VictorJuiz/thesis huggingface dataset:
Development of the Mouse Notochord
Keywords: developmental biology
embryology
mouse
notochord

During development of the vertebrate embryo, a highly conserved tissue called the organizer forms during gastrulation, and is required for establishment of the basic body plan. In mouse, the organizer gives rise to the node and notochord, which are both transient signaling centres involved in patterning the body axes. The genetic regulation and morphogenesis of these tissues, particularly in the mouse, is not well understood. To follow the formation of these tissues we used time-lapse live imaging together with conventional cell lineage tracking. This showed that the notochord has distinct morphogenetic origins along the anterior-posterior axis: anterior head process forms by condensation of dispersed midline organizer cells; trunk forms by convergent extension of node cells; tail forms from posteriorly migrating node cells—this challenges the previously accepted model that tail notochord forms by node regression. We have also found there are distinct genetic requirements within these different regions. Previous mouse mutant analysis showed that conserved transcription factors Foxa2 and Noto are required for either all notochord regions or just tail notochord, respectively. We found a novel genetic interaction between the two demonstrated Foxa2 compensates for Noto specifically in the trunk notochord. Furthermore, we found Noto has a conserved role in regulating axial (notochord) versus paraxial (somite) cell fate. Therefore, we proposed there are three distinct regions within the mouse notochord, each with its own unique morphogenetic origins and genetic control. We have also conducted two microarray-based screens to identify novel gene expression patterns in the node and notochord. First, we compared Foxa2 mutant and wild type gastrula embryos. Second, we isolated notochord progenitors from early somite stage embryos. Extensive in situ hybridization screening based on both data sets revealed over 50 node and notochord expression patterns. Lastly, we screened Foxa2-bound chromatin regions near these notochord-specific genes using a transient zebrafish expression assay, and identified two novel notochord cis-regulatory modules. Together, we found a combination of classical genetics, embryology, and novel imaging techniques, has given us a better understanding of the morphogenesis and genetic regulation of pattern formation in the developing mouse embryo.
Imagining the Afro-Uruguayan Conventillo: Belonging and the Fetish of Place and Blackness
Keywords: Uruguay
blackness
whiteness
belonging
Latin America
race
gender
fetish
foklorization
space
conventillo
domestic work
Rosa Luna
Carlos Paez Vilaro
Afro-Uruguayan
Barrio Sur and Palermo
symbolic order
psychodynamics of place

This thesis explores the symbolic place occupied by a racialized neighbourhood within the Uruguayan national imaginary. I study the conventillos (tenement buildings) of two traditionally Afro-Uruguayan neighbourhoods in Montevideo, Barrio Sur and Palermo. These neighbourhoods are considered the cradle of Afro-Uruguayan culture and identity. The conventillos have been immortalized in paintings, souvenirs, songs, and books. Over the years most of the residents were evicted due to demolitions, which peaked during Uruguay’s military dictatorship (1973-1984). I address the paradox of how a community can be materially marginalized, yet symbolically celebrated, a process that is evident in other American nations (Brazil, Colombia, etc.). I show how race, class, and gender are entangled in folkloric depictions of the conventillo to constitute a limited notion of blackness that naturalizes the relationship between Afro-Uruguayans, music, sexuality, and domestic work. The folklorization of the space and it residents is shown to be a “fetishization” which enhances the whiteness of the national identity, while confining the parameters of black citizenship and belonging. Utilizing a methodology that draws on cultural geography, critical race, postcolonial, and feminist theory, my dissertation analyzes the various ways that the Barrio Sur/Palermo conventillo has been imagined, represented, and experienced. Specifically, I examine 1) autobiographical, literary and popular (media, songs) narratives about these neighbourhoods; 2) the depiction of the conventillo by a prominent artist (Carlos Páez Vilaró); 3) spatial practices; 4) the performance of a dancer who emerged from the conventillo to become a national icon (the Carnival vedette Rosa Luna); and 5) interviews with nine key informants. My analysis focuses on how bodies, subjects, and national belonging are constituted through relations to particular spaces. By foregrounding the “geographies of identity” (Radcliffe and Westwood, 1996, p. 27), I show that the symbolic celebration of black space goes hand in hand with material disavowal. This study thus connects the imagining of a local, racialized space to how national belonging is constituted and experienced.
Molecular Characterization of the von Hippel-Lindau Ubiquitin Ligase
Keywords: VHL
CCRCC
HIF
Polycythemia
Ubiquitin
NEDD8
Cullin
JAK2

Marking proteins for degradation by the proteasome is a classical function of ubiquitination. This process of covalent attachment of a chain of ubiquitin molecules to target proteins is governed by the ubiquitin-activating enzyme (E1), the ubiquitin-conjugating enzyme (E2) and the ubiquitin ligase (E3). The von Hippel-Lindau (VHL) tumour suppressor protein forms an E3 ubiquitin ligase, ECV (Elongins BC/Cul2/VHL), which targets the alpha subunit of hypoxia-inducible factor (HIF) for ubiquitin-mediated destruction under normal oxygen tension. Tumour hypoxia promotes accumulation of HIFalpha, whose expression is associated with cancer progression, poor prognosis and resistance to conventional therapies, thus establishing HIF as a therapeutic target. Notably, VHL is functionally inactivated in VHL disease, a hereditary cancer syndrome characterized by the formation of tumours in multiple organs, as well as in the majority of sporadic clear-cell renal cell carcinomas (CCRCC) and haemangioblastomas. Recently, certain VHL mutations have been shown to cause the congenital disorder Chuvash polycythemia. Work contained in this thesis describes the temporally coordinated activation of the ECV, whereby oxygen-dependent recognition of HIFalpha by VHL triggers Cul2 modification by the ubiquitin-like molecule NEDD8, which enhances ECV ubiquitin ligase activity by recruiting the E2. In addition, the feasibility of ‘bio-tailored’ enzymes in the treatment of cancer is introduced by creating a bioengineered VHL capable of targeting HIFalpha for degradation irrespective of oxygen tension, which leads to the dramatic inhibition of CCRCC tumour growth and angiogenesis in a xenograft model. Furthermore, a ubiquitin ligase composed of two F-box proteins, VHL and suppressor of cytokine signalling 1 (SOCS1), was identified and shown to be paramount for the negative regulation of erythropoiesis by targeting phosphorylated Janus kinase 2 (JAK2) for ubiquitin-mediated destruction. The malfunction of this ubiquitin ligase explains the excessive erythrocytosis observed in Chuvash polycythemia patients and reveals a novel genetic link between the seemingly distinct genes VHL and JAK2 in the development of polycythemia.
Transient and Steady-state Creep in a SnAgCu Lead-free Solder Alloy: Experiments and Modeling
Keywords: lead free solder
creep fatigue
transient creep
steady state creep
microelectronics packaging
reliability
finite element modeling
Monte Carlo analysis

It has been conventional to simplify the thermo-mechanical modeling of solder joints by omitting the primary (transient) contributions to total creep deformation, assuming that secondary (steady-state) creep strain is dominant and primary creep is negligible. The error associated with this assumption has been difficult to assess because it depends on the properties of the solder joint and the temperature-time profile. This research examines the relative contributions of primary and secondary creep in Sn3.8Ag0.7Cu solder using the constant load creep and stress relaxation measurements for bulk tensile specimens and the finite element analysis of a chip resistor (trilayer) solder joint structure that was thermally cycled under multiple temperature ranges and ramp rates. It was found that neglect of primary creep can result in errors in the predicted stress and strain of the solder joint. In turn, these discrepancies can lead to errors in the estimation of the solder thermal fatigue life due to the changing proportion of primary creep strain to total inelastic strain under different thermal profiles. The constant-load creep and stress relaxation data for Sn3.8Ag0.7Cu span a range of strain rates 10(-8) 1/s < strain rate < 10(-4) 1/s, and temperatures 25°C, 75°C and 100°C. Creep and stress relaxation measurements show that transient creep caused faster strain rates during stress relaxation for a given stress compared to the corresponding minimum creep rate from constant-load creep tests. The extent of strain hardening during primary creep was a function of temperature and strain rate. A constitutive creep model was presented for Sn3.8Ag0.7Cu that incorporates both transient and steady-state creep to provide agreement for both creep and stress relaxation data with a single set of eight coefficients. The model utilizes both temperature compensated time and strain rate to normalize minimum strain rate and saturated transient creep strain, thereby establishing equivalence between decreased temperature and increased strain rate. The apparent activation energy of steady-state creep was indicative of both dislocation core and bulk lattice diffusion was the most sensitive model parameter. A saturation threshold was defined that distinguishes whether primary or secondary creep is dominant under either static or variable loading.
Optimizing Femoral Head Preparation in Hip Resurfacing Arthroplasty
Keywords: Hip Resurfacing
Pre-operative Templating
Imageless Computer Navigation
Femoral Head Preparation
Femoral Neck Notching
Implant Alignment

Hip resurfacing is an alternative to total hip arthroplasty for the young and active patient likely to outlive traditional means of hip joint replacement. The acetabular cup is implanted in much the same fashion as an uncemented total hip arthroplasty, however, implantation of the femoral component is unique to hip resurfacing, presenting both distinct benefits and limitations. Hip resurfacing spares much of the proximal femur including the femoral neck and portions of the femoral head. This may be advantageous if the patient requires revision surgery; however, preservation of the femoral neck bears with it the risk of femoral neck fracture. The exact mechanism of neck fracture is not fully understood. Avoiding potential fracture risks is vital to ensuring optimal patient outcomes. The current work investigated mechanical femoral head preparatory factors that may predispose to femoral neck fracture. Intra-operative computer navigation is emerging as the gold-standard in orthopaedic care. In hip resurfacing, navigation may improve the surgeon’s ability to optimally implant the resurfacing prosthesis; however, much of this technology is still in its infancy and requires investigation into the accuracy and repeatability of this peri-operative tool. Pre-operative planning can assist the surgeon in optimally determining the size and position of the resurfacing components, specifically in reference to the patient’s unique anatomy, prior to performing the operation. This may aid in correct implant selection and provide a basis on which to conduct intra-operative navigation. However, the accuracy and repeatability of pre-operative planning for hip resurfacing has not yet been established. Thus, this body of work looked to establish a clear methodology for pre-operative planning, intra-operative computer navigation and surgical technique in order to optimize preparation of the femoral head, ultimately reducing the risk of femoral neck fracture in hip resurfacing.
Evaluation of Mismatch Repair Gene Polymorphisms and their Contribution to Colorectal Cancer and its Subsets
Keywords: Colorectal Cancer
Mismatch Repair
Single Nucleotide Polymorphism
DNA Methylation

Colorectal cancer (CRC) is a major source of morbidity and mortality in the Western world. Approximately 15% of all CRCs develop via the mutator pathway, which results from a deficiency of mismatch repair (MMR) system and leads to genome-wide microsatellite instability (MSI). MLH1 promoter hypermethylation accounts for the majority of MSI CRCs. Numerous single nucleotide polymorphisms have been identified in MMR genes, however their functional roles in affecting MMR system, and therefore susceptibility to MSI CRCs, are unknown. This study uses a multidisciplinary approach combining molecular genetics, epigenetics, and epidemiology to examine the contribution of MMR gene polymorphisms in CRC. Among a panel of MMR SNPs examined, the MLH1 (-93G>A) promoter polymorphism (rs1800734) was shown to be associated with increased risk of MSI CRCs in two Canadian populations, Ontario and Newfoundland. Functional studies of the MLH1-93G>A polymorphism indicate that it has weak effects on the core promoter activity, although it dramatically reduces activity of the shorter promoter constructs in a panel of cell lines. Furthermore, MLH1 gene shares a bi-directional promoter with EMP2AIP1 gene, and the MLH1-93G>A polymorphism increases the activity of the reverse, EPM2AIP1 promoter. Examination of alternative role of the MLH1-93G>A polymorphism in MSI-H CRCs led to evaluation of a 500-kilobase pair chromosome 3 region around the MLH1 gene and identification of two additional SNPs, rs749072 and rs13098279, which are in strong linkage disequilibrium with rs1800734. All three SNPs showed strong associations with MLH1 promoter methylation, loss of MLH1 protein expression, and MSI-H CRCs in three populations, Ontario, Newfoundland, and Seattle. Such findings potentially implicate genetic susceptibility to DNA methylation. Logistic regression models for MSI-H versus non-MSI-H CRCs demonstrate that models including MLH1 IHC status and MLH1 promoter methylation status fit the data most parsimoniously in all three populations combined, however, when rs1800734/rs749072/rs13098279 was added to this model, polymorphisms no longer remained significant indicating that the observed associations of these polymorphisms with the MSI-H CRCs occur through their effect on DNA methylation. This study identified a novel mechanism in which common missense alterations may contribute to complex disease.
Drosophila melanogaster as a Model Organism to Study Human Neurodegenerative Diseases
Keywords: Models of human disease

A great deal of our current understanding about the biology of neurodegenerative diseases has come from studying the function of genes linked to inherited forms of these disorders. Work performed in animal models, including vertebrates as well as invertebrates, has been instrumental in deciphering the cellular, physiological and behavioural deficits arising from the expression of disease-causing genes. Using the fruit fly, Drosophila melanogaster, as a model we examined the normal and aberrant function of two genes linked to the onset of neurodegeneration in humans, presenilin and superoxide dismutase. Drosophila is an extremely versatile model and in many ways is ideal for studying the genetic basis of human disease. The high degree of genetic conservation coupled with low genetic redundancy make this model particularly well suited for studying the function of disease causing genes. We demonstrate a novel genetic,physical and physiological interaction between presenilin and calmodulin and describe how this interaction impacts a very early cellular defect associated with Alzheimer?s Disease, intracellular calcium dyshomeostasis. We also describe progressive locomotory deficits in flies expressing mutant alleles of the superoxide dismutase gene, which have been linked to the onset of familial amyotrophic lateral sclerosis. Collectively, our work demonstrates that Drosophila can be used to study the cellular, physiological and behavioural basis of human neurodegenerative diseases and may provide a model to identify novel therapeutic avenues for neurodegenerative diseases.
Molecular Imaging as a Tool for Predicting and Monitoring Response of Breast Cancer to Trastuzumab (Herceptin(R))
Keywords: Nuclear Medicine
Molecular Imaging
Breast Cancer
Trastuzumab
HER2
Pertuzumab

The human epidermal growth factor receptor 2 (HER2) is overexpressed in 20% of breast cancers (BCs) and confers an aggressive tumour phenotype with a poor prognosis. Trastuzumab (Herceptin®) is a humanized IgG1 monoclonal antibody (mAb) approved for treatment of HER2-positive breast cancer (BC), however many eligible patients do not respond. The hypothesis was that molecular imaging strategies that probe: i) the expression of HER2; ii) one of the mechanisms of action of trastuzumab or iii) evaluate the viability of tumour cells by their glucose utilization would be useful in predicting and monitoring the response of BC to treatment with trastuzumab. The relationship between tumour HER2 density, uptake of 111In-DTPA-trastuzumab and response to trastuzumab was evaluated by gamma camera imaging, biodistribution studies and monitoring tumour growth in mice implanted with BC xenografts. There was a non-linear relationship between HER2 expression and uptake of this radiopharmaceutical when tumour uptake was corrected for non-specific IgG accumulation and/or circulating blood radioactivity (r2=0.87-0.99). Tumour response corresponded better with the uncorrected tumour uptake of 111In-DTPA-trastuzumab. HER2 downregulation, a putative mechanism of action of trastuzumab, was noted as decreased tumour uptake on microSPECT/CT of mice bearing MDA-MB-361 xenografts administered 111In-DTPA-pertuzumab. Tumour uptake of 111In-DTPA-pertuzumab was reduced by 53% in mice treated for 3 days with trastuzumab (P<0.05) associated with an early molecular response to the drug. Furthermore, tumour uptake of 111In-DTPA-pertuzumab was reduced by 78% (P<0.001) in mice treated for 3 weeks, which corresponded with a reduction in HER2-positive tumour cells, indicating a therapeutic response. The relationship between changes in tumour uptake of 18F-2-fluoro-2-deoxy-D-glucose (18F-FDG) and response to trastuzumab was examined in mice bearing MDA-MB-361 and MDA-MB-231 BC xenografts, with high or very low HER2 expression, treated with trastuzumab. MicroPET imaging and biodistribution studies detected a 43-60% (P<0.03) reduction in tumour uptake of 18F-FDG in mice with MDA-MB-361 xenografts, treated with trastuzumab compared to PBS-treated controls. In contrast, there was no change in 18F-FDG uptake in MDA-MB-231 xenografts, that did not respond to trastuzumab. I conclude that molecular imaging is a promising tool for monitoring response of BC to treatment with trastuzumab.
Using the Cognitive Orientation to Daily Occupational Performance (CO-OP) Treatment Approach with Adults with Stroke: Efficacy and Adaptations
Keywords: Stroke
Rehabilitation
Cognitive Strategies
Motor Performance
Motor Learning

This thesis reports on a multi-phased research project conducted to evaluate the use of the Cognitive Orientation to daily Occupational Performance (CO-OP) approach with adults with stroke. Current approaches to motor recovery, called systems approaches, suggest that movement arises from a dynamic interaction among several different systems, including perception, cognition, and action, all within the context of the individual and his or her environment. CO-OP is an established treatment approach for children with motor-based performance problems that takes into account interactions among several systems, as well as individual needs and environmental factors. CO-OP is a client-centred, problem solving approach based on the theoretical foundations of learning and motor learning theory. The objectives of this project were: to examine the efficacy of CO-OP to improve motor skill acquisition and performance in adults living with chronic stroke; to explore other benefits of the approach; and to identify adaptations for use with adults with stroke. Two series of single case experimental studies were conducted, with three participants completing each. In addition, semi-structured interviews were conducted. Findings from the single case experiments provide evidence that CO-OP is associated with performance improvements in both trained and untrained self-selected goals in adults more than one year post stroke. As well, pre-post measures suggest there may be changes in performance satisfaction, motor control, generalized use of the affected upper extremity, and self-efficacy. Interview findings provided valuable information about the experiences of participants with the approach; the interview respondents enjoyed the increased sense of responsibility that came with problem solving on their own, but expressed a desire to have ongoing professional support. Suggestions for modifications to CO-OP for use adults with stroke are made. CO-OP is a promising approach to improve functional independence in adults with stroke. Future research is warranted.
Polymer Diffusion in Latex Films
Keywords: polymer

In this thesis, I describe experiments that provide a new and deeper understanding of factors that affect polymer diffusion in acrylic latex films. This is the step that leads to the growth of mechanical properties of these films. Polymer diffusion was studied by fluorescence resonance energy transfer (FRET) in films prepared from dye-labeled latex particles. Poly(n-butyl acrylate-co-methyl methacrylate) [P(BA-MMA)] was chosen for the study of copolymer composition on the polymer diffusion rate. Four sets of P(BA-MMA) copolymers were prepared from various weight ratios of BA/MMA. Polymer diffusion was monitored as a function of annealing temperature, and apparent diffusion coefficients (Dapp) were calculated from the FRET data, using a simple diffusion model. The temperature dependence of polymer dynamics (G’, G”) obtained by linear rheology measurements is in good agreement with the temperature dependence of Dapp. Increasing the BA content of the copolymer led to an apparent increase in long-chain branching, which is reflected in both the time dependence of Dapp and in the dynamic moduli measurements. To study the effect of branching on polymer diffusion rates, latex particles comprised of branched poly(n-butyl methacrylate) (PBMA) were prepared. The degree of branching was controlled by adding various amounts of bisphenol A dimethacrylate as a branching agent, plus 1-dodecanethiol as a chain transfer agent to prevent gel formation and to control the polymer molecular weight. The results of rheology (G’, G”) measurements are consistent with the absence of entanglement in these polymers. After correcting for the effects of Tg, by comparing results at a constant T- Tg, ET data show that the PBMA with the highest degree of branching had the highest diffusivity. In a separate set of experiments I tested the effect of incorporating the highly branched PBMA (HB-PBMA) into P(BA-MMA) dispersions to examine its influence on polymer diffusion in the latex films. Three different approaches were taken to combine these different polymers: latex blends, using HB-PBMA seeds in the synthesis of P(BA-MMA) by semicontinuous emulsion polymerization, and dissolving HB-PBMA in the mixture of BA and MMA for latex particles prepared by miniemulsion polymerization. ET studies indicate that HB-PBMA significantly enhances polymer diffusion rate, comparable with TexanolTM, a volatile organic coalescing agent. Tensile tests show that the films containing HB-PBMA have significant higher mechanical properties than the films containing TexanolTM.