Specific binding of the mammalian high mobility group protein AT-hook 2 to the minor groove of AT -rich DNAs: Thermodynamic and specificity studies

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a small transcriptional factor involved in cell development and oncogenesis. It contains three "AT-hook" DNA binding domains, which specifically recognize the minor groove of AT-rich DNA sequences. It also has an acidic C-terminal motif. Previous studies showed that HMGA2 mediates all its biological effects through interactions with AT-rich DNA sequences in the promoter regions. In this dissertation, I used a variety of biochemical and biophysical methods to examine the physical properties of HMGA2 and to further investigate HMGA2's interactions with AT-rich DNA sequences. The following are three avenues perused in this study: (1) due to the asymmetrical charge distribution of HMGA2, I have developed a rapid procedure to purify HMGA2 in the milligram range. Preparation of large amounts of HMGA2 makes biophysical studies possible; (2) Since HMGA2 binds to different AT-rich sequences in the promoter regions, I used a combination of isothermal titration calorimetry (ITC) and DNA UV melting experiment to characterize interactions of HMGA2 with poly(dA-dT) 2 and poly(dA)poly(dT). My results demonstrated that (i) each HMGA2 molecule binds to 15 AT bp; (ii) HMGA2 binds to both AT DNAs with very high affinity. However, the binding reaction of HMGA2 to poly(dA-dT) 2 is enthalpy-driven and the binding reaction of HMGA2 with poly(dA)poly(dT) is entropy-driven; (iii) the binding reactions are strongly depended on salt concentrations; (3) Previous studies showed that HMGA2 may have sequence specificity. In this study, I used a PCR-based SELEX procedure to examine the DNA binding specificity of HMGA2. Two consensus sequences for HMGA2 have been identified: 5'-ATATTCGCGAWWATT-3' and 5'-ATATTGCGCAWWATT-3', where W represents A or T. These consensus sequences have a unique feature: the first five base pairs are AT-rich, the middle four to five base pairs are GC-rich, and the last five to six base pairs are AT-rich. All three segments are critical for high affinity binding. Replacing either one of the AT-rich sequences to a non-AT-rich sequence causes at least 100-fold decrease in the binding affinity. Intriguingly, if the GC-segment is substituted by an AT-rich segment, the binding affinity of HMGA2 is reduced approximately 5-fold. Identification of the consensus sequences for HMGA2 represents an important step towards finding its binding sites within the genome.

Perylene Diimide Molecular Glass: Investigations of Charge Transport

A new glass-forming organic semiconductor material was synthesized using a known electron transport material, perylene diimide, and attaching it to a molecular glass in order to allow the material to be solution processed. Devices were made using a simple metal-semiconductor-metal structure and electrodes were selected to produce Schottky diodes. Experiments were carried out to characterize this new molecular glass perylene diimide. The new material shows evidence of traps, hysteresis, and other behaviours that are explored in this thesis. The material shows some potential as an electron transport layer with possibilities of memory storage behaviour.

NEIGHBORHOOD PERCEPTION OF SAFETY AND THE MOBILITY GAP BETWEEN MEN AND WOMEN IN OLD AGE

Background and Objectives: Mobility limitations are a prevalent issue in older adult populations, and an important determinant of disability and mortality. Neighborhood conditions are key determinants of mobility and perception of safety may be one such determinant. Women have more mobility limitations than men, a phenomenon known as the gender mobility gap. The objective of this work was to validate a measure of perception of safety, examine the relationship between neighborhood perception of safety and mobility limitations in seniors, and explore if these effects vary by gender. Methods: This study was cross-sectional, using questionnaire data collected from community-dwelling older adults from four sites in Canada, Colombia, and Brazil. The exposure variable was the neighborhood aggregated Perception of Safety (PoS) scale, derived from the Physical and Social Disorder (PSD) scale by Sampson and Raudenbush. Its construct validity was verified using factor analyses and correlation with similar measures. The Mobility Assessment Tool – short form (MAT-sf), a video-based measure validated cross-culturally in the studied populations, was used to assess mobility limitations. Based on theoretical models, covariates were included in the analysis, both at the neighborhood level (SES, social capital, and built environment) and the individual level (age, gender, education, income, chronic illnesses, depression, cognitive function, BMI, and social participation). Multilevel modeling was used in order to account for neighborhood clustering. Gender specific analyses were carried out. SAS and M-plus were used in this study. Results: PoS was validated across all sites. It loaded in a single factor, after excluding two items, with a Cronbach α value of approximately 0.86. Mobility limitations were present in 22.08% of the sample, 16.32% among men and 27.41% among women. Neighborhood perception of safety was significantly associated with mobility limitations when controlling for all covariates, with an OR of 0.84 (CI 95%: 0.73-0.96), indicating lower odds of having mobility limitations as neighborhood perception of safety improves. Gender did not affect this relationship despite women being more likely to have mobility limitations and live in neighborhoods with poor perception of safety. Conclusion: Neighborhood perception of safety affected the prevalence of mobility limitations in older adults in the studied population.

The impact of childhood residential mobility on mental health outcomes in adolescence and early adulthood: a record linkage study.

Background Understanding the causes of poor mental health in early childhood and adolescence is important as this can be a significant determinant of mental well-being in later years. One potential and relatively unexplored factor is residential mobility in formative years. Previous studies have been relatively small and potentially limited due to methodological issues. The main aim of this study was to investigate the relationship between early residential instability and poor mental health among adolescents and young adults in Northern Ireland.

Methods A Census-based record linkage study of 28% of children aged 0–8 years in 2001 in Northern Ireland (n=49 762) was conducted, with six monthly address change assessments from health registration data and self-reported mental health status from the 2011 Census. Logistic regression models were built adjusting for socioeconomic status (SES), household composition and marital dissolution.

Results There was a graded relationship between the number of address changes and mental ill-health (adjusted OR 3.67, 95% CIs 2.11 to 6.39 for 5 or more moves). This relationship was not modified by SES or household composition. Marital dissolution was associated with poor mental health but did not modify the relationship between address change and mental health (p=0.206). There was some indication that movement after the age of five was associated with an increased likelihood of poor mental health.

Conclusions This large study clearly confirms the close relationship between address change in early years and later poor mental health. Residential mobility may be a useful marker for children at risk of poorer mental health in adolescence and early adulthood

The influence of mobility on mental health status in young people: The role of area-level deprivation

Residential mobility during childhood has been previously associated with poor mental health; however, this association could be mediated by several aspects of moving. This paper investigated the impact of mobility across different levels of area deprivation on the individual’s mental health status in Northern Ireland. Mobility towards deprived areas was associated with an elevated risk of reporting poor mental health in both house owners and renters. However, the number of residential moves appeared to be moderating the effect of area change on the individual’s mental health. Further exploration of this relationship is warranted through the use of more in-depth mental health measures

Tooth Mobility, Periodontal Ligament Space, and the Alveolus During Periodontal Health, Disease, and Disuse

Thesis (Ph.D.)--University of Washington, 2016-07

Atomic resolution studies of oxide superlattices and ultrathin films

The ability to grow ultrathin films layer-by-layer with well-defined epitaxial relationships has allowed research groups worldwide to grow a range of artificial films and superlattices, first for semiconductors, and now with oxides. In the oxides thin film research community, there have been concerted efforts recently to develop a number of epitaxial oxide systems grown on single crystal oxide substrates that display a wide variety of novel interfacial functionality, such as enhanced ferromagnetic ordering, increased charge carrier density, increased optical absorption, etc, at interfaces. The magnitude of these novel properties is dependent upon the structure of thin films, especially interface sharpness, intermixing, defects, and strain, layering sequence in the case of superlattices and the density of interfaces relative to the film thicknesses. To understand the relationship between the interfacial thin film oxide atomic structure and its properties, atomic scale characterization is required. Transmission electron microscopy (TEM) offers the ability to study interfaces of films at high resolution. Scanning transmission electron microscopy (STEM) allows for real space imaging of materials with directly interpretable atomic number contrast. Electron energy loss spectroscopy (EELS), together with STEM, can probe the local chemical composition as well as local electronic states of transition metals and oxygen. Both techniques have been significantly improved by aberration correctors, which reduce the probe size to 1 Å, or less. Aberration correctors have thus made it possible to resolve individual atomic columns, and possibly probe the electronic structure at atomic scales. Separately, using electron probe forming lenses, structural information such as the crystal structure, strain, lattice mismatches, and superlattice ordering can be measured by nanoarea electron diffraction (NED). The combination of STEM, EELS, and NED techniques allows us to gain a fundamental understanding of the properties of oxide superlattices and ultrathin films and their relationship with the corresponding atomic and electronic structure. In this dissertation, I use the aforementioned electron microscopy techniques to investigate several oxide superlattice and ultrathin film systems. The major findings are summarized below. These results were obtained with stringent specimen preparation methods that I developed for high resolution studies, which are described in Chapter 2. The essential materials background and description of electron microscopy techniques are given in Chapter 1 and 2. In a LaMnO3-SrMnO3 superlattice, we demonstrate the interface of LaMnO3-SrMnO3 is sharper than the SrMnO3-LaMnO3 interface. Extra spectral weights in EELS are confined to the sharp interface, whereas at the rougher interface, the extra states are either not present or are not confined to the interface. Both the structural and electronic asymmetries correspond to asymmetric magnetic ordering at low temperature. In a short period LaMnO3-SrTiO3 superlattice for optical applications, we discovered a modified band structure in SrTiO3 ultrathin films relative to thick films and a SrTiO3 substrate, due to charge leakage from LaMnO3 in SrTiO3. This was measured by chemical shifts of the Ti L and O K edges using atomic scale EELS. The interfacial sharpness of LaAlO3 films grown on SrTiO3 was investigated by the STEM/EELS technique together with electron diffraction. This interface, when prepared under specific conditions, is conductive with high carrier mobility. Several suggestions for the conductive interface have been proposed, including a polar catastrophe model, where a large built-in electric field in LaAlO3 films results in electron charge transfer into the SrTiO3 substrate. Other suggested possibilities include oxygen vacancies at the interface and/or oxygen vacancies in the substrate. The abruptness of the interface as well as extent of intermixing has not been thoroughly investigated at high resolution, even though this can strongly influence the electrical transport properties. We found clear evidence for cation intermixing through the LaAlO3-SrTiO3 interface with high spatial resolution EELS and STEM, which contributes to the conduction at the interface. We also found structural defects, such as misfit dislocations, which leads to increased intermixing over coherent interfaces.

Beyond hope: Rhetorics of mobility, possibility, and literacy

When writing teachers enter the classroom, they often bring with them a deep faith in the power of literacy to rectify social inequalities and improve their students’ social and economic standing. It is this faith—this hope for change—that draws some writing teachers to locations of social and economic hardship. I am interested in how teachers and theorists construct their own narratives of social mobility, possibility, and literacy. My dissertation analyzes the production and expression of beliefs about literacy in the narratives of a diverse group of writing teachers and theorists, from those beginning their careers to those who are published and widely read. The central questions guiding this study are: How do teachers’ and theorists’ narratives of becoming literate intersect with literacy theories? and How do such literacy narratives intersect with beliefs in the power of literacy to improve individuals’ lives socially, economically, and personally? I contend that the professional literature needs to address more fully how teachers’ and theorists’ personal histories with literacy shape what they see as possible (and desirable) for students, especially those from marginalized communities. A central focus of the dissertation is on how teachers and theorists attempt to resolve a paradox they are likely to encounter in narratives about literacy. On one hand, they are immersed in a popular culture that cherishes narrative links between literacy and economic advancement (and, further, between such advancement and a “good life”). On the other hand, in professional discourse and in teacher preparation courses, they are likely to encounter narratives that complicate an assumed causal relationship between literacy and economic progress. Understanding, through literacy narratives, how teachers and theorists chart a practical path through or around this paradox can be beneficial to literacy education in three ways. First, it can offer direction in professional development and teacher education, addressing how teachers negotiate the boundaries between personal experience, theory, and pedagogy. Second, it can help teachers create spaces wherein students can explore the impact of paradoxical views about the role of literacy on their own lives. Finally, it can offer direction in public policy discourse, extending awareness of what we want—and need—from English language arts education in the twenty-first century. To explore these issues, I draw on case studies and ethnographic observation as well as narrative inquiry into teachers’ and theorists’ published literacy narratives. I situate my findings within three interrelated frames: 1) the narratives of new teachers, 2) the published works of literacy educators and theorists, and 3) my own literacy narrative. My first chapter, “Beyond Hope,” explores the tenuous connections between hope and critique in literacy studies and provides a methodological overview of the study. I argue that scholarship must move beyond a singular focus on either hope or critique in order to identify the transformative potential of literacy in particular circumstances. Analyzing literacy narratives provides a way of locating a critically informed sense of possibility. My second chapter, “Making Teachers, Making Literacy,” explores the intersection between teachers’ lives and the theories they study, based on qualitative analysis of a preservice course for secondary education English teachers. I examine how these preservice English teachers understood literacy, how their narratives of becoming literate and teaching English connected—and did not connect—with theoretical and pedagogical positions, and how these stories might inform their future work as practitioners. Centering primarily on preservice teachers who resisted Nancie Atwell’s pedagogy of possibility because they found it too good to be true, this research concentrates on moments of disjuncture, as expressed in class discussion and in one-on-one interviews, when literacy theories failed to align with aspiring teachers’ understandings of their own experiences and also with what they imagined as possible in disadvantaged educational settings. In my third and fourth chapters, I analyze the narratives of celebrated teachers and theorists who put forth an agenda that emphasizes possibilities through literacy, examining how they negotiate the relationship between their own literacy stories and literacy theories. Specifically, I investigate the narratives of three proponents of critical literacy: Mike Rose, Paulo Freire, and Myles Horton, all highly respected literacy teachers whose working-class backgrounds influenced their commitment to teaching in disenfranchised communities. In chapter 3, “Reading Lives on the Boundary,” I demonstrate how Mike Rose’s 1989 autobiographical text, Lives on the Boundary, juxtaposes rhetorics of mobility with critiques of such possibility. Through an analysis of work published in professional journals, I offer a reception history of Rose’s narrative, focusing specifically on how teachers have negotiated the tension between hope and critique. I follow this analysis with three case studies, drawn from a larger sampling, that inquire into the personal connections that writing teachers make with Lives on the Boundary. The teachers in this study, who provided written responses and participated in audio-recorded follow-up interviews, were asked to compare Rose’s story to their own stories, considering how their personal literacy histories influenced their teaching. My findings illustrate how a group of teachers and theorists have projected their own assessments of what literacy and higher education can and cannot accomplish onto this influential text. In my fourth chapter, “Horton and Freire’s Road as Literacy Narrative,” I concentrate on Myles Horton and Paulo Freire’s 1990 collaborative spoken book, We Make the Road by Walking. Central to my analysis are the educators’ stories about their formative years, including their own primary and secondary education experiences. I argue that We Make the Road by Walking demonstrates how theories of literacy cannot be divorced from personal histories. I begin by examining the spoken book as a literacy narrative that fuses personal and theoretical knowledge, focusing specifically on its authors’ ideas on theory. Drawing on Bakhtin’s notion of the chronotope—the intersection of time and space within narrative—I then explore the literacy narratives emerging from the production process of the book, in a video production about Horton and Freire’s meeting, and ultimately in the two men’s reflections on their childhood years (Dialogic). Interspersed with these accounts is archival material on the book’s editorial production that illustrates the value of increased dialogue between personal history and theories of literacy. My fifth chapter is both a reflective analysis and a qualitative study of my work at a men’s medium-high security prison in Illinois, where I conducted research and served as the instructor of an upper-level writing course, “Writing for a Change,” in the spring of 2009. Entitled “Doing Time with Literacy Narratives,” this chapter explores the complex ways in which literacy and incarceration are configured in students’ narratives as well as my own. With and against students’ stories, I juxtapose my own experiences with literacy, particularly in relation to being the son of an imprisoned father. In exploring the intersections between such stories, I demonstrate how literacy narratives can function as a heuristic for exploring beliefs about literacy between teachers and students both inside and outside of the prison-industrial complex. My conclusion pulls together the various themes that emerged in the three frames, from the making of new teachers to the published literacy narratives of teachers and theorists to my own literacy narrative. Writing teachers encounter considerable pressure to align their curricula with one or another theory of literacy, which has the effect of negating the authority of knowledge about literacy gleaned from experience as readers and writers. My dissertation contends that there is much to be gained by finding ways of articulating theories of literacy that encompass teachers’ knowledge of reading and writing as expressed in personal narratives of literacy. While powerful cultural rhetorics of upward social mobility often neutralize the critical potential of teachers’ own narratives of literacy—potential that has been documented by scholars in writing studies and allied disciplines—this is not always the case. The chapters in this dissertation offer evidence that hopeful and critical positions on the transformational possibilities of literacy are not mutually exclusive.

Household language, residential segregation and social mobility: continuity and change in eThekwini, South Africa

This article uses South African census data for 1996, 2001 and 2011 to explore the relationship between language and social mobility in the metropolitan region of eThekwini (including what was previously known as Durban). We focus particular attention on variables selected to shed light on residential segregation and social mobility, such as education level, income, race and in-migration. Data on adults at ward level (using 2011 ward boundaries) in eThekwini is used to develop a comparative spatial context for this analysis. Our main finding is that English appears in eThekwini to be the household language of the social elite as well as the language of upward mobility and empowerment.

Child-to-parent violence: the role of exposure to violence and its relationship to social-cognitive processing

Research suggests that child-to-parent violence (CPV) is related to a previous history of violence within the family setting. The current study was aimed to explore the exposure to violence in different settings (school, community, home, and TV) and its relationship to some variables of the social-cognitive processing (hostile social perception, impulsivity, ability to anticipate the consequences of social behaviors and to select the appropriate means to achieve the goals of social behaviors) in a group of juveniles who assaulted their parents. It is also examined how they differ from other young offenders and non-offender adolescents. The sample included 90 adolescents from Jaén (Spain). Thirty of them were juveniles who had been reported by their parents for being violent towards them and 30 were juveniles who had committed other types of offences. The third group was made up of 30 adolescents without any criminal charge. Adolescents answered measures of exposure to violence, perception of criticism/rejection from parents, hostile social perception, and social problem- solving skills. Results revealed that juveniles who abused their parents reported higher levels of exposure to violence at home when comparing to the other groups. In addition, exposure to violence at home was significantly correlated to the hostile social perception of adolescents in CPV cases. Implications for prevention and treatment are discussed

Mobility and emplacement in north coast Papua New Guinea: worlding the Pacific marine industrial zone

On the north coast of Papua New Guinea, the construction of the Pacific Marine Industrial Zone is catalysing movements of people, capital and things, as well as of the ideas and imaginings which accompany and make them meaningful. Drawn from literary and postcolonial studies, the concept of worlding offers a narrative framework through which to think through these movements and the ways in which they complicate prevailing narratives of globalisation. At the Pacific Marine Industrial Zone, the neoliberal worldings that inform the project do not simply catalyse movements, but also act to impose barriers to movement. Local communities assert connection to place, but also generate new circuits of mobility, and rearticulate ideas of kastom (custom) that have movement at their core. An emphasis on worlding-drawing particularly on Heidegger's distinction between world and earth-allows for a more complex reflection on the relationship between mobility and emplacement, one that more fully illuminates the complexity of the relationship itself, and the way it is experienced at the PMIZ site.

Morphology-properties relationship of gas plasma treated hydrophobic meso-porous membranes and their improved performance for desalination by membrane distillation

The impact on performance of the surface energy and roughness of membrane materials used for direct contact membrane distillation are critical but yet poorly investigated parameters. The capacity to alter the wettability of highly hydrophobic materials such as poly(tetra-fluoro-ethylene) (PTFE) by gas plasma treatments is reported in this paper. An equally important contribution from this investigation arises from illustrating how vaporized material from the treated sample participates after a short while in the composition of the plasma and fundamentally changes the result of surface chemistry processes. The water contact angle across the hydrophobic membranes is generally controlled by varying the plasma gas conditions, such as the plasma power, chamber pressure and irradiation duration. Changes to surface porosity and roughness of the bulk material as well as the surface chemistry, through specific and partial de-fluorination of the surface were detected and systematically studied by Fourier transform infra-red analysis and scanning electron microscopy. It was found that the rupture of fibrils, formed during membrane processing by thermal-stretching, led to the formation of a denser surface composed of nodules similar to these naturally acting as bridging points across the membrane material between fibrils. This structural change has a profound and impart a permanent effect on the permeation across the modified membranes, which was found to be enhanced by up to 10% for long plasma exposures while the selectivity of the membranes was found to remain unaffected by the treatment at a level higher than 99.99%. This is the first time that an investigation demonstrates how the permeation characteristics of these membranes is directly related to data from spectral, morphological and surface charge analyses, which provide new insights on the impact of plasma treatments on both, the surface charge and roughness, of PTFE porous materials.

NEIGHBORHOOD PERCEPTION OF SAFETY AND THE MOBILITY GAP BETWEEN MEN AND WOMEN IN OLD AGE

Thesis (Master, Community Health & Epidemiology) -- Queen's University, 2016-10-02 21:02:07.735

A NOVEL MODELING AND STATE OF CHARGE ESTIMATION SCHEME FOR LITHIUM-ION BATTERIES

Lithium Ion (Li-Ion) batteries have got attention in recent decades because of their undisputable advantages over other types of batteries. They are used in so many our devices which we need in our daily life such as cell phones, lap top computers, cameras, and so many electronic devices. They also are being used in smart grids technology, stand-alone wind and solar systems, Hybrid Electric Vehicles (HEV), and Plug in Hybrid Electric Vehicles (PHEV). Despite the rapid increase in the use of Lit-ion batteries, the existence of limited battery models also inadequate and very complex models developed by chemists is the lack of useful models a significant matter. A battery management system (BMS) aims to optimize the use of the battery, making the whole system more reliable, durable and cost effective. Perhaps the most important function of the BMS is to provide an estimate of the State of Charge (SOC). SOC is the ratio of available ampere-hour (Ah) in the battery to the total Ah of a fully charged battery. The Open Circuit Voltage (OCV) of a fully relaxed battery has an approximate one-to-one relationship with the SOC. Therefore, if this voltage is known, the SOC can be found. However, the relaxed OCV can only be measured when the battery is relaxed and the internal battery chemistry has reached equilibrium. This thesis focuses on Li-ion battery cell modelling and SOC estimation. In particular, the thesis, introduces a simple but comprehensive model for the battery and a novel on-line, accurate and fast SOC estimation algorithm for the primary purpose of use in electric and hybrid-electric vehicles, and microgrid systems. The thesis aims to (i) form a baseline characterization for dynamic modeling; (ii) provide a tool for use in state-of-charge estimation. The proposed modelling and SOC estimation schemes are validated through comprehensive simulation and experimental results.