VictorJuiz/thesis huggingface dataset:
Using Electronic Medical Records to Assess and Improve Primary Care Physicians’ Performance of Chronic Disease Management in Ontario
Keywords: Electronic health records
Electronic medical records
Health informatics
performance measurement
Primary care
Quality improvement

Through five original studies, this thesis studies if and how electronic medical records (EMRs) can be used meaningfully to target improvements in chronic disease management in primary care practices in Ontario. The thesis answers four areas concerning primary care EMRs. First, it identifies if EMRs can be used to accurately identify patients with chronic disease (COPD). Second, it studies if EMR systems can measure primary care physicians’ adherence to clinical practice guidelines for patients with respiratory or cardiovascular diseases (CVD) or risk. Third it looks at if EMRs can be used to assess provider or patient characteristics that are associated with the provision or receipt of guideline adherent care respiratory or vascular disease management. Finally, this thesis examines the barriers to and facilitators for the adoption and routine use of EMR tools designed to increase guideline-adherence in primary care. Identifying patients with certain conditions is essential to target quality improvement initiatives and audit current performance. The thesis demonstrates that EMRs could be used to accurately identify patients with COPD. Aspects of chronic disease care, namely primary care physicians’ adherence to clinical practice guidelines and quality indicators for CVD and COPD are possible to measure when they are quantifiable or coded in semi-structured or structured formats in the EMR. It is possible to link EMR data to external data sources to investigate if there are provider or patient characteristics associated with meeting the quality indicator criteria (including the effects of health service utilization data, socioeconomic data and clinical data). This thesis provides insight into important considerations for building a quality improvement intervention using EMR data as a platform or data source by identifying key barriers to, and facilitators for the adoption of EMR-based tools designed to increase guideline-adherence in primary care. We identified key limitations to using EMR data to measure primary care quality, which would be important to consider in future efforts to use EMRs for primary care quality improvement and performance management. It is essential that policymakers take into consideration sociotechnical aspects of the healthcare system and delivery when considering the use of EMRs for quality improvement.
Computational Analysis of Arguments and Persuasive Strategies in Political Discourse
Keywords: Argumentation analysis
Computational linguistics
Framing analysis
Machine Learning
Persuasive strategies
Reputation defence strategies

Various persuasive strategies are employed in advancing argumentation. This dissertation presents the first computational work in analyzing persuasive strategies in monological and dialogical argumentation in natural language. I begin with reputation defence strategies and show to what extent human annotators agree on these strategies. I present the first manually annotated corpus of parliamentary debates annotated with the most agreed upon face-saving strategies and show that linguistic features automatically extracted from the text of debates can differentiate between these strategies. Having shown the effectiveness of discourse parsing features in the classification of reputation defence strategies, I hypothesize that by directly using the effective features for discourse parsing, the classification results can be improved. My experiments validate this hypothesis and show that the developed methods can automatically label speeches with these strategies. I then explore whether we can automatically predict the language of face-saving in speeches and show that by leveraging the contextual information of the speeches, we can reliably distinguish between reputation defence from non-defence. I further investigate whether we can automatically classify statements in face-threatening and face-saving speeches based on truthfulness using the effective linguistic features introduced in the prior literature and show that while some of these features help identify the expression of dodge, they are not very effective in identifying the truthfulness of the statements. I further operationalize framing analysis as a classification task and show that neural language models can capture the abstract representations of frames more effectively. My experiments also show that frames are transferable across genres. Finally, in collaboration with several researchers, we examine to what extent expert and lay annotators can evaluate argumentation aspects, and show that the agreement of both groups is limited.
Associations of Amyloid Deposition and FDG Uptake in Aging and Cognitively Impaired Elders With and Without Moderate to Severe Periventricular White Matter Hyperintensities Using Simple Machine Learning Techniques
Keywords: Amyloid
Dementia
PET

Abstract Background: Cerebral small vessel disease (SVD) often coexists with Alzheimer’s Disease (AD), but subjects with significant SVD were usually considered mixed disease and excluded from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and other international cohorts. We use 2 machine learning algorithms (random forests (RFs) and K-means clustering) and 2 radiopharmaceuticals (18F-Florbetabir and 18F-FDG) to study associations of periventricular white matter hyperintensity (pvWMH), amyloid deposition and 18F-FDG uptake in aging and cognitively impaired elders. Methods: A multi-center, observational, prospective cohort study was designed to acquire data in subjects with significant pvWMH. Baseline data from the first 57 subjects recruited through tertiary memory clinics or stroke prevention clinics formed the basis for analysis. All subjects had a 3T MRI, 18F-Florbetabir PET and neurological evaluation; 18F-FDG PET was available in 55. A matched cohort of 57 subjects with minimal pvWMH was derived from ADNI. PETs were interpreted by 2 dual certified radiologists/ nuclear medicine physicians with MIM software (MIM Software Inc, Cleveland, Ohio) and processed to obtain quantitative data in regions of interest (ROIs). Algorithms programmed in MATLAB were used to classify 18F-Florbetabir PET as positive or negative for amyloid deposition, suggest ROIs for classification, and study associations with pvWMH. Discussion: This work complements current data on associations of amyloid, 18F-FDG and pvWMH. RFs (supervised) and K-means clustering (unsupervised) had similar classification accuracy for 18F-Florbetabir PET with clinical interpretation as the gold standard. ROIs for classification were, most commonly: the left posterior cingulate, left precuneus and left middle fontal gyrus; key nodes of the default node network, where amyloid deposition preferentially begins in the brain of patients with AD. Subjects with significant pvWMH had slightly more amyloid deposition across a spectrum of ROIs compared with their matched ADNI cohort. 18F-FDG uptake was slightly higher in several cortical ROIs with lower uptake in the basal ganglia. Possibly these findings can be explained by poor amyloid clearance related to venous collagenosis in subjects with significant pvWMH coupled with metabolic compensation. Future research will include evaluation of 2-year follow-up, correlation of PET with MRI, neurological assessment and ApoE4 status in the full cohort of subjects.
Peter and Julian: An Analysis of Pears and Bream’s Tenor-Guitar Performances
Keywords: Benjamin Britten
Julian Bream
performance
Peter Pears
tempo analysis

This project seeks to understand the artistic renown of the Peter Pears (1910 – 1986) and Julian Bream (b. 1933) duo by conducting a thorough analysis of their performance output as a tenor-guitar duo. Despite the acclaim they received during their lifetimes, the duo thus far has been unduly neglected in scholarly writings, and their performances, while widely celebrated, have never been analyzed. This problem is addressed primarily through the analysis of the duo’s album Music for Voice and Guitar (1965) and the development of a performance-practice guide to their distinct musical style. The analysis employs a unique methodology that combines empirical and descriptive analytical tools in order to better understand the duo’s performances from a wide array of perspectives. The resulting performance-practice guide covers several interpretive techniques that are found throughout the body of performances. This guide not only reveals the musical depth and creative choices that two of the twentieth century’s most lauded performers employed, but it can also serve as inspiration for future musicians. Indeed, as I demonstrate near the end of my thesis, the duo’s interpretations are based on principles that can be applied to other musical ventures. The overarching goal of this thesis is that the duo’s creative interpretations may help to generate ideas for other musicians to create their own meaningful musical performances.
Three Essays on the Interplay between Entrepreneurship, iInnovation and Socioeconomic Phenomena
Keywords: entrepreneurship
innovation

My dissertation is composed of three chapters that explore the relationships between entrepreneurship, innovation, and the broader economic and social dynamics that are shaping the modern world. In the area of entrepreneurship and innovation, one aspect that is often examined is that of the relationship between individuals and firms. In my work, I examine the role that social and economic factors play in shaping the environment within which entrepreneurs and innovators work and grow. The first chapter of the dissertation focuses on the impact of immigration on entrepreneurship and explores the consequences of start-up location on the number of immigrant-founded start-ups and their performance. I find that immigration has a positive effect on immigrant entrepreneurship only in non-enclave areas. Additional analyses uncovering the mechanism suggest that discrimination faced by immigrants in non-enclave areas might be the main driver for the increased entrepreneurship. In a second chapter on entrepreneurship, jointly authored with John Voorheis, we explore how entrepreneurship influences income inequality and social mobility in the United States. Shedding light on who gains from entrepreneurship is crucial to understanding whether investments in incubating potentially innovative start-up firms will produce socially beneficial outcomes. We find that entrepreneurship increases income inequality. Further, we find that this increase in income inequality arises because almost all the individual gains associated with increased entrepreneurship accrue to the top section of the income distribution. In the third chapter, joint with Michela Giorcelli and Nico Lacetera, we study the interplay between scientific progress and culture through text analysis on a corpus of about eight million books, with the use of machine learning techniques. We focus on a specific scientific breakthrough: the theory of evolution by Charles Darwin. Besides examining the diffusion of certain concepts that characterized this theory, we document their semantic changes over time. Our findings thus show a complex relationship between two key factors of long-term economic growth: science and culture. We argue that considering the evolution of these two factors jointly can offer new insights to the study of the determinants of economic development, and machine learning is a promising tool to explore these relationships.
Shade Trees in Schoolyards: their Role in Protection from Ultraviolet Rradiation and Improving Childhood Learning
Keywords: education
schoolyards
shade trees
tree canopy
ultraviolet radiation
urban forestry

Urban trees are widely recognized to improve the physical environment for humans, but little work has been done to quantify differences among tree species in their ability to mitigate ultraviolet radiation, or on tree effects on learning in the context of primary education. My research examines the environmental services of schoolyard shade trees, and specifically evaluates the potential for different tree species to attenuate UV radiation reaching the ground and to provide psychological benefits as indicated by standardized test score performance. My thesis examines three different approaches to address specific questions that add to our understanding of both mechanisms and net effects, namely: (1) the analysis of leaf optical and morphological traits and their impact on the transmittance and reflectance of UV radiation, particularly UV-B and UV-C radiation of most concern from a human health perspective; (2) the determination of typical UV radiation levels beneath different urban tree species in schoolyards and public parks across Toronto, Ontario; and (3) the assessment of tree canopy cover, diversity, and species composition on the academic performance of primary-school-age children. I found both estimated leaf-level UV reflectance and transmittance were substantially higher than prior published estimates. UV reflectance ranged from 20.06-49.69% (UV-A), 30.13-62.68% (UV-B), and 37.18-73.29% (UV-C), and UV transmittance ranged from 0.33-10.14% (UV-A), 0.44-13.13% (UV-B), and 1.61-29.73% (UV-C) among sampled leaves. When analyzed at the canopy-level, UV protection factor (PF) varied significantly among species, ranging from ~1.3-3.4. Additionally, I found crown transparency (%), crown radius/height of live crown (m), and shade tolerance were important as predictors of UV protection factors. Lastly, tree cover is a significant positive predictor of children’s academic performance, and the effects of tree cover and species composition were most apparent in schools that showed the highest level of external challenges to excel in academic settings. More broadly, this dissertation examines the potential for shade trees in typical urban settings to provide both physical and mental health benefits to children through the attenuation of UV radiation and enhanced educational performance.
Global Health and Global War: The US Military’s Health Engagement in Africa, 1952-2018
Keywords: American Imperialism
Biopolitics
Geopolitics
Health engagement
Militarism
Militarization

In this dissertation, I trace the changes in the US military’s health engagement practices in Africa from the beginning of the Cold War through to the current global war on terror. My project reveals trends in the overlaps between military and humanitarian networks and highlights how the military’s health engagement practices are articulations of a changing American imperialism. Grounded on colonial legacies, the US military’s health engagement practices are underpinned by processes of militarization, perpetuate uneven power relations, open up spaces for processes of territorialization, and are connected to larger market-centric processes. Drawing on archival material from the US National Archives and Records Administration and a wider array of documents from across the US national security complex, I focus on three interrelated case studies. First, I trace the history of the Walter Reed Army Institute of Research’s infectious disease research and surveillance practices on the continent, with a detailed focus on their work in Kenya. Secondly, I look at the changes in the US military’s medical civic action practices in Africa from the early Cold War to the current work of US Africa Command. Finally, I explore the US military’s response to the 2014 West African Ebola crisis, Operation United Assistance, and the military’s role in pandemic response going forward. Each case study brings its own discrete contributions: my study of the Walter Reed Army Institute of Research shows how the military has adapted to a changing international development context and is now embedded in a network of global health actors; my analysis of medical civic action demonstrates the ways in which military practices of care are connected to processes of territorialization and war readiness; and my study of Operation United Assistance shows the trajectory of the military’s practices in disaster response and its changing role in what are traditionally civilian practices. My project reveals an underexplored history and geography of American imperialism in Africa. In doing so, it makes important contributions to the understanding of the military’s changing position in a global humanitarian context, as well as the changing ways humanitarian practices have been co-opted towards military ends.
Output-based Error Estimation and Anisotropic AMR for Numerical Prediction of Steady Ideal Magnetohydrodynamic Flows
Keywords: Adjoint
Computational Fluid Dynamics
Error-estimation
Magnetohydrodynamics
Mesh adaptation
Space weather

An anisotropic output-based adaptive mesh refinement (AMR) scheme is proposed and developed for the numerical prediction of ideal magnetohydrodynamic (MHD) flows on three-dimensional multi-block meshes using parallel distributed memory computer architecture. A finite-volume discretization procedure with limited piecewise linear reconstruction is used to solve the governing system of partial-differential equations on multi-block body-fitted hexahedral meshes. An inexact Newton's method is used to obtain steady state solutions of the discretized governing equations. The anisotropic block-based refinement technique provides significant reductions in the size of the computational mesh by locally refining the grid only in certain directions as dictated by the flow physics and numerical solution. A flexible binary tree data structure facilitates efficient parallel AMR via domain decomposition. An output-based error estimation procedure enables formal evaluation of a posteriori estimates of the errors of solution-dependent engineering functionals of interest in terms of local estimates of the truncation error as measured by the solution residual error. These errors are calculated by solving an adjoint problem related to the functional of interest and using the adjoint solution to appropriately weigh primal flow quantity residual errors evaluated on a finer mesh using an h-refinement strategy. The resulting dual-weighted error estimate is used to direct the local anisotropic mesh adaptation and the output-based refinement strategy generates meshes which are customized for the accurate calculation of functionals of interest. The performance of the output-based mesh refinement scheme is first demonstrated for several representative steady time-invariant aerodynamic flows governed by the Euler and Navier-Stokes equations and finally for several space physics flows governed by the equations of ideal MHD. Comparisons are made between the output-based mesh refinement technique and more traditional gradient-based and uniform refinement approaches in terms of efficient reduction in error and number of cells required to obtain a certain accuracy level. A solar wind-MHD model employing photospheric magnetic field maps obtained from solar magnetograms as inputs is also developed as a test case for the proposed output-based anisotropic mesh refinement scheme.
Apprehending Black Queer Diasporas: A Study of Black Pride Festivals and Their Emplacements
Keywords: Black Expressive Cultures
HIV/AIDS Activism
Queer Diaspora
Queer Tourism
Social Cultural Geography

“Apprehending Black Queer Diasporas is a historical consideration of Black Pride festivals. Emerging as an alternative to “mainstream” Pride parades, Black Pride has its origins in grass-roots community organizing by Black LGBT+ populations in response to the HIV/AIDS crisis in major US metropolitan cities in the early 1990s. As both a celebration of Black LGBT+ life and a space for political organizing, the model of Black Pride would be adopted throughout the United States, and internationally in London, U.K., and South Africa. Examined through a “black queer diasporic analytic” this dissertation traces the movement of this festival to assess how it was enabled through diasporic affinities among Black LGBT+ populations, globally. Utilizing a transnational comparative approach this study was conducted in three global cities; Toronto, Los Angeles, and London, U.K. Through key informant interviews with the founders of the Black Pride festivals selected, this dissertation offers a cultural history of the festival to capture the political contexts that prompted their emergence. Methodologically, I supplement the ethnographic component with archival research conducted in select LGBT archives to assess what the major political priorities were that served as the impetus for Black Pride festivals. Moving between ethnography, cultural history and social and cultural geography I discuss the historical origins of the festivals, in tandem with the spatial politics that are engendered when Black LGBT+ communities assert and cultivate communal space. Through a “black queer diasporic analytic” this project traces the transnational circuits of cultural exchange among Black LGBT+ communities that enabled Black Pride to become a global movement.
Structural Studies of Membrane-tethered KRAS4B Interaction with RAF and Inhibitors, and RIT1 Disease Mutants
Keywords: Cancer
Drug discovery
NMR
Protein membrane interactions
RAF
RAS

For more than three decades, RAS genes have been recognized as among the most important cancer-causing genes. RAS mutations are found in some of the most aggressive and deadly cancers, and are generally associated with poor prognosis. However decades of research have yet to yield a drug that can effectively inhibit RAS. Failed attempts to develop RAS inhibitors, including GTP-competitive analogs and farnesyltransferase inhibitors, have driven researchers from this field and led pharmaceutical companies to abandon RAS projects. However, in the last few years, researchers have started returning to this field, recognizing that RAS is still one of the most important targets in oncology. Although now armed with improved technology and a better understanding of RAS, researchers are mindful that there are still many hurdles, including the knowledge gap in understanding bilayer-anchored KRAS. RAF is one of the most important effectors of RAS and membrane anchoring of KRAS is critical for RAF activation. The RAS-binding domain (RBD) and Cysteine-rich domain (CRD) of RAF are key elements coupling RAS GTP loading and RAF activity. Their engagement with KRAS-GTP and membrane relieves the auto-inhibition of RAF kinase domain. This proposal aims to improve understanding of structure and function of KRAS in complex with CRAF RBD-CRD on biological membranes, and develop novel approaches towards inhibiting RAS in its membrane-tethered form by exploiting its tendancy to adopt an ‘occluded’ orientation on the bilayer surface. The discovery of RAS oncogene in human cancer marked the beginning of decades' journey of exploring the structure and function of RAS superfamily members. Recently, the RAS-like wildly expressed in many tissues (RIT1) came to researchers' spotlight because of its etiologic role in Noonan Syndrome and cancer. Using a real-time NMR-based GTPase assay, we characterized the GTP hydrolysis and nucleotide exchange of RIT1 WT and five disease-associated mutants including S35T, A57G, Y89H, F82V and T83P. This characterization will facilitate understanding of the biophysical properties and disease role of RIT1 and its mutants.