identifier: Zambon, Alessandro <https://research.library.mun.ca/view/creator_az/Zambon=3AAlessandro=3A=3A.html>   (2022) Transient torsional vibration analysis of Polar-Class propulsion shafting systems under ice-propeller interaction loads.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
The design of propulsion plants for Polar-Class vessels has to ensure the safety and
preservation of ship operations in sea ice environments. In particular, the effects of ice-propeller interaction on shafting segments constitute a potential hazard for the integrity of
the entire propulsion system. Collisions of ice blocks with propeller blades induce high
torsional vibrations along shaft lines and cause the prime mover’s output torque to fluctuate
abruptly. These processes also undermine ships’ propulsion efficiency and manoeuvring
capability during ice breaking expeditions, as well as during ice navigation of commercial
vessels and offshore operations. Consequently, the development of effective design methods
dedicated to the dynamics of ship propulsion systems is fundamental to simulate the effects
of ice-induced loads correctly. To this end, full-scale measurements have proven essential
to support the evolution of robust design criteria and updated regulatory guidelines.
The research activity presented in this doctoral thesis aims to accomplish two objectives: firstly, delivering a modelling methodology to simulate the propulsion shaft lines
of Polar-Class vessels, or the analysis of the torsional dynamic response caused by ice-
propeller interaction processes; secondly, providing indications about the mathematical
characterization of the ice-propeller torque pattern. The research project includes full-scale
measurements conducted aboard the two Canadian Coast Guard icebreakers Henry Larsen
and Terry Fox.
Torsional vibration data acquired from CCGS Terry Fox’s shaft lines validate an original
mathematical model to simulate the dynamic torque delivered by Diesel engines. Besides,
an innovative integrated measurement system is installed aboard CCGS Henry Larsen icebreaker to achieve concurrent monitoring of the shafts’ dynamic response, sea ice conditions,
and propulsive performance. The experimental measures obtained in open-water navigation
are employed to validate the numerical models of both vessels’ shaft lines. Conversely, the
datasets of the ice-induced shaft responses are used to calculate the actual ice-propeller
milling torques and correlate them to the ongoing ice conditions; this represents a unique
outcome in this subject’s state-of-the-art scenario. Alterations of the main properties of the
rules’ ice-propeller excitation—defined by the current design recommendations—are then
tested to determine their influence on the shaft line dynamic response. Overall, the results
suggest that the mathematical procedure defining the ice-propeller torque pattern, which is
described in the seguidelines, might need to be reviewed.


identifier: Turanli, Fethi Tayfun <https://research.library.mun.ca/view/creator_az/Turanli=3AFethi_Tayfun=3A=3A.html>   (2022) A study of Sandikli Graben, west central Turkiye, using the vertical electrical sounding geophysical method.  Masters thesis, Memorial University of Newfoundland.

type: Thesis NonPeerReviewed

abstract:
Turkiye has a wide range of geothermal and agricultural resources. As part of Alpine-
Himalayan orogenic belt it has mountainous regions and high heat flow, with the main
sources of geothermal energy being recent volcanism. The study area, the Sandikli
graben, is located in west central Anatolia, where there are 1500 wells tapping fresh
waters from shallow aquifers for domestic and agricultural use and, within a known
geothermal field, 23 deeper thermal wells which provide heat to greenhouses and spas.
In this study, data from 384 Vertical Electrical Sounding geophysical surveys were
analysed. The data were collected in an area of 36 km x 10 km and provided information
on resistivity extending to 1.4 km depth. The aim was to delineate the subsurface
resistivity structure of the graben including the locations of hot and cold aquifers as well
as fault structures that can provide upward transfer of geothermal waters.
It is found that near surface resistivity is associated with topography and drainage. Raw
data in the known geothermal field showed large jumps which may be indicative of near
surface geothermal activity. Large lateral resistivity variations are related to known
faults. Low resistivity subsurface layers, indicating aquifers, can be seen almost
everywhere in the graben. Their depth range of 50 to 300 m suggests that they are cold
water aquifers, and there was no indication of deeper geothermal resources outside the
known geothermal field.


identifier: Leduc, Nadine <https://research.library.mun.ca/view/creator_az/Leduc=3ANadine=3A=3A.html>   (2022) The impact of organizational culture on the mental well-being of public safety communications officials.  Masters thesis, Memorial University of Newfoundland.

abstract: Public safety communicators (e.g., 911, police, fire, and ambulance call-takers), like many other public safety personnel (e.g., police, fire) suffer operational stress injuries (OSIs) that are too often hidden, and at a prevalence higher than the general population. Unfortunately, there are very little data for OSI prevalence among Canadian public safety communicators, and no known pan-Canadian studies focusing on organizational culture and its potential influence on OSIs, within the communicator context. In the current qualitative study, I focus on participant responses (n=329) to open ended items included in a larger national online survey that revealed communicator OSIs are impacted by organizational and operational factors (work environment; e.g., feeling undervalued by one’s organization, exposure to potentially traumatic psychological events, insufficient mental health supports), and interactions with others (inter-personal work relationships; e.g., management, colleagues, the community). A semi-grounded thematic approach was used to analyze what communicators reported when asked in an online survey to describe the organizational culture in their communications centre. Six dominant themes emerged; organizational affect (positive or negative characteristics), management and supervision, morale and staffing, division and exclusion, colleagues, and gender. The findings suggest that, while organizational culture is a key factor in employee well-being; it varies considerably across agencies, impacting treatment-seeking behaviours related to potential OSIs. Our new understandings of organizational culture’s role in OSIs may help reduce the frequency and severity of communicator OSIs, helping ensure that emergency services are delivered to Canadians.


identifier: Rezajooei, Nazanin <https://research.library.mun.ca/view/creator_az/Rezajooei=3ANazanin=3A=3A.html>   (2022) Machine learning prediction of dispersion interactions using the exchange hole dipole moment model.  Masters thesis, Memorial University of Newfoundland.

abstract:
Newly developed Neural Network Potentials (NNPs) like ANI are powerful tools to
describe these systems with a high level of accuracy but with a modest computational
cost. Because they use short-range cutoffs (e.g., 5 Å), interactions outside
this range are not described correctly. Significantly, London dispersion is a fundamental
intermolecular force that extends beyond 5 Å, so it is neglected by current
NNPs. The dispersion interaction in a chemical system can be estimated as the sum
of pairwise atomic interactions with 6th, 8th, and 10th order terms (i.e., C₆, C₈,
and C₁₀). The exchange hole dipole moment (XDM) model provides an accurate
ab initio method for calculating these coefficients. However, a computationally intensive
Density-Functional Theory (DFT) calculation is required to calculate these
coefficients, so they cannot be used practically with NNPs. In this thesis, we developed
a neural network to calculate these dispersion coefficients of atoms without
the DFT calculation, providing an NNP that describes dispersion rigorously while
maintaining the computational efficiency of NNPs. This new NNP is trained to reproduce
PBE0/aug-cc-pVTZ with an XDM dispersion correction. This method was
validated by comparison to high-level ab initio calculations from the DES15K test
set. This method predicted intermolecular interaction energies of neutral molecules
with a mean absolute error of 1.1 kcal/mol and a coefficient of determination of 0.91,
demonstrating that this method has comparable accuracy to the QM method with a
dramatically reduced computational cost.


identifier: Adigun, Oludoyin Adeseun <https://research.library.mun.ca/view/creator_az/Adigun=3AOludoyin_Adeseun=3A=3A.html>   (2022) Oxylipins as novel sources of soybean (glycine max) tolerance to phytophthora sojae infection.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Soybean (Glycine max) is an important staple crop currently grown worldwide. The annual global losses of the crop due to root and stem rot infection caused by oomycete Phytophthora sojae are currently estimated at approximately $2B USD. The attempt to fight this devastating disease is towards pyramiding tolerant soybean cultivars that could enhance tolerance to Phytophthora sojae infection. The initial point of infection is root and could spread to the stem. Lipids are major structural components of cellular membranes, which serve as a component of defense mechanisms used by plants against pathogen infection. I hypothesized that lipid mediated plant immunity including phyto-oxylipin anabolism culminating in unique histochemical and morphological structures appear to be part of the successful mechanisms used by tolerant soybean cultivar to limit colonization and infection by Phytophthora sojae. These greater alterations are just a component of successful strategy used by tolerant cultivar to mitigate pathogen infection. To investigate these hypotheses, we employed multi-modal lipidomics, scanning electron microscopy and histochemical techniques to determine, (1) how soybean cultivars remodel their lipid metabolism, (2) to better understand the induction and functions of phyto-oxylipins, and (3) to investigate the mechanism of infection in both soybean cultivars in response to Phytophthora sojae infection. Both soybean cultivars demonstrated alterations in lipid metabolism in response to pathogen infection. Relative to non-inoculated controls, induced accumulation of stigmasterol occurred in the susceptible cultivar whereas induced accumulation of phospholipids and glycerolipids was observed in the tolerant cultivar. A comprehensive metabolic map of soybean root and stem lipid metabolism identified unique lipid biomarkers and accumulation of phyto-oxylipins in tolerant cultivar in response to Phytophthora sojae infection. Histochemical results revealed differences in morphological changes in both susceptible and tolerant cultivars and seemed to be associated with the successful mechanisms used by tolerant soybeans to limit pathogen infection. Overall, my thesis findings demonstrate the role of lipid metabolisms and phyto-oxylipin induction in
soybeans during pathogen inversion. This information could be useful in pyramiding soybean cultivars with high tolerance to Phytophthora sojae infection and may consequently improve sustainable agriculture.


identifier: Hu, Wenting <https://research.library.mun.ca/view/creator_az/Hu=3AWenting=3A=3A.html>   (2022) Machine learning methods for multiple sclerosis detection based on raw data from an instrumented walkway.  Masters thesis, Memorial University of Newfoundland.

abstract:
Background: Multiple sclerosis (MS) patients may experience varying gait disorders. In MS disease evaluation and diagnosis, instrumented walkways using embedded pressure sensors are widely used to provide information regarding gait disturbances. The information is delivered as predefined parameters, which may obscure salient features and patterns in the raw sensor data. This thesis applied machine learning techniques to raw walkway data to distinguish MS patients from healthy controls while further distinguishing the impairment levels of MS patients.
Methods: New features were constructed to supplement the standard parameters. A severity level was determined using patients' ratings of the severity of their gait problems on the MS Impact Scale-29. Two experiments were conducted. The first experiment focused on discerning healthy controls from MS patients. The second experiment attempted to classify patients with different impairment levels.
Results: The MS vs. Healthy experiment achieved a good baseline accuracy of 81% using the standard feature set and received a 7% improvement using the augmented set. The mild MS vs. moderate MS experiment achieved an accuracy of 76% using the standard set, which was further improved by 2% using the augmented set.
Conclusion: These experiments demonstrate that the newly generated features improve the machine learning model results with excellent accuracy and precision.


identifier: Wang, Yaomei <https://research.library.mun.ca/view/creator_az/Wang=3AYaomei=3A=3A.html>   (2022) Multi-glider cooperation for underwater oil spill delineation.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Underwater oil spill reconnaissance and delineation is challenging as the spilled oil can cover a large area and may form plumes beneath the water surface. Autonomous underwater vehicles (AUVs), with improved intelligence, are used more widely for oil spill tracking nowadays. Underwater gliders, a type of AUVs, are favorable for underwater oil spill mapping as they can work for longer durations with less energy storage required. This thesis investigates the capabilities of gliders, especially multiple gliders, as platforms for mapping subsurface oil plumes.
Considering the limited payload capability and energy availability of a glider, a lightweight Cyclops submersible fluorometer and a Ping360 sonar were used on gliders to detect oil in the water in this thesis. The sensors were tested in a tank experiment with oil and the cross-validation from fluorescence measurements and sonar images was expected to improve the reliability in detecting oil. Furthermore, a Slocum glider was developed as a platform for the sensors before it was tested in the ocean with air bubbles which were used as proxies for oil droplets to avoid discharging oil into the environment. This glider was also developed with a backseat driver controller to provide it with an intelligence to adaptively map underwater oil plumes. In addition, a cooperation strategy was proposed for multiple gliders to delineate underwater oil patches simultaneously to overcome the challenges in oil spill mapping such as spatiotemporal aliasing and to improve data redundancy. In this cooperation strategy, a scout glider was commanded to follow a lawn-mower path to cover the area and find potential patches with rich information for follower gliders. A data compression method was designed for the scout glider to reduce the amount of information to be transmitted to the follower gliders. An adaptive path planning strategy was proposed for the follower gliders to
ensure they spent most of their mission time inside patches. The proposed cooperation strategy was compared with other strategies without cooperation and/or without adaptive control and the influence of having adaptive control and multiple gliders on a strategy was investigated through simulations. This developed Slocum glider was used as a follower glider to test the adaptive control in my cooperation strategy through a field experiment.
The tank experiment with oil and the field experiment with air bubbles conducted in this thesis proved the feasibility and necessity of having two or more sensors to cross-validate their measurements as a single sensor was not reliable in proving the existence of a particular substance, such as oil droplets, in the water. The developed backseat driver was able to provide the glider with an ability of adaptive control. However, having adaptive control or multiple gliders cannot guarantee a good score of performance when delineating underwater oil patches. The proposed cooperation strategy with multiple gliders was found to have the best score of performance, especially for long-endurance missions. The performance of the cooperation strategy could be further improved by having a thruster for the follower gliders to overcome the influence of the ocean environment, such as strong currents, when mapping moving underwater patches.


identifier: Huang, Xin <https://research.library.mun.ca/view/creator_az/Huang=3AXin=3A=3A.html>   (2022) Deep neural networks for conditional visual synthesis.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Conditional visual synthesis is the process of artificially generating images or videos
that satisfy desired constraints. Individual visual synthesis tasks include high-fidelity natural
image generation, artwork creation, face animation, etc. Such tasks have many realworld
applications, such as database expansion, face editing in beauty camera, and face
effects in short videos. With advances in deep learning, methods for conditional visual
synthesis have evolved rapidly in recent years. Many of these recent approaches are based
on Generative Adversarial Networks (GANs), which have strong abilities to generate samples
following almost any implicit distribution, allowing the synthesis of visual content
in an unconditional or input-conditional manner. However, GANs still have many limitations,
such as difficulty in directly approximating high-resolution image distributions, poor
model generalization ability on unpaired datasets, and limited power for mimicking human
actions. Hence, it is worth to tackle these limitations and investigate how to handle different
conditional visual synthesis tasks.
Four conditional visual synthesis tasks are investigated in this thesis. The first task studies
how to generate high-resolution images from conditioning text descriptions. The second
task simulates facial changes based on desired age inputs. How to synthesize realistic talking
face videos from conditioning audio inputs is investigated as the third task. Finally,
the forth task generates human-like painting actions based on desired target images. Both
qualitative and quantitative validations are conducted for method developed for each task.
Comparisons with existing works demonstrate the respective merits of these techniques.
Insights on how to design conditional visual synthesis approaches are summarized.


identifier: Islam, Towhidul <https://research.library.mun.ca/view/creator_az/Islam=3ATowhidul=3A=3A.html>   (2022) Rheology and surface free energy of modified asphalt binder containing anti-stripping additives.  Masters thesis, Memorial University of Newfoundland.

abstract:
Since 2008, the number of roads in Canada has been going up due to rapid urbanization and
economic growth, and by 2020, there is more than 1.08 million kilometres of roads across the
country. Around 90% of roads managed in Canada are paved with asphalt materials. During the
service life, asphalt pavement experiences various surface distresses due to aging, the effect of
environmental factors, and traffic loading. A way to mitigate the early deterioration of asphalt
pavement is to blend suitable modifiers and additives with asphalt binders during asphalt mixture
production. The current study aims to understand the relative effect of different liquid antistripping
additives on the rheological and fundamental properties of styrene butadiene styrene
(SBS)- and Gilsonite-modified binders (4 and10% by the weight of base binder, respectively)
containing various percentages of anti-stripping additives in short-term aging conditions. Four
different anti-stripping additives: ZycoTherm SP2 (0.05%, 0.075%, and 0.1%), Kling Beta 2914
(0.5%, 0.75%, and 1%), Pave Bond Lite (0.5%, 0.75%, and 1%), and AD-Here (0.5%, 0.75%, and
1%) were selected for this study. To attain our research goal, anti-stripping additives were blended
to SBS and Gilsonite modified PG 58-28 binder. Later, all binders were aged using Rolling Thin
Film Oven (RTFO) protocol. This thesis summarizes the results of rheological behaviour by
considering the rutting and cracking parameters, such as the Superpave rutting parameter,
Shenoy’s rutting parameter, non-recoverable creep compliance, and Glover-Rowe parameter.
Additionally, this study considered using the Surface Free Energy (SFE) as a fundamental material
property to evaluate the cohesive bond strength of the Gilsonite-modified asphalt binders. The
results show that anti-stripping additives significantly affect the binders’ rheological behavior and
fundamental properties, which can influence the overall performance of the asphalt binder.
Furthermore, the comparative analysis showed that Gilsonite-modified binders containing liquid
anti-stripping additives enhance the moisture damage, rutting and cracking resistance of asphalt
binders.


identifier: Huang, Zhe <https://research.library.mun.ca/view/creator_az/Huang=3AZhe=3A=3A.html>   (2021) Invasion speed determinacy for wave propagations in partial differential equation models arising from population biology.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This thesis aims at developing the study of invasion speed determinacy for wave propagation
in partial differential equations arising from population biology. Along this
direction, we first investigate a reaction-diffusion-advection equation in a cylindrical
domain with a Fisher-KPP type nonlinearity. Using the upper and/or lower solutions
method, we obtain sufficient conditions under which the linear or nonlinear selection
is realized when the model is prescribed with Neumann boundary conditions and
Dirichlet boundary conditions, respectively. To study the invasion speed determinacy
of a system, we investigate a reaction-diffusion-advection population model arising
in stream ecology. We concentrate on how the spreading speed (the minimal wave
speed) is impacted by the Allee effect in the model. Linear and nonlinear selection
mechanisms for the spreading speed are first defined, and the determinacy is further
established by way of the upper and lower solution method. It is found that the
nonlinear determinacy is realized if there exists a lower solution with a faster decay.
For a multiple species population system having diffusion, individual species possibly
invade into the far end with different spreading speeds. Predicting or determining
them (the fast and slow-spreading speeds) becomes challenging. Hence, we first analyze
a cooperative Lotka-Volterra system, which admits a single or multiple spreading
speeds (co-speed or fast-slow speeds). We successfully derive a necessary and sufficient condition for this particular model to determine whether the system has a single
spreading speed or multiple spreading speeds. We define the linear and nonlinear
speed selection mechanism for each case and derive new conditions to classify the
speed selection. After studying the former three particular models arising from population
biology, we further, in the last part, present the speed selection mechanism for
an abstract time-periodic monotone semi
ow. At the end of this thesis, we present
our future work.


identifier: Liao, Tuotian <https://research.library.mun.ca/view/creator_az/Liao=3ATuotian=3A=3A.html>   (2021) Layout-aware sizing methodology for analog integrated circuits.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract: The traditional iterative design flows for analog integrated circuit synthesis, which can help meet circuit performance requirements in the conventional technology processes, often experience longer runtime. The nonnegligible impact of layout parasitics and layout dependent effects (LDEs) on electrical performance has posed increasingly greater challenges to determining circuit parameters (i.e., circuit sizing), which makes it harder for designers to close the synthesis loop especially in the advanced nanometer technologies. This dissertation is focused on parasitic-aware and LDE-aware circuit sizing solutions in the early schematic design stage of the circuit synthesis process. A number of techniques, which include analytical modeling for devices and circuits, mathematical programming, sensitivity analysis, curve fitting, and heuristic optimization as well as machine learning, are utilized to construct the proposed circuit sizing methodologies. In this regard, we combine geometric programming and differential evolution as well as a many-objective evolutionary algorithm to construct a novel two-phase hybrid sizing methodology for dealing with parasitics. In addition, we propose to use gm/ID-based mixed-integer nonlinear programming to improve the accuracy of the first-phase sizing, and adapt it to address the layout-dependent effects with the aid of sensitivity analysis. Furthermore, we develop a machine-learning based approach called Bayesian optimization featuring high-dimensionality and many objectives to tackle parasitics and LDEs for analog circuit sizing. The ultimate objective of this research is to develop efficient methodologies and algorithms to include the consideration of parasitics and LDEs from layout design into schematic design stage as an early action to reduce the analog IC design iterations. The experimental results show the efficacy of our proposed sizing methodologies over other similar works for the layout-aware analog circuit sizing.


identifier: Arbiol González, Carlos <https://research.library.mun.ca/view/creator_az/Arbiol_Gonz=E1lez=3ACarlos=3A=3A.html>   (2022) Microanalytical approaches to the study of hydrothermal alteration in epithermal and orogenic AU-AG deposits in Newfoundland.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
The Island of Newfoundland (Canada) is an amalgamation of terranes defining the northernmost extent of the Appalachian orogen in North America. A subset of these terranes host epithermal and orogenic gold occurrences of Neoproterozoic and Silurian-Devonian age, respectively. Well-preserved examples of high- and low- sulfidation epithermal gold mineralization and associated phyllosilicate-rich alteration occur in the Neoproterozoic portion of the Avalon Zone. High-sulfidation epithermal occurrences, including the Hickey´s Pond prospect and the Hope Brook deposit, are characterized by the phyllosilicates Fe muscovite (2M1 polytypism), paragonite, Al clinochlore (ripidolite with IIb polytypism), pyrophyllite, kaolinite group minerals, and mixed layer clay phases, which formed at relatively high temperatures (200-300 ºC). Low-sulfidation epithermal occurrences, such as the Heritage prospect, feature a phyllosilicate assemblage defined by Fe-Mg muscovite (high Tschermak substitution and 2M₂ polytypism), Al clinochlore (brunsvigite with IIb polytypism), and mixed layered clay phases, which formed at lower temperatures (100-200 ºC). Raman microspectroscopy proved highly effective in characterizing alunite group minerals (alunite and natroalunite endmembers), pyrophyllite, white mica (muscovite/paragonite and phengite), and Fe-Mg chlorite (clinochlore and chamosite end-members) in these examples. The sensitivity of the white mica Raman band between 1000 cm⁻¹ and 1150 cm⁻¹ to changes in Si⁴⁺ and Al³⁺ in tetrahedral coordination revealed that compositional variations due to Tschermak substitution (muscovite-paragonite versus phengite(celadonite)) can be effectively detected by Raman microspectroscopy. The position of the main chlorite Si-O-Si Raman band shifts from >680 cm⁻¹ for Mg-rich chlorite to <670 cm⁻¹ for Fe-rich chlorite, permitting the estimation of the Fe²⁺ content in chlorite. The Baie Verte Peninsula
(Dunnage Zone) hosts abundant orogenic gold mineralization with formation of hydrothermal rutile at distances of 10s of m from the auriferous veins. The distal-to-proximal evolution of Fe-Ti phases consists of (Ti)-magnetite - ilmenite - titanite - rutile, showing a progression from Fe- to Ti-rich phases. Vein-proximal rutile from the essentially barren Animal Pond prospect contains high concentrations of Fe and Mn, while vein-proximal rutile from the auriferous Stog’er Tight and Argyle deposits contains higher concentrations of Nb, Ta, Sn, and, in particular, Sb (80-100 ppm). The Fe-Mn-poor, Sb-rich composition of rutile formed proximal to auriferous veins has potential application to gold exploration in the Baie Verte region and elsewhere.


identifier: Bennett, Brittany A. P. <https://research.library.mun.ca/view/creator_az/Bennett=3ABrittany_A=2E_P=2E=3A=3A.html>   (2022) Conceptualizing police perceptions of the parents of youth in conflict with the law.  Masters thesis, Memorial University of Newfoundland.

abstract:
Broadly defined as a member of society given certain rights and tasked with certain obligations
from the state, it is clear throughout social sciences literature that the consideration of citizenship
is tied to the age of majority. Within scholarship exploring what citizenship means for those
under the age of majority, there has been little attention paid to the position of police in young
people’s journeys toward citizenship. Drawing from qualitative data collected through one-on-one
interviews and focus groups with rural Atlantic police officers, I build on youth citizenship
literature by examining police officers’ interpretations of policing youth and their experiences
interacting with the parents of youth. In the results, I document police officers’ perceptions of
their authority and their perceptions of the authority of parents in addressing concerns with
young people. A total of 128 police officer participants took part in the study; 76 participants
engaged in one-on-one interviews and 52 participants took part in focus groups. Police in this
sample discuss how they feel parents use police as a parenting tool, how they believe parents can
contribute to youth accountability, and how they suggest parents can influence youth attitudes
towards policing legislation. Drawing on theories of governance, I argue that police officers’
perceptions of the policing and parental management of youth behaviour reflect a view of young
people as less than ideal citizens. Youth are considered unable to work toward the
responsibilities required of an ideal citizen without the guidance and mentorship from authority
figures such as parents and police working simultaneously in both the private and public arenas
of young people’s lives. This suggests that better policing policy and practice should include
engagement and communication between police and parents regarding the expected roles and
responsibilities of each authority figure in young people’s lives.


identifier: Canning, Chelsea <https://research.library.mun.ca/view/creator_az/Canning=3AChelsea=3A=3A.html>   (2022) The frequency of childhood maltreatment experiences in a national Canadian sample of adult women reporting a diagnosis of attention deficit hyperactivity disorder.  Masters thesis, Memorial University of Newfoundland.

abstract: This study examined the reported frequency of childhood maltreatment (sexual and physical abuse) in adult women reporting a diagnosis of attention deficit hyperactivity disorder (ADHD). Using data from the Canadian Community Health Survey – Mental Health (CCHS-MH) (2012), a sample of 402 women who reported being diagnosed with ADHD by a health professional was compared to a sample of age-matched women not reporting a diagnosis of ADHD on the frequency that they experienced different forms of physical and sexual abuse. Group comparisons were conducted using Pearson’s chi-square and effect sizes were assessed with Cramer’s V. The results of the study showed that women reporting a diagnosis of ADHD reported experiencing all forms of childhood maltreatment significantly more frequently than women not reporting a diagnosis of ADHD. The implications of these findings along with directions for future research are discussed.


identifier: Farahani, Mozhgan <https://research.library.mun.ca/view/creator_az/Farahani=3AMozhgan=3A=3A.html>   (2022) The deduction model for Cops and Robber.  Masters thesis, Memorial University of Newfoundland.

title: The deduction model for Cops and Robber

abstract:
A variation of the game of cops and robber on graphs is studied in which the cops must capture an invisible robber in one move. Cops know each others’ initial locations, but they can only communicate if they are on the same vertex. Thus, the challenge for the cops is to deduce the other cops’ movement and move accordingly in order to capture the robber. This game is called the deduction model for cops and robber. In this thesis, the deduction number is introduced as the minimum number of cops needed to capture the robber in this model. For some classes of graphs, the deduction number is determined. We study the deduction number of trees and provide an upper bound for the Cartesian product of graphs. In particular, we give the deduction number for
the hypercubes.


identifier: Alhowaide, Alaa Zaid Mohammad <https://research.library.mun.ca/view/creator_az/Alhowaide=3AAlaa_Zaid_Mohammad=3A=3A.html>   (2021) Towards autonomous IoT IDSs using ensemble learning and feature selection methods.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Intrusion Detection Systems (IDSs) are an efficient and effective solution against polymorphic
and zero-day cyberattacks in IoT networks. Many IDSs have failed in practice due to a
considerable number of false alarms, high False Positive Rates (FPR), and low Detection Rates
(DR). Furthermore, with the rapidly growing number of connected devices in IoT networks and
the wide variety of traffic types, it becomes challenging to develop a fast, light, and accurate
IDS.
This research provides substantial contributions to cybersecurity research on developing a
scalable, adaptive, and lightweight IDS framework for IoT networks. It considers two main
aspects, a novel ensemble feature selection method and a new ensemble detection model
approach to achieve a reliable IDS architecture.
The first contribution is developing a novel ensemble evaluation method for Feature
Selection Methods (FSMs) to automatically construct an Ensemble Feature Selection Method
(ENFSM). The proposed methodology combined five evaluation measurements. One of them is
a new evaluation measurement that integrated the reduction rate with method speed and two
new measurements that scored the whole feature set quality. Also, a novel cutoff mechanism for
filter-based FSMs is proposed.
The second contribution is developing a novel ensemble Model Selection Method (MSM) to
automatically construct an ensemble detection model. The proposed method used three new
integrated efficiency measurements and combined the recommendations in a novel way to
increase the method’s reliability.
Notably, the proposed ENFSM achieved a reduction percentage ranging from 51% to 79%
over the four datasets without compromising the accuracy of the detection models. Furthermore,
the proposed cutoff mechanism showed a noticeable improvement in the feature selection
methods’ efficiency. The proposed ENFSM F and ROC-AUC scores ranged from 0.9 to 1 using
most detection models. Furthermore, the generated feature set suited a vast range of models.
The proposed ensemble models showed 0.99, 0.95, 1, and 0.99 F scores and 1, 0.98, 1, and 1
ROC-AUC scores on NSL-KDD, UNSW-NB15, BotNetIoT, and BoTIoT dataset, respectively.
The proposed models overcame most models in terms of efficiency and showed a stable
performance using a vast range of feature sets.


identifier: Miles, William R. <https://research.library.mun.ca/view/creator_az/Miles=3AWilliam_R=2E=3A=3A.html>   (2014) Captains and colonies: Royal Navy Service in the North Atlantic world, 1660-1739.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This dissertation examines captains of the English/British Royal Navy and their service in the North Atlantic between 1660 and 1739. The navy deployed six to twelve warships as convoy escorts and station ships to royal colonies on the American mainland and the Newfoundland fisheries. Captains sent to the New England station at Boston are examined in detail. In order to explore navy professionalization and professionalism, supplementary evidence comes from captains protecting the yearly Newfoundland convoy. Reconstructing and analysing captains’ service in North America has generated little interest from historians because the scale of deployment favours the study of fleet and squadron activities after 1739. Rather than identify the captain as a state servant strictly from an operational perspective, his daily presence is examined as part of the early-modern British Atlantic Empire.
British Admiralty records provide the primary documentary evidence, especially orders and instructions and surviving captains’ correspondence. Other Admiralty records such as ship lists, ships’ logs, and correspondence from the Navy and Victualling Boards are also employed. Detailed examination of these under-utilized sources enhances our understanding of the daily routines of both navy and maritime communities. Ships dispatched to New England engaged in a variety of tasks, and the Admiralty controlled them through an evolving set of orders and instructions that focussed on the captain’s responsibility to maintain the integrity of warship and crew. Instructions to colonial governors granting them partial operational control over warships were counterbalanced by orders to captains precluding them from endangering the ship, interfering in colonial societies, or engaging in undue opportunism while on assignment. Nevertheless, the captain’s need to interact with maritime communities during day-to-day operations put him into frequent contact and conflict with other self-interested persons, in particular colonial governors and merchants.
This dissertation offers new perspectives on overseas naval service by emphasizing the considerable agency displayed by captains serving in the colonies. Encounters with contentious colonial governments, inflexible naval administrators, difficulties with resupply and repair, and even threats of incarceration demonstrate the captain’s ill-defined position as an individual within a centralized imperial institution required to negotiate through a decentralized British Atlantic World.


identifier: Benham, Philip Henry <https://research.library.mun.ca/view/creator_az/Benham=3APhilip_Henry=3A=3A.html>   (1991) Stratigraphy and palynology of cretaceous and tertiary rocks, North Bylot trough, Bylot Island, Northwest Territories, Canada.  Masters thesis, Memorial University of Newfoundland.

abstract:
Cretaceous and Tertiary strata of North Bylot Trough at
Maud Bight on Lancaster Sound are divided into five
formations representing three tectonic phases based on
lithology and palynology. In detail, late Albian Hassel
Formation fluvial quartz arenites were deposited at Maud
Bight prior to rifting in Baffin Bay and Lancaster Sound
(Phase 1). Late Campanian-mid Maastrichtian shelf mudstones
(Bylot Island Formation) and mid to late Maastrichtian
(Sermilik Formation) nearshore and beach deposited quartz
arenites reflect uplift of the Byam Martin Mountains and
separation from Eclipse Trough (Phase 2). Lower to middle
Paleocene shale and thinly bedded sandstone (Navy Board
Formation), lithic greywacke and over 200 metres of
conglomerate (Aktineq Formation including the newly defined
Maud Bight Member) are equivalent to strata in Eclipse
Trough. The Navy Board Formation consists of braided stream,
flood plain and lacustrine deposits. These strata are
overlain by meandering stream deposits (Aktineq sandstone)
and alluvial fan strata (Maud Bight Member). This
tectonically deformed coarsening up sequence indicates
renewed activity corresponding with the opening of Baffin Bay
to the east and the Lancaster Aulacogen to the north (Phase
3).
Based on spores, pollen and fungal remains three
terrestrial palynomorph assemblage zones and one subzone
containing components of both the Aquilapollenites and
Normapolles Provinces are defined for the North Bylot Trough
strata: Azonia cribrata-Aquilapollenites trialatus (AA) Zone,
Porosipollenites porosus-Wodehouseia spinata (PW) Zone and
the Paraalnipollenites alterniporus-Pesavis parva (PP) Zone.
Subzone R lies within the AA Zone and consists of >85%
recycled palynomorphs typical of mid to late Albian
assemblages such as Cicatricosisporites, Tappanispora and
Klukisporites. The AA Zone is late Campanian to mid
Maastrichtian and is characterized by Azonia,
Aquilapollenites, Trudopollis, Ceratiopsis and Lejeunia.
Characteristic genera of the mid to late Maastrichtian PW
Zone include Porosipollenites, Aquilapollenites,
Beaupreaidites, Singularia and Wodehouseia. The PP Zone is
early to mid Paleocene and is characterized by
Paraalnipollenites, Trivestibulopollenites, Momipites,
Triporopollenites, Caryapollenites and Pesavis.
Organic matter recovered from strata at Maud Bight is
thermally immature but with sufficient burial in offshore
Lancaster Aulacogen would generate liquid and gas
hydrocarbons. Stratigraphic relationships in North Bylot
Trough, when applied with geophysical data in Lancaster Sound
should allow for delineation of a series of stratigraphic and
structural traps.


identifier: Warren, Susan <https://research.library.mun.ca/view/creator_az/Warren=3ASusan=3A=3A.html>   (2018) In healthy full and late pre-term babies, does delaying the first bath until at least 24 hours of life effect in-hospital breastfeeding rates, thermoregulation and glycemic control?  Masters thesis, Memorial University of Newfoundland.

abstract:
Objective: To determine if delaying a newborn’s first bath until at least 24 hours of life, as recommended by the World Health Organization, effects in-hospital breastfeeding rates, infant hypothermia rates and/or infant hypoglycemia rates.
Methods: Retrospective cohort study comparing 680 infants bathed before 24 hours to 545 infants bathed after 24 hours. The primary outcome was comparison of the rates of in-hospital breastfeeding initiation and exclusive breastfeeding at discharge. Secondary outcomes were a comparison of rates of infant hypothermia and hypoglycemia.
Results: Exclusive breastfeeding rates were 33% higher in the delayed bathing cohort compared to the early bathing cohort (AOR 1.334, 95% CI 1.049-1.698, p=0.019). No significant difference in breastfeeding initiation rates were observed in the total population or high-risk subgroup but in the average risk subgroup there was a significant 43% increase in breastfeeding initiation rates when bathing was delayed (AOR 1.433, 95% CI 1.008-2.039, p=0.045). Infants bathed after 24 hours were 2.5 times more likely to experience a hypothermic event than those bathed before 24 hours (AOR 2.524, 95% CI 1.239-5.142, p=0.011). No significant differences in rates of hypoglycemia were observed (AOR 0.916, 95% CI 0.421-1.994, p=0.826).
Conclusions: Delaying newborn bathing was associated with increased likelihood of exclusive breastfeeding at discharge and increased rates of hypothermia.


identifier: Kundu, Pritam <https://research.library.mun.ca/view/creator_az/Kundu=3APritam=3A=3A.html>   (2022) Numerical modelling of field vane shear test in sensitive clay.  Masters thesis, Memorial University of Newfoundland.

abstract:
The undrained shear strength of clay is one of the key parameters in geotechnical design, which can be determined from laboratory or field tests. The disturbance of soil samples during sampling, transporting, storing and trimming could influence the laboratory test result, which could be significantly high for sensitive clay because the structure of the soil might be changed. Therefore, the field vane shear test (VST) is commonly used to determine the undrained shear strength of sensitive clay. Although the test is relatively simple, the interpretation of the VST results is challenging, as the failure mechanisms are still not well understood and cannot be observed in the field. Therefore, numerical simulation might be a viable option to examine such mechanisms. Some attempts have been made previously using Lagrangian-based finite element (FE) analysis but not could model the complete process, because large shear strains develop along the thin shear plane, which causes mesh distortion and numerical issues.
In the present study, VST is simulated using an Eulerian-based FE approach. In this approach, the Eulerian material (soil) flows through the fixed mesh; therefore, the simulation can be continued for a large penetration and rotation. A nonlinear strain-softening and strain-rate dependent soil model for the undrained shear strength of sensitive clays is incorporated in the FE simulation. The first set of simulations is performed for only one element of thickness (i.e., two-dimensional conditions) by applying rotation to a rigid vane. Three-dimensional simulations are then performed by penetrating the vane to the desired depth, followed by a rotation. The rotation initiates the formation of a rounded square-shaped failure block which turns into a circular one after the peak torque. The penetration of the vane can significantly disturb the surrounding sensitive clay and thereby reduce the maximum torque during rotation. The extent of disturbance depends on several factors, such as blade thickness, soil sensitivity, and post-peak strength degradation parameters.


identifier: Richardson, Christine <https://research.library.mun.ca/view/creator_az/Richardson=3AChristine=3A=3A.html>   (2016) An exploratory study of the incidental learning benefits for physician peer assessors in a formal peer assessment.  Masters thesis, Memorial University of Newfoundland.

abstract:
Clinical peer assessment, by which health care professionals evaluate each other’s
clinical and documentation practice, has been employed by physician regulatory bodies as
a quality assurance method, to ensure that standards of care are met. There are many
studies addressing the benefits of charting and practice audits for physicians, however
there is a paucity of evidence regarding the effects on the peer assessors themselves.
This study sought to explore if the review process contributes to changing the peer
assessor’s practice and documentation habits. To answer this question, eighteen
Emergency Medicine physicians, who conduct peer assessments for the College of
Physicians and Surgeons of Ontario (CPSO), were interviewed, and the data analysed
using a grounded theory methodology.
The results suggest that the peer review process motivated peer assessors to
reflect on the ways they were providing patient care or preparing documentation in
their own practices when they were exposed to different or newer information or
after having seen the value already demonstrated by the peer they were
assessing. This supports Schön’s notion of reflection-on-action, where the
practitioner spends time exploring the situation, and developing questions and ideas
before building change in a process of continuous learning.
Few physicians are engaged formally as peer assessors with the CPSO.
Publicizing the tangible learning benefits of participation in peer assessment has the
potential to assist in recruiting newer assessors and could aid in the adoption of local,
informal peer assessment groups, which would benefit both reviewee and reviewer


identifier: Langille, Barbara <https://research.library.mun.ca/view/creator_az/Langille=3ABarbara=3A=3A.html>   (2014) Mitochondrial DNA and microsatellite analysis of post-glacial dispersal and hybridization of longnose suckers (Catostomus catostomus) in Labrador: implications for conservation and management near the Trans-Labrador Highway.  Masters thesis, Memorial University of Newfoundland.

abstract: Understanding phylogeographic origins and hybridization of species are crucial when proposing effective management strategies in disturbed habitats. The longnose sucker in Labrador is an interesting species as the eastern part of the range in North America has not been studied and Labrador has recently undergone the construction of the Trans-Labrador Highway (TLH) with no assessment of the influence of this disturbance on the longnose sucker. To document genetic diversity, post-glacial dispersal, and putative hybridization with the white sucker, mitochondrial DNA and microsatellites were analysed, leading to evidence for one main glacial refugial source of longnose suckers within Labrador, the Atlantic refugium, with possible minor contributions from the Beringian and Mississippian. Significant population structure among regions and among lakes was inferred. Only four putative hybrid suckers were identified suggesting that hybridization is lower than among other catostomid species. Hence the TLH is likely not influencing hybridization of longnose and white suckers in Labrador.


identifier: May, Sandy M. <https://research.library.mun.ca/view/creator_az/May=3ASandy_M=2E=3A=3A.html>   (2014) Teenage pregnancy & mothering in the face of social exclusion: discourse, phenomenology, and an affirmation of positive maternal identity.  Masters thesis, Memorial University of Newfoundland.

abstract:
In contemporary Western society teenage pregnancy and motherhood are
understood almost exclusively as problematic, undesirable, and in need of intervention.
Social anxieties are seemingly paradoxical, however, given the decades of steadily
declining, and current historically low rates. Using poststructural analysis, psychoanalysis,
and autobiographical narrative, the purpose of this study was to examine the underlying
power dynamics inherent in discourse about teenage pregnancy and teenage mothers in
Canada and the United States, to challenge hegemonic assumptions about adolescent
pregnancy, early motherhood, and young mothers themselves, and demonstrate that
stigmatizing and marginalizing adolescent pregnancy and young mothers has
consequences that are counterproductive, and harmful to young women and their
children at the phenomenological level. While many studies have documented the effects
of adolescent pregnancy and parenting, few have examined the role of discourse itself in
shaping and impacting young women’s experiences, and moreover, its role in shaping,
and compounding many of the adverse effects associated with teenage pregnancy and
childbearing. Lastly, to my knowledge, no studies have examined the subject by drawing
on and incorporating the researcher’s own experiences of adolescent pregnancy and
mothering.


identifier: Butler, Trina Maxine <https://research.library.mun.ca/view/creator_az/Butler=3ATrina_Maxine=3A=3A.html>   (2015) The role of integrin linked kinase (ILK) in human placenta development.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
During placenta development, mononuclear villous cytotrophoblast cells
differentiate and fuse with the overlying syncytiotrophoblast, which is the epithelial
covering of the chorionic villi. Integrin-linked kinase (ILK), is known to downregulate
E-cadherin through Poly (ADP-ribose) polymerase (PARP) and Snail in during epithelial
to mesenchymal transition (EMT). Therefore, since ILK is expressed in villous
cytotrophoblast, the role of ILK in aiding trophoblast syncytialization via the downregulation
of E-cadherin was examined using the trophoblast derived BeWo cell model.
The temporal/spatial expression of ILK, PARP, Snail and E-cadherin was determined in
first and early second trimester chorionic villi and BeWo cells by immunofluorescence
and immunoblot analysis. It was found that ILK co-localized with PARP and Snail in
villous cytotrophoblast. PARP and Snail expression also persisted in some cells that
appeared to be fusing with the overlying syncytiotrophoblast, as indicated by decreased
E-cadherin expression. In BeWo cells undergoing syncytialization, ILK increasingly
localized to cell nuclei in correlation with increased nuclear Snail localization, an Ecadherin
repressor, and PARP nuclear localization. This was coincident with decreased
E-cadherin expression. Wildtype ILK or mutant ILK was also transiently overexpressed
in BeWo cells or endogenous ILK depleted by siRNA targeting. Subsequently the cell
fusion in these transfected cells, grown under syncytialization conditions, was scored by
the presence or absence of E-cadherin immunostaining. Furthermore, PARP and Snail
promoter activities were assessed in BeWo cells during syncytialization and upon ILK
overexpression and syncytialization using luciferase assays. Over-expression of ILK
ii
significantly elevated syncytialization in BeWo cells grown under syncytialization
promoting conditions, while the knockdown of ILK expression significantly reduced
syncytialization. Lastly, PARP and Snail promoter activities were significantly higher in
BeWo cells during syncytialization. Therefore, the results demonstrated that ILK aids
trophoblast syncytialization and differentiation via the downregulation of E-cadherin,
likely through an ILK-PARP-Snail pathway.


identifier: Ghamartale, Ali <https://research.library.mun.ca/view/creator_az/Ghamartale=3AAli=3A=3A.html>   (2022) Molecular-scale mechanistic investigation of asphaltene precipitation and deposition control using chemical inhibitors.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Asphaltene stability can be perturbed during oil production and transportation, leading to asphaltene precipitation and deposition. Chemical inhibitors are usually added to the crude oil to postpone asphaltene deposition. The interaction and potential bonds between asphaltene and inhibitor molecules describe the mechanisms and efficiency of inhibitors during the prevention of precipitation and deposition. As the asphaltene type varies from oil to oil, screening, designing, and developing inhibitors for a target oil are necessary. The screening process of selecting an effective inhibitor will be much more efficient if actual inhibition mechanisms are known. Although chemical inhibitors have been used in the industry for a long time, understanding of interaction mechanisms between asphaltenes and chemical inhibitors is vital in developing an efficient inhibitor. Disclosing the interaction mechanisms using an experimental strategy needs high technology tools, and it is demanding and costly. This research aims to develop a simulation workflow to understand the interaction between asphaltene molecules, inhibitors, and surfaces, which will help to figure out the main prevention/aggregation mechanisms during precipitation and deposition. In this study, molecular dynamics (MD), an advanced computational chemistry method, is employed to analyze the inhibitory effect of n-octylphenol (OP) and two 1-Butyl-3-methylimidazolium ionic liquids for three different asphaltene structures. The employed asphaltene structures include one archipelago and two continentals. Based on the knowledge gaps, we first study the impact of asphaltene structure, inhibitor concentration, pressure, and temperature on the efficiency of asphaltene aggregation inhibitors. Then, the impact of inhibitors on asphaltene binding arrangement during the aggregation process is investigated. Finally, we explore the inhibitory effect of chemicals on asphaltene deposition in the calcite pore. The asphaltene
aggregation, aggregate characterization, and deposit characterization are studied in oil bulk and confined oil systems (pore structure) to meet the objectives.
This thesis begins with an extensive literature review, and the first sets of simulations focus on the impact of asphaltene structures during the precipitation process. In this section, systems with singular and binary asphaltene types in n-heptane are simulated in the absence and presence of OP, as a surfactant inhibitor. The results show that the OP can delay the aggregation of the continental asphaltene with the potential of forming hydrogen bonds. It is also concluded that the average aggregation number needs to be coupled with the gyration radius analysis to evaluate the hierarchical paradigm of asphaltene aggregation. After that, a sensitivity analysis is conducted to investigate important aspects such as the inhibitor concentration, thermodynamic condition, and computational hardware. This part aims to optimize the screening and designing of inhibitors from both technical and economic viewpoints. It is concluded that a minimum inhibitor concentration is needed so that the inhibitor appears to be impactful. It also shows that in the pressure range of 1-60 bar, OP has the most inhibitory effect at 30 bar since the asphaltene-asphaltene aggregation energies are extremely high at 1 bar such that the asphaltene-inhibitor energy can not cope with this situation. In comparison, the asphaltene-asphaltene interaction energy is extremely reduced at 60 bar such that the aggregates are already unstable even in the absence of OP. OP is most impactful at 360 K in the temperature range of 300-360 K. The significant impact of the inhibitor on aggregate shape in this study motivates us to study the detailed arrangement of asphaltene aggregation, which is directly related to the strength and stability of the aggregation. Therefore, we concentrate on more mechanistic details by investigating the impact of two types of inhibitor, including surfactant and ionic liquid, on the asphaltene binding arrangement. The outcome reveals the OP mainly forms bonding through hydrogen bonds, and the quadrupole-quadrupole interaction
between the OP benzene ring and asphaltene core is weaker than the quadrupole-quadrupole between asphaltenes. In contrast, the ionic liquid reduces the asphaltene stacking association as the cation part of ionic liquids approaches the aromatic core of the asphaltene and beats the quadrupole-quadrupole interaction between asphaltenes. In the next step, the asphaltene deposition is studied when asphaltene-heptane is placed in a calcite pore without/with chemical inhibitors. According to the results, the OP adsorbs on the calcite surface and reduces LJ and Coulomb energies between asphaltene and calcite by 400 and 1000 kJ/mol, respectively, which reduces the asphaltene deposition on the surface. The selected ionic liquid has a short alkyl tail on its cation, which cannot provide a hindrance layer near the calcite surface. The combination of two inhibitors minimizes the precipitation and deposition of asphaltene when OP to IL ratio is 3:1. At this ratio, the aggregation number reduces from 20 to less than 10, and the deposition rate reduces from 1 to 0.8 compared to the case with no inhibitor. This thesis is a pioneering study to demystify the asphaltene-inhibitor behaviors during asphaltene precipitation and deposition, which can provide a useful workflow to screen, select, and design the effective inhibitor for the target crude oil (and asphaltene) besides saving time and money for the industry with effective pre-selection instead of conducting trial and error lab tests.


identifier: Silva, A. Madhushika M. <https://research.library.mun.ca/view/creator_az/Silva=3AA=2E_Madhushika_M=2E=3A=3A.html>   (2021) Isomorphism, cold-adaptation, and phosphorylation of sarcomeric tropomyosin.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Tropomyosin is a dimeric protein containing 284 amino acids per chain that is found, in association with F-actin and troponin, within the thin filament, a complex that regulates muscle contraction.
The thesis is composed of three results chapters:
i) The existence of beta tropomyosin (Tpm2) is demonstrated for the first time in fish (Salmo salar). Compared to the mammalian homologue, salmon Tpm2 has fewer cysteine (one per chain) and tyrosine (five per chain) residues. Tpm2 contributes half of the total tropomyosin in the jaw, tongue, and fin muscles. A Tpm1 isoform, either alpha-1 chain-like isoform X1 (cheek dark, jaw and tongue) or alpha (fin), accounts for the remainder. Salmon tropomyosins are distinguishable based on electrophoretic mobility, affinity for troponin-Sepharose, tryptic peptide mapping, and variable carboxyl-terminal regions (residues 276 - 284): beta (Tpm2), Leu-Ala-Leu-Asn-Asp-Met-Thr-Thr-Leu; alpha-1 chain-like isoform X1, His-Ala-Leu-Asn-Asp-Met-Thr-Ala-Ile, and alpha (Tpm1), Asn-Ala-Leu-Asn-Asp-Met-Thr-Ser-Ile.
ii) The relative instability of the most abundant isoform of Atlantic salmon, Tpm1, (20 substitutions vs. mammal) is due to a neutral 77th amino acid (Thr in salmon; Lys in rabbit), and glycines at 24 and 27 (Ala and Gln in rabbit). Incorporation of the respective mesophilic amino acid increases resistance to thermal unfolding as determined by calorimetry and chymotrypsin digestion at Leu-169, a site ⁓100 amino acids far away from residue-77. PyMOL indicates ion pairing between Lys-77 and Glu-82 in the opposite chain.
Binding of Tpm1 to troponin-Sepharose is influenced by N-terminal acetylation and the mutation of residues 24, 27, and 77. Furthermore, wild type Tmp1 displays a higher affinity for F-actin at 4 ℃ (KD, ̴ 0.1 μM) than 30 ℃ (KD, ̴ 1.6 μM). In contrast, the mesophilic homologue binds less tightly to actin at lower temperatures.
iii) Phosphorylation of serine 283 increases the susceptibility of mammalian Tpm1.1(α) to chymotrypsin (at Leu-169) and trypsin (at Arg-133), suggesting an induced opening of the center of the molecule >150 amino acids upstream, and shifts the corresponding portion of the circular dichroism unfolding profile. These results infer a change in exposure of actin-binding periods 4 (residues 124 - 147) and 5 (residues 166 - 189). The proposal is consistent with a two-fold increase in affinity for F-actin in co-sedimentation experiments.


identifier: d'Entremont, Kyle James Nestor <https://research.library.mun.ca/view/creator_az/d=27Entremont=3AKyle_James_Nestor=3A=3A.html>   (2022) The effects of seasonal and annual differences in prey and environmental conditions on a colonial seabird at the southern limit of its breeding range.  Masters thesis, Memorial University of Newfoundland.

abstract: The Northern Gannet (Morus bassanus) is the largest seabird breeding in the North Atlantic Ocean. Their breeding colonies stretch across a broad geographical range, and colonies near the southern extent of their breeding range have recently exhibited poor productivity. Gannets are opportunistic, generalist foragers and consume a wide range of prey including Atlantic mackerel (Scomber scombrus), capelin (Mallotus villosus), Atlantic herring (Clupea harengus) and Atlantic saury (Scomberesox saurus). The distribution and availability of these pelagic fishes depend on ocean temperature. In this thesis, I fill in critical knowledge gaps on how gannets nesting at their southernmost colony at Cape St. Mary’s, NL respond to differences in prey availability and sea surface temperature. In Chapter 2, I examine the effects of prey availability and sea surface temperature during the breeding season on gannet productivity over a multi-decadal timespan. I found that declines in mackerel availability and warming waters in late chick-rearing were associated with depressed productivity. In Chapter 3, I examine the foraging behaviour of gannets and how it differs between and within years. Gannets switched their foraging tactics from preying on capelin in early chick-rearing to larger pelagics in late chick-rearing. Gannets exhibited greater foraging effort during early chick-rearing in 2020 than 2019 which was associated with lowered capelin availability. Overall, gannets were negatively impacted by lowered prey availability and warming sea surface temperatures.


identifier: Reimer, Julie M. <https://research.library.mun.ca/view/creator_az/Reimer=3AJulie_M=2E=3A=3A.html>   (2022) Amplifying the potential of marine spatial planning for conservation and sustainability.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
The ocean is ubiquitously impacted by humans as our activities expand at an increasing rate. Marine spatial planning (MSP) is a process for analyzing and allocating space to specific human activities, while accounting for ecosystems, to inform ocean management and the use of ocean management tools. MSP has proliferated as an approach that seeks balance between social, economic, and ecological objectives to use the ocean sustainably. Despite its rapid uptake, the process continues to face critical challenges in operationalizing theoretical best practices and struggles to deliver sustainability, as socioeconomic development often takes precedence over conservation. Though MSP promises an ecosystem-based, integrated, place-based, adaptive, strategic, and participatory process, these principles have not fully come to fruition. The goal of this thesis is to explore these challenges and develop guidance to amplify the potential of MSP for biodiversity conservation and ocean sustainability, filling a void in the academic discourse that is often descriptive and disjointed from the complex reality of MSP practice.
Using mixed methods, including systematic review, expert opinion survey, case study analysis, and qualitative scoring, this thesis aims to identify how management tools might deliver sustainability targets, how conservation might be embedded in MSP, and how MSP principles might be translated into practice. Results highlight the importance of multi-sector management tools for achieving ocean sustainability targets, and gaps in evidence for social and economic outcomes from common spatial management tools. This research identifies potential strategies for recognizing biodiversity as fundamental to sustainable resource use, proposing the need for conservation ready MSP. Finally, this research produces the MSP Index, a tool for gauging MSP progress based on principles. The application of this tool to case studies revealed possibly persistent challenges in implementing adaptive and participatory MSP. MSP holds the potential to support ambitious goals for a healthy ocean; however, as processes adopt best practices, they become increasingly complex, requiring significant and ongoing investments that may be underestimated by the academic discourse. For MSP to meet its full potential, science must engage deeply with practitioners to understand the realities of MSP and co-produce sustainable solutions for a sustainable ocean.


identifier: Salehi, Vahid <https://research.library.mun.ca/view/creator_az/Salehi=3AVahid=3A=3A.html>   (2022) Modelling and optimizing socio-technical operations in healthcare using the FRAM and reinforcement learning.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
This PhD research work is intended to model, analyze, and optimize socio-technical
operations in healthcare using a systemic approach and reinforcement learning. An
extensive literature review is presented, and the main knowledge gaps related to
modelling and optimizing socio-technical operations in healthcare are clearly outlined
and addressed in this research work.
Introduction: Hospital to home transition processes of frail older adults include a set
of actions for frail people who are discharged from hospital to their home in the
community. The transition process exhibits dynamic interactions between technology,
humans, organizations, and the environment. The non-linear dependencies among
these influential parameters complicate the understanding of the transition process
and the mechanism of modelling its operations.
Objectives: The objectives of this research work are (a) To identify the strengths and
shortcomings of the FRAM in modelling complex socio-technical systems; (b) To
develop a comprehensive model of the hospital-to-home transition process for frail
patients; (c) To capture and visualize different characteristics of variability in the
transition process; (d) To monitor frail patients’ transitions from hospital to home; (e)
To identify challenges of the transition process; and (f) To explore functional
pathways to identify transition processes with the highest quality of care and services
for frail older people.
Methodology: This research work uses the Functional Resonance Analysis Method
(FRAM) to study and model the complexity of the transition process. A
complementary tool for the FRAM (DynaFRAM) is also used to characterize
functional and system variability in order to identify the challenges of successful
transition processes. Additionally, this research employs the reinforcement learning
technique to explore the functional transition model generated by the FRAM to
investigate a basic method to optimize the transition process for frail people.
Results and discussion: The results of this research work show that FRAM-generated
models can serve as a basis in further analyses regarding complexity, safety, and risk
management. The results also indicate that the DynaFRAM tool helps monitor
patients’ hospital-to-home transitions and characterize different types of variability in
functional and system outputs. A comprehensive model¹ of the transition process was
built using the FRAM. It includes a library of 38 functions classified in five
categories. The outcomes of using the DynaFRAM for monitoring patients’ transitions
revealed functions with significant variability. The variability observed in the outputs
of these functions could be challenging as the variability of a function can reinforce
the variability of down-stream functions and affect the performance of the entire
transition process. Finally, the results of coupling the FRAM to reinforcement
learning help evaluate the system performance in terms of accumulated action value
achieved by an artificial agent during functional pathways.
Conclusion: In light of the FRAM, the complexity of the transition process can be
visualized and understood better. The application of the DynaFRAM helps enhance
the situation awareness of frail patients through providing healthcare providers with
where a patient is and what they need during the transition process. Coupling the

FRAM and reinforcement learning would benefit the healthcare system by providing
guidance on how to provide the best care to frail patients in the light of various
circumstances.

¹The transition model is called comprehensive as it includes the perspectives of healthcare
professionals, patients, and caregivers. It also involves pre-discharge and post-discharge processes.


identifier: Miller Jobson, Sara <https://research.library.mun.ca/view/creator_az/Miller_Jobson=3ASara=3A=3A.html>   (2021) A study of echinoderm immune agents with a special focus on the sea cucumber Cucumaria frondosa and constructing a comprehensive understanding of its health and well-being.  Masters thesis, Memorial University of Newfoundland.

abstract: Immune responses are among the most well recognized markers of health and well-being in animals; however, they remain far less studied in invertebrate than vertebrate models. Nevertheless, research on invertebrate taxa can provide valuable information on the evolution of innate immunity and subsequently lead to groundbreaking work in vertebrates, including mammals. As deuterostomes possessing remarkable regenerative abilities, echinoderms have held interdisciplinary research interest for decades, particularly in the fields of immunology and developmental biology. Echinoderms are also keystone representatives of marine ecosystems around the globe, and many are the target of exploitation, highlighting the importance of understanding their resilience to environmental and anthropogenic stress. To explore this, I first examined the cellular immune agents of 23 echinoderm species from all five extant classes of this phylum (holothuroids, echinoids, asteroids, ophiuroids, crinoids). I determined that the formation, morphology, and dynamics of coelomocyte aggregates in response to foreign material are fairly conserved across taxa, with some characteristics distinct to each class, including the nature of initial catalysts, pigmentation and the expulsion pathways. Secondly, I examined several bioindicators of stress (cellular, hormonal, and behavioural responses) within the commercial holothuroid Cucumaria frondosa after exposure to stressors common within the fisheries industry (e.g., lower salinities and air exposure at various temperatures). Cucumaria. frondosa displayed measurables responses in all bioindicators that were proportional to the severity of the stress encountered. This research serves both an academic and industry purpose as it further characterizes echinoderm immunity and demonstrates how this information is valuable for stakeholders aiming to sustainably exploit or protect valuable marine resources.


identifier: Ye, Xudong <https://research.library.mun.ca/view/creator_az/Ye=3AXudong=3A=3A.html>   (2022) Development of emergency response systems by intelligent and integrated approaches for marine oil spill accidents.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Oil products play a pervasive role in modern society as one of the dominant energy fuel sources. Marine activities related to oil extraction and transportation play a vital role in resource supply. However, marine oil spills occur due to such human activities or harsh environmental factors. The emergency accidents of spills cause negative impacts on the marine environment, human health, and economic loss. The responses to marine oil spills, especially large-scale spills, are relatively challenging and inefficient due to changing environmental conditions, limited response resources, various unknown or uncertain factors and complex resource allocation processes. The development of previous research mainly focused on single process simulation, prediction, or optimization (e.g., oil trajectory, weathering, or cleanup optimization). There is still a lack of research on comprehensive and integrated emergency responses considering multiple types of simulations, types of resource allocations, stages of accident occurrence to response, and criteria for system optimizations. Optimization algorithms are an important part of system optimization and decision-making. Their performance directly affacts the quality of emergency response systems and operations. Thus, how to improve efficiency of emergency response systems becomes urgent and essential for marine oil spill management. The power and potential of integrating intelligent-based modeling of dynamic processes and system optimization have
been recognized to better support oil spill responders with more efficient response decisions and planning tools. Meanwhile, response decision-making combined with human factor analysis can help quantitatively evaluate the impacts of multiple causal factors on the overall processes and operational performance after an accident.
To address the challenges and gaps, this dissertation research focused on the development and improvement of new emergency response systems and their applications for marine oil spill response in the following aspects: 1) Realization of coupling dynamic simulation and system optimization for marine oil spill responses - The developed Simulation-Based Multi-Agent Particle Swarm Optimization (SA-PSO) modeling investigated the capacity of agent-based modeling on dynamic simulation of spill fate and response, particle swarm optimization on response allocation with minimal time and multi-agent system on information sharing. 2) Investigation of multi-type resource allocation under a complex simulation condition and improvement of optimization performance - The improved emergency response system was achieved by dynamic resource transportation, oil weathering and response simulations and resource allocation optimization. The enhanced particle swarm optimization (ME-PSO) algorithm performed outstanding convergence performance and low computation cost characteristics integrating multi-agent theory (MA) and evolutionary population dynamics (EPD). 3) Analysis and evaluation of influencing factors of multiple stages of spill accidents based on human
factors/errors and multi-criteria decision making - The developed human factors analysis and classification system for marine oil spill accidents (HFACS-OS) framework qualitatively evaluated the influence of various factors and errors associated with the multiple operational stages considered for oil spill preparedness and response (e.g., oil spill occurrence, spill monitoring, decision making/contingency planning, and spill response). The framework was further coupled with quantitative data analysis by Fuzzy-based Technique for Order Preference by Similarity to Idea Solution (Fuzzy-TOPSIS) to enhance decision-making during response operations under multiple criteria. 4) Development of a multi-criteria emergency response system with the enhanced optimization algorithm, multi-mode resource transportation and allocation and a more complex and realistic simulation modelling - The developed multi-criteria emergency response system (MC-ERS) system integrated dynamic process simulations and weighted multi-criteria system optimization. Total response time, response cost and environmental impacts were regarded as multiple optimization goals. An improved weighted sum optimization function was developed to unify the scaling and proportion of different goals. A comparative PSO was also developed with various algorithm-improving methods and the best-performing inertia weight function. The proposed emergency response approaches in studies were examined by oil spill case studies related to the North Atlantic Ocean and Canada circumstances to analyze the modelling performance and evaluate their practicality and applicability. The
developed optimization algorithms were tested by benchmarked functions, other optimization algorithms, and an oil spill case.
The developed emergency response systems and the contained simulation and optimization algorithms showed the strong capability for decision-making and emergency responses by recommending optimal resource management or evaluations of essential factors. This research was expected to provide time-efficient, and cost-saving emergency response management approaches for handling and managing marine oil spills. The research also improved our knowledge of the significance of human factors/errors to oil spill accidents and response operations and provided improved support tools for decision making. The dissertation research helped fill some important gaps in emergency response research and management practice, especially in marine oil spill response, through an innovative integration of dynamic simulation, resource optimization, human factor analysis, and artificial intelligence methods. The research outcomes can also provide methodological support and valuable references for other fields that require timely and effective decisions, system optimizations, process controls, planning and designs under complicated conditions, uncertainties, and interactions.


identifier: Crawford, Ashley <https://research.library.mun.ca/view/creator_az/Crawford=3AAshley=3A=3A.html>   (2021) Exploring anxiety disorders during pregnancy planning: a qualitative study of women’s experiences in Nova Scotia.  Masters thesis, Memorial University of Newfoundland.

abstract: Anxiety disorders are common in North America, especially among women of reproductive age. However, there is very little research examining women’s perspectives of pregnancy planning. The purpose of this modified grounded theory master’s thesis is to understand the factors that shape the pregnancy planning decisions of women with anxiety disorders in Nova Scotia. Qualitative semi-structured interviews (N=8) were conducted, and three themes were deduced. First, undertaking a pregnancy in the presence of an anxiety disorder is complex because of increased personal needs – specifically, choosing between anxiety disorder management and social expectations. Second, physicians may not all provide sufficient information about the impact of anxiety disorders during pregnancy. Third, which was an unexpected observation, women perceived their anxiety disorder as being associated with their fertility. Recommendations emerging from this study are: (1) health providers should discuss with women who have anxiety disorders the challenges associated with undertaking pregnancy; (2) information about pregnancy planning should be more available for women with anxiety disorders as it would help them make informed decisions; (3) women with anxiety disorders should be encouraged to consider midwives as care providers because midwives may provide the best support during pregnancy planning and throughout pregnancy.


identifier: Amegadzie, Joseph Emil <https://research.library.mun.ca/view/creator_az/Amegadzie=3AJoseph_Emil=3A=3A.html>   (2021) Pharmaco-epidemiological study of cardiorespiratory safety of β2-agonists for the treatment and management of asthma, chronic obstructive pulmonary disease (DOPD) and asthma-COPD overlap.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Despite ample evidence underpinning the efficacy of β2-agonists in asthma and
Chronic Obstructive Pulmonary Disease (COPD), the occurrence of β1-and β2-
adrenoceptors in the heart suggests that β2-agonists may have deleterious cardiac effects.
Therefore, patients who have asthma, COPD or both may be at increased risk of cardiorespiratory
(CR) events because these diseases magnify the impact of these agents on the
heart.
In this thesis, I performed a systematic review and meta-analyses of the literature
to provide a general overview of the comparative effectiveness and safety of inhaled
medications. I conducted a retrospective cohort study to investigate gender differences in
new-users of inhaled corticosteroids (ICS), short-or long-acting β2-agonist (SABA or
LABA), ICS/LABA, short-or long-acting muscarinic antagonist (SAMA or LAMA) and a
nested case-control study to test the association between β2-agonist-based medications
and safety events for cardio-respiratory outcomes of major adverse cardiovascular events
(MACE), all-cause mortality, and hospitalization for pneumonia using the United
Kingdom Clinical Practice Research Datalink of patients with asthma, COPD or asthma-
COPD overlap between 01-January-1998 and 31-July-2018.
Results from the meta-analysis suggests that for patients with asthma–COPD
overlap, LABA are associated with decreased risk of myocardial infarction in
comparisons to non-LABA; and the combination therapy of ICS/LABA appears to reduce
the risk of death or hospitalization in comparisons to placebo. Also, results from the
gender-based analysis of pharmacotherapy use showed significant gender differences in
new-users of inhaled pharmacotherapies among obstructive airways disease patients. In
regards to the cardio-respiratory outcomes, new initiation of LABA, SABA or ICS/LABA
compared to SAMA in COPD or SABA compared to ICS in asthma-COPD overlap was
associated with an increased risk of MACE. However, among asthmatics, β2-agonists
compared to ICS were not associated with risk of MACE. Consequently, starting LABA
monotherapy or SABA monotherapy treatment was associated with an increased risk of
all-cause mortality in patients with COPD. On the other hand, I observed no association
with SABA, LABA or LABA/ICS in comparison with ICS or SAMA and the risk of
pneumonia in patients with asthma, COPD or asthma-COPD overlap.


identifier: Noori (Frohlich), Rebecca J. <https://research.library.mun.ca/view/creator_az/Noori_=28Frohlich=29=3ARebecca_J=2E=3A=3A.html>   (2021) Pannexin1 in human pluripotent stem cells and its influence on early cell fate decisions.  Masters thesis, Memorial University of Newfoundland.

abstract: Human development requires cells to work together within their environment to successfully differentiate and organize into complex tissues. Pannexin1 (PANX1) is a channel-forming protein that facilitates cell-cell communication by conveying small messenger molecules across cellular membranes. PANX1 is expressed in the early embryo and persists in most adult tissues. Dysfunctional PANX1 activity has been implicated in several human pathologies including oocyte cell death and neurological disease. Given its expression in the early embryo and its link to disease, we investigated PANX1’s involvement in cell fate specification to the embryonic germ layers and during complex, 3-dimensional human cerebral organoid development. Using immunofluorescence, flow cytometry and quantitative RT-PCR, we find that human induced pluripotent stem cells (iPSCs) express PANX1. iPSCs subjected to CRISPR-Cas9 PANX1 genetic ablation show no changes in cellular morphology, pluripotency gene expression, proliferation, or apoptosis. However, spontaneously differentiated PANX1 knockout iPSCs have enhanced ability to generate mesoderm and endoderm germ layers compared to control. Furthermore, PANX1 is dynamically expressed and localized across different neural cell types at distinct stages of human cerebral organoid development. Taken together, our results suggest that PANX1-mediated cell communication actively participates in cell fate specification and human cerebral organoid development.


identifier: Galloway, Dylan A. <https://research.library.mun.ca/view/creator_az/Galloway=3ADylan_A=2E=3A=3A.html>   (2021) Investigating microRNA-mediated glial cell contributions in the pathophysiology of MS and its animal models.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Multiple sclerosis (MS) is a chronic neurological disease characterized by the
immune-mediated destruction of myelin within the central nervous system (CNS). During
the course of MS, diverse cell populations including microglia, monocyte-derived
macrophages and astrocytes contribute towards neuroinflammation and demyelination;
however, these cells can also facilitate remyelination and brain repair. Consequently,
defining the molecular mechanisms that balance inflammation and regeneration within
the CNS is essential for understanding the pathophysiology of MS and investigating novel
disease-modifying therapies. microRNAs (miRNAs) are small RNA molecules that posttranscriptionally
regulate gene expression and are of significant interest in many diseases
since they can repress several functionally related genes and robustly alter cell phenotype
and function. The overall goal of this thesis was to investigate miRNAs that control glial
cell activation and myelin repair in MS and its animal models.
Dimethyl fumarate (DMF) is a commonly prescribed MS disease-modifying
therapy. While studying the effects DMF on human astrocytes, it was observed that this
molecule, and not its metabolite, suppressed pro-inflammatory astrocyte activation and
miRNA expression. In MS patient monocytes, miR-223-3p was identified as a
differentially regulated miRNA that is essential for pro-regenerative myeloid cell
phenotypes. Specifically, miR-223-3p promoted anti-inflammatory polarization and
myelin phagocytosis by macrophages and microglia, and miR-223-3p deficiency impaired
myelin debris clearance and remyelination following experimental demyelination in vivo.
Gene expression profiling of demyelinated lesions revealed that genes associated with the
inflammasome, a complex that induces pro-inflammatory cytokine secretion and cell
death, were highly upregulated in acutely demyelinated lesions and subsided during
remyelination. In MS lesions and experimental demyelination, it was confirmed that the
NLRP3 inflammasome was highly expressed in macrophages and microglia. NLRP3 was
identified as a miR-223-3p target gene, and both miR-223-3p and a small-molecule
NLRP3 inhibitor suppressed inflammasome activation in vitro. In vivo, NLRP3 inhibition
reduced axonal injury following demyelination.
Overall, this thesis has established a role for miRNAs as regulators of glial cell
responses and are functionally relevant during CNS repair following demyelination.
Moving forward, modifying the expression of miRNAs, such as miR-223-3p, may
represent a novel therapeutic approach in the treatment of MS and other inflammatorymediated
demyelinating conditions.


identifier: King, Justin <https://research.library.mun.ca/view/creator_az/King=3AJustin=3A=3A.html>   (2020) Model-guided mutational analysis of Activation-induced cytidine deaminase (AID) to elucidate structure-function relationships.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Activation-induced cytidine deaminase (AID) is a DNA mutating cytidine deaminase enzyme that is a member of the AID/ Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases, altogether consisting of 11 members in humans. AID deaminates deoxycytidine to deoxyuridine at immunoglobulin loci in activated B lymphocytes to mediate secondary antibody diversification. AID-mediated mutations have also been implicated in epigenetic reprogramming, as well as genome-wide DNA damage and chromosomal translocations that transform healthy B cells into lymphoma/leukemia. Since its discovery in 1999, a key element missing in the AID field has been the lack of a protein structure. The goal of this thesis was to solve this problem and determine how AID binds its substrate nucleic acid and how these interactions result in its physiological and aberrant activities. In chapter 2 of this thesis, we explored the role AID plays in epigenetic reprogramming through genome-demethylation. We provided a glimpse into the AID catalytic pocket structure and how AID from humans and other species target cytidine vs 5-methylcytidine. In chapter 3, we provided the first functional and breathing structure of AID using a unique computational-biochemical approach. In this work, we provided the first fine map of AID’s structure, identified the structural details of its catalytic pocket and interactions with the DNA substrate including secondary catalytic residues that are key to cytidine stabilization in the pocket, delineated two novel substrate DNA binding grooves on the surface and studied how conformational changes in the AID structure regulate its function. The work culminated in our discovery and proof that dynamic catalytic pocket closure limits AID activity. This novel catalytic pocket state which we termed the “Schrödinger’s CATalytic pocket” has since been confirmed by multiple other structural studies and represents a novel mode of enzyme activity regulation across all known nucleic acid modifying enzymes. Our work also provided a structural rationale for many of the biochemical properties of AID including its
unusually low catalytic rate and atypically high nanomolar range binding affinity for its substrate DNA. In Chapter 5, we utilized these structural insights and the combined computational-biochemical approach developed in Chapter 3 to screen a large library of small molecule drug-like compounds against the catalytic pocket of AID. We have identified and functionally tested the first small molecule inhibitors that block the mutagenic activity of AID. We also demonstrated that several of these small molecules can inhibit several of AID’s tumorigenic APOBEC siblings. And finally in Chapter 6, we review several DNA/RNA binding grooves previously discovered on AID and explore their possible binding combinations. We explore how these plastic modes of binding DNA and RNA simultaneously may impact AID function. Finally, we examine proposed AID dimer models bound to DNA/RNA and examine how this may act as an additional regulatory bottleneck of enzymatic activity.


identifier: Orzylowski, Magdalena <https://research.library.mun.ca/view/creator_az/Orzylowski=3AMagdalena=3A=3A.html>   (2020) Living with a genetic form of arrhythmogenic right ventricular cardiomyopathy causing sudden cardiac death: symptoms of depression, anxiety and post-traumatic stress in transmembrane protein 43 p.S358L mutation positive family members with an ICD.  Masters thesis, Memorial University of Newfoundland.

abstract:
Arrhythmogenic right ventricular cardiomyopathy (ARVC) caused by a p.S358L mutation in
TMEM43 has a high incidence in Newfoundland and Labrador (NL), with sudden cardiac death
(SCD) often the first symptom. Implantable cardioverter defibrillators (ICDs) are effective at
preventing SCD. Mental health effects have not been studied in this population. This study
sought to identify symptoms of depression, anxiety, and posttraumatic stress in those with
TMEM43 p.S358L ARVC and an ICD.
TMEM43 p.S358L positive individuals with an ICD were recruited. Participants completed the
Patient Health Questionnaire-9 (PHQ-9), Zung self-rating anxiety scale (SAS), and the posttraumatic
checklist-civilian version (PCL-C). Prevalences of depression, anxiety and posttraumatic
stress symptoms were described and compared with scores in unaffected family members and
general population norms.
Fifty-three ICD patients completed the questionnaires. Univariate linear analysis revealed that
the three scales were significantly positively related to each other (Pearson’s r > 0.6). Anxiety
was related to number of appropriate ICD discharges (B=0.355, p=0.022) and the PCL-C scale
was significantly related to age (B=-.322, p=0.019). Multivariate regression models predicting
each scale score revealed that only the three scales contributed to the variance, excepting age,
which remained significant in the model predicting posttraumatic stress scale scores (B=-.215,
p=0.015). A significant percentage of participants scored above the clinical cutoff levels for
depression (28.3%), anxiety (49%) and posttraumatic stress (32%). Scoring high on one mental
health scale (PHQ-9, SAS, or PCL-C) was strongly associated with scoring high on the subsequent
scales. Findings can inform the provision of mental health services to these patients.


identifier: Buote, Richard <https://research.library.mun.ca/view/creator_az/Buote=3ARichard=3A=3A.html>   (2021) Factors associated with glycemic control, hospitalization, and mortality among Newfoundland and Labrador residents with diabetes mellitus.  Doctoral (PhD) thesis, Memorial University of Newfoundland.

abstract:
Diabetes is among the most prevalent chronic conditions in Canada. It is characterized by a body's inability to produce or efficiently use insulin. Diabetes can be effectively managed, often with the support of a primary care provider. Unfortunately, the high turnover rate of family physicians (FPs) in Newfoundland and Labrador (NL) threatens continuity of care, potentially contributing to poorer health outcomes for people with diabetes. This study examines the relationship between FP turnover and glycemic control, hospitalization, and mortality among patients with diabetes in NL. It was hypothesized that FP turnover would be related to the three outcomes of interest. Specifically, it was expected that high turnover rates would be associated with poorer glycemic control and increased risk of hospitalization and mortality. To examine these hypotheses, a cross-sectional analysis of adults (20+ years) with diabetes in NL between 2011 and 2015 was performed. Secondary data sources were linked, including the provincial Chronic Disease Registry and the Physician and Medical Practice Database. Multivariate binary logistic regression was used to examine the relationship between FP turnover, glycemic control, hospitalization, and mortality while controlling for important covariates. The analyses provided mixed support for the hypotheses. FP turnover was found to be associated with glycemic control and hospitalization but not mortality. Further, FP turnover was associated with an increased risk of hospitalization, but the direction of the relationship between turnover and glycemic control was inconsistent with the hypothesis. Findings from this study also suggest that regions with no FPs performed similarly to regions with low turnover on the outcomes of glycemic control and hospitalization. These findings may have implications for the delivery of primary care in
NL. Future studies should examine primary care models in regions with no FPs and consider whether these models could be more widely applied in NL for chronic disease management. Additionally, studies in other provinces should compare regions with high rates of primary care change (i.e., high turnover) to regions with consistent primary care availability to determine whether consistent primary care delivery, irrespective of the presence of FPs, is associated with better outcomes for patients with chronic condition.


identifier: Maziar, Aida <https://research.library.mun.ca/view/creator_az/Maziar=3AAida=3A=3A.html>   (2022) Age-related LTCC and NMDAR expression in the hippocampus and olfactory cortex in rats.  Masters thesis, Memorial University of Newfoundland.

abstract:
Neuronal calcium is a critical mediator for learning and memory. However, with age, calcium dysregulation leads to cognitive decline. L-type calcium channels (LTCCs) and N-methyl-D-aspartate receptors (NMDARs) mediate Ca2+ influx in neurons. We hypothesized that there are age-related changes of calcium channel expression in the piriform cortex (PC) and hippocampus, two areas that are crucial for olfactory and spatial learning ability respectively. We measured synaptic and extrasynaptic levels of LTCCs (Cav1.2) and NMDAR subunits (GluN1, GluN2A, and GluN2B) in neonatal, adult, and aging rats using Western blot. PSD-95 colocalizing and non-colocalizing Cav1.2 expression were compared between adult and aging brains using immunohistochemistry and confocal microscopy, and we further investigated somatic and dendritic expression of both Cav1.2 and Cav1.3 subunits. The expression of hippocampal synaptic, but not extrasynaptic, NMDARs was higher in adult and aging groups compared to neonates. However, GluN2A/2B ratios and synaptic:extrasynaptic ratios of NMDAR subunits were similar across age groups. In contrast, in the PC, GluN2A/2B and synaptic:extrasynaptic ratios were higher in adult PC compared to neonates. In hippocampal CA1 and PC, the soma:dendritic ratio of Cav1.2 expression increased with aging, but the soma:dendritic ratio of Cav1.3 expression decreased. Extrasynaptic Cav1.2 non- PSD95 colocalizing expression was also found to have higher expression in the aging PC compared to adult. Our data suggest that PC and hippocampus are different in age-related channel expression. PC maturation is accompanied by a switch from GluN2B to GluN2A subunits. Higher somatic Cav1.2, but not Cav1.3 expression in
CA1 and higher extrasynaptic Cav1.2 in the PC may correlate with aging-associated disruption of calcium homeostasis and cognitive decline.