VictorJuiz/thesis huggingface dataset:
Functional Study on the GLP-1 Based Drug Liraglutide in High Fat Diet Fed Mice
Keywords: Diabetes
GLP-1
GLP-1R agonists
Insulin Resistance
Liraglutide
Obesity

The incretin effect is essential for glucose homeostasis. Glucagon-like peptide 1 (GLP-1) based drugs, like liraglutide, and GLP-1 C-terminal fragment, GLP-128-36, have garnered attention for their weight lowering effects. However, their “preventative effects” on obesity development have not been explored in animal models. To investigate this, male C57BL/6J mice were given liraglutide or GLP-128-36 after 10 days of HFD or LFD continued for 8 weeks, with injections 6 times per week. The daily body weight and other metabolic parameters were assessed. Liraglutide moderately reduced body weight gain, fasting blood glucose and triglyceride (TG) levels, and improved glucose disposal as well as insulin-stimulated hepatic Akt (Ser473) phosphorylation in HFD fed mice and moderately increased β-catenin (Ser675) phosphorylation in INS-1 cells. Also, the body weight gain lowering effect of liraglutide gradually diminished with continued treatment. Altogether, the findings indicate that liraglutide, but not GLP-128-36, has a moderate preventative effect on obesity development.
Evaluating the Proteomic Landscape of Diffuse Intrinsic Pontine Glioma for Therapeutic Targets
Keywords: Cancer
Glioma
Metabolism
Proteomics

Diffuse Intrinsic Pontine Glioma (DIPG) is a devastating brain tumour arising in the brainstem of children. Currently there is no effective cure for this disease and new therapeutic targets are desperately needed. High performance liquid chromatography mass spectrometry was carried out on 15 DIPG tumour and 10 normal brain tissues to identify potential therapeutic targets. The methionine salvage pathway was selected from proteomic analysis and validated in vitro as a potential therapeutic target for DIPG. DIPG cells and H3K27M expressing cells have a differential dependency on methionine and homocysteine compared to control immortalized normal human astrocyte (iNHA) and immortalized oligodendrocyte (MO3.13) cells. K27M and DIPG cells are unable to survive in homocysteine supplemented methionine deprived conditions whereas iNHA and MO3.13 cells can survive, providing a therapeutic window. DIPG4 and SF8268 cell lines are deficient in 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), elucidating one potential mechanism driving the methionine dependent phenotype.
Development of a New Experimental Model for Investigating Osseointegration of Titanium Mini-screws Placed Intraorally
Keywords: Implants
Osseointegration

A novel in-vivo pilot study was developed using the rabbit mandibular diastema to evaluate the effect of implant micro- and nano-surface topography on the rate of osseointegration. Six rabbits received one titanium mini-screw from both topographies in each diastema. Two rabbits were euthanized at 6, 22 and 85d post-implantation. Harvested mandibles were measured and processed for reverse torque, microCT, SEM and histological analyses. At 22 days, the nano- surface screws had higher mean torque values but both topographies reached nearly identical mean values after 85 days. Localized areas of crestal bone resorption were seen around all screw heads at 22 days. Sub-periosteal bone formation lateral to the screw heads led to complete coverage of the screws at 85 days. The epithelium of the overlying mucosa was parakeratinized stratified squamous. This intra-oral animal model is suitable to study osseointegration.
Diversity and Drug Resistance in Plasmodium falciparum Malaria Infections
Keywords: Antimicrobial resistance
Community ecology
Drug resistance
High-throughput sequencing
Malaria
Plasmodium falciparum

Plasmodium falciparum malaria infections often consist of multiple co-infecting strains with different phenotypic traits and responses to drug treatment. Traditional techniques used to study malaria infections do not account for co-infections and are unable to reveal the presence of rare drug resistant phenotypes within diverse infections. However, high-throughput sequencing can uncover parasite genotypes (or haplotypes) at low relative abundances within individual hosts. We detect 29 infections with signatures of drug resistance by quantifying haplotype-specific clearance curves, and five infections using a novel approach inspired by Fisher’s fundamental theorem. A second set of analyses reveal that parasite density and initial haplotype richness have a positive and negative relationship with the probability of an infection persisting after 72 hours of treatment, respectively. Overall, this study shows the utility of high-throughput sequencing for detecting variation in drug sensitivity and provides insight on the within-host dynamics of diverse infections.
A Portable and Low-cost Frequency-scanned Traffic Radar with Metasurface Collimation
Keywords: frequency-scanning
metasurface
radar

Highway traffic monitoring is important for obstacle detection and collision mitigation. In this work, a portable millimeter-wave frequency-scanned radar is developed to provide a low-cost, low maintenance alternative to mechanically scanned radar sensors. For this purpose, small components and software were utilized to recreate the functionality of a function generator and oscilloscope. This allowed the radar to shrink in overall size to allow better portability while exploring opportunities in component selection toward chip-level components for use in a printed circuit board radar, which would further reduce the implementation cost significantly. The radar was tested both indoors and outdoors to operate at 33.5 to 35 GHz and allow up to a target range of 150 m with an electronic scanning ability from +5 to -20 degrees. Future development would be expected to increase the range close to 1 km with more refined components and better amplifiers.
“Grounded in the Interconnectedness of Life, Guided by love and Growing in Wisdom”: Exploring Wisdom and Moral Virtue Through the Lens of a Canadian Atheist Exemplar
Keywords: Atheism
Christianity
Moral Virtue
Religion
Wisdom

The present study explored a highly influential exemplar of moral virtue and wisdom, Gretta Vosper, using a mixed-method person-centered case study analysis. Vosper is an Atheist Christian minister at West Hill United, a Christian church within the United Church of Canada. We interviewed her in 2017, during the time she was under review by the church to see if she was deemed fit to still be a minister as well as being outspokenly Atheist. A semi-structured interview, as well as scales such as the Three-Dimensional Wisdom Scale, were administered during a three-hour session. Analysis revealed that her own theory of wisdom and virtue cultivation is a four-step process: community, empathy, moral virtue development through interconnectedness, and lastly the development of wisdom. Commentary across all scales administered is also discussed in relation to her place as an exemplar of moral virtue and wisdom.
Prehabilitation for Women Undergoing Breast Cancer Surgery: A Mixed Methods Study
Keywords: Breast cancer
Prehabilitation
Surgery
Survivorship

Research examining prehabilitation prior to cancer surgery has grown rapidly in recent years, but data in the breast cancer setting are scant. This study examined the feasibility of an exercise-centred prehabilitation intervention prior to breast cancer surgery using a mixed methods design. Participants (n=22) received an individualized exercise prescription including aerobic and upper quadrant-specific resistance and mobility training for the duration of their surgical waiting period. Primary outcomes included feasibility and acceptability. Exploratory outcomes included measures of physical and psychosocial wellbeing. Semi-structured interviews with a sub-set of participants (n=5) and health care providers (HCPs; n=2) provided further insights into acceptability. The study demonstrated feasibility based on pre-determined thresholds. Inductive thematic analysis demonstrated that prehabilitation was perceived as highly favourable by both participants and HCPs, including suggestions that it be offered to all surgical candidates. Randomized controlled trials to examine prehabilitation efficacy in people with breast cancer are warranted.
Co-packaged 100+ Gbps Optical Communication Receiver Front-ends in FinFET CMOS
Keywords: Analog Circuit Design
FinFET CMOS
High-Speed Circuit Design
Integrated Circuits
Optical Communications
Transimpedance Amplifier

Approaches for co-packaged optical receiver front-ends are presented with a 16nm FinFET CMOS prototype for over 100 Gb/s communication. A co-packaging solution for the optical receiver front-end is sought with the discrete photodetector, and CMOS dice flip-chip attached to a shared package substrate and interconnected by an on-package microstrip. The microstrip interconnect provides an opportunity to improve the passive front-end bandwidth over what is achieved with no interconnect by making an appropriate choice for characteristics impedance of the microstrip line. Furthermore, an inverter-based transimpedance amplifier consisting of a variable-gain-amplifier and programmable equalizers is proposed. Post-layout simulations predict 60 dBΩ gain, 39 GHz bandwidth and output noise of 4.3 mVrms. Simulations of -5 dBm 4-PAM input at 100 Gb/s exhibit an output eye opening of 50 mV, assuming photodetector responsivity of 0.8 A/W. Finally, a custom package substrate is prepared for co-packaged integration of the CMOS prototype alongside commercial photodetectors.
Exploring the "Home" in Home-based Exercise for People with Cancer: The Influence of Environmental Characteristics on Exercise Participation
Keywords: cancer survivors
exercise
home-based
qualitative

Home-based exercise interventions have demonstrated the ability to improve a variety of outcomes for people with cancer. However, the environments that constitute “home-based” exercise and the different benefits and barriers of various home-based settings are poorly and inconsistently described in the exercise-oncology literature. The purpose of this exploratory qualitative study was to develop an improved understanding for what constitutes the “home” for home-based exercise in oncology and how factors of the “home” environment impact exercise participation. Data collection consisted of photo elicitation semi-structured interviews with sixteen cancer survivors enrolled in a home-based exercise program. The findings of this study contribute to a foundational understanding of the diversity of environmental resources that influence home-based exercise participation, and the complexity of participant experiences regarding the implementation of a home-based exercise prescription. Specific recommendations are made to facilitate the prescription of home-based exercise according to the environmental resources available to people with cancer.
Exploring Current Nutritional Recommendation Practices by Physicians and Dietary Changes in Patients Following Sport-Related Concussion
Keywords: nutraceuticals
nutrition
sport-related concussion
traumatic brain injury

Sport-related concussion is a concern for athletes. Currently, recommendations of initial rest followed by a gradual re-introduction of cognitive and physical activities is common practice among physicians following concussion. However, there is no standard rehabilitation strategy to manage a sport-related concussion. Additionally, the literature maintains gaps addressing nutritional recommendations in the current concussion paradigm. Therefore, this thesis was two-fold: (1) To characterize current recommendation practices of physicians managing SRC, with interest examining frequency of nutritional interventions, and (2) to characterize and identify changes in nutrition status and food behaviours. Collectively, these studies found an undeniable gap between the recommendation practices of physicians regarding nutrition and the observed nutritional changes occurring post-injury in patients with concussive injury. Future research should evaluate physicians’ nutrition knowledge in greater depth and continue to characterize nutritional changes in patients.
Attitudes and Barriers Design Professionals Face in Creating Inclusive Digital Products for Older Adults
Keywords: Human-Computer Interaction
Inclusive Design
Older Adults
Usability for Seniors
User Experience Design
Web Accessibility

When websites or apps are not designed with the age-related needs of the older population in mind, they create barriers by limiting the content available to seniors. This is particularly aggravating when such content could be beneficial for their health or wellness, for their financial security, or for maintaining social connections. This research focuses on investigating the attitudes and perceptions of design professionals in the context of designing digital products for seniors. The study was conducted using an online survey with the participation of 45 design professionals. Findings reveal that very few design professionals consider senior-friendliness in their design projects, primarily due to a lack of awareness of the needs of senior users and a lack of familiarity with senior-friendly design guidelines. The study also identified several challenges design professionals faced when designing for seniors and provided recommendations to improve their design practices.
Development of an MRI-guided Robotic Platform and Optimized Treatment Parameters for Sonothrombolysis of Intraventricular Blood Clots
Keywords: cavitation
focused ultrasound
intraventricular hemorrhage
thrombolysis

Intraventricular haemorrhage develops in 3% of all live births in Canada and 50% of those babies develop post-haemorrhagic ventricular dilatation due to blood clots in the ventricles. This often leads to hydrocephalus, which can negatively impact an infant’s vision, hearing and long-term neurodevelopment. Current treatment involves invasive brain surgery that relieves the built-up pressure from hydrocephalus, but the clot is often left untreated. In this thesis, a robotically controlled focused ultrasound platform was evaluated as a method to perform sonothrombolysis of the clot. A range of focused ultrasound parameters were tested in vitro with porcine blood to determine what values effectively and efficiently induced sonothrombolysis. The robot’s current state was assessed and necessary changes to the hardware and software were implemented to bring the robot to a working condition. The thesis concludes with a robotically controlled focused ultrasound platform along with a set of optimized parameters recommended for sonothrombolysis.
In-situ Electrochemical Characterization of Ni and Amorphous Ni-based Nanoparticles in an Anion Exchange Membrane Water Electrolyser
Keywords: AEM
electrolyser
electrolysis
nanoparticles
nickel
water

Alkaline water electrolysis has regained interest as a promising technology for converting renewable energy into H2 due to the recent developments in anion exchange membranes. In this study, an anion exchange membrane water electrolyser (AEMWE) was fabricated to study the in-situ electrocatalytic performance of Ni-based materials. Ni is of particular interest due to its wide availability and intrinsic activity. Commercial Ni and amorphous (Ni, Co)-Nb-Y nanoparticles (NPs) were applied to AEMWE as electrocatalysts showing promising performance. Amorphous (Ni, Co)-Nb-Y NPs were produced through a novel two-step ball milling process. Fabrication methods (i.e. membrane electrode assembly (MEA) hot-pressing and optimized ionomer content) were critical for improving cell performance. AEMWE operating conditions (i.e. temperature and MEA compression) were investigated to enhance activity. The concentration of a supporting electrolyte dramatically increased the cell performance. Electrochemical testing showed that Ni displayed higher in-situ activity than the amorphous alloys. Cycled amorphous catalyst layers were more stable.
Vanadium Dioxide Phase Transition Modeling and Bias Control for Photodetection
Keywords: Vanadium Dioxide

Vanadium dioxide (VO_2) is a transition material that demonstrates phase transitions between the insulator and metallic states when under thermal, electrical or optical stimuli. It is a promising material for novel devices, for instance, switches, volatile memory, oscillatory neural network units, and photodetectors. Despite being a long-standing interest in the field of condensed matter physics, the numerous observed properties of VO_2 remain insufficiently explained, which impedes the progress of its utilization for electronic devices. This thesis develops theoretical explanations and corresponding analytical and numerical models that fit our fabricated VO_2 devices. This thesis also investigates the feasibility of utilizing VO_2 as photodetectors and develops a bias control circuit with low-cost off-the-shelf circuit components, enabling repeated operations despite the hysteresis effect, demonstrated the potential of VO_2 to be integrated with existing electronics.
Bio-functional Analysis of Ubiquitin Ligase UBE3D
Keywords: Cilia
DNAAF2
Dynein
Mass Spectrometry
UBE3D
Ubiquitin

The ubiquitin system is comprised of a reversible three step process: E1 activating enzyme, E2 conjugating enzyme and an E3 ligase, leading to ubiquitin molecules being post-translationally modified onto substrate proteins leading to a plethora of downstream effects (localization, function and half-life). UBE3D, a HECT (homologous to E6-AP carboxylic terminus) E3 ligase, has a relatively elusive regulatory role within the cell. Here, we systematically analyze and characterize UBE3D as well as its highest confidence interactor, Dynein axonemal assembly factor (DNAAF2) through: Autoubiquitylation assay; intracellular localization with immunofluorescence; interaction network using proximity-dependent biotin identification (BioID) to better understand the relationship of these two proteins. DNAAF2 protein interaction mapping allowed for insight into PIH domain. In summary, I have used multiple approaches to gain novel knowledge and insight into the potential functional role of UBE3D within the cell, and its putative partner protein, DNAAF2.
Generation and Characterization of Human Induced Pluripotent Stem Cell-derived Alveolar Epithelial Type II Cells
Keywords: Acute respiratory distress syndrome
differentiation
pluripotent stem cells
regenerative medicine
stem cell
Type II alveolar epithelial cells

AECIIs, local progenitors of alveoli, differentiated from human iPSCs may provide a therapeutic potential for lung diseases. However, existing differentiation protocols lack in yield and purity, and maturity lacking their functions. Transforming 3D to 2D culture conditions at crucial development phase of lung bud organoids will enhance differentiation, stability and functionality of the iPSC-derived AECIIs. The lung organoids differentiated from human iPSCs were dissociated and matured to yield highly homogeneous population of AECIIs. The AECIIs were then purified and propagated. Cells were then tested for functionality to investigate their maturity. We produced highly proliferative AECIIs verified by expression of epithelial cell adhesion molecule and presence of surfactant protein C and lamellar bodies. The functionality of the iPSC-derived AECIIs was confirmed by release of soluble We improved existing methods to differentiate human iPSCs into functional AECIIs for a greater production capacity, which provides a powerful tool for regeneration research.
A Finite Element Model for Laser Interstitial Thermal Therapy Near Large Vessels for Lung Tumor Treatment Planning
Keywords: Finite Element Model
Heat Sink Effect
Laser Interstitial Thermal Therapy
Lung Cancer

A finite element analysis was conducted to characterize the impact of the heat sink effect due to large vessels near the ablation area in laser interstitial thermal therapy of lung cancer. The model consists of a 1 cm in diameter tumor near a large vessel with properties resembling those of the secondary branches of the pulmonary artery. A parametric sweep of different laser power inputs was performed and the light, thermal, and tissue damage distributions were evaluated. Comparative simulations in liver and brain tissue were carried out to better characterize the lung tissue’s unique response. The simulation results conclude that the lung’s unique properties, specifically its relatively low density and low optical penetration, may be favorable when treating near vascular heat sinks as compared to other tissue types.
Unearthing Invasion Mechanisms: Do Plant-soil Feedbacks Facilitate the Invasions of the Dog-strangling Vine?
Keywords: dog-strangling vine
invasive species
plant-soil feedback

Human welfare is gravely threatened by invasive species. One of Canada’s most invasive plant species, Vincetoxicum rossicum (DSV), often creates virtual monocultures. Below-ground interactions are important in determining the success and impact of plant invasions. I hypothesized that DSV invasion benefits from plant-soil feedbacks; that is, DSV will outperform competitors in soils which it has already invaded. A four-factor (soil invasion level, sterilization, activated carbon, and species) growth chamber experiment with a randomized complete block design was conducted to disentangle potential plant-soil feedbacks. In addition, soil chemical properties (i.e., nutrients) were analyzed to identify potential confounding effects. Overall, the effects of soil treatments were species-specific, and there was a lack of evidence supporting the hypothesis that DSV invasion benefits from plant-soil feedbacks. However, nitrogen was more abundant in invaded soils, suggesting that the impact of DSV invasion may instead be mediated by its altering of the soil nutrient dynamics.
Comparative Transcriptomics in the Parasitic Plant Genus Cuscuta Reveals the Effects of Ploidy Level on Gene Expression
Keywords: Cuscuta
Hybridization
Parasitic plants
Polyploidy
RNA-seq
Transcriptome

Polyploidy is known to influence the rapid evolution observed in angiosperms because it can spark near instantaneous divergence among species. My study system, Cuscuta section Denticulatae, involves two diploid progenitor species, C. denticulata and C. nevadensis, and two relatively recently formed allotetraploids, C. veatchii and C. psorothamnensis. Both parental species are further distinguished into genotypic forms labeled as D1, D2 and N1, N2, respectively. In C. denticulata, autotetraploid populations from D1 have been previously identified. Transcriptomes of both parents were assembled and annotated. To investigate the effects of gene dosage in this system, the transcriptomes were analyzed for differentially expressed genes within each parental species, including between diploid and autotetraploid populations. Differential gene expression was observed between forms D1 and D2 in C. denticulata, with a bias in gene upregulation in D1. Also, a comparative orthologue analysis found a high degree of similarity between the parents and their forms.