VictorJuiz/thesis huggingface dataset:
Ground Beetles (Coleoptera: Carabidae) and Ecologically Sustainable Forest Management in the Northern Hardwood Forests of Central Ontario

Ecological sustainability is a priority in the management of Ontario’s northern hardwood forests. It is important to assess harvesting impacts, as well as the likelihood of recovery prior to the next harvest. In this thesis, I use carabid communities as indicators of forest management in sugar maple (Acer saccharum Marsh.) dominated stands in Central Ontario to compare different partial harvesting systems within a recently cut experimental forest, as well as between old-growth and mature logged stands. Greater basal area removal resulted in greater deviations in carabid communities from uncut conditions among experimental treatments, while communities were similar between old-growth and mature logged sites, despite strong difference in forest structure. These findings suggest that pre-harvest conditions may sufficiently recover between partial harvests to support ecological sustainability over time. However, the ability to recover may depend on initial logging intensity and harvesting rotation length.

Keywords: carabidae
ground beetles
northern hardwoods
old-growth forests
single-tree selection
sustainable forest management
Advisor: Malcolm, Jay R.
Non-binary Belongings in Toronto: Problematizing the Gay-friendly City

This thesis examines the experiences of non-binary transgender people in the city of Toronto through the use of photovoice and semi-structured interviews. It is concerned with the ways such individuals articulate their sense of belonging towards Toronto itself as well as the LGBTQ+ spaces of the city. This thesis argues that the ongoing gentrification of Toronto, the persistence of transphobic discrimination, and the prevalence of right-wing politics in the region marginalize non-binary individuals and challenge their ability to belong in spaces throughout the city. While participants particularly identified LGBTQ+ spaces in Toronto as important sites of belonging, networking, and ontological security, these positive experiences stand in contrast with the number of homo- and transnormativities at play within these sites, further cementing the exclusion of non-binary individuals. Therefore, I argue that the envisioning of non-binary inclusive, transgender-friendly urban spaces is a utopian endeavour as it requires a radical rethinking of social, political, and economic structures and hierarchies.

Keywords: nonbinary
non-binary
photovoice
queer geography
toronto
transgender
Advisor: Mollett, Sharlene
Roberts, David
Investigation of A Tandem Cylinder Arrangement with A Yawed Cylinder in Crossflow

A tandem cylinder (TC) arrangement of a vertical cylinder trailed by a slanted counterpart, was investigated at ReD = 1 × 105 and separation angles of 𝛬 = 30° and 45°, formed by the orientation of the cylinders. Two mean pressure states occurred at certain spanwise locations on the upstream cylinder surface. These locations corresponded to the following normalized cylinder-to-cylinder gap spacing ranges of the TC arrangement: 2.7 ≤ L/D ≤ 5 (𝛬 = 30°) and 4.6 ≤ L/D ≤ 7.6 (𝛬 = 45°). The durations of each mean pressure state were irregular. The separation angle, 𝛬, in conjunction with L/D, had a strong influence on the gap flow field and surface pressure quantities, such as the root mean square. The surface pressure data of the upstream cylinder indicated that cellular gap regimes form along the span of the gap; this is similar to the cellular vortex shedding occurring along the span of the wake of a tapered cylinder.

Keywords: Aeroacoustics
Aerodynamics
Bluff-bodies
Flow-induced noise
Fluid Dynamics
Fluid Mechanics
Advisor: Lavoie, Philippe
Elucidating the Role of Peroxisome Proliferator-activated Receptor (PPAR-δ) in Microglia Cell Function during Experimental Autoimmune Encephalomyelitis (EAE)

Microglia, the resident macrophages of the central nervous system (CNS), mediate pro- and anti-inflammatory activities during experimental autoimmune encephalomyelitis (EAE). Previous reports show that peroxisome proliferator-activated receptor (PPAR)-δ attenuates pro-inflammatory activation of peripheral macrophages and limits EAE development; however, the role of microglial PPAR-δ remained unclear. Accordingly, we generated mice with a microglia-specific PPAR-δ deletion. Following EAE induction, microglia-specific PPAR-δ knockout mice developed an exacerbated course of disease, accompanied by severe histological outcomes. In addition, microglia devoid of PPAR-δ showed activated tendencies in vivo. Magnetic resonance imaging (MRI) analyses of CNS specimens preserved after prolonged EAE revealed that microglia-specific PPAR-δ knockout mice exhibit significant atrophy of spinal cord white matter and of brain structures with microglia activation. In vitro culturing of primary microglia revealed a unique pro-inflammatory cytokine and chemokine profile in PPAR-δ-deficient cells. Collectively, these results solidify microglial PPAR-δ as an important endogenous brake to limit excessive CNS inflammation.

Advisor: Dunn, Shannon E
Measurement and State-dependent Modulation of the Excitability of a Brainstem Motoneuron Pool In-Vivo

Measuring the excitability of a central motoneuron pool in-vivo across behavioural states to identify mechanisms of control is difficult, and accordingly studies are few. Here I applied ‘optogenetics’ to optically control genetically targeted motoneurons in mice and determine their net excitability from measures of motor output. I applied this tool to a motor circuit critical to the pathogenesis of obstructive sleep apnea (OSA). OSA is caused by airway closure in sleep due to relaxation of tongue muscles. The hypoglossal motoneuron pool (HMN) is the source of motor output to the tongue, and strategies to measure and modulate its activity are needed to identify and test new pharmacological treatments for OSA. This thesis identifies that (1) an optogenetic protocol can be used to measure the endogenous excitability of the HMN in-vivo, and (2) endogenous HMN excitability is significantly reduced in rapid eye movement (REM) sleep compared to non-REM sleep and wakefulness.

Keywords: animal models
genioglossus
obstructive sleep apnea
sleep
upper airway
Advisor: Horner, Richard L
The Long-Term Psychological Impact and Sequelae of Childhood Intrusive Medical Procedures, Treatments, and/or Hospitalization(s) due to a Serious Injury or Chronic Illness

This qualitative individual case analysis explores the long-term psychological impact and developmental implications of enduring childhood medical procedures, treatments and hospitalizations, retrospectively through an adult’s personal narrative and insights. In utilizing an autoethnographic approach, the primary investigator of this study serves as the key participant and case under review. This case of childhood medical experiences is presented and analyzed within a theoretical background of Erik Erikson’s five stages of childhood psychosocial development. The goal of this study was to investigate the long-term psychological and developmental impact childhood medical procedures, treatments, and hospitalization(s) potentially pose for children with serious congenital/acquired injuries or illnesses. The psychological impact and developmental implications identified in the results of this study are discussed, along with emerging themes.

Keywords: adult case study and autoethnography
developmental and psychological impact of childhood medical events
long-term consequences of childhood medical procedures
pediatric medical traumatic stress
pediatric mental health
pediatric patients and psychosocial development
Advisor: Volpe, Richard
Longitudinal Investigation into the Role of Reading Self-concept on Reading Achievement for English as a First Language and English Language Learners

Reading self-concept—students’ perceived competence and enjoyment in reading—is theorized to influence reading development. Multi-group confirmatory factor analysis and two, cross-panel structural equation models were used to investigate the measurement invariance and structural relationship between reading self-concept and reading achievement from grade 3 to grade 6 in a cohort comprised of students with English as a first language (EL1; n= 8947) and English language learners (ELL; n= 8942). Reading self-concept and reading achievement were invariant in factor loadings, but not item intercepts, between EL1 and ELL students. Reading self-concept influences subsequent reading achievement for EL1 students, while reading achievement influences later self-concept for ELL students. Thus, to maximize the effectiveness of grade 3 reading instruction, foundational reading skills should be the primary focus of instruction for ELL students. These results highlight the unique relationship between reading self-concept and achievement among ELLs.

Keywords: English Language Learners
measurement invariance
reading achievement
reading self-concept
structural equation modeling
Advisor: Jang, Eunice E
Active Mitigation of Transformer Saturation in Dual-active-bridge Converter for Electric Vehicle Chargers

This thesis presents a non-linear active transformer saturation-mitigation-technique suitable for Dual-Active-Bridge(DAB) dc-dc converters, used in bi-directional on-board Electric Vehicle(EV) battery chargers. Bi-directional on-board EV chargers enable features such as vehicle-to-grid, and vehicle-to-vehicle capabilities. The proposed technique detects the variation in current slope near the saturation boundary. This controller operates with minimal saturation safety-margin and over-design. Compared to protection methods that regulate average current, the proposed control provides a fast and simple way to detect saturation and take corrective action with fewer sensors. The detection and reaction time of the proposed controller reduces the required operating safety-margin, increasing transformer power and converter density. Validation is done on a 450V, 6.6kW DAB with 96.8% efficiency and 80cm^3 transformer. Compared to similar DAB converters, the proposed controller halves the transformer volume with a higher efficiency. The proposed transformer is only 20% larger than those used in resonant converters with four times the frequency.

Keywords: dual-active-bridge
on-board charger
protection
saturation
slope
transformer
Advisor: Trescases, Olivier
SDX-based Security Collaboration: Extending the Security Reach beyond Network Domains

Security is becoming increasingly a threat, especially as we progress to Smart Cities and the Internet of Things. Therefore, it becomes necessary to embed greater security in the current Internet architecture, since beyond internal domains, there is little control over traffic circulating the Internet. In this thesis, we propose a collaboration between Software Defined Internet Exchange Points to enable greater control over wide area network traffic. Moreover, with recent surges of extensive DDoS attacks that exhaust and drive the victims' resources and parts of the Internet to a halt, such collaboration could really stem the tide of these attacks. Our proposal is complemented with SDN to simplify management and enable granular inter-domain traffic customization. In addition, the configurations are abstracted from the end users by utilizing the intent concept. The proposed design relies on a hierarchical architecture with a centralized entity capable of distributing the intents to the appropriate SDX's.

Keywords: Distributed Denial of Service (DDoS)
Intent Driven Networking (IDN)
Internet Core (Internet Exchange Point - IXP)
Network Security
Policy-based Management (PBM)
Software Defined Internet Exchange Point (SDX)
Advisor: Leon-Garcia, Alberto
Biomechanical Evaluation of Nosing Design on Stair Navigation in Healthy and Post-Stroke Older Adults

Stair design can influence the risk of stair falls, with stair nosings intended to provide greater foot accommodation. However, to date little is known regarding the appropriate nosing shape to guide safer stair ambulation. This thesis investigates the impact of different nosing shapes (round, square, tapered, and no-nosing) on foot trajectory measures during stair navigation among healthy and post-stroke older adults. Less resultant foot clearance and greater foot overhang during descent highlighted the increased risk of falls on stairs in the post-stroke group. For both healthy and stroke participants, the tapered and round nosing shapes resulted in the largest horizontal foot clearance, and smallest foot overhang, respectively. However, with greater step-to-step variability detected with round nosings, the tapered nosing presents as the safest choice among all evaluated designs. The results of this work can be used to inform architectural and accessible design standards to create a safer built environment.

Keywords: Aging
Kinematics
Nosing design
Stair ambulation
Stroke
Advisor: Novak, Alison C
Canadian Privacy Advocacy Groups and Bill C-51

New technologies with mass surveillance capabilities have dominated national security policies globally and nationally. The effects on privacy and freedom of expression permeate public and academic discussions; however, the contributions by the coalition of privacy advocacy groups who debate these policies have often been overlooked (Bennett, 2010). These coalitions include organizations that have different mandates and definitions of “privacy” that are effective in changing legislation. In Canada, The Anti-Terrorism Act, 2015 (Bill C-51) was met with criticism concerning its broad powers and lack of oversight. This thesis examines Canadian advocacy groups and their coalition efforts through a policy analysis of Bill C-51 and related documents. Interviews were conducted with advocacy group leaders to understand how coalitions meaningfully shape privacy legislation. With the launch of a public National Security Consultation in 2016, this thesis examines a critical juncture in Canadian security and surveillance debates.

Keywords: Advocacy
Civil Society
Coalitions
National Security
Policy
Privacy
Advisor: Shade, Leslie R
Relevance-driven Clustering Methods for Visual Interactive Search

The goal of this research is help users perform efficient and effective search in large-scale visual information displays. In order to reduce users' cognitive load, we propose to develop novel clustering methods for aggregating information in these displays. The key problem is to define what is the optimal cluster in visual search displays and how to efficiently optimize these visual clusters. Specifically, this optimization problem can be formulated as the maximization of an expected F1-Score (EF1). We show how EF1 maximization is formalized as a Mixed Integer Linear Programming (MILP) problem and then develop two fast greedy algorithms benchmarked against this optimal MILP solution demonstrating their near-optimality and efficiency. Our user study results show that users can complete their search tasks with higher efficiency and higher accuracy using greedy algorithms, thus achieving our primary objective of helping users perform efficient and effective search in visual interactive displays.

Keywords: information retrieval
Mixed Integer Linear Programming
Relevance-driven Clustering
visual cluster
visual search
Advisor: Sanner, Scott
An Evaluation of the Ethic of Neutrality in the Ontario Public Service

Work of Ontario Public Servants is determined in part by the government of the day as they set their priorities. This commitment to serve the government, regardless of individual affiliation or support, is built on the ethic of neutrality – a value that can shape the personal lives of public servants. This study sheds light on how workplace ethical values impact the personal political participation decisions of public servants. What measures does the employer take, if any, to reduce any ambiguity or burden posed by the ethic of neutrality? This research examines the measures, if any, that the employer takes to reduce any ambiguity or burden posed by the ethic of neutrality. This is important as it provides a window into the employer’s motivation to help strengthen the health of the democracy, and thereby the public service, and the employer’s motivation to support public servants through the conflict of interest process.

Keywords: Charter of Rights and Freedoms
Ethic of Neutrality
Government of Ontario
Ontario Public Service
Political Participation
Advisor: Quarter, Jack
Spatial Deep Learning for Wireless Scheduling

The optimal scheduling of interfering links in a dense wireless network with full frequency reuse is a challenging task. The traditional method involves first estimating all the interfering channel strengths then optimizing the scheduling based on the model, both of which are computationally intensive. This thesis explores approaches using deep learning for scheduling, based solely on the geographic locations inputs. We innovated a solution by using a novel neural network architecture that computes the geographic spatial convolutions for interference estimation, over multiple feedback stages to learn the optimum solution through unsupervised training. The resulting neural network gives near-optimal performance for sum-rate maximization and is capable of generalizing to larger problem sizes. Furthermore, this thesis also focuses on optimizing Proportional Fairness across the network, through proposing a novel scheduling approach that utilizes the sum-rate optimal scheduling heuristics over judiciously chosen subsets of links, showing highly competitive performances.

Keywords: Artificial Intelligence
Deep Learning
Machine Learning
Non-convex Optimization
Resources Allocation
Wireless Communication
Advisor: Yu, Wei
The Moderating Influence of Acute Stress in the Relationship between Impulsivity and Reward Processing

Previous studies have shown that acute stress and impulsivity can directly impair reward sensitivity and performance on a response inhibition task. This study attempted to validate the Maastritch Acute Stress Task (MAST) as an effective stressor and to demonstrate that acute interfered with performance on reward processing and response inhibition tasks. The study also explored acute stress as the moderator of reward sensitivity on trait and behavioural impulsivity. The study confirmed that the MAST was an effective stressor, however, the MAST neither altered reward processing or response inhibition. For individuals who scored high on behavioural impulsivity (not trait impulsivity) the stressor reduced reward sensitivity and the ability to discriminate stimuli in the probabilistic reward task. The results showed the interaction of stress and impulsivity and its influence on reward processing which contributes to our understanding of how these variables may affect basic motivational processes underlying both normal and abnormal behavior.

Keywords: acute stress
impulsivity
response inhibition
reward
reward processing
stress
Advisor: Erb, Suzanne
Whole-cell regenerating 'microbead' to capture disease antibodies using the yeast species, Pichia pastoris

Guiding appropriate medical treatment and population surveillance are examples of the crucial functions of diagnostics in health care [1]. Antibody based assays are routinely employed, however, they often require substantial resources limiting their use in low-resource settings. Richard Kil and others in Prof. David McMillen's lab proposed a synthetic biology solution: using yeast as 'microbeads' to detect disease antibodies. The yeast diagnostic combines yeast surface display and agglutination. Surface display engineers yeasts natural cell wall linked proteins to display antigens. The cells are placed in a u-shaped well settle into a dot at the bottom by default. Disease specic antibodies bridge the cells causing them to agglutinate; distinguishable by the naked eye. Preliminary work utilized Saccharomyces cerevisiae and I rebuilt the biosensor using an alternative yeast species, Pichia pastoris. It is an industrially viable yeast [2] and I investigated the viability of using P. pastoris.

Keywords: Diagnostics
Synthetic biology
Yeast
Advisor: McMillen, David R
Structure and Function of the VPS33B/VPS16B Complex

Platelet α-granules are central to the function of these cells in blood clotting and other physiological processes. α-granule biogenesis and platelet precursor megakaryocytes require functional VPS16B/VPS33B complexes, which are thought to facilitate vesicular fusion. The VPS16B/VPS33B complex was synthesized using an exogenous expression system in insect Sf9 cells and affinity-purified. The complex was gently cross-linked in a sucrose gradient by the GraFix method prior to imaging via negative-staining electron microscopy. Image analysis revealed a putative structure for VPS16B/VPS33B that resembles a dumbbell. Co-immunoprecipitation studies using truncated constructs of VPS16B confirmed that a 146 amino acid region (aa 122-268) is necessary and sufficient for binding to VPS33B: Intermolecular interactions were further examined via homology modeling. Molecular weight estimates for VPS16B/VPS33B obtained from sucrose gradients, size exclusion chromatography, and molecular modeling indicate a size of 250-350 kilodaltons.

Keywords: Sec1/Munc18
SNARE
VPS16B
VPS33B
Advisor: Kahr, Walter H
Prognostic and Therapeutic Implications of a Unique Expression Cluster in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is characterized by accumulation of myeloid cells in the bone marrow and hematopoietic insufficiency. NPM1 is among the most commonly mutated genes in AML, representing a distinct entity and indicating a low-risk prognosis. However, NPM1 mutations co-occur with high-risk mutations and have complicated patterns of co-occurrence, potentially altering prognosis. By performing RNA sequencing of NPM1-mutated patient samples, we have identified two distinct groups within NPM1-AML, one enriched for FLT3-ITD. Interestingly, a subset of patients without the ITD mutation have similar gene expression to FLT3-ITD patients; a FLT3-like phenotype. These patients possess gene fusions that may explain this phenotype. Additionally, this group has increased sensitivity to certain kinase inhibitors compared with other FLT3-ITD negative patients, and similar to FLT3-ITD patients in the same cluster. These findings support the presence of a potentially high-risk subgroup within NPM1-AML, aiding to refine classification and contributing to personalized medicine for AML.

Keywords: Genetics
Leukemia
NPM1
Advisor: Schimmer, Aaron D
Cis-regulatory Elements Controlling Expression of the Auxin Response Factor MONOPTEROS and its Irrepressible Variant MP∆

The AUXIN RESPONSE FACTORS (ARFs) mediate changes in gene expression that are associated with auxin response in plants. One of the best-characterized ARFs is ARF5/MONOPTEROS(MP), for which strong loss-of-function and gain-of-function associated defects have been reported. Recent evidence has indicated that auxin response may be driven in part by MP-mediated control of its own expression. Here it is shown that removal of individual ARF-binding auxin response elements (AuxREs) from the MP promoter results in differential expression in specific tissues, while creation of supernumerary AuxREs is associated with auxin response-related phenotypic changes. The irrepressible MP variant MP∆ was used to track potentially expression-stage specific regions of the MP promoter and to determine in which tissues MP∆ can exert its gain-of-function effects independent of the activity of other, closely related ARFs.

Keywords: ARF
Auxin
AuxRE
MONOPTEROS
MP∆
Advisor: Berleth, Thomas