VictorJuiz/thesis huggingface dataset:
Genomic responses to environmental variation and change in the ocean [electronic resource]

Abstract Human activities are driving dramatic changes in the global environment. One consequence of this change is the rapid warming and acidification of the ocean. Throughout the Earth's history, sudden environmental change has often been associated with mass extinctions. However, in some cases species can adapt to changing environments via natural selection on heritable genetic variation. Most genetic variation, however, is not important for adaptation, and instead reflects the influences of mutation and drift on variants with minimal fitness consequences. For this reason, it has been difficult to assess the adaptive potential of populations and species even when genetic data are available. This thesis uses new genome-wide approaches to the analysis of the functional consequences of genetic variation to determine the spatial distribution and abundance of the functional genetic variation that could drive adaptive responses to environmental change. In the first chapter, I use gene co-expression network analysis to identify gene networks that mediate both fixed and plastic differences between coral colonies of the species Acropora hyacinthus in susceptibility to coral bleaching, the stress-induced breakdown of coral-dinoflagellate symbiosis. In the second chapter, I show that variation in gene expression within and between marine populations, including coral, abalone, mussels, and urchins, is often related to variation in the frequencies of genetic variants that change the expression of the allele on which they are found. In the third chapter, I show that persistent differences in the frequencies of genetic variants that cause changes in gene expression and protein sequence in stress-related genes are associated with the evolution of increased bleaching resilience in a cryptic lineage of Acropora hyacinthus. In the fourth chapter, I use low-coverage whole-genome re-sequencing of 114 coral colonies to identify "supergenes, " or closely linked co-inherited sets of multiple genes, that were associated with differences in bleaching outcomes during the third global bleaching event within and between cryptic species of Acropora hyacinthus. Taken as a whole, this thesis demonstrates the existence of high levels of functional diversity spread across contemporary environmental mosaics, and suggests that this diversity will play a critical role in assessing and managing the responses of populations to rapid anthropogenic change.

Keywords: Biology.
Advisor: Palumbi Stephen R.
Fraser Hunter B. advisor. Thesis advisor
Petrov Dmitri Alex
Sherlock Gavin advisor. Thesis advisor
Genomics and cell biology of symbiois in Aiptasia, a model system for coral-algal symbiosis [electronic resource]

The health and success of coral reef ecosystems is dependent upon the symbiotic relationship between coral animals and dinoflagellate algae (Symbiodinium spp.). Under thermal stress, corals can suffer from bleaching, a loss of Symbiodinium cells from the coral tissue that can be fatal during prolonged or severe stress. If stress is mild, corals can recover from bleaching through the repopulation of remaining Symbiodinium, or acquisition of new Symbiodinium from the environment. Despite the ecological importance of these processes, little is known about the molecular and cellular mechanisms underlying the establishment of coral-dinoflagellate symbiosis or its breakdown in bleaching. In this thesis, my collaborators and I use the small, symbiotic sea anemone Aiptasia as a model system for the study of cnidarian-dinoflagellate symbiosis. Using Aiptasia, we were able to test a popular hypothesis that the susceptibility of coral to bleaching is largely determined by the thermal tolerance of its algal symbiont and found that, indeed the type of algae hosted by an anemone had a strong effect on its susceptibility to bleaching, and that there was little effect of host genotype. Next, we examined the role of lectin-like proteins in the establishment of symbiosis and symbiosis specificity in Aiptasia. We identified several genes with homology to lectins that are differentially expressed between aposymbiotic and symbiotic Aiptasia. We recombinantly expressed one of these lectin-like proteins, Ctl1, and found that it bound preferentially to a type of algae that is incapable of establishing a symbiotic relationship with Aiptasia, suggesting a possible role in discriminating between different Symbiodinium types. Finally, to further the development of Aiptasia as a model system, we sequenced and assembled the Aiptasia genome. To search for genes and pathways that may be involved in symbiosis, we compared the genome of Aiptasia to the symbiotic coral Acropora digitifera, and to the anemone Nematostella, which does not have a symbiotic relationship with dinoflagellates. We identified a novel class of lectin-like genes that are enriched in the genome of the two symbiotic cnidarians, and may play a role in symbiosis establishment. The work presented here furthers our understanding of a symbiosis that is vital to the health of coral ecosystems and may provide tangible support to conservation efforts by identifying factors that contribute to susceptibility to bleaching and the ability to recover by acquiring novel symbionts.

Keywords: Genetics.
Advisor: Pringle John
Bassik Michael advisor. Thesis advisor
Fire Andrew Zachary advisor. Thesis advisor
Schneider David (David Samuel)
Geometric deformations of orthogonal and symplectic galois representations [electronic resource]

For a representation of the absolute Galois group of the rationals over a finite field of characteristic p, we would like to know if there exists a lift to characteristic zero with nice properties. In particular, we would like it to be geometric in the sense of the Fontaine-Mazur conjecture: ramified at finitely many primes and potentially semistable at p. For two-dimensional representations, Ramakrishna proved that under technical assumptions odd representations admit geometric lifts. We generalize this to higher dimensional orthogonal and symplectic representations. The key ingredient is a smooth local deformation condition obtained by analysing unipotent orbits and their centralizers in the relative situation, not just over fields.

Keywords: Mathematics.
Advisor: Conrad Brian
Venkatesh Akshay
Yun Zhiwei
Geomorphically driven biogeochemical gradients and their influence on tropical forest canopies [electronic resource]

The Peruvian Amazon is home to over half a million square kilometers of tropical forest, more than three quarters of which exists on terrace landforms. The characteristics of terrace ecosystems have been contrasted with neighboring floodplains and compared with terraces of different ages, but the ecological and biogeochemical complexity that exists within these landscapes has not been studied in detail. These landforms are often considered to be relatively homogeneous, despite the fact that they are subject to dynamic processes driven by ongoing landscape evolution. In this dissertation, I consider the role of geomorphic gradients and biogeochemical processes in determining soil and foliar nutrient distributions across a terrace formation in Los Amigos Conservation Concession (LACC) in the southern Peruvian Amazon. I seek to determine whether the evolution of terrace landscapes has a material effect on soil properties along hillslopes and whether the interplay of topographic position and differing resource availability determines the spatial patterns of foliar nutrient concentrations of canopy trees. Chapter 2 focuses on uncovering patterns in soil concentrations of rock-derived nutrients across hillslopes with differing morphologies, as well as identifying the processes that drive these patterns. I found that hillslope erosion, driven by stream incision, is causing nutrient rejuvenation within this landscape, and that calcium in particular is tightly retained through biotic cycling by the ecosystem. Chapter 3 demonstrates that airborne high fidelity imaging spectroscopy data can be used to predict canopy foliar nutrient concentrations, as well as leaf mass per area, at the scale of emergent canopies across floodplain and terrace landforms within LACC. In Chapter 4, I utilize the understanding of soil nutrient distributions gained in Chapter 2, and the high resolution maps of canopy foliar nutrient concentrations developed in Chapter 3, to consider the role of geomorphic processes in controlling the spatial distributions of canopy foliar nutrient concentrations. Through these studies, I determine that hillslope and biotic processes drive biogeochemical gradients that are reflected in both soil nutrient availability and foliar nutrient concentrations within a terrace landform in the lowland Peruvian Amazon. These findings suggest that fine scale geomorphic processes play a significant role in determining spatial distributions of biogeochemical and ecosystem processes across tropical lowland terrace landscapes.

Keywords: Earth System Science.
Advisor: Asner Gregory P. primary advisor. Thesis advisor
Fendorf Scott advisor. Thesis advisor
Field Christopher B. advisor. Thesis advisor
Vitousek Peter Morrison advisor. Thesis advisor
Global estimate of lightning energy injected into the earth's plasmasphere [electronic resource]

Generated by lightning, 'whistlers' are electromagnetic waves that propagate through the plasma surrounding the Earth in near-Earth space known as the plasmasphere. Electromagnetic waves propagating in the plasmasphere can influence the Van Allen radiation belts, a collection of highly energetic, charged particles surrounding the Earth and trapped by the Earth's magnetic field. In particular, energy from these waves can reduce the number of electrons in the radiation belts by causing them to precipitate into the lower atmosphere. Therefore, an estimate of the amount of energy input into the radiation belts from electromagnetic waves like lightning-generated whistlers is vitally important to our understanding of the nature and dynamics of this important part of our planetary environment. Previous estimates of lightning energy in the plasmasphere failed to take into account such considerations as the distribution of lightning across the globe and the effect of the ionosphere on whistler propagation, both of which we examine here. We first present a method to automatically identify upgoing whistler waves using measurements taken from low Earth orbiting satellites. The algorithm computes cross-correlations of the frequency-time spectrogram of the wave data with the expected shape of an upgoing whistler to determine whether or not a given set of data corresponds to a whistler. The technique is validated using data from the DEMETER satellite, and an FPGA-based real time implementation of the algorithm has been built to fly on board the TARANIS satellite, scheduled to launch in 2018. Next, we provide a calculation of the lightning energy injected into the plasmasphere using a frequency domain finite element electromagnetic full wave simulation known as the full wave method (FWM) to quantitatively model the propagation of electromagnetic waves through any number of horizontally stratified layers of plasma such as the ionosphere. We first compare the FWM predicted amount of lightning energy propagating upward with extensive available measurements from the DEMETER satellite. Our comparisons indicate that the field intensities determined by the FWM tend to underestimate the measured energy from DEMETER by as much as 6 dB, although we also present evidence suggesting that the calibration of the DEMETER data may be inaccurate. Finally, we use the FWM to map the upgoing amount of electromagnetic wave energy propagating from each point on Earth for an arbitrary source. By then scaling with data on lightning occurring at each point on Earth as given by the Vaisala Global Lightning Dataset (GLD360) lightning detection network, we arrive at a global estimate of the lightning energy injected into Earth's plasmasphere. Our estimate is comparable to though slightly lower than previous estimates yet provides a more detailed picture of the distribution of lightning in the plasmasphere.

Keywords: Electrical Engineering.
Advisor: Inan Umran S. primary advisor. Thesis advisor
Poon Ada Shuk Yan
Gill John T.
Linscott Ivan advisor. Thesis advisor
Global-mode helioseismology [electronic resource] : extensions of a well-used method

Global-mode helioseismology has been used extensively to precisely infer the detailed properties of the solar interior. Multiple algorithms have been applied to several different datasets, which now span over two solar cycles. This dissertation deals primarily with two instruments, namely the Michelson Doppler Imager (MDI) onboard the Solar and Heliospheric Observatory, and the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory. For MDI, we have two velocity datasets spanning the 15 years from 1996 to 2011: high-resolution images which were taken for a few months each year, and low-resolution images which were taken almost all the time. For HMI, we have even higher resolution velocity images taken since 2010. Unlike MDI, HMI also provides intensity data. The initial motivation for this study was to address known systematic errors in the analysis of MDI data, as well as discrepancies with inferences drawn by other projects, most notably the Global Oscillation Network Group. In particular, the MDI results indicated a high-latitude peak in the solar rotation rate, which is now believed to be spurious. Also, certain fits resulted in normalized residuals that indicate the fit is not using the correct model. Lastly, MDI saw an annual periodicity in frequency shifts, which can only be because of errors in geometry. Now that MDI is no longer operating, it has also become important to achieve continuity between the MDI and HMI datasets. To that end, both have been processed in their entirety using the same set of software. Since the original software was written when computational capabilities were far less than now, this involved the application of several updates. At the same time, we have adopted better models of the physics behind the oscillations and applied various geometric corrections. In this dissertation we investigate how these changes affected the global-mode parameters from the MDI analysis and the systematic errors therein. We then apply the fully updated analysis to the HMI data, and make a comparison of mode parameters derived from the various datasets from the two instruments. We find methods that decrease or eliminate the systematic errors mentioned above. Hence, inferences of the Sun's interior rotation have become more robust. Further, the comparison between MDI and HMI encourages the concatenation of their datasets, which may allow for the detection of new oscillation modes.

Keywords: Physics.
Advisor: Scherrer Philip H.
Church Sarah Elizabeth advisor. Thesis advisor
Schou Jesper (Scientist)
Gopakumar-Vafa conjecture for genus 0 real Gromov-Witten invariants [electronic resource]

The Gopakumar-Vafa conjecture arising from string theory states that BPS counts of a Calabi-Yau 3-fold (obtained from Gromov-Witten invariants using a power series formula) are integers. A symplectic version of the conjecture was proved by Ionel-Parker. In this thesis we prove a generalization of the symplectic Gopakumar-Vafa conjecture to the case of real Gromov-Witten invariants. Namely, real genus 0 BPS states of a Calabi-Yau 3-fold with an anti-symplectic involution (which are obtained from real genus 0 Gromov-Witten invariants) are integers. The proof combines topological methods from Ionel-Parker's proof of the original conjecture and Katz-Liu's computation of local BPS counts.

Keywords: Mathematics.
Advisor: Ionel Eleny primary advisor. Thesis advisor
Eliashberg Y.
Lin Yu-Shen
Government bureaucrats in a postmodern world [electronic resource] : expectations, identity, and attacks

This dissertation is comprised of three distinct papers that address how identity creation processes affect occupational choice and workplace behaviors in the US public sector. The first paper investigates public service motivation (PSM) as the dominant rationale for choosing public sector work among educated bureaucrats. In the second paper, I examine how white-collar public workers construct their own workplace identities. Specifically, I investigate how white-collar bureaucrats' workplace identities reflect the increasing professionalization of white-collar public sector work relative to the existing union structure in public agencies. In the final paper, as in the first two, I explore the ways in which identity, values, and context explain generational stratification in mobilization patterns among white-collar, government bureaucrats, despite their connection to unions as mobilizing structures. Specifically, I look at mobilization against Wisconsin's Act 10 and Minnesota's state government shutdown, as a means for understanding differential recruitment within these preexisting mobilization networks.

Keywords: Sociology.
Advisor: McAdam Doug primary advisor. Thesis advisor
Fields Corey advisor. Thesis advisor
Grusky David B. advisor. Thesis advisor
Graded index immersion optics with application as solar concentrators [electronic resource]

Axially Graded Index LEns (AGILE), as an effective non-tracking concentrator, was conceptualized, simulated, and fabricated. The results demonstrated how modes/optical power can be confined in a smaller volume in a high refractive index media and paved the way for a passive concentration system coupled to solar absorbers with optical and mechanical bonding, which saves PV (Photo-Voltaic) material cost, and provides space for cooling and circuitry. Most importantly, AGILE prototypes were fabricated in straightforward, inexpensive, and scalable processes. Simple to test and verify, back-to-back AGILEs demonstrated a concentration of up to 10 suns (geometric area ratio) and tracked the theoretical simulations. AGILE is a simple device that rests on fundamental laws and has the potential to greatly improve solar conversion systems by reducing cost, increasing efficiency, and providing a robust modular design with natural anti-reflection and encapsulation. The operational principle of the AGILE is based on the fact that the number of states of an optical aperture is proportional to the square of the Refractive Index (RI), which allows loss-free concentration by a factor of square of RI. Development of AGILE into a practical technology presented substantial challenges in material science and fabrication techniques. After exploring various techniques for making graded index and fabricating optical devices with glass bonding and curing of polymer films, high-quality optics were also fabricated using 3D printing and smoothing technique. A UV gel smoothing technique that can be used with commercial 3D printers (resolution of tens of microns) was conceptualized and developed, and the optical surfaces fabricated gave a rms (root mean square) surface roughness of around 2 nm. Optical components made using 3D printing including mirrors, lenses, and solar concentrator arrays were demonstrated and tested. 3D printing ushers in a new era in optical device fabrication. This 3D printing technique was also used to fabricate and demonstrate high concentration AGILEs of up to 10 suns. Ultimately, AGILE requires transparent, robust, and broadband transparent materials with RI (Refractive Index) gradually ranging from 1 to 3.5 and beyond. Evolution of the AGILE basic structure into a more sophisticated design will involve a robust lens top surface, an optimized side wall profile, and a radial as well as an axial index gradient with nano structuring to couple light from the concentrator to the solar cell. The AGILE fabrication process, once transferred as a commercially technology, has the potential to not only change the way we concentrate light (applications also in illumination, coupling, anti-reflection coatings, and displays), but also the economy and adoption of solar power.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav primary advisor. Thesis advisor
Dauskardt R. H. (Reinhold H.) advisor. Thesis advisor
Fan Shanhui
Graphics processing unit accelerated tensor hypercontraction for high performance computing [electronic resource] : a reduction in computational cost of Ab initio methods

Often, the computation of molecular properties requires an accurate description of the electronic wavefunction. Unfortunately, the accuracy and computational demands of a method are typically at odds with each other. In order to reduce the computational demands of ab initio methods, we have developed the tensor hypercontraction approach. In this work, we will show how the tensor hypercontraction approximation improves the efficiency of electronic structure methods while maintaining the accuracy of the underlying ab initio approach. This work focuses on the use of tensor hypercontraction in second-order Møller-Plesset perturbation theory (MP2), second-order approximate coupled cluster singles and doubles (CC2), and the extension of CC2 for excited state computations. Recently, the high performance computing industry has incorporated the use of graphics processing units (GPUs) for general purpose computing. GPUs are massively parallel architectures that are being used to accelerate computationally intensive approaches in a variety of fields, including quantum chemistry. I will show that the tensor hypercontraction methods are highly amenable to parallelization techniques and demonstrate a performance improvement for parallel tensor hypercontraction via parallelization across compute nodes and acceleration with GPUs. I will demonstrate that the use of parallel approaches allows us to extend the applicability of tensor hypercontraction CC2 and excited state computations to chemical system sizes that are challenging for canonical CC2.

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Markland Thomas E.
Ying Lexing advisor. Thesis advisor
The great elector's table [electronic resource] : food and the rise of Brandenburg-Prussia, 1640-1688

This dissertation reexamines the rise of Brandenburg-Prussia in the seventeenth century through the lens of food culture. It explores the ways that culture, politics, the natural environment, and science intertwined to define taste at the court of Friedrich Wilhelm (1640-1688). I argue that the decisions about everyday life at court were fundamental to the larger growth of the power of this court on the European political stage and its consolidation of power at a time when most central European states fell into obscurity. This work offers an alternative to the traditional military and bureaucratic narratives of the rise of Prussia. Instead, this dissertation views the military and bureaucratic accomplishments of this dynasty as part of a wider cultural program that shaped the consolidation of the state. In studying the economic, environmental, social, and political dynamics in choices about food at court, this work exposes the micro-decisions that determine the identity of any state.

Keywords: History.
Advisor: Stokes Laura
Findlen Paula advisor. Thesis advisor
Lougee Carolyn Chappell advisor. Thesis advisor