VictorJuiz/thesis huggingface dataset:
Neutrophil Extracellular Traps as a Biomarker to Predict Outcomes in Lupus Nephritis

Neutrophil Extracellular Traps (NETs) have been implicated in Lupus Nephritis (LN) pathogenesis. Systemic Lupus Erythematosus (SLE) neutrophils release Elastase, High Mobility Group Box-1 (HMGB1) and oxidized DNA (oxDNA). These NET components are capable of amplifying the inflammatory immune response and causing tissue damage which may in turn dictate the severity of LN and it´s response to therapy. This thesis examined if the amount of serum NET remnants (Elastase-DNA, HMGB1-DNA and Elastase-oxDNA) at the time of a LN flare predicted renal outcomes in the following 24 months. To accomplish this I developed in-house-ELISA assays to measure serum Elastase-DNA, HMGB1-DNA and Elastase-oxDNA complexes. It was found that circulating NET remnants, specifically Elastase-DNA and HMGB1-DNA, are predominantly elevated in patients with active LN and may also serve as predictors of adverse renal outcomes including lack of response to therapy and decline in kidney function in the 24 months following the LN flare.

Keywords: Biomarkers
Lupus Nephritis
Renal outcomes
Systemic Lupus Erythematosus
Advisor: Urowitz, Murray
Wither, Joan
Development of a Pulsed, Diode-Pumped, Fiber-Based, Entangled Photon Source

Entangled photon sources have applications in such fields as quantum communications, quantum sensing and quantum computing. Of particular interest are pulsed entangled photon sources, as they provide an additional degree of freedom – the temporal degree of freedom – to manipulate entanglement properties, hence increasing the information capacity of the entangled photons they produce. An entangled photon source in the telecom wavelength typically requires a 780 nm pump laser. So far, in most cases, pulsed entangled photon sources are pumped by the Ti:Sapph mode-locked laser, which, due to its bulky size and high cost, has limited the widescale adoption of pulsed entangled photon sources. In this thesis, I demonstrate a simple, cost-effective, pulsed laser diode capable of competing with the Ti:Sapph for the purposes of entangled photon generation. The diode and driver are capable of pulsing at up to 60 MHz , with peak power exceeding 1 W and pulse energy in excess of 1 nJ , and with a spectral width narrower than 0.1 nm. I also demonstrate a pulsed, fully fiber-based, entangled photon source, with high entanglement quality (maximum concurrence of 0.985) and a high pair generation rate (0.15 pairs/pulse). The source is to our knowledge the first of its kind.

Keywords: Entanglement
Photonics
Quantum Optics
Advisor: Qian, Li LQ
Multimodal COACH System to Assist with Activities of Daily Living

Older adults with dementia often rely on caregivers for daily activities, resulting in a loss of confidence and independence. While many cognitive assistive technologies have been developed, limitations exist. The multimodal COACH system addresses these challenges by integrating speech and visual modalities with a socially assistive robot (SAR) to assist in handwashing. The system improves tracking performance using YOLO algorithms and facilitates human-robot interaction through speech with the SAR. In a study with healthy participants, the system achieved an 84.17% accuracy in visually detecting handwashing steps without prompts and an impressive overall task completion rate of 99.17%. Participants reported positive experiences, highlighting the robot's interactivity and engagement. This work evaluates the feasibility and effectiveness of using multiple modalities and robots, marking a significant step in system advancement. Ultimately, it aims to empower older adults with dementia to independently and safely perform a broader range of daily activities in their homes.

Keywords: Activities of Daily Living (ADLs)
Artificial Intelligence
Assistive Robotics
Conversational Interface
Dementia
Object Detection
Advisor: Mihailidis, Alex
Exploring the Impact of Minority Stress on Trauma and Dissociation Symptoms Among Sexual Orientation Minorities: A Mixed-Methods Study

The present study utilized a mixed-methods approach to explore the relationship between minority stress and trauma-related symptoms among sexual orientation minorities. The study posits that chronic identity-based stressors encountered by sexual orientation minorities may elicit mental health symptom commonly associated with trauma. The methods include a qualitative interview and quantitative self-report measures of minority stress, trauma symptoms, and dissociation symptoms. The study found a distinct relationship between elevated minority stress scores and an array of trauma-related symptoms endorsed in the qualitative interviews, including hypervigilance, emotion dysregulation, negative self- concept, and dissociation. Furthermore, the analysis revealed that trauma symptoms mediate the relationship between minority stress and dissociation symptoms, providing new insights into the underlying mechanisms that may influence mental health outcomes in this population. This research contributes to the call for innovative trauma frameworks that are inclusive and attuned to the lived experiences of sexual orientation minorities.

Keywords: dissociation
minority stress
sexual orientation minorities
trauma
Advisor: Gillis, Joseph R.
Ketamine for Bipolar Depression

Clinical trials have demonstrated therapeutic potential of intravenous (IV) ketamine in unipolar depression; however, its effectiveness and safety in treating bipolar depression (BD) remains uncertain. This thesis aimed to assess the efficacy, effectiveness, safety and tolerability of IV ketamine for BD. A systematic review was conducted to synthesize the currently available evidence on ketamine for BD. Additionally, a retrospective analysis was conducted, evaluating outcome data of outpatients with BD that received an acute course of four ketamine infusions. The systematic review found that 48% of participants receiving ketamine achieved response, whereas only 5% achieved response with placebo. Real-world data showed statistically and clinically significant antidepressant effects of ketamine in the overall sample (n=66). Preliminary evidence suggests IV ketamine has a favourable safety and efficacy profile for the treatment of BD. Future studies should focus on investigating the effects of repeated acute and maintenance infusions using a randomized study design.

Keywords: Bipolar Depression
Depression
Effectiveness
Ketamine
Suicide
Treatment-resistant
Advisor: Rosenblat, Joshua D
The Incidence and Function of Defensive Sound Production in a Nearctic Tiger Moth Community

We queried a community of Nearctic tiger moths for defensive sound production (clicks) when exposed to simulated predator stimuli, and measured several parameters of the phonoresponse to better understand how they deter predatory bats. We found that most species produced clicks and, within and between species, more responded to tactile stimulation than to ultrasonic stimuli (high frequency tone or calibrated bat attack sequence). Additionally, we found that most species respond early in the bat attack sequence, although there was a significant difference in when species responded. Using the dogbane tiger moth, Cycnia tenera, we determined when their clicks would arrive at an attacking bat relative to their returning echoes and how loud the clicks would be relative to these same echoes. We also measured click frequency and directionality. We found that the timing, sound level, and frequency point to an aposematic function, and we demonstrate that the clicks are directional.

Keywords: Aposematism
Arctiidae
Echolocation
Predator
Prey
Tiger moth
Advisor: Ratcliffe, John
Exploring NahK-mediated Metabolic Oligosaccharide Engineering with N-azidoacetylglucosamine Derivatives in Escherichia coli

N-acetylglucosamine (GlcNAc), a glycan precursor, has essential roles in bacterial survival. TheGlcNAc analog, N-azidoacetylglucosamine (GlcNAz) is a widely used glycan probe. Metabolic oligosaccharide engineering (MOE) employing NahK GlcNAc-1-kinase enables UDP-GlcNAz production and incorporation into the peptidoglycan of E. coli. In this work, the mechanism of GlcNAz import in E. coli was investigated using knockout mutant screens. Our results lead to a model for GlcNAz import, consisting of GlcNAz-6-phosphate import by the MurP-Crr phosphotransferase system, induction of transcriptional regulator NagC, and upregulation of GlcNAz import by galactose permease GalP. Additionally, the scope of this MOE strategy was explored toward novel GlcNAz derivatives and N-azidoacetylmannosamine (ManNAz). This revealed GlmU as a bottleneck to incorporating bulkier GlcNAz analogs while hinting at unexplored amino sugar metabolic pathways. This work sheds light on the promiscuity of bacterial sugar transporters and can inform the development of novel cell-permeable sugar probes and MOE strategies.

Keywords: Glycans
Metabolic labelling
Metabolic oligosaccharide engineering
N-azidoacetylglucosamine
Advisor: Nitz, Mark
Automated Morphological Grading of Human Blastocysts from Multi-focus Images

The live birth rate of in vitro fertilization (IVF) treatment cycles has remained stagnant at ~30% over the last decade. Yet with global demand for IVF treatment on the rise, there is mounting pressure to break through this long-standing plateau. The IVF community now turns its attention towards automated and data-driven Artificial Intelligence (AI) approaches for the critical task of blastocyst evaluation to potentially revolutionize the field. Despite it being routine for embryologists to grade blastocysts by viewing their morphology at multiple focal planes under a microscope, existing automated grading methods in literature predominantly use blastocyst images from a single focal plane as input. In this thesis, we design a novel CNN-based model architecture to harness the comprehensive morphology presented in multi-focus images for morphological grade prediction. Our method predicted the three grades (developmental stage, inner cell mass morphology, trophectoderm morphology) assigned to each blastocyst with ROC AUCs of 0.98, 0.95, and 0.97. Notably, our model outperformed comparable single-image models, as well as the mean performance of embryologists.

Advisor: Sun, Yu
Predicting Extubation Failure in Preterm Infants Born

In preterm infants, re-intubation is common and associated with morbidity. Predicting extubation outcome remains a clinical challenge. Our objective was to develop two prediction models: 1. Re-intubation within 7 days, and 2. Non-invasive respiratory support (NRS) failure within 72 hours. We conducted a retrospective study in 25 Canadian neonatal intensive care units, over 2.5 years, involving infants born 230/7 - 286/7 weeks gestational age, extubated from invasive mechanical ventilation. Predictors were chosen based on clinical relevance. A two-level generalized estimating equations approach was used to account for clustering. Model performance was assessed through discrimination, calibration, goodness of fit, and internal validation. Of 1816 included infants, 20% required re-intubation, and 29% NRS failure. Both models had good performance but varying discrimination: re-intubation model AUC 0.704 (95% CI 0.673 – 0.735), NRS failure model AUC 0.658 (95% CI 0.620 – 0.676). In conclusion, our prediction models may help to refine future models with the aim of improving extubation outcomes.

Advisor: Shah, Prakeshkumar
Residual Mandibular Growth in Different Facial Growth Patterns

Objective: To determine if significant differences exist in rates and amounts of post-peak residual mandibular growth in subjects with vertical, average and horizontal growth patterns. Methods: Untreated subjects with Class I characteristics from the AAOF Growth Legacy Collection were categorized into three growth pattern groups based on their change in the Y- axis from 9 to 16 years. Peak mandibular growth was determined using cephalometric measurements. Mandibular growth amount and rate were compared between groups at peak (T0), 2 years post-peak (T1) and 18 years (T2) using one-way ANOVA.Results: Inter-group differences in mandibular growth amount were not statistically significant. The mandibular growth rate between T1 and T2 was slightly lower in the horizontal facial type compared to average. Male and female subjects showed similar trends. Conclusions: No clinically significant differences in amount or rate of post-peak mandibular growth were found between different facial types or male and female subjects.

Advisor: Suri, Sunjay
The Association Between Cow Milk-Fat Percentage and Non-High-Density Lipoprotein Cholesterol in Young Children

In this thesis, the relationship between cow milk-fat percentage and non-high-density lipoprotein (non-HDL) cholesterol was investigated in 2–8-year-old children (n=2890) enrolled in The Applied Research Group for Kids (TARGet Kids!), a primary care, practice-based research network in Ontario and Quebec. Generalized estimating equations were used to evaluate associations between parent-reported cow milk-fat percentage and serum non-HDL cholesterol concentrations and odds of having high non-HDL cholesterol (≥3.75 mmol/L). Bootstrap resampling was used to assess whether volume of milk consumed mediated this association. Each percent increase in cow milk-fat was associated with a 0.024 mmol/L (95% CI: 0.005, 0.044; p = 0.01) increase in non-HDL cholesterol. Volume of cow milk mediated 28% of this association. Cow milk-fat percentage was not associated with the odds of high non-HDL cholesterol. Consumption of higher-fat cow milk was associated with small increases in non-HDL cholesterol, which may have implications for non-HDL cholesterol levels in adulthood.

Advisor: Birken, Catherine
Detection and Characterization of Pulse Field Ablation Lesion Guided by Polarization-sensitive Optical Coherence Reflectometry in Cardiac Tissue

Pulsed electric field ablation (PFA) is a new modality of cardiac ablation that uses electrical fields to cause non-thermal cell death over several hours, resulting in replacement fibrosis. Muscular tissue is known to exhibit birefringent properties and when the tissue is damaged and loses its ultrastructure there is a change in its optical properties. Polarization Sensitive Optical Coherence Reflectometry (PS-OCR) is an optical imaging technique that can detect changes in tissue birefringence in real-time. The objective of this project was to evaluate the ability of a PS-OCR system to detect acute changes in tissue birefringence during PFA which can predict the development of chronic lesions in the superior vena cava in a swine model. PS-OCR proved to be an effective method to guide PFA and lesion formation in real-time, assessing loss of tissue birefringence and potential electrical gaps. The system showed a sensitivity of 96% and a specificity of 83% to predict chronic lesion formation.

Keywords: Atrial fibrillation
Cardiac ablation
Electrophysiology
OCR
Polarimetry
Pulsed Field Ablation
Advisor: Verma, Atul
Investigating the Role of HDAC inhibition on Cell Fate Determination

As Waddington proposed, fate determination is maintained not only by a network of transcription factors but the superimposed epigenetic landscape. This epigenetic landscape governing and maintaining the earliest cell fate decisions post-fertilization remains elusive. Here I focus on epigenetic manipulation of murine blastocyst-derived stem cell lines (ESCs mainly, as well as TSCs), focusing on histone deacetylases (HDACs) and their associated complexes and their role in establishing repression of cell states after fertilization, with a specific focus on the totipotent-like state. Chemical inhibitors of HDAC isoforms are first assessed and their capacity to relieve repression on restricted blastocyst lineages in stem cell models. Class I HDAC1-3 inhibition of both ESCs and TSCs enable access to their restricted trophectoderm and epiblast lineages, respectively, after 6 days of treatment. HDAC1-3 inhibited cells replated at day 6 in optimized media and 3D non-adherent culture have the capacity to also self-assemble into blastocyst-like structures. Prior to turning on alternative lineage transcripts, around 3 days in 2D culture, totipotent-like transcripts (Zscan4, Dux and Muervl) are also expressed, suggestive of possible reprogramming through a totipotent-like state prior to restricted lineage access. I subsequently dive further into this mechanism of totipotent-specific transcript alleviation with HDAC 1-3 inhibition. Since HDAC1 through 3 do not act in isolation and are associated with four main complexes (NuRD, CoREST, Sin3a, and SMRT), chemical inhibitors specific to these complexes were tested using a Zscan4-Emerald mouse ESC line. Broad and narrow range general HDAC inhibitors were also tested alongside. HDAC 1 and 3 and associated complexes CoREST and SMRT, respectively, show most significant increase in Zscan4 endogenous protein after full treatment duration as well as most significant increase in key totipotent transcripts (Zscan4, Muervl and Dux). Therefore, results cumulatively suggest that HDAC 1 and 3 and associated complexes CoREST and SMRT are key players of the totipotency network, epigenetically.

Keywords: Blastoids
Epigenetics
HDACs
Reprogramming
Stem cells
Advisor: Cox, Brian J.
Early Detection of Polyneuropathy in Patients with Hereditary Transthyretin Amyloid Cardiomyopathy and Determining the Cost-Effective Treatment for Mixed Phenotype Patients

Transthyretin amyloidosis is a rare disease caused by the deposits of misfolded proteins known as amyloid. This disease is caused by misfolded transthyretin (TTR) proteins, that are produced in the liver and are deposited in various organs and tissues, especially in the heart and nerves. These TTR proteins are normally formed as stable tetramers; however, a mutation on the TTR gene could cause the dissociation of the TTR tetramer into monomers which would then form as TTR amyloid causing transthyretin amyloidosis (ATTR). Patients with ATTR may present cardiomyopathy and/or polyneuropathy. Although there is no cure for this disease, there are treatments available that would slow down the progression of ATTR and allow patients to have a better quality of life (QOL). The treatments include organ transplantation (liver/heart) or novel disease modifying therapies. This thesis focuses on detecting polyneuropathy among patients with hereditary transthyretin amyloid cardiomyopathy and determining its cost-effective treatment.

Advisor: Delgado, Diego H
The Association Between Prenatal Depression and Anxiety and Children's’ Sleep Patterns at Age 3: A Cohort Study

ABSTRACT Background: Behavioral insomnia of childhood has a prevalence as high as 25–30%, and has negative long-term consequences. Prenatal depression is a potential contributor to disturbed sleep patterns. However, few studies have examined children aged three and older.Objective: To evaluate the association between prenatal depression/anxiety and children's sleep patterns at age 3. A further aim is to establish whether maternal depression and anxiety in different trimesters have a differential effect. Methods: The dependent variables are maternal-reported child sleep latency, total sleep duration and nighttime awakenings. The main independent variables are the maternal depressive and anxiety symptoms assessed using the Patient Health Questionnaire score. Results/Conclusion: A multiple regression revealed a robust association between prenatal depression at 28-32 weeks of pregnancy and child awakening. While programming effects of maternal depression on child neurodevelopment may account for these findings, alternative explanations such as shared genetic risk require further consideration in future work.

Keywords: Child Health
Cohort
Depression
Developmental
Mental Health
Sleep
Advisor: Levitan, Robert RL
Piggybacking on UAV Package Delivery Systems to Enable Aerial Wireless Network in 6G

Various literature explored the idea of deploying unmanned aerial vehicles (UAVs) as last-mile package delivery agents or aerial wireless base stations in recent years. Despite the extensive exploration of these applications, nearly all of the studies assumed that the UAVs are serving just one service, and not both simultaneously; however, for reasons such as heavy traffic congestion in the sky, it seems more suitable for the UAVs to be serving both services concurrently. Stemming from the observation that there are various ongoing industrial projects in UAV-based package delivery, we investigate the possibility of piggybacking on UAV-based package delivery infrastructures to also provide wireless coverage, and address the problem of designing UAV trajectories that maximize the downlink cumulative sum rate of the ground communication users while simultaneously delivering packages under strict delivery time constraints with deep Q-learning. To conclude, we discuss several open problems in this new aerial network framework.

Keywords: 6G
Deep Q-Learning
Deep Reinforcement Learning
Multi-Purpose UAV
UAV-Assisted Communications
UAV-Based Delivery
Advisor: Sousa, Elvino
Assaying Fish Richness and Distribution Using eDNA in the Ecuadorian Amazon

To protect the Amazon's biodiversity from escalating anthropogenic threats, proactive conservation measures are crucial. Understanding the region's intricate biodiversity is pivotal for effective strategy development. This study introduces the first museum voucher-backed 12S rRNA reference library for fishes of the Ecuadorian Amazon, highlighting the pivotal role of curated libraries and museum collaborations in advancing biodiversity studies. Employing eDNA metabarcoding, this study yielded comparable outcomes to conventional sampling in estimating richness and species distributions, requiring fewer samples and reduced effort. The fusion of a reliable reference library and eDNA metabarcoding emerges as an enhanced tool for mapping species distributions, estimating richness, and monitoring environmental impacts. The study identifies the Napo drainage in Ecuador as exceptionally diverse, underscoring the need for targeted conservation in a region persistently affected by anthropogenic impacts. This study emphasizes the significance of integrating novel techniques and collaborative strategies for effectively identifying biodiversity in the Amazon.

Keywords: Amazon Biodiversity
Conservation
eDNA metabarcoding
Freshwater Fishes
Museums
Advisor: Lujan, Nathan K
Revitalizing Indigenous Languages in Toronto: The Responsibilities and Potential Roles of non-Indigenous People

In the place known as Toronto, Indigenous peoples are dedicating themselves to revitalizing and reclaiming their languages. How can the non-Indigenous people of this place end the neglect and assault on Indigenous languages and support their goals? I spoke with eleven mostly First Nations people who are engaged with languages in the Toronto area to ask for guidance. I learned about the different kinds of relationships and responsibilities that hold us together, including wampum belt treaties, reconciliation, our relationship with the land, and for some, common experiences of colonization or language oppression. I learned about the work that needs to be done, including: raising awareness, supporting Indigenous language naming, signage and arts, lobbying governments, land back, volunteering for grass roots organizations, decolonizing institutions, and perhaps learning the languages. This research is intended as a foundation for public education to stimulate informed solidarity and action in Indigenous language revitalization.

Keywords: Allyship
Anishinaabemowin (Ojibwe language)
Haudenosaunee languages
Indigenous language revitalization
Toronto
Two Row Wampum
Advisor: Wemigwans, Jennifer