VictorJuiz/thesis huggingface dataset:
Role of SPARC in Drosophila Melanogaster basal lamina homeostasis
Keywords: chaperone
Collagen IV
fat body
SPARC

SPARC is a multifunctional, evolutionarily conserved, collagen- and growth factor-binding glycoprotein that is required in Drosophila melanogaster for proper larval development and maintenance of fat body homoeostasis. I have engineered a SPARC RNAi knockdown in the larval fat body, with an emphasis on ultrastructural adipocyte morphology and basal lamina integrity, resulting in adipocyte remodeling characterized by cell rounding and accumulation of fibrous matrix material. SPARC deficient larva show increased deposition of collagen IV and other basal lamina components. How collagen IV assembles into an organized network in basal lamina remains unclear. In seeking to elucidate the potential intra- and extracellular functions of SPARC in this context, I generated five mCherry tagged SPARC constructs which failed to rescue SPARC-null mutants. Together, the data compiled by myself and others in the lab indicate that SPARC is required to maintain adipocyte morphology and basal lamina homeostasis during larval development.
Reduced Pressure Distillation of Wood Derived Pyrolysis Liquid Biofuels and their Emulsion with Diesel Fuel in a Compression Ignition, Indirect Injection Engine
Keywords: Biofuels
Compression Ignition Engines
Emulsions
Fast Pyrolysis Liquid Biofuel
Indirect Injection Engines
Pyrolysis Liquids

Reduced pressure distillation was used to reduce water content of crude WPLs from 24.81 to 14.51 wt%, named dewatered WPL (dWPL). Five emulsions were produced with 5-25 wt% dWPL, 5 wt% ethanol, 4 wt% surfactant, 0.15 wt% of a fuel additive, and remainder diesel. Emulsions were tested in a C2.2 engine at three conditions. Max engine duration was 5-25 minutes for dWPL emulsions, where key barriers were injector failure and fuel stability. Ignition delay for dWPLs was found to be 10째CA longer than diesel fuels. In a corrosion study, the mass loss rate for specimens submerged in dWPLs was found to be roughly half that of specimens submerged in WPLs. The absolute mass loss rate for dWPLs at high temperatures (50째C) is non-negligible in engine applications. SEM images of specimens show increased surface roughness, which may cause injector failure when dWPLs are used in engines.
GABA Cells in the Central Nucleus of the Amygdala Control Cataplexy
Keywords: Amygdala
Cataplexy
Chemogenetics
Narcolepsy

Cataplexy is a hallmark of narcolepsy characterized by the sudden onset of muscle weakness or paralysis during wakefulness. It can occur spontaneously but is typically triggered by positive emotions like laughter. Although cataplexy was identified over 130 years ago, its neural mechanism remains unclear. Here, we show that a newly identified GABA circuit within the central nucleus of the amygdala (CeA) may play a causal role in promoting cataplexy. We found that, in narcoleptic mice, chemogenetic activation of GABA cells within the CeA triggered a 253% increase in the number of cataplexy attacks without affecting their duration. We also show that GABA cell activation only promotes cataplexy attacks associated with emotionally rewarding stimuli such as wheel running, without impacting spontaneous attacks. Our results indicate that the CeA plays a pivotal role in controlling cataplexy onset, and that emotionally rewarding stimuli may trigger cataplexy by activating GABA cells in the CeA.
Transforming Bodies: Affect and Collage in Eating Dis/order Recovery
Keywords: Affect
Collage
Deleuze
Eating Disorder
Embodiment
Pedagogy

This thesis explores affective experience in the development of eating disorders as well as its influence and potential in the recovery process. Affect is researched within the context of identity and embodied learning. This research also explores the use of creative practices (collage) in eating disorder recovery. Four women between the ages of 18 and 30 who self-identified as having an eating disorder participated in this study. Their participation included two interviews (one individual and one group) and two group collage sessions. This research suggests that eating disorders can be understood as bodily practices (entangled with emotion and thought) that both build and fragment the sense of self. Using Deleuzoguattarian concepts such as “the fold” and “BwO”, I propose a rhizomatic understanding of eating disorder recovery in which the affective body is paramount. I suggest that arts-based practices have the potential to play an important role in the recovery process.
CCCTC-binding Factor (Ctcf) is Required for Mouse Cardiovascular Development
Keywords: Cardiovascular development
Chromatin regulators
CTCF
Long-range chromatin interactions
mouse embryonic development

Disruption of transcriptional programs controlling development of the cardiovascular system can cause congenital cardiovascular disease. These programs are tightly regulated by chromatin regulators that alter gene expression via formation of active or repressive chromatin and by mediating long-range chromatin interactions. However, how the process of long-range chromatin interactions, facilitated by chromatin mediators, regulate cardiovascular development is not understood. One potential highly conserved chromatin regulator of cardiovascular development is the CCCTC-binding factor (CTCF). Through conditional deletion of Ctcf in mouse cardiac and endothelial progenitors, I found that Ctcf is essential for cardiovascular development. Inactivation of Ctcf in cardiac progenitors induces severe cardiac defects by embryonic day 12.5, while inactivation of Ctcf in endothelial progenitors causes extraembryonic vascular defects by E9.5-10.5. Future investigations in the mechanistic involvement of Ctcf in cardiovascular development will help determine how the process of long range chromatin interactions guide developmental transcriptional programs and function of CV systems.
Three, Two, One: Three New C–C Bonds, Two C–H Activations, One Pot. A Highly Efficient Palladium-catalyzed Domino Reaction of Aryl Iodides and Aryl Bromides
Keywords: Catalysis
C-H activation
Domino reactions
Palladium

Palladium-catalyzed C–C bond formation and C–H activation have become emerging methods of choice in the industrial synthesis of pharmaceutical and agrochemical products. The development of a palladium-catalyzed domino reaction of aryl iodides and aryl bromides to form polycyclic dihydrophenanthrene structures selectively and in high yields is discussed in this thesis. The reaction involves two C–H activations and the formation of three new C–C bonds and demonstrates the high efficiency of domino reaction catalysis. A detailed description of the optimization of two reactions is given, one involving a dimerization of aryl iodides and the other featuring a selective coupling of two distinct aryl bromides. Experiments to demonstrate the scope of these reactions show the tolerance of the optimized systems for a variety of common functional groups.
Does Androgen Deprivation Therapy Impact Subjective Cognitive Function in Men with Non-metastatic Prostate Cancer?
Keywords: Androgen Deprivation Therapy
Prostate Cancer
Subjective Cognition

Androgen-deprivation therapy is used to treat almost 50% of current prostate cancer patients. Despite slowing disease progression and prolonging survival, androgen-deprivation therapy is associated with numerous side effects. However, the impact of androgen-deprivation therapy on subjective cognitive function remains uncertain, as the studies published in this area have assessed objective cognitive function and are limited by small sample sizes and inconsistent findings. The primary objective for this thesis was to determine whether there was a change in subjective cognitive scores over a 12-month period in non-metastatic prostate cancer patients receiving ADT compared to controls. The secondary objectives were to examine the relationship between subjective cognitive function and socio-demographic variables, and change in subjective and objective cognitive function over the 12-month period. Change scores between baseline and 12 months analyzed with adjusted multivariable linear regression models showed no significant change in the prostate cancer patients receiving androgen-deprivation therapy compared to the other control groups.
The Application of the Cyclic Void Growth Model to Assess the Ultra-low-cycle Fatigue Life of Steel Castings
Keywords: Fatigue
Inelastic
Seismic
Steel Castings
Yielding

Steel castings have been used increasingly to develop new seismic force resisting systems. Although they have primarily been used as elements which are to remain elastic during seismic events, recent developments have proposed and validated systems that rely on the yielding response of steel castings, taking advantage of their freedom of geometry and chemistry to obtain optimum combinations of strength, stiffness, and ductility. To this end, an understanding of their ultra-low-cycle fatigue life is paramount. To further this understanding, in this thesis, fatigue laws are calibrated for multiple cast steel heats using a fatigue model which has recently been proposed in the literature for rolled steel elements. The calibrated models are used to predict the ductile failure in multiple full-scale experiments. A method is proposed to assess the casting's fatigue life at the foundry and to utilize the model in designing prototype steel castings for ductile applications.
An Extended GASNet API for PGAS Programming on a Zynq SoC Cluster
Keywords: FPGA
GASNet
Programming Models
THe_GASNet
Zynq

This work presents a dynamic development flow to integrate FPGA accelerators into software applications for a Zynq SoC cluster. We provide a high-level library, THe\_GASNet Extended API, based on the Partitioned Global Address Space (PGAS) programming model for remote memory operations. The extended API is built using the THe\_GASNet Core API that implements a global address space view of the memory but provides distinction between local and remote data accesses. The extended API provides an expressive way to implement parallel applications on the x86-ARM-FPGA heterogeneous systems. For the benchmark, we implemented the Jacobi iterative method on the cluster. The hardware implementation of the Jacobi method performs 2.78-fold faster than the software implementation on the i5 processor for a 4096x4096 surface. Compared to the core API, the extended API performs slightly worse for all the data sizes. However, the trade-off of the reduced performance is increased ease of programming.
Single Particle Electron Cryomicroscopy of the Thermus thermophilus V/A-type Rotary ATPase and Structure of the Membrane-bound a Subunit
Keywords: a subunit
ATP synthase
Electron cryomicroscopy
Evolutionary covariance
V/A-ATPase
V-ATPase

Rotary ATPases are membrane-bound protein complexes found ubiquitously in biology that carry out ion transport and ATP synthesis. Despite variation in structure and function, conserved biochemical features dictate the mechanisms of rotary ATPase action. Structural models are available for many subunits in every class of rotary ATPase, but none exist for the membrane-bound ion-transporting a subunit. Here we present the structure of the intact Thermus thermophilus V/A-type rotary ATPase at 6.4 Ă , obtained by single particle electron cryomicroscopy. This map was used in concert with evolutionary covariance analysis and biomolecular modelling to create a model of the a subunit. Models were similarly generated for the Saccharomyces cerevisiae V-ATPase a subunit and Bos taurus F-type ATP synthase a subunit. These models display similar features despite large sequence variation, indicating a conserved path for protons and suggesting a universal mechanism of proton translocation in rotary ATPases.
Retinal Thickness Irregularities in Preclinical Diabetic Retinopathy
Keywords: diabetes
diabetic retinopathy
image analysis
optical coherence tomography
retina
type 1 diabetes

Diabetic retinopathy (DR) is the most common complication of diabetes and the leading cause of vision loss worldwide. Clinical detection relies on the manifestation of sight-threatening microvascular, macrovascular and edematous ocular insults. However, preclinical investigations detected retinal thickness irregularities. We hypothesized that retinal thickness irregularities are localized to specific retinal regions and layers. Training and validation data were collected from participants with diabetes with no/minimal DR and healthy individuals to identify and verify regions of interest. Optical coherence tomography and MATLAB速 computing were the primary tools used to measure retinal thickness in each participant. Linear mixed-effects models identified four significant regions of thickness irregularities from the training data; these were not matched by validation data. Nonetheless, retinal thickness irregularities were localized to specific regions and layers. Recognizing that there are retinal regions susceptible to retinal thickness irregularities during preclinical stages of disease is important for early disease detection.
The Impact of Alternative Oxidase on Nitrogen Stress in Nicotiana tabacum
Keywords: Abiotic Stress
Alternative Oxidase
Ammonium Toxicity
Nitrogen
Photosynthesis
Respiration

The alternative oxidase (AOX) is a stress response protein that is thought to safely dissipate excess reductant that accumulates when certain plant species are supplied with low concentrations of nitrate, or high concentrations of ammonium. To investigate whether AOX has an impact on these "nitrogen stress" scenarios wild-type Nicotiana tabacum, in addition to AOX knockdown and overexpression lines, were grown hydroponically in varying concentrations of nitrate or ammonium. Using gas exchange and chlorophyll a fluorescence, in addition to qRT-PCR and western blotting, we demonstrate that AOX was imposing photosystem stoichiometry adjustments in plants grown in low nitrate. All plant lines displayed symptoms of ammonium toxicity when grown in high ammonium; however, AOX expression was significantly positively correlated with photosynthetic capacity in later parts of the day. These results demonstrate that AOX is an important component of the nitrogen stress response in plants and could even be beneficial under extreme nitrogen stress conditions.
Investigating the Role of a Natural RecA Mutation on BCG-Russia Vaccine Properties
Keywords: BCG
BCG-Russia
RecA

The Bacille Calmette-GuĂŠrin (BCG) vaccine is the only vaccine for tuberculosis (TB) control. Although effective in preventing disseminated forms of TB in children, its efficacy in preventing pulmonary TB in adults is highly variable. BCG-Russia, one of the most widely used substrains to produce the vaccine, is a natural RecA mutant. Whether the presence of functional RecA affects the virulence and efficacy of BCG-Russia remain unknown. Here I show that a recombinant BCG-Russia expressing functional RecA, rBCG-RecA, is more attenuated than its parental counterpart in SCID mice and this difference is due to slower growth within the animals. I also demonstrate that rBCG-RecA confers equivalent protection against M. tb challenge as the parental strain in guinea pigs with similar bacterial burden in the organs. Taken together, the presence of RecA in BCG-Russia allows for a safer yet equally protective vaccine. This work provides new insight to future TB vaccine design.
Alternate Stable States in Coupled Fishery-aquaculture Systems
Keywords: alternate stable states
aquaculture
coupled human and natural systems
fisheries
salmon
theoretical modeling

Stagnating capture fisheries production has led to rapid aquaculture development due to an increasing shortfall of wild fish in meeting demand. Farmed fish can negatively ecologically affect nearby wild fish and they can interact economically by supplying similar products to the market, but general theory on how these interactions affect fishery-aquaculture population dynamics and system resilience is lacking. I develop simple theoretical models integrating the ecology, economics, and management of capture fisheries and aquaculture and demonstrate that alternate stable states and hysteresis of equilibrium population abundances can exist, indicating decreased system resilience. Abrupt transitions from a capture fishery-dominated state to an aquaculture-dominated state with few or no wild fish can occur that are difficult to reverse. Empirical patterns of salmonid capture fisheries and aquaculture production data are examined considering the developed theory, which may apply to other systems with wild and domesticated species that are coupled ecologically and economically.
Characterizing Genes Associated with Social Interactions in Drosophila melanogaster
Keywords: Drosophila melanogaster
fruit fly
genetics
microbiology

Social behaviour is seen among a variety of organisms. Drosophila melanogaster engages in many social behaviours including courtship and mating. The fly has also exhibited the ability to alter the rhythmic timing of its behaviours based on the social composition of the group. The rhythmic timing of behaviours in Drosophila is regulated by the endogenous biological clock. There are many crucial components of the circadian clock, which work together to help regulate behavioural rhythms. Some of these components, such as clock genes, can thereby be used to examine the status of the clock. The aim of this work is to characterize the role that the CG42343 locus plays in directing social interactions. We demonstrate that the CG42343 locus plays a role in regulating social interactions through changes in expression levels of clock genes, and that this phenomenon is likely mediated through chemosensory signalling.
Why do only Some Women Develop Postmenopausal Osteoporosis?
Keywords: advanced glycation endproducts
osteoclasts
oxidative stress
postmenopausal osteoporosis
receptor for advanced glycation endproducts

Although all women experience postmenopausal bone loss, only 25-30% will develop postmenopausal osteoporosis, therefore another mechanism must be working with estrogen deficiency to cause this disease. Our proposed mechanism outlines the accumulation of advanced glycation endproducts (AGEs) as the driving force behind bone loss through intracellular signaling after ligation to the receptor for advanced glycation endproducts (RAGE). The study employed a high-fructose diet to initiate production of AGEs and investigated the effects on bone loss and RAGE expression after ovariectomy. This study investigated changes in bone quality and oxidative damage due to diet and surgeries as well as levels of soluble and bone collagen bound AGEs. It also worked to evaluate RAGE expression in serum and osteoclasts. Results show there was no production of AGEs, and bone quality and oxidative damage were affected by ovariectomy only. Soluble RAGE expression was increased due to ovariectomy alone, however cell-bound RAGE was unchanged.
Quantifying Variation in Discrete Force-time Characteristics during the Sprint Start: Considerations for Monitoring Training Adaptations
Keywords: biomechanics
block start
human movement
sprint start
training
variability

Biomechanical quantities during the sprint start have been correlated with race time. “Typical” training variation in these quantities must be understood to interpret changes. Purposes were to: (1) describe variation; and (2) compare variation between-session. Using force plate-instrumented starting blocks, foot-block interactive forces were measured from four starts in two training sessions (n=10). Pre-tension (PT), reaction time (RT), block time (BT), rate of force development (RFD), peak force (PF), impulse, time of force application (TFA), time to peak (TTP), peak force offset (PFTO), and force ‘off’ offset (FOTO) were derived trial-by-trial. Variable-specific coefficients of variation (CoVs) were calculated within-session, and compared between-session. PT, BT, RFD and TTP exhibited within-session CoVs ≤ 10%. TTP CoVs were significantly different (p
Recolonization Trends of Fish Communities Following the Restoration of a Great Lakes Coastal Wetland
Keywords: Aquatic Ecology
Conservation of Fishes
Wetland Restoration

The Great Lakes coastal wetlands are in decline due to various anthropogenic factors including invasive species. An invasion by Phragmites australis in Long Point Crown Marsh, Lake Erie, reduced the amount of open-water habitat for wildlife. Dredging occurred to restore the environment and create more open water. I studied the recolonization trends of fish communities by examining changes in species richness, population density, and community composition, 2012-2014, in four created and two reference ponds. Then, I examined how water chemistry and vegetation influenced the fish communities using variance partitioning and redundancy analysis. Fishes colonized the created ponds immediately after dredging, but ponds showed variation in population density and community composition indicating that created ponds may not be functioning similar to the reference ponds. Water chemistry and vegetation accounted for very little variation in the communities indicating that other factors are influencing the fish communities.
Prevalence of Heavy Prenatal Alcohol Exposure in Uganda via Analysis of Fatty Acid Ethyl Esters in Meconium
Keywords: fatty acid ethyl esters
fetal alcohol spectrum disorder
meconium
prenatal alcohol exposure
prevalence

Fetal alcohol spectrum disorder (FASD) manifests as a continuum of permanent birth defects and neurodevelopmental impairments that originate from maternal alcohol use during pregnancy. The number of recognized FASD cases in parts of Sub-Saharan Africa is growing, which is a cause for concern. Prenatal alcohol exposure was examined via regional hospital population-based collection of meconium, and analysis of the fatty acid ethyl esters (FAEEs) contained within. Meconium samples were collected from five hundred ten neonates over a two-month period at Mbarara Regional Referral Hospital. Each meconium sample was accompanied by a maternal questionnaire. The prevalence of prenatal alcohol exposure using the maternal questionnaire was 16.1% (81 of 510). The overall prevalence of prenatal alcohol exposure via FAEE-meconium analysis in this population was 1.6% (8 of 510). This is the first population-based study of an entire local neonatal population examining fetal alcohol exposure via meconium-FAEE analysis conducted in Uganda.
Early Adoption of Aliskiren in Ontario: Prescribers’ Characteristics and Patients’ Outcomes
Keywords: adoption
aliskiren
antihypertensive
early
new
prescribers

Little is known about the patterns of adoption of new antihypertensive drugs. The objectives of this study are: 1) examining trends of aliskiren prescribing in Ontario, 2) determining physicians' characteristics associated with aliskiren prescribing, and 3) comparing morbidity and mortality outcomes, and prescription drug costs, among patients treated by early versus late and non-adopters of aliskiren. We hypothesize that early adopters are largely represent by primary care providers, and patients treated by those physicians will have worse outcomes and higher prescription costs than patients treated by late or non-adopters. We examined a population-based cohort using linked administrative databases. Results showed primary care providers were earlier and heavier prescribers of aliskiren. Patients treated by early adopters incurred higher prescription costs. However, no difference in mortality and morbidity outcomes was observed between patients treated by early vs. late or non-adopters, suggesting that early adopters provided quality of care similar to other physicians.