title: Chiral Analysis of Amino Acids in Bacterial Samples Using LC-MS/MS

contributor:
McCarry, Brian E.
Chemistry

subject: chiral analysis, amino acids, bacterial samples, LC-MS/MS, multiple reaction monitoring, bacterium, enantiomers

abstract:
An optimized method for the chiral resolution of enantiomers of amino acids in bacterial
supernatants is reported. This LC-MS/MS method is performed using a chiral Teichoplanin LC column and does not require sample clean up or chemical derivitization. This method allows for the determination of the relative amounts of the D and L enantiomers of 20 proteinogenic amino acids. The detection limits and response factors for the 20 amino acids were determined. Calibrations over three orders of magnitude showed least squares coefficient values (R^2) greater than 0.996 for eighty percent of the amino acids and greater than 0.992 for the remainder.
The amino acids and their enantiomers were identified based on their retention times and
their unique Multiple Reaction Monitoring (MRM) transitions for each amino acid. L-Aspartic
acid-2,3,3-d3 was used as the internal standard.
Cultures of Sinorhizobium meliloti (a nitrogen-fixing soil bacterium) were grown on minimal media; thus, all amino acids were biosynthesized by the bacterium. After centrifugation, supernatants were freeze dried, reconstituted in a small volume of methanol/water with internal standard and injected onto the LC column. The amino acids detected in the bacterial supernatant and the concentrations of the enantiomers were reported as the L and D isomers respectively: arginine [L, 12.6 ± 3.1 μg/L; D, 10.1 ± 3.2 μg/L], serine [L, 7.2 ± 1.16 μg/L; D, n.d.], threonine [L, n.d.; D, 11.2 ± 2.7 μg/L] and valine [L, 15.5 ± 4.3 μg/L; D, 11.3 ± 3.7 μg/L], where the term n.d. means below detection limit. The limits for detection for all amino acids ranged from 1.3 μg/L - 5.1 μg/L. In media with no added phosphate, the amino acid profiles changed somewhat under these stress conditions. Arginine was no longer detected while alanine and proline were now observed; the concentrations of the amino acids were: alanine [L, 7.7 ± 1.2 μg/L; D, 13.4 ± 2.5 μg/L], proline [L, n.d.; D, 8.63 ± 1.3 μg/L], serine [L, 7.6 ± 1.2 μg/L; D, n.d.], threonine [L, n.d.; D, 10.2 ± 3.2 μg/L] and valine [L, 11.6 ± 2.3 μg/L; D, 10.1 ± 3.1 μg/L]. These data represent the mean values of three independent bacterial growth experiments conducted over a 3 month period; the data came from the analysis of five separate aliquots from each growth experiment. The percent standard deviation for these data ranged from 15% to 33% and averaged 24%. Under both the normal and stressed growth conditions of S. meliloti produced the L enantiomer of serine, the D enantiomer of threonine and racemic valine. While racemic arginine was observed under normal growth conditions, levels were below detection under stressed conditions; under stress conditions only the D enantiomer of proline was observed while alanine was found in 1:2, L:D ratio.

abstract: Thesis

abstract: Master of Science (MSc)


title: MULTIPLE TRAFFIC LIGHT RECOGNITION SYSTEM BASED ON A MONOCULAR CAMERA

contributor:
Kirubarajan, Thia
Electrical and Computer Engineering

subject: multiple traffic light recognition

abstract: This thesis proposes a novel multiple traffic light recognition system based on videos captured by a monocular camera. Advanced driver assistance system (ADAS) and autonomous driving system (ADS) are becoming increasingly important to help drivers maneuvering vehicles and increase the vehicle and road safety in modern life. Traffic light recognition system is a significant part of ADAS and ADS, which can detect traffic light on the road and recognize different types of traffic lights to provide useful signal information for drivers. The proposed method can be applied to real complex environment only based on a monocular camera and is tested in real-world scenarios. This system consists of three parts: multiple traffic light detection, multi-target tracking and state classification. For the first step, a supervised machine learning method, support vector machine (SVM) with two integral features - histogram of oriented gradients (HOG) and histogram of CIELAB color space (HCIELAB), are used to detect traffic lights in the captured image. Then, a new multi-target tracking algorithm is presented to improve the accuracy of detection, reduce the number of false alarm and missing targets, by means of nearest neighbor data association, motion model analysis and Lucas-Kanade optical flow tracking and the region of interest (ROI) prediction. Finally, a SVM-based and a convolution neural network (CNN) based classifiers are introduced to classify the state of traffic lights, that provides the stop, go, warning, straight and turn information. Various experiments have been conducted to demonstrate the practicability of the proposed method. Both GPU-based and CPU-based programming can run real-time on the real street environment.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Comparative study of ATF for a CANDU lattice

contributor:
Novog, David
Engineering Physics

subject:
nuclear engineering
reactor physics
CANDU
accident-tolerant fuel
Serpent 2
Monte Carlo
accident-tolerant cladding

abstract:
McMaster University MASTER OF APPLIED SCIENCES (2017) Hamilton, Ontario (Engineering Physics)

TITLE: Comparative study of accident-tolerant fuel for a CANDU lattice AUTHOR: Simon Younan, B.Eng. (McMaster University) SUPERVISOR: Dr. David Novog NUMBER OF PAGES: xiii, 120

abstract:
Since the Fukushima accident in 2011, there have been an increasing number of studies on the use of accident-tolerant fuel (ATF) in light water reactors to mitigate the consequences of a future severe accident, by better retaining fission products and/or providing operators more time to implement emergency measures.
However, few studies exist for CANDU reactors in this regard. The goal of this study is to determine how different types of ATF are expected to behave in a CANDU lattice when compared to the current UO2 fuels. In particular, this study focuses on neutronic parameters calculated using the Serpent 2 code, but also models heat transfer and stylized accident scenarios. The ATF concepts tested include UO2-SiC composites, UN and UN-based composites, U-9Mo, and fully ceramic microencapsulated (FCM) fuel, along with SiC and SS-coated cladding.  Four general conclusions can be drawn:
1. Fuel temperature are lower for ATF as compared to traditional fuels.  UO2-SiC composite fuel exhibits a moderate temperature reduction compared to UO2, particularly for fresh fuel. Other ATF fuel materials exhibit a substantial decrease in fuel temperature compared to UO2. The lower fuel temperatures are also accompanied by lower melting temperatures for some fuels, hence each design requires specific assessments on safety.
2. As most ATF have a poorer neutron economy compared to standard fuel designs, enrichment is required to use ATF in a CANDU, particularly for UN and FCM fuel compositions. Coolant void reactivity (CVR) is lowest with FCM fuel and highest with U-9Mo fuel. Fuel temperature coefficient (FTC) is most negative for fuel containing UN or U-9Mo.
3. Changing the cladding material from zircaloy to SiC slightly improves neutron economy, while a FeCrAl surface layer impairs neutron economy.  The impact of many ATF sheath materials is to greatly reduce or eliminate hydrogen production in some severe accidents.  A specific assessment on hydrogen production was not performed in this study.
4. In stylized accident scenarios, all fuels exhibit only a small temperature spike due to the reactivity insertion of the LOCA as the reactor shutdown limits the power excursion. For cases where Emergency Core Cooling functions as designed, fuel and channel failures are precluded for both traditional fuels and ATF. For cases with impairment of ECC, most ATF fuels show lower fuel temperatures than UO2 fuels and adequate heat removal to the pressure-calandria tube fuel channel.  The exception would be Mo-based fuels that reach the melting point prior to establishing an adequately high sheath temperature to sustain radiative heat removal to the PT-CT assembly.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
Since the Fukushima accident in 2011, there have been an increasing number of studies on the use of accident-tolerant fuel in nuclear reactors to mitigate the consequences of a future severe accident, reducing the likelihood and severity of a radiation release.  Canadian reactors are of the CANDU design, which differs greatly from the reactors most recent studies have focused on. The goal of this study is to determine the feasibility of using accident-tolerant fuel in CANDU reactors, studying different types.
In general, the goal of accident-tolerant fuels in CANDU reactors would be to reduce fuel temperatures and improve fission product retention, reducing the likelihood/magnitude of radioactive releases in a severe accident. However, nearly all types of accident-tolerant fuel would also require the uranium to be slightly enriched as opposed to the current fuel which is based on naturally-occurring uranium. This study outlines the results obtained by computer modelling of accident-tolerant fuel in a CANDU reactor, including the enrichment requirements, changes to important reactivity feedbacks, and impacts on accident performance.


title: Expression Analysis of the Transporters of Sinorhizobium Meliloti

contributor:
Finan, T.M.
Biology

subject: expression analysis, transporters, Sinorhizobium meliloti, alpha-proteobacterium, nodulation, compounds, soil

abstract:
 Sinorhizobium meliloti is an alpha-proteobacterium that forms symbiotic nodules on the roots of Medicago sativa (alfalfa). The ability to catabolize specific compounds available in the soil is one of the best-characterized factors to increase competition for nodulation. In order to successfully attain symbiosis S. meliloti must compete for nutrients in the rhizosphere, which can be done by having a large number of transport systems encoded in its genome. Genes encoding proteins involved in transport constitute the largest (12%) class of genes in the S. meliloti genome. Great interest now lies in determining substrates for the transport systems and their role in the survival and fitness of S. meliloti.

 An estimated 824 transport genes in the genome of the soil bacterium Sinorhizobium meliloti are predicted to encode 382 transport systems. All of the S. meliloti transporters had been studied under 120 different conditions, including growth on various carbon and nitrogen sources, seed and root exudates and starvation conditions.

 From this screen of every transport system in S. meliloti, the substrates that induce expression of over 50 transport systems have been identified. We have found putative transporters for amino acids, sugars, sugar alcohols, amino sugars, betaines and other compounds that might be found in the soil. This large scale expression analysis gives insight into the natural environment of S. meliloti by studying those genes that are induced by compounds that would be found in the soil.

abstract: Thesis

abstract: Master of Science (MSc)


title: Esquesing Township: A Geographical Appreciation

contributor:
Parker, W. H.
Geography

subject: Esquesing Township, geography, land use

abstract:
<Abstract Not Provided>
Thesis
Bachelor of Arts (BA)


title: Physiological and Biochemical Responses of Yukon and Shandong Thellungiella to Water Deficits

contributor:
Weretilnyk, Elizabeth A.
Biology

subject: physiological, biochemical, Yukon, responses, Shandong Thellungiella, water deficits, plants, environmental conditions

abstract:
 Thellungiella salsuginea (also known as T. halophila), is an emerging model species for studies of plant tolerance to osmotic stress. Currently, Thellungiella plants originating from two geographical locations are being developed for research. Yukon Thellungiella is native to the saline and alkaline soils of the Yukon Territory, Canada. The seeds in this study were collected at the Takhini Salt-Flats near Whitehorse, YT, a sub-arctic and semi-arid region. Plants from the Yukon have been proposed to be a suitable species to study plant tolerance to salinity, cold temperatures, and water deficits. Shandong Thellungiella is native to the saline coast of north-eastern China in Shandong Province where the climate is temperate and affected by summer monsoons. This plant has been proposed as an ideal model for the study of salt tolerance mechanisms but is reported to show little drought tolerance.

 An objective of this study was to compare Yukon and Shandong Thellungiella plants with respect to their ability to withstand water deficits. Plants were grown simultaneously in controlled environment chambers where watering was withheld until plants visibly wilted. Wilting occurred at a leaf relative water (RWC) content of about 50-60% and then turgor was restored by re-watering. In a second experiment plants allowed to wilt and recover once were then subjected to a second wilting and recovery cycle. The third experimental approach tested the survival capacity of plants after experiencing a wilting episode where leaf RWC dropped to about 30%.

 With the first drought simulation treatment, both Yukon and Shandong plants took about 6 days to wilt when watering was stopped. After re-watering and recovery, the Yukon plants subjected to a second drought episode took almost two days longer to wilt
while the similarly treated Shandong plants showed no change in the days taken to wilt. This indicates that Yukon plants show improved tolerance to stress after a single exposure to a water deficit. Yukon plants were also able to grow and complete their life cycle following exposure to severe water deficit treatment whereas Shandong plants died. Measurements of solute potential showed that the Yukon plants re-established turgor at a lower solute potential of -2.06 +/- 0.03 MPa following recovery from a second drought treatment suggesting that this plant can undergo osmotic adjustment. No evidence of osmotic adjustment was observed for Shandong Thellungiella.

 Gas chromatography/mass spectrometry (GC/MS) was used to identify the metabolites associated with Thellungiella leaves recovering from water deficits relative to those from unstressed, well-watered controls. For comparison, metabolite profiles were also prepared from leaves of plants harvested at a Yukon field site during a dry year (2003) and a year of higher than normal rainfall (2005). The data was analyzed to identify treatment/sample-specific patterns using ANOVA to test for significance among quantitative and qualitative changes for individual metabolites. Significant changes were
then subjected to hierarchical cluster analysis (HCA) and principal component analysis (PCA). Using ANOVA and HCA, we were able to identify the most likely metabolite candidates contributing to the superior tolerance of Thellungiella, and their linkages between broad spectrums of metabolites. Using PCA we were able to assign clusters to the individual plant treatments for each plant source, and identify the most important components contributing to these clusters. Of the ca 289 components detected, only a small subset of components underwent statistically significant changes in abundance. Most of the drought-stress related changes were attributed to sugars: hexoses and disaccharides. Sugars accumulating in the more drought-tolerant Yukon plants and in a dry field season included fructose, glucose and galactose. Of the sugar alcohols, only myo-inositol showed patterns of interest in view of its enrichment in tissues showing superior tolerance to low water conditions. Similar patterns were also shown by the organic acid, threonic acid.

 A complementary approach was used to characterize metabolic traits associated with exposure to cold temperatures. In this study, a higher content of proline and citrate distinguished plants exposed to cold temperatures irrespective of whether the plants were in cabinets or in the field. Proline content, however, did not show drought-responsive accumulation under any drought treatment tested. As such, by comparison with the drought-stress data we can identify possible stress-specific signatures among metabolites undergoing changes. The study of stress-responsive traits could help develop a better understanding of plant systems and their response to specific environmental conditions.

abstract: Thesis

abstract: Master of Science (MSc)


title: Malic Enzymes of Sinorhizobium Meliloti: A Study of Metabolomics and Protein-Protein Interactions

subject: malic enzymes, Sinorhizobium meliloti, metabolomics, protein-protein interactions, oxidative, bacterium, dme gene, tme mutant

abstract:
 Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate with the
simultaneous reduction of a nicotinamide cofactor. It was previously reported that the nitrogen-fixing bacterium, Sinorhizobium meliloti, has two malic enzymes, a
diphosphopyridine-dependent malic enzyme (DME) and a triphosphopyridine-dependent malic enzyme (TME). The dme gene is essential for symbiotic nitrogen-fixation in alfalfa root nodules and this symbiotic requirement cannot be met through increased expression of tme. In order to determine if a metabolic difference exists between the dme and tme mutants which might explain the symbiotic phenotypes, we conducted an analysis of intracellular and extracellular polar metabolomes. Differences noted between the intracellular profiles of the dme and tme mutant strains hinted at osmotic stress or a disturbance in central carbon metabolism. Extracellular studies indicated that dme mutant cells excreted at least 10-fold greater concentrations of both malate and fumarate. When considered together, the metabolic data implies that the DME enzyme is primarily responsible for the conversion of malate to pyruvate to generate acetyl-CoA whereas the TME enzyme must serve a secondary function within the cell.

 While the C-terminal 320 amino acid regions from both DME and TME are similar in sequence to phosphotransacetylase enzymes, enzyme assays with DME and
TME proteins have failed to detect PTA activity. Here we report that the chimeric malic enzyme structure is conserved among various gram negative bacteria including Agrobacterium tumefaciens, Escherichia coli, Bradyrhizobium japonicum and Porphyromonas gingivalis. Moreover these chimeric proteins are also present in the archaebacteria. Halobacterium salinarum and Haloarcula marismortui. To further our understanding of the functions of DME and TME in S. meliloti, we have fused protein domains from DME to an affinity tag consisting of strepII and a calmodulin binding peptide. To identify proteins interacting with this fusion, we expressed these protein fusion constructs in S. meliloti, prepared extracts containing the soluble proteins and passed these through tandem affinity chromatography columns. All proteins that coeluted with the fusion proteins appeared to be interacting with antibodies specific for the DME protein and so may have been aggregates or break-down products of DME.

abstract: Thesis

abstract: Master of Science (MSc)


title: INVESTIGATING THE ROLE OF MANF & CDNF IN THE PATHOPHYSIOLOGY OF PARKINSON’S DISEASE

title: INVESTIGATING THE ROLE OF CEREBRAL DOPAMINE NEUROTROPHIC FACTOR (CDNF) & MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR (MANF) IN THE PATHOPHYSIOLOGY OF PARKINSON’S DISEASE

contributor:
Mishra, Ram
Neuroscience

subject:
MANF
CDNF
Parkinson's Disease
Neurotrophic
NTF
Pathophysiology

abstract: CDNF and MANF are members of a recently discovered and evolutionarily conserved neurotrophic factor family implicated in supporting the survival and protection of midbrain dopaminergic neurons in the nigrostriatal pathway, which degenerate in Parkinson’s Disease (PD). Increasing evidence demonstrated that MANF overexpression resulted in significant protection and repair of TH+ cells and DA neurons in the substantia nigra (SN). In addition, continuous infusion of CDNF demonstrated greater protection of TH-positive neurons in the SNc and fibers in striatum than GDNF in the 6-OHDA neurotoxin model. Current literature suggests that CDNF and MANF are involved in regulating ER stress and are upregulated in vitro and in vivo during the unfolded protein response (UPR). Thus, this study sought to investigate whether selective knockdown (K/D) of MANF and CDNF causes pathophysiological conditions that lead to the behavioural manifestation of PD in preclinical models. Male Sprague-Dawley rats underwent stereotaxic surgery, whereby 2 μL at 0.5 μL/minute of MANF, CDNF, MANF and CDNF combined, or a scrambled negative control (N=44) of rat lentiviral-mediated shRNA formulations were infused into the SN in reference to bregma: Anterior/Posterior=-5.3 mm, Medial/Lateral=±2.3 mm, Dorsal/Ventral=-7.8 mm. Rats were tested on a battery of behavioural tests for the assessment of PD phenotypes, such as impairments in balance, gait and motor coordination. MANF K/D rats demonstrated PD phenotypes in the rearing duration, beam traversal, rotarod and cylinder test (P <0.05). These results were largely mirrored in the combined MANF and CDNF K/D group, however, CDNF K/D rats failed to demonstrate consistent motor deficits (P >0.05). Additionally, CDNF mRNA expression from the platelets of PD patients revealed no significant differences compared to healthy controls (P >0.05). In conclusion, the etiology of PD remains to be elucidated, and this is the first study to demonstrate that MANF K/D rats recapitulate key motor features of parkinsonism.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: CDNF and MANF are members of a recently discovered and evolutionarily conserved neurotrophic factor family implicated in supporting the survival and protection of midbrain dopaminergic neurons in the nigrostriatal pathway, which degenerate in Parkinson’s Disease (PD). Increasing evidence demonstrated that MANF overexpression resulted in significant protection and repair of DA neurons in the substantia nigra (SN). Current literature suggests that CDNF and MANF are involved in regulating ER stress and are upregulated in cells and in rodents during the unfolded protein response (UPR). Thus, this study sought to investigate whether selective knockdown (K/D) of MANF and CDNF causes the underlying changes in the brain that lead to the behavioural manifestation of PD in preclinical models. 2 μL at 0.5 μL/minute of MANF, CDNF, MANF and CDNF combined, or a scrambled negative control (N=44) of rat lentiviral-mediated shRNA formulations were infused into the SN. Rats were tested on a battery of behavioural tests for the assessment of PD phenotypes, such as impairments in balance, gait and motor coordination. MANF K/D rats demonstrated PD phenotypes in the rearing duration, beam traversal, rotarod and cylinder test (P <0.05). These results were largely mirrored in the combined MANF and CDNF K/D group, however, CDNF K/D rats failed to demonstrate consistent motor deficits (P >0.05). Additionally, CDNF mRNA expression from the platelets of PD patients revealed no significant differences compared to healthy controls (P >0.05). In conclusion, the etiology of PD remains to be elucidated, and this is the first study to demonstrate that MANF K/D rats recapitulate key motor features of parkinsonism.


title: Evidence of Pollinator-Mediated Selection for Floral Display Height

contributor:
Dudley, S.A.
Biology

subject: pollinator-mediated selection, floral display height, autogamously, mating, plants, behaviour and reproduction,

abstract:
 Many floral characters have can affect plant fitness by altering the frequency or efficiency of pollinator visits. More frequent pollinator visitation may lead to larger pollen loads and greater outcrossing rates, which in tern may lead to greater numbers of offspring, with higher genetic variability and less inbreeding depression. Mating systems may moderate the strength of natural selection on traits that attract pollinators through its effects on inbreeding depression, and the ability to self-pollinate autogamously. Natural selection is expected to be stronger in largely outcrossing systems where inbreeding depression is high, but reduced in largely selfing systems where deleterious alleles have been purged.

 Here I investigate the role of floral display height in attracting pollinators, and its consequences for plant fitness in two closely related monocarpic herbs (Hesperis matronalis and Alliaria petiolata) with different mating systems. Though others have looked at height as a potential trait attracting pollinators, no one has yet clearly separated the effects of floral display height from that of plant size. I experimentally altered plant height independently of plant size by placing potted plants into either elevated or non-elevated treatments and observed pollinator foraging behaviour and reproduction.

 Pollinators preferred taller floral displays in the predominant outcrosser Hesperis matronalis. Elevated plants produced more seeds than control plants although their seeds were smaller, reflecting a strong seed size-number trade-off. Path analysis showed seed number was affected directly by plant height, presumably though greater pollinator visitation, and indirectly by plant mass through increased fruit number.

 In Alliaria petiolata, a predominant self-pollinating species, pollinators visited taller displays in field observations and experimentally elevated plants had significantly
greater seed per fruit. Experimentally outcrossed and self-pollinated plants showed no
difference in seed production, but offspring quality was significantly higher in outcrossed
plants for early traits. Measures of maternal fitness increased significantly with both maternal and seed mass. For individual seeds, seed mass was the most important factor in seed fitness, where larger seeds germinated sooner, more frequently, and had higher survivorship than smaller seeds, regardless of pollination treatment. Competition strongly affected all seedling traits, with increased density having a significant negative effect on seedling mass, total leaf area, and maximum leaf length; and, a positive effect on hypocotyl length and petiole length. Seedling mass at harvest was not significantly affected by elevation treatment, seed mass, or maternal mass, however, this may have been due to lower competition brought about by low germination and survival; thus, competition did not accentuate the effect of maternal size or elevation treatment on seedling. Taken together, the results of these two studies suggest the importance of height, in attracting pollinators, independent of size in both species. The consequences of pollinator attraction were highly significant in the predominant outcrosser Hesperis matronalis, while maternal size and seed size played more important roles in the fitness of the predominant selfer Alliaria petiolata.

abstract: Thesis

abstract: Master of Science (MSc)


title: Loss Minimization using Linear Soft-Switching with Wide Bandgap Devices in Efficient High-Frequency DC-DC Converters

contributor:
Emadi, Ali
Electrical and Computer Engineering

abstract:
Switching power converters are used for voltage-level conversions in various applications. With progress in device technology, the wide bandgap devices offer smaller parasitic capacitances and lower switching energy values. Efforts are being made to use higher frequencies to realize more power-dense converters with smaller volume of the passive components. The maximum switching frequency is limited by the ability of the switching devices to dissipate their losses. This thesis presents a framework for the design and modeling of efficient high-frequency high-energy density DC/DC converters using soft-switching techniques with wide bandgap devices. Various online switching loss estimation methods are discussed demonstrating improved accuracies, enabling a better cooling system design. A comparison is made between various soft-switching methods and the use of turn-off snubbers to reduce the switching losses. A
linear soft-switching method is proposed and validated for both SiC and GaN devices. A simpli fied analytical model is presented which predicts the actual turn-off losses very accurately. This method is found to enable buck converter operation at 1 MHz switching frequency and 1 kW output power with switch losses smaller by nearly  five times from a hard-switched system using GaN devices. These losses are further reduced with the use of SiC schottky diodes, with future scope to achieve higher efficiency using custom inductors designed for high frequency and current ripple values.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Synthesis and Characterization of Constrained Magnetism in Niobates

contributor:
Luke, Graeme M.
Physics and Astronomy

subject:
frustrated magnetism
crystal growth
niobate
muon spin relaxation
neutron scattering
specific heat
synthesis
characterization
x-ray diffraction
SQUID magnetometry
antiferromagnetism
low dimensionality

abstract:
This thesis contains the results of the extensive study into the synthesis of nickel niobate (NiNb2O6) including the formation of what was a previously unreported polymorph of the material, as well as the magnetic properties of both cobalt niobate (CoNb2O6) and nickel niobate using techniques including SQUID magnetometry, powder and single crystal x-ray scattering, powder and single crystal neutron scattering and muon spin rotation/relaxation.
In cobalt niobate we found extremely long relaxation times in the heat capacity which showed up strongly in muon spin rotation experiments but not in neutron measurements. Additionally, with field applied to the system we see the emergence of spin-wave like structures in the neutron scattering data. Within cobalt niobate the strongest interaction is ferromagnetic and along the chain. The chains themselves are laid out on a triangular fashion
and interact, although far more weakly, in an antiferromagnetic manner. This triangular patterning as well as an antiferromagnetic interaction results in interchain frustration, which protects the quasi-1D nature of the system due to the difficulty generated in creating 3D order.
In nickel niobate we found that growth conditions caused highly variable changes, and we were able to create two different polymorphs. One polymorph was in the same space group as cobalt niobate, which gave us an opportunity to explore the magnetic difference between a spin-½ and spin-1 magnetic system and in nickel niobate in the new space group we performed an ab initio characterization solving the unit cell structure, the magnetic structure with neutron scattering as well as a magnetic characterization with SQUID magnetometry and muon spin rotation, allowing us to contrast the significant crystallographic differences. For the new polymorph we were able to determine its magnetic structure, characterized by Ising-like spins arranged in frustrated tetrahedra with three of the four points lying in the same plane as the spin, and for both materials we were able to use zero-field μSR data to estimate behaviour near the critical point and determine a critical exponent near the magnetic transitions. In both polymorphs there is evidence of constrained magnetism or reduced dimensionality, although the evidence for low dimensionality is much stronger in the columbite polymorph.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
This thesis examines two different niobium-based compounds: cobalt niobate (CoNb2O6) and nickel niobate (NiNb2O6). In these systems the cobalt and nickel atoms provide interesting magnetic properties. Within a magnetic material, the magnetic atoms tend to have their spins
align in certain ways. The atoms themselves are fixed to particular sites by the way the material is assembled; an atomic framework.
In the case of cobalt niobate, the magnetic atoms are arranged in well-separated chains so that a magnetic atom interacts strongly with its magnetic neighbours within a chain, and weakly with ones that are further away. This is an example of a material that is called `low dimensional'. The chains themselves form triangular patterns, and the interactions between chains are both weaker and antialigned, which creates a frustrated competition between the chains, protecting the low dimensional state by creating conditions where it is hard for all the spins in the material to order.
For nickel niobate, the magnetic moments all want to anti-align, or be pointing in the opposite direction as its nearest neighbour. The magnetism is `frustrated' because each magnetic atom is tetrahedrally connected to three other atoms, so it cannot meet that condition. This can be visualized by drawing a triangle and trying to make each corner have an arrow pointing up
or down. The third corner of the triangle cannot satisfy this requirement for its neighbours (one up and one down arrow).
Both decreased dimensionality and frustration can lead to the emergence of novel quantum states of matter at low temperature. This thesis explores these materials with that in mind.


title: Limitations in Geophysical Processing and Interpretation: Three Canadian Case Studies

contributor:
Morris, W.A.
Earth and Environmental Sciences

subject: geophysical processing, interpretation, three Canadian case studies, limitations, natural resources, terrain corrections

abstract:
With an increasing demand on natural resources, more efficient prospecting techniques need to be developed. One important tool is geophysical methodologies. As technology develops so do these methods and availability of high-resolution information; however if this information is not properly corrected biased results are achieved. This thesis intends to explore common limitations faced by modern geophysical surveys. Processing and interpreting of geophysical data is often accomplished in frequency domain due to speed and efficiency; however this often leads to non-geologically correct results. A spatial domain filter based on potential field signal curvature analysis is a proposed alternative. By isolating specific curvatures, one is isolating specific frequencies, which are generated by sources at particular depths. The method was applied to synthetic and real-world datasets. Following
filtering two analytic routines were applied, which showed that the spatially filtered datasets provided cleaner results. Terrain corrections have always been applied to gravity datasets, but rarely are terrain corrections implemented as a pre-processing step in magnetic
survey interpretation. Therefore, interpretations based on anomalies from non-corrected
magnetic data may be of non-geological features. In a magnetic survey conducted in the mid-eighties, magnetic lows were associated with alteration; however, at that time of initial interpretation no terrain correction was applied. This dataset was revisited and terrain corrected, which showed that the magnetic lows were associated with unaccounted bathymetry. The Bathurst Mining Camp (BMC) is one of Canada's most important base metal mines, but is threatened by a fluctuating mineral resources market. By using high resolution geophysical surveys potential mineral reserves may be located. However, in order to do so a better understanding of geology is necessary, which is often difficult due to limited outcrops. Through the processing and interpretation of recent geophysical datasets, a revised
geological map of a selected portion of the BMC has been developed.

abstract: Thesis

abstract: Master of Science (MSc)


title: A CASE STUDY IN ASSURANCE CASE DEVELOPMENT FOR SCIENTIFIC SOFTWAR

contributor:
Smith, Spencer
Computing and Software

subject: Assurance Case, GSN, Goal Structuring Notation, Scientific Software, 3dfim+, SRS , Software Requirements Specification

abstract:
Assurance Cases have been effectively used for improving the safety of real-time safety systems. However, until now, Assurance Case techniques have not been applied to building confidence in the correctness of Scientific Computing (SC) software.
Our approach is to employ Assurance Case techniques to the case of a specific medical image analysis software, 3dfim+, and then generalize the results/template for other medical and SC software. Using the Goal Structuring Notation (GSN), we develop an Assurance Case to support the top goal that "Program 3dfim+ delivers correct outputs when used for its intended use/purpose in its intended environment."  This claim is supported by several sub-claims, including the claims that high-quality requirements exist and that the implementation complies with the requirements.  The full argument decomposes each sub-claim further until at the bottom level evidence is provided.  The evidence provided includes the requirements documentation, test cases and expert review.                                                                     To simplify the Assurance Case diagram, a new generic module, parameterized over quality, was developed to argue that each quality has been achieved. Evaluation of the full Assurance Case shows that this approach is feasible for building confidence in SC software, even in the practical situation where confidence is sought, but redesign and reimplementation are not possible. The exercise uncovered issues with the original documentation for 3dfim+, including missing assumptions, and ambiguity with the chosen sign convention. Furthermore, although no errors in output were found, the Assurance Case highlights that confidence in the original 3dfim+ software could be improved through additional checks for input validity.

abstract: Thesis

abstract: Master of Science (MSc)


title: Development of an Acute Biotic Ligand Model for Ni Toxicity to Daphnia pulex in Soft Water: Effects of Ca, Mg, Na, K, Cl, pH and Dissolved Organic Matter

contributor:
Wood, Chris M.
McGeer, Jim C.
Biology

subject: acute biotic ligand model, Ni toxicity, Daphnia pulex, soft water, alkalinity, dissolved organic matter, NOM

abstract:
 In this study the influence of several water chemistry parameters on the toxicity of Ni to Daphnia pulex in soft water were tested. A reconstituted soft water (pH 7.8, hardness 31.5 mg/L CaCO3) was used as the basis for culture and testing. Daphnia pulex was chosen as a typical cladoceran, one which can be acclimated to very soft water. An understanding of the influence of water chemistry on Ni toxicity in soft water is relevant because metals have higher bioavailability in soft water. The 48h EC50 in the reconstituted soft water (RSW) was 974 μg/L (16 μM) dissolved Ni (95%CI 830- 1081 μg/L). The following factors were examined for their potential for modifying Ni toxicity: Ca, Mg, Na, K, Cl, pH (3 different approaches used) and natural organic matter (NOM, 2 sources tested). Both Ca and Mg protected against Ni toxicity and the relative effect was greater for Ca. Varying the concentrations of Na, Cl or K did not alter the toxicity of Ni. Tests at different pH showed that as pH increased, Ni toxicity decreased. When the test solution pH was adjusted with the organic buffer 3-morpholinepropanesulfonic acid, there was a clear correlation between increasing pH and increasing EC50. The pH tests using bicarbonate to adjust pH did not show this relationship as clearly. Both types of NOM showed a protective effect on Ni toxicity with Nordic Reservoir NOM having a 4 fold greater effect than that of Suwannee River NOM. This research illustrated that the effect of alterations in water chemistry were generally as predicted within the context of
the biotic ligand model (BLM) approach. The data provide the information required to
develop a BLM for the acute effects of Ni in soft water.

abstract: Thesis

abstract: Master of Science (MSc)


title: RESISTANCE PROFILING OF MICROBIAL GENOMES TO REVEAL NOVEL ANTIBIOTIC NATURAL PRODUCTS

contributor:
Magarvey, Nathan
Biochemistry and Biomedical Sciences

subject:
Antibiotic Discovery
Natural Products

abstract: Microbial natural products have been an invaluable resource for providing clinically relevant therapeutics for almost a century, including most of the commonly used antibiotics that are still in medical use today. In more recent decades, the need for new biotherapeutics has begun to grow, as multi-drug resistant pathogens continue to emerge, putting into question the long-term efficacy of many drugs that we routinely depend on to combat infectious diseases. To affect this growing medical crisis, new efforts are being applied to computationally mine the genomes of microorganisms for biosynthetic gene clusters that code for molecules possessing anti-microbial activities that circumvent known resistance mechanisms. To this end, cutting-edge software platforms have been developed that can identify, with high predictive accuracy, microbial genomes that code for natural products of potential interest. However, with such analyses comes the need to thoroughly vet each predicted gene cluster, to identify those high-value candidate molecules that are not associated with known resistance mechanisms. In this work, a new strategy was developed that involved cataloguing all known ‘self-resistance’ mechanisms encoded by natural product producing microorganisms, which protect the producer from the highly toxic effects of their secreted anti-microbial agents. This collection of resistance data was leveraged and used to engineer an automated software-based pipeline that interrogates biosynthetic gene clusters and relates them to previously identified resistance mechanisms. Gene clusters that are revealed to be independent of known resistance mechanisms can then be flagged for further chemical and biological study in the laboratory. Such in-depth interrogations of microbial genomes aim to help reveal the full biological repertoire of antibiotics yet to be discovered from microorganisms, and will lead to the development of the next generation of biotherapeutics to quell the growing medical crisis of antibiotic-resistance among human pathogenic organisms.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: It would be hard to imagine a world where we could no longer use the antibiotics we are routinely being prescribed for common bacterial infections. Currently, we are in an era where this thought could become a reality. Although we have been able to discover antibiotics in the past from soil dwelling microbes, this approach to discovery is being constantly challenged. At the same time, the bacteria are getting smarter in their ways to evade antibiotics, in the form of resistance, or self-protection mechanisms. As such is it essential to devise methods which can predict the potential for resistance to the antibiotics we use early in the discovery and isolation process. By using what we have learned in the past about how bacteria protect themselves for antibiotics, we can to stay one step ahead of them as we continue to search for new sources of antibiotics from bacteria.


title: SUPPORT FEATURES FOR ONLINE COGNITIVE BEHAVIOURAL THERAPY INTERVENTIONS FOR ADOLESCENTS AND YOUNG ADULTS: A SCOPING REVIEW

contributor:
Archer, Norm
eHealth

subject:
eHealth
Cognitive Behavioural Therpay
Anxiety
Depression
Online CBT
self-help
scoping review

abstract:
Adolescent and young Canadians are a group with the highest rates of symptoms of anxiety and depression.  Such conditions, when unaddressed, negatively impact the development of a person, restricting their chances of attaining a fulfilling future and career. Even when deciding to reach out to access care, the process can be a challenging one with many barriers along the way.
Online therapies in the form of online Cognitive Behavioural Therapies, have shown to be a promising format for some, but have faced some shortcomings with low uptake and variable results. Adding guidance and support to such therapies has been shown to help address these barriers.
The objective of this research is to explore how support is currently provided for online cognitive behaviour therapies for anxiety and depression, targeting adolescents and young adults. To achieve this objective a scoping review methodology was utilized to identify relevant articles. The approach taken in a scoping review methodology allows for identification of a wide range of articles, which was necessary in this case because research isolating support features from other interventions is very limited. The scoping review identified fifty articles to be reviewed, and they were analyzed using a framework created for this review. The framework covered human, delivery, and design factors. Consultations with five key informants was also used to identify more findings related to the themes identified in the framework and to complement the findings from the articles in the scoping review.
The resulting picture identified the field of support for online CBT for anxiety and depression in adolescents and young adults, covering a field with a great diversity ranging from virtual guides to face-to-face support from therapists. The features were organized into groups of ‘toolkits’ that can be considered by CBT developers for different situations and needs.

abstract: Thesis

abstract: Master of Science (MSc)


title: Extending Growth Mixture Models and Handling Missing Values via Mixtures of Non-Elliptical Distributions

contributor:
McNicholas, Paul
Mathematics and Statistics

subject:
Growth Mixture Model
Model-Based Clustering
EM Algorithm
Missing Data
Finite Mixture Models

abstract:
Growth mixture models (GMMs) are used to model intra-individual change and inter-individual differences in change and to detect underlying group structure in longitudinal studies. Regularly, these models are fitted under the assumption of normality, an assumption that is frequently invalid. To this end, this thesis focuses on the development of novel non-elliptical growth mixture models to better fit real data. Two non-elliptical growth mixture models, via the multivariate skew-t distribution and the generalized hyperbolic distribution, are developed and applied to simulated and real data. Furthermore, these two non-elliptical growth mixture models are extended to accommodate missing values, which are near-ubiquitous in real data.

Recently, finite mixtures of non-elliptical distributions have flourished and facilitated the flexible clustering of the data featuring longer tails and asymmetry. However, in practice, real data often have missing values, and so work in this direction is also pursued. A novel approach, via mixtures of the generalized hyperbolic distribution and mixtures of the multivariate skew-t distributions, is presented to handle missing values in mixture model-based clustering context. To increase parsimony, families of mixture models have been developed by imposing constraints on the component scale matrices whenever missing data occur. Next, a mixture of generalized hyperbolic factor analyzers model is also proposed to cluster high-dimensional data with different patterns of missing values. Two missingness indicator matrices are also introduced to ease the computational burden. The algorithms used for parameter estimation are presented, and the performance of the methods is illustrated on simulated and real data.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Inorganic Asian North American Lives: Virtual Dismemberments, Copies and Wellbeing

contributor:
Goellnicht, Donald
English

subject: Asian North American, new media, techno-Orientalism, performance, virtuality

abstract:
This dissertation examines Asian North American rearticulations of the inorganic—a quality that has historically been assigned to Asians, rendering them counterfeit, abstract or not-quite-human—in new media, film and literature. By analyzing circulations of Asian North American disassembled body parts, “copies,” and gendered inter/faces, I argue that the excess, failures and ambivalence of Asian North American labour and performance constitute virtual modes of racialization that disrupt neoliberal, postracial temporalities in the Information Age.

Asian American studies has held in tension its critiques of the West’s monopoly of liberal humanism in techno-Orientalist narratives (David S. Roh, Betsy Huang and Greta A. Niu) and the oppositional strategies of reappropriating techno-Orientalist tropes. My project does not seek to recuperate the Asian North American subject from the dehumanizing processes of fragmentation, surplus reproduction or abstraction—an impulse described by Rachel C. Lee as returning the “extracted body part” to the racialized “whole” in order to resolve anxieties about subjective “incoherence” or cultural inauthenticity. Instead, I turn to modes of inorganic life that do not produce an agential, autonomous Asian North American subject, but engender racializing disassemblages that work out survival and wellbeing within the neoliberal, abstracting pulls of the Information Age.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Fuel Selection in Genetically Selected Endurance Running Rats at Submaximal Exercise Intensities

contributor:
McClelland, Grant
Biology

subject: fuel selection, genetically selected endurance, running rats, submaximal exercise intensities, oxidation, lipid, enzyme activity

abstract:
 Exercise intensity is one of the major factors determining the utilization of carbohydrates (CHO) and lipids in mammalian skeletal muscle. Using indirect calorimetry, we determined maximal oxygen uptake (VO2max) and whole-body rates of CHO and lipid oxidation in rats selectively bred for high and low running capacity (HCR's and LCR's) during exercise at 50, 60, 70 and 80%VO2max. Previous studies have revealed a pattern of selection where mammals with different aerobic capacities use the same proportions of lipids and CHO when exercising at the same relative exercise intensity and as intensity increases, CHO use increases and lipid use decreases. The present results showed that the HCR's had a VO2max and distance run to exhaustion that was 1.3 and 4.0 times greater than the LCR's respectively. Also, both groups of rats followed the pattern of fuel selection seen in previous studies where the same proportions (in%) of lipids and CHO are used at the same relative exercise intensity. On an absolute scale, the HCR's used more lipids and CHO than the LCR's at all exercise intensities but the results were not always statistically significant. We also determined the exercise intensity that elicited the greatest lipid use to be 60% VO2max in both groups.

 In order to explain these patterns of fuel selection, metabolic indicators, metabolites and enzymes, in skeletal muscle were measured at rest and post exercise for one hour at 60%VO2max. Specifically, ATP and phosphocreatine (PCr) metabolite
concentrations were determined in the medial and lateral gastrocnemius, extensor digitorum longus (EDL), tibialis anterior (TA), and soleus muscle. The medial gastrocnemius and soleus were analyzed (pre and post exercise samples were combined) for their oxidative and glycolytic enzyme activity by measuring citrate synthase (CS), cytochrome oxidase (COX), β-hydroxyacyl CoA dehydrogenase (HOAD), and lactate dehydrogenase (LDH) . PCr and ATP concentrations did not change pre and post exercise and between the HCR's and LCR's except for the EDL where there was a significant decrease (P<0.05) in both metabolites after exercise in both groups of rats. For the enzyme measurements, CS and COX activities were higher (P<0.05) in the HCR's for the soleus and HOAD activities were also higher in the HCR's medial gastrocnemius compared to the LCR's. We concluded that the HCR's have a greater
oxidative capacity as shown by their greater aerobic and endurance capacity (VO2max
and distance to exhaustion), their ability to oxidize a greater absolute amount of lipids
and CHO's at the same relative exercise intensity, and their higher activities of oxidative
enzymes in the soleus (CS and COX) and medial gastrocnemius (HOAD). Future research into the mechanisms involved in explaining these patterns of fuel selection may include examining fatty acid transport proteins, fatty acid and CHO availability, fiber types, and catecholamines.

abstract: Thesis

abstract: Master of Science (MSc)


title: Comparison of the Sodium Calcium Exchanger in the Porcine Coronary Artery Endothelial and Smooth Muscle Cells

contributor:
Grover, A.K.
Biology

subject: sodium calcium exchanger, porcine coronary artery endothelial, smooth muscle cells, cell membranes, BAPTA, NCX-SERCA linkage

abstract:
 Calcium (Ca2+) is an important signaling molecule and hence its movement across cell membranes must be tightly regulated. The intracellular Ca2+ concentration ([Ca2+]i) in smooth muscle and endothelium controls the coronary tone. After stimulation, decreasing the [Ca2+]i back to resting levels is achieved mainly by the sodium calcium exchanger (NCX), the plasma membrane calcium pump (PMCA) or the sarcoendoplasmic reticulum calcium pump (SERCA). The present study will focus on NCX and its interactions with SERCA in the smooth muscle and endothelium of pig coronary artery.

 Aim 1 of my thesis is determination of activity levels of NCX in smooth muscle cells (SMC) and endothelial cells (EC). The NCX activity in cultured cells was approximately 5 times greater in EC than in SMC. The NCX inhibitors KB-R7943 and SEA 0400 blocked the NCX mediated Ca2+ entry, as did collapsing the Na+ gradient with monensin. NCX1 is the isoform largely responsible for NCX activity in SMC and EC. NCX activity was also assayed as the Ca2+ efflux in cultured cells and as Ca2+ uptake in plasma membrane vesicles isolated from freshly isolated smooth muscle.

 Aim 2 is to assess the existence of a functional NCX mediated Ca2+ entry linked to SERCA in SMC. In the absence of thapsigargin, BAPTA loading SMC increased the NCX mediated uptake. Thapsigargin did not affect the Ca2+ uptake in BAPTA loaded cells but it inhibited the Ca2+ uptake in cells that were not loaded with BAPTA. These data are consistent with a model in which SER acts as a sink for the NCX mediated Ca2+ entry. However, with BAPTA chelation and the resulting lower intracellular Ca2+, the need for SER to act as a sink is eliminated, and NCX is driven in full force. EC did not demonstrate a NCX-SERCA linkage.

 Arterial SMC and EC differ in their structure and function. The function of SMC is the generation of tone which is achieved by the Ca2+ dependent contractile filaments. Since these filaments are distributed throughout the cell, Ca2+ must be transported to and removed from deep within the cell. As a result, the SER may play a large role in Ca2+ regulation in the SMC. Furthermore, SMC also contain higher levels of high affinity Ca2+ pumps (SERCA and PMCA) and thus Ca2+ is more tightly regulated. Endothelial cells release nitric oxide in response to an increase in [Ca2+]i, which relaxes the smooth muscle. The endothelial nitric oxide sythase produces nitric oxide and is located adjacent to the PM in EC. The SER that removes Ca2+ from deep within the cell cytosol may play a small role in Ca2+ dependent modulation of the endothelial nitric oxide synthase activity. Based on the Western blot data, EC contain a greater amount of the high capacity NCX, thus the larger quantities of Ca2+ can be removed from the cell and the vicinity of endothelial nitric oxide synthase.

abstract: Thesis

abstract: Master of Science (MSc)


title: BLAST LOAD SIMULATION USING SHOCK TUBE SYSTEMS

contributor:
El-Dakhakhni, Wael
Tait, Michael
Civil Engineering

subject: 2D axisymmetric flow simulation model, 3D flow simulation model, ANSYS Fluent, blast loads, blast shock tube, blast wave parameters, shock tube control parameters, TNT equivalent charge weights

abstract:
With the increased frequency of accidental and deliberate explosions, the response of civil infrastructure systems to blast loading has become a research topic of great interest. However, with the high cost and complex safety and logistical issues associated with live explosives testing, North American blast resistant construction standards (e.g. ASCE 59-11 & CSA S850-12) recommend the use of shock tubes to simulate blast loads and evaluate relevant structural response.
This study aims first at developing a 2D axisymmetric shock tube model, implemented in ANSYS Fluent, a computational fluid dynamics (CFD) software, and then validating the model using the classical Sod’s shock tube problem solution, as well as available shock tube experimental test results. Subsequently, the developed model is compared to a more complex 3D model in terms of the pressure, velocity and gas density. The analysis results show that there is negligible difference between the two models for axisymmetric shock tube performance simulation. However, the 3D model is necessary to simulate non-axisymmetric shock tubes.
The design of a shock tube depends on the intended application. As such, extensive analyses are performed in this study, using the developed 2D axisymmetric model, to evaluate the relationships between the blast wave characteristics and the shock tube design parameters. More specifically, the blast wave characteristics (e.g. peak reflected pressure, positive phase duration and the reflected impulse), were compared to the shock tube design parameters (e.g. the driver section pressure and length, the driven
v
section length, and perforation diameter and their locations). The results show that the peak reflected pressure increases as the driver pressure increases, while a decrease of the driven length increases the peak reflected pressure. In addition, the positive phase duration increases as both the driver length and driven length are increased. Finally, although shock tubes generally generate long positive phase durations, perforations located along the expansion section showed promising results in this study to generate short positive durations.
Finally, the developed 2D axisymmetric model is used to optimize the dimensions of a proposed large-scale conical shock tube system developed for civil infrastructure blast response evaluation applications. The capabilities of this proposed shock tube system are further investigated by correlating its design parameters to a range of explosion threats identified by different hemispherical TNT charge weight and distance scenarios.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Wisdom of Thunder: Indigenous Knowledge Translation of Experiences and Responses to Depression Among Indigenous Peoples Living with HIV

contributor:
Cain, Roy
Lee, Bill
Greene, Saara
Social Work

subject:
Indigenous
Knowledge Translation

abstract: The translation of research findings, and the development of products, has been identified as a research priority that may improve health outcomes for Indigenous peoples. Although knowledge translation is relatively new and emerging area in Indigenous science, Indigenous scholars have already been critical of Western defined knowledge translation theories and approaches as neglectful of Indigenous ways of knowing, being and doing. Within Indigenous knowledge systems, the translation of research findings is best conceptualized as a ‘sharing what we know about living a good life.’ This dissertation explores and focuses on the use of Indigenous stories and storytelling as knowledge translation products that may be better equipped to share research findings with Indigenous peoples. Grounded in an earlier study exploring experiences and responses to depression among Indigenous peoples living with HIV, this dissertation reviewed the Indigenous knowledge translation literature, adapted narrative analysis to an Indigenous context using composite character development and a scared story (i.e., Animikii and Mishebeshu), and created an Indigenized research story titled “The Wisdom of Thunder.” Meant to inspire healing, this story was also meant to create space to rethink, reorder, and re-imagine a world where HIV-positive Indigenous people and experiencing depression can learn and understand through Indigenous eyes. In ways connected to an oral body of stories, Indigenous stories, as an artful research translation practice, may make the findings of research more culturally accessible for Indigenous communities thereby promoting healing and well-being.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The sharing of research findings in cultural appropriate ways with Indigenous community stakeholders is an important endeavour. Guided by the Indigenous principle of "sharing what we know about living the good life," it is equally important that such activity be done so in ways that respect Indigenous ways of knowing, being, and doing. This dissertation explores and focuses on the use of Indigenous stories and storytelling as knowledge translation products that may be better equipped to share research findings with Indigenous peoples.


title: Studying the Effects of p120 and Kaiso-Mediated Gene Regulation on Epithelial-to-Mesenchymal-Transition

contributor:
Daniel, Juliet
Biology

subject: Kaiso-mediated, gene regulation, epithelial-to-mesenchymal-transition, E-cadherin, cells

abstract:
 Downregulation of E-cadherin is a frequent event in epithelial cancers and it correlates
with weakened cell-cell adhesion and the induction of an epithelial-to-mesenchymal transition (EMT). It is postulated that E-cadherin downregulation liberates the catenin p120 and allows p120's translocation to the nucleus where it interacts with and functionally regulates the novel BTB/POZ transcription factor, Kaiso. Kaiso mediates transcriptional repression of various tumourigenesis-associated genes via methylated CpG dinucleotides or a sequence-specific Kaiso binding site (KBS). The Kaiso/p120 interaction has been detected in E-cadherin expressing cells of various origins, but is seldom detected in N-cadherin expressing cells or cells that have undergone EMT. We hypothesize that p120 and Kaiso play a role in EMT by modulating the expression of EMT-associated genes. We demonstrated that TGF-β-induced EMT occurs in a dose- and time-dependent manner in NMuMG cells but not in FHL-124 cells. In both cells lines, the Kaiso/p120 interaction occurred irrelevant of EMT induction by TGF-β. In NMuMG cells, the expression of p120 increased with EMT induction, while the expression of
Kaiso remained unchanged. Finally, misexpression of Kaiso and p120 in mammary
epithelial cells affected TGF-β-mediated EMT induction by delaying the upregulation of the positive mesenchymal markers, N-cadherin and α-SMA.

abstract: Thesis

abstract: Master of Science (MSc)


title: Factors Determining Heterospecific Mating Success in the Sibling Fruit Fly Species Drosophila Pseudoobscura and D. Persimilis

contributor:
Dukas, R.
Psychology

subject: heterospecific mating success, sibling fruit fly species, Drosophila pseudoobscura, D. persimilis

abstract:
Patterns of heterospecific matings are important to understand in order to learn about speciation. I proposed a classical signal detection model as a representation of heterospecific mating patterns in both sexes. From the model I proposed that males would be able to achieve successive heterospecific mating success, as those males were more similar to conspecifics. I also proposed that restrictive females that rejected heterospecific matings would also be more likely to reject conspecific matings. I used the sibling species Drosophila pseudoobscura and D. persimilis to examine heterospecific mating patterns in males and females. I found that males previously accepted as heterospecific mates were more likely to achieve heterospecific matings than males that had previously been rejected as heterospecific mates. This was most likely due to decreased courtship by rejected males. Males rejected heterospecifically but mated conspecifically also were less likely to achieve heterospecific matings than males that had initially been accepted as heterospecific mates. This indicated that the same males were able to achieve successive heterospecific matings, despite rejected males also having had initial mating success. This was again likely influenced by decreased courtship in rejected males. Furthermore, I found that females that rejected heterospecific males were also more likely to reject conspecific males than naive females. There was also a non-significant trend of females that previously accepted heterospecific males were more
likely to again accept heterospecific males than females that had previously rejected
heterospecific males.

abstract: Thesis

abstract: Master of Science (MSc)


title: Modeling the Rate of Lateral Gene Transfer in Bacillaceae Genomic Evolution

contributor:
Golding, G. Brian
Biology

subject: rate of lateral gene transfer, Bacillaceae genomic evolution, species, lineages, taxonomic boundary, bacterial genomes

abstract:
Genome evolution is not always shaped by a Darwinian-fashion of vertical inheritance
from ancestral lineages. The historical gene content of a species contains many atypical gene sequences showing high similarity to those of distantly related taxa. This evolutionary phenomenon is referred to as lateral gene transfer (LGT). Lateral gene transfer permits the exchange of genetic material across lineages, completely ignoring any concept of taxonomic boundary. The rapid acquisition of foreign genes into bacterial genomes has greatly obscured the historical phylogeny of prokaryotes. In this thesis we calculate the rate of LGT on a Bacillaceae phylogeny, to determine the extent to which it controls species evolution. First, we examined the evolution of the phylogeny according to a simple model of maximum likelihood. We assume equal rates of gene insertion and deletion on the phylogeny and show high rates of evolution in the genomes of B. anthracis, B. cereus, and B. thuringiensis (Bc group), representative of adaptive evolution. We then improved the model to account for differential rates of gene insertion and deletion, thus offering a more realistic model of gene evolution. Again, we demonstrate that members of the Bc group are rapidly evolving, with the rate of gene insertion being significantly higher than the rated of gene deletion. Finally, we evaluate the sole effect of LGT on the phylogeny in a simple birth-death analysis with immigration. We show that LGT is the main vehicle of gene acquisition when the number of gene families
substantially increases from external taxa to members of the Bc group. Collectively, our
findings suggest that the Bacillaceae genome is rapidly expanding, and that laterally
transferred genes may facilitate adaptive evolution and subsistence in a new niche.

abstract: Thesis

abstract: Master of Science (MSc)


title: Functional Analysis of Rad50 Mutants

contributor:
Zhu, Xu-Dong
Biology

subject: functional analysis, Rad50 mutants, DNA, cellular processes, telomeres, fusion proteins

abstract:
 Mre11 and Rad50 form a complex with Nbs1 (MRN) in mammals and Xrs2 (MRX) in yeast. The MRN complex plays a role in many cellular processes, such as DNA damage sensing, DNA repair, cell cycle checkpoint and telomere maintenance. Rad50 contains a
conserved ATP binding motif and its ATPase activity is essential for ATM activation in vitro. Using a tethering approach, I have shown that Rad50 can be targeted to telomeres through its fusion to hRap1. The fusion of hRap1 to Rad50 did not alter the property of Rad50. The fused wild-type Rad50 promoted telomerase-dependent telomere lengthening. However, the fusion proteins containing loss-of-function mutations in Rad50 (K42E and S1202R) did not. I have also shown that the fused wild-type Rad50 was able to form irradiation-induced foci in a manner similar to unfused Rad50. In contrast, the two defective mutants of Rad50 failed to accumulate irradiation-induced foci. Expression of the fusion proteins containing Rad50 mutants also interfered with the ability of endogenous Mre11 protein to form foci post irradiation. Thus our data suggest that the Rad50 mutants may function as dominant-negative alleles in cells.

abstract: Thesis

abstract: Master of Science (MSc)


title: FUNCTIONS OF MULTIMERIN 1 (MMRN1) IN PLATELET ADHESION AND THROMBUS FORMATION, THROUGH INTERACTIONS WITH VON WILLEBRAND FACTOR (VWF)

title: FUNCTIONS OF MMRN1 IN PLATELET ADHESION & THROMBUS FORMATION

contributor:
HAYWARD, CATHERINE P.M.
Medical Sciences

subject:
Multimerin 1
von Willebrand factor

abstract: Multimerin 1 (MMRN1) is a massive, homopolymeric platelet and endothelial cell protein with functions that are emerging to support platelet adhesive processes. MMRN1 supports platelet adhesion under arterial flow conditions by a mechanism dependent on interactions with von Willebrand factor (VWF). The goals of this thesis were to further define the platelet adhesive functions of MMRN1 by: 1) characterizing the molecular mechanisms of VWF interactions with MMRN1; and 2) investigating if multimerin 1 is important for platelet adhesive functions using mice with and without a selective multimerin 1 (Mmrn1) deficiency. Studies of the mechanism of MMRN1-VWF binding indicated that MMRN1 bound to shear exposed VWF, and that MMRN1 interacted with the A1 and A3 domains in the VWF A1A2A3 region. VWF A1A2A3 also bound to MMRN1 with a physiologically relevant binding affinity, and supported platelet adhesion to MMRN1 at a high shear rate. The selective loss of Mmrn1 in mice had limited effects on tail bleeding times, although it impaired collagen-induced aggregation of washed platelets, as well as high shear platelet adhesion of whole blood on collagen surfaces, in vitro. Additionally, the selective loss of Mmrn1 in mice was associated with impaired and delayed platelet-rich thrombus formation in vivo, in arterioles treated with ferric chloride. These findings provide new insights on platelet adhesive, haemostatic functions at arterial shear rates, and the involvement of the platelet and endothelial cell protein, multimerin 1, to support these processes.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: DNA Mutation Frequency in Vitamin C Deficient Mice Using Big Blue Mice

contributor:
Schellhorn, H. E.
Igdoura, S.
Biology

subject: DNA, mutation, frequency, Vitamin C, deficient mice, oxidative stress, gene

abstract:
 Gulonolactone oxidase enzyme is important in the final stage of ascorbic acid biosynthesis. Gulonolactone oxidase is encoded by the Gulo gene. Most animals, such as mice, have the Gulo gene, through which they produce ascorbic acid from glucose, while humans, guinea pigs and primate animals carry a non functional Gulo gene. Ascorbic acid plays an important role in many biological processes. However, it is primarily essential as an antioxidant. Ascorbic acid protects genomic DNA from free radicals resulting from oxidative stress that might otherwise cause a variety of diseases such as cancer or heart disease. This thesis focuses on investigating the role of ascorbic acid in the elimination of oxidative stress-induced mutagenesis.

 To investigate how vitamin C decreases level of the DNA mutation frequency and protects DNA from free radicals, knockout Gulo and Big Blue mice were used as models to determine the ability of vitamin C to minimize oxidative stress. The Big Blue mice carry the cll gene which is a reporter gene through which DNA mutation rate can be detected in any part of body. Therefore, we generated double transgenic mice which are Gulo deficient or a Big Blue background. Homozygote Gulo cll positive (Gulo-/- cll+) were
obtained by crossing heterozygote Gulo cll Positive and homozygote Gulo mice. Five
Gulo-/-cll mice were placed under vitamin C deficient diet and another five were supplemented with vitamin C. DNA mutation frequency was analyzed in the two groups. There were no significant differences in mutation frequencies between homozygote Gulo-/- cll mice on vitamin C deficient diet and homozygote Gulo-/- cll+ mice fed vitamin C rich diet. One treatment mouse showed increased frequency in mutations but a second did not. Further tests can be done on other treated knockout mice to identify the mutation types generated by oxidative stress in the absence of vitamin C.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Effects of Carotid Body Neurotransmitters on the Efferent Glossopharyngeal Neurons

contributor:
Nurse, Colin A.
Biology

subject: carotid body neurotransmitters, efferent glossopharyngeal neurons, organ, inhibitory, calcium, nerve fibers

abstract:
 The carotid body (CB) is the main peripheral chemoreceptor organ that maintains
homeostatic control of the O2, CO2, glucose and pH levels in the blood. It is innervated by nerve fibers from the carotid sinus nerve (CSN) that consists of sensory afferents from the petrosal ganglion (PG) and "inhibitory" efferents from the glossopharyngeal nerve (GPN). The efferent innervation forms an elaborate network that is immuno-positive for neuronal nitric oxide synthase (nNOS), and is thought to inhibit the CB via release of nitric oxide (NO). The purpose of this study is to further understand the underlying mechanisms of this inhibition. Since the CB possesses various neurotransmitters, including the excitatory neurotransmitter, acetylcholine (ACh), I tested the hypothesis that the CB drives its own modulation during chemoexcitation by secreting ACh, which would directly act on receptors located on the GPN neurons (GPNs) and lead to nNOS activation via calcium entry and the subsequent release of NO. To address this, molecular and calcium imaging techniques were used to demonstrate the specific types of nicotinic ACh receptors (nAChRs) expressed in GPN neurons. It was shown that GPN neurons expressed the mRNA for ten subunits: α2-α9, excluding α8 and β2-β4 and they responded to ACh and nicotine, a nAChR agonist, in a dose-dependent manner via an
increase in intracellular calcium. The EC50 for ACh and nicotine were ~ 9.9 and 20.5 μM
respectively. The nicotine-induced calcium transients were inhibited by mecamylamine, a nAChR competitive antagonist, with an IC50 of ~ 1.2 μM. Studies using subunit-specific
antagonists, dihydro-β-erythroidine (specific for α4β2 and α3β4 in particular dose ranges) and methyllycaconitine (MLA) and α-bungarotoxin (BTX; both specific for α7) revealed that the major functional nAChR expressed in GPNs were the α4β2 and α3β4 nAChRs. The results of this study show that GPN neurons respond to ACh stimulation with an increase in intracellular calcium and thus raise the possibility that ACh secreted after stimulation/activation of receptors on the CB may contribute to the synthesis of NO and negative feedback inhibition of CB function via stimulation of GPN efferent nerve fibers.

abstract: Thesis

abstract: Master of Science (MSc)


title: LC-ESI-TOF-MS Analysis of the Polar Metabolome of Sinorhizobium Meliloti

contributor:
McCarry, Brian E.
Chemistry and Chemical Biology

subject:
Sinorhizobium meliloti
LC-ESI-TOF-MS

abstract: The goal of this thesis is to determine if Sinorhizobium meliloti can be useful as a sentinel soil microorganism for assessing the impacts of contaminant stressors on the metabolome of a microorganism. Not only is a good deal known about this organism, but it is an important organism in agriculture. Moreover, the currently available gene array and a large library of gene fusion can be used as facile pathways to explore genetic and genomic impacts in addition to metabolomic impacts of contaminants, should such studies be deemed worthwhile. In this study, the polar metabolome of the soil microorganism, Sinorhizobium meliloti, has been analyzed by LC-ESI-MS using a HILIC column coupled to a medium mass resolution time-of-flight mass spectrometer. This approach has resulted in the retention (k' > 0.7) of over 300 polar metabolites as detected in both positive ion and negative ion modes. These data do not include ions corresponding to adduct ions, isotopic features or ions resulting from in-source decay processes. The retained peaks showed excellent linear responses and did not suffer from ion suppression, a common problem in flow-injection ESI analysis. This methodology has been applied to the analysis of S. meliloti exposed to fluorene, a common PAH contaminant, and to a coal tar fraction containing low molecular mass PAHs. Multiple cultures of S. meliloti were grown on M9 glucose minimal medium in the absence and presence of fluorene (0.14 mg/L and 1.4 mg/L) and a PAH mixture (total PAH concentrations of 0.14 mg/L and 1.4 mg/L). Analyses of biological replicates were performed in pentuplicate. The retention times of the resulting chromatograms were aligned, peak areas determined and the resulting data processed using PCA and OPLS-DA methods. The retention time reproducibilities of peaks were within ± 10 seconds and the biological variabilities of over 700 components averaged 23% ± 15% (n=25) . The impacts of fluorene exposures and PAH mixture exposures on the S. meliloti metabolomes (polar) caused significant changes in the metabolome. The lower concentration exposures had less of an impact than the higher dosages. Low dosages of both fluorene and the PAH mixture produced a similar metabolic response in S. meliloti, while at higher dosages the responses were more specific to each toxin. The use of SUS plots coupled with S-plots of the OPLS-DA analysis were particularly advantageous for the identification of metabolites of interest. Changes were seen in the levels of adenine, adenosine, glutamate, and aspartate, among others. In the future, the profiles of the non-polar metabolites of each of sample will be analyzed using a previously developed 'shotgun lipidomics' method.

abstract: Thesis

abstract: Master of Science (MS)


title: Characterization of cyclin D1 as a Putative Kaiso Target Gene

contributor:
Daniel, Juliet M.
Biology

subject: characterization, cyclin d1, putative, Kaiso, target gene, DNA, tumourigenesis, transcriptional repression

abstract:
 Kaiso is a unique member of the BTB/POZ (Broad complex, Tramtrak, Bric à brac,/Pox virus and zinc finger) zinc finger family of transcription factors with established roles in development and tumourigenesis. Kaiso was originally identified as a novel binding partner of the Armadillo catenin p120^ctn, a cytosolic co-factor and regulator of the cell-cell adhesion molecule and tumor suppressor E-cadherin. In addition to their roles in cell adhesion, the multifunctional Armadillo catenins also regulate gene expression, thus providing at least two mechanisms for their contribution to tumourigenesis. The discovery of a novel interaction between p120^ctn and the transcription factor Kaiso was therefore consistent with gene regulatory roles for Armadillo catenins. Interestingly, Kaiso represses transcription via a sequence-specific DNA binding site (TCCTGCnA) as well as through methylated CpG di-nucleotides, and one role of nuclear p120^ctn is to inhibit Kaiso DNA-binding and transcriptional repression. We recently identified sequence-specific Kaiso binding sites in a subset of Wnt/β-catenin/TCF tumour-associated target genes, and here we present data
characterizing cyclin D1 as a putative Kaiso target gene.

 Kaiso binds the cyclin D1 promoter in vitro and in vivo, and artificial promoter assays revealed that Kaiso overexpression results in the repression of a cyclin D1 promoter luciferase reporter. Since cyclin D1 is highly amplified in ~50% of human breast tumours, and a cancer profiling array demonstrated that Kaiso is misexpressed in ~40% of human breast tumours, we hypothesized that Kaiso represses and regulates cyclin D1 expression to inhibit breast tumourigenesis. In fact, examination of Kaiso expression in human breast cell lines demonstrated that cyclin D1 mRNA levels were upregulated in Kaiso-depleted cells. My studies further revealed that methylation-dependent Kaiso-DNA binding may contribute to Kaiso's transcriptional repression of the cyclin D1 promoter. We also determined that Kaiso inhibits, while p120^ctn activates, β-catenin-mediated activation of the cyclin D1 promoter. These findings further support a role for Kaiso and p120^ctn in breast tumourigenesis via their modulation of the canonical Wnt signaling pathway which is highly implicated in human tumourigenesis. Together these findings support our hypothesis that Kaiso regulates cyclin D1 expression. However, further
studies are required to elucidate the mechanism employed by Kaiso to elicit cyclin D1
repression and to examine how this activity may contribute to breast tumourigenesis.

abstract: Thesis

abstract: Master of Science (MSc)


title: Nestling Provisioning in a Joint Nesting Cuckoo: The Smooth-Billed Ani (Crotophaga Ani)

contributor:
Quinn, James S.
Biology

subject: nestling provisioning, joint nesting cuckoo, smooth-Billed Ani

abstract:
Abstract Not Provided
Thesis
Master of Science (MSc)


title: The Effects of 12 Days of Uni-Lateral Immobilization on Arterial Vascular Compliance and Endothelial Function in Healthy Young Humans

contributor:
MacDonald, Maureen J.
Human Biodynamics

subject: uni-lateral immobilization, arterial vascular compliance, endothelial function, healthy young humans, cardiovascular, blood

abstract:
 Physical inactivity or deconditioning has been shown to be an independent risk factor for
cardiovascular disease. Contrary to the previously demonstrated effects of exercise training on the cardiovascular system, the vascular adaptations that occur with a deconditioned state have not been adequately characterized within a young, healthy population. Thus, it was the interest of the present study to examine vascular adaptations to 12 days of unilateral lower limb immobilization (ULI) in young, healthy humans. Previous studies have used other models to mimic a deconditioned state such as paraplegia, simulated micro gravity and bed rest; however, such models are also associated with factors that are not physiologically applicable to normal deconditioning in the able-bodied population. Fifteen young, healthy participants [age: 20.6±0.51 (mean ± SEM)] participated in the 12-day knee-braced immobilization period that consisted of PRE and 12-DAY time point testing sessions. Measurements of supine common carotid, popliteal and common femoral artery cross sectional compliance as well as popliteal artery endothelial function (using flow mediated vasodilation (FMD)) were acquired prior to the 12-day immobilization (PRE) and on the 12th day of the immobilization (12-DAY).
Arterial characteristics of the Immobilized legs (IMM) and NON-Immobilized (NIM) legs were assessed by echo Doppler ultrasound and applanation tonometry.

 Resting carotid artery cross sectional compliance and blood flow showed no change throughout the 12-day time period, (Compliance: PRE = 0.001209 ± 0.000067 mm^2/mmHg, 12-DAY= 0.001230 ± 0.00085 mm^2/mmHg; Blood Flow: PRE = 242.8±14.2 mL/min, 12-DAY = 226.0±14.27 mL/min). Popliteal artery cross sectional compliance decreased significantly over the 12 day time period in both legs (p<0.05) (IMM PRE = 5.7±0.4 10^-4mm^2/mmHg, IMM 12-DAY = 3.8±0.4 10^-4mm^2/mmHg; NIM PRE= 6.7±0.9 10^-4mm^2/mmHg, NIM 12-DAY = 5.5±0.6 10^-4mm^2/mmHg). Common femoral artery cross sectional compliance decreased in the immobilized leg but not in the non-immobilized leg (p<0.05) over 12 days of immobilization (PRE= 1.2±0.1 10^-4mm^2 /mmHg, 12-DA Y =: 0. 79±0.1 10^-4mm^2/mmHg). Neither popliteal nor common femoral artery mean blood flow changed throughout the 12 days of immobilization. Popliteal arterial mean diameter decreased significantly over time in both the IMM and NIM legs showing greater decreases in the IMM leg, while common femoral arterial mean diameter decreased in both the IMM and NIM legs through the 12 days (Popliteal: IMM PRE = 0.57±0.02 cm, IMM 12-DAY = 0.50±0.02 cm; NIM PRE = 0.59±0.02 cm, NIM 12-DAY = 0.55±0.02 cm; Common Femoral IMM PRE = 0.83±0.04 cm, IMM 12-DAY = 0.77±0.03 cm; NIM PRE = 0.81±0.03 cm, NIM 12-DAY = 0.77±0.03 cm).
Popliteal artery endothelial function, calculated as both relative FMD and FMD normalized to shear stress, increased (p<0.05) throughout the 12 days in the immobilized leg while showing no change in the non-immobilized leg (Relative FMD: IMM PRE 6.0 ± 1.4%, IMM 12-DAY = 12.6 ± 2.7%; NIM PRE = 5.8 ± 1.4%, NIM 12-DAY = 8.3 ± 1.6 %; Normalized FMD: IMM PRE = 0.023 ± 0.007%/^sec-1, IMM 12-DAY = 0.037 ± 0.008%/^sec-1; NIM PRE = 0.016 ± 0.003%/^sec-1, NIM 12-DAY = 0.022 ± 0.004%/^sec-1).

 In conclusion, 12 days of deconditioning by ULI was able to cause structural and functional changes in the arteries of the immobilized leg, but not the central elastic artery in the neck in healthy young humans. Specifically in the legs, a decrease in arterial compliance, increases in mean blood velocity and increases in endothelial function were noted, with no change in volumetric blood flow. Surprisingly, our results suggest, with regards to endothelial function, that the vascular effects of deconditioning are not simply the inverse of exercise training which also shows increases in endothelial function. Thus the present study concludes that there exists a very short time course to arterial adaptations in healthy young humans with significant changes within the vasculature occurring within 12 days of deconditioning.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Effect of Self-Regulated Practice on Motor Learning Using Tasks of Varying Complexity

contributor:
Lee, Timothy D.
Kinesiology

subject: self-regulated practice, motor learning, tasks, varying complexity

abstract: Increasing evidence indicates that giving individuals control over their practice schedule facilitates motor learning (Titzer, Shea, & Romack, 1993; Wu & Magill, 2004, 2005). A recent study within cognitive psychology (Son, 2004) found that individuals massed practice on tasks they judged as hard but spaced practice on tasks they judged as easy. The purpose of this experiment was to examine how self-regulated practice impacts motor learning and the strategies used by individuals as a function of task complexity. Participants were required to move a mouse-driven cursor through a pattern of coloured squares, pausing only long enough in each square to make an appropriate button press (white square=left button, black square=right button). Task complexity (4 easy and 4 hard patterns) was determined by the combined effects of the arrangement of the grid of squares and the hand used to manipulate the mouse (easy =dominant hand, hard=non-dominant hand). Participants were randomly assigned to one of eight groups: blocked, random, self-regulated, and yoked to self-regulated, performing either the easy or hard tasks. The number of switches between patterns were recorded as well as temporal and accuracy measures. The self-regulated groups were ineffective in acquisition, but showed the most stable and improved performance in retention, irrespective of task difficulty. Moreover, although switch strategies of the self-regulated groups differed between and within task complexity, the motor learning advantage was generalized. Taken together, these results reveal that an individual's strategic approach to practice may change as a function of task complexity, with no detriment to motor learning and adds to the growing body of literature that suggests self-regulated practice is an important variable for effective motor learning.

abstract: Thesis

abstract: Master of Science (MSc)


title: Effect of Single Light Orientation on Landing Gear Wake

contributor:
Ziada, Samir
Mechanical Engineering

subject:
Landing Gear Noise
PIV
Aircraft Noise
Airframe Noise
Landing Gear Near-wake

abstract: Within the overarching area of airplane noise, landing gear noise has been proven to be a major contributor to airframe noise. Despite a large focus given to it by past research work, landing gear noise investigations have continuously failed to include landing lights, completely disregarding their potential for seriously altering the landing gear wake structure and overall noise signature. This thesis is one of the first studies to focus on the effect of landing light orientation on landing gear wake and landing gear noise. Pressure fluctuations in the wake of a simplified single light landing gear model are investigated experimentally for several freestream velocities and at various elevations of measurement plane. The effect of the distance between the light and the landing gear strut is also investigated. Three-dimensional flow is found in the wake at the center, or zero elevation, plane. This three-dimensionality is found to be much weaker at the highest elevation from the light, where the wake is found to be primarily two-dimensional. The nature of the transition region between the three-dimensional flow and two-dimensional flow is not investigated, but it is acknowledged that a transition region exists. Complex flow behaviour leading to a wake width larger than twice the size of the light-strut assembly width is found to be present at the zero elevation, and phase-locked PIV imaging is unable to capture any periodic motion within the wake at this elevation. In contrast, the wake at the highest elevation is found to resemble the flow in the wake of circular cylinders, and phase-locked PIV imaging at this elevation clearly captures an alternate vortex shedding scheme. Due to this difference in wake structures, the periodicity at the highest elevation is found to be stronger than that observed at the zero elevation. Changes in light-strut spacing are found to inversely affect the strength of the periodicity in the wake, as larger spacing is linked to greater influence of three-dimensionality, and therefore a weaker periodicity. Changes in light-strut spacing are also found to be inversely related to the oscillation frequency of the periodicity, with the cause for this relationship possibly explained by the wider wake at increased spacing. It is found that the oscillation frequency of periodicity in the single light landing gear wake is consistently in the Strouhal number range of St=0.16-0.18 for all light-strut spacing distances, freestream velocities, and elevations. The flow around the light-strut assembly is therefore characterized as modulated flow around a cylindrical strut because alternate vortex shedding is dominant except for a slight region where the light acts to generate three-dimensionality, and because the oscillation frequency is near that of vortex shedding from a circular cylinder, St=0.19. The wakes of the single light landing gear and two-light landing gear models are compared, but neither design can be supported as quieter than the other at this time due to the unknown amount of vertical radiation from the landing gear wakes.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: A Pilot Study Determining the Influence of Cervical Manipulation on Spinal Motion During Gait in Previously Concussed Individuals

contributor:
Pierrynowski, Michael R.
Human Biodynamics

subject: influence, cervical manipulation, spinal motion, gait, previously concussed individualsn=, neck, syndrome, biomechanical

abstract:
 This pilot study was performed in order to examine the potential beneficial effects of cervical spinal manipulative therapy on volunteers suffering from post-concussive neck syndrome. The study of concussions and post-concussive neck syndrome is still a relatively new topic in the existing literature. Little research has been done in the area of spinal manipulation and the treatment of volunteers suffering from post-concussive neck syndrome, from a biomechanical standpoint.

 Forty-one volunteers who were suffering from post-concussive neck syndrome were recruited from McMaster University in Hamilton, Ontario to participate in the study. In order to assess the severity of neck complaints, the severity of their post-concussive symptoms and overall general health, the volunteers completed the Neck Disability Index, the Visual Analog Scale, the Standardized Assessment of Concussion
and the Short Form-36 Health Survey. During testing sessions, volunteers were fitted with several light emitting markers placed strategically on the head, mid-back, sacrum and heels of the volunteers' footwear. Each volunteer would then walk on a treadmill for four separate five minute trials, after an initial familiarization period. The 3D position of these markers during gait were recorded by a rear-mounted kinematic data acquisition system (Optotrak 3020). After the initial five minute walk (trial 1), the volunteer was treated with a cervical spinal manipulation, and immediately resumed walking for the second trial on the treadmill. The volunteers performed four walking trials in total.

 Both manual and automated procedures were used to identify the multiple right-heel treadmill surface contacts during each five minute walk. Objective biomechanical outcome measures used in the study included relative phase measurements between the head and thorax in the transverse plane, the Biomechanical Efficiency Quotient and the Neck-Walk Index.

 Clinically significant results in relative measurements, post-intervention, were found when certain volunteers were removed (due to slow walking velocity). These differences can be attributed to the intervention of spinal manipulation which caused a significant increase in cervico-thoracic spinal motion, which appeared to decrease again at 35 minutes. This is clinically significant because it poses the theory that initial short-term biomechanical changes in the cervical spine are caused by SMT.

 Clinically significant results in the Biomechanical Efficiency Quotient were found when specific volunteers were removed. The results however, were in the opposite direction than was previously hypothesized. The reason for the increase in BEQ post-manipulation compared to pre-manipulation could be a result of the familiarization walking period before the initial trial. By allowing volunteers several minutes to get accustomed to walking on the treadmill, a learning effect had taken place, decreasing the variability in their gait in the initial pre-intervention trial. Although BEQ increased in the second and third trials, it decreased again at 35 minutes post-intervention, meaning the walking economy had once again increased.

 The specific intervention of cervical spinal manipulative therapy was hypothesized to change the variability of head movement disturbances during gait (Neck-Walk Index). No reference in the literature is made in relation to Neck-Walk Index and how it evaluates change in head carriage, post-intervention. This study suggests however, that although results approached significance, cervical manipulative therapy did not change biomechanical head carriage in this volunteer population.

 With respect to future studies, several recommendations have been made in this thesis which are aimed at increasing the clinical significance of the results. This would be done through the incorporation of more affected volunteers (increase in functional disability due to post-concussive neck syndrome), the incorporation of a more lengthy and specific treatment protocol (to sustain biomechanical and physical changes), and an increased treadmill walking velocity (to assess antiphasic movements more easily).

abstract: Thesis

abstract: Master of Science (MSc)


title: Functional Analysis of the Role of Slit and its Receptors During D. melanogaster Heart Morphogenesis

contributor:
Jacobs, J. Roger
Biology

subject: functional analysis, role of slit, receptors, D. melanogaster, heart morphogenesis, cardiovascular, heparin sulfate proteoglycan Syndecan

abstract:
Proper formation of the heart is a critical developmental event which requires strict
regulation of coordinated cardial cell adhesion, alignment, and migration. The simple, tube-like heart of the fruit fly, Drosophila melanogaster, has proven to be an attractive system in which to study the regulatory pathways which control cardiogenesis. This is mainly due to its strikingly similarity to the vertebrate heart during early embryogenesis. In addition, many genes identified in association with congenital heart disease in humans have homologues in Drosophila, suggesting that this model organism has great potential to contribute to cardiovascular research. The extracellular matrix protein encoded by slit is a ligand for the receptors Robo, and Robo2 (lea). Recently, a third receptor for Slit has been identified as the heparin sulfate proteoglycan Syndecan. The main objective of this thesis was to use time lapse confocal imaging in order to develop further understanding of the mechanisms which result in heart assembly defects in slit, robo, lea, and syndecan mutants. We also aimed to gain a better understanding of the role of Syndecan within the Slit-Robo pathway and elucidate its relative contribution to development of the mature heart. In mutants homozygous for slit, as well as mutants doubly heterozygous for robo and lea, cardial cell alignment, adhesion, and synchronized migration were disrupted. The heart phenotype of syndecan homozygous mutants was similar that of slit and robo, lea, however the migration speed of cells to the midline did not seem to be affected. Based on our findings, we hypothesize that Slit may have Syndecan-dependent and Syndecan-independent functions in the heart.

abstract: Thesis

abstract: Master of Science (MSc)