VictorJuiz/thesis huggingface dataset:
Improvements to the Efficiency of the Radiotherapy Treatment Planning Process

Radiotherapy is one method of treating di erent diseases like cancer. It requires a treatment plan that clearly delineates target and non-target volumes, and the beams and their intensities to deliver the prescribed dose. Historical treatment plans often contain volume names that are unaccounted for. An approach is applied where desired volumes are detected and renamed to conform to current search standards. The mapped names provide an avenue for searching historical plans when performing outcomes analysis in the future to help improve quality in radiation therapy. A specific form known as intensity modulated radiation therapy is applied to total marrow irradiation, a method to remove all marrow in the body prior to bone marrow transplant. A set-covering approach is used, solved using heuristics and commercial packages to compare outcomes. Constraint programming is used in an attempt to better and to improve on the heuristic solutions.

Keywords: optimization
radiation therapy
beam orientation optimization
nomenclature
Advisor: Aleman, Dionne
Characterization of Williams-Beuren Syndrome Mouse Models: Linking Genes with Cognition and Behaviour

Deletion (Williams-Beuren syndrome (WBS)) and duplication (Dup7q11.23) of a common interval spanning 26 genes on chromosome 7q11.23 cause disorders with a spectrum of clinical, cognitive and behavioural symptoms. Studies of individuals with atypical deletions have implicated two genes, GTF2IRD1 and GTF2I. Here I describe the behavioural characterization of mice hemizygous for Gtf2i, or Gtf2ird1 and Gtf2i together, as well as mice with additional Gtf2i copies. Dosage changes in Gtf2i were associated with working memory impairment and separation anxiety, and possibly with general anxiety and repetitive behaviours. A potential cause of these phenotypes was found in brain tissue, where subcellular localization of the calcium channel TRPC3, which is regulated by GTF2I, was found to be altered. Collectively, these results provide a better understanding of the contributions of GTF2I to the cognitive and behavioural profile of WBS and Dup7q11.23 and identify a potential biological mechanism that may underlie some of the symptoms.

Keywords: Molecular biology
Williams-Beuren syndrome
Mouse models
Behaviour
Cognitive development
Neurobiology
Advisor: Osborne, Lucy
Dynamic Modeling and Control of a 6-DOF Parallel-kinematic-mechanism-based Reconfigurable Meso-milling Machine Tool

In this thesis, a methodology for rigid body dynamic modeling and control design is presented for a 6 degree-of-freedom (DOF) parallel-kinematic-mechanism-based reconfigurable meso-milling machine tool (RmMT) with submicron tracking accuracy requirement. The dynamic modeling of the parallel kinematic mechanism (PKM) is formulated using the Lagrangian method with the application of principle of energy equivalence and coordinate transformations to separate the mechanism into serial sub-systems. The rigid body gyroscopic force is also modeled using this approach and its effect as a disturbance is analyzed and compensated. The contour errors for both position and orientation are formulated to increase machining accuracy. The dynamic model of the system is linearized through feedback linearization and the contour error based feedback control law is formulated using the convex combination design approach to satisfy a set of design specifications simultaneously. The dynamic model and its control methodology are simulated and verified within the MATLAB Simulink environment.

Keywords: meso-milling
parallel mechanism
dynamic model
control
Advisor: Benhabib, Beno
Mills, James
Effects of Moderate-intensity Aerobic Cycling and Swim Exercise on Post-exertional Blood Pressure in Healthy, Young Men and Women

Aerobic exercise such as cycling is known to elicit a post-exercise hypotensive (PEH) response. However, it is not known if swim exercise produces a similar effect in normotensive individuals. We tested the hypothesis that an acute bout of swimming would elicit a PEH response that is less compared to an equivalent bout of cycling. 10 trained and 11 untrained normotensive (SBP/DBP < 120/80 mmHg) individuals (23±1 years) underwent 30 min intensity-matched cycling and swimming sessions to assess changes in BP and cardiovascular responses. While PEH was similar between modalities within groups, the magnitude and temporality of change in BP following swimming was significantly different (p < 0.01) between groups, with untrained participants showing a significant PEH response. Attenuation of PEH in trained individuals was reflective of a significant increase in sympathetic outflow and slower vagal reactivation, suggesting training in an aquatic environment leads to alterations in post-exercise BP regulatory mechanisms.

Keywords: blood pressure
swimming
cycling
exercise
post-exercise hypotension
Advisor: Goodman, Jack
Pulse Shaping Based on Integrated Waveguide Gratings

Temporal pulse shaping based on integrated Bragg gratings is investigated in this work to achieve arbitrary output waveforms. The grating structure is simulated based on the sidewall-etching geometry in an AlGaAs platform. The inverse scattering employin the Gel'fan-Levithan-Marchenko theorem and the layer peeling method provides a tool to determine grating structures from a desired spectral reflection response. Simulations of pulse shaping considered flat-top and triangular pulses as well as one-to-one and one-to-many pulse shaping. The suggested grating profiles revealed a compromise between performance and grating length. The integrated grating, a few hundred microns in length, could generate flat-top pulses with pulse durations as short as 500 fs with rise/fall times of 200 fs; the results are comparable to previous work in free-space optics and fiber optics. The theories and the devised algorithms could serve as a design station for advanced grating devices for, but not restricted to, optical pulse shaping.

Keywords: Pulse shaping
Integrated optics
Gratings
Ultrafast optics
Picosecond pulses
AlGaAs waveguide
AlGaAs gratings
Flat-top pulse shaping
Rectangular pulse shaping
Coupled-mode theory
Inverse scattering
Advisor: Aitchison, J. Stewart
Insulin Modulates Intracellular Apolipoprotein B mRNA Traffic into RNA Granules/Cytoplasmic P Bodies: Implications in Translational Control

Apolipoprotein B (ApoB) synthesis is partially regulated at the translational level; however, the molecular mechanisms that govern translational control of apoB mRNA remains largely unknown. We imaged intracellular apoB mRNA traffic and determined whether insulin silences apoB mRNA translation by trafficking into translationally-silenced cytoplasmic RNA granules called Processing Bodies (PBS). ApoB mRNA was visualized by using a strong interaction between the bacteriophage MS2 protein and a specific phage RNA sequence that binds MS2 protein. We observed a statistically significant increase in the localization of apoB mRNA into PBs, 4h, 8h, and 16h after insulin treatment. Conversely, acute insulin treatment (1h) did not show any significant effect. Insulin was also found to reduce polysomal association of apoB mRNA 4h and 16h post treatment in HepG2 cells. Overall, our data suggest that chronic insulin treatment silences apoB translation in HepG2 cells by localizing apoB mRNA into PBs and reducing translationally-competent mRNA pools.

Keywords: Insulin
Apolipoprotein B
P bodies
Polysome
Advisor: Adeli, Khosrow
Testing the Normative Hypothesis of Relational Aggression and Psychopathology through Gender and Age Moderation

The gender normative hypothesis of relational aggression and psychopathology states that relational aggression is more detrimental to boys than it is to girls because relational aggression is more normative in girls. In the present study, this hypothesis was tested in a large sample of 6-to-18-year-old children and this hypothesis was also extended to the domain of age norms. Specifically, it was tested whether relational aggression would also be most detrimental outside of the age in which it is most normative. The results showed some evidence supporting the gender normative hypothesis. Specifically, it was found that relationally aggressive boys suffered more internalizing and externalizing problems than non-relationally aggressive boys did. Relationally aggressive girls, however, suffered only more externalizing problems than non-relationally aggressive girls did. Results did not support the age normative hypothesis. Implications of these findings and future directions are discussed.

Keywords: relational aggression
psychopathology
adolescence
gender differences
Advisor: Tackett, Jennifer L.
Experimental Verification of a Three Dimensional Photonic Crystal Bandgap

Photonic crystals (PC) are periodic structures that dictate the behavior of electromagnetic radiation and can be one-dimensional, two-dimensional or three-dimensional (3D). A 3DPC was modeled and fabricated based on a three-layer design resulting in a face centered cubic structure. Different simulation methods were used to show the existence of a complete 3D bandgap, and were verified experimentally by obtaining transmission measurements in several directions. A prototype of the structure was fabricated using ECCOSTOCK HiK high dielectric sheets (dielectric of 12) and machined using a computer and numerical controlled mill. Experiments to test this structure were performed in an anechoic chamber making use of a network analyzer, a pair of horn antennas, collimating lenses, and a track for alignment. Free-space Thru-Reflect-Line measurements were taken between 10GHz and 15GHz to obtain the transmission through the prototype. Finally, a defect layer was added to the structure at different locations and localized modes observed.

Keywords: Photonic Crystal
Bandgap
Advisor: Mojahedi, Mohammad
Nutrient and Biomass Contributions of Downed Woody Debris in Boreal Mixedwood Forests of Northeastern Ontario

Harvest-related decreases of downed woody debris (DWD) in forests may have important ecological implications; however, patterns of nutrient release from decaying DWD are poorly understood. The importance of DWD was investigated relative to biomass and nutrient pools in six, second-growth boreal mixedwood forest stands, differing by harvest regime near Kapuskasing, Ontario. Nutrient concentrations and mineralization trends using ion exchange resins at three proximities during the decay of Abies balsamea and Populus tremuloides were also examined. Concentrations of N, P, Ca, and Mg increased with decay, whereas K decreased. DWD was a minor contributor to biomass and nutrient pools. Inorganic N, P, Ca, and Mn were significant between harvest types with decay class interaction for N, Ca, and Mn. Species and proximity effects were found for Al, Fe, and K. These results suggest DWD may be a minor contributor to biomass and nutrient pools, but highlights its dynamic nature.

Keywords: Biomass and nutrient pools
Downed woody debris
Doreal mixedwoods
Wood decay patterns
Advisor: Malcolm, Jay R.
Morris, Dave
Modeling Hydrogen Sulfide Adsorption by Activated Carbon made from Anaerobic Digestion By-product

Biogas, produced from anaerobic digestion of cattle manure, is an attractive alternative energy source as it is rich in methane. However, it is necessary to remove hydrogen sulfide from the biogas before it can be used in engines for electricity generation. Currently, large scale biogas systems employ physical adsorbing solvents to upgrade and purify biogas which is not economically feasible for small scale biogas systems. Activated carbon made from anaerobic digestate proves to be an effective adsorbent of hydrogen sulfide because it has minimal operating costs and essentially zero raw material cost. A model is developed to predict the adsorption capacity, carbon bed life span, and breakthrough time for this carbon material. By analyzing the reaction constant, adsorption constant, and degradation constant, adsorption behavior under different operating conditions were studied. The model can be scaled-up to model adsorption for biogas loading rates for small to large scale cattle farms.

Keywords: hydrogen sulfide
adsorption
activated carbon
modeling
Advisor: Kirk, Donald W.
Factors Influencing Ecological Metrics of Thermal Response in North American Freshwater Fish

Habitat temperature is a major determinant of performance and activity in fish. I examined the relationships between thermal response metrics describing growth (optimal growth temperature [OGT] and final temperature preferendum [FTP]), survival (upper incipient lethal temperature [UILT] and critical thermal maximum [CTMax]), and reproduction (optimum spawning [OS] and optimum egg development temperature [OE]) for 173 North American freshwater fish species. All metrics were highly correlated and associated with thermal preference class, reproductive guild and spawning season. Controlling for phylogeny resulted in an overall decrease in correlation strength, varying with metric pair relationship. ANCOVA and Bayesian hierarchical models were utilized to assess the influence of phylogeny on metric pair relationships. For both methods, FTP based metric pairs were weakly correlated within taxonomic family. Strong within family associations were found for reproduction metrics OS-OE. These results suggest that evolutionary history plays an important role in determining species thermal response to their environment.

Keywords: Thermal Ecology
Freshwater fish
Advisor: Shuter, Brian
Embodiment, Pain, and Circumcision in Somali-Canadian Women

Female genital cutting/circumcision/mutilation (FGC) is found predominantly in the Sahel, Northern Africa, removing parts/all of the clitoris, labia minora and majora in girls. Cutting the highly innervated external genitalia may change sensory processing leading to chronic pain. Fourteen Somali women in the Greater Toronto Area (21-46, Type III FGC) completed qualitative, quantitative and psychophysical methods to evaluate pain. Interviews analyzed by interpretive phenomenology form the core method, examining circumcision stories and present, embodied life. The second Short Form McGill Pain Questionnaire and quantitative sensory testing with a vulvalgesiometer form secondary components. Somali women with FGC have pain-filled stories about circumcision and daily life. Socio-cultural considerations are central for women to comprehend how their own bodies feel. SF-MPQ-2 indicates low intensity or no pain symptoms; however, many body regions were indicated. QST reveals low vulvar pressure-pain thresholds. Reports from three measures suggest that FGC may cause sensory changes including chronic pain.

Keywords: pain
women's health
female genital cutting
immigration and health
biocultural
Advisor: Einstein, Gillian
The Role of Colony-stimulating Factor 1 and its Receptor on Acute Myeloid Leukemia

Colony-stimulating factor 1 receptor (CSF1R, Fms) is an integral transmembrane glycoprotein with tyrosine specific protein kinase activity that it is found on the mononuclear phagocytes to promote their survival, proliferation and differentiation. Colony-stimulating factor 1 (CSF-1), also known as M-CSF, is a protein ligand that acts on the CSF1R. There is a variable association of Fms with the stem cell marker CD34 on acute myeloid leukemia (AML) cells and this suggests different structures of the AML hierarchy in different patients. Mouse stromal cells (MS-5) were transduced with a plasmid containing human CSF-1 because mouse CSF-1 is inactive on human CSF1R. Results show that AML cells cultured with CSF-1-expressing stroma had a much better growth and survival than the control stroma, suggesting that CSF-1 might be a stimulating factor for the growth of leukemic stem cells.

Keywords: Leukemia
AML
Cancer stem cells
Leukemia stem cells
CSF-1
M-CSF
Advisor: Minden, Mark
The Catalytic Aspartic Acid Shows a Role in Substrate Positioning in 5-methylthioribose Kinase

Methionine is involved in many cellular processes, several of which produce a feedback inhibitor. 5-methylthioribose (MTR) kinase, one protein involved in the removal of this inhibitor, has a protein kinase fold with conserved kinase motifs and several unique MTR binding motifs. Site-directed mutagenesis and characterization of the Bacillus subtilis enzyme was performed to probe the role of one motif. Active site D233 mutants show an activity profile similar to other protein kinase-like enzymes, suggesting a common mechanism that does not require a catalytic acid. An ordered sequential binding mechanism, with nucleotide binding first, was seen in wild type MTR kinase. Binding studies of the mutant proteins suggest that hydrogen bonding is important for MTR binding. The structures of the mutant proteins also show more differences in MTR binding than nucleotide binding. Overall, D233 is important for increasing the nucleophilicity of MTR, and ensuring its correct position in the active site.

Keywords: kinase
5-methylthioribose
methionine recycling
enzyme mechanism
Advisor: Howell, P. Lynne
Investigating the Role of Fwd and Potential Role of the Rab11-interacting Protein dRip11 in Drosophila Spermatocyte Cytokinesis

Cytokinesis is the final separation of daughter cells after division. Membrane trafficking increases the surface area of dividing cells and may deliver cargo needed for division. The Drosophila PI4-kinase Fwd is required for spermatocyte cytokinesis and likely acts, in part, by mediating Rab11-dependent trafficking to the furrow. To further understand the mechanism of action of Fwd, I attempted to place fwd in a pathway with other cytokinesis genes encoding Rab11, phosphatidylinositol transfer protein and a subunit of the exocyst. I also investigated a potential role for the Rab11 interacting protein dRip11 in cytokinesis. My results suggest that Rab11, like Fwd, is required for cell integrity during cytokinesis and that the Rab11 interacting protein Nuf is an important candidate to investigate along with dRip11 as a relevant Fwd/Rab11 effector during this highly conserved process.

Keywords: cytokinesis
phosphoinositides
membrane trafficking
Advisor: Brill, Julie
Maternal Dietary Restriction and the Effects of Postweaning Nutrition on Fetal Development, Insulin Signalling, Glucose Metabolism and Body Composition In C57BL/6J Mice

Mice (C57BL/6J: B6) exposed to maternal dietary restriction (DR) exhibited fetal growth- restriction and as adults develop symptoms of the metabolic syndrome. We aimed to determine the impact of DR on fetal hepatic gluconeogenic pathway and insulin sensitivity in late gestation. Second, we aimed to determine whether a postweaning diet rich in omega-3 fatty acids would alter the development of glucose intolerance, insulin resistance and obesity in DR male offspring. The reduced rate of fetal glycogen synthesis by DR male offspring and altered hepatic gene expression of enzymes involved in insulin signalling and glucose metabolism suggest abnormal fetal development in response to DR that may contribute to the later development of the metabolic syndrome. The postweaning omega-3 diet improved obesity, glucose intolerance and insulin resistance in both DR and control males. These data suggest that nutrition in pregnancy and postnatal life play important roles in determining life-long metabolic health.

Keywords: metabolic syndrome
maternal undernutrition
omega-3 fatty acids
intervention
Advisor: Lye, Stephen J.
Investigating Type I Collagen Self-assembly Processes and End Products

Segmental long spacing (SLS) collagen self-assembly was studied by analyzing aggregates formed from different nucleoside triphosphates at various protonation stages. Triple-negatively charged triphosphate groups were determined to be critical for SLS assembly, electrostatically bridging basic residues between collagen monomers. In the second part of this thesis, the nominal elastic modulus for each of the three forms of Type I collagen aggregate was measured and compared. Fibrous long spacing collagen, often associated with diseased tissues, exhibited lower stiffness in comparison to the other forms, native and SLS, suggesting decreased structural stability in diseased tissues. In the last section, a unidirectional pattern of native fibrils was assembled using mica as a template; the ability to customize and change the surface morphology was also demonstrated. For the first time, collagen monomers deposited on the mica were demonstrated to gain lateral mobility.

Keywords: collagen
atomic force microscopy
self-assembly
nanoindentation
segmental long spacing
fibrous long spacing
elastic modulus
mica
in vitro assembly
Advisor: Goh, M. Cynthia
Reusable OpenCL FPGA Infrastructure

OpenCL has emerged as a standard programming model for heterogeneous systems. Recent work combining OpenCL and FPGAs has focused on high-level synthesis. Building a complete OpenCL FPGA system requires more than just high-level synthesis. This work introduces a reusable OpenCL infrastructure for FPGAs that complements previous work and specifically targets a key architectural element - the memory interface. An Aggregating Memory Controller that aims to maximize bandwidth to external, large, high-latency, high-bandwidth memories and a template Processing Array with soft-processor and hand-coded hardware elements are designed, simulated, and implemented on an FPGA. Two micro-benchmarks were run on both the soft-processor elements and the hand-coded hardware elements to exercise the Aggregating Memory Controller. The micro-benchmarks were simulated as well as implemented in a hardware prototype. Memory bandwidth results for the system show that the external memory interface can be saturated and the high-latency can be effectively hidden using the Aggregating Memory Controller.

Keywords: FPGA
OpenCL
SDRAM
Advisor: Chow, Paul
Assembly, Integration, and Test of the Instrument for Space Astronomy Used On-board the Bright Target Explorer Constellation of Nanosatellites

The BRIght Target Explorer (BRITE) constellation is revolutionary in the sense that the same scientiﬁc objectives can be achieved smaller (cm3 versus m3 ) and lighter (< 10kg versus 1, 000kg). It is a space astronomy mission, observing the variations in the apparent brightness of stars. The work presented herein focuses on the assembly, integration and test of the instrument used on-board six nanosatellites that form the constellation. The instrument is composed of an optical telescope equipped with a Charge Coupled Device (CCD) imager and a dedicated computer. This thesis provides a particular in-depth look into the inner workings of CCD. Methods used to characterize the instrument CCD in terms of its bias level stability, gain factor determination, saturation, dark current and readout noise level evaluation are provided. These methodologies are not limited to CCDs and they provide the basis for anyone who wishes to characterize any type of imager for scientic applications.

Keywords: Charge Coupled Device
Space Telescope
Instrument Characterization
BRITE
Bright Target Explorer
Spacecraft assembly, integration and testing
CCD gain
Dark current
Readout noise
bias level
saturation level
full well saturation
Advisor: Zee, Robert E.
ED-A Fibronectin: A Storage Site for Latent TGFB-1 in the Myofibroblast Matrix?

Fibrosis, a major cause of organ failure, has no effective therapy available. Responsible for fibrosis are myofibroblasts. Mechanical stress, TGF myofibroblast differentiation, however the exact link remains elusive. I hypothesize that ED-A FN stores the latent TGF -1 in the ECM by interacting with the latent TGF -1 binding protein (LTBP-1), and that matrix stiffness is a regulator of ED-A FN and LTBP-1. Using co-IP and ED-A domain antagonists, ED-A FN and LTBP-1 associated in the ECM of human dermal fibroblasts (HDFs). The effects of the 11th_ED-A_12th recombinant FN peptide was most prominent in blocking LTBP-1 incorporation in the ECM. HDFs seeded on collagen- coated substrates, showed an increase in expression and organization for both proteins with matrix stiffness. In conclusion, the ED-A domain may require the aid of heparin linkages flanking the 12th domain of FN to bind to LTBP-1 in the ECM.

Keywords: biology
Advisor: Hinz, Boris