VictorJuiz/thesis huggingface dataset:
Investigating translational machinery heterogeneity across cell types, development, and diseases

Recent studies have shown that ribosomes with distinct compositions can differentially regulate gene expression. This compositional heterogeneity can arise from a few sources: ribosomal RNA (rRNA) sequence variation, differential incorporation of ribosomal proteins (RP), binding of ribosome-associated proteins (RAPs) that link translation to cellular processes, and rRNA and RP modifications. Although there have been a few examples of heterogeneity described in prior literature, we lack a full understanding of the extent of ribosome heterogeneity and how ribosome composition changes due to our inability to systematically characterize ribosomes among different biological samples. This dissertation focuses on the diversity in rRNA sequences and RAP compositions that contribute to translational machinery heterogeneity across cell types, tissues, and diseases. We developed novel methodologies to systematically analyze complete rRNA sequences and RAPs for the first time. With respect to rRNA, we built the first comprehensive functional human rRNA sequence variant atlas. This atlas revealed different ribosome subtypes that are genomically clustered in different chromosomes. With this resource, we then showed these variants can be expressed in a tissue-specific or cancer-specific manner. With respect to RAPs, we developed a novel, label-free methodology called RAPIDASH to enrich ribosomes and their associated proteins from any biological sample. We applied this technique to mouse embryonic forebrain, limbs, and liver tissues, which allowed us to identify RAPs with tissue-specific functions. Among these is LLPH, which forms forebrain-specific ribosomes that are important for neurodevelopment. RAPIDASH thus allows us to identify RAPs and understand their roles in modulating gene expressions in development. Together, these techniques enable an in-depth characterization of translational machinery heterogeneity and its role in gene regulation

Keywords: Medicine.
Genetics.
Advisor: Barna Maria (Professor of developmental biology)
Bassik Michael
Pritchard Jonathan (Jonathan K.)
Wernig Marius
Japanese diaspora in a WWII incarceration camp : archaeology of Gila River

"Japanese Diaspora in a WWII Incarceration Camp: Archaeology of Gila River" challenges narratives of closure and removal through an examination of the material lives of 16,000 Japanese Americans imprisoned on a Native American Reservation during WWII. Drawing from archaeological surveys conducted in collaboration with the Gila River Indian Community, as well as archival, oral historical, and ethnographic sources, it traces the connections maintained, formed, and transformed through material practices during the incarceration camp period. By weaving together these threads, I argue that the incarceration camp system reordered the social connections of the Japanese American community. I utilize community-based research methodologies to work towards building decolonized praxis in recognizing diverse community connections and Indigenous sovereignty. Through an attention to the landscape and the material, I show how the expectations of War Relocation Authority administrators were unfulfilled and incarcerees worked to safeguard individual and community health. By using the concept of diaspora to interrupt the notion of the camp, I challenge notions of isolation and control and theorize the camp as a site of connectivity

Keywords: Humanities and Sciences.
Anthropology.
Advisor: Voss Barbara L.
Chang Gordon H.
De León Jason
Ebron Paulla A.
Japan’s Security Strategies Towards China in the Scope of Defense White Papers, 1972-2014

This project explored Japan’s changing security attitudes from 1972 to 2014 under the scope of its official defense white papers, using a method of sentiment analysis. Consistent with previous studies, Japan was highly cooperative with China during the period from 1972 to 1992, a period rightfully characterized as the “Golden Age.” Starting from 1993, faced with a rising China, Japan maintained an overall neutral posture on the official and legal level towards China, but subtle attitudinal changes could be seen. While Japan had praised China for its cooperative efforts to denuclearize the Korean peninsula and active involvement in UN peacekeeping, it also pointed to China’s covert purposes for engaging in such activities and repeatedly raised concerns about a perceived violation of state sovereignty by China on the “Senkaku Islands,” as well as over Beijing’s human rights issues and lack of transparency in military spending. The current project shows that Japan has continued to adopt non-confrontation, non-provocative language even when describing its disputes with China.

Keywords: Japan-China relations
Security policies
White papers
Text
Thesis
Advisor: Tsutsui Kiyoteru
Kant and the dynamics of pure thinking : essays on Kant's theoretical philosophy

In this dissertation, I defend new readings of arguments and claims found in Kant's Critique of Pure Reason. Chapter One defends a new reading of Kant's two-step proof structure in his B-edition of the Transcendental Deduction. Chapter Two defends a new reading of Kant's distinction between general and transcendental logic; Chapter Three defends a new reading of his 'Refutation of Idealism' by examining the legal, logical, and critical uses of 'refutation' in Kant's work

Keywords: Humanities and Sciences.
Philosophy.
Advisor: Friedman Michael
Anderson R. Lanier
De Pierris Graciela Teresa
Wood Allen W.
Knowledge work reimagined : lyric life writing and the university

Postwar academic culture has seen the rise of a literary consciousness and an autobiographical mode. One instantiation of this mode is a contemporary style of writing called "autotheory." While some scholars interpret autotheory as a para-academic literary phenomenon, wishing to trace its lineage outside the university, I show that it is, in fact, rooted in the postwar university, and should be seen as a challenge to prevailing mechanistic epistemologies within the university. As a third way between strictly creative and strictly scholarly writing, autotheory works against prohibitions of self and self-assembly found in a host of humanistic discourses, including philosophy, theory, literary studies, and creative writing. However, I also show that autotheory is a direct outcome of philosophy, specifically the ordinary language philosophy of Ludwig Wittgenstein and Stanley Cavell, and that it plays out key elements of that philosophy. The self-assembly that is accomplished by autotheory is neither narcissistic nor "neoliberal." It is an antidote to the radical self-displacements found in knowledge work. These cultures of radical self-displacement, engaged in what I call the search-for-method paradigm, undermine actual insight in favor of scientism and the administration of concepts. In contrast to this, autotheoretical works, and the tradition of lyric philosophy from which they stem, can be seen as recuperating personality, the experience of meaning, and a coherent political consciousness.

Keywords: Humanities and Sciences.
Advisor: Greif Mark
Greene Roland
Landy Joshua
KRAS-dependent intercellular signaling organizes the tumor microenvironment

Cancer is amongst the leading cause of death in the world, with lung cancer being the leading cause of cancer related deaths. Over half a century of cancer research has revealed many key features of cancer, yet for many cancers we are no closer to treating cancer than the 1900s. Part of this has to do with the heterogeneity of tumors, where the genomic instability induces mutations causing heterogeneous population of cancer cells within one tumor. This would not be much of a problem if this was the only source of heterogeneity in a tumor, but research into the tumor microenvironment reveal the tumor landscape adds several degrees of complexity to tumors. The tumor microenvironment has rapidly gained attention in the cancer community, quickly moving to the forefront of cancer research. The intercellular signaling between cancer cells and its surrounding cells dictate microenvironment composition and tumor progression. Over a dozen different cell types are found in the tumor microenvironment and communicate with each other to create a stable environment for cancer. Much of this communication happens through signaling proteins secreted to the extracellular space. These secreted proteins have already been implicated in various tumor related functions such as tumor growth, angiogenesis, immunosuppression, and metastasis. Despite their importance, the composition of secreted protein in the tumor microenvironment and much of the secreted protein's function remain unknown. This is partly due to the difficulty of studying this set of protein as they are dispersed outside the cell. We expanded the understanding of cancer secreted proteins by profiling the secretome of NSCLC driven by the most prolific oncogene, KRAS, using data independent acquisition on Bruker's state-of-the-art mass spectrometer timsTOF Pro. We identify over 1000 proteins secreted by 27 NSCLC, of which 76 were significantly changed in response to KRAS inhibition. We produced these proteins and applied them to cells in various functional assays to characterize their function and reveal proteins involved in key tumor functions cell including proliferation and cell migration. We then examined signaling responses in the recipient cells by measuring global kinase activity changes in the responding cells using phosphoproteomic analysis and discovered the casein kinase 2 was upregulated in metastasis in response to cancer secreted proteins. We hope to apply our research to translational research, using combinatory treatment based off various points of vulnerability found in our study as therapy for cancer with hopes that we can eradicate this disease once and for all.

Keywords: Humanities and Sciences.
Biology.
Advisor: Jackson Peter
Dixon Scott
Gozani Or
Winslow Monte
Language, multilingualism, and power in world language teachers' ideologies about a second language education

This work questions what is meant by a "multilingual education" in the United States, including how its understandings may be perpetuating harmful power asymmetries. Drawing on interview data from high school world language teachers, it utilizes inductive coding of transcripts to surface teachers' ideologies--professed beliefs, thoughts, and feelings--about a second language education, as well as their thoughts on multilingualism and conceptions of language. Findings include six ideologies, two views of multilingualism, and five conceptions of language, leading to a discussion of two overall interpretations of language and its education: proficiency and expansiveness. The former is argued to be a monolingual view of multilingualism, and implications are considered in light of its ironic and problematic prevalence.

Keywords: Education.
Advisor: Langer-Osuna Jennifer
Goldman Shelley
Martinez Ramon
Valdes Guadalupe
Large detectors for rare event searches

In the last few decades, neutrinos proved to be an extremely rich field to explore physics beyond the Standard Model (SM). In particular, neutrino oscillations are the first substantial phenomenon not predicted by this current framework and represent a major success in this field. Nevertheless, our knowledge on this elusive particle is still lacking of fundamental pieces, such as its mass and nature, which could explain, for example, the origin of the matter/antimatter asymmetry we observe today. Neutrinoless double beta decay (0νββ) is a nuclear process that, if observed, could answer these crucial open questions. These increasingly challenging measurements require dedicated detectors specifically designed for the ultimate physics goal. In this thesis, I'll describe how the physics reach constrains the detector design. To do this, I'll focus on two projects I worked on: the first one is an exploratory study of a novel concept of liquid scintillator detector employing segmented optics, while the second is the design and characterization of two instrumentation setups deployed in liquid xenon. The latter is part of the R&D effort of nEXO, a tonne-scale time projection chamber filled with 90% enriched 136Xe aimed to improve the sensitivity to 0νββ

Keywords: Humanities and Sciences.
Physics.
Advisor: Gratta Giorgio
Graham Peter W.
Schwartzman Ariel G.
Large powers of random matrices

This dissertation comprises five papers, concerned with Wishart and Wigner ensembles. The underlying technique for its results is the method of moments, which in random matrix theory amounts to computing expectations of traces of large powers of matrices and inferring from them properties of the eigenspectrum. The main novelties are twofold, employing trace differences, and using traces to obtain eigenvector universality for a broad family of distributions. This combinatorial approach contrasts with the prevalent means for tackling questions related to eigenspaces, local laws, which rely on resolvents and stochastic differential equations

Keywords: Humanities and Sciences.
Mathematics.
Advisor: Papanicolaou George
Dembo Amir
Ryzhik Leonid
The large-misalignment mechanism for the formation of compact axion structures

Axions are some of the best motivated particles beyond the Standard Model. We show how the attractive self-interactions of dark matter (DM) axions over a broad range of masses, from 10^-22 eV to 10^7 GeV, can lead to nongravitational growth of density fluctuations and the formation of bound objects. This structure formation enhancement is driven by parametric resonance when the initial field misalignment is large, and it affects axion density perturbations on length scales of order the Hubble horizon when the axion field starts oscillating, deep inside the radiation-dominated era. This effect can turn an otherwise nearly scale-invariant spectrum of adiabatic perturbations into one that has a spike at the aforementioned scales, producing objects ranging from dense DM halos to scalar-field configurations such as solitons and oscillons. We call this class of cosmological scenarios for axion DM production "the large-misalignment mechanism." We explore observational consequences of this mechanism for axions with masses up to 10 eV. For axions heavier than 10^-5 eV, the compact axion halos are numerous enough to significantly impact Earth-bound direct detection experiments, yielding intermittent but coherent signals with repetition rates exceeding one per decade and crossing times less than a day. These episodic increases in the axion density and kinematic coherence suggest new approaches for axion DM searches, including for the QCD axion. Dense structures made up of axions from 10^-22 eV to 10^-5 eV are detectable through gravitational lensing searches, and their gravitational interactions can also perturb baryonic structures and alter star formation. At very high misalignment amplitudes, the axion field can undergo self-interaction-induced implosions long before matter-radiation equality, producing potentially-detectable low-frequency stochastic gravitational waves.

Keywords: Humanities and Sciences.
Physics.
Advisor: Dimopoulos Savas
Graham Peter
Silverstein Eva
Large-scale and continuous subsurface monitoring using distributed acoustic sensing in urban environments

This thesis investigates using Distributed Acoustic Sensing (DAS) as a scalable and cost-effective approach for continuous, large-scale monitoring in urban settings. DAS capitalizes on existing telecommunication infrastructure to establish high-resolution seismic recording arrays. The research specifically targets two critical domains: traffic management and near-surface monitoring. The central innovation of this work lies in leveraging moving vehicles as cost-efficient, non-specialized indicators for both traffic and seismic monitoring. This involves tackling various obstacles such as pinpointing the geographical positions of DAS channels, improving the clarity of traffic signals, and overcoming the processing constraints and diminished resolution typical of conventional ambient noise interferometry methods. I first conduct comprehensive field experiments and simulations to characterize vehicle-induced seismic signals, thus providing foundational knowledge for more sophisticated monitoring techniques. Subsequent chapters introduce scalable and precise mapping methods that utilize concurrent onboard GPS and DAS recordings. These methods have proven essential for tasks like fiber interruption localization, enhancing vehicle tracking accuracy, and near-surface characterization. To tackle the issue of degraded signal resolution in urban DAS applications for traffic monitoring, an advanced machine learning algorithm is developed, yielding improved vehicle detection and tracking. Finally, to overcome the limitations of conventional ambient noise interferometry, I present a targeted interferometry approach based on the Kalman filter algorithm. This method enables high-resolution, cost-effective, and time-sensitive characterizations of the near-surface environment, effectively capturing phenomena such as rainfall-induced soil saturation changes. In summary, this research signifies a substantial advancement in the application of DAS technology for urban monitoring, offering solutions that are both state-of-the-art and economically sustainable.

Keywords: Sustainability.
Geophysics.
Advisor: Biondi Biondo
Clapp Robert G. (Robert Graham)
Ellsworth William L.
Noh Hae Young
Large-scale measurements of the cosmic microwave background

The cosmic microwave background (CMB), the afterglow of the Big Bang, is a cornerstone of modern cosmology. Measuring its features with ever-increasing detail has been key to building and validating our current standard cosmological model, thus motivating further attempts to study the CMB with ever greater precision. First, we present the development of the microwave SQUID multiplexer. We show the design and validation of custom warm readout electronics and discuss studies of the fundamental properties of the device and readout combined system. We discuss the first on-sky CMB demonstration of umux and production-scale development at 910x multiplexing factor for upcoming CMB observatories. Together these efforts increase the achieved multiplexing factor for deployment-grade CMB detector systems by over an order of magnitude. Second, we present measurements of CMB E-mode polarization at large angular scales with the BICEP/Keck program. We show the design and execution of new extended-area observations with BICEP3 to map large-scale E-modes across almost 20\% of the sky. We present the updated analysis pipeline for mapmaking, curved sky power spectrum estimation, and likelihood framework. Preliminary analysis shows sensitivity to new cosmology comparable to the best satellite observation-based constraints, demonstrating the potential of future ground-based surveys. Finally, we live in privileged times in cosmology, with access to unprecedented instruments and computing power. This work cannot be done alone: large collaborations of hundreds of scientists are responsible for producing much of the stunning success of modern cosmology. We present thoughts on structural policies to ensure the diversity, equity, and inclusivity of these large-scale collaborations moving forward

Keywords: Humanities and Sciences.
Physics.
Advisor: Ahmed Zeeshan 
Kuo Chao-Lin (Physics professor)
Akerib Daniel S.
Church Sarah Elizabeth
Irwin Kent
Laser modification of nuclear fusion cross-sections

The effect of ultraintense, x-ray laser fields on the value of the nuclear fusion cross-section is studied. Analytic models of this theoretical effect are explored alongside a direct numerical approach to its governing quantum-mechanical equation of motion. Consistencies between certain models and the numerical solution suggest a simplified physical picture sharing features with atomic ionization in optical laser fields, as well as with quantum phase-modulation problems. An estimate of the laser-modified thermonuclear reaction rate in an idealized, low-temperature deuterium-tritium plasma is calculated. Results describe strong-field enhancement effects taking hold at field strengths that are of considerable magnitude, but below the Schwinger limit (taken as an upper cutoff)

Keywords: Engineering.
Advisor: Glenzer S. H.
Hara Ken
Mani Ali (Professor of mechanical engineering)
Laser path optimization strategies for laser powder bed fusion

Metal additive manufacturing promises to enable the production of complex geometries with potentially exotic material properties. One leading paradigm of metal additive manufacturing is laser powder bed fusion, where a laser shines on a powder bed to selectively fuse powder together via heating, layer by layer, to build up a part. The path of the laser strongly affects the temperature field history of the part, which in turn determines the part's microstructure, as well as the presence of defects like porosity, warping, and residual stresses/strains. With the goal of elucidating how good or optimal laser paths can be identified, this thesis presents three main contributions. After an introduction and review of existing laser path optimization strategies in Chapter 1, Chapter 2 demonstrates the viability of modeling the optimal control problem as a board game and applying deep reinforcement learning a la AlphaGo Zero (albeit with major modifications) as an optimization technique. Then in Chapter 3, we show that by making the assumption that the effect of laser heating is finite in time, our optimal control problem can be modeled as an Traveling Salesperson Problem with History, which we prove can be transformed into equivalent Equality-Generalized Traveling Salesperson Problems and Traveling Salesperson Problems. Chapter 4 demonstrates how the structure of the Traveling Salesperson Problem with History can be used to develop a dynamic programming algorithm for solving and how it affects different solvers' performances. Finally, this thesis concludes with reflections on the potential and limitations of our work to improve laser powder bed fusion beyond computational models

Keywords: Engineering.
Mechanical Engineering.
Advisor: Darve Eric
Lew Adrian
Kochenderfer Mykel J.
The last Black public high school in Oakland : what is at stake with the relationship between school closures and Black administered and attended schools

While research has documented the more tangible causes and consequences of school closures in majority-Black neighborhoods, little explores the equally significant consequences of fear of school dissolution and closure on Black children, teachers, and school communities, as caused by Black physical and cultural displacement. This dissertation argues that public non-charter schools, where Black children are educated and Black educators labor, operate under persistent threat of closure and, beyond that threat, are indeed the schools into the 21st century most likely to be shuttered. This phenomenon of school dissolution is placed in conversation with large structural scales of displacement through a novel longitudinal nationwide quantitative study which examines the likelihood that majority Black schools are closed as compared to their non-majority Black counterparts. Further, thematic analysis and ethnographic research methods were utilized to explore one school district's disappearing African American community, the impact on its last majority-Black public high school, and the developed narratives about why the school has been drastically under enrolled - ultimately, threatening its long-term viability. Finally, this dissertation challenges the notion that Black administered and attended (BAA) schools, especially those operating under the threat of closure, do not offer exceptional instruction via interrogating how the conditions of Black displacement shape and inform a veteran African American teacher's pedagogical choices

Keywords: Education.
Advisor: Ball Arnetha F.
Banks Adam J. (Adam Joel)
Rosa Jonathan
Pearman Francis A.