VictorJuiz/thesis huggingface dataset:
The Water Neutron Detector (WaND)

The Water Neutron Detector (WaND) is an efficient and non-toxic alternative to some helium-3 neutron counting applications. The detection volume is comprised of a 1.02 cubic meters homogeneous mixture of deionized water doped with 0.5% gadolinium chloride. Following neutron capture, gadolinium emits an 8 MeV gamma shower, which in turn creates Cherenkov light that can be detected with photomultiplier tubes. The WaND is particularly well-situated to perform multiplicity counting of small samples because of its high efficiency of (23.4 +/- 0.8)% and short die-away time (15 microseconds). Due to the moderate gamma sensitivity, the WaND system may be suited for neutron-based nondestructive assay of small quantities of spent fuel. It is effective at measuring and identifying minute quantities of plutonium. Using a novel algorithmic approach, the WaND system can effectively differentiate between Cf-252 and Pu-240, as well as quantify the mass of Pu-240 in milligram quantities.

Advisor: van Bibber, Karl
Dazeley, Steven
Leveraging latent structure in high-dimensional data: causality, neuroscience, and nonparametrics

Many scientific fields have been changed by rapid technological progress in data collection, storage, and processing. This has greatly expanded the role of statistics in scientific research. The three chapters of this thesis examine core challenges faced by statisticians engaged in scientific collaborations, where the complexity of the data require use of high-dimensional or nonparametric methods, and statistical methods need to leverage lower dimensional structure that exists in the data./nThe first chapter concerns the promise and challenge of using large datasets to uncover causal mechanisms. Randomized trials remain the gold-standard for inferring causal effects of treatment a century after their introduction by Fisher and Neyman. In this chapter, we examine whether large numbers of auxilary covariates in a randomized experiment can be leveraged to help improve estimates of the treatment effect and increase power. In particular, we investigate Lasso-based adjustments of treatment effects through theory, simulation, and a case study of a randomized trial of the pulmonary artery cathether. In our investigation, we avoid imposing a linear model, and examine the robustness of Lasso to violations of traditional assumptions./nThe second chapter examines the use of predictive models to elucidate functional properties of the mammalian visual cortex. We investigate the activity of single neurons in area MT when stimulated with natural video. One way to investigate single-neuron activity is to build encoding models that predict spike rate given an arbitrary natural stimulus. In this work, we develop encoding models that combine a nonlinear feature extraction step with a linear model. The feature extraction step is unsupervised, and is based on the principle of sparse coding. We compare this model to one that applies relatively simple, fixed nonlinearities to the outputs of V1-like spatiotemporal filters. We find evidence that some MT cells may be tuned to more complex video features than previously thought./nThe third chapter examines a computational challenge inherent in nonparametric modeling of large datasets. Large datasets are often stored across many machines in a computer cluster, where communication between machines is slow. Hence, nonparametric regression methods should avoid communication of data as much as possible. Random forests, among the most popular nonparametric methods for regression, are not well-suited to distributed architectures. We develop a modification of random forests that leverage ideas in nonparametric regression by local modeling. Our method allows for training of random forests completely in parallel, without synchronization between machines, with communication of sufficient statistics at test-time only. We show that this method can improve the predictive performance of standard random forests even in the single-machine case, and that performance remains strong when data is distributed.

Advisor: Yu, Bin
Cracking the Cas: Investigations into CRISPR RNA-guided bacterial immunity

In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)–/nassociated (Cas) DNA-targeting complex Cascade (CRISPR-associated complex for/nantiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets/nat sites adjacent to a trinucleotide signature sequence called the protospacer adjacent/nmotif (PAM). The Cascade complex then recruits Cas3, a nuclease-helicase that/ncatalyzes unwinding and cleavage of foreign double-stranded DNA (dsDNA) bearing a/nsequence matching that of the crRNA. Cascade comprises several Cas proteins and one/ncrRNA, forming a structure that binds and unwinds dsDNA to form an R-loop in which the/ntarget strand of the DNA base pairs with the RNA guide sequence./nSingle-particle electron microscopy reconstructions of dsDNA-bound Escherichia coli/nCascade with and without Cas3 reveal that Cascade positions the PAM-proximal end of/nthe DNA duplex at the CasA subunit and near the site of Cas3 association. The finding/nthat the DNA target and Cas3 co-localize with CasA implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the/nPAM region is unnecessary for target binding but critical for Cas3-mediated degradation./nIn addition, the L1 loop of CasA, previously implicated in PAM recognition, is essential for/nCas3 activation following target binding by Cascade. Together, these data show that the/nCasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA/ntarget sites and positioning Cas3 adjacent to the PAM to ensure cleavage./nThough the E. coli Cascade complex is well-studied, other Type I systems remain/nrelatively mysterious. We wondered how Desulfovibrio vulgaris Cascade/I-C could form/nand function with just three distinct subunits, fewer than any other Type I or III interference/ncomplex. Cas5c recognizes and cleaves the crRNA repeat via interactions with the 5′/nhandle region to which it remains associated. Cas5c binds to Cas7, which oligomerizes/ncooperatively along the crRNA, capped by the crRNA stem-loop. Interactions with Cas5c,/nCas7, and the crRNA facilitate incorporation of Cas8c, a fusion of the large and small/nsubunits found in other systems. Subnanometer resolution cryo-electron microscopy/nreconstructions of Cascade/I-C with and without target DNA reveal the dynamic role of/nCas8c, structural rearrangements for PAM recognition, the path of the displaced strand,/nand a dramatic bend in the target duplex.

Advisor: Doudna, Jennifer A
Atom probe tomographic analysis of high dose oxide-dispersion strengthened steel (alloy MA957) at selected irradiation conditions

In an effort to understand the effect of high dose neutron irradiation on fast reactor cladding candidate materials, oxide-dispersion strengthened (ODS) alloy MA957 was irradiated to doses exceeding 100 displacements per atom (dpa) at various irradiation temperatures. The finely distributed Y-Ti-O particles, which provide MA957 its attractive properties, were examined by atom probe tomography (APT). Significant increases in oxide cluster number density and reductions in oxide cluster size were observed in specimens irradiated at 412 °C and below. A substantial hardness increase, measured by nanoindentation, was also observed at these low irradiation temperatures. It was found that the increase in oxide cluster number density, reduction in oxide cluster size, and associated increase in hardness is due to the inhibition of reformation processes of the Y-Ti-O particles following ballistic dissolution by incident radiation. Redistribution of oxide particle material along the grain boundaries is also observed at the low irradiation temperatures. The intermetallic phase α’ was observed in the low temperature samples. This observation of this phase provides additional experimental evidence for the location of the phase boundary for this low temperature precipitate. The conclusion of this work is that MA957 is microstructurally stable under neutron irradiation at and above 495 °C.

Advisor: Slaybaugh, Rachel
Beautiful and Damned: Geographies of Interwar Kansas City

Between the World Wars, Kansas City, Missouri, achieved what no American city ever had, earning a Janus-faced reputation as America’s most beautiful and most corrupt and crime-ridden city. Delving into politics, architecture, social life, and artistic production, this dissertation explores the geographic realities of this peculiar identity. It illuminates the contours of the city’s two figurative territories: the corrupt and violent urban core presided over by political boss Tom Pendergast, and the pristine suburban world shaped by developer J. C. Nichols. It considers the ways in which these seemingly divergent regimes in fact shaped together the city’s most iconic features—its Country Club District and Plaza, a unique brand of jazz, a seemingly sophisticated aesthetic legacy written in boulevards and fine art, and a landscape of vice whose relative scale was unrivaled by that of any other American city. Finally, it elucidates the reality that, by sustaining these two worlds in one metropolis, America’s heartland city also sowed the seeds of its own destruction; with its cultural economy tied to political corruption and organized crime, its pristine suburban fabric woven from prejudice and exclusion, and its aspirations for urban greatness weighed down by provincial mindsets and mannerisms, Kansas City’s time in the limelight would be short lived. In the end, Kansas City's apotheosis of identity was—like that of every city's—as tenuous as it was definitive.

Advisor: Johns, Michael
Intimate Bonds: Dislocation, Survival, & Resistance in the Era of Neoliberal Punishment

This dissertation explores the life course of individuals who were convicted of violent crimes in adolescence and young adulthood and who served long prison sentences in California in the neoliberal era. It argues that the experience of “dislocation” (Polanyi, 1944) – meaning the rupture of meaningful connection to self, others, and purpose – is essential to understanding why individuals commit acts of violence and why they desist from violence. I explore this theory as it manifests in the life histories of 35 men with whom I conducted life history interviews, all of whom were convicted of violent crimes and served time in California prisons between 1980 and 2015. I focus in particular on a cohort of 15 individuals within this broader sample who were born between 1969 and 1979 and who came of age in urban neighborhoods in the 1980s and 1990s./nI argue that in their early lives, the search for compensatory intimacy resulting from dislocation in the family and community evolved into a subsequent attachment to violence and destructive lifestyles that eventually led each to incarceration. The experience of incarceration under neoliberal penality, characterized by the State’s abandonment of rehabilitation, resulted in further dislocation. As the prison population began rising, leading to the overcrowding characteristic of mass incarceration, the “strategies of control” (Messinger, 1969) promoting rehabilitation and good conduct in previous eras of penal history were replaced with strategies that incapacitated, racialized, and militarized the prisoner population, highly restricting the ability of incarcerated individuals to form genuine relationships and individual identities./nWithin these conditions, the private acts of individual prisoners, prison staff, and prison volunteers replaced the state-sponsored rehabilitative offerings previously available. In particular, incarcerated individuals worked with one another to survive and resist their conditions by mentoring one another and sharing resources, providing exposure to new ideas and perspectives, and encouraging each other to take advantage of the limited opportunities at their disposal, including college correspondence courses, the state-run educational and vocational programs that persisted into the neoliberal era, and volunteer-run therapeutic and educational programs./nThe personal accounts of individuals experiencing these conditions suggest that the development of “generativity” (Erikson, 1993), or the propensity to promote the well-being of future generations, can occur through maturation, but is also catalyzed by the formation of meaningful relationships and the sense of being attached to a path. The life histories of the young men who came of age during the neoliberal era thus suggest that intimacy – in the form of a meaningful connection to self, community, and a path – is an essential form of survival and resistance to violence and dehumanizing conditions.

Advisor: Simon, Jonathan
Gravure-printed electronics: Devices, technology development and design

Printed electronics is a novel microfabrication paradigm that is particularly well suited for fabrication of low-cost, large-area electronics on flexible substrates. Applications include flexible displays, solar cells, RFID tags or sensor networks. Gravure printing is a particularly promising printing technique because it combines high print speed with high resolution patterning. In this thesis, gravure printing for printed electronics is advanced on multiple levels. The gravure process is advanced in terms of tooling and understanding of printing physics as well as its application to substrate preparation and device fabrication./nGravure printing is applied to transform paper into a viable substrate for printed electronics. Paper is very attractive for printed electronics because it is low-cost, biodegradable, lightweight and ubiquitous. However, printing of high-performance electronic devices onto paper has been limited by the large surface roughness and ink absorption of paper. This is overcome here by gravure printing a local smoothing layer and printed organic thin-film transistors (OTFTs) are demonstrated to exhibit performance on-par with device on plastic substrates./nIf highly-scaled features are to be printed by gravure, traditional gravure roll making techniques are limited in terms of pattern definition and surface finish. Here, a novel fabrication process for gravure rolls is demonstrated utilizing silicon microfabrication. Sub-3μm features are printed at 1m/s. Proximity effects are demonstrated for more complex highly-scaled features. The fluid mechanics of this effect is studied and it is suggested how it can be used to enhance feature quality by employing assist features./nFinally, advancements are made to printed organic thin-film transistors as an important technology driver and demonstrator for printed electronics. First, a novel scanned thermal annealing technique is presented that significantly improves the crystallization of an organic semiconductor and electrical performance. Second, transistors are fully gravure printed at a high print speed of 1m/s. By scaling both lateral and thickness dimensions and optimizing the printing processes, good electrical performance, low-voltage operation and low variability is demonstrated.

Advisor: Subramanian, Vivek
The effects of anthropogenic disturbance and environmental change on multiple dimensions of microbial biodiversity

Despite recent advances in microbial ecology, including the widespread use of high- throughput sequencing and micro-array technologies, microbial taxonomic, phylogenetic, and functional diversity remain understudied and poorly understood compared to our knowledge of macrofaunal diversity. In this dissertation, I work to close this gap by: (1) addressing the challenges of quantifying and comparing modern microbial data, (2) elucidating the changes to soil microbial diversity caused by widespread land-use change in tropical ecosystems, and (3) modeling the unique evolution of marine diatoms./nThe dissertation begins in Chapter 1 with a general overview of the three original research projects that were carried out. In Chapter 2, I explore the use of diversity profiles, which are a novel way to analyze microbial datasets. Diversity profiles may be better suited than traditional ecological indices for quantifying data spanning multiple domains of life and dimensions of diversity. I evaluate the use of diversity profiles for analyzing microbial assemblages in order to determine whether the inclusion of rarity and similarity information changes the interpretation of comparative studies of microbial community diversity./nIn Chapter 3, I assess the effects of anthropogenic land-use change, soil abiotic factors, and geographic distance on the taxonomic, phylogenetic, and functional gene diversity of soil microbes. I discover and quantify multiple dimensions of bacterial, archaeal, and fungal diversity in five different land-use types (Primary Forest, Secondary Forest, Oil Palm, Rubber, and Rice) throughout a dipterocarp forest landscape in Peninsular Malaysia. In Chapter 4, I identify major shifts in lineage diversification rates during diatom evolution by building a new diatom phylogenetic tree with significantly more environmental diatom sequences than previously published phylogenies./nThe dissertation concludes in Chapter 5 with a summary of key findings: Microbial diversity comparisons may vary when taxa rarity and similarity information are considered by diversity profiles. Incorporating this information can greatly alter our comparisons and conclusions of microbial diversity in multi-community studies (Chapter 2); conversion of Primary Forest to other land-use types led to the loss of rare microbial OTUs (Chapter 3); fungal diversity was more strongly affected by land-use type than bacterial and archaeal diversity (Chapter 3); functional gene diversity was most strongly linked to abiotic soil environment (Chapter 3); and analyses of the global diatom phylogenetic tree yield estimates of diversification rate shifts across the tree with all but one of the estimated shifts corresponding to net increases in diversification rates (Chapter 4).

Advisor: Potts, Matthew D
β-delayed neutron studies of 137−138I and 144−145Cs performed with trapped ions

The β-delayed neutron (βn) emission decay mode, prevalent in a vast number of neutron- rich nuclei, influences abundances calculated in the r-process nucleosynthesis models, affects nuclear reactor safety analysis calculations, and can illuminate aspects of nuclear structure. This thesis describes a newly developed recoil ion detection technique that was applied for high-precision βn branching ratio and neutron energy measurements of 137−138I and 144−145Cs. The recoil ion measurement approach avoids difficulties associated with direct neutron detec- tion by instead detecting the daughter ion recoiling from neutron emission. The radioactive ions of interest are held in near-rest with the use of an ion trap, from which they leave the trap upon β or βn decay. The detector array surrounding the trap measures the time-of- flight of the recoil ion, as well as several associated decay products. Measuring the recoil ion’s time-of-flight determines the recoil energy, from which the emitted neutron’s energy can be deduced. Detecting other decay products gives rise to three different methods of measuring the βn branching ratio, which helps expose systematic effects. The technique builds upon a previous proof-of-principle experiment, and was expanded for the present measurements to include twice as many improved detectors, an upgraded ion trap, and a stronger source. This thesis also examines various backgrounds and detailed detector characterizations. The experimental campaign presented here serves to probe the limits of applying the recoil ion technique to explore further into the neutron-rich region.

Advisor: Norman, Eric B
Scielzo, Nicholas D
Quantification and controls of wetland greenhouse gas emissions

Wetlands cover only a small fraction of the Earth’s land surface, but have a disproportionately large influence on global climate. Low oxygen conditions in wetland soils slows down decomposition, leading to net carbon dioxide sequestration over long timescales, while also favoring the production of redox sensitive gases such as nitrous oxide and methane. Freshwater marshes in particular sustain large exchanges of greenhouse gases under temperate or tropical climates and favorable nutrient regimes, yet have rarely been studied, leading to poor constraints on the magnitude of marsh gas sources, and the biogeochemical drivers of flux variability./nThe Sacramento-San Joaquin Delta in California was once a great expanse of tidal and freshwater marshes but underwent drainage for agriculture during the last two centuries. The resulting landscape is unsustainable with extreme rates of land subsidence and oxidation of peat soils lowering the surface elevation of much of the Delta below sea level. Wetland restoration has been proposed as a means to slow further subsidence and rebuild peat however the balance of greenhouse gas exchange in these novel ecosystems is still poorly described./nIn this dissertation I first explore oxygen availability as a control on the composition and magnitude of greenhouse gas emissions from drained wetland soils. In two separate experiments I quantify both the temporal dynamics of greenhouse gas emission and the kinetic sensitivity of gas production to a wide range of oxygen concentrations. This work demonstrated the very high sensitivity of carbon dioxide, methane, and nitrous oxide production to oxygen availability, in carbon rich wetland soils. I also found the temporal dynamics of gas production to follow a sequence predicted by thermodynamics and observed spatially in other soil or sediment systems./nIn the latter part of my dissertation I conduct two field studies to quantify greenhouse gas exchange and understand the carbon sources for decomposition in a 1 km2 restored wetland in the Sacramento Delta. By coupling flux measurements at multiple-scales with remote sensing imagery I showed that large methane emissions produce an overall climate warming effect from the wetland for the next several centuries, despite relatively high productivity. I also used radiocarbon analyses of wetland sediment carbon dioxide and methane to show that both bulk peat and recently fixed carbon contribute to decomposition in the wetland, and that their relative importance is regulated by proximity to, and the phenological cycles of, emergent vegetation.

Advisor: Silver, Whendee L