VictorJuiz/thesis huggingface dataset:
Synthesis of Multifunctional Microbubbles through Precursor Microfluidic Droplet Generation

Microbubbles can resonate in response to ultrasound to enhance contrast for ultrasound imaging and to locally deliver therapy. This resonance depends on the microbubble size and shell properties. Here, a method was developed to produce perfluorocarbon gas filled microbubbles with the potential to encapsulate therapeutic molecules by lyophilizing size-controllable, lipid-stabilized precursor oil-in-water microfluidic droplets. Heat treating the precursor oil droplets increased microbubble yield by ~40%. Furthermore, microbubbles could only be formed by incorporating >= 6mg/mL of lipids into the oil phase of the droplets. Microbubble formation yield from the precursor droplets was ~40%. The final microbubbles were echogenic and could cavitate in response to ultrasound (18MHz at ~5.4MPa). Surprisingly, by adjusting the concentration of lipid in the water phase of the precursor droplets, liquid droplets could be formed via the spontaneous condensation of microbubbles after saline reconstitution of the lyophilized precursors.

Keywords: condensed
droplet
lyophilize
microbubble
microfluidic
ultrasound
Advisor: Matsuura, Naomi
Untethered Magnetic and Acoustic Micromanipulation for Microrobotic Assembly in Dry Workspace

Untethered robotic micromanipulators are devices that physically interact with components on the microscale (sizes less than a few millimeters), and usually within a remote workspace, that enhance the precision and accuracy of manipulation by an unaided hand. Addressing the low levels of dexterity, precise kinematics and dynamics, and versatility are the current limitations that have been the focus of recent studies. The two novel methods presented in this thesis use magnetic and acoustic fields to achieve dexterous and precise micromanipulation characteristics to tackle the current gaps. A magneto-acoustic system is developed for magnetic actuation, with sub-body-length precision, of magnetic microrobots for dry surface and levitated contactless micromanipulations and the performances of each method are characterized. The capabilities of both methods are shown by real-world microassembly demonstration for assembly of microscale-sized optical components. For the first time, a permanent magnet sphere was levitated open-loop with small magnetic and acoustic field magnitudes.

Keywords: Acoustic Levitation
Automated Assembly
Microassembly
Micromanipulation
Microrobotics
Untethered Manipulator
Advisor: Diller, Eric David
Age of Cow Milk Introduction and Childhood Growth

Recommendations on the age that children can start consuming cow milk vary between countries. In Canada and Denmark, cow milk can be introduced as early as 9 months; however, in most countries it is recommended to wait until 12 months. Through this thesis I aimed to determine if the age that cow milk is first introduced into the diet influences childhood growth. In this prospective study of healthy children enrolled in the TARGet Kids! cohort, introducing cow milk at a younger age was associated with greater height by age 3-5 years. Each month earlier that cow milk was introduced was associated with 0.03 higher height-for-age z score or 0.1 cm per month. There was no significant association between timing of cow milk introduction and adiposity. In this cohort of children aged 3-5 years starting to consume cow milk earlier in life contributed to gains in height, without adversely affecting adiposity.

Keywords: Child nutrition
cow milk
growth
Height
Advisor: Maguire, Jonathon
A Complete Portable and Low-cost Micro-opto-fluidic Raman Spectroscopic Measurement and Characterization System

There is a glaring, unmet demand for a healthcare analysis method which is non-invasive, rapid, portable, and flexible, to provide consistent results for novice and expert users alike. Such a technique would facilitate access to health solutions in rural settlements, where population health can suffer due to limited specialized facilities. Raman spectroscopy of biological fluids is ideal for this task. Widespread adoption requires a robust collection system and a model which can withstand routine spectrum variability, but current methods place the end-user in charge of these remedies. In this thesis we present a point-of-care system for fluidic analysis using Raman which eliminates sample preparation and optimizes analysis, independent of end-user proficiency. A micro-opto-fluidic device greatly enhances the Raman signal, and accompanying machine-learning suite optimizes preprocessing methods to compensate for routine signal variation. We demonstrate performance on artificial human tears and whole-blood, achieving user-independent predictive concentration precision below 500 microMolar.

Keywords: Biofluid Diagnostics
Machine Learning
Optofluidics
Photonic Crystal Fibers
Principal Component Analysis
Raman Spectroscopy
Advisor: Helmy, Amr S
Spinal Cord Injury and Medication Management: A Descriptive Qualitative Study Exploring the Experiences of Community-dwelling Adults in Ontario

Spinal cord injury or dysfunction (SCI/Dys) is a life-altering event that is often accompanied by numerous secondary complications, multimorbidity, accelerated aging and subsequent polypharmacy. This descriptive qualitative study aimed to explore the attitudes, beliefs and experiences of prescribed and unprescribed medications among community-dwelling adults with SCI/Dys living in Ontario. This study highlighted three main themes: the disruptive nature of medications, the fear of negative outcomes and the importance of medication self-management strategies. Findings showed that medication management is a complex and multifaceted process that does not occur in a linear fashion, and in order to gain a more comprehensive understanding of persons with SCI/Dys experiences with medication-taking, the lens through which these experiences are situated within must be broadened. Based on the findings from this study, recommendations for future practice, policy and research have been suggested.

Keywords: Medication management
Medication-taking
Polypharmacy
Qualitative
Self-management
Spinal cord injuries
Advisor: Guilcher, Sara JT
Physiological Consequences of Seasonality in Temperate Fishes: The Effect of Thermal Preferences on Energy Storage Strategies

Aquatic ectotherms are faced with seasonal fluctuations in metabolic rates and prey density that can drive distinct patterns in energy storage. Lipids are crucial for overwinter survival and successful reproduction in many aquatic organisms. My thesis investigated the effect of seasonality on lipid dynamics in fish with different thermal preferences. I conducted a comprehensive literature review of seasonal lipid levels in freshwater fishes. Then, I compared lipid and protein dynamics in a warm and cold water fish species sampled from Lake of Two Rivers in Algonquin Park. Seasonal lipid variation appeared widespread across thermal guilds, suggesting that energy acquired during warm months is universally important for overwinter survival and reproduction. Across-species, larger bodied fish had dampened seasonal lipid variation. Algonquin lake trout (cold water) exhibited more variable seasonal energy levels than smallmouth bass (warm water). These findings provide a new perspective on general physiological responses to seasonality in freshwater fish.

Keywords: Fish
Lipid
Seasonality
Winter
Advisor: McMeans, Bailey C.
Long Term Reproductive Health Outcomes in Women with Perisistent Symptoms Following Traumatic Brain Injury

Traumatic brain injury (TBI) is a public health concern, yet little is known about the long-term effects unique to women. This study examined the 1) feasibility of recruitment and study procedures; and, 2) long-term reproductive health outcomes in women living with TBI. A convenience sample of 10 women was consecutively recruited from the largest adult TBI rehabilitation program in Canada. Eligible participants were premenopausal women who sustained a TBI one or more years ago. Participants attended the research clinic and completed a structured questionnaire, Repeatable Battery for the Assessment of Neurological Status and provided a serum sample for Anti-Mullerian Hormone (AMH). Of the participants, 50% experienced low levels of AMH and all participants experienced high levels of symptomology when compared to the general population. These findings suggest monitoring of reproductive health in the long-term post TBI is needed and future research should be sufficiently powered to expand on these findings.

Keywords: anti-mullerian hormone
concussion
long-term
outcomes
reproduction
traumatic brain injury
Advisor: Colantonio, Angela
Investigating How Mammalian Cells Detect the Bacterial Metabolite, HBP

The innate immune system senses invading microbes through recognition of pathogen-associated molecular patterns (PAMPs) expressed by a variety of microbes. Our group recently discovered that a metabolic intermediate in lipopolysaccharide biosynthesis, heptose-1,7-bisphosphate (HBP), represents a new PAMP unique to Gram-negative bacteria. While the proteins, TIFA and TRAF6 have been definitively established as critical for cytosolic detection of HBP to drive an NF-κB-dependent pro-inflammatory response, other proteins upstream of TIFA in the HBPinduced signalling cascade remain unknown. Using an unbiased proteome-wide assay, we have identified 6 protein hits that are stabilized/destabilized by exposure to HBP. Genetic knockdown a top hit, Oxysterol-binding protein (OSBP)- related protein 3 (ORP3), indicates that it is involved in the HBP signalling cascade. Further examination of this potential HBP target will shed more light on the newly emerging HBP-mediated TIFA signalling pathway and give us a better understanding of the host immune response associated with Gram-negative bacterial infection.

Keywords: ADP-Heptose Biosynthesis
HBP-TIFA Signalling
Heptose 1
7- Bisphosphate (HBP)
Inflammation
NF-kB
TIFA
Advisor: Gray-Owen, Scott D
Super-Resolution Mapping of Basal Foot and the Characterization of a Novel Cilium in Human Airway Multiciliated Cells

During ciliogenesis, mother centriole-specific subdistal appendages undergo structural changes to become basal feet. This supramolecular assembly anchors the basal body to the microtubule cytoskeleton thereby regulating signaling in primary cilia and beating coordination in motile cilia. In mice, loss of the basal foot causes symptoms consistent with those observed in patients with Primary Ciliary Dyskinesia (PCD), an inherited lung disease. Despite its importance, the molecular structure of the basal foot remains to be characterized: its size is below the diffraction limit of conventional fluorescence microscopy and it is too large to be studied in vitro. By combining 3DSIM super-resolution microscopy, Electron Microscopy, and a novel tag-insertion mapping strategy, we discovered that the basal foot has a modular architecture conserved across different cilia. Moreover, we identified a new type of cilium in airway epithelial multiciliated cells with a potential mechanosensory role.

Keywords: basal foot
human airway epithelial cells
molecular architecture
motile cilia
primary cilia
super-resolution microscopy
Advisor: Mennella, Vito
Understanding the Role of the Co-Chaperone, Bcl-2 Associated Athanogene 5, in PINK1/parkin Dependent Mitophagy

Mutations in the genes encoding PINK1 and parkin are known to cause autosomal recessive familial Parkinson’s disease (PD). PINK1 and parkin act in a sequential pathway to identify and tag damaged mitochondria for selective autophagic degradation, a process termed mitophagy. The co-chaperone protein, BAG5, has been shown to interact with both PINK1 and parkin, and to inhibit parkin’s E3 ubiquitin ligase activity. Furthermore, BAG5 is known to enhance dopaminergic neurodegeneration in rodent models of PD. This thesis investigates the hypothesis that BAG5 negatively regulates PINK1 and parkin dependent mitophagy. We confirmed that BAG5 can interact with PINK1 and that this interaction requires functional BAG domains by co-immunoprecipitation. Fluorescence microscopy analysis revealed that BAG5 impairs GFP-parkin recruitment to depolarized mitochondria. This in turn impaired downstream mitophagy, as measured by a flow cytometry assay directly quantifying lysosomal engulfment of mitochondria. These findings demonstrate a potential role BAG5 in PD pathobiology.

Keywords: BAG5
Co-chaperone
parkin
Parkinson's disease
PINK1
Advisor: Kalia, Suneil
A Motor Phenotype of ɑ-Synuclein-Mediated Dopaminergic Neuron Dysfunction in a C. elegans Model

Parkinson’s disease (PD) is the most common neurodegenerative motor disorder, yet there are no treatments that ameliorate the underlying neurodegeneration. The protein alpha-synuclein (ɑSyn) has a propensity to aggregate in PD, leading to synaptic transmission failure and ultimately dopaminergic neuronal death. A major limitation of current C. elegans systems for studying ɑSyn-mediated toxicity is the lack of sensitive measures of early stage neurodegeneration. We identified a motor impairment that presents before neurodegeneration in an ɑSyn-expressing C. elegans model, and devised a methodology to measure this motor phenotype at the population level. We demonstrated that severity of the phenotype was associated with ɑSyn protein levels and dopamine signaling. Additionally, we found that proteasomal disruptions using pharmacological and genetic strategies significantly affected the motor phenotype. Thus, we have developed a new tool for studying ɑSyn-mediated toxicity that will aid drug discovery exploration and investigations into the molecular mechanisms of neurodegeneration in PD.

Keywords: 17-AAG
alpha-synuclein
C. elegans
coiling phenotype
motor impairment
Parkinson's Disease Models
Advisor: Kalia, Lorraine V
Functional Consequence of Human Missense Variants in Integrin-linked Kinase on Renal Branching Morphogenesis

Mammalian kidney function depends on the presence of a critical complement of nephrons connected to an intact collecting system. Malformation of these elements is characteristic of a phenotypically varied group of congenital kidney-urinary tract anomalies, termed CAKUT. Previously, we have shown that Integrin-linked kinase (ILK) acts via p38MAPK/ATF2 signalling to regulate murine renal branching morphogenesis. Yet, its contribution to human CAKUT is undefined. Recently, patients with CAKUT have been shown to possess point mutations in the ankyrin-repeat domain of ILK (ILK-T173I and ILK-N22S). Here, we show that these missense variants alter the MAPK signalling profile of mouse inner medullary collecting duct cells. ILK-T173I activates JNK and AKT/mTOR while ILK-N22S activates ERK. Phenotypic analysis of cultured embryonic mouse kidney explants demonstrated severe hypoplasia in ILK-T173I and a spectrum of phenotypes in ILK-N22S. Our results demonstrate that mutations in the ankyrin domain of ILK disrupt ILK-dependent signalling that regulate renal branching morphogenesis.

Keywords: hypoplasia
Integrin-linked kinase
MAPK
missense variants
renal branching morphogenesis
ureteric bud
Advisor: Rosenblum, Norman D
ProxyPhos Sensors: Beyond the Detection of Proximal Phosphorylation Motifs

This work involved the extensive characterization of a group of excimer-based fluorescent chemosensors, named ProxyPhos. ProxyPhos was designed to selectively detect proximal phosphorylation motifs on many phosphate-containing species, including phosphorylated peptides and proteins, inorganic phosphate species and nucleotides. The utility of these sensors in biological assays was demonstrated and was further expanded to include detection of negatively charged phospholipid membranes, including the detection of early apoptosis in mammalian cells and in bacteria. The potential future utility of ProxyPhos sensors as diagnostic tools is briefly explored. This work provides a strong foundation for the further development and application of ProxyPhos sensors in various biological assays and for use as diagnostic tools for the detection of apoptotic events, bacterial infection and disease states such as phospholipidosis, Alzheimer’s disease and certain cancers.

Keywords: Biomarker
Chemosensor
Detection
Diagnostics
Excimer
Phosphorylation
Advisor: Gunning, Patrick T
Beharry, Andrew A
Analysis of the Function of Protein Kinase C δ in Regulating Collective Cell Migration during Drosophila Oogenesis through Live Imaging

Border cell cluster (BCC) migration during Drosophila oogenesis has provided an excellent model to study collective cell migration. We have previously demonstrated that the serine/threonine kinase Protein Kinase C δ (PKCδ) is a regulator of BCC motility. My project aimed at examining the effects of altered PKCδ expression on BCC motility through live imaging, focusing on BCC migration behaviour and protrusion dynamics. Live imaging revealed that BCCs require normal levels of PKCδ expression to migrate at a normal speed. Increasing PKCδ expression levels in BCCs delayed detachment from the epithelium and significantly slowed down migration. Decreased PKCδ expression caused BCCs to migrate slower and less linearly during migration. In addition, PKCδ-deficient BCCs showed defects in cellular protrusion dynamics, including frequent bifurcations and multiple cycles of extension and partial retraction. In summary, my analysis contributed to understanding the function of PKCδ in regulating migration and protrusion dynamics during collective cell migration.

Keywords: Border Cell Cluster
Cellular protrusions
Collective cell migration
Confocal microscopy
F-actin
Live Imaging
Advisor: Godt, Dorothea
Spontaneous mystical experiences, mental health, and wellbeing: A qualitative study among atheist young adults

Spontaneous mystical experiences (SMEs) are common, spontaneously occurring, anomalous states, often involving spiritual/religious insight and change. Outcomes range from enhanced wellbeing to various mental health problems, and are mediated by spirituality/religiosity. This study employed a qualitative methodology to explore how atheist young adults interpret their SMEs and how their mental health and wellbeing are affected. Data was collected via semistructured interviews with adult participants, and analyzed using a grounded theory approach. Participants’ SMEs comprised an altered sense of self and connectedness, precipitating changes in self-identity, worldview, values, and goals that facilitated wellbeing across domains of functioning. Difficulties explaining the SME to self and others were linked to uncertainty and rumination, feelings of isolation and alienation, and worries about mental illness, suggesting that atheists may be at increased risk for mental health problems associated with SME. Implications for clinical practice and theory are provided, along with recommendations for future research.

Keywords: atheism
mental health
mystical experience
religion
spirituality
wellbeing
Advisor: Moodley, Roy
In Search of a Black, Indigenous Future: Awakening De/Anti-Colonization

This thesis demonstrates the need to retheorize ideas of decolonization as they relate to Black people and anti-Blackness. Placing critical texts together in a discursive engagement reveals their theoretical gaps. Numerous texts within discursive literature on decolonization pervasively absent Blackness. Those texts that do address Blackness tend to disregard Black people’s history and relationship to the Land prior to European colonial contact with the African continent. Instead, such works often discuss Blackness solely as it relates to enslavement and the afterlife of slavery (Hartman, 2007), in a stunted manner that belies white supremacist logics (Smith, 2010) and anti-Blackness. This thesis critically analyzes existing works about settler colonialism, anti-Blackness, white supremacy and de/anti-colonization theory.

Keywords: African
afropessimism
anti-blackness
anti-colonization
Black
Decolonization
Advisor: Dei, George S
Sudan to 'Sijui' and all black lives in-be-tween

In this thesis, I write from a personal, political and embodied place using first person accounts and my personal narrative as a Sudanese Muslim activist, artist, and organizer to speak back to the Canadian state and its creation of me. From a place of epistemic self-assuredness, I write, re-write, unpack and speak back to these constructions using Evocative Autoethnography and Critical Discourse Analysis. Drawing on an anti-Black racism theoretical framework, I humbly offer the beginnings of a new mode of analysis which I name Black turbulent consciousness where I present the term ‘sijui’ and ‘sijui situatedness’ as an additional entry point into existing notions such as liminality and in-betweenness. By engaging in an in-depth look at my location and linking my experiences to the condition of Black life/lives in this country, I aim to paint a larger depiction of anti-Blackness, islamophobia, and fear of a Black freedom(s) in the West.

Keywords: Activism
Anti-Black racism
Black Turbulent Conciousness
East African
Sijui
Toronto
Advisor: Walcott, Rinaldo
Parathyroid hormone and fetal growth in a pregnancy cohort in Dhaka, Bangladesh

Fetal growth restriction is prevalent throughout South Asia; yet, causes remain unclear. Parathyroid hormone (PTH) regulates calcium homeostasis and bone turnover. We investigated the association of maternal PTH with newborn anthropometry and regulators of PTH, in a pregnancy cohort in Dhaka, Bangladesh. This study was cross-sectional, using data from 492 participants enrolled in a prenatal vitamin D supplementation trial. The primary outcome was length-for-gestational-age z-scores (LAZ). Secondary outcomes included weight-for-gestational age z-scores (WAZ), head-circumference-for-gestational age z-scores (HCAZ), and rump-to-knee length. Contrary to our hypothesis, maternal PTH was positively associated with WAZ in univariate and multivariable models; however, the effect was small. In multivariable and path analysis models, vitamin D supplementation suppressed PTH, and fibroblast-like growth factor-23 (FGF23) was positively associated with PTH. This was the first study to identify an association between maternal FGF23 and newborn size. Future studies should further characterize the effect of prenatal FGF23 on birth size.

Keywords: fetal growth restriction
IUGR
Parathyroid hormone
pregnancy
skeletal growth
Advisor: Roth, Daniel E
Dissecting the Morphogenetic Circuitry of Candida albicans in Response to Phagocytosis by Macrophages

Morphogenesis is a major virulence trait in the leading human fungal pathogen, Candida albicans. Here, I sought to dissect the morphogenetic circuitry of C. albicans in response to phagocytosis by macrophages. A conditional expression library, covering ~40% of the genome, was screened for mutants that are defective in the yeast-to-hyphal transition upon phagocytosis. I identified 19 mutants that were viable but unable to filament within macrophages. Further functional analysis suggests a distinct morphogenetic program within this key phagocyte. Selection experiments were performed in the presence of macrophage lysate to restore filamentation in non-filamentous mutants. Whole genome sequencing was then used to identify suppressor mutations potentially responsible for the restored filamentation phenotype and to elucidate circuitry important for macrophage-induced hyphal growth. Lastly, characterization of macrophage lysate implicated a low molecular weight peptide as a novel filamentation inducing cue. Collectively, this work suggests new potential therapeutic strategies to combat life-threatening infectious disease.

Keywords: Candida albicans
Functional Genomic Screen
Fungi
Infectious Disease
Macrophages
Morphogenesis
Advisor: Cowen, Leah