VictorJuiz/thesis huggingface dataset:
Rehabilitation and how it Applies to Stigma using HIV as an Example

Adults living with HIV face numerous challenges and the application of rehabilitation principles may help alleviate many of them. Stigma is a challenge many individuals living with HIV face every day and it can have important consequences for their participation in valued activities and roles in their lives. The impact of stigma associated with HIV has not been well studied from a rehabilitation science perspective. This thesis explores research on the rehabilitation interventions used by adults living with HIV to help them manage their experiences of disability and investigate how stigma intersects with the rehabilitative framework of the International Classification of Functioning, Disability and Health (ICF). A series of interrelated investigations – a scoping review, a theoretical analysis and an empirical study – were completed. The scoping review revealed the extent, range and nature of research on rehabilitation interventions used by adults living with HIV to manage their experiences of disability. The theoretical investigation illustrated how stigma and rehabilitation interrelate, specifically demonstrating how three forms of stigma (enacted, self and structural) interrelated with the ICF domains of participation restrictions, environmental and personal contextual factors. A final empirical study illustrated the real-world application of the theoretical contribution through secondary analysis of interviews with Zambian women living with HIV. These women faced enacted, self and structural stigma, which were shown to interrelate with the domains of the ICF, through accounts of their lived experiences. The concepts of rehabilitation, stigma and HIV are uniquely connected in this dissertation. The findings illustrate how stigma and rehabilitation are interrelated both theoretically and empirically using HIV as an example. The resulting insights have implications for rehabilitation professionals and researchers who can apply this information to their clinical and scientific work to strengthen the role of rehabilitation in mitigating stigma as experienced by people living with HIV.

Keywords: HIV
Rehabilitation
Stigma
Advisor: Nixon, Stephanie A
Magnetic Resonance Characterization of Infarct Heterogeneity Using High-Resolution Volumetric Multicontrast Imaging

Infarct characteristics identified by gadolinum-enhanced magnetic resonance imaging (MRI) have been increasingly used to inform the management of ventricular tachycardia (VT) in patients with prior myocardial infarction (MI). Gadolinum-enhanced MRI can identify the presence, location, morphology, heterogeneity and size of MI. Heterogenous tissue in the peri-infarct zone has been associated with arrhythmic substrates determined in the electrophysiology study. Recently, the extent of infarct heterogeneity assessed by gadolinum-enhanced MRI has been shown to predict VT inducibility, the occurrence of arrhythmic events and appropriate implantable cardioverter defibrillator (ICD) therapy. However, accurate assessment of infarct heterogeneity is primarily limited by achievable spatial resolution in clinical settings restricted by the time constraints occurring with cardiac and respiratory motion as well as contrast kinetics. This thesis presents new acceleration methods for high-resolution volumetric multicontrast imaging to improve characterization of infarct heterogeneity by gadolinum-enhanced MRI. A new reconstruction using compressed sensing with low rank and spatially varying edge-preserving constraints (CS-LASER) was developed to enable reconstruction of small-scale features from highly accelerated volumetric multicontrast acquisitions. In a pig study, CS-LASER was demonstrated to provide peri-infarct characteristics on multicontrast images with excellent correspondence with histopathology. Furthermore, improved peri-infarct characterization was achieved by advancing reconstruction efficacy and robustness for cases of varying contrast-to-noise ratio (CNR) using compressed sensing and parallel imaging with low rank and spatially varying edge-preserving constraints (CP-LASER). Finally, in a clinical study of 11 patients with chronic MI, it was successfully demonstrated that CP-LASER accelerated volumetric multicontrast imaging achieves an isotropic resolution of 2.2 mm on 1.5T in a single breath-hold, and provides better delineation of infarct characteristics and improved assessment of infarct heterogeneity compared to the conventional two-dimensional (2D) late gadolinium enhancement (LGE) method. The methods presented in this thesis help translate high-resolution volumetric multicontrast imaging toward clinical utility in infarct heterogeneity assessment.

Keywords: Cardiac Magnetic Resonance Imaging
Compressed Sensing
Edge-Preserving Sparse Modeling
Low Rank Modeling
Myocardial Tissue Characterization
Ventricular Tachycardia
Advisor: Wright, Graham A.
Radical Leaders: Status, Competition, and Violent Islamic Mobilization in Indonesia

Why do some Muslim leaders radicalize while others do not? Drawing on a study of radical mobilization in Indonesia, this dissertation argues that Muslim leaders radicalize when they find religious authority hard to gain and maintain. It makes two specific points: 1) radical mobilization is more likely among weak and precarious religious leaders, those with few followers and little institutionalization; and, 2) weak and precarious leaders are more likely to radicalize in crowded and competitive religious markets, because they need to be creative if they want to survive. It argues that weak Muslim leaders, in competitive environment, are the ones most likely to use strategies of outbidding, scapegoating, and provocation. The dis-sertation’s empirical puzzle is the cross-regional variations in Islamist mobilization observed in post-transition Java, Indonesia. Since 1999, radical groups have proliferated and mobi-lized more in some regions than others. The study finds that in regions with radical groups and mobilization, most clerics have weak religious institutions, fragmented networks, and operate in competitive religious markets. In these markets, radical mobilization provides low-status clerics with a cheap and efficient way to bolster their religious authority. In re-gions where radical groups did not proliferate, most clerics have strong religious institutions with deep roots in society, extensive networks, and operate in much less competitive reli-gious environments. In these markets, clerics do not feel the same urge to mobilize, as reli-gious authority is more secure, stable, and routinized. The origins of these religious markets are traced back to sub-regional variations in the process of state building. State building strategies had long-lasting consequences on contemporary Muslim institutions by shaping subsequent political cleavages and state policies toward Islam. This dissertation is based on 13 months of fieldwork in Indonesia, 126 interviews with Muslim clerics and activists, and a new dataset of Java’s 15,000 Islamic boarding schools and their 30,000 Muslim clerics.

Keywords: Indonesia
Islam
Minorities
Moderation
Radicalism
Violence
Advisor: Bertrand, Jacques
Synthesis and Reactivity of Transition Metal and Main Group Hydrogenation Catalysts

Since its discovery by Paul Sabatier, catalytic hydrogenation of unsaturated substrates has become the single largest industrial process to date and encompasses the production of many products, such as foods, agrochemicals, pharmaceuticals, and materials. Over the last century research in the area has predominantly focused on the use of transition metals such as palladium, platinum, rhodium, and ruthenium to develop heterogeneous and homogeneous hydrogenation catalysts. The research presented herein focuses on the use of ruthenium complexes bearing electron-rich phosphorylated N-heterocyclic carbene ligands as well as the development of main-group compounds for frustrated Lewis pair catalysis. Complexes [Ru(0)LL’2(CO)] and [RuHL2(CO)][Cl], where L = N-phosphorylated N-heterocyclic carbene (NHCP), and L’ = triphenylphosphine, were prepared as a mixture by treatment of RuHCl(CO)(PPh3)3 with excess NHCP carbene and separated by crystallization. The zero-valent complex [Ru(0)LL’2(CO)] was shown to undergo rapid oxidative addition to the corresponding Ru(II) species when treated with small molecules to afford complexes of the general type [RuHXLL’(CO)], where L = N-phosphorylated N-heterocyclic carbene, L = triphenylphosphine, and X = H, SiPh3, or Si(H)Ph2. The reaction of NHCP carbene with [RuCl2(p-cymene)]2 resulted in the isolation of the piano-stool half-sandwich complex [RuCl2(p-cymene)(NHCP)] as well as an unusual arene-activated species. The half-sandwich complex was treated with a halide-abstracting agent to afford the cationic compound [RuCl(p-cymene)(NHCP)]+, which was shown to rapidly undergo dihydrogen activation via an outer-sphere mechanism involving the phosphine appended to the carbene ligand. To demonstrate the utility of main-group catalysts, trityl cations of the form [(4-MeO-C6H4)xCPh3-x][BR4] were synthesized, where x = 1 and 3, and R = F, or C6F5. Treatment of equimolar solutions of [(4-MeO-C6H4)CPh2][BF4] and sterically encumbered phosphines with dihydrogen resulted in activation of dihydrogen but no catalytic activity was observed. The air- and moisture-stable [(4-MeO-C6H4)CPh2][BF4] was shown to be a potent Lewis acid catalyst in the hydrothiolation of olefins.

Keywords: FLP
hydrogenation
inorganic
main group
organometallic
Advisor: Stephan, Douglas W
Borinic Acid Catalyzed Reactions of 2,3-Epoxy Alcohols

Epoxy alcohols are versatile intermediates that can be ring opened or rearranged to enable target-oriented synthesis. Previous studies describe the ability of borinic acids (R2BOH) to activate vicinal cis-diols via reversible borinate ester formation. These interactions lead to catalytic and site-selective transformations of carbohydrates. The current work describes investigations related to expanding the utility and modes of borinic acid catalysis by employing additional substrate classes. Chapter 1 describes a borinic acid catalyzed regioselective coupling of 2,3-epoxy alcohols with acyl chlorides. A variety of epoxy alcohols underwent the transformation, which produces chlorohydrin diol esters. Control experiments as well as kinetic and computational studies were carried out to gain information about the reaction mechanism. These studies were consistent with an initial borinic acid promoted C3-selective chlorination of the epoxy alcohol to generate a chlorohydrin diol-derived borinate ester. The activated borinate complex subsequently enabled a regioselective acylation to produce the observed products. Chapter 2 describes efforts to extend the borinic acid catalyzed chloroacylation protocol towards alternative coupling partners. Although the strategy could be successfully extended towards chlorosulfonylation of 2,3-epoxy alcohols, limited success was observed when a variety of additional coupling partners such as acyl azides, benzyl bromides, or anhydrides were employed. Challenges associated with poor regioselectivities and formation of epoxy ester side products were encountered. Chapter 3 describes the development of an unusual Type II semipinacol rearrangement of 2,3-epoxy alcohols that proceeds with net-retention of configuration. The protocol employed borinic acids and halide salts as co-catalysts and rearranged the substrates to produce β-hydroxy carbonyl compounds. Mechanistic experiments were consistent with a pathway involving an initial ring opening of the epoxide ring to generate a halo-diol borinate ester species. Although O-centered reactivity is generally observed from 1,2-diol-derived borinates, migration of the carbon–carbon bond was observed in the case of halo-diol derived borinate species generate in this system. Chapter 4 summarizes the major conclusions resulting from these studies. Preliminary attempts related to applications of the methods developed in this work towards target-oriented synthesis are described followed by a discussion concerning potential future directions.

Keywords: Boron Catalysis
Catalysis
Epoxide
Rearrangement
Semipinacol
Tandem Reaction
Advisor: Taylor, Mark S
Water Vapour Measurements in the Canadian High Arctic

This thesis provides an evaluation of atmospheric H2O measurements at the high Arctic site in Eureka, Nunavut made using ground-based and satellite instruments. The focus is on measurements acquired using a solar absorption Fourier transform infrared spectrometer (the 125HR) located at the Polar Environment Atmospheric Research Laboratory (PEARL), as part of the MUSICA project. Close agreement is observed between H2O total columns from seven PEARL instruments, with mean differences ≤ 1.0 kg/m2 and correlation coefficients (R) ≥ 0.98, except for a comparison between a microwave radiometer and a radiosonde product, which had a correlation coefficient of 0.92. Comparisons revealed a 6% wet bias in the 125HR MUSICA product. Atmospheric Emitted Radiance Interferometer measurements were shown to provide accurate H2O measurements, e.g. within 4% of radiosondes. The PEARL 125HR and Eureka radiosondes were used to demonstrate that the Atmospheric Chemistry Experiment (ACE) satellite instruments, ACE-FTS and ACE-MAESTRO, produce accurate H2O profiles in the upper troposphere and lower stratosphere. ACE-FTS showed a wet bias of up to 6 ppmv (6 to 13%) of 125HR measurements between 6 and 14 km and was within 6 ppmv (12%) of radiosondes between 7 and 11 km. ACE-MAESTRO profiles showed a dry bias relative to the 125HR of between 7% and 12% between 6 and 14 km. ACE data showed closer agreement with the radiosondes and 125HR than did other satellite datasets, e.g. MIPAS, MLS, SCIAMACHY, and TES, except AIRS, which showed mean differences within 5%. In addition, TCCON H2O and δD total column datasets, retrieved from near-infrared 125HR spectra, and not yet assessed in detail, were compared with the well-validated MUSICA products at Eureka and six other globally-distributed sites. The results showed TCCON measurements agree well with MUSICA, although the H2O product had a small dry bias (6%) and the δD had a high bias (40‰).

Keywords: arctic
atmosphere
canada
climate
satellite validation
water vapour
Advisor: Strong, Kimberly
Friendship Quality in Adolescents with Attention-deficit Hyperactivity Disorder

The majority of research investigating the social functioning of youth with ADHD has examined peer rejection and social skills deficits while generally overlooking their friendships. The goal of this dissertation was to provide detailed information about friendship quality in adolescents with and without ADHD. The first manuscript compared ratings of social support and negative interactions in same- and other-sex friendship dyads in adolescents with and without ADHD, while examining the potentially moderating effects of age and gender. The second manuscript examined empirically supported correlates of friendship quality including friendship stability, co-morbid psychopathology, and interpersonal competence. A sample of 115 adolescents, ages 13-18, were recruited to participate in the present study of whom 61 were classified as having ADHD (21 female) and 54 without ADHD (29 female). The measures used included parent and self-report rating scales and questionnaires assessing ADHD symptoms, friendship quality, friendship stability, externalizing behaviour (conduct problems, oppositional behaviour), internalizing behaviour (anxiety, depression), and interpersonal competence (social skills, social perspective taking). Results from study one indicated that ratings of friendship social support diminished across age groups in youth with ADHD, but increased in typically developing youth. Adolescents with and without ADHD, however, did not differ on ratings of negative interactions experienced in their friendships. Compared to males, females rated their friendships to be more supportive, irrespective of ADHD status. Adolescents with and without ADHD rated their same-sex friendships to be simultaneously more supportive and more conflictual than their other-sex friendships. Results from study two indicated that friendship stability, social skills, social perspective-taking, oppositional behaviour, and anxiety explained unique variance in the prediction of friendship social support. However, results of exploratory mediation analyses indicated that the direct effects of oppositional behaviour and anxiety were no longer significantly predictive of friendship quality, after controlling for the mediators social skills and social perspective-taking, respectively. These findings, clinical implications, and future directions are discussed within the context of the existing peer relations literature.

Keywords: ADHD
Adolescents
Friendship
Quality
Advisor: Wiener, Judith
The Role of the NKR-P1B:Clr-b Recognition Axis in Oncogenic Transformation and Cancer Immunosurveillance

Natural killer (NK) cells play important role in tumour elimination, virus control, transplant rejection, and the elimination of cells going under genotoxic or cellular stress. They facilitate this innate immune recognition by detecting changes in ligand expression on target cells mediated via germline-encoded NK cell receptors. Here, we elucidate the role of MHC-I-independent NKR-P1B:Clr-b receptor-ligand interactions in the detection of oncogenic transformation by NK cells. Ras and c-Myc proto-oncogene overexpression were found to promote a real-time loss of Clr-b on mouse fibroblasts and leukemia cells. Ras-driven Clr-b downregulation was mediated in part via the Raf/MEK/ERK and PI3K pathways, regulated at multiple levels, including the Clrb (Clec2d) promoter, nascent Clr-b transcripts, and cell surface Clr-b protein. Clr-b downregulation on leukemia cells in turn diminished recognition of the target cells via the NKR-P1B inhibitory receptor, augmented cytotoxicity mediated by NKR-P1B+ NK cells in vitro, and enhanced rejection by WT mice in vivo. Interestingly, genetic ablation of either one (Clr-b+/–) or two Clr-b alleles (Clr-b–/–) enhanced survival of Eμ-cMyc transgenic mice in a primary lymphoma model, despite preferential rejection of Clr-b–/– hematopoietic cells previously observed following adoptive transfer into naïve wild-type mice in vivo. Collectively, these findings suggest that the inhibitory NKR-P1B:Clr-b axis plays a beneficial role in the innate detection of oncogenic transformation via NK cell-mediated cancer immunosurveillance, in addition to a pathological role in the immune escape of primary lymphoma cells in Eμ-cMyc mice in vivo. In an attempt to discover novel pathways involved in Clr-b ligand regulation, we initiated genome-wide loss-of-function screening in lymphoma cells sorted for high or low Clr-b levels. Validation analysis of potential targets identified two genes with oncogenic properties, Ddx6 and PPARα, that are potentially involved in Clr-b downregulation. These results provide a model for the human inhibitory NKR-P1A:LLT1 system, a human homolog for NKR-P1B:Clr-b, in cancer immunosurveillance in lymphoma patients, and suggest it may represent a target for immune checkpoint therapy.

Keywords: Cancer
Clr-b
Immunology
Immunotherapy
Natural killer cells
NKR-P1B
Advisor: Carlyle, James R.
3D 3C Seismic Imaging in the Athabasca Basin, Canada

This study investigates the 3C-3D surface and downhole (VSP) seismic datasets previously collected at the Athabasca Basin McArthur River to Millennium uranium mine sites using a number of unconventional analytical methods. The objective is to understand the potential of the seismic method to delineate subsurface features such as the hydrothermal alteration footprint, the sandstone-basement unconformity and the subvertical thrust fault zone. Methodologies applied include a series of forward and data-driven approaches. First, this study accomplishes the prediction of the compressional and shear wave amplitude and traveltime using angle dependent reflectivity equations and 2D elastic finite-difference waveform models. The numerical predictions are based on the existing and estimated petrophysical data from the local area. Second, this study discovers a number of unique properties of the seismic wave attenuation from surface and downhole seismic datasets. Multiple methods applied to VSP datasets confirm that the attenuation quality factor (Q) in the study area is low and variable. Finally, this study analyzes the traveltime and waveform data collected from the unique 3C-3D-borehole seismic geometry at Millennium to delineate the subsurface geologic structures that are potentially related to the wave attenuation and velocity. A forward 3D visco-elastic waveform model is created to illustrate the observed abnormal amplitude and velocity azimuthal variations with a superimposed effect of intrinsic and scattering. The results from these series of approaches provide updated understandings of the alterations, structural geology, and their relationships with seismic data. These understandings contribute to the suggestions for future seismic imaging work such as converted shear wave processing, downhole seismic acquisition, and alteration footprint tomography.

Advisor: Milkereit, Bernd
Nanofluidics: A Window into Transport and Phase Change in Nanoporous Systems

Fluid transport and phase change in nanoporous media are of fundamental importance in a range of applications including fuel cells, water treatment, solar steam production, electrocatalytic conversion of CO2, as well as importantly natural gas and oil in nanoporous reservoirs. Shale resources are massive, controversial, and provide an increasing share of global energy with a broad group of stakeholders in academia, industry, and government. However, there is much uncertainty regarding the underlying fluid fundamentals of ultra-low permeability nonporous media – a nanoscale fluid challenge which is extremely complex, coupled and largely uncharacterized. The challenge is multi-component fluid mixtures within radically multi-scale geometries (a few nanometers to bulk), and is behind the shale resources efficient recovery as well as its global environmental impact now under debate. Probing fluid behaviors at the nanoscale is challenging due to difficulties in creating representative nanoconfinement and measuring properties within. Silicon-glass micro/nanofluidics provides an opportunity in overcoming these challenges. Here, the innovation and application of silicon-glass nanofluidic devices to directly quantify fluid behaviors in nanoconfinement using optical microscopy down to sub-10 nm is introduced. This nanofluidic approach is compatible with industrially-relevant high temperatures (up to 573 K) and pressures (up to 20 MPa). Fundamental nanoscale single component hydrocarbon condensation, hydrocarbon mixture phase transitions and large molecule diffusion are studied, deviating significantly from bulk. The results highlight mass-transport governed phase change dynamics, mixture bubble points depressed even below bulk dew points, and order of magnitude reduced molecular diffusivity at nanoscale. In addition, the nanofluidic approach is also applied to screen emerging gas injection strategies for enhanced tight oil recovery as a demonstration of its industrial application potential. Efficient evaluation of different recovery strategies indicates the significance of capillary pressure as a barrier in nanoporous shale and how it can be applied to improve recovery.

Keywords: energy system
fluid mechanics
microfluidics and nanofluidics
oil and gas
shale reservior
thermodynamics
Advisor: Sinton, David