VictorJuiz/thesis huggingface dataset:
Simulating Thermal Effects of MR-guided Focused Ultrasound (MRgFUS) in Cortical Bone and its Surrounding Tissue
Keywords: Bone
HIFU
MRI
Therapeutic
Tumour
Ultrasound

High intensity focused ultrasound (HIFU) has been proposed as an alternative treatment for osteoid osteoma and bone metastases. To overcome current issues planning and monitoring HIFU procedures, this project proposes a simulator that predicts the temperature distribution during therapy. The bone is segmented from MR images using a semi-automatic algorithm, acoustic calculations are performed using the Rayleigh integral, and thermodynamic calculations using Pennes' Bioheat equation. The algorithm segmented with a sensitivity of 85 ± 4% and a mean volume error of 5 ± 11%. The simulation had a maximum temperature error of -2.4 ± 11.7°C, had a spatial error of 3.61 ± 1.61mm, and could be computed in less than 40s on over 10^8 points. Although these results were deemed insufficiently accurate for clinical software, the fast computation time and the modifiable framework have shown that this project was a first step in developing a clinically relevant simulation.
Nature of Production Blast Malfunctions: A Creighton Mine Case Study
Keywords: Blast
Creighton
Explosive
Malfunction

The occurrence of blast malfunctions is investigated for deep underground production stopes at Vale's Creighton mine. Over the course of six years, multiple stope blasts were recorded throughout Creighton with triaxial accelerometers and borehole camera surveys to detect the frequency of blast malfunctions. The variety in stope and blast design parameters have allowed for a detailed comparison to be made regarding the frequency of malfunctions related to the size of the blasts, the type of detonators used, the type of explosive used, the relative in-situ stress of the stope, and the number of explosive decks used in the blast designs. The investigations into the malfunctions have found that the sequence of explosive performance typically is initiated by successful charges, followed by partial energy charges, followed again by failed charges. It was also discovered that single charge boreholes have a greater explosive performance success rate than multi-decked blast designs.
Mechanical Design and Development of a Modular Drag Sail for the CanX-7 Nanosatellite Mission
Keywords: Deorbiting
Drag sails
Nanosatellites
Spacecraft

The drag sail developed for the CanX-7 nanosatellite mission is an aerodynamic deorbiting device suited to small spacecraft. The drag sail enables spacecraft within a range of bus and orbit properties to comply with international regulations that require newly-launched satellites to be removed from low Earth orbit after their end of mission, with the intent of reducing the rate of orbital debris formation. The overall design uses a modular approach that enables integration with two existing spacecraft busses, and also allows for distributed mounting on notional busses yet to be designed. Additive fabrication allows for complex part geometry that enables the drag sail components to be compactly stowed within a small volume. A model of the deployment mechanism dynamics in terms of basic design parameters reproduces a simplified picture of the operation of the real system at room temperature.
Notch Signaling Mediates Tumor-CAF Crosstalk in Basal-like Breast Cancer
Keywords: cancer-associated fibroblast
Notch signaling
tumor microenvironment

Increasing evidence indicates the importance of the tumor microenvironment in cancer progression. Cancer-associated fibroblasts (CAFs), in particular, have been reported to support tumorigenesis by promoting cell proliferation, invasion and angiogenesis. However, the mechanisms by which CAFs and tumor cells, specifically the basal-like subtype of breast cancer (BLBC), interact with each other, remain unclear. Interestingly, BLBC tumors are characterized by activation of the Notch pathway. Here, we performed co-cultures of BLBC cells with CAF-like fibroblasts and investigated the role of Notch in these interactions. We showed CAF-derived TGFb drives tumor Notch signaling and expression of the Notch target uPA. Notch activation also drives expression of c-MET which is required for uPA expression. Supporting functional assays suggested CAF-like cells promote invasion of MDA-MB231, in a fashion that depends upon TGFbR1, c-MET, uPA and Notch. Therefore, Notch participates in tumor-CAF crosstalk in BLBC cells, and may represent an important target for cancer therapy.
Information Out in the Cold: Exploring the Information Practices of Homeless Queer, Trans and Two-spirit Youth in Toronto
Keywords: Homeless youth
Information practices
queer
trans
two-spirit

This study examines the information practices of homeless queer, trans and two-spirit youth living in Toronto. As part of this exploratory ethnographic study, semi-structured interviews where conducted with 11 youth who are currently homeless or have been homeless in the recent past. Data was also collected through participant observation at a Toronto drop-in program that supports homeless queer youth between the ages of 16 and 29. The ethnography provides a description of their habits regarding information seeking, sharing and use. The data introduces a wide range of needs relating to sexual or gender identity, housing, safety, sex work, harm reduction, creativity and performance, education, relationships and leisure. It also introduces key information sources including friends and peers, shelter staff and drop-in workers as well as practices such as texting, using university libraries, and the use of social media sites like Facebook and Craigslist.
X-ray and Magnetic Resonance Imaging (MRI) Fusion for Cardiac Resynchronization Therapy (CRT)
Keywords: Cardiac intervention
Cardiac resynchronization therapy
Image registration
MRI
X-ray

Cardiac Resynchronization Therapy (CRT) can effectively treat left ventricle (LV) driven Heart Failure (HF). However, 30% of the CRT recipients do not experience symptomatic benefit. Recent studies show that the CRT response rate can reach 95% when the LV pacing lead is placed at an optimal site at a region of maximal LV dyssynchrony and away from myocardial scars. Cardiac Magnetic Resonance (CMR) can identify the optimal site in three dimensions (3D). 3D CMR data can be registered to clinical standard x-ray fluoroscopy to achieve an optimal pacing of the LV. We have developed a 3D CMR to 2D x-ray image registration method for CRT procedures. We have employed the LV pacing lead on x-ray images and coronary sinus on MR data as landmarks. The registration method makes use of a guidewire simulation algorithm, edge based image registration technique, and x-ray C-arm tracking to register the landmarks and maintain correct alignment.
Identification of Cancer Susceptibility Loci by High-resolution Cancer Gene Microarray Analysis
Keywords: Cancer Syndromes
Copy Number Variants
Genetics
Genomics
Microarray
Oncology

Li-Fraumeni syndrome (LFS) is a highly penetrant familial cancer syndrome associated with inherited germline mutations in TP53. However, a causative gene has not been identified in ~25% of LFS and many LFS-like families. In this work we aim to discover possible candidate genes that contribute to the highly penetrant cancer predisposition observed in these families. We designed an ultra high-resolution CGH array to interrogate genes implicated in cancer. We detected alterations in genes such as MSH2 and PTCH1 which were successfully validated by qPCR. This also led to the detection of a novel substitution in a family by sequencing of PTCH1. Upon further investigation, we found that the proband harbouring the MSH2 deletion belongs to a kindred that satisfies the criteria for Lynch syndrome. Both the methodology and the results of this study can be expanded upon in the future to hopefully identify additional causative genes in LFS.
Design of Engineered Bacteria for Regulated Phage Release: Progress Towards Targeted Elimination of Pathogens
Keywords: mathematical modeling
phage therapy
synthetic biology

Cholera outbreaks, caused by surges in pathogenic Vibrio cholerae, recur frequently in areas with water reservoirs around unsanitary living conditions. Phage therapy is being pursued as an alternative treatment to antibiotics. A seek-and-destroy circuit was designed for implementation in probiotics so that they could be used as a controlled delivery system for the phages. These engineered bacteria (EB) were designed to fulfill two functions: to regulate their own population growth and to respond to V.cholerae by lysing to release phages. In this study, it was confirmed that the E.coli strain K-12 could represent EB, since it could be induced to produce lambda phage virions. Construction of the seek-and-destroy circuit began by characterizing a lytic cassette, which showed promise as a population growth regulator and a prophage inducer. Finally, numerical simulations of a mathematical model representing the circuit implied that EB can successfully eradicate a V.cholerae population
Influence of High-strength Reinforcing Bars on the Behaviour of Reinforced Concrete Nuclear Containment Structures Subjected to Shear
Keywords: compression tension axial
high-strength steel
nuclear containment
reinforced prestressed concrete
shear
wall

In the design and construction of complex, heavily reinforced concrete structures, such as nuclear containment structures, the use of high-strength reinforcement to replace congested patterns of normal-strength reinforcement improves constructability and concrete placement. However, the ACI Code 318-11 limits the usable yield strength of the shear reinforcement to 60 ksi, which means it is not possible to reduce reinforcement congestion by using high-strength reinforcing bars. To investigate the consequences of using high-strength bars on shear behaviour, twelve one-third-scale reinforced concrete wall elements with varying steel strengths and loading ratios were tested. It was determined that a significant benefit can be obtained by using high-strength steel reinforcing bars with yield strengths well beyond 60 ksi. The Modified Compression Field Theory was able to predict the full stress-strain response of all twelve members with a test-to-predicted ratio for the ultimate strength of 0.96 and a coefficient of variation of only 6.0%.
A Study of the Potential of Intel's Transactional Synchronization Extensions for Hybrid Transactional Memory
Keywords: concurrency
parallelization
scalability
synchronization
transactional memory
Transactional Synchronization Extensions

Hardware Transactional Memory (TM) attempts to deliver on the promises made with Software Transactional Memory by enabling scalable parallel execution with low programming effort. Intel's TSX is a recent such effort to provide hardware support for Transactional Memory on commodity hardware. This dissertation studies the limitations of TSX and proposes both manual and automated techniques for improving application parallelism. We find that using only TSX may result in high abort rates and poor performance for certain workloads due to hardware resource limitations. Using the Moldyn benchmark, we present a series of manual optimizations on TSX to achieve performance comparable to fine-grained locking. We then translate the identified manual optimizations into automated techniques in the form of a software-hardware hybrid transactional memory library called HyTM. Using a realistic benchmark, SynQuake, we experimentally show that HyTM can significantly increase the fraction of transactions that take advantage of TSX and execute in hardware.
Shoreline Modification Impacts on Lake Ecology as a Result of Intensive Cottage Cluster Development
Keywords: Cottage Development
Kawartha Lakes
Lake Ecology
Shoreline Modification
Sturgeon Lake

Sturgeon Lake located within the Kawarthas in Ontario is one of many freshwater lakes that are experiencing a transition from seasonal to permanently inhabited homes. This transition in development resulted in the intensification of clustering houses along the lake shoreline, impacting natural surroundings. This paper examines the ecological impacts housing developments have on lakes, examining the socio-economic impacts from the intensification of development. The goals of the paper are to examine the effects shoreline modifications have on lakes from cluster communities, to determine areas along Sturgeon Lake's shoreline that should be monitored to ensure that they are not further modified, and to bridge the gaps between management and sustainability plans for Sturgeon Lake's shoreline. Relationships were noticed between the type of housing, shoreline type, and type of roads in each development section. Increased habitation along the shoreline has resulted in increased nutrient discharge impacting the occurrences of eutrophication and algae.
The Role of AMP-activated Protein Kinase in Alleviating Insulin Resistance in Hypothalamic Neurons
Keywords: Energy Homeostasis
Hypothalamus
Insulin Resistance
Obesity
Type 2 Diabetes

Insulin signaling in the brain is vital to maintain whole-body glucose and energy homeostasis. AMP-activated protein kinase (AMPK) is a key enzyme that acts as a regulator of energy homeostasis within insulin sensitive tissues. To investigate the role of AMPK on insulin resistance within the hypothalamus, the rHypoE-19 and mHypoA-NPY/GFP hypothalamic cell lines were used. Both of these cell lines express the insulin receptor and accompanying downstream molecules involved in normal insulin signaling. To induce cellular insulin resistance, the neuronal cell lines were exposed to chronic insulin for sustained periods. It was found that pre-treatment with the AMPK activator, AICAR, had an effect on insulin action and was able to slightly improve the state of chronic insulin-induced resistance within both cell lines. Therefore, these studies provide a clearer understanding of the potential role of the AMPK pathway in improving the state of cellular insulin resistance within the hypothalamus.
Application of Imputation Methods in the Analysis of Freight Trip Generation in the Greater Toronto and Hamilton Area
Keywords: freight trip generation
imputation
missing data

Missing data is a common issue in empirical research, especially in complex surveys involving a large number of respondents. In 2012-13, a shipper-based, establishment survey was conducted of 1006 small and medium-sized firms and twelve large firms in the Greater Toronto and Hamilton Area; however, there exist complete records for only about 11 percent of the firms. In this study, several single and multiple imputation techniques were evaluated to determine the best method to impute this dataset. Once the entire dataset was imputed, freight trip generation models were developed using the imputed datasets and compared to models developed based on the complete data. The research concluded that imputation is useful when developing models as it allows for the usage of the full dataset, resulting in parameter estimates of greater power. It also allows for greater flexibility in modelling, as richer models with more explanatory variables can be considered.
Controlling Biomass Ash Alkalinity for Land Application
Keywords: Ash alkalinity
Carbonation

Burning biomass wastes generates large quantities of ash products which contain plant nutrients, such as Ca, Mg, K, and P. These nutrients could be returned for reforestation. However, the ash high alkalinity presents some challenges in terms of direct land application. The high alkalinity affects the leachability of various ash components and adversely affects ground vegetation. In this thesis, it will be shown that CO2 can effectively decrease ash alkalinity at room temperature. From the study, it was found that the rate carbonation depends heavily on the moisture content of the ash and the CO2 partial pressure. From a practical point of view, a combined process of ash pelletization and carbonation was tested to have some potential for industrial application. It was found that the time required for carbonation equals the time it takes for the wetted pellet, regardless of the size, to dry at 15 vol% of CO2.
Guided Wave Inspection of Supported Pipe Locations Using Electromagnetic Acoustic Transducers
Keywords: corrosion defect
EMAT
Guided Wave
Non-destructive testing
Pipe Support
Shear Horizontal

The goal of the work in this thesis is to develop a rapid and reliable NDT system to detect hidden corrosion at pipe-support interfaces using Electromagnetic Acoustic Transducers (EMATs). Since there are often many support interfaces over a piping run, information is needed on the support interface conditions to optimize subsequent detailed inspections.In this work it is important to be able to isolate the effects produced from the support interface and the incident guided wave. To do this an optimum EMAT operating point is first selected, then the support interfaces and wall loss type defects are independently analyzed through experimentally validated finite element models. It is found that operating the SH1 plate wave mode near the `knee' of its dispersion curve gives a high sensitivity to wall loss type defects while experiencing a minimal effect from the support contact region.
Implementation and Application of a Method for Measuring Traction Forces to Characterize Deficient CNP Signaling in Mouse Fibroblasts
Keywords: Aortic Valve Disease
C-type Natriuretic Peptide
Mechanobiology
Myofibroblasts
Traction Force Microscopy

Adherent cells respond to changes in their microenvironment by generating internal forces that are transferred to the substrate to which they are attached. Manipulation of cellular signaling pathways also influences the response to these changes and can direct cells to pathological outcomes. C-type natriuretic peptide (CNP), through the NPR-B receptor, has been shown to protect quiescent fibroblasts in heart valves from differentiating into myofibroblasts that contribute to development of calcific aortic valve disease (CAVD). Here, I implemented and validated a method for quantifying cellular traction forces
Surface Texture Consistency in Object and Background Perception
Keywords: context
form
global image feature
Scene and object perception
texture

Seminal work on global processing has suggested that the precedence of global image features is an inherent property of visual perception. Consequently, interference from global percepts may influence the perception of local elements. Investigations of scene processing have been consistent with this suggestion, demonstrating that the parahippocampal place area (PPA) represents scenes by processing global spatial properties. Recent investigations have further revealed that PPA is sensitive to processing non-spatial visual cues (such as surface texture) in both object and scene perception. In the present study, we investigated potential global interference effects in object-scene perception when attending to spatial and non-spatial visual features in both simple figure-ground representations and more complex real-world scenes. Results revealed that non-spatial surface properties such as texture can form a contextual link between the processing of object and background information in scene perception, and this interactive processing proceeds from the global to local scale of attention.
Local and Global Structural Architecture Supports Functional Organization in the Aging Brain
Keywords: aging
function
neuroimaging
structure

Neuroscience research suggests that local and global functional interactions throughout the human brain are modulated by the underlying anatomical architecture. Age-related changes of anatomical tracts suggest a potential for concomitant changes in structure-function coupling. We compared functional connectivity inferred from spontaneous BOLD fMRI with structural connectivity inferred from DTI in a sample of 47 adults ranging from 18 to 82 years of age. We noted that the strength of structural and functional connectivity decreased in most regions as subjects aged. Local regionwise structure-function correspondence varied across the age spectrum. We also found that the structural architecture upholds the functional modular organization at a global level, such that regions are more densely connected within their functionally defined module, and that this varies with age. Tracts from structural hubs may actually strengthen within functional modules with age, such that the structural core increasingly supports functional organization throughout the aging process.
Development of an Ambulatory Wearable Sensor System for Behavioural Neurocardiac Training
Keywords: biofeedback
mobile health
wearable sensor system

In this project, an ambulatory wearable sensor system was developed to deliver Behavioural Neurocardiac Training (BNT) with heart rate variability biofeedback for blood pressure and stress management in home settings. The system consists of a wearable ECG sensor and a smartphone application. The sensor was designed as a patient-friendly modular patch to be worn on the user's chest using standard electrodes. It wirelessly streams ECG in real-time using Bluetooth Low Energy. The smartphone application guides users through the BNT exercises using structured, audio-guided lessons that train a paced breathing technique using real-time biofeedback and stress recovery exercises. The feasibility of this system was evaluated in a pilot study with six participants. The overall response to the system was positive, and user satisfaction was high. It is expected that this system may offer a complementary approach to blood pressure and stress management at home, and reduce current accessibility barriers.
Exploring Mechanisms Underlying Retinitis Pigmentosa by Using Temperature Sensitive Alleles in Yeast
Keywords: Genetic suppression
Retinitis Pigmentosa
Spliceosome
Temperature sensitive alleles

Retinitis pigmentosa (RP) is characterized by progressive degeneration of the photoreceptors and visual field defects. No drug treatment has yet been found for this disease. Mutations in more than 60 genes are known to cause RP. One group of genes that was found to be mutated in retinitis pigmentosa is encoding pre-mRNA processing proteins; hPrp3, hPrp6, hPrp8, hPrp31, and hBrr2 that are homologous between human and Saccharomyces cerevisiae. In the project described here, I introduced the RP-related mutations into their yeast homologs and tested for temperature sensitivity. Two out of thirteen tried mutations resulted in a temperature sensitive phenotype. Using both available ts strains and ts strains containing RP point mutations, extragenic suppressors were isolated. Whole genome sequencing was used to identify the suppressor genes. As chemical perturbations may mimic genetic perturbations, these suppressor genes can potentially lead us to new alternative drug targets for this genetic disease.
Comparing the Effects of Self- and Instructor-Regulated Learning on Skill Acquisition, Retention and Trainees' Learning Approches
Keywords: Cardiac
Education
Instructor
Self-regulation

During instructor-regulated learning (IRL), trainees must reconcile the instructor's teaching approaches with their own learning approaches. Conversely, trainees engaged in self-regulated learning (SRL) may benefit from developing individualized learning approaches. We compared the effects of SRL to IRL on cardiac auscultation skill acquisition and retention, and on trainees' transfer of learning approaches to another session. After randomization (SRL or one-on-one IRL groups), novice medical students (n=32) practiced diagnosing simulated murmurs and then completed a post-test. Two-weeks later, participants completed a retention test, practiced diagnosing new simulated murmurs, and completed another post-test. There were no between-group differences on any performance-based assessment. Most IRL participants did not use the learning approach in session two that instructors taught them in session one. Interview data suggest the instructor's presence had both positive and negative impacts on learning. The findings highlight factors that prevent IRL training from having the benefits supervisors expect from their teaching.