VictorJuiz/thesis huggingface dataset:
Axisymmetric Drop Shape Analysis (ADSA) and Lung Surfactant

The objective of this thesis was to further develop a methodology for surface tension measurement called Axisymmetric Drop Shape Analysisn(ADSA) and to adapt it to studies of lung surfactants, i.e. the material that coats and facilitates the functioning of the lungs of all mammals. The key property of a functioning lung surfactant is its surface tension, which can reach extremely low values. Such values are difficult to measure; but a certain configuration of ADSA, using a constrained sessile drop (ADSA--CSD), is capable of performing such measurements. Clinically, lung surfactant films can be altered from both sides, i.e. from the airspace as well as from the bulk liquid phase that carries the film. Therefore, being able to access the interface from both sides is important. Here, ADSA--CSD was redesigned to be used as a micro film balance allowing access to the interface from both gas- and liquid-side. This allows deposition from the gas side as well as complete exchange of the bulk liquid phase. The new design was used to study lung surfactant inhibition and inhibition reversal. A dynamic compression-relaxation model (CRM) was developed to describe the mechanical properties of lung surfactant films by investigating the response of surface tension to changes in surface area. The model evaluates the quality of lung surfactant preparations -- beyond the minimum surface tension value -- and calculates the film properties, i.e. elasticity, adsorption and relaxation, independent of the compression protocol. The accuracy of the surface tension measurement can depend on drop size. A detailed analysis of drop shapes and accuracy of measured surface tension values was performed using a shape parameter concept. Based on this analysis, the design of ADSA--CSD was optimized to facilitate more accurate measurements. The validity analysis was further extended to the more conventional pendant drop setup (ADSA--PD). An overall upgrade of both hardware and software of ADSA--CSD, together with extensive numerical work, is described and applied to facilitate a more efficient operation. Finally, it is noted that the ADSA--CSD setup developed here can be used for a wide range of colloid and surface chemical applications.

Keywords: Surface Thermodynamics
Surface Tension
ADSA
Lung Surfactant
Advisor: Neumann, A. Wilhelm
Acosta, Edgar
Systematic Genetic Analysis of Dimorphism in Saccharomyces cerevisiae

Deletion mutant collections allow for the systematic study of gene function by linking a genotype to a phenotype. Furthermore, these collections permit the parallel and quantitative study of phenotypes, which is the foundation of functional genomics. I begin by summarizing the methods used and data derived from the field of functional genomics using the Baker’s yeast Saccharomyces cerevisiae, and provide important background information on the origins of the filamentous growth-competent S.cerevisiae strain Σ1278b, and the developmental process of fungal dimorphism. I describe my efforts in creating a complete deletion mutant collection in the filamentous growth-competent S.cerevisiae strain Σ1278b, and the subsequent phenotypic analysis of that deletion mutant collection. By quantitatively measuring mutant phenotypes of cells undergoing haploid invasive growth, biofilm mat formation and diploid pseudohyphal growth, I studied the clinically relevant developmental process of fungal dimorphism. I present the first genome-wide and quantitative phenotypic analysis of fungal dimorphism and identify a novel transcription factor encoded by the open reading frame YDL233W, which I named FMR1for Filamentation Master Regulator 1. By performing genetic, cell biological, biochemical, and expression analysis, I demonstrate that Ydl233w acts by forming a protein complex with the DNA-binding transcription factors Flo8 and Mss11 and this complex binds to a specific element within the promoter of the surface adherence mediating gene FLO11. I directly compare the essential gene sets between the Σ1278b deletion collection and the reference deletion collection made in the S288c genetic background completed by the Yeast Deletion Consortium in 2002. I find that most essential genes are shared between these two strains but a number of genes are essential for viability in only one genetic background, a phenomenon termed conditional essentiality. I describe the genetic basis of conditional essentiality as a consequence of the complex inheritance of background-specific alleles. Lastly, I summarize the scientific advancements of my research using the Σ1278b deletion collection, and highlight some potential applications for both the data derived from my research and the deletion mutant collection itself. The Σ1278b deletion collection provides a valuable resource for yeast geneticists, evolutionary biologists, researchers of fungal disease, and researchers interested in modeling the genetics that underlie complex traits and diseases.

Keywords: Genomics
Yeast
Advisor: Boone, Charles
Zelter, Goethe and the Emergence of a German Choral Canon

This thesis examines the dialogue between Carl Friedrich Zelter (1758-1832) and Johann Wolfgang von Goethe (1749-1832) on choral music and the role they envisioned for it within a national German repertory. The primary source for this examination is the voluminous correspondence between the two men, which spans almost 900 letters and over thirty years. In the correspondence, they discuss choral music both as an abstract and practical art. In addition, Zelter’s descriptions of concerts that he performed in and attended form a valuable record of musical life in Berlin in the early nineteenth-century. To show the importance of choral music within the correspondence, this thesis is divided into three parts: an examination of Zelter and Goethe’s engagement with (choral) music; their respective choral organizations; and two musical case studies that show the application of their discussions. The first segment allows for a fuller understanding of how choral music fit in Zelter and Goethe’s larger artistic endeavours. This context is especially important given their marginal musical legacies, which have contributed to the scholarly neglect of their discourse on choral music. The second segment examines Zelter’s work with the Berlin Sing-Akademie in detail, focussing on its performance practice, membership, and audience. This examination shows that contrary to the oft-repeated claim that the Sing-Akademie did not regularly perform in public until 1829, the chorus in fact sang for a wide audience on a regular basis from the early 1800s on. The third segment provides case studies on the music of J.S. Bach and G.F. Handel. Goethe and Zelter’s dialogue about the two composers is considered, along with their practical engagement with the repertoire. Further, the Sing-Akademie’s performance history of both composers is examined. In sum, this thesis demonstrates the central role of historical choral music in the correspondence of Goethe and Zelter; their interest in older German choral music is shown to have had a profound impact on the music performed by similar organizations across Germany.

Keywords: Zelter
Goethe
Choral
Bach
Advisor: Parker, Mary Ann
Elliott, Robin
Labour Force Participation and Health-related Quality of Life in People Living with HIV

This dissertation consists of four papers aimed at understanding the complex relationship between employment and health. One paper is a systematic review of the return to work literature, while the other three papers used secondary data from three cohorts of people with HIV to examine the association between employment and health-related quality of life. The systematic review looked at longitudinal studies that reported health outcomes associated with return to work in relation to other employment trajectories. This review supported the beneficial effect of return to work on health in a variety of populations, times, and settings, and also found evidence that poor health interferes with the prospects of returning to work. Two other papers looked at the association between employment and health-related quality of life in people with HIV; one paper used a cross-sectional sample of people with HIV, while the other paper used a longitudinal sample of men who have sex with men. These two studies found evidence to support the association between employment and both physical and mental health-related quality of life. They also found that employment had a stronger relationship with physical than mental health, suggesting an adaptation process to the experience of unemployment. Finally, another paper examined the cross-sectional association between job security and quality of life in men and women living with HIV. This study found that job security offered additional mental health quality of life benefits, over and above participation in employment alone, for men living with HIV. On the other hand, women benefited from the availability of work, but the perception of job security failed to offer additional health benefits. The current level of evidence on the relationship between work and health in HIV needs to be strengthened by further research to develop and support practical clinical and policy recommendations.

Keywords: employment
health-related quality of life
HIV
Advisor: Mustard, Cameron
Role of the Intestinal Epithelial Insulin-like Growth Factor-1 Receptor in Glucagon-like Peptide-2-mediated Small Intestinal Growth Responses

The gut hormone glucagon-like peptide-2 (GLP-2) has numerous beneficial effects on the intestinal epithelium, including increased mucosal growth and proliferation. GLP-2 is also necessary for the adaptive intestinal re-growth that occurs upon re-feeding after fasting. Although insulin-like growth factor (IGF)-1 and the IGF-1 receptor are known to be required for GLP-2-induced crypt-cell proliferation, the precise cellular localization of the IGF-1 receptor through which the intestinotrophic actions of GLP-2 are mediated remains unknown. I hypothesized that small intestinal growth responses to GLP-2 occur through an intestinal epithelial IGF-1 receptor-dependent pathway, through the use of an inducible, intestinal epithelial-specific IGF-1 receptor knockout (IE-igf1rKO) mouse. Intestinal growth and proliferative responses were examined in IE-igf1rKO and control mice following treatment with GLP-2, as well as in animals that were fasted and re-fed to induce GLP-2-dependent adaptation. In Chapter 3, it was demonstrated that IE-igf1rKO mice, as compared to control littermates, had normal small intestinal weight, morphometric parameters, proliferative index and differentiated epithelial cell lineage distribution. Administration of GLP-2 for 30 minutes increased nuclear translocation of !-catenin in non-Paneth crypt-cells, and stimulated the crypt-cell proliferative marker c-Myc 90 minutes following GLP-2 treatment, in control littermates but not in IE-igf1rKO mice. In Chapter 4, adaptive re-growth was studied by fasting IE-igf1rKO and control animals for 24 hours, or by fasting and then re-feeding mice for 24 hours. Small intestinal weight, crypt depth, villus height and crypt-cell proliferation were decreased in both control and IE-igf1rKO mice after 24 hour fasting. While re-feeding in control mice restored all of these parameters, re-fed IE-igf1rKO mice displayed abrogated adaptive re-growth of the crypt-villus axis as well as reduced crypt-cell proliferation. In Chapter 5, control mice responded to chronic GLP-2 with increased small intestinal weight, mucosal cross-sectional area, crypt depth, villus height and crypt-cell proliferation. However, the GLP-2-induced increase in crypt-cell proliferation was absent in IE-igf1rKO mice, in association with impaired growth of the crypt-villus axis. Taken together, these results indicate that the proliferative responses of the intestinal epithelium to exogenous GLP-2 administration and during conditions of GLP-2-dependent adaptive re-growth are dependent on the intestinal epithelial IGF-1 receptor.

Keywords: intestine
proliferation
insulin-like growth factor
glucagon-like peptide-2
Advisor: Brubaker, Patricia
The Left Regular Representation of a Semigroup

As with groups, one can study the left regular representation of a semigroup. If one considers such representations, then it is natural to ask similar questions to the group case. We start by formulating several questions in the semigroup case and then work towards understanding the structure of the representations given. We present results describing what the elements of the image under the representation map can look like (the semigroup problem), whether or not two semigroups will give isomorphic representations (the isomorphism problem), and whether or not the representation of a semigroup is reflexive (the reflexivity problem). This research has been funded in part by a scholarship from the Natural Sciences and Engineering Research Council of Canada.

Keywords: Operator Theory
Semigroups
Advisor: Rosenthal, Peter
The Social Organization of the Ontario Minimum Wage Campaign

My dissertation research is interdisciplinary in nature, at the nexus of three areas of scholarly work and actual practices: union renewal and non-unionized workers-rights organizing in Canada and the US; feminist, anti-racist Marxian approaches to class relations as being racialized, gendered and bureaucratic; and, the institutional ethnographic method of inquiry into social reality. My empirical focus is on the Ontario Minimum Wage Campaign (OMWC). The OMWC was a Toronto-based labour-community project to raise the minimum wage to $10 per hour. It was started in 2001 by Justice for Workers (J4W), was carried on by the Ontario Needs a Raise coalition (ONR) from 2003 to 2006, and was re-launched in 2007 by the Toronto and York Region Labour Council (TYRLC) in association with some community groups. The OMWC brought together across time and space activist groups, community agencies and labour organizations, all of whose volunteers, members, clients, educators, officials and staff were the agents and/or targets of the campaign. The apparent victory of the OMWC is quite contested. Local campaign realities were compartmentalized in numerous ways and OMWC involvement met different institutionally specific and coordinated needs. And while coalitions generally arise as vehicles to transcend such institutional separation, the campaign was challenged to materially bridge such compartmentalization. The fragmentation of reality amongst institutions and how it was managed in practice affected how collaboration, participation, and decision-making happened and appeared to have happened in organizing and educational activities. While there were at times transformative intentions, there was generally a pragmatic anti-racist organizing practice and effect. I contend that the complexity of contemporary society poses great challenges for the possibilities for human-agency based labour-community workers-rights organizing with a broad-based, political capacity for movement building orientation. I suggest that this is largely so because the social coordination of what we do and what we understand about what we do turns on at least three components of social reality: an institution-based organization of multi-layered social relations that is generally locally circumscribed but extralocally driven; a conditioned individually-driven orientation to meeting human needs; and an ideological orientation to both the content of ideas and thought, and the process of that reasoning.

Keywords: labour-community coalitions
race, gender, class
social relations
workers rights
Advisor: Mojab, Shahrzad
The Impact of the Grameen Bank upon the Patriarchal Family and Community Relations of Women Borrowers in Bangladesh

The purpose of the study is to: (1) examine the degree to which women borrowers of the Grameen Bank are being empowered to participate in familial decision-making around the management of income and expenditures like food, children’s education, dowry and teenage marriages; and (2) to examine women borrowers’ engagement in community activities such as the degree of freedom women are granted to visit public places like schools, local councils, banks and markets. In particular, the study explores the role of the Grameen Bank (GB) in women’s empowerment through the Sixteen Decisions, an educational program designed to empower women in the family and community. This study used a mixed-methods research design that included 61 GB women borrowers selected through purposive sampling. The data suggest that the participants have assumed leadership roles within their families: more than 80% of the study’s participants led decision making within their family; more than 90% supported their children’s education financially; 91% reported that they worked together with family members to manage day-to-day expenses; 80% reported that they manage their family incomes; 98% reported they do not like dowry marriages and teenage marriages; and 33% view male-dominant values as a hindrance to women’s development. The findings indicated that 98% of GB women borrower participants are engaged in community organizations and 94% do not face problems with this engagement. In the 2009 UpZilla (Municipal Sub-district) Election, out of 481 seats, 114 Female Chairs (25% of the total) were elected from the GB women borrowers and their families (Grameen Bank, 2009). In addition, the number of women borrowers serving as councilors has increased from 1,572 in 1997 to 1,950 in 2003; these data indicate that the number of women borrowers acting in formal leadership roles is increasing (Grameen Bank, 2009). The study finds the GB program has had a positive impact upon the borrowers’ relations in the family and community. In spite of these developments, one-fifth of GB women borrowers’ husbands control their wives’ loan money, an indication of the strength of patriarchy in Bangladesh. Although GB’s Sixteen Decisions have included economic issues and other social issues, none directly discusses gender inequality, which the study findings suggest is important. Hence a revision of the Sixteen Decisions is suggested.

Keywords: Grameen Bank
women empowerment
community development
patriarchy
community space
micro credit
Advisor: Quarter, Jack
Full-band Structure Calculations of Optical Injection in Semiconductors: Investigations of One-color, Two-color, and Pump-probe Scenarios

Carrier, spin, charge current, and spin current injection by one- and two-color optical schemes are investigated within 30-band k·p theory. Parameters of the band model are optimized to give full-Brillouin zone band structures for GaAs and Ge that give accurate Γ-point effective masses and gyromagnetic factors and give access to the L valley, and to the E₁ and E₁+Δ₁ critical points in the linear optical absorption. Calculations of one- and two-photon carrier and spin injection and two-color current injection are performed for excitation energies in the range of 0—4 eV in GaAs and 0—3.5 eV in Ge. Significant spin and spin current injection occurs with 30% spin polarization in GaAs and Ge at photon energy matching the E₁ critical point. Further, the anisotropy and disparity of the current injection between parallel and perpendicular linearly-polarized beam configurations are calculated. For light propagating along a <111> crystal axis, anisotropic contributions in coherent current control and two-photon spin injection give rise to normal current components and in-plane spin components. In Ge, contributions from the holes to spin, electrical current, and spin current injection are investigated. Optical orientation results in 83% spin-polarized holes at the band edge. The effects of carrier dynamics in Ge are treated within a rate-equation model. The detection of spin dynamics in a pump-probe setup is considered, and the Fermi-factor approach is justified for electrons but not for holes. Carrier and current injection are further investigated in single-layer and bilayer graphene within the tight-binding model. In single-layer graphene, the linear-circular dichroism in two-photon absorption yields an absorption coefficient that is twice as large for circularly polarized light compared to linearly polarized light. Coherent current injection is largest for co-circularly polarized beams and zero for cross-circularly polarized beams. For linearly polarized beams, the magnitude of the injected current is independent of beam polarizations. In contrast, the injected current in bilayer graphene shows disparity between parallel and perpendicular configurations of the beams. The resulting angular dependence of the current is a macroscopic, measurable consequence of interlayer coupling in the bilayer.

Keywords: bilayer graphene
carrier dynamics
carrier injection
chi(3)
coherent control
current injection
GaAs
gallium arsenide
Ge
germanium
graphene
nonlinear optics
optical injection
optical orientation
quantum interference
spin current injection
spin dynamics
spin injection
Advisor: Sipe, John E.
Injuries Among Elderly Canadians: Psychotropic Medications and the Impact of Alcohol

Psychotropic medication use is widely implicated as a risk factor for injuries, and it is believed that the adverse effect profiles of these medications are exacerbated by the consumption of alcohol. The objectives of this study are (a) to examine the associations between the use of specific classes of psychotropic medications and injuries among elderly participants of the National Population Health Survey (NPHS), and (b) to determine whether and how associations between psychotropic medications and injuries are modified by the consumption of alcohol. Data from Cycles 1 (1994/95), 2 (1996/97), and 3 (1998/99) of the NPHS household longitudinal file were used in this study, selecting community-dwelling participants aged 65 years of age and older in 1994/95. Among antidepressant medications, the magnitude of the risk of injuries was higher for users of tricyclic derivatives (OR=1.4; 95%CI: 0.7 – 2.9) than SSRIs (OR=0.3; 95%CI: 0.1 – 1.0). Benzodiazepine use for any indication increased the risk of injuries, but that effect was not consistent across indications. The use of benzodiazepine antianxiety medications resulted in an increased risk of injuries (OR=2.0; 95%CI: 1.3 – 3.1), but there were no significant effects on the injury risk among benzodiazepine hypnotic and sedative users (OR=0.8; 95%CI: 0.4 – 1.7). Results pertaining to the second objective of this study raised as many questions as they resolved. Alcohol consumption decreased the odds of injury among hypnotic and sedative users, but otherwise, no consistent results were observed. Findings from this study underscore the importance of identifying appropriate alcohol measures for research among elderly populations. They also stress the need to separately consider the impact of different classes of psychotropic medications on injuries (tricyclic antidepressants separate from SSRI antidepressants and antianxiety benzodiazepines separate from hypnotic and sedative benzodiazepines).

Keywords: epidemiology
public health
injuries
psychotropic medications
alcohol
National Population Health Survey
longitudinal
antidepressant medications
SSRI medications
benzodiazepines
antianxiety medications
hypnotics
sedatives
drinking
geriatrics
seniors
accidents
NPHS
Advisor: Chipman, Mary