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- Creators: Arizona State University
Description
Functional magnetic resonance imaging (fMRI) has been widely used to measure the retinotopic organization of early visual cortex in the human brain. Previous studies have identified multiple visual field maps (VFMs) based on statistical analysis of fMRI signals, but the resulting geometry has not been fully characterized with mathematical models. This thesis explores using concepts from computational conformal geometry to create a custom software framework for examining and generating quantitative mathematical models for characterizing the geometry of early visual areas in the human brain. The software framework includes a graphical user interface built on top of a selected core conformal flattening algorithm and various software tools compiled specifically for processing and examining retinotopic data. Three conformal flattening algorithms were implemented and evaluated for speed and how well they preserve the conformal metric. All three algorithms performed well in preserving the conformal metric but the speed and stability of the algorithms varied. The software framework performed correctly on actual retinotopic data collected using the standard travelling-wave experiment. Preliminary analysis of the Beltrami coefficient for the early data set shows that selected regions of V1 that contain reasonably smooth eccentricity and polar angle gradients do show significant local conformality, warranting further investigation of this approach for analysis of early and higher visual cortex.
ContributorsTa, Duyan (Author) / Wang, Yalin (Thesis advisor) / Maciejewski, Ross (Committee member) / Wonka, Peter (Committee member) / Arizona State University (Publisher)
Created2013
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013
Description
As an evolutionary force, hybridization outcomes include introgression, admixture, speciation, and reproductive isolation. While hybridization has been studied in several primates, the marmoset genus Callithrix is an important, but little studied example of Neotropical hybridization. Varying degrees of reproductive isolation exist between Callithrix species, and hybridization occurs at species borders or regions containing introduced and native species. Interbreeding between Callithrix species carries important implications for biodiversity and genetic integrity within the genus. However, species origins and levels of genetic admixture in marmoset hybrid zones are generally unknown, and few population genetic studies of individual Callithrix species exist. Using the mitochondrial control region and 44 microsatellite markers, this work explored the genetic diversity and species origins of two C. penicillata and C. jacchus hybrid zones, as well as genetic diversity and divergence in the parental species. Both marker types showed that C. penicillata is more genetically diverse than C. jacchus. Based on mtDNA, C. jacchus seems to have experienced a past population expansion and C. penicillata evolved under constant population size. The data revealed the existence of a previously undocumented natural hybrid zone along the São Francisco River in NE Brazil and confirmed species origins of an anthropogenic zone in Rio de Janeiro state. The data also showed much lower levels of admixture and genetic diversity within the natural hybrid zone than in the anthropogenic zone. Further, the data suggested that the São Francisco River is an important geographic barrier to gene flow in the natural hybrid zone. On the other hand, admixture patterns within the anthropogenic hybrid zone suggested collapse of reproductive barriers, and the formation of a hybrid marmoset swarm. Thus, this work suggested different evolutionary dynamics in anthropogenic vs. natural animal hybrid zones. Restriction Associated DNA sequencing (RADseq) identified a large number of single nucleotide polymorphisms within C. jacchus and C. penicillata genomes. These preliminary data were used to measure intraspecific genomic diversity and interspecific divergence. In the future, RADseq will be used to study genus-wide diversity of Callithrix species, examine past and present marmoset demographic history, and applied to the evolutionary study of marmoset hybridization.
ContributorsMalukiewicz, Joanna (Author) / Stone, Anne C. (Thesis advisor) / Nash, Leanne (Committee member) / Rosenberg, Michael (Committee member) / Hedrick, Phil (Committee member) / Ruiz-Miranda, Carlo (Committee member) / Arizona State University (Publisher)
Created2013
Description
The purpose of this study was to examine the attitudes and opinions of Navajo students toward the Navajo language and culture programs within the schools they were attending. Although in the final year of the No Child Left Behind, a majority of the 265 schools on and near the Navajo reservation have not been making Adequate Yearly Progress, a concern for the parents, teachers, administrators, school board members, and the Navajo Nation. The study entailed conducting a survey at five schools; three of which were not meeting the requirements of the No Child Left Behind. The purpose of the survey instrument (27 questions) administered to the students at the five schools was to examine their attitudes and opinions as to participating in Navajo language and culture programs, to determine if the programs assisted them in their academic achievements, and to examine whether these programs actually made a difference for schools in their Adequate Yearly Progress requirement Approximately 87% of 99 Navajo students, 55 boys and 58 girls, ages 9 through 14, Grades 3 through 8, who lived off the reservation in Flagstaff, Arizona and Gallup, New Mexico, and took the survey knew and spoke Navajo, but less fluently and not to a great extent. However, the students endorsed learning Navajo and strongly agreed that the Navajo language and culture should be part of the curriculum. Historically there have been schools such as the Rock Point Community School, Rough Rock Demonstration School, Borrego Pass Community School, and Ramah Community School that have been successful in their implementation of bilingual programs. The question presently facing Navajo educators is what type of programs would be successful within the context of the No Child Left Behind federal legislation. Can there be replications of successful Navajo language and culture programs into schools that are not making Adequate Yearly Progress?
ContributorsTsosie, David J (Author) / Spencer, Dee A. (Thesis advisor) / Appleton, Nicholas A. (Committee member) / Koerperich, Robbie (Committee member) / Arizona State University (Publisher)
Created2013
Description
The Student Performance Accomplishments Questionnaire (SPAQ) was developed and validated in two studies with two normative samples totaling 315 college students, including a subsample of undocumented students. This instrument assesses academic performance accomplishments in the context of students' academic, extracurricular, and advocacy roles. Performance accomplishments are theorized to be one of four sources of efficacy (Bandura, 1977, 1986). Study 2 tested part of the Social Cognitive Career Theory model (Lent et al., 1994) in a sample of 154 student advocates. By conventional standards, the results yielded no support for the SCCT model and suggested the need for an alternative model. Results showed that student performance accomplishments in advocacy are highly related to students' academic outcomes, particularly choice actions. Choice actions were subsequently related to career goals and academic performance. No significant differences were found between documented and undocumented students on any of the variables studied. It was found that student advocates were significantly higher in performance accomplishments in advocacy, academic self-efficacy, choice action, and academic performance in comparison to student non-advocates. Clinical and research implications of these results for the field of counseling psychology were discussed.
ContributorsCadenas, German (Author) / Bernstein, Bianca L. (Thesis advisor) / Kurpius, Sharon E. (Committee member) / Arciniega, Guillermo M. (Committee member) / Arizona State University (Publisher)
Created2013
Description
The primary goals of this study were to empirically identify subgroups of socially withdrawn youth in late childhood using latent profile analysis and to examine profiles of students' scholastic adjustment. Further, comparisons of the academic functioning for different subtypes of withdrawn children, with particular emphasis on socially disinterested and socially avoidant youth, were made. Participants were 358 fifth grade children. Results indicated that theoretical subtypes of socially withdrawn youth emerge among fifth grade students (i.e., shy, socially disinterested, socially avoidant, and nonwithdrawn). Additionally, associations among subtype membership and various indices of academic engagement and achievement demonstrated unique academic profiles depending on subgroup classification. In particular, youth who were identified as socially avoidant were at greatest risk for academic difficulties compared to their peers. Findings also emerged for socially disinterested youth indicating some degree of academic maladjustment associated with a preference for solitude. These findings have implications for students exhibiting different forms of social withdrawal for their academic functioning in later childhood.
ContributorsSechler, Casey M (Author) / Ladd, Gary W. (Thesis advisor) / Kochel, Karen P. (Committee member) / Kochenderfer-Ladd, Becky (Committee member) / Arizona State University (Publisher)
Created2012
Description
A proposed visible spectrum nanoscale imaging method requires material with permittivity values much larger than those available in real world materials to shrink the visible wavelength to attain the desired resolution. It has been proposed that the extraordinarily slow propagation experienced by light guided along plasmon resonant structures is a viable approach to obtaining these short wavelengths. To assess the feasibility of such a system, an effective medium model of a chain of Noble metal plasmonic nanospheres is developed, leading to a straightforward calculation of the waveguiding properties. Evaluation of other models for such structures that have appeared in the literature, including an eigenvalue problem nearest neighbor approximation, a multi- neighbor approximation with retardation, and a method-of-moments method for a finite chain, show conflicting expectations of such a structure. In particular, recent publications suggest the possibility of regions of invalidity for eigenvalue problem solutions that are considered far below the onset of guidance, and for solutions that assume the loss is low enough to justify perturbation approximations. Even the published method-of-moments approach suffers from an unjustified assumption in the original interpretation, leading to overly optimistic estimations of the attenuation of the plasmon guided wave. In this work it is shown that the method of moments approach solution was dominated by the radiation from the source dipole, and not the waveguiding behavior claimed. If this dipolar radiation is removed the remaining fields ought to contain the desired guided wave information. Using a Prony's-method-based algorithm the dispersion properties of the chain of spheres are assessed at two frequencies, and shown to be dramatically different from the optimistic expectations in much of the literature. A reliable alternative to these models is to replace the chain of spheres with an effective medium model, thus mapping the chain problem into the well-known problem of the dielectric rod. The solution of the Green function problem for excitation of the symmetric longitudinal mode (TM01) is performed by numerical integration. Using this method the frequency ranges over which the rod guides and the associated attenuation are clearly seen. The effective medium model readily allows for variation of the sphere size and separation, and can be taken to the limit where instead of a chain of spheres we have a solid Noble metal rod. This latter case turns out to be the optimal for minimizing the attenuation of the guided wave. Future work is proposed to simulate the chain of photonic nanospheres and the nanowire using finite-difference time-domain to verify observed guided behavior in the Green's function method devised in this thesis and to simulate the proposed nanosensing devices.
ContributorsHale, Paul (Author) / Diaz, Rodolfo E (Thesis advisor) / Goodnick, Stephen (Committee member) / Aberle, James T., 1961- (Committee member) / Palais, Joseph (Committee member) / Arizona State University (Publisher)
Created2013
Description
This study empirically evaluated the effectiveness of the instructional design, learning tools, and role of the teacher in three versions of a semester-long, high-school remedial Algebra I course to determine what impact self-regulated learning skills and learning pattern training have on students' self-regulation, math achievement, and motivation. The 1st version was a business-as-usual traditional classroom teaching mathematics with direct instruction. The 2rd version of the course provided students with self-paced, individualized Algebra instruction with a web-based, intelligent tutor. The 3rd version of the course coupled self-paced, individualized instruction on the web-based, intelligent Algebra tutor coupled with a series of e-learning modules on self-regulated learning knowledge and skills that were distributed throughout the semester. A quasi-experimental, mixed methods evaluation design was used by assigning pre-registered, high-school remedial Algebra I class periods made up of an approximately equal number of students to one of the three study conditions or course versions: (a) the control course design, (b) web-based, intelligent tutor only course design, and (c) web-based, intelligent tutor + SRL e-learning modules course design. While no statistically significant differences on SRL skills, math achievement or motivation were found between the three conditions, effect-size estimates provide suggestive evidence that using the SRL e-learning modules based on ARCS motivation model (Keller, 2010) and Let Me Learn learning pattern instruction (Dawkins, Kottkamp, & Johnston, 2010) may help students regulate their learning and improve their study skills while using a web-based, intelligent Algebra tutor as evidenced by positive impacts on math achievement, motivation, and self-regulated learning skills. The study also explored predictive analyses using multiple regression and found that predictive models based on independent variables aligned to student demographics, learning mastery skills, and ARCS motivational factors are helpful in defining how to further refine course design and design learning evaluations that measure achievement, motivation, and self-regulated learning in web-based learning environments, including intelligent tutoring systems.
ContributorsBarrus, Angela (Author) / Atkinson, Robert K (Thesis advisor) / Van de Sande, Carla (Committee member) / Savenye, Wilhelmina (Committee member) / Arizona State University (Publisher)
Created2013
Description
Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of five AWS and five paired control sites (treatments) in the surrounding Sonoran desert from October 2011 to May 2012. I measured plant species richness, density, and percent cover in the spring of 2012. A Multi-response Permutation Procedure was used to identify differences in small mammal community abundance, biomass, and species richness by season and treatment. I used Principle Component Analysis to reduce 11 habitat characteristics to five habitat factors. I related rodent occurrence to habitat characteristics using multiple and logistic regression. A total of 370 individual mammals representing three genera and eight species of rodents were captured across 4800 trap nights. Desert pocket mouse (Chaetodipus penicillatus) was the most common species in both seasons and treatments. Whereas rodent community abundance, biomass, and richness were similar between seasons, community variables of AWS were greater than CS. Rodent diversity was similar between treatments. Desert pocket mouse abundance and biomass were twice as high at AWS when compared to controls. Biomass of white-throated woodrat (Neotoma albigula) was five times greater at AWS. Habitat characteristics were similar between treatments. Neither presence of water nor distance to water explained substantial habitat variation. Occurrence of rodent species was associated with habitat characteristics. Desert rodent communities are adapted for arid environments (i.e. Heteromyids) and are not dependent on "free water". Higher abundances of desert pocket mouse at AWS were most likely related to increased disturbance and debris and not the presence of water. The results of this study and previous studies suggest that more investigation is needed and that short term studies may not be able to detect interactions (if any) between AWS and desert small mammal communities.
ContributorsSwitalski, Aaron (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2013
Description
The discovery of DNA helical structure opened the door of modern molecular biology. Ned Seeman utilized DNA as building block to construct different nanoscale materials, and introduced a new field, know as DNA nanotechnology. After several decades of development, different DNA structures had been created, with different dimension, different morphology and even with complex curvatures. In addition, after construction of enough amounts DNA structure candidates, DNA structure template, with excellent spatial addressability, had been used to direct the assembly of different nanomaterials, including nanoparticles and proteins, to produce different functional nanomaterials. However there are still many challenges to fabricate functional DNA nanostructures. The first difficulty is that the present finite sized template dimension is still very small, usually smaller than 100nm, which will limit the application for large amount of nanomaterials assembly or large sized nanomaterials assembly. Here we tried to solve this problem through developing a new method, superorigami, to construct finite sized DNA structure with much larger dimension, which can be as large as 500nm. The second problem will be explored the ability of DNA structure to assemble inorganic nanomaterials for novel photonic or electronic properties. Here we tried to utilize DNA Origami method to assemble AuNPs with controlled 3D spacial position for possible chiral photonic complex. We also tried to assemble SWNT with discrete length for possible field effect transistor device. In addition, we tried to mimic in vivo compartment with DNA structure to study internalized enzyme behavior. From our results, constructed DNA cage origami can protect encapsulated enzyme from degradation, and internalized enzyme activity can be boosted for up to 10 folds. In summary, DNA structure can serve as an ideal template for construction of functional nanomaterials with lots of possibilities to be explored.
ContributorsZhao, Zhao (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2013