VictorJuiz/thesis huggingface dataset:
Organic Materials for Energy Generation and Storage

In this thesis, I describe my efforts in developing organic materials for energy storage and generation. Chapter 1 introduces the broad classes of organic materials that are the focus of the thesis, including graphene, small molecules and conjugated polymers. It provides background into the principles of energy storage in supercapacitor devices, including the mechanism, performance metrics, and common materials. It provides a brief overview of energy generation in photovoltaic devices, with a focus on the electron transport layers of perovskite solar cells. Chapter 2 explores synthesis of a graphene quantum dot/poly(3,4-ethylenedioxythiophene) (PEDOT) film for application as a supercapacitor electrode. I demonstrate the first electrochemical polymerization of functionalized graphene quantum dots. I determined that the graphene quantum dot/PEDOT films have significantly higher capacitance than control films, but reduced cycling stability. Chapter 3 investigates a polymer comprising PEDOT with tetrachlorinated perylene diimide pendant units. This polymer was designed to serve as a stable ambipolar electrode for application in symmetric type III supercapacitor devices. It demonstrates moderate capacities, but the donor-node-acceptor architecture grants it extremely good charge cycling stabilities in both positive and negative regions. In Chapter 4, I examine a graphene quantum dot/perylene diimide material for application in perovskite solar cells. This material was demonstrated to successively quench the fluo- rescence of a perovskite material, indicating its potential as an electron transport layer. It is hoped the graphene will facilitate electron extraction at the electrodes, in addition to providing improved stability to ultraviolet, thermal and chemical degradation to perovskite solar cell. Chapter 5 examines the potential to dope graphene with tellurium for use as a non-precious metal catalyst for the electrochemical reduction of oxygen in basic aqueous medium. It was demonstrated that graphene oxide could be simultaneously thermally reduced and doped with tellurium, and the resulting Te-doped graphene showed potential as an electrocatalyst. The doping was unable to be suitably controlled and resulted in inconsistent Te-doping, tellurium oxidation states and oxygen content within the Te-doped graphene. In Chapter 6, I detail a simple microwave-assisted synthesis of carbon nanodots, and screen potential precursors to allow the controlled doping of carbon nanodots with heteroatoms. It was demonstrated that the carbon nanodots could be rapidly synthesized, and heterogeneous mixtures of precursors allowed modification of the optical properties of the synthesized carbon nanodots. Chapter 7 serves to summarize the thesis, provides future outlooks on the topics covered, and proposes future research directions in the field to generate high performance organic ma- terials for energy storage and generation.

Keywords: Energy Storage
Graphene
Polymers
Supercapacitors
Advisor: Seferos, Dwight S
Altered Excitation-inhibition Balance in Depression and Stress: Contributing Pathology and Treatment Target

Lifetime exposure to severe or lasting stressors is a shared risk factor across psychiatric illnesses that together account for one-third of global years lost due to disability, including major depressive disorder (MDD), anxiety disorders, and post-traumatic stress disorder (PTSD). Evidence from human and animal studies demonstrates alterations in cellular and molecular components of excitation-inhibition balance (EIB) as central to these illnesses. These include deficits among excitatory glutamatergic neurons, inhibitory GABAergic interneurons, and glial cells. Concurrently, first-line antidepressant drugs (ADs) achieve insufficient response, low remission, and high relapse rates, in part because they do not directly target primary pathological alterations to EIB components. Although recent advancements have been made with rapid-acting ADs targeting excitatory alterations, several pathological targets among EIB components remain unexplored. This thesis investigated how deficits in cellular and regional mediators of EIB, as informed by human pathological findings, contribute to preclinical behaviors reflecting symptoms of chronic stress-related disorders. Using transgenic mice with brain-wide low somatostatin-positive GABAergic interneuron (“SST+ cell”) function, we first identified that inhibitory SST+ cells regulate depressive-, anxiety-, and anhedonia-like behaviors, plus memory impairment, supporting evidence that primary SST+ cell deficits in humans contribute to MDD symptoms (Study 1). In chronic stress-exposed mice, we next identified that stress-related behavioral deficits emerge partly through altered EIB, specifically, enhanced functional activation of the anterior cingulate cortex and ventral hippocampus (Study 2). We then evaluated the therapeutic potential of novel AD strategies targeting excitatory homeostasis or inhibitory components of EIB. Prophylactic administration of riluzole, a drug that regulates excitatory glutamate homeostasis, enhanced resilience in chronic stress-exposed mice (Study 3). In transgenic mice with SST+ cells silenced, potentiation of α5-GABA-A receptors (that partially mediate inhibitory SST+ cell functions) revealed antidepressant potential, demonstrating a proof-of-concept for emerging therapeutic mechanisms bypassing SST+ cell pathological changes (Study 1). These studies contribute evidence linking disrupted EIB to behavioral deficits related to symptoms of psychiatric illnesses and support antidepressant mechanisms targeting components of altered EIB. The insights from this work have potential to advance precision diagnosis and treatment of MDD and other neuropsychiatric disorders linked to chronic stress.

Keywords: Depression
Excitation
GABA
Inhibition
Somatostatin
Stress
Advisor: Sibille, Etienne
Cutting the Knot: Founding Canada and Restoring the Honour of the Crown

The honour of the Crown in Canadian Aboriginal jurisprudence has taken on a prominent role in interpreting s.35 of the Constitution Act 1982, cited as grounding, at a minimum, Crown responsibilities to consult and accommodate. Yet what is not often discussed is the over 800 year long legal legacy of the honour of the Crown in common law and equity and that our understanding of Crown honour today appears greatly narrowed and underapplied in contrast. I offer a more full and complete understanding of the roots of the honour of the Crown and its relevance to the Crown's relationship to Indigenous peoples with the hope of offering a new lens through which to more properly understand those relationships, those treaties made on the basis of Crown honour, and the path of reconciliation itself.

Keywords: de jure
honour of the crown
indigenous
reconciliation
sovereignty
treaty
Advisor: Sanderson, Douglas
Characterization of 13C-Lactate Signals for the Application of Hyperpolarized 13C MRI in Intracranial Metastasis Patients

Intracranial metastasis is a clinical heterogeneous disease, commonly treated with radio- therapy. However, diverse treatment outcomes and potential side effects associated with aggressive radiotherapeutic approach makes it essential to identify which patients will benefit from such treatment. Elevated lactate production in metastatic tissues has been proposed by other researchers as a metabolic biomarker for radiation resistance in cancer patients. Hyperpolarized 13C MRI is an emerging metabolic imaging modality that can detect 13C-lactate production in tissues from the injected “hyperpolarized” 13C-pyruvate. This imaging modality has been steadily evolving towards clinical translation over the last decade, leading to a number of recent publications demonstrating the feasibility of implementing this tool to acquire 13C-lactate images in the human brains. However, even healthy brain tissues generate high 13C-lactate signals from the injected 13C-pyruvate. Moreover, there are a number of biological components involved in the 13C-lactate production from the injected 13C-pyruvate, making it difficult to accurately interpret the acquired 13C-lactate signals. As a result, the optimal approach to characterize these 13C-lactate signals for the clinical assessment of intracranial metastasis remains under investigation. In this dissertation, approaches to enhance our understanding and characterization of 13C-lactate signals is described. The pre-clinical experimental approach was designed to investigate the correlations between biological components of lactate metabolism and 13C-signals. The conventional method to characterized 13C-lactate signals (i.e. lactate- to-pyruvate ratio) was confirmed to strongly correlate to [1-13C]lactate concentration but not to the total lactate pool size in metastatic tumour xenograft model. Accordingly, a novel approach of characterizing 13C-lactate signals as ‘z-score’ in the human brain was developed. This segmentation-based approach was implemented to investigate 13C-lactate metabolism in the control human brains and revealed that the human brains have consistent region-specific lactate biology. This approach was further extended to characterize 13C-lactate signals in 14 intracranial metastatic lesions in 10 patients. A median split analysis suggested that lactate z-scores may be better predictors of clinical progression following radiation treatment than the conventional lactate-to-pyruvate ratio approach. This suggested that the approach described in this thesis can potentially improve clinical assessment of intracranial metastases in response to radiation treatment using the information stored in 13C-lactate images.

Keywords: Brain
Cancer Metastasis
Hyperpolarized 13C MRI
Lactate
Metabolic Imaging
Pyruvate
Advisor: Cunningham, Charles H
Technocracy

Technocracy is a twelve-minute, single-movement work for orchestra. Divided into three sections, Technocracy nods at the rhetorical thrust of traditional sonata form insofar as two contrasting sets of musical material are juxtaposed against one another then subsequently resolved within a single movement. However, whereas the recapitulation of a traditional sonata resolves the secondary theme to the key of the primary theme via some form of alteration, the final section of Technocracy balances the material of the prior sections without altering one to accommodate the other. Section A organizes pitch horizontally through a series of twelve chords that are constructed, as much as possible, from stacked tonal triads. These chords progress gradually from a twelve-note aggregate presented at the opening to a single note that signals the transition from Section A to Section B. Throughout Section A, there is no clear instrumental hierarchy, and sudden dynamic shifts combined with unpredictable repeating rhythms, create the impression of chaos. Section B retorts the horizontal pitch organization of Section A with a series of tone rows. While Section A lurches between dynamic extremes, Section B is a relatively steady trajectory from soft to loud. In Section A, chaos reigns, whilst in Section B, the instrumental hierarchy is clearer; winds and brass present melodic material while the strings and percussion provide support. Section C of Technocracy consolidates the ideas presented in the preceding sections. It combines the tone rows of Section B with the chord progression of Section A. By maintaining a strong sense of pulse and forward motion, it consolidates the rhythmic unpredictability of Section A and the relative stasis of Section B. Finally, Section C strikes a balance between the orchestrated chaos of Section A and the clear hierarchy of Section B.

Keywords: Arts
Communication
Composition
Music
Orchestra
Politics
Advisor: Palej, Norbert
CRISPR/Cas9-based Genetic Screens Reveal Novel Cancer Cell Mechanisms for Evading Metabolic and Immunological Stress

Genetic screening technologies with the CRISPR-Cas system have greatly expanded our ability to annotate the function of genes in mammalian models at a systems-level. While this has provided novel insight into the genetic basis for diseases such as cancer, the use of this technology remains in its infancy. Through an exploration of the contemporary CRISPR screening literature, we identified a paucity of data informing our understanding of the emerging cancer hallmarks of reprogrammed metabolism and immune evasion. To circumvent these knowledge gaps, we developed and employed CRISPR/Cas9-based genetic screening approaches to reveal new biological insight into how cancer cells adapt to metabolic stress and evade T-cell killing. This included the mapping of genetic interactions (GI) for the de novo fatty acid synthesis pathway, which identified the previously uncharacterized gene, C12orf49 (named herein as Lipid Uptake Regulator; LUR1), as a strong negative GI partner of fatty acid synthase (FASN). We demonstrate LUR1 as being required for the optimal induction of the sterol-regulatory-element binding protein 2 (SREBP2) transcriptional response following intracellular lipid depletion. Furthermore, we identify a core set of genes whose perturbation renders cancer cells more sensitive or resistant to T-cell killing across diverse genetic backgrounds. We subsequently organize these genes into a functional hierarchy through genetic co-essentiality analysis and GI mapping, revealing the power of systematically applying CRISPR screens for uncovering the genetic determinants of complex phenotypes such as immune evasion. Collectively, our data underscore core principles in applying CRISPR/Cas-based genetic screens for interrogating the genotype to phenotype relationship of cancer.

Keywords: Cancer
CRISPR
Genetic interactions
Immune evasion
Metabolism
Advisor: Moffat, Jason
Ailles, Laurie
Peter Comestor's Lectures on the Glossa ‘ordinaria’ on John (ca. 1165): An Historical Introduction with a Critical Edition

This thesis encompasses the first partial critical edition and specialised study of a series of lectures from the cathedral school of Notre-Dame, Peter Comestor’s Glosae super Iohannem glosatum. Delivered in Paris in the mid-1160s, Comestor’s lecture course on the Glossa ‘ordinaria’ on the Gospel of John has survived in seventeen manuscript witnesses, being preserved in the form of continuous transcripts taken in shorthand by a student-reporter (reportationes). Following a careful census of the manuscript tradition, I have selected ten of the best witnesses dating from between ca. 1175 and 1225 to produce a critical edition of the prothemata and the first chapter of Comestor’s lectures. In addition to the text of the original lectures, I provide two appendices containing subsequent accretions to the lecture materials contributed by Comestor and his students, as well as a third appendix containing an edition of the corresponding portion of the Glossa ‘ordinaria’ from which Comestor lectured. The second part of this thesis, comprised of five chapters, represents a critical study of the historical and intellectual context of Peter Comestor’s biblical teaching. Chapter One presents an outline of Comestor’s scholastic career and known works, a survey of the scholarship on his biblical glosses, and a general introduction to the text of the edition: its date, genre, and title. Chapter Two charts the intellectual landscape of Comestor’s lectures: namely, the tradition of biblical teaching originating at the School of Laon, preserved in the Glossa ‘ordinaria,’ and subsequently developed in the classroom by Peter Lombard and a succession of Parisian masters. Chapter Three examines more closely the portion of the Glosae presented in this thesis, encompassing: an overview of its structure and narrative sequence, an examination of Comestor’s teaching method and scholastic setting, an outline of the sources behind the master’s biblical scholarship, and a survey of his engagement in contemporary doctrinal controversies. In Chapter Four, I provide a detailed description of the manuscripts selected for this edition together with a stemmatic analysis of their relations. Finally, Chapter Five sets forth the editorial principles observed in the edition, its various apparatus, and the appendices.

Keywords: Biblical exegesis
Latin philology
Medieval commentary
Peter Comestor
Twelfth-century schools
Advisor: Andrée, Alexander
Mainland Southeast Asia Precipitation: Natural Variability, Teleconnection, and Response to External Forcing

Mainland Southeast Asia (SEA) has been considered to be a particularly vulnerable region to climate change. Reducing uncertainty in future projections of changes in SEA precipitation requires a better understanding of the processes that drive variability in present day SEA precipitation. Here we examined the impact of natural climate variability and anthropogenic forcing associated with anthropogenic aerosols on precipitation in SEA. We also investigated the resolution dependence of modeled precipitation extremes in SEA using the Community Earth System Model (CESM). The sources of moisture for local precipitation over mainland SEA and the interannual variability in precipitation during the Indian summer monsoon period were examined using a version of CESM with water tagging capability. We found that interannual variability in precipitation over mainland SEA during the monsoon onset is associated with an El Niño and Southern Oscillation (ENSO) induced shift in the Indian summer monsoon onset, whereas variations in precipitation later in the monsoon period reflect variations in the monsoon circulation and tropical cyclonic activity. We examined the capability of a variable resolution version of CESM to simulate regional climate features in SEA, especially extreme precipitation events. Compared to coarse-resolution versions of CESM, we found that variable-resolution CESM (VR-CESM) significantly improved the tail distribution of precipitation, with smaller biases in N-year-return-period events with respect to the reference data sets. In addition to a more accurate representation of the topography, the better resolved vertical moisture flux in VR-CESM increased resolved-scale precipitation, leading to better simulation of the precipitation extremes. The impact of anthropogenic aerosols on regional climate over the Asian monsoon region was also examined using VR-CESM. It was found that anthropogenic aerosols tend to cause an overall reduction in the summer mean and extreme precipitation over the Asian continent through a weakening of the Asian summer monsoon circulation. The decrease in the precipitation over mainland SEA was due to an ocean-mediated response to the aerosol forcing, whereas the reduction in precipitation over East Asia was likely caused by a direct atmosphere adjustment to the aerosol forcing.

Advisor: Jones, Dylan B
Approximating Bayes: Inference and Modeling

This thesis focuses on sources of error in modern Bayesian analysis and machine learning in the ``big data'' era. We develop new theoretical tools for analyzing and controlling different sources of error. Our work leads to new theory and methodology for providing performance guarantees for modern Bayesian methods and machine learning algorithms. The first two contributions of this thesis are new tools for studying the complexity/hardness of achieving approximation guarantees for Markov chain Monte Carlo (MCMC) in high-dimensional settings. The third contribution of this thesis is a theoretical framework for Bayesian analysis in the face of model misspecification that makes the analysis of different practical Bayesian methods possible. The fourth contribution of this thesis is a bridge between PAC-Bayes theory and Rademacher complexity, two important theoretical tools for developing the so-called generalization bounds in machine learning theory. Through the analysis of various sources of error, this thesis makes contributions to the study of: convergence of high-dimensional MCMC; optimization of high-dimensional MCMC; Bayesian model misspecification; and statistical learning theory.

Advisor: Roy, Daniel M.
Rosenthal, Jeffrey S.
Literacy Development in Canadian French Immersion Students: The Role of Oral Language

The overarching goals of this dissertation were to examine the extent to which lower-level oral language skills facilitate phonological awareness and to investigate the importance of higher-level oral language skills in the development of reading comprehension among children enrolled in Canadian French immersion programs. The first study investigated how lexical restructuring can stimulate children’s phonological awareness in their first (L1) and second (L2) languages. Sixty-two emerging English (L1) – French (L2) bilingual children were taught new English and French word pairs differing minimally in phonological contrast. The results indicated that lexical specificity in English at the beginning of Grade 1 mediated the relationship between English vocabulary and English phonological awareness both concurrently and longitudinally. Furthermore, a longitudinal relationship was established among French vocabulary, French lexical specificity, and French phonological awareness at the end of Grade 1. Notably, cross-language transfer from English was a better predictor of development in French phonological awareness, especially for words that contained phonological contrasts common to both languages. The second study was designed to understand the extent to which second graders’ comprehension monitoring predicts reading comprehension in the third grade. The ability to monitor one’s comprehension was assessed by the proficiency to detect internal inconsistencies in orally presented stories among 115 emerging bilingual children. The concurrent results revealed that in Grade 3, children’s comprehension monitoring served as a unique predictor of reading comprehension within English and French, over and above the contribution of word reading and vocabulary. This relationship was not observed in Grade 2. Moreover, the longitudinal analyses indicated that Grade 2 children’s comprehension monitoring in English made a significant contribution to English reading comprehension in Grade 3, even after controlling for word reading, vocabulary, and the autoregressor variable. However, this relationship was not established in the L2. Overall, the results from this study lay the groundwork for the development of screening measures that can be used by educators to support phonological foundations of literacy. Furthermore, the findings suggest there is a need to include support for higher-level language skills, such as the ability to monitor one’s comprehension, in the early stages of bilingual reading instruction.

Keywords: Bilingualism
Comprehension monitoring
French immersion
Lexical specificity
Phonological awareness
Advisor: Chen, Xi Becky