VictorJuiz/thesis huggingface dataset:
Resting Neural Activity Patterns in Auditory Brain Areas following Conductive Hearing Loss
Keywords: Conductive hearing loss
Auditory
c-fos
immunocytochemistry
spontaneous activity
otits media
inner hair cell
ribbon synapse

Conductive hearing loss (otitis media) in young children can effect speech and language development. However, little is known about the effects of conductive loss on neural activity in the auditory system. Hypothesis: Conductive hearing loss will change resting activity levels at the inner hair cell synapse, and lead to auditory deprivation of central auditory pathways. A conductive loss was produced by blocking the ear canals in mice. Resting neural activity patterns were quantified in brainstem and midbrain using c-fos immuno-labelling. Experimental subjects were compared to normal hearing controls and subjects with cochlear ablation. Conductive loss subjects showed a trend in reduction in c-fos labelled cells in cochlear nucleus and the central nucleus of inferior colliculus compared to normal controls. Results seen in this study may indicate the influence of conductive hearing loss on the developing auditory brain during early postnatal years when the system is highly plastic.
Cryoprecipitate Transfusion: Assessing Appropriateness and Dosing in Trauma
Keywords: Cryoprecipitate transfusion
appropriateness
dosing
trauma

Cryoprecipitate is commonly used outside guidelines. In trauma, the appropriate cryoprecipitate dose and its impact on plasma fibrinogen levels are unclear. This retrospective study aims to evaluate: (1) the appropriateness of cryoprecipitate transfusion in trauma; and (2) the plasma fibrinogen response to cryoprecipitate transfusion during massive transfusion in trauma. Fibrinogen levels of < 1.0 g/L within 2 and 6 hours of cryoprecipitate transfusion were used for assessing appropriateness. Out of 394 events, 238 (60%) and 259 (66%) were considered appropriate using 2 and 6 hour criteria, respectively. A dose of 8.7 (±1.7) units caused a mean increase in fibrinogen levels of 0.55 (±0.24) g/L, or 0.06g/L per unit. In our hospital, where transfusion guidelines and policies for rapid blood product and laboratory turnaround times exist, it is possible to achieve high rates of appropriateness for cryoprecipitate transfusion in trauma. The current recommended dose causes a modest increase in fibrinogen levels.
Enzymes and Feedstocks for Sustainable Biomass Utilisation
Keywords: biomass
biorefinery
feedstock
lignin
eastern leatherwood
carbohydrate oxidoreductase
galactose oxidase
glucooligosaccharide oxidase

Modern biorefineries provide a framework for the sustainable conversion of biomass to biofuels and biochemicals. In light of the recalcitrance of lignin in woody feedstocks, the native shrub eastern leatherwood is proposed as a model hypolignified species. Xylem tissue of this low-lignin plant contained syringyl-rich lignin that was more easily hydrolysed and did not appear to be localised in the middle lamellae. Also, leatherwood cellulose was less crystalline and the xylan was highly acetylated. While viable low-lignin plants will enable the sustainable utilisation of woody feedstocks, high-value bioproducts are needed to economise future biorefineries. The carbohydrate oxidoreductases galactose oxidase and glucooligosaccharide oxidase were studied for use in the oxidation and derivatisation of plant-derived polysaccharides for the production of such high-value bioproducts. The carbohydrate-binding module of galactose oxidase was necessary for recombinant protein production. Also, a mutant library of glucooligosaccharide oxidase variants was produced to generate enzymes with novel activity.
The Role of Starch Physicochemical Properties in Determining the Glycaemic Index of Novel Potato Varieties
Keywords: Glycaemic Index
Potatoes

Potatoes are often thought of as high GI. It is known that cooking and cooling affect GI and that these effects may be mediated through the physicochemical properties of their starch. As part of a Canadian initiative to develop low GI potatoes, novel potato varieties which differed in starch composition were tested in 2 separate studies. In study 1, we determined the GI of 8 varieties and found that cooling produced a wide range of effects (0-50% reduction in GI). In study 2, four previously tested varieties were re-examined. A significant variety-x-treatment interaction (p<0.01) was observed with cooling reducing GI in some potatoes. Examination of the starch properties and their role in determining GI showed that RDS was positively associated with GI (r2= 0.85, p= 0.001) and SDS (r2=-0.60, p= 0.02) and amylose (r2=-0.99, p=0.007) negatively associated with GI. No relationship between RS and phosphorous content and GI was observed.
Mutational Analysis of FERM Domain Proteins CG34347 and Cdep in Drosophila
Keywords: Drosophila
Cell Signalling
Crumbs
Polarity
FERM
Cell Signalling
PatJ
Armadillo
Oogenesis
Interfollicular stalk
Notch
Wingless
Hedgehog
Hippo
Follicular epithelium
Cell division
Ovaries
Yurt

Crumbs is a transmembrane protein and apical determinant in Drosophila epithelial cells. Its cytoplasmic tail contains a PDZ and a FERM domain-binding site through which Crumbs interacts with the FERM proteins Yurt, Moesin and Expanded. Recent evidence suggests that Crumbs can also interact with the uncharacterised FERM proteins CG34347 and Cdep. The main objective of my thesis was to generate mutations in CG34347 and Cdep to facilitate the functional analysis of these genes. I generated a mutation for Cdep that remains to be characterised and two mutant lines for CG34347; one lacking the first exon and one lacking the entire gene, using a FRT-based recombination strategy. Both CG34347 mutants cause severe ovarian defects. The most consistent defect is a multilayering of the interfollicular stalk. These defects are also observed when Notch, Hippo, Wingless and Hedgehog signalling pathways are overactive in ovaries suggesting that CG34347 participates in one of those pathways.
MAX-DOAS Measurements of Nitrogen Dioxide and Aerosol
Keywords: Differential Optical Absorption Spectroscopy
MAX-DOAS
tropospheric nitrogen dioxide and aerosol
vertical pollutant profiles
aerosol optical properties

Multi-axis differential optical absorption spectroscopy (MAX-DOAS) was applied to retrieve tropospheric NO2 and aerosol vertical profiles from downtown Toronto, and King City, Ontario during select periods in 2006 – 2010. Linear regression of MAX-DOAS NO2 vertical column density (VCD) versus OMI (satellite) VCD yielded a good correlation (R = 0.88) and MAX-DOAS negative bias of 20%, which was within the reported uncertainty of the MAX-DOAS and OMI VCD. The average regional Toronto VCD (remotely-sensed via MAX-DOAS and OMI) was half of the near-road VCD obtained in-situ (2.4 x 1016 ± 1.2 x 1016 molec/cm2). MAX-DOAS measurements of O4 were coupled with radiative transfer modeling to obtain vertical aerosol extinction profiles and aerosol optical depth (AOD). A strong linear agreement was observed between PM2.5 concentration and aerosol extinction coefficient (R = 0.92), and MAX-DOAS versus sun photometer AOD (slope = 0.94; R= 0.90).
Characterization of Declohorinating Populations in the WBC-2 Consortium
Keywords: WBC-2
Dechlorination
Dehalococcoides
Dehalobacter
Dehalogenimonas
1,1,2,2-Tetrachloroethane

The WBC-2 consortium was characterized using quantitative PCR and analytical techniques to associate growth of dechlorinating bacteria to each step of the 1,1,2,2-Tetrachloroethane (TeCA) degradation pathway. The consortium was found to degrade TeCA through dichloroelimination to trans-1,2-dichloroethene (tDCE), and reductive dehalogenation to Vinyl Chloride (VC) and ethene. Thus the pathway was hypothesized to provide three distinct niches for three genera of dechlorinating bacteria, Dehalobacter, Dehalogenimonas and Dehalococcoides. Using qPCR to track growth over two time course experiments at different inoculum dilutions, the Dehalobacter species showed significant growth on the first step of TeCA dihaloelimination to tDCE Dehalococcoides and Dehalogenimonas species grew on the dechlorination products. The Dehalogenimonas species, a novel non-Dehalococcoides, was found to grow only on tDCE. The Dehalococcoides species also grew on cDCE, less well on tDCE, and on VC.
The Effect of Molecular Weight on Polypropylene Foaming
Keywords: Polypropylene Foaming
Extrusion
Crystallization
Non-crosslinked

The effect of molecular weight on polypropylene (PP) extrusion foaming was investigated and the process to make soft touch, largely expanded, high cell density non-crosslinked PP foam using environmental friendly CO2 is presented. In previous research, when the cell density was high, cell opening was dominant and large expansion could not be achieved even in HMS PP materials. The effects of processing and material parameters on the foam morphologies of PP materials with three different melt flow rate (MFR) were studied using single-screw tandem foam extrusion system. By selecting proper material and die, and by tailoring the processing conditions, large expansion (25 fold) and high cell density (>109 cells/cm3) was successfully achieved in the high MFR PP without any additives. The mechanism of locally induced crystallization was found to be significantly affecting the foaming behavior of PP and was successfully verified using SEM, DSC, HPDSC, shear viscosity and solubility measurements.
Adsorption of Oligonucleotides on Quantum Dots Coated with Zwitterionic Ligands and other Water-soluble Ligands
Keywords: Quantum dots
Zwitterionic

A strategy to ameliorate non-specific adsorption of oligonucleotides onto Quantum Dots (QDs) is investigated where QDs are being used as a platform for the development of optical bioprobes for nucleic acid detection. Certain zwitterionic structures as coatings on QDs have recently been shown to reduce non-specific binding of proteins. In this thesis, a lysine side chain is attached to a dihydrolipoic acid (DHLA) derivative to create a zwitterionic bidentate ligand that has primary amine and carboxyl termini. Such coatings on CdSe/ZnS QDs were studied to assess adsorption of oligonucleotides across a range of pH to better understand the relationship between surface charge and adsorption. The change of pKa of charged terminal groups on QD surfaces for a variety of different water soluble ligands were evaluated using pseudo-titration curves, and indicated up to 3 orders of magnitude shift of pKa at a QD surface in comparison to pKa in bulk solution.
Characterization of ZHX1 in Axillary Lymph Node-negative Breast Cancer
Keywords: Breast Cancer
Gene Expression
Recurrence
Lymphatic Invasion
ZHX1

Women with breast cancer without local metastasis to the axillary lymph nodes (axillary lymph node-negative, ANN) have a good prognosis. However, 20 to 30% of patients with ANN breast cancer will still experience recurrence and distant metastases. Lymphatic invasion (LVI) is an important prognostic factor for ANN breast cancer. Zinc fingers and homeoboxes 1 (ZHX1) was identified as a candidate gene involved in LVI and associated with early recurrence of ANN breast cancer. I examined expression of ZHX1 in breast cancer cell lines and ANN breast tumour samples and discovered that it is expressed at variable levels. I also investigated ZHX1 copy number and determined that amplification does not appear to be a mechanism of its over-expression. From bioinformatic and proteomic analyses, ZHX1 was discovered to potentially be phosphorylated. Overall, these studies suggest that ZHX1 may be involved in ANN breast cancer.
The Haj in the Urbs Prima in Indis: The Regulation of Pilgrims and Pilgrim Traffic in Bombay, 1880 to 1914
Keywords: Bombay
Haj
Empire
Regulation

In this thesis I argue that the management of Muslim pilgrims and the Haj traffic in Bombay was the result of the localization of an international regime of regulation aimed at controlling Hajis as mobile threats to public health and imperial security. International scientists, doctors, and politicians problematized Hajis as diseased, dangerous and disorderly through discourse produced in print material and at international conferences taking place across the globe. Local, elite concerns over their own power, Bombay’s urban spatial order, and the city’s international trade shaped the way these larger global and imperial projects were implemented in Bombay. These findings point to the importance of local, place-based social, political and economic structures in the day-to-day governance of empire.
The Effects of Distractions and Driver's Age on the Type of Crash and the Injury Severity Sustained by Occupants Involved in a Crash
Keywords: Driver Distraction
Human Factors
Injury Severity
Crash Type
Ordered Logit Model
Multinominal Model

This thesis investigates the associations between crash outcomes, the existence and type of driver distraction as well as driver’s age. The crash outcomes considered in this thesis consist of the type of crash as well as the injury severity sustained by occupants involved in the crash. An ordered logit model was built to predict the likelihood of severe injuries and a multinomial model was developed to predict the likelihood that a driver will be involved in one of three common crash types: singular, angular, and rearend. In these models, various factors (e.g., weather, driver’s gender, and speeding) have been statistically controlled for, but the main focus was on the interaction of driver’s age and distraction type. The findings of this thesis have implications for policy making and prioritizing capabilities of distraction-related safety systems.
Lanthanide-encoded Poly(styrene-co-methacrylic Acid) Microspheres: Synthesis and Characterization
Keywords: polystyrene
dispersion polymerization
lanthanide
mass cytometry
microspheres
ion release

Lanthanide-encoded polystyrene-co-methacrylic acid (P(S-MAA)) microspheres with narrow size distributions were synthesized by two-stage dispersion polymerization. I examined how the amounts of methacrylic acid (MAA) and lanthanide (Ln) salts affect the composition of the particles formed in the reaction. Also, I performed a systematic study of Ln ion release into different aqueous solutions. In normal buffers, these particles were stable against ion leakage, even upon prolonged storage and stirring. When strong chelating agent ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) were present in buffer, the loss of Ln ions increased to 15 % after 8 weeks. A preliminary kinetic study of Ln ion incorporation was performed to help understand the particle formation mechanism.
Costimulation-mediated Rescue of Superantigen-activated T cells in an Animal Model of Kawasaki Disease
Keywords: kawasaki disease
superantigens

Lactobacillus casei cell wall extract (LCWE)- induced coronary arteritis in mice models Kawasaki disease (KD). LCWE injections consist of T-cell dependent factors that expand superantigen (SAg)-activated T-cell receptor (TCR) Vβ6+ cells, and T-cell independent factors (i.e. TLR2 activity) that localize and sustain the immune response. TLR2 can upregulate costimulatory molecules to rescue SAg-activated T-cells from apoptosis. Accordingly, SAg-activated costimulation-rescued TCRVβ6+ cells are predicted to express activation markers, produce cytokines and be able to induce coronary arteritis. MAM was identified as a SAg able to activate TCRVβ6+ cells in a manner similar to LCWE; however a combination of MAM and TLR2 agonist Pam3Cys could not induce coronary arteritis. As another marker of disease, leukocyte recruitment molecule expression in the hearts of MAM+Pam3Cys- injected mice was found to be lower than in LCWE- injected mice. Therefore, LCWE contains unique features beyond TCRVβ6 stimulation and TLR2 activity that are important for disease induction.
In Silico Metabolic Network Reconstruction of Scheffersomyces Stipitis
Keywords: metabolic model
S. stipitis
FBA

In this study, a genome-scale metabolic model was constructed using published genomic and biochemical data. By employing the flux balance analysis (FBA) framework, the model was able to accurately predict ethanol yields on various carbon substrates, secretion profiles, and key characteristics of central metabolism under various growth conditions. A by-product of the model development was the construction of a pathway genome data-base (PGDB) of the yeast, named PichCyc. The PGDB was constructed using Pathway Tools and the database contains 5,841 genes, 1,457 reactions, 994 gene-associated reactions, and 1,475 metabolites. Pathway Tools also facilitated the annotation of an additional 155 genes through the use of Pathway Hole Filler. Together with the constraint-based model, a platform for model-guided metabolic engineering, high-throughput data contextualization, and a public-access online genomic/biochemical database was created.
Improvements to the Efficiency of the Radiotherapy Treatment Planning Process
Keywords: optimization
radiation therapy
beam orientation optimization
nomenclature

Radiotherapy is one method of treating di erent diseases like cancer. It requires a treatment plan that clearly delineates target and non-target volumes, and the beams and their intensities to deliver the prescribed dose. Historical treatment plans often contain volume names that are unaccounted for. An approach is applied where desired volumes are detected and renamed to conform to current search standards. The mapped names provide an avenue for searching historical plans when performing outcomes analysis in the future to help improve quality in radiation therapy. A specific form known as intensity modulated radiation therapy is applied to total marrow irradiation, a method to remove all marrow in the body prior to bone marrow transplant. A set-covering approach is used, solved using heuristics and commercial packages to compare outcomes. Constraint programming is used in an attempt to better and to improve on the heuristic solutions.
Characterization of Williams-Beuren Syndrome Mouse Models: Linking Genes with Cognition and Behaviour
Keywords: Molecular biology
Williams-Beuren syndrome
Mouse models
Behaviour
Cognitive development
Neurobiology

Deletion (Williams-Beuren syndrome (WBS)) and duplication (Dup7q11.23) of a common interval spanning 26 genes on chromosome 7q11.23 cause disorders with a spectrum of clinical, cognitive and behavioural symptoms. Studies of individuals with atypical deletions have implicated two genes, GTF2IRD1 and GTF2I. Here I describe the behavioural characterization of mice hemizygous for Gtf2i, or Gtf2ird1 and Gtf2i together, as well as mice with additional Gtf2i copies. Dosage changes in Gtf2i were associated with working memory impairment and separation anxiety, and possibly with general anxiety and repetitive behaviours. A potential cause of these phenotypes was found in brain tissue, where subcellular localization of the calcium channel TRPC3, which is regulated by GTF2I, was found to be altered. Collectively, these results provide a better understanding of the contributions of GTF2I to the cognitive and behavioural profile of WBS and Dup7q11.23 and identify a potential biological mechanism that may underlie some of the symptoms.
Dynamic Modeling and Control of a 6-DOF Parallel-kinematic-mechanism-based Reconfigurable Meso-milling Machine Tool
Keywords: meso-milling
parallel mechanism
dynamic model
control

In this thesis, a methodology for rigid body dynamic modeling and control design is presented for a 6 degree-of-freedom (DOF) parallel-kinematic-mechanism-based reconfigurable meso-milling machine tool (RmMT) with submicron tracking accuracy requirement. The dynamic modeling of the parallel kinematic mechanism (PKM) is formulated using the Lagrangian method with the application of principle of energy equivalence and coordinate transformations to separate the mechanism into serial sub-systems. The rigid body gyroscopic force is also modeled using this approach and its effect as a disturbance is analyzed and compensated. The contour errors for both position and orientation are formulated to increase machining accuracy. The dynamic model of the system is linearized through feedback linearization and the contour error based feedback control law is formulated using the convex combination design approach to satisfy a set of design specifications simultaneously. The dynamic model and its control methodology are simulated and verified within the MATLAB Simulink environment.
Effects of Moderate-intensity Aerobic Cycling and Swim Exercise on Post-exertional Blood Pressure in Healthy, Young Men and Women
Keywords: blood pressure
swimming
cycling
exercise
post-exercise hypotension

Aerobic exercise such as cycling is known to elicit a post-exercise hypotensive (PEH) response. However, it is not known if swim exercise produces a similar effect in normotensive individuals. We tested the hypothesis that an acute bout of swimming would elicit a PEH response that is less compared to an equivalent bout of cycling. 10 trained and 11 untrained normotensive (SBP/DBP < 120/80 mmHg) individuals (23±1 years) underwent 30 min intensity-matched cycling and swimming sessions to assess changes in BP and cardiovascular responses. While PEH was similar between modalities within groups, the magnitude and temporality of change in BP following swimming was significantly different (p < 0.01) between groups, with untrained participants showing a significant PEH response. Attenuation of PEH in trained individuals was reflective of a significant increase in sympathetic outflow and slower vagal reactivation, suggesting training in an aquatic environment leads to alterations in post-exercise BP regulatory mechanisms.
Pulse Shaping Based on Integrated Waveguide Gratings
Keywords: Pulse shaping
Integrated optics
Gratings
Ultrafast optics
Picosecond pulses
AlGaAs waveguide
AlGaAs gratings
Flat-top pulse shaping
Rectangular pulse shaping
Coupled-mode theory
Inverse scattering

Temporal pulse shaping based on integrated Bragg gratings is investigated in this work to achieve arbitrary output waveforms. The grating structure is simulated based on the sidewall-etching geometry in an AlGaAs platform. The inverse scattering employin the Gel'fan-Levithan-Marchenko theorem and the layer peeling method provides a tool to determine grating structures from a desired spectral reflection response. Simulations of pulse shaping considered flat-top and triangular pulses as well as one-to-one and one-to-many pulse shaping. The suggested grating profiles revealed a compromise between performance and grating length. The integrated grating, a few hundred microns in length, could generate flat-top pulses with pulse durations as short as 500 fs with rise/fall times of 200 fs; the results are comparable to previous work in free-space optics and fiber optics. The theories and the devised algorithms could serve as a design station for advanced grating devices for, but not restricted to, optical pulse shaping.
Insulin Modulates Intracellular Apolipoprotein B mRNA Traffic into RNA Granules/Cytoplasmic P Bodies: Implications in Translational Control
Keywords: Insulin
Apolipoprotein B
P bodies
Polysome

Apolipoprotein B (ApoB) synthesis is partially regulated at the translational level; however, the molecular mechanisms that govern translational control of apoB mRNA remains largely unknown. We imaged intracellular apoB mRNA traffic and determined whether insulin silences apoB mRNA translation by trafficking into translationally-silenced cytoplasmic RNA granules called Processing Bodies (PBS). ApoB mRNA was visualized by using a strong interaction between the bacteriophage MS2 protein and a specific phage RNA sequence that binds MS2 protein. We observed a statistically significant increase in the localization of apoB mRNA into PBs, 4h, 8h, and 16h after insulin treatment. Conversely, acute insulin treatment (1h) did not show any significant effect. Insulin was also found to reduce polysomal association of apoB mRNA 4h and 16h post treatment in HepG2 cells. Overall, our data suggest that chronic insulin treatment silences apoB translation in HepG2 cells by localizing apoB mRNA into PBs and reducing translationally-competent mRNA pools.