identifier: Duggan, Chris <https://research.library.mun.ca/view/creator_az/Duggan=3AChris=3A=3A.html>   (2019) An investigation of eating pathology, emotion regulation, and stress in university student athletes.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Research investigating eating pathology in university student athletes tends to
suggest that student athletes exhibit lower risk for eating pathology and lower levels of
body dissatisfaction than their non-athlete counterparts. Given that body dissatisfaction
has been shown to predict eating pathology, it is possible that student athletes exhibit
lower eating pathology risk as a result of their relatively lower levels of body
dissatisfaction. Given that student athletes engage in regular and intense physical activity,
it is likely that their bodies more closely match the cultural ideal (lean), which would
explain the relatively low levels of body dissatisfaction observed in previous studies.
There is evidence to suggest that regular engagement in physical activity is an effective
emotion regulation strategy. Emotion regulation involves the awareness and acceptance
of emotions, the ability to behave in accordance with desired goals when experiencing
negative emotions, and the ability to use situationally appropriate emotion regulation
strategies. Difficulties in emotion regulation arise when one of these processes is
disrupted and difficulties in emotion regulation have been associated with higher risk for
eating pathology.
The current research investigated the relationships between athletic status, eating
pathology, and difficulties in emotion regulation in a sample of 123 male and female
student non-athletes and 85 male and female student athletes. It was hypothesized that the
student athletes would report lower levels of eating pathology risk and higher levels of
body satisfaction than the student non-athletes. Additionally, it was predicted that student
athletes would report fewer difficulties in emotion regulation than the student non-athletes and that difficulties in emotion regulation would mediate the relationship
between athletic status and eating pathology.
In general, the results of the current study were consistent with the predictions, in
that the student athletes reported significantly lower likelihood of scoring within the
range of clinical concern on an eating pathology assessment. Additionally, the student
athletes reported significantly higher scores on an index of body satisfaction and lower
scores on an index of difficulties in emotion regulation, but the difference merely trended
towards significance for difficulties in emotion regulation. Finally, the current study
demonstrated that the relationship between scores on an eating pathology assessment and
athletic status were mediated by difficulties in emotion regulation in a sample of male
and female student athletes and student non-athletes. This suggests that student athletes
reported less eating pathology as a result of fewer difficulties in emotion regulation.


identifier: Awad, Ibrahim Ezzeddin <https://research.library.mun.ca/view/creator_az/Awad=3AIbrahim_Ezzeddin=3A=3A.html>   (2018) Towards computing the properties of large molecules from atoms-in-molecules (AIM) densities.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

type: Thesis NonPeerReviewed

abstract:
This thesis is divided into two main parts. In the first part, we proposed new three partition
weights, namely; Fermi-Dirac, triangle, and Awad weights. In this part, we aim to develop
new weights in which the core region close to a nucleus of an atom is assigned to that
atom and not to the core or the bond of other atoms. We visually illustrate the molecular
radial electron density (RDEN) and bond electron density (BDEN) using the proposed
weights. We compared the molecular properties including the total number of electrons
Nₑ, the electron-nuclear potential energy Vne, and Coulomb potential energy Vₑₑ which are
calculated numerically using the Awad weight with those calculated by Hartree-Fock (HF)
wavefunction (the exact values). Also, the computed results using the Awad weight were
compared to the computed results obtained using Becke weight. Our findings show that the
Awad weight gives better bonding-region representations for both RDEN and BDEN than
those obtained using Becke weight. Also, the Awad weight gives better results in computing
the molecular properties than those using the Becke weight.
In the second part, we proposed a new approach for calculating the total energy of molecules
called atoms in molecules density (AIMD). In this part, we present the first version of
AIMD. In AIMD, the molecular properties of the target molecules were computed in three
steps: (i) generating small molecules (fragments) from molecules of interest, (ii) storing
some properties of these fragments in a database, (iii) using the data stored in the database
and by using the direct method to compute the molecular properties of the target molecule. The electronic molecular energy (Eᴱᴸᴱ) is obtained using AIMD as follows,
Eᴱᴸᴱ = Tsum+Vne[ρ]+J[ρ]


identifier: Lftisi, Fuzi <https://research.library.mun.ca/view/creator_az/Lftisi=3AFuzi=3A=3A.html>   (2019) Intelligent control of induction motors.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

title: Intelligent control of induction motors

abstract:
This thesis presents the development and implementation of an integral field oriented intelligent control for an induction motor (IM) drive using Fuzzy Logic Controller (FLC), and an Artificial Neural Network (ANN), employing a finite element controller and making use of a Proportional Integral (PI) adaptive controller as well. An analytical model of an induction motor drive has been developed. In order to prove the superiority of the proposed controller, the performance of this controller is compared with conventional PI-based IM drives. The performance of the proposed IM drive is investigated extensively at different operating conditions in simulation. The proposed adaptive PI-based speed controller’s performance is found to be robust and it is a potential candidate for high performance industrial drive applications. The novel work focuses on using a Finite Element Controller map (FECM) to manipulate adaptive controllers for motor control drives.
A digital signal processing (DSP) board DS1104 and laboratory induction motor were used to implement the complete vector control scheme. The test results have been compared with simulated results at different dynamic operating conditions. The effectiveness of this control scheme has been evaluated, and it has been found to be more efficient than the conventional PI controller.


identifier: Kazemi, Farhad Mohammad <https://research.library.mun.ca/view/creator_az/Kazemi=3AFarhad_Mohammad=3A=3A.html>   (2018) Automatic high content screening using deep learning.  Masters thesis, Memorial University of Newfoundland.

abstract:
Recently, deep learning algorithms have been used with success in a variety of domains.
Deep learning has proven to be a very helpful tool for discovering complicated
structures in high-dimensional and big datasets. In this work, five deep learning models
inspired by AlexNet, VGG, and GoogleNet are developed to predict mechanism
of actions (MOAs) based on phenotypic screens of a number of cells in dimly lit and
noisy images. We demonstrate that our models can predict the MOA for a compendium
of drugs that alter cells through single cell or cell population views without
any segmentation and feature extraction steps. According to these results, our models
do not need to fully realize single-cell measurements to profile samples because they
use the morphology of specific phenomena in the cell population samples.
We used an imbalanced High Content Screening big dataset to predict MOAs with
the main goal of understanding how to work properly with deep learning algorithms on
imbalanced datasets when sampling methods, like Oversampling, Undersampling, and
Synthetic Minority Over-sampling (SMOTE) algorithms are used for balancing the
dataset. Based on our findings, it is now clear that the SMOTE sampling algorithm
must be part of the deep learning algorithms when confronting imbalanced datasets.
High Content Screening technologies have to deal with screening thousands of
cells to provide a number of parameters for each cell, such as nuclear size, nuclear
morphology, DNA replication, etc. The success of High Content Screening (HCS)
systems depends on automatic image analysis. Recently, deep learning algorithms
have overcome object recognition challenges on tasks with a single centered object
per image. Present deep learning algorithms have not been applied to images that include multiple specific complex objects, such as microscopic images of many objects
such as cells in these images.


identifier: Handrigan, Stephen M. <https://research.library.mun.ca/view/creator_az/Handrigan=3AStephen_M=2E=3A=3A.html>   (2019) Investigating the effect of porosity on elastic modulus through finite element analysis and molecular dynamics simulations.  Masters thesis, Memorial University of Newfoundland.

abstract: The effect of porosity on elastic modulus was studied. First, a study with experimental load-deflection curve using Finite Element Analysis and beam theory, Euler-Bernoulli and Timoshenko, to investigate the effect of porosity on elastic modulus of a cantilever beam undergoing tip loading. It was determined that porosity amount and location affected the elastic modulus of a cantilever beam undergoing tip loading. Second, an investigation into the applicability of atomistic modelling of vacancies as a method of studying the effect of porosity on elastic modulus was completed for two materials, pure iron and iron-chromium. The study involved testing several force fields and parameter sets to determine accuracy and reliability of prediction. It was determined that vacancy amount did influence elastic modulus, with some force fields and parameter sets providing more accurate prediction in modulus and reduction in modulus due to vacancies. Results were compared to experimental data and Finite Element model from literature.


identifier: Omer, Farej <https://research.library.mun.ca/view/creator_az/Omer=3AFarej=3A=3A.html>   (2018) Starter sequences: generalizations and applications.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
In this thesis we introduce new types of starter sequences, pseudo-starter sequences,
starter-labellings, and generalized (extended) starter sequences. We apply these new
sequences to graph labeling. All the necessary conditions for the existence of starter,
pseudo-starter, extended, m-fold, excess, and generalized (extended) starter sequences
are determined, and some of these conditions are shown to be sufficient. The relationship between starter sequences and graph labellings is introduced. Moreover, the starter-labeling and the minimum hooked starter-labeling of paths, cycles, and k-
windmills are investigated. We show that all paths, cycles, and k-windmills can be
starter-labelled or minimum starter-labelled.


identifier: Watts, Erica <https://research.library.mun.ca/view/creator_az/Watts=3AErica=3A=3A.html>   (2018) Markedness and implicational relationships in phonological development: a longitudinal, cross-linguistic investigation.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This dissertation sets out to evaluate theoretical and empirical issues involved in referring to
implicational relationships (i.e., that a marked or complex sound or phonological process implies
the presence of an unmarked or simpler sound or process) for the treatment of speech sound
disorders (e.g., Gierut 2007). Due to the relatively untested and unexplored nature of
implicational relationships, and because of their potential relevance to Speech-Language
Pathology practice, I investigated the following research questions:
(1) Are implicational relationships warranted cross-linguistically in the description of
phonological development?
(2) Can factors outside of universal markedness account for attested patterns of phonological
development?
I conducted six detailed longitudinal case studies documenting typical phonological
systems in English, French, German, and Portuguese, as well as atypical development in one
English-learning child. Based on these studies, I claim that implicational relationships based on
universal markedness are theoretically and empirically questionable. The results from my
investigation highlight the influence of speech phonetics and phonological distributions in all
aspects of development. Additionally, the few implicational relationships that appear to make
valid predictions can be described in terms of articulatory complexity: the sounds that the
children acquired first are easier to articulate for a number of reasons (e.g., motoric, perceptual,
grammatical).
As claims based on universal markedness generally do not account for the data, I
investigate whether a phonetically driven view of markedness could apply. This inquiry led me to advocate for a markedness-through-mechanism (Hume 2011) approach to phonological
development, which combines perceptual distinctiveness, phonetic variability, and articulatory
simplicity; which, in child language, can be rather salient due to anatomical and motor properties
of child speech production. I combine this view of phonetically conditioned markedness with the
A-map model (McAllister Byun, Inkelas & Rose 2016), which provides a formal link relating
perceptual targets and the dimensions involved in the motor-acoustic mappings of these objects
on to patterns of speech production.
In a nutshell, combining markedness-through-mechanism with the A-map provides a way to
frame the phonological patterns that we observe in child phonological development that is both
theoretically consistent and clinically applicable. This approach expands on our understanding of
the underpinnings of speech sound disorders and provides a new model that can guide Speech-
Language Pathologists in their selection of treatment approaches to speech disorders.


identifier: Sofla, Saeed Jafari Daghlian <https://research.library.mun.ca/view/creator_az/Sofla=3ASaeed_Jafari_Daghlian=3A=3A.html>   (2019) The behaviour of silica nanoparticles in multi-phase ionic solutions: enhanced oil recovery implications.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Conventional oil production methods produce approximately one-third of the initial oil in place from a reservoir, on average. The remaining oil is a large attractive target for Enhanced Oil Recovery (EOR) techniques. Recently, the potential of using nanoparticles in EOR methods has been explored with some promising results from preliminary evaluations. However, the application of nanoparticles in real oil reservoirs is limited by knowledge gaps. The stability of nanoparticles in the injection or formation water containing diverse types and concentrations of ions is a challenge. It is still unknown whether and under which conditions nanoparticles can self-assemble at the oil-water interface and alter the oil-water interfacial properties. The wettability alteration capacity of nanoparticles usually investigated by contact angle measurements is affected by subtle experimental artefacts; hence, the result of conventional contact angle measurements may not be reliable to evaluate the effect of nanoparticles on the wettability of substrates. Moreover, the mechanism of wettability alteration by nanoparticles is not clear yet.
The stability of nanoparticles in the aqueous phase is the primary challenge to using nanoparticles in reservoir conditions. Nanoparticles are extremely unstable in high salinity seawater or formation water. Typically, seawater or formation brine is used for water-flooding and EOR purposes. Therefore, if we want to modify the fluid-fluid or fluid-rock properties by injecting nanoparticle enhanced water, then the stability of the nanoparticles in high salinity seawater or formation brine is extremely important. A novel method to stabilize silica nanoparticles in seawater is proposed. First, the stability of silica nanoparticles in the presence of different ions is investigated. The results show that the presence of multivalent counter-ions in the electrical double layer of nanoparticles can destabilize silica nanoparticles. To reduce the concentration of positive multivalent ions around silica nanoparticles, a method called “H+ protected” is proposed and its effectiveness is tested by particle size, turbidity, zeta-potential, and pH measurements. Experimental results show that the H+ protected method obtained by adding hydrochloric acid (HCl) to the solution, can effectively stabilize silica nanoparticles in seawater.
By investigating the controlling parameters of nanoparticle attachment at the interface (bulk suspension properties including the concentration of nanoparticles, concentration of HCl, salinity, size and charge of nanoparticles and operating conditions i.e., temperature and pressure) and coupling them with nanoparticles’ stability in the solution, the conditions under which silica nanoparticles can reduce oil-water interfacial tension are experimentally investigated. The maximum IFT reduction occurs when there is a packed monolayer of nanoparticles at the oil-water interface. For instance, increasing nanoparticles’ concentration and salinity to their optimum value would lead to achieving smaller IFT values. Further increasing the concentration of nanoparticles and salinity beyond the optimum value can destabilize the nanoparticles and increase their average size in the solution, which can reduce the number of nanoparticles at the interface and thus increase the IFT value. In general, the minimum IFT occurs when the surface energy reduction due to the adsorption of nanoparticles is minimum, i.e., the chance of nanoparticles desorbing from the interface due to thermal fluctuations (especially in the elevated temperatures) is high and aggregation of nanoparticles in the bulk solution is initiated. We believe that IFT reduction is partially but not fully responsible for incremental oil recovery greater than water-flooding alone. We test our hypothesis by conducting silica nanoparticles in seawater flooding experimentally and comparing the results with simulations that examine the effect of a) IFT reduction only and b) the effect of altering the relative permeability, wettability, and IFT reduction.
The mechanism of wettability alteration by silica nanoparticles is investigated. The impact of experimental methods in conventional contact angle measurements on the wettability alteration data is evaluated. In conventional contact angle measurements, the rock samples are either aged with (immersed in) nanoparticles-fluid before conducting the experiments or contacted with the nanoparticles-fluid before the oil droplet is attached to the rock substrate. In both cases, nanoparticles exist in the oil-rock interface before initiating the contact angle measurements (pre-existing nanoparticles). A real reservoir scenario would be to inject the nanoparticle-fluids into an already established equilibrium condition of oil-water-rock. Hence, the contact angle measurements are modified using a new displacement contact angle method to represent the injection of nanoparticle-fluids into a reservoir. The impact of pre-existing nanoparticles on the contact angle measurements is examined for simple (n-decane, NaCl brine, pure substrates) and complex (crude oil, seawater, and reservoir rock) systems at various wetting conditions of the substrates (water-wet and oil-wet). The effect of the surface and nanoparticle charge on the contact angle is evaluated by adjusting the aqueous phase salinity. We also differentiate between the disjoining pressure mechanism and diffusion of silica nanoparticles through the oil phase by testing the attachment of nanoparticles on the rock surface. The results illustrate that a substantial portion of the wettability alteration ability of nanoparticles reported in the literature may be attributed to the method of measuring the contact angles where nanoparticles can adsorb at the rock sample before contact angle measurements. Silica nanoparticles are shown to further reduce the contact angle (make the substrate more water-wet) only when we have water-wet condition initially. Under oil-wet conditions, nanoparticles cause no notable change on the contact angle. The synergic effect of structural disjoining pressure and capillary pressure reduction might be a possible mechanism of wettability alteration in the water-wet conditions. In oil-wet conditions, the only possible mechanism is capillary pressure reduction. This chapter is presented as a paper in the International Symposium of the Society of Core Analysts.


identifier: Minguy, Thomas <https://research.library.mun.ca/view/creator_az/Minguy=3AThomas=3A=3A.html>   (2018) Variations of immanence: Spinoza, Deleuze and a metaphysics of immanence.  Masters thesis, Memorial University of Newfoundland.

abstract: The present thesis analyses the specific philosophies of Baruch Spinoza and Gilles Deleuze, more specifically the way in which both thinkers attempted to establish immanent metaphysics. The purpose of the work is not to compare both authors, but to see the key elements of the common project they share. To summarize, the present thesis seeks to elucidate the structure of something like an immanent metaphysics through a careful reading of Spinoza and Deleuze. We first attempt to clarify the relation both authors entertain with metaphysics, then we dedicate a chapter on each philosopher in order to disclose the specific systems they created. The conclusion we reach is the following: while Deleuze’s philosophy might lack some of the insights of Spinoza’s own, both authors are able to produce a metaphysics of pure immanence through a power ontology focused on the notion of potentia.


identifier: Connolly, Ross D. <https://research.library.mun.ca/view/creator_az/Connolly=3ARoss_D=2E=3A=3A.html>   (2018) Probabilities of PTSD and related substance use among Canadian adults.  Masters thesis, Memorial University of Newfoundland.

abstract:
The aim of this study was to estimate the prevalence and probabilities of comorbidities between
self-reported PTSD and smoking, alcohol binge drinking, and substance use disorders (SUDs)
from a national Canadian sample. Data were taken from the Public Use Microdata File of the
2012 Canadian Community Health Survey–Mental Health (N = 17 311). The prevalence of (a)
smoking, (b) alcohol binge drinking, and (c) SUDs was estimated among those with a PTSD
diagnosis versus those without a PTSD diagnosis. After controlling for potential socioeconomic
and mental health covariates, self-reported PTSD acted as a significant predictor for group
membership in the heaviest smoking, heaviest drinking, and heaviest drug usage
categories. Individuals self-reporting a diagnosis of PTSD were found to have a significantly
higher likelihood of engaging in smoking and alcohol binge drinking, and were more likely to
meet criteria for SUDs than individuals not reporting a PTSD diagnosis. Implications of the
findings are discussed.


identifier: Kelly, Erin E. <https://research.library.mun.ca/view/creator_az/Kelly=3AErin_E=2E=3A=3A.html>   (2018) Potential effects of blueberries on markers of neurodegenerative disease.  Masters thesis, Memorial University of Newfoundland.

abstract: One of the main mechanisms contributing to neurodegenerative diseases (NDD) is oxidative stress, caused by the buildup of reactive oxygen species (ROS) in the brain. Chronic neuroinflammation is also involved with the pathology of NDD; when microglia are activated in response to the dysfunction and aggregation of alpha-synuclein and amyloid-beta, they release inflammatory mediators. NDD are linked to glutamate-mediated excitotoxicity as well, where cells are damaged by the excessive stimulation from glutamate via inadequate uptake by glial cells. Polyphenols, found in very high levels in blueberries, have antioxidant properties which may offer protection and intervention from neurological disorders by managing ROS and reducing the inflammatory response. Biochemical analysis was performed on extracts from frozen wild Newfoundland fruits and leaves, Vaccinium angustiform spp. Mouse-pup derived brain cultures, and pure cultures of rat neurons and microglia were exposed to 100μM glutamate, 100ng/ml alpha-synuclein or 7.5μM amyloid-beta for 24-hours, which decreased cell viability. Overall, there was an increase in the number of viable cells once blueberry extract was added, effectively reducing neuronal and microglial cell death, showing that compounds in berries are beneficial when cell death and damage is influenced by glutamate-mediated excitotoxicity or insoluble alpha-synuclein and amyloid-beta aggregates. The blueberry extracts have high antioxidant activity and therefore may be able to help combat oxidative stress and neuroinflammation in the brain.


identifier: Timmar, Mesam <https://research.library.mun.ca/view/creator_az/Timmar=3AMesam=3A=3A.html>   (2018) The computational complexity of controller-environment co-design using library selection for distributed construction.  Masters thesis, Memorial University of Newfoundland.

abstract:
Creating specified structures through the coordinated efforts of teams of simple
autonomous robots is a significant problem in distributed robotics. All previous ef-
fort, both empirical and theoretical, has focused on the problems of designing either
controllers or environments which, in tandem with given environments or controllers,
built the specified structures. In this paper, we give the results of the first computa-
tional and parameterized complexity analyses of the controller-environment co-design
problem in the simple case where teams of finite-state robots are designed by select-
ing controllers from a given library. We show that this problem cannot be solved
efficiently in general or under a number of restrictions, and give the first restrictions
under which this problem is efficiently solvable.
We also consider two elaborations on this problem. First, we analyze the controller-
environment co-design problem under a new architecture in which robots have a
transient memory. Second, we give the first definitions of and derive computational
complexity results for stigmergy-related parameters for the controller-environment
co-design problem.


identifier: Alghamdi, Naeemah <https://research.library.mun.ca/view/creator_az/Alghamdi=3ANaeemah=3A=3A.html>   (2018) Disjoint skolem-type sequences and applications.  Masters thesis, Memorial University of Newfoundland.

abstract:
Let D = {i₁, i₂,..., in} be a set of n positive integers. A Skolem-type sequence
of order n is a sequence of i such that every i ∈ D appears exactly twice in the
sequence at position aᵢ and bᵢ, and |bᵢ - aᵢ| = i. These sequences might contain
empty positions, which are filled with 0 elements and called hooks. For example,
(2; 4; 2; 0; 3; 4; 0; 3) is a Skolem-type sequence of order n = 3, D = f2; 3; 4g and two
hooks. If D = f1; 2; 3; 4g we have (1; 1; 4; 2; 3; 2; 4; 3), which is a Skolem-type sequence
of order 4 and zero hooks, or a Skolem sequence.
In this thesis we introduce additional disjoint Skolem-type sequences of order n
such as disjoint (hooked) near-Skolem sequences and (hooked) Langford sequences.
We present several tables of constructions that are disjoint with known constructions
and prove that our constructions yield Skolem-type sequences. We also discuss the
necessity and sufficiency for the existence of Skolem-type sequences of order n where
n is positive integers.


identifier: Eskandari, Saeid <https://research.library.mun.ca/view/creator_az/Eskandari=3ASaeid=3A=3A.html>   (2019) Investigation of longitudinal and transverse dispersion in porous media.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Miscible displacement processes are increasingly feasible methods for the recovery of
oil from depleted reservoirs as an enhanced oil recovery (EOR) method. However, a
fundamental understanding of the dependency of transport phenomenon to medium
properties and their consequent impact on oil recovery efficiency is lacking. Moreover,
it is generally believed that miscibility may repeatedly develop and break down in a
reservoir due to dispersion arising from velocity and reservoir heterogeneity. Thus,
miscible processes are assumed to be dependent on the pore geometry of the reservoir.
The current research uses mathematical and unique experimental approaches to investigate miscible displacement in two-dimensional media with focus on pore structure
to comprehend the relationship between the transport properties to its pore structure. Transport phenomena significantly influence EOR efficiency and this raises the
importance of dispersion and miscibility. The mathematical section of this research
uses a statistical oriented mathematical approach to investigate miscible displacement
assuming various pore properties to comprehend the relationship between dispersion
during miscible displacement and the pore structure. This study focuses on examining the dependence of dispersion in both the longitudinal and transverse directions
on heterogeneity and pore geometry using statistical models. The pore element is
defined by adjustable distribution functions indicating tortuosity and connectivity of
the porous medium. Using random walk theory that assumes the mass transfer occurs
as a sequence of discrete physical events as particles move between a series of discrete
pore elements, the stochastic functions are used to develop a model to estimate the
mechanical dispersion properties of the porous media. The introduced model decouples dispersion in the longitudinal and transverse directions and shows a more specific
relationship between dispersion and pore size distribution. An analytical approach is
applied to model miscible displacement in a fractured medium to study the effect of
velocity on the magnitude of mechanical dispersion. Various displacement scenarios are assumed to find the the effect of pore properties on dispersion. Results illustrate a
strong dependence of mechanical dispersion on pore properties of the medium. Both
longitudinal and transverse dispersion coefficients increased by increasing the velocity
and heterogeneity ratio. In the experimental section, a new experimental approach
has been developed to estimate the average longitudinal and transverse dispersion co-
efficients in a homogeneous anisotropic porous medium during miscible displacement.
A series of miscible flooding tests are conducted and studied. Traditionally, most
studies of miscible injection have focused on recovery and mechanism of the method
and Peclet number that have been used to find the dispersion and diffusion coefficients
from a mathematical correlations. This study utilizes a unique method to estimate
the mass transfer properties. A unique image processing tool is developed and used to
analyze the developing mixing zone in the process and consequently processed images
are used to collaborate with a developed Bayesian estimator tool to fit the dispersion
coefficients in analytical solution of Advection-Diffusion Equation (ADE). The de-
tails of the approach are explained and obtained images are analyzed and interpreted.
The results confirm the strong dependency of the velocity of the displacing fluid and
dispersion coefficients in both longitudinal and transverse directions. The effects of
anisotropy on miscible mass transport are investigated in this study too.


identifier: Chagas, Caroline Manto <https://research.library.mun.ca/view/creator_az/Chagas=3ACaroline_Manto=3A=3A.html>   (2018) Effects of vinblastine and its metabolites on nausea and alopecia associated receptors.  Masters thesis, Memorial University of Newfoundland.

abstract:
The effects of vinblastine (VLB) and its thirty-five known metabolites were investigated on nausea and alopecia associated receptors by means of molecular docking simulations. The in silico pharmacokinetics (PK) properties and binding affinities of VLB and its metabolites with the vinca site of tubulin were also elucidated in the present study.
VLB and its metabolites have demonstrated binding affinities mainly for the muscarinic receptors M₁, M₄ and M₅ that display significant roles in the onset of nausea during chemotherapy. The metabolites of VLB interact with the binding site of acetylcholine and share similar binding interactions with residues involved with the endogenous substrate. Furthermore, VLB metabolites have also shown binding affinities for alopecia associated receptors such as vitamin D (VDR), androgen, smoothened and MDM2, which can trigger the death of hair follicle following cancer treatment.
The predicted PK properties of VLB and its metabolites have revealed that they are all substrates and inhibitors of CYP3A4 and P-glycoprotein, and inhibitors of CYP2D6. The majority of metabolites do not cross the blood-brain barrier, do not undergo glucuronidation and have no affinity for the human ether-à-go-go-related gene receptor. Finally, VLB metabolites docked into the vinca site of tubulin have revealed that metabolites 8, 10 and 11 have binding affinities for tubulin and interact with the same residues involved with VLB. Taking into account the PK properties, metabolite 10 (20-Hydroxy-VLB) has shown to be a potential active analog of VLB.
This research project has aimed to a better understanding of the VLB-induced off-targets events such as nausea and alopecia, and how the VLB metabolites can trigger these ADRs. These findings suggest that knowing which and how the metabolites of VLB are involved with off-targets receptors of nausea and alopecia, as well as their PK properties and effects on tubulin target, ADRs during chemotherapy could be eliminated or lessened. This is possible if modifications on the chemical structure of VLB and advances in drug discovery and medicinal chemistry fields are taken into consideration in future studies. It would enhance target specificity as it could decrease formation of many metabolites and hence minimize the number of off-target interactions. That could result in providing a less unpleasant treatment for cancer patients and a higher quality of life during chemotherapy.


identifier: Cai, Qinhong <https://research.library.mun.ca/view/creator_az/Cai=3AQinhong=3A=3A.html>   (2019) Biosurfactant production and applications in oil contaminate control.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Surfactants are a versatile group of chemicals. They are amphiphilic compounds that exert impacts at interfaces among air, water, oil, and solid phases. Currently, the prevalent players in the market are chemically synthesized surfactants, which have concerns of considerable toxicity and low biodegradability. Because they are mainly derived from fossil fuels, they are not sustainable in the long run and the production costs are subjected to the price variance of raw materials. In view of these limitations, biosurfactants have been proposed as promising alternatives. They are surfactant molecules produced by microorganisms during their growth. Biosurfactants exist naturally in the environment and play some roles in the ecosystem even without human interferences. In this dissertation we define this virtue as “environmental friendly”. They are also renewable and non/less toxic. They have also been found with the intriguing advantages such as enormous structural diversity, lower critical micellar concentrations (CMCs), and the feasibility to use renewable and/or waste streams as the source of production. Biosurfactants are considered as multifunctional biomolecules of the 21st century with a thriving global market share. Their applications in environmental and oil industries are among the top market sectors thanks to their environmental friendly nature.
In order to harness the power of biosurfactants, the economic effectiveness of production of these molecules needs improvements. The inocula/microorganisms are the engine of a production process, which determine the maximum yield potential and the functionality of biosurfactants, yet limited inocula have been reported. The functional diversity of biosurfactants includes emulsification, dissolution, dispersion, emulsion breaking, reduction in viscosity, and surface activity, which result in a broad spectrum of potential applications in oil contaminate control including soil washing, enhanced bioremediation, oily wastewater treatment, and spilled oil dispersion. However, limited research efforts have been placed into evaluating the application potential of biosurfactants in oil contaminate control.
The objectives of this thesis are to 1) identify novel and robust biosurfactant producing microorganisms and develop hyper-production mutants; 2) examine the functionality of the produced biosurfactants; and 3) investigate the potential of using these produced biosurfactants in diverse applications of oil contaminate control.
The outputs of the thesis include: (1) the successful isolation, identification, characterization and functionality analysis of one-hundred-and-fourteen biosurfactant producing and oil degrading marine bacteria; (2) the discovery of a novel bacterial species, Alcanivorax atlaticus for the first time and its proposed type strain with comprehensive genotype and phenotype characterizations; (3) an in-depth characterization, functionality analysis and application demonstration of a novel bioemulsifier (exmulsins) and its bacterium (Exiguobacterium sp. N4-1P); (4) reporting of thirty-seven novel oil-in-water emulsion breaking marine bacteria for oily wastewater treatment, and a recommended screening strategy for their identification; (5) the first attempt to genetically modify Rhodococcus strains for hyper production of biosurfactant and to investigate the dispersing abilities of the the produced biosurfactants; and (6) a comprehensive investigation of 4 types of biosurfactants produced from selected isolates and mutants as marine oil spill dispersants.


identifier: Cheng, Zhenlong <https://research.library.mun.ca/view/creator_az/Cheng=3AZhenlong=3A=3A.html>   (2018) Regulation of coronafacoyl phytotoxin production in the potato common scab pathogen Streptomyces scabies.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
The genus Streptomyces consists of hundreds of species of Gram-positive,
filamentous bacteria, which have a complex developmental life cycle. Many specialized
metabolites of clinical, agricultural and biotechnological value are produced by
Streptomyces. Very few Streptomyces species have been shown to be pathogenic to plants.
The best characterized pathogenic species is Streptomyces scabies, which is the main
causative agent of potato common scab (CS) disease. CS is characterized by the formation
of lesions on the potato tuber surface, which negatively impact the market value of the
affected potatoes, leading to significant losses for growers.
S. scabies and other CS-causing pathogens produce thaxtomin A, the key virulence
factor involved in CS disease. S. scabies also produces N-coronafacoyl-L-isoleucine (CFAL-
Ile), which is a member of the coronafacoyl family of phytotoxins. The coronafacoyl
phytotoxin biosynthetic gene cluster in S. scabies consists of 15 genes, of which 13 are
enzyme-encoding genes and are co-transcribed. The remaining two genes are divergently
co-transcribed from the biosynthetic genes. The first gene, scab79591/cfaR, encodes a
PAS-LuxR family regulator that activates the transcription of the enzyme-coding genes.
The second gene, scab79581/orf1, encodes a ThiF family protein of unknown function.
This thesis examines the regulation of CFA-L-Ile biosynthesis in S. scabies and the
role of the CfaR and ORF1 proteins. Our results show that CfaR is the principle regulator
controlling expression of the coronafacoyl phytotoxin biosynthetic genes and CFA-L-Ile
production, while ORF1 augments phytotoxin production in a CfaR dependent manner and
may function as a “helper” of CfaR. Bioinformatics analysis suggests that ORF1 may catalyze AMPylation of an unknown target molecule. In addition, this thesis addresses the
effects of the plant-derived molecules cellobiose and suberin on CFA-L-Ile production as
well as the role of CFA-L-Ile in controlling its own production. While cellobiose and
suberin both induce thaxtomin A production, our results suggest that these molecules
inhibit CFA-L-Ile production in S. scabies. In vitro binding assays showed that CFA-L-Ile
inhibits the binding of CfaR to its target site in the coronafacoyl phytotoxin biosynthetic
gene cluster. This suggests that CFA-L-Ile production is subjected to negative feedback
regulation in S. scabies.


identifier: Guo, Chuanqi <https://research.library.mun.ca/view/creator_az/Guo=3AChuanqi=3A=3A.html>   (2019) Copula-based models for risk analysis of process systems with dependencies.  Masters thesis, Memorial University of Newfoundland.

abstract:
With the increasing integration of heat and mass and the complexity of process systems, process variables are becoming strongly interdependent. Ignoring these dependencies in process safety modelling is unreasonable. The present work addresses this dependency challenge. It proposes two simple yet robust risk models for process safety analysis.
The first model is the copula-based bow-tie (CBBT) model, which revises the traditional bow-tie (BT) model by considering dependencies among the causes and failures of safety barriers. Copulas are used to simulate hypothetical dependent joint probability densities. The proposed model, along with classical BT analysis, is examined under a case study of the risk analysis of a typical distillation column. Comparing the results from both approaches in terms of the estimated probability of a potential hexane release scenario, it is shown that the dependencies of process units’ malfunctions can increase the likelihood of accident scenarios to a significant extent. Further, to explore the mechanisms behind the impact of such dependencies, the effect of dependencies on the two most basic logic gates is also analyzed.
The next model developed is the copula-based Bayesian network (CBBN), which integrates linear dependence modelled by a Bayesian network (BN) and non-linear dependence by copulas. It provides more reliable estimation of accident probability when applied to real cases. Sensitivity analysis identifies the factors that play important roles in causing an accident. A diagnostic analysis is also performed to find the most probable explanation for the occurred event. Results match the accident investigation report and thus prove the effectiveness of the proposed model.


identifier: Abramov, Oleksandr <https://research.library.mun.ca/view/creator_az/Abramov=3AOleksandr=3A=3A.html>   (2018) Parallelization of a Winslow variational mesh generator.  Masters thesis, Memorial University of Newfoundland.

abstract:
Adaptive meshes appear to be preferable to the uniform meshes for the numerical
approximations of some PDEs. As the solution of large scale numerical problems
often involves solving a problem on a distributed computational systems (clusters),
it is desirable for a mesh adaptation method to also be deployable on such systems.
We study various 1D mesh adaptation methods and theoretically explore connection
between some of them. An implementation of a library for a parallel 2D Winslow
adaptive mesh method is be presented. The library is written in the C++ language
and uses the PETSc library and the Message Passing Interface (MPI) protocol. Also
an example of using the library with a Stochastic Domain Decomposition (SDD)
approach based on a Monte Carlo method is discussed with some numerical results
provided.


identifier: Maich, Kimberly <https://research.library.mun.ca/view/creator_az/Maich=3AKimberly=3A=3A.html>   (2018) Everyday mobile/assistive technology supporting adults with intellectual &/or developmental disabilities in the community setting.  Masters thesis, Memorial University of Newfoundland.

abstract: Twelve pilot project participants with intellectual and/or developmental disabilities used mobile devices (smartwatch and smartphone technology) and individualized apps focused on time management, coping, budgeting, exercise, and safety, to support independence and community engagement. Ten participants with Intellectual and/or Developmental Disabilities (IDD) and five front-line Coordinators participated in post-project focus groups in which common patterns of responses and salient findings were noted, including the emergence of a peer technology expert. Five themes emerged from focus group data, which were then developed into five broad technological, clinical, and methodological recommendations for phase two, that will follow this pilot project. Duration data showed variable change in pre-post duration of supports; related changes were part of these recommendations. The small sample size and current pilot study status suggests cautious interpretation and application of results beyond the immediate context of this project; however, this pilot project has developed a foundation for a more comprehensive intervention.


identifier: Jones-Doyle, Annique <https://research.library.mun.ca/view/creator_az/Jones-Doyle=3AAnnique=3A=3A.html>   (2018) Maritime consumption on Newfoundland's Petit Nord: material expressions of identity on the Champ Paya fishing station.  Masters thesis, Memorial University of Newfoundland.

abstract:
Excavations at the Champ Paya fishing station (EfAx-09) on Newfoundland’s Historical French Shore have revealed many insights about the seasonal cod fishery in the New World. Maps of the area, made by French naval chart-maker Georges Cloué (1850s) indicated that there had been a number of fishing stages in Crouse Harbour, and Champ Paya has proven to be a rich source of early maritime material culture.
The personal consumer goods recovered from the site have not, as yet, been thoroughly documented and analyzed. I will explore the ways in which the material culture may have helped to reinforce aspects of social identity and power for Champ Paya’s seasonal occupants by analysing the small finds collected from the site in the context of the fishing room as a socially stratified consumption site.
Historical, cartographic and archaeological evidence indicates that the Champ Paya fishing station, located on Newfoundland’s historical French Shore, was utilized since 1504. Excavations at Champ Paya (EfAx-09) have revealed many insights about the seasonal cod fishery in the New World and the daily lives of those involved in it.
Utilizing the early maritime material culture recovered from the site, in particular the personal consumer goods, this thesis explores the interpretative value of ‘small finds’ and their importance in reinforcing social identity and status hierarchy among the seasonal residents at Champ Paya.


identifier: Hennigar, Bronwen <https://research.library.mun.ca/view/creator_az/Hennigar=3ABronwen=3A=3A.html>   (2018) Effects of anthropogenic noise and light on the vocal and spatial behaviour of birds.  Masters thesis, Memorial University of Newfoundland.

abstract:
Understanding how anthropogenic disturbance affects animal behaviour is challenging
because observational studies often involve co-occurring disturbances (e.g., noise,
lighting, and roadways), and laboratory experiments often lack ecological validity. During
the 2016 and 2017 avian breeding seasons, I tested the effects of anthropogenic noise
and light on the singing and spatial behaviour of birds. I independently manipulated the
presence of anthropogenic noise and light at 110 sites in an otherwise undisturbed
boreal forest in Labrador, Canada. Each stimulus was surrounded by a microphone array
that recorded and localized singing birds throughout the stimulus presentation. Results
show that noise attracts birds, but that light and the interaction between noise and light
have little or no effect. None of the treatments affected when birds began singing. My
study provides some of the first experimental evidence of the independent and
combined effects of noise and light on the singing and spatial behaviour of wild birds.


identifier: McCuaig, Bonita <https://research.library.mun.ca/view/creator_az/McCuaig=3ABonita=3A=3A.html>   (2018) The independent partnership of Thyasira cf. gouldi and its sulfur oxidizing symbiont.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Symbiotic relationships between invertebrates and chemoautotrophic bacteria can be found in many marine environments. Here we focus on describing the genomic content of the extracellular symbionts of Thyasira cf. gouldi. Previous work described three symbiont phylotypes designated A, B, and C. These bacteria are all closely related sulfur oxidising gammaproteobacteria.
Investigation of the ribulose-1,5-bisphosphate carboxylase (RuBisCo) gene showed a high level of diversity between bacterial populations hosted by Thyasira cf. gouldi. The RuBisCo had a higher diversity than the 16S rRNA gene and showed possible horizontal gene transfer events within phylotype A. A small number of host individuals also appeared to contain mixed populations of RuBisCo phylotypes not identified in 16S rRNA sequences. Draft genomes were created from sequencing of host gill tissue. These samples were selected to include bacteria of each phylotype. The draft genomes created were highly fragmented, but many genes were identified. The metabolic capabilities were very similar and encode for carbon fixation through the Calvin-Benson-Basham cycle. Energy for this process is obtained through oxidation of sulfur compounds through both a reverse dissimilar sulfate reduction cycle and a bacterial sulfur oxidation cycle. The bacteria may also be able to utilize nitrogen or hydrogen oxidation for respiration. A functional tricarboxylic acid cycle was also identified in all three genomes suggesting the bacteria may be capable of heterotrophy. All metagenomes contained chemotaxis and flagellar genes. An extracellular chromosome encoding a type IV secretion system was identified in the draft genome of phylotype B. If this plasmid is truly from the symbiont it could be used to export compounds to the host. Both phylotypes A and B contained genes involved in biofilm formation. A biofilm would benefit extracellular bacteria by creating a barrier from the host immune system and creating a controlled environment where the symbiont can exclude other environmental bacteria. Some genes associated with host interactions were also identified, although these were less conserved than the metabolic functions. Our results support the evidence that Thyasira cf. gouldi obtains its symbionts from the environment. The draft genomes contained evidence of a flexible metabolism that can adapt to changing sediment conditions.


identifier: Sidey, Megan <https://research.library.mun.ca/view/creator_az/Sidey=3AMegan=3A=3A.html>   (2018) Aquaculture regulation in Canada: a case for modernization, standardization and collaboration.  Masters thesis, Memorial University of Newfoundland.

abstract:
As the global population is set to reach 9 billion by 2050, food production needs to be far more efficient in utilizing productive natural resources (World Bank, 2013). Aquaculture can address some of the difficult challenges that accompany global population growth.
Aquaculture regulation in Canada is shared between the provincial and federal governments. The Department of Fisheries and Oceans (DFO) is the lead regulatory authority that manages aquaculture in Canada. DFO manages aquaculture collaboratively with ten provincial governments and the Yukon Territory. There is significant potential for Canadian aquaculture to expand, with the Canadian government estimating that by 2020, domestic aquaculture production could exceed 308,000 tonnes with a processed value of USD 1.6 billion (FAO, 2018a). For future significant growth in Canada’s aquaculture industry to occur, centralized policies and regulations, with DFO remaining the lead regulator, must be implemented to continue to protect the environment, and ensure the economic viability of the sector in an increasingly competitive global market.
Throughout this report, the discussion is centered around three themes: (1) the importance of aquaculture to the Canadian economy, (2) the need for aquaculture regulation and legislation to be standardized throughout the Canadian provinces and territories to promote the efficiency and growth of the industry, (3) recommendation of the standardization of aquaculture regulations be based on aspects of the British Columbian model –the largest aquaculture producing province in Canada (FAO, 2018a).


identifier: Galagedarage Don, Mihiran Pathmika <https://research.library.mun.ca/view/creator_az/Galagedarage_Don=3AMihiran_Pathmika=3A=3A.html>   (2019) Process fault prediction and prognosis based on a hybrid technique.  Masters thesis, Memorial University of Newfoundland.

abstract: The present study introduces a novel hybrid methodology for fault detection and diagnosis (FDD) and fault prediction and prognosis (FPP). The hybrid methodology combines both data-driven and process knowledge driven techniques. The Hidden Markov Model (HMM) and the auxiliary codes detect and predict the abnormalities based on process history while the Bayesian Network (BN) diagnoses the root cause of the fault based on process knowledge. In the first step, the system performance is evaluated for fault detection and diagnosis and in the second step, prediction and prognosis are evaluated. In both cases, an HMM trained with Normal Operating Condition data is used to determine the log-likelihoods (LL) of each process history data string. It is then used to develop the Conditional Probability Tables of BN while the structure of BN is developed based on process knowledge. Abnormal behaviour of the system is identified through HMM. The time of detection of an abnormality, respective LL value, and the probabilities of being in the process condition at the time of detection are used to generate the likelihood evidence to BN. The updated BN is then used to diagnose the root cause by considering the respective changes of the probabilities. Performance of the new technique is validated with published data of Tennessee Eastman Process. Eight of the ten selected faults were successfully detected and diagnosed. The same set of faults were predicted and prognosed accurately at different levels of maximum added noise.


identifier: Nirmalkanna, Ananthika <https://research.library.mun.ca/view/creator_az/Nirmalkanna=3AAnanthika=3A=3A.html>   (2018) Efficiency of two-phase single and multiple response-dependent sampling designs.  Masters thesis, Memorial University of Newfoundland.

abstract:
In some observational studies, it may be relatively more affordable to measure
the response variable, while some covariates' data might be expensive to obtain.
Therefore, collection of the covariate information might be restricted by the available
budget of the study. In this situation, we need to consider sampling designs which
yield powerful association tests for a given sample size by selecting more informative
subjects. Using cost-efficient response-dependent two-phase sampling designs is a
way to select more informative sampling units. In phase I, we have easily measured
variables including the response variable for all individuals in the cohort or in a large
random sample from the population, and in phase II, we obtain expensive variables for
a subset of individuals selected according to their response variable and inexpensive
covariates obtained in phase I. We consider the likelihood and pseudo-likelihood
based methods for incomplete data analysis to make inference on the association
between the expensive covariate and the response variable. We also consider multiple
response-dependent sampling designs. The objective is to compare the efficiency of
estimators and to identify efficient sampling design settings under each estimation
method.


identifier: Villamizar, Ederson <https://research.library.mun.ca/view/creator_az/Villamizar=3AEderson=3A=3A.html>   (2019) Constructing a crustal-scale 3-D earth model of offshore-to-onshore western Newfoundland using seismic reflection, seismic refraction, gravity and magnetic data.  Masters thesis, Memorial University of Newfoundland.

abstract:
Western Newfoundland is characterized as a geologically complex region for which the potential field data have not been incorporated into tectonic models. To this end, a 3D density model of Western Newfoundland was constructed by means of forward gravity modelling and gravity inversion to better understand the complexity of the Appalachian structures on which Western Newfoundland is placed. This model was constrained by seismic refraction and seismic reflection data located in the study area, and surface geology. Density values were calculated from empirical velocity-density functions and gravity forward modelling adjustments.
The 3D density model, 3D gravity inversion results, and magnetic data support the presence of a high density lower crustal body in the Grenville Province. It is possible that this particular body may extend further north and could be related to the denser body found in southeast Labrador. The high resolution magnetic map for the study area showed two WNW-ESE linear magnetic anomalies in the Gulf of St. Lawrence that lie perpendicular to the Newfoundland coast. They could be explained by the presence of ancient inherited basement involved transfer faults that resulted from offset ancient ridge axis segments during the opening of the Iapetus ocean.


identifier: Chokshi, Killol <https://research.library.mun.ca/view/creator_az/Chokshi=3AKillol=3A=3A.html>   (2018) Characterizing the molecular signaling pathways in the cerebral arteries of stroke-prone spontaneously hypertensive rate (SHRsp) before and after stroke.  Masters thesis, Memorial University of Newfoundland.

abstract: Background: Hemorrhagic stroke (HS) is associated with loss of middle cerebral artery (MCA) autoregulation in the stroke-prone spontaneously hypertensive rat (SHRsp). We believe the MCA dysfunction may be due to increased inflammatory signalling (p38MAPK and ERK) and decreased contractile signalling (MLC and PKC) in the MCA during stroke, altered calcium (TRPV4) channel expression, accompanied with increased neuro-inflammation (astrocyte and microglia) and neuronal damage in brain after stroke. Methods: SHRsps were fed a high salt (4%NaCl) diet and sacrificed at nine weeks of age for pre-stroke and after evidence of stroke (~15 weeks) for post-stroke samples. The MCAs were isolated to measure protein levels and expression using immunofluorescence (IF), and western blot (WB) for inflammatory and contractile proteins. Tissues were analyzed for activation of neuro-inflammation, neuronal damage, for total and activated inflammatory proteins (ERK1/2 and p38MAPK), cerebrovascular contraction (PKC and MLC), and changes involved in transient receptor potential V4 (TRPV4) activation. Results: Results from both WB and IF indicate an increase in activated inflammatory proteins post-stroke, with an associated decrease in expression of activated contractile proteins and TRPV4 channel compared to pre-stroke SHRsp. The post-stroke samples also show significant increase in neuro-inflammation and neuronal damage compared to pre-stroke samples. Conclusion: The results show an increase in ratio of activated/total (p38 MAPK and ERK1/2) accompanied with a decrease in activated/total PKC and TRPV4 channel expression in post-stroke which may relate to a decrease in vessel structural integrity and alter vascular tone in the MCAs effecting its ability to contract in response to pressure. Significant neuro-inflammation and neuronal damage in the brain tissue surrounding the MCA in post-stroke samples confirm MCA dysfunction accompanies brain damage during stroke.


identifier: Acheampong, Lily <https://research.library.mun.ca/view/creator_az/Acheampong=3ALily=3A=3A.html>   (2019) Examining gender differences in the diagnosis of obstructive airway diseases.  Masters thesis, Memorial University of Newfoundland.

abstract:
Gender disparities in the diagnosis of cardiovascular diseases have been well established. Not much is known about gender differences in obstructive airway diseases (OADs). The aim of this thesis is to 1) conduct a systematic review and meta-analysis to synthesize the existing evidence on gender bias in the diagnosis of chronic obstructive pulmonary disease (COPD), 2) conduct a secondary data analysis to examine gender diagnostic bias in patients who meet spirometry criteria for COPD and 3) conduct a secondary data analysis to examine gender diagnostic bias in patients who meet spirometry criteria for asthma.
The Cochrane handbook for systematic reviews of interventions was used as a guide for standard methods used in systematic reviews. Literature search was conducted using MEDLINE (PubMed), EMBASE and CINAHL. Relevant articles were selected for descriptive and quantitative synthesis, and the Inverse Variance (IV) random effect model was used for analysis. For the secondary data analysis, multivariate logistic regression was used to assess the effect of sex on diagnostic outcomes (physician-diagnosed COPD or physician-diagnosed asthma, misdiagnosis, referral to a specialist, referral for spirometry and referral for chest x-ray), while controlling for additional patient factors.
Results from the meta-analysis suggests that gender disparities do exist in primary care for COPD, as men were about two times more likely to receive a correct diagnosis for COPD, and women with respiratory symptoms were less likely to be referred for spirometry. For the secondary analysis of data, no significant differences between genders were observed for all diagnostic outcomes in patients who meet spirometry criteria for COPD. However, for patients with spirometrically-defined asthma, women were less likely than men to receive a correct diagnosis for asthma, less likely to be referred for spirometry, but more likely than men to be referred for chest-x-ray.


identifier: Gillani, Syed Shah Mohioudin <https://research.library.mun.ca/view/creator_az/Gillani=3ASyed_Shah_Mohioudin=3A=3A.html>   (2018) Remote estimation of gross primary production and light use efficiency at a boreal bog and an abandoned peatland pasture in western Newfoundland, Canada.  Masters thesis, Memorial University of Newfoundland.

abstract:
The pristine peatlands store approximately 1/3 of the global soil carbon (C) pool and function as a climate cooling mechanism. A peatland’s production is persistently larger than its decomposition due to its high soil water content. However, peatlands disturbed via drainage have been identified as a potential C source. Gross primary production (GPP) and light use efficiency (LUE) are two critical indicators for studying the C budget in terrestrial ecosystems. However, the knowledge of GPP and LUE values in boreal peatlands is still limited because so few measurements have been carried out in peatlands. Field measurements in boreal peatlands cover less than 0.01% of global peatlands; this significantly limits our capacity to understand the C budget of global peatlands. Normally, estimation of the C budget for global peatlands requires field-based measurements to be up-scaled from the field level to the global level. Another commonly-adopted approach for estimating the C budget for global peatlands is to estimate the C budget based on the remotely sensed measurement with global coverage. This approach needs to use the algorithm derived from field measurements. However, there are significant uncertainties over the field-based algorithm used to estimate the GPP and LUE in boreal peatlands due to the very limited availability of field measurements. Moreover, none of the field-based estimations of GPP and LUE were done for drained peatlands. Therefore, more studies are needed to estimate the GPP and LUE for both pristine peatlands and disturbed peatlands based on field measurements. To fill this gap, I conducted a study to estimate GPP and LUE using eddy covariance tower (EC) measurements and MODIS satellite data in a boreal bog and an adjacent abandoned peatland pasture. I have assessed the relationships of GPP with photosynthetic active radiation (PAR) alone, vegetation indices (normalized difference vegetation index [NDVI] and enhanced vegetation index [EVI]), and their products (PAR×EVI, PAR×NDVI) at both research sites during both study years. The relationship between GPP and the product of vegetation indices and PAR performed better in both study sites, with a greater value of determination coefficient R² (0.70 to 0.90), than those calculated from PAR and vegetation indices alone (R² ranged from 0.56 to 0.79).
The abandoned peatland pasture had greater LUE capacity than the boreal bog. At the start and end of the growing season, the LUE value was minimum, but in the middle of the growing season, the LUE value peaked at both study sites. The LUE of the abandoned peatland pasture showed greater variations between the study years 2014 and 2015 compared to the boreal bog site. Air temperature and water table depth were the main environmental factors regulating LUE during the growing season in both study years.
Research in this thesis will help to estimate the GPP and LUE in boreal bog and drainage pasture peatlands. This research is important for GPP modeling, and spatial and temporal simulation of GPP and LUE in peatland ecosystems, because both PAR and vegetation indices are readily available from the remotely sensed data. This work will improve our understanding of how GPP and LUE vary over space and time and contribute to C cycle budget and global climate change perceptivity.


identifier: ElTantaway, Agwad Hammad ElSayed <https://research.library.mun.ca/view/creator_az/ElTantaway=3AAgwad_Hammad_ElSayed=3A=3A.html>   (2018) Aerial detection of ground moving objects.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Automatic detection of ground moving objects (GMOs) from aerial camera platforms
(ACPs) is essential in many video processing applications, both civilian and military.
However, the extremely small size of GMOs and the continuous shaky motion of ACPs
present challenges in detecting GMOs for traditional methods. In particular, existing
detection methods fail to balance high detection accuracy and real-time performance.
This thesis investigates the problem of GMOs detection from ACPs and overcoming
the challenges and drawbacks that exist in traditional detection methods. The
underlying assumption used in this thesis is based on principal component pursuits
(PCP) in which the background of an aerial video is modelled as a low-rank matrix
and the moving objects are modelled as sparse corrupting this video. The research
in this thesis investigates the proposed problem in three directions: (1) handling the
shaky motion in ACPs robustly with minimal computational cost, (2) improving the
detection accuracy and radically lowering false detections via penalization term, and
(3) extending PCP’s formulation to achieve adequate real-time performance.
In this thesis, a series of novel algorithms are proposed to show the evolution of
our research towards the development of KR-LNSP, a novel robust detection method
which is characterized by high detection accuracy, low computational cost, adaptability
to shaky motion in ACPs, and adequate real-time performance. Each of the
proposed algorithms is intensively evaluated using different challenging datasets and compared with current state-of-the-art methods.


identifier: Wang, Chenfang <https://research.library.mun.ca/view/creator_az/Wang=3AChenfang=3A=3A.html>   (2019) The role of social media in mobilizing social movements: a case study of the "Save the arctic" campaign.  Masters thesis, Memorial University of Newfoundland.

abstract: Social media plays a vital role in mobilizing social movement actors to produce and respond to a variety of issues. The development of the Internet and social media has transformed traditional social movements and provided a new means for people in modern societies to mobilize. While social media presents contemporary social movements with new opportunities, they also bring challenges. This study examines the “Save The Arctic” campaign launched by Greenpeace as a typical case of contemporary movements to explore how environmental movements intertwine with social networking platforms. Qualitative textual analysis of campaign-related content on Twitter is used to analyze who plays a role in mobilizing the campaign, what discourses social movement actors produce, and how activists use Twitter to promote campaign-related messages. The findings of this study provide insights into the changing relationship between social movement organizations and digitally networked individuals, how protest strategies shift through social media activism, how visual communication is used as part of social movement framing in digital forms of mobilization, and how the media environment for social movements shifts in the social media era.


identifier: Xu, Jiming <https://research.library.mun.ca/view/creator_az/Xu=3AJiming=3A=3A.html>   (2019) Static power analysis of cryptographic devices.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Side-channel attacks are proven to be efficient tools in attacking cryptographic devices.
Dynamic power leakage has been used as a source for many well-known side-channel
attack algorithms. As process technology size shrinks, the relative amount of static
power consumption increases accordingly, and reaches a significant level in sub-100-
nm chips, potentially changing the nature of side-channel analysis based on power
consumption. In this thesis, we demonstrate our work in side-channel attacks exploiting
static power leakage. Our research interest is particularly focused on profiled attacks.
Firstly, we present recent developments of static power analysis and provide our
results to further support some of the conclusions in existing publications. We also
give a description of the template attack we developed for static power analysis of
block ciphers. This template attack uses new distinguishers which are previously
applied to other data analysis fields. The results of our study are achieved using
simulations in a 45-nm and 65-nm CMOS environment, and demonstrate the viability
of static-power-based template attacks.
Secondly, we bring kernel density estimation into the scenario of static power
analysis. We compare the performance of the kernel method and conventional Gaussian
distinguisher. It is demonstrated in our experiments that the static power leakage
may not satisfy multivariate Gaussian distribution, in which case the kernel method
results in better attack outcomes.
Thirdly, we perform template attacks on a masked S-box circuit using static and
dynamic power leakage. We are the first to compare static power and dynamic power in the scenario of profiled attacks against masked devices. The attacks are shown
to be successful, and by performing multiple attacks and adding Gaussian noise, we
conclude that in the 45-nm environment, dynamic power analysis requires a high
sampling rate for the oscilloscopes, while the results of static-power-based attacks are
more sensitive to additive noise.
Lastly, we attempt to combine static and dynamic power leakage in order to take
the advantage of both leakage sources. With the help of deep learning technology, we
are able to propose more complex schemes to combine different leakage sources. Three
combining schemes are proposed and evaluated using a masked S-box circuit simulated
with 45-nm library. The experiment results show that the hierarchical LSTM proposal
performs the best or close to the best in all test cases.


identifier: Zhang, Liqiu <https://research.library.mun.ca/view/creator_az/Zhang=3ALiqiu=3A=3A.html>   (2018) Incorporating climate change into inland fisheries management and policy development: a systematic review.  Masters thesis, Memorial University of Newfoundland.

abstract: The impact of climate change on inland fisheries has received critical attention in science and policy cycles. Despite this attention, the consequences of these impacts are difficult to predict due to the complex dynamics of these systems, their inherent uncertainties and the long timescales upon which change occurs. Additionally, inland fisheries are often influenced by multiple external drivers which are difficult to identify and account for in assessing and predicting change. Despite a growing body of literature on climate change impacts on fisheries, few comprehensive syntheses exist. This thesis applies a systematic literature review to answer the question whether climate change is incorporated into inland fisheries management and policy development. The review found that despite the growing attention, the literature in the field could still be described as insufficient. The review revealed that in general studies did not integrate climate change into management or decision-making, and even fewer studies attempted to identify adaptive options. Integrated approaches or responses that incorporate multiple drivers of change and account for multiple sources of uncertainty are needed for policy makers and stakeholders. The complexities of these socio-ecological systems require deliberate integration of climate change in the management of inland fisheries.


identifier: London, Sydney <https://research.library.mun.ca/view/creator_az/London=3ASydney=3A=3A.html>   (2018) The neuroendocrine control of feeding and reproduction in zebrafish (Danio rerio) and glass catfish (Kryptopterus vitreolus).  Masters thesis, Memorial University of Newfoundland.

abstract:
Reproduction and feeding are two critical life processes in all vertebrates, the regulations of
which involve a complex network of interactions. It has been suggested that appetite
regulators, such as orexin, neuropeptide Y (NPY), and cocaine and amphetamine regulated
transcript (CART), and reproductive hormones, like gonadotropin-releasing hormone (GnRH),
gonadotropin-inhibitory hormone (GnIH), kisspeptin, and neurokinin B (NKB), interact to
regulate both food intake and reproduction. However, this relationship is not well characterized
in all vertebrate species, especially fish. The purpose of this study was to examine this
relationship and uncover some of the regulating mechanisms underlying these two processes.
Specifically, I investigated two species of freshwater fish; glass catfish (Kryptopterus vitreolus)
and zebrafish (Danio rerio). In glass catfish, I was able to successfully isolate two reproductive
hormones (GnRH1 and GnRH2) and three appetite regulators (orexin, NPY, and CART). I found
that fasting affected the relative brain expression levels of all of these peptides, except for
GnRH2, suggesting a link between nutritional status and endocrine regulation. In zebrafish, I
examined how nutritional status, reproductive stage, gender, and strain affected the brain
mRNA expression of certain appetite (orexin and NPY) and reproductive (GnRH, kisspeptin,
GnIH, and NKB) hormones. To compare strains, I used both wild-type and transparent Casper
zebrafish. My results suggest gender- and reproductive stage-specific, as well as strain-specific
variations in the mechanisms that regulate feeding and reproduction in zebrafish. To further
investigate these differences, I compared the brain mRNA expression of genes involved in the
melanocortin system and melanin pathway between wild-type and Casper zebrafish. I found
that the Casper zebrafish had lower levels of several of the genes examined, suggesting that these strain-specific differences may be mediated by the melanocortin system. Overall, I was
able to show a clear relationship between appetite and reproduction in both zebrafish and glass
catfish, providing new insights into the endocrine mechanisms that regulate these two
processes in fish.


identifier: Brenan, Julia <https://research.library.mun.ca/view/creator_az/Brenan=3AJulia=3A=3A.html>   (2019) Archaeology and memories on Birch Island.  Masters thesis, Memorial University of Newfoundland.

abstract:
The site of Birch Island has been targeted by the non-profit Healthy Waters
Labrador (HWL) and larger Labrador tourism initiative for conservation, environmental
education, and commemoration of the former Birch Island settlement. The settlement
existed from 1942 to 1969 when it was resettled under the Fisheries Household
Resettlement Program. The goal of this project was to gather historical data to inform the
information plaques that will be placed around the island. To fulfill this goal, an online
survey was set up, 17 individuals were formally interviewed, and a map of surface debris
from the former settlement was created. The analysis shows the changing landscape, the
island’s traditions, and everyday interactions of life. The product of this research is an
amalgamated body of knowledge including archival information, photos, interviews, and
archaeological analysis of debris and artifacts that will assist in informing the information
plaques planned for Birch Island by HWL.


identifier: Bakhshi, Mohammad Ali <https://research.library.mun.ca/view/creator_az/Bakhshi=3AMohammad_Ali=3A=3A.html>   (2019) Teachers' perceptions on self-directed professional learning in Newfoundland and Labrador.  Masters thesis, Memorial University of Newfoundland.

abstract: To fill a gap in the literature with regard to teacher self-directed professional learning practices in Newfoundland and Labrador context, this qualitative study explored the experiences and perceptions that teachers have about professional learning programs and practices, with a focus on the role of teachers as adult learners, in the planning of such programs. For this purpose, this study employed a phenomenological approach to document and explore representations of the lived experiences of nine (9) teachers [four (4) male and five (5) female] through in-depth semi-structured interviews. These participants were teaching at the elementary, junior high, and high schools in the greater St. John’s area, with one participant from Corner Brook. Based on the representations of the nine participants in this study, self-directed professional learning seems to be practiced by teachers in Newfoundland and Labrador, and the teachers interviewed say they are continuously improving their teaching skills through a variety forms of formal and informal learning strategies. The findings also show that the quality of professional learning programs seems to have improved. There is a reasonable balance between teachers’ professional needs and the system’s priorities in terms of teacher professional learning’s contents and focus, and teachers feel they have been able to contribute to the planning of formal professional learning programs in a number of ways. The research also identified some challenges such as insufficient time; lack of facility or reluctance to use technology; lack of support, anxiety and isolation among learners, and; risk of low reward for invested time and effort. Recommendations for educational leaders and areas for further research are suggested.


identifier: Crofts, Anna L. <https://research.library.mun.ca/view/creator_az/Crofts=3AAnna_L=2E=3A=3A.html>   (2019) The effect of biotic interactions on boreal conifer recruitment at alpine treeline in central Newfoundland.  Masters thesis, Memorial University of Newfoundland.

abstract: Treeline, the ecotone between forest and alpine or tundra ecosystems, is perceived as the thermal limit to tree growth, reproduction, and survival and in a warming world, we expect treelines to shift to higher elevation and latitudes. Despite increases in temperatures, there has been no ubiquitous change in treeline position. Shifts in treeline position will be dependent on increased recruitment, the production or dispersal of viable seed followed by germination and seedling establishment and survival, at treeline. To examine how biotic interactions constrain or facilitate black spruce and tamarack recruitment at alpine treeline, we conducted a series of observational and experimental studies along an altitudinal gradient in central Newfoundland, Canada. We found treeline population to be simultaneously seed and establishment limited, however if seedlings become established we found seedling survival to be high. Our results highlight the need for multiple factors to align temporally for recruitment to occur.


identifier: Cooke, Emma L. L. <https://research.library.mun.ca/view/creator_az/Cooke=3AEmma_L=2E_L=2E=3A=3A.html>   (2019) The influence of spatial and temporal scale in detecting offshore recruitment signals of Atlantic cod (Gadus morhua) based on coastal juvenile surveys.  Masters thesis, Memorial University of Newfoundland.

abstract: The moratorium on the Newfoundland Atlantic cod (Gadus morhua) fishery in 1992 motivated studies on the factors influencing population stability and tools to forecast future cod abundance. Unfortunately, short-duration time series compromised most efforts to link life stages. I used coastal seine surveys of juveniles (age-0 and -1) to predict offshore pre-adult (age-3) cod abundance at multiple spatial scales (individual bays to offshore regions), temporal scales (short and long-term time series from 7 to 18 years in length) and environmental and biological factors influencing recruitment signal strength. These analyses detected strong recruitment signals among all early age classes from the Newman Sound Survey (1995 – 2013) and demonstrated interactions between juvenile abundance and environmental variables. In contrast, a strong recruitment signal was only detectable from a single bay using the shorter Fleming Survey (1992 – 1997, 2001). For both surveys, recruitment signal strength varied with distance from the index sites, among management zones, and between areas of known ecological and biological significance. Studies evaluating year-class strength often overlook the value of coastal juvenile surveys. These results demonstrate the utility of using information from long-duration coastal seine surveys when forecasting adult population strength. The implications of my results could help stakeholders prepare for socio-economic implications of poor recruitment years, and can be used in management decision-making.


identifier: Davis, Bryan <https://research.library.mun.ca/view/creator_az/Davis=3ABryan=3A=3A.html>   (2019) Reducing fishing vessel capsizing in Newfoundland and Labrador by establishing a relationship between common causes and operators' understanding of stability and risk.  Masters thesis, Memorial University of Newfoundland.

abstract:
Commercial fishing is considered one of the most dangerous industries in the world. Among the different types of fishing vessel accidents, capsizing has one of the highest fatality rates. In Newfoundland and Labrador, fatalities, due to the loss of stability in fishing vessels, have been identified as a significant problem.
This study’s primary objective was to determine the main causes of fishing vessel capsizing and recommend preventative measures to reduce the frequency of fishing vessel capsizes in Newfoundland and Labrador. Through an analysis of fishing vessel capsizing investigation reports, and a series of discussions with operators, the study identified the primary causes of these events. In 57 of the 60 capsizes analyzed, operators’ actions were determined to play a significant role.
A second component of the discussion portion of the study focused on operator and crew understanding of vessel stability. This portion of the study revealed a correlation between the amount of formal training an operator had received and their understanding of stability. Those who had received some form of stability education appeared better equipped to avoid or manage potential capsizing events.
Many fishing vessel capsize events were attributed to operator error and operators with no stability training are more likely to make poor decisions based on common misconceptions of vessel stability. Based on this conclusion, it is recommended that a compulsory stability education course be offered in the province. An outline and proposed curriculum including potential delivery methods for such a course is presented.


identifier: Omoregie, Abiemwense Edokpayi Henry <https://research.library.mun.ca/view/creator_az/Omoregie=3AAbiemwense_Edokpayi_Henry=3A=3A.html>   (2018) A paradigm shift using circle dialogue: a narrative study to investigate the impact of restorative justice education on graduate students.  Masters thesis, Memorial University of Newfoundland.

abstract: This study examined the impact of restorative justice education (RJE) on students after completing a graduate course in ED 6936 (Restorative Justice in Education-Promises and Challenges) at Memorial University of Newfoundland. As a graduate student in this course, I experienced a paradigm shift in my worldview after completing the 3-credit course. This shift encouraged me to investigate whether my classmates experienced the same impact. Out of eleven students in the course, I selected 5 for the study. The investigation was conducted using narrative and autoethnographic methods. I collected data through narrative and semi-structured interviews. Findings from the thematic analysis revealed a change in the worldview of all the participants. Further findings revealed that the circle dialogue pedagogy, the leadership quality of the facilitator and the philosophical foundation of the course contributed to the shift experienced.


identifier: Sandhu, Gagandeep K. <https://research.library.mun.ca/view/creator_az/Sandhu=3AGagandeep_K=2E=3A=3A.html>   (2019) Interactions of antimicrobial peptides (AMPs) with model membranes at different pH values.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Antimicrobial peptides (AMPs) are important components of the innate immune
systems of many different organisms. Their amphipathic and cationic characteristics
promote interactions with the cell membrane. Gad peptides are rich in
histidine, and thus have the potential to exhibit pH-dependent activity. The major
focus of this study was to understand how Gad peptides interact with model
lipid membranes and how these interactions depend on the peptides’ overall charge
and the composition of the model membranes. ²H NMR spectroscopy was used
to study the effect of Gad peptides on lipid acyl chain order of model lipid bilayers
at different pH values. ²H NMR results revealed that membrane disruption
by Gad peptides was not pH-dependent. Zeta potential measurements were used
to study the binding of Gad peptides to model lipid membranes. The binding
studies showed that for both Gad-1 and Gad-2 at low pH, less peptide binds to
the membrane and the peptide interacts with a larger number of lipid molecules.
Experiments performed with model membranes containing cardiolipin (CL) in the
presence of Gad-1 showed that the presence of CL allows the membrane to accommodate
more Gad-1. In the presence of CL the peptide binds more strongly with
the membrane and interacts with a larger number of lipids. Taken together, these
results suggest that Gad peptides might disrupt membrane integrity by clustering
anionic lipids. Clustering of anionic lipids away from zwitterionic lipids by
cationic AMPs might be a contributing mechanism, which does not exclude other
mechanisms, including the carpet mechanism and pore formation. The chemical
shift values of ¹⁵N NMR spectroscopy can give an insight about the positioning
of peptides in lipid bilayer surfaces. ¹⁵N NMR observations showed that Gad-1
aligned parallel to the membrane surface. The study of AMP-membrane interactions
will help to identify criteria to recognize the important features of natural AMP sequences involved in the antimicrobial action and thus assist in the design of
AMP-based antibiotics to help overcome the problem of antimicrobial resistance.


identifier: Ye, Sipan <https://research.library.mun.ca/view/creator_az/Ye=3ASipan=3A=3A.html>   (2018) Evolution of social networks through smart phones and radio sensors.  Masters thesis, Memorial University of Newfoundland.

abstract:
Social interactions have been an integral part of human civilization. It reflects human society and its evolution. The first challenge in the research of social networks
is data acquisition. The high cost and low efficiency are always restrictions. In
addition, most existing studies of network problems are using single datasets to build
their network models. It is paramount to find a general method of obtaining a highly
accurate network model to represent social interactions. Therefore, we propose a
cross-platform system and strategy to collect data through radio sensors and design
a combined scheme with multiple datasets in order to settle this problem. Moreover,
we use complex network theory to build our network models. The next challenge is
network dynamic. A larger number of real-world networks are dynamic, i.e. social
networks, as the topology of a network changes over time. It is also hard to describe
the topological variance of the network using a static network model where it does
not have any time features. Thus, we propose a weighted temporal network model to
illustrate the time effect of social network problems. In this study, we also analyze
the effect of friendship on human social interactions and activities. The relationships
among networks are shown as well. Furthermore, we show the combined network
model provides a highly efficient way to construct social networks.


identifier: Koralage, Janaki <https://research.library.mun.ca/view/creator_az/Koralage=3AJanaki=3A=3A.html>   (2019) Localized quantile regression of realized volatility.  Masters thesis, Memorial University of Newfoundland.

abstract:
Volatility is a financial term that measures the dispersion of asset returns. Calculating
and predicting volatility are not simple, but there are several well-known models for
determining the volatility of assets. In recent years, researchers have been interested
in developing statistical methods to model financial volatility, and new concepts have
been applied to achieve better results. Quantile regression is another area gaining
increased attention in the analysis of financial data. In this thesis, we propose a
new quantile regression model for measuring the volatility of financial assets called
the localized quantile regression model. As the name suggests, the proposed model
is a local model rather than a global model. It takes care of possible structural
changes and makes predictions of volatility more reliable. The initial step in this
approach is to identify the longest interval of homogeneity. Identifying this interval of
homogeneity involves a sequential testing procedure. After identifying intervals, we
can apply quantile regression for each homogeneous time interval. The main advantage
of this method is that it does not require any distributional assumptions. Simulation
studies are carried out to investigate the performance of the proposed method. Results
obtained from the simulation study show that the localized quantile regression model
is appropriate for modeling the volatility of financial assets.


identifier: Eslamloo, Khalil <https://research.library.mun.ca/view/creator_az/Eslamloo=3AKhalil=3A=3A.html>   (2019) Molecular basis of antiviral immune responses in teleost fish.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
In addition to the importance of Atlantic cod (Gadus morhua) and Atlantic
salmon (Salmo salar) for fisheries or aquaculture of several countries including Canada,
these species are valuable for comparative immunological studies. The Atlantic cod
possesses a unique immune system among many teleosts, and the Atlantic salmon may
serve as a molecular model for genomics studies in salmonids. Several aspects of the
immune response in these species are yet to be determined, and a broader picture of the
immune responses of Atlantic cod and Atlantic salmon may enhance the health
management of wild or farmed populations of these species. With respect to the
importance of macrophages in innate immune responses, the objectives of my thesis were
to use a macrophage model and genomics approaches to enhance our understanding of
the antiviral immune response of Atlantic cod, and to profile the transcriptome of the
dietary fatty acid-dependent and antiviral responses of Atlantic salmon.
In Chapter 2, I used microarray and quantitative reverse transcription-polymerase
chain reaction (qPCR) analyses to identify and validate several antiviral biomarker genes
encoding receptors, signal transducers, transcription factors and immune effectors in
Atlantic cod macrophages. This study revealed that the antiviral immune responses of
Atlantic cod macrophages may be activated downstream of RIG-I-like receptor (RLR)-
and Toll-like receptor (TLR)-dependent pathways. Chapter 3 fully characterised Atlantic
cod viperin, one of the putative interferon-stimulated genes (ISGs) identified in Chapter
2. I found Atlantic cod viperin to be an evolutionarily conserved gene with an antiviral
response that is regulated through endosomal-TLRs-, protein kinase R (PKR), mitogen-activated protein kinase (MAPK)- and interferon (IFN)-mediated pathways. Using deep
sequencing and gene expression analysis, Chapter 4 profiled the immune-related
microRNAs (miRNAs) of Atlantic cod macrophages, and discovered both evolutionarily-conserved
and teleost-specific miRNAs playing roles in the antiviral immune response of
macrophages of this species. Concerning the immune-related functions of omega (n)-3
and n-6 fatty acids, Chapter 5 used an ex vivo model to evaluate if varying levels of
dietary n-3 and n-6 fatty acids influence the antiviral responses of Atlantic salmon
macrophage-like cells (MLCs). Chapter 5 showed that different levels of dietary n-3 and
n-6 fatty acids change the fatty acid composition of head kidney leukocytes, and it
identified fatty acid-dependent immune-related biomarkers in Atlantic salmon MLCs.
Moreover, this chapter identified a large number of biomarker transcripts activated by
RLR, TLR, MAPK and IFN pathways during the antiviral response of Atlantic salmon
MLCs.
This thesis contributed significantly to the development of a comprehensive
picture of the genes, non-coding RNAs and regulating pathways involved in antiviral
immune responses of teleosts. In addition, my thesis enhances the general understanding
of the immunomodulatory functions of dietary n-3 fatty acids in Atlantic salmon. The
novel results generated by this thesis contribute molecular biomarkers that may be used
in future immunological studies to aid in the development of aquafeeds and other health
management tools for teleosts.


identifier: Mukherjee, Bandhan <https://research.library.mun.ca/view/creator_az/Mukherjee=3ABandhan=3A=3A.html>   (2019) NMDAR plasticity and metaplasticity in early odor preference learning in rats.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Early odor preference learning is a classical conditioning behavioral model which can be used to understand the molecular mechanism of learning and memory, and synaptic plasticity. In this thesis the research is focused on the role of N-methyl D-aspartate receptor (NMADR) plasticity and metaplasticity in early odor preference learning.
In Chapter 2, we investigated the differential roles of L-type calcium channel (LTCC) and NMDAR in early odor preference learning. The results suggest that the NMDAR is crucial for creating stimulus-specific memory and LTCC is required for maintenance of the memory. Activation of LTCC without NMDAR can cause loss of input specificity and as a result, generalization of the memory.
Chapter 3 depicts that, the effect of altered number of NMDARs in the anterior piriform cortex (aPC) can significantly modifies future learning and synaptic plasticity. Here we show that NMDARs are down regulated at 3hr following the early odor preference learning. Repeated training at 3hr leads to unlearning and this unlearning is mediated by NMDAR itself. Inhibition of the NMDAR prior to retraining at 3hr, blocks unlearning. In continuation of Chapter 3, we have characterized the molecular mechanism underlying the NMDAR mediated unlearning in Chapter 4. Calcineurine and metabotropic glutamate receptor (mGluR) plays a vital role in NMDAR downregulation at 3hr following early odor preference training.
In Chapter 5, we have investigated whether NMDAR plasticity and its mediated metaplasiticity observed in the early odor preference learning can be induced by stronger trainings that produce prolonged memories. Previous research has shown that infusing trichostatin A (TSA), a histone deacetylation inhibitor, in the olfactory bulb (OB) extends odor preference memory up to 5 days. Our data suggests that OB TSA infusion prevents NMDAR down-regulation and unlearning. These outcomes argue that it is critical to understand the metaplastic effects of training which have implications for learning optimization.