VictorJuiz/thesis huggingface dataset:
Modelling Intraguild Predation with Adaptive Behaviour

The thesis examines the dynamics of intraguild predation models incorporating adaptive behaviour. The top predator varies its relative consumption of the intermediate consumer and the basal resource. The consumer alters its activity level in response to the threat of predation. Incorporating these adaptive behaviours facilitated three species coexistence, but restricted omnivory by promoting the formation of three species food chains. Model modifications which promoted omnivory also tended to reduce three species coexistence. It is predicted that omnivory should be most common when the intermediate and the basal species are similarly profitable to the predator. The model also predicts two types of omnivory. Strong omnivory occurs when the predator always consumes intermediate amounts of both prey items. Weak omnivory occurs when the predator preys almost exclusively on one prey at most times, but rapidly switches to include the other when the relative abundance of that second prey exceeds a certain level.

Keywords: Omnivory
Intraguild Predation
Adaptive Behaviour
Model
Advisor: Abrams, Peter
The Role of Function, Homogeneity and Syntax in Creative Performance on the Uses of Objects Task

The Uses of Objects Task is a widely used assessment of creative performance, but it relies on subjective scoring methods for evaluation. A new version of the task was devised using Latent Semantic Analysis (LSA), a computational tool used to measure semantic distance. 135 participants provided as many creative uses for as they could for 20 separate objects. Responses were analyzed for strategy use, category switching, variety, and originality of responses, as well as subjective measure of creativity by independent raters. The LSA originality measure was more reliable than the subjective measure, and values averaged over participants correlated with both subjective evaluations and self-assessment of creativity. The score appeared to successfully isolate the creativity of the people themselves, rather than the potential creativity afforded by a given object.

Keywords: latent semantic analysis
syntax
creativity
Advisor: Dunbar, Kevin
Characterization of the Drosophila HtrA2/OMI Ortholog, a Mitochondrial Protein of Pro-apoptotic Function

While mitochondria are traditionally associated with energy production, recent studies identified its function in controlling the onset of apoptosis. Mitochondrial apoptotic control results from sequestering pro-apoptotic proteins, which are secreted following cellular stress. HtrA2/OMI is secreted from mitochondria to the cytosol following apoptotic induction, binds and degrades the inhibitor of apoptosis protein, XIAP in mammals, activating the caspase cascade. This study characterizes the expression of Drosophila HtrA2/OMI, a mitochondrial protein, its processing by Rhomboid-7 and demonstrates its pro-apoptotic function. Following exposure to apoptotic stress, dOMI is secreted from mitochondria and its expression profile displays an increase in a cleaved form consistent with Rhomboid-7 processing. dOMI expression resulted in sensitization of cells to apoptotic stress, observed through an increase in caspase activity. These data further validate the use of Drosophila in the study of mitochondrial driven apoptosis while implicating a potential role for Rhomboid-7 in apoptosis through proteolytic cleavage of dOMI.

Keywords: HtrA2
OMI
Apoptosis
Rhomboid-7
Advisor: McQuibban, G. Angus
An Initial Attempt to Correlate Prefrontal Cortex mRNA Transcripts with Behavioural Variation in Lewis Rats

Despite virtually identical genomes, inbred animals often vary in phenotype, including behaviour, but the molecular basis of this phenomenon is unknown. Our hypothesis is that differences in behaviour between inbred rats are correlated with differential cortical mRNA transcript levels. 40 Lewis rats were subjected to 5 behavioural tests: two were used to categorize 10 animals into either “high” or “low” phenotype groups. Microarray gene expression profiling was performed for 5 rats from each group. Three main analyses were performed to: (1) identify differential expression between the high and low groups, (2) identify correlations between transcript levels and individual behaviour scores, and (3) determine if the results of this replicate experiment overlapped with a previous pilot experiment. Some array results were confirmed by RT-PCR. We found that this experiment did not replicate the findings from the pilot, however several genes of interest were determined and were validated by RT-PCR.

Keywords: transcriptomics
prefrontal cortex
behaviour
rat
Advisor: Wong, Albert Hung Choy
Robust Face Detection Using Template Matching Algorithm

Human face detection and recognition techniques play an important role in applica- tions like face recognition, video surveillance, human computer interface and face image databases. Using color information in images is one of the various possible techniques used for face detection. The novel technique used in this project was the combination of various techniques such as skin color detection, template matching, gradient face de- tection to achieve high accuracy of face detection in frontal faces. The objective in this work was to determine the best rotation angle to achieve optimal detection. Also eye and mouse template matching have been put to test for feature detection.

Keywords: Face detection
Face recognition
Template matching
Advisor: Venetsanopoulos, Anastasios N.
Aarabi, Parham
The Lipophorin Receptor of Drosophila melanogaster

Animals carry lipids such as hydrocarbons, fats, and sterols throughout their circulatory systems bound to a carrier protein known as lipophorin. The lipophorin receptor has been characterized in locusts, mosquitoes and cockroaches yet little is known about it in Drosophila melanogaster. An antibody against the eleven variants of the lipophorin receptor was developed and tested. Although this was the main feature of the work, several preliminary experiments using RNA interference were conducted to determine the effects of lipophorin receptor. Flies whose lipophorin receptor proteins were knocked down were found to have no major differences in locomotor activity in total darkness suggesting that their circadian rhythms are unaffected. The same flies were found to have extensive differences in their cuticular hydrocarbon profiles as compared with wild‐type flies. Whole‐mount tissue staining of Drosophila adult brains revealed that several cells in the central nervous system are immunoreactive with the anti‐Lipophorin receptor antibody.

Keywords: Drosophila
Lipophorin Receptor
antibody
Advisor: Levine, Joel
Design and Application of Discrete Explicit Filters for Large Eddy Simulation of Compressible Turbulent Flows

In the context of Large Eddy Simulation (LES) of turbulent flows, there is a current need to compare and evaluate different proposed subfilter-scale models. In order to carefully compare subfilter-scale models and compare LES predictions to Direct Numerical Simulation (DNS) results (the latter would be helpful in the comparison and validation of models), there is a real need for a "grid-independent" LES capability and explicit filtering methods offer one means by which this may be achieved. Advantages of explicit filtering are that it provides a means for eliminating aliasing errors, allows for the direct control of commutation errors, and most importantly allows a decoupling between the mesh spacing and the filter width which is the primary reason why there are difficulties in comparing LES solutions obtained on different grids. This thesis considers the design and assessment of discrete explicit filters and their application to isotropic turbulence prediction.

Keywords: Large Eddy Simulation
Explicit Filtering
Discrete Explicit Filters
LES
Advisor: Groth, Clinton P. T.
The Joint Modelling of Trip Timing and Mode Choice

This thesis jointly models the 24 hour work trip timing and mode choice decisions of commuters in the Greater Toronto Area. A discrete-continuous specification, with a multinomial logit model for mode choice and an accelerated time hazard model for trip timing, is used to allow for unrestricted correlation between these two fundamental decisions. Statistically significant correlations are found between mode choice and trip timing for work journeys with expected differences between modes. Furthermore, the joint models have a wide range of policy sensitive statistically significant parameters of intuitive sign and magnitude, revealing expected differences between workers of different occupation groups. Furthermore, the estimated models have a high degree of fit to observed cumulative departure and arrival time distribution functions and to observed mode choices. Finally, sensitivity tests have demonstrated that the model is capable of capturing peak spreading in response to increasing auto congestion.

Keywords: travel behaviour
work trip timing
mode choice
hazard model
logit model
joint model
peak spreading
time of day choice
Advisor: Miller, Eric
Determinants of Yeast Prion Stability

S. cerevisiae Sup35p inhabits two metastable states: functional translation termination factor; and prion-like aggregate [PSI+], which propagates by converting soluble Sup35p to its own misfolded form. Once initiated, Sup35p polymerization in [PSI+] cells is spontaneous, but [PSI+] prion inheritance depends on the Hsp104p disaggregase. To identify Hsp104-interacting sequences, Sup35p was subjected to a systematic deletion screen. [PSI+] maintenance by mutant Sup35p was assessed in both presence and absence of plasmid-encoded WT Sup35p in haploid sup35 cells. Large deletions abolished [PSI+], implying perturbations of prion structure, while others imparted [PSI+]-dependent toxicity. Removal of a single 25aa segment destabilised [PSI+] inheritance, resulting in enhanced rates of prion loss. This is consistent with the expected prion propagation defect in response to reduced Hsp104p interaction. However, several mutants containing this 25aa segment share the destabilised prion phenotype, suggesting chaperone/prion interactions are strongly context-dependent, and no one Sup35p region is solely responsible for Hsp104p recognition.

Keywords: Prion
Saccharomyces cerevisiae
PSI
Sup35
Hsp104
Advisor: Glover, John R.
Analyzing Spatial Diversity in Distributed Radar Networks

We introduce the notion of diversity order as a performance measure for distributed radar systems. We define the diversity order of a radar network as the slope of the probability of detection (PD) versus SNR evaluated at PD =0.5. We prove that the communication bandwidth between the sensors and the fusion center does not affect the growth in diversity order. We also prove that the OR rule leads to the best performance and its diversity order grows as (log K). We then introduce the notion of a random radar network to study the effect of geometry on overall system performance. We approximate the distribution of the SINR at each sensor by an exponential distribution, and we derive the moments for a specific system model. We then analyze multistatic systems and prove that each sensor should be large enough to cancel the interference in order to exploit the available spatial diversity.

Keywords: Radar
Distributed Detection
Neyman Pearson
Spatial Diversity
Space-Time Adaptive Processing
Advisor: Adve, Raviraj
Student Leadership for Social Justice in Secondary Schools: A Canadian Perspective

This qualitative study investigates how the views of student leaders (and some of their staff advisors) illuminate the discussion in the broader literature around issues of student leadership, conflict, diversity and social justice in secondary schools. Eighteen one-hour, semi-structured interviews were conducted with twelve student leaders and six teachers from six provinces across Canada. This study contributes to educational research by considering the ways student leaders (rather than adult administrators) can impact social justice. While students envision their leadership role in terms of social justice with the goals of inclusion and societal change in mind, the present schooling structure, established expectations and strategies chosen for initiatives often hinder the realization of such a role. Schools also seem to avoid local controversial issues by encouraging student leaders to focus on international concerns. This study explores opportunities for schools to address equity issues through reconceptualizing student leadership and its goals.

Keywords: Student Leadership
Social Justice
Diversity
Conflict
Controversial Issues
Secondary schools
Advisor: Portelli, John P.
Patterns of Cytokine Response in Patients Undergoing Curative Radiotherapy for Prostate Cancer

Ionizing radiation induces specific proteins involved in DNA repair, cell death, inflammation and tissue injury. The radiation response of proteins within a uniform prostate cancer (PCa) radiotherapy (RT) population has been studied to a limited extent. In this thesis, the proteomic responses of patients undergoing curative RT for intermediate-risk PCa were determined for a panel of pro-inflammatory cytokines from pre-RT baseline to last treatment (39 vs. 33 fractions depending on whether the cohort received primary or post-prostatectomy RT respectively). Longitudinal proteomic research is feasible at our institution based on the study design presented herein. Interferon (IFN)-g and interleukin (IL)-6 were significantly increased during RT and these changes followed consistent patterns modeled by linear and quadratic functions respectively. Furthermore, acute gastrointestinal (GI) and genitourinary (GU) toxicities were significantly associated with IL-2 and IL-1 levels respectively during RT. Taken together this research supports cytokines as potential biomarkers of normal tissue radiation response.

Keywords: prostate cancer
cytokine
biomarker
radiation therapy
Advisor: Bristow, Robert
Concurrent Design of Reconfigurable Robots using a Robotic Hardware-in-the-loop Simulation

This thesis discusses a practical approach to the concurrent analysis and synthesis of reconfigurable robot manipulators based on the alternative design methodology of Linguistic Mechatronics (LM) as well as the utilization of a modular Robotic Hardware-In-the-Loop Simulation (RHILS) platform. Linguistic Mechatronics is a systematic design methodology for mechatronic systems, which formalizes subjective notions and simplifies the optimization process, in the hope that numerous naturally different design variables can be considered concurrently. The methodology redefines the ultimate goal of design based on the qualitative notions of wish and must satisfactions. The underlying concepts of LM are investigated through a simulation case study. In addition, the RHILS platform involving physical joint modules and a control unit, which takes into account various physical phenomena and reduces the simulation complexities, is employed to the design architecture. Ultimately, the new approach is applied to redesigning kinematic, dynamic and control parameters of an industrial manipulator.

Keywords: Concurrent Design
Hardware-in-the-loop Simulation
Linguistic Mechatronics
Reconfigurable Robotics
Advisor: Emami, Mohammad Reza
The Distribution of Coral, Reefs and Coastal Habitats in North Central Cuba

Coral communities have begun to form under small inlet-style bridges along the causeway connecting Cayo Coco to Cayo Guillermo. To understand how these bridge-reefs formed and characterize their attributes relative to surrounding communities, a combination of ecological observations and 13C isotopes were analyzed from the bridges and surrounding reefs, mangrove channels and seagrass patches. Hierarchical Cluster Analysis, Detrended Correspondence Analysis and Canonical Correspondence Analysis were carried out to group which physical attributes contributed to the coral communities in the bridge-reefs and also which habitats they were most similar to, with respect to coral and benthic composition. Bridge reef coral assemblages resembled shallow patch reefs and mangrove channels, while benthic coverage was similar to mangrove channels. Organic matter was from combined seagrass and mangrove sources, with mangrove dominating in some regions more than others. This work demonstrates that habitats within the seascape are inter-related through varying mechanisms and development is multi-dimensional.

Keywords: seascape ecologoy
coral distribution
Cayo Coco
Cuba
marginal habitats
coral reefs
seagrass
mangroves
carbon isotopes
primary productivity
coastal vegetation
causeways
Advisor: Cowling, Sharon A.
Happy Distraction: Positive Affect Broadens Attention to Irrelevant Information

The present study investigated the claim that positive mood broadens the scope of attention to include irrelevant information, and if so, whether this loosening of attentional control has longer term cognitive consequences. In Experiment 1, participants in an induced happy mood were more influenced by distracting information that interfered with responses in the global-local task, particularly when this information was global in nature. Experiment 2 demonstrated that, when previously irrelevant information became solutions on a subsequent task, implicit memory for this distraction was positively correlated with naturally-occurring positive mood. This study corroborates findings that individuals in a happy mood are more affected by distracting irrelevant information. Furthermore, this widened scope of attention can facilitate performance on a subsequent task, a finding with implications for the relationship between positive mood and creativity.

Keywords: attention
emotion
distractibility
Advisor: Hasher, Lynn
Cost Based Design Optimization of a Laminated Plate

The focus of this thesis is to introduce a proof-of-concept illustrating the integration of cost and performance as primary design drivers for structural design. Of particular interest to the aerospace industry is laminated structural design, therefore an example problem of a laminated plate structure is selected. This problem presents two primary challenges: linking cost in as general a way as possible to the design variables, and dealing with the many discrete design options available in a laminated plate. The first issue is examined by using a theoretical cost model for advanced composite fabrication and using a Direct Operating Cost model. The second issue is addressed using a gradient based optimization algorithm and a Discrete Material Optimization (DMO) method, which is typically used in topology optimization of structures.

Keywords: optimization
engineering cost estimation
aerospace
laminated plate
composites
plate
cost
Advisor: Hansen, Jorn S.
Islanding Detection and Control of Islanded Single and Two-parallel Distributed Generation Units

This thesis experimentally validates the performance of an active islanding detection method under various scenarios. It is also analytically shown that the islanding detection method has a non-detection zone (NDZ), and a method to eliminate the NDZ is proposed. Moreover, the performance of an autonomous mode controller for islanded DG units is experimentally evaluated. Based on a robustness analysis, it is shown that the controller, which is basically designed for the nominal plant, can maintain the stability of the system despite of significant load uncertainties. The feasibility of the islanding detection method for islanding detection in two-DG systems is also experimentally investigated. Moreover, a control strategy for autonomous operation of two-DG systems is proposed, and its performance is experimentally evaluated. Then, adopting the islanding detection method and the proposed control strategy, the viability of smooth transitions from grid-connected modes to autonomous (islanded) modes in two-parallel DG systems is experimentally validated.

Keywords: Islanding Detection
Distributed Generation
Advisor: Iravani, Mohammad Reza
Precoding for Multiuser MIMO Systems with Multiple Base Stations

Future cellular networks are expected to support extremely high data rates and user capacities. This thesis investigates the downlink of a wireless cellular system that takes advantage of multiple antennas at base stations and mobile stations, frequency reuse across all cells, and cooperation among base stations. We identify asynchronous interference resulting from multi-cell communication as a key challenge, prove the existence of a downlink/uplink duality in that case, and present a linear precoding scheme that exploits this duality. Since this result is not directly extendable to orthogonal frequency division multiplexing (OFDM), we propose a `hybrid' algorithm for two cooperating base stations, which combines linear and nonlinear precoding. This algorithm minimizes the sum mean squared error of the system and is extendable to OFDM. Finally, we consider the problem of user selection for multiuser precoding in OFDM-based systems. We extend an available single-cell user selection scheme to multiple cooperating cells.

Keywords: downlink
multiuser
cooperation
linear precoding
MIMO
duality
multiple base stations
user selection
asynchronous interference
multicell
OFDM
Advisor: Adve, Raviraj
From Images to Maps

This work proposes a two-stage method that reconstructs the map of a scene from tagged photographs of that scene. In the first stage, several methods are proposed that transform tag data from the photographs into an intermediary distance matrix. These methods are compared against each other. In the second stage, an approach based on the physical mass-spring system is proposed that transforms the distance matrix into a map. This approach is compared against and outperforms MDS-MAP(P) when given human tagged input photographs. Experiments are carried out on two test datasets, one with 67 tags, and the other with 19. An evaluation method is described and the optimal overall reconstruction generates maps with accuracies of 47% and 66% respectively for the two test datasets, both scoring roughly 40% higher than a random reconstruction. The map reconstruction method is applied to three sample datasets and the resulting maps are qualitatively evaluated.

Keywords: maps
tags
Advisor: Aarabi, Parham
A Comparison of the Stability of Measures of Personality Traits, Self-esteem, Affective Well-being, and Cognitive Well-being

A variety of statistical models have been developed to examine longitudinal stability and change of individual differences. Kenny and Zautra’s (1995) trait-state-error (TSE) model models stability as a function of stable variance that does not change (trait), moderately stable variance that changes over time (state), and error variance. Applications of this model have been limited to panel studies with repeated observations of the same individual. The present study developed a non-linear regression model to apply the TSE model to retest correlations from different samples. This model was used to compare the stability of measures of personality traits, affective well-being (AWB), cognitive well-being (CWB), and self-esteem. After correcting for differences in reliability, age, gender, and scale length, the amount of trait (vs. state) variance was similar across constructs. Stability of the state component was highest for AWB and CWB, suggesting that situational influences have most enduring effects on these two constructs.

Keywords: stability
meta-analysis
personality
well-being
self-esteem
trait-state-error model
affect
life satisfaction
Advisor: Schimmack, Ulrich