VictorJuiz/thesis huggingface dataset:
Investigating the Role of Sublaterodorsal Tegmental Nucleus GABA Neurons in Sleep-Wake Control

The sleep-wake cycle is a continuous oscillation between wakefulness, NREM sleep, and REM sleep, which provides the fundamental backbone for all behaviors. This phenomenon is reported in both vertebrate and invertebrate animals, which branched out at an early stage of evolution. Hence, the most ancient structure of the brain -the brainstem- is hypothesized to control sleep-wake states. Growing evidence suggests that the brainstem houses all the necessary elements for regulating sleep-wake states; however, the mechanism by which these elements control sleep-wake states remains incompletely understood.The sublaterodorsal tegmental nucleus (SLD) is a brain region in the pons of the brainstem. The SLD contains GABA-releasing neurons with neuroanatomical features suitable for regulating sleep-wake states. However, their precise role in sleep-wake control remains to be determined. In my thesis, I used optogenetics, genetically assisted track tracing, and fiber photometry to identify the functional role of GABA SLD neurons in sleep-wake control and assess whether these neurons are involved in the pathophysiology of a sleep disorder, narcolepsy. From this study, I found that: 1) silencing GABA SLD neurons promotes wakefulness and activating the same neurons suppresses wakefulness, 2) GABA SLD neurons send axon projections to other wake-promoting brain areas, 3) the activity of GABA SLD neurons varies as a function of sleep-wake state: high/phasic activity during REM sleep, intermediate/phasic activity during wakefulness and low/oscillatory activity during NREM sleep, and 4) GABA SLD neurons generates sleep attacks under narcoleptic conditions. Taken together, I conclude that GABA SLD neurons play an important role in suppressing wakefulness and stabilizing sleep-wake states, but they can also pose a threat to wakefulness by generating sleep attacks under narcoleptic conditions.

Keywords: brain network
fiber photometry
narcolepsy
optogenetic
sleep
wakefulness
Advisor: Peever, John H
Exploring Beta Cell NADPH production using Organelle-targeted Apollo-NADP+ Sensors

A major function of beta cells is the production and secretion of insulin to maintain glucose homeostasis. Loss of this function is directly linked to progression of diabetes. The loss of beta cell function is exacerbated by cellular senescence associated with natural aging. Senescence impacts mitochondrial-dependent pyruvate cycling and nicotinamide nucleotide transhydrogenase (NNT) activity, which are important for production of beta cell NADPH to support biomolecule synthesis during cell growth and for the quenching of reactive oxygen species generated during oxidative stress. We hypothesized there exist changes in beta cell NADPH associated with development of beta cell senescence. We previously developed genetically encoded Apollo-NADP+ sensors to track changes in NADPH/NADP+ redox in real time. We targeted Apollo-NADP+ to various organelles to probe whether organelle compartmentalization of NADPH could create disparate impacts on beta cell metabolism. We demonstrated glucose- and glutamine-stimulated NADPH responses in the mitochondria preceded those in the cytoplasm indicating the dominant role of mitochondria in setting beta cell NADPH redox state. We subsequently aimed to develop an Apollo sensor based around pyruvate kinase M2 to allow for simultaneous tracking of NADPH and glycolytic flux. The resulting sensor was responsive to some oxidative treatments such as hydrogen peroxide and diamide, but wholly insensitive to other physiological treatments such as glucose and serine. It is likely the sensitivity of pyruvate kinase M2 to a variety of post-translational modifications made the sensor responses difficult to interpret. Finally, we explored doxorubicin as an inducer of senescence to observe changes to NADPH production during senescence. We found doxorubicin locked cells into a late G1 state consistent with induction of senescence. Senescent cells appeared to have increased glutamine-stimulated NADPH responses, consistent with reports of senescent cells being dependent on glutamine for survival. Preliminary data suggest the increased NADPH response may be due to an increased proportion of cells in G0/G1. Future work aims to identify differences in NADPH metabolism between quiescent and senescent beta cells. Overall, this thesis developed organelle targeted tools to enable simultaneous study of mitochondrial-driven NADPH responses simultaneously with other sensors.

Keywords: Fluorescent protein
NADPH redox
Protein engineering
Sensors
Advisor: Rocheleau, Jonathan V
Introverted Reflections

Introverted Reflections is a seventeen minute two-movement orchestral composition (2,2,2,2,4,3,3,1, timpani,3 perc, harp, piano, and strings) submitted in conformity with the requirements for the degree of Doctor of Music (Composition). The work summarizes most of the knowledge acquired during my residency at the University of Toronto while maintaining coherence and integrity to my preferred harmonic, melodic, and rhythmic language. As I was composing since late 2020, my world was going through turmoil. The Lebanese revolution and political/economic crisis, COVID 19, and the Beirut blast had a significant effect on me as I turned inwards looking for ways to keep moving forward with optimism despite the darkness. These paths are deeply embedded in this piece. Main influences that informed the work would be extended tonal harmony, modes of limited transposition, Late Romanticism, Minimalism, Middle Eastern modes, Middle Eastern aksak rhythms, synthetic modes, modal harmony, sonorism , and monophonic melodic writing influenced by Lebanese church music. The first movement starts off with a sonoristic asymmetrical motif that grows into a lyrical melodic section expanding from its own self gaining momentum until it reaches a contrasting minimalist section which rebuilds on the forward momentum until a climactic resolve into the initial asymmetrical motif. The second movement opens with a monophonic Middle Eastern-influenced chant that stubbornly recurs with added layers, a counter melody and woodwind textures acknowledging the tension. After reaching a cadence, the music transitions into a new minimalist section introducing a five-note woodwind motif and continuing its march with a predominant 15/8 rhythm that carries the music towards a variant to the initial melody in different modes and in 11/8. Following the climax to an octatonic variation, a new section emerges binding material from the initial melody and the first movement. Dissonant layers and textures contribute to blurring the melody, but after multiple failed attempts, the music finally lands on the major scale. The opening from the first movement is re-introduced in a much brighter tone, fusing with material from the second movement altogether embracing the cyclical infinitude of everything.

Keywords: composition
Advisor: Hatzis, Christos
Evaluating the Role of Myelin Regulatory Factor in Mouse development

During development, the precise spatiotemporal regulation of transcription is achieved through stage-specific transcription factors in response to internal and external cues. Using mouse embryonic stem cells to recapitulate early embryonic fate, Myelin Regulatory Factor (MYRF) was identified as a prominent transcription factor that increased expression upon pluripotency exit. MYRF is known for the transcriptional regulation of myelination genes in oligodendrocytes. MYRF works cooperatively with SOX10 to activate myelination genes by targeting regulatory sequences. Multiple neurological and nonneurological disorders have been linked to MYRF de novo mutations. Therefore, a better understanding of the role of MYRF during embryonic development can enhance current knowledge of genetic predispositions and medical interventions for related anomalies. Among the transcription factors that maintain pluripotency in embryonic stem cells is SOX2, which is an essential transcription factor in embryonic development where aberrations have been linked to many developmental defects. Considering the expression and relative association of MYRF and SOX10 during central nervous system development, the role of MYRF in cooperation with SOX2 was assessed in the context of pluripotency and embryonic development. In addition, novel interactors between MYRF and proteins of the nuclear lamina were discovered and assessed in a pluripotency context. A dynamic and inversely correlated association between MYRF and transcriptional complexes, or the nuclear lamina, was observed. These results indicate that MYRF may be recruited to transcriptional complexes via cell-specific SOX factors, and in the absence of such recruiters, MYRF resides in association with Lamins which mayact as a nuclear repository for this protein. Furthermore, the role of MYRF during embryonic development was evaluated using a Cre-Lox system for gene ablation. The homozygous deleted embryos show embryonic delays in development as well as lethality at E10.5. Further assessment of the cause of embryonic lethality using tissue-specific elimination in cardiac progenitors did not result in embryonic lethality, indicating that the primary cause of embryonic lethality is not relevant to the development of cardiomyocytes. However, MYRF-deficient adult mice exhibit a decline in cardiac function and cardiomyopathy with age. Similarly, adult mice with a heartspecific deletion of MYRF show a decline in heart function and cardiomyopathy.

Keywords: Mouse embryonic development
Mouse embryonic lethality assessment
Mouse embryonic stem cells
Myelin Regulatory Factor
Proximity ligation assay
Transcriptional regulation
Advisor: Mitchell, Jennifer A
Boosting 3D Reconstruction with Differentiable Imaging Systems

Imaging and 3D reconstruction are reciprocal procedures. The former employs imaging systems to measure scene properties, where it encodes various 3D-related properties (including geometry, material, and light) into specific measurements. Conversely, the latter aims to solve the inverse problem, i.e., recovering 3D-related properties back from captured data. As the reciprocal step, imaging process provides important cues to 3D reconstruction. Exploring ways to utilize imaging priors is critical to improve the performance of 3D reconstruction. Recent advances of deep learning (DL) have reshaped 3D reconstruction algorithms. Inspired by it, this dissertation provides a new framework to boost 3D reconstruction with imaging priors. The core idea is to differentiate imaging systems and embed them into reconstruction algorithms, in particular DL-based approaches. Consequently, the proposed framework allows information to be freely propagated between imaging and 3D reconstruction. It supports reconstruction algorithms to utilize inherent geometric and physical rules inside imaging systems for better recovery of 3D properties. Additionally, it enables tuning imaging systems to explore the best settings they should adopt under reconstruction tasks. We validate the superiority of our framework on two imaging systems: rendering pipelines and structured light systems. First, we present novel differentiable reformulations of rendering pipelines and apply them in unsupervised, single-view 3D object reconstruction. Compared to previous methods, our novel designs demonstrate more accurate shape and texture recovery, as well as enable new capabilities to achieve faithful material and lighting disentanglement. Next, we discover optimal illumination patterns in structured light triangulation. Unlike existing approaches that use predetermined patterns, for the first time, differentiable structured light systems allow us to optimize patterns for the chosen imaging conditions and exhibit substantial improvements in 3D triangulation accuracy.

Keywords: 3D Reconstruction
Computational Imaging
Computational Photography
Differentiable Rendering
Advisor: Fidler, Sanja
Kutulakos, Kyros
Lung Deflation Injury - Mechanism and Translational Relevance

Ventilator management in ARDS focuses less on ventilator disconnection. We hypothesized if abrupt deflation after inflation causes lung injury in animal models. Male Sprague-Dawley rats were ventilated and randomized to Control (n=6, PEEP 3 cmH2O; 100 min) or Intervention (n=6, PEEP 3 to 11 cmH2O over 70 min; abrupt deflation to zero PEEP; ventilation for 30 mins). Lung function and injury was assessed, scanning electron microscopy performed, and microvascular leak timed by Evans Blue dye (n=4/group). Echocardiography (n=4) and measurements of right (n=6) and left ventricular pressures (n=6) were performed. Abrupt deflation (vs. control) caused lower lung compliance and increased wet/dry ratio. Vascular leak was absent before deflation and maximal 5-10 min thereafter; injury was predominantly endothelial. At deflation, left ventricular preload and LVEDP increased precipitously in proportion to the degree of injury. Abrupt deflation in rats caused acute lung injury mediated by acute LV decompensation and potentiated by pulmonary vascular surge, with resultant endothelial injury and edema. Ventilator disconnections in humans often cause cardio-respiratory instability. Whether repeated disconnections (lung deflations) cause lung injury was tested in a porcine large animal model. Yorkshire pigs (~12 weeks) were studied in three series. First, like rats, we compared PEEP abruptly deflated from 26 cmH2O or from PEEP 5 cmH2O to zero. Second, pigs were randomly crossed over to receive rapid vs. gradual PEEP removal from 20 cmH2O. Third, pigs with volume overload, and ventilated with PEEP 15 cmH2O were randomized to repeated ETT disconnections (15 secs every 15 min) or none for three hours. Cardiopulmonary variables were monitored; lung histology and BAL studied. As compared to PEEP 5 cmH2O, abrupt deflation from PEEP 26 cmH2O increased PVR, lowered oxygenation, and increased lung wet-to-dry ratio. From PEEP 20 cmH2O, gradual vs. abrupt deflation mitigated the changes in oxygenation and vascular resistance. From PEEP 15, repeated disconnections led to reduced compliance; lower oxygenation; higher PVR, lung wet-to-dry ratio, lung injury score and morphometric oedema. In this porcine model, like rodents, single abrupt deflation from high PEEP, and repeated short deflations from moderate PEEP caused pulmonary oedema, impaired oxygenation, and increased PVR. Rapid deflation may thus be a clinically relevant cause of impaired lung function and injury, which may be attenuated by gradual pressure release.

Keywords: Lung Deflation
Pulmonary Endothelial Injury
VILI
Volume Overload
Advisor: Post, Martin
Torpor Use in Ruby-throated Hummingbirds (Archilochus colubris): Effects of Energy Stores, Seasonality, Temperature, and Age-Sex Class

Animals utilize various behavioral and physiological strategies to balance energy gain and energy expenditure despite seasonally changing environmental and ecological constraints. Torpor, a state of reduced metabolism, is a versatile energy conservation strategy used by many mammals and birds. Hummingbirds are known for their ability to use daily torpor to cope with energetic challenges they face throughout the annual cycle. Due to their small size and use of hovering flight, hummingbirds sustain extremely high metabolic rates and carry limited energy stores. Additionally, their body masses and endogenous fat stores vary daily and seasonally, in rhythm with environmental and ecological conditions. Thus, hummingbirds are a uniquely powerful system in which to interrogate whether the rules that govern torpor are constant or subject to individual, environmental, ecological, and seasonal contexts. My dissertation investigates torpor in ruby-throated hummingbirds (Archilochus colubris) by evaluating how the sensitivity of torpor to endogenous energy stores differs with respect to nocturnal metabolic fueling strategy, breeding, migration and wintering life history stages, nighttime air temperature, and age-sex class. First, I find that hummingbirds that perform evening hyperphagia quickly convert this sugar to fat, which they subsequently use to fuel normothermy. Second, I find that in the summer breeding period, birds use torpor to survive energy emergencies when their fat levels reach a critically low threshold, but shift to a routine fat-sparing strategy in the fall migratory period. Thirdly, I find that on colder nights in the summer, birds enter torpor more often and at higher fat levels, but in the winter, they use torpor frequently, irrespective of fat content and air temperature. Finally, I find that birds that experience natural daytime conditions in the summer use torpor more when leaner, and that developing juveniles use torpor less often than adults. These findings suggest that by reducing nightly energy expenditure through torpor, hummingbirds can maintain seasonally appropriate energy levels despite the various energetic constraints they face throughout the annual cycle. Thus, I propose that hummingbird torpor is governed by an adipostat mechanism sensitive to a fat threshold set relative to immediate (air temperature, night length) and future (seasonal, life history stage) resource availability, energy requirements, and biomechanical constraints.

Keywords: Age-Sex Class
Air Temperature
Body Composition
Hummingbird
Season
Torpor
Advisor: Welch Jr., Kenneth C
Strengthening the Circle of Tuberculosis Care: A Process Evaluation of an eHealth Intervention in Tibet Autonomous Region, China

eHealth offers an opportunity to support people in adhering to their tuberculosis (TB) medications as part of efforts to deliver high-quality TB care in communities. This work was conducted alongside a randomized controlled trial (RCT) of an eHealth digital adherence intervention in Shigatse, Tibet Autonomous Region, China that used technology to strengthen the circle of care around people with TB and improve medication adherence. This work explores the implementation context and process and aims to provide information on intervention delivery. The work includes three qualitative studies. Study 1 used an adapted access to care framework to explore the perspectives of people with TB. Study 2 explored the perspectives of health workers through the lens of the TB care cascade. Study 3 used the Consolidated Framework for Implementation Research (CFIR) to explore implementation from the perspective of all users. In Study 1 we describe barriers and enablers to accessing TB care across the region that shape the outer setting of the intervention context. Barriers include a lack of culturally tailored care, complex care pathways, and out-of-pocket costs. Family support was reported as an enabler for continuity of TB care. In Study 2 we explore the inner setting in which the intervention is implemented and highlight how TB care in the region can be strengthened by training health workers, supporting village doctors, and leveraging technology to create a circle of care. In Study 3 we identify barriers and enablers across CFIR domains and highlight how intervention adaptations can either support or undermine project goals. We highlight how infrastructure determines user experience, the importance of anticipating and documenting adaptations, the role of training to strengthen intervention delivery and health worker knowledge, as well as how implementation science must inform health policy. eHealth is a flexible and accepted tool to enhance TB health service delivery, even in high-burden, rural, and remote settings. eHealth innovations, however, must support the circle of care around patients and their families. To do so requires capacity building at the most local level of the health workforce to deliver high-quality TB care in communities.

Keywords: eHealth
Global health
Health services research
Implementation science
Process evaluation
Tuberculosis
Advisor: Wei, Xiaolin
Humour in West African Literature: Four Templates

This thesis examines texts from modern West African literature whose intention is clearly laughter. It reads novels and plays from Chuma Nwokolo, Wole Soyinka, Kobina Sekyi, Ferdinand Oyono, Amadou Hampaté Bâ, Ola Rotimi, and others. The study explores the relationship between writers, their humorous texts, and their audiences. It makes regular reference to theories of humour, but also acknowledges that by the very nature of their imprecise subject, such theories are not at all comprehensive. It does not propose a definition of “African” humour. It does point out, however, that a multilingual context, along with its differences and hierarchies, creates a unique potential for humour. Divided into four main sections, the thesis revolves around character typologies. Chapter One studies modern-day tricksters and argues that their ethos is both amoral and amusing. Chapter Two focuses on mimicry, and how anxious social climbing in a context of colonialism creates humour. Staying within the context of colonialism, while further underlining the relevance of language, Chapter Three examines the figure of the colonial interpreter. The final chapter discusses norms that are foundational for explaining how expectations can be played upon to make us laugh. Though the four are studied separately, I conclude that they are interconnected. Ultimately, the comic figures, in different ways, characterise the unique dialogue that the writer, who is presenting an African story in English or French, is engaged in with his reader. The templates embody a situation that the writer turns into a source of humour with a self-referential quality.

Advisor: Kortenaar, Neil t.
Energy- and Carbon-efficient CO2 Electrolysis

Carbon dioxide/monoxide (CO2/CO) reduction (CO2R/COR) – when powered by renewable electricity – provides a sustainable means to convert emissions into valuable products for the manufacturing, transport, and chemical industries. CO2R can contribute to sustainability through closing the carbon loop, increasing the penetration of renewables in the petrochemical industry, and achieving long-term storage of renewable electricity. Despite considerable promise, there have yet been few demonstrations of CO2R with a rate, energy efficiency, and carbon efficiency that would bring techno-economics in line with incumbents. The main objective of the thesis is to contribute to the realization of energy- and carbon-efficient CO2R. The first three technical chapters of this thesis focus on improving the performance metrics in flow cells and membrane electrode assembly electrolyzers (Chapters 3, 4, and 5). The last two technical chapters focus on implementing the performance-boosting strategies into carbonate-formation-free systems to achieve simultaneously high carbon and energy efficiencies (Chapters 6 and 7). The first work reports a new catalyst design that decouples gas, ion, and electron transport and enables, for the first time, CO2R at activities greater than 1 A cm−2 in alkaline flow cell electrolyzers (Chapter 3). Then, low overpotential and high selectivity in CO2R is achieved via an adparticle functionalization catalyst: gold adparticles formed on the silver-gold alloying interface via galvanic replacement (Chapter 4). A molecule:ionomer hierarchy is developed to lower the activation barrier for C–C coupling and control CO2, water, and proton transport – which in turn enabled record energy efficiency towards ethylene at industrially relevant reaction rates (Chapter 5). A cascade system – CO2R to CO in a solid oxide electrolysis cell (SOEC) with zero carbonate formation and COR to C2+ products in a MEA electrolyzer – is developed to achieve record low energy intensities in the electrosynthesis of C2+ products (Chapter 6). Finally, a catalyst microenvironment exhibiting cation repulsion and anion attraction is developed to combine practical energy- and carbon-efficiency in electrosynthesis of C2+ from CO2/CO feedstocks (Chapter 7).

Keywords: Carbon efficiency
CO2 reduction reaction
Electrochemical systems
Electrolyzer
Energy efficiency
Membrane electrode assembly
Advisor: Sinton, David