VictorJuiz/thesis huggingface dataset:
Validation of putative prognostic markers for non-small cell lung carcinoma

Lung cancer is the second most diagnosed cancer in North America. Several microarray studies have reported gene expression signatures capable of classifying non-small cell carcinoma (NSCLC) patients according to prognosis. However, these signatures rarely overlap and most have not been independently validated using other methods. We therefore validated putative prognostic markers from previously published NSCLC microarray expression studies in a large independent patient cohort by real-time quantitative PCR. Two independent algorithms were used to select prognostic subsets, identifying a 6- and 3-gene classifier that could significantly segregate NSCLC patients. Next, preliminary experiments examined the potential biological role of the most robust prognostic gene in the classifiers, syntaxin 1A (STX1A). Loss of STX1A expression by RNAi had no effect on cell proliferation or cell cycle, but decreased the ability of H460 cells to migrate through collagen IV and form colonies in soft agar. STX1A represents a novel target for further investigation.
Threads of connection: Addressing historic trauma of indigenous people through cultural recreational programming

An indigenous research framework formed the theoretical basis of this project - the foundation of which was the medicine wheel. The medicine wheel teachings are vast but the focus for this project was the concept of health whereby an individual's health is maintained through balance of emotional, physical, mental and spiritual well-being. Interconnection between these four realms is an important characteristic. This project began with the physical realm, specifically a physical activity program, and explored its interconnectedness to emotional, spiritual, mental and physical well-being. The physical activity was a martial arts program offered at the Native Canadian Centre of Toronto. Seventeen adults (twelve indigenous) and five from other cultural backgrounds participated in the project. Indigenous research methods, sharing circles and Anishnaabe Symbol-Based Reflection (ASBR) captured the stories of the participants. One personal interview was conducted. The stories captured in the sharing circles and the symbols from ASBR described the impact of the martial arts program on the lives of the participants. A qualitative software program was used to analyze the stories and symbols. Nine common themes emerged which describe a collective story represented through the symbol of a hydrangea flower. The nine themes were: events of the past, hopes for the future, the martial arts program, the Native Canadian Centre, the impact of physical activity on physical, emotional, mental and spiritual well-being, and how they walk in life carrying what participants have learned from the martial arts program. These findings are important in demonstrating the interconnectedness of physical activity with emotional, mental, physical and spiritual well-being. This was particularly important for indigenous participants in addressing the healing from their colonial pasts.'Threads of Connection' described their collective story accentuating how martial arts were interwoven throughout their lives. Stories of their pasts reflected the impacts of historic trauma, such as physical violence, and experiences with foster care and residential school. Yet, paradoxically, they spoke of ending this cycle of trauma in the future. The participants emphasized the importance of incorporating indigenous teachings into the physical activity program and the significance of offering it within an indigenous cultural centre.
A determination of critical periods in development at the Drosophila larval neuromuscular junction

A central objective in the field of neurobiology is to understand the developmental plasticity of neurons. The pursuit of this objective has revealed the presence of critical periods in neural development. This idea holds that there are particular developmental time windows in which certain kinds of neural remodeling can take place. Here I have taken advantage of the Drosophila melanogaster neuromuscular junction (NMJ) to investigate developmental plasticity and critical period determination of defined identifiable neurons at this model synapse. My data support the view that individual neuromuscular synapses in Drosophila melanogaster larvae possess critical periods for synapse development, but that the time windows for morphological and physiological plasticity are not identical. These studies open the door to further molecular genetic analysis of critical periods of synaptic development.
Roots of graphs

Root and root finding are concepts familiar to most branches of mathematics. In graph theory, H is a root of G = (V, E) if there exists a positive integer k such that [special characters omitted] where dH(x, y) is the length of a shortest path in H from x to y. In such a case H is a kth root of G and we write G = Hk and call G the kth power of H. In this thesis, we study the complexity of restricted graph powers recognition problems. We show the NP-completeness of recognizing squares of chordal graphs, squares of split graphs, finding square roots of chordal graphs, and recognizing cubes of bipartite graphs. On the other hand, we give the first polynomial time recognition algorithms for squares of bipartite planar graphs and squares of k-regular bipartite graphs. By using the tools developed for squares of restricted bipartite graphs, we are able to give a new and conceptually simpler algorithm to recognize squares of trees and a new proof that tree square roots are unique up to isomorphism. Last but not least, we present the first polynomial time algorithm to recognize squares of proper interval graphs and give an outline to recognize k-th powers of proper interval graphs for every natural number k.
Role of polyunsaturated fatty acids on bone development in fat-1 transgenic mice

Incorporation of n-3 PUFA into bone may optimize skeletal development. The overall thesis objective was to determine if fatty acid composition, mineral, and biomechanical strength were favourably modulated in femurs and vertebrae of fat-1 mice, a transgenic model that synthesizes n-3 from n-6 PUFA. Wild-type and fat-1 mice were studied at 12 weeks of age. In Study 1, peak load and bone mineral density (BMD) were associated with long chain n-3 PUFA and n-6/n-3 ratio at the femur. Study 2 showed greater peak load in the vertebra of fat-1 mice compared to wild-type. Long chain n-3 and n-6 PUFA were correlated with peak load and BMD at the vertebrae. In Study 3, significant associations were shown between BMD and long chain PUFA in phospholipids at both bone sites. In summary, modulating bone n-6 and n-3 PUFA levels resulted in stronger vertebrae, suggesting a positive role in bone development.
Effects of gemcitabine on APE/Ref-1 and the therapeutic potential of antisense oligonucleotides

Apurinic/apyrimidinic endonuclease (APE) is a key enzyme involved in DNA base excision repair and is also referred to as redox effective factor (Ref-1) due to its alternative role as a redox regulator of various transcription factors like NF-κB and p53. Pancreatic cancer is extremely resistant to various types of cancer treatment with the only currently clinically active agent being the nucleoside analogue; gemcitabine. Pancreatic cells treated with various doses of gemcitabine showed increases in APE/Ref-1 protein levels as well as increased endonuclease activity. These results suggest that elevated APE/Ref-1 expression might be an adaptive response contributing to the overall chemoresistance seen in pancreatic carcinomas. Combination treatments with antisense and gemcitabine inhibited further induction of APE/Ref-1 protein versus cells exposed to gemcitabine alone. This study suggests that APE/Ref-1 is an important mediator of gemcitabine resistance and that antisense have a potentially therapeutic role in the treatment of pancreatic cancers.
Minimum norm mutual coupling compensation with applications in matrix pencil direction of arrival estimation

This research introduces a new approach to compensate for the mutual coupling between the elements of an antenna array. The compensation is undertaken in the context of practical direction of arrival estimation. In this thesis, Matrix Pencil is used to provide an algorithm for a fast, yet accurate DOA estimation. It can estimate directions with great accuracy using only a single time sample. Then, a new mutual coupling compensation method is introduced to account for any mutual coupling affecting the DOA estimation. It is based on the minimum norm solution to an underdetermined system of equations. It works independent of the type of antenna element and provides good results in situations where signal strengths vary considerably. The combination of Matrix Pencil and minimum norm method provides for practical DOA estimation solution with possible real-time applications. We also show that this solution works extremely well in CDMA communication systems.
A systems biology approach to decoding the function of complex N-glycans

Embryogenesis, tissue repair and adaptive immunity involve developmental sequences of cell proliferation followed by differentiation and cell cycle arrest. Growth factors and other cytokines bind glycoprotein receptors to stimulate growth or arrest signaling, with the net response dependent on the availability of both ligands and receptors. The number of N-glycans (n), a distinct feature of each glycoprotein sequence, cooperates with the physical properties of the Golgi pathway to regulate surface levels of receptors. The Golgi pathway is ultrasensitive to hexosamine flux for the production of tri- and tetraantennary N-glycans, which bind galectins to form a molecular lattice that opposes glycoprotein endocytosis. Glycoproteins with few N-glycans (low n - e.g. TbetaR, CTLA-4, GLUT4) exhibit enhanced cell surface expression with switch-like responses to increasing hexosamine concentration, whereas glycoproteins with high numbers of N-glycans (high n - e.g. EGFR, IGFR, FGFR, PDGFR) exhibit hyperbolic responses. A bioinformatics survey shows that receptor kinases with high n play roles in metabolism and growth, while those with low n have functions in arrest and differentiation pathways. Computational modeling and experimental data reveal that these features impose a sequence of growth-to-arrest/differentiation, where growth-promoting high n receptors stimulate nutrient flux first, which then drives arrest/differentiation programs by increasing surface levels of low n glycoproteins. Interaction of the N-glycan branching pathway and N-glycan number play important roles in diseases, as evidenced by the identification of synergistic polymorphisms in Mgat1 and CTLA-4 in human multiple sclerosis patients. In order to fully understand the interaction of N-glycan functions with cellular phenotypes, we applied an unbiased screening approach to examine perturbation to N-glycan branching on a global scale. By utilizing microarray analysis and siRNA knockdown, we have identified GIcNAc-sensitive pathways that validate and extend our model, and simultaneously affect growth regulation, complex N-glycan processing, and constitutive endocytosis. Non-intuitive genes of interest identified by our screen include those associated with ionic regulation and proteoglycan biosynthesis. Our results reveal a mechanism for the metabolic regulation of the cellular transition between growth and arrest in mammals that arises from the apparent co-evolution of N-glycan number and branching.
Effect of exercise in women with polycystic ovary syndrome (PCOS): a randomized controlled trial of diet and exercise compared with diet alone

Background. PCOS affects 6% of reproductive aged women. It results in oligo/anovulation, hyperandrogenism, dyslipidemia, diabetes mellitus, and may increase risk of hypertension, endometrial cancer and coronary artery disease. Insulin resistance plays a critical role in PCOS. This randomized controlled trial was conducted to determine whether moderately intense exercise, combined with diet, is better than diet alone to improve ovulatory rates and other outcomes in women with PCOS. Interpretation. Exercise combined with diet may improve ovulatory and menstrual rates among women with PCOS. The main limitation of this trial was drop-out; however, the risk of harm with exercise is very low and therefore it should be offered as a non-pharmacologic alternative for women of reproductive age with PCOS. Results. Eighty-two women were randomized, 40 to the diet and exercise group and 42 to the diet only group. The two groups were similar at baseline. Primary outcome data were available on 38 women in the exercise group and 40 women in the control group. Secondary outcome data at 6 and 12 months were available on 26 and 21 women in the exercise group, and 27 and 28 women in the control group, respectively. There were trends favouring the exercise group for ovulation (RR [90%CI] = 1.71 [0.97, 2.41], p(1-tailed) = 0.056) and menses (RR [98%CI] = 1.36 [0.98, 1.83], p(1-tailed) = 0.014). No differences were seen in measures of insulin resistance, hyperandrogenemia, cardiovascular disease risk factors and SF-36 scores. There were trends favouring the exercise group for LH/FSH ratio (P = 0.036), Feniman-Gallwey hirsutism score (p = 0.018) and change in sleep at 6 months (p = 0.026). There was a trend towards lower BMI in the control group (p = 0.049). There were differences favouring the exercise group for percent body fat by skin folds (p = 0.010) and change in relationship satisfaction at 6 months (p = 0.001) and 12 months (p = 0.0025). Methods. Women with PCOS were randomly assigned to receive diet and exercise (exercise) or diet alone (control) for 12 months. The primary outcome was the ovulatory rate over 12 months. Secondary outcomes were other symptoms of PCOS and cardiovascular disease risk factors. The planned sample size was 80 women. Analysis was by intention-to-treat.
Values of Artin L-functions at s =1

In this thesis we prove, under GRH, several uniform estimates and upper bounds for Artin L-functions, in particular at s = 1. We begin by generalising an upper bound of Littlewood for Dirichlet L-functions. We prove logL1,c, K/F le;c1log loglogdK +O c1log dF+2, 1 where chi is an irreducible, non-trivial character of Gal(K/F), and dK and dF are the absolute values of the discriminants of K/ Q and F/ Q . This leads to an upper and a lower bound for L(1, chi). In the course of the proof of (1) we estimate log L(1, chi) by a short sum over the prime powers of F. If L(s, chi) is entire, then we sharpen the previous results. In the case F = Q this is due to Duke without a uniform error term. We use the orthogonality relations of group characters and the Chebotarev density theorem to prove several estimates for averages of L-functions associated to K/F. In particular we estimate c ne;1 cClog L1,c, K/F, 2 where C is any conjugacy class of G. We also estimate the sum and the mean square. These, in general, give sharper bounds than those given by trivial applications of (1). We discuss several examples and make comparisons with (1). We use the estimates of (2) to prove some further bounds. We prove another estimate for log L(1, chi, K/F) that is sharper than the previous estimate. We also prove a new estimate for the mean square and use (2) to conjecture an upper bound for the least prime in a conjugacy class. For all of the above, we prove sharper versions under further assumptions, in particular, if the L-functions considered are entire. Lastly we prove some convexity bounds. We prove an upper bound for the integral of L(s, chi) along the truncated line, realss = sigma from --iT to iT, where T is sufficiently large and sigma> ư + epsilon. We also prove some upper bounds for the integral along the line realss = 1 of averages of L-functions.
Evaluation of direct medical costs, lost productivity, health utility and quality of life in patients hospitalized for febrile neutropenia

Background. Febrile neutropenia (FN) is a common, serious adverse effect of chemotherapy; its treatment is costly as it typically involves hospitalisation, use of intravenous antibiotics, and sometimes expensive hematopoietic growth factors. Methods. A prospective cost-of-illness study evaluated direct medical costs of FN episodes treated in hospital. Lost productivity, health utility and quality of life were also quantified. Results. Fifty-one episodes of FN were included in the study. The mean length (+/- SD) of stay and mean cost per episode were 6.8+/-4.9 days and $6337+/- $4783CAD, respectively. Minimal lost productivity was attributable to FN. A mean health utility of 0.64 (+/- 0.22) was calculated and quality of life was decreased in FN. Conclusions. Hospitalization for the treatment of FN is expensive and quality of life is substantially decreased. The data obtained can be used as a baseline from which to evaluate cost-effectiveness of alternative interventions to treat and prevent FN.
A Navier-Stokes equation solver using agglomerated multigrid featuring directional coarsening and line-implicit smoothing

An explicit agglomeration multigrid method is presented for the Navier-Stokes equations with the Spalart-Allmaras turbulence model and applied to turbulent aerodynamic flows. The use of agglomeration provides an automated method for producing a sequence of coarse grids for use with multigrid. The solver employs a finite-volume formulation with a multistage relaxation scheme to produce steady-state solutions. Artificial dissipation is provided through a blend of an undivided Laplacian and biharmonic operator. Block-Jacobi preconditioning with matrix dissipation has been implemented. This solver is capable of using structured and unstructured grids, including mixed-element grids, with the primary focus being the use of unstructured grids. Competitive convergence rates approaching the theoretical limit of 0.75 for a second-order method are demonstrated for inviscid flow problems. Validation of inviscid and viscous results relative to two reference solvers and experimental results are presented. The main focus of this research is the improvement of convergence rates for turbulent flow problems. The performance of explicit multigrid methods applied to turbulent flow problems has typically been shown to be far slower than that for inviscid flow problems. Two techniques to improve the performance of explicit agglomeration multigrid for turbulent flow problems are presented. Directional-coarsening alters the agglomeration algorithm to directly alleviate numerical stiffness arising from grids containing high-aspect-ratio cells. Line-implicit smoothing alters the block-Jacobi preconditioner to introduce implicit terms along non-crossing lines constructed in the grid. Both methods are investigated separately and in combination to determine the best set of parameters and the limits of these methods. Substantial reductions in the cost of obtaining a solution are demonstrated for laminar and turbulent flow problems, with solutions converged over 10 orders of residual reduction being obtained in 25–33% of the time required for the base multigrid solver using isotropic coarsening.

Keywords: Navier-Stokes equations, Numerical solutions
Multigrid methods (Numerical analysis)
Turbulence, Mathematical models
Oral and written language abilities of grade 2 children: a longitudinal study

The purpose of this thesis was to characterize the oral and written language abilities of grade two children whose speech and language skills were assessed during their preschool years. The study compared these abilities through the administration of standardized assessment tools, including articulation, syntactic, semantic, metalinguistic, reading and spelling tests. Specific research goals included building a profile of each child based on the longitudinal data in order to chart particular developments across time, as well as to uncover possible oral language precursors to written language difficulties. Through the above research, it was found that the children assessed exhibited oral and/or written language difficulties during grade 2 and that their speech/language profiles changed significantly over time. The most significant oral language factors associated with grade 2 written language scores were found to be metalinguistic (including phonological awareness) and semantic language scores. Educational significance of the above findings is discussed.

Keywords: Children, Language
Language disorders in children, Longitudinal studies
The ART of representation: memory reduction and noise tolerance in a neural network vision system

The Feature Cerebellar Model Arithmetic Computer (FCMAC) is a multiple-input-single-output neural network that can provide three-degree-of-freedom (3-DOF) pose estimation for a robotic vision system. The FCMAC provides sufficient accuracy to enable a manipulator to grasp an object from an arbitrary pose within its workspace. The network learns an appearance-based representation of an object by storing coarsely quantized feature patterns. As all unique patterns are encoded, the network size grows uncontrollably. A new architecture is introduced herein, which combines the FCMAC with an Adaptive Resonance Theory (ART) network. The ART module categorizes patterns observed during training into a set of prototypes that are used to build the FCMAC. As a result, the network no longer grows without bound, but constrains itself to a user-specified size. Pose estimates remain accurate since the ART layer tends to discard the least relevant information first. The smaller network performs recall faster, and in some cases is better for generalization, resulting in a reduction of error at recall time. The ART-Under-Constraint (ART-C) algorithm is extended to include initial filling with randomly selected patterns (referred to as ART-F). In experiments using a real-world data set, the new network performed equally well using less than one tenth the number of coarse patterns as a regular FCMAC. The FCMAC is also extended to include real-valued input activations. As a result, the network can be tuned to reject a variety of types of noise in the image feature detection. A quantitative analysis of noise tolerance was performed using four synthetic noise algorithms, and a qualitative investigation was made using noisy real-world image data. In validation experiments, the FCMAC system outperformed Radial Basis Function (RBF) networks for the 3-DOF problem, and had accuracy comparable to that of Principal Component Analysis (PCA) and superior to that of Shape Context Matching (SCM), both of which estimate orientation only.

Keywords: Control theory
Manipulators (Mechanism), Design and construction
Computer vision
Remote control, Equipment and supplies
Fuzzy systems
Experimental determination of the modulation transfer function for high quantum efficiency electronic portal imaging detectors

Increasing the quantum efficiency, eta, of electronic portal imaging detectors (EPIDs) will enable the use of cone-beam megavoltage CT (MVCT) for image-guidance of radiotherapy by lowering dose requirements to obtain soft tissue contrast. As eta is increased the interaction of scattered photons within the detector causes signal blur, potentially limiting useful improvements in eta. An experimental model was developed to measure the expected modulation transfer function, MTF, for a large range of high-eta detectors without requiring a priori development of a detector prototype. For the range of eta studied, 0.02--0.86, the MTF does not drop considerably from the initial MTF. Measurements using both medium and high density build-up layers demonstrated that blur due to photon scatter is not greatly dependent on the material used to construct a high-eta EPID. Therefore, resolution in a high-eta EPID is not constrained by photon blur, and development of a high-eta EPID looks promising.