VictorJuiz/thesis huggingface dataset:
Parametric and semi-parametric approaches to missing data [electronic resource]

In this dissertation, I consider models that are designed to deal with missing data, in two very different areas of application, forecast combination and longitudinal studies. In both these areas, naive imputation methods can be shown to be justified only under the most restrictive and unrealistic assumptions, while going beyond naive imputation is challenging as it requires including more variables in the model, and so introduces nuisance parameters. Two distinct approaches to overfitting in the nuisance parameters are applied here. The empirical Bayes approach treats model parameters as random variables, and shrinks them towards some prior mean. In the first chapter, I apply the empirical Bayes approach to forecast combination. Using this approach to combine fore- casts from the Survey of Professional Forecasters, I find that the empirical Bayes model outperforms other models for short forecast horizons, but there is no clear result for longer forecast horizons. This can be attributed to the model failing to include serial correlation that exists in the data. In the second chapter, I consider a semiparametric approach to longitudinal studies where patients drop out at various points in time, creating a monotone missing data pattern. The semiparametric approach uses a variable number of parameters, in this case controlled by a choice of series order, so that the number of parameters in the model can vary with the size of the data set. In addition to a semiparametric estimator, we provide data driven method for the selection of the series order. This improvement, combined with other theoretical and practical advantages of our model, make it a practical alternative for empirical researchers, who have so far preferred likelihood based models that make very restrictive parametric assumptions.

Keywords: Economics.
Advisor: Hong Han primary advisor. Thesis advisor
Romano Joseph D.
Wolak Frank A. advisor. Thesis advisor
Part I: development of novel fluorescence quenchers, part II: improving catalysis of hydrazone and oxime formation at biological pH [electronic resource]

This thesis is composed of two parts. In the first part, the development of novel fluorescence quenchers is discussed. The design and properties of Multiple Pathway Quenchers (MPQs) that display broadened absorption properties that allow for greater quenching of a wider variety of fluorophores than common commercial quenchers is examined. The prepared quenchers display complex electronic pathways that provide considerably red-shifted absorption maxima and widened spectra relative to the parent dyes. Particularly in FRET quenching, these new compounds are observed to perform better than other quenchers previously reported. Further studies discuss new quenchers designed for oxime and hydrazone bioorthogonal attachment to fluorescently labeled biomolecules. Hydrazine-containing dyes in particular afford powerful properties for fluorescence quenchers upon hydrazone formation. These quenchers allow for new means of attaching fluorescent molecules to biologically relevant probes and provide the first example of quenching a fluorophore in a living cell without the need for photobleaching. The second part of this thesis explores the design and properties of new catalysts for bioorthogonal hydrazone and oxime formation at physiological pH. Traditionally, aniline has served as the recommended catalyst for hydrazone or oxime formation at pH 7.4, but exceedingly high concentrations are required that hinder simpler applications. Anthranilic acid derivatives are reported as the first enhanced catalysis for both hydrazone and oxime formation at pH 7.4. Further studies display that optimizing the pKa of the ortho proton donor in the anthranilic acid scaffold to match that of the buffer pH affords further enhanced catalysis, with 2-aminobenzenephosphonic acids discussed as the optimal class of catalysts at biological pH.

Keywords: Chemistry.
Advisor: Kool Eric T. primary advisor. Thesis advisor
Chen James
Huestis Wray advisor. Thesis advisor
Phase competition in strongly correlated materials [electronic resource]

Strongly correlated electron materials display a wide variety of collective electronic phenomena including high-temperature superconductivity, magnetic phases, and charge and orbital ordered states. Rich phase diagrams with multiple competing or cooperating orders often arise, making these materials promising candidates for future device applications. An important step towards being able to understand, predict, and control collective phenomena in strongly correlated systems is to elucidate how these phases relate to each other. This thesis investigates the role of phase competition in strongly correlated materials, utilizing multiple methods and perspectives. One large area of focus in this work is the cuprate high-temperature superconductors, and in particular the relation between the superconducting and pseudogap phases in the hole doped compounds. Through combined experimental and theoretical studies, progress is made towards elucidating the interplay of these orders. The second part of the thesis considers phase competition in strongly correlated systems more generally. Focusing on a model system that incorporates strong electron-electron and electron-phonon interactions, the competition between antiferromagnetic and charge density wave orders is investigated, and evidence for an intervening emergent metallic phase is presented. These findings help clarify how new emergent phases can arise between different phases of matter and the competition between them.

Keywords: Physics.
Advisor: Devereaux Thomas Peter
Fisher Ian R. (Ian Randal) advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
Photoemission and X-ray absorption studies of magnetic materials [electronic resource]

The works presented in this thesis investigate magnetic materials using various synchrotron techniques. Since the magnetic properties of a material are due to the behavior of the electrons, it is fruitful to measure the electronic structure of magnetic material with synchrotron techniques and make comparisons with theoretical model. Our main interest is in the 3d transition metal oxides, Silicides, and intermetallic compounds. The issues studied are that of colossal magneto-resistance, narrow band insulators, and half-metals. The first phenomenon discussed is CMR (colossal magneto-resistance). It simply means that the electrical conductivity is very sensitive to an applied magnetic field. Most magnetic materials possess some magneto-resistance (less than a few percent), however certain perovskite manganite show many orders of magnitude change in conductivity near a ferro-paramagnetic transition temperature with a strong applied magnetic field. Using photoemission and x-ray absorption, we have tried to extract the electronic structure of the material, understand its temperature and doping dependence, and compare our results with leading theoretical models. In particular, the physics of double exchange, polaron mechanism and charge inhomogeneuity are discussed. We have also determined many of the key parameters of these compounds such as the one electron bandwidth, the Hund's rule coupling energy and the Jahn-Teller energy. These parameters are keys to microscopic models. Second interesting magnetic material system we focused on is FeSi. The unusual magnetic susceptibility of FeSi over a wide temperature range has puzzled physicists for a long time. Various theoretical models have been proposed to explain the phenomenon. By discovering evidence of a narrow band near the Fermi level from angle-resolved photoemission spectra, we support the existence of a sharp density of states between a semiconductor gap in this compound. This may put FeSi into a class of narrow band insulator that is seen only in rare earth compounds. Another interesting family magnetic compound is the Heusler alloys. According to band calculations, this class of alloy is metallic for spin-up electrons and semiconducting for spin-down electrons ("Half-metallic"). However it lacks definite experimental evidence to prove or disprove the calculation. We have performed resonance photoemission, X-ray magnetic circular dichroism, and X-ray photoemission spectroscopy studies of the Heusler alloy and have compared these results with the predictions of band calculations. These results gave qualitative information about the density of states of various orbital/elemental contributions, and found them to be consistent with the band calculation. However, since we do not measure the spin directly, our data can't provide a definitive test.

Keywords: Physics.
Advisor: Shen Zhi-Xun primary advisor. Thesis advisor
Doniach S. advisor. Thesis advisor
Raghu Srinivas
The physical genome [electronic resource] : structure, elasticity, and transport in packaged DNA

The packaging and expression of the genome requires a cell to overcome elastic and entropic forces to form a highly compact structure that remains dynamically accessible to transcription machinery. The eukaryotic genome is packaged into a hierarchical structure collectively termed chromatin and the prokaryotic genome is also condensed and structured by the binding of architectural proteins along the DNA. We use a combination of analytic theory and computational techniques to study how the mechanical properties of DNA and associated proteins impact genome structure and dynamics across a wide range of length and time scales. We demonstrate that the elasticity of the DNA molecule can give rise to tension-mediated cooperative binding between DNA-bending proteins, allowing them to sense each other across a tunable length scale. At the lowest level of eukaryotic chromatin packing, DNA is wound around protein cores to form nucleosomes, which then condense into regular helical fibers under physiologic conditions. Using energy landscape optimization methods, we investigate the role of DNA mechanics in determining the structure of these compact chromatin fibers. We then proceed to examine how he statistical properties of DNA at long length scales are modulated by its interactions with proteins that modify its geometry. To this end, we develop a generalized approach for coarse-grained modeling of polymer systems by mapping to continuous and discrete elastic models. Moving into the realm of dynamics, we uncover an important role for force fluctuations in biomolecular kinetics, demonstrating how microsecond fluctuations can qualitatively alter nucleosomal transcription by RNA polymerase, an essential process for eukaryotic gene expression. Finally, we use a combination of analytic reaction-diffusion models and simulations to study the target site search process of DNA-binding proteins under a variety of conditions relevant to in vitro and in vivo systems, elucidating a key role for confinement and a surprising robustness to DNA configuration. These multi-scale studies further our fundamental understanding of how the complex hierarchy of genome packing and processing arises from the basic physical properties of DNA and interacting proteins.

Keywords: Biophysics.
Advisor: Spakowitz Andrew James primary advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor
Straight Aaron
Point-contact spectroscopy in novel materials [electronic resource]

This thesis describes point-contact spectroscopy (PCS) experiments on BaPb$_{1-x}$Bi$_x$O$_3$ (BPBO) and KWO$_3$ with both an aluminum tip to probe the tunneling regime and a gold tip to probe the Andreev regime. In the case of BPBO, when in the tunneling regime, we find a suppression in the density of states above the transition temperature which has not been previously commented about in the literature. With further support from resistivity measurements, we conclude that a disorder-driven metal insulator transition is present in this material which seemingly occurs before the onset of the charge-disproportionated charge density wave. We suggest that a scaling theory might be applicable to our tunneling results. We also present a method to estimate the transition temperature without disorder. When using a gold tip, we find that the coherence peaks are larger than can be fit with traditional Blonder-Tinkham-Klapwijk theory and more theoretical work is needed to describe results in this low tunneling barrier limit. Preliminary PCS of KWO$_3$ with a Au tip display some results with a suppression in the density of states around zero-bias above the transition temperature as well. Given the high residual resistivity of this material, we thought that disorder was also a likely factor in this material. Hence we decided to measure KWO$_3$ with an Al tip to probe the tunneling regime. However, surprisingly the junction resistance was too low to probe the tunneling regime. While more experiments are necessary to uncover whether disorder plays a major role in this material, we apply similar calculations as in BPBO to measure the disorder-free critical temperature and find that this provides further support to the disorder claim.

Keywords: Physics.
Advisor: Beasley Malcolm primary advisor. Thesis advisor
Devereaux Thomas Peter
Fisher Ian R. (Ian Randal) advisor. Thesis advisor
The politics of judgment [electronic resource] : dispute resolution and state formation from the homeric world to Solon's Athens

In the eighth century BCE, the relatively small and relatively simple Dark Age settlements of the Greek world start changing, as a demographic boom takes place. At the beginning of the fifth century, we are looking at a much more complex ecology of poleis, each with its own particular internal institutional structure as well as external relations. My driving question in this study is why and how these particular institutions were formed in the intervening seventh and sixth centuries BCE to produce this complexity and progress. This is a question that spans the fields of literary and historical analysis: institutions emerge as a result of a society's fears and hopes, and often out of a set of competing alternatives; these are well documented in the products of the public song culture of early Greece. More specifically, I argue that in early Greece, resolving disputes, which by definition is a costly endeavor in terms of time spent and enmities risked, was not carried out by elite rulers simply because it was part of their job description. On the contrary, there was a significant payoff to be gained if one developed a reputation as a successful arbitrator: in the absence of a legislative process, the elites who became established as sources of legal order would see the rest of the community start referring to them as authorities. Institutions then emerge in several cities precisely in order to curtail the payoff and power of the arbitrator, but their introduction has far-ranging implications, as it shapes and accelerates state formation.

Keywords: Classics.
Advisor: Martin Richard P. primary advisor. Thesis advisor
Ober Josiah primary advisor. Thesis advisor
Nightingale Andrea Wilson advisor. Thesis advisor
Peponi Anastasia-Erasmia advisor. Thesis advisor
Poly(hydroxybutyrate-co-valerate) biodegradable foams [electronic resource] : the effects of processing, nanoscale additives, and aging

Biodegradable polymers can reduce the environmental impact of petroleum-based polymers by eliminating plastic accumulation in nature. Poly(hydroxybutyrate-co-valerate) (PHBV), one such polymer, is completely biorenewable and has potential for significant commercial growth if suitable applications are found. In addition to cost barriers, PHBV has not been widely adopted due to technical challenges associated with melt processing because PHBV has a high melting point and low thermal degradation temperature. These two complications create a narrow processing window in which the melt strength is too low for several common processing techniques, including foaming, blow molding, and film/fiber drawing. The application of interest in this work, foaming, requires high melt strength due to the rapid expansion of molten plastic around growing bubbles in order to prevent unwanted cell coalescence and collapse. Foaming of PHBV with a carbon dioxide producing blowing agent was performed in this thesis research to improve upon the thermodynamic limit witnessed in previous studies with nitrogen-generating blowing agents. The result was an additional decrease in the bulk density of more than 30%, but this was accompanied by a loss of the desired closed-cell morphology. Rapid water quenching at the die in extrusion foaming led to faster cooling and better bubble stabilization in the more expanded foams, as verified by thermal modeling. Next, silica nanoparticles were used as an additive in PHBV foams, and, in addition to bubble nucleation, particles were found to induce crystallization in PHBV. This solidification mechanism stabilized the cell morphology, even in the absence of a water quench. Silica treated with fluorinated silane coupling agents became hydrophobic and also acted as a nucleation agent. However, particle depletion due to aggregation limited the overall nucleation efficiency at high loading with hydrophobic nanoparticles. Ultimately, the rapid quenching of PHBV/silica nanocomposite foams led to synergistic stabilization of heterogeneously nucleated bubbles. As a result, foams with expansion ratios near six and closed-cell morphology were observed under these conditions. Products made from PHBV, including foams, will experience mechanical property degradation as the material ages. Because there is ambiguity as to the specifics of the embrittlement mechanism, the mechanical properties of aged poly(3-hydroxybutyrate) (PHB) and PHBV were examined over a 168 day period. The tensile modulus increased while the ultimate strain decreased, but the thermal characteristics showed no signs of secondary crystallization at 15°C. The aging of PHAs at ambient conditions, near the glass transition, led to a constriction of the rigid amorphous fraction, which decreased the ductility of the samples with little impact on the strength imparted by crystalline regions.

Keywords: Chemical Engineering.
Advisor: Frank C. W. primary advisor. Thesis advisor
Billington Sarah L. (Sarah Longstreth)
Criddle Craig advisor. Thesis advisor
Postsynaptic vesicular cycling and its role in local redistribution of surface receptors [electronic resource]

The spatial distribution of membranes and receptors along neuronal dendrites, in both surface and internal compartments, is important for remodeling of dendritic morphology and receptive properties. Applying a hypertonic solution, a well-established method for evoking presynaptic vesicle release, to dendrites expressing pHluorin-tagged transferrin receptors, rapidly induces new dendritic protrusions enriched in those receptors. Kinetic studies reveal that the protrusion formation precedes the receptor enrichment, suggesting distinct steps in receptor redistribution. These protrusions likely form due to exocytosis, as their number is significantly reduced when SNARE-mediated fusion is blocked by tetanus toxin or botulinum A toxin. Receptor redistribution, on the other hand, likely occurs through both coupled endo- and exocytosis and surface diffusion, as receptor endocytosis and depletion are observed in the adjoining regions of the protrusions. Additionally, the frequency of induced protrusions depends on the degree of tonicity much like presynaptic release, although they form in non-synaptic regions and do not require glutamate or a rise in intracellular calcium. Moreover, neurons co-expressing tagged GluA1 and transferrin receptors show co-trafficking of both receptors into the protrusions induced by hypertonic solution. Taken together, these findings unveil a microdomain centered on dendritic protrusions, where synaptic resources such as key surface receptors, are drawn from nearby regions and gathered in those protrusions. Thus, this domain serves to enhance local response to signaling without altering global responsiveness.

Advisor: Tsien R. W. (Richard W.) primary advisor. Thesis advisor
Baccus Stephen A. advisor. Thesis advisor
Malenka Robert C. advisor. Thesis advisor
Shen Kang
The practical demand of means-end rationality [electronic resource]

In this dissertation I provide a vindication of the normative requirement on persons to intend and take means to their ends. One basic intuition that we have is the thought that if a person is not intending or taking the means to an intended end of hers, then she is "irrational". Another basic intuition is that a requirement of rationality cannot be true if it simply entails that a person ought to take means to her ends. The tension between these two thoughts leads to the philosophical problem at the heart of this dissertation. That problem is to account for what we take to be a genuine requirement of "means-end rationality" that makes a normative demand on persons. In Part I, I clarify these intuitions and situate the problem within some appropriate constraints. I take as a backdrop very recent work of philosophers whom I call the "Myth Theorists". I show that the Myth Theorists are best understood as presenting those who accept the prevailing contemporary view of the requirement of means-end rationality with a challenge. I present this challenge in what I call the Argument of Superfluity. I show that the advocate of the prevailing view of the normative requirement of means-end rationality supports a "requirement" that appears to have no explanatory work to do in our attributions of "rationality" and "irrationality". I therefore go on to propose an account that allows us to salvage both of our basic intuitions while also incorporating lessons that we learn from the Myth Theorists. On the account that I offer, our decisions and intentions are significant in altering what it is that we have reason to do. Sometimes, but not always, they can determine what it is that we ought to do. The activity of persons therefore has a special significance on my view. The special significance of a person's intentional action is that it is the expression of a person taking something or other to be at least minimally worth bringing about. On my view, a person thereby has at least a pro tanto reason to intend and take the means that she believes are required to realize her end. I argue that satisfaction of the normative requirement of means-end rationality by a person just is the practical expression of her autonomy. In Part II of the dissertation, I distinguish between different conceptions that we have of "autonomy". I also show how two leading contemporary accounts take the normative requirement of means-end rationality to be grounded in the value of what turn out to be different conceptions of a person's autonomy. I argue that one of these conceptions of a person's "autonomy" does not allow us to resolve our philosophical problem while incorporating the lessons that we learn from the Myth Theorists. My account therefore emphasizes the importance of the form of autonomy that is anchored in our understanding of persons as accountable and responsible for their activity.

Keywords: Philosophy.
Advisor: Schapiro Tamar
Bratman Michael advisor. Thesis advisor
Hussain Nadeem J. Z. advisor. Thesis advisor