VictorJuiz/thesis huggingface dataset:
Ecological and evolutionary connections between genetic and species diversity [electronic resource]
Keywords: Biology.

Understanding the causes and consequences of biological diversity remains the unifying goal of ecology and evolutionary. One promising avenue to understand the causes and consequences of genetic diversity within populations is to consider correlations between that genetic diversity and species diversity of the community in which it resides. Both genetic and species diversity can respond to locality characteristics, or each level can influence and be influenced by the other. First, I investigate how area connectivity and gene flow affects the population genetic diversity patterns in the California vole (Microtus californicus). I show that migration across the landscape produces an identical genetic patterns at the local and regional spatial scales in this small mammal (Chapter 1). Next, I explored two ways in which genetic and species diversity influence each other. In one approach, I examine the effects of a species-rich competitor community on the genotypic diversity of a focal community when genetic diversity allows for differential strength of competition with different species. Using computer simulations, I show that species diversity of competitors can act as an important promoter of genotypic diversity within species (Chapter 2). Next, moving to a riparian community in northern Utah, I demonstrate that the genetic diversity of a foundation tree correlates positively with the species diversity of understory plants, including forbs, grasses, and vines (Chapter 3). Finally, I show that both genetic diversity and species richness across the globe show a similar pattern: genetic markers in over 70 vertebrate species show a significant trend of higher diversity at low latitudes than at higher latitudes (Chapter 4). By taking a broad approach to understanding the causes and consequences of intraspecific genetic diversity, with a particular focus on links to species diversity patterns, my dissertation finds general principles that operate across systems. The two levels of diversity can influence each other by creating spatially-varied selection regimes, but gene flow and mutation are two processes operating on the genetic level whose power to scale up to influence species-level patterns is highly contextual.
Ecological importance of large fishes [electronic resource]
Keywords: Biology

In this dissertation I explore how ecosystems change when their largest faunal residents are removed. Specifically I consider how coral reef ecosystems respond to the removal or depletion of a variety of functionally and taxonomically unique large reef fish. There are seven chapters in this thesis. Chapter 1 critically examines the performance of four methods for estimating coastal shark abundance. I compare outputs from field survey trials conducted at Palmyra to results from computer simulations to evaluate the efficacy of these selected methods. In Chapter 2 I present the results of an experiment conducted at our near-pristine reef site where I excluded large fish and tracked the effects of their absence. I observed that the removal of these larger ecosystem constituents affected a variety of responses including algal growth, fish behavior, and invertebrate recruitment. These changes occurred rapidly and were observed to interact in complex ways with one another. Chapter 3 relies on the use of stable isotopes to identify how large fish build linkages across ecosystems. I use isotopes of C and N and mixing models to determine what energy sources large reef predators rely upon and to infer how these utilization patterns influence ecosystem connectivity and functioning. In Chapter 4 I examine some provocative observations made in unfished and fished reefs which suggest that large fish predators control the temporal niche structure of their prey. I observed that the removal of day-time active predators from fished reefs appears to have caused an increase in the abundance of nocturnal prey fishes. Chapter 5 is an investigation of the functional ecology of the world largest parrotfish B. muricatum. Using this animal as a model, I consider how ecologically dominant animals affect the functioning of ecosystems. Conclusions are drawn from intensive field observation and simulation exercises. Chapter 6 utilizes a diversity of research approaches (biogeochemical tools, ecological surveys, animal tracking) to chronicle a long ecological interaction chain that links forests to manta rays. By contrasting processes in disturbed and undisturbed study sites I consider how anthropogenic disturbance more generally affects the length of ecological interaction chains. Finally, in chapter 7 I discuss the importance of protecting remote ecosystems that often harbor intact communities of large animals. I argue that extremely remote environments are critically important and yet vulnerable repositories of biodiversity and I review how existing conservation strategies may be adapted to help protect these special environments.
Ecological studies on seed dispersal networks [electronic resource] : insights from a diverse tropical ecosystem
Keywords: Biology.

Mutualisms between animals and plants, such as pollination, seed dispersal and ant-plant protection, are key ecological processes in many ecosystems throughout the world. Like any other ecological interaction, plant-animal mutualisms occur in a community context. Therefore, one-to-one interactions are very rare in nature and the majority of species, both animals and plants, have more than one partner. Recently, studies on mutualistic interactions at the community level have used the "network approach" in order to simplify complex interactions and to determine both the pattern of interaction and the properties of species in networks. In this dissertation, I use network theory combined with long-term field work, phylogenetic and multivariate analysis, species extinctions simulations and experimental manipulation to identify the pattern of interaction in a seed dispersal network, to assess the contribution of particular animal species to network stability and robustness, and to address the extent to which seed dispersal interactions can structure plant communities. To do so, I studied a hyper-diverse seed dispersal network sampled in the Brazilian Pantanal, which includes interactions among plant species from 28 families and seed dispersers, both native and exotic species, from 25 families and 4 taxonomic groups. This study contributes novel information on seed dispersal at the community level, especially because I examined a diverse and relatively complete seed dispersal network, which may provide insights for other diverse systems, especially in the tropics. Besides generating information on the ecology and evolution of plant-animal interactions, this study also shows that not all seed disperser species are equal at the community level; and body size of dispersers seem to be a useful proxy of relative importance for dispersal services. Since contemporary defaunation differentially affects species depending on body size, this work illustrates how human activities, such as hunting, land use and climate change, affect not only taxa, but also crucial processes in which animals of different body size play different roles. This study emphasizes that conservation science needs to look at the conservation of ecological processes driven by species interactions.
The effect of grain boundaries on scintillation in rare-earth doped transparent ceramics [electronic resource]
Keywords: Materials Science and Engineering

The need for large-scale, low-cost, novel materials for the active component in nuclear detector systems has sparked an interest in optically transparent ceramic scintillators as an alternative to single crystals. Ceramics may be produced in large sizes and to near net shapes, using standard methods of ceramic forming and sintering. Additionally, bulk slabs of certain materials compositions that may not be accessible by single-crystal growth may be produced as ceramics. Although ceramic scintillators have been used in commercial CT scanners for some time now, in other applications, they have not reached the levels of performance that single-crystal scintillators have. Research into the properties of ceramic scintillators has been restricted to a small number of materials, processed under a limited number of conditions. Many studies on ceramic scintillators point to possible "defects at the boundaries" as a source of degraded scintillator performance and an origin of deep trapping, but the true effect of grain boundary defect states on scintillator performance has not been well-characterized. Additionally, the unique processing methods required to produce not only dense, but transparent ceramics had only been used on a handful of materials prior to 15 years ago, and limited work has been done on materials with non-cubic crystal structures. In order to address these two limitations, this dissertation focuses on the sintering and scintillation properties of ceramics of three model materials, Eu:Y2O3, Ce:Y3Al5O12 (Ce:YAG) and Eu:SrI2. Transparent ceramics of these materials were sintered, including non-cubic Eu:SrI2 for the first time by inducing grain texture in ceramics of the material. Eu:SrI2 ceramics were found to have as proportional a response as single crystals and a light yield of 25% of single crystals and 55% of Tl:NaI. Through parametric studies of ceramic processing parameters, grain size, and bulk scintillation, the effect of grain boundaries on scintillator performance was compared to that from other sources of charge carrier trapping and light yield degradation. Using models for charge carrier generation and transport in a ceramic and a new micro-scintillation technique, X-ray radioluminescence microscopy, the localized effect of grain boundaries on scintillation was also characterized. Based on these micro-scale studies, a greater understanding of the effect of grain boundaries on bulk scintillation was developed. Based on the conclusions of these sintering and scintillation studies, a number of criteria are suggested for identifying new and existing scintillator materials that may be of interest for further investigation as ceramics, because of their potential to maintain high levels of scintillator performance and optical transparency when fabricated in ceramic form.
The effects of college diversity experiences on student academic and democracy outcomes [electronic resource]
Keywords: Education.

Institutions of higher education claim they prepare their students to be leaders and positive contributors to society. In pursuit of these aims, institutions promote opportunities for diversity experiences among schoolmates. The legality of these claims has been challenged in court, and social science research on the effects of diversity experiences has played a pivotal role in shaping court rulings. Mixed results in previous studies and important unexamined questions in this research area prompt this examination of college diversity experiences. Classroom-based experiences, participation in diversity events, and the informal interactions students have with racially/ethnically dissimilar schoolmates are the foci of the study. Their relationships with democracy and academic outcomes are examined, and investigative emphasis is placed on the racial/ethnic heterogeneity of friendship groups and the relative position of students as outliers or majority-group members in primarily racially/ethnically homogeneous friendship groups. In addition to analyses of the full sample of University of Michigan students, analyses are performed on students based on their primary racial/ethnic identification and their status as racial/ethnic outliers or majority-group members. The results suggest that the three types of college diversity experiences benefit students. They are orthogonal to student outcomes for Asian-Americans, but significant positive relationships are seen across the analyses of White and Underrepresented Minority student groups. Outliers appear to benefit from diversity experiences in fewer ways than majority-group members, but the results are equivocal due to a statistical power issue. Implications for the research community are discussed.
Effects of priming and work relationship on linguistic alignment in computer-mediated communication and human-computer interaction [electronic resource]
Keywords: Communication

People engaged in a conversation tend to express themselves in similar ways by using comparable or identical words, phrases, sentence structures, accent, speech rate, etc. This process and end results are termed "linguistic alignment, " and have also been observed in both computer-mediated communication (CMC) and human-computer interaction (HCI). Many researchers have demonstrated that linguistic alignment can be easily induced through priming, while others focus on the social aspect of linguistic alignment. Moreover, previous research work on linguistic alignment mostly focused on conversation within dyads. In this dissertation, I report two experimental studies that, in the context of a triadic conference chat setting, investigated the co-presence of alignment as a result of priming and alignment attributable to difference in work relationship (cooperation vs. competition). Similarities and differences observed in the HCI and CMC conditions were also examined. Results show that priming is a strong predictor of alignment even when interlocutors do not directly communicate with each other, but work relationship between interlocutors and communication type (i.e., HCI vs. CMC) could also sway the degree of alignment. Additionally, the priming effect on certain stylistic dimensions (e.g., vocabulary complexity) lasted relatively longer than the effect on other features (e.g., capitalization). As a whole, the dissertation proposes a holistic way of examining and understanding linguistic alignment, and offers researchers a new methodology utilizing realistic user contexts and tasks to study human language behaviors in general and those specific to HCI and CMC.
The effects of viscoelasticity on the transitioning cylinder wake [electronic resource]
Keywords: Mechanical Engineering

Using a newly developed three dimensional, time dependent finite volume code designed to compute non-Newtonian flows over a large range of Reynolds number (Re), we performed simulations of viscoelastic flow past a circular cylinder. Our goal was to elucidate elastic effects during transition to turbulence in a bluff body wake. Based on its ability to capture essential physical processes in turbulent drag reduction studies, the FENE-P rheological model was employed in the calculation, and the numerical method utilized was such that a large range of rheological parameters (polymer length L, dimensionless Weissenberg number (Wi), and polymer concentration (beta) in the FENE-P model) could be probed. Simulations were performed for Reynolds numbers ranging from Re = 100 to Re = 3900. Within this range, the Newtonian cylinder wake first undergoes a series of secondary instabilities, transitioning the wake structure from a two-dimensional, laminar vortex shedding state to one exhibiting three-dimensional motion. This transition is characterized first by the mode A instability, which develops in the region of primary vortex development at a Reynolds number of Re = 190. The mode B instability then follows at Re = 260, resulting from unstable perturbation growth in the braid region between primary vortices. At still higher Reynolds numbers, Re = O(1000), the separated shear layer immediately behind the cylinder begins to transition prior to primary vortex shedding. Through nonlinear simulations as well as a Floquet linear stability analysis, viscoelasticity was observed to stabilize both regimes of three-dimensional transition. Full nonlinear simulations revealed that for high enough polymer extensibility L at Re = 300, where mode B instability structures dominate for Newtonian flow, the wake could be reverted back to a state resembling two-dimensional, laminar vortex shedding. This was then confirmed using a Floquet stability analysis, showing significantly suppressed growth rates for both the mode A and mode B instabilities in the linear regime of their development. Mechanisms of this stabilization are presented. At Re = 3900, viscoelasticity again stabilizes the flow, though at this point through a suppression of the Kelvin-Helmoltz rollup instability present in the separated shear layer for Newtonian flows. Once a primary Karman vortex is allowed to form without the influence of a transitioned shear layer, the wake then reverts back to one resembling the mode B instabilities. Confirming this, a study was then performed at the same Reynolds number but allowing for an inhomogeneous polymer concentration throughout the flow field. By injecting polymer additives on the upstream side of the cylinder, it was found that stabilization of the shear layer and of the subsequent wake could be achieved without the presence of polymeric stresses in all downstream locations of the flow.
Efficiencies of slowness [electronic resource] : the politics of contemporary collective creation
Keywords: Drama

This project focuses on the process and performance of three contemporary collective creation groups: Goat Island, Elevator Repair Service, and Nature Theater of Oklahoma. I draw processual and aesthetic connections between collective creation methodologies and the consequences of those methodologies in performance, claiming that processes leave footprints that are ultimately visible to audiences, though their visibility requires new ways of seeing. Taking into account an American genealogy of collective creation, I outline the footprints of method through the images of everyday employment, instances of untrained bodies enacting danced gesture, and the speeds and velocities that characterize the work of these three contemporary groups. Through these aesthetics we can locate evidence of methodological principles that constitute a politics. In the work of Goat Island, Elevator Repair Service, and Nature Theater of Oklahoma, this politics does not play out through the ideological content of performance, but is embedded within collaborative acts of making.
Efficient access to bryostatin and functional bryostatin analogs [electronic resource] : design, synthesis and evaluation of potent bryostatin analogs and the total synthesis of bryostatin 9 using B-ring annulative macrocyclization strategies
Keywords: Chemistry

The bryostatins are a family of structurally complex natural products isolated from the marine bryozoan Bugula neritina. Bryostatin 1 is currently being investigated for cancer, Alzheimer's and HIV/AIDS indications. Despite these remarkable activities, research on the bryostatins is hampered by their low natural abundance. Efficient access by total chemical synthesis has been in large part precluded by the bryostatins' structural complexity. This dissertation describes the design, synthesis, and preliminary biological evaluation of functional bryostatin analogs that possess biological activities comparable or superior to the natural product. These fully synthetic analogs were convergently assembled in a uniquely step-economical manner using novel macrocyclization strategies, including macroacetalization and Prins-driven macrocyclization approaches. Bryostatin analogs were identified that possess unique affinities (subnanomolar) and selectivities for protein kinase C (PKC). Synthetic bryostatin analogs also exhibit subnanomolar antileukemic activity in in vitro assays. The convergent total synthesis of bryostatin 9, a highly potent congener of the natural product family, is also described.
Electrical and optical characterization of molecular junctions [electronic resource]
Keywords: Chemical Engineering

Electronic transport through molecules has been intensively studied in recent years, due to scientific interest in fundamental questions about charge transport and the technological promise of nanoscale circuitry. A variety of experimental platforms have been developed to electronically probe molecular junctions. However, it remains challenging to fabricate reliable electronic contacts to molecules, and the vast majority of molecular electronic architectures are not amenable to standard characterization techniques, such as optical spectroscopy. Interesting phenomena like switching and rectification are observed in molecular junctions. However, due to limited quantitative information about the junction, the mechanism remains unknown and many fundamental questions about electronic transport remain unanswered. The first part of the thesis will introduce the fabrication of Metal-Insulator-Metal (MIM) cross bar junctions using soft deposition technique. In this method, we softly deposit the premade metal contacts that are being supported with a polymer backing layer onto the organic layer. Using this method, we can efficiently fabricate large area, non-shorting devices, which are required for optical characterization of the molecular junctions. Having established a means of fabricating reliable molecular devices, we have investigated the switching mechanism in molecular junctions based on n-type semiconductor Perylene tetracarboxylic diimide (TE-PTCDI) molecules. Using Surface Plasmon Resonance Spectroscopy (SPRS) we have been able to perform simultaneous optical-electrical measurements to study the molecular behavior quantitatively. Using in- situ optical spectroscopy on active molecular junctions, we find that only a small fraction of the molecules are actually switching in the junction. Next, metal filament formation, a common phenomenon in thin film devices has been investigated. Metal filaments are observed to lead to non-molecular conductance variations in molecular junctions. Employing electrical and optical methods, the possible mechanisms responsible for the formation of metal filaments in the junction were studied. Finally, I present the results of our studies on the molecular rectification in C60- diamondoid hybrid molecules in large area junctions, as well as in smaller ensemble of molecules.
Electroabsorption mechanisms in germanium quantum well material [electronic resource]
Keywords: Electrical Engineering

One possible solution to make viable optoelectronic modulators that meet strict targets down to the scale of on-chip communication is to use germanium-rich materials. Ge/SiGe quantum wells grown on silicon substrates provide the strongest mechanism, the quantum-confined Stark effect (QCSE), and thereby can meet the strictest requirements for optical interconnects, including CMOS-compatibility. Using such a strong effect, Ge-based modulators can be ultra-compact, ultralow-power, large bandwidth and high-speed, making them a strong contender for the future of optoelectronic device integration to solve the bottleneck problem. In this thesis, we will discuss the physical properties of the Ge and SiGe material system then present designs of optoelectronic modulators at the important 1310 nm and 1550 nm communication wavelengths using a program we developed called the Simple Quantum Well Electroabsorption Calculator (SQWEAC). SQWEAC takes the important physical mechanisms present, such as QCSE and indirect absorption, to predict the electroabsorption profile of Ge-based quantum wells. QCSE was experimentally determined on a wide range of samples to show the predictive powers of SQWEAC. Additionally, indirect absorption was also experimentally determined to optimize the physical model for these Ge quantum well devices. In being able to design both 1310 nm and 1550 nm devices using this Ge material system, we provide a platform for designing optoelectronic devices that are Si CMOS compatible and operate over a wide range of wavelengths. These modulators have the capability of providing the large density of information at very low energies per bit required for future interconnect technologies.