title: Subalpine Spruce Forest Carbon Flux: The Role of Hylocomium Splendens

title: Ecosystem Carbon Flux: The Role of Hylcomium Splendens

subject:
forest
carbon
spruce
hylocomium
hylocomium splendens

abstract: Pulse release and uptake of carbon by forest floor Hylocomium splendens moss mats was examined in a subalpine white spruce/subalpine fir forest. Optimal conditions for net photosynthesis in Hylocomium splendens were 14 °C, 240-480 μmol m⁻² s⁻¹ and between 200-400% water content by weight. These conditions were rarely met under field conditions. However, release of CO₂ from organic soils frequently elevated CO₂ concentrations within moss mats by up to 200 ppm CO₂ above ambient, suggesting that elevated CO₂ concentrations within forest floor moss mats may counteract the effect of suboptimal microclimate conditions experienced by Hylocomium splendens, allowing it to achieve positive carbon balance under a much wider range of conditions. Observation in the summer of 1992 and 1993 show that pulse release of organics from Hylocomium splendens contributes between 10-110 mg ⁻¹ m⁻² total organic carbon (TOC) to groundwater leachate during the rehydration phase of every rain event. I hypothesize that mineralization of this TOC release and resaturation respiration from the moss mat contributes significantly to carbon cycling within mat environments. The pulse release of carbon may also have major influence on ecosystem function stimulating microbial decomposition, increasing net mineralization of nitrogen, and stimulating asymbiotic nitrogen fixation. Thus, Hylocomium splendens functions as both a source and sink for ecosystem carbon. It's most important contribution is that of an ecosystem capacitor. H. splendens accumulates gaseous carbon from the atmosphere through photosynthesis. Then, during rehydration, the bryophyte releases carbon in a water soluble form at concentrations higher than those found in the atmosphere.

abstract: Thesis

abstract: Master of Science (MS)


title: Characteristics of Endothelial Permeability in Tumours and the Role of Neutrophils

title: Endothelial Permeability in Tumours

contributor:
Arsenault, A. L.
Biology

subject: endothelial permeable tumour neutrophil

abstract: Vascular hyperpermeability is a common characteristic among many tumour types, especially those that grow in ascites form. With these, the exudate that flows out of the circulation collects as ascites fluid in the cavities within which these tumours are growing. In the past, this hyperpermeability has been attributed to the production of vascular permeability factor (VPF) by tumours. VPF has been found to bind to endothelial cells and lead to an increased vascular permeability. In the present study, the role of polymorphonuclear leukocytes (neutrophils) in tumour vascular hyperpermeability was investigated. Hey-3 tumour cells were grown into masses on the chick embryo chorioallantoic membrane (CAM). Interstitial neutrophilia was found to be a common feature at the tumour-host interface. Horseradish peroxidase was injected into the circulation and allowed to perfuse for five minutes. The density of labelled vesicles within the endothelial cell cytoplasm was calculated to be 0.99 +/-0.28 vesicles/μm². This vesicular density was comparable to that of N-formyl-methionine-leucine-phenylalanine (a chemotactic peptide for neutrophils)-treated CAM (1.04 +/-0.09 vesicles/μm²), but very different from control CAM (0.51 +/- 0.09 vesicles/μm²). In order to rule out any immune response to foreign cells, immune hepatocyte masses were grown on the CAM and vesicular density was calculated to be 0.54 +/-0.03 vesicles/μm². Through chemotaxis assays with the Boyden chamber, it was observed that Hey-3 tumour cells in culture were producing a chemotactic factor that is an attractant for human neutrophils. Once in the area, neutrophils do possess the potential to increase vascular permeability. Thus, neutrophils play a role in vascular endothelial hyperpermeability in tumours.

abstract: Thesis

abstract: Master of Science (MS)


title: The Effects of Food Quality on the Life History Tactics of the American Cockroach, Periplaneta americana

title: Effects of Food Quality on the American Cockroach

contributor:
Rollo, C. D.
Biology

subject:
food
quality
cockroach
periplaneta
periplaneta americana

abstract:
The American cockroach, Periplaneta americana, is an abundant and globally distributed species. Much of its success is attributed to its remarkable ability to alter rates and utilization efficiencies of behavioural and physiological processes so as to maintain growth and reproduction within nutritionally variable environments. This study utilized artificial diets diluted with cellulose to investigate the impact of food quality on the life history tactics of this species and the compensatory mechanisms
involved in offsetting these impacts. To investigate the impact of diet quality on the life history tactics of the American cockroach, seven dietary regimes were implemented. The control condition consisted of an unaltered 100% quality diet. The remaining six treatments were diluted with cellulose resulting in diet qualities of 50%, 25%, 10%, 5%, 2.5%, and 0%.
The parameters examined included mortality, longevity, instar number, instar durations, growth, maturation dates, maturation sizes, dry mass budgets, and reproduction. The dry mass budgets involved observations of growth rate, feeding rate, assimilation rate, respiration rate, assimilation efficiency, efficiency of conversion of ingested food into biomass, and efficiency of conversion of digested food into biomass. Reproductive studies entailed observations of oothecal production, oviposition intervals, inter-oviposition intervals, mass of oothecae, oothecal dimensions, egg number, oothecal cannibalism, and hatching dates. Strongly canalized development was achieved by resilient compensatory responses indicative of altered physiological and behavioural features. Cockroaches developed and reproduced adequately even when nutrient concentration was reduced to 25% of the controls. The declines in various key parameters were considerably less than expected from the degree of dietary dilution. In addition, elevated consumption and enhanced conversion efficiencies strongly suggest that cockroaches normally function at submaximal levels. The applied relevance of this research entails possible ramifications into the regulation and control of cockroaches. Furthermore, such knowledge enhances our understanding of not only diverse lifestyles but also the degree of variability to which insects may modify life history features in response to resource supply.

abstract: Thesis

abstract: Master of Science (MS)


title: The Development of Ion Regulation in Embryonic Rainbow Trout, Oncorhynchus mykiss

contributor:
O'Donnell, M. J.
McDonald, D. G.

subject:
trout
ion
ion regulation
embryo
oncorhynchus
oncorhynchus mykiss

abstract:
This study investigated the regulation of Na⁺ Ca²⁺ Cl⁻ during development in embryonic rainbow trout (Oncorhynchus mykiss). Because there is a close relationship between pH regulation and ion uptake mechanisms in adult teleosts, pH, pCO₂, and NH₄⁺ levels in unstirred layers (USLs) adjacent to whole eggs and dechorionated embryos were determined using double-barrel ion-selective microelectrodes (ISMEs).
Whole eggs accumulated Na⁺, Ca²⁺ and Cl⁻ during the last 20 days of embryonic development, suggesting an ionoregulatory ability prior to hatching. Na⁺ uptake by whole eggs was linearly related to external [Na⁺], suggesting that Na⁺ crosses the chorion by diffusion. The uptake by dechorionated embryos was saturable, indicating the presence of active transport or facilitated diffusion mechanisms on the surface of embryos prior to hatching. Ca²⁺ uptake by whole eggs and dechorionated embryos was saturable, suggesting that specific pathways or binding sites are present in the chorion, and that active transport or facilitated diffusion mechanisms are present at the surface of embryos. The much higher Jₘₐₓ for whole eggs than dechorionated embryos suggests a role of the perivitelline fluid (pvf) or chorion in ion uptake. Jₘₐₓ was lower in dechorionated embryos than in hatchlings suggesting that Ca²⁺ uptake mechanisms may not be fully developed in dechorionated embryos. Low pH and high [NH₄⁺] were measured in the USLs adjacent to whole eggs and dechorionated embryos, relative to the bulk water. A high Pcₒ₂ measured adjacent to the gills suggests that CO₂ excretion was the primary source of USL acidification. pH was lower in the USL adjacent to the gills and trunk than in the USL adjacent to the yolk sac. [NH₄⁺] was highest adjacent to the gills and trunk than adjacent to the yolk sac. There was no change in the extent of USL acidification or in [NH₄⁺] over the last half of embryonic development. After hatching, however, there was a significant increase in [NH₄⁺] adjacent to the gills, which was not accompanied by a change in USL pH. It is possible that a change in permeability of the transporting surfaces (i.e. gills, trunk, yolk sac) occurs after hatching.

abstract: Thesis

abstract: Master of Science (MS)


title: Arterial Compliance, Brachial Endothelial Function and Blood Pressure Adaptations to Resistance Training in Young Healthy Males

title: Arterial Adaptations to Resistance Exercise Training

contributor:
MacDonald, Maureen
Human Biodynamics

subject:
artery
endothelial
blood pressure
resistance
male

abstract: The current study evaluated the potentially detrimental effects of daily resistance training on cardiovascular health using a longitudinal study design. This study also addressed the effects of resistance training on vascular endothelial function. Recent cross-sectional studies have shown resistance trained individuals have reduced whole-body arterial compliance compared to sedentary controls and that the age-associated reduction of arterial compliance is augmented in resistance trained athletes. The effect of resistance training on vascular endothelial function has not been addressed to date in the literature. Twenty-eight young healthy males (age: 23±3.9 [mean±SD]) were whole body resistance trained five times a week for twelve weeks, using a split body design. Measurements of supine resting arterial blood pressure at the brachial artery, carotid, brachial and femoral cross-sectional compliance, and brachial vascular endothelial function (using flow-mediated dilation) were acquired prior to, halfway through and following the exercise training protocol. Strength of various body segments increased significantly following the resistance training program. Shoulder press one repetition maximum (1RM) lifts increased from 141.4±7.6 lbs. to 185.2±8.8 lbs. and double leg press 1RM from 483.0±29.0 lbs. to 859.8±52.1 lbs. Resting diastolic blood pressure increased significantly from Mid to Post training (61.8±1.3 mmHg to 65.4±1.2 mmHg) yet was not significantly changed from Pre values (62.9±1.2 mmHg). Pulse pressure was reduced significantly with exercise training by the Post training time-point (Pre 63.3±1.9 mmHg; Mid 59.0±2.4 mmHg; Post 53.7±2.8 mmHg). Mean arterial carotid and femoral artery diameters were not changed with resistance training; however, mean brachial artery diameter increased by the Mid training time-point and remained elevated at the Post training time-point (Pre 3.81±0.10 mm; Mid 4.03±0.1 0 mm; Post 4.04±0.11 mm). Cross-sectional compliance did not change at the carotid or the brachial arteries, however the femoral artery experienced a reduction of compliance by the Mid time-point that remained to the Post training time-point (Pre 0.162±0.012 mm²/mmHg; 0.125±0.013 mm²/mmHg; Post 0.129±0.015 mm²/mmHg). Brachial vascular endothelial function measured using flow-mediated dilation did not show a significant change with resistance training. When normalized for shear rate (which was also unaltered with resistance training) there were no changes in endothelial function. Peak and 1 0-s average brachial post-occlusion blood flow was enhanced with resistance training (Pre 247.5±14.0 ml/min; Mid 331.1±18.5 ml/min; Post 290.5±21.0 ml/min) possibly revealing enhanced resistance vessel function. In conclusion, resistance exercise training results decreased PP, reduced femoral compliance, an increase in mean brachial artery diameter and enhanced post-ischemic blood flow. The exact mechanisms responsible for such changes remain unknown and require further investigation.

abstract: Thesis

abstract: Master of Science (MS)


title: A Multichannel Single Fiber EMG Recording System

contributor:
DeBruin, H.
Electrical Engineering

subject: EMG multichannel fiber record

abstract: A multichannel single fiber EMG recording system has been developed and tested. This system is based on a multichannel needle electrode which has the ability to record EMG signals from multiple sites within the muscle under study without reinsertion. Therefore, not only is the recording volume of the electrode. increased but also enhancement of the single channel electrodes is possible through spatial filtering. The recording system, currently implemented on a PDP-11/34 computer, amplifies, filters and digitally stores the multichannel EMG signals for further signal processing. Signal processing techniques were developed to detect and extract motor unit action potentials from the EMG signal. Due to the large amount of data recorded by the multichannel electrode, slower sampling rates for digitizing the action potentials were required. Even with near Nyquist sampled signals the accuracy of this technique was shown to be nearly equivalent to conventional extraction of action potential features samples at four times the Nyquist rate. Finally, the problem of superpositioning of action potentials was addressed. By modifying the interpolation routine an algorithm for resolving superpositions was developed.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Characterization of Electrohydrodynamic (EHD) heat transfer enhancement mechanisms in melting of organic Phase Change Material (PCM)

contributor:
Cotton, James S.
Mechanical Engineering

subject:
Electrohydrodynamic
Phase change material
Octadecane
Thermal storage
Heat transfer enhancement
Shadowgraph
Melting
Numerical modelling

abstract:
The effect of using high voltage DC and AC on the heat transfer process during the melting of a Phase Change Material (PCM) in a rectangular enclosure was studied experimentally and numerically. The experiments were conducted for two configurations: (a) a horizontal rectangular enclosure in which the initial melting process is governed by heat conduction, (b) a vertical rectangular enclosure in which the initial melting process is governed by heat convection.
The level of heat transfer enhancement was quantified by using a novel experimental facility for the horizontal configuration. The experimental methodology was verified first against non-EHD melting cases and then was further expanded to include the EHD effects. The experiments showed that EHD forces can be used to enhance a conduction dominated melting up to a maximum of 8.6-fold locally and that the level of enhancement is directly related to the magnitude of the applied voltage. It was found that the main mechanism of enhancement in these cases can be attributed to the electrophoretic forces and that the role of the dielectrophoretic forces is minimal under the applied voltages.
In the vertical configuration, the effect of the magnitude of the applied voltage, the applied voltage wave-form, the gravitational Rayleigh number, Stefan number and the aspect ratio of the enclosure on the heat transfer enhancement were investigated experimentally. A novel shadowgraph experimental measurement system was developed and verified against the analytical correlations of natural convection in rectangular enclosures and the non-EHD melting performance was verified against the bench mark experiments of Ho (1984). The shadowgraph system was used to measure the local heat transfer coefficient across the heat source wall (the heat exchanger surface). The local heat transfer measurements along with the melting temporal profiles were used to explain and visualize the coupling between the Electrohydrodynamics (EHD) forces and the gravitational forces.
It was found that the EHD forces could still enhance the melting process even for an
initially convection dominated melting process. The mechanism of enhancement was found
to be a bifurcation of the initial convection cell into multiple electro-convective cells
between the rows of the electrodes. The shadowgraph system was used to assess the interaction between the electrical and the gravitational forces through the visualization of these cells and quantifying their size. The EHD heat transfer enhancement factor was found to increase by the increase of the applied voltage, reaching a 1.7 fold enhancement at the lower gravitational Rayleigh number tested and 1.45 fold for the highest gravitational Rayleigh and Stefan number. The effect of the polarity of the applied voltage was tested for the different cases and it was found that there was no significant difference between the positive and the negative polarities when the magnitude of the applied voltage was below 4 kV. At higher voltages- 6kV- the negative polarities showed better level of enhancement when compared to the positive applied voltage. It was again found that the main mechanism of enhancement is attributed to charge injection from the high voltage electrodes.
A scaling analysis was conducted based on the previous conclusions and the dominant mechanism of enhancement to describe the problem in non-dimensional form. An electrical Rayleigh number was introduced and its magnitude was correlated to the magnitude of the injected current. The melt volume fraction was then represented against the non-dimensional parameter (n+1)(H/W)Fo.Ste.RaE^0.25 and the melt fraction temporal profiles for the different voltages collapsed well against this parameter.
Finally, a numerical analysis was conducted on the role of the dielectrophoretic forces during the melting of Octadecane and when they would become of significant importance. The results of the numerical model supported the experimental findings and suggested that a minimum of 15 kV is needed in order to realize the effect of the dielectrophoretic forces. The numerical model was used to understand the interaction between the gravitational and the dielectrophoretic forces at different ranges of both gravitational Rayleigh number and electrical Rayleigh number. The model was complemented with scaling analysis to determine the governing scales of the problem and the dielectrophoretic Rayleigh number was deduced from the study.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Analysis of Rodent Mitochondrial and Nuclear DNA

contributor:
Golding, G. B.
Biology

subject: rodent mitochondria nuclear DNA

abstract:
Thesis
Master of Science (MS)


title: Informatic strategies for the discovery and characterization of peptidic natural products

contributor:
Magarvey, Nathan
Biochemistry and Biomedical Sciences

subject:
Natural Products
Cheminformatics
Bioinformatics
Data Science
Machine Learning

abstract:
Microbial natural products have served a key role in the development of clinically relevant drugs. Despite significant interest, traditional strategies in their characterization have lead to diminishing returns, leaving this field stagnant. Recently developed technologies such as low-cost, high-throughput genome sequencing and high-resolution mass spectrometry allow for a much richer experimental strategy, allowing us to gather data at an unprecedented scale. Naive efforts in analyzing genomic data have already revealed the wealth of natural products encoded within diverse bacterial phylogenies. Herein, I leverage these technologies through the development of specialized computational platforms cognizant of existing natural products and their biosynthesis in order to reinvigorate our drug discovery protocols.

As a first, I present a strategy for the targeted isolation of novel and structurally divergent ribosomally synthesized and post-translationally modified peptides (RiPPs). Specifically, this software platform is able to directly compare genomically encoded RiPPs to previously characterized chemical scaffolds, allowing for the identification of bacterial strains producing these specialized, and previously unstudied metabolites. Further, using metabolomics data, I have developed a strategy that facilitates direct identification and targeted isolation of these uncharacterized RiPPs. Through these set of tools, we were able to successfully isolate a structurally unique lasso peptide from a previously unexplored \textit{Streptomyces} isolate.

With the technological rise of genomic sequencing, it is now possible to survey polymicrobial environments with remarkable detail. Through the use of metagenomics, we can survey the presence and abundances of bacteria, and further metatranscriptomics is able to reveal the expression of their biosynthetic pathways. Here, I developed a platform which is able to identify microbial peptides exclusively found within the human microbiome, and further characterize their putative antimicrobial properties. Through this endeavour, we identified a bacterially encoded peptide that can effectively protect against pathogenic \textit{Clostridium difficile} infections.

With the wealth of publicly available multi-omics datasets, these works in conjunction demonstrate the potential of informatics strategies in the advancement of natural product discovery.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Biochemistry is the study in which life is built upon a series of diverse chemistry and their interactions. Some of these chemicals are not essential for the maintaining basic metabolism, but are instead tailored for alternative functions best suited to their environment. Often, these molecules mediate biological warfare, allowing organisms to compete and establish dominance amongst their neighbours. Understanding this, several of these molecules have been exploited in our modern pharmaceutical regimen as effective antibiotics. Due to the ever rising reality of antibiotic resistance, we are in dire need of novel antibiotics. With this goal, I have developed several software tools that can both identify these molecules encoded within bacterial genomes, but also predict their effects on neighbouring bacteria. Through these computational tools, I provide an updated strategy for the discovery and characterization of these biologically derived chemicals.


title: Lay Perceptions of Health and Health Care in Small Town Ontario

contributor:
Eyles, John
Geography

subject: perception health ontario

abstract:
The focus of this research is to examine people's perceptions around issues of health and health care. Using the qualitative research method of in-depth interviewing, the perceptions of twenty-four individuals are explored. This sample is taken from a middle class, white collar community in Southern Ontario. The major emphasis of this work is upon re-creating a human experience in order to come closer to understanding how people's attitudes and beliefs influence their health seeking behaviour.
This research found that health is a taken for granted state which is important for daily functioning. It is a difficult term for people to explain and it was found that changing the term to healthy made it easier for the informants to describe. Some of the determinants of health were explored and it was found that behaviours such as exercise, diet, and drinking alcohol as well as occupation and environment were all perceived as factors which could shape the types of illnesses people suffer. The only behaviour which was seen as a determinant of health was smoking. The informants saw other factors as having a greater influence on determining their health. These were fate, fault (blame), and family(heredity). This study also explored illness behaviour and perceptions about physicians and health care. People are aware of the signals that their bodies give thus signifying that something is wrong. People feel that they go to considerable extent in treating their own illnesses before they seek medical care. They also have expectations about their physician and failure of the physician to meet these expectations can result in a disruption in treatment or termination of the relationship. The Canadian health care system is seen by these informants as being the best in the world. People are very proud of this country's system for the delivery of health care. They are concerned about the health care crisis but perceive a reduction in government spending on health as being irresponsible. This work uncovers many of their ideas about problems in the delivery of health care services and possible solutions to these problems. This work seeks to contribute to the body of knowledge about lay perceptions. It is one of a few formal studies of its type done in Ontario. It represents an additional dimension to the investigation of the delivery of health services. By coming closer to understanding the human experience of health and health care, we can assist in creating a health care system that not only treats illness and diseases but also delivers health to all.

abstract: Thesis

abstract: Master of Arts (MA)


title: Encapsidation of RNA by VSV N Protein In Vitro

title: Encapsidation of RNA by VSV N Protein

contributor:
Prevec, Ludvik
Biology

subject:
RNA
VSV
protein
in vitro

abstract: Sequences at the 5' end of the nascent RNA are known to be important as signals for encapsidation of the genome of vesicular stomatitis virus. In order to define the specific sequences involved in this process and to develop an in vitro encapsidation system, in vitro transcription from SP64-based plasmids was used to synthesize RNA molecules corresponding to various portions of the viral 5' plus strand sequence. Some of these RNAs were tested for their ability to bind the capsid N protein in vitro. N protein in this assay was provided either from VSV mRNA programmed reticulocyte lysates or from infected cell extracts or, in collaboration with Dr. Sue Moyer (Gainesville, Florida), purified from viral nucleocapsids. This thesis describes the construction of the SP64-based plasmids and the use of their RNA transcription products in the experiments described above. I also constructed a series of plasmids that could direct the synthesis of RNA molecules which have many of the features of VSV defective particle genomes. Two of the constructs generate a defective-like RNA carrying a reporter gene capable of expressing the bacterial lac Z protein. These RNAs have the potential, after in vitro encapsidation and transfection into mammalian cells, of producing readily detectable helper-dependent virions.

abstract: Thesis

abstract: Master of Science (MS)


title: Exploring User Requirements for the Design of an Electronic Patient Decision Aid for Guardians Making Treatment Decisions about Congenital Adrenal Hyperplasia

contributor:
Braga, Luis
Lokker, Cynthia
Valaitis, Ruta
Agoritsas, Thomas
eHealth

subject: Patient Decision Aid

subject: Congenital Adrenal Hyperplasia

subject: Feminizing Genitoplasty

subject: Feminizing Genital Reconstructive Surgery

subject: Persona-scenario

subject: Requirements Analysis

abstract:
Congenital Adrenal Hyperplasia (CAH) describes a set of autosomal recessive diseases which affect enzymes mediating steroid biochemistry in the adrenal glands. In chromosomal females, the excess androgens associated with CAH cause virilization. Females with a high degree of virilisation can undergo feminizing genitoplasty in infancy or later in life. Parents and guardians are the medical proxies for their infants and therefore make decisions on their behalf. However, decision-making about feminizing genitoplasty can be very difficult. One tool that could help in such a situation is an electronic patient decision aid (PtDA). However, a PtDA for feminizing genitoplasty does not exist and there is insufficient information in existing literature to inform its design and development.
Thus, the objectives of this study were to:
(1)	Identify user requirements,
(2)	Develop specifications for the design and development of the PtDA, and
(3)	Understand the best way to implement and distribute the PtDA
We used the persona-scenario methodology to acquire user-requirements. Persona-scenario sessions were conducted with four parents of children with CAH, two adult patients with CAH, and four healthcare practitioners. Participants created fictitious personas, and scenarios wherein their personas interacted with an idealized version of the PtDA. Transcripts of these persona-scenarios and facilitator notes were analyzed to identify user-requirements, which were interpreted into specifications.
Participants provided user requirements about (1) information and decisional content in the PtDA, (2) proposed functionalities for the PtDA, (3) web usability, and (4) implementation context. Many of these requirements are supported by existing literature. The requirements identified in this project will inform the design and development of a PtDA for feminizing genitoplasty in patients with CAH. However, further research is necessary to understand how to best implement these requirements and to ensure that the gathered information is useful for a broad range of potential end users.

abstract: Thesis

abstract: Master of Science (MSc)


title: Effects of Feeding and Temperature on Acid-Exposed Juvenile Rainbow Trout (Oncorhynchus Mykiss Walbaum) During a Global Warming Scenario

title: Effects of Feeding and Temperature on Acid-Exposed Trout

contributor:
Wood, C. M.
Biology

subject:
rainbow trout
trout
acid
global warming
feeding
temperature

abstract: Juvenile rainbow trout were chronically exposed to acidified softwater, alone and in combination with a slight temperature increase in order to understand the possible effects of global warming and environmental acidification in freshwater fish. The second goal was to determine the role of diet in the response to acid stress and elevated temperatures. In the first two exposures, a simulated global warming scenario (+2°C) was applied for 90 days in winter (8-12 °C), in the presence and absence of sublethal acidity (pH 5.2). In the first trial, fish were fed to satiation twice daily, while in the second trial, fish were fed only 1% of their wet body weight every four days (~0.25% daily). A slight increase in temperature caused a marked increase in oxygen consumption, nitrogenous waste excretion and growth, although there did not appear to be any specific pH effects. During the Satiation Exposure, fish exposed to low pH especially at slightly elevated temperatures had increased appetites compared to non-acid exposed fish. This increased appetite suggested that NaCl losses brought about by low pH exposure, stimulated appetite in some way, thereby alleviating any ionoregulatory disturbances. During the Limited Ration Exposure, ionoregulatory disturbances occurred during low pH exposure, with more dramatic effects in fish at slightly elevated temperatures. Trout maintained on a limited diet had a higher mortality rate, lower plasma and whole body Na⁺ and Cl⁻ concentrations, and elevated cortisol levels compared with fish fed to satiation. Thus, it became clear that fish could use food to compensate for the stresses of increased temperature and low pH. The third exposure was conducted to determine whether food simply provided the necessary fuel to meet the increased cost of living in a low pH environment, or whether food directly provided the dietary salts necessary to replace branchial ion loss. Diets were formulated at two levels of energy (regular: 16.31MJ/kg or low: 9.77MJ/kg) and two levels of NaCl (regular: 263 mmols/kg or low: 43 mmols/kg) using a factorial design (2x2=4 treatments). In addition, a fifth group of fish were not fed during the exposure. All five groups of fish were challenged with pH 4.0 to induce a rapid ionoregulatory disturbance and then held at pH 5.2 for the next 28 days. During this month, fish were fed 0.6% of their body weight of one of the four diets. Fish fed the low salt diets incurred typical long-term ionoregulatory disturbances with decreased whole body Na+, K+ and Cl concentrations. These effects were not seen in fish fed regular salt diets, regardless of energy content, showing that it is the salt content of the food rather than the energy content which is critical in protecting against the deleterious effects of low environmental pH. Interestingly, fish fed the regular energy/low salt diet had high cortisol levels and increased mortality while fish fed the regular salt diets, low energy/low salt diets and starved fish did not have a high rate of mortality. These results may have been due to differences in metabolic rate and therefore oxygen consumption (M₀₂). Starved fish had the lowest M₀₂. Fish fed the regular energy diet had increased post-prandial M₀₂ due to the specific dynamic action evoked in fish by ingestion of protein-rich food. An increase in oxygen consumption may have caused an increase in branchial ion loss, thereby exacerbating the ionoregulatory deficit associated with chronic acid exposure. This is detrimental when dietary salts are unavailable to replace branchial losses. Overall, the salt content of food may play an important role in ameliorating the deleterious effects of chronic low pH, while the energy content of food may complicate the response.

abstract: Thesis

abstract: Master of Science (MS)


title: Electrophysiological and Ion Transport Characteristics of Cultured Branchial Epithelia from Freshwater Rainbow Trout

title: Studies on Cultured Freshwater Branchial Epithelia

contributor:
O'Donnell, M. J.
Wood, C. M.
Biology

subject:
ion
transport
rainbow trout
trout
electrophysiology
branchial epithelia

abstract:
Thesis
Master of Science (MS)


title: Effects of Exhaustive Exercise on Oxygen Consumption and Metabolism of Juvenile Rainbow Trout: An Evaluation of the O_2 Debt Hypothesis

title: O_2 Consumption and Metabolism of Trout After Exercise

subject:
exercise
oxygen
rainbow trout
trout
oxygen debt
metabolism

abstract: This thesis examined the effects of exhaustive exercise and post-exercise recovery on metabolism and respiratory gas exchange in juvenile rainbow trout, in relation to the classical oxygen (O₂) debt hypothesis (Hill & Lupton, 1923). The initial study was a detailed quantitative analysis of the metabolic cost of post-exercise recovery in terms of O₂ and ATP equivalents. A 5 min bout of exhaustive exercise resulted in about a 2.0-2.5 fold increase in O₂ consumption (MO₂), a 6-8 fold increase in whole-body lactate (LAC) levels and a near depletion in whole-body glycogen (GLY), adenosine triphosphate (ATP) and creatine phosphate (CP) stores. Recovery of MO₂, LAC and GLY was usually complete by 6 h, though GLY did not always return to resting levels. Recovery of resting whole-body ATP required 1.0-1.5 h, whereas restoration of CP required only 5 min. Quantitative budgets of the cost of recovery were prepared, based on two opposite assumptions. The first scenario (A) assumed that all the GLY resynthesized came from LAC, and that the remaining 25% of the total LAC cleared was oxidized. This scenario accounted for 48% of the excess post-exercise O₂ consumption (EPOC) and 94% of the ATP budget. The alternative scenario (B), attributed 100% of the EPOC to LAC oxidation (64% of the total LAC cleared), while the remaining LAC (36%) was resynthesized into GLY. As scenario B accounted for only 35% of the ATP budget, scenario (A) appeared more probable. Subsequent experiments attempted to experimentally dissociate LAC disappearance from EPOC, via repetitive exercise bouts and prior GLY depletion. A 2nd bout of exhaustive exercise, given 6 h after the 1st, significantly reduced EPOC by 40%, whereas metabolite status (LAC disappearance and GLY, ATP, and CP restoration) remained essentially unchanged. In contrast, prior GLY depletion by 5 days starvation significantly lowered the LAC burden while EPOC remained unchanged. Neither the two scenarios of the theoretical analysis could adequately explain the relationships between EPOC and the various metabolites. It is likely that some blend of the two approaches may be more realistic. Nevertheless, these approaches all point to the conclusion that the EPOC is not directly related to the metabolism of LAC after exercise in the rainbow trout. Thus, in contrast to the classical O₂ debt hypothesis, LAC disappearance does not determine the magnitude EPOC after exhaustive exercise in rainbow trout.

abstract: Thesis

abstract: Master of Science (MS)


title: Digital Signal Processing of Hemodynamic Singals

contributor:
Kamath, Markad
Electrical and Computer Engineering

subject: digital hemodynamic signal

abstract: Physiological signals when subjected to digital signal processing algorithms often reveal information about their origin and how they are regulated. Recently, it has been shown that when power spectrum of the heart rate variability signal is computed, physiological mechanisms about how the autonomic nervous system modulates the sinus node of the heart can be unraveled. During the past several years, computation of the power spectrum of heart rate variability has progressed from Blackman-Tukey algorithm and autoregressive modelling to Wigner-Ville distribution. In this thesis, we describe the development of appropriate algorithms for QRS detection from an ECG signal to obtain a heart rate signal, interpolation of heart rate variability signal and the computation of power spectrum. We also describe mathematical details underlying time-frequency analysis, specifically for the Wigner-Ville distribution. We present a software package in C++, for computing the Wigner-Ville distribution of the heart rate variability signal. As applications of these methods in physiology and clinical medicine, we found that the power spectrum of the heart rate variability of premature infants can help us understand the ontogeny of the autonomic nervous system. Similarly, physiological effects of atropine, methacholine and allergen challenges can be elucidated using the power spectrum of heart rate variability in small animals, such as a rat model. Furthermore, a progressive tilt model in human subjects is used to compare power spectrum obtained from the Blackman-Tukey method, autoregressive modelling and the Wigner-Ville distribution. Finally, an application of the Wigner-Ville distribution technique to study the changes that take place in the autonomic regulation of the heart during different stages of sleep is presented.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Effects of Chronic Cadmium Exposure on Juvenile Rainbow Trout: Protective Effects of Calcium and Application of Biotic Ligand Modelling

title: Effects of Chronic Cadmium Exposure on Trout

contributor:
Wood, C. M.
McDonald, D. G.
Playle, R. C.
Biology

subject:
chronic
cadmium
rainbow trout
trout
calcium
biotic
ligand

abstract: Juvenile rainbow trout were chronically exposed to cadmium in hard water, soft water, and in calcium-supplemented soft water in order to understand the effects of long term cadmium exposure in freshwater fish. A particular goal was to characterize changes in gill cadmium burden and the cadmium-binding properties of the gills during chronic sublethal exposures, so as to examine the applicability of the acute gill surface metal binding model or Biotic Ligand Model to trout chronically exposed to cadmium. Trout were exposed for 30 days to sublethal concentrations of cadmium in: a) moderately hard, Hamilton tap water (Ca = 1000 μM), b) synthetic soft water (Ca = 130 μM), or c) calcium-supplemented soft water (Ca = 260, 470, 770, and 1200 μM Ca). For both the hard and soft water cadmium exposures, no effects were observed on growth, swimming performance, and whole body ions. Growth and whole body and plasma Ca²⁺ concentrations were similar for all treatments in the calcium-supplemented soft water experiment; however, swimming performance was significantly reduced for the 470 μM Ca + Cd exposed fish. Acclimation to cadmium occurred in the hard water and lower concentrations of calcium-supplemented exposures but not in the soft water exposure. Cadmium accumulation was greatest in kidneys and gills and was directly related to cadmium exposure concentration. Tissue metal burdens were reduced with increased water calcium concentrations. Affinity of the gill for cadmium and the number of binding sites for cadmium decreased at higher water calcium concentrations. Affinity of the gill for Cd decreased with chronic cadmium exposure but binding site numbers increased with chronic Cd exposure. The acute gill binding model or Biotic Ligand Model, originally developed in soft water, was successfully applied to fish in both hard and soft water; however, complications arose when extending the model to fish chronically exposed to cadmium at various water calcium concentrations.

abstract: Thesis

abstract: Master of Science (MS)


title: The Development of a DC Micro-grid model with Maximum Power Point Tracking for Waste Heat Recovery Systems

contributor:
Cotton, James
Mechanical Engineering

subject:
DC-microgrid
Thermoelectric generators
TEG
Maximum power point tracking
MPPT
Energy management
Waste heat recovery
WHR
Load Matching
Load Shedding
Power losses

abstract:
Research in sustainable energy sources has become the interest of many studies due to the increasing energy demand and the amount of wasted energy released from existing methods, along with their effect on climate change and environment sustainability. Thermo-Electric Generators (TEGs) are a potential solution that is being studied and implemented as they can convert low grade thermal energy to useful electrical energy at various operating conditions.
The integration of a TEG within a heat exchanger (TEG/HX) system connected to an electrical DC micro-grid, using a Maximum Power Point Tracking (MPPT) system is the focus of this study. Using a numerical TEG/HX model from a previous study and a developed DC micro-grid model the interaction between the thermal and electrical aspects were investigated with the focus on the electrical performance of the system.
The main concern of this study is to investigate the effect of the sub components of the DC micro-grid on the overall available energy. An analytic model was developed to estimate the power loss in the electrical circuit of the micro-grid, the model utilizes the equations for switching and conduction losses which have been used by several studies. Other variables such as the battery characteristics and electrical load profiles were also investigated by simulating several case studies including changing operating conditions.
 This study shows the effect of a TEG configuration on the power loss in an electrical system using power loss curves in comparison with the Open Circuit Voltage (OCV) of such configuration. It also covers important modes of operation for the battery, loads and MPPT for a stable and reliable operation of an isolated DC micro-grid system were TEGs are the only source of power.

The result of the study presented is a system design that is able to maximize the electrical energy harvested from the TEGs to extend the operation of the dc-micro-grid first by applying a suitable TEG configuration and consequently a suitable electrical circuit. Secondly, by adapting to the changing operating conditions of the TEGs and the loads; and compensating for these changes using the battery storage system.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Effects of Adenovirus Region E1B Mutations on the Accumulations of Viral Specific RNAs

title: RNA Accumulations in Adenovirus E1B Mutants

contributor:
Mak, Stanley
Biology

subject: adenovirus E1B viral RNA mutation

abstract: The expression of the adenovirus (Ad) genome is co-ordinately regulated and the various early regions of the genome are known to exert feedback controls on each other. The region E1B is known to encode functions which are required for oncogenic transformation by adenovirus yet its potential regulatory role is poorly understood. In this study the regulatory role(s) of the region E1B was investigated at the level of RNA accumulation. The Northern blot technique using various cloned early regions as probes and RNAs from E1B mutants Ad 12, Ad 2 and Ad 5 were used. The levels of region E1A specific RNAs were found to be aberrant. Thus for Ad 12 cyt 68 and Ad 2 dl 250 the levels were higher than wild type ones at late times whereas for Ad 5 dl 313 hr-6 the levels were consistently lower than Ad 5. This implies that the region E1B normally encodes functions which are involved either directly or indirectly in the efficient accumulation of region E1A specific RNA. Other regions also seemed to be affected in these mutants. In cyt 68, region E1B RNA was higher than wild ones at late time, indicating an auto-regulatory mode of control for this region. The expression of region E3, E4 and LS RNA were all perturbed by the E1B mutation as some of the mutants either accumulated higher or lower than wild type levels of RNA.

abstract: Thesis

abstract: Master of Science (MS)


title: The Effects of Basis FGF and Endothelin-1 on the Mitotic Activity and Survival of Cultured Carotid Body Chemoreceptor Cells

contributor:
Nurse, Colin
Biology

subject: carotid FGF endothelin chemoreceptor

abstract:
Thesis
Master of Science (MS)


title: Effects of Acute and Chronic Zinc Exposure on Juvenile Rainbow Trout: Influence of Water Chemistry and Biotic Ligand Modelling

subject:
znic
chronic
acute
rainbow trout
trout
water
ligand

abstract:
Thesis
Master of Science (MS)


title: Development of a Teaching Module on Water Quality that Involves Two Local Communities

contributor:
Sorger, G. J.
Blizzard, A. C.
Teaching

subject: water quality teach local community

abstract: This project describes the development of microbiology laboratory exercises to be used in the teaching of first year undergraduates. One of the main goals of this project, is to try to make these laboratory exercises relevant to the life of local communities. Two local communities were chosen in the Hamilton area. The communities of Hamilton Beach and Dundas were involved and their water was tested for the presence of faecal coliform bacteria. The design of these laboratory exercises includes relevant aspects of educational theory intended to stimulate the students' interests in Biology and, simultaneously, strengthen the relationship between the students and their local communities. The main conclusions drawn from this project are: 1. The primary objectives established for the course seem to have been fulfilled. 2. The majority of the students considered these laboratory exercises to be socially and educationally relevant. 3. It is important to stimulate dialogue amongst the students. 4. It is desirable to make educational programs immediately relevant to the lives and the experiences of the students.

abstract: Thesis

abstract: Master of Science (Teaching)


title: Assessing the Influence of Elastic Recovery in a Stretch-Shortening Cycle Task: A Muscle Modelling Approach

title: Assessing Elastic Recovery in a Stretch-Shortening Task

contributor:
Dowling, James
Human Biodynamics

subject: elastic muscle modelling influence recovery

abstract: A Hill-based muscle model was used to assess the influences of series elastic recovery in stretch-shortening cycle (SSC) contractions at the human elbow. Elbow torque, EMG and joint kinematics were recorded as eight male subjects performed a vari ety of elbow flexion and extension tasks. A significant performance enhancement was observed in SSC vs non-SSC elbow flexions (20% greater angular impulse). The muscle model used activation-force, length-tension and force-velocity functions to estimate instantaneous elbow flexor and extensor moments. These moments were summed with a passive elbow moment to obtain estimates of net elbow moment and angular impulse. The estimated values were compared to actual measures of joint torque and angular impulse. The model accurately estimated the angular impulse generated by non-SSC contractions, but demonstrated substantial underestimation errors in SSC contractions. The majority of the SSC performance enhancement could not be attributed to either neural potentiation or to a better exploitation of contractile component mechanics. Since the model was designed to account for these influences but did not possess an ability to account for series elastic recovery, the performance enhancement which was not accounted for by the model was attributed to the recovery of strain energy stored in the SEC of the flexor muscles during the stretch phase. Past studies of SSC enhancement in voluntary movements have been unable to discern between the influences of elastic recovery, neural potentiation and other SSC phenomena. The methods employed in this study permitted the influence of elastic energy recovery to be partitioned from a net SSC performance enhancement. The results indicate that elastic recovery can play an important role in human movement, and that Hill-based muscle models offer a useful tool for studying physiological phenomena which can not be isolated experimentally.

abstract: Thesis

abstract: Master of Science (MS)


title: A Self-Directed Instructional Manual for Health Professionals

contributor:
Neufield, V.
Humphreys, D. A.
Health Care Practice

subject: instruction manual health education

abstract: In this project the author establishes that health teaching is a major function of all health professionals, but very little emphasis is given on teaching-learning principles in their curricula. Based on literature review the author develops a self-directed instructional manual for health professionals. Teaching-learning principles with examples are introduced throughout the manual. Twelve health professionals from medicine, nursing, occupational and physiotherapy have evaluated the manual for its content and process.

abstract: Thesis

abstract: Master of Science (Teaching)


title: An Investigation of the Role of the Corpus Callosum in the Lateralised Skilled Reaching Task

title: The Corpus Callosum in the Lateralised Reaching Task

contributor:
Racine, R. J.
Psychology

subject:
corpus callosum
investigation
skill reaching

abstract: Long-term potentiation (LTP), a long-lasting enhancement of synaptic efficacy, is believed to be the mechanism by which memory storage occurs in the brain. Several studies have shown that LTP can be induced in various neural sites, not only by electrical stimulation, but also as a result of behavioural modifications. It has previously been shown that LTP in the primary motor cortex accompanies motor skill learning. One study showed that potentiation occurred following training on a lateralised skilled reaching task. In this task, animals are trained to use only one paw to grasp a small food pellet. An interesting finding that has been uncovered from these studies is that, although only one hemisphere actively participates in the task (the trained hemisphere), the other hemisphere (untrained hemisphere) also shows potentiation. This has led to the hypothesis that the corpus callosum is involved in the transfer of information from one hemisphere to another during training on the reaching task. The nature of this communication, however, is unknown. Two possibilities were considered. The first was that the callosum transfers information that allows the animal to maintain its balance while the reaching paw is elevated. Careful observation of videorecording made while animals performed the task however, failed to reveal any deficits in balance in animals that had undergone a callosal transection. A second possibility is that the corpus callosum transfers information about the task from the trained to the untrained hemisphere such that, even though it does not actively participate in the task, the untrained paw may "know" how to perform above chance level. Analysis of the rate of successful reaching with the untrained paw revealed no advantage for normal animals over transected animals. Work is however, currently underway to increase the number of animals in the study in order to obtain a more conclusive result.

abstract: Thesis

abstract: Master of Science (MS)


title: Studies of Functionalized Polyurethanes for Blood Contacting Applications

contributor:
Brash, J. L.
Chemical Engineering

subject: polyurethane blood application functional

abstract:
The synthesis of novel polyurethanes for use in blood contacting applications was investigated. A series of polyurethanes containing biologically active groups in the hard segment was synthesized. Sulphonate-containing polyurethanes were produced using a sulphonated chain extender (biphenyl diamino disulphonic acid) and these polymers were subsequently reacted to incorporate arginine methyl ester groups via sulphonamide bonds.
The novel polyurethanes were initially evaluated using elemental sulphur analysis and nitrogen analysis, gel permeation chromatography and Fourier transform infrared spectroscopy to verify reaction of the sulphonated chain extender and addition of arginine methyl ester. Three sulphonated polyurethanes covering a range of sulphonate content were produced by varying the prepolymer and hard segment lengths. These three polymers and the three corresponding arginine methyl ester containing polymers were characterized to relate both bulk and surface structure to physical and biological properties. Elemental analysis, gel permeation chromatography and Fourier transform infrared spectroscopy were used to characterize the molecular structure. These techniques provided results consistent with the expected reaction mechanisms. Electron spectroscopy for chemical analysis and contact angle measurements were used to analyse the surface structure. Preliminary contact angle data indicate that the sulphonated polyurethane surfaces are hydrophilic, but further investigation is required before a firm conclusion can be reached. ESCA results indicate that while soft segment surface enrichment is taking place there are significant numbers of sulphonate groups present at the polyurethane surface. Mechanically these polymers have similar ultimate tensile strength but lower elongation than polyurethanes produced using aliphatic diamines, like ethylene diamine. This is probably due to increased microphase segregation arising partly from incompatibility of the aromatic chain extender with the aliphatic soft segment and possibly partly to ion cluster formation. The incorporation of arginine methyl ester groups increases both the elongation and the tensile strength, probably due to reduced phase segregation. Fibrinogen adsorption experiments in plasma were conducted to evaluate the blood response of these polymers. The plasma adsorption "isotherms" for the novel polyurethanes do not show transient fibrinogen adsorption (Vroman effect) which has been observed on a number of other surfaces including a wide range of polyurethanes. Instead, the initially adsorbed fibrinogen remains adsorbed. Also the levels of fibrinogen adsorption from plasma are three to four times greater than observed on previously studied surfaces. Conversion of some of the sulphonate groups to sulphonamide-bonded arginine methyl ester restores the Vroman effect and results in lower levels of retained fibrinogen. These data suggest the possibility of a specific interaction between sulphonate groups and fibrinogen.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Identifying determinants of body composition in undergraduate students: a systematic review and protocol for a prospective observational study

title: Determinants of body composition in undergraduate students

contributor:
Meyre, David
Health Research Methodology

subject:
Undergraduate
Systematic review
Obesity
Genetics
Freshman fifteen

abstract: Young adulthood is an important period in the development of obesity. Undergraduate students are particularly at-risk since they gain more weight than those not attending university. As students transition from high school to university, they often adopt unhealthy lifestyle behaviours which are thought to lead to weight gain. On average, students gain three to five pounds (1.4-2.3 kg) during their first year of undergraduate education. However, less is known about how body composition changes throughout the four-year course of undergraduate education and what causes these changes. We thus conducted a systematic review to synthesize a comprehensive list of factors associated with obesity traits (e.g. body mass index, body fat percentage, muscle mass) in undergraduate students. Two hundred thirty-eight studies were included (175 cross-sectional, 49 cohort, 11 interventional, 3 qualitative). We identified age, sex, ethnicity, socioeconomic status, religion, diet, eating habits, physical activity, sedentary activity, sleep, stress, university campus life, alcohol use, smoking, psychiatric disorders, body image, eating attitude, eating regulation, personality, and social/cultural influences as factors which are associated with obesity traits. These factors guided the design of the Genetic and EnviroNmental Effects on weight in University Students (GENEiUS) study, a prospective observational study which investigates the genetic and environmental determinants of body composition in undergraduate students over four years. The GENEiUS study will recruit 2500 multiethnic first- year undergraduates aged 17–25 years and will follow them every six months for four years. Primary outcomes are body mass index, waist circumference, waist-to-hip ratio, body fat mass and body fat percentage. This study will help design obesity prevention programs in universities.

abstract: Thesis

abstract: Master of Science (MSc)


title: Novel Mechanisms of Antibiotic Resistance in Soil Organisms

contributor:
Wright, G. D.
Biochemistry

subject: antibiotic resistance soil organism

abstract:
Thesis
Master of Science (MS)


title: Investigation of Platelet-Surface Interactions Using a Novel Cone and Plate Device

subject: platelet cone device plate

abstract:
Polymers are frequently utilized in blood-contacting biomaterials. Although, these materials exhibit generally favourable mechanical properties, the presence of these artificial surfaces in contact with blood initiates the mechanisms of thrombosis. This occurrence may, in turn, lead to a variety of serious clinical complications. A great deal of work has been done in this laboratory in the past to investigate the interactions of a variety of proteins (particularly coagulation proteins) with artificial surfaces. This interaction is believed to be the initial step in the physiological response to artificial surfaces in contact with blood. A secondary but equally important process is the adhesion and activation of blood platelets to artificial surfaces which may then lead to the formation of thrombi. The work performed here involves the investigation of platelet-surface interactions with a variety of surfaces, primarily a series of sulphonate ion-containing polyurethanes. Similar polymers have been shown by other researchers to exhibit favourable blood-contacting responses while retaining the attractive mechanical properties of polyurethanes in general. To perform the work outlined above, a novel cone and plate device was designed and built which enables the experimenter to investigate platelet-surface interactions under varying shear flow conditions. Collagen and albumin-coated test surfaces were utilized to investigate the platelet adhesion results generated in the device with varying fluid shear rate and time. A typical adhesion time response curve was generated with increasing levels of adhesion noted for increasing shear rate, as expected due to increased platelet transport to the surface. As well, effective platelet diffusion coefficients were calculated from the adhesion data collected using the collagen surface and was found to agree broadly with those found by other researchers. A series of sulphonated polyurethanes were synthesized and both the bulk and surface properties were characterized. A variety of polymer sulphonate concentrations were achieved by use of different constituent molecules (specifically chain extenders and polyols). The polymers, in general, showed high levels of water absorption and increased hydrophilicity in comparison to non-sulphonated analogs.
The cone and plate device was used to investigate the platelet adhesion response in a shear flow environment to these surfaces. In general, sulphonate incorporation resulted in a dramatic increase in the level of adhesion to the polyurethane surfaces, indicating that platelets are able to form adhesive interactions with sulphonate functional groups. Platelet adhesion levels to the sulphonated polyurethanes exhibited both time and shear rate dependence. However, differences in adhesion levels between the sulphonated polyurethanes did not appear to be a simple function of the sulphonate concentration. This may indicate that the local environment of the incorporated sulphonate groups in the polyurethane can affect the ability of these groups to interact with the platelet membrane.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Over-Expression, Purification and Crystallization of the DNA Binding and Dimerization Region of Epstein-Barr Nuclear Antigen-1

title: Over-Expression, Purification and Crystallization of Epstein-Barr Nuclear Antigen-1

contributor:
Frappier, Lori
Biochemistry

subject: purify expression crystallize Epstein-Barr nuclear antigen

abstract: EBV episomes replicate once per cellular S phase, during latent infection of host cells. Only one viral protein, Epstein-Barr Nuclear Antigen-1 (EBNA-1) is required for replication; the rest of the replication machinery is provided by the cell. EBNA-1 is an excellent model to study the molecular events required for DNA replication and its regulation because viral replication is limited to once per cell cycle. EBNA-1 is a member of a special class of DNA binding proteins called origin binding proteins (OBPs). These specialized proteins bind to distinct DNA sequences in the genome called origins of replication, where DNA replication is initiated. Origin binding proteins may serve to distort the DNA at the origin and may also attract the cellular replication machinery. Structural studies of the DNA binding and dimerization region of EBNA-1 using X-ray crystallography were undertaken in order to better understand how OBPs bind to origin DNA sequences and facilitate the assembly of the cellular replication apparatus. Six truncation mutants of EBNA-1, all containing the DNA binding and dimerization region of EBNA-1, were cloned, over-expressed in bacteria and purified to apparent homogeneity. Four of these clones were crystallized using the method of hanging-drop vapour-diffusion. Two fragments, EBNA₄₇₀₋₆₁₉ and EBNA₄₇₀₋₆₀₇, formed well-ordered crystals that diffracted beyond 2.5 Å resolution. In addition , this study also demonstrates the value of finding the most suitable piece of the protein for crystallization. This piece should fold into a compact domain for efficient packing into a crystal. Finding the optimal piece of the protein reduces the time spent searching for crystallization conditions.

abstract: Thesis

abstract: Master of Science (MS)


title: A Functional Analysis of the EBNA1 Origin Binding Protein of Epstein-Barr Virus

subject: EBNA1 protein Epstien-Barr virus

abstract:
Thesis
Doctor of Philosophy (PhD)


title: McMaster Patient Management Problems a Clinical Evaluation Tool

title: McMaster Patient Management Problems

contributor:
Keech, G.
Computation

subject: patient clinical problem manage

abstract: Patient Management Problems is a paper and pencil self-assessment procedure administered by the American College of Surgeons. The participant is presented with a number of problems, each of which describes a patient with an illness or injury. For each problem, the participant must assume the role of surgeon on duty and make decisions as to what he would do next in order to formulate a diagnosis. Each decision is scored in a prescribed manner. Upon completion of the problem, the participant's score reflects his knowledge and clinical competence. Dr. C. B. Mueller (Health Sciences, McMaster University) has defined a requirement to investigate the feasibility of evaluating a surgeon's ability to discriminate between critical and noncritical information available from a patient. This investigation will employ an evaluation process similar to the one used in Patient Management Problems but will be computerized and will be scored in terms of completeness and efficiency. This computerized evaluation tool will be referred to as McMaster Patient Management Problems (MPMP). This project paper will describe the activities surrounding the development of McMaster Patient Management Problems.

abstract: Thesis

abstract: Master of Science (MS)


title: Rearrangements of the Adenovirus Genome Induced by Embedded Inverted Terminal Repeat Sequences

title: Rearrangements of Adenovirus Genome

contributor:
Graham, F. L.
Biology

subject: adenovirus genome inverted terminal sequence

abstract: The adenovirus genome is a linear double stranded DNA molecule and the current widely accepted model of viral DNA replication proposes linear viral DNA intermediates at all stages of replication. Although the experimental evidence for this mechanism of replication is very strong, circular forms of adenovirus serotype 5 (Ad5) DNA molecules have also been detected in both permissive and non-permissive cell lines. In some experiments the circular structures were detected before the onset of viral DNA replication and thus suggested a possible role for circular forms of Ad5 DNA in the life cycle of the virus after infection. This study was undertaken to better understand the role of circular forms of the adenovirus genome in virus replication. The approach was to subclone the viral junction internally into the linear genome thus creating mutant viruses with embedded terminal sequences and to study the effect of such inserts on DNA structure. A total of five mutant viruses were constructed containing a variety of inserts and viral DNA from infected cells and banded viruses was analyzed by Southern Blot hybridization. The data clearly showed that embedded viral junctions have biological activity in that they generated novel, rear ranged viral DNA molecules, and that embedded single ITR sequences were also biologically active, but to a lesser extent. It was also observed that the copy numbers of the rearranged molecules were variable. It appeared that the embedded viral junction was active in recombination and replication of the viral genome, creating the rearrangements through these two processes. However, the results suggested that circular forms are not obligatory intermediates in DNA replication. The analysis of banded viral DNA in this study suggested that the encapsidation signal from the left end of the linear genome was required in cis for packaging of the viral genome, confirming previous results which identified an encapsidation signal for viral DNA packaging. The banding experiments also showed that truncated viral DNA molecules containing 75% of the viral genome were packaged.

abstract: Thesis

abstract: Master of Science (MS)


title: Construction of a Herpes Simplex Virus Type 1 (HSV-1) Expression Vector Containing the Bacteriophage T4 Den V Gene: Effect of this Gene on UV-Survival of HSV-1 in Normal and Zeroderma Pigmentosum Fibroblasts

title: Construction of an HSV-1 Recombinant Expressing the Bacteriophage T4 Den V Gene

contributor:
Rainbow, Andrew
Biology

subject:
herpes
herpes simplex virus
bacteriophage
UV
gene
xeroderma
fibroblasts

abstract: In order to examine the potential of HSV-1 as a vector to study the expression of DNA repair genes in mammalian cells, a recombinant virus containing the den V gene from bacteriophage T4 has been constructed. This gene encodes a pyrimidine dimer-specific endonuclease that has the capacity to initiate excision repair of DNA. Transfection studies indicate that excision repair deficient xeroderma pigmentosum (XP) group A cells are able to carry out excision repair initiated by the den V gene product. This gene along with the 3' LTR of Rous Sarcoma Virus and the SV40 polyadenylation signals were inserted into the non-essential glycoprotein I gene of HSV-1. Immunoprecipitation studies confirmed the production of the den V protein in virus infected cells. The uv survival of this HSV-1:den V recombinant virus was examined in various primary cell types. The cells examined in this study were primary fibroblasts from a normal individual, a Trichothiodystrophy patient and five XP patients as well as a mouse L cell line. The ability of the virally encoded den V gene to restore the excision repair deficiency in these cells was measured by monitoring the uv survival of HSV-1:den V as compared to wildtype HSV-1. Increased survival of HSV-1:den V was detected in Trichothiodystrophy cells, and in cells from XP complementation groups A, C and D, but not in XP cells from complementation groups E and F or in mouse L cells. These results demonstrate that HSV can be effectively used to study the expression of a cloned DNA repair gene in a variety of cell types. HSV has a substantial capacity of gene insertion and a wide host range including cells of human and rodent origin.

abstract: Thesis

abstract: Master of Science (MS)


title: Establishing Verifiable Trust in Collaborative Health Research

contributor:
Samavi, Reza
Computing and Software

subject:
Trust
Transparency
Privacy
Security
Blockchain
Provenance
Linked Data
Integrity
Collaboration
Artificial Intelligence
Audit Logs
Data Sharing

abstract: Collaborative health research environments usually involve sharing private health data between a number of participants, including researchers at different institutions. Inclusion of AI systems as participants in this environment allows predictive analytics to be applied on the research data and the provision of better diagnoses. However, the growing number of researchers and AI systems working together raises the problem of protecting the privacy of data contributors and managing the trust among participants, which affects the overall collaboration effort. In this thesis, we propose an architecture that utilizes blockchain technology for enabling verifiable trust in collaborative health research environments so that participants who do not necessarily trust each other can effectively collaborate to achieve a research goal. Provenance management of research data and privacy auditing are key components of the architecture that allow participants’ actions and their compliance with privacy policies to be checked across the research pipeline. The architecture supports distributed trust between participants through a Linked Data-based blockchain model that allows tamper-proof audit logs to be created to preserve log integrity and participant non-repudiation. To maintain the integrity of the audit logs, we investigate the state-of-the-art methods of generating cryptographic hashes for RDF datasets. We demonstrate an efficient method of computing integrity proofs that construct a sorted Merkle tree for growing RDF datasets based on timestamps (as a key) that are extractable from the dataset. Evaluations of our methods through experimental realizations and analyses of their resiliency to common security threats are provided.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Collaborative health research environments involve the sharing of private health data between a number of participants, including researchers at different institutions. The inclusion of AI systems as participants in this environment allows predictive analytics to be applied on the research data to provide better diagnoses. In such environments where private health data is shared among diverse participants, the maintenance of trust between participants and the auditing of data transformations across the environment are important for protecting the privacy of data contributors. Preserving the integrity of these transformations is paramount for supporting transparent auditing processes. In this thesis, we propose an architecture for establishing verifiable trust and transparency among participants in collaborative health research environments, present a model for creating tamper-proof privacy audit logs that support the privacy management of data contributors, and analyze methods for verifying the integrity of all logged data activities in the research environment.


title: A Quantitative Evaluation of the Relationship Between Income and Self-Reported Health in Canada, 1996-1999

title: An Evaluation of the Relationship Between Income and Health

contributor:
Veall, Michael
Mathematics

subject: evaluate income health canada

abstract: The focus of the research is on quantitative characterization of a potential relationship between income and health. The study is conducted in both levels and increments contexts. As a background, the research relies on Grossman's standard economic model of health as well as on previous empirical investigations. The source of the data is the Survey of Income and Labour Dynamics, administered by Statistics Canada. The set of instruments implemented includes ordered probit and ordered logit models, gamma GLM models, the OLS method and bootstrapping techniques in linear models. The results of the study suggest that there exists a strong association between the levels of health and income, whereas no evidence of significant association between the increments is present.

abstract: Thesis

abstract: Master of Science (MS)


title: Studies on HPV Infection and Persistence in a University Undergraduate Population

title: HPV Infection and Persistence

contributor:
Harnish, D. G.
Biology

subject: HPV population infect persist

abstract: Cervical cancer is preceded by a spectrum of abnormalities in the cervical epithelium. Research supports an etiological role for certain types of human papillomaviruses (HPVs) in cervical pathology. More than 70 HPV genotypes have been characterized based on complete genome sequences and of these, about half infect the genital tract. Genital HPVs are further classified as either "high risk" or "low risk" types based on their association with cervical cancer. The demonstration that there is a relationship between HPV infection and cervical cancer has been dependent on a number of viral nucleic acid-based detection systems such as Southern blot and polymerase chain reaction. However, the lack of methods which discriminate between a specific HPV type and a large number of related HPV genotypes has made studies of disease association difficult. In the first part of this study, a recently developed Amplicor HPV Genotyping Kit was evaluated with respect to its ability to define HPV infection status. The L1 region was directly sequenced from the PCR product in 16 clinical samples to determine which genotype(s) was/were present. Sequencing data from one sample suggested a mixed infection and therefore the PCR product was cloned and sequenced to see if more than one genotype was present. Fifteen out of the sixteen samples sequenced were HPV genotypes which are not represented on the Amplicor Genotyping Kit test strips. The samples are rare HPV types (HPV 61, 62, CP6108 and CP8304). The second part of this study examined the issue of persistence and in particular, I have considered the issue of an appropriate definition of persistence. A number of patients who had evidence of HPV 16 or HPV 18, 6 and 66 were investigated using samples obtained on at least two occasions. Molecular variants of either the LCR gene for HPV 16 or the L1 gene for the other HPV types were studied. No differences in LCR or L1 gene sequence in sequential same patient samples were observed. Two HPV 16 LCR alleles were seen for six patients of which 8/10 showed one nucleotide change at base 7518 and 2/10 were identical to the prototype. Based on a compilation of published studies on HPV 16 variants and subtypes for the long control region, the number of HPV 16 LCR alleles, worldwide, was determined. One HPV 66 and two HPV 18 and HPV 6 L1 alleles were observed. When examining persistence, one must consider the frequency of specific variants (alleles) in the study population. A common variant detected over time could either be a persistent infection or a reinfection with the same viral variant.

abstract: Thesis

abstract: Master of Science (MS)


title: MULTI-INK 3D PRINTING OF UV-CURABLE SILICONES

contributor:
Ravi Selvaganapathy, Ponnambalam
Mechanical Engineering

abstract: Silicones are an important implant material, and as additive manufacturing technologies are revolutionizing many fields, one interesting application is the production of patient-specific silicone bio-implants where the stiffness of the material may not be homogenous over the entire part. 3D printing technology is well suited for construction of such custom parts. However, current 3D printing methods for silicone are not capable of printing multiple materials to mimic the heterogeneous properties of real tissue. The objective of this thesis is the development of additive manufacturing method for silicone objects with multiple constituent inks. To this end, a pneumatic 3D printer to print multiple silicone UV-curable inks based on thiol-ene chemistry was developed. The effect of parameters such as nozzle diameter, applied pressure, feedrate and Z offset on the ink deposition process was investigated and optimized printing conditions determined. The results showed that a successful creation of a continuous ink trace depends on correlating these parameters, a simple model for this correlation is presented. By optimizing parameters, traces of 600µm in width and 80µm in height were produced. Another key factor for the trace dimensions and for preventing clogging failures was found to be the UV illumination pattern in the vicinity of the nozzle. By optimizing exposure, continuous printing for 30 mins was demonstrated. The complete system was shown capable of printing 3D objects composed of three different silicone inks with capabilities such as disconnected feature printing, printing of overhangs and two modes of ink switching. Such a printer can be potentially applied in the fabrication of custom implants, production of meta-materials and bio-printing.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Hamiltonian Methods in PT-symmetric Systems

contributor:
Pelinovsky, Dmitry
Mathematics and Statistics

subject: PT-symmetry, Nonlinear Schroedinger Equation, existence of breathers, spectral and orbital stability, Krein signature

abstract: This thesis is concerned with analysis of spectral and orbital stability of solitary wave solutions to discrete and continuous PT-symmetric nonlinear Schroedinger equations. The main tools of this analysis are inspired by Hamiltonian systems, where conserved quantities can be used for proving orbital stability and Krein signature can be computed for prediction of instabilities in the spectrum of linearization. The main results are obtained for the chain of coupled pendula represented by a discrete NLS model, and for the trapped atomic gas represented by a continuous NLS model. Analytical results are illustrated with various numerical examples.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Dual Wavelength Time Resolved Reflectance Measurements for the Determination of Hemoglobin Oxygenation in Tissue

title: Measuring Hemoglobin Oxygenation by Time Resolved Reflectance

contributor:
Patterson, Michael
Physics

subject: hemoglobin oxygen tissue time reflectance

abstract:
Thesis
Master of Science (MS)


title: Mechanistic Modeling of Station Blackout Accidents for CANDU Reactors

contributor:
Novog, David
Engineering Physics

subject:
CANDU
Severe Accidents
Station Blackout
RELAP/SCDAPSIM

abstract:
Since the Fukushima Daiichi nuclear accident, there have been ongoing efforts to enhance the modelling capabilities for severe accidents in nuclear power plants. The primary severe accident analysis code used in Canada for its CANDU reactors is MAAP-CANDU (adapted from MAAP-LWR). In order to meet the new requirements that have evolved since Fukushima, upgrades to MAAP-CANDU have been made most recently by the Canadian nuclear industry. While the newest version (i.e. MAAP5-CANDU) offers several important improvements primarily in core nodalization and core collapse modelling, it still lacks mechanistic models for many key thermo-mechanical deformation phenomena that may significantly impact accident progression and event timings. It is also a general consensus that having alternative analysis tools is beneficial in improving our confidence in the simulation results, especially given the complex nature of severe accident phenomena in CANDU and the limited experimental support. This thesis seeks a novel approach to CANDU severe accident modelling by combining the best-estimate thermal-hydraulic code RELAP5, the severe accident models in SCDAP, and several CANDU-specific mechanistic deformation models developed by the author.
This work mainly consists of two parts. The first part is focused on the assessment of natural circulation heat sinks following crash-cooldown in the early-phase of a Station Blackout (SBO) accident where fuel channel deformation can be precluded. The effectiveness of steam generator heat removal after crash-cooldown and that of the several water make-up options were demonstrated through the simulation of several SBO scenarios with/without crash-cooldown, sensitivity studies, as well as benchmarking against station and experimental measurements.
In the second part, several mechanistic severe accident models were developed to enhance the simulation fidelity beyond the initial steam generator heat sink phase to the moderator boil-off and core disassembly phases.  This includes models for predicting the pressure tube ballooning and sagging phenomena during the fuel channel heat-up phase and models for the sagging and disassembly of fuel channel assemblies during the core disassembly phase. After benchmarking against relevant channel deformation experiments, the models were successfully integrated into the RELAP/SCDAPSIM/MOD3.6 code as part of the SCDAP subroutines. The advantage of utilizing a code such as SCDAP is that generic models for fission product release and hydrogen generations, which are well benchmarked, can be directly applied to CANDU simulations.  With the modified MOD3.6 code the early-phase SBO simulations were extended to include the later stages of SBO until the calandria vessel dryout. The current modelling approach replaced the simple threshold-type models commonly seen in the integrated severe accident codes such as MAAP-CANDU with more mechanistic models thereby providing a more robust treatment of the core degradation process during severe accident in CANDU.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Peptide Modified Gold Coated Polyurethane Surfaces as Thrombin Scavengers

subject: gold polyurethane peptide thrombin

abstract:
Gold, as a chemically inert metal, does not form a stable oxide, but has strong specific interactions with sulfur functions. It has been found that thiols or disulfides can chemisorb to gold under mild conditions (room temperature), and form densely packed monolayers on the gold surface due to the high density of binding sites (gold atoms). Thus, it is possible to form closely packed and stable monolayers of thiolates containing
desirable bioactive moieties. Thiol-gold chemistry may therefore be considered as a potentially important tool in the surface modification of materials for biomedical applications. In order to develop surfaces with antithrombogenic properties, a number of thrombin inhibitors (heparin, hirudin and PPACK) have been bonded or immobilized to the material surfaces. In the present study, a series of short peptides, cys-pro-arg (CPR),
cys-phe-pro-arg (CFPR) and cys-(D)-phe-pro-arg (C[D]FPR), analogues of PR and FPR respectively, were chosen as potential thrombin inhibitors to attach to gold-coated polyurethane surfaces via the cysteine residue. Their inhibitory activity against thrombin was verified by a chromogenic substrate assay. C(D)FPR, showed a relatively high level of inhibition activity. The surfaces were characterized by water contact angle, XPS, AFM, SEM, ellipsometry, and infrared reflection-absorption spectroscopy, and the adsorption of thrombin from buffer and modified plasma was investigated. It was found that the peptide modified gold surfaces adsorbed significantly more thrombin than the unmodified control surfaces. The C(D)FPR-modified gold surface showed the highest thrombin adsorption both from buffer and plasma. This results is in accord with previous studies
showing that the D form of phenylalananine in the FPR peptide creates a favourable site geometry for binding to thrombin. The activity of thrombin adsorbed on these peptide modified gold surfaces was also investigated using a chromogenic substrate assay. Inhibition of adsorbed thrombin was demonstrated, and the C(D)FPR surface showed the strongest inhibitory activity. The presence of thrombin on the peptide surfaces following exposure to modified plasma was verified by elution of proteins and identification of thrombin in the eluate.
Probing of the eluates with antibodies to 25 plasma proteins showed that the peptide surfaces are relatively non-adsorptive, suggesting they have some degree of selectivity for thrombin binding.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Characterization of Protein COmplexes Interacting with Adenovirus Type 5 E1A Proteins and Identification of Novel E1A Phosphorylated Forms within these Complexes

contributor:
Branton, Philip
Biology

subject:
protein
adenovirus
adenovirus type 5
phosphorylation

abstract:
Thesis
Master of Science (MS)


title: The Murine Cell-Mediated Immune Response to Adenovirus Recombinant AdG12

contributor:
Rosenthal, K. L.
Biology

subject:
immune
immune response
murine
adenovirus
AdG12

abstract:
This study was undertaken to examine the specificity of the cell-mediated immune response to vesicular stomatitis virus in mice, using the recombinant adenovirus vector AdG12. AdG12 contains the coding region for VSV glycoprotein (G) within the genome of adenovirus type 5. Ultimately, these studies attempted to provide a model for the use of adenovirus vectors to elicit specific CTL responses in mice against an inserted foreign protein. Cell-mediated immunity was examined using a standard ⁵¹Cr release assay. Splenocyte effectors from VSV or AdG12 primed mice were tested for their ability to lyse labelled infected target cells.
A number of target cell lines were analyzed for productive infection by AdG12 and expression of VSV-G. Of the lines tested, B10.D2 (H-2ᵈ) and PAK (H-2ᵇ) lines were shown to be infectible with AdG12 and expressed VSV-G 36 hours post infection. Cell lines P815 (H-2ᵈ) and EL-4 (H-2ᵇ) did not appear to be AdG12 infectible. Responses were measured in mice intravenously infected with AdG12. Results demonstrated that peak cytotoxic activity from AdG12 primed mice occurred six days post-infection against syngeneic target cells infected with AdG12, Ad5 wt or VSV. However, these effectors also significantly lysed allotargets infected with VSV, implying that VSV infected targets were lysed in a non-MHC restricted manner. In subsequent experiments, it was discovered that VSV infected B10.D2 and PAK targets were markedly lysed by effectors from immunized and non-immunized Balbic, C57B1/6 and CBA/J mice. Thus, it appeared that these mouse strains contained an inherent or natural cytotoxic activity against VSV infected targets that was unlike classical CTL killing. Depletion experiments showed that this activity was not due to adherent or Thy1 bearing cells within spleen cell populations. To further characterize this activity, splenocyte effectors were tested for their ability to lyse NK-sensitive YAC-1 targets, but no significant lysis was demonstrated. However, despite these results, it appeared that this activity was that of an NK-like effector. The presence of NK-like cytotoxicity against VSV infected targets precluded efforts to define specific anti-VSV responses in these mice.

abstract: Thesis

abstract: Master of Science (MS)


title: Comparison of Two X-ray Detection Systems Used to Investigate Properties of Normal and Malignant Breast Tissues

contributor: Radiation Sciences (Medical Physics/Radiation Biology)

subject: x-ray, x-ray fluorescence, Breast cancer, x-ray diffraction

abstract: The present study was implemented using two different X-ray detection systems; a monochromatic X-ray system for X-ray Fluorescence (XRF) and Angular Dispersive X-ray Diffraction (ADXRD) techniques, and a combined Polarized Energy Dispersive X-ray Fluorescence (PEDXRF) and Energy Dispersive X-ray Diffraction (EDXRD) system. As both of these systems involve different techniques, the primary objective of this study was to evaluate the performance and accuracy of each system using results achieved from XRF measurements. The assessment of the two systems was carried out by investigating invasive ductal carcinoma (IDC) of breast and normal surrounding breast tissues.  The results established from the two XRF systems are in a very good agreement with each other. The statistical analysis reveals a significant and measurable increase at P<0.01 in the concentration of K, Ca, Zn, Rb and Fe (P<0.05) in the tumor tissue when compared with the healthy tissue.  However, the levels of Cl, Cu and Br attained by both systems have not demonstrated a statistically significant difference between the normal and cancerous tissues. Investigating the structural components of the same breast tissues using of the X-ray Diffraction (XRD) spectrometers incorporated in both systems indicated a statistically significant difference in the components of normal and malignant samples. Furthermore, the results have shown a remarkable increase in the fibrous and water contents of the tumour tissue at P<0.01, and a significant increase in the adipose content of the normal tissue at P<0.01. The results acquired from both XRD approaches were shown to be statistically compatible with each other. Overall, the comparisons between the two X-ray detection systems have shown tremendous results for the combined PEDXRF and EDXRD system for the purpose of classifying normal and tumor breast tissues.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characterization of Monoclonal Antibodies of Herpes Simplex Virus Type 2 Antigens

title: Monoclonal Antibodies to Herpes Simplex Type 2 Antigens

contributor:
Prevec, L.
Biology

subject:
herpes
herpes simplex virus
antigen
monoclonal
antibodies

abstract: A HSV 2 immediate early antigen was prepared and used as an immunogen in an attempt to produce monoclonal antibodies to this set to proteins. The results of three screening assays, ELISA, immunodiffusion and radioimmunoprecipitation with cell extracts and Protein A-Sepharose beads indicated that the hybrid cell lines are nonsecretors of antiHSV 2 antibodies. Other monoclonal cell lines from Dr. Bacchetti's laboratory were characterized by radioimmunoprecipitation with Protein A-Sepharose beads and cell extracts.

abstract: Thesis

abstract: Master of Science (MS)


title: Political Discourse and Policy Change: Health Reform in Canada and Germany

contributor:
Coleman, William
Political Science

subject: discourse politic policy health reform canada germany

abstract:
Thesis
Doctor of Philosophy (PhD)


title: ADVANCES IN MODEL PREDICTIVE CONTROL

contributor:
Mhaskar, Prashant
Chemical Engineering

subject:
System identification
Subspace identification
Closed-loop identification
Model predictive control
Re-identification
Lyapunov-based model predictive control
Economic model predictive control
Nonlinear model predictive control

abstract:
In this thesis I propose methods and strategies for the design of advanced model predictive control designs. The contributions are in the areas of data-driven model based MPC, model monitoring and explicit incorporation of closed-loop response considerations in the MPC, while handling issues such as plant-model mismatch, constraints and uncertainty.

In the initial phase of this research, I address the problem of handling plant-model mismatch by designing a subspace identification based MPC framework that includes model monitoring and closed-loop identification components.
In contrast to performance monitoring based approaches, the validity of the underlying model is monitored by proposing two indexes that compare model predictions with measured past output. In the event that the model monitoring threshold is breached, a new model is identified using an adapted closed-loop subspace identification method. To retain the knowledge of the nominal system dynamics, the proposed approach uses the past training data and current input, output and set-point as the training data for re-identification.
A model validity mechanism then checks if the new model predictions are better than the existing model, and if they are, then the new model is utilized within the MPC.

Next, the proposed MPC with re-identification method is extended to batch processes. To this end, I first utilize a subspace-based model identification approach for batch processes to be used in model predictive control. A model performance index is developed for batch process, then in the case of poor prediction, re-identification is triggered to identify a new model. In order to emphasize on the recent batch data, the identification is developed in order to increase the contribution of the current data.
In another direction, the stability of data driven predictive control is addressed. To this end, first, a data-driven Lyapunov-based MPC is designed, and shown to be capable of stabilizing a system at an unstable equilibrium point. The data driven Lyapunov-based MPC utilizes a linear time invariant (LTI) model cognizant of the fact that the training data, owing to the unstable nature of the equilibrium point, has to be obtained from closed-loop operation or experiments. Simulation results are first presented demonstrating closed-loop stability under the proposed data-driven Lyapunov-based MPC. The underlying data-driven model is then utilized as the basis to design an economic MPC.

Finally, I address the problem of control of nonlinear systems to deliver a prescribed closed-loop behavior. In particular, the framework allows for the practitioner to first specify the nature and specifics of the desired closed-loop behavior (e.g., first order with smallest time constant, second order  with no more than a certain percentage overshoot, etc.). An optimization based formulation then computes the control action to deliver the best attainable closed loop behavior.  To decouple the problems of determining the best attainable behavior and tracking it as closely as possible, the optimization problem is posed and solved in two tiers. In the first tier,  the focus is on determining the best  closed-loop  behavior attainable, subject to stability and tracking constraints. In the second tier,  the inputs are tweaked to possibly improve the tracking of the optimal output trajectories given by the first tier. The effectiveness of all of the proposed methods are illustrated through simulations on nonlinear systems.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Characterization and Protein-Drug Release Studies of a Novel Copolymer of HEMA

contributor:
Brash, J. L.
Sheardown, H.
Chemical Engineering

subject: protein drug characterization copolymer HEMA

abstract:
Thesis
Master of Applied Science (MASc)


title: Mutational Analysis of the Hydrophobic Region of Herpes Simplex Virus-1 Glycoprotein gB

title: Mutational Analysis of Herpes Simplex Virus Glycoprotein gB

contributor:
Ghosh, H. P.
Biochemistry

subject:
glycoprotein
hydrophobic
herpes simplex virus
herpes
mutation

abstract:
The role of highly conserved amino acids within the carboxy-terminal hydrophobic domain of herpes
simplex virus I (HSV-I) glycoprotein gB was studied by introducing point mutations using the method of site
directed mutagenesis. A segment of this hydrophobic domain of glycoprotein gB contains a nuclear envelope
(NE) targeting signal and the effect of these point mutations on targeting to the nuclear envelope was
determined. A complementation assay was employed to determine the effect these mutations have on HSV-I infectivity .The point mutations created within the transmembrane domain of glycoprotein gB had no effect on nuclear envelope targeting and localization. However, single point mutations introduced into the first and
second hydrophobic domains of glycoprotein gB, G₇₄₃R and F₇₇₀S, affected the targeting and localization of
full-length glycoprotein gB at the nuclear envelope. When the transmembrane domain ofHSV-I glycoprotein
gB containing the following point mutations A₇₉₀Q, A₇₉₁S, A₇₈₆S, A₇₈₆Y and A₇₉₀S, was introduced into a
chimeric protein consisting of the cytoplasmic domain and ectodomain of a plasma membrane protein,
vesicular stomatitis virus glycoprotein G, NE targeting and localization were affected. These point mutations
may affect the targeting of glycoprotein gB by altering the structure of the targeting signal within the protein.
It can be hypothesized that the presence of the cytoplasmic domain. ectodomain domain, and the first and
second transmembrane domains within full-length glycoprotein gB can compensate for the effect these point
mutations have on nuclear envelope targeting. since the same point mutations had no effect on the targeting · and localization of full-length glycoprotein gB. Complementation assays showed that the glycoprotein gB mutants, A₇₈₆S, A₇₈₆Y, A₇₈₆N, A₇₉₀Q, A₇₉₁S, F₇₇₀S, or G₇₄₃R, were unable to complement a gB-null virus even though these mutant proteins are localized at the nuclear envelope. These proteins may not have been incorporated into the viral capsid due to misfolding or due to the fact that sequences required for interaction with other viral proteins were lost. Another possibility is that the mutant proteins were incorporated into the HSV virion but were not biologically active.

abstract: Thesis

abstract: Master of Science (MS)