VictorJuiz/thesis huggingface dataset:
Generic interconnectivity in fifteenth-century music [electronic resource]
Keywords: Music.

In his Dictionary of Musical Terms (ca. 1475) and Art of Counterpoint (1477), theorist and composer Johannes Tinctoris famously articulated a threefold hierarchy of music genres consisting of song, motet, and mass. Musicologists have traditionally attached significant weight to Tinctoris's tripartite scheme, analyzing each genre independently, considering the origins of each separately, and organizing modern editions in terms of genre. My dissertation focuses on the myriad ways in which musicians connected genres to one another in the fifteenth century, quoting secular songs in masses and motets; composing motets in the style of songs, re-texting songs so that they could be sung as motets, and subsuming liturgical chant into the texture and context of courtly songs; combining motets into substitute mass cycles, and even extracting mass sections and re-texting them as songs. Whereas some of these interconnections, masses based on songs in particular, have received a good deal of scholarly attention, others such as motets based on songs, have largely gone unrecognized. By considering genres not in isolation but in communication with one another, my dissertation makes the case for genre as a determinant of borrowing practices. Moreover, I argue that dissimilarity between genres was a driving force behind their commingling. Recognizing the significance and pervasiveness of generic interconnectivity sheds new light on some of the thorniest issues of the fifteenth century, including the style of Josquin's famous Ave Maria...virgo serena; the origins of and relationship between Ockeghem's D'ung aultre amer, the motet Tu solus, qui facis mirabilia, and the Missa D'ung aultre amer, both attributed to Josquin; and the motet cycle Vultum tuum.
Genetic control of T cell proliferation with synthetic RNA devices [electronic resource]
Keywords: Bioengineering.

The tools of synthetic biology offer the potential to design, construct, and reprogram natural biological systems. Programmed cells can interface with existing biological networks and introduce novel functionality that is otherwise difficult to reproduce from nature. Recent advances in the field have led to growing interest in constructing complex genetic systems in mammalian cells for various applications in health and medicine. One area that has gained significant interest is in cell-based therapy, where cells are used as therapeutic agents to treat diseases. In particular, the application of engineered autologous T cells for adoptive immunotherapy of cancer is currently under intensive translational research. This treatment modality has demonstrated remarkable success in clinical trials, but efficacy has been hampered by severe toxicities that were difficult to anticipate. Here, we present the development of RNA-based regulatory systems that can control T cell proliferation in response to a small molecule drug input. The RNA devices engineered in this work respond to (6R)-folinic acid, a pharmaceutical drug that is readily available and safe for prolonged administration in clinical settings. Through rational design and structural engineering, we constructed drug-responsive ribozyme- and miRNA-based devices to regulate the expression of transgenes and endogenous genes, respectively. To explore the possibility of implementing multiple layers of control, we further integrated the individual control systems into a single platform to exert stringent control over T cell proliferation. The RNA regulatory devices are also versatile and may be adapted more broadly for other therapeutic applications that require transgene or endogenous gene control.
Genetic fecal indicators [electronic resource] : environmental behavior and associated health risks
Keywords: Civil and Environmental Engineering.

Microbial source tracking (MST) markers that target bacterial DNA from the feces of particular animal hosts have been developed over the past two decades. Scientists, regulators, and managers are interested in using MST markers to better understand the problem of microbial contamination at recreational beaches. Certain knowledge gaps exist, however, that hinder our ability to interpret environmental measurements of MST markers. The goal of the research in this dissertation is (1) to characterize the fate and transport of the gull-associated MST marker, both absolutely and relative to Enterococcus (ENT), the standard fecal indicator; (2) to investigate through-beach transport as a pathway by which the gull marker and ENT reach the surf zone; and (3) to predict the health risks of swimming in water contaminated with a gull MST marker, or with a mixture of gull and human MST markers. Chapter 2 presents a study measuring the decay rates of a gull marker and ENT in beach sand and seawater. Indicator concentrations were measured over time in laboratory microcosms filled with natural beach sand and seawater. We found differences in the decay rates among indicators. Therefore, the ratio of indicators from a given contamination event will vary depending on how much time has elapsed since the event. Chapter 3 examines whether seawater circulating through nearshore sand can carry fecal indicators from sand to the surf zone. Laboratory column studies and numerical modeling were used to estimate transport rate coefficients. These transport rate coefficients, as well as decay rate coefficients from Chapter 2, were then input to a field-scale model to calculate transport distances. We found that through-beach pathways only allow the transport of fecal indicators over short distances. In Chapter 4, a Quantitative Microbial Risk Assessment (QMRA) is presented that predicts the probability of illness from swimming at a beach with gull fecal pollution. Monte Carlo simulations were carried out to find risk distributions for different concentrations of the gull MST marker. We found that risk is only elevated above a threshold level at beaches with very high gull impact. Chapter 5 is another QMRA, that examines the risk associated with swimming in water with both gull and human sources. We found that the source of the human marker matters: at all concentrations of the human marker, risk is much greater from a sewage source than a treated effluent source. In addition, we found that at a beach with both gull and human MST markers, the risk is determined by the human marker.
Genomic data compression and processing [electronic resource] : theory, models, algorithms, and experiments
Keywords: Electrical Engineering.

Recently, there has been growing interest in genome sequencing, driven by advancements in the sequencing technology. Although early sequencing technologies required several years to capture a 3 billion nucleotide genome, genomes as large as 22 billion nucleotides are now being sequenced within days using next-generation sequencing technologies. Further, the cost of sequencing a whole human genome has dropped from billions of dollars to merely \
Genomic responses to environmental variation and change in the ocean [electronic resource]
Keywords: Biology.

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.
Genomics and cell biology of symbiois in Aiptasia, a model system for coral-algal symbiosis [electronic resource]
Keywords: Genetics.

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.
Geometric deformations of orthogonal and symplectic galois representations [electronic resource]
Keywords: Mathematics.

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.
Geomorphically driven biogeochemical gradients and their influence on tropical forest canopies [electronic resource]
Keywords: Earth System Science.

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.
Global estimate of lightning energy injected into the earth's plasmasphere [electronic resource]
Keywords: Electrical Engineering.

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.
Global-mode helioseismology [electronic resource] : extensions of a well-used method
Keywords: Physics.

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.
Gopakumar-Vafa conjecture for genus 0 real Gromov-Witten invariants [electronic resource]
Keywords: Mathematics.

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.
Government bureaucrats in a postmodern world [electronic resource] : expectations, identity, and attacks
Keywords: Sociology.

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.