VictorJuiz/thesis huggingface dataset:
Operations Research Methodologies to Improve the Quality, Accessibilty and Equity of Primary Care
Keywords: Healthcare
Optimization
Primary Care

A growing body of evidence reveals the importance of primary care to the overall health of populations, resulting in an increasing interest in efficient, effective, timely and equitable delivery of primary care services. This research focuses on two perspectives of delivering primary care. First, the work focuses on the quality of primary care delivery, represented by distribution of facilities that provide primary care on different quality levels and incur varying costs on the regulator. The proposed model optimizes the geographic distribution of facilities (locations and types) and provides tradeoffs between two objectives - the quality of provided care and the annual operating cost. The Pampalon deprivation index is incorporated directly as a proxy of varying needs, as it was correlated with complex health-care problems, more frequent visits and barriers to obtain care. Results are showcased on the area of Kingston, Ontario. Second, the distribution of general practitioners is addressed, measured in terms of general practitioners (GPs) per population. Many countries are experiencing inequitable distribution of GPs, such that does not match the distribution of the population. It usually results from the fact that health professionals are choosing practice locations according to their own preferences and considerations. To address this issue, human choice is incorporated into the modeling approach explicitly, using Huff’s spatial interactions approach. The utilities of the professionals when choosing communities are modeled, affecting in turn the probabilities of location choice. The presented model explores the option of modifying policies so that the resulting distribution of general practitioners in the studied geographic area will be more equitable. As an example, educational policies are explored, devising the optimal locations of residency training of family physicians and their background combinations (at each training location) for Ontario. The developed methodologies showcased for the province of Ontario, Canada, however they are general enough to be used in any jurisdiction with similar characteristics.
Sexual and Viability Selection on a Wild Population of Tree Crickets Experiencing Female-biased Predation
Keywords: Mating systems
Natural selection
Nuptial gifts
Predator-prey interactions
Sex-biased predation
Sexual selection

Sex-biased predation can have important evolutionary consequences for prey, however female-biased predation is uncommon in nature and understudied in science. Understanding female-biased predation is necessary to create a complete picture of the costs of sex-specific behaviours and phenotypes. In this thesis, I used a system of tree crickets, Oecanthus nigricornis, which suffer female-biased predation by wasp predators, Isodontia mexicana, to 1) test hypotheses about the causes of female-biased predation; 2) quantify how viability selection caused by such predation may affect male and female traits differently; and 3) test if sexual selection opposes or reinforces viability selection among each sex. To address the first objective, I compared tree cricket prey taken from I. mexicana nests to surviving tree crickets, and found that wasps took significantly more adult females only when females were larger than males. I also found that females with more ovarian eggs were more likely to be caught by wasps, and laboratory experiments showed that female jumping ability is negatively affected by egg load. To address the second objective, I compared viability selection (from wasp predation) on males and females over several years. Within single study seasons, male and female phenotypes were affected differently by viability selection, but temporal variation in selection across years resulted in overall weak nonlinear selection on both sexes, and no significant effect on sexual dimorphism. To address the third objective, I compared the direction and form of sexual selection (calculated using estimates of mating success) in males and females to those of viability selection, and found that sexually selected traits had viability costs in males but not in females. Thus, in this predator-prey system, I found that females pay a viability cost for investing in fecundity traits, and males pay a viability cost for investing in sexual traits.
Interactive Visual Data Exploration: A Multi-focus Approach
Keywords: Human-computer interaction
Information visualization
Multi-focus visualization
Visual analytics
Visual data exploration

Recently, the amount of digital information available in the world has been growing at a tremendous rate. This huge, heterogeneous, and complicated data that we are continuously generating could be an incredible resource for us to seek insights and make informed decisions. For this knowledge extraction to be efficient, visual exploration of data is demanded in addition to fully automatic methods, because visual exploration can integrate the creativity, flexibility, and general experience of the human user into the sense-making process through interaction and visualization techniques. Due to the scale and complexity of data, robust conclusions are usually formed by coordinating many sub-regions in an information space, which leads to the approach of multi-focus visual exploration that allows browsing different data segments with multiple views and perspectives simultaneously. While prior research has proposed a myriad of information visualization techniques, there still lacks comprehensive understanding about how visual exploration can be facilitated by multi-focus interactive visualizations. This dissertation investigates issues and techniques of multi-focus visual exploration through five design studies, touching various types of data in a range of application domains. The first two design studies address the exploration of numerical data values. KronoMiner presents a multi-purpose visual tool for exploring time-series based on a dynamic radial hierarchy; and the ChronoLenses system supports exploratory visual analysis of time-series by allowing users to progressively construct advanced analytical pipelines. The third design study focuses on the exploration of logical data structures, and presents DAViewer that facilitates computational linguistics researchers to explore and compare rhetorical trees. The last two design studies consider the exploration of heterogeneous data attributes (or facets). TimeSlice facilitates the browsing of multi-faceted events timelines by organizing visual queries in a tree structure; and PivotSlice aids the mining of relationships in multi-attributed networks through a dynamic subdivision of data with customized semantics. This dissertation ends with critical reflections and generalizations of the experiences obtained from the case studies. High-level design considerations, conceptual models, and visualization theories are distilled to inform researchers and practitioners in information visualization for devising effective multi-focus visual interfaces.
The Solidarity Encounter between Indigenous Women and White Women in a Contemporary Canadian Context
Keywords: Indigenous/non-Indigenous relations
liberal subject
settler colonialism
solidarity
subjectivity
whiteness

This dissertation tracks the gendered operation of white settler liberal subjectivity at a specific site of settler colonial relations—the “solidarity encounter” between Indigenous women and white women in Canada. Through in-depth qualitative analysis of interviews and self-reflection (as a white settler woman ally), I examine the encounter’s intersubjective relations, shining the theoretical spotlight on how white women negotiate our tenuous status as settlers. Attentive to the complexity of these relations, including how white women allies grapple with our dominant positionality, I signal the perniciousness of white settler liberal subjectivity and the deep quest for legitimacy/innocence at its core. This quest, I argue, manifests itself as a white desire for proximity to Indigenous women, which in turn takes various forms and is often experienced by Indigenous women as invasive. I dedicate three chapters to mapping the sometimes subtle expressions of this desire (e.g., the need for acceptance, inclusion, forgiveness, healing, empowerment/purpose, friendship) and its role in liberal self-making projects, i.e., how it serves to negate colonial hierarchies and/or white settler women’s colonial complicity therein. Further, I develop the concept of the “impulse to solidarity”—the bundle of desires and discursive practices that propels white settler women in their pursuit of proximity, an impulse related to, but distinct from the “helping imperative” (Heron, 2007). White women allies find it difficult to resist the gendered dictates of liberal subjectivity, which in a settler colonial context demand our reproduction as legitimate national subjects vis-à-vis Indigenous women Others. Despite the inescapability of the “colonial present” (Gregory, 2004), I also note a cautious optimism among participants regarding the possibility of non-colonizing solidarity. I propose a framework for reconfiguring intersubjective relations in the solidarity encounter best encapsulated by the directive “step back, but not out.” Struck by pervasive spatial references in participant narratives, I characterize the problem (colonizing solidarity) and its solution (non-colonizing solidarity) in spatialized terms—white settler women must interrogate and curb our solidarity impulse and related practices of proximity. We must recognize when settler liberal self-interest takes centre stage, compels us to “come too close” and diminishes the collective political work of solidarity.
Programmed Cell Death is Intrinsic to Yeast Gametogenesis
Keywords: autophagy
cell death
meiosis
mitochondria
sporulation
vacuole

Studies of the yeast Saccharomyces cerevisiae have provided many critical insights into fundamental eukaryotic cell biology. Programmed cell death (PCD) is integral to animal and plant development, contributing to tissue homeostasis and morphogenesis by removing unneeded cells. Although PCD is of widespread importance to many organisms, studies of yeast have provided relatively limited insight into the mechanisms and physiological roles of PCD. Investigations of yeast cell death pathways have almost exclusively been restricted to cells undergoing vegetative growth, leaving no exploration of their potential functions during developmental transitions in the yeast life cycle. Here, I characterize a novel PCD intrinsic to yeast gametogenesis, or sporulation. Upon sporulation induction under severe carbon limitation, yeast cells subject only a fraction of their potential gametes to spore differentiation. Meiotic products which are not subject to spore development are shown to adopt an alternative fate of programmed destruction. I characterize the elimination of aborted gametes as programmed nuclear destruction (PND), a phenomenon which exhibits hallmarks of animal and plant PCD. Cells executing PND display fragmentation of genomic DNA by endonuclease G, a hallmark of animal apoptosis. The destruction of nuclear protein during PND is mediated by vacuolar proteases which undergo programmed release from the vacuole during sporulation. To understand the mechanisms underlying PND, I consider PND as part of a broader cell death program executing the demise of the meiotic mother cell. Accordingly, I find that the mother cell adopts characteristics of a dying cell following meiosis, including mitochondrial depolarization, vacuolar swelling and the loss of plasma membrane integrity. The timely execution of the mother cell depends on the development of its daughter spores, as cells lacking regulators of spore morphogenesis are unable to execute mother cell demise normally. As an extension of my studies of PCD, I also present preliminary, unanticipated evidence that Nuc1 contributes to mitochondrial genome metabolism. Overall, I propose that PCD of the meiotic mother cell is an intrinsic aspect of yeast gametogenesis which shares common genetic regulation with spore morphogenesis.
The Role of Peroxisome Proliferator-activated Receptor Alpha in the Regulation of Sex Differences in T Helper 1 Immunity
Keywords: Histone modification
Nuclear receptor
Sex difference
T cells
Transcription factor

It is reported that female CD4+ T cells are biased towards T helper (Th) 1 cytokine production, whereas male CD4+ T cells are biased towards Th2. It has been suggested that the female bias in Th1 immunity is the reason why females not only generate enhanced anti-viral and anti-tumour responses, but also are more likely to develop certain autoimmune diseases than males. Our group previously reported that the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARα) has a sex-specific role in negatively regulating Th1 immunity in mice. The objective of the thesis is to further explore the roles of PPARα in the regulation of sex differences in Th immunity. We first investigated sex differences in Th cytokine production in SJL mice and human primary CD4+ T cells. We observed that female CD4+ T cells of both species produced higher levels of interferon (IFN)-γ and lower levels of IL-17 than male counterparts. Furthermore, we showed that this sex bias in Th immunity was controlled by androgens. The effects of androgens in suppressing Th1 immunity were shown to be mediated through PPARα. Moreover, we showed that PPARα activity negatively correlated with IFN-γ production by CD4+ T cells. Subsequent studies in mice identified IFN-γ as the gene repressed by PPARα. We showed that this repression was mediated through the recruitment of PPARα and the nuclear receptor co-repressor 1(NCOR)-containing co-repressor complex to certain conserved non-coding sequences (CNS) at the Ifng locus in male T cells. Conversely, repressing PPARα activity with the antagonist NXT-1120 lead to global derepression at the Ifng locus and increased IFN-γ production. This control of IFN-γ production by PPARα in male T cells also extended to natural killer (NK) T cells and CD8+ T cells. On the other hand, we found that the sex difference in Th17 immunity was regulated by PPARγ. Androgens decreased PPARγ mRNAs in murine and human CD4+ T cells. Furthermore, knocking down PPARγ expression using siRNAs was associated with higher IL-17 production by female CD4+ T cells. Taken together, these findings have furthered the understanding of sex differences in Th immunity.
Regeneration in Recall and Verb Phrase Ellipsis
Keywords: anaphora
ellipsis
recall
regeneration

In this thesis, I propose the Ellipsis Regeneration Hypothesis, whereby resolution of verb phrase ellipsis (VPE) involves accessing a conceptual/propositional representation of the antecedent, and regenerating structure using recently activated lexical items. This hypothesis pulls together strands from two independent areas of research: anaphor resolution and recall. Previous research on the processing of VPE constructions has demonstrated that the linguistic structure of the antecedent appears to be accessed and reactivated during resolution. At the same time, in a series of experiments investigating immediate recall, Potter and Lombardi (1992, 1998) and Lombardi and Potter (1992) argue that such linguistic representations do not persist in memory. Under their view, immediate recall (which is normally highly accurate) entails access to a conceptual (rather than linguistic) representation of the target and regeneration of structure using recently activated, but unordered, lexical items. The primary piece of evidence for this hypothesis is lure intrusion: if recall consults a surface representation of the target, then it should not be possible to induce changes to lexical items or structure. And yet, Potter and Lombardi show that when subjects are presented with synonyms (lures) to a word in the target, they will sometimes select the synonym in recall. Moreover, if that synonym is a verb (e.g., donate) that requires a different structure to that of the target (e.g., give), subjects will make the appropriate structural changes in recall. Bringing the two strands together, one comes to an intriguing possibility: that VPE does not access a linguistic representation of the antecedent but rather, like recall, accesses a conceptual representation and regenerates using recently activated lexical items. Taking lure intrusion to be a hallmark of regeneration, three experiments were designed to determine whether the lure intrusion effect would obtain: a recall study, an ellipsis study, and a study using 'do it'. The prediction of the current thesis is that lure intrusion should occur with both recall and ellipsis, but not with 'do it'.. Evidence from the three experiments supports the hypothesis that the structural output of VPE is, like recall, not accessed, but regenerated.
Applications of Quasi-fixed-Frequency Current-mode Power Converters
Keywords: Current Mode Control
Integrated Circuit
Power Converter
Power Management

This thesis presents the small-signal analysis and implementations of two Quasi-Fixed Frequency (QFF) Current-Mode Control (CMC) schemes: 1) ripple Hysteretic CMC (HCMC) with frequency regulation and 2) Peak CMC (PCMC) with controlled off-time. The QFF CMC schemes eliminate the need for slope compensation and its negative impact on the converter stability; therefore, offering reduced compensator complexity and suitability for applications with wide input and output voltage range. The two QFF CMC schemes with different implementation complexities are applied in three emerging applications: 1) Hybrid Energy-Storage System (HESS) for Internet of Things (IoT) applications, 2) cell-level differential power processing in Concentrating-PV (CPV) system, and 3) applications of high-voltage Gallium-Nitride (GaN) High-Electron-Mobility Transistors (HEMTs). In addition to the practical implementations of the QFF CMC schemes, efficiency/power-density improvements and integration issues are also addressed. In particular, a cell-level Power Management Integrated Circuit (PMIC) operating at 3.6 MHz is the first on-chip realization of ripple HCMC with frequency regulation using a Phase-Locked Loop (PLL). With light-load operating modes, integrated driver and controller supplies, and low-voltage start-up capability, the low-cost PMIC can increase the power output of a CPV system by over 10%. A dual-mode driver/controller IC is designed for a depletion-mode HEMT, with monolithic negative gate-drive capability and digitally programmable slope control. PCMC with controlled off-time is used to simplify the current sensing. The co-packaged driver/controller IC with a customized high-voltage GaN HEMT were operated at 1 MHz in a 35W boost converter prototype.
The Effect of Material Properties on Dynamo Generation in Planets
Keywords: Dynamo
Exoplanet
Magnetic Field
Mercury
Planet
Super Earth

In this thesis I use a three dimensional numerical dynamo model to explore the effect of novel material properties and core states on magnetic field generation in the planet Mercury, and in rocky extra-solar planets. In the first part of this work I focus on the recent evidence of pressure induced metallisation in materials which commonly comprise planetary mantles. In this scenario the materials which make up the lower mantle of a planet conduct electricity with a conductivity similar to that of iron. I show that a metallised mantle changes the way in which magnetic field is generated by providing a new source of magnetic shear between the fluid outer core and the solid mantle. I then show that this has the effect of making planetary magnetic fields more difficult to observe from Earth. The second and third parts of this work focus on the planet Mercury. First, I incorporate recent evidence of buoyancy sources mid-way through Mercury’s liquid core (known as “snow zones”) to show that they can explain the weak observed magnetic field of Mercury. In a second project on Mercury I test whether recent evidence of a dense solid layer at the top of Mercury’s core, attributed to a solid, electrically conducting layer of FeS, could help explain Mercury’s weak magnetic field. I find that the addition of this layer causes the dynamo to generate a strong, dipolar magnetic field, which does not match the observations made by the MESSENGER spacecraft.
Analyzing Phenotypes in High-content Screening with Machine Learning
Keywords: Bioinformatics
High Content Screening
Machine Learning

High-content screening (HCS) uses computational analysis on large collections of unlabeled biological image data to make discoveries in cell biology. While biological images have historically been analyzed by inspection, advances in the automation of sample preparation and delivery, coupled with advances in microscopy and data storage, have resulted in a massive increase in both the number and resolution of images produced per study. These advances have facilitated genome-scale imaging studies, which are increasingly frequent. Although the sheer volume of data involved strongly favours computational analysis, many assays continue to be scored by eye. As a scoring method, visual inspection limits the rate at which data may be analyzed, at increased cost and decreased reproducibility. In this thesis, we propose computational methods for data analysis of HCS data. We begin with feature data derived from confocal microscopy fluorescence images of yeast cell populations. We use machine learning methods trained on a small labeled subset of that feature data to robustly score each population with respect to a DNA damage focus phenotype. We then introduce a method for using deep autoencoders trained using a label-free objective to perform dimensionality reduction. This allows us to model the non-linear relations between features in high-dimensional data. The computational complexity of our approach scales linearly with the number of examples, allowing us to train on a much larger number of samples. Finally, we propose an outlier detection method for discovering populations that present significantly different distributions of cellular phenotypes as com- pared to wild-type using nonparametric Bayesian clustering on the low-dimensional data. We evaluate our methods against comparable alternatives and show that they either meet or exceed the level of top performers.