VictorJuiz/thesis huggingface dataset:
The Evolution and Molecular Basis of Substrate Specificity in 3-Ketoacyl-CoA Synthases from Populus trichocarpa
Keywords: fatty acid biosynthesis
lipid synthesis
natural product biosynthesis
plant biochemistry
substrate specificity
very-long-chain fatty acids

3-Ketoacyl-CoA synthases (KCSs) catalyze the substrate specific elongation of very-long-chain fatty acids (VLCFAs), precursors to membrane lipids and plant cuticular waxes. Though members of the large KCS family have been shown to use diverse substrates, the molecular basis for their substrate specificity is still unclear. In this thesis, a KCS gene cluster in poplar (Populus trichocarpa) was used to examine the evolution and molecular determinants of VLCFA substrate specificity. Characterization of five paralogs showed differential preferences towards substrates based on carbon length, saturation, and stereochemistry. Furthermore, the paralogs showed differential inhibitor sensitivity in response to K3 herbicides. Homology models, site-directed mutants, and chimeric proteins were used to identify two key regions (helix-4 and position 277) as being major determinants of substrate specificity, results which were corroborated with a more distantly related KCS. Together, these results shed light on key molecular changes driving the evolution of KCS substrate specificity.
Effects of High-intensity Interval Training on Blood Lactate Levels and Cognition in Healthy Adults: Systematic Review and Meta-regression
Keywords: cognition
exercise
high-intensity interval training
lactate

Background. High-intensity interval training (HIIT) may confer cognitive benefits through apathway involving lactate – an exercise metabolite. R1: Individually, what is the work-interval duration, work-interval volume, work-to-rest ratio, and session volume that is most effective in increasing peripheral lactate accumulation. R2: What is the relationship between peripheral lactate levels and post-exercise cognitive performance in healthy adults? Methods. R1: Network meta-analysis, categorical meta-analysis, and mixed effects meta- regression were performed. R2: Correlation and determination coefficients were generated. Results. R1: A low work-interval volume, medium session volume, and low work-to-rest ratio may elicit peak peripheral lactate accumulation. R2 Hypotheses: i) higher blood lactate post- HIIT increases interference performance for a longer duration, and ii) predicts better interference performance at 30 mins post-HIIT. Discussion. The above parameters may elicit peak peripheral lactate levels, which may be related to improved interference performance post-exercise. Our findings need to be validated using randomized controlled trials.
Improving Biosensor-based Circuits for Dynamic Control of Metabolic Pathways
Keywords: Biosensor
Dynamic control
Metabolic Engineering
Model-based analysis
Synthetic Biology

Bioproduction of chemicals in microorganisms using renewable feedstocks is a sustainable and greener alternative to traditional processes. Dynamic control of metabolism using biosensors has evolved as a common approach to partition cellular resources efficiently However, biosensor development requires several iterations of DBTL cycles to optimize for any application. In this work, we modeled and studied the effect of various parameters on the switching characteristics of an autonomous biosensor-regulator system, qCRIPSRi by simulating the dynamics of the circuit and performing sensitivity analysis. In addition, the effect of stringency of transcriptional activator LuxR on the switching characteristics and dynamics was investigated and validated through in vivo experiments. We also designed and modeled a novel biosensor architecture that enables tuning dose-response curve using small molecule inducers. Furthermore, we demonstrated the ability of the system to tune dynamic range, threshold, and sensitivity of dose response curves of adipic acid and resorcinol biosensors in silico.
Relating Patient-specific Computational Fluid Dynamics Simulations to Coronary Artery Bypass Graft Remodeling
Keywords: computational fluid dynamics
coronary artery bypass graft
patient-specific modeling
vascular remodeling
wall shear stress

The benefits of coronary artery bypass graft (CABG) surgery are limited by graft failure, and the underlying mechanisms remain incompletely understood, though they are likely related to hemodynamics. Contributing to a better understanding of the mechanisms that lead to graft failure is the goal of this thesis. Patient-specific image-guided computational fluid dynamics (CFD) simulations were performed in 24 bypass grafts of 10 participants 1 month after surgery. Several hemodynamic measures were obtained from the 1-month CFD simulations and compared to existing clinical measures of bypass graft function. All measures were then correlated to graft lumen remodeling measured 1 year after surgery, as remodeling may precede graft failure. This thesis demonstrated for the first time prospectively a significant correlation between 1-month abnormal wall shear stress area derived from CFD and 1-year graft lumen remodeling, which suggests that abnormally low WSS could potentially play a mechanistic role in graft failure.
Improving Metabolic Modelling by Considering Small Molecule Regulation
Keywords: Enzymatic Reaction
Kinetic Parameter
Mathematical Modelling
Metabolic Regulation
Metabolism
Proteome

Metabolism is a densely connected network of enzymatic reactions, and regulatory interactions, which fuel the cell with biomass building blocks. Organisms modulate their metabolism by changing the capacity of metabolic enzymes– termed proteomes when exposed to environmental stresses. Small Molecule Regulation (SMR) is an essential component of the metabolism that enables cells to adapt to environmental fluctuations. However, it has not been incorporated into the metabolic models extensively. In this project, we have proposed a workflow to assess the accuracy of mathematical models for proteome demand calculation after integrating them with the kinetics of metabolic regulation. Here, we have developed a standard database that provides in vitro kinetic parameters of 9,814 species. Then, this database was used to generate the inhibition power imposed on 3,883 enzymes of 972 organisms. Finally, we showed that the accuracy of traditional models improved after incorporating the SMR into protein abundance calculation in Escherichia coli.
Computational Modeling of Closed-loop Geothermal System
Keywords: biodiesel processing
biofuel processing
closed-loop geothermal
geothermal energy
phase change materials
renewable energy

Emerging closed-loop geothermal systems have the potential to offer dispatchable energy without the limitations of conventional geothermal technology. However, to be competitive, closed-loop geothermal requires a fluid that exceeds water with respect to heat capacity and thermosiphon effect. Employing phase change slurries (PCS) is one strategy to enhance the performance of closed-loop systems. A model was built to assess the viability of PCS-based closed-loop geothermal, the result of which shows 12.5% enhancement in thermal output compared to the water base case and achievement of additional energy by removing the need for pumping. To take advantage of the uniquely high-pressure and high-temperature conditions within the loop, idea of biofuel processing inside the loop has been proposed. A numerical model was built to assess the viability of this idea. An economic analysis of results shows that biofuel processing in the geothermal loop could potentially outperform electricity generation from water-based geothermal loop.
Characterization of the Phage Protein LES4-4 and its Impact on Quorum Sensing in Pseudomonas aeruginosa
Keywords: Anti-phage defence
Bacteriophage
Cell signaling
Phage genes
Pseudomonas aeruginosa
Quorum sensing

Bacteria protect against virus infection using a variety of anti-phage defence systems, many of which are regulated by quorum sensing. While findings have been limited to phage proteins that inhibit individual defences, recently an anti-quorum sensing protein (Aqs1) was discovered to inhibit LasR, a global transcriptional regulator of quorum sensing. This suggests that phages can prevent the activation of numerous defences simultaneously. LES4-4 is a phage protein that shares 61% protein sequence identity with Aqs1. Herein I show that LES4-4 interacts with PilB, the Type IV assembly ATPase. The interaction with PilB resulted in inhibition of twitching motility, increased resistance against pilus-dependent phage infection, and reduction of pili on the cell surface. In addition, a bacterial two-hybrid assay indicates that LES4-4 binds Vfr, a positive transcriptional regulator of LasR – suggesting that LES4-4 may also disrupt quorum sensing in bacteria.
Investigating Metabolomic and Transcriptomic Signatures of Metabolic Dysfunction in Antipsychotic-naïve Patients
Keywords: Antipsychotics
Diabetes
Metabolomics
Psychosis
Transcriptomics
Weight Gain

Psychosis spectrum disorders (PSDs) are characterized by metabolic dysfunction, arising from intrinsic and external factors, including antipsychotic (AP) treatment. Transcriptomics and metabolomics may help explore underlying causes of the metabolic comorbidity. The thesis comprises two studies. In study one, peripheral transcriptomic datasets of AP-naïve first-episode psychosis patients, early dysglycemia patients, along with hypothalamic and hippocampal datasets of central insulin perturbation rodent models were meta-analyzed to identify overlapping gene expression signatures. Overlapping gene expression signatures included pathways of endoplasmic reticulum stress, mitochondrial dysfunction, lipid metabolism, inflammation, and neuroplasticity. In study two, 25 AP-naïve cases and 6 controls underwent metabolomic and metabolic measures at baseline. Cases were followed over 12 weeks of AP treatment. Fatty acids distinguished AP-naïve cases from controls. Baseline adrenic acid was higher for cases who gained weight. Transcriptomics and metabolomics may identify biomarkers of metabolic dysfunction intrinsic to PSDs and predict individuals at risk for AP-induced weight gain.
Community Pharmacists as Antimicrobial Stewards: A Focus on Acute Otitis Media
Keywords: acute otitis media
antimicrobial stewardship
community pharmacy
pharmacists

Background: Programs that optimize antibiotic use in primary care are important since most antibiotics are prescribed for outpatients. Although community pharmacists are gatekeepers for antibiotics, they are often absent from antimicrobial stewardship programs. Methods: This quasi-experimental uncontrolled before-and-after study was conducted with pharmacists in two community pharmacies. Patient participants were 6 months to 12 years of age presenting with an antibiotic prescription for acute otitis media (AOM). Study interventions included one-on-one pharmacist education, clinical decision support tools, and personalized monthly audit and feedback. Pharmacists were encouraged to adapt prescriptions as permitted. The primary outcome was the percentage change in guideline-congruent AOM antibiotic prescriptions attributable to pharmacist intervention. Results: The overall guideline adherence for AOM antibiotic regimens increased by 28% in the post-intervention study arm (p<0.0001), which was driven by optimization of the dose of antibiotic and duration of therapy. Conclusion: A community pharmacy-based intervention can leverage pharmacist expertise to improve antibiotic use for AOM.
Spatial Heterogeneity and Immune Microenvironment of Early Invasive ER+ Breast Cancer
Keywords: ER+ Breast Cancer
GeoMx Digital Spatial Profiler
Immunology
Regulatory T cells
Tumor Microenvironment

Estrogen receptor-positive (ER+) breast cancer makes up approximately 80% of all breast cancer cases. This subtype is known to have distant recurrences for a subset of a patient after adjuvant endocrine therapy, which can partially be attributed to the heterogeneity of the disease, requiring revision of the treatment approach. The increase in popularity of immunotherapy resulted in some cancers such as ER+ breast cancer being overlooked as immunologically cold. This study characterizes the immune microenvironment in the tumour and tumour microenvironment (TME) compartments using the GeoMx Digital Spatial Profiler. Using spatial analysis, metric of heterogeneity and multi-omic approach this study demonstrates that ER+ breast cancer presents with a rich immune microenvironment, one that can be leveraged by future immunotherapies. Significantly higher expression of CD127 in the tumour compartment versus the TME was observed, along with variable ERα expression in ER+ breast cancer that may be associated with a variable immune response.
Expansion and Characterization of Tumour Derived T Lymphocytes from Undifferentiated Pleomorphic Sarcoma
Keywords: Adoptive Cell Therapy
Cytokine
Immunotherapy
Sarcoma
T cell
TIL

Sarcoma is a group of rare bone and soft tissue tumours with over 50 distinct subtypes. Survival rate of metastatic sarcoma is poor due to the lack of efficacious treatments and therapeutic strategies such as adoptive cell therapy (ACT), which utilizes TDLs, has drawn significant interest due to its precedence in treating metastatic melanoma. However, the low abundance of sarcoma TDLs may be a limiting factor during ACT, which necessitates a large quantity. Additionally, IL-2’s use during ACT promotes FOXP3+ and terminal T cells and may further exacerbate this challenge. As such, this study optimized the Tumour Fragment and Rapid Expansion protocols to robustly expand sarcoma TDLs. Non-IL-2 gamma chain cytokines were also identified as promising IL-2 alternatives to promote T helper and CD8 TDLs with clinically favorable memory phenotype and pro-inflammatory functionality. Future approaches to ACT could explore IL-7+IL-15+IL-21 to expand TDLs, and PD-1 and TIM-3 blockades as adjuvants.
N-acetylcysteine in the Rotenone Model of Mitochondrial Complex I Dysfunction in THP-1 Monocytes
Keywords: Bipolar disorder
Complex 1
Mitochondria
N-acetylcysteine
NDUFS7

Mitochondrial Complex I dysfunction and oxidative stress have been consistently reported in bipolar disorder (BD). Neuronal cell lines and rotenone, an inhibitor of Complex I, were previously used to model Complex I dysfunction in the brain. We used rotenone and THP-1 cells, a human monocytic cell line, to model Complex I dysfunction and oxidative stress potentially present in the peripheral blood mononuclear cells of BD patients and to explore N-acetylcysteine (NAC) in preventing the mitochondrial effects of rotenone. Rotenone upregulated NDUFS7, a Complex I subunit dysregulated in BD, and induced production of mitochondrial superoxide. NAC pre-treatment prior to rotenone exposure prevented NDUFS7 upregulation but had no effect on mitochondrial superoxide production. Our results suggest a reactive oxygen species-linked adaptive mechanism to mitochondrial Complex I dysfunction, providing insights to how NAC antioxidant therapy may be effective in BD.
Methods for Modulation of Surface Calreticulin and Subsequent Phagocytosis
Keywords: Calreticulin
Glycans
Macrophage
Phagocytosis

An increase in surface calreticulin (CRT) can promote recognition of cells by macrophages and the immunogenicity of cell death, and is a desirable response in current chemotherapeutics. Using standard hematopoietic cell lines, Jurkat, THP-1 and HL-60, a range of small molecules postulated to increase surface CRT were tested. Overall, raphin1, sephin1, nelfinavir and ritonavir showed promise for increasing surface expression of CRT, which led to an increase in both THP-1 and RAW 263.7 mediated phagocytosis with raphin1 and ritonavir. A second method of increasing surface CRT was also explored. THP-1 pre-treated with P-3Fax-Neu5Ac were found to have a reduction in terminal α2, 3 and α2, 6 N-acetylneuraminic acids, exposing an obscured Tri/ Mii glycan, which allowed for increased binding of exogenous CRT, and subsequent phagocytic uptake by differentiated THP-1 macrophage-like cells.
Three-dimensional Imaging of Bacterial-induced Dental Caries using Truncated-correlation Photothermal Coherence Tomography and Computationally Optimized Modalities
Keywords: Dental Caries
Linear Iso Phase (LIOP)
Signal Processing
Thermophotonics
Truncated-Correlation Photothermal Coherence Tomography (TC-PCT)

Dental caries is a highly prevalent chronic disease which is easily treatable when detected early in its formation. The primary diagnostic imaging modality used by clinical dentists, radiography, is insensitive to early caries and unsuitable for frequent use due to the health risks associated with ionizing radiation. Photothermal imaging shows great promise in the caries detection field thanks to its non-ionizing nature and the co-operative optical and thermal properties of healthy and diseased dental tissue making it highly sensitive to early caries. In this thesis, two existing photothermal modalities: Truncated-Correlation Photothermal Coherence Tomography (TC-PCT) and Enhanced Truncated-Correlation Photothermal Coherence Tomography (eTC-PCT) as well as a newly introduced TC-PCT phase algorithm: the Linear Iso Phase (LIOP) are applied to bacterial-induced dental caries imaging of human teeth. The findings demonstrate higher sensitivities to early-stage caries than micro-CT, the non-destructive gold stand of caries detection, while operating as clinically safe energy levels.
Surfactant-oil-Water (SOW) Behaviour of Surfactant Mixtures Containing Naphthenic Species
Keywords: HLD-NAC
hydrophilic linker
interfacial tension
lipophilic linker
Microemulsions
Naphthenic Acid

Recent studies have indicated naphthenic acid (NA) and its salt form, sodium naphthenates (NaN), both of amphiphilic nature, are the main agents in the formation of emulsions during the bitumen production process. Although similar fatty acids have shown ultra-low (< 0.1 mN/m) interfacial tensions (IFT) in surfactant-oil-water (SOW) systems, NA and NaN do not achieve such levels of IFT. In this work, HLD-NAC simulations guided a stoichiometric neutralization of the NA to find an ultra-low IFT interval. As experiments did not achieve ultra-low IFT, we explored potential explanations for the deviation. The work defined that NaN partitioned to the oil phase upon production. On the other hand, simulated neutralizations showed that by increasing NaNconcentration in the aqueous phase, forcing NaN to stay in it, the system could experience IFT reductions. However, NaN was then also lost to the oil phase. The zipper-like linker self-assembly, using a mixture of two balanced surfactants AOT-SDHS, was partially confirmed as a mechanism to enhance the interaction of the NA-NaN at the interface and even increased the retention of NaN in the aqueous phase. From the scenarios experimentally explored as a function of HLD (>0, ~0, and < 0), the systems with intrinsic HLD ~0 and < 0 suggested better NaN retention and potential NaN recovery even without neutralization. Emulsion stability studies confirmed the findings, achieving the separation of the water-in-oil emulsions in 15 minutes and were congruent with the HLD-NAC simulation once the critical aggregation concentration was revisited.
Clinical Evaluation of the ONETest, a Target-capture Next Generation Sequencing Platform for the Identification of Respiratory Pathogens
Keywords: Diagnostics
Infectious Diseases
Next generation sequencing
Respiratory

We clinically evaluated the diagnostic capabilities of a target capture next generation sequencing (NGS) platform called the ONETestTM. The ONETest facilitates the simultaneous detection of respiratory pathogens through a comprehensive pipeline that includes specimen processing, NGS, and bioinformatic analysis. Clinical specimens (n=655) were collected from November 2019 to April 2020 at two hospitals in Toronto, Ontario, and another 251 specimens were collected in December 2020 from healthy community participants. All specimens were evaluated using the ONETest and conventional diagnostic techniques. Agreement statistics indicate a high level of agreement between the ONETest and conventional diagnostic techniques. The overall sensitivity, specificity, positive predictive value and negative predictive value of the ONETest was 90.9% [95% CI 87.8% - 93.4%], 97.6% [95% CI 97.1% - 98.0%], 77.7% [95% CI 73.9% - 81.2%], and 99.1% [95% CI 98.8% - 99.4%], respectively. These findings highlight the efficacy of the ONETest to detect respiratory pathogens accurately.
Modelling Hyperexcitability in Human Cerebral Organoids: A Platform for Epilepsy Drug Testing
Keywords: brain
cannabis
epilepsy
organoid
pharmacology
seizures

Epilepsy is a complex neurological condition characterized by recurrent seizures, that affects 1% of the population. A third of people with epilepsy do not respond to drugs and there is not one drug that treats all; thus, better models of epilepsy are needed for drug development. Human cerebral organoids resemble the 3D complexity of the human brain and have the potential to augment current drug development pipelines. In the present work, human cerebral organoids are used along with electrophysiological methods to explore various means of inducing seizures. The resulting activity is characterized through signal processing and manual event analysis. Furthermore, this hyperexcitable activity is investigated in its response to current anti-seizure drugs. These findings demonstrate the presence of hyperexcitable changes in the cerebral organoid tissue, which supports the use of organoids as a platform for modelling epilepsy, as well as provides a framework for testing anti-seizure drug efficacy.
The Impact of COVID-19 Restrictions on Healthcare and Caregiving Access among Community-dwelling Adults Living with Spinal Cord Injury in Southwestern Ontario
Keywords: caregiving access
COVID-19
healthcare access
spinal cord injury

Restrictions implemented during the novel coronavirus (COVID-19) pandemic may disproportionately affect healthcare and caregiving access among individuals living with disabilities. A unique longitudinal survey was used to examine changes to healthcare and caregiving access among community-dwelling adults living with spinal cord injury (SCI) in southwestern Ontario, Canada before and during the COVID-19 pandemic. The results of this research demonstrated that most of the participants were able to access virtual care, but not in-person healthcare services during the COVID-19 pandemic. Longer time since injury was associated with accessing in-person healthcare services and attending all scheduled appointments. A large proportion of participants reported increased spousal participation in caregiving services early during the pandemic and understaffed formal caregiving agencies. Findings from the current study highlight the need for improved healthcare and caregiving access for individuals living with SCI during the COVID-19 pandemic and can be used to inform ongoing and future pandemic responses.
Envelope Tracking Power Supplies for 5G RF Amplifiers
Keywords: Envelope Tracking
Supply Modulator

Envelope tracking is a technique to improve the power efficiency in 5G wireless networks. Center to this technique is a supply modulator which adjusts the supply voltage to the radio-frequency power amplifier (RF PA) according to the incoming modulated signal. In this thesis, a hybrid parallel supply modulator design is proposed. It consists of a linear amplifier connected in parallel to a non-inverting buck boost converter. The linear amplifier is responsible for providing the AC current while the buck boost converter is responsible for providing the DC current. Simulation results show that the proposed supply modulator can achieve an efficiency of over 80% with a maximum output voltage of 4.79 V, a maximum output power of 3.82 W, and an envelope bandwidth of up to 100 MHz.