VictorJuiz/thesis huggingface dataset:
Tongue Pressure and Hyoid Kinematics in Dysphagia

This dissertation explores the relationships of tongue pressure and hyoid kinematics with swallowing function in healthy participants and in patients with oropharyngeal dysphagia post-stroke. The first chapter of this dissertation provides an overview of normal swallowing including the roles of the tongue and hyoid kinematics. Next, we discuss oropharyngeal dysphagia and the use of exercise rehabilitation programs that target tongue pressure. Chapter 2 is a systematic review exploring the current evidence base for tongue pressure training as an intervention for dysphagia. Our review deemed this intervention successful for increasing isometric tongue pressure generation, however generalization to swallowing function revealed mixed findings. As a result of this review, we identified limitations in reporting and design in prior studies that we addressed in our prospective studies (Chapters 5, 6). Expanding beyond the tongue, we designed a study in to examine variations in hyoid kinematics in healthy swallowing in Chapter 3 and obtained normative data. A retrospective study was then conducted in Chapter 4 using a large sample of patients presenting with risk of neurogenic dysphagia from varying etiologies. The normative data collected in Chapter 3 were used to classify hyoid parameters as typical or atypical and to explore the relationships of hyoid bone kinematics to unsafe swallowing in this study. Through this analysis we demonstrated significant associations between hyoid parameters and laryngeal vestibule closure parameters, however hyoid measures were not significant independent predictors of swallowing safety. Expanding on these analyses, a study was designed with the objective of quantitatively outlining patterns in swallowing (patho)physiology in a homogeneous cohort of patients presenting with impaired tongue strength post-stroke in Chapter 5. Following the characterization of swallowing in this cohort, Chapter 6 describes a tongue pressure treatment protocol designed to overcome limitations identified in Chapter 2. The intervention was implemented with one participant who presented with reduced tongue strength and swallowing safety. Improved tongue pressure generation and swallowing safety was achieved in this study, however limitations of this single case study design are discussed. Finally, we outline the overall findings and limitations of the studies undertaken in this dissertation in Chapter 7 and discuss future research directions arising from this work.

Keywords: Dysphagia
Hyoid
Stroke
Swallowing
Tongue
Videofluoroscopy
Advisor: Steele, Catriona M
The Emergence of Family Medicine and Its Impact on Primary Health Care: The Experience of India

Many low- and middle-income countries are introducing family medicine (FM) to strengthen primary care and primary health care (PHC). However, there is little research on how FM emerges in a new context and how FM can strengthen PHC. Insight into these areas can help ensure implementation is effective and achieves the desired outcomes: improved health and well-being. In my dissertation, I use multiple methods to explore these two objectives. First, I look at how FM emerges in multiple countries and the trajectory of implementation using comparative policy analysis. Findings suggest four essential components, that often take place over several decades, including government commitment, educational reforms, the development of professional organizations and stakeholder buy-in. Second, I explore the implementation of FM in India and the role of early cohort family physicians in this process using a qualitative descriptive study. Findings show they developed and implemented the first FM training programs and professional organizations that supported the field's spread. They played key roles as leaders, educators, mentors, and advocates. Third, I delve into the potential mechanisms by which FM strengthens primary care and PHC through the experiences of early cohort family physicians in India using a qualitative descriptive study. They are skilled primary care providers that support the ongoing training of family physicians and mid and low-level healthcare providers and motivate the workforce. They change how care is delivered by ensuring providers' skills match the needs and engage communities as partners in healthcare. They develop relationships with specialists ensuring appropriate referral systems and, when necessary, work with governments safeguarding access to the necessary resources. Finally, using a cross-sectional survey, I assess the current landscape of FM in India to understand the implementation of FM to date and the impact of postgraduate training on family physicians and their ability to practise. Findings suggest that FM training is associated with increased confidence and skills and consequently family physicians deliver a broad range of services. In our sample, almost half of family physicians work in the primary care sector, and a greater proportion of family physicians work in rural areas compared to physicians overall.

Keywords: Family Medicine
Implementation
India
Low and Middle Income Countries
Primary Care
Primary Health Care
Advisor: Bhattacharyya, Onil
Impact of Noise and Spike Initiation Properties on the Encoding and Transmission of Neural Information

Neurons use action potentials, or spikes, to process information. Different aspects of spiking, such as its rate or timing, are used to encode information about different features of an input. But noise can influence how robustly information is represented in each coding scheme. Additionally, information can be lost if neural representations are not transmitted with high fidelity to downstream neurons. In both cases, properties of the input (its amplitude and kinetics) and properties of the neuron (its spike initiation mechanism and excitability) impact neural information processing. In my thesis, I first investigated how axons are optimized to transmit spike-based representations. Using patch clamp electrophysiology combined with optogenetics, I showed that the axon of CA1 pyramidal neurons spikes transiently in response to sustained depolarization, in contrast to the soma and axon initial segment, which spike repetitively. These distinct spiking patterns are due to the differential expression of ion channels, supporting functional specialization of neuronal compartments. Specifically, low-threshold potassium channels (Kv1) cause the axon to behave as a high-pass filter, enabling high fidelity transmission of spike-based information so that the axon selectively responds to inputs with fast kinetics. Together with biophysical modeling, my findings demonstrate that spike initiation properties in each part of the neuron are well matched to the signals normally processed in that neuronal compartment. I then investigated how background synaptic activity (noise) affects rate and temporal coding of vibrotactile stimuli. Using patch clamp electrophysiology and dynamic clamp in vitro, I found that layer 2/3 pyramidal neurons in primary somatosensory cortex spike intermittently to inputs repeated at frequencies perceived as vibration. The fraction of inputs evoking a spike varies with input amplitude, enabling firing rate to encode stimulus intensity. Despite being small in amplitude, inputs are abrupt in onset, which allows them to evoke precisely timed spikes, even under noisy conditions. Unreliable spiking allows noise to produce irregular skipping, enabling spike times (patterns) to encode stimulus frequency. The reliability and precision of spikes depend on input amplitude and kinetics, respectively. With the help of simulations, my results show that noise helps multiplexed rate and temporal coding.

Advisor: Prescott, Steven A
Architecture and CAD Techniques for Efficient FPGA Implementation of Machine Learning and Other Applications

Field-programmable gate arrays (FPGAs) offer an alternative to application-specific integrated circuits (ASICs) that is attractive in scenarios where flexibility may be required or where chip volumes are not sufficiently high enough to justify the costs of a custom chip. The flexibility of FPGAs offer users the power/performance benefits of a custom hardware implementation, compared to software running on a processor, without committing to one specific design. However, the flexibility can lead to inefficiencies in terms of development time, area, performance, and power. FPGAs are used for a variety of applications and different optimizations can be applied to increase efficiency of FPGA implementations. This thesis considers techniques that can be applied to achieve efficient implementation of machine learning and other applications on an FPGA from the perspectives of architecture and computer-aided design (CAD). We consider the use of a high-level synthesis (HLS) tool to synthesize an accelerator for deep convolutional neural networks (CNNs) on an FPGA. We implement a complete end-to-end system running on an Arria 10 SoC FPGA. The accelerator implements zero-skipping and reduced-precision convolution with minimal impact on accuracy. We evaluate various versions of the accelerator through software changes and tool constraints alone. Then, we propose architecture changes to the carry-chain architecture in FPGAs to improve the resource utilization of binarized CNNs (BNNs). We add additional carry-chain circuitry that propagates sum instead of the carry. We demonstrate that we are able to reduce FPGA resource utilization while keeping the additional circuit area small. Lastly, we propose to re-map some of the look-up-tables (LUTs) to use the existing carry-chain architecture in order to increase performance by adding a post-LUT mapping step to the FPGA CAD flow. Using a subject graph that closely matches the underlying hardware, we are able to select critical paths to take advantage of the existing fast dedicated carry-chain routing.

Keywords: FPGA architecture
FPGA CAD
Machine Learning
Advisor: Anderson, Jason H
Quasiconformal Geometry of Metric Measure Spaces and Applications to Stochastic Processes

We study three topics of quasiconformal and quasisymmetric geometry; the quasisymmetric embeddability of metric Sierpi\'nski carpets, the quasisymmetric embeddability of weak tangents and the conformal dimension of stochastic spaces. The common tools we use to attack these three topics are different versions of Moduli and the convergence of spaces. For the first problem, the problem of quasisymmetrically embedding spaces homeomorphic to the Sierpi\'nski carpet into the plane, we use transboundary modulus to study it. This allows us to give a complete characterization in the case of dyadic slit carpets. Every such slit carpet $X$ can be embedded into a ``pillowcase sphere" $\widehat{X}$ which is a metric space homeomorphic to the sphere $\mathbb{S}^2$. We show that $X$ can be quasisymmetrically embedded into the plane if and only if $\widehat{X}$ is quasisymmetric to $\mathbb{S}^2$ if and only if $\widehat{X}$ is Ahlfors $2$-regular. For the second problem, the problem of quasisymmetric embeddability of weak tangents of metric spaces, we first show that quasisymmetric embeddability is hereditary, i.e., if $X$ can be quasisymmetrically embedded into $Y$, then every weak tangent of $X$ can be quasisymmetrically embedded into some weak tangent of $Y$, given that $X$ is proper and doubling. However, the converse is not true in general; we will illustrate this with several counterexamples. In special situations, we are able to show that the embeddability of weak tangents implies global or local embeddability of the ambient space. Finally, we apply our results to Gromov hyperbolic groups and visual spheres of expanding Thurston maps. For the third problem, the conformal dimension of stochastic spaces, we develop tools related to the Fuglede modulus to study it. In order to achieve this goal, we study the conformal dimension of deterministic and random Cantor sets and investigate the situation of conformal dimension $1$. We apply our techniques to construct minimal (in terms of conformal dimension) planar graph. We further develop this line of inquiry by proving that a "natural" stochastic object, the graph of the one dimensional Brownian motion, is almost surely minimal.

Keywords: Brownian motion
Conformal dimension
Gromov-Hausdorff convergence
Quasiconformal geometry
Quasisymmetry
Sierpinski carpet
Advisor: Binder, Ilia I.
Beyond Pleasure: Effects of Depression, Anhedonia, and COVID-19 Stress on Hedonic and Eudaimonic Reward Functioning

Reward processing encompasses multiple psychological processes, including appraisals of the incentive value of a reward (reward valuation), behavioral motivation to earn it (reward wanting), and affective responses to its receipt (reward liking). Disruptions in reward processing and the vulnerability of this system to chronic stress are argued to contribute to the development of a depressive disorder and anhedonia specifically. However, research has been limited to examining responses to “hedonic” rewards as the study of “eudaimonic” reward processing presents methodological challenges. Addressing these aims, this study developed the Hedonic and Eudaimonic Incentive Delay Task (HEID) for a comprehensive assessment of reward processing across multiple reward domains, including hedonic (HE), eudaimonic (EU), and neutral-intrinsic (NT-I) rewards. The central objectives were to examine the effects of (1) depression and anhedonia-related symptoms (e.g., wellbeing, anhedonia), (2) chronic stress exposure, using the COVID-19 pandemic and case fatality rates (CFR) as objective stress measures, and (3) interventions, such as the cultivation of dispositional mindfulness and self-affirmation, on reward processing across multiple reward domains. Two samples of participants were recruited, before (N = 180) and during the COVID-19 pandemic (N = 189), completing self-report measures of depression, anhedonia, wellbeing, and mindfulness, and the HEID. Participants during COVID-19 were also randomly assigned to one of three induction conditions (Stressor Salience, Self-Affirmation, Control) to investigate stress and intervention effects. Consistent with hypotheses, (1) depression and anhedonia were associated with impaired reward processing; however, depression was more robustly associated with impairments in reward wanting, particularly the wanting of EU rewards, while reward valuation and liking were uniquely implicated in anhedonia. Chronic stress hypotheses (2) were partially supported, such that COVID-19 was associated with blunted reward wanting across reward domains (particularly NT-I), but not reward valuation and liking. Consistent with theory (3), self-affirmation helped buffer the effects of stress on reward wanting, but only at high CFR, while dispositional mindfulness was associated with greater wellbeing during COVID-19 by virtue of enhanced reward valuation and liking. This study provides new insights into reward pathways underlying stress, depression, and wellbeing/anhedonia, shedding light on disruptions to target in treatment.

Keywords: Depression
Eudaimonia
Mindfulness
Reward
Self-Affirmation
Stress
Advisor: Segal, Zindel V.
Farb, Norman A.S.
The Ghost in the Machine: Organ Transplantation and the Phenomenology of Embodiment

This dissertation examines phenomenological embodiment via an analysis of the experiences of solid organ transplant recipients. Attending to breakdown at the level of the body, I show that embodiment is a duality made up of (a) an actor’s set of “embodiment knowledge,” developed via practical activity throughout the lifecourse and (b) the flesh and blood of their physical body. Chapter two deploys this understanding of embodiment to improve our understanding of the illness experience. Specifically, I demonstrate how thinking about illness from the perspective of phenomenological embodiment clarifies the existing literature on the illness experience and provides a coherent, generalizable framework with which to understand the subjective experience of illness. Chapter three examines bodily breakdown in the context of transplant institutions, and shows that breakdown at the level of the body provokes a situation that facilitates the discursive construction of the body in the image of biomedicine. Chapter four attends to the experience of rehabilitation after transplant surgery. In this chapter, I show that embodiment is not a discrete phenomenon (as it is generally understood in contemporary sociological theory). Rather, embodiment is best understood as being made up of distinct but overlapping phenomenological layers. Chapters two-four of this dissertation are presented as stand-alone articles.

Keywords: Disability Studies
Embodiment
Medical Sociology
Organ Transplantation
Sociology of Culture
Advisor: Leschziner, Vanina
Computational Tools and Analyses for Improved Inference of Variant Effects

Personalized medicine requires rapid and accurate classification of pathogenic human variation. With over 50% of clinically interpreted missense variants classified as “variants of uncertain significance” (VUSes), multiple approaches are needed to improve variant interpretation. Multiplexed assays of variant effect (MAVEs) can experimentally test nearly all possible missense variants in selected protein targets, while computational methods seek to infer missense variant impacts using statistical modelling. Here I describe work to assist and exploit both MAVE and computational studies.To assist in planning and to promote collaboration and efficient communication for MAVE studies, I developed: 1) strategies to prioritize genes likely to have a greater impact on clinical variant interpretation, 2) MaveQuest, a resource to help researchers identify MAVE target genes and explore potential assays, and 3) MaveRegistry, a community resource for sharing MAVE progress and finding collaborators. To compare the performance of variant effect predictors and to exploit both experimental and computational information about variant impact, I 1) assessed computational variant effect predictors using a large prospective cohort, and 2) developed a pipeline to screen human pseudogenes for which different genetic variant interpretation might re-classify these pseudogenes to be protein-coding genes, refining human genome annotation.

Advisor: Roth, Frederick P
Predictors of and Reasons for Early Discharge from an Inpatient Withdrawal Management Service

Early discharges, also known as against medical advice discharges, are a significant concern in inpatient withdrawal management settings. Early discharges are associated with negative outcomes for patients and are costly for the healthcare system. A recent scoping review found gaps in the literature regarding patient perspectives, and a lack of research exploring predictors of early discharge according to demographic factors such as sex or gender which are known to influence healthcare experiences. It is vital to advance our understanding of patient perceptions of early discharges and what may predict them in order to prevent early discharges from occurring.The aim of this research was to investigate possible predictors of early discharge and patient experiences of early discharge from an inpatient withdrawal management service in Toronto, Ontario, Canada. This aim was accomplished using 2 studies. A retrospective cohort study using administrative health data was conducted to examine independent predictors of early discharge among patients admitted to an inpatient withdrawal management service between 2016 and 2020. Sex-stratified analyses using logistic regression and generalized estimating equations revealed that weekends and younger age were the strongest predictors of early discharge for both males and females. Among females only, being part of an ethnic minority group predicted early discharge. A qualitative descriptive study was conducted to explore patient perceptions of precipitants and processes related to early discharge. Thirteen people who had recently experienced an early discharge participated in the study and reported that precipitants to early discharge included external pressures, concerns about COVID-19, and dissatisfaction. Participants also described hitting a wall or reaching a breaking point prior to early discharge. Further, they often described difficult conversations about their desire to leave early and had mixed perceptions of their early discharge experience. This research demonstrates that there may be opportunities to prevent early discharges by responding to sources of dissatisfaction and exploring contributing factors during high-risk times such as weekends. Further, this research indicates that patient experiences could be improved by modifying processes associated with early discharge when they cannot be prevented.

Keywords: addiction
against medical advice
early discharge
inpatient
substance use disorder
withdrawal management
Advisor: Cleverley, Kristin
How Approaches to Value Creation, Appropriation, and Distribution by Private-sector Organizations Address the United Nations' Sustainable Development Goals

This dissertation investigates how organizational approaches to value creation, appropriation, and distribution affect the achievement of the United Nations' Sustainable Development Goals (SDGs). My objective is to contribute to strategic management theory by showing how organizational governance and design influence the achievement of socioenvironmental objectives.The first core chapter investigates how e-commerce firms operate in disadvantaged urban communities. The study argues that spatial inequalities are associated with socioeconomic disparities experienced by disenfranchised consumers living in Brazilian favelas (urban slums). E-commerce firms make fewer products available and charge higher delivery prices to customers inside Brazilian favelas than they do to customers immediately outside favelas, despite the absence of infrastructure impediments at the favela borders. This phenomenological chapter investigates firm heterogeneity in these practices. The second core chapter of my dissertation (authored jointly with my doctoral supervisor, Professor Anita M. McGahan) investigates how firms design incentives compatible with environmental protection. The new institutional economics identifies the challenges of governing common-pool resources and the difficulties of internalizing environmental externalities into regular market transactions. New stakeholder management theory suggests that firms may avoid the tragedy of the commons by aligning incentives with critical proximate stakeholders. This chapter integrates and evaluates these theoretical claims by analyzing the activities of Natura, a Brazilian cosmetics company, regarding Amazon rainforest preservation. The third core chapter of my dissertation investigates the unintended consequences of efforts to enfranchise low-income favela dwellers into the labor market. This research contributes to the management literature by showing that, while interventions designed for enfranchisement may effectively achieve targeted economic outcomes, they paradoxically may lead participants into discriminatory systems where they are stigmatized on the exact same characteristics of their prior disenfranchisement. The SDGs were developed in 2015 through widespread consultation across countries, governments, private-sector leaders, expert scholars, and other stakeholders in the global community. These goals set an agenda for addressing the most pressing and important problems of the 21st century. The central contribution to knowledge of this dissertation is to identify the theoretical and phenomenological implications of this agenda in three empirical settings where these problems are particularly acute and compelling.

Keywords: Climate Change
Global South
Mixed Methods
New Stakeholder Theory
Poverty and Inequality
Sustainable Development Goals
Advisor: McGahan, Anita