VictorJuiz/thesis huggingface dataset:
Discrete emotion sequences and marital satisfaction in middle-aged and older couples

Research indicates that positive emotions are associated with satisfied marriages while negative emotions are associated with dissatisfied marriages. Still unknown is whether all negative emotions are equally associated with dissatisfied marriages and all positive emotions equally are associated with satisfied marriages. Also unknown is whether sequences of discrete emotion between spouses (i.e., how each spouse responds to the emotions of their partner) are related to marital satisfaction. This study examined middle-aged (N = 82) and older (N = 74) couples engaged in a 15-minute conflict conversation to determine how discrete emotion sequences between spouses were related to marital satisfaction. It further examined whether age and gender moderated the relationships between discrete emotion sequences and marital satisfaction. Emotional behavior was coded using the Specific Affect Coding System (SPAFF), consisting of five positive codes, ten negative codes, and a neutral code. The study focused on discrete emotion sequences initiated by three antecedent emotions (anger, contempt and sadness) previously associated with distressed marriages. Consequent emotions included any SPAFF code. Conditional probabilities were computed using the method of Allison and Liker (1982). Results revealed significant associations between discrete emotion sequences and marital satisfaction for 11 of the 39 discrete emotion sequences examined. The significant associations were found for discrete emotion sequences with negative emotion consequents, but not positive emotion consequents. The results were consistent with the predicted pattern in all cases with one exception: spouses who had a greater likelihood of expressing sadness consequents in response to anger antecedents were in more satisfied marriages. There was no evidence of differences in the relationships between discrete emotion sequences and marital satisfaction for husbands and wives. The findings indicated that the relationships between discrete emotion sequences and marital satisfaction did not consistently differ as a function of age, but when they did, they tended to be stronger for older couples. This study revealed important differences in how discrete emotion sequences relate to marital satisfaction. It shows that anger, contempt, and sadness, three emotions that have previously been linked to marital distress, are not always associated with less satisfied marriages. Instead, these emotions are associated with distressed marriages when partners respond to them with certain emotions, but not others.

Advisor: Levenson, Robert W
Self/Non-self Discrimination by Toll-like Receptor 9

Recognition of nucleic acids as a signature of infection by Toll-like receptors (TLRs) 7 and 9 exposes the host to potential self-recognition and autoimmunity. It has been proposed that intracellular compartmentalization is largely responsible for reliable self/non-self discrimination by these receptors. Our lab has previously shown that TLR9 and TLR7 require processing prior to activation, which may further restrict TLR9 and TLR7 compartmentalization and reinforce self/non-self discrimination; although, this possibility has remained untested. We have identified residues within the TLR9 transmembrane (TM) region that confer the requirement for ectodomain proteolysis. TLR9 TM mutants responded to extracellular DNA and mice expressing such receptors died from systemic inflammation and anemia. This inflammatory disease did not require lymphocytes and appears to require recognition of self-DNA by dendritic cells. These results provide the first demonstration that TLR-intrinsic mutations can lead to a break in tolerance and support the hypothesis that ectodomain processing has evolved to reinforce self/non-self discrimination by nucleic acid-sensing TLRs.

Advisor: Barton, Gregory M
Proteomic Applications for Engineering Escherichia coli for Biofuel Production

Concerns over energy security, carbon emissions, and other limitations of petroleum-based chemicals have led to increased interest in using biological systems for the production of commodity chemicals such as fuels. It is vital that the microbes used for these processes be able to grow with minimal nutrients, produce large amounts of the target molecule, and be tolerant to the chemicals being produced. Naturally occurring strains are unable to meet all these criteria and need to be further optimized as production hosts. Proteomics is the study of cellular proteins. It has become a powerful tool for host engineering, and can give vital information about pathway performance and strain responses. Using LC-MS/MS mass spectrometry, proteomics strategies were utilized to study cellular responses to a potential biofuel, n-butanol, and to overexpression of the carbon storage regulator, which increased flux through three key biofuel production pathways./nFor each study, proteomics provided valuable cues for understanding how the host was adapting to an engineered environment. In the case of product toxicity, n-butanol stressed cells were iTRAQ labeled, separated into 20 fractions using HPLC, and spectra collected on an ESI-Q-TOF instrument. Analysis of the data indicates that n-butanol stress has components common to other stress responses including perturbation of respiratory functions, oxidative stress, heat shock and cell envelope stress, and metabolite transport and biosynthesis. Results from these analyses allow identification of key genes, such as degP, nlpD, and phoU, which were used to alleviate stress. Proteomics work was also vital for studying the cellular effects of the carbon storage regulator and the increased flux through biofuel pathways. Extracted proteins were analyzed on a 5600 Triple-TOF mass spectrometer. Increased levels of proteins involved with energy metabolism, particularly TCA cycle, were noted, along with approximately 20 proteins that were strongly up regulated, indicating previously unknown regulation. This dataset is the first cell-wide proteomics study of this global regulator, and may provide further clues for studying its complex regulation./nFinally, a novel method for multiplexing targeted proteomics samples is described, along with an outline of key experiments to validate its accuracy and usefulness to synthetic biologists. A concluding chapter outlining future work on butanol responsive genes, a targeted proteomics stress diagnostic, and challenges in developing beneficial phenotypes for biofuel production is included with several previously unpublished results.

Advisor: Keasling, Jay D
Native Defects in CdO and CdCuO Alloys

Indium tin oxide (ITO) is the most extensively researched and most commonly used transparent conductive oxide. Despite ITO's popularity its long term use by industry presents several significant challenges. Indium is an expensive and a non-abundant metal. The demand for optoelectronic devices is growing far faster than the supply of indium. In the future, this will result in even higher prices for an already expensive material. In addition to cost, ITO has a critical performance flaw. All ITO films and current substitutes for ITO, such as doped zinc oxide and doped tin oxide, achieve low resistivies because they have very high carrier concentrations, not because they have very high mobilities. Significant free carrier absorption exists in the low energy portion of the visible and near infrared solar spectrum. For many devices, this results in a loss of transparency that can negatively affect device performance./nCadmium oxide (CdO) does not suffer from either the cost or the performance limitation of ITO. CdO displays exceptional mobilities that are approximately five times greater than most ITO. This means free carrier absorption is significantly reduced. Despite CdO's promise, it has not displaced ITO in the market. The main reason is that this material is not well understood. Before a new transparent conductive oxide is used in a device, a detailed understanding of the optimal deposition parameters, defect behavior, dopant behavior and processing behavior all have to be established. The goal of this work is to provide that understanding. It is shown that the amphoteric defect model can be used to provide a unified explanation for several unresolved questions in CdO, namely, why the carrier concentration in CdO is typically between 2*1019 to 2*1020 cm-3, why no p-type films have been fabricated and why there is such a large spread in the reported optical absorption edge, ranging from 2.2 to 2.6 eV. In addition, the optimal deposition and annealing conditions have been determined which yield the lowest carrier concentration and highest mobility undoped CdO ever published. This is an important step for commercialization. Finally, the influence of high doses of irradiation on CdO and CdCuO is considered. Here, it is shown that irradiation provides a method to increase the optical absorption edge and reduce the resistivity by increasing the number of free carriers. However the irradiation dose must be carefully chosen because doses that are too small provide little improvement whiles doses that are too large lead to poor optical performance.

Advisor: Haller, Eugene E
Transatlantic Circuits of Power: A Comparative Study of Late 19th Century Caribbean and Spanish Novels

This dissertation brings together Spanish, Cuban, and Puerto Rican novels written in the late 19th century, a period covering the 1868 Revolution and the Restoration, up to independence. These novels expose the conflictive political and economic integration of both peninsular and overseas territories, which configures social relations in a web of mutual influence. I focus in particular on the representation of imperial discourses as articulated by, and informing, discourses of gender, class, sexuality, race and geopolitical situation./nA fundamental claim of my work is that these novels cannot be understood apart from the transatlantic economic, political, social and cultural ties between peninsular Spain and the Caribbean. Thus, my dissertation attempts to question the concept of the `national' as it has been applied to Spanish and Spanish-Caribbean cultural traditions of the 19th century. This approach requires detailed engagement with the historiography of the period, both because of Spain's troubled relationship with its imperial past throughout much of the 20th century, mirrored in the historical record until recently, and because of a predominance of post-independence interpretations of Caribbean novels./nI begin with Hostos' La Peregrinación de Bayoán (1863) and Alas' La Regenta (1884-5), focusing on the representation of imperialism before and after the Six Year Revolution, from the point of view of the Puerto Rican white Creole class and the Spanish provincial bourgeoisie respectively. I show how these two perspectives present different and opposed political models, which are illuminated and enacted by different gender discourses. Chapter Three offers a comparative reading of Pardo Bazán's La Tribuna (1884) and Morúa Delgado's Sofía (1894) focusing on the representation of exploited parties within the realist/naturalist genre. In both novels women are depicted through discourses of race and slavery, but in different ways and to different ends. Chapter Four, on Galdós' La Desheredada (1881) and Villaverde's Cecilia Valdés (1882), addresses the failure of modern society to live up to its liberal ideals, such as social equality and mobility, especially because of self-reinforcing social structures of exploitation and consumerism. These exploitative structures, based on gender and class distinctions, are connected figuratively and materially with colonial exploitation, especially the slave trade.

Advisor: Dougherty, Dru
Iarocci, Michael
Light-induced Electrokinetics: A path to a versatile micro total analysis system

The micro total analysis system (μTAS) has seen great interest and advances since its definition over two decades ago. By harnessing the fabrication tools of the semiconductor industry and exploiting the unique physical phenomena that dominate at the micro- to nano-scale, these devices aim to address applications ranging from point-of-care diagnostics to pharmaceutical development. A truly versatile μTAS technology platform will enable reconfigurable, parallel, and high resolution analysis, processing, and sorting/purification. To this end, we present the concept of light-induced electrokinetics, which enables the patterning of electric fields using low-intensity light. This platform allows for the manipulation of both fluids (optoelectrowetting (OEW)) and particles (optoelectronic tweezers (OET)) over a featureless substrate. In this work, we will discuss three examples of how this technology demonstrates each of the μTAS requirements. Specifically, we will use this platform to assess the developmental potential of preimplantation-stage embryos, perform high throughput light-induced electroporation of single cells, and, finally, demonstrate the ability to unify the OET and OEW device enabling both droplet and particle manipulation on a single device. Within the context of these examples, the potential of light-induced electrokinetics as a generic μTAS platform is elucidated.

Advisor: Wu, Ming C
The Problem of Pleasure: Disciplining the German Jewish Reading Revolution, 1770-1870

Focusing on learned men and women from traditional Jewish societies in Germany, between 1770 and 1870, my dissertation examines the emergence of an intellectual practice critical to the process of becoming modern: reading for pleasure. Unlike the written word that is its stimulus and object, the experience of reading in general is thought to be transitory and accessible only to individuals. But for Jewish intellectuals who were becoming modern by elaborating new selves outside the confines of traditional culture, pleasure reading, like writing, played a central role in their formations as modern individuals. Pleasure reading and the habit of sharing impressions of that reading in written correspondences, diaries, and memoirs, which were then re-read with equal pleasure, amounted to a revolution of traditional Jewish culture. In their discoveries of pleasure reading, Jewish men and women followed their feelings and imagination inside new interior spaces of individuality carved out by themselves. My dissertation traces this process by pursuing the discoveries of pleasure reading by three connected figures: the salonnière Henriette Herz (1764-1847), the founder of the critical study of Judaic literature Leopold Zunz (1794-1886), and the great historian of the Jews Heinrich Graetz (1817-1891).

Advisor: Efron, John
Jay, Martin
Forward genetics to identify Listeria monocytogenes components that activate mammalian cytosolic surveillance pathways

Listeria monocytogenes is Gram-positive facultative intracellular pathogen that is ubiquitously present in the environment. During infection, L. monocytogenes is phagocytosed by host cells and then rapidly escapes from the phagosome into the host cytosol. In the cytosol the bacterium is able to replicate and spread to neighboring cells without leaving the intracellular compartment. Maintenance of the intracellular niche is critical for L. monocytogenes pathogenesis, but there have been several reports indicating cytosolic bacteria can induce inflammasome-mediated host cell death. Additionally, our laboratory previously identified a host transcriptional profile induced by L. monocytogenes upon entry into the cytosol termed the cytosolic surveillance pathway, characterized by the robust upregulation of IFN-beta; and co-regulated genes. Although the host components of the signaling pathways leading to cell death and IFN-beta; production are becoming better defined, the bacterial ligands were largely unknown. To gain insight into the bacterial components and ligands required for stimulation of these two pathways, we performed a forward genetic screen and isolated mutants that affected induction of host cell death and/or IFN-beta./nWe identified a transposon insertion in lmo2473 that caused hyperstimulation of inflammasome-mediated cell death, pyroptosis. Further characterization revealed these mutants, and to a lesser extent wild-type L. monocytogenes, lysed in the macrophage cytosol. Intracellular bacteriolysis released bacterial DNA that was detected by the cytosolic DNA sensor AIM2 to trigger pyroptosis. Tight regulation of other bacterial factors capable of stimulating inflammasomes, such as flagellin, likely contribute to the low levels of pyroptosis induced by L. monocytogenes./nWe also isolated a mutant that harbored a transposon insertion in the gene lmo0052, renamed pdeA. Biochemical characterization of the gene product determined PdeA was a cyclic di-AMP phosphodiesterase. Inactivation of this protein resulted in accumulation of the nucleotide and increased stimulation of IFN-beta;. As cyclic di-AMP was only recently identified as a bacterial second messenger, we used mutants that modulate enzymatic processing of c-di-AMP to interrogate the role of its signaling in L. monocytogenes physiology and pathogenesis. This work implicates c-di-AMP, not only as the IFN-beta;-stimulatory ligand, but also as a critical molecule involved in bacterial growth, response to stress, and cell wall stability./nIn summary, using a forward genetic approach, we have identified mechanisms by which host cells recognize and respond to L. monocytogenes invasion of the cytosol. Other mutants isolated in this screen merit further characterization to potentially unveil additional bacterial components involved in these responses.

Advisor: Portnoy, Daniel A
Epitaxial Stabilization of a Morphotropic Phase Boundary in Lead-Free Ferroelectric Thin Films

This dissertation details the synthesis and characterization of compressively strained epitaxially grown bismuth ferrite thin films in an effort to improve their piezoelectric properties with the goal of finding a viable lead-free alternative to lead zirconate titanate. It is found that under compressive epitaxial strain a morphotropic phase boundary, the hallmark of high performance piezoelectrics, is stabilized in this material. The structural characterization of these films reveals complex mixed-phase morphologies whereby nearly energetically degenerate monoclinically distorted tetragonal and rhombohedral ferroelectric phases coexist with apparent crystallographically coherent interfaces. This mixed phase morphology is found to be responsive to perturbations both via mechanical indentation and an applied electric field, whereby a reversible phase transition is observed in the films. Electrical characterization of these films indicates a pronounced increase in their piezoelectric and ferroelectric properties.

Advisor: Ramesh, Ramamoorthy
The Role of Social Support for Physical Activity among Young Survivors of Breast Cancer

BACKGROUND: There is strong evidence that physical activity mitigates negative psychosocial effects and sequelae associated with adjuvant chemotherapy among cancer survivors. Given the many benefits of physical activity in this population, it is important to understand the factors that influence continued participation post diagnosis. One possible determinant that has received little attention to date is the influence of social support. This study is unique in that it is the first to explore the role of social support for physical activity among young survivors through the use of mixed methods./nMETHODS: Survey data (n=273) were used to determine actual levels of moderate and vigorous physical activity. These data were subsequently used to identify women of interest to participate in face-to-face qualitative interviews. Semi-structured interviews (n=31) were conducted with a subset of women from the quantitative sample. Participants were Bay Area women who were age 55 or less and premenopausal at the time of diagnosis and who also received adjuvant chemotherapy. Following qualitative analyses, hypotheses were developed to test the association between social support and obtaining recommended levels of physical activity through the use of logistic regression analyses using a sample of 273 women./nFINDINGS: Qualitative analyses indicated that women who have a partner with whom they engage in physical activity are more likely to adopt and maintain physical activity behaviors over time. Regression analyses provide evidence that women who have support specifically for physical activity are more likely to meet recommended activity guidelines (β=.030, OR=1.030 per unit of scale, p=.003, C.I.=1.01 - 1.05)./nCONCLUSION: When considering correlates of physical activity, social support specific to physical activity may be important or even pivotal in assisting survivors to adopt and/or maintain participation in a given activity at recommended levels.

Advisor: Bloom, Joan R
Algorithms and Representations for Visual Recognition

We address various issues in learning and representation of visual object categories. A key component of many state of the art object detection and image recognition systems, is the image classifier. We first show that a large number of classifiers used in computer vision that are based on comparison of histograms of low level features, are "additive", and propose algorithms that enable training and evaluation of additive classifiers that offer better tradeoffs between accuracy, runtime memory and time complexity than previous algorithms. Our analysis speeds up the training and evaluation of several state of the art object detection, and image classification methods by several orders of magnitude./nMany successful object detection algorithms localize an object by simply evaluating a classifier at multiple locations and scales in an image, and finding peaks in the classifier response. In this setting, the overall speed of the detector can be improved not only by improving the efficiency of the classifier, which we addressed earlier, but also by efficient search, which we address next. We develop a discriminative voting algorithm based on Hough transform, which cuts down the complexity of this search./nIn the last part of the thesis, we propose a representation for fine scale category recognition such as, action and pose of people in images, which is aided by more supervision. Leveraging on "crowdsourcing", we collect annotations of various kinds - keypoints, segmentations, attribute labels, pose, etc., for several tens of thousands of objects. The problem of comparing two instances visually can then be replaced by a simpler problem of comparing their annotations. The similarity function over the annotations provides us a flexible notion of correspondence between instances of a visual category, which we use to learn appearance models relevant to the task. We apply this framework to build a system for action recognition, that captures salient pose, appearance and interactions with objects, of people performing various actions in static images.

Advisor: Malik, Jitendra