VictorJuiz/thesis huggingface dataset:
Apollo in Thebes: Using a Genetically Encoded Family of Sensors to Study NADP+ Dynamics using Deep Learning
Keywords: Deep Learning
Fluorescence Anisotropy
Microscopy
NADPH/NADP+ Redox
Type 2 Diabetes

Accumulation of reactive oxygen species (ROS) lies at the core of many diseases including cardiovascular disease, neurological disorders and type 2 diabetes (T2D). In turn, ROS is scavenged through antioxidant pathways powered via intracellular NADPH/NADP+ redox. The relationship between NADPH/NADP+ redox and ROS accumulation is particularly important to T2D as there is evidence that both ROS and NADPH/NADP+ are under looser regulatory control due to their roles as signaling molecules in the pancreatic beta-cell. Understanding how these dual roles contribute to beta-cell dysfunction under metabolic stress is therefore critical to an etiological understanding of the disease. Unfortunately, a lack of suitable NADPH/NADP+ redox sensors have left this field understudied. To that end, we use a novel application of fluorescence polarization (Apollo) to develop the NADPH/NADP+ redox sensor Apollo-NADP+ and adapt it for various subcellular compartments including the mitochondria and the nucleus. Using this sensor, we were able to show that significant NADPH/NADP+ depletion precedes ROS accumulation, which highlights the importance of NADPH/NADP+ as a tool to study the mechanisms behind ROS accumulation. Using mitochondrial-targeted Apollo-NADP+, we were also able to identify the mitochondria as a root of NADPH/NADP+ dysfunction under lipotoxicity. Further investigation of these results in the context of beta-cell heterogeneity requires both a high-throughput imaging and a high-throughput analysis platform. High-throughput imaging was accomplished through the creation of a custom, three-colour, widefield polarization microscope, while high-throughput analysis was accomplished through the Thebes analysis pipeline, which used deep learning in order to split the tasks into: cell boxing, cell masking, and subcellular segmentation. Although performing widefield imaging for Apollo sensors requires additional optimization, we were able to demonstrate some key results including apparent cell heterogeneity in the beta-cells in dispersed islets. Overall, this project furthers the field of sensor design through the Apollo family of sensors as well as providing a set of tools that can be used towards the study of NADPH/NADP+ redox beyond the context of T2D.
Aeroacoustics of Shallow Cylindrical Cavities with Specific Application to the Inter-wheel Region of Aircraft Nose Landing Gears
Keywords: Aeroacoustics
Aerodynamics
Cavity
Landing Gear

Cylindrical cavities located on the interior sidewalls of aircraft nose landing gear wheels generate high amplitude tones when subject to grazing flow at aircraft approach speeds. These geometries consist of two, closely spaced shallow cavities, with depth-to-diameter ratios typically less than h/d
Rhodium-Catalyzed Enantioselective Desymmetrizations of Oxabicyclic Alkenes and Alkene Difunctionalization via Nickel-Catalyzed Arylcyanation
Keywords: Catalysis
Enantioselective
Heterocycles
Nickel
Rhodium
Ring Opening

The synthesis of heterocycles using transition metal catalysis is a topic of broad interest in the field of organic chemistry. Transition metal catalysts allow many diverse bond disconnections to be realized, allowing for many ways to assemble heterocycles. Many of the transformations developed in the Lautens group are aimed at atom economical bond construction processes that streamline synthesis and minimize waste. The arylcyanation reaction and the asymmetric ring opening (ARO) reaction are two examples of methods developed in our group that embody this design principle. Chapter 1 of this thesis describes the development of a nickel-catalyzed arylcyanation reaction for the synthesis of 3,3-disubstituted oxindoles. This method was inspired by our work on the palladium-catalyzed arylcyanation reaction, originally developed to address challenges in the formal synthesis of (+)-corynoline. This nickel-catalyzed reaction uses an air-stable catalyst precursor to achieve a highly practical synthesis of a nitrile-containing oxindole via a domino Heck-cyanide capture cascade. Derivatizations of the nitrile group affords a series of novel heterocyclic scaffolds. Chapter 2 details the discovery and development of a novel enantioselective cycloisomerization reaction of oxabicyclic alkenes. Our work on developing the intramolecular asymmetric ring opening reaction led to the discovery of a novel epoxide synthesis. Specifically, when bridgehead substituted oxabicyclic alkenes with non-nucleophilic side chains are reacted with the [Rh(cod)2]OTf/PPF-PtBu2 catalyst in the absence of an external nucleophile, chiral epoxides are obtained. The synthesis of epoxides through cycloisomerization reactions possesses 100% atom economy and avoids the use of external oxidant. Chapter 3 describes an asymmetric ring opening reaction, specifically to address gaps in the methodology concerning amine nucleophiles. We were inspired by our group’s previous attempts to use amino acid derived nucleophiles in the ARO reaction. We developed a way to incorporate amino acids into the ARO reaction by employing their 2-nitrobenzenesulfonamide (nosyl) derivatives as pronucleophiles. Intriguingly, we observed a divergence in reactivity between the diastereomeric hydroxyester products, in that one diastereomer was capable of lactonization and the other was not. This led to the enantioselective synthesis of chiral oxazinones, which are similar to the naphthoxazine class of compounds which possess dopaminergic activity.
Tracing the Distribution of Pb and Trace Elements in the Canadian Arctic from the Atmosphere to the Ocean
Keywords: aerosols
Arctic Ocean
Baffin Bay
Canadian Arctic Archipelago
trace elements
trace metal isotopes

Trace elements (TEs) play important roles in biogeochemical processes in the Arctic and understanding their cycling along with their isotopes will help us understand better the warming induced changes in the Arctic. This dissertation measured Pb, its isotopes and other TEs in aerosols and seawater samples collected in the Canadian Arctic. Lead and its isotopes are useful particulate source tracers and can be used to understand particulate contaminant inputs and oceanic circulation. Iron is also evaluated because it is an important micronutrient for primary production in the ocean. This study shows that anthropogenic aerosols from Europe and Russia (Eurasia) still dominate during the Arctic Haze period (winter–spring) and particulate pollution levels are relatively stable in the Arctic since the 2000s. This study also traced the anthropogenic Pb from aerosols to the Canadian Arctic seawater using Pb isotope measurements. Historic Eurasian Pb with distinctively low 206Pb/207Pb (
Ultra-Diffuse Galaxies and Ultra-compact Dwarfs in the Hubble Frontier Fields
Keywords: dwarf galaxies
galaxy clusters
low-surface-brightness galaxies
ultra-compact dwarfs
ultra-diffuse galaxies

Large low surface brightness galaxies have recently been found to be abundant in nearby galaxy clusters. In this thesis, I investigate these ultra-diffuse galaxies (UDGs) in the six Hubble Frontier Fields galaxy clusters: Abell~2744, MACSJ0416.1-2403, MACSJ0717.5+3745, MACSJ1149.5+2223, Abell~S1063 and Abell~370. These are the most massive (1-3 × 1015~Mo) and distant (0.308 < z < 0.545) systems in which this class of galaxy has yet been discovered. The clusters host an estimated ~200-1400 UDGs inside the virial radius (R200), consistent with the UDG abundance halo-mass relation found in the local universe, and suggests that UDGs may be formed in clusters. Within each cluster, however, I find that UDGs are not- evenly distributed. Instead their projected spatial distributions are lopsided, and they are deficient in the regions of highest mass density as traced by gravitational lensing. While the deficiency of UDGs in central regions is not surprising, the lopsidedness is puzzling. The UDGs, and their lopsided spatial distributions, may be associated with known substructures late in their infall into the clusters, meaning that I find evidence both for formation of UDGs in clusters and for UDGs falling into clusters. Also included is a catalog of UDGs in the Frontier Fields. I also investigate the ultra-compact dwarfs (UCDs) residing in the clusters, and find the spatial distributions of UDGs and UCDs appear anti-correlated. Around 15% of UDGs exhibit either compact nuclei or nearby point sources. Taken together, these observations provide additional evidence for a picture in which at least some UDGs are destroyed in dense cluster environments and leave behind a residue of UCDs.
Music by the Ducat: Giuliani's Guitar and Vienna's Musical Markets, 1806-1819
Keywords: Classical Guitar
Congress of Vienna
Folk Music
Mauro Giuliani
Nineteenth-Century Vienna
Virtuosity

Amidst ambivalent attitudes held toward the guitar, Italian-born guitar virtuoso Mauro Giuliani (1781-1829) composed and performed in Vienna from 1806 to1819. Giuliani’s time in the city was punctuated by his participation in the market for goods related to the Congress of Vienna. He entered this market by gearing his performances and publications towards representing the Congress’s mandate of cooperation and conversation, as well as the recent interest in Austrian folk songs alongside patriotic sentiments for an emerging Austrian state. Giuliani’s solo guitar performances were defined by his unique ability to overcome what critics regarded as the guitar’s seemingly unsurmountable deficiencies. His active participation in the virtuoso concert culture of Vienna—a market that was removed from a growing “serious” concert culture—was defined by his increasing involvement in the commercially-driven subscription concert. Underlying Giuliani’s participation in the Congress of Vienna and the popular virtuoso concert was his interest in the burgeoning folk music movement. Related to Austrian patriotic sentiments, Giuliani’s folk-inspired Ländler and variation sets reveal his preoccupation with a more quotation-based approach to folk song composition, an approach that—while attractive in terms of print music sales—jeopardized the longevity of his folk-inspired works by obscuring his authorial ingenuity. The early nineteenth century is regarded by guitar scholars as the “Golden Age of the Guitar,” and Giuliani is often positioned as one of the foremost contributors to the development of classical guitar repertoire during this time. However, I argue that Giuliani’s approach to guitar composition and performance reveals not a desire to cultivate a solo classical guitar repertoire, but a concerted effort to present the guitar, and by extension, himself, as a commodity for Viennese markets associated with the Congress of Vienna celebrations, the lucrative virtuoso concert, and the burgeoning folk music movement. Underlying each of these markets was a demand for public and private performances, as well as a desire for printed music. The result of Giuliani’s efforts were performances and works that, while meant for consumption by the wider public, engage with the intimate, easily digestible, and sociable aspects of Vienna’s musical culture.
Fabrication of Carbon-based Nanocomposite Materials for Energy Storage Processes
Keywords: Carbon-based composite materials
Energy storage Processes
Methanation of CO
Zn-air batteries

Our society’s development depends on the way we use, store, and transform the energy. Currently, we have multiple sources of clean energy to cover the demand of a growing population. However, a big gap remains in the technology to efficiently store the energy that is not being consumed. The purpose of this thesis is to explore carbon-based composite materials to promote the development of new systems for the efficient conversion, use, and storage of energy: first, at small-scale storage (batteries) and second, at large-scale storage (power to gas). In both cases, different carbon allotropes and functionalization methods were considered. The first half of the thesis describes materials and methods to improve the air cathode in Zn-air batteries. These batteries are considered promising energy storage devices because of the numerous advantages such as high energy density, low-cost and abundance of Zn, environmental friendliness, and safety. The first study is focused on developing a double layer membrane fabricated with thermoplastic polyurethane, carbon nanotubes, and activated carbon membrane to improve the oxygen diffusivity and to prevent electrolyte leakage. For the second study, we developed a bifunctional electrocatalyst to promote the oxygen reactions in Zn-air batteries and achieve an electrically rechargeable configuration. The electrocatalyst was fabricated with Co3O4 particles attached to a functionalized carbon support. The second half of the thesis is focused on the catalytic methanation of CO. This process allows the reduction of the main greenhouse gas, through the power-to-gas technology. Renewable energy can be used to power a reactor where the CO/CO2 is reduced to methane, which can be transported and stored in current systems. We considered Ni-based catalysts and carbon-based supports with the purpose of improving the CO conversion, the selectivity to CH4, and the catalyst stability. This study first compares Ni supported on AC and Ni3Sn supported on AC to determine the effectiveness of Sn as a carbon fiber suppressor. In a second step, the study describes the fabrication method and catalyst performance of a core-shell structure using silica spheres grown on SWCNTs coated with the catalysts Ni3Sn and FeNi3 to improve the thermal stability and catalyst activity.
Dual Roles of Nerve-Derived Precursor Cells During Adult Mammalian Tissue Regeneration
Keywords: Growth factors
Mesenchymal precursor cells
Peripheral nerves
Schwann cells
Tissue regeneration
Wound healing

Accumulating evidence suggests that endogenous tissue-resident precursors and stem cells play an important role in mediating the repair and regeneration of various adult tissues. Peripheral nerve innervation, found throughout all organs, is known to be an essential component of this regenerative injury response across various tissues and species, but through predominantly ill-defined mechanisms. Thus, here we utilized lineage tracing strategies combined with other approaches in order to ask how peripheral nerve-derived precursor cells might contribute towards mammalian tissue repair and regeneration. Using the adult mouse digit tip as a model to study multi-tissue regeneration, we first showed that following amputation of the distal digit, neural crest-derived Sox2-positive Schwann cells associated with nerves dedifferentiate to a precursor-like state and secrete growth factors including PDGF-AA and oncostatin M which stimulate the proliferation of surrounding mesenchymal cells. While normal regeneration was perturbed following surgical denervation or targeted genetic ablation of Sox2-positive Schwann cells, we showed that it could be largely rescued by transplantation of exogenous Schwann cells or their secreted ligands into denervated digits.
Methodological Considerations and Findings of a Vowel Perturbation Study in Typically Developing Children
Keywords: Auditory feedback perturbation
Speech development
Speech motor control
Vowel formants

Background: Auditory feedback enables the speech production system to compensatively correct for articulatory errors and to adaptively calibrate feedforward commands. Less is known about how these feedback control processes develop. Development can be probed by comparing how younger and older children compensate and adapt for experimentally-perturbed vowels in their auditory feedback. Aims: The aims of this work were to evaluate methods for real-time vowel estimation and tracking; to devise appropriate methods for meaningful analysis of data; and to apply those methods in a vowel perturbation study with children aged 4 to 9 years old, towards furthering an understanding of developmental speech motor control. Evaluation of vowel estimation and tracking: Audapter vowel perturbation software was tested on real and synthetic speech samples. The software was evaluated to be appropriate for use in children aged 4 to 9, within error margins of 60 Hz for F1 and 180 Hz for F2. Development of analyses: Circular statistical methods were demonstrated as a means to gain insight from directional vowel changes in F1-F2 space during compensation and adaptation; these methods supplement existing approaches to analyze changes in F1 and F2 separately. Vowel perturbation study: Children compensated and adapted for vowel perturbation, but younger and older children accomplished this in different ways. While older children compensated more directly to oppose the perturbation, younger children altered their vowels less directly, indicating that the role of auditory feedback within the speech system changes during development. Adaptation to perturbation was more variable than compensation in both groups. Contributions: This work contributes performance metrics for Audapter research software in children. The application of descriptive circular statistics to analyze vowel perturbation data was demonstrated. Preliminary evidence indicates that there are developmental differences in the manner in which children respond to vowel perturbation. There may be developmental differences in the manner in which sensory information is integrated (i.e. auditory with somatosensory) that could underlie these findings. Future research, using the circular analytical methods described in this dissertation, is needed to investigate this possibility, and to generate additional evidence towards furthering the understanding of auditory feedback integration in developing speech motor control.
Studying Abroad: An Anti-Colonial Inquiry
Keywords: study abroad

Study abroad has the potential to provide a valuable learning opportunity, provided students are supported throughout their experience to critically think and challenge the reification of knowledge hierarchies that are endemic of a colonial education system. This dissertation employs an anti-colonial discursive framework to explore the supports that exist in Ontario’s college system for domestic students engaging in a study abroad experience. Representatives from Ontario’s colleges were interviewed to gain insights into what pedagogical strategies were being used to support domestic students’ critical thinking pre-departure, while abroad, and upon return. Challenges to the implementation of a pedagogical framework, as well as participants’ views on best practices, were also explored. Thematic analysis was used to analyze the data. Findings indicate that the export commodity and human capital development models of internationalization inform the availability of study abroad support for domestic students. Despite the existence of some support, participants referenced a lack of a well-established framework to guide the experience. Pre-departure supports emphasized culture and safety, whereas, while abroad and upon return, reflection was a frequently used pedagogy. Participants emphasized the need for greater pedagogical supports throughout the study abroad experience. There is an opportunity to further develop the framework for pedagogical strategies, as participants reported a time of change at their respective institutions, with the formalization of processes and the centralization of resources underway. Recommendations are provided.
Effects of Motivation for Prosocial Spending on Subsequent Positive Affect
Keywords: empathy
moral elevation
motivation
positive affect

The present research compared the effects of empathy, moral elevation and a control condition as motivations for charitable donations on subsequent feelings of positive affect. Empathy and moral elevation have strong emotional aspects that provide the impetus for prosocial behavior. Empathy is defined as an other-oriented and congruent affective reaction that is concerned with the perceived well-being of another person (Batson, Ahmad, Lishner, 2009), while moral elevation is the warm, uplifting feeling people experience after witnessing moral beauty (Haidt, 2000). Empathy often induces negative feelings from seeing others in distress, while moral elevation often induces positive emotions. Thus, the initial difference in affective valence may have different effects on the positive affect experienced after acting prosocially. Furthermore, a number of personal characteristics are known to influence positive affect after prosocial behavior, such as personal values, internalized prosocial motivation and the satisfaction of basic psychological needs, namely autonomy, relatedness and competence. Therefore, the present study compared the effects of empathy and moral elevation, as well as a control condition, on individuals’ donations to charity and their subsequent positive affect while controlling for personal characteristics. Participants were 249 students from an introductory psychology class at the University of Toronto. The results suggested that participants in both the empathy and moral elevation conditions experienced significant decreases in positive affect following the induction of motivations, but that donating only helped restore positive affect to baseline measures in the moral elevation condition. Donating to charity was unable to restore participants to baseline measures in the empathy condition. The results also indicated that needs for competence and relatedness, internalized prosocial motivation and emotion regulation positively predicted positive affect after donation, while prosocial and pro-self values both negatively predicted positive affect after donation. As well, the association between affective empathy and positive affect after donating was negative for participants in the empathy condition, but positive for participants in the moral elevation condition. Similar differences by condition were found for internalized prosocial motivation and positive affect after donating. The theoretical and practical implications are discussed.