VictorJuiz/thesis huggingface dataset:
Precursor-directed biosynthesis of macrolide antibiotics [electronic resource]

Macrolides have long been among the most widely used antibiotics. Despite this utility, development of new macrolides through traditional synthetic and semisynthetic approaches has been greatly hindered by the inherent structural complexity of these compounds. Precursor-directed biosynthesis is a technique which circumvents this difficulty by incorporating simple synthetic precursors into a biosynthetic pathway, allowing the bulk of the molecule to be constructed enzymatically. This dissertation describes the evolution and application of a system for the facile production of new macrolides through precursor-directed biosynthesis. The results of this work are the discovery of an unexpected macrolide structure-activity relationship and the ultimate discovery of a promising new lead for macrolide development.

Keywords: Chemistry
Advisor: Khosla Chaitan
Pande Vijay advisor. Thesis advisor
Puglisi Joseph D. advisor. Thesis advisor
Predicting wind power in marine and coastal environments [electronic resource]

Offshore wind power has the potential to provide substantial carbon-free electricity near large urban load centers, yet it represents only about 1.5% of the total installed wind power capacity (about 200 gigawatts) worldwide in late 2011, with nearly all of those installations in Europe. Despite thousands of megawatts of potential in the coastal areas of the US and hundreds of megawatts proposed off the US East Coast, a single offshore turbine has yet to be built. The dissertation analyzes the offshore wind energy resource of 74% of the contiguous US at high temporal and spatial resolution using mesoscale weather modeling, to determine the potential of this renewable energy resource to drastically reduce US carbon emissions. It was found that all of the electricity used in California and all of the electricity used on the East Coast could be generated using offshore winds. In addition, unlike their onshore counterparts, which generally peak at night, offshore winds were found to provide ample resource during daytime hours, when electricity demand is highest.

Advisor: Jacobson Mark Z. (Mark Zachary) primary advisor. Thesis advisor
Chow Fotini Katopodes advisor. Thesis advisor
Street Robert L. advisor. Thesis advisor
Preschoolers' use of communicative cues to guide inductive inference [electronic resource]

In constructing a conceptual understanding of the world, children must actively evaluate what information is idiosyncratic or superficial, and what represents generalizable, essential information about kinds and categories. In six experiments (N = 312), preschoolers observed identical evidence about a novel object's function produced in subtly different manners: accidentally, intentionally, or demonstrated communicatively and pedagogically. This subtle distinction had a powerful impact on children's inductive inferences. In Part One, this distinction influenced not only the strength of children's inferences about generalizability, but resulted in a fundamentally different conception of a novel kinds as defined not by superficial appearances but by deeper, functional properties. In Part Two, children showed surprising sophistication in navigating pedagogical interactions, judiciously identifying which specific actions in an ongoing interaction were meant as communicative demonstrations for their benefit. Taken together, these experiments illustrate a powerful learning mechanism for facilitating children's conceptual development.

Keywords: Psychology
Advisor: Markman Ellen M.
Clark Herbert H. advisor. Thesis advisor
Frank Michael C. (Professor of human biology) advisor. Thesis advisor
Pricing options for acquiring a complete set of land [electronic resource]

Whenever an entrepreneur wishes to acquire unique, complementary assets which are all required to complete a project, the entrepreneur faces the risk of one of the asset owners refusing to sell his asset. This risk is the holdout problem. If the entrepreneur proceeds with buying the assets as he completes negotiations he faces the possibility that one of the remaining owners refuses to sell or demands more than he is willing to pay. Because of this, the entrepreneur faces the prospect of sinking a lot of unrecoverable money into the project only to find out he cannot complete the project. This prospect can diminish the value of the project to the point where the entrepreneur would chose not to attempt it. As a solution to the holdout problem, this thesis proposes the use of options to secure assets for which negotiations have been completed. After negotiations are completed, the entrepreneur pays the owner a small fee up front for the right, but not the obligation, to purchase the asset at a later time. The entrepreneur will then only exercise the option and purchase the asset if he has secured all the assets. This thesis develops a way to price these options so that the entrepreneur can maximize her value by incorporating the outcome of past negotiations and her beliefs about future negotiations. This model allows for the consideration of multiple sets of assets so that the developer has alternatives for completing the project. After the basic model is developed, it is extended to allow for the analysis of more situations.

Keywords: Management Science and Engineering
Advisor: Howard Ronald A. (Ronald Arthur)
Anderson Terry L. (Terry Lee)
Shachter Ross D. advisor. Thesis advisor
Prior-independence [electronic resource] : a new lens for mechanism design

We propose to study revenue-maximizing auctions in the prior-independent analysis framework. The goal is to identify a single auction mechanism for all underlying valuation distributions, so that its expected revenue approximates that of the optimal mechanism tailored for the underlying distribution, under standard weak conditions on the distribution. We use the prior-independent analysis framework to analyze natural and practical auction mechanisms such as welfare-maximization with reserve prices, limiting supply to induce artificial scarcity, sequentially posting prices, etc. Our framework allows us to argue that these simple mechanisms give near-optimal revenue guarantee in a very robust manner.

Advisor: Roughgarden Tim primary advisor. Thesis advisor
Goel Ashish advisor. Thesis advisor
Plotkin Serge A. advisor. Thesis advisor
Probabilistic and statistical modeling of fixed income assets [electronic resource]

Fix income market is a very dynamic field in the eyes of finance modelers. There have been many models in the extant literatures trying to describe the dynamics of the short rate and default intensity as realistically as possible so that some of the most important credit assets can be better priced and have their risk better understood. Here we are going to propose first of all two Monte Carlo algorithms for simulating the default times of the financial entities in a certain portfolio. The first algorithm is unbiased but more computationally expensive than the second one, which introduces some bias as tradeoff. We also show that the bias introduced in the second algorithm can be controlled by a prespecified small constant. Moreover, we present a method based on measure change to solve the pricing and risk management of these credit assets that can accommodate many different model settings, and at the same time extend the computational tractability of some well understood models to more complicated ones. In particular, by applying our measure change one can allow the company defaults to be self- and cross-excited, as well as correlated with interest rate and recovery rate. These features have been observed in empirical studies and they are quite essential in pricing multi-name credit portfolios. Another part of this thesis work focuses on predicting the trade prices of corporate bonds with benchmark prices coming from some probabilistic models given. The discrepancy between the actual trade prices and theoretical benchmarks is determined more by the market microstructures trade information so a statistical approach might be more useful here. We have tried some models based on supervised learning techniques on a certain dataset and compared their performance in bond trade price prediction.

Keywords: Statistics
Advisor: Giesecke Kay primary advisor. Thesis advisor
Lai T. L. primary advisor. Thesis advisor
Dembo Amir advisor. Thesis advisor
Probabilistic models for warning of national security crises [electronic resource]

Intelligence analysts have experimented with static forms of Bayesian inference since the late 1960's. However, their static probabilistic approaches have proven unsuitable for warning analysis. In this dissertation, I develop an analytic framework for crisis early warning that addresses four challenges: (i) it has the flexibility to incorporate geographical variation; (ii) it reflects the dynamics of a crisis in order to enable lead time estimation; (iii) it incorporates conditional dependencies among signals and data; (iv) it treats an analyst's decision of when to warn, and type of warning to give, in decision-theoretic terms. The framework is rooted in a general warning system developed by Paté-Cornell and expands on the work of Schrodt. The models comprising the framework are illustrated using a historical example, the lead up to Japan's attack on Pearl Harbor in 1941. They are then demonstrated through a contemporary case study, the warning of violence against civilians in Guatemala being perpetrated by a transnational criminal organization. From the Pearl Harbor illustration, using parameters that are entirely illustrative, the model would have issued an alert for an attack on Oahu on December 2, 1941. Despite the illustrative nature of the results, the exercise highlights the importance of incorporating decision analytic techniques in the warning process. It also demonstrates the process of entity tracking through the inference of signals, which is broadly applicable. From the transnational criminal organization case study, I demonstrate how one's belief regarding the likelihood of violence in particular municipalities, distributed over time, changes with the observation of successive signals of organizational activities. I also identify two routes spanning the width of Guatemala, which, over the period February 1 to August 31, 2012, are consistently the most secure smuggling routes.

Keywords: Management Science and Engineering
Advisor: Paté-Cornell M. Elisabeth (Marie Elisabeth) primary advisor. Thesis advisor
Hecker Siegfried S. advisor. Thesis advisor
Oliver Robert advisor. Thesis advisor
Probing the atomic limit of forces and engineered electronic structure with single molecules [electronic resource]

We use the atomic manipulation capabilities of a custom-built scanning tunneling microscope (STM) to manipulate individual molecules to study the limits of force sensing and electronic structure engineering. The system studied is CO molecules adsorbed on the Cu(111) surface. Both the molecular vibrational modes and the electron wave scattering properties of the CO molecules are used in these studies. First, the evolution of the molecular vibrational modes of a single CO molecule adsorbed on the surface are studied during the formation of a single molecule junction through isotopic labeling. Electrical contact to the molecule is made for point contact measurements. Second, the vibron virtualization experiment illustrates the non-local detection of the vibrational properties of the CO molecule through inelastic scattering by engineering the electronic states of a quantum corral. Third, a novel molecular cantilever is created by functionalizing the STM tip with a CO molecule. The molecular cantilever is used as a non-contact atomic force microscope probe by detecting the shifts in vibrational mode energy of the attached CO molecule through inelastic tunneling spectroscopy. Lastly, CO molecules are used as a periodic potential to pattern a two-dimensional electron gas to create the electronic band structure of graphene, realizing Dirac quasiparticles. Control over the hopping texture is exercised to open an energy gap at the Dirac point and to impart a pseudo-magnetic field on the lattice. The molecular cantilever experiment and artificial graphene experiment both represent techniques and concepts that can be extended upon in the future by using different molecules and building different lattices, respectively. These experiments show that one can use single molecules to study and make new materials and devices.

Keywords: Electrical Engineering
Advisor: Manoharan Harindran C. (Harindran Chelvasekaran)
Goldhaber-Gordon David
Wong Hon-Sum Philip
Processing short message communications in low-resource languages [electronic resource]

This dissertation explores the nature of the variation inherent to short message communications in the majority of the world's languages, and the extent to which modeling this variation can improve natural language processing systems. Text messaging may be the most linguistically diverse form of digital communication that has ever existed, but it is almost completely unstudied. Three sets of short messages are studied, in the Haitian Kreyol, Chichewa, and Urdu languages. It is found that all three contain the substantial spelling variations that result from a productive use of affixes/compounds, from phonological/orthographic variation, and from the typographic errors that arise from speakers with varying literacy. For example, the 600 Chichewa messages have more than 40 spellings for the word odwala ('patient'), with most appearing just once. This is problematic for many current approaches to natural language processing, which assume the level of standardization that is found in formal written English. However, as the variation is linguistically predictable it follows patterns that can be modeled. The dissertation first looks at automated methods for modeling this variation, finding that language independent methods can perform as accurately as language specific methods, indicating a broad deployment potential. Turning to categorization, it is shown that by generalizing across the spelling variations, we can, for example, implement classification systems that can more accurately distinguish emergency messages from those that are less time critical, even when incoming messages contain a large number of previously unknown spellings of words. Looking across languages, the words that vary the least in translation are named entities, meaning that it is possible to leverage loosely aligned translations to automatically extract the names of people, places and organizations. Taken together, it is hoped that the results will lead to more accurate natural language processing systems for low-resource languages and, in turn, lead to greater services for their speakers.

Keywords: Linguistics
Advisor: Manning Christopher D. primary advisor. Thesis advisor
Jurafsky Dan
Parikh Tapan S.
The promotion of criminal justice in times of transition, the inter-American system of human rights and the cases of Argentina, El Salvador and Peru [electronic resource]

Abstract Late twentieth-century Latin America was characterized by a succession of authoritarian regimes, state-sponsored death squads, paramilitary activities and a resulting dismaying number of victims. These victims suffered old and new modalities of state terror. Together with the human rights attorneys who assisted them, the victims have been the primary artifices of innovative methods to hold perpetrators accountable. To their credit is the successive outlawing of amnesty provisions in the sub-region, either by the domestic judiciaries or by the political branches of power. Indeed, Latin American states have recently prosecuted an impressive number of perpetrators of human rights abuses, chief among them former military and democratically elected heads of state. In the wake of the policy debate between peace and justice, the states of the sub-region have preponderantly veered toward justice. Due to its widespread nature, this trend has been characterized as a "justice cascade." Scholars from within and outside the region have started to acknowledge the influence of a regional force in the cascade's formation and, more notably, expansion. This influence is first and foremost a regional force, namely the normative, procedural and structural directives coming from both the Inter-American Commission on Human Rights and the Inter-American Court of Human Rights. My dissertation describes the contribution made by the victims of state terror to the creation, expansion and eventual reformulation of the Inter-American directives on this front. At the same time, it explores the role played by the victims of state terror, their legal representatives and criminal law judges in advancing states' compliance with the Commission and the Court's directives in a context of public hostility to the idea that those accused of criminal offenses deserve human rights. On this note, my dissertation highlights the obstacles faced by the victims of state terror and their legal representatives in promoting fair and effective prosecutions of the crimes of the past and of the present, as well as the key alliances they forged in their pursuit. Finally, my dissertation identifies crucial variables to be taken into consideration when designing an explanatory study of the differentiated impact of the Inter-American case law upon the several Latin American transitions.

Keywords: Law.
Advisor: Martinez Jenny S. primary advisor. Thesis advisor
Karl Terry Lynn
Stacy Helen advisor. Thesis advisor
Protein engineered biomaterials for muscle tissue engineering applications [electronic resource]

Abstract There is a tremendous need for muscle regeneration therapies to replace tissue that is lost due to disease or injury. This work is focused on developing engineered replacement therapies for lost or damaged skeletal and cardiovascular muscle tissue. In order to create viable, clinically relevant regenerative therapies, I have used recombinant protein technology to synthesize a family of protein-engineered biomaterials that incorporate critical cues for the recapitulation of in vivo muscle tissue conditions. Crucially, these biomaterials allow the independent tuning of multiple biomaterial properties including cell adhesivity, biomaterial stiffness, and topographical cues. Each of these biomaterial properties impacts muscle cell behavior independently as well as in concert. I have exploited the range of biomaterial tunability available to us to identify biomaterial conditions that enable production of striated muscle tissue using primary human skeletal muscle myoblasts (hMBs) that may be electrically paced. I have further demonstrated that mouse model skeletal muscle cell lines do not accurately recapitulate primary human myoblast behavior in response to biomaterial properties, particularly with respect to integrin-matrix interactions. Importantly, the expression of mature muscle markers that indicate muscle cell differentiation could be accelerated simply by changing biomaterial stiffness and introducing biomaterial microtopography. Finally, as demonstration that this protein-engineered biomaterial strategy may have application in the regeneration of myocardial as well as skeletal muscle tissue, cardiomyocytes derived from human embryonic stem cells exhibited good cell viability and improved contractility on these biomaterials. This thesis represents important advancements in the development of regenerative muscle tissue engineered constructs.

Keywords: Chemistry
Advisor: Heilshorn Sarah primary advisor. Thesis advisor
Huestis Wray advisor. Thesis advisor
Khosla Chaitan
Provenance in data-oriented workflows [electronic resource]

Data-processing tasks are commonly managed using data-oriented workflows, in which input data sets are processed by a graph of transformations to produce output data. In data-oriented workflows, it can be useful to track data provenance (also sometimes called lineage), which describes where data came from and how it has been manipulated and combined. We begin by giving a new general definition of provenance, introducing the notions of correctness, precision, and minimality. We then: (1) Describe a wrapper-based approach for capturing provenance in workflows in which all transformations are either map or reduce functions; (2) Describe a provenance-based approach for selectively refreshing one or more elements in the output data, i.e., computing the latest values of particular output elements based on modified input data; (3) Show how logical provenance, i.e., provenance information stored at the transformation level, can often capture precise provenance relationships in a compact fashion; (4) Describe our prototype system called Panda (for Provenance And Data) that supports refresh in data-oriented workflows, as well as debugging and drill-down using logical provenance. Overall, our work provides a comprehensive foundation, set of algorithms, and prototype system for provenance in data-oriented workflows.

Advisor: Widom Jennifer primary advisor. Thesis advisor
Das Sarma Anish
Garcia-Molina Hector advisor. Thesis advisor
Providential empire [electronic resource] : Russia's religious intelligentsia and the First World War

"Providential Empire: Russia's Religious Intelligentsia and the First World War" analyzes and contextualizes controversial commentary on the First World War by Russian religious philosophers, primarily Nikolai Aleksandrovich Berdiaev, Vladimir Frantsevich Ern, Sergei Nikolaevich Bulgakov, Prince Evgenii Nikolaevich Trubetskoi, and the Symbolist Vyacheslav Ivanovich Ivanov. Examining the prominence of the concept of Providence in their thought, the dissertation shows how Christian Providentialism can become the basis of an ideological worldview. Belief in the ability of the human mind to perceive the hand of God in history and unfolding events, along with belief in the need to interpret this ostensible evidence of the hand of God as callings to which individual believers or collective actors, such as nations, are meant to respond, leads to the emergence of a "politics of Providentialism." While expressed in a specifically Russian idiom and shaped by a specifically Russian context, the religious intelligentsia's politics of Providentialism was not unique to Russia, and was derived naturally from a traditionalist Christianity that arose in late modern Europe to stand against the perceived cultural threat of nihilism. This politics of Providentialism was one of the defining characteristics of the late imperial Russian religious intelligentsia, and, a socially significant phenomenon, it had a substantial presence in late imperial Russian civil society.

Keywords: History
Advisor: Crews Robert D.
Freidin Gregory advisor. Thesis advisor
Kollmann Nancy Shields