VictorJuiz/thesis huggingface dataset:
Regional and Cross-Network Brain Dynamics in Acute and Chronic Pain

Chronic pain is a major societal burden, affecting nearly 1 in 5 Canadians. Chronic pain patients demonstrate a great degree of variability in the way they perceive and cope with pain, experience symptoms, and respond to treatment. These individual differences may in part be due to the brain dynamics associated with the processing and modulation of nociceptive signals. Thus, the overall goal of this thesis was to understand the role of regional brain dynamics in acute and chronic pain. Towards this goal, I first established a link between regional BOLD signal variability and pain sensitivity and the effect of pain on cognitive performance in healthy individuals. I then examined frequency-specific regional BOLD signal variability abnormalities in chronic pain patients with ankylosing spondylitis (AS) and related these abnormalities to pain intensity. Finally, I investigated the brain plasticity in regional and cross-network brain dynamics that subserve successful response to ketamine therapy in patients with refractory chronic neuropathic pain (NP). Healthy individuals and chronic pain patients (AS and NP) underwent a resting-state fMRI scan and completed a psychophysical session and a battery of questionnaires (e.g., assessing pain intensity etc.). The main findings of this thesis are: 1) Regional BOLD signal variability within the ascending nociceptive pathway and networks of the dynamic pain connectome are increased in healthy individuals who are less pain sensitive and have good cognitive performance during a pain-interference task; 2) Patients with AS exhibit elevated regional frequency-specific BOLD signal variability in the ascending nociceptive pathway and networks of the dynamic pain connectome; these abnormalities are related to chronic pain intensity; 3) Ketamine reduces regional BOLD signal variability within the default mode network (DMN); and 4) Effective ketamine-treatment outcome is associated with decreased static functional connectivity of the DMN with the salience network and with the sensorimotor network. Therefore, this thesis demonstrates that regional BOLD signal variability serves as a functional metric that underlies individual differences in acute pain, and the clinical symptoms and treatment outcomes in chronic pain. These findings provide novel insight into chronic pain etiology that serve to advance the knowledge base needed to develop new treatment options.

Keywords: Chronic pain
fMRI
Advisor: Davis, Karen D
Automated Interconnect Synthesis and Optimization for FPGAs

One of the key challenges for the FPGA industry going forward is to make the task of designing hardware easier. A significant portion of that design task is the creation of the interconnect pathways between functional modules. Interconnect synthesis tools and Network-on-Chip architectures have been developed to solve this problem. They allow the designer to specify desired connectivity at an abstract logical level, and automate the physical details of the interconnect implementation. In this work, we introduce a new approach to automatically synthesizing interconnect, based on the composition of many simple hardware primitives that each perform an elementary routing, translation, storage, or delay function. This approach is embodied in a new design tool called GENIE, which produces RTL implementations of complete systems containing a designer’s functional modules connected with automatically-generated interconnect, whose generation is guided by an initial logical system specification. GENIE leverages its piecemeal approach to interconnect generation to offer more automation and optimization capabilities to the designer than are provided by existing tools. One such capability is the generation of interconnect for “fine-grained” applications in which the overall small size of the system, need for simple communication protocols, and tight latency requirements would incur too high of a performance or area penalty to make productive use of automation with existing methods. We also introduce a new type of user design specification called synchronization constraints that allow GENIE to build low-cost, backpressure-free interconnect for applications with fixed-latency modules and achieve correct cycle-level timing using a minimum amount of automatically-inserted delay elements. GENIE’s other optimization capabilities include automatic clock domain crossing insertion, interconnect pipelining, and a limited form of network topology generation guided by application performance requirements. Using both FPGA synthesis and RTL simulation of the generated systems, we evaluate GENIE and its features using two applications that serve as extensive and detailed case studies. We also compare GENIE against other system generation tools, NoC architectures, and hand-written RTL interconnect implementations, and are able to show equivalent or higher quality implementations with lower design effort.

Keywords: Automation
CAD
FPGA
HLS
Interconnect
NoC
Advisor: Rose, Jonathan
Intersections of Ethics of Indigenous Health Research and Health Research Education

Health research involving Indigenous peoples is regulated by guidelines based on the ethics of Indigenous health research, which establish routes to knowledge development in order to support and improve health for Indigenous communities. Despite these guidelines, health imbalances remain and continue to negatively impact Indigenous peoples. This thesis explores some of the barriers and strengths of ethical guidelines of Indigenous health research in Canada. Using a community-based approach, this research shifts the focus away from a study of Indigenous peoples themselves, to a study of the practices that health researchers employ when conducting health research involving Indigenous peoples. An online survey was developed and distributed via email and through social networks to health researchers who work in the field of Indigenous health research. The survey consisted of 22 questions using and a Likert scale (Likert, 1932) to explore perceptions of ethical guidelines in use by researchers who engage in Indigenous health research. After data quality control analysis, 228 respondents were considered valid and constituted the data set. Results suggest a general level of agreement (Somewhat Agree) with the value of the health ethical guidelines used by researchers. High agreement was found for basic items such as ethical guidelines being easy to access and the amount of information offered was appropriate. However, low agreement was found on items that rated the perceived characteristics of ethical guidelines: their clarity, and whether they reflected the current social context of Indigenous peoples; the inclusion of Indigenous paradigms inside ethical guidelines and whether the guidelines enhanced health researchers’ understanding of Indigenous worldviews. Results also describe some other characteristics of Indigenous health research, such as exploring who is researching what, when, and how with special attention to research methodologies, approaches and perceived engagement with Indigenous communities. A major implication of these results suggests the need for the inclusion of Indigenous research perspectives in health research and health research education much more broadly if they are to effectively support Indigenous healthier communities.

Keywords: Community Based Research
Health Education
Health Research
Indigenous Ethics
New Knowledge
Research Practices
Advisor: Brett, Clare
Denaturalizing Information Visualization

This dissertation investigates how, behind the recent proliferation of information visualization technologies, a number of opaque epistemic conventions structure distinct practices of data analysis, sensemaking, argumentation, and persuasion. The dissertation's primary claim is that contemporary infovis practices and tools naturalize specific representational forms and modes of interaction (e.g. ocularcentric objectivity) at the expense of others. It examines this naturalization process through a series of four interconnected case studies that consider, in turn, the translation of 2D images and graphics into tangible 3D objects; the development of two multimodal visualization projects; scale experiments in a virtual reality-based visualization environment; and an empirical study of 14 blind and visually impaired citizens interacting with tactile data objects. By surfacing specific naturalizations and attempting to denaturalize them, these four case studies illuminate a host of critical issues (e.g. a long-simmering tension between truth and aesthetic concerns) raised by the appearance of new interactive approaches to visualization. In doing so, they also demonstrate alternative visualization methods that might be deployed in service of a more critical infovis practice. As a result, the dissertation contributes to an emerging body of critical infovis research that spans domains ranging from HCI to critical data studies. Visualization media has become the de facto currency of data interpretation, and a rich and nuanced understanding of the epistemology of information visualization is absolutely necessary. Discussions around the challenge of multimodal representation, the tendency for new media to produce epistemic conflict, and the benefits of critical data literacy, all of which appear in the dissertation, will help colour in this rich and nuanced picture of visualization.

Keywords: 3D Printing
Critical Data Studies
Data Literacy
Infovis
Representation
Visualization
Advisor: Ratto, Matt
Looking for Beyond the Standard Model Physics in Dijet-Plus-Lepton Final-State Events Collected with the ATLAS Detector

A search for a new resonant state decaying exclusively to two quarks in events with at least two jets and one isolated charged lepton using 139 fb−1 of proton-proton collision data collected by the ATLAS detector at √ s = 13 TeV is presented. Requiring a charged lepton in dijet final states provides sensitivity to extensions of the Standard Model which predict the production of dijet resonances in association with leptonically-decaying vector bosons or top quarks. Whereas inclusive searches are limited to resonance masses greater than 1 TeV due to jet-based triggers which have a minimum jet transverse momentum of about 400 GeV, lepton triggers can be as low as 24 GeV, thereby permitting access to resonance masses of order 100 GeV. The search presented in this thesis considers a dijet invariant mass range between 0.22–6.3 TeV. The largest deviation between the number of observed events and the Standard Model background estimate was found at a dijet invariant mass mjj = 1.3 TeV with a global statistical significance of 0.5 standard deviations. In the absence of a statistically significant deviation of the data from the background expectation, exclusion limits are set at a 95% confidence level on the presence of generic Gaussian-shaped signals of different masses and widths. Such signals are excluded with cross sections ranging from 40–0.03 fb between 0.25–6.0 TeV. Limits are also set in the context of a Technicolor model and a Simplified Dark Matter model. A follow-up search using a machine learning approach is discussed last.

Keywords: ATLAS
BSM
CERN
dijet resonance
leptons
LHC
Advisor: Krieger, P.
Subgraph Density and Graph Clustering

Graph clustering, also often referred to as network community detection, is an unsupervised learning task. It is the process of grouping vertices into sets of vertices that share common relations. Graph clustering is a pivotal topic in the field of network science. It has applications in various areas such as the analysis of chemical, biological and social networks and any other area where a macroscopic systems point of view is important. Currently, three open problems emerge from the literature: determining if a graph is clusterable before any clustering effort is undertaken, assessing the quality of clusterings identified by an algorithm and the development of fast accurate clustering techniques. In this dissertation, we attempt to answer these three open questions. We use heterogeneity in local densities to determine whether a graph is suited for clustering, if it has a clustered structure to begin with. We also compare global, mean intra-cluster and mean inter-cluster densities to assess the quality and strength of the clusters identified by any clustering algorithm. Finally, as a minor contribution, we examine the possibility of using intra-cluster density maximization as a clustering algorithm. Our clusterability test is shown to be more accurate than techniques proposed in the very recent literature and to rely on fewer assumptions. We demonstrate how heterogeneous densities can be used to identify graphs that display a clustered structure. On the topic of clustering quality assessment, we offer an alternative to the very widely used and problematic modularity quality function. This alternative is consistent with the sets of axioms defining good clustering quality functions, which have been presented by numerous authors. We base our measures on our own definition of clustering quality and accompanying necessary and sufficient conditions. Our approach is shown to be more responsive to connectivity patterns than both modularity and conductance measures. Finally, we also explore intra-cluster density as an objective function to be maximized, for the purpose of clustering. We show how an ensemble optimization meta-heuristic may offer a solution to the clustering problem.

Keywords: Data Science
Graph Clustering
Unsupervised Learning
Advisor: Lawryshyn, Yuri
Pardalos, Panos M.
How to Work Wisely: Work Wisdom Arising from Three-dimensional Mindfulness

While research on the benefits of mindfulness for organizational well-being and performance has dramatically increased during the past decade, rarely has it revealed obstacles experienced by practitioners in integrating mindfulness into work. Further, I argue that the literature on mindfulness fails to fully integrate three dimensions of Buddhism: virtue, concentration and wisdom, referred to as ‘Three-Dimensional Mindfulness,’ which together increase the effectiveness of mindfulness in ending stress. To facilitate this integration, I explore two research questions: 1) ‘How do Buddhist-informed and secular-informed mindfulness practitioners reduce work stress and improve work performance through mindfulness practice in work-life?’ and 2) ‘What obstacles do they experience in integrating mindfulness into work?’ Critical reflexivity and critical phenomenology are employed as a methodological framework for qualitative interviewing. Data are drawn from interviews with 21 long-term Buddhist mindfulness practitioners, 16 of whom are from Buddhist traditions and 5 from secular traditions. Findings show that practicing Three-Dimensional Mindfulness helped both groups reduce work stress and improve work performance. However, both groups constantly experienced internal difficulties of not being able to accept stress instantaneously and external difficulties due to unsupportive external work conditions and attributing causes of stress to these conditions. To embrace, transform or overcome these difficulties, participants tried to put more effort into practicing Three-Dimensional Mindfulness and/or change or accept external work conditions. However, some external difficulties, such as the contradiction between compassion and competition, were viewed by some participants as more complicated to overcome. In handling these difficulties, participants showed four patterns: A) prioritizing work, B) prioritizing Three-Dimensional Mindfulness, C) not prioritizing either, and D) combining them. Most Buddhist-informed participants fell within the first three patterns; secular-informed participants and one Buddhist-informed participant fit the last pattern. Patterns A and C show positive organizational outcomes of resilience and retention, while Patterns B and D have mixed results of resilience or resistance and retention or turnover. To remedy this disconnect between Three-Dimensional Mindfulness and work, I propose that organizations align their values with Buddhist values. These findings contribute to the fields of adult education, Buddhist studies and human resources management in transforming work-life. Keywords: mindfulness, Buddhist wisdom, work stress, organizational values, well-being, virtue

Keywords: Buddhist wisdom
mindfulness
organizational values
virtue
well-being
work stress
Advisor: Magnusson, Jamie
A Cognitive Work Analysis of a Pedagogical Documentation Technology in Ontario's Kindergarten Program

Abstract Research has shown that factors related to the home learning environment are roughly twice as significant in influencing the social and cognitive development of young children as any factors related to preschool (Siraj-Blatchford, Taggart, Sylva, Sammons, Melhuish, 2008). Therefore, maintaining a reciprocal connection between the home learning environment and school has become a critical component of early childhood educational programs in Canada. Recently, early childhood practitioners have been turning to pedagogical documentation technology (PDT) to forge this connection. This study examined the impact of a PDT, called Storypark, on the home-school connection in 11 kindergarten classrooms at four schools in a large, urban school district in Ontario. By applying Vicente's (2003) Human-tech framework to cognitive work analysis (CWA), this study followed a design research methodology to examine the impact of and promising practices for PDT use in Ontario’s Kindergarten Program. Eight lessons pertaining to PDT and two lessons pertaining to CWA resulted from these analyses. PDT lessons showed that PDT supported: 1) Parent-educator communication, 2) The parent-educator relationship, 3) Parents’ understanding of their children’s classroom learning, 4) Educators’ and parents’ understanding of The Kindergarten Program curriculum, 5) Conversations between parents and their children, 6) Student learning and 7) Parents’ involvement in their children’s learning. However, while PDT supported these areas of the home-school connection, the eighth PDT lesson showed that the Human-tech relationship could be improved to support a stronger home-school connection. CWA lessons showed that CWA: 1) Predicted the extent to which a PDT was successfully adopted and 2) Provided useful information about which Human-tech factors need to be modified in order to support a more effective adoption of PDT. More specifically, factors pertaining to the political and organizational levels of the work environment were identified. This thesis makes important contributions to a growing evidence base, which demonstrates the positive impact that PDT can have in promoting educator-parent communication and partnerships, parent-child conversations and student learning in early childhood educational settings. Furthermore, it is the first study of its kind to identify promising practices for PDT use in the context of an early learning program in Canada.

Keywords: Digital
Documentation
Kindergarten
Ontario
Pedagogical
Technology
Advisor: Woodruff, Earl
Ligand Chemistry and Ultrafast Carrier Dynamics of Perovskite Quantum Well Photovoltaics

Metal halide perovskites are solution-processed materials that exhibit remarkable optoelectronic properties combined with the prospect of inexpensive manufacturing. Bulk 3D metal halide perovskite lattices exhibit limited stability, in part a result of ions within their lattice that are labile; and rapid decomposition in the presence of moisture. 3D perovskites can be rendered into two-dimensional perovskite quantum wells (PQWs), and these are stabilized and protected by van der Waals-bonded organic molecular ligands, leading to longer material lifetimes. Mixtures of variably confined PQWs lead to new photophysical properties that have important consequences for light harvesting and light emitting devices. In this thesis I present new ligand chemistry and ultrafast photophysical properties of next-generation mixed dimensionality perovskite materials. First, I use the novel ligand allylammonium to synthesize PQW thin films with superior well width monodispersity compared to conventional ligands. This results in a smooth energy landscape and enhanced photovoltaic performance and is the first study to determine that highly confined PQWs act as traps in otherwise dimensionally pure films. Next, I use another novel ligand, 4-vinylbenzylammonium, to form 2D/3D mixed dimensional heterostructures whose interfaces can be photochemically crosslinked to improve the ambient and operational stability of solar cells, while also improving their performance to exceed 20% PCE. Lastly, I study ultrafast energy and charge transfer processes between mixed PQWs and organic dye ligands. I use ultrafast transient absorption and two-dimensional electronic spectroscopy to determine that interwell exciton transfer occurs on timescales of 100s of femtoseconds, whereas charge transfer occurs over 10s – 100s of picoseconds. When PQWs are synthesized using naphthalenediimide ligands, subpicosecond electron transfer from PQWs to organic ligands is observed, leading to the formation of charge separated states between the organic and inorganic components of the type-II heterostructure. The contributions within this thesis provide new understandings of how PQW ligands can be used to alter ultrafast photoinduced dynamics; tailor molecular interfaces; and control size polydispersity in lead halide perovskite quantum wells towards more efficient and stable optoelectronic devices.

Keywords: Exciton
Ligand
Perovskite
Photovoltaic
Quantum Well
Ultrafast
Advisor: Kelley, Shana O
Sargent, Edward H