fear memory
H2A.Z
Histone variant
Sex difference
Advisor: Zovkic, Iva B
Monks, Douglas A
Risk Factor Epidemiology and Predictive Modelling Approaches to Understanding Chronic Disease Incidence

The chronic disease burden is a public health priority with most Canadian adults having chronic disease. Addressing this burden is a complex task requiring multiple stakeholders, including researchers. While researchers have traditionally studied chronic diseases individually “in silos”, studying multiple chronic diseases together is important because the results provide a comprehensive understanding of the overall health of the individual and the population. This dissertation contributes to the field of chronic disease research by elucidating the relationships between a person’s first chronic disease with shared lifestyle risk factors and applying this knowledge to create a predictive tool. To enable fresh perspectives about chronic disease incidence, various survival analysis techniques were applied. The first objective examined the relationships between shared lifestyle risk factors and the incidence of first chronic disease at a given age over the life course. This study found that most individuals will develop chronic disease prior to death, and heavy, daily smoking was the most important lifestyle factor for chronic disease incidence at a given age. The second objective focused on the Royston-Parmar model and its application for prognostic modelling in health research. The study found that this relatively new model was suited for prediction but has not been widely adopted for health research. The third objective developed and validated the Chronic Disease Population Risk Tool (CDPoRT), a population risk algorithm that predicted the incidence of multiple chronic diseases simultaneously over a ten-year period in the general adult population using routinely-collected data. The end product was a tool that consistently demonstrated strong predictive performance in estimating chronic disease risk. Overall, the studies capitalized on representative health survey data linked to administrative data to study the relationships between shared lifestyle risk factors and multiple chronic diseases, and leveraged these findings to create CDPoRT using traditional and novel survival analysis methods.

Keywords: CDPoRT
Chronic disease
Lifestyle risk factors
Prediction modelling
Royston-Parmar model
Advisor: Rosella, Laura C