Now showing items 1-20 of 18303

• Development of Bioanalytical Assays Using Scintillant Polymer-Core Silica-Shell Nanoparticles

(The University of Arizona., 2018)
Ideal nanosensors of biomolecules are sensitive, selective, stable, minimally invasive, amenable to mass production with low-cost, and applicable for reproducible in vitro and in vivo analyses. The nano scintillation proximity assay (nanoSPA) presented here is based on a composite architecture of polystyrene-core and silica-shell nanoparticles, with a high surface area to volume ratio (ca. 2×107 m-1) and density of approximately 1.6 g/cm3. nanoSPA obviates the need for separation of bound from free radiolabeled molecules prior to measurements, with minimized complexity and maximized versatility. Selected β-emitter radioisotopes were utilized for the development of radioassays for analysis of biological processes using nanoSPA. 35S was employed for thiol/disulfide ratio analysis for the first time. Thiolresponsive nanoSPA was used for quantification of 33S-cysteine and 33S-cystine as models of 35S-thiol and 35S-disulfide. Synthetic samples of 33S-cysteine and 33S-cystine and human embryonic kidney (HEK293) cell lysates were analyzed using thiolresponsive nanoSPA for evaluation of thiol/disulfide ratio as a measure of redox status of the sample. Limit of detection for 35S-thiol analysis was <1.1 pM (<1.1 nCi) with a signal to background ratio over 10-fold. 33P-labeled adenosine triphosphate (ATPγ33P) was utilized for the development of kinase activity assays. Three nanoSPA platforms were developed for kinase activity analysis including adsorption, binding, and immuno-nanoSPA that respond based on electrostatic non-specific adsorption, covalent binding, and antibody-antigen binding, respectively. Signal to background ratio up to 24 was observed using separation-free analyses with nanoSPA, compared to approximately 11.5 using liquid scintillation analysis after many washing steps. 3H emits the lowest energy β-particles and it was utilized with nanoSPA for development of saccharide sensors. Dynamic binding of 3H-D-glucose to nanoSPA functionalized with several monoboronic acids (monoBAs) and diboronic acids (diBAs) was evaluated. The signal to background ratio was up to 2.2-fold that must be improved. Further platforms may be developed based on phospholipid-nanoSPA with minimal nonspecific adsorption and more specificity.
• Impact of Geographic Variation, Disability, Socioeconomic Status and Risk Adjustment on High-Risk Medication Use among Elderly Medicare Beneficiaries

(The University of Arizona., 2018)
• Examining Three Levels of Social Integration and Health in Minorities: A Bioecological Perspective

(The University of Arizona., 2018)
• Effects of Stress, Sleep Hygiene, and Exercise on Academic Engagement in Undergraduate Students

(The University of Arizona., 2018)
• Machine Reading for Scientific Discovery

(The University of Arizona., 2018)
• Supporting Parents as College Advisors: A Qualitative Study of First Generation College Students' Parents

(The University of Arizona., 2018)
• The Nature of the Vertical Distribution of Seismic Responses in Multi-Story Structures

(The University of Arizona., 2018)
This Ph.D. research investigates the vertical distribution of seismic responses and controlling seismic response patterns in multi-story reinforced concrete and steel structures. Seismic responses of buildings designed by conventional force-based or displacement-based approaches result in significant force demands compared to nominal design as observed in both experimental studies and earthquake simulations. Furthermore, force patterns suggest that the floor forces are predominantly controlled by higher modes especially when modal properties of buildings alter due to inelastic deformations. Therefore, actual force patterns experienced by buildings may not comply with the design code assumptions such as equivalent lateral force or response spectrum analysis. The main assumption in those methods, that the response of a building is dominated by the first mode excitation, may not be valid under strong earthquakes when inelastic deformations contribute significantly to the total response. Design code assumptions imply inelasticity to have same effects in all modes of response, though it may have significant effects on the demands associated with the first mode, higher modes may not be affected the same way. Further the distribution of seismic responses may differ for different types of lateral force resisting systems since each system possesses different response mechanisms such as formation of inelastic deformations. To better understand the distribution of seismic demands, response intensity measures obtained through nonlinear time history analysis are examined closely in terms of magnitude and shape along the height of buildings for different types of lateral force resisting systems in this study. This dissertation examines various types of buildings to address and shade light on those issues and observations mentioned above.
• Planetary Granular Topography: Slope Angles & Crater Concentric Ridges

(The University of Arizona., 2018)
In the first portion of this dissertation I examine the effect of gravitational acceleration on the angle of repose of granular features. To do this I have used HiRISE DTMs to compare the slipface angles of Martian sand dunes with those measured on Earth. In doing this I have found that the slopes of active dunes on Mars do not differ from their terrestrial counterparts, and as such I have concluded that gravitational acceleration does not effect the angle of repose. In the second, larger portion of this dissertation I examine the morphology and formation of Crater Concentric Ridges (CCRs). These features, formerly known as 'Lunar Concentric Dunes', are ridges oriented concentrically to fresh craters a few kilometers in diameter. Using LROC NAC data I have created a catalog of 77 craters that have these features in their ejecta blankets. Further, I have used this data to map and measure the CCRs around eight craters of varying diameters in order to analyze their distributions. I have also been able to characterize the morphology of these ridges and how that morphology changes with distance from the host crater. Using DTMs made from NAC images I have studied the three-dimensional topography of CCRs in order to fully describe the morphology of these features. This morphological analysis has allowed me to refute several hypotheses for the formation of these features, including the previously accepted ballistic impact sedimentation and erosion hypothesis. In order to formulate a new theory for the formation of these features I have created simulations of crater ejecta flowing over regolith using discrete element modeling. In these simulations I found that Kelvin-Helmholtz instabilities form at the interface between the ejecta and regolith. I posit that these instabilities are responsible for the formation of Crater Concentric Ridges. This hypothesis is supported by the observation that the topography produced in my simulations strongly resembles that which I have measured and described around real lunar craters.
• Socially Constructed Narratives for Exploring the Impacts of Air Pollutant Infiltration in Built Environments

(The University of Arizona., 2018)
This dissertation is an autoethnographic (self-guided) interdisciplinary process done by an empathetic entity (me) who noted a problem sorting out the effects of outdoor air pollutants that infiltrate indoors from those of other indoor pollutants. This problem is the lack of understanding by architects, planners, and other experts of relevant implications of their lack of attention to the infiltration of airborne dust indoors in the arid regions of Arizona. This systematic process of informed reflections is written in a continuous narrative, and breakouts or Vignettes. Each Vignette corresponds to a topic directly relevant to the research and contains the evidence that answers an inquiry followed by a reflection based on my experience and observations. In the study of arid lands, autoethnographic Vignettes provide an alternative approach for taking a scientific point of view to reveal complex interactions between the natural and built environments for arid regions and other regions that may experience drier and warmer climatic conditions in the future.
• Statistical Methods for Next Generation Sequencing Data

(The University of Arizona., 2018)
Statistical genetics is a scientific field concerned with the development of statistical methods for drawing inferences from genetic data. Research in statistical genetics generally involves developing theory or methodology to support research in one of three related areas: population genetics, genetic epidemiology and quantitative genetics. This dissertation is an ensemble of my research work in statistical genetics, including three projects with varying focuses. The first project applies a rare variant region-based test to identify sets of common or rare variants aggregated in and around genes associated with Dravet Syndrome. The second project proposes a score-based test to investigate the association for a set of rare variants and ordinal traits. The third project describes an implement of dimensionality reduction method in genotype data for population inference.
• The European Yankee: A Study and Performance Guide of George Chadwick’s A Flower Cycle

(The University of Arizona., 2018)
This document examines the solo vocal music of American composer, George Whitefield Chadwick (1854-1931), and focuses on his 1892 collection, A Flower Cycle, with poetry written by Arlo Bates (1850-1918). It highlights the European influence in Chadwick’s writing style that created a Euro-American hybridized style in the United States. Though his instrumental works have been widely performed and analyzed, his art songs have not received the same amount of attention. Excerpts of the songs in A Flower Cycle will be analyzed and compared to various German lied and French mélodie to show the similarities in style and Chadwick’s penchant for being influenced by these European composers. The second intent of this document is to provide a guide with which to perform any or all of the pieces therein with proper understanding of the text and how it is set musically. The poetry is believed to have been written specifically to be set to the music for this collection with the exception of The Jacqueminot Rose, which was the inspiration for the construction of A Flower Cycle
• L1 Biases in Learning Root-And-Pattern Morphology

(The University of Arizona., 2018)
• Residential Flood Risk and Knowledge Assessment in the Tucson Metropolitan Area

(The University of Arizona., 2018)
This research explores the challenges of reducing arid land flood risk among a diverse and growing community, plus reveals how population demographics can play a role in determining vulnerability to flooding. Communities make an effort to become more resilient when natural disasters occur. Ideally, these efforts will lessen the physical and economic impacts during and after subsequent events. For the Tucson Metropolitan Area (TMA), a major push to build resilience was initiated after a 1983 flood event. Those efforts proved successful, reducing damage and recovery time when other major floods hit the area. However, homes remain in high risk flood areas and data show Hispanic homeowners may be the most vulnerable to flooding in the TMA. But, data also indicate all homeowners, no matter their race or cultural heritage, in high risk areas may be able to better afford flood insurance, which is a policy supplemental to home insurance. Plus, survey results show homeowners may be more likely to accept personal responsibility for the financial impacts of floods as compared to an earlier study also completed in the TMA. Tailored education efforts addressing why a homeowner would choose or not choose a flood insurance policy could increase the number of policies in force, which potentially builds personal resilience, while also strengthening the community’s ability to withstand the impacts of the next big event.
• The Transit Light Source Effect

(The University of Arizona., 2018)
Transmission spectroscopy provides a powerful probe of exoplanet atmospheres, enabling constraints on their compositions and structures. Recent advances in instrumentation and observational techniques have enabled detections of molecules in the atmospheres of exoplanets as small as Neptune as well as provided constraints on cloud properties for Earth-sized and super-Earth exoplanets. However, these precise observations have also revealed that the heterogeneous nature of stellar photospheres presents a significant challenge to high-precision transit depth determinations. This owes to a fundamental limitation of the transmission spectroscopy technique, which is that transiting exoplanet atmospheres are illuminated by a spatially resolved region of the stellar photosphere, the spectrum of which we cannot directly measure. Any difference between the out-of-transit disk-averaged emergent spectrum of the star—our necessary reference by which we measure transit depths—and the average emergent spectrum of the transit chord—the true light source for the transmission measurement—will imprint on the observed transmission spectrum. This phenomenon is what I term the transit light source effect. In this thesis, I present my work to understand the transit light source effect in F to M dwarf systems and constrain stellar contamination signals in transmission spectra from two M dwarf systems. I first describe a modeling effort to constrain spot and faculae covering fractions and the concomitant stellar contamination spectra on M dwarfs. I find that large covering fractions of active regions are possible for typically active M dwarfs, and therefore stellar contamination signals can be likewise large and even overwhelm planetary atmospheric features produced by small transiting planets. This is indeed what I find in two observational studies of transiting M dwarf systems: the M4.5V GJ 1214 system and the M8V TRAPPIST-1 system. I then expand the analysis to F5V to K9V spectral types, investigating stellar contamination signals with a model similar to that presented for M dwarfs. I find that stellar contamination signals are much weaker for typical F to K dwarfs than for M dwarfs, though signals are detectable in high-precision transmission spectra, and active G and K dwarfs, in particular, can impart relatively large transit depth changes. Finally, I summarize the findings of this thesis and conclude with a look toward future prospects for disentangling stellar and planetary signals in exoplanet transmission spectra.
• Characterization, Setting, and Drama: Rhetorical Practice in Schütz’s Weihnachtshistorie, SWV 435

(The University of Arizona., 2018)
This study demonstrates how the compositional choices Heinrich Schütz made while completing Weihnachtshistorie reflect the influence of musica poetica and musical rhetoric. The study examines how selected musical processes accomplish rhetorical or persuasive goals. Special attention is paid to the musical-rhetorical methods Schütz used to individualize, illuminate, and highlight the personal qualities of each of the mortal characters through musical means to strengthen the overall credibility of the story. The study reveals that the colorful manner in which Schütz paints his characters, while aesthetically pleasing, is a consequence of the application of rhetorical principles to musical composition meant to persuade the listener of the central theological proposition of the work.
• In Questo Proposito: Formal Innovations in the Vespers by Chiara Margarita Cozzolani

(The University of Arizona., 2018)
The focus of the current study is the use of form in the collection of Vespers music by Chiara Margarita Cozzolani (1602-c.1678), an Italian Benedictine nun living in Milan who spent her entire life cloistered within the walls of the Santa Radegonda convent. Although her life was typical of upper-class Milanese women, her compositions demonstrate that her approach to music is anything but typical. She composed in every genre of her day and published a large amount of music during her lifetime. Cozzolani’s collection of Vespers music comes from her final publication of 1650. With the exception of a few historians who have focused specifically on convent music, such as Robert L. Kendrick and Craig Monson, this music has largely been overlooked. The reasons for this are unclear given the wealth of material and the quality of musical aesthetic of this music. It is, however, heartening to see the body of research into Cozzolani’s music grow due to the renewed interest in music by female composers both past and present.
• Challenging the Status Quo: What Arizona Principals of High Performing Urban Schools are Doing to Improve the Outcomes of Latino Students

(The University of Arizona., 2018)
Molecular Dynamics (MD) is a numerical simulation technique which is used to obtain the time evolution trajectory of a system of interacting particles. Consideration of the molecular movement in the space of generalized internal coordinate rather than in Cartesian coordinate is an efficient way to deal with the constraints such as fixed angles and lengths. This type of molecular dynamics is called Internal Coordinate Molecular Dynamics (ICMD). To integrate the equation we need to invert the dense mass matrix. Since the direct calculation of mass matrix inversion is cubically scaled with the number of atoms in a molecule, a more efficient method is required for macro-molecules simulation. Fixman's work in 1974 and the follow-up studies have developed a method that can factorize the inverse of mass matrix into an arithmetic combination of three sparse matrices—one of them is positive definite and need to be further factorized by using the Cholesky decomposition or similar methods. When the molecule subjected to study is of serial chain structure, this method can achieve $\mathcal{O}(n)$ computational scaling, where $n$ is the number of atoms within a specific molecule. However, for molecules with long branches and loops, the nonzero structure of this positive definite matrix makes its decomposition in scaling of $\mathcal{O}(n^3)$. We have presented a new method which can guarantee for no fill-in in doing the Cholesky decomposition. As a result, the inverting of mass matrix will remain the $\mathcal{O}(n)$ scaling, no matter the molecule structure has long branches or not. Based on the above $\mathcal{O}(n)$ method in inverting mass matrix, an $\mathcal{O}(n)$ framework for internal coordinated molecular dynamics has been built. It has the following properties: has $\mathcal{O}(n)$ time complexity; constraints such as constant bond lengths and angles can be arbitrarily applied\added{ on tree structures}; suitable to complex geometries such as branches, \added{flexible }loops, dummy atoms/sites; and is singularity free in inverting mass matrix. When compared to traditional MD methods, the new method is especially powerful in macromolecule simulations. The ICMD utilizes the bond angle $\theta_i$, torsional angle $\phi_i$, and bond length $b_i$ as the basic types of internal coordinate parameters. However, there is a serious problem of using $\theta_i$ and $\phi_i$ as the internal coordinates. When $\theta_i$ is very close to $0$ or $\pi$, the mass matrix becomes singular and its inverse does not exist, so that the numerical integration of the equations of motion is unstable in this situation. In this work, we will introduce a convention switch method which can prevent the singularity by adopting two alternative rotation conventions. According to our test, this method is suitable to any size of molecule. In addition, it only requires a very small amount of additional computational cost. The conservation of total energy in microcanonical (NVE) ensemble simulation is extremely important because the NVE ensemble simulation is a statistical sampling over the constant energy surface in the hyperdimensional phase space. A symplectic numerical scheme can make the error of the total energy be bounded even for exponentially large simulation time. On the other hand, non-symplect time integrators such as 4th order Runge-Kutta (RK4) would give monotonic increasing or decreasing total energy. In internal coordinate molecular dynamics, the Hamiltonian is a strongly coupled equation which depends both on the momentum and position vectors, and very few explicit symplectic numerical methods existing for inseparable Hamiltonian. In this work, the influence of symplectic and non-symplectic time integrators on the energy conservation of ICMD have been studied.