title: Hydrogen Embrittlement Susceptibility of Ca-Treated Linepipe Steel Skelp

title: Hydrogen Embrittlement Susceptibility of Linepipe Steel

contributor:
Kish, Joseph
Materials Engineering

subject:
Hydrogen Embrittlement
Hydrogen Trapping
Pipeline Steel

abstract:
The aim of this research is to identify problematic microstructural features as hydrogen traps in linepipe steel that serve to increase the hydrogen embrittlement susceptibility. A comparison is made between the hydrogen trapping capacity and associated hydrogen embrittlement susceptibility of Ca-treated X60 grade steel skelp and X70 grade steel skelp: the latter typically being more susceptible to hydrogen-induced cracking in sour environments.
	Through-thickness variations in the steel skelp microstructure were characterized across multi-length scales using light optical microscopy (LOM) and scanning electron microscopy (SEM) equipped with X-ray energy dispersive spectroscopy (EDS). Key features under study include the composition, shape, and distribution of non-metallic inclusions, as well as differences in features present between the quarterline (¼ and ¾ depths) and centerline (½ depth) microstructures. The type, count, and average size of inclusions present in both steel skelp grades were analyzed using an automated SEM-EDS technique called ASPEX®. Major types of inclusions detected in both grades of steel skelp include those containing Ca, Al, Mn, Mg and Ti as major elements. Overall, the area fraction of inclusions detected in the X70 steel was larger than those detected in the X60 with the exception of Ti-containing inclusions, which had a larger area fraction within the X60 steel. Comparing the number of detected inclusions shows that there was overall slightly less Ca-containing inclusions and significantly less Ti-containing inclusions detected in the X70 steel but there was generally more Al-containing, Mg-containing, and Mn-containing inclusions than those detected in the X60 steel.
Thermal desorption spectroscopy (TDS) measurements were made on samples prepared from the ¼, ½, and ¾ depths of X60 and X70 steel skelps after galvanostatic cathodic charging in an As2O3-containing solution using an applied current density of −10 mA/cm2. Hydrogen release was measured using a HYDROSEEL® probe while the sample was heated from 20°C to 650°C to detect temperature values at which hydrogen gas release peaks occurred, and thus provide information on types of reversible and/or irreversible traps present. The TDS results suggests that non-metallic inclusions indeed serve as irreversible traps along with grain boundaries and dislocations, which serve as reversible traps. Hydrogen permeation measurements were also made on samples prepared from the ¼, ½, and ¾ depths after galvanostatic cathodic charging in an As2O3-containing solution using an applied current density of −10 mA/cm2. Hydrogen gas release was measured using a HYDROSEEL® probe while the sample remained at room temperature (~20°C), providing information regarding the potency of reversible hydrogen traps when subjected to a flux of hydrogen. Only reversible traps can be detected at room temperatures due to their low binding energies. Higher temperatures are required to overcome the larger binding energies associated with irreversible traps. The hydrogen permeation results indicate no significant effect of through-thickness variations in the X60 steel, but the centreline depth of the X70 steel skelp trapped a larger quantity of hydrogen than either of the two quarterline depths, indicating the presence of a distinct problematic trap. The X70 steel skelp was also observed to trap more hydrogen than the X60 steel skelp.
The observed hydrogen trapping capacity was linked to the hydrogen embrittlement susceptibility by comparing the uniaxial tensile behaviour of centreline samples with and without hydrogen charging applied as a pre-treatment step. Hydrogen charging was achieved by galvanostatic cathodic polarization at an applied current density of −10 mA/cm2 for 24 h in an NH4SCN-containing solution while simultaneously loading the samples to 85% of the yield strength using a proof ring tensile test cell. An increase in hydrogen embrittlement as a result of pre-charging was confirmed through tensile plots by comparing the area of reduction and failure strain of charged samples to uncharged samples. A decrease in both values was observed in the charged samples indicating a loss in ductility as a result of hydrogen charging. Fracture surfaces were imaged using SEM and inclusions of interest were analyzed for elemental composition using EDS. Inclusions observed along the fracture surfaces include oxysulfides of Ca and Al, oxides of Mg, Al-Ca-Si oxides, and Al2O3-containing inclusions which are likely to be heterogeneous Al-Ca-O inclusions.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Functional Significance of novel molecular markers specific for Deinococcus and Chlamydiae species

contributor:
Gupta, Radhey
Biochemistry and Biomedical Sciences

abstract:
The Deinococcus species are highly resistant to oxidation, desiccation, and radiation. Very few characteristics explain these unique features of Deinococcus species. This study reports the results of detailed comparative genomics, structural and protein-protein interactions studies on the DNA repair proteins from Deinococcus species.  Comparative genomics studies have identified a large number of conserved signature indels (CSIs) in the DNA repair proteins that are specific for Deinococcus species. In parallel, I have carried out the structural and protein-protein interactions studies of CSIs which are present in nucleotide excision repair (NER), UV damage endonuclease (UvsE)-dependent excision repair (UVER) and homologous recombination (HR) pathways proteins. Comparative genomics studies have identified a 30 amino acid (aa) conserved signature indel (CSI) in the UvrA1 protein and a 1 aa CSI in the UvsE protein that are  specific for Deinococcus species. I also have identified a 1 aa CSI in the RecA protein that is specific for Deinococcus-Thermus phylum. Structural analysis delineates that these CSIs are located at the surface loop of the protein. Protein-protein interactions analyses reveal that the UvsE protein of Deinococcus species is present in a genetic linkage with Zn-ribbon protein. RecA protein is also present in a genetic linkage with two proteins in Deinococcus-Thermus phylum. UvsE and RecA proteins are predicted to be part of same operon with the interacting proteins. The UvrA protein is also present in genetic linkage with disulfide oxidoreductase (DsbA), disulfide bond formation protein (DsbB) and one of our labs identified conserved signature protein (CSP). These four proteins are indicated to be part of the same operon. We have proposed a model to understand the functional role of these four proteins in together in DNA repair. According to our model, the predicted linkage of the UvrA protein via CSP to the DsbA/DsbB is expected to restore the activity of the NER pathway in Deinococcus species upon radiation exposure. Further experimental studies may lead to prove our hypothesis and to understand the functional role of CSI and CSP among Deinococcus species.
Similarly, I have carried out the comparative genomics studies in the GyrA and GyrB protein sequences which are supposed to play role in regulation of temporal gene expression during intracellular development. I have identified a number of molecular markers in the form of CSIs in the GyrA and GyrB protein sequences which are specific for all the members of Chlamydiae. Structural analysis indicates that two of these CSIs may play role in enhancing the supercoiling activity of GyrA and GyrB proteins of chlamydial species.  I have carried out protein-protein interactions analyses to understand the functional role of other two CSIs of GyrA and GyrB proteins. Protein-protein interactions analyses delineate that the GyrA and GyrB proteins of chlamydial species are present in a unique genetic linkage with thymidylate kinase (TMK), DNA polymerase III subunit δ' (HolB) and one of the chlamydial specific CSP. We have proposed a model to understand the functional role of CSIs, CSP and also to delineate the functional role of these proteins together to chlamydial intracellular development. According to our model, these five proteins together play a role to increase the replication rate during the midcycle of intracellular development. CSP and CSIs are responsible for these unique associations among these proteins. Further experimental studies may lead to prove this hypothesis and will guide to decipher the intricateness of chlamydial intracellular development.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: Estimating Veterans' Health Benefit Grants Using the Generalized Linear Mixed Cluster-Weighted Model with Incomplete Data

contributor:
McNicholas, Paul
Jevtic, Petar
Mathematics and Statistics

subject:
Cluster-weighted models
Mixture models
Generalized linear models
Clustering
Mixed-type data
Incomplete data

abstract: The poverty rate among veterans in US has increased over the past decade, according to the U.S. Department of Veterans Affairs (2015). Thus, it is crucial to veterans who live below the poverty level to get sufficient benefit grants. A study on prudently managing health benefit grants for veterans may be helpful for government and policy-makers making appropriate decisions and investments. The purpose of this research is to find an underlying group structure for the veterans' benefit grants dataset and then estimate veterans' benefit grants sought using incomplete data. The generalized linear mixed cluster-weighted model based on mixture models is carried out by grouping similar observations to the same cluster. Finally, the estimates of veterans' benefit grants sought will provide reference for future public policies.

abstract: Thesis

abstract: Master of Science (MSc)


title: Multi-Dimensional Characterization of Bone and Bone-Implant Interfaces

contributor:
Grandfield, Kathryn
Materials Science and Engineering

subject: Osseointegration, bone-implant interface, electron tomography, atom probe tomography, liquid-phase TEM, 4D

abstract:
Metallic bone implant devices are commonly used to tackle a wide array of bone failures in human patients. The success of such implants relies on the biomechanical and functional bonding between the living bone tissue and implant, a process defined as osseointegration. However, the mechanism of osseointegration is still under debate in the scientific community. One efficient method to help understand this complex process is to characterize the interface between human bones and implant devices after the osseointegration has been established, while another approach is to visualize mineralization in real-time under simulated body conditions. Both of these approaches to understand mineralization have been explored in this thesis.

    Firstly, due to the inhomogeneous nature of bone and complex topography of implant surfaces, a suitable sample geometry for three-dimensional (3D) characterization was required to fully understand osseointegration. Electron tomography has been proven as an efficient technique to visualize the nanoscale topography of bone-implant interface in 3D. However, resulting from the thickness and shadowing effects of conventional transmission electron microscope (TEM) lamellae at high tilt angles and the limited tilt-range of TEM holders, “missing wedge” artifacts limit the resolution of final reconstructions. In Chapter 3, the exploration of a novel sample geometry to explore osseointegration is reported. Here, on-axis electron tomography based on a needle-shaped sample was applied to solve the problem of the “missing wedge”. This resulted in a near artifact-free 3D visualization of the structure of human bone and laser-modified titanium implant, showing bone growth into the nanotopographies of the implant surface and contributing to the evolution of the definition of osseointegration towards nano-osseointegration.

    One of the key issues regarding the mechanism of osseointegration that remains is that of the chemical structure at the implant interface, namely distribution of calcium-based and carbon-based components at the interface and their origins. Thus, the second objective of this thesis aimed to push characterization techniques further to four dimensions (4D), by incorporating chemical information as the fourth dimension after the spatial X,Y,Z coordinates. In Chapter 4, correlative 4D characterization techniques including electron energy-loss spectroscopy (EELS) tomography and atom probe tomography (APT) and other spectroscopy techniques were used to probe the nanoscale chemical structure of the bone-implant interface. This work uncovered a transitional biointerphase at the bone-implant interface, consisting of morphological and chemical differences compared to bone away from the interface. Also, a TiN layer between the surface oxide and bulk metal was identified in the laser-modified commercial dental implant. Both findings have implications for the immediate and long-term osseointegration.

    Since bone formation at the implant interface is a dynamic process, which includes calcium phosphates (CaP) biomineralization as a basis of these reactions, the third objective of this work focused on exploring real-time mineralization processes. Liquid-phase transmission electron microscopy (LP-TEM) is a promising technique to enable real-time imaging with nanoscale spatial resolution and sufficient temporal resolution. In Chapter 5, by using this technique, we present the first real-time imaging of CaP nucleation and growth, which is a direct evidence to demonstrate that CaP mineralization occurs by particle attachment.

    Overall, this thesis has applied state-of-the-art advanced microscopy techniques to enhance the knowledge and understanding of osseointegration mechanisms by investigating established biointerfaces and real-time mineralization. The developed correlative 4D tomography workflow is transferable to study other interfacial applications in materials science and biological systems, while the LP-TEM work forms a basis for further mineralization research.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: TOOTH TALES: WHAT INTERNAL DENTAL STUCTURES REVEAL ABOUT VITAMIN D DEFICIENCY AND AGE ESTIMATION

contributor:
Brickley, Megan
Prowse, Tracy
Anthropology

subject: vitamin D deficiency, interglobular dentin, nutritional rickets, histology

subject: dental radiographs, older adult age estimation

abstract:
Exploration of the internal structures of teeth is complex and has the potential to add greatly to existing information about the lifecourse of archaeological individuals, but has yet to realize its full interpretative value as an avenue of bioarchaeological inquiry. This thesis consists of three papers that focus on the potential for internal dental structures to provide important information on chronological age, and physiological alterations linked to vitamin D deficiency.

The first paper used SEM, microscopic imaging, and histological investigation of tooth dentin to determine the presence of mineralisation defects, observed as interglobular dentin (IGD) (spaces following incremental lines) in living (with known medical history) and archaeological individuals with clear healed rickets. This paper demonstrated that incremental bands of IGD are indicative of vitamin D deficiency.

The second paper expands identification of those with deficiency by quantifying morphological changes in pulp chambers of living and archaeological individuals. Pulp chambers were radiographed, evaluated histologically, and measured. Those with evidence of past vitamin D deficiency displayed constricted or chair shaped pulp horns. This radiographic technique provides a non-destructive tool to identify individuals that experienced childhood vitamin D deficiency.

The role vitamin D plays in the development of IGD over the lifecourse requires that accurate age estimates be conducted on older as well as younger adults. The third paper used a new version of pulp/tooth area ratios to provide an accurate estimation of age-at-death in older adults (50+). ImageJ software was used to calculate areas on sectioned teeth and results provided a mean absolute error (MAE) of ±3.9 years in older adults.

The results described in this thesis contribute to broader topics of discussion in anthropology, such as investigating health and metabolic disease in human populations, and adds to the ongoing discussion and evaluation of age-at-death techniques used to extend our ability to study the lifecourse of archaeological individuals.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Teeth record life events and the three papers in this thesis use dental structures to provide methodological foundations to evaluate the occurrence and severity of vitamin D deficiency in early life. The potential long-term consequences of such events are investigated through accurate recognition of older adults. Vitamin D regulates skeletal health by mediating calcium absorption and phosphorous homeostasis and deficiency is recognised as an important health concern. Accurate identification of older adults is also a widely recognised problem in skeletal studies. Age-at-death estimation in older individuals was calculated and the exploration of abnormal pulp chamber shape and mineralisation defects in tooth dentin was done to determine vitamin D status in both younger and older individuals. This research established that internal dental structures enables past episodes of vitamin D deficiency to be recognized in cases where skeletal indicators are not clear and permits increased precision in age-at-death estimations in the older individual.


title: Pricing Asian Options and Basket Options by Monte Carlo Methods

contributor:
Pirvu, Traian
Mathematics and Statistics

abstract: In this thesis, we investigate pricing Asian options and basket options under different Monte Carlo methods. It is observed that the prices of Asian options and basket options are based on the combinations of stocks prices, while the stocks follow a geometric Brownian motion (GBM). For the price of Asian options, a benchmark price is computed first. A partial differential equations (PDE) (one dimension in time and one in space) due to Veˇceˇr with the constant volatility of Asian call option is numerically solved and gives the option prices which we use as a benchmark. After that, three Monte Carlo methods are used to simulate Asian option prices: naive Monte Carlo, antithetic Monte Carlo and control variate. Comparing them with the benchmark and by evaluating the absolute error, mean square error and computation time, we eventually find that control variate method is the most efficient method for pricing Asian options. Next, to price basket options, we choose two different control variate, a classical one and a novel one. After applying these two control variates, we evaluate the performance by mean square error, length of 95% confidence interval and computation time. Taking all factors into consideration, the new control variate is more useful for pricing basket options.

abstract: Thesis

abstract: Master of Science (MSc)


title: Unmet Need for Community Based Physiotherapy in Canada

contributor:
Richardson, Julie
Rehabilitation Science

subject: unmet need, physiotherapy

abstract:
This thesis includes four manuscripts with overarching objectives to identify if Canadians experience unmet need for physiotherapy. McIntyre et al.’s framework was utilized across the manuscripts to explore reasons why unmet need may exist.
	The first manuscript presents a scoping review investigating unmet need for physiotherapy across Canada. The objective was to describe current evidence for unmet need for community-based physiotherapy services (CBPTS). Adults with chronic conditions versus those without, or who lived in rural versus urban communities were more likely to report unmet need for CBPTS. Availability and affordability were identified as reasons for unmet need.
	The second manuscript presents a secondary data analysis of three Canadian Community Health Survey (CCHS) cycles (2001, 2003, 2005) for three provinces: Ontario (ON), Alberta (AB), British Columbia (BC). This study investigated factors that explain variations in self-reported unmet needs of individuals with specific chronic conditions. Unmet need for treatment of a physical health problem (PHP) was the most common type of need in all three cycles.  Affordability was the only domain with significant differences between cycles in two provinces. Women were less likely than men, and older persons less likely than persons 40 – 45 years, to report unmet need for treatment of a PHP.
	The third manuscript analyzed CCHS data for ON, AB and BC to investigate which socio-demographic variables were associated with reporting a visit to a physiotherapist in three cycles. People with lower income were less likely to report a physiotherapy visit compared to people with higher income. Women, and individuals with an injury or physical activity limitation were more likely to report a physiotherapy visit.
	The fourth manuscript presents themes from key informant interviews that explored the partial removal of physiotherapy from the Ontario Health Insurance Plan (“delisting”). Partial delisting contributed to increased unmet need immediately following, and more than ten years post implementation. Longstanding unmet need due to affordability and availability was identified.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Physiotherapy is a health profession that works with people to help them stay healthy and maintain physical function. There are many people with chronic conditions who would benefit from receiving physiotherapy treatment, but are not able to do so. Three reasons that may explain why people do not receive physiotherapy are they: cannot afford to pay; cannot find a physiotherapist close to where they live or work; or they do not believe a physiotherapist will improve their health.  This thesis includes four papers aimed at better understanding the reasons why people in three Canadian provinces, Ontario, Alberta and British Columbia, do not see a physiotherapist when their health would benefit from doing so.  The results suggest that cost and the location where physiotherapy services are provided are reasons why some people do not receive physiotherapy care - even if they believe physiotherapy is needed. The findings from this thesis may help to inform the future organization and delivery of physiotherapy services.


title: Rigorous defect control and the numerical solution of ordinary differential equations

contributor:
Nedialkov, Nedialko
Computational Engineering and Science

subject:
Reliable computing
Taylor models
Automated stepsize control
Ordinary Differential Equation
Taylor series
Sollya
Rigorous Polynomial Approximation
Continuous output
Backward error analysis

abstract:
Modern numerical ordinary differential equation initial-value problem
(ODE-IVP) solvers compute a piecewise polynomial approximate solution
to the mathematical problem. Evaluating the mathematical problem at
this approximate solution defines the defect. Corless and Corliss
proposed rigorous defect control of numerical ODE-IVP.

This thesis automates rigorous defect control for explicit,
first-order, nonlinear ODE-IVP. Defect control is residual-based
backward error analysis for ODE, a special case of Wilkinson's
backward error analysis. This thesis describes a complete software
implementation of the Corless and Corliss algorithm and extensive
numerical studies. Basic time-stepping software is adapted to defect
control and implemented.

Advances in software developed for validated computing applications
and advances in programming languages supporting operator overloading
enable the computation of a tight rigorous enclosure of the defect
evaluated at the approximate solution with Taylor models. Rigorously
bounding a norm of the defect, the Corless and Corliss algorithm
controls to mathematical certainty the norm of the defect to be less
than a user specified tolerance over the integration interval. The
validated computing software used in this thesis happens to compute
a rigorous supremum norm.

The defect of an approximate solution to the mathematical problem
is associated with a new problem, the perturbed reference problem.
This approximate solution is often the product of a numerical procedure.
Nonetheless, it solves exactly the new problem including all errors.
Defect control accepts the approximate solution whenever the sup-norm
of the defect is less than a user specified tolerance. A user must be
satisfied that the new problem is an acceptable model.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Many processes in our daily lives evolve in time, even the weather.
Scientists want to predict the future makeup of the process. To do
so they build models to model physical reality.

Scientists design algorithms to solve these models, and the algorithm
implemented in this project was designed over 25 years ago. Recent
advances in mathematics and software enabled this algorithm to be
implemented.

Scientific software implements mathematical algorithms, and
sometimes there is more than one software solution to apply to the
model. The software tools developed in this project enable
scientists to objectively compare solution techniques.
There are two forces at play; models and software solutions.
This project build software to automate the construction of the
exact solution of a nearby model. That's cool.


title: IMMUNO-ENDOCRINE INTERACTIONS IN INTESTINAL INFLAMMATION

contributor:
Khan, Waliul
Medical Sciences

subject: Enterochromaffin cells, EC cells, Serotonin, 5-HT, Immunology, Interleukin-13, IL-13, Gut, Intestine, Infection, Inflammation, Inflammatory bowel disease

abstract: Mucosal inflammation in conditions ranging from infective acute enteritis or colitis to inflammatory bowel disease (IBD) is accompanied by alteration in enterochromaffin (EC) cell numbers and serotonin (5-hydroxytryptamine; 5-HT) content in the gut. Previously we had shown that CD4+ T cells, via production of T helper (Th)2 cytokines, regulate EC cell biology in the Trichuris muris-infectious colitis model. I further examined the mechanisms of immuno-endocrine interactions in the context of intestinal inflammation. In chapter 3, utilizing human EC cell line and Trichuris muris-mouse model of infectious colitis we identified a critical role of interleukin (IL)-13, a key Th2 cytokine, in increasing EC cell numbers, tryptophan hydroxylase (TPH)1 expression (rate-limiting enzyme of mucosal 5-HT bio-synthesis), and 5-HT production. In chapter 4, we show that IL-13 driven intestinal inflammation is critically dependent on increased 5-HT production using dextran sulfate sodium (DSS) and dinitrobenzene sulphonic acid (DNBS) models of colitis. In DSS-induced colitis, we were the first to identify the increased production of IL-13 and its pathogenic role as IL-13 knockout (IL-13-KO) mice had less severe inflammation compared to wild-type, which was exacerbated following replenishment of 5-HT in IL-13-KO mice. In chapter 5, biopsy examination revealed, higher mucosal IL-13 expression accompanied inflammation in Crohn's disease (CD), which was additionally associated with increased TPH1, 5-HT receptor (5-HTR)3A, 5-HTR7 and decreased 5-HT transporter (5-HTT) expressions. Moreover, CD patients had elevated plasma and platelet-poor plasma 5-HT levels compared to healthy controls (HCs). Furthermore, 5-HTT polymorphism associated genotypes causing inefficiency in 5-HT re-uptake were more common in our patient cohort than HCs. The findings included in this thesis further emphasize the role of immuno-endocrine interactions in intestinal inflammation, which may be a step toward a better diagnosis or management or even a cure for a disease that is of growing concern, and in understanding IBD pathogenesis.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The gut produces most of the serotonin found in our body, where it regulates many normal functions. A group of special cells, named enterochromaffin cells, produces nearly all of the serotonin in the gut. In diseases of the gut, especially ones that involve inflammation resulting in symptoms like abdominal pain, diarrhea and bleeding, the number of these cells and serotonin concentration are different from that in the normal gut. I found that these changes are controlled by a particular protein produced by immune cells, called interleukin-13, and alteration in serotonin levels, in turn, contributes to the inflammatory process. Our laboratory experiments with cells and animals establish this connection between interleukin-13 and serotonin in gut inflammation. We further confirm this association between interleukin-13 and serotonin in human inflammatory bowel disease. Moreover, we identify a potential genetic cause of these changes in serotonin concentrations which may ultimately result in inflammatory bowel disease.


title: Electrochemical protein detection by target-responsive programmable dynamic DNA assembly

contributor:
Soleymani, Dr. Leyla
Biomedical Engineering

subject: Protein responsive strand displacement assay.

abstract:
Nucleic acid amplification is responsible for pushing the limit-of-detection of molecular
diagnostic assays to unprecedented levels. We developed an assay based on protein-responsive programmable dynamic DNA assembly (PRPDA) to detect proteins via an
intermediate process involving nucleic acids for taking advantage of nucleic acid amplification strategies. PRPDA has previously been designed for sensitive protein analysis in
fluorescent assay formats. To further push the detection limit and to achieve assay
miniaturization and multiplexing, we sought to combine PRPDA with electrochemical
readout. We were able to achieve LOD of 1 pM by employing wrinkled gold electrode
for the PRDA protein detection scheme. Which is 2800 times improvement compare to
the 2.8 nM demonstrated by fluorescent transduction.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: INVESTIGATING NOVEL β-CATENIN SIGNALLING MECHANISMS IN AN EMBRYONIC STEM CELL MODEL

contributor:
Doble, Bradley
Biochemistry and Biomedical Sciences

subject:
β-catenin
Stem Cells

abstract: The Wnt/β-catenin pathway is a fundamental regulator of embryonic development and adult tissue homeostasis. The key effector, β-catenin, is a multifunctional protein that occupies dual roles in signalling and intercellular adherens junctions. β-catenin primarily signals though the TCF/LEF transcription factors; however, many transcription factors, in addition to TCF/LEFs, interact with β-catenin, and the function of these interactions is poorly understood. To investigate novel β-catenin regulated signalling mechanisms with certainty, we developed TCF/LEF quadruple knockout (QKO) mESCs. In vitro differentiation of QKO cells reveals a neural differentiation bias, which is attenuated by overexpression of stabilized β-catenin. Our data indicate the presence of a TCF-independent β-catenin regulated neural differentiation blockade in mESCs. In addition to directly challenging the central dogma of canonical Wnt signalling, this finding has the potential to unveil new therapeutic targets for the treatment of many β-catenin-associated diseases, including forms of brain cancer that may arise from the oncogenic stimulation of neural stem cells. Furthermore, we describe an attempt to identify genome-wide TCF-independent β-catenin binding sites in QKO cells by ChIP-seq. Optimization trials provide proof of concept that the fold enrichment method of interpreting ChIP-qPCR results can be highly misleading when compared to the more comprehensive % input method of analysis. This conclusion has important implications for all fields of scientific research in which ChIP-seq methodology is employed.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Theoretical Model and Study of Mathematical Anxiety

contributor:
Wolkowicz, Gail
Mathematics

subject: Mathematical anxiety, mathematical model of learning, mathematical education.

abstract: The study of mathematical anxiety has seen an increased importance in the past few decades in the field of mathematical education. As this topic is of great interest in education research, this thesis investigates the previous contributions made by other researchers via a literature review of mathematical education papers. Furthermore, a literature review of mathematical models of learning is presented. In the hopes of closing the gap between these two streams of research, this thesis conducts a study of mathematical anxiety at the first year university level through a survey and data analysis, and proposes a theoretical model of learning. Throughout the data analysis, the prevalence, effects, and correlates of mathematical anxiety are examined. Using a version of the Mathematical Anxiety Rating Scale refined by Plake \& Parker in 1982, factors such as gender, high school performance, and program choices are shown to be correlated to mathematical anxiety, as is consistent with previous literature. On the other hand, the model of learning offers a theoretical perspective in understanding the relationship between knowledge, effort, and anxiety, and how these variables interact during a learning experience. This model suggests that given an individual's aptitude, drive, and susceptibility for anxiety, that they may reach various levels of knowledge, effort, and anxiety throughout an academic term.

abstract: Thesis

abstract: Master of Science (MSc)


title: HIV-KILLER: A SOCIAL CONSTRUCTIONIST ANALYSIS OF THE  CRIMINALIZATION  OF HIV NON-DISCLOSURE DEBATE

title: HIV-KILLER: THE CRIMINALIZATION OF HIV NON-DISCLOSURE

contributor:
Pawluch, Dorothy
Sociology

subject:
Social Constructionism
HIV
Non-Disclosure
Criminalization
Social Problems
Qualitative Media Analysis

abstract: Over the past decade, there has been a dramatic increase in the number of cases of criminal charges laid against those who do not disclose their HIV-positive status to their sexual partners. The criminalization of HIV non-disclosure has generated an intense debate which is the object of this analysis. Using a social constructionist framework, particularly the work of Donileen Loseke, a leading social problems theorist, and documentary data drawn primarily from the internet, my goal is to shed light on the debate. More specifically, I am concerned with definitional contests or competing constructions inherent in the debate.  The dissertation is organized around three papers. The first paper explores how the condition of HIV itself is socially constructed in the debate.  Claims-makers who support criminal sanctions construct the disease as deadly and devastating, while claims-makers who oppose criminalization construct HIV as chronic and manageable.  The second paper explores the rhetorical strategies used by those who support criminalization to construct non-disclosers as villains. I coined the term techniques of vilification to capture these strategies.  The third paper examines the rhetorical strategies used by those who oppose criminalization to neutralize the label of victim for partners of non-disclosers.  As a whole, the dissertation contributes to a better understanding of social problems claims-making processes, particularly around the construction of conditions and people. The dissertation also makes contributions to ongoing discussions in the sociology of health and illness, and victimology.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This thesis investigates the debate around the criminalization of HIV non-disclosure with an emphasis on the Canadian context.  Adopting a social constructionist approach, particularly as it has been used in the sociological study of social problems, and building on the work of social problems theorist Donileen Loseke, the thesis explores three themes: 1) how claims-makers understand HIV as a condition based on whether they support or oppose criminalization, 2) how claims-makers who support criminalization vilify those who do not disclose their HIV-positive status, and 3) how claims-makers who oppose criminalization work to downplay claims to victimhood by partners of non-disclosers.  This work contributes to our understanding of the definitional contests underlying the debate. More broadly, it contributes to our understanding of social problems claims-making processes.


title: On Platforms and Algorithms for Human-Centric Sensing

contributor:
Rong, Zheng
Computer Science

subject:
wearable technology
machine learning

abstract:
The decreasing cost of chip manufacturing has greatly increased their distribution and availability such that sensors have become embedded in virtually all physical objects and are able to send and receive data -- giving rise to the Internet of Things (IoT). These embedded sensors are typically endowed with intelligent algorithms to transform information into real-time actionable insights. Recently, humans have taken on a larger role in the information-to-action path with the emergence of human-centric sensing. This has made it possible to observe various processes and infer information in complex personal and social spaces that may not be possible to obtain otherwise. However, a caveat of human-centric sensing is the high cost associated with high precision systems.

In this dissertation, we present two low cost and high performing end-to-end solutions for human-centric sensing of physiological phenomena. Additionally, we present a post-hoc data-driven sensor synchronization framework that exploits independent, omni-present information in the data to synchronize multiple sensors. We first propose XTREMIS -- a low-cost and portable  ECG/EMG/EEG platform with a small form factor that has a sample rate comparable to research-grade EMG machines. We evaluate XTREMIS on a signal level as well as utilize it in tandem with a Gaussian Mixture Hidden Markov Model to detect finger movements in a rapid, fine-grained activity -- typing on a keyboard. Experiments show that not only does XTREMIS functionally outperforms current wearable technologies, its signal quality is high enough to achieve classification accuracy similar to research-grade EMG machines, making it a suitable platform for further research. We then present SiCILIA  -- a platform that extracts physical and personal variables of a user's thermal environment to infer their clothing insulation. An individual's thermal sensation is directly correlated with the amount of clothing they are wearing. Indeed, a person's thermal comfort is crucial to their productivity and physical wellness, and is directly correlated with morale. Therefore it becomes important to be aware of actions such as adding or removing clothing as they are indicators of current thermal sensation. The proposed inference algorithm builds upon theories of body heat transfer, and is corroborated by empirical data. SiCILIA was tested in a vehicle with a passenger-controlled HVAC system. Experimental results show that the algorithm is capable of accurately predicting an occupant's thermal insulation with a low mean prediction error. In the third part of the thesis we present CRONOS -- a sensor data synchronization framework that takes advantage of events observed by two or more sensors to synchronize their internal clocks using only their data streams. Experimental results on pairwise and multi-sensor synchronization show a significant drift improvement for total drift and a very low mean absolute synchronization error for multi-sensor synchronization.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Small-Volume Blood Collection Tubes to Reduce Anemia and Transfusion in Intensive Care Unit Patients

title: Reducing Blood Sampling Volumes in the Intensive Care Unit

contributor:
Crowther, Mark
Heddle, Nancy
Health Research Methodology

subject:
blood loss
laboratory testing
intensive care
cluster trial
pilot study
administrative data

abstract:
Blood sampling causes significant blood loss in intensive care unit (ICU) patients (up to 41 mL per day). Only 10% of the blood collected is used for testing suggesting that volumes can be reduced without compromising patient care or laboratory processes. Blood loss contributes to anemia which is highly prevalent in the ICU (>90% after 3 days) and is associated with major adverse cardiovascular outcomes and death.
     Diagnostic blood loss increases the likelihood of red blood cell (RBC) transfusion which is administered to about 40% of ICU patients (half are given in absence of hemorrhage) and has significant health risks. Small-volume blood collection tubes, which collect about 50% less blood, are available, but rarely used in adults. They have the same cost as standard-volume tubes and are compatible with laboratory equipment. The rationale for the continued use of standard-volume tubes is a theoretical concern about inadequate volume for testing, and the absence of data showing the benefit of small-volume tube use on an important clinical outcome.
     A study is needed to show that small-volume tubes reduce blood loss, anemia and RBC transfusion without harms or negative consequences on patient care and hospital procedures compared to standard-volume tubes. If this could be shown, it may lead to practice change regarding blood collection for laboratory testing. A stepped-wedge cluster randomized trial is the ideal study design for this low-risk intervention. By incorporating the small-volume tubes into routine clinical practice and using administrative and hospital electronic medical record data, this study would be a pragmatic, cost-effective way to evaluate effectiveness and implementation. However, prior to conducting a full-scale trial powered on clinical outcomes, a pilot study is needed to determine whether a larger study will be feasible.
     The goals of this thesis are to (i) summarize the existing evidence regarding small-volume tubes; (ii) discuss cluster randomized trial methodology;(iii) discuss the use of health care administrative data for research; (iv) discuss the role of pilot studies; and (v) present the design of a pilot stepped wedge randomized trial of small-volume versus standard-volume blood collection tubes to evaluate the feasibility of a full-scale trial.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Blood testing is a preventable cause of blood loss. Patients in the intensive care unit (ICU) have about 41 mL of blood taken per day for testing (like donating 1 unit of blood every 8 days). This contributes to anemia (low red blood cells) and transfusion, which are harmful. About 40% of ICU patients get at least one red blood cell transfusion which is a limited resource with health risks. Most of the blood sent to the laboratory is discarded (up to 90%) suggesting that volumes can be reduced without compromising care.
     The goals of this thesis are to (i) summarize the evidence for reducing blood loss for laboratory testing; (ii) discuss cluster randomized trials; (iii) discuss use of health care administrative data for research; (iv) discuss the role of pilot studies; and (v) present a pilot stepped wedge cluster randomized trial of small-volume versus standard-volume blood collection tubes in ICU patients.


title: An Integrated Array-based Microfluidic Device for Parallel Loop-Mediated Isothermal Amplification (LAMP)

contributor:
Selvaganapathy, Ponnambalam Ravi
Mechanical Engineering

subject:
Microfluidic
LAMP
Parallel DNA Amplification
Array-based

abstract:
Nucleic-based acid technology (NAT) is a reliable and well-established method in molecular diagnosis for the detection of bacterial infection. Specifically, PCR (polymerase chain reaction) is the most popular technique to amplify the number of DNA or RNA copies in the sample. However, due to the thermal cycles in the PCR method, advanced equipment and technologies are required to precisely control the temperature during the cycles. To overcome this limitation, isothermal amplification methods have been developed which function at constant temperatures and help reduce the need for state-of-the-art machines to perform the amplification. Among isothermal amplification methods, LAMP (loop mediated isothermal amplification) has demonstrated robustness and sensitivity compared to PCR. Additionally, microfluidic lab-on-a-chip (LOC) technology can facilitate the intensive processes which have been used traditionally in laboratories by automating the required procedures, reducing the volume of the reagents and minimizing the cost and the time of experiments. Although many microfluidic LOC devices have been developed in order to be used in resource poor settings, there is still a need for a simple setup which is inexpensive, accurate and can be performed without the need for a trained technician.
In this thesis, a disposable microfluidic device was developed which is capable of performing high-throughput DNA amplification by using a simple segmentation method in order to digitize the sample into multiple micro-wells. Moreover, design and fabrication of a disposable, inexpensive flexible heater which is an inevitable part of the setup using a direct write process was introduced in order to provide the required energy for the LAMP reaction. Parallel real-time DNA amplification with limit of detection down to few copies per micro-well in less than an hour was illustrated. Using E. coli 0157, it was demonstrated that the detection time of E.coli can be as quick as 11 to 55 minutes with sample concentrations varying from 700,000 copies/micro-well (11 minutes), 70,000 copies/micro-well (18 minutes), 700 copies/micro-well (31 minutes), 7 copies/micro-well (40 minutes) and 0.07 copies/micro-well (55 minutes). Finally, the capability of the device for on chip reagent storage up to 3 days without using any coating methods was illustrated.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor:
Mascher, Peter
Engineering Physics

subject:
Silicon carbonitride
Photoluminescence
ECR PECVD
Annealing
Hydrogen
Luminescence Mechanism
Structral
Optical
Deposition Temperature
Carbon

abstract:
McMaster University DOCTOR OF PHILOSOPHY (2017) Hamilton, Ontario
(Engineering Physics)
TITLE: Luminescent Silicon Carbonitride Thin Films Grown
using ECR PECVD: Fabrication and Characterization
AUTHOR: Zahra Khatami , M.A.Sc. (Shahid Behehsti University)
SUPERVISOR: Professor Peter Mascher
NUMBER OF PAGES: xx, 268

abstract:
Silicon, the cornerstone semiconductor of microelectronics, has seen growing interest
as a low-cost material in photonics. Nanoscience has employed various strategies to
overcome its fundamentally inefficient visible light emission such as developing new
silicon-based nanostructures and materials. Each of the proposed materials has its
own advantages and disadvantages in attempting to reach commercialization. Silicon
carbonitride (SiCxNy) is a less-studied and multi-functional material with tunable
optical features. Despite reports on promising mechanical properties of SiCxNy thin
films, they have not yet been well explored optically.  This thesis presents the first in-depth analysis of the luminescent properties of
SiCxNy thin films at a broad range of compositions and temperatures. To better understand
this ternary structure, the reported data of the two fairly well studied binary
structures was used as a reference. Therefore, three classes of silicon-based materials
were produced and explored; SiCxNy, SiNx, and SiCx. Samples were fabricated using
one of the common methods in the semiconductor industry; electron cyclotron resonance
plasma enhanced chemical vapour deposition (ECR PECVD). A multitude of
characterization techniques were utilized including; optical methods (ultraviolet-visible
spectroscopy (UVVIS), variable angle spectroscopic ellipsometry (VASE), photoluminescence
(PL)) and structural techniques (elastic recoil detection (ERD), Rutherford backscattering spectrometry (RBS), X-ray photoelectron spectroscopy (XPS), Fourier
transform infrared spectroscopy (FTIR), high-resolution transmission electron microscopy
(HR-TEM)).
In view of the exploring of emission properties of SiCxNy materials, our approach
was towards the enhancement of the visible emission by adjusting the film composition
and subsequent thermal treatment. First, a systematic study of the influence of
carbon on the optical, compositional, and structural properties of SiCxNy was carried
out. This investigation was followed by an exploration of influence of growth conditions
on the visible emission and its connection with the other film properties including
hydrogen concentration, microstructure, and composition. In addition, hydrogen
diffusion was explored and associated with two featured annealing temperatures.
The key element of this thesis is the comprehensive report on the interdependency
of the visible light emission and all optical, structural, and compositional features of
SiCxNy structures. Unlocking the potential of this ternary and less studied material
can appeal to the silicon photonics community to implement it in anti-reflection,
solar cell, and sensing applications, and in particular as a substitution of SiNx used
in existing microelectronic devices.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Clinical application of the Web-Accessible Population Pharmacokinetic Service – Hemophilia (WAPPS-Hemo): proposal for a pilot study of a population pharmacokinetic approach to tailored prophylaxis in hemophilia.

contributor:
Iorio, Alfonso
Health Research Methodology

abstract:
Background
A possible way to improve the global clinical benefit of hemophilia treatment could be adopting a tailored prophylaxis regimen. To execute a tailored prophylaxis treatment scheme is necessary the evaluation of pharmacokinetic (PK) parameters acquired after the infusion of clotting factor concentrates at the individual patient level. However, an individual, complete, PK study for either FVIII or FIX can be demanding and impractical. An alternative to the traditional PK studies is the population PK (popPK) approach. The Web Accessible Population Pharmacokinetic Service - Hemophilia (WAPPS-Hemo) is an independent population PK calculator developed at McMaster University by Dr. Alfonso Iorio. Sparse data from individual patients are fitted using a Bayesian iterative approach to estimate terminal half-life and times to critical concentrations and to produce an interactive graphical display of the concentration time curve.
Objective
The aim of this project is to develop a protocol for a pilot study to assess the feasibility of an interventional trial designed to test the efficacy of the PopPK approach to tailored prophylaxis in hemophilia.
Methods
Design: The proposed study is multi-centre, prospective (pre-post), open label, clinical trial. This study is designed to be primarily a feasibility study. Setting: Canadian Hemophilia Treatment Centers. Study population: In this study, we will enroll severe congenital hemophilia A and B patients (baseline factor level <1%) who have been on factor with any factor concentrate for at least 12 months and have reached a minimum of 150 exposure days. Intervention: The study intervention is the new personalized dosing recommendation based on PopPK, produced through the WAPPS-Hemo application. Feasibility Criteria for success: We’ll consider the pilot study to be feasible and successful if at least 50% of enrolled patients are eligible for a regimen adjustment (switch to personalized dosing regimen); at least 75% of patients who start the new prophylaxis regimen based on the personalized dosing recommendation complete the 12 months’ follow-up.
Conclusion
The goal of dose individualization for clotting factor concentrates is to improve the outcomes in severe hemophilia patients. The PopPK approach has this potential, but whether the use of PopPK will be will translate into clinically or economically meaningful changes in the practice of hemophilia care remains to be demonstrated. The pilot study described in this proposal will assess the feasibility of a full-scale interventional study designed to this purpose.

abstract: Thesis

abstract: Master of Science (MSc)


title: Algorithms for Multiple Ground Target Tracking

contributor:
Kirubarajan, Thia
Electrical and Computer Engineering

subject:
ground target tracking
visual tracking

abstract:
In this thesis, multiple ground target tracking algorithms are studied. From different aspects of the ground target tracking, three different types of tracking algorithms are proposed according to the specialties of the ground target motion and sensors employed.
Firstly, the dependent target tracking for ground targets is studied. State dependency is a common assumption in traditional target tracking algorithms, while this may not be the true in ground target tracking as the motion of targets are constraint to certain path. To enhance the tracking algorithm for ground targets, starting with the dependency assumption, Markov Random Field (MRF) based Probabilistic Data Association (PDA) approach is derived to associate motion dependent targets. The driving behavior model is introduced to describe motion relationship among targets. The Posterior Cramer-Rao Lower Bound (PCRLB) is derived for this new motion model. Experiments and simulations show that the proposed algorithm can reduce the false associations and improve the predictions. Eventually, the proposed approach alleviates issues like the track impurity and coalescence problem and achieves better performance comparing to standard trackers assuming state independence.

Ground target tracking using cameras is then studied. To build an efficient multi- target visual tracking algorithm, fast single target visual tracking is an important component. A novel visual tracking algorithm that has high speed and better or comparable performance to state-of-the-art trackers is proposed. The proposed approach solves the tracking task by using a mixed-motion proposal based particle filter with Ridge Regression observation likelihood calculation. This approach largely reduces the exhaustive searching in common state-of-art trackers while maintains efficient representation of the target appearance change. Experiments on 100 public benchmark videos, as well as a high frame rate benchmark, are carried out to compare the performance with the state-of-art published algorithms. The results of the experiment show the proposed tracker achieves good performance while beats other algorithms in speed with a large margin.

The proposed visual target tracker is integrated into a new multiple ground tar- get tracking algorithm using a single camera. The multi-target tracker addresses the issues in the target detection, data association and track management aside from the single target tracker. A perspective aware detection algorithm utilizing the re- cent advanced Convolutional Neural Networks (CNN) based detector is proposed to detect multiple ground targets and alleviate the weakness of CNN detectors in detecting small objects. A hierarchical class tree based multi-class data association is presented to solve the multi-class association problem with potential misclassified detections. Track management is also improved utilizing the high efficiency detectors and a Support Vector Machine (SVM) based track deletion is proposed to correctly remove the dead tracks. Benchmarking is presented in experiments and results are analyzed. A case study of applying the proposed algorithm is provided demonstrating the usefulness in real applications.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Learning-Based Multi-Channel Spectrum Access in Full-duplex Cognitive Radio Networks with Unknown Primary User Activities

contributor:
Zheng, Rong
Davidson, Tim
Electrical and Computer Engineering

subject:
cognitive radio
spectrum sensing
spectrum access
sequential learning
full-duplex

abstract: Cognitive radio had been proposed as a methodology for overcoming the inefficiency of the conventional static allocation of the available spectrum in wireless communication networks. The majority of opportunistic spectrum access schemes in cognitive radio networks (CRNs) rely on the Listen-Before-Talk (LBT) model due to the half-duplex nature of conventional wireless radios. However, LBT su ers from the problem of high collision rates and low secondary user throughput if time is misaligned among the secondary users (SUs) and the primary users (PUs). This problem can be mitigated by leveraging full-duplex (FD) communications that facilitate concurrent sensing and transmission. This thesis considers the problem of optimal opportunistic multi-channel spectrum sensing and access using FD radios in the presence of uncertain primary user (PU) activity statistics. A joint learningand spectrum access scheme is proposed. To optimize its throughput, the SU sensing period has to be carefully tuned. However, in absence of exact knowledge of the PU activity statistics, the PU's performance may be adversely a ected. To address this problem, a robust optimization problem is formulated. Analysis shows that under some non-restrictive simplifying assumptions, the robust optimization problem is convex. The impact of sensing periods on the PU collision probability and the SU throughput are analyzed, and the optimal sensing period is found via convex optimization. An "\epsilon-greedy algorithm is proposed for use by the SU to learn the PUs' activity statistics in multichannel networks. It is shown that sublinear regrets can be attained by the proposed estimation and robust optimization strategy. Simulation studies demonstrate that the resulting robust solution achieves a good trade-o  between optimizing the SU's throughput and protecting the PU.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Role of the GABARAP Tumor Suppressor in the Control of E.R. Stress and Cell Apoptosis

contributor:
Bédard, André
Campos, Ana
Biology

subject:
GABARAP
Endoplasmic Reticulum
Unfolded Protein Response
Stress
Autophagy
CHOP
Apoptosis

abstract:
In response to starvation, mis-folded proteins accumulate in the endoplasmic reticulum (E.R.) causing E.R. stress. This triggers a series of signaling pathways known as the unfolded protein response (UPR). The response helps to both enhance protein folding capacity and initiate mis-folded protein degradation, reducing E.R. stress. Alternatively, misfolded proteins are degraded and nutrients are recycled through autophagy. Thus, E.R. homeostasis depends on both UPR and autophagy. However, if E.R. stress is not resolved, UPR and autophagy can also cause apoptosis by mechanisms that are not fully understood. In chicken embryo fibroblasts, gamma-aminobutyric acid receptor-associated protein or GABARAP (a protein involved in autophagy) can promote apoptosis in conditions of prolonged starvation (Maynard et al. 2015). In these conditions, the down-regulation of GABARAP by shRNA/RNA interference reduces the expression of the pro-apoptotic CHOP (CAAT-enhancer-binding protein homologous protein) transcription factor (a marker of E.R. stress) and enhances cell survival. This suggests that elevated levels of autophagy compromises E.R. homeostasis and promotes the expression of CHOP in UPR lethal pathways. While GABARAP induction and processing/activation has been linked to the expression of CHOP upon prolonged starvation (Maynard et al. 2015), nothing is known about the pathway mediating CHOP expression and the relationship with other pathways of the UPR in cells with GABARAP mis-expression. Understanding these pathways will allow us to determine if GABARAP is a general determinant of E.R. stress or acts specifically on the expression of CHOP to control cell survival.
Elucidating mechanisms which are involved in E.R. stress and the cellular transition between pro-survival to pro-apoptotic roles can allow understanding of processes associated with several pathological conditions like cancer and neuro-degenerative diseases. Additionally, establishing a role for GABARAP tumor suppressor in the control of the UPR and cell fate is also important.

abstract: Thesis

abstract: Bachelor of Science (BSc)

abstract: In response to starvation, mis-folded proteins accumulate in the endoplasmic reticulum (E.R.) causing E.R. stress. This activates both the Unfolded Protein Response (UPR) and Autophagy as both processes help to reduce E.R. stress. GABARAP, a protein involved in autophagy, has been shown to be involved in the promotion of apoptosis in conditions of prolonged starvation as its downregulation reduces apoptosis and CHOP expression (Maynard et al. 2015). However, how GABARAP regulates apoptosis remains unknown.  Here, we investigate if GABARAP mis-expression affects multiple pathways in the UPR relieving global E.R. stress or if its specifically involved in blocking CHOP expression.


title: PALEOHYDROLOGIC RECONSTRUCTION OF YAX CHEN CAVE (YUCATAN PENINSULA, MEXICO) IN RESPONSE TO HOLOCENE CLIMATE CHANGE

contributor:
Reinhardt, Eduard
Earth and Environmental Sciences

subject: Yucatan Peninsula

abstract:
Four sediment cores and ten sediment trap samples were collected from Yax Chen cave, part of the Ox Bel Ha cave system on the Yucatan Peninsula in Mexico, for microfossil and micro-XRF geochemical analysis. In cores, Cl ̄trends (measuring salinity changes in meteoric water mass) show a direct relationship with microfossil (specifically the foraminifer Elphidium spp.) and weathering proxies (K, Ti, and Fe) used for measuring wet/dry conditions. Micro-XRF measurements of Cl ̄are derived from pore water in the cores, allowing for a more accurate observation of change in the cave system. Conversely, weathering proxies are measured from transported sediments.
All four cores show a general decrease in groundwater salinity up core. Two of the cores, which were collected above the present halocline (~11m), show salinity changes in the meteoric water mass. One core was collected at the halocline and measures its movement in response to precipitation and Holocene sea-level rise. These findings are in agreement with other studies from the Yucatan coast (e.g. cenotes Aktun Ha and Sac Actum) as well as other paleoclimate records in the region. Additionally, these findings correlate with archaeological evidence, revealing several droughts that occurred throughout late Pre-Classic to late Classical Maya. High resolution analysis of Cl ̄offers new insights on how coastal aquifers respond to climate change and may have implications for regional archaeology. The use of micro-XRF geochemical analysis is an effective tool which can be used to understand the spatial and temporal complexities of Yucatan coastal aquifers.

abstract: Thesis

abstract: Master of Science (MSc)


title: Prospects for Sustainable Micro-Factory Retailing in Canada: A Case Study of 3D Printed Electric Vehicles

contributor:
Newbold, K. Bruce
Geography

subject:
Micro-Factory Retailing
Sustainable Automobility
Electric Mobility
Electric Vehicles
Additive Manufacturing
3D Printing
Direct Digital Manufacturing
Product-Service System
Business Model Innovation
Industrial Ecology
Biomimicry
System Innovation
Multi-Level Perspective
Canadian Auto Industry

abstract: The contemporary global automotive industry has persisted, relatively unchanged, since its inception over a century ago. However, it appears that major changes may be underfoot with increasing environmental, social, and economic pressures to improve the industry's long-term sustainability. An alternative model, known as Micro-Factory Retailing (MFR), guided by the emerging field of Industrial Ecology (IE) has been proposed as a possible solution to the industry’s sustainability crisis. This thesis will explore the prospects of MFR in Canada and propose the use of 3D printed electric vehicles as a means to facilitate sustainable system innovation. To demonstrate the feasibility of this proposed technological pathway, three entrepreneurial firms attempting to disrupt the way in which cars are made, sold, and used will be studied. Although the timeline of such a major transition is currently unknown, Canada should act proactively to transition its role in the global automotive sector and lead the way towards a more sustainable automotive ecosystem through MFR.

abstract: Thesis

abstract: Master of Science (MSc)


title: THE EFFECT OF TOOL EDGE RADIUS ON CUTTING CONDITIONS BASED ON UPDATED LAGRANGIAN FORMULATION IN FINITE ELEMENT METHOD

contributor: Mechanical and Manufacturing Engineering

subject: UPDATED LAGRANGIAN FORMULATION, FEA, Metal Cutting

abstract: Tool wear is a significant problem for manufacturing companies and represents a major challenge in their operations, but it is also a way they can gain a competitive advantage.  To do this it is important to set up a standard procedure to develop high performing tooling. This thesis outlines how the Finite Element (FE) method can be used to understand and develop tool geometry. FE based simulation, as a numerical method, is a reliable method to assess the performance of a cutting tool before conducting machining tests based on the force and temperature profile predicted by the FE model. Defining a mathematical model which can be used as a built-in algorithm for tool wear prediction is very challenging and time consuming. Instead there is a possibility of using other factors such as stress distribution and temperature profile and correlate them to tool wear. In this research, the performance of different tool edge radius in cutting has been studied through experiments and in parallel Updated Lagrangian Models have been developed through ABAQUS/EXPLICIT for various cutting conditions, and experimental data was used to validate the data that has been generated from the finite element models. These models are very convenient to develop and capable of being applied for other types of material and cutting conditions. Thus, they represent an efficient way to reduce the amount of experiments needed to improve a tooling, the machining process, and thereby provide an effective way to increase the machining productivity of manufacturing companies.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Decentralized Crash-Resilient Runtime Verification

contributor:
Bonakdarpour, Borzoo
Computing and Software

subject: Runtime Verification, Distributed Monitoring, Linear Temporal Logic, Fault Tolerance

abstract: This is the final revision of my M.Sc. Thesis.

abstract: Runtime Verification is a technique to extract information from a running system in order to detect executions violating a given correctness specification. In this thesis, we study distributed synchronous/asynchronous runtime verification of systems. In our setting, there is a set of distributed monitors that have only partial views of a large system and are subject to failures. In this context, it is unavoidable that monitors may have different views of the underlying system, and therefore may have different valuations of the correctness property. In this thesis, we propose an automata-based synchronous monitoring algorithm that copes with f crash failures in a distrbuted setting. The algorithm solves the synchronous monitoring problem in f + 1 rounds of communication, and significantly reduces the message size overhead. We also propose an algorithm for distributed crash-resilient asynchronous monitoring that consistently monitors the system under inspection without any communication between monitors. Each local monitor emits a verdict set solely based on its own partial observation, and the intersection of the verdict sets will be the same as the verdict computed by a centralized monitor that has full view of the system.

abstract: Thesis

abstract: Master of Science (MSc)


title: White Antiracism in Southern Ontario: Frames, Praxis and Awareness

contributor:
McLaughlin, Neil
Sociology

subject:
White antiracism
Activism
White racial identity
Whiteness
Hamilton, Ontario, Canada
Frames
Praxis
Action
Strategies
Racial awareness
Enablers
Obstacles
Racism

abstract:
There has been an increase in reactionary racial violence in the past eight years following the presidency of Barack Obama, and in response to perceived threats to the racial and cultural order posed by movements for racial justice and the refugee crisis. Complicit to the spate of organized racial violence are passive white bystanders, who, through their inaction, have tolerated and given free reign to a resurgence of racial violence. Only a minority of whites have responded to calls for solidarity from Black, Indigenous and People of Color (BIPOC). This study set out to uncover how these minority of whites respond to racism.

Drawing on narratives and questionnaires of thirty-eight white persons, I begin with an exploration of the frames that shape participants’ understanding of antiracism. Three frames are discussed: the (a) equality and human rights frame, (b) anti-oppression frame, and (c) whiteness-centered frame.

The core of this study is on antiracism praxis. I discuss two categories of praxis: quotidian antiracism and organizational antiracism. In the former category are three types of antiracism strategies: (a) confrontation, (b) counterclaiming, and (c) covert and clandestine antiracism. The latter category consists of equality and equity focused strategies in education that I distinguish based on setting: (a) classroom antiracism and (b) administrative antiracism. This discussion is enriched by an investigation of the enablers and obstacles of antiracism and what respondents consider when deciding to engage in bystander action.

In conversation with Frankenberg’s (1993) ‘race-cognizance’ concept, I present a subsidiary antiracism awareness that I call self-implication cognizance. I detail five ways participants stop themselves from ‘racing to innocence’ by implicating themselves in the hegemonic order of whiteness.

This study contributes a typological model of frames and praxis and a situated picture of enablers of antiracism to the scholarship of white antiracism. It also offers insights for progressive whites and organizations interested in racial justice, equality and equity.

Subject keywords: antiracism, activism, whiteness, white racial identity, racial awareness, frames, enablers, obstacles, racism

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Crystal Growth and Neutron Scattering Study on High Tc Superconductors La_{1.6-x}Nd_{0.4}Sr_{x}CuO_{4}

contributor:
Gaulin, Bruce
Physics and Astronomy

subject: Superconductivity Cuprate

abstract:
Superconductivity has been a topical dicovery of materials research and condensed
matter physics since its discovery in 1911. It has seen applications appear within
cutting edge technology, yet the mechanism for this exotic quantum phenomena remains
unclear. This thesis is centred on the preliminary study on one family of the cuprate
high Tc superconductors, the La1.6−xNd0.4SrxCuO4 (Nd-LSCO) system. We were
able to synthesize single phase polycrystalline material of Nd-LSCO across its phase
diagram from x   0.02 to x   0.4. We were also able to grown three large, high quality
single crystal samples of this system at high doping, for the first time. Large single
crystals of La1.6−xNd0.4SrxCuO4 (x=0.17, 0.19 and 0.24) were successfully grown using
the traveling solvent floating zone technique. This thesis focuses on an introduction
to the relevant materials preparation and crystal growth techniques and a discussion
of some of the characterization of the samples which necessarily is involved in such a
systematic study.

abstract: Thesis

abstract: Master of Science (MSc)


title: Regulation of S-Adenosyl-L-Methonine Phosphoethanolamine-N-Methyltransferase Activity in Spinach

contributor:
Weretilnyk, Elizabeth
Science

subject: solute glycine betaine, chloine,metabolite,methionine, phosphoethanolamine

abstract: The compatible solute glycine betaine accumulates in many plants including spinach (Spinacea oleracea) under conditions of water deficit stress. The precursor to glycine betaine is choline, a ubiquitous metabolite in plants as a component of phosphotidylcholine. In spinach choline is synthesized from phosphocholine, a product of three sequential N-methylations of phosphoethanolamine catalysed by the cytosolic enzyme S-adenosyl-L-methionine: phosphoethanolamine-N-methyltransferase (PEAMT). PEAMT activity shows diurnal changes with peak activity at the end of the photoperiod and a decrease overnight. The activity of this enzyme is up-regulated 2 to 3-fold in salt-stressed plants relative to unstressed plants. The objective of this thesis is to determine how PEAMT activity is regulated in vivo. Thus, PEAMT activity, protein and transcript levels were quantified in spinach leaves from plants subjected to different light and salinity conditions. A spinach PEAMT eDNA sequence was used to over-express recombinant PEAMT in the protein expression vector pET30a (+). The presence of a polyhistidine-tag on the overexpressed protein allowed for purification by a cobalt metal affinity column. The affinity purified protein was used to produce polyclonal antibodies for immunoblot hybridization analysis. For these studies, PEAMT protein was first immunoaffinity purified from soluble extracts prepared from leaves and then the protein subjected to electrophoresis by SDS-p AGE. Enzyme assays and immunoblot analysis show PEAMT activity and protein levels increase and become relatively constant in leaves of plants exposed to continuous light. In continuous darkness, PEAMT activity and protein levels decrease and remain low and constant. Thus the pattern of changes in PEAMT activity levels are associated with changes in PEAMT protein levels. In contrast, Northern blot hybridizations show that under conditions of constant light, peamt transcript levels undergo cyclical changes with peak levels at 20 and 40 h and troughs at 28 and 52 h after the continuous light treatment was imposed. These peaks coincide with the dark and light cycles of the normal photoperiod. The same cyclical changes in peamt transcript levels was seen for plants transferred from a normal photoperiod to continuous darkness. Since these changes persist in the absence of a day/night cue we conclude that peamt transcript levels are circadian-regulated. The peamt transcript levels of control unstressed and salt-stressed plants also show circadian rhythms, however the levels found in salt-stressed plants were 0.5 to 2-fold higher than the controls. Therefore, while salinization of plants increases peamt transcript abundance, it does not alter the circadian rhythm that transcripts of this gene display. Changes in PEAMT activity and protein levels are likely controlled by other as yet unknown post-translational mechanisms, processes that override and obscure operation of a circadian rhythm in regulating the level of peamt transcripts.

abstract: Thesis

abstract: Master of Science (MS)


title: Dosage-Sensitive Modifiers of Slit Function in the Drosophila Embryonic CNS

contributor:
Jacobs, J. Roger
Biology

subject: drosophila Slit

abstract:
Genetic screens provide information on phenotype interactions as a step to uncovering functional interactions in vivo. In this study, I conducted genetic modifier screens in Drosophila that might reveal genes expressed in the embryonic CNS that interact genetically with slit. These screens include a blind genetic screen, stable line double mutant analysis, transheterozygote interactions and a dosage-sensitive dominant modifier screen. Differences in CNS phenotypes between the blind screen and the double mutant analysis were uncovered for some of the crosses, indicating background effects of genotype can influence phenotypes observed. A group of candidate genes were chosen based on motif composition for potential
interaction with slit, and spatial and temporal expression patterns coinciding with Slit. The
majority of these genes show a mutant CNS phenotype on their own. slit-interacting genes
were identified by their ability to alter midline axon guidance, as assayed with antibodies
specific to CNS-expressing proteins. The interacting genes include those encoding receptor and second messengers thought to function in growth cones, integrins and extracellular matrix proteins. From these interactions, I could then propose models of function in axon guidance. The first model I propose adds to a currently known repressor-derepressor model
of axon guidance at the midline of the CNS, involving the Netrin, Commissureless and
Robo signaling molecules, whereby Slit is locally suppressed by Netrin function to allow
axons to cross the midline via Comrnissureless-mediated intemalisation of Robo. In my
second model, Slit may also be involved in integrin signaling, especially through the αPS3
and βPS integrins, in concert with the Laminin molecule. Included in this model is the
intersection of cytoplasmic Dock signaling within the growth cone. Thirdly, I demonstrate
a genetic interaction with other molecules expressed by the midline glia, Masquerade, Toll
and Neurexin. Masquerade and Toll may function in a common pathway, but in parallel to
Slit function. Likewise, Neurexin may function in a parallel pathway to Slit. Slit has shown to interact genetically with a number of molecules that appear to be involved in different aspects of axon guidance. This study was meant to provide a survey of molecules that may functionally interact with Slit and provides a good basis upon which to explore the interactions in detail in future work.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characterization of S-Adenosyl-L-Methionine Phosphomethylethanolamine N-Methyltransferase from Spinach

contributor:
Weretilnyk, Elizabeth A
Biology

subject: metabolite, glycinebetaine, phospholipid,choline

abstract:
In response to salinity and drought, some higher plants accumulate the secondary
metabolite glycinebetaine which functions as a compatible osmolyte (Rhodes and
Hanson, 1993). Choline, a precursor of glycinebetaine (Rhodes and Hanson, 1993), is
also a component of a primary metabolite phosphatidylcholine, an ubiquitous membrane
phospholipid (Moore, 1982). In leaves of the glycinebetaine accumulator spinach,
choline is synthesized as phosphocholine (PCho) and PCho is synthesized by three
sequential N-methylations of phosphoethanolamine (PEA) ~ phosphomethyl-EA
(PMEA) ~ phosphodimethyl-EA (PDEA) ~ PCho. The methyl group donor is Sadenosyl-
L-methionine, SAM (Summers and Weretilnyk, 1993). The enzyme SAM:
PMEA N-methyltransferase (PMEAMeT) is suggested to N-methylate PMEA ~ PDEA
~ PCho (Weretilnyk and Summers, 1992).
A four-step strategy was developed for the partial purification of PMEAMeT on
the basis of PMEA-dependent methylations (PMEAMeT activity) that involved the
extraction of soluble leaf protein, ammonium sulfate precipitation, and column
chromatography on DEAE Sepharose, Phenyl Sepharose and High Q Anion matrices.
PDEA-dependent methylating activity co-purified with PMEAMeT activity which
suggested PMEAMeT may N-methylate PMEA ~ PDEA ~ PCho. PMEAMeT was
purified 43-fold and has specific activities of 14.7 and 18.0 nmol•min-1•mg-1 protein with
PMEA and PDEA as substrates, respectively. Thin layer chromatography was used to
identify the reaction products formed during the 30 minute assay incubation: with PMEA
as the substrate, PDEA and PCho were detected in a ratio of 9: 1 as products; and with
PDEA as the substrate, PCho was detected as the only product.
PMEAMeT was estimated to have a native molecular mass of 76 kDa by HPLC
gel filtration chromatography. Both PMEA and PDEA N-methylating activities have an
alkaline pH optimum between 8.5 and 9.0 in 0.1 M Tris-HCl buffer. Neither activity was
iii
affected by the omission of Na2-EDT A from the assay. The addition of 10 mM Mg2+ to
the assay inhibited PMEA and PDEA-dependent methylation by approximately 49% and
32%, respectively; whereas, the addition of 1 and 10 mM Mn2+ to the assay completely
inhibited both activities.
Both activities were inhibited by the reaction products S-adenosyl-Lhomocysteine
by over 90% at 0.2 mM and PCho by approximately 80% at 10 mM. Of
the products ofPCho hydrolysis, choline inhibited PMEA-dependent methylation by 10%
at 10 mM; whereas, Pi inhibited PMEA and PDEA-dependent methylation by 38 and
19%, respectively at 10 mM. The compatible osmolyte glycinebetaine inhibited PMEA
and PDEA-dependent methylation by between 20 and 30% at 140 mM; however, the
inibition of PMEA-dependent methylation can be partly accounted for by the presence of
cr ions in the assay. If present at these concentrations in the same subcellular
compartment, these metabolites could serve as regulators ofPMEAMeT activities in vivo.
Study of PMEAMeT contributed to identifying the number of enzymes that Nmethylate
PEA ~ PMEA ~ PDEA ~ PCho and possible regulatory metabolites for
choline biosynthesis in vivo. These data are pertinent to basic research and also to
genetic-engineering studies aimed at introducing the glycinebetaine-accumulating trait
into crop plants as an approach to enhancing osmotic-stress resistance.

abstract: Thesis

abstract: Master of Science (MSc)


title: Inferential Latent Variable Models for Combustion Processes

contributor:
MacGregor, John F.
Chemical Engineering

subject: inferential, latent, variable models, combustion processes, multivariate analysis, energy costs, lime kiln operation

abstract:
This thesis investigates the application of latent variable methods to three combustion
processes. Multivariate analysis of flame images and process data is performed to predict
important quality parameters and monitor flame stability. The motivation behind this work is to decrease operational costs and greenhouse gases in these energy intensive processes. The three combustion processes studied are a lime kiln, a basic oxygen furnace and a coal-fired boiler. In lime kiln operation, the main goal is to stabilize final product temperature in order to reduce fouling and energy costs. Due to long process dynamics, prediction of product temperature is required at least one hour in advance for potential use in a control scheme. Several methods for extracting features from flame images were investigated for the prediction of the temperature. The best method is then combined with process data in a PLS
model that also incorporates dynamic information. The analysis revealed that prediction one hour into the future is successful using latent variable methods. In the basic oxygen furnace analysis, the main goal is to predict end-point carbon of the batch process. Termination of the batch as soon as the desired carbon is attained reduces oxygen consumption and thus operational cost. Traditional image analysis is used to identify a constant field of view in the flame images. Multivariate image feature extraction methods were then used in combination with process data to successfully predict the final carbon
content of the heat. The coal-fired boiler analysis focuses on monitoring of flame stability at different production and air to fuel levels of the boiler. Prediction of energy efficiency and off-gas chemistry from flame images is also investigated. An unexpected result was the ability to use the installed cameras for localized fouling monitoring. This thesis showed that the use of multivariate analysis of flame images and process data in combustion process is very promising.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Rules of Engagement

contributor:
Freeman, Bonnie
Social Work

subject:
child protection
engagement

abstract: The first version that was uploaded to Macsphere was the incorrect version.  I was advised to re-upload the correct version.

abstract:
This research project interviewed child protection workers to understand how they used strengths-based theory and the Signs of Safety model in practice to facilitate engagement and build rapport with families. In addition, child protection workers were asked for their definitions of engagement and rapport building, since these concepts have multiple definitions in child welfare. In semi-structured individual interviews, child protection workers provided their perspectives regarding what fostered or hindered their efforts to engage with families. A structural and critical lens was applied to the analysis of the data, to reveal what organizational and relational factors positively or negatively influenced engagement.
This study found that all workers identified strengths-based theory and the Signs of Safety model as producing positive outcomes. The workers‟ descriptions of strengths-based practice included positive aspects such as being forthright about their role and their mandate, and working from the family‟s strengths instead of focusing solely on risk. Workers‟ responses regarding the Signs of Safety model varied. Two workers were from an agency (CAS-A) that promoted and used Signs of Safety with families, and two workers were from an agency (CAS-B) that had just began to use the model in settings with colleagues. Workers‟ descriptions of the model were positive and highlighted the collaborative aspects of the model, its inclusion of the family in planning, and affording the workers with a balanced assessment that contained elements of safety and risk.
In contrast, this study found that despite the strengths-based focus of these approaches, they had limitations. Workers described factors within and external to the worker/client relationship that influenced whether or not workers would use either approach. All workers discussed instances when engagement with a family was not successful, and consistently
MSW Thesis – L.A. Mabo McMaster School of Social Work
iv
described client resistance as a barrier to the process. However, this study found that client resistance was connected to power dynamics present in the worker/client relationship, and the dual role workers had to assume to do their job and satisfy their agency mandate.
The workers interviewed for this study described reverting to their role of investigator, when the family was resistant. This study found that a worker‟s authority was implied, and related to a family‟s feelings of powerlessness and fear. All workers provided examples of both types of resistance. As a result, this study concluded that strengths-based approaches could not address the issue of power, and were effective only with the family‟s cooperation.
Workers described wanting to apply strengths-based approaches but felt overwhelmed by organizational factors such as time constraints due to caseloads, and excessive administrative burden. This study found that these factors were influenced by Provincial policy, which emphasizes productivity and cost efficiency over family engagement. Workers identified lack of agency support to apply strengths-based approaches as a barrier, with the exception being CAS-A, that promoted the Signs of Safety model and permitted its workers to be interviewed for this study.
The findings of this study have direct implications for practice and future research. To address the issues identified by this research, practice and policy may need to be modified to promote strengths-based practices to offer services that will meet the needs and safety of the child and family. Further research is recommended, with a larger sample from an agency that uses strengths-based practice and the Signs of Safety model, to determine whether positive outcomes can be linked with these approaches. It is also recommended that research include the perspectives of child protection workers and families.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Purificaation and Properties of S-Adenosyl-L-Methonine: Phosphomethylethanolamine N-Methyltransferase from Spinach

contributor:
Weretilnyk, Elizabeth
Biology

subject: spinach phosphomethylethanolamine

abstract: Under conditions of osmotic stress such as drought and salinity, many plants accumulate compatible organic solutes such as glycine betaine (Rhodes and Hanson, 1993). The primary metabolite choline is a precursor for glycine betaine synthesis in addition to being a component of phospholipids. In spinach leaves, choline synthesis involves three sequential N-methylations of phosphoethanolamine (PEA) in order to generate phosphocholine (PCho) via the pathway PEA -+ phosphomethylethanolamine (PMEA) -+ phosphodimethylethanolamine (PDEA) -+ PCho. The S-adenosyl-L-methionine (SAM) dependent N-methyltransferase phosphomethylethanolamine N-methyltransferase (PMEAMeT) can catalyze two of the three sequential steps: PMEA -+ PDEA -+ PCho (Dhadialla, 1999). This thesis describes a seven-step strategy for PMEAMeT purification from spinach leaves and provides evidence for the existence oftwo distinct enzymes with apparently overlapping capacities to use both PMEA and PCho as substrates. A seven step purification strategy was used in this project which included the initial four-step strategy used by Dhadialla ( 1999) to partially purify PMEAMeT approximately 70-fold. The seven steps included precipitation of soluble leaf protein from spinach leaves by 1.8-2.6M (NH^4)^2SO^4 fractionation followed by open column chromatography on DEAE Sepharose CL-6B, Phenyl Sepharose CL-4B, Macro-Prep® High Q, and Sephacryl S-100, then high performance chromatography on Mono QHR 5/5 and Protein Pak SW-300. The highest fold purifieation achieved for PMEAMeT was 7,507-fold and yielded a specific activity of 3,243 nmol min^-1 mg^-1 protein. SDS-PAGE analysis of this sample and silver staining of the polyacrylamide gel revealed that approximately 15 polypeptide bands are present in this sample and included two polypeptides with estimated molecular masses of 30 and 50 kDa. Anion exchange chromatography on a Mono Q matrix followed by photoaffinity cross-linking with aliquots of individual fractions shown to have high PMEAMeT activity, shows that the 30 and 50 kDa photoaffinity cross-linked species can be partially resolved from each other by this matrix. This observation is best explained if the two polypeptides are not subunits of the same methyltransferase enzyme. Evidence that both the 30 and 50 kDa [^3H]SAM-binding polypeptides contribute to PMEAMeT activity was provided by showing that the inclusion of either PMEA or PDEA in the photoaffinity cross-linking assay prevented the binding of [3H]:;AM to either polypeptide; a result consistent with PMEA and PDEA serving as substrates for the enzyme(s) associated with both polypeptides. In addition, the presence of PEA in the photoaffinity cross-linking assay did not prevent the binding of [^3H]SAM to either polypeptide showing that in these species cross-linking is not prevented by phosphobases that are not suitable substrates for PMEAMeT. This report describes for the first time the existence of two enzymes in spinach leaves that possess PMEAMeT activity. The role of these enzyme(s) in spinach might involve the maintenance of low PMEA and PDEA pool sizes. Low pools for these metabolites may be required to prevent the incorporation of PMEA and PDEA into the polar head groups of phospholipids in place of PCho. Whether the substitution of PMEA or PDEA for PCho is deleterious to phospholipid structure or function in plant membranes is unknown.

abstract: Thesis

abstract: Master of Science (MSc)


title: Frequency-Domain Self-Adjoint S-Parameter Sensitivity Analysis for Microwave Design

contributor:
Nikolova, Natalia K.
Electrical and Computer Engineering

subject: frequency-domain, self-adjoint, s-parameter, sensitivity, microwave design, electromagnetic, optimization, finite-element simulator

abstract:
 This thesis proposes a sensitivity solver for frequency-domain electromagnetic (EM) simulators based on volume methods such as the finite-element method (FEM). The proposed sensitivity solver computes S-parameter Jacobians directly from the field solutions available from the EM simulation. It exploits the computational efficiency of the self-adjoint sensitivity analysis (SASA) approach where only one EM simulation suffices to obtain both the responses and their gradients in the designable parameter space. The proposed sensitivity solver adopts the system equations of the finite-difference frequency-domain (FDFD) method.

 There are three major advantages to this development: (1) the Jacobian computation is completely independent of the simulation engine, its grid and its system equations; (2) the implementation is straightforward and in the form of a post-processing algorithm operating on the exported field solutions; and (3) it is computationally very efficient-time requirements are negligible in comparison with conventional field-based optimization procedures utilizing Jacobians computed via response-level finite differences or parameter sweeps.

 The accuracy and the efficiency of the proposed sensitivity solver are verified in the sensitivity analysis and the gradient-based optimization of filters and antennas. Compared to the finite-difference approximation, drastic reduction of the time required by the overall optimization process is achieved. All examples use a commercial finite-element simulator.

 Suggestions for future research are provided.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Oxygen and Carbon Stable Isotope Analysis of the Otoliths of Atlantic Cod (Gadus Morhua L.)

contributor:
Schwarcz, H.P
Geology

subject: oxygen, carbon stable isotope, otoliths, Gadus morhua

abstract:
The purpose of this study was to apply oxygen and carbon stable isotope microsampling
techniques to the seasonal banding of the otoliths of the Atlantic cod, Gadus morhu~ in order
to determine their potential use in reconstructing the environmental conditions experienced by
cod. A reconstruction of the changes in environmental temperature is seen as particularly
applicable to the determination of cod migration routes based on the known temperature profile
of the North Atlantic. Transverse thin sections of six otoliths from cod taken off the coast of
Atlantic Canada were prepared using standard methods. Material was sampled from each semiannual
band of the otoliths and run on a Finnigan MAT 251 ratio mass spectrometer to determine
0180 and 013C.
The results for 0180 indicated that the otoliths had an approximate initial value of either
1.4%o or l.O%o for sample material taken from the nucleus. The 0180 signal was characterized
by oscillating values in which sample material from hyaline bands corresponded predominantly
with the troughs and sample material from the opaque bands corresponded with the peaks. The
average range of 0180 was found to be 0.87%o corresponding to a temperature range of 3.6°C
which was within the expected 3 to 4 °C seasonal average temperature shift experienced by cod.
Seasonal cycling was apparent in three of the otoliths, with semi-annual values alternating
between high opaque bands and low hyaline bands.
It was concluded that seasonal temperature changes due to migration from offshore to
inshore waters are recorded in the 0180 signal and that future sampling should attempt to resolve
several samples within each seasonal band in order to resolve the migratory changes in temperature on an sub-annual basis. It is also suggested that experiments be carried out to
determine the species specific 0180 versus temperature relationship for cod to make accurate
interpretation of the data possible.
The o13C signal was found to be characterized by an increasing logarithmic trend in o13C.
The 013C signal was observed to increase over the first three years of growth and to level off at
age 4 and fluctuate at a value close to O%o. The otoliths of cod were found to contain a high
proportion of inorganic carbon with a minimum 013C value of -4.53%o and a maximum of 0.23%o.
It was suggested that the initial increase in 013C was a product of a combination of factors
affecting metabolic rate and therefore, indirectly, the amount of metabolically derived carbon
circulating in the blood. It was concluded that further research into the growth and development
of cod was necessary in order to reach a comprehensive understanding of the biological processes
responsible for the observed trends in 013C.
0180 was plotted against 013C for samples from growth bands of age four or greater and
found to have a positive correlation with a slope of 0.269 (S.E. 0.049) and an r-squared of 0.537,
P < 0.0001 when the results for otolith 176 were excluded due an anomalous trend in that data
set. Two hypotheses were suggested to account for the observed positive correlation, a
metabolic/temperature effect, and a depth/temperature effect.
It was concluded that, with further research into the controlling factors behind the
fluctuations in 013C, the 013C signal may provide a second source of information with regards to
changes in habitat and environmental characteristics over the life time of the cod. It is suggested
that a study be carried out to determine the amount of metabolic carbon incorporated into the
otolith in order to clarify the observed trends.

abstract: Thesis

abstract: Candidate in Philosophy