VictorJuiz/thesis huggingface dataset:
Identification and characterization of a novel polyubiquitin binding protein involved in virus maturation [electronic resource]
Keywords: Biology.

The covalent attachment of ubiquitin (Ub), a 76-amino-acid protein, to another protein is a highly occurring and conserved post-translational modification. Ub functions in a plethora of diverse signaling pathways including proteasomal degradation, endocytosis and trafficking of membrane receptors and DNA repair when conjugated to substrate proteins. Ub is unique in that it can also be conjugated to itself to create an assortment of polyubiquitin chains, through either its amino terminus or any of its seven internal lysines, where a large part of its diverse signaling is ascribed to these polyubiquitin chains. Previous work has identified proteins, which specifically recognize these different types of Ub linkages to contain domains or motifs termed Ub binding domains (UBDs). Studies on the various and diverse roles of Ub signaling along with its own diversity of conjugates present on substrates and their recognition by UBDs have uncovered the existence of a Ub syntax or code. The main goal of the work entailed in this thesis was to contribute to decryption of this code by identifying new linkage specific polyubiquitin binding proteins and characterizing their function and mechanism of polyubiquitin recognition. We developed and used a K63 linkage specific polyubiquitin affinity reagent in conjunction with shotgun LC-MS/MS to identify novel polyubiquitin binding proteins. We found that the majority of polyubiquitin dependent identified proteins were previously known Ub binders as well as a few previously unidentified Ub interacting proteins, demonstrating this as a valid approach for the identification of polyubiquitin binding proteins. One such previously unidentified protein we identified was ALIX, a a component of the Endosomal Sorting Complex Required for Transport (ESCRT) machinery known to be involved in Human Immunodeficiency Virus (HIV) budding. We characterized ALIX and found that it binds directly and selectively to K63-linked polyubiquitin via two potential Ub binding sites on a single [alpha]-helical surface within a coiled-coil region, where mutation of these sites impaired retroviral release. Our study demonstrates ALIX as the first example of a K63 chain specific polyubiquitin receptor in the endosomal sorting pathway that supplies evidence for a functional link between K63 polyubiquitin binding and ESCRT function, specifically in retrovirus budding. In summary the findings in our study contribute to the understanding of the role of K63-linked polyubiquitin in the ESCRT pathway. Our work also demonstrates the power of using unbiased affinity capture and tandem mass spectrometry to identify polyubiquitin receptor proteins to further decryption of the Ub code.
Ideological osmosis [electronic resource] : Asian immigrants' understanding of racial inequalities in the U.S.
Keywords: Sociology

This dissertation aims to understand the social psychological process of ideology of racial inequalities, and makes both theoretical and empirical contributions. Theoretically, it tests the utility of a conceptual framework that combines a number of social psychological approaches to long-lasting intergroup inequalities. It assumes that inequalities and ideologies feed into each other, and intends to find out the osmotic strength of the dominant race ideology in the US society by examining micro-level intergroup ideologies in immigrants. It adopts a relatively new model of stereotype contents in looking at the interrelations among status, competence and warmth traits and how they jointly legitimize existing social inequalities, and applies it to an immigrant population that has rarely been studied in this light. Empirically, the project consists of two sets of studies. I first used data from the Los Angeles Study of Urban Inequality to examine the micro processes delineated in the theoretical framework, comparing first-generation and later-generation Asian Americans—a purportedly high-status group—to whites, the high-status dominant group. Next, I used data I collected through an online questionnaire to gauge the association between cultural orientation and social categorization as bases of racial stereotypes, comparing Asian respondents to whites. Key findings include a fairly consistent racial ideology among whites which I interpret as the dominant racial ideology because it conforms to principles of individual-based meritocracy ascribable as a quintessential American character. I find Asians, especially the foreign-born, to be less "ideologically consistent" compared to whites if holding the dominant ideology as the standard. In addition, in certain aspects, foreign-born Asians resemble whites more than native-born Asians do in embracing the principles of hard work, while the native-born show signs of stronger solidarity with other minority groups. Ideological assimilation, therefore, is not a straight line process that "improves" across generations. For Asians, convergence to a core "American" ideology may be stronger in the first generation but weaker in the second generation as a result of the combination of racialization and birthright. Implications and suggestions for future studies are discussed.
Il mestiere di scrivere [electronic resource] : Italo Calvino e Natalia Ginzburg, posizioni, pratiche, opere di due professionisti della scrittura
Keywords: French and Italian Literature.

This project examines the intersection of fictional writing and editorial work in the careers of two of post-war Italy's leading literary figures, Natalia Ginzburg and Italo Calvino. I explore the ways in which these writers, working for Einaudi -- the most prestigious Italian publisher of the time -- could control the forms in which their works came to be published and at the same time sought to shape the reception, both nationally and internationally, of their own books. At the same time, I analyze how the aesthetic choices of these writers are influenced by their privileged position as editors, literary agents, and readers of others' works for publication.
Imaging of spin torque switching and ultrafast spectroscopy at X-ray free electron lasers [electronic resource]
Keywords: Applied Physics

In this thesis, I present the results of two distinct sets of experiments relating to x-ray measurements performed on solid metal transmission samples. In the first part, I present time-resolved scanning transmission x-ray microscopy (STXM) measurements that were performed to study the current-induced magnetization switching mechanism in nanopillars exhibiting strong perpendicular magnetic anisotropy. The switching in these devices occurs in the relative alignment (anti-paralllel or parallel) between two ferromagnetic layers: a fixed and free layer. The STXM technique provides both short-time (70 ps) and high-spatial (25 nm) resolutions. Direct imaging of the magnetization demonstrates that, after an incubation time of 1.3ns, a 100nm x 300 nm ellipsoidal device starting in an antiparallel configuration switches in 1 ns via a central domain nucleation and opposite propagation of two domain walls toward the edges. High domain-wall velocities on the order of 100 m/s are measured. Micromagnetic simulations are shown to be in good agreement with experimental results and provide insight into magnetization dynamics during the incubation and reversal periods. For the reverse process, from parallel to antiparallel, the situation is less clear, however I can surmise that switching still occurs via domain wall but with less certainty in the location of nucleation. In the second half of the thesis, I explore x-ray absorption spectroscopy at free- electron lasers (FEL). First, I demonstrate the feasibility of near edge x-ray absorption fine structure spectroscopy (NEXAFS) on solids by means of femtosecond soft x-ray pulses from the free-electron laser at hamburg (FLASH). The experiments used a special sample geometry, spectrographic energy dispersion, single shot position- sensitive detection, and a data normalization procedure that eliminates the severe fluctuations of the incident intensity in space and photon energy. As an example, I present a NEXAFS spectrum recorded the 3D1 N4,5 edge absorption resonance of La3+ ions in LaMnO3. Later experiments, done at the Linac Coherent Light Source (LCLS), aim to understand the role of electronic damage under intense x-ray pulses. I wish to understand the point at which an intense x-ray pulse can no longer be treated as a small perturbation on the electronic structure of a sample. Because of problems with the normalization of the detection scheme used in the first soft x-ray spectrometer at LCLS, I cannot answer this question definitively, however, initial data is discussed.
The importance of dedication [electronic resource]
Keywords: Philosophy

In this dissertation I develop a philosophical conception of an extraordinary kind of commitment, what I call "dedication, " that is exhibited in people like religious martyrs, those devoted to secular ideals, and others whose lives revolve around grand personal passions. The motivation for this project is two-fold: one, this kind of commitment is interesting because it is significantly valuable; two, analysis of dedication reveals insights into fundamental areas of ethical thought. I argue that dedication itself is intrinsically, invariably, and significantly valuable in virtue of its intimate relationship to a special and valuable mode of integrity that is disposed to persist in the face of adverse circumstances, what I call "robust" integrity. I argue that integrity is significantly valuable because it is tantamount to a disposition to what I call "self-endorsement, " or happiness with oneself and the way one leads one's life. And, robustness contributes further value to this by providing its bearer with the ground for what I call "self-assurance." This self-assurance brings peace of mind regarding one's future self-endorsement, and satisfaction with the quality of one's current self-endorsement. The general ethical upshots of this investigation are the following. The relation between dedication and robust integrity, a species of metaphysical sufficiency plausibly understood as realization, allows for intrinsic value to be inherited across its lines. Also, all instances of dedication appear to be organic unities, wholes whose value is not necessarily equal to the value of the sum of the parts, which helps to explain possible misevaluation of dedication. And, in the course of investigating whether the value of robust integrity and dedication translates into reasons for action, I uncover a puzzle the most plausible solution of which leads to far reaching consequences for practical reasons generally: particularly, value does not entail a reason for action, reasons for ends are holistic, and the concept of reasons "transmission" from ends to means is inapt, reasons "coordination" is more fitting.
Improving the cathode/electrolyte interface [electronic resource] : from alloying electrodes to refining grain boundaries
Keywords: Applied Physics

Solid oxide fuel cells (SOFCs) have been demonstrated to have great potential for efficiently converting chemical energy to electrical energy. Recent studies have focused on reducing the operating temperature of SOFCs to below 500°C. At such low temperatures, the cathode/electrolyte interface is one of the bottlenecks for better fuel cell performance. In this work, improving the cathode/electrolyte interface was first attempted by replacing pure platinum electrodes with platinum alloy electrodes. Pure platinum electrodes suffer degradation of microstructure over time at elevated temperatures due to The Ostwald ripening. The results show, that in solid oxide fuel cells employing nanoporous Pt-Ni cathodic catalysts instead of pure Pt, better microstructural stabilities, lower electrode impedances, and higher power densities can be achieved at elevated operating temperatures (350-550°C). Independently, improving the cathode/electrolyte interface was also attempted by improving surface structures of the electrolyte. Grain boundary regions of electrolytes were postulated to enhance the rate of oxide ion incorporations. A continuum model was developed to simulate oxide ion diffusion under the influence of electrical fields in polycrystalline oxides. Based on experimental O-18 tracer diffusion data, the model is consistent with enhanced oxide ion incorporation rates in close proximity of the grain boundaries. The results suggest that employing electrolytes with high densities of surface grain boundaries may enhance the performance of low-temperature SOFCs.
In a time of prophets [electronic resource] : healing, gender, and politics in the Nazareth Baptist Church of South Africa, c.1870-1939
Keywords: History

The Nazareth Baptist Church (NBC) took root during the Zulu Zion, a surge in the growth of faith healing churches throughout South Africa (but especially among Zulu speakers) in the early twentieth century. It has since become one of South Africa's oldest and largest faith healing churches. Drawing upon oral traditions, oral history interviews, and government archives, this study traces the history of the NBC from the birth of its first prophet (Isaiah Shembe) through an act of violence in 1939 that secured the succession of the second prophet. It argues for the salience of understanding ideas of healing in the making, un-making, and maintenance of communities in South Africa in the early twentieth century. In so doing, it also shows how the community transformed from a group coalescing around women's grievances into an institution with property and resources as men gained new interest and authority in the church.
In the right place at the right time [electronic resource] : understanding basic microrna biology through the control of developmental timing by lin-4 and let-7 in caenorhabditis elegans
Keywords: Genetics

MicroRNAs are an important class of short RNA molecules that regulate gene expression in diverse organisms. Despite their short history, extensive research on microRNAs has revealed how microRNAs are made, their regulatory mechanisms and functions in different biological processes. In addition, novel experimental techniques and computational algorithms have been developed to study microRNAs. Our knowledge of microRNAs is constantly evolving as newer studies turn up exceptions to canonical models established by early studies. This highlights how our understanding of microRNAs is far from complete and much work is still needed to investigate unexplored aspects of the microRNA world. The founding microRNAs, C. elegans lin-4 and let-7, have well-characterized heterochronic defects in mutant animals and their target genes have been genetically validated. Combined with powerful experimental tools available in C. elegans, the microRNA function of lin-4 and let-7 in developmental timing of C. elegans is an ideal in vivo model system for testing microRNA-related hypotheses. Using functional assays to evaluate lin-4 and let-7 rescue activities in transgenic animals, we have investigated several poorly understood aspects of microRNAs, from biogenesis to functional mechanism. In this work, we first demonstrated the cell autonomous nature of lin-4 in C. elegans temporal development. Through tissue/cell-specific expression of lin-4 and the use of tissue/cell-specific reporters and microRNA sponges, we have shown that lin-4 rescue activities were limited to sites of lin-4 expression, despite its broad endogenous expression and function in many tissues. Next, we showed that intron-containing microRNAs ("inc-miRs") are functional in C. elegans, raising the possibility that mature microRNAs need not be encoded as contiguous units in the genome. This result also highlights a blindspot in our current novel microRNA discovery methods that assume inc-miRs do not exist. Lastly, we investigated the partnership between microRNA "seed" and "non-seed" sequences in providing microRNA function during C. elegans temporal development. By assessing microRNA function in transgenic mutant animals expressing lin-4 or let-7 mutant microRNA, we found contrasting results between lin-4 and let-7. While the results suggest a functional requirement for lin-4 seed sequence, mutations in either let-7 seed or non-seed sequences provided similar levels of functional activities. Using C. elegans lin-4 and let-7 as an experimental model, this work has furthered our understanding on microRNA autonomy, microRNA biogenesis and functional partnership between microRNA seed and non-seed sequence.
In vitro analysis of the complete fatty acid biosynthetic pathway from Escherichia coli and implications on metabolic engineering of E. coli for the production of fatty acid based biofuels [electronic resource]
Keywords: Chemical Engineering

With increasing demands of energy, depletion of global fossil fuel reserves, and unsustainable emission rates of greenhouse gases, there is considerable impetus for the development of renewable fuel sources. Fatty acid derived biofuels, being energy-dense and compatible with existing infrastructure, represent a promising supplement to petroleum-based fuels. Earlier work has led to extensive genetic and biochemical characterization of the fatty acid biosynthesis pathway in Escherichia coli. More recently, the potential of using E. coli as a biocatalyst for converting biomass into fatty acid derivatives in an economically viable manner has been explored. The dissertation focuses on in vitro analysis of the complete fatty acid biosynthetic pathway from E. coli, and discusses strategies for enhancing biosynthesis of fatty acids and derivatives in vivo based on findings from the in vitro analysis. The entire pathway has been successfully reconstituted in vitro, providing a powerful starting point to understand and engineer rate-limiting and regulatory steps in the complicated pathway, thereby rationally guiding future metabolic engineering efforts for E. coli -- catalyzed biofuel production.
Incentive mechanisms for societal networks [electronic resource]
Keywords: Electrical Engineering

A "societal network" is an interconnected structure of resources and consumers that drives a societal process. Examples include roads, electricity grids, health-care systems, and waste management networks. Societal networks are plagued by two pressing problems: (i) the demand for resources exceeds their supply, especially at "peak'' hours, and (ii) inefficiencies due to wastage are highly permeable, i.e., while the loss to an individual is very small, the overall loss to the societal network as a whole can be substantial. This suggests that small changes in the behavior of each user can lead to significant gains in the efficiency of societal networks. More importantly, such a change in each user is necessary to combat systemic problems such as congestion. There is a strong urgency to the problems in societal networks -- the scale of the problems has reached epic proportions. Fortunately, help is at hand. Over the past few decades, there have been great technological inventions such as the creation of the global Internet, the Web, cellular telephony and cloud computing. Now is the right time to address the problems in societal networks making use of the ubiquitous presence of smart sensing technology. This thesis presents a first attempt at that -- making use of a variety of sensing technology to monitor user behavior, informing the users about their actions and incentivizing them to adopt a desirable behavior. This thesis develops a general approach to affect change in the behavior of the users of societal networks. At the first level, it is based on fine-grained sensing of user behavior and communicating this information to a platform, and using incentives of monetary, social and other kinds to change user behavior. At the second level, the approach is concerned with the design of low-cost and accurate sensors, and backend algorithms to inform, engage and incentivize users to affect the desired behavior change. We describe some pilot projects which we have conducted to test and verify the effectiveness of this approach. The first project, INSTANT (Infosys-Stanford Traffic project), was conducted over 6 months in Bangalore, India, to incentivize roughly 14,000 commuters of Infosys Technologies to shift their commute to off-peak hours. The second project is a recycling experiment conducted over one week at Stanford to incentivize the members of the Stanford community to recycle. Third, we outline our contributions to Steptacular, an employee wellness program run at Accenture, USA. Finally, we describe CAPRI (Congestion and Parking Relief Incentives), a research project currently underway at Stanford University to incentivize off-peak travel and "off-center" parking.
Incentive problems concerning the timing and quality of dialysis [electronic resource]
Keywords: Business.

This dissertation is composed of three essays that analyze incentive problems concerning the health care of end stage renal disease (ESRD) in the United States. The first essay is concerned with the unintended consequences of a proposed change to the system for allocating kidneys to patients on the transplant waiting list. In particular, policymakers in the United States have recently proposed to modify the kidney allocation system by assigning higher priority to patients who are on dialysis longer. The essay examines how this change may create an incentive for physicians to start their patients on dialysis prematurely and investigates how to mitigate this unintended behavior. The second essay investigates physician behavior directly from data, analyzing why the kidney function at which patients start dialysis has been rising over time in the United States. That is, why do patients seem to be starting dialysis earlier and earlier over time? The third essay is concerned with the quality of care of profit-maximizing dialysis providers. In particular, Medicare recently restructured its reimbursement system and publicly released previously confidential data on the quality of care of dialysis facilities. The essay analyzes how such policy changes influence the quality of care decisions of profit-maximizing dialysis providers. On the whole, this dissertation is intended to help policymakers as they make difficult decisions about kidney allocation policies, ESRD-related spending, dialysis reimbursement, and disclosing dialysis facility performance information.