VictorJuiz/thesis huggingface dataset:
Context-dependent interactions in an ant-plant-hemipteran symbiosis [electronic resource]
Keywords: Biology.

The cost-benefit outcomes of potentially mutualistic interactions between species can range on a continuum between mutualism and parasitism, depending on context. Here I use ecological, behavioral, physiological, theoretical, phylogenetic, and comparative approaches to understand the effects of context on the strength of an ant-plant-hemipteran mutualism. I examine how the strength of mutualism changes with variation in the density and behavior of individuals, the ontogenetic stage of individuals, resource availability in the surrounding environment, and the evolutionary history of a partner guild. The mutualism studied here occurs among the widespread neotropical tree Cordia alliodora, ants of the genus Azteca, and phloem-sucking scale insects of the superfamily Coccoidea. The ants live and tend scale insects inside specialized, hollow branch nodes of the tree, the scale insects excrete a concentrated sugar that forms a key component of the ants' diet, and the ants defend the trees against leaf-eating herbivores. In Chapter 1, I examine the indirect effects of increased densities of scale insects on the tree, and find that higher densities of scale insects increase the effectiveness of ant defense against leaf-eating herbivores. In Chapter 2, I investigate how ant defense of trees changes as trees and ant colonies grow in the course of ontogeny, and find that larger trees suffer from higher herbivore pressure and less effective ant defense. In Chapter 3, I consider the effects of water availability and covariation in tree growing-season duration on the mutualism, and find that as water availability increases, the strength of the mutualism decreases. In Chapter 4, I reconstruct the evolutionary history of the Azteca ant symbionts of the tree in Middle America, and, through the use of comparative methods, I find that the effectiveness of defense that ants provide to trees is conserved across the ant phylogeny. Taken together, these results show that biotic, abiotic, and evolutionary context can strongly affect the strength of an ant-plant-hemipteran mutualism, and that the direction of these effects may be predicted from key contextual variables.
Contracting over actions [electronic resource]
Keywords: Business.

I consider models in which contracts are written over the verifiable actions taken by an agent in multiple decisions. The principal's preferences over actions depend on underlying states of the world, but only the agent observes the states. The principal cannot audit the agent's information or punish her ex post for having taken inappropriate actions. Moreover, the principal is uncertain about the agent's preferences conditional on the states. Chapter 2 extends the concept of a quota contract to account for discounting and for the possibility of infinitely many periods: a discounted quota fixes the number of expected discounted plays on each action. Discounted quotas are optimal contract forms, even if arbitrary dynamic transfer payments are available, if the agent is assumed to have state-independent preferences. I recursively characterize the optimal discounted quotas for an infinitely repeated problem with independent and identically distributed states. Then I give a more explicit description of these contracts in the limit as interactions become frequent, and when only two actions are available. In Chapter 3 I allow the agent's preferences to depend on the states of the world. Under a variety of assumptions on the timing of the game and on the set of possible agent utility functions, I solve for the max-min optimal mechanisms -- those which maximize the principal's payoff against the worst possible agent preference type. These mechanisms are characterized by a property which I call "aligned delegation." Max-min optimal mechanisms may take the simple forms of simultaneous ranking mechanisms, sequential quotas, or budgets.
Contributions of the deltoid and rotator cuff to shoulder mobility and stability [electronic resource] : a 3D finite element analysis
Keywords: Mechanical Engineering

The shoulder bones provide few constraints on motion. Therefore, stability must be maintained by muscles and ligaments. Shoulder mobility allows versatility of function, but makes the shoulder prone to injury. A better understanding of the role of muscle in shoulder mechanics is needed to improve the treatment of shoulder injuries and pathologies. Computational models provide a valuable framework for characterizing joint mechanics. Previous shoulder models have used simple representations of muscle architecture and geometry that may not capture the details needed to fully understand muscle function. The purpose of this dissertation was to create a detailed 3D finite element model of the deltoid and the four rotator cuff muscles. This model was then used to characterize the muscle contributions to joint motion and stability. The model was constructed from magnetic resonance images of a healthy shoulder. From the images, the 3D geometry of the muscles, tendons and bones was acquired. A finite element mesh was constructed and the 3D trajectories of the muscle fibers were mapped onto the finite element mesh. A hyperelastic, transversely-isotropic material model was used to represent the nonlinear stress-strain relationship of muscle. Bone motions were prescribed and the resulting muscle deformations were simulated using an implicit finite element solver. To characterize muscle contributions to joint motion, we calculated moment arms for each modeled muscle fiber. We found that 3D models predicted substantial variability in moment arms across fibers within each muscle, which is not generally represented in line segment models. We also discovered that for muscles with large attachment regions, such as deltoid, the line segment models under constrained the muscle paths in some cases. As a result, line segment based moment arms changed more with joint rotation than moment arms predicted by the 3D models. Glenohumeral instability is common, and difficult to treat. To better understand the mechanics of instability we used the 3D model to investigate the role of the muscles in stabilizing the glenohumeral joint by simulating joint translations. We found that at the neutral position, anterior deltoid provides the largest potential to resist anterior translation which counters the conclusions of conventional line segment models. This is the result of compression generated by muscle contact, which must be considered when characterizing the ability of muscle to resist joint translation. This dissertation provides a new computational method for analyzing shoulder mechanics, and demonstrates the importance of 3D analysis when investigating the complex function of shoulder muscles.
Controlled vapor deposition of azide-terminated siloxane monolayers [electronic resource] : a platform for tailoring oxide surfaces
Keywords: Chemical Engineering

The controlled deposition of mixed, azide-terminated siloxane monolayers onto oxide surfaces provides a platform for the covalent attachment of alkyne-terminated species such as oligonucleotides using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. A convenient method for the vapor deposition of dense siloxane monolayers onto oxide surfaces was developed. A selectively deuterated silane, (CD3O)3-Si-(CH2)13-CH3, was synthesized and then vapor deposited in the presence of controlled amounts of water vapor from the in situ dehydration of MgSO4[multiplication dot]7H2O at 110°C. Monolayer densification was characterized using ellipsometry, Fourier transform infrared (FTIR) spectroscopy, water contact angle, and electrochemical capacitance measurements. The formation of dense, completely hydrolyzed monolayers required excess amounts of silane and water reactants. The optimized vapor deposition conditions were used to form mixed, azide-terminated monolayers. Dilution of the azide groups with unreactive methyl groups was achieved from the co-deposition of two silanes. Enrichment of the monolayers with the higher vapor pressure silane reactant was observed. Quantitative CuAAC reactions of the azide groups in mixed monolayers were demonstrated with azide surface compositions up to approximately 40%. Steric hindrance presumably prevented the quantitative reaction of a purely azide-terminated monolayer. Alkyne-terminated oligonucleotides were covalently attached to azide-terminated monolayers on glass followed by hybridization with complementary oligonucleotides. However, the azide-terminated monolayers were susceptible to the nonspecific adsorption of oligonucleotides even after thorough rinsing in aqueous detergents and buffers. A two-step reaction sequence was developed that involved one CuAAC reaction to attach oligonucleotides at low density followed by a second CuAAC reaction with ethynyl phosphonic acid to make the surface more resistant to nonspecific adsorption.
COSA-1, a meiotic crossover site associated protein [electronic resource]
Keywords: Genetics

The formation of crossovers during meiosis is important both for the reassortment of genetic traits, and for creating a physical connection between homologous chromosomes to ensure faithful segregation. This thesis explores the role of a novel protein, COSA-1 (crossover site associated-1), in forming crossovers in the nematode C. elegans. cosa-1 was isolated in a screen for dead embryos, signaling missegregation of the autosomes, and a high incidence of males, signaling missegregation of the X chromosome. Interestingly, obvious orthologs of COSA-1 are only present in metazoans with the notable exception of Drosophilids. Thus no obvious orthologs of COSA-1 exist in the common model organisms, S. cerevisiae, S. pombe, D. melanogaster, and A. thaliana, making C. elegans one of the few organisms in which COSA-1 could have been isolated and studied. Yet, COSA-1 is conserved into humans suggesting the study of COSA-1 will have implications for human reproduction. Not only does C. elegans cosa-1 play a crucial role in promoting the formation of crossovers, evidenced by the lack of chiasmata in the cosa-1 mutant, GFP::COSA-1 exhibits an interesting localization pattern to presumptive crossover sites. In particular, unlike other crossover promoting proteins MSH-5 and ZHP-3, GFP::COSA-1 does not exhibit an initial broader localization but instead localizes to just 6 foci, 1 focus for the 1 crossover on each of the 6 chromosomes. This localization of GFP::COSA-1 to 6 foci was robust under various conditions. Mathematical modeling of the relationship between irradiation dose and COSA-1 foci revealed a relationship between obligate crossover, the phenomenon in which at least one crossover is formed per chromosome, and crossover interference, the phenomenon in which the formation of a crossover inhibits the formation of other crossovers nearby. In addition, analysis of GFP::COSA-1 foci in mutants that form extra crossovers, in particular rtel-1 and dpy-28, revealed a separation between the number of GFP::COSA-1 foci, 6, and the number of COs made, more than 6, suggesting that interference is still operating on GFP::COSA-1foci. Thus GFP::COSA-1 may serve as a better readout for crossover interference than crossovers per se. The ability to visualize GFP::COSA-1 in live worms holds great potential for elucidating the mechanisms involved in crossover interference, crossover distribution, and crossover designation.
Coupling optional pólya trees and the two sample problem [electronic resource]
Keywords: Statistics

Testing and characterizing the difference between two data samples is of fundamental interest in statistics. Existing methods such as Kolmogorov-Smirnov and Cramer- von-Mises tests do not scale well as the dimensionality increases and provide no easy way to characterize the difference should it exist. In this work, we propose a theoretical framework for inference that addresses these challenges in the form of a prior for Bayesian nonparametric analysis. The new prior is constructed based on a random-partition-and-assignment procedure similar to the one that defines the standard optional Pólya tree distribution, but has the ability to generate multiple random distributions jointly. These random probability distributions are allowed to "couple", that is to have the same conditional distribution, on subsets of the sample space. We show that this "coupling optional Pólya tree" prior provides a convenient and effective way for both the testing of two sample difference and the learning of the underlying structure of the difference. We provide both simulated and real data examples to illustrate the work of this method and compare its performance to several existing methods, both frequentist and Bayesian. We demonstrate through an analysis of the Wellcome Trust Case-control Consortium data how the method can be applied to conduct multiple marker association tests. We also discuss some practical issues in the computational implementation of this prior and explore techniques that can be utilized to improve the computational efficiency in the appendices.
Creating destiny [electronic resource] : youth, arts, and social change
Keywords: Education.

In this ethnographic study, I examine the work of a company of youth artists who create art to create social change. I explore how they define social change, and how they make it through a process of creating and performing an original work of hip hop, modern dance, and theater. The company is the Destiny Arts Youth Performance Company in Oakland, CA, which brings together 15 to 20 young people each year to work with the company's adult co-directors to create an original performance for social change. The company members are high-school-aged and diverse with regard to race, ethnicity, gender, sexual orientation, and socio-economic background. Its work is part of a larger tradition of programs in which artists "apply" the tools and processes of the arts to social problems (McCammon, 2007). Through inductive analysis of field data that I collected documenting the company's ten-month process, I surfaced a theory of social change embedded in the company's work. The company posits social change as a process of changing relationships--that is, changing how we relate to ourselves, to one another, and to the world around us. This process requires understanding how our ways of relating are shaped by social structures and our positions within them; imagining new possibilities for these relationships that would exist in the world in which we want to live; and then transforming our relationships to embody these possibilities. Transforming our relationships in this way, the company suggests, is a means to create the world we have imagined. In this study, I elaborate this theory and it's potential to complement more traditional notions of social change, which focus on changing social structures more directly. Such theories rely on the imposition of social structures to align human activity with principles of equality and social justice. By contrast, the company focuses on how social change created among small groups can radiate outward to effect change in communities and to shift social structures. Through fieldnote, interview, and photographic data that I gathered in the role of participant observer, I describe what dance and writing offer the company as media for social change during their creative process. I also explore the impact of the company performance through audience focus group and survey data. My analyses elaborate the concept of third space in the arts and the ways in which it functions to facilitate social change at an individual, interpersonal, group, and community level. They also illuminate the importance of cross-cultural collaborations among youth to creating social change.
Cross-validation and regression analysis in high-dimensional sparse linear models [electronic resource]
Keywords: Statistics

Modern scientific research often involves experiments with at most hundreds of subjects but with tens of thousands of variables for every subject. The challenge of high dimensionality has reshaped statistical thinking and modeling. Variable selection plays a pivotal role in the high-dimensional data analysis, and the combination of sparsity and accuracy is crucial for statistical theory and practical applications. Regularization methods are attractive for tackling these sparsity and accuracy issues. The first part of this thesis studies two regularization methods. First, we consider the orthogonal greedy algorithm (OGA) used in conjunction with a high-dimensional information criterion introduced by Ing& Lai (2011). Although it has been shown to have excellent performance for weakly sparse regression models, one does not know a priori in practice that the actual model is weakly sparse, and we address this problem by developing a new cross-validation approach. OGA can be viewed as L0 regularization for weakly sparse regression models. When such sparsity fails, as revealed by the cross-validation analysis, we propose to use a new way to combine L1 and L2 penalties, which we show to have important advantages over previous regularization methods. The second part of the thesis develops a Monte Carlo Cross-Validation (MCCV) method to estimate the distribution of out-of-sample prediction errors when a training sample is used to build a regression model for prediction. Asymptotic theory and simulation studies show that the proposed MCCV method mimics the actual (but unknown) prediction error distribution even when the number of regressors exceeds the sample size. Therefore MCCV provides a useful tool for comparing the predictive performance of different regularization methods for real (rather than simulated) data sets.
Curricular program implementation in the context of randomized field trials [electronic resource]
Keywords: Education.

Abstract curricular program implementation in the context of randomized field trials Gloria Isabel Miller This study examined three cases of commercially available curricular program implementations to determine if a unified approach to measuring the level of implementation was possible (proof of concept). Further, the study investigated whether the level of curriculum and implementation plan specificity made a difference to the strength of implementation achieved in classrooms; and described the implementation evolution in different contexts. The study sample consists of a total of 163 teachers in eight school districts across the United States. In each case teachers were randomly assigned to using the curricular innovation or their currently used materials and processes. The three cases, HS-Math, NewScience, and MathIntervention, were purposely chosen to represent three different points of curricular and implementation specificity and two different subject areas, math and science. Each case features a commercially available program that also had opportunities for teachers to use "electronic" technology to enhance their learning or to engage their students. The cases represent differing student grade levels. The cases are different enough to provide a range that exercises the measurement techniques introduced in this study so results can begin to generalize across curricular programs and grades. However, the cases are similar enough in research design, instrumentation, and data collection methods to make them comparable. A key contribution of this investigation is the creation of a framework to measure the level of implementation (the extent to which the teacher and students display the actions, behaviors, and interactions expected by using the innovation). The unified conceptual framework arrived at by using an Activity Theory perspective together with the analytical methods employed provide a way to view the rich complex interaction of implementation as a system with the larger system of the school organization. Data from the analysis revealed that variations in the level of implementation were no different regardless of the level of specificity. A strong finding of this work is that implementation evolves slowly even when the curricular program is scripted and coaching support is provided to teachers. The paper concludes with implications for policy and future research.
A data-estimation-based approach for quasi-continuous seismic reservoir monitoring [electronic resource]
Keywords: Geophysics

Current strategies and logistics for seismic data acquisition impose restrictions on the calendar-time temporal resolution obtainable for a given time-lapse monitoring program. One factor that restricts the implementation of a quasi-continuous monitoring program using conventional strategies is the time it takes to acquire a complete survey. Here quasi-continuous monitoring describes the process of reservoir monitoring at short time intervals. This dissertation describes an approach that circumvents the restriction by requiring only a subset of a complete survey data each time an image of the reservoir is needed. Ideally, the time interval between survey subset acquisitions should be short so that changes in the reservoir properties are small. The accumulated data acquired are used to estimate the unavailable data at the monitor survey time, and the combined known and estimated data are used to produce an image of the subsurface for monitoring. Quasi-continuous seismic monitoring can be used to monitor geologic reservoirs during the injection phase of a carbon dioxide sequestration project. It can also be used to monitor reservoir changes between injector and producer wells during the secondary recovery phase in an oil field. The primary advantage of a quasi-continuous monitoring strategy over the conventional strategy is the high temporal resolution of the reservoir changes obtainable. Naturally, the spatial resolution of the image obtained using a subset of the data from a full survey will be worse than the spatial resolution of the image obtained using the complete data from a full survey. However, if the unavailable data are estimated perfectly, the spatial resolution is not lost. The choice of estimation algorithm and the size of the known data play an important role in the success of the approach presented in this dissertation.
Decision analytic approach to customer experience design [electronic resource]
Keywords: Management Science and Engineering

Customer experience influences purchasing behavior. How do we measure this subjective phenomenon called customer experience? What are the best approaches to design customer experience? In my dissertation I present a new approach to assessing customer experience using emotion cues, which is a departure from commonly used self-reporting methods like surveys. I also demonstrate a modeling approach to designing customer experience that can offer more actionable insights than best practices and basic principles. I call this the Decision Analytic Approach to Customer Experience Design.