identifier: Pratt, Allison <https://research.library.mun.ca/view/creator_az/Pratt=3AAllison=3A=3A.html>   (2016) Entre Montesquieu et l'encyclopédie. Voltaire face à l'inquisition Espagnole.  Masters thesis, Memorial University of Newfoundland.

abstract: Nous étudions la progression, au siècle des Lumières en France, de la critique de l'Inquisition espagnole à partir de l'oeuvre de Montesquieu, en montrant comment Voltaire, principal défenseur de la tolérance religieuse du siècle, a approfondi l'analyse de Montesquieu pour faire de l'Inquisition espagnole un modèle exemplaire du fanatisme religieux, et comment finalement Voltaire a pour sa part influencé les articles sur le sujet rédigés par Louis de Jaucourt pour l'Encyclopédie.


identifier: Lubben, Kelsey <https://research.library.mun.ca/view/creator_az/Lubben=3AKelsey=3A=3A.html>   (2016) The dual effect of normobaric hypoxia on heart rate variability and substrate partitioning following interval cycling.  Masters thesis, Memorial University of Newfoundland.

type: Thesis NonPeerReviewed

abstract:
Recent studies have shown the importance of the beat-by-beat changes in heart
rate influenced by the autonomic nervous system (ANS), or heart rate variability (HRV).
The purpose of this study was to examine the lasting effects of hypoxic exercise on HRV,
and its influences on substrate usage. Results from this study could lead an increased
understanding on this topic. Eight active healthy males (age: 31±11 years; height: 180±7
cm; weight: 83±8 kg; VO₂max (maximal oxygen consumption): 4.4±0.6 L•min⁻¹)
underwent normoxic and hypoxic (FᵢO₂= 0.15) conditions during high-intensity interval
(HIIT) cycling (70%-high interval, 35%-rest interval). Cycling intensity was determined
by a peak power output cycling test. Each experimental session consisted of a basal
metabolic rate determination, up to 45-minutes of HIIT cycling, and three 30-minute
post-exercise metabolic rate measurements (spanning 3 hours and 15 minutes after
exercise). During exercise, RPE was higher (p<0.01) and LAC (lactate) increased
(p=0.001) at each point of time in hypoxia, with no change in normoxia. After hypoxic
exercise, the SNS/PNS ratio (overall ANS activity) was significantly higher (p<0.01) and
significantly decreased through time in both conditions (p<0.01). In addition, a
significant interaction between time and conditions (p<0.02) showed a decrease in LAC
concentration through time post-hypoxic exercise. The findings showed that a single bout
of hypoxic exercise alters ANS activity post-exercise along with shifting substrate
partitioning from glycolytic to lipolytic energy production. The significant decrease in
LAC concentration post-hypoxic exercise supports the notion that hypoxic HIIT induces
a greater muscle glycogen depletion leading to increased fat oxidation to sustain
glycogenesis and gluconeogenesis to maintain blood glucose level during recovery.


identifier: Sagmeister, Linda <https://research.library.mun.ca/view/creator_az/Sagmeister=3ALinda=3A=3A.html>   (2016) How does employer support and educational background effect an Ergonomics Practitioner’s awareness of the relationship between ergonomics and psychosocial hazard control?  Masters thesis, Memorial University of Newfoundland.

abstract: There is a growning need to address psychological health and safety in the workplace. Ergonomics tends to be widely recognized for its physical applications, such as ¨office¨ and ¨manual materials handling¨ however the other domains of specialization of ergonomics (cognitive and organizational) appear to be less well known. This study evaluates the level of understanding that professionals who practice ergonomics have of the relation between ergonomics and the control of psychosocial hazards in the workplace. A survey was distributed to ergonomics practitioners and asked them about their awareness of the relation between ergonomics and workplace psychosocial hazard control. Ergonomists and human factors specialists demonstrated a greater awareness of this relationship than other allied occupational groups that also practice ergonomics, however they indicated that there may be difficulties in the “real world” applying these areas of knowledge into practice. Participants who demonstrated a high level of awareness of the relation between ergonomics and psychosocial hazard control demonstrated stronger organizational commitment than participants with a low awareness. Ergonomics practitioners who reported having employer support for professional development also demonstrated a higher degree of awareness of the relation between ergonomics and psychosocial hazard control, as did the professionals who had been practicing in the field the longest. This research provides some insight for professional associations for Ergonomists, employers of Ergonomists, and human resource professionals about how ergonomics practitioners perceive the ergonomics field and the profession as well as their employing organization.


identifier: Khan, Muhammad Akhtar <https://research.library.mun.ca/view/creator_az/Khan=3AMuhammad_Akhtar=3A=3A.html>   (2016) Ad-atoms and their enhancement effects on Pt activity for formic acid oxidation.  Masters thesis, Memorial University of Newfoundland.

abstract: Formic acid oxidation has been widely studied at Pt as a model reaction to understand fundamental aspects of electrocatalytic reactions in fuel cells. Electrocatalytic oxidation of formic acid takes place through two parallel pathways (direct and indirect). The indirect pathway proceeds via CO as an intermediate, which is known to be responsible for the poisoning of Pt and its consequent decrease in activity. Surface modification of Pt with ad-atoms is known to hinder this poisoning and promote the direct pathway. The incorporation of polymers (polyaniline, polycarbazole, polyindole) as supports also increases activity. Irreversibly adsorbed Sb and Bi on Pt are known to show high electrocatalytic activity for formic acid oxidation. This work presents the dependence of Sb and Bi irreversible adsorption on immersion time, metal solution concentration and pH. The activity of Sb and Bi modified Pt was correlated against immersion time and percent coverage of Pt by ad-atoms. Polyaniline support effects in combination with a Bi modified Pt catalyst showed enhancement in oxidation current compared to Pt-Bi.


identifier: Nalepa, Mariella <https://research.library.mun.ca/view/creator_az/Nalepa=3AMariella=3A=3A.html>   (2016) Synthetic modelling study of marine controlled-source electromagnetic data for hydrocarbon exploration.  Masters thesis, Memorial University of Newfoundland.

abstract:
The marine controlled-source electromagnetic method (CSEM) is a geophysical technique
for mapping subsurface electrical resistivity structure in the offshore environment. It has
gained ground in recent years as a tool for remote detection and mapping of hydrocarbon
reservoirs as it serves as an independent yet complementary method to seismic acquisition.
While CSEM data contains useful information about the subsurface, modelling and
inversion are required to convert data into interpretable resistivity images. Improvement
of modelling tools will assist in closing the gap between acquisition and interpretation of
CSEM data. The primary focus of this study was to explore the limits of our present modelling
capabilities in the context of marine electromagnetic scenarios. Software based on
the three-dimensional CSEM finite-element forward code CSEM3DFWD (Ansari and Farquharson,
2014; Ansari et al., 2015) was employed in this study. While testing of this
software had been expanded to models of relevance to mineral exploration, its performance
for models which are representative of marine geologic environments, in particular those
which are encountered in offshore oil and gas exploration, had not yet been investigated.
In this study, marine models of increasing complexity were built and tested, with the ultimate
goal of synthesizing marine CSEM data for three-dimensional earth models which
were complete in their description of the subsurface. Computed responses were compared
to results existing in the literature, when available. To investigate the capability of the code
in modelling realistic scenarios, forward solutions were computed for a marine reservoir
model based on the real-life North Amethyst oil field, located in the Jeanne d’Arc Basin,
offshore Newfoundland. When the capability of modelling realistic earth models is fully
realized, forward modelling may be used to assess the utility of the marine CSEM method
as a tool for hydrocarbon detection and delineation in specific offshore scenarios.


identifier: Liu, Ming <https://research.library.mun.ca/view/creator_az/Liu=3AMing=3A=3A.html>   (2016) Experimental and numerical studies of hydrodynamic interaction of two bodies in waves.  Masters thesis, Memorial University of Newfoundland.

abstract:
This thesis focuses on experimental and numerical studies of the hydrodynamic interaction
between two vessels in close proximity in waves. In the model tests, two
identical box-like models with round corners were used. Regular waves with the same
wave steepness and different wave frequencies were generated. Six degrees of freedom
body motions and wave elevations between bodies were measured in a head sea
condition. Three initial gap widths were examined. In the numerical computations,
a panel-free method based seakeeping program, MAPS0, and a panel method based
program, WAMIT, were used for the prediction of body motions and wave elevations.
The computed body motions and wave elevations were compared with experimental
data.


identifier: Malik, Rania <https://research.library.mun.ca/view/creator_az/Malik=3ARania=3A=3A.html>   (2016) A comparison of modality effect performance in children: how reading achievement performance is influenced by echoic memory.  Masters thesis, Memorial University of Newfoundland.

abstract: This study investigates if less skilled readers suffer from deficits in echoic memory, which may be responsible for limiting the progress of reading acquisition. Serial recall performance in auditory, visual, and noisy conditions was used to assess echoic memory differences between skilled and less skilled readers. Both groups showed the typical modality effect, demonstrating that each had a functioning echoic memory. Less skilled readers performed more weakly than skilled readers on noisy serial recall, suggesting that the recall of less skilled readers is more vulnerable to interference than the recall of skilled readers. Nonword repetition performance indicated that all participants had reduced recall as a function of word complexity and word length. No difference between reading groups was found on this task; however, as nonword repetition and size of modality effect did not correlate, this task may not be a measure of echoic memory.


identifier: Memarpour, Pegah <https://research.library.mun.ca/view/creator_az/Memarpour=3APegah=3A=3A.html>   (2016) Ritual and routine: a means of adaption.  Masters thesis, Memorial University of Newfoundland.

title: Ritual and routine: a means of adaption

abstract:
Researchers have demonstrated how engaging in rituals or ‘patterned’ behaviours can
help people cope with stressful situations and significant life changes. However, limited
knowledge exists on the role of ritual practices in prison and how federally incarcerated
Canadian men use these rituals to deal with their imprisonment. To respond to this lacuna in the
literature, transcripts from 56 semi-structured interviews with former male federal prisoners
released on parole into Ontario, Canada, were analyzed for emergent themes identifying the
purpose of ritual and routine practices across prisons with different security classifications.
Findings reveal the effectiveness of rituals for managing and mitigating the stresses of
incarceration, specifically that prisoners’ routine behaviours constitute a positive strategy of
adaption to incarceration (e.g., alleviating stress and passing time) in preparation for life postincarceration
(e.g., anticipatory socialization). Structural Ritualization Theory frames the
analyses and implications presented in this study.


identifier: MacDonald, Sarah <https://research.library.mun.ca/view/creator_az/MacDonald=3ASarah=3A=3A.html>   (2016) The effect of note taking on memory for details in investigative interviews.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Across 3 experiments, the effect of different styles of note taking, summary and access to
notes was examined for memory for the details contained in a witness interview. In
Experiment 1, participants (N = 40) were asked to either take notes or listen as they
watched a witness interview. In Experiment 2, participants (N = 84) were asked to either
take notes in one of three ways (i.e., conventional, linear, spidergraph) or listen as they
watched a witness interview. In Experiment 3, participants (N = 112) were asked to take
notes using the conventional or spidergraph method of note taking while they watched a
witness interview and were subsequently given an opportunity to review their notes or sit
quietly. Participants were then either granted access to their notes during testing or were
not provided with their notes. Results of the first two experiments revealed that note
takers outperformed listeners. Experiment 2 showed that conventional note takers
outperformed those who used organizational styles of note taking, and post-hoc analyses
revealed that recall performance was associated with note quality. Experiment 3 showed
that participants who had access to their notes performed the best. The implications of
these findings for police training programs in investigative interviewing are discussed.


identifier: Palamakumbura, Sudharaka <https://research.library.mun.ca/view/creator_az/Palamakumbura=3ASudharaka=3A=3A.html>   (2016) Homomorphic encryption and database query privacy.  Masters thesis, Memorial University of Newfoundland.

abstract:
Homomorphic encryption is a particular type of encryption method that enables
computing over encrypted data. This has a wide range of real world ramifications
such as being able to blindly compute a search result sent to a remote server without
revealing its content.
In the first part of this thesis, we discuss how database search queries can be
made secure using a homomorphic encryption scheme based on the ideas of Gahi
et al. Gahi’s method is based on the integer-based fully homomorphic encryption
scheme proposed by Dijk et al. We propose a new database search scheme called the
Homomorphic Query Processing Scheme, which can be used with the ring-based fully
homomorphic encryption scheme proposed by Braserski.
In the second part of this thesis, we discuss the cybersecurity of the smart electric
grid. Specifically, we use the Homomorphic Query Processing scheme to construct a
keyword search technique in the smart grid. Our work is based on the Public Key Encryption with Keyword Search (PEKS) method introduced by Boneh et al. and a
Multi-Key Homomorphic Encryption scheme proposed by L´opez-Alt et al.
A summary of the results of this thesis (specifically the Homomorphic Query
Processing Scheme) is published at the 14th Canadian Workshop on Information
Theory (CWIT).


identifier: Romani, Shadab <https://research.library.mun.ca/view/creator_az/Romani=3AShadab=3A=3A.html>   (2016) Succinct representations of Boolean functions and the Circuit-SAT problem.  Masters thesis, Memorial University of Newfoundland.

abstract:
We study the question whether there is a computational advantage in deciding properties
of Boolean functions given a succinct description of the function (such as a Boolean circuit)
as opposed to black-box access to the function. We argue that a significant computational
advantage for a large class of properties implies a non-trivial algorithm for the Circuit Satisfiability (Circuit-SAT) problem. In particular, we show that if there is a property with
strong black-box lower bounds yet decidable in BPP, which also has a highly sensitive instance
computable by a small circuit, then there is a non-uniform sub-exponential algorithm
for the Circuit-SAT problem. Additionally, we analyze variants of this question for other
computational models.


identifier: Shahnaz, Shuhana <https://research.library.mun.ca/view/creator_az/Shahnaz=3AShuhana=3A=3A.html>   (2016) Modeling the distribution of crossovers and interference with mice DNA data.  Masters thesis, Memorial University of Newfoundland.

abstract:
Chiasma and crossover are two related biological processes of great importance in
the understanding genetic variation. The study of these processes is straightforward
in organisms where all products of meiosis are recovered and can be observed. This
is not the case in mammals. Our understanding of these processes depends on our
ability to model them. In this study I describe the biological processes that underline
chiasma and crossover as well as the two main inference problems associated with these
processes: i) in mammals we only recover one of the four products of meiosis and, ii)
in general, we do not observe where the crossovers actually happen, but we find an
interval containing type-2 censored information. NPML estimate was proposed and
used in this work and used to compare chromosome length and chromosome expansion
through the crosses.


identifier: Haghshenas, Sadegheh <https://research.library.mun.ca/view/creator_az/Haghshenas=3ASadegheh=3A=3A.html>   (2015) Packings and coverings of the complete graph with trees.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
In this thesis, we define the spectrum problem for packings (coverings) of G to be
the problem of finding all graphs H such that a maximum G-packing (minimum G-
covering) of the complete graph with the leave (excess) graph H exists. The set of
achievable leave (excess) graphs in G-packings (G-coverings) of the complete graph is
called the spectrum of leave (excess) graphs for G. Then, we consider this problem
for trees with up to five edges.
We will prove that for any tree T with up to five edges, if the leave graph in a
maximum T-packing of the complete graph Kn has i edges, then the spectrum of leave
graphs for T is the set of all simple graphs with i edges. In fact, for these T and i
and H any simple graph with i edges, we will construct a maximum T-packing of Kn
with the leave graph H.
We will also show that for any tree T with k ≤ 5 edges, if the excess graph in
a minimum T-covering of the complete graph Kn has i edges, then the spectrum of
excess graphs for T is the set of all simple graphs and multigraphs with i edges, except
for the case that T is a 5-star, for which the graph formed by four multiple edges is
not achievable when n = 12.


identifier: Shafiei Zadeh, Shirin <https://research.library.mun.ca/view/creator_az/Shafiei_Zadeh=3AShirin=3A=3A.html>   (2016) Toxic metal recovery from spent hydroprocessing catalyst.  Masters thesis, Memorial University of Newfoundland.

abstract:
Spent hydroprocessing catalysts (HPCs) are solid wastes generated in refinery industries
and typically contain various hazardous metals, such as Co, Ni, and Mo. These wastes
cannot be discharged into the environment due to strict regulations and require proper
treatment to remove the hazardous substances. Various options have been proposed and
developed for spent catalysts treatment; however, hydrometallurgical processes are
considered efficient, cost-effective and environmentally-friendly methods of metal
extraction, and have been widely employed for different metal uptake from aqueous
leachates of secondary materials. Although there are a large number of studies on hazardous
metal extraction from aqueous solutions of various spent catalysts, little information is
available on Co, Ni, and Mo removal from spent NiMo hydroprocessing catalysts.
In the current study, a solvent extraction process was applied to the spent HPC to
specifically remove Co, Ni, and Mo. The spent HPC is dissolved in an acid solution and
then the metals are extracted using three different extractants, two of which were aminebased
and one which was a quaternary ammonium salt. The main aim of this study was to
develop a hydrometallurgical method to remove, and ultimately be able to recover, Co, Ni,
and Mo from the spent HPCs produced at the petrochemical plant in Come By Chance,
Newfoundland and Labrador. The specific objectives of the study were: (1) characterization
of the spent catalyst and the acidic leachate, (2) identifying the most efficient leaching agent
to dissolve the metals from the spent catalyst; (3) development of a solvent extraction
procedure using the amine-based extractants Alamine308, Alamine336 and the quaternary
ammonium salt, Aliquat336 in toluene to remove Co, Ni, and Mo from the spent catalyst; (4) selection of the best reagent for Co, Ni, and Mo extraction based on the required contact
time, required extractant concentration, as well as organic:aqueous ratio; and (5) evaluation
of the extraction conditions and optimization of the metal extraction process using the
Design Expert® software.
For the present study, a Central Composite Design (CCD) method was applied as the main
method to design the experiments, evaluate the effect of each parameter, provide a
statistical model, and optimize the extraction process. Three parameters were considered
as the most significant factors affecting the process efficiency: (i) extractant concentration,
(ii) the organic:aqueous ratio, and (iii) contact time. Metal extraction efficiencies were
calculated based on ICP analysis of the pre- and post–leachates, and the process
optimization was conducted with the aid of the Design Expert® software.
The obtained results showed that Alamine308 can be considered to be the most effective
and suitable extractant for spent HPC examined in the study. Alamine308 is capable of
removing all three metals to the maximum amounts. Aliquat336 was found to be not as
effective, especially for Ni extraction; however, it is able to separate all of these metals
within the first 10 min, unlike Alamine336, which required more than 35 min to do so.
Based on the results of this study, a cost-effective and environmentally-friendly solventextraction
process was achieved to remove Co, Ni, and Mo from the spent HPCs in a short
amount of time and with the low extractant concentration required. This method can be
tested and implemented for other hazardous metals from other secondary materials as well.
Further investigation may be required; however, the results of this study can be a guide for
future research on similar metal extraction processes.


identifier: Werdyani, Salem <https://research.library.mun.ca/view/creator_az/Werdyani=3ASalem=3A=3A.html>   (2016) Characteristics of the germ-line Copy Number Variations (CNVs) in colorectal cancer patients.  Masters thesis, Memorial University of Newfoundland.

abstract:
INDELs and CNVs are types of structural variations. This project aimed to
computationally predict and examine the possible biological consequences of the
INDELs/CNVs in colorectal cancer patient genomes using the QuantiSNP and PennCNV
algorithms. A total of 69,290 INDELs/CNVs were identified in 495 patients and satisfied
the quality control criteria. These variations constituted 3,486 distinct INDELs/CNVs and
clustered in 1,527 CNV regions. The majority of the variations were CNVs (~79%) and
deletions (~81%). Around 63% of the distinct variations were identified to completely or
partially cover the sequences of 1,673 genes, and a large number of these genes were
observed to act in cancer related biological pathways. In summary, this project detected a
number of biologically interesting INDELs/CNVs in the genomes of colorectal cancer
patients. Further studies in the Savas lab will investigate these variants in detail including
their possible associations with the disease characteristics and outcomes in colorectal
cancer.


identifier: Mohammed, Zakiyah <https://research.library.mun.ca/view/creator_az/Mohammed=3AZakiyah=3A=3A.html>   (2015) Modelling the growth of Northern Cod.  Masters thesis, Memorial University of Newfoundland.

title: Modelling the growth of Northern Cod

abstract:
We develop a body size growth model of Northern cod (Gadus morhua) in Northwest
Atlantic Fisheries Organization (NAFO) Divisions 2J3KL during 2009-2013. We
use individual length-at-age data from the bottom trawl survey in these divisions during
2009–2013. We use the Von Bertalanffy (VonB) model extended to account for
between-individual variations in growth, and variations that may be caused by the
methods which fish are caught and sampled for length and age measurements. We
assume between-individual variation in growth appears because individuals grow at
a different rate (k), and they achieve different maximum sizes (l∞). We also included
measurement error in length and age in our model since ignoring these errors can
lead to biased estimates of the growth parameters. We use the structural errors-invariables
(SEV) approach to estimate individual variation in growth, ageing error
variation, and the true age distribution of the fish. Our results shows the existence of individual variation in growth and ME in age. According to the negative log likelihood
ratio (NLLR) test, the best model indicated: 1) different growth patterns across
divisions and years. 2) Between individual variation in growth is the same for the
same division across years. 3) The ME in age and true age distribution are different
for each year and division.


identifier: Fay, Amelia E. M. <https://research.library.mun.ca/view/creator_az/Fay=3AAmelia_E=2E_M=2E=3A=3A.html>   (2016) Understanding Inuit-European contact along the Labrador Coast: a case for continuity.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This dissertation examines the effects of an increasing European presence on Labrador Inuit society from the late sixteenth- through early nineteenth centuries. Previous research on this topic has tended to focus on site-specific analyses and often divided the coast into North and South, creating a dichotomy that ignored Inuit mobility and emphasized the arrival and placement of Europeans along the coast. I explore this topic diachronically, highlighting the Inuit response to their changing social landscape by investigating its effects on constructions of gender, status, and prestige within Inuit society.
Archaeological data collected from Black Island, Labrador were selected as the focal point for this research as the occupants of this dwelling were noted in a 1776 Moravian census and included Mikak, a Person of National Historical Significance. The data from this site was compared with extant collections from eight other sites (10 houses and 3 middens) spanning over 200 years from various locations along the Labrador coast. Using quantitative and qualitative analyses I compare artifact categories representing both European-made and traditional Inuit materials to explore any significant changes over time or regional differences. Quantitatively these assemblages differ, but not in a uniform pattern, suggesting that access to these items was not limited to a particular region along the coast nor did it differ greatly from the earliest encounters to the established period of intensive contact. The same cannot be said for the qualitative analysis as some sites presented unique and prestigious artifacts in their assemblages.
The results of this study show that for roughly 250 years Inuit sites spanning the coast had more in common than previously assumed; perceived changes in their settlement, subsistence, and material culture strategies were not simply reactionary. Instead these changes were part of gradually evolving relationships within their physical, social, and material worlds. I suggest that exploring the nature of Inuit-European contact through a long-term perspective situates these changes and removes the peaks from previous work that highlighted change over continuity and emphasized difference over similarity.


identifier: Mbakwe, Anulika Blessing <https://research.library.mun.ca/view/creator_az/Mbakwe=3AAnulika_Blessing=3A=3A.html>   (2016) Investigating factors that influence the catch rates of northern stone crab (Lithodes maja).  Masters thesis, Memorial University of Newfoundland.

abstract:
Natural resources in marine and coastal areas are of crucial economic importance for the province of Newfoundland and Labrador. They sustain the livelihoods and natural heritage of communities, and provide stable income for current and future generations, provided they are well-managed. Not all fisheries in Newfoundland and Labrador are fully exploited, and there are ongoing efforts to establish new sustainable industries in the province. For commercial fisheries, management requires a detailed assessment of the gear used in the fishery to ensure a sustainable industry. Assessing the effectiveness of fishing gears, and understanding the extent of fishing gear impacts on marine ecosystems, can provide unique protection for aquatic habitats and help ensure sustainability of marine species.
In this study, I assessed a potential fishing gear for use in a northern stone crab (Lithodes maja: Linnaeus, 1758) fishery, and investigated how abiotic factors - water current direction, hourly variation in water current direction, turbidity and interspecific interractions, influence catch rates of this species, with the aid of an underwater video-camera. Results demonstrate that the Norwegian two-door pot is effective in capturing this species, and catch rates of this species is partly influenced by water current directions, hourly variation in water current direction and interspecific interactions of species. Turbidity had no effect on the catch rates of northern stone crab. In addition, there was little or no impact of the pot on the sea bed, there were no cases of escape and discard mortality, ghost fishing, lost pot, or injury to both target or non-target species in the study. Conscientious fishery management strategies remain essential in the effort towards ensuring sustainable existing and emerging commercial fisheries, as well as the benthic ecosystem.


identifier: Hameed, Abdul <https://research.library.mun.ca/view/creator_az/Hameed=3AAbdul=3A=3A.html>   (2016) Risk-based shutdown inspection and maintenance for a processing facility.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
In this research, a risk-based shutdown inspection and maintenance interval optimization for a processing facility is proposed. Often inspection and maintenance activities can’t be performed until the processing unit or plant is taken into a non-operational state, generally known as “shutdown”. Extensive work on inspection and maintenance interval estimation modeling is available in the concerned literature however, no to very limited application on shutdown inspection and maintenance modeling is observed for a continuous operating facility. Majority of the published literature deals to optimize individual equipment inspection and maintenance interval without considering the overall impact of plant unavailability due to shutdown. They all deal to optimize individual equipment inspection and maintenance interval considering cost, risk, availability and reliability. The efforts towards finding an optimal inspection and maintenance interval is not considered in these studies especially when it requires unit or plant to be in shutdown state from an operational state for performing inspection and maintenance. This topic is selected to bridge the existing gap in the available literature and to provide a means to develop a methodology to estimate the shutdown inspection and maintenance interval for a continuous processing unit or plant, rather an inspection and maintenance interval for each piece of equipment considering the overall asset availability, reliability and risk.
A component failure due to wear or degradation is a major threat to asset failure in a processing facility. A carefully planned inspection and maintenance strategy not only mitigate the effects of age-based degradation and reduce the threat of failure but also minimize the risk exposure. Generally failure caused by wear or degradation is modeled as a stochastic process. For an effective inspection and maintenance strategy, the stochastic nature of failure has to be taken into consideration. The proposed methodology aims to minimize the risk of exposure considering effect of failure on human life, financial investment and environment by optimizing the interval of process unit shutdown. Risk-based shutdown inspection and maintenance optimization quantifies the risk to which individual equipment are subjected and uses this as a basis for the optimization of a shutdown inspection and maintenance strategy.


identifier: Alkasasbeh, Ahmad <https://research.library.mun.ca/view/creator_az/Alkasasbeh=3AAhmad=3A=3A.html>   (2016) Cyclic packing designs and simple cyclic leaves constructed from Skolem-type sequences.  Masters thesis, Memorial University of Newfoundland.

abstract:
A Packing Design, or a PD(v; k; λ) is a pair (V; β) where V is a v-set of points
and β is a set of k-subsets (blocks) such that any 2-subset of V appears in at most λ
blocks. PD(v; k; λ) is cyclic if its automorphism group contains a v-cycle, and it is
called a cyclic packing design. The edges in the multigraph λKᵥ not contained in the
packing form the leaves of the CPD(v; k; λ); denoted by leave (v; k; λ) :
In 2012, Silvesan and Shalaby used Skolem-type sequences to provide a complete
proof for the existence of cyclic BIBD(v; 3; λ) for all admissible orders v and λ.
In this thesis, we use Skolem-type sequences to find all cyclic packing designs with
block size 3 for a cyclic BIBD(v; 3; λ) and find the spectrum of leaves graph of the
cyclic packing designs, for all admissible orders v and λ with the optimal leaves, as
well as determine the number of base blocks for every λ when k = 3.


identifier: Moffatt, Amelia <https://research.library.mun.ca/view/creator_az/Moffatt=3AAmelia=3A=3A.html>   (2016) The use of statin drug therapy for primary prevention of cardiovascular disease in primary care: a retrospective cohort study.  Masters thesis, Memorial University of Newfoundland.

abstract:
Statin drugs have been widely studied for their efficacy in secondary prevention by preventing
the recurrence of cardiovascular disease (CVD), however their use as a primary prevention
strategy in individuals without documented CVD, especially at low risk, is highly controversial
among the medical community. The current research study used data from the Canadian Primary
Care Sentinel Surveillance Network (CPCSSN); a database that houses point-of-care data from
physician electronic medical records (EMR) from primary care practices all across Canada. It is
a valuable resource to conduct outcomes research on diseases and conditions managed in
primary care.
This retrospective inception cohort study assessed whether statin drug use over a period of five
years (January 1, 2009 to December 31, 2013) reduced outcomes of CVD and all-cause mortality
in a group of primary prevention patients (i.e. patients who have never had CVD) from
Newfoundland and Labrador (NL). The CPCSSN database was linked to both the Clinical
Database Management System and Mortality Registry housed at the Newfoundland and
Labrador Center for Health Information (NLCHI).
The results based on univariate analysis suggested that statin drug use was associated with
increased rates of CVD, hospitalization and coronary artery disease (CAD). However, these
apparent harmful effects of statins in causing CVD were no longer present when other risk
factors of CVD (sex, age, BMI, LDL-C, HDL-C, HTN, smoking status, total cholesterol, total
triglycerides and blood pressure) were controlled for using logistic regression. Statin drugs were
also significantly associated with decreased rates of all-cause mortality, and this beneficial effect
persisted after controlling for CVD risk factors. Our results also demonstrated that statins were
significantly associated with an increase in diabetes mellitus (DM) over the study period. The
results obtained were similar when we considered compliance and used only those in the
exposure group who had used statins for ≥ 80% of the five year follow up period.
The use of statin drugs in a primary prevention situation is still controversial, and the results of
this study provide real world data from EMR practices in NL on the effects of statins on CVD
outcomes and death. This study concludes that at best, statins had no effect on CVD outcomes
but decreased all-cause mortality. The results of a “real-life” assessment of the benefits of using
statins in a primary prevention situation are not nearly as impressive as what clinical trials
suggest.


identifier: Bakhit, Amir Halim Zaky <https://research.library.mun.ca/view/creator_az/Bakhit=3AAmir_Halim_Zaky=3A=3A.html>   (2016) Rare earth elements (REEs) in shallow and deep water articulated brachiopods: sensitive tracers of paleo-oceanography.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Through time, oceans have experienced physicochemical variations in a response to the evolution of the earth and its atmosphere. Geochemical proxies are employed to define these variations, evaluate their magnitudes and identify the responsible factors. Because of the unique behavior of the rare earth elements (REEs) within the oceanic system, they have been proven to be a leading proxy for tracing changes in the marine geochemical cycle (Elderfield et al., 1988; Holser, 1997). However, obtaining a reliable rare earth element (REE) proxy seems to be very difficult. Several archives were investigated for their REE proxy potential but with limited success. The biggest difficulty which complicates our understanding is perhaps the ambiguous REE compositions acquired from both modern and fossil archives.
REEs are incorporated into the crystal lattice of the marine components in very small fractions. Investigating their REE contents and fractionations in the different modern and ancient archive requires complete elimination of the internal and the external contaminants. Without their removal, inputs from the bound oxides, detritus and/or organic matter overprint the archives’ REE compositions. Despite the importance of the cleaning procedures, reviewing the literature reveals the lack of a rigorous methods or steps that should be followed to acquire uncontaminated REE signals. Therefore, the establishment of a reliable sample processing protocol that satisfies the most stringent demands for procuring reliable and robust REEs from marine materials is among the objectives of the thesis. To achieve this goal, five different cleaning procedures (P) were applied on Liothyrella neozelanica valves dredged from the deep water of the South Pacific Ocean (north of New Zealand). P-1 consisted only of rinsing the specimens extensively with distilled water. P-2 was the immersion of the specimens in hydrogen peroxide for 3 continuous days. Physically cleaning the shells under binocular microscope using a sharp stainless-steel blade comprised the P-3 procedure. In P-4 the specimens were physically cleaned, then leached with 10% hydrochloric acid until they deemed white. In P-5 the specimens were processed using all above cleaning procedures (water washing, physical cleaning, H2O2 treatment, and HCl leaching).
The P-1 specimens yielded high concentrations of Mn, Fe, U and ΣREEs particularly Ce resulting from the primary layer, periostracum and the adsorptive particulates and detritus. P-2 specimens yielded similar trend as P-1, but with partial depletion in the Ce/Ce* anomalies. Specimens of P-3 (physical cleaning only) yielded depleted ΣREEs and lower Mn, Fe, and U concentrations with slightly negative Ce anomaly. P-4 and P-5 fragments yielded remarkable reductions if the ΣREE, Mn, Fe, U concentrations and ‘normal’ Ce anomaly, however, the P-4 fragments are slightly enriched in their ΣREE contents. The P-5 seems to be the ultimate protocol for modern shells but P4 should be applied to fossil shells due to the absence of the organic remnants adhering to the outermost shell.
The reproducibility of the clearing protocol on individuals of different water masses was evaluated by applying the P-3 and P-5 procedures on deep water shells recovered from the abyssal depths of the Caribbean Sea. Its validity for archives of different settings, on the other hand, was assessed by applying the P-1, P-2, P-3 and P-5 on shallow water shells from the Irminger Sea, west of Iceland. The results were uniform and consistent supporting the reliability and robustness of the proposed protocol. However, it is infallible and its completion must be verified in the light of the archives’ elemental composition.
The P-4 was applied to Ordovician, Silurian, Pennsylvanian and Permian brachiopods and near-micritc whole rock to test the efficiency of the suggested protocols on the ancient archives. The fossils yielded ΣREE, Mn, Fe, U concentrations and Ce anomalies comparable to their modern counterparts, while the whole rock are slightly to extensively enriched. Those with higher Fe and Mn contents than 300 and 100 ppm, respectively, their Ce/Ce* values should be adjusted by −13% to be considered for the paleoredox investigations.
One of the thesis main objectives is to evaluate the REE proxy potential of the brachiopods archive for paleooceanographic and paleoenvironmental investigations. This evaluation required minimizing the impact of variations in the environmental conditions on seawater REE compositions. It was, consequently, conducted by assessing the REE uptake of the deep water shells (>500 m) of the orders Rhynchonellids and Terebratulids obtained from the Caribbean Sea, North Atlantic, South Pacific and Southern Oceans. The shells display gradual enrichment REESN patterns with increasing atomic numbers that are punctuated consistently with the negative CeSN excursions. The REE contents of their secondary fibrous calcite layers are elevated relative to the ambient water masses by an average factor of 0.81x10⁵. The REE distribution coefficients between the shells’ crystal lattice and the ambient seawater vary consistently within the series in response to changes in ionic radii relative to that of the Ca²⁺ cation. The calculated log KD values for the shells of two orders are remarkably similar and consistent with those of foraminiferal calcite.
The deep water shells yielded L:H and L:M ratios similar to those of their water masses, while their M:H ratios are notably different, defining a secondary trend that is directly proportional to the shells’ depths. Although their Ce/Ce* anomalies are consistently negative, they vary significantly but in a manner reflecting the variations in the prevalent oceanographic conditions. The open water shells display a vertical Ce/Ce* profile relatively similar to the Ce vertical curve in seawater.
To assess the REE incorporation into different parts/layers of the brachiopod shell structure, and the impacts of changes in the seawater physicochemical parameters on the REE fractionations and distributions of the brachiopod archives, articulated shells of the orders Terebratulida and Thecideidina were obtained from the shallow waters (<500 m) of the Norwegian, the Irminger and the Ross Seas, the Denmark Strait, Bonne Bay and Bay of Fundy and Friday Harbor. Their REE compositions were correlated to those of the deep water settings. The umbo region is secreted with either selective REE uptake or species dependency during the growth of the juvenile stage, whereas the primary layer’s REE incorporation is variable and incidental. Precipitation of the pedicle and brachial valves’ secondary layers occur with a small range of differences that falls within the natural variation of the brachiopod’s lattice. The Thecideidinid shells yielded remarkable variations in their elemental, REE compositions and the REESN patterns due to the domination of the primary layers over their structures. Seawater parameters of temperature, salinity and depth seem to have controls on the shells’ REE composition. Depth plays a major rule on the shell REE fractionations, while temperature and salinity have moderate to minor impacts on the REE contents.
The shallow water shells have been divided into six depth intervals, and their L:H ratios were utilized to estimate the paleobathymetry of several Paleozoic formations. The evaluation was successful in placing the Permian Gyanyima, the Pennsylvanian Naco, Boggy and the Silurian Chicotte, Becscie and Jupiter Formations in shallow depths (<15-50 m).


identifier: Ghosh, Abhinaba <https://research.library.mun.ca/view/creator_az/Ghosh=3AAbhinaba=3A=3A.html>   (2016) Age dependent differential effect of norepinephrine on the pyramidal neurons of the anterior piriform cortex in mouse model of early odor preference learning.  Masters thesis, Memorial University of Newfoundland.

abstract: Rodent pups show preference to an odor when it is paired with a tactile stimulation- stroking the back with a paintbrush- only within a critical period of postnatal (P) 10-12 days of age. Norepinephrine (NE) released from the locus coeruleus during stroking plays a crucial role in this learning. Here we established the learning model in mouse pups and showed that it was β-adrenoceptor dependent. Next we investigated the developmental changes in pyramidal cell excitability and NE responsiveness in the anterior piriform cortex layer II neurons. Two concentrations (0.1 and 10 μM) of norepinephrine did not alter intrinsic properties in either group, although there was an age-related difference in those properties. In P8–11 pups, norepinephrine at 0.1 μM presynaptically decreased miniature inhibitory postsynaptic current (IPSC) and increased miniature excitatory postsynaptic current (EPSC) frequencies, opposite to the effect of norepinephrine at 10 μM. This suggested involvement of different receptors with different concentrations. In P14 and older pups both concentrations promoted inhibition.


identifier: Maybank, Allison <https://research.library.mun.ca/view/creator_az/Maybank=3AAllison=3A=3A.html>   (2016) Factors associated with people going to the emergency department for non-urgent visits rather than attending a family physician.  Masters thesis, Memorial University of Newfoundland.

abstract: Context: Poor access to primary care (PC) has been associated with increased use of emergency departments (ED) for non-urgent reasons. Identifying PC factors associated with non-urgent ED use will inform the development of policies designed to lower this usage. Objective: Determine PC factors associated with non-urgent ED use. Design: 1) Canada-wide, and 2) St. John's, NL ED cross-sectional surveys. Participants: 1) Adult PC patients across Canada 2) adult ED patients at Health Sciences Centre, St. John's, NL. Outcome Measures: Patient attended the ED for non-urgent reasons. Results: Limited availability of after-hours services (OR=2.08,p<0.0001) and the ability to arrange an appointment as soon as wanted (OR=0.56,p<0.0001) were significantly associated with non-urgent ED use within the Canada-wide data. Non-urgent St. John’s ED users report that restricted hours of operation influenced them to attend the ED, more than other users (62.5%vs.25.0%, p=0.0083). Conclusions: Limited hours and timely availability of services affect patients’ decisions to attend the ED for non-urgent issues.


identifier: Ahmed, Abdelrahman <https://research.library.mun.ca/view/creator_az/Ahmed=3AAbdelrahman=3A=3A.html>   (2016) StableFlow: a physics inspired digital video stabilization.  Masters thesis, Memorial University of Newfoundland.

abstract:
This thesis addresses the problem of digital video stabilization. With the widespread use
of handheld devices and unmanned aerial vehicles (UAVs) that has the ability to record
videos, digital video stabilization becomes more important as the videos are often shaky
undermining the visual quality of the video. Digital video stabilization has been studied
for decades yielding an extensive amount of literature in the field, however, current approaches
suffer from either being computationally expensive or under-performing in terms
of visual quality . In this thesis, we firstly introduce a novel study of the effect of image
denoising on feature-based digital video stabilization. Then, we introduce SteadyFlow, a
novel technique for real-time stabilization inspired by the mass spring damper model. A
video frame is modelled as a mass suspended in each direction by a critically dampened
spring and damper which can be fine-tuned to adapt with different shaking patterns. The
proposed technique is tested on video sequences that have different types of shakiness
and diverse video contents. The obtained results significantly outperforms state-of-the
art stabilization techniques in terms of visual quality while performing in real time.


identifier: Rasmussen, Andrea N.  <https://research.library.mun.ca/view/creator_az/Rasmussen=3AAndrea_N=2E_=3A=3A.html>   (2016) Contrasting effects on HLA and PD-L1 expression through inhibition of MAPK pathway in triple negative breast cancer cells.  Masters thesis, Memorial University of Newfoundland.

abstract:
Expression of human leukocyte antigen (HLA) molecules is essential for antitumour
immune responses. Interferon gamma (IFN-γ) up-regulates HLA and,
paradoxically, programmed cell death ligand-1 (PD-L1), which inhibits immune
activation. The mitogen-activated protein kinase pathway (MAPK), overactivated in
triple negative breast cancer (TNBC), is implicated in HLA and PD-L1 expression. We
hypothesized that its inhibition may modulate HLA and PD-L1 expression in TNBC.
Human TNBC and non-TNBC cell lines were treated with various MEK inhibitors
(MEKi) in the presence/absence of IFN-γ. Flow cytometry, immunofluorescence and
Western blotting were used to assess MEKi mediated changes in constitutive and
inducible HLA and PD-L1 expression.
U0126 antagonized cell surface HLA expression, but not total HLA protein, while
the clinically relevant MEKi(s), Trametinib and Selumetinib, generally augmented
constitutive and inducible cell surface HLA class I. All MEKi (s) reduced PD-L1 expression.
These results have important implications for MEKi in targeting immunotherapy for
TNBC.


identifier: Rahimi, Ayda <https://research.library.mun.ca/view/creator_az/Rahimi=3AAyda=3A=3A.html>   (2016) Processing, modeling and interpretation of wide-angle seismic data of an active plate boundary, south of Cyprus.  Masters thesis, Memorial University of Newfoundland.

abstract: Cyprus lies at the southern edge of the Aegean-Anatolian microplate, caught in the convergence of Africa and Eurasia. Subduction of the African plate below Cyprus has probably ceased and this has been attributed to the docking of the Eratosthenes Seamount microcontinental fragment on the northern edge of the African plat in the subduction zone. In early 2010, on R.V. Maria S. Merian, we conducted a wide-angle seismic survey to test the hypothesis that the Hecataeus Ridge, another possible microcontinental block lying immediately offshore SE Cyprus, might be related to an earlier docking event. The upper crust of southern Cyprus is dominated by ophiolites, with seismic velocities of up to 7 km s⁻¹. A wide-angle seismic profile along Hecataeus Ridge was populated with 15 Canadian and German ocean-bottom seismometers at 5 km intervals and these recorded shots from a 6000 cu. in. air gun array, fired approximately every 100 m. Rough topography of the seabed has made picking of phases and their modeling a demanding task. Bandpass and coherency filtering have enabled us to pick phases out to around 80 km. Tomographic inversion of short-range first arrivals provided an initial model of the shallow sub- seabed structure. Forward modeling by ray-tracing, using the code of Zelt and Smith, was then used to model crustal structure down to depths of around 25 km, with no evidence of reflections from Moho. Modeling results provide good control on P-wave velocities in the top 20 km and some indications of deeper events. There is no evidence of true velocities approaching 7 km.s⁻¹ in the top 20 km below the Ridge that might indicate the presence of ophiolitic rocks. Regional gravity and magnetic field data tend to support this proposition. We thus conclude that Hecataeus Ridge is not composed of characteristically ophiolitic, Cyprus (upper plate) crust, and most likely it might be derived from the African (lower) plate.


identifier: Richter, Anna <https://research.library.mun.ca/view/creator_az/Richter=3AAnna=3A=3A.html>   (2016) E-storybooks and paper storybooks for preschoolers: effects on attention, learning and engagement.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
The increasing availability of electronic storybooks (e-books) for preschoolers has raised
a variety of concerns regarding their potential to distract children and diminish prereading
skill acquisition as well as change the nature of the parent-child interaction during
book reading. Alternatively, because e-books are delivered via popular mobile devices, it
has been suggested that they might motivate children to read more, allow children to
benefit from built-in reading aids, and increase their focused attention to story details.
The current study investigated the utility of e-books for facilitating early literacy skills in
a sample of 79 3 to 5-year-olds. Children read an e-book and paper storybook with an
experimenter and were asked story comprehension questions following each book
reading. Children then completed two measures of executive function (Day-Night Task
and Digit Span Task) as well a measure of receptive vocabulary. Dependent measures
were children’s (1) recall of factual and inferred story detail (2) duration of looking to
book, adult, and off-task during reading, (3) engagement and communication during story
reading. ANOVAs revealed that: (1) there was a significant increase in recall of story
information across age, but no difference as a function of story format (2) all children
were highly attentive during story reading but looked relatively more at the e-book than
the paper book and more at the adult during the paper book reading (3) children were
engaged with and communicated about both stories, but more so with the e-book than the
paper book. The results of the current study suggest that carefully designed e-books
support story comprehension similarly to paper books and also increase children’s
engagement and communication during book reading.


identifier: Odeyemi, Ayoola Samuel <https://research.library.mun.ca/view/creator_az/Odeyemi=3AAyoola_Samuel=3A=3A.html>   (2016) Structured decision making as a tool for facilitating stakeholder engagement in non-renewable resource management: using the case study of hydraulic fracturing in the Green Point Shale formation in western Newfoundland.  Masters thesis, Memorial University of Newfoundland.

abstract: This thesis examines the importance of effective stakeholder engagement that complies with the doctrines of social justice in non-renewable resources management decision-making. It uses hydraulic fracturing in the Green Point Shale Formation in Western Newfoundland as a case study. The thesis uses as theoretical background John Rawls’ and David Miller’ theory of social justice, and identifies the social justice principles, which are relevant to stakeholder engagement. The thesis compares the method of stakeholder engagement employed by the Newfoundland and Labrador Hydraulic Fracturing Review Panel (NLHFRP), with the stakeholder engagement techniques recommended by the Structured Decision Making (SDM) model, as applied to a simulated case study involving hydraulic fracturing in the Green Point Shale Formation. Using the already identified social justice principles, the thesis then developed a framework to measure the level of compliance of both stakeholder engagement techniques with social justice principles. The main finding of the thesis is that the engagement techniques prescribed by the SDM model comply more closely with the doctrines of social justice than the engagement techniques applied by the NLHFRP. The thesis concludes by recommending that the SDM model be more widely used in non- renewable resource management decision making in order to ensure that all stakeholders’ concerns are effectively heard, understood and transparently incorporated in the nonrenewable resource policies to make them consistent with local priorities and goals, and with the social justice norms and institutions.


identifier: McCrate, Farah R. <https://research.library.mun.ca/view/creator_az/McCrate=3AFarah_R=2E=3A=3A.html>   (2016) The Newfoundland and Labrador colorectal cancer screening program for the average risk population: A pre-implementation study of the family physician and target population perspective on fecal occult blood testing.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Background
Newfoundland and Labrador (NL) has the highest incidence and mortality rates of colorectal cancer (CRC) in North America. In March 2010, funding was announced for a fecal occult blood test (FOBT) screening program for those aged 50 – 74 years and at average risk for CRC. The main goal of this program is to reduce mortality from CRC through the detection of pre-cancerous polyps or early-stage cancer. Research was undertaken prior to program implementation to survey the average risk population regarding their intention to participate in screening and to ascertain family physicians’ knowledge of screening guidelines, current screening practices and level of support for an organized screening program.
Methods
Average risk individuals living in three different areas of the province were surveyed (n = 959): a rural area with a familial cluster of high genetic risk CRC, and a rural and an urban area without familial clusters of high genetic risk CRC. It was hypothesized that those living in the area with a presence of high genetic risk CRC would be most likely to report positive intention to participate in screening. It was further hypothesized that between the two areas without any familial clustering of CRC, urban respondents would be more likely to report a positive intention to screen.
The intent of the family physician survey (n = 274) was to enhance understanding of FOBT screening practices and level of physician support for an organized screening program. It was posited that the majority of physicians would be supportive of an organized FOBT screening program but would not necessarily be screening their average risk patients according to recommended guidelines.
Results
No significant association was found between intention to screen and a) presence of a familial cluster of high genetic risk CRC (p = 0.17), or b) residing in a rural versus urban region (p = 0.30). In multivariate analysis, prior awareness of FOBT [OR = 1.92, 95% CI 1.32 – 2.77, p = 0.001] and prior use of FOBT [OR = 1.87, 95% CI 1.18 – 2.97, p = 0.008] were significant predictors of positive screening intention.
Almost all family physicians indicated support for an organized screening program (n = 256, 94.8%). Despite this, colonoscopy was the most commonly recommended procedure for screening average risk patients. Most physicians were compliant with the guideline- recommended age to start screening, (n = 228, 83.5%), but fewer were compliant with the recommended age for stopping (n = 66, 25%).
Conclusions
Presence of a familial cluster of high genetic risk CRC did not appear to positively impact the screening intention of average risk individuals. Based on previous research, a higher than expected level of positive intention to screen was reported across all regions that were sampled. Similarly, it was unanticipated that almost all family physicians would be supportive of an organized screening program. Follow-up research, post-implementation of the screening program, will provide an opportunity to determine whether reported intention and support translate into high rates of participation and physician referral for screening.


identifier: Septama, Erlangga <https://research.library.mun.ca/view/creator_az/Septama=3AErlangga=3A=3A.html>   (2015) The late Quaternary deep-sea depositional system in the Gulf of Papua: linking source, dynamic sedimentation process and depositional architecture.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This study was undertaken to explore interactions among eustatic sea level change, fluvial
sediment supply, oceanic processes, and seabed morphodynamics, and their controls on delivery
of terrestrial sediments to the deep sea, using the Gulf of Papua (GoP), between New Guinea and
Australia, as a natural laboratory. The GoP is a 500 km wide embayment that contains excellent
examples of adjacent passive and active terrestrial-oceanic margins with multiple sources of
terrestrial and neritic carbonate sediments. This work examines source to sink sediment delivery
from river systems to the slope and deep-sea basins of the GoP, over the last ~40 ky, at
millennial temporal resolution and finer. The results offer new insights into the development of
sedimentary successions in deep-sea basins, and also into approaches for provenance analysis.
Mapping and integration of acoustic facies with core physical properties, sedimentary fabric, and
chronostratigraphy allows placement of seafloor evolution into a well-defined temporal
framework. Chronological constraints permit an assessment of changes in sediment supply and
depositional environments across time and space, from marine isotope stage (MIS) 3 to MIS 1.
Sand provenance provides additional insights regarding sediment sources and routing.
In summary, the study yields a narrative of sediment delivery along a ~500 km basin margin that
is more complex than initially imagined. The sediment delivery to and conduit connectivity
between deep-sea basins evolves over time due to the combined effects of eustasy, oceanic
processes, and dynamic seabed morphology. Multiple terrestrial sediment sources along a ~500
km basin margin initially converge to form one continuous deep-sea system of channels and two
major basins prior to 30 ky BP, that become bathymetrically separated by a large mass-transport deposit. Subsequent sea-level fall approaching the late glacial maximum (LGM) initially drives
re-partitioning of sediment sources to create multiple compositionally distinct depocentres,
presumably due to migration and incision of individual rivers across the newly exposed coastal
plain. Multiple separate deep-sea channels then regain compositional similarity near the end of
the LGM, due to regional erosion into compositionally similar catchment rocks. Furthermore
sand transport shuts down, except for one depocentre (MV22), fed by local volcanic, that
remains active at least into the Middle Holocene.


identifier: Modir-Rousta, Ali <https://research.library.mun.ca/view/creator_az/Modir-Rousta=3AAli=3A=3A.html>   (2015) Analysis of N-nitrosames in water using micellar electrokinetic chromatography (MEKC) and development of online and offline methods of extraction and enrichment of neutral polar analytes.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Evaluation of the quality of the environment is essential for human wellness as pollutants in trace amounts can cause serious health problem. Nitrosamines are a group of compounds that are considered potential carcinogens and can be found in drinking water (as disinfection byproducts), foods, beverages and cosmetics. To monitor the level of these compounds to minimize daily intakes, fast and reliable analytical techniques are required. As these compounds are relatively highly polar, extraction and enrichment from environmental samples (aqueous) are challenging. Also, the trend of analytical techniques toward the reduction of sample size and minimization of organic solvent use demands new methods of analysis. In light of fulfilling these requirements, a new method of online preconcentration tailored to an electrokinetic chromatography is introduced. In this method, electroosmotic flow (EOF) was suppressed to increase the interaction time between analyte and micellar phase, therefore the only force to mobilize the neutral analytes is the interaction of analyte with moving micelles. In absence of EOF, polarity of applied potential was switched (negative or positive) to force (anionic or cationic) micelles to move toward the detector. To avoid the excessive band broadening due to longer analysis time caused by slow moving micelles, auxiliary pressure was introduced to boost the micelle movement toward the detector using an in house designed and built apparatus. Applying the external auxiliary pressure significantly reduced the analysis times without compromising separation efficiency. Parameters, such as type of surfactants, composition of background electrolyte (BGE), type of capillary, matrix effect, organic modifiers, etc., were evaluated in optimization of the method. The enrichment factors for targeted analytes were impressive, particularly; cationic surfactants were shown to be suitable for analysis of nitrosamines due to their ability to act as hydrogen bond donors. Ammonium perfluorooctanoate (APFO) also showed remarkable results in term of peak shapes and number of theoretical plates. It was shown that the separation results were best when a high conductivity sample was paired with a BGE of lower conductivity. Using higher surfactant concentrations (up to 200 mM SDS) than usual (50 mM SDS) for micellar electrokinetic chromatography (MEKC) improved the sweeping.
A new method for micro-extraction and enrichment of highly polar neutral analytes (N-Nitrosamines in particular) based on three-phase drop micro-extraction was introduced and its performance studied. In this method, a new device using some easy-to-find components was fabricated and its operation and application demonstrated. Compared to conventional extraction methods (liquid-liquid extraction), consumption of organic solvents and operation times were significantly lower.


identifier: Barnes, Melanie C. <https://research.library.mun.ca/view/creator_az/Barnes=3AMelanie_C=2E=3A=3A.html>   (2015) Miocene to recent tectonic and kinematic evolution of the Rhodes, Finike and Antalya Basins and the Anaximander Mountains, Eastern Mediterranean Sea.  Masters thesis, Memorial University of Newfoundland.

abstract:
Interpretation of ~14,000 km of high-resolution seismic reflection
profiles, together with 2,500 km of industry seismic reflection profiles and
chronostratigraphic data from several onland exploration wells revealed a complex tectonic and sedimentary history for the northwestern segment of the
eastern Mediterranean Sea. Three seismic stratigraphic units are defined
across the Rhodes, Finike and Antalya Basins and the greater Anaximander
Mountains at the junction of the Hellenic and Cyprus Arcs: the uppermost Unit 1 (early Pliocene-Quaternary) is a strongly reflective laterally continuous
package of high frequency reflections which extends from the seabed to the M-reflector. Beneath this, Unit 2 (Messinian-earliest Pliocene) is a weakly reflective package displaying complex internal architecture with weak,
discontinuous and often chaotic reflections bounded at their top and base by the M- and N-reflectors, respectively. Unit 3 (pre-Messinian Miocene) is a strongly reverberatory, high reflective package of low amplitude reflections with significant lateral continuity. The structural architecture of the northwestern segment of the eastern
Mediterranean Sea is characterised by two prominent phases of deformation,
separated by a period of tectonic quiescence. A protracted interval of contraction in the Miocene created a prominent belt consisting of northeast-
southwest striking and predominantly south-verging thrusts across the Rhodes
and Finike basins, which assumed a broadly east-west strike across the Anaximander and Anaximenes Mountains. Farther to the east in the Anaxagoras Mountain and the Antalya Basin, the belt exhibits a northwest-
southeast strike and is invariably southwest verging. This phase of contraction culminated in the latest Miocene and was followed after a period
of tectonic quiescence by an interval of spatially-partitioned strain in the early Pliocene-Quaternary which resulted in the development of discrete domains
characterized by extensional, contractional, transpressional and transtensional structures. The Anaximenes and Anaxagoras Mountains in the east and
southeast exhibit contractional/transpressional deformation and form the
linkage with the Florence Rise to the southeast. An arcuate and extensively faulted and folded region immediately northwest of the Anaximenes and
Anaxagoras Mountains (i.e., the Sırrı Erinç Plateau) forms a 30-40 km-wide zone which separates the Anaximander Mountain in the west and northwest and the Anaximenes and Anaxagoras Mountains. The Miocene-Recent tectonic evolution of the eastern Mediterranean reflects the various phases of the closure of the Neotethys Ocean, and the stepwise collision of microplates and continental fragments. The collision and
suturing of the African Microplate with the Eurasian Plate resulted in the west-directed tectonic escape of the Aegean-Anatolian Microplate during the Pliocene, which in turn, resulted in the partitioning of strain across the southern boundary between the African Plate and the Aegean-Anatolian
Microplate. Mapping and interpretation clearly show that this boundary is a very wide zone of deformation extending from the southern fringes of the Mediterranean Ridge across the entire forearc region into Taurus Mountains
of southern Turkey.


identifier: Rahman, Taufiqur <https://research.library.mun.ca/view/creator_az/Rahman=3ATaufiqur=3A=3A.html>   (2016) Design synthesis & prototype implementation of parallel orientation manipulators for optomechatronic applications.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This thesis documents a research endeavor undertaken to develop high-performing
designs for parallel orientation manipulators (POM) capable of delivering the speed
and the accuracy requirements of a typical optomechatronic application. In the
course of the research, the state of the art was reviewed, and the areas in the
existing design methodologies that can be potentially improved were identified, which
included actuator design, dimensional synthesis of POMs, control system design, and
kinematic calibration. The gaps in the current art of designing each of these POM
system components were addressed individually. The outcomes of the corresponding
development activities include a novel design of a highly integrated voice coil actuator
(VCA) possessing the speed, the size, and the accuracy requirements of small-scale
parallel robotics. Furthermore, a method for synthesizing the geometric dimensions
of a POM was developed by adopting response surface methodology (RSM) as the
optimization tool. It was also experimentally shown how conveniently RSM can be
utilized to develop an empirical quantification of the actual kinematic structure of
a POM prototype. In addition, a motion controller was formulated by adopting the
active disturbance rejection control (ADRC) technology. The classic formulation of
the ADRC algorithm was modified to develop a resource-optimized implementation
on control hardware based on field programmable gate arrays (FPGA).
The practicality and the effectiveness of the synthesized designs were ultimately
demonstrated by performance benchmarking experiments conducted on POM prototypes constructed from these components. In specific terms, it was experimentally
shown that the moving platforms of the prototyped manipulators can achieve highspeed
motions that can exceed 2000 degrees/s in angular velocity, and 5×105 degrees/s2
in angular acceleration.


identifier: Li, Zelin <https://research.library.mun.ca/view/creator_az/Li=3AZelin=3A=3A.html>   (2016) Parameterization of modeling subsurface hydrocarbon contamination and biosurfactant enhanced remediation processes.  Masters thesis, Memorial University of Newfoundland.

abstract:
Subsurface hydrocarbon contamination caused by accidental spills or operational leakages of petroleum products is a global environmental concern. In order to cost-effectively and eco-friendly recover the contaminated sites, biosurfactant enhanced aquifer remediation (BSEAR) technologies have become a popular subject in both research and practice. However, the inherent uncertainties and complexities of the subsurface systems make it challenging in numerical simulation of the hydrocarbon transport and fate as well as remediation processes. Efforts in developing more efficient and robust parameterization approaches for such modeling purpose, therefore, are highly desired.
This research aims to help fill the gap by developing a novel hybrid stochastic – design of experiment aided parameterization (HSDP) method for modeling BSEAR processes. The method was developed and tested based on an integrated physical and numerical modeling system comprised of a set of intermediate scale flow cells (ISFCs) and a numerical simulator named BioF&T 3D. Generally, the HSDP method was performed by: 1) building the design of experiment (DOE) models based on screened parameters and defined responses, which could reflect the goodness of fit between observed and simulated data; 2) identifying the and interactions among parameters and their significance; 3) optimizing the DOE predicted responses; 4) introducing stochastic data within reduced intervals based on the optimized parameters; 5) running Monte Carlo simulation to find the optimal responses with the corresponding combinations of parameters. The flow cell tests proved that the HSDP method could improve both
efficiency and robustness of modeling parameterization and significantly reduce the computational demand without compromising the effectiveness in quantifying parameter interactions and uncertainties.
Furthermore, a specific lab synthetized surfactin was applied in this study. The effect of dissolution enhancement was observed from parallel flow cell experiments especially during the first 12 hours following the initial hydrocarbon release. The HSDP method was demonstrated to be capable of advancing BioF&T 3D, which lacks the capacity of simulating surfactant. By incorporating the HSDP method, the BSEAR processes were effectively simulated with a satisfactory overall goodness of fit (R² = 0.76, 0.81, 0.83, and 0.81 for benzene, toluene, ethylbenzene, and xylene, respectively). The enhanced dissolution effect was also reflected in the modeling parameterization by increasing the first 12 hours hydrocarbon loading ratio (12LR) compared to non-biosurfactant processes.
This research developed a new parameterization method HSDP, which is capable of revealing interactions of parameters, as well as quantifying their uncertainties, in a robust and efficient manner. Also, using this method, this study initiated the attempts to advance simpler numerical models in simulating complicated BSEAR processes, which is particularly attractive for the potential applications in practice.


identifier: Huo, Xiaotong <https://research.library.mun.ca/view/creator_az/Huo=3AXiaotong=3A=3A.html>   (2016) A study of mechanical integrity for unequal wall thickness transition joints in pipeline.  Masters thesis, Memorial University of Newfoundland.

abstract:
Unequal wall thickness transition joints are used in energy pipelines to connect straight pipe segments to thicker walled pipe sections such as cold bends and fittings. Due to the operational loads, changes in the pipe horizontal and vertical alignment, and variations in the soil type, axial loads and bending moments are generated along the pipeline. Through the wall thickness transition, stress concentrations develop due to the differences in pipe geometry, stiffness, material grade and mechanical strength.
Current engineering practice and standards provide guidance on back-bevel design for wall thickness transitions. An alternative configuration, the counterbore-taper design recommended by TranCanada PipeLines, is intended to reduce stress concentration effect across the transition, facilitate welding processes, and improve NDT quality, productivity and reliability.
Through a parametric study, using finite element methods, the relative mechanical response of the back-bevel and counterbore-taper wall thickness transition is evaluated. The numerical modelling procedures are verified with analytical equations and numerical simulations available in the public domain literature. The influence of element type, mesh topology, wall thickness mismatch (t₂/t₁), material grade on the limit load, pressure containment response, associated with the onset of plastic collapse, are evaluated. In terms of strength performance associated with stress concentration effects, the significance of element type, mesh topology, pipe diameter (D), pipe diameter to wall thickness ratio (D/t), wall thickness mismatch (t₂/t₁), material grade on the limit load, counterbore length, taper angle and radial girth weld offset (i.e., Hi-Lo) are examined.
The improved performance of the counterbore-taper weld transition; relative to the back-bevel design as recommended by current practice, was demonstrated in this study through equivalent limit load capacity for pressure containment and reduction in the stress concentration factor for combined loading. The minimum counterbore length was found to be consistent with industry recommended practices, and was related to the pipe diameter and wall thickness mismatch. Guidance on the selection of joining methods to advance current engineering practice is provided.


identifier: Ma, Zhenguo <https://research.library.mun.ca/view/creator_az/Ma=3AZhenguo=3A=3A.html>   (2016) Metabolism of antioxidants and nitrosothiols in barley (Hordeum vulgare L.) seeds during germination and seedling growth.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: In the process of seed germination, antioxidant metabolism in barley seeds is intensified. Production of reactive oxygen and nitrogen species, and activities of enzymes scavenging these reactive species such as ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, glutathione reductase, catalase, superoxide dismutase and S-nitrosoglutathione reductase, increased in germinating barley seeds instead of non-germinated more dormant Sundre seeds. Meanwhile the content of total ascorbate and glutathione and the rate of fermentation dropped in germinating seeds. Sharp decrease in glutathione content in embryos of barley seeds led to a dramatic increase in reduction potential of glutathione disulfide/glutathione couple. High levels of adenosine triphosphate and adenosine diphosphate were observed during the first few hours of germination but later their content decreased with a concomitant increase in their ratio in germinating seeds. Expression of the gene encoding alcohol dehydrogenase III declined in Harrington seeds from the onset of germination, while expression of the gene encoding hemoglobin was elevated within the first few hours and later declined, and the expression of the both genes did not change significantly in Sundre seeds. In the process of further transition from imbibition of dry Harrington seeds to seedling growth, glyoxylate cycle and citric acid cycle in scutellum became more active in the first few days, as evidenced by the increased activities of isocitrate lyase and malate synthase in glyoxylate cycle and succinate dehydrogenase and fumarase in citric acid cycle. During this period, the content of malic acid, succinic acid, and overall pH value declined in both scutellum and endosperm of Harrington seeds. In the endosperm, the content of succinic acid was much lower than malic acid and citric acid. The level of citric acid in scutellum was high and maintained stable while its level in endosperm was low. The increase of H₂O₂ production was observed during the process of seed germination and early period of seedling growth. In summary, the antioxidant metabolism, metabolism of reactive oxygen and nitrogen species, glyoxylate cycle and citric acid cycle were found to be more active during seed germination and early period of seedling growth.


identifier: Clark, Jo-Anna B. J. <https://research.library.mun.ca/view/creator_az/Clark=3AJo-Anna_B=2E_J=2E=3A=3A.html>   (2016) Emergence of hereditary hyperplastic gingivitis in Newfoundland and Labrador, Canada: an exploration into the molecular aetiology at both the gene and genome levels.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: Hereditary hyperplastic gingivitis (HHG) is a benign fibrous enlargement of the gingival tissue to dental encapsulation in ranched silver foxes (Vulpes vulpes). It is an autosonal recessive condition displaying male sex-biased penetrance HHG demonstrates a pleiotropic association with superior fur quality. In 2004, after the introduction of a Finnish fox line, HHG emerged in Newfoundland and Labrador, Canada. While the underlying HHG aetiology is unknown, an analogous condition called hereditary gingival fibromatosis (HGF) occurs in humans, providing a platform for investigation into the molecular mechanisms of HHG. A mutation in the son of sevenless homolog 1 gene causes one form of HGF. Candidate gene sequencing of this and related genes including epidermal growth factor receptor (EGFR), growth factor receptor bound protein 2, and mitogen-activated protein kinase kinase 6 did not uncover any putative coding sequence or splice-site mutations. HHG was also examined at the genomic level, integrating knowledge of the chromosomal loci associated with the analogous human condition, HGF. This exploration was divided into the known genetic causes of isolated HGF and HGF-associated sundromes characterized by both gingival and hair overgrowth. Global gene expression differences between affected adn unaffected foxes pinpoint SOS2 and RASA1 as candidate gene for HHG; overall, the genomic expression patterns strongly indicate the involvement of the mitogen-activated protein kinase (MAPK) signalling pathway. Specifically, the error could occur prior to the Rat sarcoma protein in this pathway. Future exploration of the pathway could elucidate the genetic basis of HHG and more broadly the molecular aetiology of gingival overgrowth in humans and canines. Additional information regarding the HHG phenotype was revealed, including the potential involvement of androgens in disease severity. The steroid-5-alpha-reductase, alpha polypeptide 2 gene was found to be up-regulated in the HHG-affected foxes, and the link between androgens and gingival sensitivity in dogs might help explain the perceived sex biased penetrance originally noted in HHG. Overall the molecular mechanisms underpinning the HHG phenotype and future work revolve around the MAPK signalling pathway including influences that other gene products like androgens have on it.


identifier: Komatsu, Yumiko <https://research.library.mun.ca/view/creator_az/Komatsu=3AYumiko=3A=3A.html>   (2016) Active RAS/MEK pathway downregulates expression of IFN-inducible genes by targeting IRF1: implications for understanding molecular mechanisms of viral oncolysis.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Oncolytic viruses exploit common molecular changes in cancer cells, which are
not present in normal cells, to target and kill cancer cells. Ras transformation and defects
in type I interferon (IFN)-mediated antiviral responses are known to be the major
mechanisms underlying viral oncolysis. The Hirasawa lab has previously demonstrated
that oncogenic Ras/Mitogen-activated protein kinase kinase (Ras/MEK) activation
suppresses the transcription of many IFN-inducible genes in human cancer cells,
suggesting that Ras transformation underlies type I IFN defects in cancer cells. The
objective of my PhD project was to elucidate the mechanisms underlying how Ras/MEK
downregulates IFN-induced transcription.
By conducting promoter deletion analysis of IFN-inducible genes, the IFN
regulatory factor 1 (IRF1) binding site was identified to be responsible for the regulation
of transcription by MEK. MEK inhibition promoted transcription of the IFN-inducible
genes in wild-type mouse embryonic fibroblasts (MEFs), but not in IRF1− / − MEFs.
Furthermore, IRF1 expression was lower in RasV12 cells compared with vector control
NIH3T3 cells, which was restored to equivalent levels by inhibition of MEK. Similarly,
MEK inhibition restored IRF1 expression in human cancer cells. IRF1 re-expression in
human cancer cells increased cellular resistance to infection by the oncolytic vesicular
stomatitis virus strain. Together, these results indicate that Ras/MEK activation in cancer
cells downregulates transcription of IFN-inducible genes by targeting IRF1 expression,
resulting in increased susceptibility to viral oncolysis.
I further sought to determine how active Ras/MEK downregulates IRF1
expression. MEK inhibition restored IRF1 expression at the protein level prior to mRNA
induction; however, it did not affect IRF1 protein stability. The expression of IRF1-
targeting microRNA, activity of IRF1 5’ and 3’-UTRs, and polysome loading of IRF1
mRNA in response to MEK inhibition were analyzed; however, the translational
regulation of IRF1 mRNA by Ras/MEK remained inconclusive. To determine whether
Ras/MEK modulates post-translational modifications (PTMs) of IRF1, phosphorylation,
ubiquitination, sumoylation, and acetylation of IRF1 were examined. MEK inhibition
promoted ubiquitination and inhibited sumoylation of IRF1, indicating that active
Ras/MEK alters PTM of IRF1 protein.
Lastly, siRNA screens and overexpression experiments identified RSK3 and
RSK4 to be the ERK downstream effectors involved in Ras/MEK-mediated IRF1
regulation.


identifier: Li, Yake <https://research.library.mun.ca/view/creator_az/Li=3AYake=3A=3A.html>   (2016) Frequency-modulated continuous-wave synthetic-aperture radar: improvements in signal processing.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
With the advance of solid state devices, frequency-modulated continuous-wave (FMCW) designs have recently been used in synthetic-aperture radar (SAR) to decrease cost, size, weight and power consumption, making it deployable on smaller mobile plat-forms, including small (< 25 kg) unmanned aerial vehicle(s) (UAV). To foster its mobile uses, several SAR capabilities were studied: moving target indication (MTI) for increased situational awareness, bistatic operation, e.g. in UAV formation flights, for increased range, and signal processing algorithms for faster real-time performance.
Most off-the-shelf SAR systems for small mobile platforms are commercial proprie-tary and/or military (ITAR, International Trades in Arms Regulations) restricted. As such, it necessitated the design and build of a prototype FMCW SAR system at the early stage to serve as a research tool. This enabled unrestricted hardware and software modifica-tions and experimentation.
A model to analyze the triangularly modulated (TM) linear frequency modulated (LFM) waveform as one signal was established and used to develop a MTI algorithm which is effective for slow moving targets detection. Experimental field data collected by the prototyped FMCW SAR was then used to validate and demonstrate the effectiveness of the proposed MTI method.
A bistatic FMCW SAR model was next introduced: Bistatic configuration is a poten-tial technique to overcome the power leakage problem in monostatic FMCW SAR. By mounting the transmitter and receiver on spatially separate mobile (UAV) platforms in formation deployment, the operation range of a bistatic FMCW SAR can be significantly improved. The proposed approximation algorithm established a signal model for bistatic FMCW SAR by using the Fresnel approximation. This model allows the existing signal processing algorithms to be used in bistatic FMCW SAR image generation without sig-nificant modification simplifying bistatic FMCW SAR signal processing.
The proposed range migration algorithm is a versatile and efficient FMCW SAR sig-nal processing algorithm which requires less memory and computational load than the traditional RMA. This imaging algorithm can be employed for real-time image genera-tion by the FMCW SAR system on mobile platforms. Simulation results verified the pro-posed spectral model and experimental data demonstrated the effectiveness of the modi-fied RMA.


identifier: Hasan, Tahrim <https://research.library.mun.ca/view/creator_az/Hasan=3ATahrim=3A=3A.html>   (2016) Evaluation of cell line-derived xenografted tumors as controls for immunohistochemical testing for estrogen receptors and progesterone receptors.  Masters thesis, Memorial University of Newfoundland.

abstract:
Current Quality Control (QC) practices for diagnostic immunohistochemistry (IHC) use
archived breast cancer specimens and breast cancer cell lines as control materials for
Estrogen Receptor (ER) and Progesterone Receptor (PR) testing in breast cancer.
However, archived breast tumors show inherent heterogeneity within and between
specimens and cell lines are not histologically representative of patient-derivedtumor
controls. In an effort to generate standardized controls for ER and PR IHC
testing, I hypothesized breast cancer cell line-derived xenografted tumors are
representative of patient-derived-tumor controls that can be used for QC
purposes. Well-characterized breast cancer cell lines with varying steady-state levels
of ER and PR expression – MCF7, T47D and MDAMB468 – analyzed by immunoblot
and IHC were implanted in immune-deficient mice to generate cell line-derived
Xenografted (CDX) tumors. ER and PR expression of the Xenografted tumors was
consistent with the derivative cell lines. Three pathologists expert in breast biomarker
reporting assessed CDX tumors for reproducibility from different Mammary Fat Pad
(MFP) sites in the mice. The CDX tumors were indistinguishable regardless of the MFP
sites. The xenografted tumors from the three cell lines represented the range of
biomarker expression levels exhibited by the patient-derived-tumor controls. These
results suggest the possible potential applications of CDX tumor as controls to assist
in reporting of ER and PR test results.


identifier: Tailor, Sapan Pravinbhai <https://research.library.mun.ca/view/creator_az/Tailor=3ASapan_Pravinbhai=3A=3A.html>   (2016) Diversity analysis of blueberry clones and cultivars using EST-PCR and microsatellite markers.  Masters thesis, Memorial University of Newfoundland.

abstract:
The blueberry (Vaccinium spp. L.) is a health promoting and economically important fruit crop. Genetic diversity and relatedness were studied in 63 blueberry genotypes, using eleven EST–PCR and nine microsatellite markers. Markers found to be polymorphic and detected 436 and 272 alleles, respectively. Other parameters such as PIC, expected and observed heterozygosity were also high for both the markers.
Cluster analyses such UPGMA, NJ and PCO identified clustering of genotypes according to their geographic collection site. Fingerprinting data was used for the STRUCTURE analysis which also separated clones and cultivars based on their geographic collection site. Similarity was found among the results of UPGMA, NJ, PCoA and STRUCURE analyses for both the markers analysed individually and combined. AMOVA analysis revealed high genetic diversity among genotypes. Results from the present study will help in germplasm management and for evaluating and selecting promising blueberry genotypes in the current blueberry improvement program.


identifier: Wang, Yunfei <https://research.library.mun.ca/view/creator_az/Wang=3AYunfei=3A=3A.html>   (2015) Carboxyl and ethynyl-substituted dithiafulvenes and tetrathiafulvalene vinylogues: synthesis, properties, and applications.  Masters thesis, Memorial University of Newfoundland.

abstract:
This thesis describes a systematic study of new dithiafulvene (DTF) and tetrathiafulvalene
vinylogue (TTFV) derivatives as redox-active π-conjugated molecular materials.
The content of this thesis work is divided into two major parts. In the first
part, a series of carboxylate ester and carboxyl-substituted DTFs and TTFVs were
synthesized and their electronic and electrochemical redox properties were characterized
by UV-Vis spectroscopic and cyclic voltammetric analyses. The carboxyl-TTFV
was applied as a redox-active ligand to complex with zinc ions, forming a stable Zn-
TTFV coordination product. The structural, electrochemical, and thermal properties
of the coordination product were investigated by infrared spectroscopy, powder X-ray
diffraction, cyclic voltammetry, and differential scanning calorimetric analyses. Furthermore,
the microscopic morphological and porosity properties of the Zn-TTFV
coordination product were measured by scanning electron microscopy and nitrogen
gas adsorption experiments. In the second part, a series of ethynyl-substituted DTF
regioisomers was synthesized and then used as starting materials to construct further
π-extended derivatives through oxidative dithiafulvenyl coupling and Cu-catalyzed
alkynyl homocoupling reactions. The resulting π-conjugated systems were subjected
to UV-Vis absorption and cyclic voltammetric analyses to examine their electronic
properties and redox reactivity. Based on the characterization studies, a understanding
of the structure-property-reactivity relationships for these compounds has been
established.


identifier: Nguyen, Truong X. <https://research.library.mun.ca/view/creator_az/Nguyen=3ATruong_X=2E=3A=3A.html>   (2016) Development of seabed friendly bottom trawls.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Concerns over the impacts of fishing practices, especially bottom trawling, on the ocean environment have been expressed at the local, national and international scale. While physical alterations of the seabed by bottom trawling are known to occur, the biological effects on benthic communities and their recovery rates depend on substrate types, depth, and natural disturbance in the fishing area, as well as how trawl gears are designed and operated. In this thesis, I investigate different key research aspects regarding the subject of development of seabed friendly bottom trawls, in particular shrimp trawling in Newfoundland and Labrador, Canada. The complementary use of different research approaches (e.g., underwater video observations, numerical modeling and simulation, flume tank testing, and at-sea experiments) were applied for each of the research questions.
First, I investigated the behavioural interactions of individual snow crab in response to the rockhopper footgear of a traditional inshore shrimp trawl used in Newfoundland and Labrador, Canada. I found that snow crab were quickly overtaken under the footgear of the approaching trawl and over half of the snow crab (i.e., 54%) observed experienced an encounter with the rockhopper footgear components. The majority of the snow crab observed appeared to be aware of the trawl and were actively responding and/or reacting to the approaching threat. Second, the strengths and limitations of different commercially available trawl simulation software (i.e., DynamiT, SimuTrawl, and Trawl Vision PRO) in terms of design capability, simulation capability, and reliability of results, were investigated and interpreted. The study provides valuable knowledge and reference for stakeholders (e.g., gear designers, researchers, and educators) who are considering using numerical simulation methods to optimize their gear design concepts during the early stages of development of seabed friendly bottom trawls (e.g., predict expected mechanical stresses of trawl components on the seabed). Next, I addressed the question of how well computer simulation and flume tank testing of scale engineering models actually predict full-scale at-sea performance of bottom trawls. The results demonstrated that the complementary use of two or three methods should be encouraged for assisting the gear development cycle given their own weakness and merits. For instance, the flume tank testing method was successfully utilized to estimate the percentage of contact area made by trawl footgear with the seabed, while at-sea experiments were not designed to measure such impacts. Moreover, I clarified that the precision and accuracy of the predictions depends on many factors. Thus, thoroughness and care must be emphasized in order to reduce bias in predicted performance. Finally, I examined the effectiveness of a reduced seabed impact footgear (i.e., drop chain) over a traditional rockhopper footgear on identical bottom trawls targeting northern shrimp (Pandalus borealis) in Newfoundland and Labrador, Canada. The results demonstrated that seabed impacts of shrimp trawling can be reduced if the trawl footgear is made lighter and/or designed to have less contact with the seabed. In particular, it was revealed that with the experimental drop chain footgear trawl we are able to reduce the interaction or encounter of snow crab.
In summary, the knowledge presented in this thesis is believed to significantly contribute to the research and development of low-impact bottom trawls both in theoretical and practical aspects. While the potential impact of bottom trawling activities on habitats and benthic communities is not easy to predict and characterize for various reasons, I do believe that further development and application of fishing gears and techniques that reduce impacts on seabed habitats and associated benthic communities will be essential to achieve ecosystem objectives.