VictorJuiz/thesis huggingface dataset:
The Alchemy of Capital: Industrial Waste and the Chemicalization of United States Agriculture

Along with mechanization and scientific plant breeding, modern forms of industrial agriculture are premised on the use of synthetic chemicals to sustain yield, irrigate fields, decrease erosion, and provide defense against pests and disease. Chemicalized agriculture has its origins in the late 19th and early 20th centuries as the presence of industrially produced chemicals became available on domestic and international markets, as crop production specialized, and as scientists, farmers, and policy makers turned to chemicals to “fix” fertility, pest, and labor issues. While the use of agricultural chemicals has created the conditions for astonishing yields, their generalized use has also resulted in the pollution and degradation of ecosystems, harmful effects on consumers and farm workers, and large greenhouse gas emissions./nThis dissertation investigates the relationships between the late 19th and early 20th century US mining, chemical, and petroleum refining industries, their waste byproducts, and the promotion and naturalization of economic poisons in US agriculture. Specifically, I explore the transition from the ad hoc use of economic poisons on US farms to the use of economic poisons as an agricultural necessity by focusing on the complex and multidirectional links between industrial and chemical waste and the use of a rapidly industrializing and specializing agriculture as an efficacious and profitable outlet for industrial byproducts. Drawing from fourteen archives across the US, I use the history of mining and smelting companies, chemical and petrochemical manufacturers, marketers and dealers, industrial R&D, governmental institutions, university scientists and extension agents, capital investment, environmental regulation, the military, along with politics of an inchoate toxicological science, to narrate the political economic thresholds of industrial waste’s transmutation and US agriculture’s chemicalization. In other words, I relay the historical and political economic origins of economic poisons in US agriculture from the mid 1860s to the end of WWII through the lens of industrial waste.

Advisor: Sayre, Nathan F
Regulation and Genetic Manipulation of Ligands for the Immunoreceptor NKG2D

NKG2D is an important activating receptor expressed by natural killer (NK) cells and some subsets of T cells. NKG2D recognizes a family of cell surface protein ligands that are typically not expressed by healthy cells, but become upregulated by cellular stress associated with transformation or infection. Engagement of NKG2D by its ligands displayed on a target cell membrane leads to NK cell activation, cytokine secretion, and lysis of the target cell. Despite the importance of NKG2D for controlling tumors, the molecular mechanisms driving NKG2D ligand expression on tumor cells are not well defined./nThe work described in this dissertation was centered on the identification of novel regulators of ULBP1, one of the human NKG2D ligands. Using a forward genetic screen of a tumor-derived human cell line, we identified several novel factors supporting ULBP1 expression, and used the CRISPR/Cas9 system to further investigate these hits. Our results showed stepwise contributions of independent pathways working at multiple stages of ULBP1 biogenesis, including transcription of the ULBP1 gene, splicing of the ULBP1 mRNA, and additional co-translational or post-translational regulation of the ULBP1 protein./nOne of the novel regulators of ULBP1 we identified was ATF4, a stress-induced transcription factor. ATF4 drives the constitutive expression of ULBP1 on some cancer cell lines and causes further upregulation of ULBP1 in response to stresses such as amino acid starvation or activation of the unfolded protein response. We found that ATF4 drives ULBP1 transcription by binding directly to the ULBP1 locus./nThe screen also identified the RNA-binding protein RBM4 as a driver of ULBP1 expression. Analysis of RBM4-deficient cells revealed that RBM4 suppresses a novel alternative splicing event in the ULBP1 transcript. The alternative isoform of ULBP1 mRNA is unlikely to encode a functional protein. As such, RBM4 supports ULBP1 expression by promoting the splicing of the functional mRNA isoform./nThis dissertation also describes the use of the CRISPR/Cas9 methodology to generate mice lacking two key NKG2D ligands, RAE-1ε and RAE-1δ. These mice are being used by other lab members to test hypotheses concerning regulation of NK cell activation imparted by RAE-1 expression on host cells within tumors. Additionally, these mice will soon be used to generate mice lacking all known NKG2D ligands./nThe findings presented here highlight diverse mechanisms for the control of NKG2D ligand expression, and offer insight into the stress pathways that alert the immune system to danger. Furthermore, this work demonstrates the power of forward genetic screens and the CRISPR/Cas9 system for both discovery- and hypothesis-driven research.

Advisor: Raulet, David H
Kinetic Inductance Detectors for Dark Matter Searches

Decades of astrophysical observations suggest that 23% of the mass energy of the universe is dark. Meanwhile, particle physics theories favor the existence of a stable and weakly interacting particle, which has yet to be detected. These realities combine to formulate a very well motivated particle dark matter candidate, which was produced in the early universe and still lingers in abundance today. The expectation of a small weak interaction cross-section enables the instrumentation of experiments designed to discover the nature of the dark matter which continues to be an overarching question of cosmology. A detector for this dark matter candidate senses energy from occasional collisions between the dark matter and atomic nuclei; the more nuclei in the detector, the greater its sensitivity to dark matter. The detectors of the Cryogenic Dark Matter Search (CDMS) measure phonons and charge emanating from recoiling germanium nuclei. Its phonon sensors, though exquisitely sensitive, are relatively complicated to fabricate and deploy. Responding to the scientific imperative to increase dark matter sensitivity, we look for a simpler phonon sensor technology. Kinetic inductance based phonon sensors (KIPS) are superconducting thin film microwave frequency resonant circuits. Phonon energy impinging on the film alters its surface impedance, which alters the characteristics of the resonance. KIPS can be made with relatively large, millimeter sized features which makes them easier to fabricate and reduces variations between detectors. This instrumentation focused thesis shows that KIPS can be used as a simple and sensitive phonon sensor for the CDMS detector. KIPS design aspects, competitiveness to the current transition edge phonon sensors, readout considerations and suggestions on how to instrument them in future dark matter experiments will be presented. The broader applicability of KIPS in nuclear non-proliferation and other physics investigations is also discussed.

Advisor: Sadoulet, Bernard
The Betrayal of Brown v. Board of Education: How Brown’s Promise is Unfulfilled and What it Says About the Continuing Problem of Race in Education

As we stand on the cusp of another Supreme Court opinion concerning the use of racial considerations in education from Fisher v. University of Texas, the Court’s final verdict may potentially be another set back for affirmative action policies in education. However, the historical trajectory of the Court’s approach to racial issues in and beyond education suggests a more critical assessment of legal moments such as Fisher is needed. That is, Fisher must be placed within a historical racial narrative carefully orchestrated by the Court. The Court’s racial narrative adjudicates social cleavages on race in areas such as voting rights, employment law, criminal justice, and education. A comprehensive engagement of the Court’s discursive trajectory on race is necessary in order to accurately understand the significance of Fisher in the aftermath of Brown v. Board of Education. Without an engagement of the Court’s previous moments, our understanding of Fisher’s significance becomes limited and trapped within the mainstream colorblind racial narrative that all but dismisses the salience of racial subordination in society. This study will show that by engaging the Court’s long and unfortunate history adjudicating racial issues, white privilege and whiteness has been protected and perpetuated by the Court’s powerful authority. Furthermore, regardless of Fisher’s outcome, an engagement of how the Court has defined, protected, and perpetuated whiteness will fundamentally understand Fisher not only as a defeat or victory for racial considerations in education, but as an instantiation of the continuing problem of race in society. As a result, the persistence of racial subordination in the ‘colorblind’ era is anything but coincidental.

Advisor: Leonardo, Zeus
3D Modeling of Interior Building Environments and Objects from Noisy Sensor Suites

In this dissertation, we present several techniques used to automatically generate virtual models of indoor building environments. The interior environment of a building is scanned by a custom hardware system, which provides raw laser and camera sensor readings used to develop these models. Our modeling techniques can be separated into three categories: 2D floor plan models, simplified 2.5D extruded models, and fully complex and detailed 3D models. All models are produced automatically from the output data of a backpack-mounted ambulatory scanning system, which can scan multiple floors of a building efficiently. We can capture the entirety of a large building in only a few hours, including staircases and other hard to reach locations, which improves upon the state-of-the-art static scanning by several orders of magnitude. Our algorithms are capable of producing many kinds of 3D virtual building models while traversing through a GPS-denied environment, including point clouds, 2D floor plans, and 3D building models./nThe novel contributions of this dissertation fall into three groups. First, we present multiple methods for producing 2D floor plans in a scalable fashion. We automatically partition these floor plans into separate building levels and separate rooms within each level. These floor plans can also be extruded into simplified 2.5D models of the building environment. Second, we present multiple techniques to produce complex 3D models of the scanned environment, capturing all observed detail. Third, we present several techniques that combine these two types of building models -- simple and complex -- to perform additional analysis of the building environment. Such analysis includes segmenting objects and furniture in the environment as separate models, reducing noise and artifacts within the models, and demonstrating novel visualization techniques. Additionally, we show several example datasets generated by the system in real-world environments, including buildings of over 40,000 square feet. We demonstrate how such building models are applicable in many fields of study, including architecture, building energy efficiency, virtual walk-throughs of buildings, indoor navigation, and augmented and virtual reality.

Advisor: Zakhor, Avideh
A Convenient Partnership: The Ribosome and the Nascent Chain Interact to Modulate Protein Synthesis and Folding

During translation, the ribosome reads the genetic code of the messenger RNA, adding one amino acid at a time to the nascent protein. The sequence of the polypeptide determines the three dimensional structure of the natively folded protein, and thus encodes its biological activity. Because folding rates are often fast compared to translation, many proteins likely undergo folding transitions during synthesis, with folding potentially modulated by the sequential appearance of the polypeptide and the chemical environment of the ribosome. Traditional experimental approaches to study protein folding employ chemical, temperature or pH-induced denaturation and would irreversibly destroy the ribosome; thus, such techniques cannot be used to probe folding on the ribosome. In this work, we implement a novel single-molecule optical tweezers assay to probe folding transitions of the nascent polypeptide as it emerges from the ribosome. We demonstrate that the ribosome can modulate the kinetics of folding through interactions between the nascent chain and the charged ribosomal surface. Additionally, the ribosome can prevent misfolding of incompletely synthesized protein fragments. These observations point to a chaperone-like role for the ribosome in guiding the nascent protein to its native state./nIn addition to interacting with the exterior of the ribosome, some nascent chain sequences can form specific contacts with the ribosome exit tunnel. These contacts lead to conformational changes of the ribosome, and reduced translation rates. The Secretion Monitor protein stalls the ribosome upon translation of a 17 amino acid motif. Arrest release requires targeting of the stalled ribosome-nascent chain complex to the translocon; thus, it has been hypothesized that arrest is released by a mechanical pulling force generated as the polypeptide is translocated across the membrane. By applying force to the nascent polypeptide of stalled ribosomes, we demonstrate that translation arrest at SecM is released by mechanical force. Additionally, we show that the force needed to release stalling can be generated by a protein folding in close proximity to the ribosome tunnel exit. Our results demonstrate the feasibility of a feedback mechanism, whereby a folding protein can modulate its synthesis through the generation of force. More generally, since the nascent polypeptide in the cell can undergo a number of potentially force-generating events–chaperone binding, protein or ligand binding, translocation and membrane insertion–force applied to the nascent chain may be an important modulator of protein synthesis.

Advisor: Bustamante, Carlos J
Spontaneous Symmetry Breaking in Nonrelativistic Systems

The subject of condensed matter physics is very rich — there are an infinite number of parameters producing a diversity of exciting phenomena. As a theorist, my goal is to distill general principles out of this complexity — to construct theories that can coherently explain many known examples altogether./nThis thesis is composed of several attempts to develop such theories in topics related to spontaneously symmetry breaking. A remarkable feature of many-body interacting systems is that although they are described by equations respecting various symmetries, they may spontaneously organize into a state that explicitly breaks symmetries. Examples are numerous: various types of crystalline and magnetic orders, Bose-Einstein condensates of cold atoms, superfluids of liquid helium, chiral symmetry in QCD, neutron stars, and cosmic inflation./nThese systems with spontaneously broken continuous symmetries have gapless excitations, so called Nambu-Goldstone bosons (NGBs). Although the properties of NGBs are well understood in Lorentz-invariant systems, surprisingly, some basic properties of NGBs such as their number and dispersion in nonrelativistic systems have not been discussed from a general perspective. In the first part of this thesis, we solve this issue by developing and analyzing an effective Lagrangian that coherently captures the low-energy, long-distance physics of many different symmetry-breaking states all at once./nNext, we examine whether these NGBs originating from spontaneous symmetry breaking remain to be well-defined excitations inside a metal, where low-energy electrons near Fermi surface can collide with them. Our result is a one equation criterion that specifies whether the interactions between electrons and NGBs can be ignored, or whether it completely changes their character. In the latter case, unusual phases of matter such as non-Fermi liquids may arise; in that case, NGBs are overdamped and cannot form particle-like excitations in spite of the assumed symmetry breaking./nIn the last part of this thesis, we investigate the possibility of spontaneously breaking of Hamiltonian itself. The homogeneity of time is one of the most fundamental symmetries of nature, underlying the conservation of the energy. The question is whether this symmetry can be spontaneously broken, as suggested recently by Wilczek, in analogy with ordinary crystals. Contrary to his proposal that attracted a significant attention and stimulated many further studies, we prove a no-go theorem that rules out spontaneously breaking of time translation, in the ground state or in the canonical ensemble of a general Hamiltonian.

Advisor: Vishwanath, Ashvin
Production and Photodissociation of Neutral Free Radicals

The primary photochemistry of several combustion-relevant free radicals have been in- vestigated via photofragment translational spectroscopy. The relevance of radical photo- chemistry will be discussed, along with methodologies and details of each experiment. The experimental apparatus will also be described, especially with regard to the recent installa- tion of a tunable energy electron ionizer. The upgraded ionizer has been a significant advance, allowing for more detailed characterization of the radical source employed in this thesis./nThe photochemistry of the phenyl radical (c-C6H5), a combustion intermediate and pre- cursor to polycyclic aromatic hydrocarbons, was investigated at 248 and 193 nm. At 248 nm, an H-atom loss pathway was found, while at 193 nm both H-atom loss and C2H2 loss pathways were observed. For both wavelengths, P(ET) distributions suggested internal con- version to the ground electronic state followed by energy randomization and dissociation. The branching ratio between the two 193 nm dissociation pathways was found to be 0.2 ± 0.1 in favor of H-atom loss, in good agreement with statistical Rice–Rampsperger–Kassel–Marcus (RRKM) theory./nAn initial investigation of the methyl perthiyl radical (CH3SS) at 248 nm suggested the surprising results of both CH3 + SS and CH2S + SH dissociation channels with no evidence for S-atom loss. In both cases, the translational energy distributions were inconsistent with the expected energetics. Upon reinvestigation, the assumption of radical production—and there- fore radical photodissociation—was shown to be incorrect. The new results demonstrated S-loss and CH3 loss pathways, with the former appearing to involve a repulsive electronic excited state.

Advisor: Neumark, Daniel M
Observational constraints on upper tropospheric NOx emissions, lifetime, and oxidative products

Nitrogen oxides (NOx ≡ NO + NO2) regulate tropospheric ozone (O3) production rates. In the upper troposphere (~8 – 15 km above ground level), where O3 is an important greenhouse gas, there are few detailed measurements of NOx and its oxidation products. As a result, the chemical reactions that involve NOx are poorly characterized under the low temperature conditions in this region of the atmosphere. For the reactions that have been studied under these conditions (e.g., daytime nitric acid, or HNO3, and pernitric acid, or HO2NO2, production), the results from various experiments indicate a 20 – 50% disagreement for the rate constants, and the other important NOx oxidation reactions (production of acyl peroxy nitrate, like PAN and PPN, and alkyl and multifunctional nitrates) have not been well characterized for the conditions characteristic of the upper troposphere. Besides the poorly understood NOx oxidation rates, recent calculations have indicated there is an important upper tropospheric NOx oxidation product (methyl peroxy nitrate, or CH3O2NO2) that has not been measured in the atmosphere. These uncertainties in the products and oxidation rate constants affect the characterization of the input of NOx from lightning./nIn this dissertation, I report observations obtained during two airborne field campaigns, the Deep Convective Clouds and Chemistry (DC3, May – June, 2012) and the Studies of Emissions and Atmospheric Composition, Clouds, and Climate Coupling by Regional Surveys (SEAC4RS, August – September, 2013) experiments, and use these observations to investigate the reaction products and rate constants for the oxidation of NOx to less reactive reservoirs. The observations focused on fresh lightning emissions in deep convective outflow, and the subsequent chemical aging of the outflow downwind./n/nFirst, I present the first ambient observations of CH3O2NO2, and recommendations on how to measure upper tropospheric in situ NO2 with minimal interferences from the thermal decomposition of CH3O2NO2 during sampling. I show that CH3O2NO2 is ubiquitous in the upper troposphere and is as important NOx oxidative product as HNO3. Then, using observations from one quasi-Lagrangian flight during DC3, I derive constraints on the daytime NOx oxidative rate constants for the reactions that remove upper tropospheric NOx. The reactions include the production of CH3O2NO2, HO2NO2, PAN, PPN, alkyl and multifunctional nitrates, and HNO3. These constraints indicate that NOx lifetime is longer than currently believe due to the daytime HNO3 and HO2NO2 production rate constants being 30 – 50% slower than currently assumed. Finally, the implications of the longer lifetime are used to show that lightning NOx emission rates are at least 33% larger than current estimates. As a consequence, model predictions indicate O3 in the upper troposphere increase by 5 – 10% with a resulting increase in radiative forcing.

Advisor: Cohen, Ronald C
Visualizing Sound: Cross-Modal Mapping Between Music and Color

Within the realm of perception, the phrase "cross-modal correspondences" refers to consistent associations between features in two different sensory domains, such as the fact that people commonly associate low-pitched tones with larger visual images and high-pitched tones with smaller visual images. These cross-modal correspondences play an important role in helping our brains solve the multisensory binding problem, that is, deciding what information from one domain to combine with information from another/ndomain. It is less obvious what kind of role cross-modal correspondences might play in music perception and music visualization. In this dissertation, I will describe three different research projects that explore questions about cross-modal correspondences within the context of music: 1) Do people have consistent associations between different colors and musical intervals and chords? 2) Do consistent visual associations exist for musical timbre? 3) What is the relationship between normal cross-modal correspondences and the/nneurological condition known as synesthesia, in which individuals actually experience visual sensations when they are listening to music. Across all three projects, I found that participants had a surprising level of consistency in their associations between visual and musical features, as well as intriguing evidence for a role of semantic and emotional features in guiding these cross-modal correspondences.

Advisor: Palmer, Stephen