VictorJuiz/thesis huggingface dataset:
The Metals from the Cenote Sagrado, Chichén Itzá as Windows on Technological and Depositional Communities

This project is the first to reconcile metals recovered from the Cenote Sagrado at Chichén Itzá, Mexico from three museums in the US and Mexico in which Cenote objects are held. 148 of these metals were characterized through archaeometric studies. Through non-invasive and nondestructive analyses, this project involved the documentation of individual metals, including bells, sandals, and figurines, searched for patterning across the assemblage to identify distinct technological styles, and then compared data to published literature to determine the/nmetallurgical communities in Mesoamerica and Lower Central America indexed by these styles. After performing a visual inspection of each object with a magnifying glass and recording measurements with calipers, optical microscopy with visible, ultraviolet, and infrared light was then employed to comprehensively document object surfaces. Bulk compositions were evaluated with portable-Energy-Dispersive-X-Ray Fluorescence spectrometry. After carrying out these analyses in museum storerooms, with the permission of the Peabody Museum of Archaeology/nand Ethnology, 15 objects were brought to laboratories in New York for finer-resolution studies, including synchrotron-based X-Ray Diffraction and Rutherford Backscattering Spectroscopy, which permitted the evaluation of artificial enrichments on the metals./nThe assemblage consists of copper-based objects, including bronzes of arsenic and/or tin as well/nas brass, and tumbaga, a metal containing gold, silver, and copper. Many show post-fabrication alteration, including indentation, tearing, and wrinkling, practices that may have taken place in ritualized deposition. Two zoomorphic bells were hammered to shape after their lost-wax/ncasting. Two sandals were artificially enriched in silver and gold through electrochemical replacement gilding. Reconciliation of the data with pre-existing literature reveals the contributions of metallurgists in Guerrero and Michoacán (axe-monies), the Tarascan state (tweezers), Veraguas/Chiriquí (anthropomorphic figurines), and Gran Coclé (rolled tubes) to the Cenote deposit. The documentation of sandals in 16th-century literature and the presence of brass suggest that the deposition was developed through connections to the Mexica tributary system/nand through the working of metal imported from Europe, thus, centuries after the main occupation of Chichén (8th-11th century AD). Experimental lost-wax casting and hammering has allowed for exploration of metallurgy as a performative and fully embodied practice and to recognize that the individuals who altered the objects after their fabrication were themselves/nmetallurgists, enacting technical knowledge.

Advisor: Shackley, Steven
The Effect of Inflammatory Stimuli on Cryptic Peptide Presentation for Immune Surveillance

Cytolytic T cells eliminate infected cells by recognizing intracellular peptides presented by MHC class I molecules. The antigenic peptides are derived primarily from newly synthesized proteins including those produced by cryptic translation. Previous studies have shown that in addition to the canonical AUG codon, translation can be initiated at non-AUG codons. Furthermore, translation initiation at non-AUG codons such as CUG is mechanistically distinct from canonical translation initiation as it is resistant to protein synthesis inhibitors that cause global translation shutdown. Here, we show that Toll-like receptor (TLR) signaling pathways involved in pathogen recognition enhance presentation of the cryptically translated peptides. Moreover, infection of bone-marrow derived macrophages with different viruses and bacteria or treatment with pro-inflammatory cytokines also enhances presentation of cryptically translated peptides. Thus, translation and presentation of cryptic peptides may allow the immune system to detect intracellular pathogens that inhibit host translation and presentation of peptides from conventional sources.

Advisor: Shastri, Nilabh
Statistical Methods for Genome Assembly

In the last decade, sequencing technology has progressed rapidly, leading to much faster and cheaper production of short-read data. The challenge of \emph{assembling} the reads into an accurate reconstruction of the sequenced genome, however, has increased. This is because the assembly problem is made more difficult when the reads are shorter, especially for genomes of most higher organisms, which contain complicated repeat structures. In this thesis we study the algorithmic problem of \emph{de novo} DNA sequence assembly, focusing on the challenge of dealing with genomic repeats. We develop two new assembly tools, as well as initiate the study of information-theoretic limits of shotgun sequencing for realistic genomes./nOur first novel algorithm for DNA assembly, Telescoper, is designed for assembly of telomeres. Due to their many repeats, telomeric regions are notoriously difficult to assemble. Telescoper iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. The algorithm utilizes both short and long-insert libraries in an integrated way throughout the assembly process. This approach is shown to effectively resolve some of the complex repeat structures found in the telomeres of yeast genomes./nOur second novel algorithm for DNA assembly, Piper, takes a statistical approach to resolving ambiguity caused by repeats. A lot of potentially useful information is present in paired-end reads, but due to the inherent noise in the insert length and the combinatorial nature of the problem, it is not clear how to best use this information. Piper selects a {\em set} of candidate paths through the contig-graph, and scores them based on their likelihood given a generative model for the reads. The output consists of a ranked set of assemblies (rather than a single assembly) in order to give the maximum information available, while still explicitly encoding unresolved ambiguity. On small simulated datasets, Piper produces excellent error-free assemblies./nIn the final portion of the thesis, we investigate the information-theoretic limits of DNA sequencing, focusing on the effect of repeats. Specifically, we ask: how many reads of a given length are necessary in order to perfectly reconstruct with a certain target probability? We focus on a simple read model, with noiseless single-end reads, but consider arbitrary genomic sequences. We first prove a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on known algorithms, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction.

Advisor: Song, Yun S
"Other Lovings": Abjection, Love Bonds, and the Queering of Race

This dissertation discusses the intersection of racial abjection and love bonds in late 20th-century and 21st-century African-American and Asian-American literature and culture. The manuscript deploys affect studies and queer theory to discuss works by Audre Lorde, Amiri Baraka, David Henry Hwang, Adrian Tomine, and Gayl Jones, in addition to the cultural phenomena of "Linsanity" and "afro-pessimism." Whereas most critical readings of failed love in minority literature have emphasized the tragic interpersonal consequences of internalized racism, this dissertation argues that these writers narrate love's apparent failure in order to explore the positive content emergent in the felt rupture of breakups. Through readings of dissolved love relationships in these authors' works, I inquire into love's operation as an affect that always desires more and better sociality. The appearance of love's failure is precisely what illuminates the ineluctably positive content of love, and I situate this content in the context of recent theoretical discussions of love as narcissistic, not-yet-here, oppressive, or antisocial. The project ultimately argues that blackness, yellowness, and queerness share a privileged access to and familiarity with love's affective positivity.

Advisor: JanMohamed, Abdul
Development of an air-stable, high energy density printed silver oxide battery for printed electronics

Printed batteries are an emerging battery technology that has the potential to enable the production of cheap, small form factor, flexible batteries capable of powering a diverse set of existing and emerging applications such as RFID tags, flexible displays, and distributed sensors. Partially printed battery systems have been demonstrated with various chemistries, but what is needed is a low cost, air stable method of fully printing a high energy density battery. The silver oxide chemistry is attractive for developing a printed battery as this chemistry has demonstrated high energy densities and is capable of air stable fabrication processes due to its aqueous based chemistry. To facilitate the advancement of this technology, material components and printing techniques need to be developed to demonstrate a printed silver oxide battery./n/nIn this thesis, I will present a printed, high energy density silver oxide battery using stencil printing. A key development of this work is the demonstration of a novel photopolymerized polyacrylic acid separator layer. The mechanical and conductivity properties of this layer are characterized and optimized for an alkaline silver oxide battery. The incorporation of this layer has enabled a printed battery capable of high rates of discharge. The batteries show no difference in discharge upon flexing at a bend radius of 1.0 cm, indicating their potential in flexible applications. The fabricated batteries have demonstrated high energy densities of 10 mWhr cm -3 and areal capacities of 5.4 mAhr cm-2, which satisfies the power and capacity requirements for most of the proposed applications. In addition, we have examined several printed encapsulation schemes (epoxy and silicone caulk) for encapsulating an alkaline battery.

Advisor: Subramanian, Vivek
Characters of Design: Writing and Materiality in Early China

This dissertation examines ornamental writing on bronze vessels, ceramic eave tiles, and silk textiles dated from the Spring and Autumn period (ca. 771-476 BCE) to the end of the Eastern Han dynasty (25-220 CE). These inscriptions--cast, inscribed, incised, or woven for display--provide an analytically rich site for providing a theory of writing because part of, if not all, of their identity is defined by an artisan's deliberate occlusion of their readability. I use a two-part method to study these scripts. The first approach attends to the recursive and replicatory design process of artisanal practice through epigraphical studies of extant characters and analyses of technological limitations and developments during the period in which these objects were produced. The second path explores how ornamental writing visually elaborates and conveys information. While the initial step addresses design and material technology, this line of inquiry provokes its audience in asking, "What do we see?" and "What do we read?" when confronted with ornamental script at various stages of its production. Research into excavation sites, workshop practices, and artisanal literacy informs my reconstruction of the conditions under which these inscriptions were seen.

Advisor: Berger, Patricia
The Paradox of Poverty and Plenty: Egypt, India, and the Rise of U.S. Food Aid, 1870s to 1950s

This study show how American food production became a pillar of U.S. global power after the Second World War. To analyze the character of that power and the global scale on which it was exercised, the study traces its historical roots in two regions of the former British Empire. From the 1950s to the 1970s, countries across what had come to be called the "Third World" became reliant on imports of U.S. food aid to manage their domestic food supply, in an international political and economic arrangement that sociologists Harriet Friedmann and Phillip McMichael have called the post-war "food regime." Focusing on the largest consumers of U.S. food aid by the 1960s--Egypt and India--my study examines the foundations of this regime beginning in the late nineteenth century./nDrawing on sources in Arabic, French, and English from Egyptian, Indian, British, and U.S. archives, the dissertation shows how a range of actors in Egypt, India, and the United States contributed to produce institutions and ideas to regulate and make sense of volatile and unruly global markets between the late nineteenth century and the Second World War. Those institutions and ideas came to undergird a food regime structured around the U.S. export of food aid by the 1950s. Small and large farmers, wageworkers, consumers, and social scientists interacted with one another, and with government administrators and policymakers, in the making of this world. The study traces this history through social scientific writings, political tracts, private letters, propaganda, government records and reports, labor and farm newspapers, and petitions from farmers, workers, and consumers to state officials./nThrough the history of food and agriculture, the dissertation offers a new lens for understanding how the United States emerged as a global power out of a British imperial world. It also shows in a practical way a different mode of writing global history. In order to understand how food became such a significant international political tool for American policymakers beginning in the 1950s, the study suggests, we must recognize that its power was contingent on particular struggles, conflicts, and compromises, not only within the United States, but also in countries like Egypt and India. Global processes did not simply affect local and national politics, but were also constituted by them.

Advisor: Candida-Smith, Richard
The impacts of sleep and sleep deprivation on human brain and behavioral incentive processing

Despite an emerging link between alterations in motivated behavior and a lack of sleep, the impact of sleep deprivation as well as the potential benefit of sleep, when it is achieved, on human brain mechanisms of reward and punishment remain largely unknown. Targeting these unanswered questions, this thesis aims to determine the impact sleep loss on human brain incentive processing in topics of 1) food desire and 2) monetary gains and losses. From these investigations four main findings have emerged that make up the first four chapters of this report: 1) In the context of food choices, sleep deprivation leads to significantly decreases activity in appetitive evaluation regions within the human frontal cortex and insular cortex during food desirability choices, combined with a converse amplification of activity within the amygdala ultimately leading to increased high calorie food choices. 2) In the context of monetary rewards and losses, sleep deprivation did not lead to measurable changes in activation to the anticipation of rewards and losses in the nucleus accumbens or insula respectively. However, sleep deprivation did lead to diminished medial prefrontal cortex responses to gain outcomes and increased anterior insula response to loss outcomes. 3) Although there were no observable sleep deprivation group effects on anticipation of monetary gains and losses, there was a significant interaction of sleep deprivation with a trait dopamine transporter genetic polymorphism that determined the impact of sleep deprivation on anticipatory response to gain and loss in the nucleus accumbens and anterior insula respectively. 4) In the context of learning from monetary incentives, sleep deprivation led to a specific deficit in the ability to learn from monetary gains but no change in the learning profile for monetary losses. Finally, in addition to these four findings on the impacts of sleep deprivation on human incentive processing, the final chapter (5) focuses on the relationship between sleep, when it is achieved, and next day reward responsivity. Here there is a significant relationship between individual differences in REM sleep beta power and next day nucleus accumbens response to anticipation of rewards. Beyond these basic scientific insights, such results offer potential clinical relevance given that sleep disruption is highly co-morbid with numerous psychiatric and neurological conditions associated with dysfunctional dopaminergic reward processing (e.g., Parkinson's disease, substance abuse, and obesity). Such findings further indicate that sleep intervention may represent an under appreciated and novel therapeutic target particularly for disorders of the reward system.

Advisor: Walker, Matthew P
From Cores to Envelopes to Disks: A Multi-scale View of Magnetized Star Formation

Observations of polarization in star forming regions have been made across many wavelengths, many size scales, and many stages of stellar evolution. One of the overarching goals of these observations has been to determine the importance of magnetic fields—which are the cause of the polarization—in the star formation process. We begin by describing the commissioning and the calibration of the 1.3 mm dual-polarization receiver system we built for CARMA (the Combined Array for Research in Millimeter-wave Astronomy), a radio telescope in the eastern Sierra region of California. One of the primary science drivers behind the polarization system is to observe polarized thermal emission from dust grains in the dense clumps of dust and gas where the youngest, Class 0 protostars are forming. We go on to describe the CARMA TADPOL survey—the largest high-resolution (∼1000 AU scale) survey to date of dust polarization in low-mass protostellar cores—and discuss our main findings: (1) Magnetic fields (B-fields) on scales of ∼1000 AU are not tightly aligned with protostellar outflows. Rather, the data are consistent both with scenarios where outflows and magnetic fields are preferentially misaligned (perpendicular) and where they are randomly aligned. (2) Sources with high CARMA polarization fractions have consistent B-field orientations on large scales (∼20'', measured using single-dish submillimeter telescopes) and small scales (∼2.5'', measured by CARMA). We interpret this to mean that in at least some cases B-fields play a role in regulating the infall of material all the way down to the ∼1000 AU scales of protostellar envelopes. Finally, (3) While on the whole outflows appear to be randomly aligned with B-fields, in sources with low polarization fractions there is a hint that outflows are preferentially perpendicular to small-scale B-fields, which suggests that in these sources the fields have been wrapped up by envelope rotation. This work shows that the ∼1000 AU protostellar envelope may be a turning point: at larger scales B-fields may still retain the memory of the global B-field drawn in from the ambient medium; but at smaller scales the B-fields may be affected by the dynamics of both envelope and disk rotation. This sets the stage for ALMA (the Atacama Large Millimeter/submillimeter Array), which will soon reveal the morphology of B-fields in circumstellar disks themselves.

Advisor: Plambeck, Richard
"What the Heart Unites, the Sea Shall Not Divide": Claiming Overseas Czechs for the Nation

This is a study of nation-building, liberal politics, and overseas migration among a small people in a supranational empire. By 1914 around one million Czechs (from a nation of six million) permanently resided outside the Bohemian Lands. About half of these expatriates settled in the United States. In feuilletons, travel narratives, brochures, works of scholarship, theatrical plays, popular fiction, and above all in journalism, patriotic Czechs grappled with the question of mass emigration. What did it mean for the existence of a small people in a supranational empire that one of every six co-nationals lived outside the homeland? When confronting this question, leaders of the Czech national movement reacted with ambivalence. As self-proclaimed liberals they lacked a language with which to oppose the free movement of labor. But as nationalists they worried over the loss of Czech hands and hearts. Ambivalence was at the core of the emigration question; a discourse that developed from an appeal to the emigrant's sense of patriotism to a systematic critique of the Habsburg state and the call for State Rights. This dissertation examines the first decades of mass labor migration from Bohemia and the emergence of the Czech national movement between 1848 and 1873. It argues that Czech liberals adapted a vocabulary of European expansion in order to justify their claim to State Rights within the Habsburg Empire and their leadership role within the national movement. Mass emigration made this possible; the presence of co-nationals in distant lands enabled national leaders to portray their nation as a carrier of civilization to backward parts of the world. By the period's end this project of overseas nation-building had adopted ethnic, even racial overtones. The image of Czech national expansion (a surprising formulation for a stateless and landlocked people) was projected as far afield as the American West and the Russian Far East, and national activists worked to transform Bohemian emigrants into Czech colonists.

Advisor: Connelly, John
Structural and biochemical studies of sigma 54 dependent Gene transcription Initiation

This thesis addresses several questions regarding the structure details of the proteins involved in sigma 54 dependent gene transcription initiation both in E.coli and Aquifex aeolicus. In order to place each topic in its appropriate context, a general introduction is provided in the first chapter, and supplemented with additional, more detailed introductions in each subsequent chapter. The second chapter reflects the central project of this thesis, the determination of the -24 DNA binding domain of sigma 54 from E.coli using Nuclear Magnetic Resonance spectroscopy. The structure, which is a three-helix fold, was compared with the same domain in the sigma 54 from A. aeolicus. DNA binding affinity with the -24 promoter element was also determined by using native gel./nIn the third chapter, I describe the previous biochemical studies of histidine kinase sensor protein 4 from Aquifex aeolicus. Then I present my work towards the structural studies of PAS domain of Hksp4 using X-ray crystallography. Diffraction data with 2.8 Angstrom resolution was analyzed, which showed the completeness of the data is below 90%. Molecular replacement was used to build the initial electron density map with no success due to the low sequence identities between the target protein and the models. Experimental phasing was also tried with no success in growing crystals./nIn the fourth chapter, I work on the structure determination of NtrC from Salmonella typhimurium, which is among the very first few proteins studied in the sigma 54 dependent gene transcription initiation process. The initial attempt was to use NMR. Beryllofluride was used to activate the RC domains of NtrC. Without the DNA binding domain, RC domains can not be activated by beryllofluride like the full length. Then X-ray crystallography was used for the full-length NtrC to determine the structure of NtrC in the activated state. However, the studies were complicated by low solubility and protein aggregation problems. No crystals were formed in the activated state.

Advisor: Wemmer, David E.