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Title: Characterizing the Epigenetic Regulation of ABA-Induced Transcriptional Responses in Zea Mays.
Creator: Vendramin Alegre, Stefania, McGinnis, Karen M., Li, Hong, Bass, Hank W., Chadwick, Brian P., Dennis, Jonathan Hancock, Florida State University, College of Arts and Sciences,...
Show moreVendramin Alegre, Stefania, McGinnis, Karen M., Li, Hong, Bass, Hank W., Chadwick, Brian P., Dennis, Jonathan Hancock, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: Plants are often subjected to extreme environmental conditions and must adapt rapidly. The phytohormone abscisic acid (ABA) accumulates under abiotic stress conditions, signaling transcriptional changes that trigger physiological responses. Epigenetic modifications are also required to facilitate transcription, particularly at genes exhibiting temporal, tissue-specific and environmentally induced expression. In maize (Zea mays), MEDIATOR OF PARAMUTATION 1 (MOP1) is required for progression of...
Show morePlants are often subjected to extreme environmental conditions and must adapt rapidly. The phytohormone abscisic acid (ABA) accumulates under abiotic stress conditions, signaling transcriptional changes that trigger physiological responses. Epigenetic modifications are also required to facilitate transcription, particularly at genes exhibiting temporal, tissue-specific and environmentally induced expression. In maize (Zea mays), MEDIATOR OF PARAMUTATION 1 (MOP1) is required for progression of an RNA-dependent epigenetic pathway that regulates transcriptional silencing of loci across the genome. As critical regulators of gene expression, MOP1 and ABA pathways predictably regulate specific genes in a coordinated manner. In one project, the amino acid sequence of DNG103 and the gene promoter region were analyzed for conserved domains and cis-responsive elements, respectively. DNG103 is similar to the Arabidopsis ROS1, contains the conserved domains of a DNA glycosylase with DNA demethylase activity, and contains ABA-responsive elements (ABREs) in its promoter region. Transcript levels of Dng103, and the ABA-responsive gene Viviparous 1 (Vp1), were monitored in maturing embryos from two genotypes placed in culture under different conditions. Expression of both genes decreased after culture in hormone-free medium and was induced by ABA in Mop1 wildtype. Dng103 and Mop1 showed decreased expression in mop1-1 and dng103 mutants, respectively. Dng103 is not responsive to ABA in the mop1-1 mutant and Vp1 has reduced sensitivity. Therefore, DNG103, MOP1 and ABA might have common regulatory targets. Protoplast isolation and transfection protocols were standardized alongside the production of reporter constructs containing the Dng103 and Vp1 promoters. This technology will allow for the promoter characterization of genes of interest through quantifiable luciferase expression, using different conditions and genotypes. To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses, mop1-1 and Mop1 homozygous seedlings were subjected to exogenous ABA and RNA-sequencing. A total of 3,242 differentially expressed genes (DEGs) were identified in four pairwise comparisons. Overall, the loss of MOP1 exaggerated some ABA-induced changes in gene expression. The highest number of DEGs were identified in ABA-induced mop1-1 mutants, including many transcription factors. A gene regulatory network was used to predict relationships between DEGs; suggesting multifaceted regulatory scenarios including direct and indirect transcriptional responses to genetic disruption (mop1-1) and/or stimulus-induction of a hierarchical, cascading network of responsive genes. Additionally, a modest increase in CHH methylation at putative MOP1-RdDM loci in response to ABA was observed in some genotypes, suggesting that MOP1 might be necessary to achieve environmentally induced transcriptional responses in maize. To understand the multistep ABA response of identified ABA-induced genes, an ABA-time course was carried out in another project using four different time points. The previously predicted ABA-responsive transcription factors Hb41 and Bzip4 showed an early induction to ABA and the late embryogenesis abundant Rab17 gene was induced during the transition from early to late response. Together, these results indicate that MOP1 and ABA act at multiple levels within complex, connected transcriptional networks to mediate tissue-specific growth and responses to some abiotic stresses. LIST OF SUPPLEMENTARY FILES 1. Significant differentially expressed genes in analysis groups I-VIII. 2. GO term enrichment in groups I, II, V and VI. 3. Arabidopsis and maize homologous transcription factors and target genes in ABA transcription factor hierarchical network and their corresponding gene expression. 4. Transcription factors and target genes in ABA transcription factor hierarchical network separated by transcriptional levels. 5. Group model parameters per gene. 6. Genome-wide siRNA changes in mop1-1 mutant. 7. TGS2 target genes. 8. Sequence Capture (SeqCap) DNA methylation ratios in all sequence contexts. 9. Promoter DNA methylation for Mop1 wildtype ABA-responsive DEGs. 10. MOP1-ABA targets with a loss of siRNA and DNA methylation at ABRE sites.
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Date Issued: 2019
Identifier: 2019_Fall_VendraminAlegre_fsu_0071E_15503_P
Format: Set of related objects

Title: Nutrition Interests of FSU Students, Their Preferred Information Sources and Perceived Credibility.
Creator: Liu, Anni, Spicer, Maria T., Cui, Ming, Arjmandi, Bahram H., Florida State University, College of Human Sciences, Department of Nutrition, Food and Exercise Sciences
Abstract/Description: Purpose Due to ease of access to nutritional misinformation, it becomes difficult for the public to identify credible and current information. Adding to this, many individuals have not learned how to distinguish between trustworthy and untrustworthy information sources (Wansink, 2006). This study investigated the preferred sources of nutrition information by FSU students, reasons for their preference, their belief in the reliability of these sources, students’ confidence in their ability to...
Show morePurpose Due to ease of access to nutritional misinformation, it becomes difficult for the public to identify credible and current information. Adding to this, many individuals have not learned how to distinguish between trustworthy and untrustworthy information sources (Wansink, 2006). This study investigated the preferred sources of nutrition information by FSU students, reasons for their preference, their belief in the reliability of these sources, students’ confidence in their ability to find credible nutrition related information. Methods Internet surveys were distributed using Qualtrics to students over 18 years old at Florida State University. Surveys were emailed to students through departmental emails and word of mouth. Data collection was completed through Qualtrics. Data analysis was completed with IBM SPSS Statistics 25 software for Windows, Version 25.0. released in 2017. Results 293 student participants (24.6% males and 75.1% females) were included in this study from at least 8 different areas of study. The top three most preferred nutrition information sources were Social Media (Instagram, Facebook, Pinterest) (12.4%), Medical Doctors (9.4%), and Nutritionists (7.6%). The most important reasons for selecting preferred sources of nutrition information included: credibility (50.17%), convenience (31.7%), and possible effectiveness (9.6%). The most credible nutrition information sources were shown to be Registered Dietitians (87.7%), Nutritionists (81.9%) and Medical Doctors (77.8%). The least credible sources of nutrition information were Celebrities (34.8%), Social Media (27.9%), and Television (25.3%). The sources which were considered to be backed by sufficient research all of the time included: Registered Dietitians (63.1%), Nutritionists (58.4%) and Medical Doctors (52.7%). Social media was one of the least credible sources and the least likely to have information backed up by sufficient research. 90.8% of the participants in this study were at least somewhat confident of their ability to find credible nutrition information. Only 6.8% of participants have passed a nutrition course in college. This group of individuals valued credibility no more than the rest of the participants. Conclusion The students studied were confident in their own ability to find credible nutrition information sources and viewed credibility of information as the most important reason when it comes to choosing nutrition information sources. They are aware of the unreliable information they get from their most preferred source which is social media, and of the availability of more reliable nutrition information sources. However, students do not choose to use sources with information supported by sufficient research, the reason for which was not explored. Further research to explore the cause of this behavior and incongruous thinking is recommended. Every college student should have evidence-based nutrition and health education.
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Date Issued: 2019
Identifier: 2019_Fall_Liu_fsu_0071N_15041_P
Format: Set of related objects

Title: Developing New Datasets to Evaluate Tropospheric Photochemistry and the Effects of Ozone Uptake in the Biosphere.
Creator: Ducker, Jason Alexander, Holmes, Christopher D., Miller, Thomas E., Misra, Vasubandhu, Bourassa, Mark Allan, Florida State University, College of Arts and Sciences, Department...
Show moreDucker, Jason Alexander, Holmes, Christopher D., Miller, Thomas E., Misra, Vasubandhu, Bourassa, Mark Allan, Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: In the presence of water vapor, photolysis of tropospheric ozone (O3) produces the hydroxyl radical (OH), which is a strong oxidant that directly and indirectly controls a host of greenhouse gases and air pollutants. When tropospheric O3 reaches the surface, its oxidative effects perturb plant transpiration and photosynthesis. Although these effects have been included in climate and air quality models, there are limited observational datasets to constrain key aspects of atmospheric...
Show moreIn the presence of water vapor, photolysis of tropospheric ozone (O3) produces the hydroxyl radical (OH), which is a strong oxidant that directly and indirectly controls a host of greenhouse gases and air pollutants. When tropospheric O3 reaches the surface, its oxidative effects perturb plant transpiration and photosynthesis. Although these effects have been included in climate and air quality models, there are limited observational datasets to constrain key aspects of atmospheric photochemistry and O3 deposition on regional to global scales. This dissertation develops and uses two new datasets to better understand the ozone photochemistry and impacts. Photolysis, the breaking of chemical bonds by sunlight, is the engine for reactive atmospheric chemistry. It controls production of atmopsheric oxidants, especially O3 and OH, which then influence the lifetimes of other air pollutants and climate forcing agents. Global chemistry and climate models differ in their estimates of these photolysis rates and there have been datasets capable of discriminating among different models. Here, we integrate satellite-retrivals of clouds and aerosols into a photolysis code and produce a 3-D global photolysis dataset called Sat-J. We show that Sat-J is tightly correlated with in-situ measurements of pholysis rates from airborne chemistry campaigns, with errors (4-20%) mainly attributed to differences in nonuniform cloud sampling and time match differences. By comparing regional, not necessarily collocated, averages of aircraft data, SatJ, and a chemistry model (GEOS-Chem); we demonstrate that SatJ provides a representative climatology of photolysis rates across the globe and can serve as a benchmark for photochemistry models. Using surface micrometeorological fluxes and surface O3 monitoring networks, we also develop and evaluat a method to estimate O3 deposition and stomatal O3 uptake across networks of eddy covariance flux tower sites where O3 concentrations and O3 fluxes have not been measured. This method, called SynFlux, reproduces the variability in daily stomatal O3 uptake at sites with O3 flux measurements, with a modest bias (21% or less) attributed to gridded O3 concentrations. Across SynFlux sites, we highlight environmental factors controlling spatial patterns in O3 deposition and showed that previous O3 concentration-based metrics for plant damages did not correlate with SynFlux O3 uptake, which is a better predictor for plant damage than ambient concentration in air. SynFlux has dramatically expanded the the available data on surface O3 deposition, which can now be used for performing ecosystem impact studies across a species and climates in the US and Europe. Past controlled experiments involving single plant species have shown that O3 uptake can degrade water-use efficiency (WUE), which is the ratio of carbon uptake in photosynthesis (GPP) to water loss in plant transpiration (T). Using SynFlux sites, we can quantify this effect for whole ecosystems under natural environmental variability, which has not been previously studied. Across 74 SynFlux sites, we find a significant negative relationship (–0.02% per μmol m-2 d-1) between daily cumulative O3 uptake (CUO) and WUE anomalies, with the largest impacts occurring at forest sites. Past controlled studies of selected individual species also observed a similar O3 reduction of WUE over the growing season, indicating a consistent response to O3 across multiple species with an ecosystem. When we analyze the relationships between daily CUO and GPP or T anomalies, we also find that CUO degrades GPP and increases T over the growing season. We postulate that O3 degrades WUE through O3 non-stomatal biochemical factors, which result in a reduction of GPP or an increase in T. Our SynFlux results here provide climate models the ability to incorporate O3-dose response relationships between O3 uptake and ecosystem carbon and water vapor fluxes across ecosystems that have not previously been studied. For chapters 2-4, we have separate supplementary documents for each chapter.
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Date Issued: 2019
Identifier: 2019_Fall_Ducker_fsu_0071E_15515_P
Format: Set of related objects

Title: Large-Scale Multi-Target Tracking Problem for Interacting Targets.
Creator: Vo, Garret Dan, Park, Chiwoo, Srivastava, Anuj, Liang, Zhiyong (Richard), Vanli, Omer Arda, Florida State University, FAMU-FSU College of Engineering (Tallahassee, Fla.),...
Show moreVo, Garret Dan, Park, Chiwoo, Srivastava, Anuj, Liang, Zhiyong (Richard), Vanli, Omer Arda, Florida State University, FAMU-FSU College of Engineering (Tallahassee, Fla.), Department of Industrial and Manufacturing Engineering
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Abstract/Description: The unique physical properties of nanoparticles depend on their sizes and shapes. Therefore, an ability to precisely control the size of nanoparticles and tune their morphology will allow scientists and engineers to modify their physical properties, which will lead to many potential applications. To precisely control nanoparticles' sizes and shapes requires a deep understanding of their growth mechanism. To understand their growth mechanism, a direct observation and its quantitative analysis...
Show moreThe unique physical properties of nanoparticles depend on their sizes and shapes. Therefore, an ability to precisely control the size of nanoparticles and tune their morphology will allow scientists and engineers to modify their physical properties, which will lead to many potential applications. To precisely control nanoparticles' sizes and shapes requires a deep understanding of their growth mechanism. To understand their growth mechanism, a direct observation and its quantitative analysis are both necessary. In the direct observation study, the electron microscopy method has shown promises, because the in situ method enables researchers to see the growth process using video recordings. In these video recordings, each frame displays an image from an electron microscope. However, this method yields a vast number of electron images; therefore, analyzing these images to monitor the nanoparticles' growth is a challenging task. The objective of this dissertation is to develop an automation process to capture the complex growth event of nanoparticles in a sequence of electron microscope images. The automation process consists of two tasks: detect nanoparticles in an electron microscope image that has a non-uniform background and significant noise; and then track these detected nanoparticles in a large number of video frames obtained from a single camera. In each frame, complex interaction among these nanoparticles exists; therefore, the tracking algorithm will capture the complex interaction among these nanoparticles. Two solutions are proposed in this dissertation. To detect nanoparticles, an electron microscope image is converted to a binary image through a process called image binarization. To perform the image binarization step, the background of the electron microscope image is first estimated with a robust regression technique; then, it is subtracted from the input image. Afterwards, a global thresholding algorithm is applied to the subtracted outcome in order to achieve the binary image. To track these detected nanoparticles in a large number of video frames, an online algorithm has been created. This algorithm leverages the multi-way data association, which is capable of tracking complex interaction among nanoparticles but suffers from computational inefficiency for a large number of video frames. The online algorithm forms fragmented trajectories between two consecutive frames (i.e. frame-by-frame data association). When missed-association between nanoparticles occur, the algorithm augments these missed-associated nanopartiles to nanoparticles in the second frame in the frame-by-frame data association step. Then, the algorithm continues forming trajectories with the multi-way data association for the incoming video frame. When these augmented nanoparticles are associated within the sliding window, the algorithm initiates the creation of tracks, which connect missed-associated nanoparticles at their respective time frames to their correspondents at the incoming video frame. While working on the second solution, we also created a computer simulation model to generate multi-target datasets with their respective ground-truth associations.The generated datasets and their respective ground-truth associations will serve as a benchmark data to test and evaluate multi-target tracking algorithms. The simulation model serves two purposes: cover all complexity of multi-target tracking scenarios, which public datasets lack; and provide the ground-truth target tracking and association so that the evaluation of multi-target tracking algorithms can be performed without any manual video annotation process.
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Date Issued: 2019
Identifier: 2019_Summer_Vo_fsu_0071E_15279_P
Format: Set of related objects

Title: Smartwatch Adoption within the Running Community.
Creator: Ramos, Nathaniel, Mon, Lorri M., Dennen, Vanessa P., Burnett, Kathleen M., Kazmer, Michelle M., Florida State University, College of Communication and Information, School of...
Show moreRamos, Nathaniel, Mon, Lorri M., Dennen, Vanessa P., Burnett, Kathleen M., Kazmer, Michelle M., Florida State University, College of Communication and Information, School of Information
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Abstract/Description: This research investigates the adoption of smartwatches within the running community. By using a mixed methods design consisting of quantitative surveys and qualitative interviews, this study asks runners what factors influence their adoption of smartwatches, what information is valued and most utilized, and the impact of these devices on their behavior. This study primarily relies on Diffusion of Innovations theory as a lens through which to view the factors of adoption for runners, but it...
Show moreThis research investigates the adoption of smartwatches within the running community. By using a mixed methods design consisting of quantitative surveys and qualitative interviews, this study asks runners what factors influence their adoption of smartwatches, what information is valued and most utilized, and the impact of these devices on their behavior. This study primarily relies on Diffusion of Innovations theory as a lens through which to view the factors of adoption for runners, but it also utilizes questions from the Technology Acceptance Model to attempt to better understand the role of these devices within the running community. Through the utilization of surveys and interviews, this study identifies relative advantage to be the primary factor in adopting smartwatches and trialability to be an unimportant factor. Further, all interview participants in this study reported that smartwatches made them more aware of their behavior, and 14 of 15 interview participants stated that their behavior and/or training regimens had changed due to data they obtained via smartwatches. The findings of this study suggest that more research is needed to determine whether these changes are temporary or part of a larger, permanent trend. Further, based on this study, there is a need for more research into the impact of smartwatches in other communities to determine whether the effect of smartwatches on behavior is isolated to athletes who are actively training or whether more fitness data and greater awareness of one's activity spurs greater movement in the population more generally.
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Date Issued: 2019
Identifier: 2019_Summer_RamosJr_fsu_0071E_14988_P
Format: Set of related objects

Title: RIF1 Is Necessary to Maintain Epigenetic State in Human Cells.
Creator: Klein, Kyle N., Gilbert, David M., Gunjan, Akash, Bass, Hank W., Yu, Hong-Guo, Chadwick, Brian P., Florida State University, College of Arts and Sciences, Department of...
Show moreKlein, Kyle N., Gilbert, David M., Gunjan, Akash, Bass, Hank W., Yu, Hong-Guo, Chadwick, Brian P., Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: DNA is replicated in a defined temporal order termed the RT program. Ordered DNA replication is conserved in eukaryotes, yet its biological significance remains enigmatic. 3D genome organization as assayed by Hi-C has revealed that RT is highly correlated with genome architecture at two scales. Developmentally programmed changes in RT occur in units that align with sub-megabase chromatin architectural units known as TADs and early and late replicating chromatin is segregated into separate A...
Show moreDNA is replicated in a defined temporal order termed the RT program. Ordered DNA replication is conserved in eukaryotes, yet its biological significance remains enigmatic. 3D genome organization as assayed by Hi-C has revealed that RT is highly correlated with genome architecture at two scales. Developmentally programmed changes in RT occur in units that align with sub-megabase chromatin architectural units known as TADs and early and late replicating chromatin is segregated into separate A and B sub-nuclear compartments respectively. Transcriptionally permissive histone modifications are associated with early replication and A nuclear compartmentalization. Conversely, transcriptionally repressive histone modifications are associated with late replication and B nuclear compartmentalization. However, studies of mechanisms linking RT and chromatin architecture with epigenetic chromatin modifications have been difficult since mutation of chromatin regulatory proteins have found only small, localized changes in the RT program, not global disruption of ordered replication. Indeed, depletion of key architectural proteins such as CTCF and cohesin disrupts TAD structure but has little effect on compartments or RT. RIF1 is the only protein shown to have a conserved role in regulating RT genome wide. To address the role of RT in organizing epigenetic chromatin modifications and genome structure we have generated RIF1 knockouts via CRISPR/Cas9 genome editing in hESCs and the cancer cell line HCT116. While RT changes in HCT116 mirrored those seen in previously published human and mouse RIF1 null cell lines, remarkably, hESC null cells lose almost all detectable temporal replication specificity, despite retaining pluripotency, a nearly normal transcriptome, and cell cycle progression. In both cell lines, the effect on RT was due to increased stochastic cell to cell variation in RT, rather than discrete RT changes as previously thought. Hi-C detected significant changes in compartments driven by changes in interactions between peaks of specific histone marks that coordinately increase or decrease in intensity. Heterochromatic H3K9me3 peaks were globally reduced in intensity, but highly enriched in both peak intensity and interaction strength at certain loci that remained late replicating. H3K27me3 showed cell line specific changes, becoming enriched or excluded from H3K9me3-rich domains in hESCs or HCT116, respectively. H3K27ac peaks also showed a global decrease in peak intensity and interactions between peaks were significantly weakened. H3K4me3 peak intensity and inter-peak interactions were depleted in the A nuclear compartment and enriched in the B nuclear compartment. TAD architecture and Rad21 binding was largely unaffected in both cell lines. We conclude that RIF1 is necessary to maintain the global epigenetic landscape and suggest a model in which RT regulates chromatin and compartment identity in human cells.
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Date Issued: 2019
Identifier: 2019_Summer_KLEIN_fsu_0071E_15412_P
Format: Set of related objects

Title: A Structural Equation Modeling Analysis of Chinese Undergraduate English Language-Learners' Personal Factors and Contextual Factors Based on Self-Determination Theory.
Creator: Chen, Yanyan, Turner, Jeannine E., Sunderman, Gretchen L., Yang, Yanyun, Roehrig, Alysia D., Florida State University, College of Education, Department of Educational Psychology...
Show moreChen, Yanyan, Turner, Jeannine E., Sunderman, Gretchen L., Yang, Yanyun, Roehrig, Alysia D., Florida State University, College of Education, Department of Educational Psychology and Learning Systems
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Abstract/Description: This study investigated the relationships among Chinese undergraduate English learners' motivation for learning English (i.e., students' internal choice, students' external pressure), integrative orientation (i.e., students' engagement with the target language culture or community), students' perceptions of psychological need satisfaction, English self-efficacy, classroom engagement, and their English academic achievement. The theoretical framework underlying this study is Self-Determination...
Show moreThis study investigated the relationships among Chinese undergraduate English learners' motivation for learning English (i.e., students' internal choice, students' external pressure), integrative orientation (i.e., students' engagement with the target language culture or community), students' perceptions of psychological need satisfaction, English self-efficacy, classroom engagement, and their English academic achievement. The theoretical framework underlying this study is Self-Determination Theory (Ryan & Deci, 2000a, 2000b, 2017). To investigate the relationships among the variables, a quantitative research methodology of a full structural equation model with single indicators was used. Although language learners' motivation for learning a second/foreign language is a well-studied construct, there is a paucity of studies to investigate whether or not Self-Determination Theory applies to Chinese collectivistic culture for understanding Chinese college English language learners' motivation for learning English. The purpose of this dissertation study was to investigate the relationships among Chinese undergraduate English language learners' personal variables (i.e., motivation for learning English, integrative orientation, English self-efficacy, classroom engagement, and English academic achievement) and contextual variables (i.e., students' perceptions of psychological need satisfaction) in a full structural model. The participants of this study were 1,378 Chinese undergraduate English majors from middle-level national public universities in the Southeast of China. Findings of the current study showed that Chinese undergraduate English language-learners, who were primarily regulated by internal choice (i.e., intrinsic regulation, identified regulation), were likely to perceive that teachers met their psychological-needs for intrinsic motivation, and to have greater intentions to engage in the target-language culture and community, which in turn predicted their learning-related beliefs (e.g., a high sense of English efficacy), learning-related behaviors (e.g., active involvement in learning activities), and English achievement. Nevertheless, students who were primarily regulated by externally-controlled reasons for learning English, including introjected regulation (i.e., performing a task to avoid feeling guilty), external regulation (i.e., performing a task for obtaining rewards), and parental persuasion (i.e., parents' influence toward learning English) were also likely to perceive that their teachers met their psychological-needs, which may have influenced their intention to integrate into the target-language culture and community. This dissertation study investigated Chinese undergraduate English learners' motivation for learning English as a foreign language and the consequent learning outcomes. Findings of this study broadened understandings of students' motivation for learning a language by showing how students' initial reasons for learning a language may influence their learning beliefs, classroom engagement, and language achievement. Keywords: Chinese undergraduate English majors, motivation, psychological need satisfaction, integrative orientation, self-determination theory
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Date Issued: 2019
Identifier: 2019_Summer_Chen_fsu_0071E_15311_P
Format: Set of related objects

Title: Excessive Exercise, Eating Pathology and Suicidality: Investigating the Role of Capability for Suicide.
Creator: Buchman, Jennifer M. (Jennifer Marie), Joiner, Thomas, Winegardner, Mark, Cougle, Jesse R. (Jesse Ray), Eckel, Lisa A., Patrick, Christopher J., Florida State University,...
Show moreBuchman, Jennifer M. (Jennifer Marie), Joiner, Thomas, Winegardner, Mark, Cougle, Jesse R. (Jesse Ray), Eckel, Lisa A., Patrick, Christopher J., Florida State University, College of Arts and Sciences, Department of Psychology
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Abstract/Description: Eating disorders (EDs) are associated with increased risk for suicide. Recent research suggests that excessive exercise (EE), an ED compensatory behavior, may increase suicide risk via increasing one's capability for suicide which is comprised of an elevated pain tolerance and a diminished fear of death. However, additional research is needed to determine the exact mechanisms by which EE may influence capability for suicide. Specifically, no studies to date have examined the influence of EE...
Show moreEating disorders (EDs) are associated with increased risk for suicide. Recent research suggests that excessive exercise (EE), an ED compensatory behavior, may increase suicide risk via increasing one's capability for suicide which is comprised of an elevated pain tolerance and a diminished fear of death. However, additional research is needed to determine the exact mechanisms by which EE may influence capability for suicide. Specifically, no studies to date have examined the influence of EE and eating pathology on behavioral indices of capability for suicide. The present study had two aims: 1) this study sought to examine how EE engagement and ED status influences pain avoidance behaviors in comparison to controls; and 2) the second aim of the present study was to determine how EE engagement and ED status influence fear of death and avoidance of death-related stimuli. We recruited 87 participants based on ED and EE status (22 controls, 22 EE only, 21 ED only, and 22 ED+EE). Hierarchical regression with dummy coding was used to compare our groups on the following outcomes: 1) breakpoint and total key presses on a pain avoidance progressive ratio task (CPT); and 2) breakpoint and total key presses on a death avoidance progressive ratio task (viewing and rating of suicide images). The results of the present study provide preliminary, albeit mixed support for our hypotheses. Specifically, we found that the EE only (β = -0.31, p = .017) and ED only (β = -0.30, p = 0.02) groups differed significantly from controls on one measure of pain avoidance (CPT PR breakpoint); the ED only group (β = -0.31, p = .017) differed significantly from controls on one measure of death avoidance (suicide-related images PR total presses). However, our ED group characterized by EE did not differ significantly from controls on any of our behavioral measures. See supplementary file for Tables 1 and 2 which provide group comparisons on main variables of interest (Table 1) and a correlation matrix for continuous variables (Table 2). Exploration of these findings, limitations, and areas for future research are included in our general discussion.
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Date Issued: 2019
Identifier: 2019_Summer_Buchman_fsu_0071E_15405_P
Format: Set of related objects

Title: Exploring the Growth of Charge Balanced Tetrelide Phases from Mg/Al Flux.
Creator: Vasquez, Guillermo, Latturner, Susan, Siegrist, Theo, Albrecht-Schmitt, Thomas E., Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of...
Show moreVasquez, Guillermo, Latturner, Susan, Siegrist, Theo, Albrecht-Schmitt, Thomas E., Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: Flux synthesis is a useful method for the exploration and development of new tetrelide Zintl phases. Reactions of heavy divalent metals (A = Ca, Sr, Ba, Eu, Yb) with tetrels (Tt = Si, Ge, Sn) in Mg/Al flux mixtures produce charge-balanced tetrelides with the general formula (A/Mg)2Tt; these compounds have hexagonal structures analogous to those of a large family of rare earth transition metal phosphides. Initial reactions of ytterbium, barium and silicon in Mg/Al melts produced three new...
Show moreFlux synthesis is a useful method for the exploration and development of new tetrelide Zintl phases. Reactions of heavy divalent metals (A = Ca, Sr, Ba, Eu, Yb) with tetrels (Tt = Si, Ge, Sn) in Mg/Al flux mixtures produce charge-balanced tetrelides with the general formula (A/Mg)2Tt; these compounds have hexagonal structures analogous to those of a large family of rare earth transition metal phosphides. Initial reactions of ytterbium, barium and silicon in Mg/Al melts produced three new phases: Ba2Yb0.9Mg11.1Si7, Ba5Yb2Mg17Si12, and Ba20Yb5Mg61Si43, isostructural to the ternary phosphides Zr2Fe12P7, Ho5Ni19P12, and Ho20Ni66P43 respectively. Later a fourth silicide (Ba6Yb1.84Mg18.16Si13, analogous to Zr6Ni20P13) was synthesized. All these phases exhibit Pauli paramagnetic behavior, indicative of divalent Yb2+ ions. From the density of states (DOS) calculations on Ba2Yb0.9Mg11.1Si7, Ba5Yb2Mg17Si12 and Ba6Yb1.84Mg18.16Si13, these compounds are expected to be poor metals/semimetallic. Due to the very complex nature of the Ba/Yb/Mg/Si system (there are four competing, structurally related compounds) quenching experiments and in situ neutron powder diffraction studies were carried out to determine the reaction parameters that favor certain products. Under slow cooling conditions, Ba5Yb2Mg17Si12 precipitates from the flux at 800 °C. A faster cooling rate of an identical reaction results in the formation of single crystals of Ba20Yb5Mg61Si43 in the flux at 640 °C. This indicates that the crystallization of products in this metal flux reaction does not involve precipitation and interconversion of different phases but instead depends on the rate of cooling across the supersaturated metastable zone in this system. The other two compounds (Ba2Yb0.9Mg11.1Si7 and Ba6Yb1.84Mg18.16Si13) were not seen in the in situ neutron diffraction experiments. These phases might form under rare and difficult to reproduce conditions (caused by temperature fluctuations that occur when opening the furnace door) that position the reaction at a specific point in the metastable zone. Further exploration of reactions of tetrels with divalent alkaline earth or rare earth metals in Mg/Al flux was carried out. All the (A/Mg)2Tt products are tetrelide analogs of hexagonal ternary phosphides (Zr2Fe12P7, Ho5Ni19P12, Zr6Ni20P13 or Ho20Ni66P43 structure types). The charge-balanced stoichiometries result in semimetallic behavior, and the complex structures and heavy element incorporation yield low thermal conductivity, confirmed by thermoelectric measurements on two representative compounds. Ba5Eu2.85Mg16.15Si12 and Ba5Yb2.26Mg16.74Si12 have room temperature thermal conductivities of 2 – 3 W/mK, and Seebeck coefficients of +160 uV/K and -75 uV/K respectively, with Ba5Eu2.85Mg16.15Si12 exhibiting magnetoresistance around 2 K. These materials are promising for thermoelectric applications at high temperatures. Incorporation of europium results in compounds exhibiting very weak magnetic transitions at low temperatures. Magnetic susceptibility measurements on Ba5Eu2.85Mg16.15Si12 and Eu4.64Yb2.32Mg18.04Si12 indicated that both phases show no ordering below 3 K and that their Eu ions are divalent.
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Date Issued: 2019
Identifier: 2019_Summer_Vasquez_fsu_0071E_15324_P
Format: Set of related objects

Title: A Study of the Musical Style of Elliott Carter's Piano Sonata (1945-46) and of Mei-Fang Lin's Disintegration and Mistress of the Labyrinth.
Creator: Wang, Yingying, Kalhous, David, Darrow, Alice-Ann, Dumlavwalla, Diana Teresa, Williams, Heidi Louise, Florida State University, College of Music
Abstract/Description: The purpose of this treatise, which is in two parts, is to investigate piano solo works of Elliott Carter and Mei-Fang Lin. Part I of the treatise focuses on American composer Elliott Carter and his Piano Sonata (1945-46). Part II discusses contemporary Taiwanese composer Mei-Fang Lin and her two solo piano works, Disintegration and Mistress of the Labyrinth. Elliot Carter’s Piano Sonata is a representative example of his distinctive modernist style. After his early works written largely in...
Show moreThe purpose of this treatise, which is in two parts, is to investigate piano solo works of Elliott Carter and Mei-Fang Lin. Part I of the treatise focuses on American composer Elliott Carter and his Piano Sonata (1945-46). Part II discusses contemporary Taiwanese composer Mei-Fang Lin and her two solo piano works, Disintegration and Mistress of the Labyrinth. Elliot Carter’s Piano Sonata is a representative example of his distinctive modernist style. After his early works written largely in Neoclassical idiom, Carter embarked on a new musical path in this work. His innovative approach to form, harmony, thematic design, metric elements, sound, and timing according to the common sonata structures differ significantly from the traditional approaches to this form. The compositional aesthetic of this work has become one of the hallmarks of American musical modernism, foreshadowing the compositional direction of piano sonatas in the latter half of the twentieth century. Carter’s music has known for his metrical complexity, in which metric modulation and polyrhythmic application largely emerged after 1948. The trademark is specifically launched in his Cello Sonata (1948). The 1945 piano sonata is the piece a few years earlier in which rhythmical complexity began to expose. In this treatise, I demonstrate the layer of rhythmical pulse through the method of thematic analysis, rather than merely focusing on metric modulation technique. In contrast to most scholarships that have a rigorous study for Carter’s eclectic deed on the fusion of European neoclassicism and American avant-garde, I discuss the composer’s new compositional approach in the Sonata. My analysis concentrates on specific innovative aspects that make the work unconventional, showing why Carter is one of the most important voices of American modernism. Part II of the treatise focuses on the contemporary Taiwanese composer Mei-Fang Lin’s two piano solo works, Disintegration and Mistress of the Labyrinth. Lin’s compositional aesthetic are intrinsically related to her educational background and cultural identity, and I show how this particular aesthetic is revealed in these two pieces. Lin’s musical language demonstrates a strong duality. On one hand, her European and American musical training imbued her music with an unmistakably Western voice. On the other hand, Lin’s studies of Eastern philosophy and traditional Chinese music infused her style with Eastern elements. My analysis illustrates how these two tendencies coexist in these two pieces.
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Date Issued: 2019
Identifier: 2019_Spring_WANG_fsu_0071E_15077_comp
Format: Set of related objects

Title: Teachers' Sense of Self-Efficacy Scale in the Virtual Setting.
Creator: Walker, Reddick Russell, Park, Toby J., Dennen, Vanessa P., Gawlik, Marytza A., Herrington, Carolyn D., Florida State University, College of Education, Department of Educational...
Show moreWalker, Reddick Russell, Park, Toby J., Dennen, Vanessa P., Gawlik, Marytza A., Herrington, Carolyn D., Florida State University, College of Education, Department of Educational Leadership and Policy Studies
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Abstract/Description: What is interesting is virtual learning seems to go against the very nature of teachers and teaching. For example, many teachers are in the profession to change the lives of students, to have an impact, for interaction, to motivate and aspire students. Some teachers find that these are all diminished and even sometimes eliminated in the virtual environment. Given the expansion of K-12 virtual education across the United States, there is scarce evidence on virtual teachers’ and their...
Show moreWhat is interesting is virtual learning seems to go against the very nature of teachers and teaching. For example, many teachers are in the profession to change the lives of students, to have an impact, for interaction, to motivate and aspire students. Some teachers find that these are all diminished and even sometimes eliminated in the virtual environment. Given the expansion of K-12 virtual education across the United States, there is scarce evidence on virtual teachers’ and their acclimation to this setting. Therefore, the purposes of this study were twofold: i) identify and modify a scale for use in the virtual setting; and ii), analyze the data collected from virtual teachers to describe and explore their sense of self-efficacy. This exploratory study found that a group of virtual teachers had a moderately high sense of self-efficacy. T-tests revealed significant differences between teachers’ sense of self-efficacy scores and grade-level taught, content delivery, and prior participation in a virtual course. Multiple regression was used to show that virtual teaching experience (years), course content, and grade-level taught explained some of the variations in teachers’ sense of self-efficacy composite scores. Furthermore, teachers’ that incorporate synchronous and asynchronous lessons have a higher sense of self-efficacy than those that do not. In addition to providing evidence that supports the scale design and use, an unexpected finding emerged from this cross-sectional study: Teachers’ age had strong positive correlation with overall teaching experience but there was no correlation between age and years of virtual teaching experience. On average, research suggests that teaching experience, gained over a career, is positively associated with student achievement. Therefore, it seems plausible that the quality of virtual courses could vary widely due to variations in virtual teachers’ experience. With a better understanding of scale utilization, a profile of virtual teachers’ perceptions and points for future research, researchers and practitioners can enhance instructional practices.
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Date Issued: 2019
Identifier: 2019_Spring_Walker_fsu_0071E_15118_comp
Format: Set of related objects

Title: Elaborations of Classical-Model Sentences and Periods in Richard Strauss's Songs for Voice and Piano.
Creator: Tanis, Joshua, Kraus, Joseph Charles, Buchler, Michael Howard, Fisher, Douglas L., Jones, Evan Allan, Florida State University, College of Music
Abstract/Description: In this dissertation, I address several ways in which Richard Strauss elaborates the Classical-model sentence and period paradigm: through harmonic elaborations by way of Strauss’s chromatic, Romantic-style harmonic palette; through formal elaborations by way of phrase expansion; or through elaborations of many musical parameters, which yield hybrid variants of sentences and periods. I offer labels for these hybrids based on their melodic-motivic, harmonic, and phrase-length profile: the...
Show moreIn this dissertation, I address several ways in which Richard Strauss elaborates the Classical-model sentence and period paradigm: through harmonic elaborations by way of Strauss’s chromatic, Romantic-style harmonic palette; through formal elaborations by way of phrase expansion; or through elaborations of many musical parameters, which yield hybrid variants of sentences and periods. I offer labels for these hybrids based on their melodic-motivic, harmonic, and phrase-length profile: the Straussian Hybrid Sentence, the Straussian Hybrid Period, and the Lone Antecedent Phrase. These labels encapsulate a sense of their musical shape, showing how the resulting formal structures derive from familiar Classical models, but in some Strauss-specific ways. My methodology for analyzing Strauss’s songs takes on its own hybrid approach, which responds to Janet Schmalfeldt’s 1991 article on reconciling form-function theory with Schenkerian theory and analysis. It is often the case that where Strauss obfuscates normative Classical theme-types, he embeds the inherent unification of their formal structure in other ways, namely through voice leading and the melodic-motivic interplay between voice and piano. Accordingly, I present form overlays and voice-leading sketches for each song excerpt or full-song analysis. By so doing, I highlight how one kind of analysis informs the other, especially when one or the other type of analysis does not seem to fully account for a particular passage of music. To be sure, the form overlays and voice-leading sketches work in tandem with my analysis of poetic structure, meaning, and text-setting in each song. In Chapter 2, I investigate Classical-model sentences, sixteen-measure sentences, and Straussian hybrid sentences in excerpts from seven songs. Instances of Classical-model sentences and sixteen-measure sentences in Strauss’s songs adhere strictly to the melodic-motivic, harmonic, and phrase-length features described by William Caplin, such as in “Befreit,” Op. 39, No. 4, and “Ich trage meine Minne,” Op. 32, No. 1. In some cases, Strauss expands Classical-model sentences by various phrase-expansion techniques, such as in “Mohnblumen,” Op. 22, No. 2, and “Leises Lied,” Op. 39, No. 1. Yet in other songs, Strauss expresses elaborations of sentences whose melodic-motivic organization is noticeably different from the Classical model; specifically, these structures—which I label the Straussian Hybrid Sentence—exhibit a “presentation” phrase comprising a compound basic idea rather than a basic idea and its repetition (like Caplin’s Hybrid 3 model). I identify these structures in “Winternacht,” Op. 15, No. 2, “Wiegenliedchen,” Op. 49, No. 3, and “Allerseelen,” Op. 10, No. 8. In Chapter 3, I analyze examples of Classical-model periods, in addition to two related categories: the Straussian Hybrid Period and the Lone Antecedent Phrase. Straussian Hybrid Periods comprise a normative antecedent phrase (4-bar compound basic idea, ending with a weak cadence) followed by a hybrid consequent phrase that is guised as one of several possible formal outcomes, such as a sentence, a continuation phrase (like Caplin’s Hybrid 1 model), or a cadential unit (like Caplin’s Hybrid 2 model). In the case of any of these three options, the hybrid consequent phrase ends with a stronger cadence than the one at the end of the antecedent phrase. The final formal structure I address is the Lone Antecedent Phrase, which describes an antecedent phrase that is not followed by a consequent phrase, whether normative or hybrid. In these cases, it is difficult to speak of a “true” periodic design; rather, the first half of a perceived period is present, but there is no musical (or even rhetorical) completion of a complementary musical unit. In all, I survey six excerpts: “Für fünfzehn Pfennige,” Op. 36, No. 2, and “Ach weh unglückhaften Mann,” Op. 21, No. 4 (Classical-model periods); “Mit deinen blauen Augen,” Op. 56, No. 4, “Die Zeitlose,” Op. 10, No. 7, and “Schön sind, doch kalt die Himmelssterne,” Op. 19, No. 3 (Straussian Hybrid Periods); and “Das Bächlein,” Op. 88, No. 1 (Lone Antecedent Phrase). In Chapter 4, I provide three full-song analyses: “Zueignung,” Op. 10, No. 1, “Allerseelen,” and “Befreit.” Through analyses at multiple levels of formal and voice-leading structure, I highlight the inherent interaction between these two musical parameters, showing specifically how they relate to the poetry. In “Zueignung” and “Allerseelen,” there is a progression from obscurity to clarity that spans the duration of the song. Conversely, the poem from which “Befreit” is derived poses the opposite rhetorical effect—that is, “Befreit” traces a progression from clarity to obscurity. The analyses presented in Chapter 4 depict how Strauss’s use and elaboration of Classical theme-types is done so in the service of conveying poetic meaning over the span of an entire song.
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Date Issued: 2019
Identifier: 2019_Spring_Tanis_fsu_0071E_15125_comp
Format: Set of related objects

Title: Humicrete in Northwest Florida an Analysis of Formation and Characteristics.
Creator: Shelfer, Megan L. (Megan Lee), Kish, Stephen A., Ray, Peter, Wang, Yanchang, Means, Guy H., Florida State University, College of Arts and Sciences, Department of Earth, Ocean...
Show moreShelfer, Megan L. (Megan Lee), Kish, Stephen A., Ray, Peter, Wang, Yanchang, Means, Guy H., Florida State University, College of Arts and Sciences, Department of Earth, Ocean and Atmospheric Science
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Abstract/Description: The formation process by which sand becomes cemented with humate compounds to form humicrete is not well understood, likely due in part to limited exposures of this material around the world. Humicrete layers along the Intracoastal Waterway in northwest Florida are some of the most well exposed units in the western hemisphere. Over a length of about ten kilometers, multiple beds with varying humate cementation can be observed throughout the lower two-thirds of bluffs that are nine to fifteen...
Show moreThe formation process by which sand becomes cemented with humate compounds to form humicrete is not well understood, likely due in part to limited exposures of this material around the world. Humicrete layers along the Intracoastal Waterway in northwest Florida are some of the most well exposed units in the western hemisphere. Over a length of about ten kilometers, multiple beds with varying humate cementation can be observed throughout the lower two-thirds of bluffs that are nine to fifteen meters high. Dune deposits overlay the humicrete layers. The most prominent humicrete layer is approximately one to two meters thick and can be traced nearly continuously for over a kilometer. These layers were catalogued, photographed, and sampled for this study, in an effort to learn more about their depositional conditions, chemical composition, and the age of the material hosting the humate cementation. Specifically, this project sought to understand whether the organic matter present in the humate layers was transported laterally from nearby areas with high organic accumulation, or leached from overlying peat layers. Samples of disaggregated humate were analyzed via Fourier Transform Infrared (FTIR) spectroscopy and carbon/nitrogen isotopic analysis. The FTIR data produced indicated high concentrations of lignins and hydroxyls, similar to the chemical signature of younger humicrete samples. A table of the individual FTIR data points is included as a supplementary file titled “Appendix B - FTIR.pdf.” Isotopic analysis of these samples yielded δ13C values of -23.6‰ to -26.8‰ and a C/N ratio of 62 to 85, both of which point to terrestrial plants as the originating vegetation. Results of these tests, as well as observation of the current environment along the northwest Florida coastline, suggest that the organic matter found in these humicrete layers was carried laterally by near-surface groundwater from nearby forested swamps. The age of these host layers and the humicrete cementation is believed to be around 115,000-130,000 years old, as they are thought to have formed by interaction with groundwater during the Sangamonian interglacial period. Additional testing, especially with regard to extent, age and nature of movement of organic-rich water, would be helpful in further understanding how humicrete forms.
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Date Issued: 2019
Identifier: 2019_Spring_Shelfer_fsu_0071N_15012_comp
Format: Set of related objects

Title: Mieczysław Weinberg: Concerto for Cello and Orchestra, and 24 Preludes for Solo Cello.
Creator: Pereverzeva, Aleksandra, Sauer, Greg, Brewer, Charles E. (Charles Everett), Punter, Melanie, Jiménez, Alexander, Florida State University, College of Music
Abstract/Description: The purpose of this treatise is to introduce the music of the Soviet composer of Polish-Jewish origin, Mieczysław Weinberg (1919-1996) to a wide audience. Weinberg’s life took place during the very difficult period following World War I through the second world war. Not only did he feel the terrible consequences of the Nazi efforts to exterminate Jews, but he also experienced the terrors associated with being an artist in the Soviet Union under Stalin. Weinberg’s music reflects its historical...
Show moreThe purpose of this treatise is to introduce the music of the Soviet composer of Polish-Jewish origin, Mieczysław Weinberg (1919-1996) to a wide audience. Weinberg’s life took place during the very difficult period following World War I through the second world war. Not only did he feel the terrible consequences of the Nazi efforts to exterminate Jews, but he also experienced the terrors associated with being an artist in the Soviet Union under Stalin. Weinberg’s music reflects its historical context and the tragic events that impacted his own life and the lives of so many others. This is one reason his compositions are important and valuable. He also had a close friendship with Dmitry Shostakovich, and they inspired one another’s creative work in many ways. Weinberg’s music reflects a diversity of genres and styles. In addition to the large-scale works dedicated to the heavy themes of war, fascism, and death, he also wrote music for movies, cartoons, circuses, and children. Like Weinberg’s life, his music had a difficult fate, as it was obscured for many years. Fortunately, Weinberg’s music has gained increased attention in recent years, especially in Europe. There have been several festivals dedicated to his work held in Liverpool (UK), Rochester (USA), Bregenze (Switzerland), and Moscow (Russia). Recordings of his compositions have been released by large record labels, including “Olympia” (UK), and "Russkiy disk” (Russia). The Danel String Quartet, a Belgian group, recently made a complete recording of all seventeen quartets written by Weinberg. Several renowned conductors have contributed to the promotion of Weinberg’s music, including Thomas Sanderling, the co-initiator of the International Mieczysław Weinberg Society, and Thord Svedlund. This treatise provides information about the composer’s life, an overview of his work, and style analyses of his Concerto for Cello and Orchestra Op. 43 (1948) and his 24 Preludes for Solo Cello (1960). The Concerto and the Preludes are historically significant and musically engaging additions to the standard cello repertoire. The Concerto consists of four contrasting and highly expressive movements with different characters and moods—lyrical, dramatic, powerful, sorrowful, and triumphant. The diversity in the work, in its melodic features and dramatic qualities, make it accessible to a wide range of audiences. The 24 Preludes is a challenging work that features technical variety and extended techniques. In this collection we see Weinberg demonstrating his musical experience, knowledge, and creativity. Practice suggestions for the Concerto and the Preludes are provided at the end of their respective chapters.
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Date Issued: 2019
Identifier: 2019_Spring_Pereverzeva_fsu_0071E_15016_comp
Format: Set of related objects

Title: Americans at the Leipzig Conservatory (1843–1918) and Their Impact on American Musical Culture.
Creator: Pepple, Joanna, Seaton, Douglass, Williamson, George S., Eyerly, Sarah, Quinn, Iain, Von Glahn, Denise, Florida State University, College of Music
Abstract/Description: In 1842 Felix Mendelssohn gained approval from the Prussian King Friedrich Wilhelm IV to apply the late Supreme Court Justice’s Heinrich Blümner’s 20,000-Thaler gift to the founding of Germany’s first music education institution dedicated to the higher-level training of musicians. The establishment of the Leipzig Conservatory in 1843 was a milestone in Germany’s history, as this was Germany’s first national conservatory of music, with the goal to train and educate “complete” musicians in both...
Show moreIn 1842 Felix Mendelssohn gained approval from the Prussian King Friedrich Wilhelm IV to apply the late Supreme Court Justice’s Heinrich Blümner’s 20,000-Thaler gift to the founding of Germany’s first music education institution dedicated to the higher-level training of musicians. The establishment of the Leipzig Conservatory in 1843 was a milestone in Germany’s history, as this was Germany’s first national conservatory of music, with the goal to train and educate “complete” musicians in both applied and theoretical studies. Due to its highly-esteemed faculty, the Leipzig Conservatory immediately drew attention from music students not only nationally but also internationally. The Leipzig Conservatory was known for its “conservative” leanings as well as the strong foundation students received in harmony, counterpoint, and voice-leading. The pedagogy of the Leipzig Conservatory not only had a great impact in Germany and the surrounding European countries, but its influence reached across the Atlantic to American musical life. Nineteenth-century Americans held German musical training in high regard. Between 1846 and 1918 over 1,500 Americans traveled across the Atlantic to study with the renowned faculty at the Leipzig Conservatory. Receiving a comprehensive music education and being exposed to world-class visiting soloists such as Clara Schumann and Franz Liszt, these American students returned to the United States as music teachers, administrators, music writers and publishers, and performers, prepared to influence their music culture in numerous ways. These American individuals had a great impact in numerous cities throughout the United States, and several of them had a role in founding America’s first music conservatories: Oberlin Conservatory of Music (1865) and New England Conservatory of Music (1867). By studying the original documents and concert programs at these institutions, one can trace direct pedagogical approaches and institutional policies transferred from Leipzig to Oberlin and Boston. Furthermore, many early faculty members at Oberlin and NEC themselves had studied at the Leipzig Conservatory, bringing Leipziger tastes and pedagogy to American students. While the Leipzig influence impacted Oberlin and NEC greatly, its pedagogy and principles shaped many other aspects of American music life and education throughout multiple cities and regions in the United States, leaving lasting imprints on American music culture, including music education, concert life, music criticism, and composition. The supplementary Excel spreadsheet shows Leipzig Conservatory faculty members and the duration of their tenure at the Conservatory.
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Date Issued: 2018
Identifier: 2019_Spring_Pepple_fsu_0071E_14966_comp
Format: Set of related objects

Title: The Impact of Vehicle Modal Activity and Green Light Optimized Speed Advisory (GLOSA) on Exhaust Emissions through the Integration of VISSIM and Moves.
Creator: Karabag, Hasan H. (Hasan Huseyin), Ozguven, Eren Erman, Sobanjo, John Olusegun, Moses, Ren, Florida State University, FAMU-FSU College of Engineering, Department of Civil and...
Show moreKarabag, Hasan H. (Hasan Huseyin), Ozguven, Eren Erman, Sobanjo, John Olusegun, Moses, Ren, Florida State University, FAMU-FSU College of Engineering, Department of Civil and Environmental Engineering
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Abstract/Description: Air pollution is a very critical non-natural hazard that adversely affects human health as well as the environment itself in the context of climate change. One of the biggest contributors to air pollution is the transportation industry. According to the U.S. Environmental Protection Agency (EPA), transportation is the second leading source for greenhouse gas (GHG) emissions, contributing to GHG emissions by 28%. Researchers and practitioners have been working on developing techniques to...
Show moreAir pollution is a very critical non-natural hazard that adversely affects human health as well as the environment itself in the context of climate change. One of the biggest contributors to air pollution is the transportation industry. According to the U.S. Environmental Protection Agency (EPA), transportation is the second leading source for greenhouse gas (GHG) emissions, contributing to GHG emissions by 28%. Researchers and practitioners have been working on developing techniques to estimate and reduce transportation-related emissions by the help of various types of technologies. As such, this study aimed to investigate the effect of vehicle operating modes (i.e., constant running, idling, accelerating, and braking) on vehicle exhaust emissions in order to highlight the importance of occasionally disregarded factors that exacerbate the transportation-related air pollution problem. In order to accomplish this goal, this study adopted an approach involving two frequently used software for estimating emissions, namely VISSIM (a microscopic traffic simulation software) and EPA’s Motor Vehicle Emission Simulator (MOVES). The input data required for these software was collected, processed, and introduced into the models in order to estimate the emissions. First, a corridor was simulated within the VISSIM. This corridor is located in the City of Tallahassee, Florida, which is highly congested during the peak hours, and approximately 7.7 miles long, with 22 signalized intersections. Next, the outputs of VISSIM were collected and provided to MOVES by developing an integration tool. First, average speed and volume data were provided to MOVES only for the whole corridor, and VISSIM and MOVES emissions for carbon monoxide (CO) and nitrogen oxides (NOx) were compared. Note that VISSIM provides only emissions for CO and NOx. After observing the massive difference between VISSIM and MOVES emissions, the importance of using operating mode distribution file in MOVES was pointed out. To meet this end, the integration tool was enhanced to compute the vehicle operating mode distribution file based on second-by-second vehicle trajectory output. This was provided to MOVES in order obtain more accurate emission estimation results since only average speed and volume data could not provide accurate emission values disregarding the different vehicle operating modes. For this purpose, an algorithm, named as operating mode calculation algorithm (OMCA), was developed in Python 3.0 to create operating mode distribution input by using second-by-second vehicle trajectory data of VISSIM. This type of analysis focusing on the emissions of individual vehicles provided more accurate emission results. Now that these results were obtained, the focus of the thesis shifted towards analyzing the impact of vehicle connectedness on the air pollution. Two intersections of the selected highway corridor were modelled and simulated with a connected environment using one of the widely used vehicle-to-infrastructure (V2I) communication application called Green Light Optimized Speed Advisory (GLOSA). The GLOSA was implemented on the major leg of these intersections only with different Connected Vehicle (CV) penetration rates. One of the selected legs was the most congested link of the corridor. After extensive simulations, second-by-second VISSIM trajectory data were provided to OMCA, which converted them to MOVES operating mode distribution input files. Finally, MOVES was run in order to estimate carbon monoxide (CO), nitrogen oxides (NOx), primary exhaust smaller than 2.5 micrometer (PM2.5) and primary exhaust smaller than 10 micrometer (PM10) emissions. Findings of the study can aid researchers in understanding the effect of different operation modes on the exhaust emissions, understanding the effect of smoother and lower number of stop-and-go driving operations in the context of the connected vehicle impact on the exhaust emission, and quantifying the potential operational and environmental benefits of connected vehicles (CV’s).
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Date Issued: 2019
Identifier: 2019_Spring_Karabag_fsu_0071N_15065_comp
Format: Set of related objects

Title: Left-Hand Techniques in Aldo Pais' La Tecnica del Violoncello: An Electromyographic Comparison.
Creator: Galvarino, Jordan Lee, Sauer, Greg, Jones, Evan Allan, Stillwell, Corinne, Thomas, Shannon, Florida State University, College of Music
Abstract/Description: The purpose of this treatise is to use surface electromyography (sEMG) in a study with human subjects to compare techniques found in Aldo Pais’ La Tecnica del Violoncello. Statistical research regarding the following exercises found in La Tecnica is provided: compressing the hand (avvicinamenti), enlarged extensions (allargamenti), finger independence, and repetitive motions. Data is recorded from the left extensor digitorum and abductor digiti minimi using sEMG, and each subject’s data is...
Show moreThe purpose of this treatise is to use surface electromyography (sEMG) in a study with human subjects to compare techniques found in Aldo Pais’ La Tecnica del Violoncello. Statistical research regarding the following exercises found in La Tecnica is provided: compressing the hand (avvicinamenti), enlarged extensions (allargamenti), finger independence, and repetitive motions. Data is recorded from the left extensor digitorum and abductor digiti minimi using sEMG, and each subject’s data is compared to one another, in order to reveal these common trends and outliers. Wearing biosensors, six anonymous participants performed two control exercises and four modified versions of Pais’ exercises that each exhibit a specific technique. Participants also completed a short survey at the conclusion of their session, regarding education level and their experience practicing the examples. There was no correlation between education level and sEMG results. Lowered sEMG results result in improved musical performance, and female participants produced lower microvolt ratings than males in every category. Despite their absence in standard cello pedagogy, avvicinamenti and allargamenti produced significantly lower sEMG results than the exercises of finger independence and repetitive motions. This is an important finding because it removes any assumption that Pais’ techniques should be shunned on the basis that they produce an excess of tension. Including these techniques in standard cello pedagogy would expand upon the fingering possibilities available to cellists in numerous musical contexts.
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Date Issued: 2019
Identifier: 2019_Spring_Galvarino_fsu_0071E_15150_comp
Format: Set of related objects

Title: Understanding Variation in Complex Displays and Mate Choice in a Lekking Species with Cooperative Dual-Male Courtship.
Creator: Vanderbilt, Carla Curry, DuVal, Emily H., Johnson, Frank, Lemmon, Emily C., Travis, Joseph, Winn, Alice A., Florida State University, College of Arts and Sciences, Department of...
Show moreVanderbilt, Carla Curry, DuVal, Emily H., Johnson, Frank, Lemmon, Emily C., Travis, Joseph, Winn, Alice A., Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: Motor displays (displays that involve visible body movements) are an integral component of many courtship displays and have the potential to be important signals of male quality to females during mate choice. The whole organism is used in the execution of movements, and so the performance of motor displays may be an even more valuable signal than static traits commonly studied in sexual selection literature. In lekking species where a female chooses a mate from among displaying males, motor...
Show moreMotor displays (displays that involve visible body movements) are an integral component of many courtship displays and have the potential to be important signals of male quality to females during mate choice. The whole organism is used in the execution of movements, and so the performance of motor displays may be an even more valuable signal than static traits commonly studied in sexual selection literature. In lekking species where a female chooses a mate from among displaying males, motor displays provide an especially interesting opportunity for studying mate choice. Which male a female decides to mate with is dependent on which males she observes. Therefore, it is important to not only look at variation in male motor performance and mating success across the entire lek, but also at the phenotypic variation between the males each female is actively choosing between. My dissertation research investigates the causes of variation in the performance of complex, acrobatic displays in the lance-tailed manakin (Chiroxiphia lanceolata; Aves: Pipridae), and the resulting fitness consequences of that variation. Courtship displays in this species vary from being cooperative, with a dominant alpha and subordinate beta male present, to solo, involving only the alpha. Males also perform displays in the absence of females that are very similar to courtship displays. One potential cause of variation in the performance of complex displays is social context. I examined the effects of social context on male displays by quantifying the predictability of display elements in the presence and absence of females. I found that the predictability of individual performance within the dual-male interaction did not differ with female presence; however, entropy metrics describing the interaction of the alpha and beta male indicated that displays for females were more predictable and coordinated. This suggests that the dual-male phenotype is likely an important factor in female mate choice for cooperatively displaying species. The use of male-male cooperation in displays is also variable in this species, and so I next investigated what influences a male’s decision to cooperate and how this decision, in addition to other factors, influences female choice. I found that more experienced alphas were less likely to display cooperatively. Surprisingly, females were more likely to copulate after a solo display, independent of alpha experience. Females that were older, renesting, and closer to egg-laying were more likely to copulate after any given display. Considering effects of the sequence of displays viewed by individual females revealed that females were more likely to observe cooperative displays if they had done so in their previous visit, and more likely to copulate if they had copulated during their previous visit. My results demonstrate non-independence of female visits, suggesting females accumulate information in extended mate searches. These results also challenge the view that cooperative courtship primarily serves to enhance mating success via female choice, and more generally challenges the tendency to assume that the most obvious traits are the most salient for female choice. The complexity of displays and the limitation of current analytical techniques for incorporating sequences of events led me to discover a novel approach called multi-channel sequence analysis (MCSA) to analyze simultaneously the sequences of male and female behaviors during courtship. This approach, to my knowledge, has never before been applied to behavioral ecology. I identified three distinct clusters of display types, based on the combination of male and female behavioral sequences. Displays belonging to the first cluster were more likely to involve male-male cooperation, and those belonging to the second cluster more likely to end in copulation. These results suggest that behavioral sequences from multiple interacting individuals can be productively combined to provide new perspectives on displays, and that MCSA has the potential to be an important new tool in the field of behavioral ecology. In summary, mate choice is a complicated process, and various factors including social context and individual characteristics of males and females can influence the performance of complex displays. This research provides insight into cooperative behavior and utilizes novel statistical approaches that provide a more holistic view of complex displays. This dissertation includes two supplementary video files “Video B-1-Cooperative display example-Chiroxiphia lanceolata.mp4” and “Video B-2-Solo Display Example-Chiroxiphia lanceolata.mp4” that correspond with Appendix B for Chapter 3. These videos are examples of a lance-tailed manakin cooperative and solo display, respectively.
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Date Issued: 2019
Identifier: 2019_Spring_Vanderbilt_fsu_0071E_15007_Comp
Format: Set of related objects

Title: Enabling Intergration of Arabic Art Song into the Applied Voice Music Curriculum.
Creator: Qudourah, Feryal, Brister, Wanda, Gunderson, Frank D., Jackson, Margaret R., Chandler, Yuell, Florida State University, College of Music, College of Music
Abstract/Description: This treatise will discuss the need for essential information that will enable the integration of Arabic song and art song into the applied voice music curriculum. It will begin with a brief history of the cultural and religious understanding and viewpoints of the term "music," as well as sounds through recitation and poetry found in Islam. Middle Eastern singers such as Fairouz will be discussed for her use of western vocality, and Umm Kulthum for her political and religious influence...
Show moreThis treatise will discuss the need for essential information that will enable the integration of Arabic song and art song into the applied voice music curriculum. It will begin with a brief history of the cultural and religious understanding and viewpoints of the term "music," as well as sounds through recitation and poetry found in Islam. Middle Eastern singers such as Fairouz will be discussed for her use of western vocality, and Umm Kulthum for her political and religious influence throughout the Arab world. Composers of art song who have used translations of Arabic poetry will be presented along with examples of well-known artists that have incorporated Arabic lyrics to their songs, such as Shakira, Sting and Sarah Brightman among others. An interview with Lebanese composer, Iyad Kanaan will provide more insight on his compositional style and thoughts on Arabic Art Song. The score for Art songs in Arabic on poems by Said Akl Op.19 for soprano and piano will be provided as supplemental material at the end of this treatise. The second chosen work also provided, is Spanish composer Francisco Javier Jáuregui's art song entitled The Religion of Love with poetry by Ibn Arabi. Several other composers' works will be briefly discussed for students and voice teachers who wish to expand their knowledge of Arabic art song repertoire. There will be an online recording available on YouTube of my lecture recital with selected songs by Iyad Kanaan, Francisco Javier Jáuregui, and Fairouz and the Rahbani Brothers. A proposed IPA chart has been made in the final chapter for English speakers who wish to sing Arabic Art Song. Supplemental files at the end of this treatise include the following scores for use: Art songs in Arabic on poems by Said Akl Op.19 for soprano and piano by Iyad Kanaan, Qadmus by Iyad Kanaan, and The Religion of Love by Francisco Javier Jáuregui.
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Date Issued: 2018
Identifier: 2018_Fall_Qudourah_fsu_0071E_14904_Comp
Format: Set of related objects

Title: Lignin-Based Polymers via Graft Copolymerization.
Creator: Liu, Hailing, Chung, Hoyong, Schlenoff, Joseph B., Guan, Jingjiao, Florida State University, FAMU-FSU College of Engineering, Department of Chemical and Biomedical Engineering
Abstract/Description: Lignin can be an important source of synthetic commodity materials owing to its abundance in nature and low production cost. The current main usage of lignin, however, is very limited to cheap and poorly defined nonfunctional materials, because of undefined chemical structure of lignin and difficulties in chemical modification. This dissertation presents fundamental studies of chemical modifications for natural lignin, leading to advanced functional lignin-based polymers that contains...
Show moreLignin can be an important source of synthetic commodity materials owing to its abundance in nature and low production cost. The current main usage of lignin, however, is very limited to cheap and poorly defined nonfunctional materials, because of undefined chemical structure of lignin and difficulties in chemical modification. This dissertation presents fundamental studies of chemical modifications for natural lignin, leading to advanced functional lignin-based polymers that contains covalently linked natural lignin and synthetic polymers (or other natural biopolymers). The presented graft copolymerization methods of lignin emphasis on 1) natural lignin modification to possess alkyne or alkene groups, 2) synthesis of well-defined functional polymer grafts, 3) covalent bond linkages between lignin and polymers, and 4) mechanical and thermal property studies for material applications. Based on the fundamental method to produce lignin-based polymers, a new lignin-based self-healing polymer, lignin-graft-poly(5-acetylaminopentyl acrylate) (lignin-graft-PAA) was synthesized. The natural lignin and PAA was covalently integrated by a copper catalyzed azide-alkyne cycloaddition using graft-onto method. Prior to the click reaction, lignin was modified to convert abundant hydroxyl groups to alkyne groups. The PAA was synthesized by reversible addition fragmentation-chain transfer (RAFT) polymerization that produces low molecular weight distribution polymers containing chemically active terminal, azide end groups. The synthesized lignin-graft-PAA showed excellent automatic self-healing function which was achieved by hydrogen bonding from the acetylamino groups in PAA. In this lignin-graft-PAA, lignin functioned to strengthen the mechanical strength. The mechanical properties of Young's modulus, energy, maximum strength, and ultimate elongation were enhanced with more lignin content. After using click chemistry as a graft method, a visible light induced thiol-ene reaction was applied to lignin polymeric modification. This is the first time that lignin is modified by Ru(bpy)3Cl2 photoredox catalyzed reaction. Among photoredox catalysts and UV initiators for thiol-ene reaction, including Eosin Y, Ru(bpy)3Cl2, and 2,2-Dimethoxy-2-phenylacetophenone, Ru(bpy)3Cl2 was found to be the most efficient on lignin modification. This modification was efficient between lignin and various thiol compounds, even with a polymer example, poly(ethylene glycol). This new modification method is an important synthetic tool for the further materials applications because of its features of low energy consumption, high efficiency, temporal and spatial control, and no need of special reaction facilities. Using this thiol-ene reaction, a new lignin-based shape memory polymer, crosslinked lignin-polycaprolactone (PCL) was synthesized. Lignin was modified from abundant hydroxyl groups to alkene groups to prepare for the thiol-ene reaction. PCL was synthesized by ring opening polymerization with a 4-arm architecture, which was designed for a dense crosslinking. The hydroxyl end groups from PCL was easily modified to thiol group through an esterification reaction. The alkene groups functioned lignin and thiol groups ended PCL were densely crosslinked by the thiol-ene reaction. The crosslinked lignin-PCL possessed an advanced shape memory function by the crosslinking structure with lignin as netpoints and PCL as switching segments. During the shape memory process, lignin netpoints hold the permanent structure and PCL switching segments allowed shape change. In this system, the role of lignin was a crosslinker additive. Moreover, the content of lignin crosslinker provided adjustment to melting temperature of the crosslinked lignin-PCL. More lignin content lowered the melting temperature by introducing defect to the PCL crystalline structure. Overall, lignin was integrated with polymers by precisely synthesis in this dissertation. The role of lignin was used as an important base polymer that occupies large portion, as well as a small amount additive. Both of the two roles can significantly change polymer properties to strengthen mechanical property and tune thermal property. The overall lignin-based polymer research in the dissertation may be very useful for advanced levels of material applications such as self-healing and shape memory polymers.
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Date Issued: 2018
Identifier: 2018_Fall_Liu_fsu_0071E_14885_Comp
Format: Set of related objects

Title: Characterizing Gene Networks and RNA-Mediated Gene Regulation in Maize.
Creator: Huang, Ji, McGinnis, Karen M., Lemmon, Alan R, Jones, Kathryn M., Chadwick, Brian P., Dennis, Jonathan Hancock, Florida State University, College of Arts and Sciences,...
Show moreHuang, Ji, McGinnis, Karen M., Lemmon, Alan R, Jones, Kathryn M., Chadwick, Brian P., Dennis, Jonathan Hancock, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: Controlling spatial-temporal gene expression patterns is a fundamental task for maize growth and development. With the emergence of massively parallel sequencing, genome-wide expression data production has reached an unprecedented level. This abundance of data has greatly facilitated maize research, but may not be amenable to traditional analysis techniques that were optimized for other data types. In one project, using publicly available data, a Gene Co-expression Network (GCN) was...
Show moreControlling spatial-temporal gene expression patterns is a fundamental task for maize growth and development. With the emergence of massively parallel sequencing, genome-wide expression data production has reached an unprecedented level. This abundance of data has greatly facilitated maize research, but may not be amenable to traditional analysis techniques that were optimized for other data types. In one project, using publicly available data, a Gene Co-expression Network (GCN) was constructed and used for gene function prediction, candidate gene selection and improving understanding of regulatory pathways. To build an optimal GCN from plant materials RNA-Seq data, parameters for expression data normalization and network inference were evaluated. A comprehensive evaluation of these two parameters and ranked aggregation strategy on network performance using libraries from 1266 maize samples was conducted. Three normalization methods (VST, CPM, RPKM) and ten inference methods, including six correlation and four mutual information (MI) methods, were tested. The three normalization methods had very similar performance. For network inference, correlation methods performed better than MI methods at some genes. Increasing sample size also had a positive effect on GCN. Aggregating single networks together resulted in improved performance compared to single networks. In another project, a maize mutant, transgene reactivated 9-1 (tgr9-1) in the transcriptional gene silencing (TGS) pathway, was cloned. The B-A translocation lines were used to map tgr9-1 on chromosome 3 and this result was consistent with molecular markers. To further locate tgr9-1, next-generation sequencing (NGS) combined with bulk segregant analysis was applied to the tgr9-1 mapping population. Using coexpression analysis, our result indicates a maize dicer-like3a (Zmdcl3a) gene is a high-confidence candidate gene for tgr9. Zmdcl3a is involved in the RNA-directed DNA methylation (RdDM) pathway. This pathway is driven by two plant-specific DNA-dependent RNA polymerases, Polymerase IV (Pol IV) and Polymerase V (Pol V). Several kinds of non-coding RNAs are involved, including long single-stranded RNAs, double-stranded RNAs, and small interfering RNAs. The identification of tgr9-1 uncovered the role of non-coding RNAs in TGS and revealed the diversity of TGS pathways in maize. One primary focus of gene regulation study is by studying transcription factors (TFs). Transcription factors (TFs) are proteins that can bind to DNA sequences and regulate gene expression. Many TFs are master regulators in cells that contribute to tissue-specific and cell-type-specific gene expression patterns in eukaryotes. Little is known about tissue-specific gene regulation through TFs in maize. In this project, a network approach was applied to elucidate gene regulatory networks (GRNs) in four tissues (leaf, root, shoot apical meristem and seed) in maize. We used GENIE3 machine-learning algorithm combined with the large quantity of RNA-Seq expression data to construct four tissue-specific GRNs. Although many TFs were expressed across multiple tissues, a multi-tiered analysis predicted tissue-specific regulatory functions for many transcription factors. Some well-studied TFs emerged within the four tissue-specific GRNs, and the GRN predictions matched expectations based upon published results for many of these examples. The GRNs were also validated by ChIP-Seq datasets (KN1, FEA4, and O2). Key TFs were identified for each tissue and matched expectations for key regulators in each tissue, including GO enrichment and identity with known regulatory factors for that tissue.
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Date Issued: 2018
Identifier: 2018_Sp_Huang_fsu_0071E_14421_comp
Format: Set of related objects

Title: Genome Editing of the Disease Locus D4Z4 as a Means to Ameliorate Gene Misregulation in Facioscapulohumeral Muscular Dystrophy.
Creator: Das, Sunny, Chadwick, Brian P., Arbeitman, Michelle N., Keller, Thomas C. S., Gilbert, David M., Dennis, Jonathan Hancock, Florida State University, College of Arts and Sciences...
Show moreDas, Sunny, Chadwick, Brian P., Arbeitman, Michelle N., Keller, Thomas C. S., Gilbert, David M., Dennis, Jonathan Hancock, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: D4Z4 is a subtelomeric macrosatellite repeat on chromosome 4q that codes for DUX4, a gene that is causal to the muscle wasting disease Facioscapulohumeral muscular dystrophy (FSHD). DUX4 expression is influenced by a number of genetic and epigenetic modifiers, including variation in D4Z4 copy number, single nucleotide polymorphisms (SNPs) on 4q, DNA and histone methylation changes, modifier genes like SMCHD1 and DNMT3B, and telomeres. The overarching goal of the research presented in this...
Show moreD4Z4 is a subtelomeric macrosatellite repeat on chromosome 4q that codes for DUX4, a gene that is causal to the muscle wasting disease Facioscapulohumeral muscular dystrophy (FSHD). DUX4 expression is influenced by a number of genetic and epigenetic modifiers, including variation in D4Z4 copy number, single nucleotide polymorphisms (SNPs) on 4q, DNA and histone methylation changes, modifier genes like SMCHD1 and DNMT3B, and telomeres. The overarching goal of the research presented in this dissertation was to demonstrate the feasibility of targeting the disease locus using genome editing tools. To achieve this, we first needed to identify suitable cellular platforms for subsequent genome editing experiments. Through genotyping analysis, we were able to identify a cell line (HCT116) that was well-suited to studies investigating D4Z4/DUX4 expression, given that it harbors a disease-permissive 4qA allele. Using HCT116 and three of its DNA methyltransferase knockouts (1KO, 3BKO and DKO), we probed for factors that influence DUX4 expression in these cell lines. These experiments revealed that H3K9me3 loss and CpG hypomethylation can independently result in DUX4 expression in non-myogenic cell types. HCT116 and its DNMT KOs offer a new platform for studying DUX4 expression, albeit with some caveats. Importantly, we showed existence of D4Z4 transcripts in a variety of adult human tissues in addition to testis, with notably high expression in the thymus. Using these cell lines, we next explored the mechanism by which modifiers of D4Z4, such as SMCHD1 and telomeres might influence DUX4 expression. We generated several independent SMCHD1 knockout clones in HCT116 using TALENs. Characterization of these KOs revealed that despite no detectable changes in H3K9me3 or CpG methylation at D4Z4, SMCHD1 loss causes expression of unspliced DUX4, a phenomenon that was phenocopied by treatment of cells with a chemical inhibitor of telomerase. Spliced and pathogenic DUX4 was only expressed in these KOs upon treatment with 5-Aza-C, which demethylates DNA and lowers H3K9me3 levels at D4Z4. Given these results and the previously known importance of H3K9me3 enrichment in transcription and splicing, we speculate on a model, where SMCHD1 protein and telomeres, may act in coordination to provide an extra layer of transcriptional repression in addition to H3K9me3, at D4Z4. To achieve the main goal of this project, we took four independent approaches aimed at directly or indirectly repressing DUX4. In the first approach, we successfully deleted the array from a 4q permissive allele (in HCT116 and DKO cells), generating recombinants that likely had a shortened 4q chromosomal end and harbored an exogenously provided telomere seeding construct. Although we were unable to isolate clones of D4Z4-deleted cells, these results showed that the entire array can be deleted, also highlighting adverse side-effects of such targeting on cell viability. For our second approach, we used a CRISPR-based effector system to upregulate SMCHD1 transcript levels. Using a dCas9-VP64 activator construct, we were able to affect >2-fold upregulation in SMCHD1 in 293T cells. This avenue can be explored further to assess the effect of such upregulation on DUX4 and its target gene expression, in clinically relevant cell types. A SNP, resulting in a non-canonical polyadenylation (poly-A) sequence in DUX4 exon 3 is believed to stabilize pathogenic DUX4 transcripts in somatic cells. In a novel third approach, we designed pairs of gRNAs flanking the poly-A and deleted it using Cas9 nuclease recruited by these gRNAs. Significant lowering of DUX4 transcription in a mutant clone of HCT116, which contains a deletion of the pathogenic poly-A highlighted the importance of this sequence in transcript stabilization. Additionally, through lentiviral transduction of patient myoblasts, we showed that this approach can not only repress DUX4 expression, but also alleviate misregulation of a subset of its downstream target genes that are also biomarkers of FSHD. For our final approach, we enriched H3K9me3 at D4Z4 using a the dCas9-KRAB repressor system and a suitable gRNA. In both DKO cells and patient myoblasts, targeting repressed DUX4 expression significantly. Additionally, DUX4 target genes were also repressed in myoblasts and we showed that this repression was a consequence of increase and spread of H3K9me3 at D4Z4. Taken together, the results from these studies have generated promising future directions that can help understand the mechanism of how modifiers regulate D4Z4 expression. More importantly, by demonstrating the feasibility of targeting the disease locus in different cell types (including patient myoblasts), we have laid the foundation for development of future cell-based therapies to alleviate patient suffering in FSHD.
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Date Issued: 2018
Identifier: 2018_Sp_Das_fsu_0071E_14319_comp
Format: Set of related objects

Title: Utilities for Off-Target DNA Mining in Non-Model Organisms and Querying for Phylogenetic Patterns.
Creator: Mechtley, Alisha, Lemmon, Alan R, Arbeitman, Michelle N., Meyer-Bäse, Anke, Beerli, Peter, Slice, Dennis E., Florida State University, College of Arts and Sciences, Department...
Show moreMechtley, Alisha, Lemmon, Alan R, Arbeitman, Michelle N., Meyer-Bäse, Anke, Beerli, Peter, Slice, Dennis E., Florida State University, College of Arts and Sciences, Department of Scientific Computing
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Abstract/Description: High throughput sequencing data are rich in information and contain many off-target sequences (reads) that are often ignored but may be biologically relevant. Seed extension, a combination of reference and de novo based assembly methods, can be used to extract the information but it is time-consuming to implement because it requires that multiple seeds (sequences from one or many closely related species) be gathered in advance. A new tool is presented here, SeedSQrrL, that can automatically...
Show moreHigh throughput sequencing data are rich in information and contain many off-target sequences (reads) that are often ignored but may be biologically relevant. Seed extension, a combination of reference and de novo based assembly methods, can be used to extract the information but it is time-consuming to implement because it requires that multiple seeds (sequences from one or many closely related species) be gathered in advance. A new tool is presented here, SeedSQrrL, that can automatically crawl the web to gather the seeds from the closest taxonomic relative for each gene and store it into a relational database. The seeds can then be used to create multiple seed extensions which are later combined into a reference or used for downstream phylogenetic analysis. Patterns in the resulting gene trees can be searched for using the traditional methods of tree comparison (Robinson-Foulds topological distance and branch-length comparison methods). Currently, no open source tree pattern matching program exists that allows the user to modify algorithms and create their own custom pattern matching functions. I have worked on such a tool, called Treematcher, and it will be made available in the ETE Toolkit (a Python Environment for Tree Exploration). Three biological case studies will be included included to demonstrate the capabilities of the two programs: 1) a custom function in Treematcher to perform a regular expression-like query, 2) SeedSQrrL will be used to isolate mitochondrial genes from snakes and chloroplast genes from angiosperms, and 3) a large case study of animals will be assembled.
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Date Issued: 2018
Identifier: 2018_Sp_Mechtley_fsu_0071E_14520_comp
Format: Set of related objects

Title: Baroclinic Geostrophic Turbulence and Jets in the Laboratory.
Creator: Smith, Carlowen Andrew, Speer, Kevin G., Landing, William M., Dewar, William K., Sura, Philip, Florida State University, College of Arts and Sciences, Program in Geophysical...
Show moreSmith, Carlowen Andrew, Speer, Kevin G., Landing, William M., Dewar, William K., Sura, Philip, Florida State University, College of Arts and Sciences, Program in Geophysical Fluid Dynamics
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Abstract/Description: Baroclinic, geostrophic turbulence is random, chaotic flow characterized by significant vertical gradients in density (Bu
Show moreBaroclinic, geostrophic turbulence is random, chaotic flow characterized by significant vertical gradients in density (Bu << 1) in which rotation plays a major role (Ro << 1). In the presence of a large-scale background gradient of potential vorticity (a β-effect ), a symmetry-breaking occurs which admits anisotropy in the system. These conditions form the fundamental dynamical basis of many natural geophysical flows on a planetary scale (Rh << 1), and even fairly simple models of these phenomena can exhibit quite complex behavior. One such aspect that is common to these flows is that of multiple, zonal jets. These are spontaneous flow structures characterized by fast East-West (azimuthal) motion. This thesis describes the creation of multiple jets in the laboratory within a fully-stratified, baroclinically-forced fluid subject to rotation and a β-effect. By carefully controlling the forcing parameters, we observe the transition between a single “classical” baroclinic wave and regimes that closely resemble conditions of natural planetary flows. Observing this transition in the laboratory shows that the proposed scaling arguments are valid and have predictive power in the case of multiple zonal jets in a baroclinic fluid. Spontaneous eddy forcing of the mean flow is shown to be the ultimate driving force of the jets, whose evolution is observed in time. A long-duration drift in the jet structure is observed and quantified to be an order of magnitude less than the Rossby wave phase speed. A detailed quantitative analysis of the structure the flow field sheds further light. This is done through both a standpoint of the Eulerian flow fields, and the raw data associated with the (Lagrangian) tracks of neutrally buoyant particles within the flow. There is a significant transition of the power law scaling of Fourier spectra between dynamically significant scales. As the flow changes between experiments, the power law of the Eulerian spectra can change over particular scale ranges, which is direct evidence of a regime change. Access to raw Lagrangian tracks of the fluid allow a direct characterization of the flow field that is independent of the Eulerian. The structure function technique is introduced and shows a fundamental change in behavior between dynamic scales, and between experiments, in a way consistent with theory. A preliminary analysis is carried out of an experiment studying the competing mechanisms of buoyancy and wind forcing present on a single zonal jet. This is simulated in a rotating annulus of fluid by imposing a radial temperature gradient across the annulus gap, while applying mechanical forcing at the surface through the differential rotation of a rigid lid in contact with a surface layer of oil. A radially-sloping bottom creates a fluid depth gradient and simple topography in the form of five regularly spaced meridional ridges creates azimuthally varying f/h contours that steer the first-order flow. By varying the strength of wind and thermal forcing on the fluid, several regimes of flow are produced. Analysis of the Eulerian field shows the response of zonal transport and eddy kinetic energy to these different forcing regimes. The thesis concludes with a description of the development of an apparatus to push the observations into a more turbulent dynamical range. This includes information about the spin-up and maintenance of a large-scale sloping thermal gradient in the apparatus, as well as some preliminary results.
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Date Issued: 2018
Identifier: 2018_Sp_Smith_fsu_0071E_14453_comp
Format: Set of related objects

Title: The Computationally-Assisted Analysis of Select Songs by Sergei Prokofiev.
Creator: Lomax, Micah Aaron, Efimov, Nina A., Kraus, Joseph Charles, Buchler, Michael Howard, Florida State University, College of Music, College of Music
Abstract/Description: Sergei Prokofiev's songs for solo voice and piano hold a special place in his oeuvre both biographically and stylistically. The works were composed almost continuously throughout his entire lifetime, with only a short lapse in output from 1922-1931. The chronological consistency with which his songs were produced stands in stark contrast to other genres like his concertos, sonatas, symphonies, oratorios, and film music, which were either subject to large chronological gaps between subsequent...
Show moreSergei Prokofiev's songs for solo voice and piano hold a special place in his oeuvre both biographically and stylistically. The works were composed almost continuously throughout his entire lifetime, with only a short lapse in output from 1922-1931. The chronological consistency with which his songs were produced stands in stark contrast to other genres like his concertos, sonatas, symphonies, oratorios, and film music, which were either subject to large chronological gaps between subsequent works or were composed exclusively in his Soviet Period (1936-1953) resulting in separate snapshots of Prokofiev's changing compositional practice instead of a more panoramic and dynamic view. Therefore, his songs for solo voice and piano offer a perspective of his stylistic evolution not available when examining his works from other genres. Even so, very few scholarly works engage with more than a handful of these songs within the same study. Eugenia Joukova attempts to examine all of his solo vocal songs from a historical perspective, noting the subject matter of each song and how it relates to the surrounding political and cultural environment, but her study is unique, as no other scholarly investigations, either historical or analytical in their focus, attempt to address all of Prokofiev's works in this genre in a single project. This dissertation not only demonstrates that an analytical investigation of these songs can lead to a deeper understanding of Prokofiev's compositional style, but also fills a gap in the literature and contributes to the well-established body of Prokofiev scholarship. Producing a thorough, in-depth analysis of a large corpus of music can prove challenging and, at times, unattainable due to various factors. The sheer size of a musical corpus can discourage these studies from being undertaken, and the time and resources required for hand analysis of a large corpus can result in incomplete analyses even after a significant effort has been made. To overcome these challenges, this dissertation will leverage computationally-assisted analytical tools, which are guided by a bi-directional analytical procedure that moves fluidly between the analysis of the underlying song texts and the accompanying song melodies to identify shifts and patterns that distinguish Prokofiev's pre-Soviet (1891-1936) songs from his Soviet (1936-1953) songs. Further, the analysis will contextualize these findings historically, drawing connections between the socio-political environment in which Prokofiev worked and his compositional style to demonstrate that in both stylistic periods, his compositional decisions were often driven by the philosophical dogma of the day. The findings of both the computationally-driven text and music analyses will also be compared to songs by other Russian and Soviet composers, to further identify musical features that are statistically distinctive of Prokofiev's compositional style. The result is a robust, holistic analysis of Prokofiev's songs that not only advocates for the use of computationally-assisted analytical tools in the field of music theory, but also fills a gap in the scholarly literature and provides a clearer picture of Prokofiev's compositional evolution utilizing a corpus of music that, up to this point, has received little analytical investigation.
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Date Issued: 2018
Identifier: 2018_Sp_Lomax_fsu_0071E_14340_Comp
Format: Set of related objects

Title: New Approaches of Differential Gene Expression Analysis and Cancer Immune Evasion Mechanism Identification.
Creator: Liu, Yuhang, Zhang, Jinfeng, Sang, Qing-Xiang, Mai, Qing, She, Yiyuan, Florida State University, College of Arts and Sciences, Department of Statistics
Abstract/Description: Background: Genomic and epigenomic data analyses has been a popular research area in the 21st century. Common research problems include detecting differentially expressed genes between groups, clustering and classification using genomic data in order to study the heterogeneity of a disease, and dividing a sequence of measurements along a genome into segments to identify different functional regions of the genome. This study gives a comprehensive investigation of the aforementioned tasks, with...
Show moreBackground: Genomic and epigenomic data analyses has been a popular research area in the 21st century. Common research problems include detecting differentially expressed genes between groups, clustering and classification using genomic data in order to study the heterogeneity of a disease, and dividing a sequence of measurements along a genome into segments to identify different functional regions of the genome. This study gives a comprehensive investigation of the aforementioned tasks, with emphasis on developing new computational methodologies. Normalization is an important data preparation step in gene expression analyses, in order to remove various systematic noise, therefore reduce sample variance and increase the power of subsequent statistical analyses. On the other hand, variance reduction is made possible by borrowing information across all genes, including differentially expressed genes (DEGs) and outliers, which will inevitably introduce bias to the data. A question of interest is how to avoid inflation of type I error rate and loss of statistical power incurred by this bias. Breast cancer (BRCA) can escape immune surveillance using 6 known evasion mechanisms, yet the complexity of combination of these mechanisms used by subsets of human BRCA patients is not fully understood. In the era of immunotherapy and personalized medication, there is an urgent need for advancing the knowledge of immune evasion clusters (IEC) in BRCA and identifying reliable biomarkers, which is essential for better understanding of patients’ response to immunotherapies and for rational clinical trial design of combination immunotherapies. Identification of functional enriched regions of a genome often requires dividing a sequence of measurements along the genome into segments where adjacent segments have different properties (e.g. mean values). Despite dozens of algorithms developed to address this issue, accuracy and computational efficiency still need to be improved, to tackle both existing and emerging segmentation problems in genomic and epigenomic research. Results: In chapter 1 of this study we propose a new differential gene expression analysis pipeline super-delta, that pairs a modified t-test derived based on large sample theory with a robust multivariate extension of global normalization, designed to minimize the bias introduced by DEGs. In simulation studies, Super-delta was compared to four commonly used normalization methods: global, median-IQR, quantile, and cyclic loess normalization, and shown to have better statistical power with tighter type I error control. We then applied all methods to a microarray gene expression dataset on BRCA patients who received neoadjuvant chemotherapy. Super-delta was able to identify marginally more DEGs than its competitors, in addition to the substantial overlap of DEGs identified by all of them. Appropriate adaptations are under active development to make this procedure framework incorporated with RNA-Seq data and more general between-group comparison problems. In chapter 2, we developed a sequential biclustering (SBiC) method based on existing biclustering approach using the plaid model and applied it to the log2 normalized RNA-seq data of immune related genes of BRCA patients from The Cancer Genome Atlas (TCGA). We identified seven clusters for 81% of the studied samples. We found that 78.8% of these samples evade through TGF-β immunosuppression, 57.75% through DcR3 counterattack, 48% through CTLA4, and 27.8% through PD-1. Interestingly, combination of TGF-β and DcR3 was pronounced in 57.75% of patients and evasion through DcR3 was exclusive to the lobular invasive subgroup. In addition, triple negative breast cancer (TNBC) patients split equally into 2 clusters: one with impaired antigen presentation and another with high leukocyte recruitment but a combination of 4 evasion mechanisms. We also identified biomarkers that play important roles in distinguishing immune evasion mechanisms. These findings provide a better understanding of patients’ response to immunotherapies and shed light to rational design of novel combination immunotherapies. In chapter 3, We designed an efficient algorithm called iSeg, for segmentation of genomic and epigenomic profiles. It first utilizes dynamic programming to identify candidate significant segments, then uses a novel data structure based on coupled balanced binary trees to detect overlapping significant segments and update them simultaneously during searching and refinement stages. Merging of significant segments are performed at the end to generate the final set of segments. The algorithm can serve as a general computational framework that works with different model assumptions of the data. As a general procedure, it can segment different types of genomic and epigenomic data, such as DNA copy number variation, nucleosome occupancy, and (differential) nuclease sensitivity. We evaluated iSeg using both simulated and experimental datasets and showed that it performs satisfactorily when compared with some popular methods, which often employ more sophisticated statistical models. Implemented in C++, iSeg is very computationally efficient, well suited for long sequences and large number of input data profiles.
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Date Issued: 2018
Identifier: 2018_Su_Liu_fsu_0071E_14757_Comp
Format: Set of related objects

Title: Sparsity-Regularized Learning for Nano-Metrology.
Creator: Li, Xin, Park, Chiwoo, Srivastava, Anuj, Liang, Zhiyong, Vanli, Omer Arda, Florida State University, College of Engineering, Department of Industrial and Manufacturing Engineering
Abstract/Description: The key objective of nanomaterial metrology is to extract relevant information on nano-structure for quantitatively correlating structure-property with functionality. Historic improvements on in- strumentation platforms has enabled comprehensive capture of the information stream both glob- ally and locally. For example, the impressive scanning transmission electron microscopy (STEM) progress is the access to vibrational spectroscopic signals such as atomically resolved electron en- ergy loss...
Show moreThe key objective of nanomaterial metrology is to extract relevant information on nano-structure for quantitatively correlating structure-property with functionality. Historic improvements on in- strumentation platforms has enabled comprehensive capture of the information stream both glob- ally and locally. For example, the impressive scanning transmission electron microscopy (STEM) progress is the access to vibrational spectroscopic signals such as atomically resolved electron en- ergy loss spectroscopy (EELS) and the most recent ptychography. This is particularly pertinent in the scanning probe microscopy (SPM) community that has seen a rapidly growing trend towards simultaneous capture of multiple imaging channel and increasing data sizes. Meanwhile signal pro- cessing analysis remained in the same, depending on simple physics models. This approach by definition ignores the material behaviors associated with the deviations from simple physics models and hence require more complex dynamic models. Introduction of such models, in turn, can lead to spurious growth of free parameters and potential overfitting etc. To derive signal analysis pathways necessitated by large,complex datasets generated by progress in instrumentation hardware, here we propose data-physics inference driven approaches for high- veracity and information-rich nanomaterial metrology. Mathematically, we found structural spar- sity regularizations extremely useful which are explained at corresponding applications in later chapters. In a nutshell, we overview the following contributions: 1.We proposed a physics-infused semi-parametric regression approach for estimating the size distribution of nanoparticles with DLS measurements, yielding more details of the size distribution than the traditional methodology. Our methodology expands DLS capability of characterizing heterogeneously shaped nanoparticles. 2.We proposed a two-level structural sparsity regularized regression model and correspondingly developed a variant of group orthogonal matching pursuit algorithm for simultaneously estimating global periodic structure and detecting local outlier structures in noisy STEM images. We believe this an important step toward automatic phase. 3.We develop and implement a universal real-time image reconstruction algorithm from rapid and sparse STEM scans for non-invasive and high-dynamic range imaging. We build up and opensource the systematic platform that fundamentally push the evolution of STEM for both imaging and e-beam based atom-by-atom fabrication, forming a marriage between the imaging and manipulation modes via intelligent and adaptive responses to the real-time material evolution.
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Date Issued: 2018
Identifier: 2018_Su_Li_fsu_0071E_14718_Comp
Format: Set of related objects

Title: Glucose Sensing in the Olfactory System: Role of Glucose Transporter Type 4.
Creator: Al Koborssy, Dolly, Fadool, Debra Ann, Blaber, Michael, Meredith, Michael, Keller, Thomas C. S., Overton, J. Michael, Florida State University, College of Arts and Sciences,...
Show moreAl Koborssy, Dolly, Fadool, Debra Ann, Blaber, Michael, Meredith, Michael, Keller, Thomas C. S., Overton, J. Michael, Florida State University, College of Arts and Sciences, Department of Biological Science
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Abstract/Description: Olfactory perception affects the food choice of most living species. A strong set of data have been accumulated to demonstrate that the olfactory bulb, the first relay of olfactory information, as a metabolic sensor. Mitral cells of the olfactory bulb project to central processing areas such as the piriform cortex. Our laboratory has recently determined that a subpopulation of mitral cells can modulate their firing frequency in response to changes in extracellular glucose concentration, thus...
Show moreOlfactory perception affects the food choice of most living species. A strong set of data have been accumulated to demonstrate that the olfactory bulb, the first relay of olfactory information, as a metabolic sensor. Mitral cells of the olfactory bulb project to central processing areas such as the piriform cortex. Our laboratory has recently determined that a subpopulation of mitral cells can modulate their firing frequency in response to changes in extracellular glucose concentration, thus acting as glucose sensors. Glucose sensors are found throughout the brain in the hypothalamus, the brainstem, amygdala, septum and hippocampus. Glucose has been extensively studied in non-neuronal tissues given its essential role as the main cellular fuel. In glucose sensing neurons, however, where glucose acts as a signal, this process remains largely unknown. My dissertation project focused on providing further evidence of glucose-sensing in the olfactory system, specifically the olfactory bulb and the anterior piriform cortex. I hypothesized that glucose-sensing happened via the insulin-dependent glucose transporter type 4. I first mapped the presence of the glucose transporter type 4 in the different cellular layers of the olfactory bulb and the piriform cortex. mRNA of the glucose transporter type 4 and the voltage-gated potassium channel Kv1.3 were present in the mitral cell layer of the olfactory bulb. In the piriform cortex, the glucose transporter type 4, Kv1.3, and insulin receptors exhibited a broad diversity of distribution. Neurons in the different layers of the piriform cortex expressed one of the three proteins, two of them, or the three proteins co-expressed together. Both mitral cells in the olfactory bulb and pyramidal neurons in the piriform cortex had glucose-sensing properties whereby glucose modulated the electrical behavior of these cells. Mitral cells increased or decreased their firing frequency in response to low glucose (1 mM) while the electrical activity of pyramidal neurons was dependent on extracellular glucose concentration. Switching glucose concentration from high (10 mM) to low (0.5 mM) decreased the instantaneous frequency in pyramidal neurons. Switching glucose concentration from moderate (5 mM) to low (1 mM) revealed two subpopulations of pyramidal neurons that either decreased their instantaneous frequency or were unresponsive to the change in glucose concentration. Pyramidal neurons were responsive to insulin as well, and both mitral cells and pyramidal neurons required glucose metabolism to sense glucose as demonstrated in vitro by using the glucose analog 2-deoxyglucose, or alloxan, a glucokinase inhibitor. Furthermore, I bilaterally implanted cannulas into the anterior piriform cortex of rats, micro-injected insulin (172 nM), glucose (10 nM), or a small peptide Kv1.3 inhibitor margatoxin (0.1 nM). Animals were then subjected to an olfactory habituation/dishabituation paradigm. Results showed that insulin and glucose reduced olfactory discrimination but blocking Kv1.3 improved olfactory habituation and discrimination. My work is the first to demonstrate the presence of the glucose transporter type 4 in the anterior piriform cortex, it is also the first to provide insights into the glucose sensing transduction cascade in the olfactory system, a process that appears to be modulated by insulin and glucose metabolites. The results of this study help provide a better fundamental understanding of the physiological regulation of olfactory perception in relationship with the metabolic status. This study might also pave the way towards identifying a potential therapeutic target to control overeating; a main cause of obesity in western countries.
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Date Issued: 2018
Identifier: 2018_Su_AlKoborssy_fsu_0071E_14756_Comp
Format: Set of related objects

Title: The Impact of Interpersonal Trauma Exposure and Posttraumatic Stress Disorder on Suicide-Related Outcomes.
Creator: Blankenship, Allison Paige, Canto, Angela I., Tripodi, Stephen J., Becker, Martin Swanbrow, Osborn, Debra S., Florida State University, College of Education, Department of...
Show moreBlankenship, Allison Paige, Canto, Angela I., Tripodi, Stephen J., Becker, Martin Swanbrow, Osborn, Debra S., Florida State University, College of Education, Department of Educational Psychology and Learning Systems
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Abstract/Description: Relationships have been previously established between trauma exposure and suicide, particularly when the trauma exposure occurs during childhood, and when the event results in symptoms of Posttraumatic Stress Disorder (PTSD). Interpersonal types of trauma (i.e., trauma within a human relationship) have been found to exhibit stronger relationships with both suicidal ideation (SI) and suicide attempts (SA) than noninterpersonal trauma (e.g., natural disaster). More specifically, interpersonal...
Show moreRelationships have been previously established between trauma exposure and suicide, particularly when the trauma exposure occurs during childhood, and when the event results in symptoms of Posttraumatic Stress Disorder (PTSD). Interpersonal types of trauma (i.e., trauma within a human relationship) have been found to exhibit stronger relationships with both suicidal ideation (SI) and suicide attempts (SA) than noninterpersonal trauma (e.g., natural disaster). More specifically, interpersonal events that are physically assaultive exhibit stronger relationships with suicide-related outcomes than other types of trauma. Existing research has compared individual trauma events; however, there is a need to understand the differences between overarching types of trauma, and to explore the relationships between interpersonal trauma, age at time of exposure, PTSD, and suicide-related outcomes. The Interpersonal-Psychological Theory of Suicide (IPTS; Joiner, 2005) theorizes that death by suicide occurs when an individual possesses perceived burdensomeness (PB), thwarted belongingness (TB), and acquired capability for suicide (AC). Empirical evidence for IPTS is emerging, and relationships have been established between PB, TB, and AC with suicide-related outcomes. While interpersonal trauma exposure has been speculated to increase risk for PB, TB, and AC, there is a need to examine these relationships further, and to identify the interactions between trauma type and IPTS constructs. The first aim of the present study was to explore the relationships between trauma type (i.e., interpersonal assaultive, interpersonal non-assaultive, and noninterpersonal), age at time of trauma exposure, PTSD symptomology, and suicide-related outcomes (i.e., SI, SA, and severity of suicide-related outcomes (SSRO; a single variable that encompasses both SI and SA)). Given the existing relationships noted in literature, it was hypothesized that all variables would be significantly related to all suicide-related outcomes, and predictive of SSRO. Specifically, it was hypothesized that interpersonal assaultive trauma would demonstrate a stronger relationship with SSRO than the other trauma types. The second goal of the present study was to explore the relationships between trauma type and the IPTS constructs of PB, TB, and AC (Joiner, 2005) with suicide-related outcomes, as well as to explore interactions between IPTS constructs and trauma type. It was hypothesized that each IPTS construct would be significantly related to all suicide-related outcomes, and predictive of SSRO. Based on the conceptual understanding that assaultive trauma events increase habituation to painful experiences (Joiner, 2005), it was further hypothesized that interactions would be found between interpersonal assaultive trauma and AC. The current sample included 515 individuals. Of this sample, 426 individuals (82.7%) endorsed a traumatic event that met the minimum threshold of stressfulness to be included in the primary analyses. Participants completed an online survey that included a Demographic Questionnaire, the Trauma Experience Questionnaire (TEQ), a Worst Event Sampling Questionnaire, an Event Stressfulness Rating item, the Posttraumatic Stress Disorder Checklist for DSM-5 (PCL-5; Weathers, Litz, Keane, Palmieri, Marx & Schnurr, 2013), a questionnaire regarding history of SI and SA, an abbreviated form of the Interpersonal Needs Questionnaire (INQ; Van Orden, Witte, Gordon, Bender, & Joiner, 2008), and finally, an abbreviated form of the Acquired Capability for Suicide Scale (ACSS; Van Orden et al., 2008). Participants’ qualitative reports of their “worst traumatic experience” were coded by a trauma-focused research team into one of the three trauma types: interpersonal assaultive, interpersonal non-assaultive, and noninterpersonal. Statistical analyses included bivariate correlational analyses and a series of hierarchical regression analyses. Regression analyses examined the relationships between trauma type, age at time of trauma exposure, PTSD symptomology, PB, TB, and AC with SSRO, as well as the interactions between trauma type and IPTS constructs. Results indicated that age at time of trauma exposure and PTSD symptomology were both significant predictors of SSRO, but that trauma type did not predict SSRO when the aforementioned variables were controlled for. In regard to IPTS constructs (Joiner, 2005), PB was determined to be a positive predictor of SSRO after controlling for age at time of exposure and PTSD, when interaction effects were also included in the model. However, TB and AC were both found to have significant interactions with interpersonal assaultive trauma. Implications of this study include the clinical focus on elevated PTSD symptomology, younger age at time of trauma exposure, and feelings of burdensomeness in the assessment and treatment of individuals with history of trauma exposure. Limitations include the cross-sectional nature of this research as well as limited generalizability due to characteristics of the participants. This study further contributes to empirical evidence for IPTS by supporting the relationship between constructs and suicide-related outcomes, and by being the first known study to explore the interactions between IPTS constructs and trauma type.
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Date Issued: 2018
Identifier: 2018_Su_Blankenship_fsu_0071E_14669_Comp
Format: Set of related objects

Title: Peptide Mediated Delivery of Inorganic Nanomaterials.
Creator: Kapur, Anshika, Mattoussi, Hedi, Grant, Samuel C., Miller, Brian G, Li, Hong, Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department of...
Show moreKapur, Anshika, Mattoussi, Hedi, Grant, Samuel C., Miller, Brian G, Li, Hong, Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: The unique chemical, optical and physical properties of inorganic nanocrystals have generated tremendous interest to develop a variety of applications, most importantly as novel probes in biology. Recent developments have advertised them as promising platforms for sensing, drug delivery, imaging cells and tissue, and as diagnostic tools. However, one impediment to achieve these goals has remained the lack of effective means to deliver them into the cytosol of live cells. A variety of...
Show moreThe unique chemical, optical and physical properties of inorganic nanocrystals have generated tremendous interest to develop a variety of applications, most importantly as novel probes in biology. Recent developments have advertised them as promising platforms for sensing, drug delivery, imaging cells and tissue, and as diagnostic tools. However, one impediment to achieve these goals has remained the lack of effective means to deliver them into the cytosol of live cells. A variety of techniques have been explored to achieve this goal including receptor mediated internalization, lipid-based transfection, electroporation and viral peptide-mediated delivery. Nevertheless, most if not all those approaches tend to sequester the nanoparticles within endocytic vesicles. This prevents them from reaching intracellular targets, thus limiting their use in cellular studies. Despite several strategies and efforts there is still a need for an easy and reproducible approach to deliver exogenous nanomaterials to cells directly via membrane translocation. In this dissertation, we summarize different approaches to overcome this issue by employing two distinct peptides to deliver nanoparticles into the cell cytoplasm through the plasma membrane. We also describe the use of gold nanoparticles to develop a potential platform for thiol sensing. In Chapter 1, we introduce the optical and physical properties of inorganic nanomaterials including, quantum dots (QDs), gold nanoparticles (AuNPs) and gold nanorods (AuNRs). We further briefly describe their syntheses approach followed by an overview of surface functionalization and bio-conjugation strategies employed to assemble colloidally stable and biocompatible nanoparticle-biomolecule conjugates. This followed by a brief discussion about various recent applications of nanoparticles in biology and biomedicine focused on imaging, biosensing, drug delivery and photothermal therapy. Finally, we conclude by presenting several approaches that have been applied for intracellular delivery of nanoparticles into the cell cytoplasm. In Chapter 2, we characterize the energy transfer quenching of mCherry fluorescent proteins immobilized on AuNPs via metal-imidazole coordination, where parameters such as NP size and number of attached proteins were varied. Using steady-state and time-resolved fluorescence measurements, we recorded very high mCherry quenching, with efficiency reaching ≈ 95-97%, independent of the NP size or number of bound fluorophores (i.e., conjugate valence). We further describe the use of this system to develop a solution phase sensing platform targeting thiolate compounds. This is based on the use of Energy Transfer (ET) as a transduction mechanism to monitor the competitive displacement of mCherry from the Au surface upon the introduction of varying amounts of thiolates with different size and coordination numbers. We then demonstrate that the competitive displacement of mCherry depends on the thiolate concentration, time of reaction and type of thiol derivatives used and also provide a measure for the equilibrium dissociation constant (Kd-1) for these compounds. In Chapter 3, we describe a new quantum dot (QD)-conjugate prepared with a lytic peptide, derived from a non-enveloped virus capsid protein, capable of bypassing the endocytotic pathways and delivering large amounts of QDs to living cells. The polypeptide, derived from the Nudaurelia capensis Omega virus, was fused onto the C-terminus of maltose binding protein that contained a hexa-HIS tag at its N-terminus, allowing spontaneous self-assembly of controlled numbers of the fusion protein per QD via metal-HIS interactions. We illustrate how the efficacy of QD-peptide conjugate uptake by several mammalian cell lines was substantial even for small concentrations (10-100 nM). Upon internalization the QDs were primarily distributed outside the endosomes/lysosomes. We further provide evidence indicating an entry mechanism that does not involve endocytosis, but rather the perforation of the cell membrane by the lytic peptide on the QD surfaces. In Chapter 4, we propose the use of a chemically-synthesized anticancer peptide, SVS-1, as an efficient vehicle to promote the rapid delivery of ligated quantum dots across the cell membrane and directly into the cytoplasm of live cells. We describe the assembly of QD-SVS-1 bioconjugates by functionalizing the QD surface with maleimide groups, which were then subsequently reacted with the N-terminal thiol of a cysteine containing SVS-1 analogue (CGG-SVS-1) to form a stable thioether linkage. We provide epi-fluorescence, confocal microscopy, and flow cytometry data, combined with specific endocytosis inhibition measurements to demonstrate that conjugates stain the cytoplasm, without interactions with endosomes or the nuclei. We have also provided QD-conjugate internalization data collected by live cell imaging as supplemental files. Finally, in Chapter 5, we demonstrate the use of SVS-1 to promote non-endocytic uptake of both small size gold nanoparticles (AuNPs) and larger size gold nanorods (AuNRs) into mammalian cells. We describe the preparation of colloidally stable AuNPs and AuNRs with an amine-functionalized polymer, His-PIMA-PEG-OCH3/NH2, as their capping ligand. Subsequently, the amine groups were utilized for covalent attachment of cysteine terminated SVS-1 (via a thioether linkage) and NHS-ester-Texas-Red dye onto the nanocrystal surface. We further demonstrate nanocrystal staining throughout the cytoplasmic volume of the cells incubated with these conjugates via fluorescence microscopy. We further provide additional endocytosis inhibition experiment results to confirm that physical translocation of these conjugates takes place through the cell membrane independent of endocytosis.
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Date Issued: 2018
Identifier: 2018_Su_Kapur_fsu_0071E_14514_comp
Format: Set of related objects

Title: Enhancing the Business Traveler Experience Though Hotel Design.
Creator: Flock, Brittany Jean, Waxman, Lisa K., Huber, Amy M, Ransdell, Marlo E, McLane, Yelena, Florida State University, College of Fine Arts, Department of Interior Design
Abstract/Description: The purpose of this study was to explore hotel design features and amenities that provide opportunities for business travelers to complete essential tasks, reduce stress, and enhance their travel experience. In this global economy, travel to conduct business negotiations, facilitate inter-organizational knowledge transfers, and other important company operations have become essential (Mäkelä, Kinnunen, & Suutari, 2015; Demel & Mayrhofer, 2010). Rates of business travel are expected to...
Show moreThe purpose of this study was to explore hotel design features and amenities that provide opportunities for business travelers to complete essential tasks, reduce stress, and enhance their travel experience. In this global economy, travel to conduct business negotiations, facilitate inter-organizational knowledge transfers, and other important company operations have become essential (Mäkelä, Kinnunen, & Suutari, 2015; Demel & Mayrhofer, 2010). Rates of business travel are expected to continue rising, impacting more people as they strive to meet the demands of their careers (Statistica, 2017). Stress related to business travel often leads to health concerns, such as sleep deprivation, unhealthy diet, anxiety, weight gain, susceptibility to allergies and illness, and depression (Chen, 2017; Demel & Mayrhofer, 2010). Business travel stress occurs during three travel phases: pre-trip, destination, and post-trip (Chen, 2017; Carlson Wagonlit Travel Solutions Group, 2012). This research and design solution placed an emphasis on the destination phase of business travel, and how the design of hotels plays an influential role on business traveler well-being. Through the improvement of hotel interior environments, designers may be able to help reduce stress and improve travel well-being by enhancing the travel experience for business travelers during their destination phase of travel. By conducting a literature review, original research in the form of a survey and interviews, and onsite observations of two different hotels, the preferences of business travelers provided insights that formed the foundation of design guidelines for the thesis project. The survey targeted business travelers and was designed to gather information on business traveler preferences, travel stress triggers, valued hotel attributes, amenities, and design features. Interviews with business travelers provided further elaboration on answers from the survey. Interviews and observations were conducted in two hotels in San Antonio, Texas, a business traveler hub infused with deep history and culture. To better understand the spaces, interviews with hotel management, and observations of the hotels’ social spaces using behavioral mapping techniques were conducted. The hotel was also evaluated through the lens of the WELL Building Standard, which was used as a benchmark to explore how each hotel is considering the well-being of their guests. Findings from these research methods show that the most valued hotel attributes by business travelers are cleanliness followed by sleep quality; the most valued hotel amenities are the restaurant, fitness center, and café; the most valued design features are a meaningful integration of art and a celebration of local culture through art and building materials. Most business travelers expressed their preference for chain hotels over boutique hotels, but they desire a chain hotel that blends boutique hotel characteristics such as unique amenities and design features. The research culminated in the design of a hotel space in San Antonio, Texas, that utilizes the research to create a space that enhances the business traveler experience. Concepts from the WELL Building Standard provided by the International WELL Building Institute were also incorporated for guiding design decisions throughout the hotel that promote physical and mental well-being. The results of this study have the potential to positively impact hotel design to better accommodate the needs of business travelers.
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Date Issued: 2018
Identifier: 2018_Su_Flock_fsu_0071N_14762_Comp
Format: Set of related objects

Title: Atmospheric Mercury Wet Deposition along the Northern Gulf of Mexico: Seasonal and Storm-Type Drivers of Deposition Patterns and Contributions from Local and Regional Emissions.
Creator: Krishnamurthy, Nishanth, Landing, William M., Miller, Thomas E., Holmes, Christopher D., Fuelberg, Henry E., Salters, Vincent J. M., Florida State University, College of Arts...
Show moreKrishnamurthy, Nishanth, Landing, William M., Miller, Thomas E., Holmes, Christopher D., Fuelberg, Henry E., Salters, Vincent J. M., Florida State University, College of Arts and Sciences, Department of Earth, Ocean and Atmospheric Science
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Abstract/Description: Continuous event-based rainfall samples were collected at three sites throughout the Pensacola airshed from 2005 - 2011. Samples were analyzed for total mercury (Hg), a suite of trace metals (TMs), and major ions in order to understand how thunderstorms aﬀected their wet deposition and concentrations in rainfall, estimate the contributions from regional coal combustion and other anthropogenic sources to Hg and TMs in rainfall along the Gulf Coast, and investigate the possible inﬂuence that a...
Show moreContinuous event-based rainfall samples were collected at three sites throughout the Pensacola airshed from 2005 - 2011. Samples were analyzed for total mercury (Hg), a suite of trace metals (TMs), and major ions in order to understand how thunderstorms aﬀected their wet deposition and concentrations in rainfall, estimate the contributions from regional coal combustion and other anthropogenic sources to Hg and TMs in rainfall along the Gulf Coast, and investigate the possible inﬂuence that a local 950 megawatt coal-ﬁred power plant had on rainfall chemistry in the Pensacola airshed. Mercury was measured with a Tekran 2600 using a method that was a variation of the standard method used by the US Environmental Protection Agency (EPA) to measure total Hg in water which allowed for the analysis of TMs from the same bottle without having to worry about contamination from reagents during sample preparation. Trace metals were measured used an Agilent 7500cs quadrupole inductively coupled plasma mass spectrometer (ICP-MS) while utilizing an octopole reaction cell (ORC) which allowed for the detection of key coal-combustion tracers like arsenic (As) and selenium (Se). Our ﬁndings show that summertime rainfall Hg concentrations are higher compared to other months despite higher rainfall amounts. In contrast, other measured pollutant TMs and ions did not show a consistent seasonal pattern. By incorporating Automated Surface Observing System data from nearby Pensacola International Airport and WSR-88D radar data from Eglin Air Force Base, we were able to classify the storm type (thunderstorms or non-thunderstorms) and analyze altitudes of hydrometeor formation for individual rain events. This showed that mid-altitude and high-altitude composite reﬂectivity radar values were higher for both thunderstorm and non-thunderstorm ”warm season” (May - Sept) rain events compared to ”cool season” (Oct - Apr) events including cool season thunderstorms. Thus, warm season events can scavenge more soluble reactive gaseous Hg from the free troposphere. Two separate multiple linear regression analyses were conducted on log-transformed data using interaction and non-interaction terms to understand the relationship between precipitation depth, season, and storm-type on sample concentrations. The regressions without interaction terms showed that the washout coeﬃcients for more volatile TMs like Hg and Se were less pronounced compared to other pollution-type elements and that their concentrations were therefore less diluted for a given increase in precipitation depth, but otherwise displayed similar coeﬃcients for season and storm-type. The regression model with interaction terms revealed a more interesting dynamic where thunderstorms caused enhanced Hg concentrations in rainfall regardless of season or precipitation depth while showing a more volume-dependent relationship with TM concentrations as concentrations increased with increasing rainfall amounts relative to non-thunderstorm events. This suggests a vacuum cleaner eﬀect such that for increasing storm strength, non-Hg aerosol TMs in the boundary layer are further entrained into a storm cell. With this understanding, a positive matrix factorization (PMF) analysis was conducted using the EPA PMF 5.0 software to estimate the contribution of diﬀerent sources to Hg deposition. Our results suggest that approximately 84% (72 - 89%; 95% CI) of Hg in rainfall along the northern Gulf of Mexico is due to long-range transport from distant sources while a negligible amount (0 - 21%; 95% CI) comes from regional coal combustion. However, we found that anthropogenic sources like regional coal combustion and ore smelting were signiﬁcant contributors to rainfall concentrations of other pollution-type TMs like copper, zinc, As, Se, and non-sea salt SO42-. Using modeled wind proﬁles via the HYSPLIT trajectory model, we assessed whether plumes from a local coal-ﬁred power plant (”Plant Crist”) could be detected in the rainfall chemistry of rain events occurring downwind of the plant. We limit this analysis to cool season rain events between June 2007 (when the model began) and December 2011 (when the study ended) because modeled wind proﬁles showed better agreement with observations during this time period compared to the warm season. We also limit this analysis to cool season events since the spatial distribution of rainfall throughout the area is more even during this time which makes sample comparisons between sites easier since Hg/TM concentrations are aﬀected by precipitation depth. Furthermore, we focus on Hg and other pollution-type TMs and major ions such as As, Se, and non-sea salt SO42- in this analysis as they serve as tracers of coal combustion. For our ”unpaired-site” analysis, we analyzed, for each individual site, the rainfall chemistry in a given sample as a function of the proportion of rain events associated with that sample that occurred downwind of Plant Crist. Using this method, we were not able to ﬁnd evidence that the plant had a signiﬁcant inﬂuence on Hg/TM concentrations or Hg/TM:Al enrichment ratios in rainfall. Similarly, for our ”paired-site” analysis, we consider the diﬀerences in rainfall chemistry between two sites - an upwind and downwind site pair - that were impacted by the same rain event where the downwind site was exposed to plumes from Plant Crist while the upwind site was not. As with the unpaired-site analysis, we did not ﬁnd signiﬁcant diﬀerences in the rainfall chemistry between upwind-downwind site pairs with regards to sample concentrations or enrichment ratios. A multiple linear regression analysis was then conducted using interaction terms to understand the relationship between the operation of a wet ﬂue-gas desulfurization system (which began operation at the plant during the middle of the study), the relative exposure a rainfall sample had to the plumes coming from the plant, and the log-transformed precipitation depth on log-transformed sample concentrations. Besides for As, the ﬁrst regression analysis did not ﬁnd coeﬃcient values of any statistical signiﬁcance for any of the variables that would indicate that the scrubber aﬀected the rainfall chemistry at the two urban sites nearest to the plant. The calculations for As gave mixed results as the coeﬃcients for the non-interaction terms suggested that the scrubber and the plumes emanating from Plant Crist aﬀected the concentration of As in rainfall while the interaction terms suggested that they did not. We perform another multiple linear regression analysis, but remove the complicating eﬀects of precipitation depth on Hg/TM concentrations and instead analyze the eﬀects that the scrubber and the plumes coming from the plant might have had on Hg/TM:Al ratios. Again, these results were inconclusive as the regression coeﬃcients suggested that the scrubber helped reduce Hg and TM emissions from the plant while also suggesting that samples with more exposure to the plant’s plumes had lower enrichment ratios. We propose that we were unable to detect a chemical signal from Plant Crist in our rain samples due to a few possible reasons including quick scavenging of TMs from the plume at the onset of a rain event before reaching our sites, the reliance on radar data to determine start and stop times for rain events at the sites as opposed to on-site measurements, and relatively low spatiotemporal resolution for the wind trajectory model.
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Date Issued: 2018
Identifier: 2018_Su_Krishnamurthy_fsu_0071E_14732_comp
Format: Set of related objects

Title: Is There a Biofeedback Response to Art Therapy?: A Multidisciplinary Approach for Reducing Anxiety and Stress in College Students.
Creator: Beerse, Megan E., Van Lith, Theresa, Gussak, David, Stanwood, Gregg, Parker-Bell, Barbara Faye, Florida State University, College of Fine Arts, Department of Art Education
Abstract/Description: Although the field of art therapy has made enormous headway in quantitative research within the last ten years, there are still significant gaps that need explored. Most quantitative research on art therapy and stress is organized in either pretest-posttest single sessions or multi-week, rigorous art therapy interventions. Researchers have failed to address an intervention strategy that meets in the middle, a strategy that emphasizes mental health as a habitual practice. Mindfulness and art...
Show moreAlthough the field of art therapy has made enormous headway in quantitative research within the last ten years, there are still significant gaps that need explored. Most quantitative research on art therapy and stress is organized in either pretest-posttest single sessions or multi-week, rigorous art therapy interventions. Researchers have failed to address an intervention strategy that meets in the middle, a strategy that emphasizes mental health as a habitual practice. Mindfulness and art therapy independently demonstrate efficacy in reducing stress and symptoms of anxiety with higher-education students, but again, these interventions require a substantial time commitment that many students will not make. To address the mental health crisis on college campuses, this study evaluated the feasibility of a minimal contact, technology-assisted Mindfulness-Based Art Therapy (MBAT) intervention for higher-level education students over the course of ten weeks. The experimental MBAT group was compared to a neutral clay task (NCT) comparison group. Participants of the MBAT condition were provided a variety of yoga videos and meditation clips, which have been uploaded as supplementary files associated with this manuscript. These supplementary files include: MBAT Week 2 Meditation, MBAT Week 3 Yoga Sequence, MBAT Week 4 Meditation, MBAT Week 5 Meditation, MBAT Week 6 Yoga Sequence, MBAT Week 7 Meditation, MBAT Week 8 Yoga Sequence, and MBAT Week 9 Meditation. All meditations are audio files adapted by Dr. Sean Sullivan from Limbix; the researcher, Megan Beerse, produced all yoga sequence videos. Self-report outcomes were collected on perceived stress and levels of generalized anxiety. Salivary cortisol sampling was conducted on the first and last weeks of the study to determine any presence of a physiological impact on participants. Fifteen participants were recruited and nine maintained participation through all 10 weeks. Reduced symptoms of generalized anxiety were observed in the MBAT condition but not the NCT condition. MBAT participants’ salivary cortisol concentrations significantly decreased pretest to posttest on Week 10 but not on the first week, while the NCT participants experienced the opposite. Further data is needed, but results suggest the possibility of a biofeedback response to art therapy as well as anxiety-reducing benefits from practicing mindfulness-based art therapy directives in the form of a minimal contact, technology-assisted approach.
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Date Issued: 2018
Identifier: 2018_Su_Beerse_fsu_0071N_14796_comp
Format: Set of related objects

Title: Parma: Applications of Vector-Autoregressive Models to Biological Inference with an Emphasis on Procrustes-Based Data.
Creator: Soda, K. James (Kenneth James), Slice, Dennis E., Beaumont, Paul M., Beerli, Peter, Meyer-Baese, Anke, Shanbhag, Sachin, Florida State University, College of Arts and Sciences,...
Show moreSoda, K. James (Kenneth James), Slice, Dennis E., Beaumont, Paul M., Beerli, Peter, Meyer-Baese, Anke, Shanbhag, Sachin, Florida State University, College of Arts and Sciences, Department of Scientific Computing
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Abstract/Description: Many phenomena in ecology, evolution, and organismal biology relate to how a system changes through time. Unfortunately, most of the statistical methods that are common in these fields represent samples as static scalars or vectors. Since variables in temporally-dynamic systems do not have stable values this representation is unideal. Differential equation and basis function representations provide alternative systems for description, but they are also not without drawbacks of their own....
Show moreMany phenomena in ecology, evolution, and organismal biology relate to how a system changes through time. Unfortunately, most of the statistical methods that are common in these fields represent samples as static scalars or vectors. Since variables in temporally-dynamic systems do not have stable values this representation is unideal. Differential equation and basis function representations provide alternative systems for description, but they are also not without drawbacks of their own. Differential equations are typically outside the scope of statistical inference, and basis function representations rely on functions that solely relate to the original data in regards to qualitative appearance, not in regards to any property of the original system. In this dissertation, I propose that vector autoregressive-moving average (VARMA) and vector autoregressive (VAR) processes can represent temporally-dynamic systems. Under this strategy, each sample is a time series, instead of a scalar or vector. Unlike differential equations, these representations facilitate statistical description and inference, and, unlike basis function representations, these processes directly relate to an emergent property of dynamic systems, their cross-covariance structure. In the first chapter, I describe how VAR representations for biological systems lead to both a metric for the difference between systems, the Euclidean process distance, and to a statistical test to assess whether two time series may have originated from a single VAR process, the likelihood ratio test for a common process. Using simulated time series, I demonstrate that the likelihood ratio test for a common process has a true Type I error rate that is close to the pre-specified nominal error rate, regardless of the number of subseries in the system or of the order of the processes. Further, using the Euclidean process distance as a measure of difference, I establish power curves for the test using logistic regression. The test has a high probability of rejecting a false null hypothesis, even for modest differences between series. In addition, I illustrate that if two competitors follow the Lotka-Volterra equations for competition with some additional white noise, the system deviates from VAR assumptions. Yet, the test can still differentiate between a simulation based on these equations in which the constraints on the system change and a simulation where the constraints do not change. Although the Type I error rate is inflated in this scenario, the degree of inflation does not appear to be larger when the system deviates more noticeably from model assumptions. In the second chapter, I investigate the likelihood ratio test for a common process's performance with shape trajectory data. Shape trajectories are an extension of geometric morphometric data in which a sample is a set of temporally-ordered shapes as opposed to a single static shape. Like all geometric morphometric data, each shape in a trajectory is inherently high-dimensional. Since the number of parameters in a VAR representation grows quadratically with the number of subseries, shape trajectory data will often require dimension reduction before a VAR representation can be estimated, but the effects that this reduction will have on subsequent inferences remains unclear. In this study, I simulated shape trajectories based on the movements of roundworms. I then reduced the number of variables that described each shape using principle components analysis. Based on these lower dimensional representations, I estimated the likelihood ratio test's Type I error rate and power with the simulated trajectories. In addition, I also used the same workflow on an empirical dataset of women walking (originally from Morris13) but also tried varying amounts of preprocessing before applying the workflow as well. The likelihood ratio test's Type I error rate was mildly inflated with the simulated shape trajectories but had a high probability of rejecting false null hypotheses. Without preprocessing, the likelihood ratio test for a common process had a highly inflated Type I error rate with the empirical data, but when the sampling density is lowered and the number of cycles is standardized within a comparison the degree of inflation becomes comparable to that of the simulated shape trajectories. Yet, these preprocessing steps do not appear to negatively impact the test's power. Visualization is a crucial step in geometric morphometric studies, but there are currently few, if any, methods to visualize differences in shape trajectories. To address this absence, I propose an extension to the classic vector-displacement diagram. In this new procedure, the VAR representations for two trajectories' processes generate two simulated trajectories that share the same shocks. Then, a vector-displacement diagram compares the simulated shapes at each time step. The set of all diagrams then illustrates the difference between the trajectories' processes. I assessed the validity of this procedure using two simulated shape trajectories, one based on the movements of roundworms and the other on the movements of earthworms. The result provided mixed results. Some diagrams do show comparisons between shapes that are similar to those in the original trajectories but others do not. Of particular note, diagrams show a bias towards whichever trajectory's process was used to generate pseudo-random shocks. This implies that the shocks to the system are just as crucial a component to a trajectory's behavior as the VAR model itself. Finally, in the third chapter I discuss a new R library to study dynamic systems and represent them as VAR and VARMA processes, iPARMA. Since certain processes can have multiple VARMA representations, the routines in this library place an emphasis on the reverse echelon format. For every process, there is only one VARMA model in reverse echelon format. The routines in iPARMA cover a diverse set of topics, but they all generally fall into one of four categories: simulation and study, model estimation, hypothesis testing, and visualization methods for shape trajectories. Within the chapter, I discuss highlights and features of key routines' algorithms, as well as how they differ from analogous routines in the R package MTS \citep{mtsCite}. In many regards, this dissertation is foundational, so it provides a number of lines for future research. One major area for further work involves alternative ways to represent a system as a VAR or VARMA process. For example, the parameter estimates in a VAR or VARMA model could depict a process as a point in parameter space. Other potentially fruitful areas include the extension of representational applications to other families of time series models, such as co-integrated models, or altering the generalized Procrustes algorithm to better suit shape trajectories. Based on these extensions, it is my hope that statistical inference based on stochastic process representations will help to progress what systems biologists are able to study and what questions they are able to answer about them.
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Date Issued: 2017
Identifier: FSU_SUMMER2017_Soda_fsu_0071E_13917_P
Format: Set of related objects

Title: Mantle Source Compositions by LA-ICP-MS Analyses of Volcanic Glasses from Hawaii and the Mid-Oceanic Ridges.
Creator: Yang, Shuying, Humayun, Munir, Siegrist, Theo, Salters, Vincent J. M., Landing, William M., Florida State University, College of Arts and Sciences, Department of Earth, Ocean,...
Show moreYang, Shuying, Humayun, Munir, Siegrist, Theo, Salters, Vincent J. M., Landing, William M., Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: The chemical compositions of basaltic melts from diverse tectonic settings on Earth are interpreted in terms of mantle sources that are either a single lithology (peridotite) or composed of two mixed lithologies (peridotite + pyroxenite). The observation of an elevated Fe/Mn ratio in Hawaiian lavas relative to Mid-Oceanic Ridge basalts (MORBs) has been attributed to either Fe-addition from core-mantle interaction or to Mn-retention in pyroxenitic mantle sources. The discrimination of...
Show moreThe chemical compositions of basaltic melts from diverse tectonic settings on Earth are interpreted in terms of mantle sources that are either a single lithology (peridotite) or composed of two mixed lithologies (peridotite + pyroxenite). The observation of an elevated Fe/Mn ratio in Hawaiian lavas relative to Mid-Oceanic Ridge basalts (MORBs) has been attributed to either Fe-addition from core-mantle interaction or to Mn-retention in pyroxenitic mantle sources. The discrimination of pyroxenitic melts from peridotitic melts is a first-order issue in mantle geochemistry. The first-row transition elements (FRTEs), Ga and Ge are mildly incompatible to compatible during mantle partial melting so the abundances of these elements are sensitive to lithological heterogeneities in the mantle source. Recent experimental determinations of partition coefficients (Ds) of FRTEs, Ga and Ge have made it possible to quantitatively model partial melting of mantle sources of various lithologies, which are now limited by the dearth of high-quality measurements of these elements. To effectively test the hypotheses, in this study, we analyzed 60 elements, including FRTEs, Ga and Ge, in 319 mid-oceanic ridge basalt (MORB) glasses and 199 Hawaiian oceanic island basalt (OIBs) glasses by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). A particular emphasis was placed on obtaining precise Ge abundances. The MORB dataset was used to revise the composition of MORB mantle. The available experimental data were carefully examined to assess the dependence of the partitioning behavior of FRTEs, Ga and Ge on the variation of temperature, pressure and mineral compositions. The Ge/Si ratio was developed as a useful discriminator of pyroxenite melts since such melts are high in silica but low in Ge/Si. It was found that enriched (E)- MORBs have lower Ge/Si than depleted (D)- MORBs due to the presence of a few percent recycled pyroxenite in E-MORB mantle. For Hawaiian glasses, we found that Ge is volatile during volcanic degassing from subaerially erupted lavas, but the effect is suppressed in submarine glasses. Submarine Hawaiian glasses exhibit correlated variations in Ge vs. SiO2 that overlap MORB glasses, and even the Mauna Kea high-SiO2 glasses show no evidence of the presence of pyroxenite melts. This discovery should prove transformative in petrological models of lithologic heterogeneity in the mantle.
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Date Issued: 2015
Identifier: FSU_SUMMER2017_Yang_fsu_0071E_14040_P
Format: Set of related objects

Title: Investigation of the Impacts of Greenland Ice Sheet Melting on the along-Shelf Flow on Greenland Shelves and the Labrador Sea Deep Convection.
Creator: Sangmanee, Chalermrat, Clarke, Allan J., Tam, Christopher K. W., Knapp, Angela N., Bourassa, Mark Allan, Dewar, William K., Florida State University, College of Arts and...
Show moreSangmanee, Chalermrat, Clarke, Allan J., Tam, Christopher K. W., Knapp, Angela N., Bourassa, Mark Allan, Dewar, William K., Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: Gravity measurements from the Gravity Recovery and Climate Experiment (GRACE) satellite measuring system show that Greenland is losing mass as water is lost to the ocean. Past work has suggested that the freshwater flux from Greenland, particularly along the southeastern coast, may be affecting the Labrador Sea deep convection, a major driver of the world deep ocean circulation. The main objectives of this thesis are to examine (1) the relationship between Greenland freshwater flux and the...
Show moreGravity measurements from the Gravity Recovery and Climate Experiment (GRACE) satellite measuring system show that Greenland is losing mass as water is lost to the ocean. Past work has suggested that the freshwater flux from Greenland, particularly along the southeastern coast, may be affecting the Labrador Sea deep convection, a major driver of the world deep ocean circulation. The main objectives of this thesis are to examine (1) the relationship between Greenland freshwater flux and the near-surface Labrador Sea salinity; (2) the response of the Greenland shelf water flow to the freshwater flux from the coast; and (3) to predict when the Labrador Sea deep convection will shut down because of the near-surface Labrador Sea freshening. Using the GRACE results and analysis of Argo float hydrographic data showed that there is a strong correlation between the anomalous annual freshwater flux onto the southeastern Greenland shelf and the freshening of the Labrador Sea several months later. The corresponding regression coefficient is physically reasonable and the delay in freshening is what you would expect based on eddy propagation from the west Greenland coast to the site of Labrador Sea deep convection. Satellite altimeter data was used to estimate the interannual shelf water flow, but the flow trend was too small to be determined. Calculations of the heat flux during winter in the Labrador Sea region of deep convection showed that if the freshening continues at the present rate, in about 31 years the cooling heat flux in water will not be able to overcome the freshwater near-surface buoyancy and deep convection will cease.
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Date Issued: 2017
Identifier: FSU_SUMMER2017_Sangmanee_fsu_0071E_13961_P
Format: Set of related objects

Title: Roy Harris' West Point Symphony for Band (1952): A Working Edition.
Creator: Harris, Thomas L. (Thomas Lloyd), Clary, Richard, Madsen, Clifford K., Kelly, Steven N., Florida State University, College of Music
Abstract/Description: Roy Harris (1898-1979) was one of the leading American composers of the early and mid-twentieth centuries. Audiences were polarized in their appreciation of him and his music. Some adored it and labeled it truly American while others were critical. However, both groups respected his talent as a unique voice within American music. He was known for his style which included long-meandering phrases and atypical diatonic harmonic progressions. His compositions were commissioned and championed by...
Show moreRoy Harris (1898-1979) was one of the leading American composers of the early and mid-twentieth centuries. Audiences were polarized in their appreciation of him and his music. Some adored it and labeled it truly American while others were critical. However, both groups respected his talent as a unique voice within American music. He was known for his style which included long-meandering phrases and atypical diatonic harmonic progressions. His compositions were commissioned and championed by the likes of Sergei Koussevitsky and the Boston Symphony Orchestra, William Revelli and the University of Michigan Band as well as others. Over the course of his compositional career, he wrote no less than 21 original works for wind band, most of which are seldom performed. In 1952, the command staff of the West Point Band commissioned a series of original band works for the Sesquicentennial Celebration of the United States Military Academy at West Point. Roy Harris's West Point Symphony for Band was a product of this series. However, for many reasons, this piece has lived in relative obscurity having never been published or regularly performed. The purpose of this dissertation is to create a new, working and critical edition of this piece with the goal of creating more performances of a masterwork by this truly American composer.
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Date Issued: 2017
Identifier: FSU_2017SP_Harris_fsu_0071E_13825_C
Format: Set of related objects

Title: Rapid and Selective Syntheses of Trisubstituted -1,2,3-Triazoles Through Copper Mediated Azide Alkyne Cycloaddition.
Creator: Brassard, Christopher J., Zhu, Lei, Deng, Wu-Min, Dudley, Gregory B., Shatruk, Mykhailo, Florida State University, College of Arts and Sciences, Department of Chemistry and...
Show moreBrassard, Christopher J., Zhu, Lei, Deng, Wu-Min, Dudley, Gregory B., Shatruk, Mykhailo, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
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Abstract/Description: This dissertation describes the development of alternative products from the copper-catalyzed azide-alkyne cycloaddition (CuAAC). The first chapter provides an introduction to the CuAAC through the historic timeline of the development of reaction conditions. Finally the current mechanistic understanding and three applications of the commonly used reaction are described. The second chapter describes a method for the preparation of 5-iodo-1,2,3-triazoles directly from organic azides and...
Show moreThis dissertation describes the development of alternative products from the copper-catalyzed azide-alkyne cycloaddition (CuAAC). The first chapter provides an introduction to the CuAAC through the historic timeline of the development of reaction conditions. Finally the current mechanistic understanding and three applications of the commonly used reaction are described. The second chapter describes a method for the preparation of 5-iodo-1,2,3-triazoles directly from organic azides and terminal alkynes. The reaction is mediated by in-situ generated copper(I) catalyst and iodinating agents. The method described is a follow-up of the protocol developed by Dr. Brotherton in 2012. The methodological enhancements of the procedure described in Chapter 2 provides high conversion as well as high iodo/protio selectivity through the reduction in equivalents of alkyne, and employment of [Tri(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (TBTA). Through these improvements the method became more synthetically practical and increased the reaction substrate scope to include unreactive azides and alkynes. Chapter three describes the synthesis of 5,5’-bis(1,2,3-triazole)s (bistriazoles). These compounds have been proposed to be employed as chiral ligands in enantioselective synthesis. Previously reported methods for the synthesis of bistriazoles mainly require decreased reaction temperatures (0-35 oC) and long reaction times (20-48 hours) while applying a limited substrate scope. The method described in Chapter 3 is a simple and rapid process for the synthesis of bistriazoles from organic azides and terminal alkynes under oxidative conditions ( oxygen atmosphere) with a broad substrate scope. The reactions are mediated by copper(II) acetate, and completed within 3 hours, with ≥ 50% isolated yields. TBTA has been employed in the CuAAC to accelerate the formation of 1,2,3-triazoles, in addition TBTA accelerates the formation of bistriazoles. Employing K2CO3 as a basic additive in MeOH or EtOH as the solvent promotes the oxidative reaction that produces the bistriazole at the expense of the 1,2,3-triazole. In Chapter 4 the initial development of 5-alkynyl-1,2,3-triazoles is reported. The previously reported methods require extended reaction times with varying temperature (rt-60 oC) with a limited substrate scope. The method described in Chapter 4 is a simple and rapid process for the synthesis of 5-alkyny-1,2,3-triazoels from organic azides and terminal alkynes under oxidative conditions (oxygen atmosphere) with a developing substrate scope. The reactions are mediated by copper(II) acetate, completed within 3-5 hours, and produce ≥ 50% isolated yields. Employing 1,5-diazolbicyclo[4.3.0]non-5-ene (DBN) as the basic additive in MeOH or EtOH as the solvent promotes the oxidative reaction that produces the 5-alkynyl-1,2,3-triazoles at the expense of the 1,2,3-triazole and 5,5’-bis-(1,2,3-triazole)s. Chapter 5 summarizes the work conducted on modifying the conditions applied to the copper catalyzed azide alkyne cycloaddition (CuAAC). Modifications to enhance the synthesis of the 5-iodo-1,2,3-triazoles via CuAAC are the first addressed Which was followed by the unsuccessful application of the Ullmann reaction for the synthesis of 5,5’-bis(1,2,3-triazole)s. The subsequent employment of potassium carbonate in the CuAAC, afforded the desired bistriazoles with moderate to high selectivity over 1,4-disubstituted-1,2,3-triazoles. In addition, changing the base from potassium carbonate to DBN allowed for the 5-alkynyl-1,2,3-triazole to be produced as the major product while diminishing the bistriazole and protiotriazole.
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Date Issued: 2016
Identifier: FSU_2016SU_Brassard_fsu_0071E_13324-C
Format: Set of related objects

Title: Maximizing Electron Signal: Development and Integration of Techniques in Cryogenic Electron Microscopy and Tomography.
Creator: Noble, Alex James, Stagg, Scott, Zhou, Huan-Xiang, Taylor, Kenneth A., Piekarewicz, Jorge, Rikvold, Per Arne, Florida State University, College of Arts and Sciences, Department...
Show moreNoble, Alex James, Stagg, Scott, Zhou, Huan-Xiang, Taylor, Kenneth A., Piekarewicz, Jorge, Rikvold, Per Arne, Florida State University, College of Arts and Sciences, Department of Physics
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Abstract/Description: The field of cryogenic electron microscopy (cryoEM) has greatly benefitted from improvements upon the integration of complementary structural determination methods and the development of high-throughput processing workflows aimed at producing high-resolution structures of proteins. Herein I will present a study integrating cryoEM with mass spectrometry and atomic modelling followed by two studies covering the development of a high-throughput cryogenic electron tomography (cryoET) workflow...
Show moreThe field of cryogenic electron microscopy (cryoEM) has greatly benefitted from improvements upon the integration of complementary structural determination methods and the development of high-throughput processing workflows aimed at producing high-resolution structures of proteins. Herein I will present a study integrating cryoEM with mass spectrometry and atomic modelling followed by two studies covering the development of a high-throughput cryogenic electron tomography (cryoET) workflow aimed at high-resolution cryoET. The development and continued adoption of direct electron detectors (DEDs) over the past ten years has opened up new avenues for software development. DEDs have brought a substantial increase in detection efficiency over the entire frequency range relative to previous generation cameras, increasing the signal-to-noise ratio (SNR) of electron interference patterns generated by thin, frozen-hydrated biological specimen. In addition to the increase in SNR, the rapid pixel readout of DEDs allows for multiple frames to be recorded per exposure. With these advances has come the ability to align frames together to account for beam induced specimen movement and the ability to account for structural degradation over the course of an exposure due to beam damage. The technique of tilt-series alignment by cross correlation in cryoET where the sample is tilted at increments during a single exposure then iteratively aligned had previously been limited for most samples by the relatively low SNR of CCD cameras. The increase in SNR of DEDs has allowed for robust tilt-series alignment by cross correlation, defocus estimation, and frame alignment. These hardware advances have paved the way for the development and optimization of cryoET processing workflows using cross-correlation based tilt-series alignment. High throughput, high-resolution cryoET workflow development will likely broaden the types of samples whose native or near-native structures have not yet been solved that are not amenable to single particle cryoEM often due to structural or compositional heterogeneity. Facilitating the determination of near-native protein structure and interactions with an improved cryoET workflow potentially allows for a better rational understanding of diseases and for more rational drug development. In Chapter 1 of this dissertation, I will introduce the theoretical and practical aspects of cryoEM. In Chapter 2, I use the highest resolution cryoEM structure of the conformationally heterogeneous COPII cage, collected with a CCD camera, in conjunction with known crystallography structures of its constituents and differential hydrogen/deuterium exchange mass spectroscopy results to create a pseudo-atomic model of the whole cage. In Chapter 3, I introduce the integration of a semi-automated implementation of the Protomo correlation-based tilt-series alignment software into the Leginon/Appion software suite, allowing for high-throughput and standardized cryoET processing. In Chapter 4, I introduce a complete, streamlined protocol for sub-nanometer sub-tomogram alignment from grid preparation to complete structure. In Chapter 4, I also present an application of this protocol to the determination of the structure of Adeno-Associated Virus serotype DJ with a bound drug, Arixtra, to sub-nanometer resolution, exemplifying the accuracy of correlation-based alignment as being comparable to fiducial-based alignment. Videos are included as supplementary files and a List of Videos with their descriptions is included on page xii.
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Date Issued: 2016
Identifier: FSU_2016SU_Noble_fsu_0071E_13334-C
Format: Set of related objects

Title: Geology of the Dadeville Complex in the Camp Hill 7.5’ Quadrangle, Appalachian Inner Piedmont of Alabama.
Creator: Davis, Benjamin Lee, Tull, James F., Farris, David W., Kish, Stephen A., Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
Abstract/Description: The Dadeville Complex is a large klippe located in the Alabama Inner Piedmont of the southern Appalachian orogen lying immediately above rocks of the eastern Blue Ridge and Brevard Zone, in the core of the Tallassee synform. Structural field data outline the overall nature of the Tallassee synform in the Dadeville Complex. The Camp Hill 7.5' quadrangle contains the two major Dadeville Complex lithostratigraphic sequences, from southeast to northwest: the Ropes Creek Amphibolite, a bimodal...
Show moreThe Dadeville Complex is a large klippe located in the Alabama Inner Piedmont of the southern Appalachian orogen lying immediately above rocks of the eastern Blue Ridge and Brevard Zone, in the core of the Tallassee synform. Structural field data outline the overall nature of the Tallassee synform in the Dadeville Complex. The Camp Hill 7.5' quadrangle contains the two major Dadeville Complex lithostratigraphic sequences, from southeast to northwest: the Ropes Creek Amphibolite, a bimodal metabasalt/metatuff, metadacite at the base, overlain by the Agricola Schist, a metaturbidite consisting of metapelitic, metagreywacke, and minor metabasalt. These sequences are intruded by felsic plutonic rocks, with the Chattasofka Creek Gneiss (granite) intrusive into the Agricola Schist, and the Camp Hill Granite (tonalite) intrusive into the Ropes Creek Amphibolite. Also intrusive into the Agricola Schist is a mafic complex consisting of the Doss Mountain suite and the Slaughters Gabbro suite. The Doss Mountain suite is characterized by having an abundance of interlayered metaorthopyroxenite and metanorite, and their metamorphosed equivalents. The Slaughters Gabbro suite consists of both olivine and non-olivine bearing gabbro. Within the mafic complex, there are various felsic dikes cutting through metagabbro and amphibolite, which suggest that intrusions of felsic and mafic rocks could have overlapped temporarily. Distinctive major and trace element geochemical signatures of the Chattasofka Creek Gneiss, Camp Hill Granite, Ropes Creek Amphibolite, Doss Mountain suite, and Slaughters Gabbro suite on tectonic discrimination diagrams all suggest formation within a volcanic arc environment. Preliminary U/Pb dating of detrital zircons in the Agricola Schist and igneous zircons in the Chattasofka Creek Gneiss yield Middle Ordovician ages, with the Agricola Schist also containing a subordinate fraction of Grenville ages. These relationships suggest that the Dadeville Complex arc resulted from subduction of Iapetus lithosphere beneath the distended Laurentian plate, and that the Dadeville Complex could potentially be a key fragment of the missing Taconic arc in the southern Appalachians. A supplementary file of a detailed geologic map of the Camp Hill 7.5' quadrangle is included with this document.
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Date Issued: 2015
Identifier: FSU_2015fall_Davis_fsu_0071N_12882
Format: Set of related objects

Title: Interactive 3D GPU-Based Breast Mass Lesion Segmentation Method Based on Level Sets for Dce-MRI Images.
Creator: Zavala Romero, Olmo S., Meyer-Baese, Anke, Sussman, Mark, Erlebacher, Gordon, Slice, Dennis E., Wang, Xiaoqiang, Florida State University, College of Arts and Sciences,...
Show moreZavala Romero, Olmo S., Meyer-Baese, Anke, Sussman, Mark, Erlebacher, Gordon, Slice, Dennis E., Wang, Xiaoqiang, Florida State University, College of Arts and Sciences, Department of Scientific Computing
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Abstract/Description: A new method for the segmentation of 3D breast lesions in dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) images, using parallel programming with general purpose computing on graphics processing units (GPGPUs), is proposed. The method has two main parts: a pre-processing step and a segmentation algorithm. In the pre-processing step, DCE-MRI images are registered using an intensity-based rigid transformation algorithm based on gradient descent. After the registration, voxels...
Show moreA new method for the segmentation of 3D breast lesions in dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) images, using parallel programming with general purpose computing on graphics processing units (GPGPUs), is proposed. The method has two main parts: a pre-processing step and a segmentation algorithm. In the pre-processing step, DCE-MRI images are registered using an intensity-based rigid transformation algorithm based on gradient descent. After the registration, voxels that correspond to breast lesions are enhanced using the Naïve Bayes machine learning classifier. This classifier is trained to identify four different classes inside breast images: lesion, normal tissue, chest and background. Training is performed by manually selecting 150 voxels for each of the four classes from images in which breast lesions have been confirmed by an expert in the field. Thirteen attributes obtained from the kinetic curves of the selected voxels are later used to train the classifier. Finally, the classifier is used to increase the intensity values of voxels labeled as lesions and to decrease the intensities of all other voxels. The post-processed images are used for volume segmentation of the breast lesions using a level set method based on the active contours without edges (ACWE) algorithm. The segmentation algorithm is implemented in OpenCL for the GPGPUs to accelerate the original model by parallelizing two main steps of the segmentation process: the computation of the signed distance function (SDF) and the evolution of the segmented curve. The proposed framework uses OpenGL to display the segmented volume in real time, allowing the physician to obtain immediate feedback on the current segmentation progress. The proposed implementation of the SDF is compared with an optimal implementation developed in Matlab and achieves speedups of 25 and 12 for 2D and 3D images, respectively. Moreover, the OpenCL implementation of the segmentation algorithm is compared with an optimal implementation of the narrow-band ACWE algorithm. Peak speedups of 55 and 40 are obtained for 2D and 3D images, respectively. The segmentation algorithm has been developed as open source software, with different versions for 2D and 3D images, and can be used in different areas of medical imaging as well as in areas within computer vision, such like tracking, robotics and navigation.
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Date Issued: 2015
Identifier: FSU_2015fall_ZavalaRomero_fsu_0071E_12893
Format: Set of related objects

Title: Miocene–Pliocene Calcareous Nannofossil Biostratigraphy of IODP Site U1457, Arabian Sea.
Creator: Routledge, Claire Marie, Wise, Sherwood W., Kulhanek, Denise Kay, Parker, William C., Odom, A. L. (A. Leroy), Florida State University, College of Arts and Sciences, Department...
Show moreRoutledge, Claire Marie, Wise, Sherwood W., Kulhanek, Denise Kay, Parker, William C., Odom, A. L. (A. Leroy), Florida State University, College of Arts and Sciences, Department of Earth, Ocean, and Atmospheric Science
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Abstract/Description: International Ocean Discovery Program (IODP) Expedition 355 drilled two sites (U1456 and U1457) in Laxmi Basin, located in the eastern Arabian Sea. The primary objective of Expedition 355 is to better understand the impact that the Indian (southwest) summer monsoon has on weathering and erosion of the Himalayas and how this in turn affects mountain building. Laxmi Basin is located within the Indus Fan, the second largest submarine fan in the world that has primarily been fed by the Indus...
Show moreInternational Ocean Discovery Program (IODP) Expedition 355 drilled two sites (U1456 and U1457) in Laxmi Basin, located in the eastern Arabian Sea. The primary objective of Expedition 355 is to better understand the impact that the Indian (southwest) summer monsoon has on weathering and erosion of the Himalayas and how this in turn affects mountain building. Laxmi Basin is located within the Indus Fan, the second largest submarine fan in the world that has primarily been fed by the Indus River and its associated tributaries since the collision of India and Eurasia in the Paleogene. Thus, the drill sites are ideally situated to record changes in erosion from the Himalayas through time, which requires a robust chronostratigraphic framework. Analysis of 275 samples for calcareous nannofossil biostratigraphy from Hole U1457C has refined the age model that was produced onboard during Expedition 355. The section is assigned to nannofossil Zones NN11–17 (late Miocene to early Pleistocene). In conjunction with shipboard magnetostratigraphy and planktonic foraminifer biostratigraphy, the age model indicates variable sedimentation rates as well as the presence of an unconformity that spans at least 1.46 m.y. between ~5.5 and 4 Ma. Late Miocene sedimentation was variable at ~27 cm/k.y. before 7.42 Ma, but averaged ~2.4 cm/k.y. between 5.94 and 7.42 Ma. Sedimentation rates increased again from 5.94 to 5.59 Ma to ~20 cm/k.y., when deposition was interrupted for at least 1.46 m.y. until ~4 Ma. After the hiatus and through the Pliocene, sedimentation rates were lower at ~3.6 cm/k.y. until the early Pleistocene when sedimentation rates reached ~8.9 cm/k.y. before slowing to ~3.4 cm/k.y. through 2.39 Ma. Further work to incorporate additional biostratigraphic and paleomagnetic constraints, should produce a robust chronostratigraphic framework that is necessary to examine the evolution of the Himalayas as well as climate in the late Miocene through Pliocene.
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Date Issued: 2015
Identifier: FSU_2015fall_Routledge_fsu_0071N_12962
Format: Set of related objects

Title: The Songs of Luigi Gordigiani (1806-1860), "Lo Schuberto Italiano".
Creator: Cimarusti, Thomas M., Seaton, Douglass, Trujillo, Valerie, Brewer, Charles E., -Powell, Jeffery Kite, Leparulo, William, College of Music, Florida State University
Abstract/Description: Music historians have long acknowledged the importance of opera in nineteenth-century Italy. Few musicologists, however, have explored the more intimate genre that also played an important role in Italy's artistic, political, and social sphere – the Italian art song. This study begins with a discussion as to why few scholars have unjustifiably dismissed Italian song in favor of Italian opera – a genre that evidently eclipsed the recognition of Italian song. Although the operas of Rossini,...
Show moreMusic historians have long acknowledged the importance of opera in nineteenth-century Italy. Few musicologists, however, have explored the more intimate genre that also played an important role in Italy's artistic, political, and social sphere – the Italian art song. This study begins with a discussion as to why few scholars have unjustifiably dismissed Italian song in favor of Italian opera – a genre that evidently eclipsed the recognition of Italian song. Although the operas of Rossini, Donizetti, Bellini, and Verdi highlight the century's musical achievements, an examination of primary sources reveals that Italy possessed a rich and active concert life outside the opera house. Yet although most significant opera composers experimented with song, only one would claim international attention in this genre, the Tuscan-born composer Luigi Gordigiani (1806-1860). Beginning with the composer's childhood, a brief biographical sketch of the composer reveals a figure determined to compose for the stage – attempts that mostly met with disappointment. His failed attempts at securing a career as an opera composer, along with financial difficulties, led Gordigiani to compose more intimate works, most importantly his eight collections of Canti popolari toscani for voice and piano. These pieces would lead Gordigiani to the intimate salons and concert halls of Europe, places where he would establish himself among the most elite figures of his day. An examination of primary sources from the period reveals a composer whose circle of friends belonged to the elite of London and Florence, including Queen Victoria, Giuseppe Poniatowski, and Nikolai and Anatole Demidov. His reputation as a song composer among these figures and the public brought him the attention from over fifty publishers across Europe, including firms in France, Germany, Russia, Poland, England, and Belgium. This study also examines the historical context in which Gordigiani composed his songs. Arguably, Italy's political turmoil, excessive tax, and French and Austrian domination, may have spoiled the country's piano industry, resulting in a large number of piano imports from France, Germany, and Austria. Nevertheless, the public's interest for song, whether operatic arias or romanze, brought about an increase in the number of song publications, an aspect that may have stimulated the growth of the piano industry later in the century. The poems and poets of the risorgimento also investigated. From examination of the poets of the period, it becomes evident that Gordigiani was less interested in the works of major Italian figures like Foscolo, Manzoni, and Leopardi; rather, the composer generally looked to local poets who more likely had an affinity toward folk idioms. Gordigiani's choice of poetry also reveals that he not only used song as a form of entertainment, but also as an expression of nationalistic and political sentiments. Finally, this study shows that Gordigiani, unlike many of his Italian contemporaries, assimilated the German Lied tradition. His gift for melody, rich harmonic vocabulary, and clever musico-poetic techniques set him apart from his contemporaries, earning him the nickname "lo Schuberto italiano" – an appellation which begs the question: was Luigi Gordigiani an "Italian" Schubert or an Italian "Schubert"?
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Date Issued: 2007
Identifier: FSU_migr_etd-3601
Format: Set of related objects

Title: A Night Time Rain.
Creator: Zarou, Richard, Callender, Clifton, Wingate, Mark, Jones, Evan, College of Music, Florida State University
Abstract/Description: A Night Time Rain is a work for five live performers with four channels of prerecorded sound and two channels of click track. At this point in 2005 DVD-A, SACD, and a computer are options for playback.
Date Issued: 2005
Identifier: FSU_migr_etd-0592
Format: Set of related objects

Title: Phase Equilibria of Fe-C Binary Alloys in a Magnetic Field.
Creator: England, Roger Dale, Kalu, Peter N., Okoli, Okenwa, Shih, Chiang, Oates, William S., Ludtka, Gerard, Florida State University, College of Engineering, Department of Mechanical...
Show moreEngland, Roger Dale, Kalu, Peter N., Okoli, Okenwa, Shih, Chiang, Oates, William S., Ludtka, Gerard, Florida State University, College of Engineering, Department of Mechanical Engineering
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Abstract/Description: The deployment of high flux magnetic processing in industry requires the ability to model the expected results of a proposed processing, and the current assumptions in the literature did not reflect the actual outcome in measurements of ductile iron. Simple binary iron-carbon alloys of less than one weight percent carbon were thermo-magnetically processed and then compared with Gibbs free energy phase transformation predictions. The data was used to quantify the change in the Gibbs free...
Show moreThe deployment of high flux magnetic processing in industry requires the ability to model the expected results of a proposed processing, and the current assumptions in the literature did not reflect the actual outcome in measurements of ductile iron. Simple binary iron-carbon alloys of less than one weight percent carbon were thermo-magnetically processed and then compared with Gibbs free energy phase transformation predictions. The data was used to quantify the change in the Gibbs free energy associated with the addition of a static high flux magnetic field, which is complicated by the change in magnetic response as the iron carbon alloys pass through the Curie point. A current common practice is to modify Gibbs free energy by -12J per mole per Tesla applied, as has been reported in the literature. This current prediction practice was employed in initial experiments for this work and the experimental data did not agree with these predicted values. This work suggests two specific influences that affect the model, chemistry and magnetic dipole changes. First, that the influence of alloying elements in the original chemistry, as the samples in the literature were a manganese alloy with 0.45 weight percent carbon, as well as not being precisely controlled for tramp elements that commonly occur in recycled material, created a change that was not predicted and therefore the temperatures were incorrect. Also, the phase transformation in a high flux magnetic field was measured to have a different response under warming versus cooling than the normal hysteresis under ambient magnetism. The change in Gibbs free energy for the binary alloys was calculated as -3J per mole per Tesla in warming, and -8J per mole per tesla in cooling. The change from these values to the -12J per mole per Tesla previously reported is attributed to the change in chemistry. This work attributes the published increase in physical properties to the Hall-Petch relation as a result of the finer product phase nucleation created by the addition of a high flux magnetic field. Additionally, a pure iron sample was analyzed and found to be unique, in that the transformation temperature decreased with the application of a static magnetic field, opposite to what occurs in the iron carbon alloys. While the presence of a two-phase field is a viable cause due to the chromium impurity content in the sample creating a dilute binary alloy versus a pure element, this effect could also be attributed to the high magnetic field increasing the number of state variables present.
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Date Issued: 2014
Identifier: FSU_migr_etd-9170
Format: Set of related objects

Title: Dynamic Modeling and Motion Planning for Robotic Skid-Steered Vehicles.
Creator: Gupta, Nikhil, Collins, Emmanuel G., Edrington, Chris S., Clark, Jonathan, Oates, William S., Department of Mechanical Engineering, Florida State University
Abstract/Description: Skid-steered robots are commonly used in outdoor applications due to their mechanical simplicity, high maneuverability, and robustness. The maneuverability of these robots allows them to perform turning maneuvers ranging from point turns to straight line motion under ideal conditions (e.g., flat terrain and powerful actuators). However, sloped terrain, terrain with high friction, or actuator torque and power limitations can limit the achievable turning radii. The aim of this research is to...
Show moreSkid-steered robots are commonly used in outdoor applications due to their mechanical simplicity, high maneuverability, and robustness. The maneuverability of these robots allows them to perform turning maneuvers ranging from point turns to straight line motion under ideal conditions (e.g., flat terrain and powerful actuators). However, sloped terrain, terrain with high friction, or actuator torque and power limitations can limit the achievable turning radii. The aim of this research is to analyze and experimentally verify the dynamic and power models for skid-steered autonomous ground vehicles equipped with non-ideal (i.e., torque and power limited) actuators and moving on sloped terrains. In particular it investigates the ability of the proposed models to predict motor torques (including motor saturation), power requirement, and minimum turn radius as a function of terrain slope, vehicle heading, payload, terrain parameters and actuator characteristics. The experimental results show that the model is able to predict motor torques for the full range of turning radii on flat ground, i.e., from point turns to straight line motion. In addition, it is shown that the proposed model is able to predict motor torques (including motor saturation) and minimum turn radius as a function of terrain slope, vehicle heading, payload, terrain parameters and actuator characteristics. This makes the model usable for curvilinear motion planning tasks on sloped surfaces. The research uses these results along with Sampling Based Model Predictive Optimization to develop an effective methodology for generating dynamically feasible, energy efficient trajectories for skid-steered autonomous ground vehicles (AGVs) and compares the resultant trajectories with those based on the standard distance optimal trajectories. The simulated and experimental results consider an AGV moving at a constant forward velocity on both wood and asphalt surfaces under various loads. They show that a small increase in the distance of a trajectory over the distance optimal trajectory can result in a dramatic savings in the AGV's energy consumption. They also show that it is not difficult for distance optimal planning to produce trajectories that violate the motor torque constraints for skid-steered AGVs, which can result in poor navigation performance. In addition, the research motivates and provides a methodology that integrates the robot's dynamic model and actuator limitations, and the terrain models with SBMPO to exploit the vehicle momentum as a way to successfully traverse the difficult terrains such as steep hills, mud, or stiff vegetation patches. These scenarios are particularly critical for smaller robots with torque and power limited actuators, which as experimentally shown in this research can easily fail to accomplish their tasks in these environments. In particular, the experimental results showing the efficacy of the proposed methodology are presented for a vegetation patch and a steep hill. Finally, a discussion of the necessary perception work to fully automate the process is included. Further, for walking and running robots, analysis of the power consumption is particularly important for trajectory planning tasks as it enables motion plans that minimize energy consumption and do not violate power limitations of the robot actuators. The research here is motivated by the hypothesis that for certain regimes of operation (i.e., certain gait parameters), legged robots from the RHex family behave in a similar fashion to skid-steered robots while in general curvilinear motion. Hence, using the experience gained from skid-steered wheeled vehicles, presents models of the inner and outer side torques and power requirements for the XRL hexapedal robot. In addition, the applicability of the power model to energy efficient motion planning is illustrated for a walking gait on a vinyl surface.
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Date Issued: 2014
Identifier: FSU_migr_etd-8997
Format: Set of related objects

Title: Beatboxing and the Flute: Its History, Repertoire, and Pedagogical Importance.
Creator: Kuhns, Christopher, Amsler, Eva, Mathes, James, Meighan, Patrick, Bish, Deborah, Trujillo, Valerie, College of Music, Florida State University
Abstract/Description: "Beatbox Flute" is a contemporary technique in which a performer creates complex polyphonic percussive effects while playing the flute. Developed in the early 2000s, it has only recently begun to gain widespread acceptance. The current popularity of beatboxing on the flute, especially with the younger generation, can prove to be an effective vehicle for delivering a variety of pedagogical concepts, including support, breathing, rhythm, tone, and compound melodies. In the flute choir setting,...
Show more"Beatbox Flute" is a contemporary technique in which a performer creates complex polyphonic percussive effects while playing the flute. Developed in the early 2000s, it has only recently begun to gain widespread acceptance. The current popularity of beatboxing on the flute, especially with the younger generation, can prove to be an effective vehicle for delivering a variety of pedagogical concepts, including support, breathing, rhythm, tone, and compound melodies. In the flute choir setting, it is also a wonderful way to provide interest in an ensemble that is traditionally viewed as old fashioned or "boring" to a younger generation. This document begins with an examination of vocal beatboxing and its transference to flute. Non-lexical vocables and onomatopoeic percussive syllables have long been used in many different musical cultural traditions. Vocal beatboxing expands on these effects by deliberately masking vocal cues and more closely imitates the effects of electronic drum machines (or beat boxes). The use of percussive articulatory effects in flute music is not a new phenomenon, compositions featuring similar techniques have existed for decades. The style of playing that has come to be called beatbox flute has taken these earlier procedures and added to them with the inclusion of bass drum effects and inhaled sounds. Important pioneers in developing the field of beatbox Flute include Tim Barsky and Greg Pattillo; their specific contributions and innovations are discussed throughout this text. The current notated repertoire for beatbox flute is sparse. Background information of the available repertoire and a brief description of these works are discussed in chapter two. Compositions/arrangements examined include those by Randall Woolf, Greg Pattillo, Project Trio, Dirko Juchem, Andrea La Rose, Tilmann Denhard, and the author. In an effort to increase the number of compositions that feature beatbox flute, the appendix includes two new works: an arrangement of Joseph Bodin de Boismortier's Solo Suite no. 5, mov. 4 for solo beatbox flute, and Camille Saint-Saëns Dance Bacchanale from the opera Samson et Dalila for beatbox flute choir. Chapter three focuses on the different beatbox flute techniques and attempts to provide an exact phonetic transcription of all effects currently used in the repertoire. The effects are grouped by the category of instrument that they are intended to represent and each effect is described in detailed prose and is compared to similar effects. All effects are presented in International Phonetic Alphabet (IPA) shorthand and recorded examples are included. As with many extended techniques, there is not a standard way to notate beatbox effects in music. Chapter four compares the different notational systems currently in use by composers of vocal beatbox and flute beatbox works. A compilation of all effects currently in use by different composers/arrangers and their differing notational short-hands is also included. The potential pedagogical uses of beatbox flute within the collegiate curriculum are discussed in chapter five. Increased kinesthetic awareness and increased focus and concentration are emphasized. It can be used to strengthen rhythmic stability and as a solmization system can provide a fun and engaging experience for today's students. When applied to earlier music, beatbox effects can amplify (or reshape) important concepts such as compound melodies or metric hierarchy. Finally, its use within the flute choir setting can serve as a tool for audience development and to provide contrast to the homogeneity of the traditional ensemble.
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Date Issued: 2014
Identifier: FSU_migr_etd-8827
Format: Set of related objects

Title: Time Synchronized Sonification of Paleoclimatic Data: Orbital Eccentricity, Ecological Abundance and Stable Isotopes.
Creator: Goddard, Jay Daniel, Parker, William, Odom, Leroy, Wang, Yang, Department of Earth, Ocean and Atmospheric Sciences, Florida State University
Abstract/Description: Paleoclimatic data including orbital eccentricity, mollusk species counts and carbonate isotope data are combined in an event based, time synchronized, parameter mapped sonification that plays backwards through geologic time from ~3.2 million years ago to ~7.4 million years ago. Interpretations of the sonified data are compared to the interpretations of previously published studies and insight has been gained regarding the usefulness of auditory display methods in this scientific context. The...
Show morePaleoclimatic data including orbital eccentricity, mollusk species counts and carbonate isotope data are combined in an event based, time synchronized, parameter mapped sonification that plays backwards through geologic time from ~3.2 million years ago to ~7.4 million years ago. Interpretations of the sonified data are compared to the interpretations of previously published studies and insight has been gained regarding the usefulness of auditory display methods in this scientific context. The field of auditory display has grown exponentially in recent years but there is a lack of papers that use sonification to explore science-based data within a legitimate scientific framework. The end result allow users to monitor a substantial portion of the Late Neogene period (around 4.2 million years in length) in less than 2 minutes. Users perceive shifts in mollusk counts (a temperature proxy) as the pink noise changes structure and travels L and R in the sound field. Low frequency discrete tones mimic the changing eccentricity of Earth's orbit as bell tones (representing isotope trends) move chaotically in the center channel. It is shown that sonification can preserve both simple and advanced structures in scientific data as shown in numerous sound examples and verified with unique figures that compare sonification waveforms or spectrograms to original publication figures.
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Date Issued: 2014
Identifier: FSU_migr_etd-8791
Format: Set of related objects

Title: Carnival of Souls: A Symphony for Winds, Percussion, Harps and Low Strings.
Creator: Vollen, Guy James, Kubik, Ladislav, Croft, James, Mathes, James, Spencer, Peter, Stebleton, Michelle, College of Music, Florida State University
Abstract/Description: Carnival of Souls is a work in three movements with a brief prelude, played without break, approximately eighteen minutes in duration. It is scored for conventional wind band with added low strings, harps, and electronics. The three movements were inspired by the three sections of Dante's Divine Comedy and their respective moods: "Inferno," "Purgatorio," and "Paradiso." The dramatic trajectory of Carnival of Souls is a progression upwards from dark, heavy textures representing spiritual...
Show moreCarnival of Souls is a work in three movements with a brief prelude, played without break, approximately eighteen minutes in duration. It is scored for conventional wind band with added low strings, harps, and electronics. The three movements were inspired by the three sections of Dante's Divine Comedy and their respective moods: "Inferno," "Purgatorio," and "Paradiso." The dramatic trajectory of Carnival of Souls is a progression upwards from dark, heavy textures representing spiritual bondage to the bright and lyrical content of the third movement. The relationship between the worldly--even sensual--materials of the beginning and the heavenly apotheosis of the end is more complex than one of simple opposition. As in Dante's poem, the most rarefied spiritual states are tempered by references to lived human experience; the progression toward a reconciliation of the musica mundana and musica humana is exemplified by the epigraphs of the first and third movements (below). Believe me, ill will it go with mortal women in that heaven of which thou speakest if only the spirits be more fair, for their lords will never turn to look upon them, and their Heaven will become their Hell. H. Rider Haggard, She The creature whose substance is bliss is everywhere at home. All sounds, even to the roaring of Lions, the screeching of the nightly Owls, the laments and groans of those entrapped in Hell, are as sweet Musick to her. All odours, even to the foulest stench of Corruption, are to her as the delight of roses and Lilies. All savours, even to the banquettable of the Harpys of heathen lore, are as Sweet loaves and spiced Ale. Wandering at noon through the Waste-Places of the world, it seems to her she is refreshed by Canopies of flocking Angels. . . . Thrust a keen Sword-blade through her and it will seem as a fountain of Divine and Pure pleasure. Jane Lead, The Wonders of God's Creation
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Date Issued: 2003
Identifier: FSU_migr_etd-4580
Format: Set of related objects

Title: Something to Be Happy About: Solo for Tenor Pan and Orchestra.
Creator: Catania, Michael, Wingate, Mark, Spencer,, Peter, Jones,, Evan, College of Music, Florida State University
Abstract/Description: Something To Be Happy About: Concerto for C Tenor Pan and Orchestra is the first concerto for orchestra and steel drum to be composed in American. Divided into three movements, this 18 minute work is scored to capitalize upon the nuances of the C Tenor Pan and to provide a solid piece for the new wave of pan musicians that are clamoring for music written for the instrument.
Date Issued: 2003
Identifier: FSU_migr_etd-4023
Format: Set of related objects

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