VictorJuiz/thesis huggingface dataset:
The relationship between nuclear magnetic resonance and permeability in near-surface unconsolidated materials [electronic resource]

Essential to the effective assessment of groundwater aquifers is a comprehensive understanding of permeability (k), which defines the ease with which a fluid flows through a material. Although methods exist for obtaining estimates of k in the field, depending on the applications, they can be limited in their effectiveness. A promising alternate method for obtaining estimates of k is through proton nuclear magnetic resonance (NMR) logging. The NMR measurement provides information about water-filled porosity and pore space geometry, both of which can be used to obtain estimates of k. For decades, k has been reliably predicted from NMR logging data in petroleum applications where the materials are consolidated and the pores are typically small. However, in unconsolidated materials where pores are large, studies have shown that k is not reliably estimated. The goal of this research was to improve the reliability of NMR-derived permeability estimates in near-surface unconsolidated materials. The differences between the NMR-derived permeability estimates in small and large pores were analyzed through field and laboratory data, numerical modeling, and theoretical assessments. This thesis showed that including bulk fluid relaxation and assuming slow diffusion affects the reliability of the NMR-derived permeability estimates in unconsolidated sands and gravels. Additionally, this work showed that horizontal permeability is most reliably predicted when the measured NMR T2 distribution is represented as a single value by taking its arithmetic mean. This research establishes NMR logging as a promising tool for characterizing relevant hydrological parameters in near-surface groundwater applications.

Keywords: Geophysics.
Advisor: Knight Rosemary (Rosemary Jane)
Mavko Gary
Mukerji Tapan
Religion, science, and value in Nietzschean life-philosophy [electronic resource]

This dissertation explores the relationship between philosophy, science, and religion by reconstructing a "Nietzschean" tradition of "life-philosophy" [Lebensphilosophie] in late 19th-century Germany and analyzing an influential critique of this tradition. I argue that in the context of the impact of Darwin and the German historicist tradition, philosopher Friedrich Nietzsche, church historian Franz Overbeck, and sociologist Georg Simmel developed "naturalistic" theories of religion that drew from the life-sciences to give an account of the place of human values in the natural world. I then examine the most trenchant critic of life-philosophy, Heinrich Rickert, and argue that Rickert attempted to outline a "Kantian" alternative that rejected naturalistic and genealogical accounts for failing to capture the role values play in practical life. Further, I show that these debates over naturalism and value were the basis of each thinker's understanding of religion and assessment of its fate in modernity. In conclusion, I venture some remarks concerning the potential contribution of philosophical insights won from my reconstruction of "Nietzscheanism" and "Kantianism" for theoretical discussions in the contemporary study of religion.

Keywords: Religious Studies.
Advisor: Sockness Brent W.
Bashir Shahzad
Hussain Nadeem J. Z. advisor. Thesis advisor
Yearley Lee H. advisor. Thesis advisor
Reprogramming fibroblasts to pluripotency [electronic resource]

Reprogramming of somatic nuclei to a pluripotent state can be achieved by two approaches: somatic cell nuclear transfer (cloning) and transcription factor transduction to generate induced pluripotent stem cells (iPS). Early molecular events in reprogramming are not well understood, in large part due to the inefficiency of nuclear transfer and iPS generation. This inefficiency has led to the hypothesis that early reprogramming is a stochastic rather than a deterministic process. We hypothesized that iPS generation could be improved by the identification of early molecular events and pathways that may enhance reprogramming. In order to model reprogramming of fibroblasts towards pluripotency, we generated mouse embryonic stem cell X human fibroblast heterokaryons in which somatic cell pluripotency gene activation and promoter demethylation occurs rapidly and without cell division. We show that heterokaryon cell fusion based reprogramming is rapid and extensive, and that active DNA demethylation of the somatic OCT4 and NANOG promoters requires Activation Induced Deaminase. Heterokaryon bi-species RNA- Seq identified a role for a secreted factor which enhanced iPS generation and could replace constitutive viral expression of the reprogramming factor c-Myc. These data demonstrate that heterokaryons can serve as a discovery tool for novel reprogramming factors and that findings in cell fusion based reprogramming can inform early events in iPS generation. Mixed species heterokaryons are an attractive model system for investigating mechanisms of active DNA demethylation in the context of the mammalian genome and provide a viable approach for investigating early events in cellular reprogramming.

Keywords: Microbiology and Immunology.
Advisor: Blau Helen M. primary advisor. Thesis advisor
Chen Chang-Zheng advisor. Thesis advisor
Sarnow P. (Peter) advisor. Thesis advisor
Wernig Marius advisor. Thesis advisor
Rereading as requirement [electronic resource] : the cognitive demands of Mallarmé, Krysinska, and Proust

This dissertation claims that three French-language authors from the late-nineteenth century designed their works to demand rereading. Worried that the public favored goal-oriented approaches to literature that narrowed their perceptions of the texts, they solicited rereading to cultivate alternative interpretive practices. For Stéphane Mallarmé, the problem was that readers targeted semantic content--an approach that he feared would diminish his poetry's sensorial effects. In Marie Krysinska's view, the issue was that people's inclination to assimilate new concepts based on what they already knew caused them look for familiar features and discard leftover details. Marcel Proust attacked the common practice of reading for the wisdom of the author because doing so seems to make readers struggle to evaluate the reliability of the information that they are given. By causing these approaches to fail and then inciting us to reexamine the passages that we misread, all three of these writers disperse our attention to aspects of literature that we otherwise tend to neglect. Ultimately, the claim is that Mallarmé, Krysinska, and Proust designed their texts to challenge interpretive habits that arise from what are now called "cognitive biases, " or mental inclinations that can be inferred from the patterns of errors that most people when they make intuitive judgments about uncertain situations. By cultivating our awareness of these biases and by furnishing us with opportunities to practice working through them, certain literary texts seem to have the potential to restructure our interpretive habits so that we learn to recognize, anticipate, and avoid some of the irrational interpretations to which we are prone.

Keywords: French and Italian.
Advisor: Landy Joshua
Alduy Cécile advisor. Thesis advisor
Wittman Laura advisor. Thesis advisor
Resistive random access memory device scaling and integration with complementary metal-oxide-semiconductor [electronic resource]

Resistive random access memory (RRAM) is a promising candidate to meet future density and power challenges. RRAM has fast switching speed, low programming power, and many other advantages. However, there are still a few imperative issues to be tackled before RRAM can compete with, and eventually, replace flash or other memory technologies. This dissertation explores two issues: 1) RRAM scaling potential below 10 nm and 2) integration of RRAM with complementary metal-oxide-semiconductor (CMOS), which leads to the first threedimensional (3D) field programmable gate array (FPGA) based on RRAM.

Keywords: Electrical Engineering.
Advisor: Wong S. Simon primary advisor. Thesis advisor
Nishi Yoshio
Wong Hon-Sum Philip
Resource constrained scheduling problems in next-generation computing and networking [electronic resource]

With the explosion of traffic on computer networks along with the proliferation of applications that grow increasingly demanding of device and network resources, it has become imperative to find efficient algorithms for scheduling the delivery of this traffic. Starting with a focus on wireless communications, and continuing with a discussion of related issues in sensor networking and failure management in computing, we offer both a methodology for modeling these issues as well as algorithms for optimizing performance under the resource constraints at hand. We first investigate a key issue of scheduling the transmission of data frames across lossy channels when there is simultaneously a constraint on channel usage as well as a deadline by which all transmissions must be made. A tradeoff between throughput and power usage is profiled, and concepts from dynamic programming and control are applied to solve the real-time scheduling decision problem in question. This general type of resource limited scheduling problem appears in a number of areas in addition to wireless communications, including remote sensing and failure management in computing systems, which we also discuss at length. This work also addresses decision problems in which rather than a limitation on power, the key issue is a limitation on the routes that can be taken through a switch controlling the passage of packets to their respective destinations. A hard deadline by when packets must be delivered is once again considered. Routing constraints of this type are profiled in both a wireline as well as wireless communications framework, and we offer powerful yet intuitive solutions for these problems.

Keywords: Management Science and Engineering.
Advisor: Bambos Nicholas primary advisor. Thesis advisor
Apostolopoulos John G. advisor. Thesis advisor
Ye Yinyu advisor. Thesis advisor
Response spectrum compatibilization and its impact on structural response assessment [electronic resource]

Quantification of the seismic performance of structures is a critical step in the design and analysis of our built environment. This is sometimes accomplished using response history analysis, which requires ground motions resulting from (or attempting to simulate) real earthquakes. This thesis describes statistical studies of structural analysis results obtained from ground motions developed using response spectrum compatibilization (a.k.a. ``spectrum matching''), in order to evaluate whether the compatibilization approach produces ground motions that induce lower levels of demand on structures relative to those developed using other methods. Ground motions strong enough to cause significant damage are rare yet inevitable, motivating research on how to select, modify, or synthesize appropriate records for analysis. The spectrum matching process is a modification procedure used to provide such ground motions through nonlinear modification of spectral shape, and may be useful either to reduce spectral variability among a suite of records, or to change unsuitable spectral shapes to make them suitable. Response history analysis can be quite time-consuming, and a reduction in spectral variability generally leads to a reduction in nonlinear structural response variability, implying fewer ground motions (and fewer hours) are required to obtain an estimate of mean response. A drawback of using matched ground motions is that there is not yet consensus as to whether they will produce biased structural response results relative to results obtained from ground motions that were not matched. This thesis demonstrates the existence of a statistically significant and unconservative response bias for a variety of structural models and response parameters when ground motions are matched to reduce spectral dispersion. The cause for this bias is fully attributed to the impact of spectral shape variability, as characterized within a suite of ground motions by conditional spectral dispersion. A modified variable-target matching methodology is then proposed to provide rare, intense ground motions that produce unbiased response estimates by maintaining appropriate spectral shape variability. Finally, general recommendations are provided on the use of spectrum matching for design and analysis, and both the limitations of this study and future opportunities are discussed.

Keywords: Civil and Environmental Engineering.
Advisor: Baker Jack W. primary advisor. Thesis advisor
Kiremidjian Anne S. (Anne Setian) advisor. Thesis advisor
Miranda Eduardo (Miranda Mijares) advisor. Thesis advisor
Retino-hypothalamic regulation of light-induced sleep in mice [electronic resource]

The daily organization of sleep is regulated by a complex interaction between circadian and homeostatic processes. Light indirectly modulates sleep through its ability to phase shift and entrain the circadian system. However, light can also exert a direct, circadian-independent effect on sleep. In diurnal animals, an acute exposure to light promotes arousal whereas the same exposure induces sleep in nocturnal animals. The mechanisms whereby light directly influences sleep are not well understood. Chapter 1 reviews both the neurobiology and current hypotheses of how light acutely modulates sleep at the level of the retina and hypothalamus. Chapter 2 highlights the selective effects of light on murine sleep. By using single light pulses of different intensities and durations, the data demonstrate that (1) mice are highly responsive to the sleep inducing properties of light during the dark phase, (2) the transition to sleep is characterized by a rapid induction, period of maintenance, and a rapid compensatory recovery, and (3) the melanopsin photoreceptors in the eye are primarily important for maintenance of light-induced sleep. Chapter 3 focuses on the modulation of light-induced sleep by the melanopsin photoreceptors and histamine H3-receptors. We found that (1) millisecond light flashes are able to induce sleep in mice over a fairly large range of intervals, and similar to studies using continuous light, the response is melanopsin dependent. (2) We further show that the acute administration of ciproxifan, a selective histamine H3 receptor antagonist, attenuated the increase in sleep by continuous light early in the dark period. Chapter 4 contains a summary of the main findings of this dissertation and a discussion of new avenues for research on this topic which is still in its early stages. Overall, the work here highlights fundamental characteristics of light-induced sleep in mice. Such knowledge will be important for future studies assessing the mechanisms involved in the acute modulation of sleep by light in mammals.

Keywords: Biology.
Advisor: Heller H. Craig
Sapolsky Robert M. advisor. Thesis advisor
Zeitzer Jamie Marc advisor. Thesis advisor
Lecea Luis de advisor. Thesis advisor
Retroviral impact on mammalian placenta evolution [electronic resource]

The placenta plays a fundamental role supporting pregnancy in all mammals, but exhibits unexpected and striking morphological and physiological variation across species. The rapid evolutionary diversification of the mammalian placenta is hypothesized to be a product of recurrent genetic conflict between parent and offspring. In this work, I investigate the genetic basis of rapid placenta evolution by using high-throughput genomic approaches, and address three major issues in placental biology. First, given that highly conserved genes govern placental development, the molecular mechanisms underlying the rapid diversification of placental morphology have remained unresolved. Our study reveals that the genome-wide regulatory landscape of placental development is highly divergent between closely related species, strongly implicating non-coding regulatory evolution as the major force driving placental morphological diversity. Second, endogenous retroviruses (ERVs) that are normally repressed throughout the embryo are rampantly expressed in the placenta, but the biological rationale—if any— behind this apparent paradox has been unclear. We demonstrate that species-specific ERVs serve as a major source of functional enhancers during placental development, which provides a clear mechanism where placental ERV activity may facilitate the evolutionary diversification of placental morphology. Finally, our findings suggest a novel evolutionary model where placental ERVs provide an adaptive benefit under parent-offspring conflict. Given that genetic conflict predicts rapid diversifying evolution to maintain maximal fitness, we propose that placental ERVs act to dramatically increase the developmental evolvability of the placenta by serving as a rapidly evolving, epigenetically restricted source of polymorphic regulatory elements.

Keywords: Genetics.
Advisor: Baker Julie (Professor of genetics) primary advisor. Thesis advisor
Bustamante Carlos (Carlos D.) advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Revenue‐Maximizing Mechanism Choice in Divisible Good Auctions: An Empirical Analysis of the Thai Treasury Auction Market

An important question that prevails in the theory of divisible-good auctions is to determine whether a discriminatory auction yields higher revenues to the auctioneer than a uniform price auction or Vickrey auction. One way to answer this question empirically is to use estimates of the bidders’ true marginal valuations on the auctioned goods. This Honors Thesis conducts empirical studies of revenue comparisons under discriminatory and uniform price auction mechanisms and the studies of collusion on winning bid data from Thai Treasury bill auctions in 2008 and 2010. This Honors Thesis is one of the first to perform an empirical analysis using a structural econometric approach suggested by the recently developed approximate Linear Bayesian demand function equilibria (LBDFE) by [Ollikka(2011)] to estimate the model primitives and bidder valuations and simulate counterfactual auction outcomes from estimated structural parameters, then make analysis similar to methods in [Horta¸csu and Mcadams(2010)] and [Kastl(2011)]. Bank of Thailand currently employs discriminatory auctions in distributing Treasury bills. But results are generally in favor of uniform price mechanism except for those auctions with longer maturities where both auction mechanisms perform equivalently. However, practical auction experiments are necessary since the analysis modified from [Athey et al.(2011)Athey, Levin, and Seira] suggest the existence of collusion opportunities, which would not allow the uniform price mechanism to outperform the discriminatory one. Moreover, this Honors Thesis provides an indicative regression-based test for valuation implied by the data. The approaches suggested in this Honors Thesis can be extended to analyze divisible-good auctions.

Keywords:  Department of Economics
Stanford Department of Economics
Multi-unit auctions
Treasury auctions
Collusion
Thesis
Advisor: Hong Han
Reversing the brain drain? Skilled return migration and the global movement of expert knowledge [electronic resource]

My dissertation explores how skilled return migrants adapt the expertise they gained working abroad to workplaces in their home countries. To study this, I conducted a survey of 4,183 skilled returnees from 81 countries, who had worked abroad in the U.S., as well as 161 interviews with skilled returnees from 25 countries. The respondent pool came from U.S.'s largest organizational sponsor of J1 Visas for professionals. As the largest survey of skilled return migrants ever compiled, the dataset includes information on the respondents' career histories, attitudes, and work activity. My data analysis generated three main findings. One, less than half of the respondents report implementing some aspect of their professional knowledge gained overseas in the workplaces of their home countries. Whether returnees are successful channels of cross-border knowledge depends less on their ability to demonstrate or articulate novel ideas and more on the normative conditions of the professional environments in their home countries. Two, returnees who are effective brokers of knowledge bring back ideas about organizational and management practices, such as new methods of training, more than they do technical knowledge. Three, returnees are more likely to venture into self-employment if they have strong local ties to their home countries; moreover, the effect of these local ties on entrepreneurial transitions is stronger for returnees in home countries with high rates of self-employment. Finally, I show that the very returnees who are most successful as knowledge brokers are also most likely to venture abroad again. Thus, the returnees who could benefit their home countries the most are also the least like to stay. These findings challenge the conventional notion of return migrants as agents of economic transformation, suggesting that many institutional and cultural challenges stand in the way of their ability to broker knowledge and resources across country borders. This work also ties contributes to theoretical perspectives on international migration, organizational learning, social networks, and the sociology of knowledge.

Keywords: Sociology.
Advisor: Granovetter Mark S. primary advisor. Thesis advisor
Powell Walter W. advisor. Thesis advisor
Walder Andrew G. (Andrew George)
The rhetoric of realism [electronic resource] : American literature and democratic form

ABSTRACT The key to American realism lies in the author's construction of a narrator who at first glance may appear reliable and authoritative but who on closer examination is clearly constructed as one voice among many, none of which definitively provide the text with an absolute moral center. Critics have for the past three decades consistently argued, first, that American realism is not a coherent genre and, second, that if it were a genre, it would tend towards endorsing a rather regressive political program. I argue, first, that American realism is a coherent genre if we view it as a distinct form based on various stylistic constructions of anti-authoritative narration. Defining American realism through form and style rather than--as most current scholarship would have it--as a purely historical period will aid us in writing a more accurate history of American literature than we have at present. Second, I argue that American realism is a relatively democratic form. By undermining the narrator's authority, realism works to redistribute authority to multiple character positions, creating a formal polyphony of voices that has its political analog in the ideals of democratic governance. In short, I use concepts of genre, form and style to show how American realism can be made into a rigorous, critically useful term for the purpose of both literary history and literary-political interpretation.

Advisor: Jones Gavin Roger
Rampersad Arnold advisor. Thesis advisor
Woloch Alex