VictorJuiz/thesis huggingface dataset:
Deoxygenation of Respiratory and Limb Muscles during Exercise in COPD and Healthy Adults

The overall objective of the thesis is to investigate deoxygenation of limb and respiratory muscles in chronic obstructive pulmonary disease (COPD), and to compare exercises that recruit these muscles in healthy participants.The first study, a scoping review that searched 7 databases, demonstrated that, compared to healthy participants, COPD patients display more rapid increases in vastus lateralis deoxygenated hemoglobin and blood flow; and lower muscle tissue saturation during cycling exercise. For the second study, two different exercises were compared in order to investigate alternative ways to train the inspiratory muscles. In healthy participants, we found submaximal intermittent neck flexion (INF) induced quicker and greater deoxygenation of sternocleidomastoid than inspiratory threshold loading (ITL) in healthy participants. INF induced significant metabolic activity of the sternocleidomastoid at a lower perception of effort than ITL. The merits of INF compared to ITL may be advantageous for applications of respiratory muscle training clinically.

Advisor: Reid, Darlene WDR
Rozenberg, Dmitry
Estimating Adult Age Using Radiographs of the Proximal Femur

Most skeletal age estimation techniques are based on assessing wear on joints or bone involution. Bone involution refers to microscopic bone loss. Pryce (2012) proposed a five-trait proximal femoral bone involution method to estimate age. The purpose of this research was to test Pryce’s (2012) age estimation method and to determine whether a Bayesian approach improves the method, using radiographs from the University of Toronto at Mississauga’s radiograph database. The objectives were to determine Pryce’s (2012) inter-observer reliability, to modify the method with transition analysis, and to test the new method. The revised method using 95%-CI and 50%-CI were created. Pryce’s (2012) method had a poor inter-observer reliability, but for the revised method, four of the five traits had an accuracy rate greater than 90%. The revised method can be invaluable when it is part of a multifactorial approach; however, further research is required to investigate potential limitations.

Keywords: age estimation
bone involution
forensic anthropology
Advisor: Rogers, Tracy L.
Flex and Flow: Microfluidic Platform for Application of Mechanical Stimulation in an Articular Joint-On-a-Chip

Osteoarthritis is a disease of the joint that greatly impacts the quality of life of 1 in 6 Canadians but has no known cure. In vitro models of the joint can enable advances in osteoarthritis research, but current systems are insufficient for adequately capturing the complexity of multi-tissue interactions and mechanical stimuli. A microfluidic joint-on-a-chip platform was developed for modelling osteoarthritis that incorporates cartilage, vascularized synovium, and circulating immune cells with dynamic mechanical forces. In particular, a compliant flexure-based mechanism was created to apply cyclic compression to an array of cartilage explants where their metabolic responses were measured under 10% and 30% compressive strain compared to static controls. Additionally, a model of the joint-on-a-chip fluidic network was created to test techniques for gravity perfusion. The compression and flow prototype subsystems establish capabilities required to replicate physiological mechanical stresses in a combined joint-on-a-chip for future evaluation of new treatments.

Keywords: cartilage
mechanical stimulation
microfluidics
micromilling
Organ-on-a-chip
osteoarthritis
Advisor: Young, Edmond W.K.
Tuning of Hydrogen Charge State in Silicon: Towards Improved a-Si/c-Si Passivation for Heterojunction Solar Cells

High-efficiency silicon heterojunction solar cells rely on the excellent surface passivation achieved by amorphous silicon on crystalline silicon surfaces. Anneals ranging from 100oC to 250oC improve the interfacial passivation quality for these interfaces, but the underlying physics is yet to be fully understood. This thesis investigates the basis of this improvement by modelling the charge state dynamics in response to thermal annealing vis-à-vis hydrogen present interstitially within silicon. Analytical models produced were used to calculate the atomic hydrogen concentration within silicon while stepwise anneals are carried out to achieve these conditions experimentally. A strong correlation between the minority carrier lifetime and the calculated atomic hydrogen content is observed. The dependence of improvement in passivation on doping concentration in silicon is discussed. Infra-red spectroscopy reveals that interstitial hydrogen charge state distribution influences silicon-hydrogen bonding configuration, indicating the role of the tuning of hydrogen charge states in improving passivation.

Keywords: Amorphous Silicon
Passivation
Silicon-Hydrogen
Advisor: Kherani, Nazir
Screening Anti-inflammatory Properties of Histone Deacetylase (HDAC) Inhibitors for Psoriatic Disease

Collectively known as the psoriatic disease, psoriasis and psoriatic arthritis (PsA) are immune-mediated inflammatory diseases in which patients have cutaneous and musculoskeletal inflammation. Despite current treatments, there remain unmet therapeutic needs in both psoriasis and PsA. In this thesis, I describe the screening of a new class of isoform-selective HDAC inhibitors in keratinocytes and macrophages as a potential anti-inflammatory treatment for psoriatic disease. Based on cytotoxic and anti-inflammatory evaluations, I identified 11 isoform-selective HDAC inhibitors that may exert anti-inflammatory effects by suppressing TNF-stimulated IP-10 secretion in HaCaT cells without inflicting cellular toxicity. Overall, my findings present the first study demonstrating the potential efficacy of isoform-selective HDAC inhibitors as anti-inflammatory agents in keratinocytes. Their use as anti-inflammatory agents in other psoriatic disease models warrants further investigation.

Keywords: Anti-inflammatory
HDAC
HDAC inhibitor
Psoriasis
Psoriatic arthritis
Psoriatic disease
Advisor: Chandran, Vinod VC
Gunning, Patrick PG
ORP3 Promotes ALPK1-TIFA Dependent NF-κB Activation upon Detection of Bacterial Heptose Phosphate containing Metabolites

The innate immune system identifies microbe-associated molecular patterns (MAMPs) via pattern recognition receptors (PRRs). Heptose phosphates (HPs) are bacterial-derived metabolic intermediates of lipopolysaccharide biosynthesis (LPS) and a novel class of MAMP. HPs bind the PRR Alpha kinase 1 (ALPK1) in the cytosol of mammalian cells, triggering TIFA dependent activation of NF-κB. Here I show that Oxysterol binding protein-like 3 (ORP3), originally identified in a screen for HP interactors, facilitates TIFA dependent NF-κB activity in response to HPs. I stably integrated a CRISPR construct into HEK293T cells with small guide RNAs (sgRNAs) targeting OSBPL3. I confirmed the knockout in the resulting monoclonal cell lines by sequencing and immunoblot. I found NF-κB luciferase reporter activity to be significantly reduced upon stimulation with ADP-heptose and heptose-1-phosphate (HMP) in ORP3 knockouts which suggests ORP3 contributes to the ALPK1-TIFA PRR response. I further propose three possibilities which may explain the mechanism by which this occurs.

Keywords: ALPK1
Heptose Phosphate
NF-κB
ORP3
OSBPL3
TIFA
Advisor: Gray-Owen, Scott SG
Nano-porous Polymer Thin Films from Polymerizable Bicontinuous Microemulsion Templates

Bicontinuous microemulsions (BµE) can be used as templates for porous membrane coatings with tunable chemistry and domain length. During polymerization, phase separations and domain length distortions have been commonly reported. This work investigates the effect of the coating surface as well as the crosslinkers, initiators, and surfactant concentration in preserving the BµE nanostructure in the thin film. Commercially available raw materials and atmospheric process conditions were used when defining a composition and a process that could be scaled. Small angle x-ray scattering (SAXS) confirmed it was possible to produce BµEs films with a layered structure consistent with a layered configuration calculated via the Net-Average Curvature (NAC) framework. FTIR, microscopy, and TOC analysis show these distortions via phase separations are reduced when polymerized on surfaces with low surface free energy. Filtration studies confirmed that pure water flux, permeability, and wettability of commercial membranes are significantly improved while MWCO is unchanged.

Keywords: Bicontinuous Microemulsion Polymer
Reaction Surface
Self-Assembly
Synchrotron
Thin Film
Ultrafiltration Membrane Coating
Advisor: Acosta, Edgar J
The Association between Maternal and Paternal Preconception BMI and Child zBMI Growth Rates

Background: The association between parental preconception BMI and childhood growth is unclear.Objectives: 1) To assess the association between maternal preconception BMI and child age- and sex-standardized WHO BMI z-score (zBMI) growth rates and mean zBMI in 0–10-year-olds. 2) To examine these associations in fathers. Methods: Piecewise linear mixed models were used to determine the association between maternal preconception BMI and child zBMI growth rates. Linear mixed effect models were performed to assess associations with mean zBMI. Associations with paternal preconception BMI were explored using similar methods. Results: Maternal preconception BMI was associated with mean child zBMI, and zBMI growth rate from 0-4 and 30-60 months. Accounting for maternal weight status, paternal preconception BMI was associated with mean zBMI in boys, and zBMI growth rates in boys of mothers with preconception overweight. Conclusions: The preconception period may be an important focus of early intervention to address child zBMI outcomes.

Keywords: Childhood growth
Childhood obesity
Growth rate
Obesity
Preconception
Prepregnancy
Advisor: Birken, Catherine S
BRCA1 in DNA Damage-induced Senescence and Sex Specific Outcomes following Repeated Mild Traumatic Brain Injury

DNA damage-induced senescence is proposed to be a pathophysiological mechanism driving brain dysfunction following repeated mild traumatic brain injury (rmTBI). Breast cancer type 1 (BRCA1) is a DNA repair protein, functions in the brain, and its dysregulation has been implicated in senescence and neurodegeneration. Using mice heterozygous for BRCA1, this study investigated the consequences of deficient BRCA1-driven DNA repair in DNA damage-induced senescence and its effects on sex-specific outcomes post-rmTBI. Behavioural outcomes and molecular markers for DNA damage, repair, and cellular senescence revealed sex differences in the DNA damage response (DDR) attributed to BRCA1, where females rely more on BRCA1 compared to males, resulting in impaired DDR signalling and diminished senescence onset specifically in females. With evident disparities in outcomes between males and females in mTBI, this study highlights the role of BRCA1 in sex-specific outcomes post-rmTBI, and introduces novel insights into the development of sex-specific treatments.

Keywords: BRCA1
cellular senescence
DNA damage
DNA repair
mild traumatic brain injury
sex differences
Advisor: Hazrati, Lili-Naz
Reactively Sputtered Aluminum Oxynitride Deposited at Ambient Temperature: A Material Platform for Tunable Optical Applications

The objective of this study is to assess the material system of Aluminum Oxynitride, deposited through a low-temperature reactively sputtered process, as a potential thin film material platform for tunable optical applications across a broad UV-NIR spectral region. A thorough design of experiment assessment of the compositional and optical properties of the thin films is carried out with respect to the deposition parameter space explored herein. The as-deposited films exhibit distinct relationships between the deposition parameters explored and the realized atomic compositions, extending from AlN on the one end to approaching the γ- and spinel- AlON. Moreover, the deposition parameters and compositions obtained correspond strongly to the calculated optical properties, which exhibit a maximum change in refractive index of Δn1550,720=0.4 and a Δn320=0.6. Supplemental electrical characterization was undertaken on samples deposited with and without oxygen, where improved ion interflow is observed in the oxygenated samples. The demonstrated experimental results suggest that the aluminum oxynitride material platform has the potential for broad-spectrum tunable photonic applications.

Keywords: Ionic diffusion
Tunable Materials
UV Optical Materials
Advisor: Kherani, Nazir P
Tissue Stiffness Mapping by Light Sheet Elastography

The interplay of biophysical forces and tissue stiffness in guiding morphogenesis has been increasingly investigated over the past decades. Stiffness is an intrinsic biomechanical property of tissues and can be evaluated through externally introduced deformation. However, an improved understanding of its dynamic role in morphogenesis is hindered by the insufficiency including invasiveness and low throughput of available stiffness mapping techniques. Here we introduce stiffness mapping of embryonic tissues through a technique we developed and refer to as light sheet elastography. By coupling ultra-low frequency shear waves with light sheet fluorescence microscopy, we achieved quantitative and non-invasive stiffness mapping of an intact organ-stage mouse embryo in vivo with a cellular mapping resolution. Having quantifiable evidence at various developing stages of interest will enable us to comprehensively examine how local tissue stiffness can affect the global morphogenetic patterns and manifest the role of mechanical cues in congenital malformations.

Keywords: Developmental Biology
Elastography
Non-invasive Imaging
Stiffness Mapping
Advisor: Sun, Yu
Hopyan, Sevan
Decentralizing Recombinant Protein Biomanufacturing using Cell-Free Synthetic Biology: The Development and Application of MANufacturing on the GO (MANGO)

Recombinant proteins are of extreme importance globally, comprising therapeutics, diagnostics, research tools, and more. Currently, recombinant proteins are synthesized using living hosts in well-resourced laboratories, then distributed globally – often refrigerated – along sometimes fragile supply chains. This model poses a challenge for low-resource and remote communities, and results in a slow-to-respond system when facing outbreaks and emergencies. Cell-free in vitro protein synthesis systems offer a portable small-scale alternative that can be freeze-dried into a room-temperature stable reaction pellet, then rehydrated at the point of need to initiate production of the protein of interest. While cell-free protein synthesis has been used to express proteins in laboratory settings, expansion into the field requires deployment of companion devices to automate the protein synthesis and purification process. This work reports the design, fabrication, and demonstration of MANGO (MANufacturing on the GO), a purpose-built device for portable small-scale protein production.

Keywords: Biomanufacturing
Biotechnology
Cell Free
Protein Expression
Synthetic Biology
Advisor: Pardee, Keith I
Targeting α-Synuclein Pathology Spread Using an α-Synuclein-specific Nanobody

Synucleinopathies, such as Parkinson’s disease (PD), are characterized by the intracellular accumulation of misfolded and aggregated alpha-synuclein (α-syn), which is mostly phosphorylated (p-α-syn). This aggregated α-syn can spread throughout the brain in a prion-like manner through templated misfolding. Small extracellular vesicles, like exosomes, are one mechanism by which α-syn is transferred intercellularly. First, we found that primary neurons develop progressive p-α-syn pathology following exposure to brain exosomes isolated from synucleinopathy-affected mice. We then tested a potential therapeutic, VH14-PEST, to reduce the spread of α-syn and its intracellular aggregation in a seeded-synucleinopathy cellular model. VH14-PEST is a single-domain antibody fragment (nanobody) targeting α-syn and previously shown to reduce its accumulation. Upon intracellular expression in primary neurons, VH14-PEST significantly reduced p-α-syn up to 14 days. This work demonstrates that exosomes can transport pathological α-syn contributing to its prion-like spread, and that reducing α-syn with nanobody expression is helpful in mitigating α-syn pathology.

Keywords: Immunotherapy
Neurodegeneration
Parkinson's Disease
Synucleinopathies
Advisor: Tandon, Anurag
Effects of Ionizing Radiation on the Biophysical Properties of Type I Collagen

Ionizing radiation is used routinely in clinical practice for diagnostic and therapeutic purposes. However, its effects on collagen, one of the most abundant structural proteins in the human body, are not well characterized. This study aims to assess the effects of ionizing radiation at three dose levels and in two hydration states on the morphology, mechanical properties, protein stability, and fluorescence lifetime of engineered acellular type I collagen samples. We demonstrate that ionizing radiation can alter the mechanical properties of collagen fibrils with minimal morphological change and that these changes arise from inter-fibrillar changes. We also demonstrate that the direction of mechanical change (stiffening or softening) and change in inter-fibrillar biochemistry (increased or decreased fluorescence lifetime) varies based on hydration status at the time of irradiation, suggesting different underlying mechanisms. Clinically, these changes may have implications in the pathophysiology and management of radiation-related sequelae, including osteoradionecrosis and cancer dissemination.

Advisor: Bozec, Laurent
Vitkin, Alex
Immunometabolism of Dendritic cells in Porphyromonas Gingivalis-stimulated Hyperglycemic Microenvironment

Chronic inflammation associated with immune dysregulation is the key mediator to connect periodontitis and diabetes mellitus. These two chronic diseases have a bidirectional relationship to each other. Dendritic cells (DC) have a significant role to link the chronic infection by regulating the activation of adaptive immune T cells. This project aimed to assess the impacts of periodontal bacterial lipopolysaccharides, diabetes mellitus hyperglycemia, and advanced glycation end product on DC immunometabolism and subsequent effect on their phenotype and immunogenic functions. Immunometabolism of DC were dysregulated with increased glycolytic activities in case of hyperglycemia. Exposure to lipopolysaccharides, and advanced glycation end product further led to polarization of DC toward an inflammatory morphology, phenotype, and increased cytokine secretions. DC function characterized by phagocytosis and T cell priming ability was impaired in hyperglycemia, suggesting an important role of DC in chronic inflammation and dysregulated adaptive immune responses following periodontal bacterial challenge.

Keywords: Dendritic cell
Hyperglycemia
Porphyromonas gingivalis
Advisor: Shrestha, Annie
Drug Delivery Methods to help Mitigate Antibiotic Resistance

The emergence of antibiotic resistance has become a public health threat. A major contributor to this global healthcare problem is poor efficiency of drug delivery. To help mitigate this threat, we present our work using the photothermally active polydopamine nanospheres (PDNS) to develop laser-responsive drug delivery systems. First, we investigated the impact of antibiotic structure on PDNS’s drug loading efficiency and laser-induced drug release. The results show that both structure and manner of loading are important determinants in optimizing the efficiency of PDNS as a laser-responsive nanocarrier. Next, PDNS was used to develop a laser-responsive drug-releasing hydrogel. Here, PDNS and two different liposomes, loaded with different but synergistically acting antimicrobials, were embedded in a hydrogel. Using PDNS’s photothermal capability and capitalizing on phospholipids’ different transition temperature (??), drugs were released sequentially, in a temperature-dependent manner. Overall, these PDNS-based systems promise to mitigate resistant development by providing spatial and temporal control to drug delivery systems.

Advisor: Sullan, Ruby
Remote Tissue Oxygenation Monitoring using Spatial Frequency Domain Imaging and Depth Sensors

Remote vital signs monitoring provides valuable information about a patient’s health and wellbeing, in a low-cost, non-intrusive way. These systems have a variety of applications, from detecting patient deterioration in clinical settings to monitoring at-risk individuals in at home. This thesis describes the design and development of a remote tissue oxygenation measurement system that can map tissue oxygenation from various distances. We use Monte Carlo simulations of light interaction with tissue to guide our system design. The prototype imaging system uses spatial frequency domain imaging to extract optical property values from tissue phantoms. We incorporate an independent depth sensor to increase the tolerance to subject motion. Additionally, we test preliminary motion compensation algorithms to improve motion robustness.

Keywords: Biophotonics
Remote monitoring
Vital signs
Advisor: Levi, Ofer
SARS-CoV-2 Antibodies in Human Milk: Validation of Methods and Response to Infection and Vaccination

We explored SARS-CoV-2 RNA, antibodies, and neutralizing capacity in milk from COVID-19+, milk bank, and vaccinated donors. We also validated a commercial SARS-CoV-2 IgA and IgG ELISA kit in milk, which demonstrated acceptable performance with 4% cross-reactivity/non-specificity for IgA and a new dilution suggested for IgG. SARS-CoV-2 RNA was absent in 1,254 samples from COVID-19+ and milk bank donors. IgA was found in 52.7% and 4.3% of COVID-19+ and milk bank donors, respectively. mRNA-1273 and short vaccine intervals induced significantly higher IgA and IgG than BNT162b2 and long intervals, respectively. Although neutralizing capacity was present after vaccination and infection, it only correlated with antibody presence after infection, however, was also present in samples before vaccination and in antibody negative samples after infection, suggesting contributions of other milk components. Overall, this work provides evidence for the safety and importance of human milk feeding during and after COVID-19 infection and vaccination.

Keywords: Antibody
COVID-19
Human Milk
Neutralization
SARS-CoV-2
Vaccine
Advisor: O'Connor, Deborah L
Generating Single Subunit Variants of the Fungal Fatty Acid Synthase: Toward Single ACP Domain Tracking

Fatty acid synthase (FAS) is an evolutionary conserved enzyme that enables de novo fatty acid biosynthesis in cells. Eukaryotic and some prokaryotic FAS proteins are highly efficient by embedding all necessary catalytic domains into a large biosynthetic machine. While the multi-step and iterative chemical process of fungal fatty acid biosynthesis has been known for decades, the mechanism of substrate shuttling between the catalytic centers in these mega-enzymes remains poorly characterized. This is largely due to the six-fold symmetry of the fungal FAS architecture and the fungal FAS gene split, encoding two polypeptides that assemble into one functional FAS subunit, which results in the inability to coordinate mutations within the functional unit. By fusing the two FAS chains and inserting a large tag (i.e. MBP tag), asymmetric fungal FAS complexes containing different chain types can be successfully purified via a tandem affinity purification scheme. Using cryoEM, an image processing pipeline capable of tracing and reconstructing the MBP-tagged chain with visible ACP densities was developed. Together, these results enable single-domain tracking to experimentally interrogate the FAS substrate shuttling mechanism.

Keywords: Acyl Carrier Protein
Fatty acid biosynthesis
Fatty acid synthase
Fungal FAS
S. cerevisiae
Substrate shuttling
Advisor: Mazhab-Jafari, Mohammad T