VictorJuiz/thesis huggingface dataset:
Bayesian Growth Mixture Model for Clustering Longitudinal Data

Studies of growth patterns of longitudinal characteristics are vitally important to improve our understanding of the development course of diseases. In these studies, it is often of great interest to cluster individual trajectories based on repeated measurements collected over time. Non-linear growth trajectories are often seen in practice, and individual data can also be measured sparsely at irregular time points, which may complicate the modeling process. This thesis begins with proposing a shape invariant growth mixture model for better clustering growth trajectory data with these features (Chapter 3). In the proposed model, non-linear patterns are captured by cluster-specific cubic B-spline smoothing functions within a latent class mixed effect model framework, and random effects reflecting the size, timing and intensity of the individual growth trajectories are modeled within each cluster to account for variation that is not explained by latent classes. We also compare our model to the commonly used standard growth mixture model and functional clustering approach. To better understand the clinical implication of different growth patterns, interests are usually not limited to which individuals belong to which subgroup, but also what factors are associated with individuals' class membership. This information could help clinicians provide early intervention to prevent the development of abnormal trajectories and therefore the development of diseases. Despite its importance in facilitating medical findings, little work has been done in selecting the predictors related to class membership in the context of growth mixture models. Therefore, we aim to extend the shape invariant mixture model we proposed to a unified Bayesian growth mixture model to allow incorporating covariates. To achieve this objective, in Chapter 4 we first review the currently available Bayesian variable selection approaches and compare their performance in terms of variable selection and prediction. And in Chapter 5, we propose a unified growth mixture model allowing for simultaneously clustering growth trajectories and selecting important covariates that are associated with the class membership. Bayesian inference via Markov chain Monte Carlo (MCMC) algorithm is implemented to estimate the parameters of interest. Results from analyzing real and simulated data are presented and discussed throughout this thesis.

Keywords: Bayesian Analysis
Clustering
Growth Mixture Model
Longitudinal data
Non-linear Growth Trajectory
Variable selection
Advisor: Lou, Wendy
The Feasibility and Usefulness of Applying a Health Economic Framework to Prioritize Quality Indicators: A Demonstration with Chronic Obstructive Pulmonary Disease

The modern quality movement has placed increased attention on health care performance. As a result, quality indicators, which are quantitative measurements of health care performance, have become increasingly prevalent in health care systems. Although many health systems define improving population health and reducing health care costs as priorities, many quality indicators are selected using criteria that do not always align with these priorities. Health economics offers a framework for explicitly bringing considerations of population health and health care costs into the process of prioritizing quality indicators. This research sought to demonstrate the feasibility of operationalizing the health economic framework to prioritize quality indicators and explore the usefulness of this method. Quality indicators for smoking cessation and oxygen therapy in chronic obstructive pulmonary disease were used as examples to demonstrate the feasibility of associating variations in indicator values with variations in quality-adjusted life years (QALYs) and costs. The joint variation in QALYs and costs was represented as incremental net health benefit (INHB), which represents the QALYs gained less its opportunity cost. The first two studies demonstrated how quality indicators could be ranked by their relationships to QALYs and costs. However, uncertainty in the values of candidate indicators could affect how quality indicators are prioritized. Linear meta-models offer a method that is partially successful in prioritizing indicators in the presence of uncertain indicator levels. Focus groups, with participants representative of stakeholders who would select or use quality indicators, were conducted to explore their perceived usefulness of prioritizing quality indicators under a health economic framework. The usefulness and applicability of the framework appeared to revolve around three main themes of incorporation of evidence, ease of understanding or interpretation of health economic outputs, and the scope of the framework. Ease of interpretation appeared to be the main barrier to the utility of the health economic framework in prioritizing quality indicators. Collectively, these studies show how a health economic framework can be operationalized to prioritize quality indicators in a way that is potentially useful, but resource requirements and barriers in interpretation of the health economic framework may limit its adoption.

Keywords: chronic obstructive pulmonary disease
health economics
quality indicators
Advisor: Krahn, Murray D
Part I: Strategies for the Synthesis of Monodisperse Polymers and Cyclic Polymers. Part II: Synthesis of Dipyrromethenes and Aza-dipyrromethenes from Aromatic Nitriles

This thesis is presented in two parts. Part I begins with an introduction to some contemporary problems in polymer chemistry, but also contains what is essentially a mini-review of catalyst transfer polymerization (CTP). This part of the chapter elucidates a number of common misunderstandings of CTP that are present in the literature. It goes onto suggest a new set of design principles to design new CTP systems for a wider variety of monomers. This leads into the first homogenous synthesis of monodisperse polymers. Through cycling between low and high temperatures and carefully controlling monomer activation, we show that it is possible to add exactly one monomer per temperature cycle to each chain in solution, resulting in monodisperse polymers with quantitatively controlled end groups. Part I also describes a project in which macrocyclic poly(3-hexylthiophene) (P3HT) and poly(3-heptylselenophene) (P37S) were synthesized from their linear counterparts. The approach used to accomplish this differs from more common syntheses of cyclic polymers, in that the relatively long persistence length of the polymers makes it unreasonable to assume 100\% cyclization. The approach presented in this chapter is meant to be as general as possible, and to have applications in other cases where polymers need to be separated based on chemical functionality. Part II is an introduction to dipyrromethene and aza-dipyrromethene dyes, along with common methods for their syntheses. It goes on to present a new synthesis of aza-dipyrromethene dyes, which provides an easy route to a number of previously inaccessible compounds, as the previously existing procedures for these dyes are very limited. During the course of this project, it was discovered that one of the starting materials reacted under the same conditions to give a completely different major product. Understanding the mechanism through which it is produced may enable the development of a previously unknown chemical transformation.

Advisor: Seferos, Dwight S
Invasion in the Light of Evolution: An Integrative Approach Using Two Widespread Widow Spider Species

As invasive species spread around the world, understanding the factors underlying invasion success has become increasingly important. Using an evolutionary perspective to examine biological invasions, I investigated how organisms are able to rapidly adapt to new environments, and how selection on phenotypic traits changed over time during sequential stages of the invasion process. In this thesis, I used lab and field studies to assess the importance of behaviour, physiology, morphology, and plasticity to widow spider invasion success. Using this variation in invasion history, I explored patterns across organismal, population, and species-level scales. In Chapter Two, investigated the effects of metabolic rate on behaviour in Australian redback spiders, Latrodectus hasselti, and links between behavioural variation and fitness components measured in the field and laboratory. My work showed that metabolic rate influences fitness via correlation with multiple behaviours, but that metabolic rate alone does not drive all individual behavioural differences. In Chapter Three, I tested preadaptation and local adaptation in a native and an invasive population of L. hasselti to investigate tolerance of novel environmental conditions experienced in the invasive range. In this chapter, I showed that invasive populations may be able to thrive in novel environmental conditions because of increased behavioural plasticity, tolerance of temperature fluctuations, and higher fecundity. In Chapter Four, I compared populations of L. hasselti that are native, established invasive, and newly invasive, and assessed the relative importance of phenotypic traits likely to predispose a species to invasion success. I found that invasive populations of Australian redback spiders diverged from the native Australian population in behaviour, life history, and morphology. In Chapter Five, I tested hypotheses of behaviourally mediated spatial sorting and changes in tradeoffs during invasive spread using two independent invasions of brown widow spiders. I found similar patterns of increased dispersal propensity in two independent invasions of brown widow populations in Israel and the United States. These common patterns suggest that dispersal ability under positive selection in invasive populations, particularly the recently established populations. I infer that behavioural plasticity and dispersal propensity, together with a preference for human-disturbed environments, may underlie invasion and establishment in invasive widow species. In sum, my thesis has expanded our knowledge of how evolutionary processes affect the spread of invasive species through local adaptation, selective filters in the invasion process, and spatial sorting.

Keywords: behaviour
dispersal
invasive species
local adaptation
physiology
plasticity
Advisor: Andrade, Maydianne CB
Mason, Andrew C
A Foucauldian Discourse Analysis of Diabetes Knowledge Translation and the Governance of Family Physicians and Endocrinologists in Canada

Over the past thirty years, improving the health and lives of people with diabetes has been discussed from the perspective of diabetes knowledge translation: the process of implementing clinical practice guidelines into the care of as many people with diabetes (PWDs) as possible. While the majority of research has focused on discovering and implementing knowledge translation initiatives to overcome the problem of clinical inertia, there is less attention being awarded to what is actually happening in these well-intentioned practices. This thesis uses a critical social theoretical perspective from which to examine the ways in which we think and talk about good diabetes care shape the possibilities for physician scope of practice. The conceptual framework used to inform this study is built primarily from Michel Foucault’s concept of governmentality - a historically locatable way of thinking about how we “conduct the conduct” of ourselves and others to achieve specific goals through a variety of explicit and implicit practices, techniques, knowledge and power relations (Dean, 2010). More specifically, I examined the manner in which family physicians and endocrinologists in Canada are governed by, and also govern themselves through discourses of good diabetes care. Data collection, conducted from September 2014 to April 2017, involved analysis of formal documents and 15 semi-structured interviews with family physicians and endocrinologists. Analysis was informed through Dean’s (2010) analytics of government. My findings reveal shifts in the expected conduct of physicians over the past ninety years related to dominant discourses in different historic times. My analysis makes visible the material effects, diversity, contradictions and conflicts as physicians enact historically-constituted roles to engage with PWDs as both passive recipients of care and active participants in care. I bring attention to how discourses of good diabetes care intersect and intertwine in ways that have implications for the success of diabetes knowledge translation initiatives, the intraprofessional relationship between family physicians and endocrinologists, and the provision of patient- centered care.

Keywords: diabetes
discourse
governmentality
power
qualitative research
social sciences
Advisor: Whitehead, Cynthia R
Development of Bioanalytical Assays for Biomolecular Interactions Using Surface Plasmon Resonance

This thesis explores the applicability of surface plasmon resonance (SPR) with the aim to improve and suggest novel improvements in the subject matter with respect to biomolecular interactions. Such analytical techniques could be applied in the field of environmental, biological, and pharmaceutical chemistry, as well as surface science. In the first chapter, the backgrounds of Legionella pneumophila and Alzheimer’s disease (AD) were introduced. The chapter also described the key physical and chemical aspects of SPR and electrochemical impedance spectroscopy (EIS). Based on these analytical techniques, we explored the interactions of Legionella collagen-like (Lcl) proteins with glycosaminoglycans in Chapter 2. Moreover, the effect of tandem repeat units and self-aggregation analysis of Lcl proteins was also performed using SPR. Chapter 3 looked at the interaction of two AD-related proteins, amyloid-beta (Aβ) and apolipoprotein E4 (ApoE4). The interaction between these two proteins has been hypothesized to play a significant role in the early stages of AD. Lastly, from the practice of surface-based analytical techniques, an improvement in surface chemistry was suggested to achieve better sensitivity and anti-non-specific adsorption (anti-NSA) properties. A novel surface modification linker for gold surfaces was synthesized by our group to have improved stability and anti-NSA characteristics as described in Chapter 4. The linker was synthesized and characterized to support structure and function. The anti-NSA properties of the novel linker were demonstrated by both SPR and cyclic voltammetry (CV). To optimize the performance on studying protein-protein and protein-small molecule interactions, it would be most ideal to use our linker in conjunction to a surface spacer. In the end, we concluded the findings from the above-mentioned research studies and the future directions on those topics were expressed in detail (Chapter 5).

Keywords: Alzheimer's disease
biomolecular interaction
electrochemical impedance spectroscopy
surface plasmon resonance
Advisor: Kerman, Kagan
Macrophage Surveillance and Immunity: Eating, Drinking, and Digesting

Professional phagocytes actively patrol the tissues to remove debris, pathogens, and apoptotic bodies. This daunting task requires clearance of hundreds of billions of apoptotic cells produced each day and the never-ending assault by external pathogens. In the phagocyte toolbox are macropinocytosis to sample large volumes of extracellular fluid, and phagocytosis to internalize objects >0.5 μm in diameter. These processes form the core of phagocyte activity and require 1) efficient formation of the macropinosome/phagosome, 2) maturation of the resultant compartment, and finally 3) fusion with acidic lysosomes. In this dissertation, I explore each of these three topics presented as self-contained chapters. I characterize the organization of integrins and F-actin within the forming phagocytic cup to form podosome-like structures under the coordination of phosphoinositide signaling. The function of these structures is demonstrated to be the formation of a progressively expanding sealing zone with the phagocytic prey. I also explore the fate of luminal calcium in the maturing macropinosome and its transport into the phagocyte cytosol. In the final study I characterize a novel sensor for the labeling and study of acidic compartments, including phagolysosomes. Crucially, this probe, cresyl violet, is demonstrated to be both more stable and affordable than current alternatives.

Keywords: Cresyl violet
Lysosome
Macrophage
Macropinocytosis
Phagocytosis
Podosome
Advisor: Grinstein, Sergio
An exploration of the Role of Mentorship in Advancing Women in Coaching

Women coaches continue to be underrepresented in the coaching domain (LaVoi, McGarry, Fisher, 2019) despite the growth and advancement of women in non-sport fields (Statistics Canada, 2017). A notable strategy used to develop and advance women in non-sport sectors is mentorship and while mentorship initiatives currently exist for women in the coaching domain, we know little about women coaches’ experiences of mentorship, what they learn and how they develop through mentorship, and how they can be better supported through mentorship to facilitate career advancement. The purpose of this dissertation, therefore, is to explore the role of mentorship in the advancement of women in coaching. A mixed methods approach was used in this study, which led to the production of three manuscripts: 1) Towards a process for advancing women in coaching through mentorship; 2) Benefits of a Female Coach Mentorship Program on women coaches’ development: An ecological perspective; and 3) Key considerations for advancing women in coaching. The findings from these studies provide much needed empirical data on the role of mentorship in women coaches’ growth and advancement, and more specifically, on the importance of process-driven and group-based mentorship for women coaches, the need for greater organizational involvement and macro-level changes in mentoring women coaches, and the need to shift to sponsorship to help advance women in coaching.

Keywords: Ecological model
Mentorship
Mixed-methods
Sponsorship
Women in coaching
Advisor: Kerr, Gretchen
Chercher La Vie: Births, Deaths, Labour and Militarized Border-crossing among Sex Workers in an Area of Armed Conflict in Eastern Democratic Republic of Congo

This dissertation is a study of sociality and power in armed conflict. It is based on ethnographic research with two groups of women who sell sex in eastern Democratic Republic of Congo, self-identified “bambaragas”. These women travel back and forth across militarized lines in areas of armed conflict to perform sex work and other complementary labour and to trade with a variety of different state and non-state armed groups. This study argues that any attempt to understand sociality and power in war must grapple centrally with non-violent death. The combined effects of armed conflict and privatization contributed to mass infant, child and maternal death. Bambaragas and their children bore a distinct and disproportionate death burden. Hospitals sat at the intersection of governance of health as a private commodity rather than a public entitlement, by both the state and non-state armed groups. This resulted in policies within hospitals of refusing emergency care, abusing and punishing women suspected of abortion, imposing debt and extracting payment, and forcibly detaining women who couldn’t pay for their or their children’s care. This study also contends that gender is central to the workings of power in armed conflict. Armed groups’ governance of bambaragas fluctuates around a central tension: while their labour was relied upon by armed groups, to the point of becoming at times a stake in the conflict, their gendered independence and border-crossing meant they were treated with suspicion and, at times, targeted and killed not as civilans nor as military actors but as what I call “sovereign women/gendered traitors”. Bambaragas’ mutual recognition and collective practices of assistance, secrecy, care and housing allowed women to navigate dangerous conflict environments and predatory privatized health governance and was, at times, what allowed women to keep their children alive and in their care.

Keywords: Armed Conflict/War
Gender/Sexuality
Health
Maternal and Child Mortality
Political Economy
Sex Work
Advisor: Krupa, Christopher
Wardlow, Holly
Socio-cognitive Dynamics of Knowledge Building Communities: A High-school Physics Case Study

The results of this research provide an account of advances in foundational knowledge of black-hole physics through analysis of idea improvement and social presence in Grade 12 Knowledge Building classes. The purpose of this study is to collect and analyze student discourse and interactions to uncover socio-cognitive dynamics in an online environment—Knowledge Forum®—designed to support Knowledge Building. Questions students raised were assessed along a continuum from simple clarification and fact-seeking to explanation seeking; explanations were analyzed along a continuum from unelaborated facts to elaborated explanations. Conversation thread length was analyzed, in addition to quality of foundational knowledge of physics represented in student notes, as judged by experts in modern physics. As a separate check on adequacy of foundational knowledge, one Grade 12 group was administered a test designed for first-year university students taking a course in cosmology. The Grade 12 students did as well as the university students. Social interactions were quantified within discussion threads using social presence to identify affective, cohesive and interactive markers of engagement. According to both expert judgment and co-occurrence of the broad array of measures of idea improvement and social presence, students demonstrated impressive levels of understanding black-hole physics. Additionally, all markers pointed to one group displaying especially high-levels of collective responsibility for community knowledge. Those results are consistent with the teacher's impression that a Knowledge Building esprit de corp characterized the most successful student group. Accordingly, exploratory work to develop an analytic tool was conducted — a tool to combine measures and indicators to allow teachers and students to monitor socio-cognitive markers of collective responsibility for community knowledge as work proceeded.

Keywords: building
knowledge
physics
presence
social
Advisor: Scardamalia, Marlene
Queer isn’t a Choice! Queer is my Family! Collaborative Performance as Affective Pedagogy

This research documents an applied theatre workshop for youth aged 10-13 and had two points of focus: the first was how young people and artist-educators collaboratively used theatre to learn about themselves, each other, and the world around them; and the second was about how young people from LGBTQ2S+ families used theatre and performance as a form of advocacy by sharing their stories and experiences through their artwork. Working alongside youth participants, this research attuned to the relational aspects of theatre creation by drawing on affective encounters through aesthetic learning. Youth and artist-educators were active agents in the research process guiding the path of inquiry as they shared their stories, wrote songs, choreographed movement, played with puppets, and made books. The applied theatre work was self-revelatory, deeply personal, and created a powerful space for the youth to understand their everyday experiences on their own terms. Applied theatre as an aesthetic and participatory art form materialized in the space between creation, story, and research, building an affective performance that encompassed the stories of participants as depicted through intra-actions, movements, and art.

Advisor: Goldstein, Tara