VictorJuiz/thesis huggingface dataset:
Optical Parametric Devices
Keywords: Bandwidth
Bragg Reflection Laser
Bragg Reflection Waveguide
Difference Frequency Generation
Near-IR
Self pumping

In this thesis, a continuous range of NIR generation from 1650nm to 2160nm, for the first time, has been experimentally demonstrated in a monolithic BRW semiconductor platform when pumped at non-degenerate wavelength. When pumped at degenerate wavelength, the wavelength conversion in BRW has experimentally shown a 3dB bandwidth of 100nm with -37dB conversion efficiency. The potential of optical parametric amplification in BRW is studied through NLSE solver and experimentally characterized. BRW diode laser, which is designed for self-pump process with pump power at least an order higher than external pump can achieve, is characterized for the laser and nonlinear performance and is shown to work at 780nm regime. Experimental results and simulation model suggests that self-pumping process is highly feasible and can operate at room temperature. To alleviate the difficulties self-pumping imposed on the phasematching, acceptance bandwidth enhancement from 0.5nm to 17nm through tapering is experimentally demonstrated.
Biogenesis and Maturation of Asbestos-containing Phagosomes in Macrophages
Keywords: Asbestos
Filamentous morphology
Phagocytosis
Phagosomal maturation

Exposure to asbestos has been linked to the development of many diseases. Fibres are inhaled and circumvent the ciliated airways, depositing in the alveoli where they become targets for removal via phagocytosis. The fibre pathogenicity structure: activity paradigm states that fibres exceeding 15 Îźm are problematic for removal, purportedly causing frustrated phagocytosis. However, the cellular mechanisms involved in this process are not well understood. Our results demonstrate that the fibre length internalized by macrophages surpasses this threshold length, and that the time required for uptake is length-dependent. Following phagosome formation, maturation progresses to different stages based on the cell type. In all cells, however, asbestos-containing phagosomes fail to acidify, suggesting a defect in maturation that may contribute to pathogenicity. Altogether, our results indicate that length is not the primary factor in asbestos-induced toxicity and suggest that surface chemistry may contribute to a greater extent to the development of asbestos-related diseases.
Trafficking Dynamics in Arabidopsis Pollen-stigma Interactions
Keywords: Reproduction
Self-Incompatibility
Signalling

Reproduction in the Brassicaceae family depends on self-recognition, where cross-compatible pollen is distinguished from self-incompatible pollen prior to acceptance by the stigma. The stigma only gives compatible pollen the resources required for hydration and germination of a pollen tube for fertilization. These resources are sequestered away from self-incompatible pollen, inhibiting inbreeding. Many questions remain surrounding the specific signalling events that govern this self-recognition system. This research investigates how resource delivery to self-incompatible pollen is prevented in Arabidopsis. Topics explored include the localization of Sec5a, an exocyst complex member that delivers secretory vesicles to compatible pollen; the localization of ARC1, an E3 ubiquitin ligase which prevents the exocyst from delivering resources; and autophagyâ s degradation of the sequestered resources.
Investigating the Effect of scyllo-Inositol Treatment on the Brain in a Mouse Model of Alzheimer's Disease
Keywords: aggression
agitation
Alzheimer
neuropsychiatric
scyllo-inositol

scyllo-Inositol is a potential therapeutic for the treatment of agitation and aggression in patients with Alzheimer's disease. scyllo-Inositol reduces aggregation of beta-amyloid peptide, reduces amyloid plaques, and reduces myo-inositol concentration in the brain. The change in gene expression in the brain of TgCRND8 mice after scyllo-inositol treatment has not been previously investigated. I hypothesized that scyllo-inositol treatment would cause changes in expression of genes involved in neurodegenerative diseases and neuropsychiatric disorders. Affymetrix gene expression microarrays were used to analyze changes in the hippocampus and cerebral cortex of TgCRND8 mice as well as in non-transgenic littermates after 30 days of scyllo-inositol treatment. Analysis of the data with the Database for Annotation, Visualization and Integrated Discovery and Ingenuity Pathways Analysis program showed gene expression changes in synaptic function, calcium, dopamine receptor, glutamate receptor, and myo-inositol signalling pathways. In light of these results, I concluded that my hypothesis was correct.
Enrichment and Analysis of Proteasome Storage Granules
Keywords: enrichment
proteasome
PSG
quiescence
ubiquitin
yeast

Ubiquitin-proteasome system (UPS) is a conserved eukaryotic pathway essential for the turn-over of short-lived or unwanted proteins, through the coordination of substrate ubiquitylation, and subsequent degradation by proteasomes. Proteasomes are complexes predominantly located in the nucleus of mitotic eukaryotic cells. However, upon entry into quiescence, cultured yeast cells sequester proteasomes into stable cytoplasmic bodies named proteasome storage granules (PSGs), which dissociate rapidly upon growth resumption. Our group seeks to understand the functional significance and dynamic nature behind proteasome sequestration. Through systems biology approaches, our group has previously identified 21 genes spanning several functional groups to be involved in PSG formation. In this thesis, I complemented our systems biology findings through affinity purification and enrichment of PSG from chemically-fixed yeast cells, and subsequent biochemical and proteomic analyses. I showed that PSG primarily constitutes proteasomal proteins, and implicated free mono-ubiquitin as an organization factor in PSG. Further structural analysis of PSGs is underway using ubiquitin probes.
The Development of Positive Symptoms in Young Adults with Schizotypal Traits: A Cognitive Model
Keywords: psychosis
schizophrenia
schizotypy
subsyndromal positive symptoms

Objective: We sought to determine what cognitive mechanisms contribute to the development of positive symptomatology in schizophrenia. We hypothesized that the constellation of schizotypal traits would be a risk factor for the presentation of subsyndromal positive symptomatology. In order for subsyndromal positive symptomatology to be present, however, fantasy proneness and an externalizing bias must also be present and automatic thoughts must be externalized. Method: Undergraduate students (N = 215) completed self-report measures to assess schizotypal traits, externalizing bias, fantasy proneness, and automatic thoughts, with subsyndromal positive symptomatology as the outcome variable. Self-esteem and depressive symptom measures were included as covariates. Results: Schizotypal traits, fantasy proneness, and depressive symptoms were significantly related to subsyndromal positive symptomatology, explaining 39.7% of the variance. Conclusions: An externalizing bias may not be associated with subsyndromal positive symptomatology, possibly because the mechanism underlying positive symptoms differs depending on the severity of the symptoms.
Type I Interferon Responses Drive Intrahepatic T cells to Promote Metabolic Syndrome
Keywords: Adaptive Immunity
Immunology
Insulin Resistance
Metabolic Syndrome
Non-alcoholic Fatty Liver Disease
Obesity

Obesity-related insulin resistance is driven by low-grade chronic inflammation of metabolic tissues mediated by innate and adaptive immunity. During obesity, the liver undergoes steatosis, leading to non-alcoholic fatty liver disease that is associated with hepatic insulin resistance and systemic glucose dysregulation. The immunological factors supporting these processes are poorly understood. We found that the liver accumulates pathogenic CD8+ T cell subsets which control hepatic insulin sensitivity and gluconeogenesis during diet-induced obesity. Accumulation and activation of these cells are supported by type I interferon (IFN-I) responses in the liver. Livers from obese mice upregulate critical interferon regulatory factors (IRFs) and interferon stimulatory genes (ISGs), while IFNaR1-/- mice, or CD8-specific IFNaR1-/- chimeric mice are protected from disease. IFNaR1 inhibitors improve metabolic parameters in mice, while CD8+ T cells, IFN-I IRFs and ISG expression correlate with fatty liver disease activity in human patients. IFN-I responses govern intrahepatic T cell pathogenicity during metabolic disease.
Upper Small Intestinal Protein Sensing in the Regulation of Glucose Homeostasis
Keywords: Amino Acids
Diabetes
Glucose Production
Nutrients
Obesity
Protein

High-protein diets improve glucose control in both healthy and type 2 diabetic individuals. Given that upper intestinal lipids trigger a pre-absorptive, gut-brain-liver neuronal axis to suppress glucose production (GP), it is urgent to assess the potential glucoregulatory capacity of intestinal protein sensing. We here demonstrate that in healthy rodents in vivo, upper small intestinal infusion of protein hydrolysate improved intravenous glucose tolerance. This was due at least in part to insulin-independent effects on the liver, given that the same infusion suppressed hepatic GP during a basalinsulin euglycemic clamp. Co-infusion of tetracaine reversed the ability of protein to improve glucose tolerance, indicating that a neuronal network is initiated at the level of the gut to regulate glucose homeostasis. Collectively, these findings show for the first time that pre-absorptive protein sensing in the upper small intestine improves glucose tolerance by triggering a neuronal network to lower GP.
Defects in sialylation cause glomerular injury
Keywords: atypical hemolytic uremic syndrome
endothelial biology

Atypical hemolytic uremic syndrome (aHUS) is a rare disease characterized by hemolytic anemia, thrombocytopenia, and renal impairment. Complement dysregulation is associated with most cases, especially deficiency in the regulator complement factor H (CFH). Recessive mutations resulting in loss of the sialyltransferase activity of ST3GAL1 were identified in three siblings with aHUS with normal systemic complement laboratory indices. To test whether ST3GAL1 deficiency causes complement activation by reducing available CFH binding sites, complement deposition was assessed by flow cytometry on endothelial cells with decreased sialic acid content. Treatment with neuraminidase, which cleaves sialic acids, and genetic knockout of ST3GAL1 did not cause complement activation. Global blockade of sialyltransferases, which previously caused kidney failure in mice, did not induce a phenotype in rats. Glycoproteins lacking sialic acid residues in ST3GAL1 knockout endothelial cells were isolated and identified using a pull-down approach followed by mass spectrometry, providing targets for future study.
The Informational Body: A Sociomedical Theory of Disability and the Ethics of the Brain-Machine Interface (BMI)
Keywords: brain-machine interface
disability
ethics
heuristics
information
sociomedical

Cybernetic and bionic technologies hold great emancipatory potential for people with disabilities. Yet, scientists and disability scholars are polarized in their views on developing biotechnologies. Different discourses converge upon the brain machine interface—a link between the central nervous system and an external device—that augments sensory information and mobility for people with disabilities. This study combines philosophical, cultural studies, and social sciences methods to examine perceptions of these technologies held by people with physical, mobility disabilities and those of the researchers who develop them. Participants with acquired disabilities were more open to brain-machine technologies than those with congenital disabilities; scientists focused on patient “quality of life” and the ethics surrounding biotechnologies. I propose a “sociomedical” theory of disability that reconciles opposed medical and social models through an “informational body heuristic” that delineates the disabled body as a functionally-impaired cybernetic system. Ideological reconciliation would facilitate access to biotechnologies, thus improving the quality of life for people with disabilities.
The Spatial and Temporal Variability of Greenhouse Gas Fluxes within an Urban Bay-mouth Bar Coastal Marsh that has undergone Sediment Restoration
Keywords: Diffusion
Ebullition
Freshwater Mineral Wetland
Greenhouse Gas
Plant assisted transport
Restoration

Wetlands contribute to carbon cycling through integrated aerobic and anaerobic redox processes within their ecosystem. Despite overwhelming support that climate and land use changes threaten to alter greenhouse gas (GHG) status, both coastal marsh wetlands and the effects of dredging restoration are understudied. To address this, a field experiment was conducted to monitor GHG fluxes through ebullition, diffusion, and plant-assisted transport in Rattray Marsh (Mississauga, Ontario, Canada). This research aims to answer two questions: (i) What is the spatial variation and temporal variability of GHG fluxes across inorganic sediment exposure? and (ii) What are the driving factors for GHG fluxes? The experiment results reveal that (i) Elevated diffusive and ebullitive fluxes were observed at restored locations; (ii) GHG fluxes are seasonally driven; and (iii) GHG driving factors are highly variable. This suggests that the removal of inorganic sediment through dredging results in an elevated emission of GHG to the atmosphere.
Motion Compensation using Principal Component Analysis and Projection onto Dipole Fields for Abdominal Magnetic Resonance Thermometry
Keywords: High-Intensity Focused Ultrasound
Magnetic Resonance Thermometry
Motion compensation
MRI

High-intensity focused ultrasound is a non-invasive heat-based therapy, which is often guided by magnetic resonance (MR) thermometry. MR thermometry provides accurate temperature measurement at the target and in surrounding tissue. This is critical to ensure that sufficient thermal dose is achieved and to monitor for collateral damage. Unfortunately, MR thermometry is severely compromised by motion and susceptibility artifacts that are caused by respiration (periodic motion) and peristalsis (aperiodic motion). A hybrid method has been designed to correct these artifacts using principal component analysis as a multi-baseline method, and projection onto dipole fields as a near-referenceless approach. In vivo measurements in porcine and human kidneys, achieved a temperature stability and precision of 0.85 째C and 1.00 째C, respectively, without the need for any user-interaction or supplementary tracking tools. This is about twice as accurate as the leading hybrid method, which scored 1.97 째C and 2.22 째C, respectively, on the same data.
The Potential Effect of Alpha-Linolenic Acid on Prostate Specific Antigen
Keywords: ALA
Alpha-Linolenic Acid
prostate
prostate cancer
Prostate Specific Antigen
PSA

The objectives were to investigate the effect of alpha-linolenic acid (ALA) on prostate specific antigen (PSA) through two studies: 1) Determine the effect of ALA-enriched diet on PSA levels and serum ALA concentrations, through a secondary analysis of a randomized controlled trial in type 2 diabetes patients. 2) Determine the effect of ALA on prostate cancer cell growth and PSA production. Results: 1) ALA supplementation resulted in a reduction of 0.43 ng/ml on PSA (P=0.014). 2) ALA-enriched diet increased percentage composition of ALA in total lipids, phospholipids, free fatty acids and triglycerides (P
The Effect of Legumes on Blood Pressure
Keywords: Blood pressure
Hypertension
Legumes
Pulses

Our objective was to assess the effect on blood pressure (BP) of legumes through a secondary analysis of a 6-month randomized controlled trial (RCT), and a systematic review and meta-analysis of RCTs. In the first study, diastolic BP (DBP) was significantly lower on a low-glycemic index (GI) diet which included legume recommendations, versus a high-cereal fibre diet. Furthermore, total legume intake was associated with lower systolic BP (SBP), DBP, and mean arterial pressure (MAP) in baseline-adjusted analyses. When subgrouping legumes by type, effects were stronger and more robust for pulses versus non-pulse legumes. Significance was lost after adjustment for legume characteristics. Meta-analysis of 44 trials (n=2319) found legume diets significantly lowered SBP and DBP versus control diets. Strongest effects were in hypertensive study populations. Results of these studies suggest that legume consumption lowers BP.
Optimal Discharge Control in Capacity-constrained Systems: A Dynamic Programming Approach
Keywords: Dynamic programming
Healthcare management
Operation research
Stochastic control

In this thesis, we study a stochastic discharge control problem with patient readmissions in a capacity-constrained hospital unit. The problem is formulated as a multi-stage dynamic program where the objective is to determine the optimal discharge policy so as to minimize the expected total number of patients in the system until it is emptied. In the one-bed unit case, we fully characterize the optimal policy as a two-threshold policy (TTP). In the multi-bed unit case, the problem is more challenging since the associated dynamic programming equations are not fully decomposable bed-by-bed. To this end, we propose a so-called Marginal Policy Iteration (MPI) algorithm, that decomposes the joint optimization problem into easier one-bed marginal optimization problems and establish convergence of this algorithm to the optimal policy.
The Fresh Prince Syndrome: Experiences of Urban Black Males in Educational Settings
Keywords: anti-racism
black masculinity
cultural studies
hip-hop
pop culture

This thesis examines how urban Black males shape and negotiate their identities and how they situate themselves within schooling experiences. I take a phenomenological approach and use principles of CART to explore and analyze the stories of six individuals who claim an urban Black identity, including myself. This study is distinct in that it examines how identity is fostered inside of schooling environments as well as how it undergoes transformation from high school to university. This study also closely examines identity of urban Black males who find themselves clinging to a hip-hop cultural allegiance and the implications that has on their schooling. These experiences of aesthetic representation, space, and peer relationships combine to extend a narrative regarding urban Black male experience in school while providing insight into how educational institutions can facilitate more productive and engaging learning environments.
Local Delivery System to Reduce Pain in a Model of Back Surgery
Keywords: Biomaterial
Drug Delivery
Pain

Lumbar disc herniation is a common cause for lower back pain and reason for spinal surgery. Inevitably, patients will feel acute post-operative pain following surgery, thus local analgesics are given to patients after the surgery to alleviate pain. Existing drug delivery methods are limited by large doses, quick clearance rate from the injury site, short pain-relief period and multiple injections. As a result, there is an unmet need for a local, controlled and sustained drug delivery system following spine surgery. We propose to investigate a novel biomaterial to prolong the delivery of drugs to the local injury site. The drug-loaded hydrogel was characterized in terms of its release profile (where different factors were considered to prolong the release of the drug), storage modulus and swelling ratio. Behavioural tests and a pharmacokinetic study were conducted to determine the effects of the drug-loaded hydrogel in vivo.
SFMBT2 Function in Chromatin Architecture Mediates Trophoblast Stem Cell Maintenance
Keywords: chromatin structure
LINEs
lncRNAs
Major Satellites
SFMBT2
Trophoblast

The mammalian Polycomb Group gene Sfmbt2 is implicated in embryonic viability through the maintenance of the trophoblast stem (TS) cells and their contribution to development of the placenta. To elucidate the regulatory role SFMBT2 plays in TS cell maintenance, I performed ChIP-seq analyses against endogenous and FLAG-SFMBT2. Genome-wide SFMBT2 localization analyses revealed broad binding profiles suggesting SFMBT2 recruitment is more complex than its Drosophila counterpart dSfmbt. Analysis of SFMBT2 peaks revealed preferential localization to repetitive elements, specifically LINEs, major satellite sequences, and lncRNAs. A consistent pattern of histone and transcription factor accumulation across SFMBT2 peaks was observed. RNA-seq analysis of extraembryonic tissues of SFMBT2-null murine embryos revealed that 75% of differentially expressed genes were upregulated, as expected for loss of a transcriptional repressor. Collectively, the data suggests that SFMBT2 plays a complex regulatory role in mediating chromatin architecture which may contribute to the maintenance of stemness in TS cells.
The Role of Drosophila α-Catenin in Growth Regulation and EMT
Keywords: adherens junctions
Drosophila
growth regulation
Îą-Catenin

α-catenin (Drosophila α-Cat) links the cadherin-catenin complex to actomyosin at adherens junctions (AJs) in epithelial cells. I investigated the role of α-Cat in proliferation control and whether α-Cat acts as a mechanosensor at the AJs to regulate Hippo signaling. I showed that α-Cat has a dosage-dependent effect on proliferation and survival. α-Cat has distinct functions in growth regulation and adhesion, acting through JNK and the Hippo pathway. α-Cat null cells undergo EMT. Intermediate loss of α-Cat resulted in overgrowth. I found that α-Cat acts as an AJ component to regulate growth. Moreover, I showed that the mechanosensitive M region of α-Cat is dispensable for adhesion and proliferation control. My work identified a novel role for α-Cat as a growth regulator at the AJs, in addition to adhesion. This work will stimulate future investigations into how the α-Cat-centered protein network contributes to growth regulation in development and cancer progression.
Structure and Role of P. aeruginosa AlgL in Alginate Biosynthesis
Keywords: Alginate
Bacteria
Biofilm
Infection
Lyase
Polysaccharide

During chronic infection, Pseudomonas aeruginosa generate alginate-containing biofilms in the lungs of cystic fibrosis patients. Mature bacterial alginate is a heteropolymer of Îą-L-guluronic acid and partially acetylated Î˛-D-mannuronic acid. P. aeruginosa alginate biosynthesis requires thirteen proteins, including an alginate lyase, AlgLPa, which has been proposed to have a bi-functional role, both as a lyase and as an integral part of the cell envelope biosynthetic complex. How AlgLPa performs these functions is currently poorly understood. We have used an in vitro structure-function approach to explore the substrate recognition and catalytic mechanism of AlgLPa, and in vivo complementation to explore the role of its activity in alginate biosynthesis. The results presented suggest that AlgLPa is an endo-acting lyase with at least six subsites, and that the loop containing K66 is critical for substrate binding and/or catalysis. The complementation data supports the hypothesis that AlgLPa assembles into the cell envelope biosynthetic complex.