VictorJuiz/thesis huggingface dataset:
Gymnastics in Translation—Deciphering Ribosomal Frameshifting Dynamics

The genetic content of a messenger RNA (mRNA) can be recoded and hence expanded when the translating ribosomes are programmed to switch reading frames. For instance, the dnaX gene mRNA from Escherichia coli programs ribosomes to synthesize not one but two protein products: the 0-frame encoded τ subunit and the -1-frameshifted γ subunit for DNA polymerase III. It was thought that the latter product is translated via a probabilistic -1-nucleotide slip midway during translation across a slippery sequence, AAAAAAG. mRNA structural barriers flanking the slippery sequence—i.e. a Shine-Dalgarno:anti-Shine-Dalgarno mini-helix and a stable hairpin—can further “actuate” the ribosome to frameshift with an efficiency as high as 80% (= (γ/(γ+τ))×100%). However, the mechanism, including the timing and location of such a -1-slip, remain unresolved./nIn my PhD work presented here, I attempted to determine when within one translation cycle a slippage occurs by following a single ribosome translating a frameshift-programming mRNA held on optical tweezers. To complement the translation dynamics observed in real time, by mass spectrometry, I surveyed the entire pool of synthesized polypeptides to identify on which codon the ribosome slipped./nMass spectrometry of translated products shows that ribosomes enter the -1 frame from not one specific codon but various codons along the slippery sequence and slip by not just -1 but also -4 or +2 nucleotides. Coincidentally, single-ribosome translation trajectories detect distinctive codon-scale fluctuations in ribosome-mRNA displacement across the slippery sequence, representing multiple ribosomal translocation attempts during frameshifting. Flanking mRNA structural barriers mechanically stimulate the ribosome to undergo back-and-forth translocation excursions, thereby permitting the ribosome to explore alternative reading frames. Both experiments reveal aborted translation around mutant slippery sequences, indicating that subsequent fidelity checks on newly adopted codon position base pairings lead to either resumed translation or early termination. What has then emerged from our results is a versatile ribosomal frameshifting scheme during mRNA translocation, mediating broad branching of frameshift pathways./nOccurrence of the unsuccessful frameshifting thus prematurely terminated events had been previously overlooked and now provides a proper metric accounting for every frameshifting attempt. These events not only represent a biological context where translation quality critically relies on retrospective fidelity checks conducted by the ribosome. They result in stalled ribosomes on the mRNA—which are known targets constantly under cellular surveillance—and hence implicate canonical signaling critical for cellular regulation network.

Advisor: Tinoco, Jr., Ignacio
Efficient Multi-Level Modeling and Monitoring of End-use Energy Profile in Commercial Buildings

In this work, modeling and monitoring of end-use power consumption in commercial buildings are investigated through both Top-Down and Bottom-Up approaches. In the Top-Down approach, an adaptive support vector regression (ASVR) model is developed to accommodate the nonlinearity and nonstationarity of the macro-level time series, thus providing a framework for the modeling and diagnosis of end-use power consumption. In the Bottom-Up approach, an appliance-data-driven stochastic model is built to predict each end-use sector of a commercial building. Power disaggregation is studied as a technique to facilitate Bottom-Up prediction. In Bottom-Up monitoring and diagnostic detection, a new dimensionality reduction technique is explored to facilitate the analysis of multivariate binary behavioral signals in building end-uses.

Advisor: Spanos, Costas J
How Authoritarian Survival Strategies Affect Civil War Onset

This dissertation studies causes of civil war from a game theoretic perspective. It aims to understand not only how authoritarian leaders can strategically mitigate prospects for civil war, but also why authoritarian rulers may pursue activities that increase conflict propensity—despite the large adverse welfare consequences of civil wars. Each essay focuses primarily on one particular authoritarian survival strategy: building military capacity, extracting resources from society, and excluding threatening ethnic groups from power at the center. The dissertation applies these strategic considerations to engage two major debates in comparative politics: how each of oil wealth and inter-ethnic relationships affect prospects for fighting. The first essay argues that although oil wealth exerts certain effects that increase incentives for rebel groups to fight to control the capital, oil wealth also increases government revenues and exerts an overall effect of decreasing center-seeking civil war propensity. The second essay focuses on a different aspect of oil production, showing how local oil wealth facilitates government territorial encroachment and increases incentives to fight a separatist civil war for oil-rich ethnic minority groups. The third essay extends the focus on inter-ethnic bargaining by showing ethnic groups organized as pre-colonial kingdoms in Sub-Saharan Africa undermined inter-ethnic institution building and increased incentives for ethnopolitical exclusion, civil wars, and military coups after independence.

Advisor: Powell, Robert
The Archaeology of Economic Systems in the Central Levant during the Middle Bronze Age: A Case Study from Kamid el-Loz (Lebanon)

This dissertation investigates the economic systems operating during the Middle Bronze Age (2000-1600 BCE) at Kamid el-Loz, a decentralized settlement situated in the Beqa’a Valley of Lebanon. The scope is to examine trade structures that involved peripheral exchange centers found throughout the Beqa’a Valley and their interaction with the commercial hubs of the Lebanese coast and the hinterland settlements of southwestern Syria. During this time, settlements throughout the ancient Near East witnessed a process of regeneration that followed the collapse of Early Bronze Age IV (c. 2200-2000 BCE) societies. The development of more complex economic networks and political relationships, as well as the arrival of new ethnic groups, characterized this renewal./nThis dissertation sets forth two main research questions: How can the material culture and the geographical setting of Kamid el-Loz shed light on the economic systems of the central Levant and southwestern Syria? And, to what degree was the Beqa’a Valley integrated into the cultural milieu of the Eastern Mediterranean during the Middle Bronze Age? To answer these queries, the ceramic vessels found in the storage rooms of the Kamid el-Loz palace were analyzed and thematic maps using Geographic Information System (GIS) software were created to reconstruct the commercial paths through which materials circulated./nThe results from this study indicate that Kamid el-Loz had a well structured palatial organization that shared the same international exchange networks that involved the coastal Middle Bronze Age centers. The Beqa’a Valley was linked to this greater system of trade through paths used to surmount the obstacles posed to circulation by the mountain ranges that border this area. Interactions between these different regions are visible in the material culture recovered at Kamid el-Loz, which evidences a process of adaptation and selection of non-local motifs./nOne contribution of this project to the archaeology of the Middle Bronze Age Levant is the reconstruction of the ceramic vessel economy of Kamid el-Loz. In addition, the recreation of ancient networking trails in the Beqa’a Valley will provide a model useful for the understanding of exchange systems across the region, especially in the central Levant. Finally, determining the level of foreign interaction among settlements belonging to three different geographic areas will contribute to the social sciences by providing insight into how ancient societies received and reacted to external cultural influences.

Advisor: Feldman, Marian H
Porter, Benjamin W
Cavite Chabacano Philippine Creole Spanish: Description and Typology

This dissertation provides a grammatical description and sociohistorical account of the Cavite variety of Philippine Creole Spanish (PCS), also known as Cavite Chabacano (CC); and analyzes how this language informs standard typological characterizations of contact languages. CC is one of three surviving varieties of Chabacano, a Spanish-lexified contact language of the Philippines. The unique status of Chabacano as the only Spanish-lexified creole in Asia presents a number of typological challenges to standard views of colonial contact languages based on prototypical plantation creoles. Most work on Chabacano assumes that it is a creole language, and only a few recent works on the Zamboanga variety of Chabacano have questioned this classification. The current work reexamines the status of Chabacano as a creole language by providing linguistic data from an understudied Chabacano variety and examining it from a typological perspective./nOn the descriptive front, the dissertation provides a sketch grammar that constitutes the most complete description of the language to this date. The linguistic description is supplemented with a sociohistorical reconstruction that proposes different stages in the development of CC: an initial period of koineization, a period of hispanization or ‘decreolization’, and a latter period in which more Tagalog forms were incorporated from the adstrate. Comparative linguistic evidence from CC and two other Chabacano varieties supports this account./nThe latter part of the dissertation evaluates the CC using typological accounts of contact languages. It is argued that the language poses two main challenges to previous models of language contact outcomes; first, it shows continuity between the lexifier and the creole, and second, it shows that the language's classification into a category such as koiné or creole may shift during the development of the language. A model of radial categories (Lakoff 1987) is suggested as an alternative to more restrictive categorizations of language contact outcome

Advisor: Michael, Lev D
Improvements in Energy Decomposition Analysis for Single Determinant Methods

This thesis is concerned with the decomposition of intermolecular interaction energies computed by Hartree-Fock theory or Kohn-Sham density functional theory into physically meaningful contributions. While there is no unique way to perform this energy decomposition analysis (EDA), such methods can be judged based on formal properties, physical content, and descriptive power. Throughout this work we assess and address the weaknesses of the Absolutely Localized Molecular Orbital (ALMO) energy decomposition scheme to develop a new scheme with terms describing five distinct physical contributions: permanent electrostatics, Pauli repulsion, exchange-correlation, polarization, and charge transfer. This scheme moreover has many desirable formal properties, satisfying all of the criteria for a good EDA method that we outline in the introduction.

Advisor: Head-Gordon, Martin
Adolescents' and Young Adults' Understanding of Others' Moral Decisions

This study examined adolescents’ and young adults’ understanding of others’ moral decisions in situations involving competing concerns. The study combines the work of theory-of-mind and social domain theory as it pertains to how people develop a social and moral understanding of others, respectively. The participants (N = 102), approximately equally divided by sex and from two age groups (adolescents and young adults), were posed questions about decisions made in hypothetical situations involving conflicts between a moral concern and a nonmoral concern. For each situation, half of the participants responded to the decision consistent with the moral concern and the other half responded to the decision consistent with the nonmoral concern. Participants were asked to attribute intentions to the actor, evaluate the decision, and provide justifications for their evaluations. Findings showed that participants generally endorsed the decisions consistent with the moral concern for two of the three situations. In addition, partial support was found for the hypotheses that their understanding of each situation would include multiple considerations and be related to the actor’s decision. Findings are discussed in terms of the role of construals in understanding and evaluating moral decisions in multifaceted situations, as well as implications for future research.

Advisor: Turiel, Elliot
In Situ Investigations into CaCO3 Nucleation

Classical theories of nucleation were developed over a hundred years ago starting with Gibbs. However, much remains unknown about the process of phase transition in aqueous electrolyte solutions due to the lack of experimental tools able to probe dynamic processes at the time and length scales of the phase transformation. In the calcium carbonate system, recent discovery of an amorphous phase, as well as the suggested existence of potential precursor states such as so-called 'pre-nucleation clusters' or dense liquid droplets, has called into question the utility of the classical framework in making accurate predictions of nucleation./nAdded to these questions are those regarding the effects that chemical templates have on nucleating calcium carbonate. Many organisms use complex organic matrices to form architecturally complex functional structures out of sea water at ambient temperatures. By contrast, laboratory methods to materials synthesis often require extreme conditions yet maintain at best a low level of control over the development of the resulting material. With the goal of tightly controlling formation of functional materials, scientists have looked to such biomineral systems for inspiration. Self-assembled monolayers (SAMs) of functionalized alkanethiols have been found to act as idealized chemical templates for calcium carbonate nucleation, controlling the nucleating plane of the calcite phase for many surface functionalities. Yet there remain many open questions as to the fundamental mechanisms by which these templates achieve this control./nIn this dissertation many investigations of calcium carbonate nucleation are discussed, which examine the nucleation pathways of calcium carbonate and mechanisms of control by which alkanethiol surfaces direct the oriented formation of calcite. Traditional in situ microscopy techniques are used to make nucleation rate measurements of templated calcite nucleation on alkanethiol SAMs to test the applicability of the predictions of classical nucleation theory to this system. Low resolution microscopy techniques are further used to provide indirect evidence for the formation pathways of calcite on SAMs exhibiting different surface chemistries. The development of a platform for liquid phase transmission electron microscopy (TEM) utilizing a sealed liquid cell is described, and its utility in making novel observations of materials formation processes is demonstrated. Liquid phase TEM is further employed, using an open cell system which allows for mixing reagents, to directly observe formation pathways in the CaCO3 system.

Advisor: Minor, Andrew M
De Yoreo, James J
Maize RNA polymerase IV complexes and their control of gene function

Plants have acquired and maintained an expanded suite of DNA-dependent RNA polymerases (RNAPs) compared to other eukaryotes. Although their exact roles remain unclear, plant-specific RNAPs (Pol IV and Pol V) are involved in epigenetic silencing of transposable elements (TEs). Zea mays (maize) Pol IV is required for proper plant development as well as the establishment and maintenance of paramutations, which are trans-homolog interactions that facilitate heritable gene silencing. Maize has duplications of Pol IV catalytic subunits, which define multiple Pol IV subtypes, and accessory proteins associated with these subtypes define distinct Pol IV complexes. Understanding the roles of Pol IV will require identifying the composition and function of these Pol IV subtypes and complexes. In exploring interactions between the genes encoding a Pol IV catalytic subunit and a putative accessory protein, I identified two new alleles of the Pol IV subunit and a family of potential Pol IV accessory proteins conserved in multicellular plants. Together, these Pol IV complexes are proposed to function through two, potentially overlapping, general mechanisms to control of gene function: direct competition with Pol II and/or generation of 24-nucleotide RNAs that guide de novo cytosine methylation. I analyzed nascent transcriptome data of seedlings lacking Pol IV and their wild-type siblings, which identified a global effect of Pol IV on gene boundary transcription. Pol IV-affected loci serve as molecular and phenotypic models for dissecting the involvement of various Pol IV subtype and complex components. Such analysis implicated a Pol IV-affected allele as being controlled by Pol IV competition with/nPol II. Through expanded sequencing of a paramutation participating allele (Pl1-Rhoades), I identified a new Pol IV target of five tandem repeats that may serve as an enhancer element. I used the Pl1-Rhoades allele in particular to compare and contrast the effects of Pol IV loss with that of Pol IV accessory proteins. Together, the work presented here explores the involvement of an uncharacterized protein family of putative Pol IV accessory proteins in/nPol IV complexes, expands the roles of Pol IV complexes in controlling maize gene function, and identifies new Pol IV-affected loci for future study.

Advisor: Hollick, Jay B
Rine, Jasper D
Towards Secure and Privacy-Preserving Online Social Networking Services

Online social networking services (e.g., Facebook, Twitter, and Blogger) bring new benefits to almost all aspects of our lives. They have completely transformed how we communicate with each other, how we process information, and how we diffuse social influence. However, these social networking services are also plagued by both conventional and emerging threats to security and privacy. For instance, two fundamental security risks are 1) users’ accounts are compromised by attackers or get lost and 2) attackers create massive fake (or Sybil) accounts to launch various malicious activities. In this thesis, we first design secure and usable account recovery methods based on users’ trusted friends to recover compromised or lost user accounts. Second, we construct a scalable semi-supervised learning framework, which is based on probabilistic graphical model techniques, to detect Sybil accounts. Third, we demonstrate that diverse private information (e.g., private user demographics and hidden social connections) can be inferred with high accuracies from data that is publicly available on social networking sites, which has implications for the design of privacy-preserving online social networking services.

Advisor: Song, Dawn
Establishing reference in Máíhĩ̵̀kì

In this dissertation, I investigate the hierarchical nominal lexicon of Máíhĩ̵̀kì, an endangered Western Tukanoan language spoken in northern Peruvian Amazonia. With data from original fieldwork, I establish eight types of nouns in Máíhĩ̵̀kì, each of which patterns distinctly from the others with respect to at least seven different morphosyntactic behaviors. I argue that these patterns can be predicted from the inherent semantic properties of the nouns, and provide a formal account of the parameters that govern the structure of the proposed hierarchy. In particular, I establish the notion of a `reference ratio'---the ratio of properties that are requisite to the entities in some set to the properties that are incidental of those entities./nThe first half of the dissertation provides an in-depth grammatical description of Máíhĩ̵̀kì. A chapter on Máíhĩ̵̀kì phonetics and phonology includes a detailed description of the language's nasal spreading and tone systems, and a chapter on Máíhĩ̵̀kì morphosyntax includes extensive treatments of deixis, event structure, and clause-linking devices./nThe latter half of the dissertation discusses the semantics of Máíhĩ̵̀kì nouns and nominal morphology. I provide a summary of the literature on nominal hierarchies, then argue for one such hierarchy in Máíhĩ̵̀kì based on the distinct morphosyntactic behaviors of nouns. I look at two of these morphosyntactic behaviors---the availability of plural morphology and the ability to be suffixed with or serve as a nominal classifier---in depth. A chapter on noun classification provides background on the typology of the phenomenon, including a discussion of the features of noun categorization devices common to northwest Amazonia. In addition to the typological survey, I provide a novel semantic analysis of Máíhĩ̵̀kì classifiers that has implications for the theory of both classification and nominal compounding. In a chapter on plurality, I provide a formal semantic analysis that addresses the complexities of number marking in Máíhĩ̵̀kì, including the availability of multiple pluralization strategies and their apparent optionality. The role of both classifiers and plurals in altering the reference ratio of nouns is examined throughout.

Advisor: Michael, Lev D.
Synthesis, Reactivity and Catalytic Applications of Two-Coordinate First Row Transition Metal Complexes

Recently, the development of more sustainable catalytic systems based on abundant first-row metals, especially nickel, for organic transformations has attracted significant interest. This thesis describes the development of new synthetic methods for the preparation of two-coordinate complexes of a variety of first row transition metals. The physical and spectroscopic properties of these complexes are discussed and the reactivity and catalytic applications of these compounds are also explored. Species of this type are found to catalyze a variety of useful organic transformations using inexpensive metals and ligands.

Advisor: Tilley, T. Don