VictorJuiz/thesis huggingface dataset:
Helicobacter pylori [electronic resource] : molecular mechanisms for the utilization of the cell surface as a replicative niche
Keywords: Microbiology and Immunology

Helicobacter pylori is a bacterium that chronically infects the stomachs of more than half the human population, in some cases leading to serious diseases such as gastric cancer and ulcers. H. pylori intimately interact with the gastric epithelial surface, but much remains unknown about its life on the cell surface. The bacterium possesses several tools for its close interaction with the gastric epithelia, including a type IV secretion system, through which the virulence factor CagA is directly translocated into host cells. This dissertation focuses on how H. pylori's close interactions with the epithelial cells allows it to modify the apical cell surface to turn it into a replicative niche for the bacterium. Using live-cell microscopy to follow the fate of individual bacteria on the cell surface, we find that H. pylori is able to utilize the apical cell surface as a replicative niche, even in conditions that do not support the growth of free-swimming bacteria. Experiments with a polarized epithelial model system show that the bacterium's major virulence factors CagA and VacA both play important roles in enabling H. pylori growth and microcolony formation on the apical cell surface, by mediating perturbation of host cell polarity and intracellular trafficking processes. We find that iron is one important micronutrient that H. pylori acquires from host cells during colonization of the polarized epithelium. CagA and VacA act in concert to affect the polarized process of transferrin/transferrin receptor recycling and iron uptake in the host cells, resulting in the mis-sorting of a subset of the transferrin/transferrin receptor complex to the colonizing bacteria on the apical cell surface. This process is functionally important for the bacteria, as downregulation of transferrin receptor expression resulted in a decreased ability of H. pylori to colonize the polarized epithelium. These studies establish the cell surface as a replicative niche, which presents challenges that require bacterial adaptation for its successful utilization. Our findings also illustrate the concept that contact-dependent bacterial virulence factors may be used for the perturbation of host cell physiology for the bacterium's benefit, allowing acquisition of needed factors directly from host cells, and colonization of the apical cell surface.
The heroine's journey [electronic resource] : representing female desire and self in premodern Chinese romance
Keywords: East Asian Languages and Cultures.

This dissertation examines the evolution of the caizi-jiaren mode, and ideas about the self, gender, and ethics exhibited in it. My investigation will cover a broad range of texts spanning from the ninth century through the eighteenth century--from Tang chuanqi tales, through Ming-Qing drama, fiction, and tanci--aiming to show how the conventions of romance address cultural and ideological changes, and participate in broader social discourses. I argue that the heroine's quest for love and self is always part of a larger cultural project, fostered by a questioning and new awareness of the place of the individual within the social matrix. I read these romances in the light of the more dynamic modes of gender and desire, with a focus on the working of desire as a dialogue with moral systems and public power, and gender's relation to cultural expression.
Hidden conditional random fields for speech recognition [electronic resource]
Keywords: Electrical Engineering

This thesis investigates using a new graphical model, hidden conditional random fields (HCRFs), for speech recognition. Conditional random fields (CRFs) are discriminative sequence models that have been successfully applied to several tasks in text processing, such as named entity recognition. Recently, there has been increasing interest in applying CRFs to speech recognition due to the similarity between speech and text processing. HCRFs are CRFs augmented with hidden variables that are capable of representing the dynamic changes and variations in speech signals. HCRFs also have the ability to incorporate correlated features from both speech signals and text without making strong independence assumptions among them. This thesis presents my current research on applying HCRFs to speech recognition and HCRFs' potential to replace the current hidden Markov model (HMM) for acoustic modeling. Experimental results of phone classification, phone recognition, and speaker adaptation are presented and discussed. Our monophone HCRFs outperform both maximum mutual information estimation (MMIE) and minimum phone error (MPE) trained HMMs and achieve the-start-of-the-art performance in TIMIT phone classification and recognition tasks. We also show how to jointly train acoustic models and language models in HCRFs, which shows improvement in the results. Maximum a posterior (MAP) and maximum conditional likelihood linear regression (MCLLR) successfully adapt speaker-independent models to speaker-dependent models with a small amount of adaptation data for HCRF speaker adaptation. Finally, we explore adding gender and dialect features for phone recognition, and experimental results are presented.
High harmonic generation from multiple orbitals in molecular nitrogen [electronic resource]
Keywords: Applied Physics

The high harmonic amplitude and phase is modulated by the electronic structure in atoms and molecules. Past studies of high harmonic generation (HHG) attribute features in the high harmonic spectrum to solely the highest occupied molecular orbital (HOMO). Molecular electrons that are energetically below the HOMO should contribute to laser-driven high harmonic generation. We present the first evidence of HHG from multiple orbitals in molecular nitrogen. We describe measurements of the amplitude and phase of the HHG from aligned nitrogen molecules. The HHG phase from aligned nitrogen is measured interferometrically by beating the nitrogen harmonics with those of an argon reference oscillator in a gas mixture. A rapid phase shift of 0.2 pi is observed in the vicinity of the HHG spectral minimum. We compare the phase measurements to a simulation of the HHG recombination step in nitrogen that is based upon a simple interference model. The results of the simulation suggest that modifications beyond the simple interference model are needed to explain HHG spectra in molecules. Possible modifications are the inclusion of the molecular potential and multiple orbital effects. The importance of multiple orbital contributions to HHG is seen in measurements of the alignment dependent HHG amplitude from aligned nitrogen molecules. Measurements of the HHG spectrum in nitrogen molecules aligned perpendicular and parallel to the laser polarization show new features that indicate the influence of the electrons that occupy the orbital just below the molecular nitrogen HOMO, referred to as the HOMO-1. Evidence of the HOMO-1 is seen in the HHG spectrum obtained at the half revival of a rotational wave packet. Such observations of lower lying orbitals are essential to understand the influence of electron motion on atomic dynamics in laser-excited molecules.
High performance reconfigurable computing for learning Bayesian networks with flexible parameterization [electronic resource]
Keywords: Electrical Engineering

As improvements in high-throughput biology experiments outpace the advancement in processor performance, the gap between conventional processing capacities and new computational demands grows at exponential rates. In order to address this problem and keep pace with the new computing demands, traditional tool development approaches, where software and methods are developed independently of the hardware platform, need to be replaced by Hardware/Method co-development approaches. This new approach can achieve orders of magnitude higher performance as well as better power efficiency as the chip resources are customized to the particular computation demands of the problem. This work is an Algorithm/Architecture co-development effort to address a computationally intensive problem in modeling interaction networks using Bayesian statistics. Learning interaction networks from data uncovers causal relationships and allows scientists to predict and explain systems' behavior. Interaction networks have applications in many fields, though we will discuss them particularly in the field of personalized medicine where state of the art high throughput experiments generate extensive data on gene expression, DNA sequence and protein abundance. I will present how the FPGA-based HPC system we built, ParaLearn, is capable of modeling interaction networks in human T-Cells at orders of magnitude faster than conventional approaches.ParaLearn includes problem specific parallel/scalable algorithms, system software and hardware architecture to address this complex problem. ParaLearns accelerated and integrated solution enables scientists to use computationally intensive Bayesian network inference algorithms in real time settings. Also since it has been designed for high performance and flexibility, it creates new opportunities to develop network inference algorithms that are more robust to model parameterization and hence makes Bayesian network modeling a more useful and reliable tools for scientists.
High performance solution processed transparent electrodes for optoelectronic devices [electronic resource]
Keywords: Materials Science and Engineering

Many thin-film optoelectronic devices, including displays and photovoltaic cells, require transparent conducting films as part of their device architecture. Sputtered indium tin oxide (ITO) is the most commonly used material and has high performance but is expensive and has some performance limitations, especially on flexible substrates. This dissertation presents high-performance composite transparent conducting films comprised of silver nanowires and polymer films for use as a replacement for ITO in these devices. These composites have lower sheet resistance than ITO with comparable transmission on both glass and plastic substrates and are demonstrated in this work to be compatible with high-efficiency organic photovoltaic devices. They are also more mechanically robust to ITO and show nearly substrate-independent performance. These composites have the potential to enable both low-cost photovoltaics and flexible displays.
High speed, low driving voltage vertical cavity germanium-silicon modulators for optical interconnect [electronic resource]
Keywords: Electrical Engineering

Information processing requires interconnects to carry information from one place to another. Optical interconnects between electronics systems have attracted significant attention and development for a number of years because optical links have demonstrated potential advantages for high-speed, low-power, and interference immunity. With increasing system speed and greater bandwidth requirements, the distance over which optical communication is useful has continually decreased to chip-to-chip and on-chip levels. Monolithic integration of photonics and electronics will significantly reduce the cost of optical components and further combine the functionalities of chips on the same or different boards or systems. Modulators are one of the fundamental building blocks for optical interconnects. Previous work demonstrated modulators based upon the quantum confined Stark effect (QCSE) in SiGe p-i-n devices with strained Ge/SiGe multi-quantum-well (MQW) structures in the i region. While the previous work demonstrated the effect, it did not examine the high-speed aspects of the device, which is the focus of this dissertation. High-speed modulation and low driving voltage are the keys for the device's practical use. At lower optical intensity operation, the ultimate limitation in speed will be the RC time constant of the device itself. At high optical intensity, the large number of photo generated carriers in the MQW region will limit the performance of the device through photo carrier related voltage drop and exciton saturation. In previous work, the devices consist of MQWs configured as p-i-n diodes. The electric field induced absorption change by QCSE modulates the optical transmission of the device. The focus of this thesis is the optimization of MQW material deposition, minimization of the parasitic capacitance of the probe pads for high speed, low voltage and high contrast ratio operation. The design, fabrication and high-speed characterization of devices of different sizes, with different bias voltages are presented. The device fabrication is based on processes for standard silicon electronics and is suitable for mass-production. This research will enable efficient transceivers to be monolithically integrated with silicon chips for high-speed optical interconnects. We demonstrated a modulator, with an eye diagram of 3.125GHz, a small driving voltage of 2.5V and an f3dB bandwidth greater than 30GHz. Carrier dynamics under ultra-fast laser excitation and high-speed photocurrent response are also investigated.
A homotopy-theoretic view of Bott-Taubes integrals and knot spaces [electronic resource]
Keywords: Mathematics

We construct cohomology classes in the space of knots by considering a bundle over this space and "integrating along the fiber'' classes coming from the cohomology of configuration spaces using a Pontrjagin-Thom construction. The bundle we consider is essentially the one considered by Bott and Taubes, who integrated differential forms along the fiber to get knot invariants. By doing this "integration'' homotopy-theoretically, we are able to produce integral cohomology classes. Inspired by results of Budney and Cohen, we study how this integration is compatible with homology operations on the space of long knots. In particular we derive a product formula for evaluations of cohomology classes on homology classes, with respect to connect-sum of knots. We then adapt the construction to be compatible with tools coming from the Goodwillie-Weiss embedding calculus, in particular Sinha's cosimplicial model for the space of knots.
How does context matter? Comparing achievement scores, opportunities to learn, and teacher preparation across socio-economic quintiles using TIMSS and PISA [electronic resource]
Keywords: Education.

Many people have touted education as a great equalizer because it provides students with the skills and opportunity to succeed in life based on their own merit. While this attitude has helped increase access to education around the world, the quality of that education varies. Globally, education has multiple challenges. On the micro level, educational quality remains inconsistent, and on the macro level, increasing economic inequality has potential to deleteriously affect education. This study analyzes the relationships between micro level education phenomena and these macro level economic forces to determine how economic inequality relates to education quality. This study engages the infamous educational "black box" in three different areas that capture, in aggregate, a meaningful portion of the classroom experience: opportunity to learn (OTL), teacher preparation, and student achievement. The analysis situates educational quality in the context of country-level economics by comparing students across three types of economic disparities: inequality between countries, inequality within countries, and inequality in the socio-economic status (SES) of students. Between-country inequality consists of differences in overall country income while within-country inequality concerns the distribution of income. Between-student inequality gauges the relative SES of families and their ability to provide resources conducive to education. The main hypothesis is that high SES students in more-unequal countries have relatively more access to educational resources, leading to relatively better teachers, relatively more OTL, and higher math scores. The converse would hold true for low SES students. Findings from international comparisons using the international assessments in 2003 (PISA and TIMSS) show that income inequality adversely relates to educational factors for students in all SES groups. Both high and low SES students in more-unequal countries have lower achievement scores, less prepared teachers, and less OTL. More detailed analysis at the country level does not identify any "silver bullets" for low or high income inequality countries, but does show that OTL has a greater relationship to achievement for higher SES students, while environmental factors such as community size matter for low SES students. Theses findings imply that high SES students have the foundation to take better advantage of their educational settings while low SES students must first manage their social and economic environments.
How observers discriminate between dependent and self-critical women [electronic resource]
Keywords: Psychology

This dissertation applied a novel method of analysis using aggregated written descriptions of naïve observers to compare dependent and self-critical women as they interacted with their boyfriends. The terms "dependent" and "self-critical" have been used to describe two personality styles that reflect two different types of vulnerability to depression, as measured by the DEQ. Theoretically, this difference is thought to arise developmentally from an overemphasis on relationships (for the dependent person) or from an overemphasis on protecting the self from potential criticisms (for the self-critical person). Past research has relied primarily upon self- and peer-reports to examine the differences between women with each type of vulnerability, and little attention has been given to differences between the two groups in their actual interpersonal interactions. According to interpersonal theorists, interpersonal interactions should be more informative than personality descriptors in differentiating between the two groups. Self-report measures already exist for identifying dependent and self-critical women, but behavioral differences between the two groups have not yet been demonstrated. My primary hypothesis was that observers' descriptions of actual behaviors (he did this to her; and she did that to him) would clearly reveal the difference in behavioral strategies used by the two types of women. Panels of naïve observers were asked to describe the behaviors they considered important, and their descriptions were aggregated across observers to identify the most commonly generated observations. My results clearly showed that the observer-reported behavioral sequences were superior to personality trait descriptions in discriminating between the two groups.
Hybrid Simulation of the Eulerian Method and the Streamline Method: Investigating the Role of Cross-Product in Cross-Over Time Between the Two Methods
Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Thesis

The streamline method is ideally suited for simulating large 3D heterogeneous multi-well systems when fluid transport is dominated by convection. For such systems the Eulerian method becomes too expensive because of strong non-linearity. Decoupling of the 3D problem into a set of 1D problems reduces the computational time in the streamline method. However, the streamline method cannot address the cross-flow effect effectively when it is strong. In field scaled problems, the cross-flow effect is not always strong and one can still benefit from using the streamline method. Motivated by this, the possibility of a hybrid approach was investigated. The hybrid approach consisted of using the Eulerian method when the cross flow was strong and shifting to the streamline method when the cross flow was negligible. The present research dealt with the finding of a robust measure for the cross-over time in the hybrid approach. The cross-product of phase fluxes was found to be a reasonable measure to determine the cross-over time in the hybrid simulation. It was observed that the cross-product decreased at a faster rate initially and it stabilized at later times. The time when the cross-product stabilized was considered the optimal cross-over time. However, the optimal cross-over times were found to be very large due to very low relative error tolerance. The rate of decrease in relative error was not linear with the increase in cross-over time. The relative error decreased at a faster rate initially. Therefore, to benefit from the computational efficiency of the streamline method and also to have an acceptable relative error tolerance, a cross-over time less than the optimal cross-over time was considered. The maximum reducible cross-product is the difference of the maximum cross-product and the stabilized cross-product. A criterion for selecting the cross-over time was found to be the time when the maximum reducible cross-product reduces by 90%. This criterion resulted in 70% and 98% reduction in the relative error for gas injection and water injection cases, respectively. The average run time using the Eulerian method in the hybrid simulation was around 30% and 10% of the total simulation time for gas injection and water injection cases, respectively.
Identification and characterization of genes that affect the coordination of cell division with DNA replication in Bacillus subtilis [electronic resource]
Keywords: Biological Sciences

Dividing cells must ensure that their DNA is accurately replicated and that both copies of the chromosome are faithfully segregated into the new daughter cells before cell division completes. Here, I describe the identification and characterization of mechanisms that contribute to the coordination of cell division with DNA replication in the Gram-positive soil bacterium Bacillus subtilis. I developed a genetic screen to isolate mutations that increase the frequency with which B. subtilis cells erroneously divide over their chromosome when DNA replication is perturbed. Seventeen mutations were isolated in genes involved in a range of cellular processes including DNA repair, chromosome organization, cell wall structure, and central carbon metabolism. Six mutations affecting cell cycle coordination in B. subtilis were characterized, including detailed studies of the mechanism by which the DNA translocase SftA promotes chromosome separation at nascent division septa. I also investigated the role of YycJ, a putative metallo-beta-lactamase, in regulating cell division.
Identifying Aberrant Segments in Permanent Downhole Gauge Data
Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Thesis

Data from permanent downhole gauges are needed for interpretation of subsurface conditions in a well. The data from permanent downhole gauges are voluminous and usually contains aberrant segments. Using this aberrant data to characterize the reservoir leads to generation of inaccurate reservoir parameters (permeability, skin and storage). The approach used in this work to solve the problem of interpretation of permanent downhole gauge data was by generation of multisegment synthetic pressure data using the pressure equation with all the reservoir parameters known. An aberration was introduced in the form of a pressure segment that went against the reservoir physics; it decreased with a production shut in, when it should increase. An algorithm based on direct Kalman filtering technique was developed which was independent of the reservoir model and extracted a signal with the minimum error (mean square deviation) from the noisy/aberrant signals. In this way, aberrant segments were successfully identified, removed and the original signal with actual reservoir parameters recovered.