VictorJuiz/thesis huggingface dataset:
Discovering novel roles for the RNA binding protein Whi3 during stress [electronic resource]
Keywords: Biology.

Whi3 is an RNA binding protein that regulates cell cycle entry by binding to mRNA of the G1 cyclin CLN3 and to the cyclin-dependent kinase Cdc28. Cln3 binds to Cdc28 to promote passage through Start. whi3[delta] cells have a small size phenotype, and Whi3 may regulate cell size by sequestering CLN3 mRNA and Cdc28 protein in the cytoplasm to delay G1 entry (Wang et al., 2004). We observe that Whi3 reversibly localizes from the cytosol to cytoplasmic puncta in response to glucose deprivation and heat shock. This phenotype is shared by components of stress granules (SGs), which are large RNP complexes that form in yeast in response to various stress conditions; SGs sort and process mRNAs during the stress response (Buchan et al., 2008). Because Whi3 shares several characteristics with known SG components, including an RNA binding domain and stress-dependent relocalization, we hypothesize that Whi3 is a novel component of SGs. We show that Whi3 colocalizes with SG markers in response to glucose deprivation and heat shock. Preventing SG formation inhibits Whi3 foci formation. Like SG components, Whi3 is enriched in insoluble cell fractions during stress. Whi3 is not required for SG formation, but may be targeted to SGs to carry out a previously unknown function. We conclude that Whi3 is a novel component of yeast stress granules. This observation suggests an alternative model for Whi3 function: that Whi3 might regulate mRNA translation during stress by transporting mRNA to stress granules. We demonstrate that Whi3 regulates many of its interacting RNAs, and that this regulation may promote stress-dependent survival.
Discrete sampling in continuous time, band-limited signals [electronic resource]
Keywords: Electrical Engineering

During more than 60 years, the paradigm implied by the celebrated Shannon sampling theorem has been the basis of most ADC and DAC architectures, with the exception of the so called oversampling converters. The improvements in semiconductor technology allowed for little change in these design architectures while faster, lower power converters and new generations of manufacturing processes were developed. Over the last 5 to 10 years, the point of diminishing returns with respect to scaling seems to have been reached. As a result, there is a renewed interest in researching alternative sampling paradigms to Shannon's. Discrete Sampling is one of the numerous sampling alternatives proposed recently. In this research we show how Discrete Sampling can be extended to work with the class of continuous time band-limited signals. In addition to several mathematical results on the matter, the actual implementation of the paradigm is also considered. It will be shown that the proposed scheme results in a particular type of Hybrid Filter Bank. Several examples of such banks are presented together with their performance when sampling and reconstructing real life audio signals.
Dissecting mechanisms of bacterial pathogenesis using chemical probes [electronic resource]
Keywords: Chemical and Systems Biology.

Host-pathogen interactions are highly regulated at the post-translational level, making small molecules useful tools for dissecting many aspects of these events. This dissertation describes the development and application of chemical probes to examine aspects of bacterial infection on either side of the host-pathogen interface. We rationally designed a set of inhibitors and activity-based probes to study the substrate recognition and activation mechanisms of the internal cysteine protease domain (CPD) of Clostridium difficile's large gluocosylating toxin TcdB; a major virulence factor of this important nosocomial pathogen. Subsequent work with these tools has helped elucidate the biochemical details of CPD allosteric activation within a eukaryotic environment, and has provided evidence that TcdB contributes to hypervirulence in some C. difficile strains. We also developed an optimized activity-based probe for studying inflammasome-mediated caspase-1 activation, which is a fundamental part of the host's response to intracellular bacterial pathogens. We used this tool to discover that when cells are unable to activate caspase-1 upon intracellular bacterial infection, they instead undergo apoptosis. This work provides insight into a potential intracellular arms race between the host and pathogens capable of suppressing caspase-1 activation, and also highlights the balance that exists between pro- and non-inflammatory cellular responses. Together, these studies show there is much to be gained from adding chemical probes to the repertoire of tools used to study mechanisms of bacterial pathogenesis.
Dissecting multiple origins of heterogeneity in RNA folding [electronic resource]
Keywords: Chemical Engineering

Structured RNAs are central to many biological processes. For structured RNAs to carry out their function, they must fold into a correct structure and often undergo conformational changes while carrying out their function. When RNA folding, conformational change and function have been studied at the single molecule level, it has been commonly observed that individual molecules can have distinct properties that persist over long timescales. However, the origins of this molecular heterogeneity were unknown. The research presented in this dissertation uncover that heterogeneity in RNA folding can arise from multiple sources. This understanding helped elucidate features of RNA folding landscapes that were not previously appreciated. Furthermore, it demonstrated that understanding the origins of heterogeneity for a particular RNA is key to developing models that accurately describe the overall folding.
Dissecting the holy body [electronic resource] : between medicine and religion in early modern Europe
Keywords: History.

This dissertation explains how the body provided proof of holiness in early modern Catholicism. Tradition had long asserted that the bodies of especially saintly or sinful individuals should reveal signs of their elect status. In the early modern period, Church officials sought to make such vague ideas exact: they required medical proof of bodily holiness. This requirement arose out of developments in both medicine and Catholicism. After the Reformation, many Christians doubted how or even if they should venerate the saints. In response, the Catholic Church centralized and formalized canonization procedures. As part of this reform, canonization officials began to require that medical practitioners examine the cadavers of holy individuals. Medical and anatomical knowledge had progressed during this period to the point where dissection was thought to yield unique information about the lifestyle and habits of the deceased. This information could also include signs of a person's spiritual state. The body, interpreted through expert eyes, could now reveal a person's true nature. Together, medical practitioners and canon lawyers in the city of Rome created standards through which to interpret bodily signs of holiness. The methods of proof employed in these examinations presaged many techniques of knowledge production that would become a part of experimental practice in the early modern world. This dissertation therefore demonstrates that instead of being opposed, science and religion worked together to define the boundaries of the natural in human bodies.
Distribution problems in number theory [electronic resource]
Keywords: Mathematics

Four separate problems are considered. The first chapter concerns the average equidistribution of Heegner points attached to elements of fixed order in the class group of imaginary quadratic fields. Some discussion of the Cohen-Lenstra heuristics is also included. Chapter 2 treats the distribution of the logarithm of two families of L-functions at the central point. The most easily stated consequence is that the central values of L-functions attached to modular forms of large weight converge to 0 in distribution as the weight tends to infinity. Chapter 3 concerns omega results for large sums of Dirichlet characters. The length N of the sum is treated as a parameter that is allowed to vary with the modulus q of the characters. For N small compared to q the large values exhibited are related to the distribution of smooth numbers, while for larger N the results are analogous to omega bounds known for the corresponding L-functions. The final chapter gives a mixing time analysis for the random k-cycle walk on the symmetric group. The main new analytic ingredient is an asymptotic formula for many character ratios evaluated at a k-cycle.
Does Carbon Pricing Improve Clean Tech Profitability? A Comparative Analysis of the United States and Australia
Keywords:  Department of Economics
carbon tax
cap-and-trade
clean energy
event study
Australia
United States
Stanford Department of Economics
Thesis

The literature on optimal climate change abatement policy stresses that a price on carbon dioxide emissions could play a crucial role in driving clean energy technology innovation. The premise underlying this theory is that forcing emissions-intensive energy production to internalize the externality will increase the profitability of clean energy production, thereby enhancing the incentive to innovate. This paper tests that assumption by using event study methodology to evaluate whether political events indicating the prospect of a price on carbon in Australia and the United States increased the share prices of clean energy firms in the two countries. I find that in Australia, investors responded to expectations of a carbon tax by bidding up the valuation of Australian clean energy firms substantially. I identify a similar response in the United States, but these effects are smaller in magnitude and not as statistically robust. I offer two possible explanations for the asymmetry of these results: differing political institutions between the two countries that make policy promises more credible in Australia than in the U.S. and variations in the proposed policies that could have caused investors to project that the Australian carbon tax would be a more effective driver of clean energy than the U.S. cap-and-trade system.
Does making a test high stakes for students artificially inflate acheivement gap by race & gender? Evidence from the California High School Exit Exam [electronic resource]
Keywords: Education.

In a prior study of high school exit exams, my co-authors and I found that socio-economically disadvantaged students -- female, low income, English Language Learners (ELLs) and students of color -- are less likely to pass a high school exit exam than their more socio-economically advantaged peers, even when controlling for prior and concurrent achievement on a similar exam with no individual stakes for students (Reardon, Atteberry, & Arshan, 2011). These findings raise significant concerns about the accuracy of standardized test scores and the role they may play in reproducing societal and educational inequality. In this dissertation I use the same data to more thoroughly explore the achievement gaps on the high stakes California High School Exit Exam (CAHSEE) and low stakes California Standards Test (CST). I posit that the reasons we may observe a CAHSEE/ CST gap fall into three broad categories. The first category consists of statistical artifacts resulting from measurement error and violations of statistical assumptions. The second category of explanations consists of unintended consequences to policy decisions. These decisions may exacerbate achievement differences between groups but do not stem from performance differences between different groups introduced along with the high stakes of the test. If there is no evidence that the CAHSEE/ CST gaps are driven by true differences in ability -- either due to differences in student knowledge (including test prep) or differences in rigor of content or preparation—then these gaps are most likely the direct result of the "high stakes" nature of the exam. I use student level administrative data from three large California districts to examine these possibilities. I demonstrate that these measures are not driven by school segregation or measurement error using school fixed effects, multiple measures of ability, test scores shrunken to the group mean and instrumental variables. I find that women overperform on the English Language Arts (ELA) exam and underperform on the mathematics exam. Other groups underperform on both exams. Breaking down the exams by the content substrands, I find that the writing sample, which is included in the high stakes CAHSEE, but not the low stakes CST, drives the female overperformance on the ELA section. I conclude that the patterns of these gaps, including dramatic differences by school attended, are consistent with a stereotype threat explanation. In an era of increasing accountability for students, these performance differences on meaningful tests need to be considered both by policymakers as a possible negative unintended consequence to student level accountability and by educators as an impediment to the current of future success of their students.
Domesticating Prince Shōtoku [electronic resource] : Tokugawa sacred geography and the construction of a national landscape
Keywords: History.

The cult of Prince Shōtoku in the ancient and medieval periods was developed through the geographical logic of a satellite (Japan) struggling to break free from a superpower (China). Over time, the prince's images accreted numerous sacred and powerful layers as a national symbol in response to the political, religious, and cultural opportunities of each new age. After the encounter with Europe and the shift in the socio-political structure of the country, the burden of Shōtoku's image as a national symbol also changed accordingly. Shitennōji Temple in Osaka, as a hub of the Shōtoku cult, had always been at the middle of the cult's transformations. After surviving tough times including the turbulence of the Oda-Toyotomi decades in the late sixteenth century, Shitennōji was integrated directly into the new Tokugawa regime by Tenkai, a Tendai monk and the key architect of Ieyasu's new religious policy. Tenkai's vision was more than a mere revival of Shitennōji's physical plant or a stabilization of its role as a center of the Shōtoku cult. Rather, Shitennōji was designated as one of the most politically important temples to ensure success in institutionalizing Buddhism under the Tokugawa regime. To further that project, Tenkai appropriated Shōtoku narratives in order to construct a new national ideology for deifying Ieyasu by combining Buddhism and Shintō. Tenkai's thoroughly designed scheme caused an unintentional discourse-battle between Tenkai and Hayashi Razan. As a representative Tokugawa scholar, Razan attempted to reorganize Japan's national landscape based on Neo-Confucianism and Shintō, and he severely attacked Buddhism, criticizing Shōtoku narratives. The legacies of this battle for the next generations included new functions for Shōtoku narratives. One was as agencies to support Shintō Japan--rather than Buddhist or Confucian Japan. Another was as gazetteers, or travel guidebooks. Under the Tokugawa publishing boom, Shōtoku-related gazetteers contributed to the popularity not only of Shōtoku-related sites but also of other pilgrimages all over Japan. Thus, the broader public could start recognizing concrete geographies of Japan, while at the same time imagining Japan as a unified sacred field. Meanwhile, Tokugawa intellectuals began to struggle with conceptualizing sacred Japan in the world. Needless to say, Shōtoku narratives also responded to this movement, serving to legitimate Shintō Japan and confirming the construction of a national landscape.
Drag augmentation via supersonic retropropulsion for atmospheric deceleration [electronic resource]
Keywords: Aeronautics and Astronautics

With sample-return and manned missions on the horizon for Mars exploration, the ability to decelerate high-mass systems upon arrival at a planet's surface has become a research priority. Mars' thin atmosphere necessitates the use of advanced entry, descent, and landing (EDL) systems to aid in deceleration to sufficiently low terminal descent velocities, and the limits of current state-of-the-art Mars EDL technologies are being challenged by evolving mission requirements. Supersonic retropropulsion (SRP), the application of jets facing into the freestream during the supersonic portion of flight, has been proposed as a candidate enabling technology for future high-mass Mars missions. Moving beyond the current "jets as thrust" paradigm, this work explores augmentation of the decelerative forces experienced during Mars entry through a flow control approach which increases aerodynamic drag through SRP jet manipulation of the bow shock. A drag augmentation model is developed based upon attainable shock physics seen in high-fidelity simulations of SRP jets. This flow model uses SRP jet manipulation to recover shock losses normally associated with the strong high-Mach number bow shock on the entry vehicle. Flow control through SRP allows for partial recovery of stagnation pressure and thus significant deceleration without the burden of substantial fuel mass, increasing both the mass of deliverable payloads and the payload mass fraction. To quantify maximum achievable benefits, an analytical study determines the upper limit on drag coefficients for probable jet-induced cascading shock structures (oblique shocks followed by a normal shock). Subsequent trajectory studies reveal a tremendous potential for aerodynamic drag generation which is substantial even if only a modicum of the stagnation pressure losses can be recovered through SRP shock manipulation. Finally, attainable drag coefficient values and candidate configurations are presented based on well-validated CFD simulations of modeled jets and the resulting shock structures, establishing this novel SRP-based flow control concept as a technology capable of increasing the deliverable payload mass for future Mars missions.
The Drosophila Myb and RB/E2F2 complex transcriptionally regulates cytokinesis [electronic resource]
Keywords: Genetics

The Myb gene family plays a role in several types of human cancers. For example, high expression levels of c-Myb in colon cancer and B-Myb in breast cancer correlated with poor prognosis for the patient. B-Myb, the vertebrate homolog of invertebrate Myb, activates transcription of mitotic genes. In Drosophila, mutation of Myb reduced expression of mitotic genes, such as the regulatory kinase genes polo and ial (AurB). Previous studies revealed multiple mitotic defects in Myb mutant cells, including disrupted chromosome condensation and abnormal spindles. I now show that binucleate cells, the hallmark phenotype of cytokinesis failure, accumulate in Myb-null ovarian follicle cell and wing disc epithelia. Myb functions as an activator in the generally repressive Drosophila RBF, E2F2, and Myb (dREAM)/Myb-MuvB complex. Absence of the dREAM subunits Mip130 or E2F2 suppressed the Myb-null cytokinesis defect. While previous Myb-null mitotic phenotypes were difficult to quantitatively assay, the binucleate phenotype was binary, countable, and had a near zero background level in wild-type tissues. This offered a unique opportunity to use the Myb-null binucleate phenotype to study how the dREAM complex represses transcription. In the absence of Myb, repression by the dREAM complex was sensitive to the decreased dose of the subunits E2F2, Mip120, Caf1, and interestingly Lin-52, which was previously genetically implicated as an activator in the complex. Surprisingly, reducing the dose of His2Av also suppressed the Myb-null binucleate phenotype, suggesting a novel role for this variant histone in transcriptional repression by the dREAM complex.
Dual-band CMOS power amplifiers [electronic resource]
Keywords: Electrical Engineering

The past five years have seen the explosive growth of smartphones and tablets. In 2011, worldwide smartphone sales reached 473 million units, and since the iPad's launch in 2010, it has sold 84.1 million units. These popular mobile devices connect to a variety of wireless standards, such as Wi-Fi, Bluetooth, FM radio, GPS, and cellular, which each operate in different frequency bands. Today each frequency band requires its own wireless radio, but there is an effort to design dual-band radios capable of operating across multiple frequencies. These dual-band radios could reduce components, lower costs, and improve the energy efficiency in wireless devices. Some RF circuit blocks, such as the voltage-controlled oscillator (VCO) and low-noise amplifier (LNA), have already been designed in dual-band, but a dual-band power amplifier (PA) has remained elusive. This thesis investigates dual-band PAs in CMOS for the 802.11n WLAN standard that operates in both 2.4GHz and 5.0GHz bands. First a broadband PA that could cover both frequencies, 2.0GHz to 5.0GHz, was designed. The disadvantage of this approach was the strong 2.4GHz second harmonic at 4.8GHz that fell within the broadband range. Normally a filter could be placed after the PA to eliminate this second harmonic, but with a dual-band 2.4GHz / 5.0GHz PA, a filter cannot eliminate the 4.8GHz second harmonic without also severely degrading the 5.0GHz signal. So then tunable filters, both on-chip and off-chip, were designed to eliminate the second harmonic only during 2.4GHz operation. First a PA with on-chip tunable filter that could also serve as a dual-band matching network was designed. Next an off-chip tunable filter on PCB using discrete components was designed. This off-chip tunable filter was then integrated with the broadband and dual-band PAs to show second harmonic filtering using both on-chip and off-chip filters.
Dynamic amplifiers for high-speed pipelined A/D conversion [electronic resource]
Keywords: Electrical Engineering

Analog-to-digital converters (ADC) are a vital part of a many applications that require an interface with real-world analog signals. Fueled by the ever increasing demand for higher bandwidth and lower power consumption in many areas, the energy efficiency of ADCs becomes a critical performance criterion. Today, there exist a variety of ADCs that provide high energy efficiency solutions only for low bandwidths (below ~100 MHz). In the high-speed space (above 100 MHz), however, the energy efficiency of ADCs degrades dramatically, and this is especially visible for pipelined ADCs, which take 3-5 times more energy than other architectures that do not emphasize high speed. Furthermore, existing non-pipelined solutions for this bandwidth range are few in numbers, and this presents an opportunity for innovation at both the architectural and circuit design level. This thesis explores a pipelined ADC design that employs a variety of low-power techniques such as dynamic residue amplification and incomplete settling in a unique way to maximize the speed while maintaining low energy (98 fJ/conv-step). The resulting work advances the state-of-the-art by simultaneously achieving a high conversion rate (500 MS/s), low power (5.1 mW), moderate resolution (8 bits), and low input capacitance (55 fF). The experimental converter was implemented in a 65-nm Silicon-on-Insulator (SOI) CMOS process and is among the first high-performance ADCs employing this technology.