VictorJuiz/thesis huggingface dataset:
Control of transcriptional programs of aging by NF-kappaB [electronic resource]

Aging is a degenerative process accompanied by tissue deterioration, decline in function and increased susceptibility to disease. It is now understood to be a genetically and environmentally regulated process, rather than simply the result of wear and tear. We developed a systematic approach to identify combinatorial cis-regulatory motifs that drive age-dependent gene expression across different tissues and organisms, and identified the transcription factor NF-[kappa]B as a candidate regulator of aging. Using multiple independent models, we show a role for NF-[kappa]B in regulating transcriptional programs of aging. First, we found that aged mice subjected to NF-[kappa]B blockade for two weeks exhibit reversion of the tissue characteristics and global gene expression programs to those of young mice. Next, we detected deregulated transcriptional activity of NF-[kappa]B in Sirt6-deficient mice, which exhibit premature aging-like symptoms. We show that Sirt6 interacts with the NF-[kappa]B RelA subunit and deacetylates histone H3 lysine 9 (H3K9) at NF-[kappa]B target gene promoters. Computational genomics analyses revealed increased activity of NF-[kappa]B-driven gene expression programs in multiple Sirt6-deficient tissues in vivo. Moreover, haploinsufficiency of RelA rescues the early lethality and degenerative syndrome of Sirt6-deficient mice, suggesting that hyperactive NF-[kappa]B-dependent transcription in the absence of Sirt6 promotes premature aging-like syndromes. Finally, we performed a genome-scale survey of RelA and Sirt6 location on chromatin in mouse embryonic fibroblasts (MEFs) via chromatin immunoprecipiation (ChIP)-on-chip to understand to what extent Sirt6 and RelA act coordinately to regulate gene expression. These results indicate that RelA and Sirt6 co-occupy the promoters of a large population of genes at sites less than 500kb apart and/or require RelA to enable binding of Sirt6. Expression analysis of these shared targets reveals direct regulation of 301 promoters, including genes such as Shc1 (encoding p66), Cdkn2a (encoding p16), Wnt2 and Jmjd3, which have been separately implicated in the aging process. We propose that hyperactive NF-[kappa]B signaling contributes to premature and normal aging.

Keywords: Cancer Biology.
Advisor: Chang Howard Y. (Howard Yuan-Hao)
Chua Katrin Faye advisor. Thesis advisor
Khavari Paul A. advisor. Thesis advisor
Sweet-Cordero Eric advisor. Thesis advisor
Controls on Landscape Denudation Between Lhasa and Namche Barwa, Southeastern Tibet

Twenty new 10Be-derived basin-averaged denudation rates from the region upstream of the Namche Barwa massif resolve the relationship between these rates, and tectonic and climatic variables. Denudation rates correlate well with channel steepness and local relief; precipitation, in contrast, serves as a poor predictor of denudation. In the Yarlung River, denudation rates steadily increase from the headwaters towards the Namche Barwa massif, which is apparently undergoing rapid exhumation over the million-year timescales recorded by low-temperature thermochronologic measurements. North of the Yarlung in the Nyang River, accelerated denudation rates somewhat correspond with the location of active footwall uplift associated with extensional structures. My data, in combination with previously reported 10Be-derived denudation rates from the Parlung River, suggest that regional order-of-magnitude variations in denudation rate are associated with profile knickpoints in the vicinity of Namche Barwa and within the Parlung. Thus, it appears that regional base-level changes, as well as local tectonic effects associated with extension within the Plateau and uplift along its margin, act to steepen the landscape, and in doing so, accelerate denudation.

Keywords:  Department of Geological and Environmental Sciences
School of Earth Energy &amp; Environmental Sciences
Tibet
Thesis
Advisor: Hilley George E.
Klemperer Simon
Coordinated execution and goal management in a reactive cognitive architecture [electronic resource]

Coordinated execution and goal management are important human-level capabilities studied in cognitive science and psychology. Evidence suggests there are several di erent types of constraints that govern the coordinated execution of multiple, concurrent tasks. We took three of these types - shared objects, logical relations, and resource requirements - and developed an extension to a cognitive architecture, Icarus, that supports coordinated execution under such constraints. The extended architecture assumes that it should consider subgoals in its procedures concurrently unless the constraints prevent such execution. The existing framework supports constraints on shared objects and logical relations, but it requires a new facility to handle resource constraints. We specify resource requirements for each action that Icarus can use in the world, and the system assigns resources to executable skill paths during the skill retrieval process. The architecture prevents the execution of any skill path that requires already assigned resources and ensures that execution is coordinated according to the resource constraints. We are also interested in the ability to manage goals that arise through changes in the environment. Such changes can lead people to pursue a new goal, abandon an old goal, and revise priorities among existing goals. This ability is especially important when executing multiple tasks at the same time, because concurrently pursued goals can interact with each other in both positive and negative ways. An agent should be able to give priority to more important ones if other goals are known to interfere. In response, we made a second extension to the Icarus architecture that lets the system manage its top-level goals in a reactive manner. The revised Icarus distinguishes long-term and short-term goals, and it nominates instantiated versions of long-term goals when the state matches their corresponding relevance conditions. During the nomination process, the architecture computes the degree of match for the relevance conditions and uses it to modulate priority values of nominated goals. Icarus revises the priority of nominated goals based on the modulated values. To evaluate these extensions, we chose a variety of scenarios in an urban driving domain to demonstrate the new abilities. Due to the high-level nature of our research on cognitive architectures, the demonstrations focus on ability and parsimony of the extended Icarus framework. We have also examined connections to earlier work on these topics and explored future directions for research.

Keywords: Aeronautics and Astronautics
Advisor: Rock Stephen M. primary advisor. Thesis advisor
Lall Sanjay advisor. Thesis advisor
Langley Pat advisor. Thesis advisor
Cost-effective wireless architectures achieving enhanced capacity and coverage [electronic resource]

Achieving higher coverage and capacity while at the same time reducing the cost of cell site deployment, maintenance and backhaul is always the goal of wireless operators. Femtocell and relay are two promising architectural candidates for mobile operators to achieve coverage and capacity improvement in a cost-effective manner. The first half of this dissertation focuses on the relay systems. Relay stations are devices that assist transmission from the information source to the destination. The capacity of a wireless relay network composed of a large number of nodes that operate in an amplify-and-forward mode and that divide into a fixed number of levels is analyzed. We consider both cases where the direct link towards destination nodes is present or not. The capacity computation relies on the study of products of large random matrices, whose limiting eigenvalue distribution is computed via a set of recursive equations. The femtocell network is explored in the second half of this dissertation. The idea of femtocells is to overlay low-power and low-cost base station devices, namely Femto-APs, on the existing cellular network, where each Femto-AP provides high speed wireless connection to subscribers within a small range. Simulation results show that significant areal capacity (throughput per unit area) gain can be achieved via intense spatial reuse of the wireless spectrum. However, Femto-APs introduce more interference to the existing cellular network and degrade the coverage. Fractional frequency reuse can be applied for interference mitigation. Acceptable coverage can be provided while retaining similar order of areal capacity gain.

Keywords: Electrical Engineering.
Advisor: Cioffi John M.
Cox Donald C. advisor. Thesis advisor
Kahn Joseph M. (Joseph Mardell) advisor. Thesis advisor
Coupling fluorophores molecules to nanophotonic structures [electronic resource]

Fluorescence imaging and spectroscopy is an important tool in many areas of research. Biology has particularly benefitted from fluorescence techniques, since a single molecule's position, local environment, and even activity can be studied in real time by tagging it with a fluorescent label. It is, therefore, important to be able to understand and manipulate fluorescence. One way to control fluorescence is to shape the local electromagnetic fields that excite the fluorescent molecule. This thesis studies the interaction between fluorescent molecules and two nanophotonic structures that highly modify local electromagnetic fields: the bowtie nanoantenna and the photonic crystal cavity. The study of plasmons, or coherent excitations of free electrons in a metal, has led to the fabrication of antennas at optical frequencies. In particular, gold bowtie nanoantennas have been shown to concentrate light from the diffraction limit at 800 nm (~300 nm) down to ~20 nm, while also enhancing the local electric field intensity by a factor of 1,000. This huge change in the local field greatly alters the absorption and fluorescence emission of nearby molecules. This thesis will show that the fluorescence from an initially-poor single-molecule emitter can be enhanced by a factor of 1,300, allowing for the measurement of one highly enhanced molecule over a background of 1,000 unenhanced molecules. By extending this experiment to molecules in solution, dynamics of single molecules in concentrated solutions can also be measured. While bowtie nanoantennas act to concentrate light, light does not remain in the structure for long. The photonic crystal cavity can be used to trap and store light, which has interesting implications for molecular emitters located nearby. This thesis will show that molecules can be lithographically positioned onto a photonic crystal cavity and that the molecule's fluorescence emission is coupled to the cavity modes.

Keywords: Applied Physics
Advisor: Moerner W. E. (William Esco)
Brongersma Mark L. advisor. Thesis advisor
Kino Gordon S. advisor. Thesis advisor
Cross-border enforcement of patents [electronic resource]

The dissertation complements the existing literature at the intersection of intellectual property and private international law by providing new insights into cross-border enforcement of patent rights. It is a case study of one specific type of patent enforcement problems − problems associated with enforcement across national borders − and also a study of the impact that private international law mechanisms may have on substantive law. The dissertation shows that notwithstanding patent law territoriality, even under current substantive and procedural laws, patent cases arise in which cross-border enforcement is necessary. It explains why such cases exist and what kind of cross-border enforcement problems they generate; it also analyzes current proposals aimed at facilitating smoother recognition and enforcement abroad of decisions issued in such cases, and concludes that the proposals can function only if countries agree on deeper harmonization of patent laws. In the short-term, the U.S. may solve the problem by entering into bilateral or limited regional treaties on cross-border enforcement because the problem is, at least for now, geographically confined. In the long-term, countries should complement discussions on the proposals that will facilitate cross-border enforcement with a reopening of negotiations on creating a world patent or a regional patent. The dissertation is based on an empirical study of patent cases filed in the U.S. and Germany; it also draws on an extensive comparative study of the legislative and jurisprudential development of the patent laws of the two countries.

Keywords: Law.
Advisor: Kessler Amalia D. primary advisor. Thesis advisor
Goldstein Paul
Lemley Mark A.
Crossing the efficiency frontier [electronic resource] : understanding consumers' responses to opportunities

Although consumers face many options that can potentially be construed as opportunities, they are usually quite selective in pursuing them and often form subjective perceptions of the offer's true value. How, then, do consumers evaluate the attractiveness of marketing offers? In this dissertation, I propose a framework for understanding consumers' responses to offers and the cues they use as indicators of above-normal value. I hypothesize that consumers are often enticed by options that they perceive as particularly valuable to them due to a combination of personal circumstances "unforeseen" by the marketer. Contrary to a common assumption, I propose that under certain conditions, customized marketing offers that are presented as tailored to the consumer's individual preferences may be perceived as less attractive than self-discovered opportunities that are believed to match the consumer's preferences by coincidence. The findings also suggest that when the offer appears valuable to the consumer in a less obvious or more difficult to process manner, its attractiveness increases. Examination of the process underlying these results suggests that these effects are mediated by the extent to which the offer is perceived as providing consumers with a relative advantage or above-normal value, compared to normal circumstances. This effect does not appear to interact with the chronic tendency to experience psychological reactance. Moreover, the effects tends to be particularly pronounced when concepts and norms related to competition and self-interestedness are more accessible, highlighting the role of lay beliefs about the competitive and efficient nature of the market in these effects. The findings suggest that consumers try to "beat the market" by taking advantage of offers they believe were designed to appeal to people who would find them less attractive than they would. The findings have theoretical implications for understanding consumers' perceptions of opportunities and marketing offers, as well as important practical implications for designing customized offers and targeted promotions.

Keywords: Business.
Advisor: Simonson Itamar primary advisor. Thesis advisor
Kivetz Ran advisor. Thesis advisor
Shiv Baba
Cultural psychology of the Middle East [electronic resource] : three essays

This dissertation addresses one of the central concerns of the social sciences, the relationship between social formations and psychological processes. It does so by: a) describing differences in the psychological functioning of individuals located in Middle Eastern and North American socio-cultural contexts; and b) linking this variation to specific features of the Middle Eastern and North American socio-cultural systems. I offer three essays on the socio-cultural psychology of the Middle East, each exploring a different set of cognitive, emotional and motivational processes. The first essay describes culture-specific forms of reasoning about complex political and military events. A series of studies demonstrate that individuals in Middle Eastern settings tend to locate the cause of an event in particular individuals or groups rather than in impersonal or social factors. The second essay examines the motivations to conform and to self-enhance. Four studies demonstrate that individuals in the Middle East exhibit a constellation of psychological tendencies not observed in the prototypical collectivist and individualist cultures of East Asia and North America, namely self-enhancement and a preference for conformity. The third essay explores cultural variation in the tendency to feel emotions in response to events which affect others but not oneself. Three studies support the hypothesis that individuals in Middle Eastern settings tend to experience such emotions more frequently and intensely than do North Americans and in response to different types of events. Each essay describes the macro- and meso-level features of the Middle Eastern socio-cultural system likely to foster these culture-specific modes of psychological functioning and considers implications of the findings presented here for our understanding of the Middle Eastern social and political landscape.

Keywords: Sociology
Advisor: Cook Karen S. primary advisor. Thesis advisor
McDermott Monica
Ridgeway Cecilia L. advisor. Thesis advisor
Custom integrated amplifier chip for VLF magnetic receiver [electronic resource]

Electronic systems for collecting measurements in harsh, remote environments face special challenges that often require custom designs. These systems must have the power capacity, data storage, and robustness to record high fidelity data for many months with no human contact. In this work, an integrated preamplifier for a magnetic sensor is designed to satisfy the size, weight, power, temperature, and noise specifications for long term deployment in Antarctica. The low impedance magnetic antenna (1 [ohm] --1 mH) requires a low input impedance amplifier and operates in the VLF (Very Low Frequency) range (50 Hz--30 kHz). At these low frequencies, 1/f noise becomes the dominating issue that limits performance. Due to the higher 1/f noise corner of MOSFET devices, only bipolar-junction transistors (BJTs) must be used in noise-critical parts of the design. Because of recent interest in BJTs for their superior performance at high frequencies in the gigahertz range, they are becoming available in the fabrication processes for integrated chips. With these new opportunities for using BJTs in integrated designs, low frequency amplifiers used in low noise applications can be integrated for the first time. In this thesis, a low impedance custom amplifier is presented that was implemented in National Semiconductor Corporation's BiCMOS process which meets the impedance and temperature requirements while achieving 2 pA/pHz current noise in band with only 5 mW of power. This noise level corresponds to a magnetic field noise of 0.25 fT/pHz for the loop antenna that is used for this application. The amplifier is field tested at the South Pole, successfully collecting data suitable for science research.

Keywords: Electrical Engineering
Advisor: Inan Umran S. primary advisor. Thesis advisor
Linscott Ivan primary advisor. Thesis advisor
Pauly John (John M.) advisor. Thesis advisor
Data integration and inverse methods for characterization of multicomponent hydrologic systems [electronic resource]

This work is motivated by the need for tools that can be used to accurately characterize subsurface environments at a range of scales, and given a range of different data sources. There is a pressing need for such tools, since tuning subsurface models is often the most critical step in making accurate predictions about groundwater flow and transport of contaminants. Increasingly, dense instrumentation at groundwater sites is becoming more common, and a range of different testing methods, both hydrologic (pumping tests, tracer tests) and geophysical (GPR, seismic, electrical resistivity), may be used in order to produce images of subsurface heterogeneity. At sites such as these, key questions include how to integrate all measurements at a site into a single model, how to efficiently and accurately "invert" all data, and how to interpret the meaning of geophysical information. In five separate studies, advancements in inverse modeling and parameter estimation were introduced in order to provide useful tools for solving such subsurface imaging problems. The key contributions of this thesis are as follows 1) Derivation of a generalized, continuous-form adjoint state equation, which accelerates the numerical solution of a range of inverse problems; 2) Application of a simplified groundwater flow model and geostatistical inverse methods to a field problem at the Boise Hydrogeophysical Research Site; 3) Development of a level set-based method for joint inversion of parameter fields dominated by structural features; 4) Development of a maximum likelihood method for estimating petrophysical relations, which aid in the application of joint inversion; and 5) Development of a stochastic method for integration of multiple data sources and optimization of groundwater cleanup operations. Overall, the methods presented in these studies provide novel methods for integrating multiple data sources in order to identify the features of hydrologic systems.

Advisor: Kitanidis P. K. (Peter K.) primary advisor. Thesis advisor
Freyberg David L. advisor. Thesis advisor
Knight Rosemary (Rosemary Jane)
Data-Parallel Rasterization of Micropolygons

We present two data-parallel algorithms for rasterizing micropolygons. Our approaches differ from current techniques by parallelizing across polygons. The first, LOCKSTEP, processes micropolygons in lockstep and runs with high utilization (65%) for a small number of SIMD units, despite variance in the amount of rasterization work for each micropolygon. The second, REPACK, compacts works and is able to maintain high utilization (85%) even for large number of SIMD units. While REPACK operates with high utilization, it incurs overhead from repacking data. We study the performance and utilization of our algorithms on simulated hardware with varying amounts of SIMD units. We make predictions about the overall cost of rasterizing micropolygons in a future real-time system.

Keywords: Computer Science.
Raster data > Computer programs
Image processing > Computer programs
Computer graphics
Thesis
Advisor: Hanrahan Patrick
De la hetaera a la ramera [electronic resource] : el viaje alegórico de la prostituta hacia la modernidad latinoamericana

This study explores the prostitute's allegorical role throughout the history of Western literature, culminating in the late 19th century and early 20th century Latin American novels, where this character was established as a symbol of modernity and, more specifically, as symbolizing the destructive influence of the Latin American modernization process on the region's incipient national projects.

Keywords: Iberian and Latin American Cultures.
Advisor: Ruffinelli Jorge primary advisor. Thesis advisor
Predmore Michael P. advisor. Thesis advisor
Rosa Richard advisor. Thesis advisor