VictorJuiz/thesis huggingface dataset:
The Undiscovered CO: Charting the Molecular Gas of the Early Universe

Molecular gas, observed through tracers such as CO rotational transitions, is a vital component of galactic evolution and star formation. Recent detections of the CO molecule in massive galaxies at high redshift have demonstrated its existence in the early Universe, and have motivated its use as a means of exploring large-scale structure and as a probe of galaxy evolution in the early Universe. But many questions about molecular gas and the evolution of galaxies in the early Universe still remain: its distribution at high redshift understood is so poorly that theoretical models of the mean abundance of CO for the first several billion years of cosmic history span orders of magnitude. Direct detection of molecular gas in galaxies at these redshifts have only found the largest and most luminous of galaxies in the early Universe, whereas the bulk of the molecular gas is expected to be in the unseen masses of smaller galaxies. While difficult to detect individually, these smaller galaxies are likely detectable as an integrated ensemble with the technique of ``intensity mapping". This technique, similar to those employed by HI epoch of reionization experiments, utilizes measurements of different 3D Fourier modes to construct a power spectrum./nIn this thesis, I present results from the CO Power Spectrum Survey (COPSS), an intensity mapping experiment performed with the Sunyaev Zel'dovich Array (SZA). I present power spectrum constraints from of the first and second phase of this project, utilizing an archival dataset (covering 44 fields in 1400 hours observing time) and a 5000-hour observing campaign (covering 19 fields) with the SZA. With these data, we are capable of observing CO(1-0) emission arising from $z=2.3{-}3.3$, surveying a volume of more than ten million cubic megaparsecs. With this measurement, we place the first-ever constraints on the CO autocorrelation power spectrum, and place constraints on the CO(1-0) galaxy luminosity function and the cosmic molecular gas density at $z\sim3$./nI also present a series of simulations designed to probe the impact of cosmic variance, continuum foregrounds, and systematic errors on our measurement with the SZA. I will also present simulations designed to probe the challenges that will face intensity mapping experiments with the Yuan-Tseh Lee Array (YTLA). Finally, I will present some preliminary work on CO(3-2) and [CII] intensity mapping experiments.

Advisor: Heiles, Carl E
Refractive Cogito: An Ethnography of Relational Imagination

Refractive Cogito explores the production of intersubjective intimacy through psychotherapy and visual technologies. I have conducted one year of ethnographic research in Argentina, a global center for psychotherapeutic treatments. In Buenos Aires, I researched “systemic couple therapy.” This therapeutic model utilizes visual technologies like the one-way mirror or Closed Circuit Television in order to allow teams of therapists to observe or supervise live sessions of therapy. Building on my “observant participation” of live sessions of therapy, I argue that this setting exemplifies how late modern affectivity is mediated through the optical apparatus, which includes visual technologies but also the anonymous gazes of the observing therapists and the ethnographer’s I/eye. This visual mediation foregrounds the emergence of the “couple image,” an interpersonal imaginary that filters the normative reproduction of coupled intimacy./nAdding to research on therapeutic lifeworlds in Latin America, the work challenges the notion that modern institutions such as psychotherapy and the romantic couple have produced reflexive and self-transparent identities. I draw from the systemic setting to describe a constitutive non-coincidence and visual dispossession of late modern subjects in respect to themselves. I contribute to qualitative methodology defining ethnography as a genre of presence that involves the use of non-conscious imagination. To consider the ethnographic enterprise as an experience of refractive dispossession, I describe sessions of hypnosis I underwent to as a patient/researcher during my fieldwork.

Advisor: Cohen, Lawrence
Whitmarsh, Ian
Multi-scale Modeling of Heat Transfer

The dynamics of a complex fluid or fluid close to interfaces is affected by its microscopic structure. Because the molecular level dynamics is playing a role, and macroscopic scale is effected by lower levels, in these situations the fluid cannot be completely described by continuum theory and Navier-Stokes equation. However, molecular dynamics also is not a practical approach; the large number of particles in the large scales makes it computational impossible. I solve the problem with a Mesoscopic simulation methods by making use of information from different length scale, macroscopic and microscopic, and solve the problem in middle ground in the mesoscale level. However, by using the coupling of continuum and a mesoscale method, I could solve an industry size problem with accuracy of lower scale problem. For the first time, I present a novel coupling method of dissipative particle dynamics to continuum model to calculate heat transfer. The results of the method shows an excellent agreement with a broad range of experimental results in various cases.

Advisor: Zohdi, Tarek
Evolutionary Comparison of X-Chromosome Dosage Compensation Across Caenorhabditis Species

Many species determine sex by assessing sex-chromosome dose. In flies, mammals, and nematodes, males have one X chromosome and females or hermaphrodites have two. However, both sexes require the same level of expression for most genes; thus they evolved a process called dosage compensation to equalize X-linked gene expression between the sexes. Failure to carry out this process causes lethality in one sex. Flies, mammals, and nematodes have independently evolved very different dosage compensation mechanisms, showing that multiple strategies can be employed to achieve dosage compensation. We chose to investigate four nematode species with shared ancestry to ask whether and how essential dosage compensation mechanisms are able to evolve over time. Examples of dosage compensation mechanisms in closely related species provide evidence to better understand how genes with different expression constraints can be regulated simultaneously across chromosome-wide territories./nHere, I compare chromosome-wide dosage compensation mechanisms across four Caenorhabditis species (less than 30 million years diverged): C. elegans}, C. briggsae, C. nigoni, and C. tropicalis. We took advantage of improved sequencing technology to create chromosome-level genome assemblies for C. nigoni and C. tropicalis. We also devised genome editing strategies for the non-model species C. briggsae, C. nigoni, and C. tropicalis. Using genome editing, we created strains for phenotypic and biochemical assays to assess the function of orthologous genes in dosage compensation. Key subunits of the dosage compensation machinery and the genetic hierarchy that regulates the sex-specific function of the machinery share conserved action across species. However, remarkably, the binding sites on the X chromosome and the DNA sequence motifs within binding sites that drive X-specific binding have diverged at least twice within 30 million years of evolution. Since the dosage compensation machinery acts to modify the structure of the C. elegans X chromosome by bringing binding sites together, divergence in binding site location could result in a different X-chromosome structure in these species. Future studies of the rapid divergence of binding sites that characterize X-chromosome structure and X-linked gene expression could bring us closer to understanding how nematode dosage compensation operates.

Advisor: Meyer, Barbara J
Bilinear Quadratures and Their Applications

A bilinear quadrature numerically evaluates a continuous bilinear map, such as the $L^2$ inner product, on continuous $f$ and $g$ belonging to known finite-dimensional function spaces. The evaluation of such maps is common in Galerkin methods for differential and integral equations. A framework for constructing bilinear quadratures over arbitrary domains in $\R^d$ is developed. We provide rigorous error estimates under general conditions. We prove that in one dimension, these integration rules include Gaussian quadrature for polynomials and the trapezoidal rule for trigonometric polynomials as special cases. Lastly, we demonstrate that in higher dimensions, bilinear quadratures computed using this framework achieve similar or better performance in evaluating $L^2$ inner products than existing quadrature rules.

Advisor: Strain, John A
The Power of Place: Ideology and Ecology in the Bering Strait, 1848-1988

At the Bering Straits, Russia and Alaska share a common ecology: rolling tundra and icy mountains divided by the narrow ocean. Every living thing exists without plentiful solar energy, curtailing the productivity evident in temperate climates. Yet over the course of the long twentieth century, Russians and Americans were drawn north by its potential riches, from the energy in walrus blubber to the currency of gold. They stayed to make converts, fortunes, and states. This dissertation chronicles the environmental, political, economic and cultural revolutions that came in their wake. These revolutions map onto the distribution of energy in arctic space. Europeans began by harvesting whales, moved to hunting walrus on coasts, attempted to farm reindeer on land, sought gold underground, and finally returned to hunting whales at sea. Organized around these spaces, the following five chapters trace a narrative from the stateless meetings of indigenous Yupik, Inupiat, and Chukchi with commercial hunters, to the inception of national borders and ideas of citizenship, through to the region’s division along ideological lines. Using ecological and anthropological scholarship and sources from twenty local, regional, and national archives in the U.S. and Russia, it examines how capitalism and communism, which imagine history as universal, progress as inevitable, and production as infinite, met with the constraints of the far north./nThe common extremity of the Beringian environment provides a unique space in which to compare the twentieth century’s two great economic systems. The resulting insights transcend the peripheral geography, and contribute to major questions in the histories of capitalism, socialism, and the environment. First, comparing how people understood their northern environs, and how they chose to change them, demonstrates how both economies were laced with normative assumptions about the trajectory of people’s lives and history. Capitalism was never simply about how commodities were owned and traded, any more than communism was only about collective ownership of the means of production. Rather, both were ideologies that shaped what was thinkable, valuable, and rational. Second, these ideas did not exist outside environmental context. In ways specific to marine, coastal, and terrestrial habitats, local ecologies changed the practice of communism and capitalism. By investigating how intent became action, and action shaped new intents, this project shows instances of socialist rationality, market irrationality, and unexpected resemblance. Above all, both economic and ideological systems were contingent on factors beyond human control. Attention to the non-human, from animal behavior to climate, demonstrates how agency, in the sense of individual or collective will working on the world, was situational. The result is a history of how human intention and action were negotiated in concert with the environments they inhabited.

Advisor: Slezkine, Yuri
Revitalizing Educators using RENEW (Revitalizing Educators through a New Experience of Work)

Teachers have the capacity to change lives. They can change the academic trajectory of a young person, or inspire a student to continue. Nothing is sadder than a once vigorous teacher who loses the desire to transform lives in the classroom. It is estimated up to 30% of teachers burnout from the profession, but remain in the classroom, either too close to retirement or unprepared for other work. As the nation faces an ongoing teacher shortage, it is frustrating to fund these experienced teachers who should be top-performers./nIf these teachers could find a way to renew their passion for their subject, or their enthusiasm for teaching, it might make all the difference in the classroom./nThis problem of practice has vexed me for many years: How can veteran teachers sustain their enthusiasm and engagement for the profession, especially when working at challenging urban schools? The field of positive psychology holds some promise for professional renewal./nUsing the Job-Demands Resource model, an increase in personal resources, such as optimism, hope or self-efficacy, and job resources such as collegiality, should allow teachers to sustain their engagement no matter how challenging the work situation. I developed an eight-session professional development series using collegial conversation and positive psychology exercises to help teachers in a challenging work situation build these assets. To determine the effectiveness of this intervention, I measured work engagement, self-efficacy, well-being and analyzed the process of each session./nThe results from this study were subtle and mixed. Obviously personal change in positive affect is individualized, but the results of the positive psychology exercises as a method to support urban teachers shows promise. Future investigations of this area may show this is a simple, low-cost intervention that supports the social-emotional development of teachers and provides enough support to increase teacher retention.

Advisor: Mintrop, Heinrich
The Effect of Ethanol Addition to Gasoline on Low- and Intermediate-Temperature Heat Release under Boosted Conditions in Kinetically Controlled Engines

Abstract/nThe Effect of Ethanol Addition to Gasoline on Low- and Intermediate-Temperature Heat Release under Boosted Conditions in Kinetically Controlled Engines/nby/nDavid Malcolm Vuilleumier/nDoctor of Philosophy in Mechanical Engineering/nUniversity of California, Berkeley/nProfessor Jyh-Yuan Chen, Chair/nThe detailed study of chemical kinetics in engines has become required to further advance engine efficiency while simultaneously lowering engine emissions. This push for higher efficiency engines is not caused by a lack of oil, but by efforts to reduce anthropogenic carbon dioxide emissions, that cause global warming./nTo operate in more efficient manners while reducing traditional pollutant emissions, modern internal combustion piston engines are forced to operate in regimes in which combustion is no longer fully transport limited, and instead is at least partially governed by chemical kinetics of combusting mixtures. Kinetically-controlled combustion allows the operation of piston engines at high compression ratios, with partially-premixed dilute charges; these operating conditions simultaneously provide high thermodynamic efficiency and low pollutant formation./nThe investigations presented in this dissertation study the effect of ethanol addition on the low-temperature chemistry of gasoline type fuels in engines. These investigations are carried out both in a simplified, fundamental engine experiment, named Homogeneous Charge Compression Ignition, as well as in more applied engine systems, named Gasoline Compression Ignition engines and Partial Fuel Stratification engines. These experimental investigations, and the accompanying modeling work, show that ethanol is an effective scavenger of radicals at low temperatures, and this inhibits the low temperature pathways of gasoline oxidation. Further, the investigations measure the sensitivity of gasoline auto-ignition to system pressure at conditions that are relevant to modern engines. It is shown that at pressures above 40 bar and temperatures below 850 Kelvin, gasoline begins to exhibit Low-Temperature Heat Release. However, the addition of 20% ethanol raises the pressure requirement to 60 bar, while the temperature requirement remains unchanged./nThese findings have major implications for a range of modern engines. Low-Temperature Heat Release significantly enhances the auto-ignition process, which limits the conditions under which advanced combustion strategies may operate. As these advanced combustion strategies are required to meet emissions and fuel-economy regulations, the findings of this dissertation may benefit and be incorporated into future engine design toolkits, such as detailed chemical kinetic mechanisms.

Advisor: Chen, Jyh-Yuan
Courting Carcerality: The Rise of Paraprisons in the Era of Neoliberal Racial Statecraft

My project examines the legal, political-economic, and ideological manifestations of the U.S. neoliberal racial state through the lens of parapublic carcerality. I introduce and elaborate the term parapublic carcerality throughout this exploration to describe more accurately the incursionary, politico-regulatory technology of what has heretofore been indexed by the lingua franca of “private prison” and/or “for-profit prison.”/nParapublic carcerality is a significant conceptual contribution to the subfield of carceral studies in that it invites a shift in scholarly analysis from prison as a static, readymade punitive institution to carcerality as a tentacular (re)iterative site of regulatory social practice and meaning-making all while avoiding the analytic snares inherent to public/private dichotomization./nMoreover, my project explores the ways in which the internal logic of the U.S. neoliberal racial state is operationalized and crystallized in modern carcerative sites and practices. That is, it considers the techniques by which the neoliberal racial state pits law against capital and courts against corporations in order to broker temporary socio-political balances that maintain hierarchies of social difference oriented toward white supremacy and black subjugation./nMore specifically, my project challenges the notion that the expansion of the U.S. prison state in the mid-20th century, as well as the emergence of profit-generating companies like Corrections Corporation of America (CCA) and the GEO Group (GEO)—firms which embody the praxis of parapublic carcerality—represents a unidirectional backlash to victories achieved during the modern civil rights movement. Instead, I argue that the emergence and expansion of such companies and practices, in part, is also a consequence of efforts to remedy the “problem” of prison crowding as defined by the federal courts./nI contend that the federal courts throughout the 1970s and 1980s absorbed radical critiques of white supremacy in the form of lawsuits filed by black prisoners and their organizational allies like the NAACP and ACLU in two interrelated ways: 1) by reframing lawsuits explicitly filed to remedy racial injustice as a (neoliberal) colorblind issue of crowding and 2) by generally refusing to rule in favor of prisoners unless crowding allegations were central to their suits./nAnd finally, my examination assesses the extent to which the praxis of parapublic carcerality is tethered to the larger project of neoliberal racial statecraft, a project of both “governance and a state of condition” in which whiteness serves as a proxy for social deservedness and blackness approximates criminality and what I term the “anti-citizen.”

Advisor: Scott, Janelle
Using Explanatory Item Response Models to Evaluate Complex Scientific Tasks Designed for the Next Generation Science Standards

This dissertation includes three studies that analyze a new set of assessment tasks developed by the Learning Progressions in Middle School Science (LPS) Project. These assessment tasks were designed to measure science content knowledge on the structure of matter domain and scientific argumentation, while following the goals from the Next Generation Science Standards (NGSS). The three studies focus on the evidence available for the success of this design and its implementation, generally labelled as “validity” evidence. I use explanatory item response models (EIRMs) as the overarching framework to investigate these assessment tasks. These models can be useful when gathering validity evidence for assessments as they can help explain student learning and group differences./nIn the first study, I explore the dimensionality of the LPS assessment by comparing the fit of unidimensional, between-item multidimensional, and Rasch testlet models to see which is most appropriate for this data. By applying multidimensional item response models, multiple relationships can be investigated, and in turn, allow for a more substantive look into the assessment tasks. The second study focuses on person predictors through latent regression and differential item functioning (DIF) models. Latent regression models show the influence of certain person characteristics on item responses, while DIF models test whether one group is differentially affected by specific assessment items, after conditioning on latent ability. Finally, the last study applies the linear logistic test model (LLTM) to investigate whether item features can help explain differences in item difficulties.

Advisor: Wilson, Mark
Induction, Specification and Differentiation of Neural Crest Cells in Xenopus and Danio rerio

The neural crest (NC) is a vertebrate-specific population of multipotent cells, often referred to as the fourth germ layer because of its unique ability to migrate to all parts of the body and contribute to a variety of tissues. Positional information allows neural crest cells to determine their location relative to each other and in complex 3D environments, and to respond accordingly. A central question in developmental biology is how these positional cues are imparted to cells, and how the cells interpret them for the appropriate response. The work in this thesis sets out to determine 1) how Wnt and BMP gradients define cells as neural crest, 2) how the position along the AP axis determines neural crest fate and 3) how abolishing one positional cue results in a craniofacial phenotype./nPrecise control of BMP and Wnt signaling in both space and time is necessary for proper neural crest induction. While the Wnt signaling pathway has been extensively studied, it is not clear how the cells interpret and respond to the Wnt signals. Knowing the importance of these pathways in setting up the embryo axes, I wanted to further our understanding of the precise way these pathways initiate the neural crest program. An important first step toward determining how the intersection of the Wnt and BMP signaling pathways set up the neural crest cell program in space and time was to develop a method to rapidly and uniformly manipulate the signaling pathways in Xenopu laevis embryos. I was able to validate that small molecules can replace the use of mRNA injections in order to manipulate signaling pathways./nThe next chapter of my thesis determines how neural crest cells are specified at different axial levels. The derivatives and migratory paths of neural crest cells in the cranial and non-cranial regions are very distinct, so the gene regulatory networks are likely to differ as well. Previous work has focused on the cranial neural crest cells, and therefore, regulation of the non-cranial neural crest program remains poorly understood. By taking advantage of transgenic zebrafish lines, I show that a neural crest cell’s position along the AP axis during early development determines its fate./nIn the final chapter of this thesis, I examine how abolishing one cue (Wnt signaling) affects patterning of neural crest-derived cells without affecting earlier aspects of neural crest formation, such as proliferation and differentiation. Analysis of the craniofacial structures in mutants for multiple components of non-canonical Wnt signaling provides evidence that each component is required for proper formation in different axes.

Advisor: Harland, Richard M