VictorJuiz/thesis huggingface dataset:
Nutritionally Adequate Protein Sources in Diets During Gestation, Lactation and Weaning Influence Food Intake and the Risk of Characteristics of Metabolic Syndrome in Offspring of Wistar Rats

The hypothesis that source of protein in a nutritionally adequate diet during gestation, lactation and weaning alters food intake and characteristics of metabolic syndrome in the offspring was investigated. Pregnant Wistar rats were randomized to either the AIN 93-G casein (C) or soy protein (S) diets (n=12/group) during gestation only or during gestation and lactation. Male offspring in each dams’ diet group were weaned to either C or S diets (n=12/group). Food intake, body weight (BW), fat pad mass, systolic (SBP) and diastolic (DBP) blood pressure, and plasma homocysteine (p<0.05) were higher in offspring born to dams fed the S diet. Fasting blood glucose (BG), BG in response to a glucose gavage and Homeostatic Model of Assessment of Insulin Resistance (HOMA-IR) index were higher only in male offspring born to dams fed the S diet. Moreover, gene expression of Agouti Related Protein (AgRP) was higher in offspring born to dams fed the S diet at weaning. Extending the dams’ diet during gestation and lactation magnified the effect of the gestational S diet on BW and composition and glucose metabolism in male offspring. Although composition of the weaning diets interacted with that of the dams’ diets, the latter was the dominant factor in determining metabolic outcomes in the offspring. In conclusion, the soy protein diet, compared to the casein diet when consumed during gestation or throughout gestation and lactation increased food intake and the presence of characteristics of metabolic syndrome in the offspring.

Keywords: protein source
fetal programming
blood pressure
metabolic syndrome
food intake
Advisor: Anderson, G. Harvey
Cholera and Crisis: State Health and the Geographies of Future Epidemics

In the fall of 1892, fear of cholera was pervasive in North America. Ten years into the fifth international cholera epidemic -- that lasted from 1881 to 1896 -- cholera had been raging in the Middle East, India, and Europe, but the disease had yet to cross the Atlantic Ocean. The maritime traffic of immigrants from Europe was continuous, and each migrant ship potentially carried the disease. Doctors, government officials, and politicians were not asking 'will cholera come?', but rather when. While no one got sick or died of cholera in the city of Toronto in 1892, the crisis and fear of imminent cholera was very real. Drawing on archival research, this dissertation maps how a cholera crisis was shaped by urgency, immediacy, and speculation on the future. My argument will show how the geography of an epidemic is not limited to the presence of a disease. If crises are times of profound activity, how does this event need to be substantiated in order to produce change? This dissertation follows how cholera was integral to producing an object called proliferating life that held together: migrating populations, growing cities, and degeneration; marshland as the source of disease; the medical theory of zymosis that explained how disease outbreaks got out of control; and Malthusian 'laws' of population. Health experts used correlation and synecdoche to visualize these relations. However, these experts needed a stable institutional base to articulate both their fears and their recommendations, which included: professionalized expanding health boards, as social infrastructures; reclaiming Toronto’s marshland of Ashbridge's Bay; and a health ideology built upon the fear of future epidemics, immigration, and a growing economic rationale for health. By the early 20th century, state health became instrumental to a "national vitality", a practice of government intervention that I frame as bureaucratic bio-economy.

Keywords: cholera
crisis
health
disease
epidemic
history
science
Advisor: Prudham, W. Scott
Development of High-order CENO Finite-volume Schemes with Block-based Adaptive Mesh Refinement (AMR)

A high-order central essentially non-oscillatory (CENO) finite-volume scheme in combination with a block-based adaptive mesh refinement (AMR) algorithm is proposed for solution of hyperbolic and elliptic systems of conservation laws on body- fitted multi-block mesh. The spatial discretization of the hyperbolic (inviscid) terms is based on a hybrid solution reconstruction procedure that combines an unlimited high-order k-exact least-squares reconstruction technique following from a fixed central stencil with a monotonicity preserving limited piecewise linear reconstruction algorithm. The limited reconstruction is applied to computational cells with under-resolved solution content and the unlimited k-exact reconstruction procedure is used for cells in which the solution is fully resolved. Switching in the hybrid procedure is determined by a solution smoothness indicator. The hybrid approach avoids the complexity associated with other ENO schemes that require reconstruction on multiple stencils and therefore, would seem very well suited for extension to unstructured meshes. The high-order elliptic (viscous) fluxes are computed based on a k-order accurate average gradient derived from a (k+1)-order accurate reconstruction. A novel h-refinement criterion based on the solution smoothness indicator is used to direct the steady and unsteady refinement of the AMR mesh. The predictive capabilities of the proposed high-order AMR scheme are demonstrated for the Euler and Navier-Stokes equations governing two-dimensional compressible gaseous flows as well as for advection-diffusion problems characterized by the full range of Peclet numbers, Pe. The ability of the scheme to accurately represent solutions with smooth extrema and yet robustly handle under-resolved and/or non-smooth solution content (i.e., shocks and other discontinuities) is shown for a range of problems. Moreover, the ability to perform mesh refinement in regions of smooth but under-resolved and/or non-smooth solution content to achieve the desired resolution is also demonstrated.

Keywords: computational fluid dynamics
finite-volume method
high-order scheme
adaptive mesh refinement (AMR)
ENO scheme
essentially non-oscillatory
CENO
body-fitted multi-block mesh
high-order spatial discretization
numerical method
hyperbolic and elliptic PDE
fixed stencil reconstruction
piecewise linear reconstruction
smoothness indicator
Euler and Navier-Stokes equations
advection-diffusion equation
smooth and non-smooth solution content
k-exact least-squares reconstruction
hybrid numerical scheme
compressible gaseous flows
refinement criteria
high-performance parallel computing
solution monotonicity enforcement
large-eddy simulation (LES)
interpolation technique
structured grid
inviscid and viscous flow
TVD scheme
h-p-adaptation
high-order boundary conditions
complex curved geometries
Advisor: Groth, Clinton P. T.
Cell Non-autonomous Regulation of Death in C. elegans

Programmed cell death (PCD or apoptosis) is an evolutionarily conserved, genetically controlled suicide mechanism for cells, which when deregulated, can lead to developmental defects, cancers and degenerative diseases. In C. elegans, DNA damage induces germ cell death by signaling through cep-1/p53 ultimately leading to the activation of the CED-3/caspase. It has been hypothesized that the major regulatory events controlling cell death occur by cell autonomous mechanisms, that is within the dying cell. In support of this, genetic studies in C. elegans have shown that the core apoptosis pathway genes ced-4/APAF1 and ced-3/caspase are required in cells fated to die. However, it is not known whether the upstream signals that activate apoptosis function in a cell autonomous manner. Here I show that two genes, kri-1, an ortholog of KRIT1/CCM1 that is mutated in the human neurovascular disease cerebral cavernous malformations (CCMs) and daf-2, an insulin-like receptor, are required to activate DNA damage-dependent cell death independently of cep-1/p53. Interestingly, I found that both genes can regulate cell death in a non-autonomous manner, revealing a novel role for non-dying cells in eliciting death in response to DNA damage.

Keywords: C. elegans
apoptosis
Advisor: Derry, William Brent
Dynamic Demand for New and Used Durable Goods without Physical Depreciation

This thesis studies the interaction between new and used durable goods without physical depreciation. In product categories such as CDs/DVDs and video games, the competition from used goods markets has been viewed as a serious problem by producers. These products physically depreciate negligibly, but owners' consumption values could depreciate quickly due to satiation. Consequently, used goods that are almost identical to new goods may become available immediately after a new product release. However, the existence of used goods markets also provides consumers with a selling opportunity. If consumers are forward-looking and account for the future resale value of a product in their buying decision, used goods markets could increase the sales of new goods. Thus, whether used good markets are harmful or beneficial to new-good producers is an empirical question. To tackle this question, I extend the previous literature in three ways. First, I assemble a new data set from the Japanese video game market. This unique data set includes not only the sales and prices of new and used goods, but also the resale value of used copies, the quantity of used copies retailers purchased from consumers, and the inventory level of used copies at retailers. Second, I develop a structural model of forward-looking consumers that incorporates (i) new and used goods buying decisions, (ii) used goods selling decisions, (iii) consumer expectations about future prices of new and used goods as well as resale values of used goods, and (iv) the depreciation of both owners' and potential buyers' consumption values. Third, I develop a new Bayesian estimation method to estimate my model. In particular, my method can alleviate the computational burden of estimating non-stationary discrete choice dynamic programming models with continuous state variables that evolve stochastically over time. The estimation results suggest that consumers are forward-looking in the Japanese video game market and the substitutability between new and used video games is quite low. Using the estimates, I quantify the impact of eliminating the used video game market on new-game revenues. I find that the elimination of used video game market could reduce the revenue for a new game.

Keywords: Used Goods Markets
Discrete Choice Models
Dynamic Programming
Bayesian Estimation
Consumption Satiation
Forward-Looking Behavior
Advisor: Ching, Andrew
Moorthy, Sridhar
Canadian Refugee Policy Paradigm Change in the 1990s: Understanding the Power of International Social Influence

This dissertation explores the factors which contributed to a change in the paradigm that framed Canadian refugee policy over the course of the 1990s. This change is characterized in the dissertation as a shift from a refugee protection paradigm that dominated policy-makers’ thinking in the 1970s and 1980s, to a security-control paradigm by at the end of the 1990s. This change is puzzling because it occurred prior to the events of 9/11 rather than in response to them and because domestic motivations for change do not provide a complete explanation of the shift. The dissertation argues that although factors in the domestic and international environments may have enabled paradigm change, a more complete explanation of shift needs to consider the process through which Canadian policy-makers were socialized into a developing international norm. This process of international socialization occurred through bureaucrats’ international interaction in bilateral and Regional Consultative Processes akin to Anne-Marie Slaughter’s global government networks. Using data generated from primary document analysis and a series of interviews of key policy-makers this dissertation maps paradigm change over the two periods. This data is then used to provide evidence of the importance of bureaucratic socialization through a global government network for migration in explaining this change.

Keywords: Canada
Refugee Policy
Global Goverment Networks
Socialization
Advisor: Bertoldi, Nancy
'The Deep Slumber of Decided Opinion': How Teachers and School Administrators Understand Controversial Issues Policy

Recognition that social and global issues are important to education has re-ignited interest in policy approaches to controversial and sensitive issues(CI).Without a policy framework for CI education, educators become 'de-skilled' by their working conditions. This qualitative study researches teachers and school administrators' understanding of CI policy (CSI 2003) using a theoretical framework structured on critical democracy and a conceptual lens of critical discourse and narrative analyses. Research findings reveal CSI lacks a cogent conceptual framework; it supports curricula and board policies. Some school administrators use CSI to support the system against community-based challenges to policy and programs. In this way, the process of CSI is not democratic. Further, a critical discourse analysis reveals deeply-embedded contradictions through competing voices for authority. Teachers report feelings of fear and experiencing surveillance in conditions of inadequate and inequitable CI policy support. The findings locate inattention to students' roles is defining what (and how) CI enter the classroom. The research findings sharpen our knowledge of local-level policy activity among users. For these and other reasons, the work censures CI policy for 'white privilege' and 'liberalism.'From a theoretical perspective, the thesis asserts the need for more work on the intersections of critical policy, critical democracy and citizen engagement in policy processes.

Keywords: Educational Administration
Policy
Advisor: Portelli, John P.
Investigating the Integration of Alternative Splicing and Transcriptional Regulation in Mammalian Gene Expression

Alternative splicing functions to generate proteomic diversity and to regulate gene expression in higher eukaryotes. Genome-wide analyses suggest that alternative splicing and transcription typically regulate different gene sets to achieve cell- and tissue-type specificity. However, within individual cell-types, most alternative splicing events occur co-transcriptionally and are impacted by the transcriptional machinery. Despite many focused studies on co-transcriptional regulation of alternative splicing, its mechanisms and functions in regulation of gene expression are still poorly understood. To investigate relationships between transcription and alternative splicing, I performed microarray profiling of alternative splicing and transcript levels during activation of a T cell line. This experiment revealed that different sets of genes and associated functional categories are regulated by alternative splicing and transcription during T cell activation. I next employed inhibitors of RNA polymerase II (Pol II) elongation and microarray profiling to identify genes with coupled changes in splicing and transcript levels when transcription is impeded in activated T cell. Genes that were affected at both levels were significantly enriched in RNA binding and processing functions, and generally displayed increased alternative exon inclusion and decreased transcript levels when transcription elongation was disrupted. Similar effects were observed when transcription was driven by mutant polymerases with reduced elongation activity, and when cells were subjected to stress treatments. Many of the elongation inhibition-sensitive exons from the affected genes introduce premature termination codons into the mRNA, resulting in spliced mRNAs that are substrates of the nonsense-mediated decay pathway and further reduction in mRNA levels. ChIP-Seq experiment demonstrated that Pol II occupancy specifically increased in introns flanking the affected exons. These results provide evidence that a physiological function of transcription elongation-coupled alternative splicing regulation is to regulate the levels of RNA processing factors under conditions that reduce elongation activity, including cell stress. In summary, my thesis research has provided new insights into the integration of transcription and splicing control. While these two regulatory levels can control different gene sets during the activation of T cells, within a given cell type, they are closely coupled to control specific alternative splicing events that appear to coordinate mRNA and RNA processing factors levels.

Keywords: transcription
alternative splicing
RNA polymerase II
T cell activation
Advisor: Blencowe, Benjamin
The Malleability of Music Preferences: Effects of Individual Differences and the Listening Context

Despite the ubiquity of music and its importance to one’s identity, there has been limited research on individual differences in music preferences. The aim of this dissertation was to examine how music preferences vary across individual differences in stable traits (e.g., gender, personality) and states (e.g., mood) over three studies. The focus of Study 1 was on the influence of the listener’s mood on emotion-based music preferences. The typical preference for happy- over sad-sounding music was found to be mood-dependent, evident after happy and neutral but not sad mood inductions. When the music was emotionally ambiguous (i.e., with cues to both happiness and sadness), happy listeners liked the music more than other listeners, whereas sad listeners perceived it to be more sad-sounding. Study 2 examined how emotion-based music preferences develop. Adults and children 5, 8, and 11 years of age listened to short pieces expressing emotions that varied in arousal and valence: happiness (high, positive), scariness (high, negative), peacefulness (low, positive), or sadness (low, negative). Adults preferred pieces with a positive valence (happy and peaceful), whereas children preferred excerpts depicting high-arousal emotions (happy and scary). Identification accuracy was predictive of a positive-valence bias among 5- and 8-year-olds. A number of other findings related to accuracy and gender differences were also evident. Study 3 examined whether personality differences affect the influence of exposure on liking. Undergraduates completed the Big Five Inventory and provided liking ratings for novel music excerpts as well as for excerpts they heard 2, 8, or 32 times. Higher scores on Openness-to-Experience were related to greater liking for novel excerpts and more rapid satiation. In sum, these three studies highlight that music preferences vary as a function of individual differences and the listening context.

Keywords: Music
Liking for Music
Emotion
Openness to Experience
Musical Development
Exposure and liking
Advisor: Schellenberg, E. Glenn
Quantification of Blood Flow Using Ultrasound Contrast Agents

Contrast enhanced ultrasound offers a unique method to measure the blood flow, perfusion, vascular volume and morphology of microvascular networks. This is achieved by exploiting the ability of microbubble contrast agents to be disrupted and preferentially detected with contrast specific imaging techniques – using a method known as disruption-replenishment. In its current form, disruption-replenishment suffers from poor reproducibility and accuracy, largely due to the inappropriate application of a mono-exponential model of microbubble replenishment, and an incomplete understanding of the dependencies of the measurement. In this thesis, we hypothesize that disruption-replenishment measurements can be improved by applying a perfusion model that considers the physical elements of the measurement, including the haemodynamics and morphology of the vascular system, the ultrasound field distribution and microbubble properties. We present a flexible, theoretical framework to model microbubble replenishment within the microvasculature. The replenishment model is further developed by in vitro and in vivo validation, and clinical translation in a trial of anti-angiogenic therapy in patients, resulting in a proposed clinical protocol. The presented formalism was shown to be more robust and demonstrated better agreement of both ﬁtting quality and estimates of flow velocity when compared to the established model (accuracy to within 3-9%). The reproducibility of repeated in vivo disruption-replenishment flow measurements was 11.9% using the proposed perfusion model compared to 24% using the established model. Variability of clinical perfusion measurements was also reduced with a method that discards the contribution of flow from larger arteries. Excluding the large vessel component in clinical measurements of tumour blood volume decreased the inter-plane variability by up to 20%. The proposed perfusion model can be used to generate parametric maps of vascularity through which additional quantitative parameters become available. These improvements will help translate the method of disruption-replenishment into routine clinical practice and clinical trials.

Keywords: Ultrasound
Blood flow
Ultrasound contrast agents
Microbubbles
Advisor: Burns, Peter N.
Essays on Human Capital, Wage Dispersion and Worker Mobility

This dissertation is comprised of three papers. In Chapter 1 I analyze if career heterogeneity in terms of life-cycle earnings, occupational mobility and unemployment is predominantly driven by skills acquired prior to labor market entry or by decisions made and shocks accumulated over the working life. My study is based on a Dynamic Discrete Choice model that enriches the proto-typical dynamic Roy-model with a number of potentially important sources of career heterogeneity, such as match heterogeneity and permanent shocks to skills. I find that a large fraction of life-cycle income inequality is driven by match heterogeneity among workers with the same observable and unobservable credentials. Differences in comparative advantages, though quantitatively important as well, have a much smaller impact than what has been found in research that relies on estimates from more restrictive dynamic Roy models. In Chapter 2 I estimate a flexible non-stationary variance components model of residual earnings dynamics and investigate if recent increases in residual inequality are caused by an increase of the variances of permanent, persistent or transitory shocks. My results suggest that underlying sources of increasing wage inequality are very different across education groups. Most importantly, only the lesser educated experience a large increase in earnings instability. Chapter 1 and 2 utilize a unique administrative data set from Germany that follows workers from the time of labor market entry until twenty-three years into their careers. In the last chapter I investigate empirically if a particular set of pre-labor market skills – namely university student achievement – can be fostered by assigning male teachers to male students and female teachers to female students. I find that being taught by a same-sex instructor helps students to improve their relative grade performance and the likelihood of completing a course, but the magnitudes of these effects are small.

Keywords: Earnings Dynamics
Mobility
Inequality
Human Capital
Advisor: Oreopoulos, Philip
Shi, Shouyong