VictorJuiz/thesis huggingface dataset:
Sex, Alternative Lifestyles, and a Graphic Study of a Model

The genus of Ascomycete molds, Neurospora, has served as a valuable model for the cellular and molecular biology of multicellular fungi, and more recently for the evolution of fungi. In this thesis I present three studies of Neurospora which each expand the knowledge and utility of this model./nFirst, I expand collections of rare Neurospora species by 113 strains and 149 whole genome sequences, including the first conidial homothallic (self-fertile) Neurospora as well as genome sequences for endolichenic Neurospora from two species, both aconidial. These data provide insight into Neurospora’s mysterious lifestyle, and show that at least some Neurospora species live part of their lives as endosymbionts. These collections also expand the utility of Neurospora as a model for breeding system evolution by showing that every combination of reproductive system seen in Ascomycota is also seen in Neurospora./nSecond, I use this collection of genomes, along with 43 previously published genomes, to study the population biology of Neurospora species with diverse reproductive ecologies. While homothallic Neurospora had previously been assumed to be dominantly or exclusively selfing, I show that at least one aconidial homothallic lineage is recombining at least as much as heterothallic (self-sterile) species. I further detail the population structure and biogeography of diverse groups of Neurospora, showing how differing ecologies and mating paradigms work at different scales to shape populations./nThird, I address the question: How does the rate of genomic rearrangements vary across the genome? Genomic rearrangements are an important source of adaptive variation, but studying them has been challenging due to a lack of suitable (i.e. whole genome) data/nand the computational complexity of the problem. Leveraging this collection of Neurospora genomes, I present a method to estimate the rearrangement rate across the genome. I phrase the problem in graph theoretic terms and find it to be an instance of the well known clique cover problem. I use this method to find evidence that in N. crassa, like other Eukaryotes, rearrangements are more common in the subtelomeric regions of the chromosomes, which facilitates the evolution of novel genes.

Advisor: Taylor, John W.
A Century of Denying Child Labor in America

“A Century of Denying Child Labor in America” analyzes the influence of agrarian ideology on agricultural child labor policy in the United States over the course of the twentieth century. The project places agrarianism at the heart of the child labor question by arguing that agrarian sensibility uncompromisingly viewed children’s farm labor as a beneficial and healthful activity, and a natural and integral part of the rural family economy—even among children who did not live on family farms. Throughout the twentieth century, rural parents and agricultural interests invoked reason that was rooted in agrarianism to limit or thwart legislation that aimed at regulating agricultural child labor. As a result, children’s agricultural labor has never been regulated on a par with that of other sectors./nThis dissertation demonstrates the strength of agrarian reason and reveals the ramifications for working children by tracing the evolution of the agricultural exemption to the child labor provision of the 1938 Fair Labor Standards Act. This project challenges conventional narratives that mark the New Deal as the end point for the history of child labor in America. It moves the discussion beyond the 1930s and pushes it outside the bounds of eastern industrial America. In doing so, it draws out the experiences of racially and ethnically diverse groups of children while shedding light on the power of cultural myths to influence public policy. In challenging conventional narratives, this project contributes significantly to our understanding of the history of American politics, labor, and childhood in the twentieth century. It is the first project to argue that child labor was a critical component in FDR’s 1937 battle with the Supreme Court; to analyze the nation’s increased dependence on child farm labor during World War II; and to highlight the ways that children were activists in the United Farm Worker labor movement of the 1960s and 1970s. Moreover, this project calls attention to the fact that the child labor problem is not yet solved./nUltimately, this dissertation demonstrates the ways that agrarian reason veiled exploitation, denied children legal protection, and perpetuated multi-generational cycles of poverty and structural inequality that were in contradistinction to the tenets of agrarianism.

Advisor: Fass, Paula
Searching for the 0νββ Decay of 130Te with the Ton-Scale CUORE Bolometer Array

CUORE---the Cryogenic Underground Observatory for Rare Events---is an experiment searching for the neutrinoless double-beta ($0\nu\beta\beta$) decay of $^{130}$Te, based at the Laboratori Nazionali del Gran Sasso in Italy. The detector consists of 988 5$\times$5$\times$5 cm$^3$ TeO$_2$ crystals operated as bolometers at temperatures of $\sim$10 mK inside the world's largest and most powerful dilution refrigerator. CUORE began physics data collection in the spring of 2017, and has recently released its first limit on the $0\nu\beta\beta$ decay half-life of $^{130}$Te from 24 kg $\cdot$ y isotope exposure ($\sim$2 months live time). This result---T$^{0\nu}_{1/2} > 1.5 \cdot 10^{25}$ y (Bayesian) and T$^{0\nu}_{1/2} > 2.3 \cdot 10^{25}$ y (Frequentist) at $90 \%$ C.L.---is the most stringent to date and, together with two alternative analyses necessary to calculate it, forms the centerpiece of this thesis. In the future, with five years of live time, CUORE is projected to reach a median sensitivity of $9 \cdot 10^{25}$ y on this half-life. Besides the main physics conclusions, in this work I present an analysis modeling the spectral line shape of the bolometer, which is used for constructing the region of interest fit PDF. Additionally, I discuss the major CUORE hardware projects to which I have contributed in a significant way. Specifically, these are our world-leading cryostat, a cryogenic feedback temperature control system, a radon-free detector installation environment, and a room temperature detector calibration system.

Advisor: Kolomensky, Yury G
The Utility of Dynamic Assessment of Phonological Awareness for Bilingual Children in Singapore

Early detection of reading difficulties is crucial in order to facilitate early intervention efforts. However, it may not be as straightforward to identify reading difficulties in children from bilingual backgrounds. This may be due to the considerable variability in their home language environment, and the fact that some difficulties faced by English language learners may present as similar to those with language learning disabilities. Dynamic assessment provides a potential mechanism to disaggregate these factors. In contrast to standardized assessment procedures, dynamic assessment allows the examiner to modify a prompt or provide extra scaffolding following a student’s response, which helps to clarify the types of supports needed for the student to undertake a task successfully. Dynamic assessment has been lauded as a viable alternative for use with culturally and linguistically diverse populations because it may provide a more accurate measure of the young child’s potential and response to instruction./nThis study was conducted in Singapore, a multicultural society, with 99 preschool children (ages 4 to 5) from diverse language backgrounds. Parents and teachers filled in a Language Background Questionnaire and the children were grouped according to whether their family was Balanced Bilingual, English-dominant, or L2-dominant, depending on the languages spoken in the home. A battery of tests was administered to assess the children’s receptive and expressive language in English, as well as a standardized and dynamic test of phonological awareness. Four to 6 months after the initial assessment, the children were again assessed on letter and word reading outcome measures./nResults demonstrated that both home language background as well as the child’s receptive and expressive language in English impacted independently and significantly on phonological awareness. Hierarchical linear regression analyses indicated that prior letter identification/word reading explained close to 88% of the variance in the word reading outcome measure. However, the dynamic assessment task was found to be useful with children who had not yet learned to read at the time of the initial assessment. This study reveals the importance of language-specific skills for phonological awareness, highlights the importance of early intervention in reading, and supports the notion of the differential predictive validity of dynamic assessment.

Advisor: Cunningham, Anne E
Prinz, Philip M
Autocratic Courts in Africa

This dissertation examines how judicial institutions in sub-Saharan Africa were used to both legitimize repression and maintain autocratic survival during the postcolonial period, as well as the enduring legacies of these tactics on post-autocratic rule of law. When autocrats turn to courts, these moves are often heralded as signs of democratic opening. However, courts can also become forums of repression, where political rivals are criminally prosecuted for anti-regime behavior. Despite these trends, courts remain relatively understudied in repression research. In fact, conventional definitions of repression are almost exclusively extrajudicial, defined as the arbitrary use of coercive violence to threaten or intimidate its target. While a separate scholarship on authoritarian judiciaries draws attention to the autocratic functions of law and order, these findings tend to be disconnected from research on repression. This has limited theory-building on how and why courts are used to contain democratic dissent./nTo analyze the politicization of courts in comparative and historical perspective, I develop a theoretical framework that extends beyond conventional notions of judicial independence, re-conceptualizing judicial power along the following three dimensions: jurisdiction, function, and compliance. Jurisdiction refers to the scope of judicial decision-making, or whether judges are allowed to decide cases of political import. Once jurisdiction is granted, function refers to the actual tasks judges are required to perform in service of the regime. For example, one critical function of courts under autocratic rule is to provide a forum for the government to formally prosecute political rivals. Finally, compliance describes whether judges ultimately obey regime objectives, in this case, by convicting rivals for crimes against the state. Evaluated jointly, these three dimensions of judicial power help explain why judges become major political players in some autocratic contexts, but not others./n/nUsing this framework, I argue that courts help autocrats both punish challengers and deter future coordination against the regime. These outcomes are achieved through a trial, defined as a formal, ritualized routine which generates common knowledge regarding the rules of political order. Establishing such rules or laws is vital towards regulating insider conflict within the regime, which is important towards maintaining autocratic survival. I refer to this process, wherein laws and courts are used to repress political rivals, as a judicial strategy of repression./nMy findings utilize archival research, fieldwork interviews, and natural language processing of both web-scraped media and historical documents. My research contributes to broader debates on autocratic governance, judicial politics, postcolonial legacies, and varieties of state repression.

Advisor: Arriola, Leonardo
Noise, Quantization, and Priors in Neural Networks

A fundamental task for both biological perception systems and human-engineered agents is to infer underlying causes from incoming measurements. Approximate inference in a probabilistic graphical model is a method to generate algorithms that solve such a problem. Not only does the approximate inference seek to reduce the exponential computation necessary in a naive application of Bayes theorem, but approximations are made to handle varied hardware constraints./nThe first chapter explores the computations done by the brain in order to decode the signals from a moving retina to achieve high acuity vision. In this case, the problem is formulated as a probabilistic generative model and the decoding computations are a result of doing approximate Bayesian inference. The parameters of the inference computation are derived from the parameters of the generative model instead of being learned./nThe second chapter explores the problem of prediction of noisy temporal sequences. Here, recurrent neural networks which are good at learning non-linear temporal dependencies are combined with Kalman filters which are good at dealing with noise and uncertainty. While the resulting computations could, in principle, be approximated by a neural network, our model results in better prediction performance for eye movements than a simple neural network./nThe third chapter explores neural networks with binary weights and activations. Such networks are constrained to be binary and need a modified learning algorithm, but they both use less power and less time to execute. This work develops a theory, based on high-dimensional geometry, that explains why binary neural networks have similar performance to their 32 bit floating point counterparts.

Advisor: Olshausen, Bruno A
DeWeese, Michael R
Stress-Strain Response and Fracture Mechanics of the Cuboctahedral Lattice for Aerospace Applications

Architected lattice materials are some of the stiffest and strongest materials at ultra-light density (< 10 mg/cm3), making them ideal for aerospace structural applications. However, many factors inhibit their use in practical application. The first is scalable manufacturing. Though roll-to-roll process have been developed for 2D lattices, 3D architectured lattice materials rely on manufacturing methods that face scalability challenges when considering aircraft-sized applications. The second challenge is safety. Safety-critical applications demand a high understanding of fracture mechanics and fatigue mechanisms, but the fracture mechanics of lattice materials is a relatively nascent field that has demonstrated several challenges compared to continuum fracture mechanics./nThis thesis addresses both of these concerns. The first section presents a mass-manufacturable discrete lattice material. The mesoscale, ultra-light (5.8 mg/cm3) fiber-reinforced polymer composite lattice structure is reversibly assembled from building blocks manufactured with a best-practice high-precision, high-repeatability, and high-throughput process: injection molding. The chopped glass fiber-reinforced polymer (polyetherimide) lattice material produced with this method display absolute stiffness (8.41 MPa) and strength (19 kPa) typically associated with metallic hollow strut microlattices at similar mass density. Additional benefits such as strain recovery, discrete damage repair with recovery of original stiffness and strength, and ease of modeling are demonstrated./nThe second section characterizes the fracture toughness of the cuboctahedral lattice using experimental and computational methods. Novel experimental methods for use of the compact tension specimen are described, which enable the testing of higher unit cell resolutions than three-point bend fracture bend specimens. 3D printed acrylic compact tension specimens were manufactured and tested with relative densities of 5-15 % and compared to FEA models. The normalized toughness is shown to increase linearly with relative density, matching scaling performance of the higher connectivity octet truss. Effects of specimen geometry are computationally investigated, and limitations of the applicability of long crack fracture theory to cellular materials are discussed. Additionally, a potential toughening mechanism for lattices is addressed by characterizing crack deflection in a heterogeneous lattice. The He-Hedgepeth criterion for crack deflection in a bi-material is adapted to lattice materials, providing a single parameter to predict crack deflection in a reinforced lattice.

Advisor: Pruitt, Lisa
The economics of environmental change: Essays on climate and water

Many questions of importance for sustained human progress on a planet of finite resources remain unanswered. As environmental change accelerates, there is growing urgency to build an understanding of how the environment and society influence one another. This dissertation mobilizes novel, large-scale datasets in combination with methodological advances in casual inference and original theoretical contributions to study the interdependence between societies, economies, and two of the world's most vital natural endowments: the climate and freshwater. Throughout these essays, I estimate causal, policy-relevant relationships between global-scale processes of environmental change and human wellbeing. The first three essays provide new estimates of the climate's influence over market and non-market outcomes, generating insights in climate impact attribution, climate impact mechanisms, and the estimation of adaptation costs and benefits under anthropogenic climate change. The final essay studies the other direction of the society-environment relationship, measuring how changes in economic systems influence freshwater. This chapter uses satellite data to uncover links between agricultural policies and water depletion at a scale that has been impossible to investigate with standard water monitoring tools. Together, these essays aim to demonstrate that combination of data and methods across physical and social sciences can yield valuable answers to questions that have been discussed, debated, and left unresolved for generations.

Advisor: Hsiang, Solomon M
Auffhammer, Maximilian
Computational Design of Ceramic Matrix Composites for Turbine Blade Applications

Turbine technology is a critical part of the today's energy and transportation infrastructures, and turbine manufacturers constantly aim to increase the operating efficiencies of their products to yield better technical and economic performance. The thermodynamic efficiency of a turbine system is bounded by its operating temperature, which is often limited by the materials used to construct the turbines blades. The blade materials need to withstand very demanding conditions, including rotational loads from rotations of over 3,000 rpm and thermal loads from temperatures above 1,000 C. Informed materials design of turbine blades is therefore crucial for enhancing the performance of turbine systems./nCeramic Matrix Composite (CMC) materials are a new series of material systems that have recently received substantial interest from turbine manufacturers due to their exceptional ability to retain their mechanical properties at significantly higher temperatures than commercial superalloy compounds. Given the high cost of experimental CMC research, computation can be a very helpful tool to aid the design of novel CMC compounds by allowing the designer to test the performance of large sets of material systems quickly and effectively through targeted simulations./nThis study presents a computational framework that can be applied for exploratory design of CMC compounds. The design framework combines continuum mechanics based simulation tools, such as the finite element method, with evolutionary algorithms to enable computer driven design of CMC compounds. The evolutionary algorithms, driven by numerical and reduced order models, prototype various material and microstructure design choices and evaluate their performance against a set of target properties. As the evolutionary algorithms progress in their parameter choices, they create better and better material design choices until a stopping criterion is reached. Following the down-selection from the evolutionary algorithms, the computer-generated CMC design are then subjected to further virtual tests, including preliminary structural scale finite element simulations of a turbine blade geometry composed of the algorithmically designed CMC compound.

Advisor: Zohdi, Tarek I
Asta, Mark D
Neuronal Circuits of NREM Sleep Control in the Basal Forebrain and Midbrain

Sleep is a fundamental behavior in the animal kingdom. It is essential for optimal cognition,/ngeneral health, immune function and neuronal plasticity. Irregular or insufficient sleep may/ncause emotional disturbances, abnormal homeostasis of physiological functions. About 30%/nadults in the US suffered from insomnia. Therefore, understanding of the sleep‐wake circuit will/ncontribute to the cure of not only sleep disorders, but also other psychiatric diseases. A crucial/nstep in understanding the neural circuits controlling sleep is to identify the sleep neurons. In my/nthesis, I used transgenic Cre mouse lines, virus‐mediated circuit tracing, and optogenetic/nmanipulation to identify the sleep‐promoting neurons and dissect the neural circuits for/ncontrolling sleep and arousal./nIn chapter 2: The basal forebrain (BF) contains a spatially intermingled diverse population of/nneurons that play key roles in multiple brain functions, including sleep‐wake regulation,/nattention, and learning/memory. For sleep‐wake regulation, the cholinergic, glutamatergic, and/nparvalbumin‐expressing (PV) GABAergic neurons have been shown to promote wakefulness,/nwhereas the somatostatin‐expressing (SOM) GABAergic neurons promote NREM sleep. To/nunderstand how these cell types in the same area have different functions in sleep‐wake/nregulation, we used rabies virus ‐mediated monosynaptic retrograde tracing to label the inputs/nand adeno‐associated virus to trace axonal projections. We identified numerous brain areas/nconnected to the BF. These results reveal the long‐range wiring diagram of the BF circuit with/nhighly convergent inputs and divergent outputs and point to both functional commonality and/nspecialization of different BF cell types./nIn chapter3: We identified the neurotensin (NTS) neurons in the preoptic area, posterior/nthalamus (pTh), and ventrolateral periaqueductal gray (vlPAG) as NREM sleep‐promoting/nneurons based on optogenetic manipulation. Using rabies virus‐mediated monosynaptic/nretrograde tracing combined with fluorescent in situ hybridization (FISH) experiment, we also/nshowed that cholecystokinin (CCK) and calcitonin gene‐related peptide alpha (Calca) neurons in/nthe EW (CCKEW), and NTS neurons in the vlPAG (NTSvlPAG) form reciprocal connections to each/nother. These cell types may cooperate to promote NREM sleep.

Advisor: Dan, Yang