VictorJuiz/thesis huggingface dataset:
Polarimetric Second-Harmonic Generation Microscopy for Histopathology

Second-harmonic generation (SHG) is one of the modalities of nonlinear microscopy, which can provide structural visualization and characterization, as well as 3D optical sectioning of the material without the need for staining. Polarimetric SHG microscopy can reveal an immense amount of structural information about the specimen beyond the diffraction limited spatial resolution of the microscope by extracting the second-order nonlinear susceptibility tensor elements ratios. SHG microscopy as well as polarimetric SHG microscopy have become important imaging techniques, specially in the study of biological materials such as collagen. Collagen is the most abundant protein in human body which plays an important role in a number of biological processes including wound repair, tumour development, and cancer metastasis. This thesis focuses on studying the nonlinear optical properties of collagen using polarimetric SHG microscopy and utilizing these nonlinear optical parameters as new metrics for the field of histopathology.Two polarimetric SHG techniques, double Stokes-Mueller polarimetry (DSMP) and reduced DSMP known as linear polarization-in, polarization-out (PIPO) were utilized to study the nonlinear optical properties of collagen fibres in thin tissue sections. Two most commonly assumed symmetry classes for collagen fibres, C6 and C6v were experimentally investigated. C6 class is a more precise description of collagen fibres, as it accounts for chirality of collagen. Measurement of the chiroptical properties of collagen is shown to be linked to the 3D organization of collagen fibres, the polarity of collagen, as well as the relative phase differences between susceptibility tensor elements. Further, PIPO SHG microscopy provides the molecular susceptibility ratios of collagen. Polarimetric SHG microscopy revealed the structural alteration of collagen in tissues with pathological conditions through three main parameters: the susceptibility components ratio, degree of linear polarization of the outgoing SHG and the angle distribution of collagen fibres in the image plane. Polarimetric SHG microscopy shows great potential for understanding the tissue morphology and function, and ultimately as a diagnostic tool in histopathology. The polarimetric SHG technique was further implemented into a large area scanning system for the first time. A large area polarimetric SHG image can elucidate the morphological changes of collagen in diseased tissues such as cancer and can be used as a complementary method to the currently existing techniques in histopathology.

Advisor: Barzda, Virginijus
Developing “PEP”: A Personalized, Web-Supported Energy Conservation Education Program for People on Chronic Dialysis Therapy with Fatigue

Background: Fatigue is a common and disabling symptom experienced by people with end-stage renal disease on chronic dialysis therapy (CDT). Energy conservation education (ECE) is an approach to fatigue management that provides people with energy-saving strategies, to reduce their fatigue and improve their life participation. ECE has yet to be trialed in the CDT population. Objective: To explore the potential for energy conservation education to improve fatigue and life participation outcomes in people on CDT. Methods: A three-step process was undertaken: 1. A scoping review was conducted to investigate what is known about energy conservation education in people with chronic diseases who experience fatigue. 2. The Word Health Organization framework was used to develop an ECE program, tailored specifically to meet the needs of people on CDT. Feedback on the program was collected via key informant interviews and usability testing, to inform program revisions. 3. Preliminary efficacy testing was conducted using a mixed-methods sequential explanatory design, including a single-case, tri-phasic, time-series study with four replications, and qualitative post-intervention interviews. Results: The majority of evidence on ECE in people with chronic diseases focused on a specific, group-based ECE program in people with MS. There was a dearth of evidence to demonstrate positive effects of ECE on life participation outcomes across chronic disease populations, and a lack of programs that would be feasible for people on CDT. A personalized, web-supported ECE program (The “PEP” Program) was therefore created to meet the CDT population’s key needs. Key informant interviews suggested the program was perceived positively, and usability testing found people on CDT could complete the program independently. Efficacy testing revealed consistently positive changes in fatigue and life participation associated with the program in three of five participants, while all participants reported experiencing benefits during the qualitative interviews. Conclusion: The PEP program has the potential to improve fatigue-related outcomes in people on CDT. Further robust testing of the program is warranted.

Keywords: Chronic Kidney Disease
Dialysis
Energy Conservation
Fatigue
Occupational Therapy
Advisor: Polatajko, Helene J
Becoming bilingual readers: Examining orthographic processing in learning to read English and French

This dissertation is comprised of three studies examining the role of orthographic processing in word reading among children enrolled in Canadian French immersion programs. Print awareness, as well as lexical and sublexical aspects of orthographic processing were examined. Study 1 evaluated the within- and cross-language relations between print awareness and word reading among 92 emergent readers from senior kindergarten to Grade 1. Concurrently, there was a within-language relation between English print awareness and English word reading; there was also a cross-language relation between English print awareness and French word reading in senior kindergarten. Longitudinally, English print awareness in senior kindergarten predicted progress in French word reading in Grade 1, but not in English. These results suggest that print awareness measured in the dominant language can be used to predict word reading development in emergent bilingual readers attending French immersion. Study 2 investigated the development of early knowledge of print conventions and its within- and cross-language relations to early word reading skills with the same sample as Study 1 from senior kindergarten to Grade 1. Results revealed a systematic development of knowledge in several aspects of print from senior kindergarten to Grade 1 in both English and French. Hierarchical linear analyses revealed significant within-language relations between print convention knowledge in kindergarten and word reading in both English and French. Across languages, English print convention knowledge in senior kindergarten predicted progress in French word reading in Grade 1; French print convention knowledge in senior kindergarten was not correlated with progress in English word reading in Grade 1. Finally, Study 3 investigated the predictors of English and French word reading in 69 children from first through third grade. The role of phonological awareness, orthographic processing (both lexical and sublexical), and vocabulary knowledge in English and French on the achievement and growth of word reading in the two languages were evaluated with growth curve analyses. Results showed that Grade 1 measures of English phonological awareness and orthographic processing predicted Grade 3 English word reading achievement; English orthographic processing in Grade 1 also predicted growth in English word reading in Grade 3. French phonological awareness and orthographic processing in Grade 1 predicted French word reading achievement in Grade 3. Additionally, at-risk readers (n = 6) identified in Grade 1 generally fell behind their typically-developing peers across all measures, although evidence of improvement emerged over time. Taken together, these studies suggest that orthographic processing is a key predictor of word reading in emergent bilingual readers.

Keywords: bilingualism
orthographic processing
reading
Advisor: Chen, Xi Becky
Prognostic applications for Alzheimer's disease using magnetic resonance imaging and machine-learning

Alzheimer’s disease (AD), the most common form of dementia, is a neurodegenerative disorder that leads to cognitive deficits, particularly in the memory domain. Recent advances in magnetic resonance (MR) imaging techniques and computational tools, such as machine-learning (ML), provide promising opportunity for prognostic applications in AD. Imaging biomarkers can improve our understanding of etiology and progression of the disease, as well as assist clinicians in decision-making pertaining to patient monitoring, intervention, and treatment selection. The overarching goal of this thesis is to develop several computational methods that facilitate the use of MR imaging data in translational applications to improve personalized patient care. The work in this thesis is divided into three projects. The first project aims to improve MR image segmentation - a commonly used MR image processing step to delineate anatomical structures used in a multitude of downstream quantitative analyses. The goal of the second project is to leverage MR-based anatomical features towards subject-level clinical severity prediction. Methodologically, the work provides a novel ML framework for high-dimensional, multimodal analysis customized for MR imaging data. The third project extends the subject-level prediction towards longitudinal prognosis with several practical considerations. The methodological contributions involve modeling and prediction of clinical trajectories from longitudinal MR and clinical measures using ML approaches. The work addresses many challenges faced in a clinical setting, such as missing data points, and provides a powerful framework for early detection and accurate prognosis of at-risk AD patients via continuous monitoring. The comprehensive validation of the methods presented in this work with multiple datasets and studies demonstrates the utility of MR images towards AD prognosis. The tools proposed complement existing clinical workflow and can be leveraged in conjunction with current clinical assessments. With the increasing availability of large-scale datasets, further improvements and validations can be made to adopt this work for individual intervention and prognosis, as well as for improving recruitment strategies for the clinical trials in AD.

Keywords: Alzheimer's disease
Machine-learning
MR imaging
Advisor: Chakravarty, Mallar
Contributions to the Stable Derived Categories of Gorenstein Rings

The stable derived category Dsg(R) of a Gorenstein ring R is defined as the Verdier quotient of the bounded derived category Db (modR) by the thick subcategory of perfect complexes, and was introduced by Ragnar-Olaf Buchweitz as a homological measure of the singularities of R. This thesis contributes to its study, centered around representation-theoretic and Koszul duality aspects. In Part I, we first complete (over C) the classification of homogeneous complete intersection isolated singularities R for which the graded stable derived category DZ sg(R) (respectively, Db (coh X) for X = proj R) contains a tilting object. For this, we prove the existence of a full strong exceptional collection of vector bundles on a 2n-dimensional smooth complete intersection of two quadrics X = V (Q1, Q2) ⊆ P 2n+2, building on work of Kuznetsov. We then use results of Buchweitz-Iyama-Yamaura to describe the indecomposable objects in DZ sg(RY ) for RY the homogeneous coordinate rings of 4 points on P 1 and 4 points on P 2 in general position, and classify their Betti tables. In Part II, for R a Koszul Gorenstein algebra, we study a natural pair of full subcategories whose intersection Hlin(R) ⊆ DZ sg(R) consists of modules with eventually linear projective resolutions. We prove that such a pair forms a bounded t-structure if and only if R is absolutely Koszul in the sense of HerzogIyengar, in which case there is an equivalence of triangulated categories Db (Hlin(R)) ∼= DZ sg(R). We then relate the heart to modules over the Koszul dual R! . This extends the Bernstein-Gel’fand-Gel’fand correspondence to any pair of Koszul dual algebras (R, R! ) with R absolutely Koszul Gorenstein, applying in particular to the coordinate ring of elliptic normal curves of degree ≥ 4 and to the anticanonical model of del Pezzo surfaces of degree ≥ 4. We then relate our results to conjectures of Bondal and Minamoto on the graded coherence of Artin-Schelter regular algebras and higher preprojective algebras; we characterise when these conjectures hold in a restricted setting, and give counterexamples to both in all dimension ≥ 4.

Keywords: Artin-Schelter regular algebras
BGG Correspondence
Higher preprojective algebras
Koszul Algebras
Singularity Category
Stable Derived Category
Advisor: Kamnitzer, Joel
Ingalls, Colin
Picking up the Pieces: The Economic Crisis and the Transformation of the Contemporary Peninsular Novel

This dissertation examines changes in the genre of the Peninsular novel resulting from the impact of the World Economic Crisis that deeply affected Spain beginning in 2008. It analyzes how the novels published in Spain between 2007 and 2014 by ten contemporary authors explore the causes of the Economic Crisis and its impact on individuals, social structures, and patterns of relationships. Changes in the genre of the novel occur both on the levels of form and content. Through my initial analysis of novels by Pablo Gutiérrez, Doménico Chiappe, and Elvira Navarro, I argue that the Crisis changed the perception of public and private spaces in Spain. The real estate bubble and mass evictions laid foundations for new forms of participatory democracy such as squatters and later the 15M movement. I then build on the work of Berlant and Butler and explore categories of debt and precarity in novels by Recaredo Veredas, Benjamín Prado, and Javier López Menacho as fundamentals for the new emerging Crisis consciousness. Next, I consider the epic and symbolic nature of the Crisis as it is depicted in the novels of Rafael Chirbes. I contend that through multiple intertexts and an appeal to universal values, Chirbes inscribes the local Crisis in the national literary tradition and global context. Finally, I analyze how the texts by Lucía Extebarría, Cristina Fallarás, and Marta Caparrós depict the evolution from individual struggle to collective action. I show the transition from a reliance on failed social institutions to the creation of alternative networks of power and the social movements made possible through solidarity. I suggest that the Economic Crisis as reflected through the lens of the novels analyzed has slowly transformed into a continuity in the present with no chronological end point. This shift has transformed the national worldview and resulted in the rejection of the idea of uninterrupted progress and constant development in Spain that rooted the national consciousness from the 1990s through to the early 2000s.

Keywords: Economic crisis
Genre transformation
Peninsular novel
Spanish literature
XXI century
Advisor: Davidson, Robert A
Increasing the Stability and Turnover Number of a Highly Active Iron Catalyst for the Asymmetric Transfer Hydrogenation of Ketones

A highly active iron catalyst for the asymmetric transfer hydrogenation (ATH) of ketones was reported by the Morris group in 2013. This catalyst surpassed the activity of platinoid metals by reaching TOFs up to 200 per second, but the highest reported turnover number (TON) was only 6060. To compete with the platinoid metals industrially, the focus of this thesis was to increase the TON of the iron catalyst through mechanistic investigation of potential deactivation pathways, switching to potassium formate and water as the hydride and proton source to obtain quantitative conversion, as well as the heterogenization of the precatalyst for eventual use in a continuous flow system. The orthophenylene catalysts in Chapter 3 displayed lower activity due to the rigidity of the triphenylphosphine donor, which places a phenyl group into the active site of the catalyst. Despite this hindrance, one catalyst achieved a TON of 8821 while retaining a remarkably high ee of 90%. The maximum TON of this catalyst was 150 000 which was achieved by heating the reaction at 75 °C with sequential injections of acetophenone and isopropanol (iPrOH). Unfortunately, since the ATH with iPrOH is an equilibrium process, the product alcohol racemized over time. The ATH in water using potassium formate as the hydride source lead to decreased activity due to the mass-transfer limitations caused by the formation of a biphasic reaction mixture. The maximum TON was 199, which rivals platinoid metal catalysts in similar biphasic systems. Finally, a variant of the iron catalyst was successfully covalently bonded to polystyrene, silica gel, and polyethylene glycol for use in batch chemistry. While maintaining a pH of 12.6, the iron catalyst remained covalently bonded to the polymeric support and could be recycled one time to achieve a total turnover number (TTN) of 164. Further studies are required to optimize the batch chemistry reaction for later use in a continuous flow system.

Keywords: Aqueous Biphasic
Asymmetric Transfer Hydrogenation
Green Chemistry
Heterogenization
Iron Catalyst
Mechanistic Investigation
Advisor: Morris, Robert H
A groupoid approach to geometric mechanics

We consider numerous variations of a rigid body in an inviscid fluid. The different cases are specified by the properties of the fluid; the fluid may be compressible or incompressible, irrotational or not. By using groupoids we generalize Arnold’s diffeomorphism group framework for fluid flows to show that the well-known equations governing the motion of these various systems can be viewed as geodesic equations (or more generally, Newton’s equations) written on an appropriate configuration space. We also show how constrained dynamical systems on larger algebroids are in many cases equivalent to dynamical systems on smaller algebroids, with the two systems being related by a generalized notion of Riemannian submersion. As an application, we show that incompressible fluid-body motion with the constraint that the fluid velocity is curl- and circulation-free is equivalent to solutions of Kirchhoff’s equations on the finite-dimensional algebroid se(n). In order to prove these results, we further develop the theory of Lagrangian mechanics on algebroids. Our approach is based on the use of vector bundle connections, which leads to new expressions for the canonical equations and structures on Lie algebroids and their duals. The case of a compressible fluid is of particular interest by itself. It turns out that for a large class of potential functions U, the gradient solutions of the compressible fluid equations can be related to solutions of Schrödinger-type equations via the Madelung transform , which was first introduced in 1927. We prove that the Madelung transform not only maps one class of equations to the other, but it also preserves the Hamiltonian properties of both equations.

Keywords: Geometric Mechanics
Groupoids
Hydrodynamics
Advisor: Khesin, Boris A.
A Nonparametric Bayesian Approach to Causal Modelling

The Dirichlet process mixture regression (DPMR) method is a technique to produce a very flexible regression model using Bayesian principles based on data clusters. The DPMR method begins by modelling the joint probability density for all variables in a problem. In observational studies, factors which influence treatment assignment (or treatment choice) may also be factors which influence outcomes. In such cases, we refer to these factors as confounders and standard estimates of treatment effects will be biased. Causal modelling approaches allow researchers to make causal inferences from observational data by accounting for confounding variables and thus correcting for the bias in unadjusted models. This thesis develops a fully Bayesian model where the Dirichlet process mixture models the joint distribution of all the variables of interest (confounders, treatment assignment and outcome), and is designed in such a way as to guarantee that this clustering approach adjusts for confounding while also providing a flexible model for outcomes. A local assumption of ignorability is required, as contrasted with the usual global assumption of strong ignorability, and the meaning and consequences of this alternate assumption are explored. The resulting model allows for inferences which are in accordance with causal model principles. In addition to estimating the overall average treatment effect (mean difference between two treatments), it also provides for the determination of conditional outcomes, hence can predict a region of the covariate space where one treatment dominates. Furthermore, the technique's capacity to examine the strongly ignorable assumption is demonstrated. This method can be harnessed to recreate the underlying counterfactual distributions that produce observational data and this is demonstrated with a simulated data set and its results are compared to other common approaches. Finally, the method is applied to a real life data set of an observational study of two possible methods of integrating mental health treatment into the shelter system for homeless men. This analysis of this data demonstrates a situation where treatments have identical outcomes for a subset of the covariate space and a subset of the space where one treatment clearly dominates, thereby informing an individualized patient driven approach to treatment selection.

Keywords: Bayesian
Causal inference
Dirichlet process
Nonparametric statistics
Advisor: Escobar, Michael D
Olympus Mons Concerto for Violoncello and Orchestra

Commissioned by Edouard Claerhout for Belgian cellist Marie Hallynck, Olympus Mons is a concerto for violoncello and orchestra in two movements with a total duration of approximately 30 minutes. The orchestral forces consist of piccolo, 2 flutes, 2 oboes, English horn, 2 clarinets in B-flat, 2 bassoons, contrabassoon, 4 French horns in F, 3 trumpets in C, 2 tenor trombones, 1 bass trombone, 1 tuba, 1 piano (+celesta), 3 percussion and a string orchestra of amble size to balance the above wind, keyboard and percussion forces. Olympus Mons is dedicated to two giants of contemporary music: Sofia Gubaidulina and Henri Dutilleux, hence its bipartite structure. The piece is paying homage to these two older composers but does not quote directly from their music nor does he make stylistic references to them. The only, albeit veiled, quotation in Olympus Mons is from a chorale by Johann Sebastian Bach, who arguably represents the Olympian summit of classical music and who in a metaphorical manner raises onto himself the two dedicatees. The title of the composition refers to the Martian mountain Olympus Mons, which is the tallest mountain in our Solar System, three times taller than Mount Everest. Drawing a parallel between these two great composers, two great peaks in the world of musical composition, and the tallest mountain in our solar system is an apt metaphor, particularly since the music of this concerto is an homage to their geniuses.

Keywords: Canadian Music
Concerto
New Music
Orchestra
Violoncello
Advisor: Hatzis, Christos