VictorJuiz/thesis huggingface dataset:
Toxoplasma gondii co-opts host immune signaling by secretion of a polymorphic tyrosine kinase, ROP16 [electronic resource]
Keywords: Microbiology and Immunology.

Toxoplasma gondii is an obligate, intracellular parasite of the Apicomplexan phylum that is able to infect nearly all warm-blooded vertebrates. This capability for survival in a variety of host niches is reflected in the diversification of Toxoplasma strains. Strains differ dramatically in their interaction with hosts, and a fruitful approach towards understanding the molecular underpinnings of disease has been to identify and characterize drivers of strain-specific differences in host response. Chapter 1 provides a general introduction to Toxoplasma gondii and its ability to modulate host immunity, with special attention given to what is known about the mechanisms behind strain-specific phenotypes and the role of one particular player, ROP16. Chapter 2 describes experiments demonstrating that Toxoplasma secretes a polymorphic tyrosine kinase, ROP16, that can directly phosphorylate host STAT6. These experiments made use of a targeted disruption of the ROP16 locus in Type I parasites to identify ROP16-dependent signaling pathways, and used biochemical approaches to dissect the mechanism by which ROP16 is able to induce rapid STAT6 activation. Chapter 3 describes work demonstrating that ROP16 activation of STAT6 directs murine macrophage polarization towards an alternatively activated (M2) phenotype. In Chapter 4, the avian host response to Toxoplasma is examined to determine whether strain-specific differences in host response might be inverted in non-mammalian hosts. We show that strain-specific transcriptional host response, as well as transcriptional host response modulated by ROP16, appears very similar in chickens as in mice and humans. This suggests that variance between mammalian and avian host species in general may not be the source of selective pressure for the success of these common strains, or of ROP16's variability. Chapter 5 concludes with a discussion of future directions for further characterization of ROP16's role in modulating host response. We show that ROP16 interacts with host chromatin and suggest that investigation of ROP16's function in the host nucleus might yield further molecular insights as to how Toxoplasma is able to co-opt host cells and influence the course of infection.
Trading mechanisms for financial exchanges [electronic resource]
Keywords: Economics

The first part of this thesis discusses the structure of the US equities market and the regulatory challenges involved, with respect both to particular venues and order types, and to the market as a whole. This part addresses the role of public equities markets, their objectives, and the market-design concepts relevant to evaluating them, it describes the market structure before and after the significant regulatory reforms of 2005, goes on to detail some specific market-design challenges and current proposals from the SEC, and concludes with an analysis and evaluation of several trading mechanisms and three order types, from a mechanism-design perspective. The second part of the thesis presents a theoretical model of an exchange and analyzes optimal order submission in a one-shot game in which a buyer and seller, each of whom can have two (privately known) types, can trade up to two units of an asset through an order book, which is empty at the beginning of the game. In both a setting with private values and interdependent values, equilibria in four games are characterized: a basic game with limit and market orders, and games involving one of the three order types from the first part of the thesis- iceberg, discretionary, and volume orders. The effect of the introduction of the different order types is analyzed with respect to volume and transparency. Each setting also includes an analysis of the buyer-optimal mechanism and its relation to equilibria of the games involving orders.
The transformations of Baijie Shengfei [electronic resource] : gender and ethnicity in Chinese religion
Keywords: Religious Studies.

The goddess Baijie is worshipped only in the Dali Bai Autonomous Prefecture of Southwest China's Yunnan province, home to the Bai "nationality" (minzu). Most people today see Baijie as the widow martyr of a local ruler from the eighth century, but she first appears as a Buddhist goddess in scriptures of the Dali Kingdom (937-1253). In the Ming (1368-1644) a legend appears in which Baijie is the mother of Duan Siping, founder of the Dali Kingdom. Baijie's widow martyr identity finally emerges in the Ming and Qing (1644-1911). Today, Baijie is worshipped in her widow martyr form as a tutelary village deity throughout Dali Prefecture. This dissertation examines Baijie's transformations in relation to the themes of ethnicity and gender in the religious history of Dali. I argue that the changes in Baijie's identity reflect changes in the representation of ethnicity in Dali religion from the twelfth century to the present. Baijie's gendered symbolism, particularly in her later widow martyr form, additionally illuminates the intersections of ethnicity and gender in Dali religion. The Dali region, and Yunnan as a whole, has long fallen just inside or outside the sphere of Chinese state control. Despite Dali's proximity to India, Tibet, and Southeast Asia, historical records strongly suggest that Dali elites looked to China for their systems of writing, government, and to some extent, religion. Baijie's transformations show how religious symbols reflected and shaped Dali elites' self-representation in relation to Chinese culture and the Chinese state. The first two chapters provide background by examining issues of religion and ethnicity in the independent Nanzhao (649-903) and Dali kingdoms. Chapters three through five cover Baijie's first three identities of Buddhist goddess, king's mother, and widow martyr from the Dali kingdom through the Qing dynasty. Chapter six looks at contemporary Baijie worship and is based primarily on field research conducted in Dali in 2007-08.
Transport measurements on graphene p-n junctions [electronic resource]
Keywords: Physics

Klein tunneling is a relativistic quantum effect standing at the base of the Quantum Electrodynamics (QED) theory. It describes a relativistic process where a particle obeying the Dirac equation - called a Dirac Fermion - propagates through a strong repulsive potential step without the exponential attenuation typical to quantum tunneling. Counter-intuitively, the stronger the potential step, the more transparent it becomes for the particle. Although the QED theory had proven to be a successful theory describing reality accurately, Klein tunneling has not yet been observed experimentally. The extreme conditions required to observe such an effect may occur in collisions of super-heavy nuclei or pair production at the horizon of a black hole, difficult or impossible to realize in a laboratory. However, a recently discovered material called graphene, which is a one atom-thick lattice of carbons, can be used as a testbed for such an effect. Since graphene carriers have been proven to be Dirac-like Fermions, the analog of Klein tunneling can be investigated in a commonly used condensed matter setup via electrical transport measurements. In this work we present experimental evidence for graphene carriers obeying Klein tunneling transport using a set of metallic gates on graphene to create p-n junctions. These p-n junctions incorporate a potential step for graphene Dirac-like Fermions allowing us to investigate Klein tunneling in graphene. Finally, we also discuss the existence of p-n junction-like structures between metal contacts and graphene, a topic that has an impact on graphene's electronic device applications.
Transposable regularized covariance models with applications to high-dimensional data [electronic resource]
Keywords: Statistics

High-dimensional data is becoming more prevalent with new technologies in biomedical sciences, imaging and the Internet. Many examples of this data often contain complex relationships between and among sets of variables. When arranged in the form of a matrix, this data is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, and introduce transposable regularized covariance models by placing penalties on inverse covariance matrices. We give theoretical results exploiting the structure of our transposable models that give computationally feasible algorithms for parameter estimation and calculation of conditional expectations. These contributions make the matrix-variate normal accessible for application to high-dimensional data. We apply our model to two applications: missing data imputation and large-scale inference with the matrix-variate normal distribution. Examples, simulations and results are given using the Netflix movie-rating data and microarrays, demonstrating the flexibility and functionality of our transposable models.
Tuning the shape of semiconductor nanowires for advanced photovoltaics [electronic resource]
Keywords: Electrical Engineering

Tuning the shape of nanostructures can have a strong effect on photon management and charge carrier collection for photovoltaics. Here two examples of nanowire shape designing are demonstrated: nanocones and branched nanowires. Photon management, involving both absorption enhancement and reflection reduction, is critical to all photovoltaic devices. It can improve the efficiency by minimizing optical and electrical losses, and cut cost by reducing material usage, process time and capital investment. Here I demonstrate a novel solar cell structure with an efficient photon management design. The centerpiece of the design is a novel nanocone structure, which is fabricated by a scalable low temperature process. With this design, devices with very thin active layer can achieve near perfect absorption because of both efficient antireflection and absorption enhancement over a broad spectral range and a wide range of angles of incidence. More strikingly, the design and process is not in principle limited to any specific material system, hence it opens up exciting opportunities for all classes of photovoltaic devices. I have used amorphous silicon and dye sensitized solar cells as two examples to demonstrate the concept. The device efficiencies of this design are significantly better compared to conventional devices. Moreover, I also have explored absorption enhancement on a sub-wavelength scale, compared to "classical" light trapping limits. PbSe nanocrystals have shown a greatly enhanced multi exciton generation (MEG) effect, one important step toward third generation solar cells. However, it is difficult to extract generated carriers from nanocrystals without good transport pathways. Three dimensional branched nanowire or nanotube networks, with strong quantum confinement within two dimensions, and the connected third dimension as an efficient charge carrier pathway, could be ideal for enhancing the MEG effect, light absorption, and carrier collection. I successfully demonstrate a large area growth of PbSe hyperbranced and chiral branched nanowires on a variety of substrates. More excitingly, Chiral branched nanowires reveal a new nanowire growth mechanism, dislocation driven growth, which can be applied to a variety of materials.
Tunnel barrier engineering for flash memory technology [electronic resource]
Keywords: Materials Science and Engineering

The conventional Flash memory faces two critical obstacles in the future: density and voltage scaling. Density is associated with scaling the gate length. The gate length cannot be reduced beyond a point because it requires a commensurate gate stack, specifically, tunnel oxide scaling for maintaining good gate control and short channel effects. However, the gate-tunnel oxide (TO) reduction has a practical lower bound of ~ 7-9nm (depending upon NAND or NOR flash architecture) due to leakage and data retention constraints. Below this TO thickness, irrespective of how inter-poly dielectric (referred as ONO) is scaled, the electric field across it during charge retention increases, leading to unacceptable levels of tunneling current. The second major challenge with scaling is to reduce the programming and erase operation voltages. The usual operation voltages for these processes are much greater (15-18 Volts). With scaling, it is imperative for operating voltages to reduce. Typically, read voltages are low, while erase and program operations stress the charge pump requirements and dictate the maximum voltages. The major impediment in erase voltage scaling is, once again, the inability to scale the gate oxide. Recently, engineered tunnel barriers were proposed as solutions to scaling gate oxide. It is postulated that engineered barriers offer faster program/erase yet maintain excellent retention. However, a detailed characterization of engineered tunnel dielectrics and a deeper understanding of the erase/program mechanism are sought to establish its implementation. In the first half of the thesis, we perform simulations to establish the feasibility of tunnel barriers under Flash memory device constraints. We look at different higher-k materials as a replacement for SiO2 and perform global optimization over different materials. This is first done under absence of traps in these materials. Later the assumptions are relaxed and traps are incorporated in these materials. In the second part, we implement engineered tunnel barriers based on the simulation results. However, it is observed that presence of traps in these materials degrades performance. Retention loss and endurance degradation are identified as two major problems, hindering implementation and scaling. In the third and final part, we discuss solutions to these problems. Fluorine is well known as a passivating agent for traps in high-k dielectrics. We incorporate fluorine in engineered tunnel stacks and show electrical & physical characterization results to emphasize its advantages. Finally, alternative tunnel barrier structures and materials are discussed to continue scaling of gate dielectrics.
Ultrafast 2D-IR spectroscopy of chemical and conformational dynamics in ionic solutions [electronic resource]
Keywords: Physics

The solute-solvent interactions dictate many physical and chemical properties of ionic solutions, as well as the equilibrium structure of ionic assemblies in solution, ranging from free ions, ion pairs, ion-pair dimers, ion-pair tetramers to nanoparticles and ionic crystals. These interactions include hydrogen bonding, charge-charge, charge-dipole, dipole-dipole interactions, etc. Because of the very fast timescales involved, we need novel time-resolved spectroscopic techniques to investigate the microscopic dynamics in the solution. Ultrafast two-dimensional infrared (2DIR) spectroscopy is a unique tool to study equilibrium chemical dynamics on the picosecond timescale. In this thesis, I present my graduate studies of chemical and conformational dynamic in ionic solutions using 2DIR, focusing on two main systems: aqueous ionic solutions and organic ionic solutions. In aqueous solutions, we have applied polarization-selective 2DIR to investigate the H-bond exchange mechanism in aqueous NaClO4 solution, using hydroxyl stretches of water as vibrational markers. The results show that a water molecule shifts its H-bond partners between water and perchlorate by means of large, prompt angular rotation. Using a jump-exchange kinetic model, we extract an H-bond exchange dynamics of ~6 ps and an average jump angle of 50 degree, in agreement with the jump angle observed in molecular dynamics simulations. We also investigate ligand exchange dynamics between different anions in the first solvation shell of magnesium cation in aqueous solution at an exchange time of 50 ps, with CN stretch of thiocyanate as a marker. In nonaqueous ionic solutions, we study the dynamics of ionic assemblies, including the ion pairing and dimerization processes in different organic solvents. The dimerization of LiNCS ion-pair to form (LiNCS)2 dimer is measured to happen on 20-50 ps, while ion pairing dynamics is as slow as hundreds of picoseconds. The ion pairing study complicates from multiple exchange process involved, such as self-ligand exchange which is also investigated by concentration dependent measurements.
Ultrafast optical control of semiconductor donor electron spins [electronic resource]
Keywords: Applied Physics

Robust qubits and reliable techniques to control those qubits are essential for quantum computing applications. In this work, I investigate the use of fast optical pulses to prevent decoherence and manipulate semiconductor electron spins in two material systems. I also demonstrate a novel technique for decoherence measurements that may improve imaging capabilities and yield new information of solid-state materials. In the first system investigated, electrons bound to silicon donors in GaAs, I show partial coherent control of the electron spins using an ultrafast (picosecond) pulse. I find it possible to rotate the spins an angle > pi/3 at a fidelity of 0.9 with the limited rotation angle likely due to the presence of unwanted excitations. I use a sequence of these pulses to perform a small-angle, optical, spin-echo experiment and measure a decoherence time of 7 microseconds, presumably caused by magnetic noise from nuclear spin diffusion. This technique is significant because of its improved time resolution, spatial resolution, and power requirements over existing methods. The second material studied, electrons bound to fluorine donors in ZnSe, has the potential to be an excellent qubit. Its larger binding energy, potential for isotopic purification of the host-lattice nuclear spins, and presence of fluorine nuclear spin 1/2 coupled to the electron spin will likely lead to higher fidelity manipulations and longer spin-memory times than seen for electrons bound to Si:GaAs. In this work, I show preliminary optical measurements that identify emission from single donors and verify the presence of a three-level Lambda-system, laying the foundation for fast optical control and decoherence studies. The work in this thesis helps establish the qubit potential of both materials, and the techniques developed to control and measure these spins are applicable to almost any optically active, solid-state, electron-spin system.
Unconventional magnetic order and excitations in the pseudogap phase of mercury barium copper oxide [electronic resource]
Keywords: Physics

A major open issue about the cuprate high-temperature superconductors is the nature of the pseudogap phenomenon. In this Thesis, I report results of neutron scattering studies on the model hole-doped compound HgBa2CuO4+d (Hg1201). I first report polarized neutron diffraction results, which show evidence in Hg1201 for a novel "hidden" magnetic order in the pseudogap phase that preserves the translational invariance of the crystal lattice, and a lack of evidence for any additional order that would break this invariance. The observations are consistent with either unconventional spin order or magnetic order due to orbital charge currents. I then present a systematic study of the high-energy magnetic excitations in Hg1201 using inelastic neutron scattering. The investigation started with measurements of the magnetic "resonance" mode, and then unexpectedly led to the discovery of novel magnetic excitations that have not been previously identified in the cuprates. These excitations seem to be associated with the hidden magnetic order in the pseudogap phase, and they have highly unusual characteristics that go outside of the conventional wisdom for the cuprates. Finally, I present results for Hg1201 from two other experimental techniques: magnetometry for uniform susceptibility and X-ray photoelectron spectroscopy. The main conclusion of this Thesis is that there exist significant magnetic correlations that are fundamentally different from the well-studied antiferromagnetic correlations. The novel magnetism seems to involve hole carriers that reside not only in the copper-oxygen layers, but also in other orbitals that likely involve the apical oxygens.
Underpinnings of institutions [electronic resource]
Keywords: Business.

This dissertation investigates the role of historical events on institutions. In particular, it provides empirical evidence that the timing of agricultural adoption during the Neolithic Revolution, when humans adopted agriculture for the first time, has a strong inverse relationship with the level of constraints that political executives face in modern periods, such as the extent to which they can raise local tax levels. It also provides evidence that certain cultural traits known to foster economic and institutional development, including the level of participation in local community, beliefs in tolerance, obedience, control in life, trust and parental responsibility, have strong ties back to the Neolithic Revolution. The findings come from analyzing novel vegetation data and carbon dates showing the initial agricultural adoption from various Neolithic archaeological sites, as well as data on the level of executive power and local tax levels in Europe and East Asia. The analysis also uses the World Value Survey in order to compare current cultural differences across geographic regions. The results suggest that the regions adopting agriculture early also developed autocratic, extractive institutions in modern periods, while those adopting agriculture late witnessed democratic, egalitarian institutions. They also show that the respondents in regions which adopted agriculture late are more willing to participate and volunteer in social organizations, take active roles in local communities, and value tolerance, control in life and trust over obedience and parental responsibility. The dissertation interprets the diffusion of Neolithic farmers as one potential explanation for how the Revolution influenced modern institutions. As farmers spread out to new lands during the Neolithic Revolution, they developed strong hunter-gatherer traits, and established institutions as outcomes of past institutions, new environment and smaller population. The institutions in the origin of agriculture therefore differed substantially from the ones in the later settlements. While in the origin, large communities formed centralized political systems with hierarchical orders, later migrants established egalitarian political systems that were more suitable for smaller population and new environment. Once these institutions were established, their differences remained persistent in the long run. The dissertation concludes with a current example of the dynamics between cultural divergence and institutions in China between 1990 and 2000, in which the empirical analysis looks modern ethnic cleavages as manifestations of cultural divergence, and the level of public goods provision as a defining characteristic of institutional performance.