VictorJuiz/thesis huggingface dataset:
On the Use of Median-joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology

A phylogenetic tree is a branching diagram illustrating the inferred evolutionary history of taxa. It only represents the vertical transmission of DNA due to its structure. Phylogenetic networks have been proposed to overcome this limitation and to show complex scenarios such as hybridization in a cyclic structure known as reticulation. Median-Joining Networks (MJNs) are one of the most popular approaches to discovering reticulations, but it has been used hastily in evolutionary studies without critical examination of its assumptions, performance and suitability. The MJ algorithm is based on phenetics, and the networks lack evolutionary direction. I evaluate the extent of congruence between MJNs and Bayesian inference phylogenies through likelihood-based tests and detect a significant difference in branching order between the two methods in more than one-third of unambiguous cases. Analyses document that MJNs are inappropriate for evolutionary inference, and I encourage the biologists to take a pause and reassess its usage.

Keywords: Cladistics
Median-Joining Network
Phenetics
Phylogenetic Networks
Phylogenetic Trees
Shimodaira-Hasegawa Test
Advisor: Murphy, Robert W
Passive Acoustic Monitoring of Dissolving Tank Activity and Modelling of Underwater Vapour Explosions

Violent dissolving tank operation can pose a safety hazard, damage equipment, and in extreme cases lead to a dissolving tank explosion. This study investigates the characteristics of smelt-water interaction and the dynamics and acoustics of underwater vapour explosions. Observations carried out at pulp mills indicate that the dissolving tank soundscape becomes more intense and more variable when the smelt stream is not being shattered. Spectral analysis reveals that the smelt-water interactions carry more energy in low frequencies. Equations of motion describing a vapour bubble size in time are derived from rst principles. The resulting equation is a modied version of the Geers-Hunter doubly asymptotic approximation, which builds upon the Rayleigh-Plesset equation. Using numerical methods, the pressure wave caused by a single smelt droplet explosion is calculated. Droplet statistics simulates the total variation of pressure inside the dissolving tank. Acoustic characteristics of the synthetic pressure waves are consistent with previous observations.

Advisor: Wong, Willy
Predicting Cell-type Specific Active Properties by Developing Multi-compartment Models using Databases and Electrophysiological Feature Constraints: Application to Interneuron Specific 3 (IS3) Cells in the Hippocampus

In hippocampus, interneuron specific 3 (IS3) cells have been shown to make inhibitory synapses onto specific types of inhibitory interneuron dendrites with the ability to control their firing patterns. Morphological and synaptic aspects of IS3 cells are being examined, but what type, how much and where voltage-gated channels (VGCs) are present on IS3 cells has not been determined. Using a combination of the NEURON and MATLAB software environments, we have developed an approach that uses experimental IS3 data to generate databases of multi-compartment models that show appropriate activity for IS3 cells. Given their correspondence with data, our models predict relative conductance balances and distributions of different channel types in IS3 cells and can be used as a basis for understanding the functional roles of IS3 cells in hippocampus, a central structure in memory formation.

Keywords: Computational Neuroscience
Dendrites
Multi-Compartment Modeling
Voltage-Gated Channels
Advisor: Skinner, Frances K
The Anoxic Corrosion of Copper in Pure Water and Chloride Rich Brines

The Nuclear Waste Management Organization (NWMO) is developing an approach for the permanent geological disposal of nuclear waste. The waste will be encased in copper coated used fuel containers (UFCs) and placed in a deep geological repository (DGR). To support the NWMO in their investigations on the long-term corrosion of copper a lab scale simulation of the DGR environment was created. Copper wires were placed in glass electrochemical cells and exposed to one of two environments; pure anoxic water or chloride-rich anoxic brine. The systems were allowed to freely corrode and accumulate hydrogen within their headspaces over extended durations at 30 to 75 °C. The hydrogen was periodically purged and subsequently analyzed using a highly sensitive amperometric sensor; these measurements were utilized to calculate the corresponding copper corrosion rates. Corrosion with hydrogen evolution was demonstrated in both pure water and brines at slow rates below 1 and 10 nm/year, respectively.

Keywords: Copper
Corrosion
Deep Geological Repository
Hydrogen
Nuclear Waste
Advisor: Newman, Roger C
Effects of Age and Motor Training on Prefrontal-motor Cortical Excitability

The dorsolateral prefrontal cortex (DLPFC) is a critical substrate for motor learning. However, how DLPFC is involved in goal-directed, sequence-specific learning remains unclear, and effects of age on learning and DLPFC-to-primary motor cortex (M1) connections have not been tested. We studied 14 right-handed healthy subjects, 20-80 years old, in a combined TMS-pinch experiment. We examined DLPFC-M1 connections in human subjects and how they change with motor training, whether sequence training changes M1 intracortical and DLPFC-M1 neurophysiology differently than motor training not containing a sequence, and whether age influences the TMS neurophysiological measures. All subjects were unable to regenerate the sequence, and behavioural/TMS measures suggest that they implicitly acquired the sequence. Sequence acquisition correlated with DLPFC-M1 facilitation. The results suggest that the brain processes sequence information differently from non-specific information during motor training. The DLPFC may play a role in processing sequence-specific information through an excitatory functional connection to M1 during acquisition.

Keywords: aging
DLPFC
motor learning
neurophysiology
tms
transcranial magnetic stimulation
Advisor: Chen, Robert
Isolation and Characterization of the Corticotropin Releasing Factor-like Diuretic Hormone Receptor in Rhodnius prolixus

Rhodnius prolixus is a hemipteran insect which undergoes rapid post-feeding diuresis following ingestion of a large blood meal that can be up to 10 times initial body weight. Corticotropin releasing factor-like diuretic hormone (Rhopr-CRF/DH) is involved in the neurohormonal synergism that increases rates of fluid secretion by Malpighian tubules over 1000 fold during rapid post-feeding diuresis. In this study, the Rhopr-CRF/DH receptor was isolated and characterized from fifth instar R .prolixus. The receptor is a family B G-protein coupled receptor (GPCR) and was deorphaned using a Chinese hamster ovary (CHO) cell line. RT-qPCR demonstrated strong receptor expression in the digestive tissues, upper Malpighian tubules and the reproductive tissues. Finally, a modified Human embryonic kidney (HEK293) cell line was used to verify the initiation of the cyclic adenosine monophosphate (cAMP) pathway upon activation of the receptor. Characterization of the CRF/DH receptor will serve to elicit better understanding into the precise coordination of diuresis and other physiological processes.

Advisor: Orchard, Ian
Identifying Effective Instructional Design Features of Simulation in Nursing Education: A Realist Review

Simulation is increasingly being used as an instructional strategy, yet evidence-informed guides for how to use simulation effectively in nursing training is lacking. A realist review of the nursing simulation literature was conducted to determine how simulation is currently being used in nursing training. Unfortunately, the majority (69%) of primary studies were excluded due to missing information about the context, mechanism, or outcome of the study. In the remaining 13 studies, four themes of instructional design features emerged including: feedback, debriefing, self-regulated learning, and the intersection between feedback and self-regulated learning. However, the small number of studies permits only cautious recommendations for nursing educators. Improved reporting standards in nursing education journals are imperative so that authors of original studies are prompted to report all relevant information, and so authors of knowledge syntheses are better able to make recommendations about when simulation should be used, for which trainees, under which circumstances, and why.

Keywords: Debriefing
Feedback
Instructional Design
Realist Review
Self-Regulated Learning
Simulation
Advisor: Cockerill, Rhonda
Brydges, Ryan
Wood Ash as a Forest Soil Amendment: Effects on Seedling Growth and Nutrition, and Red-backed Salamander Abundance

Wood ash is being considered as a soil amendment on acidified forest soils of eastern North America. However, research is required to ensure ash does not negatively affect native species. The short-term effects of ash on growth and nutrition of tree seedlings native to eastern North America was assessed in greenhouse experiments, finding relatively neutral effects up to dosages of 10 Mg ha-1, and negative effects at dosages of 15-20 Mg ha-1. Responses of red-backed salamander (Plethodon cinereus) abundance to ash additions up to 8 Mg ha-1 in a tolerant hardwood forest were also assessed in a field trial. Neutral and positive effects of ash on salamander abundance were observed, and positive effects were driven by increases in soil pH and moisture. These results tentatively support ash additions in acidified forests of eastern North America, but more research is needed into the longer-term effects of ash and its potential toxicants.

Keywords: Biomass boiler
Salamanders
Seedlings
Soil
Wood ash
Advisor: Caspersen, John P
Basiliko, Nathan
Modeling Multibody Frictional Contact Problem in a CANDU Fuel Rod

A three-dimensional multibody frictional contact problem in a CANDU nuclear fuel rod is studied in this thesis. To account for the effect of friction on fuel rod deformations, a computational model is developed based on an existing model. For the contact algorithm, a set of complementary equations involving complementarity variables inequality is introduced to deal with the three-dimensional frictional contact. The algorithm is implemented into a computer program. Three cases are studied to show the feasibility and efficiency of the numerical scheme for handling frictional contact among multiple bodies. The application of the research work offers the assessment of deflection as to safety evaluation for the nuclear industry under different scenarios.

Advisor: Zu, Jean
Yu, Shudong
An Integrated Modelling and Analytics Platform for Service Planning of Bus Stops Using Archived AVL, APC, and Schedule Data

Decision-making by transit agencies in response to dynamic system and external conditions has significant impact on transit system performance. Analysis of Automatic Data Collection (ADC) system data has meaningful potential to improve transit agencies’ decision-making related to system planning and operations. The objective of this research was twofold. First, a set of analytic models was defined to estimate changes in bus performance and passenger travel times, given user-specified stop layout changes to an existing transit trip pattern. The models drew upon archived Automatic Vehicle Location (AVL), Automatic Passenger Counter (APC), and schedule data, and were constructed to accommodate bus stop removal, stop addition, and introduction of limited-stop service. Second, a data analytics platform was created to present ten Key Performance Indicators (KPIs) which drew upon the analytic models. Software was created to integrate analytic modelling with a frontend graphical user interface for defining stop layout changes, and returning resulting KPIs.

Keywords: APC
bus
CAD/AVL
data analytics
service planning
transit
Advisor: Shalaby, Amer S
On the Morphological Adaptations of the Thorax of Sphagniana sphagnum (Ensifera, Tettigoniidae) that Enable Complex Stridulation via the Forewings

Males of the flightless tettigoniid Sphagniana sphagnorum generate a complex two-spectrum signal via stridulation, using acoustically adapted forewings (tegmina). Complex-wave rapidly decaying pulses in trains, made upon the distal half of the file, have a broad-band (17-25 kHz) spectrum; short, spaced, ultrasonic and strongly sinusoidal 35 kHz pulses are emitted as trains over the file's proximal half. I studied how S. sphagnorum tegminal morphology enables the production of these two different spectra with the same forewings. The storage of elastic energy in the scraper is hypothesized to play a key role in driving the scraper over the file at a necessary tooth-contact rate. Scraper morphology indicates structural adaptations enabling storage of elastic energy. Wax loading tested the role of scraper-pit flexibility in scraper movement. Sound levels in resonant spectra were more substantially affected than those associated with broadband generation. Morphology and alignment of pteralia during tegmino-tegminal stridulation is also investigated.

Keywords: Axillary Sclerites
Elastic Energy
Stridulation
Tettigoniidae
Advisor: Morris, Glenn K
Opposing Effects of Acute Stress in a Rodent Model of Gambling Behaviour

Impulsive decision-making is characteristic of both pathological gambling and depression. It remains unclear why some individuals are prone to make risky decisions and develop gambling behaviours. Stress is known to increase the risk for addiction, depression, and disrupt optimal decision-making. The goal of this study is to explore the effects of stress-induced depressive behaviours on gambling-like decision-making in rodents. We hypothesized that stress will increase impulsive decision-making in rats. Rodents were exposed to acute stress using a stress paradigm known to induce depressive-like behaviours and the animal’s decision-making was assessed using a rodent model of gambling-like behaviour. As expected, we found that inescapable footshocks increased impulsive decision-making. Surprisingly, we found that escapable footshocks improved decision-making. Furthermore, high levels of baseline impulsivity in addition to inescapable footshocks increased impulsive decision-making. Our findings suggest that the observed effects of both types of shocks on decision-making could be modulated by baseline levels of impulsivity.

Advisor: Lobo, Daniela S.S.
I Eat; Therefore I Am: Constructing Identities Through Food

This autoethnography focuses on the role food played in my identity formation. In approaching this, the following thesis is divided into the three "meal times" where my personal narratives will function as entry points for a discussion on: how the ethnic food I ate created self-loathing problematizing a sense of belonging yet at the same time, was also capable of bonding a community, the beginnings of curiosity and an appetite for culinary adventure including an exploration of my food related practices, and finally how the gendered food identities of my father, mother, and grandmother contributed to my identity. By highlighting the impact of my food past on my sense of self, I provide insight into how it is sometimes the seemingly mundane, such as our food histories, which inform what we consume that largely define who we are, not only as individuals, but as a culture and society.

Keywords: autoethnography
culture
ethnicity
food
identity
narratives
Advisor: Trifonas, Peter P
Miller, Jack P
Surface Modification of Metals by Means of an Ultrasound Irradiation Technique in Liquid Media

Ultrasound irradiation has recently received considerable attention due to its abilities in nanoparticle synthesis and also in modifying surfaces and depositing nanoparticles on a surface. Such a sonochemical method facilitates the deposition of nanoparticles on various substrates in a one-step process. The aim of this work is to use the ultrasound irradiation technique to deposit silver particles on the surface of metals in particular copper as a model system. By controlling the concentration of silver ions in the solution, reaction temperature and sonication time a homogeneous coating of silver particles formed on the surface of copper. However, the electrochemical studies of the silver deposited copper sample compared to a pure copper, showed an increase in corrosion rate after the treatment. Electrochemical measurements were used to quantify the roughening of the copper substrate. Electrochemistry also enabled the mass transfer enhancement due to sonication to be quantified.

Keywords: Corrosion
Limiting Current Density
Silver Coating
Sonochemistry
Surface Modification
Ultrasound Irradiation-Assisted Deposition
Advisor: Newman, Roger C.
The Immunogenic Effect of Local Radiation Therapy in a Murine Model of Mesothelioma

Malignant pleural mesothelioma (MPM) is a rare cancer that arises from the mesothelial surfaces of the pleural cavity. It is associated with asbestos inhalation, with 70% of cases being associated with documented asbestos exposure. MPM has a poor prognosis and the outlook has not been improved by newer therapeutic interventions. A new approach developed in our lab, focusing on Surgery for Mesothelioma After Radiation Therapy (SMART) showed promising results in a phase I/II clinical trial. We believe that radiation is important to achieving activation of the immune system and may contribute to the benefits observed in patients. The goal of this project was to develop a mouse model to analyze the immunogenic effect of Local Radiation Therapy (LRT) and its impact on immune cell recruitment and activation in the context of MPM. Results from these studies may have clinical implication for the treatment of MPM, where combination of LRT and other treatments such as immunotherapy may prove useful.

Keywords: Immunology
Immunotherapy
Mesothelioma
Mouse model
MPM
Radiotherapy
Advisor: De Perrot, Marc
Pathogen Removal Through Biological Filtration and Quantitative Microbial Risk Assessments for Drinking Water Purification

Biological filtration is a novel concept for drinking water purification that allows for the colonization of rapid granular filters with native bacterial organisms in order to reduce organic compounds in the final treated effluent. There is little published material on the efficacy of these filters for the removal of pathogens, specifically protozoa such as cryptosporidium and giardia which are difficult to inactivate using chlorine disinfection. This study utilizes aerobic endospores as a surrogate for cryptosporidium to characterize the removal performance of biologically active filters. Biological filtration was shown to achieve

Keywords: Aerobic Spores
Biological Filtration
Drinking Water
Quantitative Microbial Risk Assessment
Water Purification
Advisor: Andrews, Robert C
Probabilistic Urban Stormwater Quantity Modeling

Analytical probabilistic models (APMs) for urban drainage systems analysis have been progressively developed by numerous researchers spanning the globe over the last four decades. The first task of this thesis is the synthesis of models for quantity analysis among these developments. Quantity models characterize the frequency of occurrence of stormwater impacts of varying magnitudes, such as peak flood flow rate or reservoir spill volume, as opposed to water quality impacts such as pollutant concentration. The second thesis task is to bridge the existing spectrum of models in a manner ensuring their seamless presentation. To this end, new models are derived to complete missing links. The third task is the improvement of a runoff volume model and a storage-treatment model. For the storage-treatment model, this constitutes an entirely reworked derivation due to prior conceptual errors. The final task is the integration of innovative approaches from related disciplines into the APM framework.

Keywords: analytical probabilistic models
bivariate copulas
quantity control analysis
Advisor: Adams, Barry J
Guo, Yiping
Metformin Promotes Tissue Repair and Functional Recovery in a Model of Postnatal Brain Injury

The development of cell replacement strategies to repair the injured brain has gained considerable attention with a particular interest in mobilizing endogenous neural stem and progenitor cells (known as neural precursor cells, NPCs) to promote brain repair. Recent work demonstrated that metformin, a drug used to manage type II diabetes, promotes neurogenesis when administered in vivo. Moreover, metformin enhanced the formation of neural and glial progeny from NPCs derived from the embryonic brain. Based on these observations, we sought to determine metformin’s potential role in neural repair following brain injury. We found that metformin administration activates endogenous NPCs and promotes their migration and differentiation in the neonatal brain in a hypoxia ischemia (H/I) injury model and importantly, leads to sensory-motor recovery. Our results indicate that the activation of endogenous NPCs is a promising target for therapeutic intervention in childhood brain injury models.

Keywords: functional recovery
hypoxia-ischemia
metformin
neural stem cells
Advisor: Morshead, Cindi M
Domains of Socialization and Adolescent Internalization of Prosocial Values

The present study examined the relation between effective parenting behaviours and adolescents' internalization of prosocial values for 41 mother-adolescent dyads. Utilizing a Domains-of-Socialization framework proposed by Grusec and Davidov (2010), we focused specifically on how appropriate parenting behaviours in different domains influenced adolescents’ internalization of prosocial values measured as a function of reasons given for engaging in prosocial behavior. The results indicated that maternal behaviours in the control domain hindered adolescent internalization whereas maternal behaviours in both the mutual reciprocity and protection domains fostered adolescent internalization of prosocial values. Furthermore, since parenting behaviours between domains were, at most, moderately correlated with each other, this would suggest that each of the domains of socialization are composed of relatively unique parenting behaviours with very little overlap. Lastly, maternal and adolescent personality contributed to appropriate parenting behaviours across several domains. The theoretical and practical implicates are discussed.

Keywords: Internalization
Prosocial Values
Socialization
Advisor: Grusec, Joan E
Malti, Tina
The Impact of Variable Precipitation on the Performance of Wetland and Grassland Plants

Climate change is causing increased precipitation variability, leading to large, infrequent precipitation events. This will have ecological consequences for plants because hydrological inputs will become transient. Despite this, there is a lack of evidence explaining the impact of variable precipitation on plant performance. To address this, this thesis asked three questions: (i) How does variable precipitation impact wetland and grassland plant performance? (ii) Does variable precipitation impact plant functional groups differently? And, (iii) do wetland and grassland plants respond similarly or differently to variable precipitation? A greenhouse and field experiment was conducted with wetland and grassland monocot and eudicot species, the amount and frequency of precipitation was manipulated, and plant performance was measured. This thesis reveals that large, infrequent precipitation events negatively impacted plant performance with larger effects on eudicots than monocots. This suggests that variable precipitation could have implications for the diversity and abundance of species in plant communities.

Keywords: climate change
grassland
plants
precipitation
wetland
Advisor: Duval, Tim P
Johnson, Marc TJ