VictorJuiz/thesis huggingface dataset:
System-level effects of soft errors [electronic resource]

Radiation-induced transient errors (soft errors) are a major reliability concern for digital systems in advanced silicon CMOS technologies. Soft errors create unexpected changes in signal values during system operation, mostly in on-chip memories and flip-flops, resulting in undetected data corruption or expensive downtimes. This dissertation focuses on soft errors in flip-flops because design techniques to protect flip-flops are generally expensive. To protect on-chip memories, coding techniques are routinely used. Error injection simulations are widely used for characterizing system-level effects of soft errors in a given design. These techniques generally inject single-bit errors into randomly-chosen locations (flip-flops, software-visible registers and memories) during randomly-chosen clock cycles. Flip-flop-level error injections suffer from slow Register-Transfer-Level (RTL) simulations. High-level error injections, that inject errors into software-visible registers or memories, are generally fast. Unfortunately, very little literature exists on the accuracies of high-level error injection techniques. We demonstrate that existing high-level error injections can be highly inaccurate by over an order of magnitude, and present detailed error propagation analysis to quantitatively explain the causes of such inaccuracies. For fast, yet accurate, error injection simulations, we present a new mixed-mode simulation platform that combines simulators at two different abstraction levels. This platform achieves 20,000× speedup over RTL-only simulation for an industrial multi-core chip consisting of approximately half-a-billion transistors. This platform targets soft errors in uncore components (e.g., memory subsystem, I/O controllers) that occupy significant portions of the overall chip area. Using this platform, we demonstrate, for the first time, that flip-flop soft errors in uncore components can significantly impact system-level reliability. We also demonstrate that recovery from uncore soft errors can be challenging for traditional system-level checkpointing techniques. A new replay technique overcomes these challenges for uncore components belonging to the memory subsystem.

Keywords: Electrical Engineering.
Advisor: Mitra Subhasish primary advisor. Thesis advisor
Gill John T.
Olukotun Oyekunle Ayinde advisor. Thesis advisor
Table-Top THz Pulses via Large-Area Photoconductive Antennas

THz pulses have a variety of applications in atomic and molecular physics. As molecular probes, they are broadband excitation pulses to study dynamics on a unique time scale. This time scale (on the order of picoseconds) is associated with the "THz gap," or the regime in the electromagnetic spectrum previously difficult to create due to the gap between electronic frequencies and optical frequencies. Given this technological gap, THz pulses pose many engineering challenges for table-top generation. Photoconductive switches offer an elegant solution to this challenge. They take advantage of the time scale associated with charge carrier dynamics in certain semiconductor materials to generate radiation in the THz regime. These devices are triggered by laser pulses, and the majority of their radiative energy is stored in a bias field applied to the semiconductor material itself. Their power is also derived from the area of semiconductor that is triggered. Hence, these devices are easily scalable from a theoretical point of view. We have developed a large-area array of photoconductive antennas for generating high-field, broadband THz pulses in such applications. The device is a 50 cm^2 patterned array of interdigitated leads on GaAs driven by a 50 fs pulse of IR light. We also report improvements for fabrication and experimental setup using the antenna array.

Keywords:  Department of Physics
THz pulses
THz emitter
molecular orientation
photoconductive switch
antenna array
water spectroscopy
Thesis
Advisor: Bucksbaum Phil
Kasevich Mark
Tackling radio polarization data of high energy pulsars [electronic resource]

The focus of this thesis is on understanding the pulsar magnetosphere particularly with the exploitation of radio polarization. The rotating vector model (the standard pulsar polarization model) can be modified to estimate emission altitude. However, more realistic treatment of relativistic and sweep-back effects show that such augmentations break down relatively quickly. This break-down is quantified and fitting functions are provided that preserve accuracy to higher altitude. The rotating vector model has proven particularly poor for modeling energetic pulsars. We remedy this by including the effects of orthogonal mode jumps, multiple emission altitudes, open zone growth via y-point lowering, and interstellar scattering. A large number of discrepancies can be understood while retaining the geometric picture. The model is systematically applied to six Fermi-detected pulsars (PSR J0023+0923, PSR J1024−0719, PSR J1744−1134, PSR J1057−5226, PSR J1420−6048, and PSR J2124−3358). Several other examples of utilizing polarization modeling to understand pulsar geometry and emission characteristics are also presented. Finally, a bidirectional emission model is applied to the polarization data of PSR J1057−5226 and PSR J1705−1906. Overall, we push the limit of what can be learned from a geometrically based model and emphasize the importance of tying such models to data.

Keywords: Applied Physics.
Advisor: Bucksbaum Philip H. primary advisor. Thesis advisor
Romani Roger W. (Roger William) primary advisor. Thesis advisor
Blandford Roger D.
Targeting lymphoma with precision using semi-synthetic anti-idiotype peptibodies [electronic resource]

B-cell lymphomas express a functionally active and truly tumor-specific cell-surface product, the variable region of the B-cell receptor, otherwise known as idiotype. The tumor idiotype differs from patient to patient, however, making it a technical challenge to exploit for therapy. We have developed a method of targeting idiotype using a semi-synthetic personalized therapeutic that is more practical to produce on a patient-by-patient basis than monoclonal antibodies. In this method, a small peptide with affinity for a tumor idiotype is identified by screening a library, chemically synthesized, and then affixed to the amino-terminus of a pre-made IgG Fc protein. We demonstrate that the resultant semi-synthetic anti-idiotype peptibodies kill tumor cells in vitro with specificity, trigger tumor cell phagocytosis by macrophages, and efficiently clear human lymphoma in a murine xenograft model. Our results suggest that this method could be used to target tumor with true precision on a personalized basis.

Advisor: Levy Ronald
Alizadeh Ash advisor. Thesis advisor
Weissman Irving L. advisor. Thesis advisor
The teacher labor market in Brazil [electronic resource]

This dissertation explores the significance of the bargaining power of the players involved in the wage decisions for teachers in Brazil, namely the teacher unions and the municipal governments. The dissertation is divided in two parts, which together form a broad analysis of the labor market for public school teachers in Brazil and the underlying institutional factors that have determined its functioning in the past twenty years. This research indicates that the bargaining power of municipal governments and teacher unions plays an essential role in setting wages. Moreover, the results suggest that the bargaining power is more important to the wage levels than the available budget of the municipalities, and that market power is driven by the lack of alternative job opportunities to the teachers. The first paper analyzes the degree of monopsony power held by municipal public employers in teacher hiring. It shows evidence of very low elasticities for the teachers' labor supply curve (of 0.11 - 0.36, depending on the model specifications), suggesting that the market power held by municipal governments allows them to enjoy rents that are, in absence of other players to counterbalance their action, as large as 275% - 901% of the teachers wage value. It also indicates that the proportion of female teachers increase the power that municipalities have to set wages, given the relatively lower elasticity of women's supply curve. The second paper examines the actual behavior of governments in teacher hiring and uses two models -- the Monopoly-Monopsony and the Insider-Outsider -- as possible interpretations of the results. I use the FUNDEF funding reform in Brazil that has redistributed funds across municipal and state systems within each Brazilian state to identify the wage-setting decisions. It shows evidence that municipalities that benefitted from the redistribution were more likely to increase teacher salaries (by an average of 3.9%), while municipalities relatively harmed by the redistribution tended to increase the number of teachers (by 8.8%) and to decrease salaries (by -4.4%). Surprisingly, the analyses of the value transferred to the municipalities reveal that receiving more funds for education does not necessarily translate to higher teacher salaries, suggesting that the bargaining power of the municipal governments and teacher unions matter more to wage determination than the amount of funds the school systems have. This dissertation provides evidence, in the context of Brazil, that policies focused on raising across-the-board wages can be desirable as a counterforce to the market power held by municipal governments. Moreover, it suggests that federal policies focused on changing the bargaining power of the municipalities would be more effective in influencing wage levels than the amount of grants given to local governments.

Keywords: Education.
Advisor: Carnoy Martin primary advisor. Thesis advisor
Dee Thomas S. (Thomas Sean) advisor. Thesis advisor
Hoxby Caroline Minter advisor. Thesis advisor
Loeb Susanna advisor. Thesis advisor
Telomerase and the male germline [electronic resource]

Telomerase is required for maintaining the male germline in worms, fish and mice. Underlying the continuous production of sperm in these species are poorly characterized germline stem and progenitors. Telomere attrition is strictly avoided during sperm production, thus avoiding the inter-generational transmission of ageing phenotypes. The work described in this dissertation aims to answer fundamental questions regarding the behavior of germline stem cells and the control of telomerase within those cells. Firstly, we describe the generation of telomerase reverse transcriptase reporter mice, allowing the prospective isolation of germ cells with discrete telomerase levels, and uncovering the basis principles of telomerase regulation in vivo. We discover that high telomerase levels are a hallmark of the male germline stem cell lineage, regardless of proliferation status, and that telomere attrition depletes the stem cell pool. Secondly, we exploit the pattern of telomerase expression in the adult testis to understand germline stem cell heterogeneity. We fractionate purified spermatogonia into GFRa1+ and GFRa1- populations, enabling functional studies by transplantation and molecular characterization by RNA-Seq. Although GFRa1+ cells were thought to represent the predominant self-renewing population by lineage tracing, GFRa1+ and GFRa1- cells exhibit comparably high stem cell activity by transplantation. The transition from GFRa1+ to GFRa1- is accompanied by a reduction in GDNF and FGF signaling and a marked decrease in proliferation. Upon transplantation, GFRa1- cells replenish the GFRa1+ population, revealing that GFRa1- cells are in a poised state, retaining stem cell potential and the ability to be reprogrammed by a vacant niche. In the final part of this dissertation, we again exploit TERT-reporter mice to determine the transcriptomes of defined spermatogonial subtypes. These datasets established a pipeline for the rapid discovery and validation of new markers for undifferentiated spermatogonia (MSI2 and SDC4), differentiated spermatogonia (ALCAM), GFRa1- cells (OCT4-delta-PE-GFP), and finally GFRa1+ cells (MCAM).

Advisor: Artandi Steven E. primary advisor. Thesis advisor
Lipsick Joseph Steven
Oro Anthony
Sage Julien advisor. Thesis advisor
Temperature-compensated silicon MEMS resonators with high quality factors and low motional impedances [electronic resource]

Microelectromechanical systems (MEMS) have become ubiquitous today, existing alongside electronics in many products and fabricated using standard semiconductor fabrication techniques. The focus of this work is on furthering the performance of silicon resonators for frequency / time references, based on the epi-seal encapsulation process that has been demonstrated to be crucial for the stability of MEMS. Temperature-compensation via heavy doping is investigated and the temperature dependence of the elastic constants of silicon is extracted for several doping types and concentrations. The values are shown to be able to predict the frequency-temperature dependence of various resonators operating in the linear regime. Also addressed is the relatively large motional impedance of capacitive resonators (typically ~100 kΩ) in the epi-seal process. The motional impedance can be significantly decreased by having narrower capacitive gaps, and two methods compatible with the epi-seal process are demonstrated: the first by adding a selective epitaxial deposition step to the epi-seal process, and the other by designing movable electrodes that can pull-in closer to the resonator. Furthermore, high quality factor Lamé mode resonators are demonstrated here with f × Q products of 2 × 1013 Hz, in conjunction with first-order temperature compensation and low second-order temperature dependences. Lastly, charge-biasing is presented as a viable alternative to voltage-biasing for lower power consumption: charges introduced on the resonator body within the epi-seal cavity via mechanical switches show no signs of leakage even after a year. All these features can co-exist simultaneously on the same resonator with the demonstrated epi-seal stability, providing a pathway for further enhancing the performance of MEMS resonators.

Keywords: Mechanical Engineering.
Advisor: Howe Roger Thomas primary advisor. Thesis advisor
Howe Roger advisor. Thesis advisor
Pruitt Beth advisor. Thesis advisor
The Backup Plan: Visualizing Disappearing Groundwater Resources on the US-Mexico Border

The absence of groundwater treaties is a global trend despite the fact that groundwater crosses the majority of international boundaries. Why have property rights over groundwater failed to evolve from the national level to the international level? Given the broad scope of the question, this thesis narrows its geographic focus and asks: What explains the absence of a groundwater treaty for the US-Mexico border?
Visibility is the obvious difference between groundwater and other resources such as surface water which are regulated by treaties. As a result, current research on groundwater treaties assumes the role of visibility and moves on to look at other issues such as institutional dynamics.1 This is a mistake. This thesis argues that visibility does not play the traditional role it is assumed to have. Its customary role is one that creates ambiguity. For example, negotiators cannot act due to underground data gaps.
This reveals a critical misunderstanding. These explanations look at groundwater as a singular resource rather than through its relationship with surface water. Within the larger system, groundwater is the dependable resource – it is the backup plan. It lets people know that even in times of a drought they will have water. Groundwater serves as the lack of ambiguity. It lowers the perception of scarcity and with it incentives to manage use.
To test this argument, this thesis tracks three periods of rapid change in the visibility of groundwater and the reaction in the Mexicali and Imperial Valleys. These three periods are: the completion of the lining of the All American Canal in April 2010, the 7.2 Sierra El Mayor Cucapah Earthquake in April 2010, and Minute 319 in November 2012. Interviews and written accounts provide an understanding of how visibility, specifically its rate of change, impacted bilateral action on groundwater.
This thesis looks not only at the perception of groundwater’s dependability, but also at what will happen when it is no longer dependable. An analysis of n-level datasets on surface water conflict and cooperation illuminates the role of groundwater in reducing conflict and the implications of its absence.
These findings provide a novel understanding of the roadblocks to a groundwater treaty, and the implications of inaction.

Keywords: groundwater
conflict
treaty
Center for International Security and Cooperation
Thesis
Advisor: Cain Bruce
Casado-Perez Vanessa
The C1ql3 gene affects emotional memory

The complement component 1, q subcomponent-like 3 (C1ql3) gene is expressed in neurons in important brain regions such as the hippocampus, the basolateral amygdala and the insular cortex, which are known to regulate spatial memory, emotional memory, and interoception, respectively. Interoception is the brain’s awareness of bodily states, and it is important for mammals to feel the rewarding effects of a drug like cocaine. Preliminary cocaine conditioned place preference experiments on C1ql3 mutant mice showed that C1ql3 may have a role in drug reward behavior. Based on the literature and preliminary data, we hypothesized that C1QL3 has a role in regulating the interoception necessary for such drug-associated conditioning. In order to test our hypothesis, adult mice with conditional alleles for C1ql3 were intracranially injected with either control viruses or viruses expressing Cre recombinase to knock out C1ql3 expression in the insular cortex. Incidentally, the virus also diffused into the amygdala, removing C1ql3 expression in a region known as the basolateral amygdala. After recovery, several behavior assays were performed on the mice to understand the nature of the cocaine CPP phenotype. The virus-injected conditional mutant mice showed normal drug-associated conditioning, yet they exhibited emotional memory deficits, suggesting that our original hypothesis needed refinement. A thorough behavioral characterization of the mutant mice demonstrated that, rather than specifically affecting drug-associated conditioning through alterations in interoception, C1QL3 has a more general role in regulating short-term emotional memory, which is most likely due to its expression in the amygdala. The lack of CPP phenotype after virus targeting to the insular cortex is likely due to the only partial inactivation of the basolateral amygdala. Further research is required to definitively demonstrate that C1QL3 expressed in the basolateral amygdala is required for mice to form memory associations between contexts and emotional salient stimuli.

Keywords:  Department of Biology
Biology
Neuroscience
Behavior
Thesis
Advisor: Sudhof Thomas
McConnell Susan
The Cancer Enhancer

Amplification of fibroblast growth factor receptor 2 (FGFR2) has been demonstrated to correlate with bone, skin and cancer pathologies. A recent study identified a particular single nucleotide polymorphism (SNP) in an intronic region of FGFR2 that is associated with increased risk of breast cancer in Chinese women using oral contraceptives. However, the molecular mechanism for the impact of this SNP on the expression of FGFR2 is unknown. The data presented here proposes that this particular intronic region contains an enhancer for the FGFR2 gene which, when mutated, amplifies FGFR2 expression, potentially leading to disease. Using cultured human skin cells as a model for epithelial tissue, we examined the enhancer activity of the SNP-containing region via an enhancer reporter assay.
We found that when the SNP was present, the enhancer demonstrated significantly amplified activity in keratinocytes as compared to wild-type. Analysis of the transcription factor binding motifs present in the region suggests that the wild-type region binds HLTF, a transcription factor which can be activating or repressive, whereas the mutated region instead binds MYC, a highly activating transcription factor. Further research will seek to confirm these protein-DNA interactions. If confirmed, this interaction could serve as a potential therapeutic target for women suffering from breast cancer caused by oral contraceptive usage.

Keywords:  Department of Biology
Biology
Epigenetics
Enhancers
Stanford University
Thesis
Advisor: Khavari Paul
Simon Michael
The Effect of Myelin Debris Components on Purified Rodent Astrocytes

Disease and trauma to the mammalian central nervous system (CNS) result in persistent, functional deficits because axons fail to regenerate and the tissue never fully recover. Glial cells maintain the structure and function of the nervous system, but following injury these cells become reactive and undergo significant molecular and functional changes. These phenotypic changes result in the formation of a glial scar, which is composed almost entirely of reactive astrocytes. Oligodendrocytes release myelin debris and microglia release cytokines into the site surrounding the injury, which can determine and perpetuate the subsequent astrogliosis. It is crucial to understand the causes and nature of this astrogliosis and its effect on the regenerating neurons so that potential treatments could reverse this reactivity to facilitate neuron recovery. The present study treats purified astrocytes in vitro with myelin debris, myelin-associated proteins, and the potent cytokine, TNFα and quantifies the subsequent astrogliosis by gene-induction, morphology, motility, and toxicity to other CNS cell types. We found reactivity is heterogeneous and dependent on the specific treatment. TNFα induced high levels of astrogliosis and we found that oligodendrocyte membrane proteins, Nogo molecules, reduce this level of reactivity.

Keywords:  Department of Biology
Stanford department of Neurobiology
Thesis
Advisor: Barres Ben
Nelson William
The Effectiveness of the Wassenaar Arrangement as the Non-Proliferation Regime for Conventional Weapons

Sovereign countries assume they have the right to purchase weapons to strengthen their national security; however, unrestricted arms trade destabilizes regions, contributes to human rights violations, and drives interstate conflicts. Over the past century, major weapon exporting states have recognized arms trade regulation as critical for international security and, in 1996, formed the Wassenaar Arrangement as an export control group for conventional weapons. However, critics of the regime claim that the principles designed to make it successful, namely its emphasis on cooperation and transparency, lead to ineffectiveness at regulating weapons transfers.
This thesis examines the Wassenaar Arrangement and asks to what extent it has achieved its stated purpose of preventing “destabilizing accumulations” of conventional weapons. Findings show that regional trends of weapon imports and economic activity between 1980-2013 reveal no clear evidence of a shift in arms trade as a result of the regime’s formation: weapons import data for select countries from 2003-2013 indicate that members of the Wassenaar Arrangement have not limited or altered their sales in any noticeable way. This study concludes that economic incentives may undermine cooperation within the arrangement.

Keywords: Center for International Security and Cooperation
Wassenaar Arrangement
export control regimes
conventional weapons
non-proliferation regimes
non-proliferation
COCOM
Coordinated Committee for Multilateral Export Controls
Freeman Spogli Institute
transparency
weapons transfer
arms trade
Thesis
Advisor: Goldstein Judith