VictorJuiz/thesis huggingface dataset:
Structure and Dynamics of AcrA, a Periplasmic Component of a Multidrug Efflux Pump
Keywords: Site-directed spin labeling
Electron paramagnetic resonance
Membrane fusion protein
TolC
Conformational change
Proton-motive force

AcrA is the periplasmic component of an efflux system AcrA-AcrB-TolC, which can expel different classes of antibiotics. AcrB is the inner membrane (IM) pump that utilizes proton-motive force for the active transport, TolC is the outer membrane (OM) channel, and AcrA coordinates the actions of AcrB and TolC, so that substrates are expelled across the two membranes, bypassing the periplasm. It has been proposed that AcrA either provides a static seamless link between AcrB and TolC, or acts like its analogous viral membrane fusion protein (MFP) and actively brings the IM and OM closer for substrate transfer. To better understand the role of AcrA in the efflux mechanism, site-directed spin labeling (SDSL)/EPR (electron paramagnetic resonance) spectroscopy is used to investigate the structure and dynamics of AcrA in solution. My results demonstrated that AcrA is a dynamic protein that undergoes pH-dependent and reversible conformational changes. AcrA contains an interrupted alpha-helical, coiled-coil domain flanked by a pair of beta-stranded lipoyl motifs, and my SDSL/EPR analysis revealed that the pH-induced conformation change mainly involves the coiled-coil and the lipoyl domains. In addition, I found that each AcrA monomer folds into an intra-molecular hairpin and AcrA monomers oligomerize with their coiled-coil hairpins aligned in parallel. Unlike the pH-induced conformational rearrangement of a viral MFP, change in pH alters both intra- and inter-molecular interaction along the coiled-coil of AcrA without rearranging the hairpin fold. The organization of AcrA protomers and its pH-induced conformational switching are, however, congruent with the TolC coiled-coil hairpins in the iris-like opening of the TolC channel. Together, my studies suggest that rather than being a passive structural linkage between AcrB and TolC, AcrA plays an active role mediating the drug efflux. The reported AcrA dynamics provides new insights into the AcrA-TolC interactions for the channel opening during the efflux process.
Seismic Imaging of Gas Hydrate Reservoir Heterogeneities
Keywords: Gas Hydrate
Seismic Imaging

Natural gas hydrate, a type of inclusion compound or clathrate, are composed of gas molecules trapped within a cage of water molecules. The presence of gas hydrate has been confirmed by core samples recovered from boreholes. Interests in the distribution of natural gas hydrate stem from its potential as a future energy source, geohazard to drilling activities and their possible impact on climate change. However the current geophysical investigations of gas hydrate reservoirs are still too limited to fully resolve the location and the total amount of gas hydrate due to its complex nature of distribution. The goal of this thesis is twofold, i.e., to model (1) the heterogeneous gas hydrate reservoirs and (2) seismic wave propagation in the presence of heterogeneities in order to address the fundamental questions: where are the location and occurrence of gas hydrate and how much is stored in the sediments. Seismic scattering studies predict that certain heterogeneity scales and velocity contrasts will generate strong scattering and wave mode conversion. Vertical Seismic Profile (VSP) techniques can be used to calibrate seismic characterization of gas hydrate expressions on surface seismograms. To further explore the potential of VSP in detecting the heterogeneities, a wave equation based approach for P- and S-wave separation is developed. Tests on synthetic data as well as applications to field data suggest alternative acquisition geometries for VSP to enable wave mode separation. A new reservoir modeling technique based on random medium theory is developed to construct heterogeneous multi-variable models that mimic heterogeneities of hydrate-bearing sediments at the level of detail provided by borehole logging data. Using this new technique, I modeled the density, and P- and S-wave velocities in combination with a modified Biot-Gassmann theory and provided a first order estimate of the in situ volume of gas hydrate near the Mallik 5L-38 borehole. Our results suggest a range of 528 to 768×10^6 m^3/km^2 of natural gas trapped within hydrate, nearly an order of magnitude lower than earlier estimates which excluded effects of small-scale heterogeneities. Further, the petrophysical models are combined with a 3-D Finite Difference method to study seismic attenuation. Thus a framework is built to further tune the models of gas hydrate reservoirs with constraints from well logs other disciplinary data.
Massage Therapy Visits By The Aged: Testing a Modified Andersen Model
Keywords: Andersen Model
Massage Therapy

Growing evidence suggests that chronic health conditions and disability act as reliable predictors of complementary/ alternative medicine (CAM) use. Such use may have the potential for some to increase independence and quality of life. Moreover, research indicates that older people are significant consumers of CAM services. Yet, understanding profiles of older individuals of these services continues to remain under researched. Here, a widely used type of CAM was considered – massage therapy (MT). Towards better understanding MT user profiles, this study tested a modified version of the Andersen Health Behavior Model to help ascertain if it is useful towards understanding factors associated with massage therapy (MT) utilization. Respondents represented an elderly sample (aged 60+) that resided within a large urban city in Ontario Canada (Toronto). Eligible respondents at the time of the study were non-institutionalized and self-reported having one of more current chronic illness conditions which they have had for six months or more, and had been diagnosed by a medical doctor. Using a quantitative method, retrospective data were gathered using a pre-tested English-only mail questionnaire, developed specifically for this study. Data were gathered over a period of 6 months, between late 2000 to mid 2001. Bivariate analysis suggests that inequity exists whereby the ability to access massage therapy varies according to one’s socioeconomic status. This is further supported using backwards step-wise regression analysis, whereby one’s total annual household income was a strong predictor of MT use status. One’s CAM-related health and social network as well as having back problems also emerged as strong predictors of MT use. Overall findings suggest that a modified Andersen model as used in this study does have utility in relation to helping to identify potential factors associated with the utilization of massage therapy. Based on regression analysis, findings here suggest, for example, that those with higher incomes are 1.5 times more likely to use MT. This provides support that there are existing inequities regarding access to rehabilitation-oriented health care services. With population aging and rising numbers of people needing restorative and rehabilitation services, study findings will increasingly have important public health as well as health care policy related implications.
Organic Residue Analysis and the Earliest Uses of Pottery in the Ancient Middle East
Keywords: Organic residues
Near Eastern prehistory
First uses of pottery
Stable isotope geochemistry

In this dissertation, I discuss the role of organic residue analysis in identifying economic activities and subsistence practices associated with the first uses of pottery in the Middle East, and present the results of my analyses of 280 potsherds recovered from 22 Neolithic and early Chalcolithic settlements dating between 7300 and 4300 cal BC. The adoption of pottery vessels in the early agricultural villages and pastoral encampments of the Middle East was not a uniform phenomenon, with this new technology not immediately of benefit, apparently, to all human groups. Results of my analyses have demonstrated that ‘conventional’ solvent extraction and alkaline hydrolysis techniques have limited utility in the recovery of diagnostic organic compounds from pottery from early ceramic horizons in the Middle East (Gregg et al. 2007), and that increased yields can be achieved through the use of a microwave-assisted liquid chromatography protocol (Gregg et al. 2009; Gregg and Slater in press). My research has established that there is greater diversity in the fractionation of stable carbon isotopes associated with the synthesis of fatty acids in domesticated animals than has previously been reported. In many instances, the ranges of modern isotopic values that have been used to categorize animal fats in archaeological potsherds in northern Europe cannot distinguish between the ∂13C ratios of ancient dairy residues and carcass fats of ruminant and non-ruminant species in central Europe or the Middle East (Gregg et al. 2009; Gregg and Slater in press). In light of these results, I evaluate the diagnostic potential and limitations of different methodological approaches in the recovery and characterization of organic residues, and propose a series of measures that will allow more confident categorization of the substances in early pottery vessels from the Middle East. I also make a number of recommendations for archaeologists considering the use of organic residue analysis, and suggest some practical ideas on how to develop the degree of confidence necessary to assess the methods used in acquisition of molecular and isotopic data, and ultimately, to evaluate the adequacy of the analytical criteria used to address specific archaeological research questions.
A Design-rule-Based Constructive Approach To Building Traceable Software
Keywords: Traceability
Software Maintenance
Design Rules

The maintenance of large-scale software systems without trace information between development artifacts is a challenging task. This thesis focuses on the problem of supporting software maintenance through a mechanism for establishing traceability relations between the system requirements and its code elements. The core of the proposed solution is a set of design rules that regulates the positional (e.g., package), structural (e.g., class), and behavioral (e.g., method) aspects of the system elements, thus establishing traceability between requirements and code. We identify several types of requirements each of which can be supported by design rules. We introduce a rule-based approach to software construction and demonstrate that such a process can support maintainability through two mechanisms: (a) traceability and (b) reduction of defect rate. We distinguish our work from traditional traceability approaches in that we regard traceability as an intrinsic structural property of software systems. This view of traceability is in contrast to traditional traceability approaches where traceability is achieved extrinsically through creating maps such as the traceability matrices or allocation tables. The approach presented in this thesis has been evaluated through conducting several empirical studies as well as building a proof-of-concept system. The results we obtained demonstrate the effectiveness and usefulness of our approach.
Race, Ethnicity, Immigration And Jobs: Labour Market Access Among Ghanaian And Somali Youth In The Greater Toronto Area
Keywords: Race
Ethnicity
Immigration
Labour Market
Youth
Black
Social Capital
Transnationalism

This thesis uses focus group interviews and survey questionnaires to examine perceptions of Ghanaian and Somali youth, residing in Toronto, about barriers to their labour market access. The emphasis is on perceptions that deal with labour market discrimination based on race, ethnicity and recency of immigration. The results show that perceptions of discrimination based on these factors are widespread among all of the participants interviewed or surveyed. This suggests a very strong belief that employment discrimination is pervasive and persistent in the Toronto labour market. The findings also show that the perceptions of discrimination are largely driven by ‘lived discriminatory’ experiences faced by the participants as well as revealing their desire for fairness and equality in society. The perceptions of discrimination negatively affected the level of trust the research participants have in people and institutions as well as impacting their sense of belonging to their communities and the wider society. The relationship between perceptions of discrimination and low levels of trust and sense of belonging is established in the findings of the Ethnic Diversity Survey. The consequences of this impact on the research participants and their communities are high levels of unemployment, high poverty rates and participant dissatisfaction with their own communities and society at large. It is my belief that this thesis contributes to the debate about the significance of discrimination due to race, ethnicity and immigrant status in the Canadian labour market.
Synthesis, Characterization and Thermal Decomposition of Hybrid and Reverse Fluorosilicones
Keywords: fluorosilicone
decomposition
polymer
synthesis
fluoropolymer
supercritical carbon dioxide
chlorotrifluoroethylene
vinyl acetate
polyhedral oligomeric silsesquioxane
flammability
thermal
thermo-oxidative

Traditional fluorosilicones contain a siloxane backbone and pendant fluorinated group leading to low temperature ductility and excellent thermal stability. However, acidic or basic catalysts can reduce the thermal stability from a potential 350 °C to 150 °C. The predominant decomposition mechanism is through chain scission and it is hypothesized that preventing this will result in polymers with higher thermal stability. Three approaches were taken to prevent chain scission. First, a series of hybrid fluorosilicones based on (trifluorovinyl)benzene were synthesized through condensation polymerization with initial decomposition temperatures of approximately 240 °C. These were compared to similar aromatic polyethers and removal of the ether oxygen lowered the initial decomposition temperature by approximately 190 °C demonstrating the importance of this oxygen to the stability of polyethers. Second, reverse fluorosilicone (fluorinated backbone and pendant siloxane) terpolymers of chlorotrifluoroethylene (CTFE), vinyl acetate (VAc) and methacryloxypropyl-terminated polydimethylsiloxane (PDMSMA) were synthesized in supercritical CO2 (scCO2) or by emulsion polymerization. Chain scission was prevented as initial decomposition occurred between 231 and 278 °C. In both the emulsion and scCO2 cases, VAc was essential in facilitating cross-propagation between CTFE and PDMSMA and the branching was similar suggesting polymerization media does not affect polymer structure. Emulsion-based polymers had higher molar masses and thermal stability whereas comparable scCO2 polymers had higher yields and incorporated more PDMSMA. Third, a series of homo-, co-, and terpolymers of CTFE, VAc and methacryloxypropyl-terminated silsesquioxane (POSSMA) were synthesized representing the first synthesis of POSSMA containing polymers in scCO2 and demonstrating reverse fluorosilicones can be synthesized without VAc. Chain scission was prevented as initial decomposition occurred from 244 to 296 °C with thermal stability increasing with CTFE content to a limit. Decomposition of the polymers was examined and mechanism elucidated. In air, the copolymers give 40 to 47 wt% char since the silsesquioxane oxidizes to SiO2 while in N2, no residue is seen. In contrast, the terpolymers give a carbonaceous residue of approximately 20 wt% in N2. The flammability and surface properties of the polymers were examined with the terpolymers having flammability similar to p(CTFE) and surface properties comparable to p(POSSMA) giving a low-flammability, hydrophobic polymer.
Low-income Mothers, Provisioning, and Childcare Policy: A Vision of Shared Caring
Keywords: childcare policy
family policy
low income
mothers
poverty
immigrants
government policy making
provisioning

This research examines how childcare policy in Ontario, Canada assists and constrains low-income urban women’s strategies of provisioning for their children. Childcare policy refers to the range of programs that assist families in reconciling paid work and parenthood. In Ontario, Canada, these programs include childcare fee subsidies, tax deductions, parental leave policies, child benefits/allowances and a program regulating live-in caregivers. Provisioning is used to capture an array of daily work-related activities (e.g. paid, unpaid and caring labour) that mothers perform to ensure their children’s survival and well-being. The qualitative study, based on individual semi-structured interviews with 20 low-income mothers living in an urban community, found that women carry out various activities in provisioning for their children. Some of these are familiar and visible activities such as providing domestic caring labour, engaging in the labour market, and undertaking volunteer work in the community. Others are less visible tasks such as sustaining their health and that of their children, making claims/asserting their rights, and ensuring safety. Low-income urban mothers provision under numerous constraints. A continuous shortage of money and childcare issues are at the core of these constraints. The study also found that the mothers encounter a variety of barriers in the community, such as a limited availability of social and community services and a high level of violence/criminal activity in their neighbourhoods. Issues related to poor health, an inadequate diet, or the necessity of caring for children with special needs further constrain women’s lives. Limited English language skills, racial barriers, and the struggles of adapting to a new country add to the multi-dimensional barriers facing low-income urban mothers. The research indicates that mothers use a variety of strategies to counter these barriers; however, these strategies cost women in terms of their time as well as their physical, mental and emotional energy. Childcare policy assists to a certain extent by providing some support to low-income mothers. Enhancements to the existing policies have potential benefits; however, they are like patches on a leaky bucket. Ultimately, the bucket needs to be replaced with a new way of envisioning family responsibilities, work and childcare.
Almost CR Quantization via the Index of Transversally Elliptic Dirac Operators
Keywords: Quantization
Contact geometry
Transversally elliptic operators
Equivariant index theory

Let M be a smooth compact manifold equipped with a co-oriented subbundle E ⊂ TM. We suppose that a compact Lie group G acts on M preserving E, such that the G-orbits are transverse to E. If the fibres of E are equipped with a complex structure then it is possible to construct a G-invariant Dirac operator [special characters omitted] in terms of the resulting almost CR structure. We show that there is a canonical equivariant differential form with generalized coefficients [special characters omitted](E, X) defined on M that depends only on the G-action and the co-oriented subbundle E. Moreover, the group action is such that [special characters omitted] is a G-transversally elliptic operator in the sense of Atiyah [Ati74]. Its index is thus defined as a generalized function on G. Beginning with the equivariant index formula of Paradan and Vergne [PV08b], we obtain an index formula for [special characters omitted] computed as an integral over M that is free of choices and growth conditions. This formula necessarily involves equivariant differential forms with generalized coefficients and we show that the only such form required is the canonical form [special characters omitted](E, X). In certain cases the index of [special characters omitted] can be interpreted in terms of a CR analogue of the space of holomorphic sections, allowing us to view our index formula as a character formula for the G-equivariant quantization of the almost CR manifold (M, E). In particular, we obtain the “almost CR” quantization of a contact manifold, in a manner directly analogous to the almost complex quantization of a symplectic manifold.
Numerical Experiments in Core-collapse Supernova Hydrodynamics
Keywords: supernovae
hydrodynamics

The explosion of massive stars involves the formation of a shock wave. In stars that develop iron cores, this shock wave stalls on its way out due to neutrino emission and the breakup of heavy nuclei flowing through the shock. For the explosion to succeed, a fraction of the gravitational binding energy of the collapsed core that is radiated in neutrinos needs to be absorbed by the material below the shock. How much energy is needed depends on the interplay between non-spherical hydrodynamic instabilities, neutrino heating, and nuclear dissociation. This thesis seeks to understand this interplay through numerical experiments that model the key physical components of the system and separate them out to examine their individual effects. Specifically, one- and two-dimensional time-dependent hydrodynamic simulations are performed to study the effects of non-spherical shock oscillations, neutrino-driven convection, and alpha particle recombination on the dynamics of the system and the critical heating rate for explosion. We find that nuclear dissociation has a significant effect on the linear stability and saturation amplitude of shock oscillations. At the critical neutrino heating rate for an explosion, convection due to a negative entropy gradient plays a major role in driving dipolar shock motions. One dimensional explosions are due to a global instability involving the advection of entropy perturbations from the shock to the region where the accretion flow cools due to neutrino emission. Large scale shock expansions in two-dimensions are due to a finite amplitude instability involving the balance between buoyancy forces and the ram pressure of the flow upstream of the shock. During these expansions, a significant amount of energy is released when nucleons recombine into alpha particles, constituting a significant last step in the transition to explosion. The critical neutrino heating rate for an explosion depends sensitively on the starting radius of the shock relative to the radius at which the binding energy of an alpha particle is comparable to the gravitational binding energy.