Shape represents a complex and rich source of biological information that is fundamentally linked to underlying mechanisms and functions. Many fields of biology employ mathematical tools for the statistical analysis of shape variation. However, difficulties in reliably quantifying biological shape, especially for newly emerging shape data, still present an obstacle for researchers to understand how shape variation relates to biological functions and development processes. To overcome these difficulties, it is desirable to build efficient ways to quantify shapes. Having a quantitative tool in hand, we can further design methods to correlate shape with biological information. The integration of these models with machine learning and statistical inference methods will allow biologists to explore how morphological variation correlates to biological variates and to help advance various areas of research. One goal of this dissertation is to construct new type of shape representation to quantify gene expression data. Advances in microscopy and techniques such as Optical Projection Tomography (OPT) allow researchers to visualize and to study 3D morphological patterns of gene expression domains. Quantitative analysis of gene expression domains and investigation of relationships between gene expression and developmental and phenotypic outcomes are central to advancing our understanding of the genotype-phenotype map. However, quantification of shape variation in gene expression domains poses particularly challenging problems, as these domains typically have no clearly defined forms, often appearing seemingly amorphous. Those properties of the gene expression domains make it difficult to analyze shape variation with the tools of landmark-based geometric morphometrics. In addition, 3D image acquisition and processing introduce many artifacts that further exacerbate the problem. To overcome these difficulties, we present a method that combines OPT scanning, a shape regularization technique and a landmark-free approach to quantify variation in the morphology of sonic hedgehog expression domains in the frontonasal ectodermal zone (FEZ) of avians and investigate relationships with embryonic craniofacial shape. The landmark-free approach quantifies variation in shape of amorphous gene expression domains, enhancing their most salient morphological characteristics and being robust to uninformative local shape variation and irregularities associated with image acquisition. The correlation analysis reveals axes in FEZ and embryonic-head morphospaces along which variation exhibits a sharp linear relationship at high statistical significance. Combined with qualitative findings, these results have the potential to benefit biologists in exploring the gene expression pathway and in understanding the underlying expression mechanisms. The techniques we used to deal with FEZ meshes should be applicable to analyses of other 3D surface-like biological structures that have ill-defined shape and are relevant to understanding developmental processes and phenotypic variation. Existing biological shape models, such as those based on landmarks, rely on sparse landmarks on the shapes to model shape variations. However, on soft-tissue surfaces as the face there are few such landmarks. Across the cheek and forehead, for instance, there are no points that have exact biological correspondence and yet aspects of their shape contains useful biological information. The analysis based on the sparse landmarks will compromise the deep and comprehensive morphological information collected by advanced image processing technologies. Thus, instead of using only the limited number of landmarks, we propose to use the spline method to construct dense surface model which covers the entire shape. This brings another goal of this dissertation - to develop such a spline method to build a dense correspondence across all shapes. Although, spline is an active area in shape analysis and also in many other disciplines for interpolation, approximation and regression. Most results have been focused on Euclidean domain. However, data living on manifold occurs often, especially when dealing with shape surfaces, so constructing spline with manifold domain and providing effective computation method for such spline are desirable in real-life problems. To fulfill this goal, we present a general theoretical framework of spline in which the Euclidean domain can be extended to manifold domain. Additionally, we provide computationally effective algorithm to compute such spline function based on bounded rectangular domain. We demonstrate the advantages of this framework by using examples on closed and open manifold domains and by comparing performance with other spline methods. The computation framework shows comparable result with the spline directly constructed on the manifold and also shows clear improvement respect to the thin plate spline method. This manifold spline method has been applied to construct dense surface models of avian embryos shapes. Those dense surface models can establish a correspondence of thousands of points across each 3D image and provide dramatic visualization of shape variation. / A Dissertation submitted to the Department of Mathematics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2015. / March 19, 2015. / Biological shape, Quantifying variation, Shape analysis, Statistical modeling / Includes bibliographical references. / Washington Mio, Professor Directing Dissertation; Piyush Kumar, University Representative; Richard Bertram, Committee Member; Xiuwen Liu, Committee Member; Jack Quine, Committee Member.

Many states within the U.S., including Florida, have seen steady population growth since the 1950s. While population growth can lead to economic growth, excessive growth of urban areas can lead to negative externalities such as road congestion, air and water pollution, decreased access to open space, habitat loss, and habitat fragmentation. This realization has led to increasing political and stakeholder pressure to more comprehensively assess impacts of land-use planning projects on human-natural systems. The Ecosystem Services Assessment (ESA) approach is a relatively new approach which is described in the peer-reviewed literature as comprehensive and holistic. This dissertation study researched the potential of an ESA approach as a planning tool in Florida by addressing the following research questions: 1) What are the guidelines for best practices in ESAs from the literature? 2) How are ESAs currently used in land-use planning projects in Florida? 3) How is the traditional approach used in land-use planning projects in Florida? 4) What are key differences between the ESA approaches used in the case studies and the guidelines for best practices in ESAs? 5) What are key differences between an ESA approach and a traditional approach as they are currently used in Florida? The research questions were investigated through the use of an online survey, in-depth interviews, and analysis of three Florida case studies. Experts in the field of ecosystem services research were interviewed to assess how ESAs are used in Florida and to gather background information for the online survey and case studies. The target group for the online survey included respondents working for local, state, regional, federal and tribal government agencies, non-profit organizations, research institutes, universities, and other relevant persons who had been involved in projects in which ecosystem services were valuated, quantified, or described. The case studies that were assessed for this research are the Central Everglades Planning Project, the Florida Conservation Lands study, and the Tampa Bay Project. / A Dissertation submitted to the Department of Urban and Regional Planning in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / May 19, 2015. / Ecosystem Services, Integrated Systems Analysis, Natural-human Systems, Natural Resource Management, Sustainable Development, Valuation / Includes bibliographical references. / Timothy Chapin, Professor Directing Dissertation; Keith Ihlanfeldt, University Representative; Christopher Coutts, Committee Member; Jeffrey Chanton, Committee Member.

Previous studies have found interactions between the meaning of a word and the spatial position of the word (Barsalou, 2008; Zwaan and Yaxley, 2003). Some studies find that words or sentences with a directional component facilitate detection toward the congruent spatial direction (e.g., Šetić & Domijan, 2007; Dils & Boroditsky, 2007; Dils & Boroditsky, 2010; Pecher et al; 2010). For instance, the word "jump" would cue toward the top of a screen. Other studies find the opposite effect, where words with implicit spatial meaning show an interference effect (e.g., Bergen et al, 2007; Estes et al, 2008; Dils & Boroditsky, 2010). In these cases the word "jump" would result in faster reaction times to stimuli in the bottom of the screen. This experiment attempts to answer this controversy by looking at temporal effects. These differences might be due to inhibition of return (Posner & Cohen, 1984). If that is the case, you would expect to see a timeline where there is a facilitation effect followed by interference. Results of the study show no effect of time, however there were strong item effects. Most sentences consistently showed either a facilitation or inhabitation effect across all times. This suggests that these effects are modulated by the items that are used. / A Thesis submitted to the Department of Psychology in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester 2015. / July 16, 2015. / Language, Spatial / Includes bibliographical references. / Michael Kaschak, Professor Directing Thesis; Walter Boot, Committee Member; Arielle Borovsky, Committee Member.

Significant disparities in healthcare among African-Americans are still prevalent in the U.S. with black patients having a higher incidence of common chronic diseases (heart disease, cancer and strokes), die at a higher rate, and lose more years of life as a result of the conditions. One area where the healthcare gap is particularly prevalent is clinical trial participation, with 1% of trial participants identifying as black despite a comprehensive meta-analysis including 70,000 subjects indicating that minority patients are just as willing to participate in medical trials as non-Hispanic White patients. Mistrust of the medical community and a long history of malpractice in experiments on minorities (i.e. Tuskegee Syphilis experiments, Vertus Hardiman case, and the Henrietta Lacks cases for example) could easily be used as justification of this mistrust, however several studies have shown that while African Americans are aware of the past abuse, awareness of those events does not significantly affect attitude toward participation. A structural model utilizing Ajzen and Fishbein's Theory of Planned Behavior was used in an attempt to explain the inconsistency between the positive attitudes of minority patients regarding participation in clinical trials and the distinct lack of actual participation. The model included measures of attitude, social norms, control and difficulty as functions of behavioral intention to participate in clinical trials and multiple-group structural equation modeling analysis of survey data from 117 black and 457 white participants was used to test group differences. Despite strong loadings on intentions by attitude, based on the structural model it cannot be concluded that the TPB model predicts intentions to participate well for this sample. None of the other constructs had any meaningful effect on intentions, indicating the TPB model does not work well for this sample. Moreover, due to insignificant loadings by social norms, control, and difficulty, it is impossible to distinguish any differences between groups on the constructs with the exception of attitude, which was not significantly different between groups. This study confirmed previous research that showed similar attitudes toward participating in clinical trials by black and white participants and did not find any evidence for including other constructs in future recruiting efforts. / A Dissertation submitted to the School of Communication in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / July 14, 2015. / African-American, Behavioral Intentions, Clinical Trials, Cross-Cultural, Structural Equation Modeling, Theory of Planned Behavior / Includes bibliographical references. / Jay Rayburn, Professor Directing Dissertation; Michael Hartline, University Representative; Davis Houck, Committee Member; Felipe Korzenny, Committee Member.

Nonmainstream American English, or dialect, among children may have important implications for reading research and practice. The purpose of this dissertation study was to examine dialect use in various language contexts and to investigate potential relations between dialect and reading outcomes among elementary students. First, a meta-analysis of recent empirical research examining quantitative relations among dialect use and reading, spelling, and writing outcomes is presented. In summary, the meta-analysis revealed a negative and moderate relationship between dialect production and literacy. Next, the study analyzed and compared dialect production across an oral language task and specifically between two different written language samples, one elicited by a narrative prompt and the second by an expository prompt, among 250 second and third grade students. The study also examined dialect use in the oral narrative task and the two writing samples in relation to concurrent and longitudinal reading outcomes. Finally, the study examined the dialect-reading relationship for students diagnosed with speech, language, and learning disabilities in comparison to their typically developing peers. The study found that overall, most students used features of dialect in their oral language samples and that students generally used several features of dialect in their written language samples as well. However, the frequency of dialect use was greater in the written narrative sample than in the written expository samples. In addition, dialect use, particularly in the oral and written narrative, was predictive of reading outcomes in the same year and two years later. Moderator analyses for students with speech, language, and learning disabilities indicated that relationships between dialect use and reading did not differ for students identified with these particular disabilities. However, students with these disabilities who also use dialect may be at increased risk for reading difficulties. Implications for practice and future research are provided. / A Dissertation submitted to the School of Teacher Education in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / June 17, 2015. / African American English, dialect, oral language, reading, writing / Includes bibliographical references. / Jeanne Wanzek, Professor Directing Dissertation; Christopher Schatschneider, University Representative; Barbara Foorman, Committee Member; Young-Suk Kim, Committee Member.

Though there are many feature selection methods for learning, they might not scale well to very large datasets, such as those generated in computer vision data. Furthermore, it can be beneficial to capture and model the variability inherent to data such as face detection where a plethora of face poses (i.e. parameters) are possible. We propose a parameter sensitive learning method that can learn effectively on datasets that can be prohibitively large. Our contributions are the following. First, we propose an efficient feature selection algorithm that optimizes a differentiable loss with sparsity constraints. We note that any differentiable loss can be used and will vary depending on the application. The iterative algorithm alternates parameter updates with tightening the sparsity constraints by gradually removing variables based on the coefficient magnitudes and a schedule. Second, we show how to train a single parameter sensitive classifier that models the wide range of class variability. The sole classifier is important since this reduces the amount of data necessary for training compared to methods where multiple classifiers are trained for each parameter value. Third, we show how to use nonlinear univariate response functions to obtain a nonlinear decision boundary with feature selection; an important characteristic since the separation of classes in real world datasets is very challenging. Fourth, we show it is possible to mine hard negatives with feature selection, though it is more difficult. This is vital in computer vision data where 10^5 training examples can be generated per image. Fifth, we propose an approach to perform face detection using a 3D model on a number of face keypoints. We modify binary face features from the literature (generated using random forests) to fit into our 3D model framework. Experiments on detecting the face keypoints and on face detection using the proposed 3D models and modified face features show that the feature selection dramatically improve performance and come close to the state of the art on two standard datasets for face detection . We also apply our parameter sensitive learning method with feature selection to detect malicious websites, a dataset with approximately 2.4 million websites and 3.3 million features per website. We outperform other batch algorithms and obtain results close to a high performing online algorithm but using far fewer features. / A Dissertation submitted to the Department of Statistics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / June 12, 2015. / Classification, Face detection, Feature selection, Large data / Includes bibliographical references. / Adrian Barbu, Professor Directing Dissertation; Kumar Piyush, University Representative; Fred Huffer, Committee Member; Yiyuan She, Committee Member; Jinfeng Zhang, Committee Member.

What explains why and how America fought the civil war? This thesis argues that industrial modernization can be a useful analytical tool for understanding the causes of the American Civil War. The argument is developed by analyzing the social, political, and military events of the era through the lens of industrialization. This study will show that the American Industrial Revolution lay at the core of the social, political, and military events that shaped this great conflict. Understanding the causes of human events is as critical as understanding their effects. By grasping the root causes of the war, we can better understand how and why it was fought. This analysis of American society, American politics, and the country's military establishment will provide the rich context needed to apprehend the reasons for the American Civil war beyond the dichotomy of slavery and economics. / A Thesis submitted to the Department of History in partial fulfillment of the requirements for the degree of Master of Arts. / Spring Semester 2015. / April 27, 2015. / Civil War, Industrialization, Modernization / Includes bibliographical references. / Michael Creswell, Professor Directing Thesis; Ronald E. Doel, Committee Member; G. Kurt Piehler, Committee Member.

Eating disorders (EDs) and alcohol use disorders, as well as less severe eating disorder symptoms and alcohol use, are behaviors that can result in severe physical, social, psychological, occupational, and academic consequences; the risk of premature death may also be increased. These behaviors are often seen comorbidly. When comorbid, negative consequences may be amplified or increased and the outcome, prognosis, and recovery of the disorders may be hindered. A population particularly at risk of developing eating disorder symptoms as well as alcohol use and misuse, and therefore, potentially experiencing severe negative consequences, is college students. Understanding the reasons why eating disorder symptoms and alcohol use and misuse occur among college students is vital, as this allows effective intervention and prevention efforts to occur. The present study strived to provide insight into these reasons. A particular theory describing the reasons behind this relationship that has received support among college students is the Acquired Preparedness Theory (Fischer & Smith, 2008). This theory involves the constructs of negative urgency, eating and thinness/dieting expectancies, and alcohol expectancies. The present study examined these variables among 189 college women and 79 college men gathered through an online and subject pool sample. The predictor variables of gender and negative urgency were measured by the Demographic Information Survey and UPPS Impulsive Behavior Scale, Urgency subscale (Whiteside & Lynam, 2001), respectively. The moderator variables of eating and thinness/dieting expectancies and alcohol expectancies were measured by the Eating Expectancy Inventory Eating Leads to Feeling Out of Control subscale (Hohlstein, Smith, & Atlas, 1998), Thinness and Restricting Expectancy Inventory (Hohlstein et al., 1998), and Comprehensive Effects of Alcohol Questionnaire Positive Expectancy factors (Fromme, Stroot, & Kaplan, 1993), respectively. The criterion variables of ED symptoms, alcohol use, and alcohol-related negative consequences were measured by the Eating Disorder Examination - Questionnaire 6.0 Global Score (Fairburn & Beglin, 2008), Timeline Followback - Alcohol (Sobell & Sobell, 1992), and Brief - Young Adult Alcohol Consequences Questionnaire (Kahler, Strong, & Read, 2005), respectively. Six hierarchical multiple linear regression analyses, with moderator variables, were used to examine the research questions. Three analyses were run utilizing a subsample of college women while three analyses were run utilizing a subsample of college men. Results revealed that mean (i.e., average) and high (i.e., one standard deviation above the mean) levels of eating and thinness/dieting expectancies moderated the relationship between negative urgency and ED symptoms among college women. Results also revealed that mean and high levels of alcohol expectancies moderated the relationship between negative urgency and alcohol-related negative consequences among college women. No other significant moderating relationships were found. Further, eating and thinness/dieting expectancies were associated with ED symptoms among both college women and men. Alcohol expectancies were associated with alcohol use as well as alcohol-related negative consequences among both college women and college men. Negative urgency also were associated with ED symptoms and alcohol-related negative consequences among college women and ED symptoms, alcohol use, and alcohol-related negative consequences among college men. The results of this study provide valuable implications for college administrators, faculty, and staff, as well as for mental health professionals working with college students with negative urgency, ED symptoms, and/or alcohol use. By identifying and challenging expectancies that are associated with ED symptoms, alcohol use, and alcohol-related negative consequences, these behaviors and consequences may be decreased. Further, by increasing college students' distress tolerance skills (i.e., increasing one's ability to manage negative urgency), ED symptoms, alcohol use, and alcohol-related negative consequences may also be avoided or decreased. Of utmost importance, dire and potentially fatal negative consequences of comorbid ED symptoms and alcohol use may be prevented. / A Dissertation submitted to the Department of Educational Psychology and Learning Systems in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / May 29, 2015. / acquired preparedness theory, alcohol use, college students, eating disorder, expectancies, negative urgency / Includes bibliographical references. / Deborah J. Ebener, Professor Directing Dissertation; Mary Frances Hanline, University Representative; Angela Canto, Committee Member; Shengli Dong, Committee Member.

There is an operational need for accurate tropical cyclone (TC) genesis forecasts. Global numerical models are an important genesis guidance tool, but each model has biases. Further, the interpretation of when genesis occurs in a model forecast field can be subjective. Thus, this study seeks to create an automated, objective, statistical-dynamical TC genesis guidance tool for the North Atlantic and eastern North Pacific basins based on output from the CMC, GFS, and UKMET global models. Another goal is to determine how well important genesis processes in global models agree with those theoretically proposed. This research also attempts to identify the characteristics of successful and failed genesis forecasts. First, historical global model forecasts of TC genesis over the past decade are verified. Using this genesis forecast archive, univariable logistic regression equations are created to reveal the statistical relationships between relevant variables and genesis probability. These statistical relationships are compared to theoretical relationships between atmospheric variables and TC genesis. Results show several expected and counterintuitive statistical relationships, with some disagreement among the models. Multiple logistic regression equations then are developed to provide probabilistic genesis forecasts. Separate equations are developed for each global model, basin, and forecast window. Additionally, a consensus regression equation is developed. These equations are tested operationally during the 2014 hurricane season. Verification of the independent data indicates generally well-calibrated guidance. Homogeneous comparisons of the consensus regression equation and National Hurricane Center Tropical Weather Outlook genesis probabilities are presented. Case studies and composite analyses are conducted to gain further insight. Case studies from the following categories are selected: (1) African Easterly Wave genesis over the Main Development Region; (2) genesis from stalled frontal boundaries; (3) genesis via tropical transition; and (4) genesis over the Gulf of Mexico. Hit, miss, and false alarm events are compared. Storm centered composite analyses also are constructed to examine differences in the environments between hit and false alarm forecasts. Separate composites are made for the eastern Main Development Region (where the GFS false alarm rate is greatest) and the remainder of the North Atlantic basin. Statistically significant differences between hit and false alarm cases are found for all variables analyzed with various areal extents. Results from the case studies and composite analyses will help guide new predictors to test for inclusion into the multiple logistic regression equations. Additionally, the case study of Sean (2011) suggests that changes to the TC identification algorithm are needed to better detect subtropical to tropical transition. Real-time guidance products based on the logistic regression equations are being evaluated by hurricane specialists at the National Hurricane Center. It is possible that the products will be selected for operational implementation pending further testing and evaluation during 2015. / A Dissertation submitted to the Department of Earth, Ocean, and Atmospheric Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2015. / June 1, 2015. / forecasting, genesis, global models, hurricane, tropical cyclone, verification / Includes bibliographical references. / Henry E. Fuelberg, Professor Co-Directing Dissertation; Robert E. Hart, Professor Co-Directing Dissertation; Kristine C. Harper, University Representative; Jeffrey M. Chagnon, Committee Member; Guosheng Liu, Committee Member.

Suicide and depression are serious and growing public health problems. Despite their substantial global health burden, relatively few interventions have been found to be efficacious at preventing these conditions. The aims of the current study were to (a) determine whether two brief, cost-effective, and easy-to-disseminate prevention interventions (gratitude and priorities) were efficacious at preventing suicidality and depressive symptoms among individuals at risk for these conditions based on their psychological histories; (b) compare the efficacy of a gratitude intervention to a stringent active control condition (priorities) and an inactive control condition; and (c) address why the two prevention interventions might be efficacious by testing possible mechanisms (e.g., belongingness, sleep quality, optimism, gratitude) through which the interventions operate. In the current study, participants (N = 192) who were currently asymptomatic but who endorsed a history of suicidality and/or depression were randomly assigned to one of three intervention conditions (gratitude, priorities, control). These at-risk participants were followed for two months following the intervention period to determine if the interventions were efficacious at preventing future symptoms of suicidality and depression. Testing the efficacy of these interventions in an at-risk sample is crucial, as it is important to know whether such interventions are efficacious, have no effect, or are potentially harmful to a subgroup of individuals. Results provided evidence that participants in the gratitude condition experienced a poorer trajectory of depressive symptoms over time, a shorter length of time to suicidal ideation, and equivalent trajectories of life satisfaction and subjective happiness compared to participants in the control condition. Results also provided evidence that participants in the priorities condition experienced a poorer trajectory of satisfaction with life, and equivalent trajectories of depressive symptoms, suicidal ideation, and subjective happiness compared to participants in the control condition. None of the proposed mediators were found to mediate the relationship between condition and outcome. Overall, results suggest that participating in a gratitude or priorities intervention may not be an efficacious means of improving well-being and preventing suicidality and depressive symptoms among individuals with a history of suicidality and/or depression. Future research should continue to test the efficacy of positive psychology interventions among vulnerable individuals before techniques and interventions are endorsed to the public via self-help campaigns. / A Dissertation submitted to the Department of Psychology in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2015. / July 9, 2014. / Depression, Gratitude, Intervention, Prevention, Priorities, Suicide / Includes bibliographical references. / Thomas E. Joiner, Professor Directing Dissertation; Mark D. Winegardner, University Representative; Norman B. Schmidt, Committee Member; Christopher Schatschneider, Committee Member; E. Ashby Plant, Committee Member.