identifier: Chowdhury, Rafiqul I. <https://research.library.mun.ca/view/creator_az/Chowdhury=3ARafiqul_I=2E=3A=3A.html>   (2012) Inferences in longitudinal multinomial fixed and mixed models.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Analyzing categorical data collected over time is an important research topic. Even though there exists numerous studies on analysis of categorical data in cross sectional setup, the analysis of this type of data in the longitudinal setup is, however, not adequately addressed. In this thesis, we develop two correlation models for multinomial (> 2 categories) longitudinal data, namely, a conditional linear probability based model and a non-linear logistic probability based model; and provide likelihood inferences for category effects, fixed covariate effects and correlations or dynamic dependence parameters. The inferences are done for both complete history and contingency tables based data. For the history based data, the thesis also models the influences of individual random effects in addition to the fixed covariate effects. Furthermore, as in many practical situations the number of individuals involved in the study may be small, in the thesis, we have examined the finite sample performance of the likelihood estimates both in fixed and mixed model setups.


identifier: Clarke, Erica L. <https://research.library.mun.ca/view/creator_az/Clarke=3AErica_L=2E=3A=3A.html>   (2012) Involvement of Galnt12 variants in inherited susceptibility to colorectal cancer.  Masters thesis, Memorial University of Newfoundland.

type: Thesis NonPeerReviewed

format: application/pdf application/pdf

abstract: Colorectal cancer (CRC) is a major health concern in the Canadian province of Newfoundland and Labrador (NL), as this population has the second highest incidence of CRC in North America. Previous mutation analysis in the NL CRC population has revealed that the high frequency of hereditary CRC in NL is likely attributable to novel susceptibility genes. A recent study suggests that N-acetylgalactosaminyltransferase 12 ( GALNT12 ) may be a novel gene associated with CRC susceptibility. The purpose of this study was to investigate the impact ofGALNT12 germline variants in CRC families from NL and in 481 cases from the Newfoundland Colorectal Cancer Registry (NFCCR) with an unknown molecular basis for their disease. -- GALNT12 was first sequenced in 129 CRC families to investigate if variants within this gene segregate with the disease. Probands included in the study have a high family incidence of CRC and were referred to the Provincial Medical Genetics Program. DNA from 481 patients from the NFCCR was also sequenced in exons 4 and 6 to identify causal variants. -- Two putatively pathogenic variants were identified in the GALNT1 2 gene within four clinical family probands - c.907G>A, p.Asp303Asn (three probands), and c.1187A>G, p.Tyr396Cys. Two families showed partial segregation of c.907G>A with CRC or adenomas. The c.907G>A variant was identified in an additional two cases after sequencing 481 cases from the NFCCR. Another variant, c.889C>T, was also identified that was previously reported in a CRC case. This study provides some support for the association between GALNTI2 and CRC susceptibility and suggests that further investigations should be performed.


identifier: Cooney, David Stephen <https://research.library.mun.ca/view/creator_az/Cooney=3ADavid_Stephen=3A=3A.html>   (2012) The post-moratorium condition: contemporary interactions between tourism and the surplus population of labour in a rural Newfoundland town.  Masters thesis, Memorial University of Newfoundland.

abstract: Newfoundland's cod moratorium was an ecological, social and economic shock so grand that its reverberations continue to be felt today. Seventeen years after the fishery collapse, many rural residents maintain their struggle to find meaningful and stable work, and as a result, poverty remains a pervasive issue across the province. To mitigate these negative effects, all three levels of government, in cooperation with local organisations, have promoted and developed a tourism industry. While this tertiary sector has no doubt brought economic relief to the countryside, questions remain surrounding its benefits and drawbacks. Based on three months of participant observation, interviewing and a literature review, the following dissertation provides a grounded study of Bonavista, a northeastern town that was devastated by the cod collapse and has turned to tourism for support. It focuses on the relationship between residents who continue to struggle as a result of the cod moratorium, and the newfound tourism sector that was developed to help deal with the surplus population of labour. The results show that the provincial and federal governments are significantly involved in the funding of tourism, while many of the workers that this funding employs have become dependant on this type of work to survive.


identifier: Crane, Amanda <https://research.library.mun.ca/view/creator_az/Crane=3AAmanda=3A=3A.html>   (2012) Genetic contribution to colorectal cancer in Newfoundland and Labrador based on family history and tumour molecular analyses for an incident cohort.  Masters thesis, Memorial University of Newfoundland.

abstract: Background and Purpose: Colorectal cancer (CRC) is an insidious cancer associated with significant morbidity and mortality. In Canada, it is the second leading cause of cancer death. Newfoundland and Labrador has the highest rate of CRC of all ten Canadian provinces and is ideal for examining founder effects and studying incidence of hereditary disease in what is essentially a closed community. Family history is the strongest risk factor for this disease. Inherited deleterious variants in the mismatch repair (MMR) genes play a critical role in the development of some cases, but families exist who have a family history consistent with autosomal dominant inheritance and no known predisposing genes (Familial colorectal cancer type X, FCCTX). The aim of this study is to determine the genetic basis of CRC in Newfoundland and Labrador, defined by family history, molecular pathology of the CRC and molecular genetics, in an incident cohort of CRC cases occurring in the population during one year. -- Methods: A study population of 262 consecutively diagnosed CRC cases from the Newfoundland population were identified and following application of the recruitment protocol 148 participants, 144 families, completed the study. Eligible probands were contacted for consent and with this permission tumour blocks were obtained. Detailed family histories were obtained and risk classified. Tests of microsatellite stability and immunohistochemistry for mismatch repair proteins in tumour blocks were performed. Cancer phenotypes in family members of patients with CRC were compared in various high risk groups. -- Results: 12.5% of families (n=18) were classified as high risk according to Amsterdam criteria (AC) and Age and Cancer modified Amsterdam criteria (ACMAC). An additional 33.3% fulfilled the revised Bethesda guidelines for intermediate risk classification and 53.5% were low risk. Fifteen (10.9%) families demonstrated microsatellite instability with thirteen (86.7%) of these having a corresponding deficiency in mismatch repair proteins. Eleven of the fifteen high risk families (61.1%) were microsatellite stable (MSS) and had no mismatch repair protein deficiency and family history was consistent with FCCTX or age modified FCCTX. FCCTX family members had a lower frequency of both CRC and Lynch syndrome associated cancers as well as a later age of cancer onset compared to possible Lynch syndrome. -- Conclusions: The incidence of CRC with high or intermediate risk family history is high in Newfoundland and Labrador. Families with a history consistent with autosomal dominant disease occurred in 12.5%; possible Lynch syndrome was suspected in a minority (35%) of these families, and FCCTX/age modified FCCTX in the majority. Phenotype differences exist between FCCTX and suspected LS families in both age of onset and cancer frequency among relatives. Opportunity for novel gene discovery exists because the molecular genetic basis for most of those with familial CRC was not determined.


identifier: Dancyger, Alex <https://research.library.mun.ca/view/creator_az/Dancyger=3AAlex=3A=3A.html>   (2012) Biochemical analysis of activation-induced cytidine deaminase (AID) from bony fish: insights into the mechanisms of AID.  Masters thesis, Memorial University of Newfoundland.

abstract: The properties of Activation-induced cytidine deaminase (AID) necessary for its role in immunity and lymphoma generation are currently unknown. AID mutants and species-variants, as compared to wild-type human AID, were identified so as to map out responsible residues/domains. Variant AIDs were analyzed by alkaline cleavage and EMSA. AID from bony fish species (Ictalurus punctatus and Danio rerio) were identified as the most divergent from human AID. Dr-AID acted enzymatically similar to H-AID, while Ip-AID was less mutagenic. Point mutations within Ip AID were generated, substituting the human counterpart amino acid. One mutant rescued Ip-AID enzyme activity to levels seen in H-AID and Dr-AID. The reverse mutation in H-AID almost fully abolished the deaminating ability of H-AID. DNA-binding kinetics were tested at different temperatures to analyze if the disparity in activity levels was due to binding of DNA. The single mutation in IP-AID increases the affinity of AID to bind ssDNA and this effect is substantially more pronounced at lower temperatures. These results have provided novel information on AID domains/residues necessary for its function.


identifier: Dar, Imran Riaz <https://research.library.mun.ca/view/creator_az/Dar=3AImran_Riaz=3A=3A.html>   (2012) Experimental testing of microcontroller based protection for three phase power distribution transformer.  Masters thesis, Memorial University of Newfoundland.

abstract: The differential protection technique is very popular for protecting power transformers of various ratings and configurations and is based on the differences between the primary side and secondary side currents. The difference currents contain information when adequately processed and provide a clear picture about the transformer operating conditions. Among several approaches developed to process differential currents, harmonic analysis is widely employed for several utilities, industrial, commercial and residential applications. -- The extraction of certain harmonic components present in the differential currents can be critical in distinguishing between the magnetizing inrush current and any internal fault current. The discrete Fourier transform can be the preferred choice in the analysis that leads to an improvement in the protection of power transformers. The implementation of a digital filtering approach is usually accomplished using microprocessor platforms, which offer accuracy, speed, reliability and simplicity for protection of distribution transformers. -- This thesis implements, for the first time, harmonic analysis of differential currents for protection of power transformers in a microcontroller. The analysis is based on a discrete Fourier transform and is realized using a c-code for testing the 3-phase laboratory transformer. Performances of the microprocessor digital relay show simple implementation, reliability, speed and accuracy for distribution type transformers.


identifier: da Silva, Robin <https://research.library.mun.ca/view/creator_az/da_Silva=3ARobin=3A=3A.html>   (2012) Amino acid metabolism in the liver and pancreas.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: This thesis presents four research papers dealing with the metabolism of creatine and amino acids in the liver and pancreas. Creatine is synthesized in two enzymatic reactions that utilize the amino acids arginine, glycine and methionine. The first step in creatine synthesis is the transfer of the amidino group of arginine onto the amine of glycine resulting in ornithine and guanidinoacetate, catalyzed by the enzyme arginine:glycine amidinotransferase. The guanidinoacetate can then be methylated by the universal methyl donor S-adenosylmethionine to form creatine and S-adenosylhomocysteine. The first two papers investigate the role of the rat liver and pancreas in creatine biosynthesis respectively, using both in vivo and in vitro techniques. I provide evidence that the liver does not perform the first step of creatine synthesis but does perform the second step and has the capacity to methylate all of the guanidinoacetate that is synthesized in the kidney. The third paper examines the effects of creatine-supplementation in high-fat diet fed rat model of non-alcoholic fatty liver disease. This paper shows that dietary creatine-supplementation prevents the accumulation of lipids in the livers of rats fed high-fat diets as well as a number of the negative observations associated with non-alcoholic fatty liver disease. The fourth paper deals with the fate of perivenous hepatocytes in rats that have undergone portacaval shunts. It is known that the expression of hepatic glutamine synthetase is markedly down-regulated in portacaval anastomosis and it has been suggested that there is a loss of the perivenous hepatocytes which contain this enzyme activity. I provide evidence that ornithine aminotransferase activity and the expression of an ammonium transporter RhBG, proteins known to be localized in the perivenous cell population, are increased and unchanged respectively in rats with portacaval anastomosis. The papers presented in this thesis a) show the major role of the liver in creatine synthesis, b) demonstrate a possible role for the pancreas in creatine synthesis, c) introduce creatine as a potential treatment for fatty liver disease, and d) demonstrate that perivenous hepatocytes are not lost during portacaval shunting. These constitute important contributions to the current body of literature relating to creatine metabolism and hepatic zonation.


identifier: Dewage Don, Awantha Jayasiri <https://research.library.mun.ca/view/creator_az/Dewage_Don=3AAwantha_Jayasiri=3A=3A.html>   (2012) Supervisory control of fuzzy discrete event systems with applications to mobile robotics.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Fuzzy Discrete Event Systems (FDES) were proposed in the literature for modeling and control of a class of event driven and asynchronous dynamical systems that are affected by deterministic uncertainties and vagueness on their representations. In contrast to classical crisp Discrete Event Systems (DES), which have been explored to a sufficient extent in the past, an in-depth study of FDES is yet to be performed, and their feasible real-time application areas need to be further identified. This research work intends to address the supervisory control problem of FDES broadly, while formulating new knowledge in the area. Moreover, it examines the possible applications of these developments in the behavior-based mobile robotics domain. An FDES-based supervisory control framework to facilitate the behavior-based control of a mobile robot is developed at first. The proposed approach is modular in nature and supports behavior integration without making state explosion. Then, this architecture is implemented in simulation as well as in real-time on a mobile robot moving in unstructured environments, and the feasibility of the approach is validated. A general decentralized supervisory control theory of FDES is then established for better information association and ambiguity management in large-scale and distributed systems, while providing less complexity of control computation. Furthermore, using the proposed architecture, simulation and real-time experiments of a tightly-coupled multi-robot object manipulation task are performed. The results are compared with centralized FDES-based and decentralized DES-based approaches. -- A decentralized modular supervisory control theory of FDES is then established for complex systems having a number of modules that are concurrently operating and also containing multiple interactions. -- Finally, a hierarchical supervisory control theory of FDES is established to resolve the control complexity of a large-scale compound system by modularizing the system vertically and assigning multi-level supervisor hierarchies. As a proof-of-concept example to the established theory, a mobile robot navigation problem is discussed. This research work will contribute to the literature by developing novel knowledge and related theories in the areas of decentralized, modular and hierarchical supervisory control of FDES. It also investigates the applicability of these contributions in the mobile robotics arena.


identifier: Dumaresq, A. Dean <https://research.library.mun.ca/view/creator_az/Dumaresq=3AA=2E_Dean=3A=3A.html>   (2012) Dendroclimatilogy and dendroecology of the dominant coniferous tree species in eastern Labrador, Canada.  Masters thesis, Memorial University of Newfoundland.

abstract: Eastern Labrador is a region in Canada relatively unexplored both ecologically and climatologically. In light of recent extensive dendroclimatic and dendroecological studies conducted in the northern and western regions of Labrador, eastern Labrador represents the last area in a contiguous sampling grid across this large forested area. This thesis fills this gap by employing similar sampling and analytical methods to other studies in adjacent regions in order to form strong analytical tools that are applicable both on a local and regional scale. -- This thesis employs a systematic sampling grid consisting of three north-south transects and four east-west transects. Two tree-ring chronologies were developed from the dominant species present at each node. In total eight chronologies of black spruce (Picea mariana (Mill) B.S.P.), nine chronologies of balsam fir (Abies balsamea (L.) Mill), two chronologies of white spruce (Picea glauca (Moench) Voss) and one chronology of eastern larch (Larix laricina (Du Roi) K. Koch) were developed. -- This thesis is centered on two manuscripts. The first is focused on the radial growth-climate relationship of the dominant tree species in eastern Labrador. This study identifies four distinct zones of growth response; the 'maritime zone', a continuance of a zone already identified in western Labrador; the 'subarctic zone' acontinuance of a zone identified in northern Labrador; the 'hyper-maritime zone' a previously unidentified zone in southern Labrador; and the 'upland maritime zone' also a potential zone previously unidentified zone along the southeastern coast of Labrador. -- The second manuscript is focused on spruce budworm (Choristoneura fumiferana ) outbreaks in eastern Labrador. This study identifies three major outbreaks in eastern Labrador in 1930s, 1950s and the 1970s. These outbreaks are consistent with regional outbreaks in eastern Canada, and are found to be moving in a west-to-east dispersal pattern from eastern Quebec, through western Labrador and finally into eastern Labrador.


identifier: Dwyer, Allan <https://research.library.mun.ca/view/creator_az/Dwyer=3AAllan=3A=3A.html>   (2012) Atlantic borderland: natives, fishers, planters and merchants in Notre Dame Bay, 1713-1802.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Notre Dame Bay in northeastern Newfoundland was a political, socio-economic, and ecological borderland where four economic cultures converged and competed for access to the contested biota of the region. After the Treaty of Utrecht (1713) Newfoundland English entrepreneurs began to move north from the old English Shore into the French migratory fishing territory above Bonavista. Notre Dame Bay was an ecologically and climatically discrete bioregion and was the homeland of the indigenous Beothuk. The Beothuk pursued their economy over the three biogeographic zones of the Bay. They camped at Boyd's Cove in the borderland to be close to European material culture. Incoming English fur trappers, and then salmon and seal fishers, settled in three principal harbours: Twillingate (Toulinguet), Fogo (Fougue) and Tilting. After 1750, aggressive merchants from Poole, Dorset capitalized on wider French losses in the Atlantic world to commence trading into the Bay. The borderland attracted merchants John Slade and Benjamin Lester. They adapted novel business systems for the procurement and shipment of the Bay's salmon, seals, lumber, peltry and other resources, in addition to cod. The borderland, however, was a place of social as well as economic innovation. Permanent settlement by Europeans saw the evolution of a planter group who, with families that included hired servants, acted as the hinge between networked Atlantic merchants and abundant local commodities. Tilting evolved rapidly into an exclusively Irish and Catholic parish. Conflict erupted after 1763 when French officials orchestrated a final attempt at reclaiming territory in the borderland. By the 1780s, English and Irish planters had successfully crowded out the migratory French. When Benjamin Lester died in 1802, the Beothuk had virtually abandoned the coast for the interior of the island of Newfoundland. With their demise came the end of the Notre Dame Bay borderland event and the incorporation of the region into British imperial systems of administration and commerce.


identifier: Enguehard, René A. <https://research.library.mun.ca/view/creator_az/Enguehard=3ARen=E9_A=2E=3A=3A.html>   (2012) Extracting patterns from large movement data sets using hybrid spatio-temporal filtering: a case study of geovisual analytics in support of fisheries enforcement activities.  Masters thesis, Memorial University of Newfoundland.

abstract: The ubiquitous nature of location tracking technologies has resulted in an increase in movement data being collected. These data are used in many contexts, such as understanding animal migration, aiding in fisheries enforcement, or managing fleets of taxicabs. Such large volumes of data call for more efficient data visualization and analysis methods. This research provides a general approach to the analysis of movement data, named Hybrid Spatio-temporal Filtering (HSF), which allows analysts to filter data based on characteristics of movement within a geovisual analytics environment. Filtering signatures are defined by combining movement path complexity (fractal dimension) and velocity, to extract behavioural patterns from data sets. An evaluation within a fisheries enforcement case study (using VMS data), and comparison to other approaches, confirmed the approach is useful, easy to use, and superior to some other approaches. This research demonstrates the value of signature-building filtering approaches for large movement data sets.


identifier: Fazilatunnessa <https://research.library.mun.ca/view/creator_az/Fazilatunnessa=3A=3A=3A.html>   (2012) Techniques for developing verified concurrent programs based on monitors and semaphores.  Masters thesis, Memorial University of Newfoundland.

abstract: In concurrent programming, mutual exclusion algorithms are used to avoid the simultaneous access of a common resource. Monitors are objects that can be used safely by more than one thread, as their methods are executed with mutual exclusion. In order for threads to wait for some condition to be met, monitors also provide a mechanism for threads to temporarily give up exclusive access. Monitors also have a mechanism for signaling other threads that some condition has been met. -- In this thesis, a general approach to monitors specification and verification code is developed which can be used for solving synchronization problems in an operating system. Specifications are given at the level of C code using the annotation language of Microsoft's Verifying C Compiler (VCC). VCC takes the annotated C program and tries to prove that the program meets these specifications. Later the proposed methodology is demonstrated with example applications.


identifier: Ford, Jessica <https://research.library.mun.ca/view/creator_az/Ford=3AJessica=3A=3A.html>   (2012) Fire: the elemental nature of Draupad?  Masters thesis, Memorial University of Newfoundland.

title: Fire: the elemental nature of Draupad?

abstract: My thesis focuses on the elemental characteristics of Draupadi, the heroine of the classical Sanskrit epic, the Mahabharata. I examine key scenes from the classical Sanskrit Mahabharata that demonstrate Draupadi's link to the element fire, a link the epic makes, I argue, through the attribution to Draupadi of characteristics firepossesses according to Hindu thought; power, destruction, and purification. Draupadi's fiery characteristics often influence the plot of the epic significantly, and it becomes clear that these characteristics play a role in the grand cosmic scheme of the epic. Draupadi is among the instigators of the great war that causes massive destruction. However, this violent destruction occurs at the end of an age (yuga) and as part of the god Krsna's divine plan and thus entails purification of the world prior to the beginning of a new age. -- In the Mahabharata, Draupadi's association with fire begins from her birth from a sacrificial fire altar and colors her behavior throughout the epic, but her connection with fire is also emphasized and developed further in living traditions of worship of her as a goddess. Indeed, traditions of worship exist in which fire is an essential element in the nature of the goddess Draupadi, and in ritual observances centered on her, most notably the firewalking ceremony.


identifier: Fudge, Korrina R. <https://research.library.mun.ca/view/creator_az/Fudge=3AKorrina_R=2E=3A=3A.html>   (2011) The role of key amino acids in the cold-adaptation of the coiled-coil protein tropomyosin.  Masters thesis, Memorial University of Newfoundland.

abstract: The structural basis of cold-adaptation in a rod-shaped (α-helical, coiled-coil) protein tropomyosin was investigated by site-directed mutagenesis. An a -type tropomyosin from Atlantic salmon skeletal muscle having twenty amino acid substitutions compared to a warm-blooded counterpart (rabbit) was used as a model. Two adaptive-strategies were elucidated. The conformational stability of tropomyosin was shown to be enhanced by the presence of a polar amino acid, threonine-179, within the hydrophobic core and the presence of a pair of closely-spaced glycines at positions 24 and 27. The specific details are outlined below in point form: -- 1) Four mutants of Atlantic salmon fast skeletal muscle alpha-tropomyosin were engineered using the QuikChange Lightning site directed mutagenesis kit. Mutations were chosen in order to investigate the role of a pair of unique glycines near to the amino-terminal end as well as threonine 179 which occurs in a core position of the coiled coil. The four mutants were: Gly24Ala, Gly27Ala, Thr179Ala and a double mutant, Gly24Ala/Gly27Ala. Mutations were confirmed by DNA sequencing. -- 2) Recombinant (mutated and non-mutated) tropomyosins were obtained by expression in BL21 cells and induction with isopropylthiogalactopyranoside. Enriched protein was isolated, without exposure to organic solvents or high temperatures, by salt-induced precipitation and chromatography on ion exchange column and hydroxyapaptite columns. -- 3) Far-UV circular dichroism was used to investigate the conformational stability of the recombinant tropomyosins (0.1M NaCI, 20mM sodium phosphate , 1-2 mM dithiothreitol, 0.01 % mass/vol NaN₃). The observed melting temperatures of the three glycine mutants were similar to each other and that of the non-mutated recombinant tropomyosin: Gly24Ala, 36.9 °C; Gly27Ala, 37.3°C; Gly24AlaGly27Ala, 38.1°C and non-mutated, 37.0°C. However, the Thr179Ala mutant showed significant stabilization, 40.7°C. -- Melting profiles of the four tropomyosin mutants and non-mutated recombinant tropomyosin showed that the four mutants displayed more cooperative unfolding profiles compared to the non-mutated protein. -- 4) Limited chymotrypsin digestion (buffer: 50 mM NH₄HCO₃, 0.1 M NaCl, 1 mM DTT, pH 8.5), as monitored by SDA PAGE, revealed that the non-mutated tropomyosin is more susceptible to proteolysis than the Thr179Ala mutant (37°C, ~1:500 enzyme:substrate mole ratio). After 30 min, none of the intact non-mutated protein was detected in the reaction mixture whereas not all of the Thr179Ala mutant had been digested. At ~25 and ~10°C, the difference in the rate of digestion between the two, was not as significant. -- 5) From points 3 and 4 it can be concluded that threonine in the 179 position of salmon tropomyosin is destabilizing compared to the alanine in the same position of rabbit skeletal alpha-tropomyosin. -- 6) Sequencing of two fragments from the chymotrypsin digestion of non-mutant recombinant tropomyosin indicates that the initial cleavage site is between Leu 11 and Lys 12. -- 7) Omp-T digestion (buffer: 0.1 M NaCl, 50 mM sodium phosphate, 5 mM EDTA, 1 mM DTT, pH 7.0) patterns, as monitored by SDS PAGE, were compared between GLY24Ala, Gly27Ala, Gly24AlaGly27Ala, and non-mutated tropomyosin at ~10, ~25, or ~37°C. At all three temperatures, non-mutated tropomyosin was digested faster compared to the glycine mutants, which were different to each other. The observed rate of breakdown decreased in the order: Gly27Ala>Gly24Ala>Gly24AlaGly27Ala, indicating that both glycines influence the conformational stability of the amino-terminal region and that Gly24Ala is more influential than Gly27Ala. -- Note: Some of the above findings were reported in preliminary form at this year's Biophysical Society Meeting (Fudge, K.R. and Heeley, D.H. (2011) A mutant of Atlantic salmon fast muscle tropomyosin. 55th Biophysical Society (Baltimore)). A full manuscript is in preparation for submission to Biochemistry.


identifier: Goldhar, Christina Alison <https://research.library.mun.ca/view/creator_az/Goldhar=3AChristina_Alison=3A=3A.html>   (2012) Water ways: vulnerability to freshwater changes in the Inuit settlement region of Nunatsiavut, Labrador.  Masters thesis, Memorial University of Newfoundland.

abstract: This thesis explores the vulnerability of Nunatsiavut residents to changes in freshwater through case studies in Nain and Rigolet. The current implications of these changes on community water security, food security, and livelihoods are discussed through an approach that emphasizes local perceptions and preferences, considering the experiential dimensions of freshwater changes. A total of 121 individual and household interviews and 13 targeted interviews were conducted in Nunatsiavut in fall 2009 and fall 2010. These findings were complemented by climate data, river discharge records, municipal water system characteristics, and other data gathered from secondary sources. Findings reveal residents have experienced freshwater changes that are presently challenging their ability to access preferred drinking water sources and food sources, and are exacerbating existing financial barriers that restrict time spent on the land. These challenges may intensify in future due to projected implications of climate variability and change on freshwater ecosystems in the region.


identifier: Grimes, Matthew T. <https://research.library.mun.ca/view/creator_az/Grimes=3AMatthew_T=2E=3A=3A.html>   (2012) The molecular signaling of the unconditioned stimulus in rat pup long-term odor preference memory: support for parallel, not serial, memory models.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The formation of memory was originally thought to occur through learning causing the formation of early short-term memory (STM), which transitions into long-term memory (LTM) through the process of consolidation. Work in Aplysia found that memory consists of three distinct phases that are defined by their unique dependence on protein synthesis. Through altering serotonin exposure, experimenters could selectively generate a translation-independent STM, a translation-dependent intermediate-term memory (ITM), and a transcription- and translation-dependent LTM. Here we specifically examine the memory mechanisms of LTM using neonatal odor preference learning, which is a well-defined, associative mammalian learning and memory model. Within this model a single pairing of the conditioned stimulus (CS) of novel odor exposure with the unconditioned stimulus (US) of the activation of bulbar beta -adrenoceptors within rat pups causes the formation of a preference for the conditioned odor that lasts for 24 h. Previous analysis of molecular signaling found that odor preference learning increased bulbar cAMP levels and the phosphorylation of CREB. Manipulating the US of beta -adrenoceptor activation causes the alteration of cAMP signaling resulting in the formation or impairment of neonatal odor preference memory such that there is an optimal level of activation, either too little or excessive activation of the US does not produce learning. -- In the present thesis, we set out to identify the underlying molecular mechanisms that produce 24 h neonatal odor preference memory with specific focus on the US of cAMP signaling. In earlier work we had shown, using translational and transcriptional protein synthesis inhibitors, that as in Aplysia , neonatal odor preference memory includes a translation-independent STM lasting till 3 h after learning, a translation-dependent ITM occurring 5 h after learning, and a transcription- and translation-dependent LTM occurring 24 h after learning. Altering the US through decreasing beta -adrenoceptor activation causes the selective generation of ITM, demonstrating the three characteristics of invertebrate memory in mammalian memory (see Appendix). Neonatal odor preference learning causes the activation of bulbar PKA 10 min after training (Chapter 2) and the activation of bulbar ERK immediately after training (Chapter 3). The direct activation of bulbar PKA acts as a sufficient US to selectively generate ITM and LTM and extend odor preference memory to 72 h (Chapter 2). The activation of Epac is also a sufficient US for the generation of long-term neonatal odor preference memory (Chapter 3), demonstrating that cAMP can work through the PKA or Epac/ERK pathway to generate longer protein synthesis-dependent phases of neonatal odor preference memory. Inhibition of either PKA (Chapter 2) or ERK (Chapter 3) prevented the LTM of rat pup odor preference learning with a normal US, suggesting both pathways contribute synergistically to LTM. LTM can be rescued from the inhibition of either bulbar PKA (Chapter 2) or ERK (Chapter 3) through increasing (3-adrenoceptor activation to a level which normally would not produce learning. Thus higher levels of activation of either pathway alone are sufficient to produce LTM. However, the simultaneous inhibition of both kinases inhibits LTM at any level of beta -adrenoceptor activation tested. PKA (Chapter 2) and Epac (Chapter 3) activation, when given alone, as an intracellular US do not produce STM. Thus ITM and LTM occur independently of STM. In addition a high level of (3-adrenoceptor activation in the presence of either a PKA (Chapter 2) or ERK (Chapter 3) antagonist does not lead to ITM although LTM is now supported. Thus, while PKA and Epac/ERK synergistically generate normal LTM through odor preference learning, the distinct memory phases of STM, ITM and LTM can occur without the prior occurrence of the temporally earlier memory. Here we have demonstrated for the first time that PKA and/or Epac activation can act directly as an US for a long-term mammalian memory. In addition, we find that memory is likely composed of parallel intracellular processes which are quasi-independent rather than occurring as a set of serial, interdependent "consolidating" processes.


identifier: Grineva, Marina <https://research.library.mun.ca/view/creator_az/Grineva=3AMarina=3A=3A.html>   (2012) The use of TV news in teaching culture in foreign language classrooms.  Masters thesis, Memorial University of Newfoundland.

abstract: The issue of integrating language and culture teaching has been a focus of research for several decades. The discourse builds on the idea of inseparability of language and culture and the need to explore effective methods of incorporating target culture into foreign language instruction. The purpose of this study was to explore whether and how integration of TV news clips into the target language teaching facilitates the learning of the target culture. The study adopted a combination of data collection methods which involved questionnaires, follow-up interviews, and participant observations. Analysis of the themes generated from the findings and comparisons with the literature proved the importance and benefits of the use of authentic TV news clips to teach the target culture. Implications for teaching Russian as a foreign language and the Russian culture, as well as recommendations for further research in the area are provided.


identifier: Hann, Allan F. <https://research.library.mun.ca/view/creator_az/Hann=3AAllan_F=2E=3A=3A.html>   (2012) Empathy and fisheries: an introduction.  Masters thesis, Memorial University of Newfoundland.

title: Empathy and fisheries: an introduction

abstract: Over the past two decades the world of industrial fishing has undergone a period of creative reorganization resulting in an influx of potential stakeholders and a move towards an ecosystem-based approach. Traditional 20th century approaches, narrowly defined in terms of utility and efficiency, have given way to a more holistic perspective. As fisheries became redefined as an urgent environmental stewardship issue, the 'Green Agenda' has gained considerable policy-making power. The emerging philosophical tension now revolves around the underlying societal image of what fisheries stewardship should look like. By using Rifkin's (2009) thesis, this paper attempts to introduce the increasingly popular idea of empathic progress as a conceptual framework to better understand fisheries stewardship. Ultimately, the ecosystem-based approach is identified as a unifying medium that is dependent upon more collaborative forums of stakeholder participation. This paper concludes that fisheries stewardship would be better understood if redefined through an empathic model of human nature. Also, the ecosystem-based approach, in both theory and practice, can indeed be explained as a manifestation of expanding empathy as described by Rifkin (2009).


identifier: Haque, Tanjila <https://research.library.mun.ca/view/creator_az/Haque=3ATanjila=3A=3A.html>   (2012) Modeling the comparison of dynamics of AC and DC coupled remote hybrid power systems.  Masters thesis, Memorial University of Newfoundland.

abstract: In this research two different types of remote hybrid power systems are designed using solar, wind and diesel power sources. In both designs load and renewable resources data of an isolated site in St.John's, Newfoundland Canada is considered. The sizing and steady-state performance of the systems are analyzed by the HOMER software tool. While maintaining the same renewable fraction a comparison is made between an AC coupled and a DC coupled hybrid power systems. In first case a 100% AC load is considered. Most of the load in North America is heating type of load, so for the second case a 70% DC and a 30 % AC load is considered. Detailed comparison indicates that the DC coupled hybrid system is better than the AC Coupled hybrid system. Comparison is made based on diesel saving, component required, system cost and environmental impact. The dynamic and transient analysis of two hybrid systems are analyzed by using the Matlab/Simulink software tool. Each component is individually simulated in Simulink, and then the models are combined to form a system.


identifier: Harvey, Brendan <https://research.library.mun.ca/view/creator_az/Harvey=3ABrendan=3A=3A.html>   (2012) Supercritical adsorption testing of porous silicon, activated carbon, and zeolite materials.  Masters thesis, Memorial University of Newfoundland.

abstract: The supercritical adsorption of methane gas on porous silicon, activated carbon, and zeolite materials was studied. An apparatus that utilizes the volumetric adsorption measurement technique was designed and constructed to conduct the experiments. Activated carbon materials consisted of Norit RX3 Extra, Zorflex FM30K woven activated carbon cloth, and Zorflex FM10 knitted activated carbon cloth. Zeolite materials consisted of 3A, 4A, 5A, and 13X zeolites. Porous silicon materials consisted of stain etched and electrochemically etched porous films, and stain etched porous powder. All adsorption tests were conducted at room temperature (approximately 298 K) and pressures up to approximately 5 MPa. Overall, the Norit RX3 Extra granulated activated carbon produced the highest excess adsorption and effective storage capacities. Effective storage and delivery capacities of 109 and 90 [Special characters omitted.] were obtained at a pressure of 3.5 MPa and a temperature of approximately 298 K.


identifier: Hasan, Kamrul <https://research.library.mun.ca/view/creator_az/Hasan=3AKamrul=3A=3A.html>   (2012) Iron catalysts for the epoxidation of olefins and C-C Cross coupling.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: This thesis describes the synthesis, structure and catalytic activity of aminebis(phenolate)Fe(llI) complexes. Fe(III) halide complexes were synthesized supported by tetradentate amine-bis(phenolate) ligands. The general formulae of these ligands are abbreviated as [O₂N₂]RR’ and [O ₂NO’]RR’R”, where [O₂N₂] and [O₂NO’] to describe the four donor atoms of the ligands, R and R'('Bu or Me) represent the substituents at the 2-and 4- positions on the phenolate rings and R" defines the pendant donor functionality such as methoxyethyl (Meth) or tetrahydrofurfuryl (Furf). These paramagnetic complexes were characterized by a variety of methods including elemental analysis, MALDI-TOF mass spectrometry, UV-vis spectroscopy, and magnetic moment measurements. Three iron complexes, FeCl[O₂N₂]BuBu (1), FeBr[O₂N₂]BuBu  (2) and FeBr[O₂NO’]BuMeMeth (3) were structurally characterized by single crystal X-ray diffraction. Magnetic moment measurements of these complexes show high-spin d⁵ Fe(lll) centers. Also, variable temperature magnetic susceptibility measurements of the three structurally characterized complexes were conducted using a SQUID magnetometer. -- For epoxidation of olefins, H₂O₂ was chosen as terminal oxidant because it is convenient and produces water as a by-product. The catalytic activity of these aminebis(phenolate)Fe(III ) halide complexes were investigated for the epoxidation of trans-stilbene. The complex FeCl[O₂N₂]BuBu (1) gave modest yield (36%) of trans-stilbene oxide after 19 h stirring of the reaction mixture at 25°C. However, a practical method for the epoxidation of olefins was discovered by the combination of FeCl₃·6H₂O and 1-methylimidazole in acetone. Heating the reaction mixture to 62°C for 19-21 h significantly improved the product yields. The optimized catalytic conditions were applicable for both aromatic and aliphatic internal and terminal olefins. Also, in-situ generated Fe(III) complexes, made by adding to FeCl₃·6H₂O solutions of selected amine-bis(phenol) ligands, were investigated for the epoxidation of trans-stilbene to see whether any enhancement of reactivity could be obtained. Tridentate amine-bis(phenol) ligands (abbreviated H₂[O₂N]RR’) improved the product yields up to 64% but these yields were less than the epoxidation activity (93%) while using FeCl₃·6H₂O and I-methylimidazole alone. -- Finally, six amine-bis(phenolate)Fe(IlI)(acac) (acac = acetylacetonate) complexes were synthesized by employing previously reported tetradentate amine-bis(phenolate) ligands including [O₂NN’]RR’R”, where R” is the pendant donor functionality such as N,N-dimethylaminoethyl (NMe2). These paramagnetic complexes were also characterized by a variety of methods including elemental analysis, MALDI-TOF mass spectrometry, UV-vis and lR spectroscopy, cyclic voltammetry, and magnetic moment measurements. Four of these complexes, Fe(acac)[O₂N₂]BuBu (9), Fe(acac)[O₂NN’]BuBuNMe2  (10), Fe(acac)[O ₂NN’]BuMeNMe2 (11), and Fe(acac)[O₂NO’]BuMeMeth (13) were structurally characterized by single crystal X-ray diffraction. Magnetic moment measurements of these complexes indicate high-spin d⁵ Fe(III) centers. Cyclic voltammetry of these complexes show ligand-centered reversible redox processes. Preliminary catalytic activity of these complexes was investigated for the C-C cross-coupling of aryl Grignard reagents with alkyl halides. Secondary cyclic halides such as cyclohexyl chloride and bromides gave high yields, however, benzyl chloride and bromide gave moderate and acyclic 2-chloro- and 2-bromobutanes gave poor yields of cross-coupled product.


identifier: Asadollahi Kalviri, Hassan <https://research.library.mun.ca/view/creator_az/Asadollahi_Kalviri=3AHassan=3A=3A.html>   (2012) Dehydration reactions of benzylic alchohols and preparation of palladium nanocrystals in imidazolium and phosphonium ionic liquids.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Palladium catalyzed dehydrative etherification of benzyl alcohols in imidazolium ionic liquids (ILs) were studied. Several hydrophobic and hydrophilic imidazolium ionic liquids were employed and as expected, higher yields were obtained when hydrophobic ionic liquids were used as the reaction media. Among the transition metal complexes studied, Pd(CH₃CN)₂ Cl₂ demonstrated the highest catalytic activity. [BMMIm]PF₆([BMMIm]= 1-butyl-2,3-dimethylimidazolium) was also used to study the possibility of N-heterocyclic carbene (NHC)-palladium complex formation. A catalytic cycle is proposed that supports the important roles of the ionic liquids and Pd in this reaction, in which ionic liquids stabilize the proposed ionic intermediates. -- Phosphonium ILs were found to catalyze the above-mentioned reactions and an added metal was not needed. Benzyl ethers and alkenes were obtained from primary and secondary benzylic alcohols in good to excellent yields. Commercially available hydrophobic phosphonium ionic liquids containing the trihexyl(tetradecyl)phosphonium cation paired with six different anions were used for the reactions under microwave irradiation. NOESY NMR, in addition to some other NMR techniques, were used to study the interaction of substrates and ILs in order to gain insight into the reaction mechanism. The acidic properties of the phosphonium ionic liquids were also investigated in order to potentially correlate the pH of the ionic liquids and the reaction yield. There was no correlation. -- Trihexyl(tetradecyl)phosphonium ILs were also found to support the formation of Pd(0) nanoparticles without the addition of reducing agents such as NaBH₄. Upon varying the Pd(II) sources and the anions of the phosphonium ILs, crystalline Pd nanoparticles grew as truncated octahedrons, octahedrons and trigonal plates with a narrow size distribution. No nanoparticle formation was observed when phosphonium ionic liquid with chloride anions were used. The presence of chloride anions is proposed to lead to oxidative etching of the particles and this process is reduced in the presence of certain anion partners including bis(2,4,4-trimethylpentyl)phosphinate. Two possible reduction mechanisms based on reactions of the phosphonium cation were suggested for the formation of the Pd(0) species. Different techniques such as TEM, XRD, FT-IR and TGA were employed to characterize the prepared nanocrystals and assess the role of the phosphonium ILs in their synthesis. The in situ prepared Pd nanocrystals in phosphonium ILs were used in a Suzuki coupling reaction and high yields were obtained.


identifier: Hassan, Imtiaj <https://research.library.mun.ca/view/creator_az/Hassan=3AImtiaj=3A=3A.html>   (2012) Twisted savonius turbine based marine current energy conversion system.  Masters thesis, Memorial University of Newfoundland.

abstract: The Ocean Network Seafloor Instrumentation (ONSFI) Project is a multidisciplinary research and development project that aims to design, fabricate and validate a proof-of-concept seafloor array of wireless marine sensors for use in monitoring seabed processes. The sensor pods, known as Seaformatics, will be powered by ocean bottom currents and will be able to communicate with each other and to the Internet through surface master units to facilitate observation of the ocean floor from the shore. This thesis explores the use of the twisted Savonius turbine as a means of converting the kinetic energy of the free flowing water into electrical energy for the pods. This will eliminate the need for battery replacement. A physical model of the turbine was constructed and tested in the Water Flume at the Marine Institute of Memorial University and in the Wind Tunnel in the Engineering Building at Memorial University. A mathematical model of the turbine was constructed in SolidWorks. This was tested in the Computational Fluid Dynamics or CFD software FLOW-3D. Experimental results were compared with CFD results and the agreement was reasonable. A twisted Savonius turbine emulator was developed to test a dc-dc boost converter. A low cost microcontroller based MPPT algorithm was developed to obtain maximum power from the turbine. Overall the thesis shows that the twisted Savonius turbine can provide the power needed by the sensor pods. It also shows that CFD is a viable way to study the performance of the Savonius type of turbine.


identifier: Hayden, Victor C. <https://research.library.mun.ca/view/creator_az/Hayden=3AVictor_C=2E=3A=3A.html>   (2012) Computational analysis of the effect of surface roughness on the deflection of gold coated silicon micro-cantilevers due to molecular adsorption.  Masters thesis, Memorial University of Newfoundland.

abstract: In this work numerical simulations were performed in order to study the effects of surface roughness on the deflection of gold coated silicon cantilevers due to molecular adsorption. The cantilever was modeled using a ball and spring system where the spring constants for the Si-Si, Si-Au, and Au-Au bonds were obtained from first principal calculations. The molecular adsorption process was simulated by elongating the natural bond length at available bonding sites chosen randomly on the cantilever. Increasing the bond length created a surface stress on the cantilever causing it to deflect. In all cases the structure refinement was performed by minimizing the energy of the system using a simulated annealing algorithm and a high quality random number generator called Mersenne Twister. The system studied consisted of a 1 micrometer by 1 micrometer portion of a cantilever of various surface roughnesses with variable boundary condition and was processed in parallel on the ACEnet (Atlantic Computational Excellence Network) cluster. The results have indicated that cantilevers with a rougher gold surface deflected more than those with a smoother surface. The increase in deflection is attributed to an increase in stress raisers in the gold film localized around the surface features. The onset of stress raisers increases the differential stress between the top and bottom surfaces and results in an increase in the deflection of the cantilever.


identifier: Heath, Peter Jonathan James <https://research.library.mun.ca/view/creator_az/Heath=3APeter_Jonathan_James=3A=3A.html>   (2012) Funny in the funnies: the formalist comedy of comic strips.  Masters thesis, Memorial University of Newfoundland.

abstract: Comics is a limited, static, and silent medium; comics artists use visual tools to represent narrative aspects that exist beyond the still-life panels, such as timing, unseen sights, sounds, and diegetic worlds. These visual tools recruit reader expectations about comics: readers must possess a "comics literacy" to understand such tools. The modern comics form began as comedy, dating back to the late nineteenth century and strips such as Richard F. Outcault's Hogan's Alley . Despite the comical origin of comics, many comics theorists see comic strips as "essentially ... illustrated joke[s]" (Kunzle "Voices" 8). These theorists fail to consider that since comics requires a specific literacy, comics comedians can defy this literacy to create jokes that are specific to the medium. Such jokes undermine the visual tools of comics and thereby challenge reader expectations about the form. Comic strips are far from illustrated jokes: they are illustrations and jokes, a century-old comedy form that is inexplicably overlooked.


identifier: Heffernan, Paul Michael <https://research.library.mun.ca/view/creator_az/Heffernan=3APaul_Michael=3A=3A.html>   (2012) Socioeconomic status, asthma, and emergency department use in Ontario, Canada.  Masters thesis, Memorial University of Newfoundland.

abstract: Socioeconomic factors are associated with asthma-related emergency department (ED) visits in the USA. This thesis reviewed the literature examining the association between socioeconomic status (SES) and asthma-related ED visits and hospitalizations. Secondly, it investigated if the SES of adult patients with asthma who visit the ED in Ontario, Canada is related to the frequency of ED visits. Using data from the Ontario Asthma Regional Variation Study and Statistics Canada's 2001 Census, the following SES characteristics of asthma-related ED visitors were described: age, sex, household income, marital status, highest level of educational achievement, and employment status. Using additional data from the Canadian National Ambulatory Care Reporting Service, univariate and multivariate Poisson regression analyses of SES characteristics on ED visit counts were conducted and demonstrated that lower household income and lower level of educational attainment were related to an increased risk of ED visits.


identifier: Hemmati, Vahid <https://research.library.mun.ca/view/creator_az/Hemmati=3AVahid=3A=3A.html>   (2012) Monte Carlo simulations of the ABC-Stacked kagome spin structure of XY and Heisenberg models.  Masters thesis, Memorial University of Newfoundland.

abstract: For many years, Ir-Mn alloys have been widely used by the magnetic storage industry in thin-film form as the antiferromagnetic pinning layer in GMR (Giant Magneto Resistance) and TMR (Tunnel Magneto Resistance) spin valves. Despite the technological importance of this structure, it has not previously been noted that the magnetic Mn-ions of fcc IrMn 3 reside on Kagome layers ABC stacked along < 111 > axes normal to the film plane. Results of Monte Carlo simulations will be reported on the bulk fcc Kagome lattice for both XY and Heisenberg models including the eight NN exchange interactions. Degeneracies persist in the 3D case and there is strong evidence for a fluctuation-driven first-order transition to well-defined long-range order characterized as the layered q=0 120-degree spin structure. Effects of varying the inter-layer coupling are also examined.


identifier: Hoben, John L. <https://research.library.mun.ca/view/creator_az/Hoben=3AJohn_L=2E=3A=3A.html>   (2012) Learning what you cannot say: public school teachers and free speech, an exploratory qualitative study.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: This thesis examines the impact of teacher perceptions of free speech on teacher identity and school cultures. Based on interviews with twenty-two teachers in Newfoundland and Labrador, the research explores how perceptions of free speech influence teachers' understanding and performance of their professional identities. Results suggest that teachers are uncertain about the nature and meaning of free speech and that this has a detrimental impact on teaching and learning as well as their ability to participate in school governance initiatives. -- Informed by critical, democratic theories of education, the study explores demands faced by teachers as employees who are also professionals. Participants described a type of professionalism that was rooted in service, obedience and compliance and, which, along with the notion of the reasonable limitation, acted as a disciplinary norm. Significantly, when talking about free speech most teachers emphasized the importance of learning what one cannot say. More specifically, many teachers commenced their exploration of the concept of free speech by focusing on the notion of a reasonable limitation rather than considering the nature and existence of any right. Teachers treated free speech in the workplace as more of a privilege than a right and expressed great reluctance about speaking critically in the public sphere where their views could contribute to an informed public dialogue about contemporary educational issues. -- Free speech, participants suggest, rather than being speech without limits, is the ability to express oneself with minimal administrative interference and often within the context of a "troubled agency". The latter results when teachers are forced to contest professional identities in school systems whose objectives are sometimes at odds with the best interests of students. Between the poles of speech and silence a broad range of speech practices and conceptions of free speech exist. Collectively, these findings suggest a need for further research as well as a renewed emphasis on the democratic role of public schooling within professional associations, teacher-education programs and schools themselves.


identifier: Hori, Tiago S. <https://research.library.mun.ca/view/creator_az/Hori=3ATiago_S=2E=3A=3A.html>   (2012) Stress physiology and immune responses of Atlantic cod (Gadus Morhua) subjected to various challenges.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The Atlantic cod is an economically important species in Canada, as well as in several European countries including Norway, Iceland and Scotland. However, collapse of Atlantic cod stocks has threatened the global Atlantic cod fishing industry. The aquaculture of Atlantic cod could be an alternative source of fish for these markets, but its establishment has been slow, due to the lack of knowledge with regards to certain aspects of this species' biology (e.g health/disease, optimal diet formulation and early maturation). Therefore, the objectives of this thesis were to develop tools to study the stress physiology and immune function of cod, and to apply these to aquaculture relevant questions. In Chapter 2, I: 1) demonstrated that cortisol responsiveness was negatively correlated with growth parameters; and 2) identified differences in the magnitude of the cortisol stress response to handling and potential quantitative trait loci (QTL) associated with this phenotype. In Chapter 3, I investigated the molecular mechanisms that mediate differences in cortisol responsiveness by measuring the mRNA expression of genes involved in cortisol synthesis and tissue responsiveness in Atlantic cod with different magnitudes of cortisol response. In Chapter 4, I report on a stress relevant gene discovery effort conducted as part of the Atlantic C[barbelow]od G[barbelow]enomics and Broodstock Development P[barbelow]roject (CGP), that involved the sequencing and characterization of over 5000 ESTs. Several of the genes identified in this work were validated using quantitative real-time reverse transcription-polymerase chain reaction (QPCR) as heat shock responsive genes, and were subsequently incorporated into the CGP 20K Atlantic cod microarray. Finally, in Chapter 5, I used this microarray platform to study the effect of a gradual temperature increase (from 10 to 16°C over several weeks) on immune-relevant gene transcription, and demonstrated that these increases in temperature dysregulated the anti-viral transcriptomic response of Atlantic cod; fish held at 16°C responding earlier than Atlantic cod held at 10°C. This research has contributed significantly to the resources available for investigating aquaculture relevant questions in Atlantic cod, and generated novel information that can be used to develop molecular markers for use in Atlantic cod broodstock selection programs.


identifier: Hossain, Zahangir <https://research.library.mun.ca/view/creator_az/Hossain=3AZahangir=3A=3A.html>   (2012) Towards the development of a multi-scale model for thermally driven circulations.  Masters thesis, Memorial University of Newfoundland.

abstract: In this thesis, we have studied the development and assessment of a multi-scale Computational Fluid Dynamics (CFD) model for simulating thermally driven flows. Using a constant eddy viscosity model, mean momentum and energy equations, an urban heat island circulation is derived. To resolve the localized spatial features of such a circulation, we have studied the use of an adaptive mesh method based on wavelet transformation. We have proposed a second order fully implicit time integration scheme such that the momentum and the energy equations are solved simultaneously on an adaptive collocated grid. At each time step, a system of nonlinear equations is solved using a multi-scale method, where we have used a Krylov method for improving the rate of convergence, which is a distinct feature of the proposed CFD model. To the best of our knowledge, this is the first time attempt to use an adaptive mesh and a Krylov method to optimize a multi-scale solver for heat island circulation. -- With a brief presentation of the scientific problem and the methodology in Chapters 1-3, the performance of the proposed model has been verified in Chapters 4-5, where we have simulated a shear-driven flow, a thermally driven natural convection flow, and a heat island circulation. We have found that our numerical results agree well with previously published benchmark simulation results of similar flows. First, the numerical error is proportional to the given tolerance. Second, a large CFL number does not affect the accuracy significantly. Finally, the computational cost grows linearly with the number of grid points if the mesh is refined locally. The proposed model is a novel contribution to the field of mesoscale meteorology, which would help for further development of multiscale meteorological modelling.


identifier: Hossain, Mohammad Zahid <https://research.library.mun.ca/view/creator_az/Hossain=3AMohammad_Zahid=3A=3A.html>   (2012) Chemical analysis and potential neuroprotective effects of Newfoundland berries.  Masters thesis, Memorial University of Newfoundland.

abstract: The research in our laboratory involves the study of nutraceuticals, which are foods claimed to have a medicinal effect on human health. Powdered samples of bilberry, blueberry, black currant and lingonberry were provided from Natural Newfoundland Nutraceuticals (NNN Inc., Markland Newfoundland). Whole berries were also collected. For the analysis, various solvent extractions of the berry samples were conducted. The extract solutions were analyzed using a liquid chromatography-mass spectrometry (LC-MS) method for compound detection. Two distinct elution regions for anthocyanins and flavonols were obtained with near base line separation of different compounds. For proper identification of these compounds, two standards (delphinidin-3-glucoside and cyanidin-3-galactoside) were run to obtain a standard retention peak with MS value. LC-MS analysis revealed that various polyphenolic compounds, such as flavonoids (e.g. anthocyanins and flavonols), are present in these species of berries. In addition, our analysis revealed that bilberry and blueberry extracts appear to contain a greater array of antioxidant compounds when compared to black currant and lingonberry extracts. We have also conducted some quantitative analysis in order to compare compounds from native Newfoundland berries to those detected in these species from other regions. The bilberry extract was examined for neuroprotection by applying them to cultured rat brain cortical cells. Cells were injured using an in vitro model of trauma. High levels of lactate were measured after injury, showing that cells were unhealthy. When extracts were added to the cells 15 minutes before injury lactate levels dropped significantly. Aging experiments showed that up to day 17 cell cultures demonstrated no significant death of neurons, but by day 20 there was a dramatic loss of neurons. For glial cells, proliferation was noticed by day 17, but by day 20 there was no significance further change in glial cells. Extracts were added on days 17, 18 and 19 in vitro . By counting neurons and glia on day 20 it was found that no noticeable effect was shown on the glia and neurons with the addition of the extracts. Therefore, bilberry extracts appear to have a more prominent effect on trauma than on aging in cell cultures.


identifier: Hu, Zhenzhong <https://research.library.mun.ca/view/creator_az/Hu=3AZhenzhong=3A=3A.html>   (2012) Copper coordination chemistry with Pyridyl-Imine ligands and their application in aerobic oxidation reactions.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Recyclable catalysts and oxidation chemistry are two important areas in the field of Green Chemistry. In this thesis, research efforts towards the development of a re-usable aerobic oxidation catalyst arc described. The background to this field and a review of relevant literature are presented in Chapter 1. -- In Chapter 2, the preparation and characterization of a series of six potentially tetradentate di(pyridyl-imine) ligands presented. In each case the pyridyl-imine groups were separated by a different linking unit (in L1, CH₂CH₂CH₂(SiMe₂O)₂₀SiMe₂Ch₂CH₂CH₂ ; in L2, CH₂CH₂CH₂SiMe₂OSiMe₂CH₂Ch₂CH₂ ; in L3, CH₂CH₂ ; in L4, CH₂(CH₂)₄CH₂ ; in L5, CH₂(CH₂)₇CH₂ ; in L6, CH₂CH₂CH₂OCH₂CH₂OCH₂CH₂ OCH₂CH₂CH₂). The solubilities of L1 and L2 in supercriticaI carbon dioxide were determined. The coordination chemistry of L1-L2 with Cu(I) was studied by UV-Vis, multinuclear NMR and IR spectroscopies, MALDI -TOF and ESI mass spectrometries and elemental analysis. Dicopper complexes of L3-L6 were prepared for comparison. PGSE (pulsed-gradient spin-echo) NMR spectroscopy was used to determine the hydrodynamic radii of the species in solution and comparison of these data with computational models for the complexes was made. There is no evidence to support linear metallopolymer formation but data suggest that [2+2] and [1+1] metallomacrocyles were formed, with siloxane linking groups encouraging the formation of [1+1] species. Solid-state NMR data on [Cu(Li)]PF₆) indicate the presence of two different environments for the PF₆⁻ anions and this could be due to the location of PF₆⁻ anions both inside and outside the metallomacrocyclic species. -- In Chapter 3, an investigation into the ability of L1-L6 in catalytic oxidations of alcohols when combined with copper bromide (CUBT2) and 2,2,6,6-tetramethylpiperidyl-1-oxy (TEMPO) is described. Analogous bidentate ligand (L 7) showed poorer catalytic activity than L 1- IA Also, the ratio of Cu:ligand was of crucial importance in maintaining high yields. The polydimethylsiloxane (PDMS) derived pyridyl-imine terminated ligand L1 combined with copper (II) ions afforded an effective and selective catalyst for aerobic oxidations of primary and secondary alcohols under aqueous conditions. Preliminary mechanistic studies suggested that bimetallic complexes may be playing a role in the catalytic transformation.  -- In Chapter 4, oxidation of amines using a copper-containing catalytic system is described. CuBr₂ with TEMPO was successfully employed for the aerobic oxidation of primary and secondary benzyl amines in aqueous acetonitrile. The same catalyst system was also used for oxidative cross-couplings of benzylamines with anilines. The electronic and steric properties of the aniline partner were found to be of crucial importance in determining reactivity or lack thereof. A mechanism for these reactions is proposed based on the data obtained to date. In the absence of benzyl amines, electron-rich anilines were found to undergo dehydrogenative coupling and yields of the resulting azo products could be increased by replacing CuBr₂  with CuBr. No ligand (e.g. pyridine) is required for either reaction to proceed and presumably water and acetonitrile solvate the copper-containing intermediates. -- Chapter 5 contains a summary of the thesis and suggestions for future research in this area.


identifier: Hulburt, Jennifer <https://research.library.mun.ca/view/creator_az/Hulburt=3AJennifer=3A=3A.html>   (2012) Biopsychosocial factors influencing physical activity participation among older adults with chronic pain.  Masters thesis, Memorial University of Newfoundland.

abstract: This mixed methods study examined biopsychosocial factors (pain, stress, and exercise self-efficacy) associated with physical activity participation among older adults with chronic pain (CP). A two phase sequential design was implemented through a cross-sectional self-administered survey collected from adults ranging in age from 19-79 years ( N = 99), and one-on-one interviews with six female survey respondents. Interview questions were aimed at exploring study variables and survey responses in greater depth. Mediation analyses in Phase One confirmed the buffer effect of physical activity participation on the association between stress and pain among the oldest adults (i.e. 70+ years). Phase Two found evidence for a theme labeled "self-kinesis", defined as an individual's self-chosen movement dependent upon internal and external stimuli. The focus of kinesiology was expanded in this study, to include a biopsychosocial understanding of the way people with CP move in their lives.


identifier: Hulburt, Sean Corey <https://research.library.mun.ca/view/creator_az/Hulburt=3ASean_Corey=3A=3A.html>   (2012) Seismic modeling and interpretation of porosity in the upper St. George group (Ordovician) Carbonates, Port au Port Peninsula, western Newfoundland.  Masters thesis, Memorial University of Newfoundland.

abstract: The geophysical and lithological heterogeneous nature of the Ordovician St. George Group Carbonates complicates the exploration process on the West coast of Newfoundland. Preferential hydrothermal dolomitization, uplift along the St. George Unconformity, and multiphase structural deformation are responsible for reservoir development in the Upper St. George Group. The ability to map porosity in a heterogeneous dolomitized reservoir such as the Upper St. George Group, prior to drilling, on 2-D seismic data is particularly advantageous for cost effective exploration. Porosity alters the acoustic response of seismic data and a synthetic seismogram study is designed to reveal the effect of porosity on waveform. Block porosity models are designed by statistical analysis in reservoir intervals known from well log data in the Upper St. George Group. The block models are representations of petrophysical changes in bulk density and sonic interval transit time caused by increasing porosity. Since the synthetic seismic trace is a product of the two petrophysical parameters, bulk density and sonic interval transit time, attributes displaying changes fromporosity can be recorded and used as proxies for finding porosity related attribute changes on 2- D seismicdata. Four well data sets on the Port au Port Peninsula (Port au Port -1, Long Range A-09, St. George's Bay A-36, and Long Point M-16) are used in generating models for this study. Synthetic seismograms are designed from block models at 0, 5, 10, and 15% porosity at 20, 40 and 80Hz Ricker wavelets. Multiple Ricker wavelets are implemented to determine which frequency best reveals porosity effects on the synthetics. Complex trace attributes (Instantaneous phase, instantaneous frequency, and reflection strength) are analyzed on each modeled synthetic seismogram. Ultimately, this process creates a predictive tool for mapping porosity in the vicinity of a well in 2-D seismic sections by matching attributes from models to attributes from the real seismic data.


identifier: Hyde, Angela J. <https://research.library.mun.ca/view/creator_az/Hyde=3AAngela_J=2E=3A=3A.html>   (2012) Characterization of colorectal cancer and identification of prognostic determinants.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Newfoundland and Labrador has the highest rate of colorectal cancer (CRC) in Canada, and its rate of familial CRC is among the highest worldwide. The goal of this PhD programme was to further characterize CRC in this province, to gain a better understanding of the heterogeneity of this disease, and to identify clinically relevant differences in the tumours that could be exploited to personalize and improve clinical care. -- The molecular genetic, protein expression, and histological heterogeneities of colorectal cancer were evaluated in three large projects. First, the molecular features related to mismatch repair proficiency were assessed and correlated with family history. In a population-based cohort of 296 patients younger than 70 years at diagnosis, 60% met high or intermediate risk of hereditary CRC according to family history criteria, while only 13% of the associated tumours had defects in the mismatch repair system compatible with Lynch Syndrome. Although Newfoundland has a very high proportion of familial colorectal cancer, Lynch Syndrome does not account for the majority of these cancers; there are likely other, novel hereditary factors contributing to the burden of disease. -- Next, the heterogeneity in protein expression was assessed, using tissue microarray technology and immunohistochemistry, in two studies. To determine if the expression of selected proteins can predict patient outcome, expression scores for 12 proteins were assessed together in unsupervised hierarchical clustering analysis using data from 280 tumours from population-based patients along with another 111 from unselected CRC patients diagnosed younger than age 75 years. This analysis identified three tumour subgroups, one ofwhich had statistically significant reduced disease-specific survival after adjustment for known prognosticfactors (adjusted hazard ratio 1.82). The conclusions were that expression of specific proteins studied may have prognostic utility, and that the statistical methods used were valuable for identifying prognostically relevant subgroups of CRC. -- In the same cohort, lamin A/C protein expression in tumour nuclei was assessed to determine whether it predicted prognosis. Stage III patients whose tumours expressed lamin A/C in >25% of cells were four times more likely to die of their disease when compared to stage III patients with lower levels of expression (adjusted hazard ratio 4.14). -- Finally, to determine whether features of tumour histology were good predictors of microsatellite instability, hemotoxylin and eosin-stained tumour sections were studied from a population-based group of 710 incident CRCs. A number of histological features were associated with microsatellite instability, and an algorithm (PREDICT) was developed to predict this status using multivariate modelling. In a validation cohort of 280 population-based incident CRCs, PREDICT had a sensitivity of 96.9% and a specificity of 76.6% for identifying microsatellite instable tumours. Microsatellite instability can be used to assist in the identification of Lynch Syndrome, and in both the prediction of patient outcome and response to standard adjuvant chemotherapy. This algorithm has been adopted into clinical practice in parts of Ontario, and as part of a Community Genetics initiative in Newfoundland and Labrador.


identifier: Ivany, Ian <https://research.library.mun.ca/view/creator_az/Ivany=3AIan=3A=3A.html>   (2012) Marine Protected areas sustainability: issues of complexity and stewardship.  Masters thesis, Memorial University of Newfoundland.

abstract: The success rate for MPA implementation both in Canada and globally is low. Tools such as 'How is Your MPA Doing?' exist that do assess MPAs, but neglect to assess them long term. This thesis examines MPAs from the point of view of sustainability through the use of various tools, and highlights the issues of complexity and stewardship as factors influencing this sustainability. Specifically, stewardship is a term often linked with MPAs and other environmental initiatives, but rarely defined with any depth or operationalized. This thesis proposes to begin understanding the concept of stewardship through literature review and community dialogue, using the case study of the Eastport Peninsula MPA, in Eastport, Newfoundland, Canada. A set of questions were developed from this dialogue that can begin to assess stewardship in the Eastport region.


identifier: Jahouh, Farid <https://research.library.mun.ca/view/creator_az/Jahouh=3AFarid=3A=3A.html>   (2012) Oligonucleotides sequencing and glycation sites determination of neoglycoconjugate vaccines using tandem mass spectrometry.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Mass spectrometry (MS) has turn out to be a fundamental technology which has produced tremendous strides in the biological sciences. In the last three decades, MS has witnessed convincing growth. Mass spectrometry has rapidly evolved to the forefront of analytical techniques; its ability to analyze proteins, deoxyribonucleic acid (DNA) and carbohydrate biomolecules has been a major driving force in the field of proteomics, genomics and glycomics. The level of performance that is achievable with MS today allows scientists to study various biomolecules in ways that were inconceivable 25 years ago. In this thesis, two different kinds of biomolecules will be covered: oligonucleotides and carbohydrate-protein neoglycoconjugates. -- First of all, the differentiation and sequencing of three constitutional isobaric 18-mer DNA oligomers, namely: GATTC A TAG CTACGAATC 1 , A ATTCG TAG CTACGAATC 2 , and A ATTCG TAC CTACGAAT G 3 were investigated using electrospray ionization (ESI) mass spectrometry with a hybrid QqTOF-MS/MS instrument. Our main objective was to differentiate and to sequence these oligonucleotides. The hypothesis was that the single scan ESI-QqTOF-MS analyses of the DNA oligomers will afford the same series of deprotonated molecular ions and that low-energy collision tandem mass spectrometric analyses (CID-MS/MS) will allow us to differentiate and to sequence the three DNA oligomers using the Mongo Oligo Software. Another objective was also to establish a mass fingerprint of these three oligonucleotides. This will aid to characterize the structure of covalently linked carcinogens to these three isobaric oligonucleotides. -- The second part of the thesis, which includes several chapters, is concerned with the use of MS for the localization of the glycation sites of neoglycoconjugate vaccine models formed by the covalent attachment of specific immunogenic carbohydrates obtained from different virulent bacteria to the protein carrier bovine serum albumin (BSA). This can be accomplished using a methodology based on squaric acid chemistry which was developed to conjugate carbohydrate antigens to lysine residues in proteins. Three different examples of hapten-BSA glycoconjugate vaccines were used: the Vibrio cholerae O1 antigenic specific hapten conjugated to the BSA, the tetrasaccharide side chain of the Bacillus anthracis exosporium conjugated to the BSA, and finally the model β-D-galactopyranosyl-(1→4)-β- D-glucopyranoside (β-lactoside) conjugated to the protein carrier BSA. Initially, the recording of the MALDI-TOF-MS of the different hapten-BSA glycoconjugate vaccines allowed us to determine the hapten-to-BSA ratios. The neoglycoconjugates were then digested and analyzed by MALDI-TOF/TOF-MS/MS and LC-ESI-QqTOF-MS/MS for the determination of the glycation sites. Our hypothesis was that the trypsin digestion will not allow a complete digestion of the protein, since the glycated lysines are not reactive with trypsin. Thus we had to use another protease, the GluC V8 which is known to digest proteins at the C-terminus of the aspartic acid and glutamic acid residues. We also suspected that the LC-ESI-QqTOF-MS/MS analysis was going to afford the identification of a higher number of glycation sites than the MALDI-TOF/TOF-MS/MS analyses.


identifier: Jeffers, Matthew <https://research.library.mun.ca/view/creator_az/Jeffers=3AMatthew=3A=3A.html>   (2012) Post-stroke augmentation of rehabilitation-mediated functional recovery with growth factor adminstration.  Masters thesis, Memorial University of Newfoundland.

abstract: Behavioural rehabilitation is the only treatment option for chronic stroke deficits. Unfortunately, even lengthy rehabilitation often provides incomplete recovery. This study used an animal model of stroke that incorporates key features of sensorimotor impairment commonly observed in stroke patients. A novel combination of growth factor administration and rehabilitation therapy was employed to facilitate functional recovery in this model. -- Sprague-Dawley rats received a stroke via injection of endothelin-1 at two sites in the sensorimotor cortex. This was followed by either a 2-week infusion of epidermal growth factor (EGF) and erythropoietin (EPO) or artificial cerebrospinal fluid (aCSF). Two weeks post-ischemia, animals began either a 6-week enriched rehabilitation program or standard housing treatment: (1) EGF/EPO + rehab; (2) aCSF + rehab; (3) EGF/EPO + no rehab; and (4) aCSF + no rehab. Functional assessments were performed pre- and post-ischemia and after 14, 28, and 42 days of rehabilitation thereafter (approximately every 3 weeks) using the Montoya staircase reaching task, beam traversing and cylinder test of forelimb asymmetry. -- The combination of EGF/EPO + rehab led to a significant acceleration in recovery on the Montoya staircase reaching task after only 2 weeks of therapy compared to rehabilitation-alone. Although the combination of EGF/EPO + rehab resulted in accelerated recovery, animals exposed to rehabilitation-alone recovered to a similar extent after 6 weeks of therapy. This effect was observed in both the staircase and beam traversing tasks where animals that received rehabilitation recovered to a significantly greater extent than standard-housed animals. -- Combining behavioural rehabilitation with growth factors that promote endogenous stem cell mobilization may accelerate recovery beyond that of rehabilitation alone. This has the potential to reduce the length of rehabilitation necessary to recover from stroke deficits.


identifier: Khan, Ahmed <https://research.library.mun.ca/view/creator_az/Khan=3AAhmed=3A=3A.html>   (2012) Is rebuilding collapsed fisheries a wicked problem ?:lessons from a fish chain analysis of northern gulf cod fisheries.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: As with many collapsed fisheries worldwide, the rebuilding of Newfoundland's Northern Gulf cod fishery has been a huge challenge to coastal communities, resource users, scientists, and policy makers. Almost twenty years after a moratorium was declared in the early 1990s, the cod stocks are below conservation limit reference points; only small quotas are available for commercial and recreational fisheries, and a strong possibility exists that the stocks will be listed as endangered. Not only have these and other regional Atlantic cod stocks been slow to rebuild, the cod fishing industry also faces challenges along the production chain, from harvesting to processing, and marketing. While the fishing industry has been restructured from reliance on groundfisheries towards an emphasis on shellfisheries, challenges persist and fishing dependent communities in regions such as the Great Northern Peninsula are struggling to survive. -- A review of global experience with rebuilding collapsed fisheries demonstrate that rebuilding is a 'wicked' problem; meaning that the challenges go beyond scientific and technical solutions, to socioeconomic and sociopolitical concerns. Rebuilding differs from recovery in that it perceives fisheries as coupled social-ecological entities connected to larger societies and the global economy. Rebuilding also takes into account both current and future generations and related equity issues including who pays for the costs of rebuilding and who benefits in the long term. The imperatives for rebuilding fisheries are multidimensional and include food security, livelihoods, revenue, cultural heritage, and ecosystem services. Using a case study of Newfoundland's Northern Gulf cod fisheries, the thesis examines the reasons why rebuilding collapsed fisheries is a wicked problem, and explores governance options for dealing with such multifaceted problems. It employs a 'fish chain' approach (that entails three production stages - the pre-harvest, harvest, and post-harvest stages) in order to generate insights into why the stocks collapsed in the early 1990s, identify reasons for the stalled rebuilding, as well as seek opportunities for collaborative rebuilding efforts. The analysis relies on existing statistical data, peer-reviewed literature, taskforce and policy documents, and findings from key informant interviews conducted along the fish chain for the pre-and post-collapse era. -- The case study findings suggest that ecosystem changes, fishing patterns, transitional livelihood options, changing global seafood markets, consumer preferences for certified seafood, power relations, and policy instruments at different stages in the fish chain have contributed to stall rebuilding. These factors illustrate how and why rebuilding collapsed stocks is a wicked problem. Findings along the fish chain also indicate that rebuilding could be facilitated using multispecies and ecosystem-based approaches that pay attention to by-catch and discards; incorporating effective gear use policies, stewardship incentives, integrated livelihood programs, seafood value-addition, and bridging scale-mismatches between ecosystems, fishing activities, and institutions. Addressing distributional and intergenerational equity concerns, community capacity building, along with changes in power relationships between stakeholders are central to successful rebuilding in the longer term. Related to this, the analysis suggests that 'clumsy' governance options that bring together insights from diverse perspectives from multiple stakeholders could play a key role in creating more institutional spaces towards rebuilding. Some of these clumsy options include stronger support for bottom-up initiatives that respond to regional economic development needs; the development of effective co-governance arrangements with stakeholder and community groups; marketing initiatives that take advantage of local, regional and global consumer choices; and meeting local food security needs and stewardship concerns. Finally, institutional partnerships across different levels of government, in addition to industry and civil society inputs, are critical to rebuilding collapsed groundfisheries in Newfoundland and could provide lessons for efforts to rebuild fisheries worldwide.


identifier: Heath King, Sara-Lynn <https://research.library.mun.ca/view/creator_az/Heath_King=3ASara-Lynn=3A=3A.html>   (2012) Physician knowledge, perception and attitudes towards electronic medical record systems in Newfoundland and Labrador.  Masters thesis, Memorial University of Newfoundland.

abstract: Objectives: To illustrate the knowledge, perceptions, and attitudes of Newfoundland and Labrador (NL) physicians towards electronic medical record (EMR) systems and their use in the practice of health care. -- Methods: A self-administered mail-out survey was used to collect information on physician characteristics, computer experience, perceptions about EMR systems, and opinions on acceptable costs of these systems. -- Results: Forty percent of eligible physicians responded. Physicians agreed that an EMR system should be implemented and that using an EMR would improve the access to and the efficiency of health care. -- Conclusions: The major concern regarding the use and implementation of an EMR system is cost-related. Examining potential subsidy models for implementation and use of EMR systems for NL physicians should be undertaken.


identifier: Kirby, Raie Lene <https://research.library.mun.ca/view/creator_az/Kirby=3ARaie_Lene=3A=3A.html>   (2012) Studies on organocatalytic ketone/nitroalkene Michael addition reactions.  Masters thesis, Memorial University of Newfoundland.

abstract: The organocatalytic Michael addition of aldehydes to ketones is of continuing interest in development of organocatyists for asymmetric synthesis. The Pansare laboratory has focused on research surrounding organocatalysts developed to aid in fundamental carbon-carbon bond forming reactions including the Michael addition reaction. -- Due to the ability to generate up to three stereocenters and products that are useful synthetic intermediates, the organocatalytic Michael addition reaction continues to be of special interest. The work described in this thesis focuses on activation of the nucleophile (Michael donor) through enamine formation with a chiral amine. Simple pyrrolidine-based diamine catalysts showed moderate to high enantioselectivities (up to 92% ee) for conjugate Michael addition reactions of cyclic ketones to nitroalkenes without acid additive. Details regarding the effect of catalyst side chain p Ka on the stereoselectivity as well as the importance of secondary-secondary diamine motif and H-bond donor functionality in the organocatalyst for Michael addition reactions of cyclic ketones to nitroalkenes are discussed


identifier: Lake, Gordon D. <https://research.library.mun.ca/view/creator_az/Lake=3AGordon_D=2E=3A=3A.html>   (2012) Dnmt1 and Dnmt3 of the winter skate (leucoraja ocellata).  Masters thesis, Memorial University of Newfoundland.

abstract: Chromatin management throughout vertebrate development is a stringently controlled and dynamic process. One event involved in that process is the covalent modification of cytosine nucleotides by the addition of a methyl group to the fifth carbon atom of the pyrimidine ring. Enzymes involved in establishing and maintaining DNA methylation patterns (DNA-methyltransferases: Dnmts) have been isolated and characterized in the teleost and mammalian lineages. There are structural similarities between enzymes as well as basic developmental expression patterns but there are fundamental differences in gene number and function in the context of two very different reproductive strategies. Subclass Elasmobranchii displays a wide variety of reproductive strategies and studying genome management in this subclass could provide great insight into the key differences and similarities in DNA methylation observed in the tetrapod and teleost models. I have isolated and characterized the first full length cDNAs of the maintenance and de novo methyltransferases ( Dnmt1 andDnmt3 respectively) from the Winter Skate (Leucoraja ocellata ), a member of subclass Elasmobranchii. Evidence is presented for multiple Dnmt3 splice variants as well as at least two Dnmt3 retrotransposed pseudogenes. Preliminary experiments indicate that the early developmental methylation dynamics observed in both mammals and teleosts may also be present in L. ocellata.


identifier: Laracy, Ashley Juliette <https://research.library.mun.ca/view/creator_az/Laracy=3AAshley_Juliette=3A=3A.html>   (2012) The promise of another spin: identity and stigma among video lottery players in St. John's, Newfoundland and Labrador.  Masters thesis, Memorial University of Newfoundland.

abstract: Gambling in Canada has expanded in recent decades following two Criminal Code amendments. The growth of this sector has resulted in gambling being accepted as a more mainstream leisure activity with reduced social stigma. Video lottery terminals (VLTs) however are somewhat of an exception. First introduced to Newfoundland and Labrador in 1991, there is evidence that VLT players suffer from social stigmatization, which may be attributable to negative public and media constructions of this form of gambling. Social constructionists argue that what is defined as deviance by public actors is culturally embedded, therefore resulting in many VLT players being aware of, and potentially internalizing, these negative attitudes. -- Using concepts from the sociology of deviance, this thesis will map the medicalization of VLT gambling in Canada as a result of a rapid expansion of the gaming sector. Drawing upon observations and interview data with Gamblers Anonymous members in St. John's Newfoundland, the thesis proceeds by answering the following questions: How do VLT players see themselves and their gambling activity? What kinds of stigma do they suffer from as a result of their gambling? What types of management techniques are employed by individuals to ensure that they are able to cope with the label of compulsive gambler?


identifier: Lehman, Graeme <https://research.library.mun.ca/view/creator_az/Lehman=3AGraeme=3A=3A.html>   (2012) Correlation of throwing velocity to the results of lower body field tests in male college baseball players.  Masters thesis, Memorial University of Newfoundland.

abstract: Baseball specific athleticism, potential and performance have been difficult to predict. Muscle strength and power has shown to help increase throwing velocity through resistance training research however themajority of research has focused on the upper body. The present study sought to determine if bilateral or unilateral lower body field testing correlates with throwing velocity and if so to what extent. Throwing velocity scores were correlated to the following tests; medicine ball scoop toss and squat throw, bilateral and unilateral vertical jumps, single and triple broad jumps, hop and stop in both directions, lateral to medial jumps, 10 and 60 yard dash, and both left and right single leg 10 yard hop for speed in 42 college baseball players. It was hypothesized that the concentric strength of the trail leg and the eccentric strength of thelead leg will correlate positively with throwing velocity. A stepwise multiple regression analysis, assessing therelationship between shuffle and stretch throwing velocities and lower body field test results determined that right handed throwing velocity from the stretch position was significantly predicted by lateral to medial jump right (LMJR) and body weight (BW) R² =0.322, whereas lateral to medial jump left (LMJL) R² = 0.688 significantly predicted left stretch throw. Right handed shuffle throw was significantly related to LMLR and Medicine Ball scoop R² =0.338; whereas, LMJL, BW and LMJR significantly contributed to left handed shuffle throw R²=0.950. Overall, this study found that lateral to medial jumps were consistently correlated with highthrowing velocity in each of the throwing techniques, in both left and right handed throwers. This is relevant because it is the first study to our knowledge to correlate throwing velocity with a unilateral jump in thefrontal plane, mimicking the action of the throwing stride.


identifier: Lethbridge, Grant David <https://research.library.mun.ca/view/creator_az/Lethbridge=3AGrant_David=3A=3A.html>   (2012) A geological model of the hibernia formation in the vicinity of the Terra Nova and Hebron/Ben Nevis oil fields, Jeanne D'Arc basin, offshore Newfoundland.  Masters thesis, Memorial University of Newfoundland.

abstract: The Hibernia Formation is a stacked siliciclastic sequence of interbedded sandstone and shale up to one kilometer thick that was deposited across the Jeanne d'Arc Basin. It represents coarse-grained progradation into the Jeanne d'Arc Basin during the second half of east-west oriented extension of the North Atlantic Rifting phase. Published literature regarding deposition of the Hibernia Formation has been focused on the Hibernia oil field, located along the western basin margin, or as broad, generalized regional studies across the entire Jeanne d'Arc Basin. No publications exist regarding the depositional environment of the Hibernia Formation along the eastern basin margin in the vicinity of the Terra Nova, Hebron, and Ben Nevis oil fields. This thesis presents the available data in the region surrounding the Terra Nova oil field and aims to refine the depositional model of the Hibernia Formation. -- Three dimensional seismic data and fifty-one wells compose the raw data used in this study. Three wells have recovered core, totaling 150 meters over three zones, however these wells are all located in the northern half of the study area. Together the geophysical and geological data were combined to vertically subdivide the Hibernia Formation into ten depositional intervals that can be correlated across the study area. These depositional units record variations in rate of sedimentation and depositional direction as well as fluctuations between progradational and retrogradational trends. The Hibernia Formation is finally summarized as a series of block diagrams illustrating changes between successive units and overall evolution of the Hibernia Formation.


identifier: Liu, Hanze <https://research.library.mun.ca/view/creator_az/Liu=3AHanze=3A=3A.html>   (2012) Improving web search personalization using Luhn-Inspired vector re-weighting.  Masters thesis, Memorial University of Newfoundland.

abstract: Web search personalization has been studied as a way to tailor Web search results to individual users based on their interests and preferences. Commonly, document and personalization profile features are stored in vector space models using measures such as term frequency (TF) and term frequency-inverse document frequency (TF*IDF). Inspired by Luhn's model of term importance, a novel approach is proposed in this thesis to identify and re-weight significant terms in the vector-based personalization models. Evaluations with a set of ambiguous queries illustrate that the order of the search results using this approach is superior to the TF approach and comparable to the TF*IDF approach. However, it is based only on the information stored in the personalization profiles, rather than requiring access to the distribution of each term across the document collection. As such, it can be applied more broadly when only limited information regarding the collection being searched is available.