VictorJuiz/thesis huggingface dataset:
hCF-chip: A Model for Human Cardiac Fibrosis
Keywords: heart-on-a-chip
organ-on-chip

Cardiac fibrosis is a strong contributor to heart failure, but a lack of suitable human models limits our understanding of disease progression. We engineered a human cardiac-fibrosis-on-a-chip (hCF-chip) model that allows for real-time assessment of cardiomyocyte function and aims to provide an accessible platform for studying human cardiac fibrosis in vitro. The hCF-chip is a microfabricated device with co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes that uses transforming growth factor-β1 as a trigger for fibrosis. The hCF-chip shows increased expression of BNP and reproduces key hallmarks of cardiac fibrosis including decreased force of contraction, increased excitation threshold, increased extracellular matrix deposition, increased tissue stiffness, and an transcriptomic profile consistent with human cardiac fibrosis. Treatment with the standard of care drugs losartan and carvedilol decreased BNP secretion, the anti-fibrotic drug pirfenidone decreased tissue stiffness and BNP secretion, and the senolytics dasatinib and quercetin showed improved tissue functional parameters.
The Effect of Remyelination on Behavioural Recovery following Mild Traumatic Brain Injury in Mice
Keywords: behaviour
concussion
magnetic resonance imaging
myelin
traumatic brain injury

Mild traumatic brain injury (TBI) is a serious public health concern, representing 80-90% of all TBI cases. While symptoms are often transient, 10-15% of patients with mild TBI experience persistent symptoms. We investigated the role that white matter damage and repair may play in the etiology of symptom generation and recovery. Results indicate that mice with mild TBI experience working memory impairment at 3 days post-impact but recover to sham levels by 6 weeks post-impact. The optic tract, corticospinal tract, and anterior commissure were white matter regions found to be particularly vulnerable to damage following mild TBI. Results also indicate that preventing the formation of new myelin after mild TBI may prolong working memory impairment, suggesting that myelin repair may be necessary for functional recovery.
Prediction of Local Control in Brain Metastases following Stereotactic Radiosurgery Treatment
Keywords: Brain Metastasis
Local Control
Neuro-oncology
Radiomics
Response Prediction

Radiomics shows promise for predicting local failure (LF) in brain metastases (BM) treated with stereotactic radiosurgery (SRS). This investigation sought to determine if radiomic features provide complementary information to routinely available clinical variables. We trained a Random Forest (RF) classifier for LF prediction on a dataset of 408 BMs from 87 patients in a cross-fold validation manner, to observe the change in predictive power from including radiomic features alongside clinical features. The addition of any one of the top nine radiomic features to the set of clinical variables resulted in a significant (p
Investigating the Mechanistic Basis of T-cell Functional Regulation Mediated by PTPN2-WAVE2 interaction
Keywords: Autoimmune Disease
Cytokine receptor signaling pathway
Phosphatase
Protein-protein interaction
T-cell receptor signaling pathway
T-cells

PTPN2 is implicated in risk for various autoimmune diseases; however, the mechanistic interactions involved in PTPN2-mediated T-cell regulation remain elusive. The Siminovitch lab has identified actin regulatory protein WAVE2 as a PTPN2 interacting partner from T-cells. To assess the mechanism whereby this interaction influences T-cell function, we investigated the possibility that PTPN2-WAVE2 binding enables PTPN2 to shuttle nucleocytoplasmically to modulate regulators of T-cell responses. Here, we show that WAVE2 and PTPN2 translocate to the nucleus after IL-4 treatment, together with increased WAVE2 binding to PTPN2 C-terminus, thereby giving PTPN2 access to its nuclear substrates. PTPN2 nuclear translocation is impaired in WAVE2-deficient T-cells and pSTATs levels are significantly altered in WAVE2-deficient and overexpressing T-cells compared to wild-type after γc cytokine treatment. These findings show that WAVE2 may regulate PTPN2 nuclear translocation, consequently, regulating PTPN2-mediated dephosphorylation of nuclear pSTATs. Together, these results reveal a significant role for PTPN2-WAVE2 interaction in T-cell regulation.
Multi-scale Design of a Lithium Ion Battery Pack for Electric Vehicles
Keywords: Battery Heat Exchanger
EV Battery Pack Design
EV thermal management
Lithium ion battery module
Parallel liquid battery cooling
Pouch cell cooling

Lithium-ion batteries have emerged as the most affordable and convenient energy storage solution to power electric vehicles (EV). However, further advances are still needed to improve their performance, lifespan, and safety, which requires better control of their tightly coupled electrical and thermal responses. This thesis project designed, simulated, built, and tested a lithium-ion battery module with a focus on battery thermal management. The core component of this design is a state-of-the-art heat-exchanger made of a network of low-cost extruded microchannel tubes for parallel liquid-cooling of pouch cells, a lightweight aluminum structure that accounts for only 10\% of the total module’s weight and also provides structural support for the cells. The parallel cooling approach yields a superior cooling performance because it minimizes temperature gradients across the pack. This thesis also demonstrates the scalability of this modular battery design by building a functional battery pack that will be deployed in a concept EV.
Ketamine Prevents a Persistent Increase in α5 GABAA Receptor Activity Induced by General Anesthetic Drugs
Keywords: Anesthetic drugs
Cognitive deficits
Ketamine
Persistent effects
Tonic inhibition
α5GABAARs

GABAA receptors mediate two distinct forms of inhibition: phasic inhibition and tonic inhibition. In the hippocampus, tonic inhibition is mainly mediated by extrasynaptic α5 subunit-containing GABAA receptors, and sustained overexpression of these receptors contributes to cognitive deficits and mood disorders. Recently, ketamine, a NMDA receptor antagonist, was shown to prevent postoperative cognitive deficits and exert long-lasting antidepressant effects in patients. Given this relationship, we hypothesize that ketamine prevents a persistent increase in α5 subunit-containing GABAA receptor activity. Using whole-cell patch-clamp recordings, we show for the first time that ketamine prevents this overactivity in mouse hippocampal neurons in vitro. Furthermore, this effect is mediated by key proteins implicated in ketamine’s antidepressant actions including BDNF and GSK3β, but not by inhibition of NMDA receptors. Interestingly, ketamine acts through both neurons and astrocytes to prevent this overactivity. Our study provides a novel mechanism for the cognition-sparing and antidepressant properties of ketamine.
Single Cell Profiling of Signaling Pathways and Phenotypic Marker Expression in Philadelphia-like B-cell Acute Lymphoblastic Leukemia
Keywords: Acute Lymphoblastic Leukemia
B cells
Cancer
Mass Cytometry
Philadelphia-like

B-cell Acute Lymphoblastic Leukemia (B-ALL) is the most common childhood cancer, but also occurs in adults. It is caused by a broad spectrum of genetic alterations which are used for risk stratification. Across all ages, the Philadelphia-like (Ph-like) subtype is associated with lower survival rates. Kinase activating mutations that converge on either ABL or JAK2 signaling are found in >80% of Ph-like cases. Although clinically approved targeted therapies are available for both subgroups, there is currently no test to rapidly identify them. Therefore, I built a mass cytometry panel to profile signaling and phenotypic markers in 7 BCR-ABL and 4 Ph-like samples. I identified blasts with activating ABL or JAK2 mutations based on expression of pSTAT5 and its reduction by targeted inhibitors. Furthermore, I distinguished Ph-like and BCR-ABL specific clusters that differed in CD14 and CD127 expression. My thesis demonstrates how mass cytometry can be used to identify Ph-like samples.
Uncovering Differences in the Learning Cultures of the Engineering and Education Departments
Keywords: engineering education
interdisciplinary collaboration
learning culture

This thesis examines the influence of a discipline on the learning culture exhibited and perpetuated within the engineering and education department through open-ended interviews with 10 graduate-level faculty, in a major Canadian public university. The research uncovers how students perceive of what is valued as knowledge and the processes that their discipline encourages them to use in the pursuit of new knowledge through a grounded theory approach using ten professors’ perceptions on how learning occurs within their disciplines. The research question motivating this study is: What differences can be understood between learning cultures in engineering and education departments? Findings highlight that ways of thinking, critical learning, dealing with uncertainty and training of graduate students are informed by disciplinary expectations. The differences in the ways individuals learn and reason based on their academic identities will lead to a better understanding of one another and provide insight into ways to collaborate effectively.
No Effect of Leucine-enriched Essential Amino Acids on Myofibrillar Protein Synthesis and Strength or Soreness Recovery after a Novel Bout of Resistance Exercise in Young Recreationally Active Males
Keywords: essential amino acids
performance
post-exercise recovery
protein synthesis
stable isotopes

We examined the effect of a single dose of leucine enriched essential amino acids (LEAA) on myofibrillar protein synthesis (MyoPS) up to 4h and thrice daily LEAA on muscle strength and soreness up to 96h after a novel bout of lower body resistance exercise in recreationally active young men. Exercise increased MyoPS (by oral D2O) with no difference between LEAA and placebo (by or L-[ring-2H5]phenylalanine) over 1.5-4h of recovery. Isokinetic peak torque at 270°/s and 60°/s decreased ~27% and ~26%, respectively, at 48h and returned to baseline by 96h with no difference between conditions. Total muscle soreness increased ~83% at 48h and returned to baseline by 96h with no difference between conditions. Small to large effect sizes (0.21-0.95) were in favor of LEAA for total muscle soreness and total peak torque over 96h of recovery. LEAA does not enhance acute MyoPS and has equivocal effects on performance recovery after exercise.
Close, but not Quite: Memory Accuracy Across Spatial Frames of Reference in Cognitive Aging
Keywords: Aging
Frames of Reference
Spatial memory

Aging is associated with deficits in spatial memory for object locations across egocentric and allocentric spatial frames of reference. However, little is known about how this age-related decline interacts with cognitive status. In this study, we used desktop virtual reality to compare object location memory across spatial frames of reference in older adults, both healthy and at-risk for mild cognitive impairment, relative to younger adults. A coarse-grained accuracy measure was not sensitive to differences in task performance across frames of reference driven by cognitive status. With a fine-grained measure of accuracy, healthy older adults showed no impairments relative to younger adults except when the task required a switch from an egocentric to an allocentric frame of reference. This condition also failed to differentiate healthy from at-risk older adults. Taken together, these findings provide novel insights into the interaction of cognitive status and aging for spatial memory across frames of reference.
The Proteomic Architecture of Human Fetal Neurogenesis
Keywords: cerebral organoids
development
fetal
neurogenesis
proteomics

Fetal neurogenesis is a highly complex process that produces the full complement of neurons required for an adult brain yet many of its regulatory mechanisms are unknown. Here, we aim to elucidate some of these pathways by conducting a spatial proteomic profile of human fetal brain regions (n = 8) implicated in fetal neurogenesis. We quantified ~2000 proteins and identified region-specific proteins which may play a functional role in neuronal maturation. Well-established regional markers such as SATB2 in the cortex were found to be significantly upregulated (FDR
Path Integration Using Eye and Hand Movements
Keywords: entorhinal cortex
eye-tracking
path integration
spatial navigation
tablet

Although there is neurological evidence suggesting that the entorhinal cortex performs similar computations on whole-body and eye movements in space, behavioural evidence of the same is lacking in the current literature. Humans can track current position relative to the starting point of a journey using only self-motion cues through the process of path integration. We tested if path integration, a process dependent on the entorhinal cortex, uses movements other than whole-body movements to update self-position. We used novel eye-tracking and tablet tasks in which participants followed a sequence of locations guided by visual or auditory cues. Consistent with results from other real-space studies, we found that participants used different strategies to update position in space depending on task demands. Retracing behavior seen with hand and eye movements suggests that retracing precedes computation of the homing vector during real-space path integration, but future studies are necessary to investigate this further.
Characterization of AcrIE8: A Novel Family of Type I-E Anti-CRISPR Proteins
Keywords: anti-CRISPR
bacteria
bacteriophage
CRISPR

Bacteria and their viruses (phages) have been undergoing an evolutionary arms race for billions of years. One of the antiphage defense systems bacteria employ is CRISPR-Cas; however, some phages have evolved to inhibit this system by expressing small proteins called anti-CRISPRs. The work of this thesis focuses on characterizing the diversity, function, and mechanism of action of a novel family of anti-CRISPRs called AcrIE8. Putative homologs of AcrIE8 were tested for their anti-CRISPR activity against the type I-E CRISPR-Cas systems of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica. AcrIE8 robustly inhibited both the P. aeruginosa and E. coli systems but not the S. enterica system. Furthermore, initial work on elucidating the AcrIE8 mechanism of action suggests an interaction with the CRISPR-Cas complex to prevent it from binding to its target DNA. Understanding the diversity of anti-CRISPRs and how novel families function will provide greater insights into the evolutionary arms race between bacteria and phages.
Development, Characterization and Evaluation of Advanced Thermoplastic and Metal Hybrid Composite Structure
Keywords: Adhesion of dissimilar material
Hygrothermal degradation
Mechanical interlocking
Polyketone
Polymer degradation and stability
Polymer-metal hybrid composites

There is a need for the development of advanced thermoplastic and metal hybrid composites structures in automotive, aerospace and biomedical applications to reduce weight and improve the properties of the constituent materials. Herein, a novel thermoplastic, polyketone (PK), was studied in aggressive hygrothermal condition, in order to understand and characterize the alterations in mechanical, chemical and thermal properties of the polymer in application. A novel polymer-metal hybrid composite fabrication process by mechanical interlocking was then developed, with PK and a chemically etched aluminum, to improve the barrier and structural stability of the PK material. The adhesion performance of the PK-aluminum composite structure was optimized and studied. Finally, various thermoplastics, polyethylene (PE), polypropylene (PP) and polyphenylene sulfide (PPS) were constructed with the mechanical interlocking adhesion mechanism to form novel thermoplastic-metal hybrid composites, and each hybrid composite system was optimized and studied.
System-level Design of Coded-exposure Cameras for Computational Imaging Applications
Keywords: coded-exposure
computational imaging
systems
time-of-flight

This thesis presents several contributions to system-level design, implementation and testing of computational cameras for computer vision applications, such as coded-exposure imaging and time-of-flight imaging. The contributions are in the areas of PCB design, firmware design and interfacing software design, and are elements of a larger-scale team-based research project on next-generation computational cameras. Three printed circuit boards (PCBs) and a re-usable firmware bridge have been designed to implement, test and deploy three custom cameras. The functionality of two camera designs in coded-exposure imaging has been validated by our team through two single-frame imaging applications: photometric stereo imaging, and multispectral imaging, respectively. The distance measurement performance of the third camera design in time-of-flight imaging has been improved by a pulse-based time-of-flight distance sensing method and verified experimentally.
The Role of NOD1 in the Control of the Non-canonical Inflammasome
Keywords: immunity
Inflammasome
LPS
Nod1
PRM
sepsis

During infection, one of the cell’s defense mechanisms is to activate the inflammasome. Activation results in a form of cell death called pyroptosis and in the release of pro-inflammatory cytokines. Although normally a protective mechanism that aids in the clearance of intracellular pathogens, widespread and constitutive activation has been implicated in several inflammatory disorders. There exists an inflammasome independent of caspase-1 known as the non-canonical inflammasome. Although this inflammasome has been well studied in murine macrophages, how it functions in cell types other than immune cells is poorly understood. We found that NOD1 is required for proper activation of the non-canonical inflammasome in the human intestinal epithelial cell line HCT116. Interestingly, NOD1’s role did not translate to murine macrophages suggesting that it’s role may be unique to epithelial cells. Our research reveals a novel form of inflammasome activation unique to epithelial cells that could provide insight into gut innate immunity.
A CRISPR/Cas9-Mediated FACS Screen Reveals Novel Regulators of Wnt/β-catenin Signalling in Human Embryonic Stem Cells
Keywords: CRISPR
ESC
METTL3
screen
signaling
Wnt

An important signalling mechanism in stem cell fate determination is the Wnt/β-catenin signalling pathway, which is critical in self-renewal and determination of multiple cell lineages. However, the underlying mechanisms involved in regulating Wnt signalling during self-renewal and differentiation of human embryonic stem cells (ESCs) are not fully understood. This thesis aims to identify and characterize regulators of Wnt/β-catenin signalling in hESCs using a CRISPR-Cas9 genome-wide screening approach. A fluorescent GFP reporter was knocked into the AXIN2 locus of a human ESC line containing an inducible Cas9, to enable screening using flow cytometry for regulators of AXIN2 expression. Validating our approach, several known regulators of Wnt/β-catenin signalling were identified. Novel regulators were also identified as negative regulators of AXIN2 expression, including METTL3 and other genes involved in the N6-methyladenosine RNA modification. While the mechanism remains to be elucidated, this study uncovers a novel link between m6A and Wnt/β-catenin signalling in hESCs.
Using C. elegans as a Drug-discovery Model for the Childhood Liver Disease Progressive Familial Intrahepatic Cholestasis 3
Keywords: C. elegans
chemical genetics
chemical screen
molecular genetics
PFIC3
pharmacology

Progressive familial intrahepatic cholestasis 3 (PFIC3) is a rare liver disease with limited treatment options. PFIC3 is caused by mutations in the phosphatidylcholine transporter, ABCB4. ABCB4 transports phosphatidylcholine to the cell surface to alleviate the hepatotoxicity of bile acids. The C. elegans homologue of ABCB4, PGP-14, is a probable phosphatidylcholine transporter whose mutations lead to sphingomyelin deficit in the pharynx. We postulate that sphingomyelin abundance sensitizes wild type worms to hydrophobic nematocidal molecules including wact-190. In my project, I exploited C. elegans pgp-14 mutants to identify drugs that circumvent the loss of phosphatidylcholine transporters. I screened 2,560 compounds and identified three robust suppressors of pgp-14’s wact-190 resistance: terconazole, nicardipine and amiodarone. I found that terconazole alone can suppress the sphingomyelin deficit of pgp-14 mutants. Therefore, terconazole may induce phosphatidylcholine transport in C. elegans. This work has the potential to make an impact on the health of children afflicted with PFIC3.
Circulating Osteocalcin and Memory Performance in People with Type Two Diabetes Mellitus and in the Mouse High Fat Diet Model
Keywords: Bone
Diabetes
Metabolism
Neuroendocrinology
Osteocalcin

Osteocalcin circulates in carboxylated (cOCN) and uncarboxylated (unOCN) forms, and unOCN is thought to have widespread neuroendocrine effects. In type 2 diabetes mellitus (T2DM), circulating cOCN and unOCN concentrations are lower, and cognitive decline is accelerated. In the high fat diet mouse model of T2DM, injections with unOCN improved cognition in a puzzle box test, and when combined with exercise, enhanced cortical expression of brain derived neurotrophic factor. In people with T2DM, fasting serum concentrations of unOCN were significantly associated with long-delayed free recall (β=0.110, p=0.010), as assessed by the California Verbal Learning Test (2nd Ed.) controlling for age, sex and HbA1c. The results show cognitive benefits of unOCN treatment in animals, highlight neurobiological benefits of unOCN when combined with exercise, and identify the relevance of a bone-derived neuroendocrine mediator in human memory.
Alternative Splicing of Exon 5 in GluN1 Controls Glycine-stimulated Recruitment of AP-2 to NMDA Receptors
Keywords: alternative splicing
NMDA receptor

The number of surface expressed NMDA receptors (NMDARs) at synapses is dynamic and undergoes clathrin-dependent endocytosis. Aside from gating, glycine triggers the recruitment of the endocytic AP-2 adaptor protein complex to NMDARs and primes them for endocytosis. Here, I provide evidence for the involvement of tyrosine kinases and phosphatases in glycine-mediated AP-2 recruitment. Furthermore, I demonstrate glycine-priming depends on the splicing state of GluN1 exon 5 by measuring glycine-mediated AP-2 binding to endogenous NMDARs from transgenic mice that either completely lack or contain exon 5. Glycine induced AP-2 recruitment and dephosphorylation events at the C-terminus of exon 5-lacking NMDARs, which were absent in exon 5-containing NMDARs. Moreover, the inclusion/exclusion of exon 5 alters basal phosphorylation levels at sites implicated in NMDAR trafficking. Thus, these findings suggest exon 5 may selectively control the stability of cell-surface NMDARs and expands our understanding on GluN1 splice variants and their impact on intracellular signaling.