VictorJuiz/thesis huggingface dataset:
Centriole assembly regulation by Plk4 [electronic resource]
Keywords: Biology

Regulation of centriole number is important to ensure proper cell division and formation of the correct number of cilia, a signaling organelle. Activity of the polo-like kinase Plk4 regulates the number of centrioles formed each cell cycle. To study Plk4 function and the mechanism of centriole assembly we developed a system in Xenopus laevis egg extract, where we show Plx4 (Xenopus Plk4) overexpression drives de novo centriole assembly. Centriole assembly regulation in this system mimicked regulation of centriole duplication in somatic cells, suggesting that mechanisms identified in the egg extract would apply to centriole formation in general. By analyzing the functionality of Plx4 mutants we determined that Plx4 activity is not regulated by proteolysis in vitro in the extract, and likely not in vivo during early embryogenesis. To identify potential Plk4 regulators and effectors we took two approaches in egg extract: 1) chemical genetics to specifically modify Plk4 substrates in egg extract, and 2) pull-down and mass spectrometry identification of co-purifying proteins. Using the second approach we identified an interaction between Plx4 and the centrosomal protein Cep152. We found that Cep152 directly interacts with human Plk4, and that Cep152 is required for centriole duplication and Plk4-based centriole amplification. Cep152 is required to recruit the early centriole assembly protein Sas-6, but not Plk4, to the centriole. Finally, Cep152 was phosphorylated by Plk4 in vitro, suggesting that Cep152 acts with Plk4 to initiate centriole formation.
Challenges to drawing generalized causal inferences in educational research [electronic resource] : methodological and philosophical considerations
Keywords: Education.

This work is concerned with external validity in educational research. The first part is an empirical work that examines the levels of two kinds of bias that can figure into the estimate of a program effect, where the intervention is being administered at multiple sites. The first (Bias 1) is due to differences in average performance between sites in the absence of treatment, the second (Bias 2) is due to variation in the treatment effect across sites. Data from the Tennessee STAR multisite trial of the effects of reduced class size is used to investigate both forms of bias. Findings include that both kinds of bias are significantly different from zero, Bias 1 is larger than Bias 2, regression adjustments are more effective at reducing Bias 1 than Bias 2, and in the case of reading but not math outcomes, certain covariates account for both forms of bias. The main conclusion is that both types of bias are large and difficult to reduce to a level where a local school official can feel confident that the impact estimates based on information from other location apply locally. The second work is a critique of the heterogeneity of replication approach to establishing generalized causal inferences. The argument is made that generalized causal inferences stemming from meta-analyses of randomized trials of nominally the same intervention are deficient for several reasons, the main one being that they ignore context. The empirical nature of causal generalizations in the social sciences makes them tentative and more akin to working hypotheses than immutable laws. Alternatives are considered, and the argument is made for an approach that admits a broader range of evidence for seeking appropriate and adequate warrants for drawing generalized causal inferences.
Characterization and modeling of thermal diffusion and aggregation in nanofluids [electronic resource]
Keywords: Mechanical Engineering

Fluids with higher thermal conductivities are sought for fluidic cooling systems in applications including microprocessors and high-power lasers. By adding high thermal conductivity nanoscale metal and metal oxide particles to a fluid the thermal conductivity of the fluid is enhanced. While particle aggregates play a central role in recent models for the thermal conductivity of nanofluids, the effect of particle diffusion in a temperature field on the aggregation and transport has yet to be studied in depth. The present work separates the effects of particle aggregation and diffusion using parallel plate experiments, infrared microscopy, light scattering, Monte Carlo simulations, and rate equations for particle and heat transport in a well dispersed nanofluid. Experimental data show non-uniform temporal increases in thermal conductivity above effective medium theory and can be well described through simulation of the combination of particle aggregation and diffusion. The simulation shows large concentration distributions due to thermal diffusion causing variations in aggregation, thermal conductivity and viscosity. Static light scattering shows aggregates form more quickly at higher concentrations and temperatures. An optimum nanoparticle diameter for these particular fluid properties is calculated to be 130 nm to optimize the fluid stability by reducing settling, thermal diffusion and aggregation.
Characterization of Listeria monocytogenes growth and colonization of the murine gallbladder [electronic resource]
Keywords: Microbiology and Immunology

Listeria monocytogenes is a facultative intracellular pathogen that causes severe invasive disease in susceptible populations. Using in vivo bioluminescent imaging, it was recently discovered that this bacterium can colonize the murine gallbladder of otherwise asymptomatic mice. This finding was surprising as L. monocytogenes, after invasion of the intestines, was thought to survive only intracellularly in an infected host and in the gallbladder the bacteria lived extracellularly. It was also surprising that a bacterium could grow and replicate in the pure bile environment of the gallbladder lumen as bile is a potent antimicrobial compound. In this study, we characterized how Listeria monocytogenes is able to reach the gallbladder during infection and examined how this pathogen is able to survive in this environment. Using a mouse adapted L. monocytogenes which expresses a modified InlA capable of binding murine E-cadherin we were able to follow the kinetics of gallbladder colonization after oral infection using in vivo bioluminescent imaging. We then utilized surgical manipulation of the mouse host and repeated the oral infection to determine how L. monocytogenes reaches the gallbladder. Once we had determined the mechanism of gallbladder entry, we then utilized whole genome microarrays to characterize the transcriptome of L. monocytogenes during in vivo growth in the gallbladder and in freshly isolated murine bile. Finally, we attempted to determine what nutrients are utilized by L. monocytogenes during growth in bile and looked at the ability of other bacterial species to grow in this environment. Through these experiments we demonstrated regular asymptomatic gallbladder colonization by L. monocytogenes after oral infection and that L. monocytogenes reaches the gallbladder via the hepatic duct only after first causing systemic infection and escaping the liver. We also demonstrated that the lifestyle in the gallbladder is similar to that in the intestine with the exception of the need for bile resistance genes, and finally that it appears as though simple carbon sources may be utilized during bile growth and that bile may not be as toxic to bacteria as has been thought. Our work suggests that gallbladder colonization may not be exclusive to only L. monocyctogenes and Salmonella Typhi since other bacteria can grow, and in some cases better than L. monocyctogenes, in pure bile.
Characterization of the Chibby family of centrosomal proteins [electronic resource]
Keywords: Biological Sciences

The Chibby protein antagonizes Wnt/Beta-Catenin signaling, a prominent regulator pathway of development, via direct interaction with the transcriptional activator domain of Beta-Catenin. Chibby mutant mice have a defect in the formation of motile cilia in the airway epithelium. The centrosome is the major microtubule organizing center of animal cells and includes two centrioles, termed mother and the daughter based on their age and replicative history. The mother harbors subdistal and distal appendages, which, respectively, anchor the interphase microtubule array and are required for ciliation. Several lines of published evidence suggest a link between the primary cilium, a single, non-motile structure found on many cells, and Wnt/Beta-Catenin signaling. Based on this evidence I investigated Chibby, and related members of the Chibby protein family, to determine its role in centrosome and cilium structure and function. I report here that the Chibby family of proteins is associated physically and functionally with the centrioles of the centrosome in mammalian cells. The Chibby family consists of Chibby (Cby1), Nurit/Cby2, and the previously uncharacterized, Chibby3 (Cby3). Fluorescence microscopy revealed that Cby1 localized to the mother centriole of the centrosome, and that this localization was partially shared with Nurit/Cby2 and Cby3. Cby1 colocalizes at the mother centriole with phospho-Beta-Catenin, a modified form of Beta-Catenin that, in some contexts it is targeted for proteasome-mediated degradation. I also found that Cby1 partially colocalized with phospho-Beta-Catenin at a ring-like structure at the midbody during cytokinesis, where they might regulate abscission. The localization of Cby1 to the mother centriole was similar to that described for proteins for the distal appendages of the mother centriole. I found that Cby1 colocalized with, and exhibited cell cycle dynamics similar to, Cep164, a known distal appendage protein that is required for primary cilium formation. Consistent with a role for Cby1 in these centriolar structures, Cby1-/- mouse embryonic fibroblasts exhibited a strong reduction in primary cilium formation that could be complemented by expression of the wild-type Cby1 protein. Remarkably, overexpression of either GFP-tagged Beta-Catenin or GFP-Cby1 in hTERT-RPE1 cells resulted in fewer, but longer, cilia than controls suggesting that both of these proteins are important for structure and function of the primary cilium. In summary, I propose that Cby1 is associated with the distal appendages of the mother centriole, that defects in those structures are the likely cause of the failure of cilium formation in cells lacking Cby1, and that both primary and motile cilia display this requirement for Cby1.
Characterizing the mechanism of continued primer synthesis at stalled replication forks and its contribution to checkpoint activation [electronic resource]
Keywords: Chemical and Systems Biology.

Stalled replication forks activate and are stabilized by the ATR-mediated checkpoint, but ultimately they must also recover from the arrest. While primed ssDNA is sufficient for checkpoint activation, it is still unknown how this signal is generated at a stalled replication fork. Furthermore, it is not clear how recovery and fork restart occur in higher eukaryotes. Using Xenopus egg extracts, we show that DNA replication continues at a stalled fork through the synthesis and elongation of new primers independent of the checkpoint. This synthesis is dependent on the activity of PCNA, Pol[lowercase Delta] and Pol[Epsilon], and it contributes to the phosphorylation of Chk1. We also used defined DNA structures to show that for a fixed amount of ssDNA, increasing the number of primer-template junctions strongly enhances Chk1 phosphorylation. These results suggest that new primers are synthesized at stalled replication forks by the leading and lagging strand polymerases and that accumulation of these primers may contribute to checkpoint activation.
Charge in composite micromechanical resonators [electronic resource]
Keywords: Electrical Engineering

Silicon micromechanical resonators have recently come into view as competitors to quartz technology for frequency reference applications. Several researchers have investigated techniques for improving the frequency stability of silicon resonators against temperature. In particular, a promising temperature compensation technique exploiting the positive temperature coefficient of elastic modulus of silicon dioxide (a dielectric material) has been demonstrated both for MEMS, as well as for surface acoustic wave devices. The coating of silicon resonators with silicon dioxide enables a significant reduction of the temperature sensitivity. Broadly, dielectrics such as silicon dioxide play an important role in many classes of MEMS. They are frequently used for electrical isolation, as structural elements, for enhancing the transduction within electrostatic actuators and more generally, as sacrificial layers. However, it is also well known that dielectrics are susceptible to various charging phenomena. Charge build-up and charge motion can screen electrode potentials, affecting the overall electromechanical properties of the device. Such adverse effects due to charging are also seen in oxide-coated silicon resonators. Since charging is not always avoidable, techniques that can circumvent the undesirable effects of charge can be of value. In this work, we investigate the effects of dielectric charge on resonant frequency in thermally oxidized silicon resonators in a hermetic wafer-level package, with a double-ended tuning fork (DETF) design. We present theoretical models for the electromechanical effects of charge trapped in the dielectrics within a resonator. In addition, observations of time-varying resonator frequency indicate the presence of mobile oxide charge in a series of voltage biasing and temperature experiments. This work also introduces the use of ac polarization for resonant electrostatic MEMS as a drift-circumvention technique, that eliminates the frequency drift caused by dielectric charging and charge screening. It is mathematically and experimentally shown that an ac-polarized resonator can sustain stable oscillations when used in a positive feedback oscillator circuit. We also demonstrate an oscillator topology that generates a low-drift reference frequency signal (0.15 ppm/week of drift over 21 days) with this technique in spite of using a resonator that exhibits very large frequency drifts under dc polarization (about -90 ppm in 42.5 hours). Long-term data is presented for these drift-susceptible devices, showing more than 2 orders-of-magnitude improvement in frequency stability. In addition to reducing the drift due to charge motion in oxidized resonators, ac polarization provides a path to the independent control of resonance frequency and response amplitude in two-port electrostatic resonators without the need for additional electrodes. We also note a reduced frequency sensitivity to dc offset voltages, and discuss oscillator noise characteristics that differ from the dc polarization case.
Chemerin and IL-17 in inflammation, obesity, and metabolism [electronic resource]
Keywords: Immunology.

Inflammation is characterized by the influx and activation of leukocytes to sites of tissue damage. Upon recruitment, immune cells become activated and can secrete pro-inflammatory cytokines and chemoattractants that can modulate cellular responses and leukocyte trafficking. However, if inflammation occurs inappropriately, it can lead to unwanted tissue damage to the host or can affect metabolic processes (e.g. glucose metabolism or bone metabolism). Evidence indicates inflammation also occurs in adipose tissue during obesity and that adipose tissue leukocytes secrete cytokines that can contribute to systemic, chronic inflammation. The mechanisms that regulate inflammation and mediate its effects on metabolism are not fully understood. To help clarify what factors mediate inflammation, we sought to determine the role that the chemerin receptor, CMKLR1, may play in mediating immune cell trafficking to inflamed tissue. We found CMKLR1 is expressed by murine peritoneal macrophages, which can migrate to chemerin in vitro. CMKLR1 was upregulated by TGF[Beta] and downregulated by pro-inflammatory cytokines and TLR ligands. Furthermore, we found that CMKLR1 exacerbated the progression of experimental murine autoimmune encephalomyelitis (EAE). Chemerin was expressed in inflamed central nervous system (CNS) tissue, and microglial cells and CNS-associated myeloid dendritic cells expressed CMKLR1 in mice with EAE. Additionally, we discovered CCRL2 as a novel receptor for chemerin and determined it is a non-signaling decoy receptor which may bind and present chemerin to CMKLR1. We found that CCRL2 is expressed by mouse mast cells and can enhance tissue swelling and tissue leukocyte infiltration during mast cell-dependent passive cutaneous anaphylaxis. In an attempt to uncover a role for chemerin/CMKLR1 in obesity development or obesity-related inflammation, we discovered an unexpected role for the pro-inflammatory cytokine, IL-17, in adipocyte metabolism. IL-17 was upregulated in obese adipose tissue by T cells. IL-17 KO mice were more susceptible to diet-induced obesity. IL-17 inhibited adipocyte development and insulin stimulated glucose uptake by adipocytes. Furthermore, young IL-17 deficient mice were more insulin sensitive than their WT counterparts. Overall, our data indicate a role for chemerin and chemerin receptors in leukocyte migration and function in inflammatory diseases, and suggest that IL-17 regulates metabolic responses associated with obesity.
Chemical reaction modeling in a subsurface flow simulator with application to in-situ upgrading and CO2 mineralization [electronic resource]
Keywords: Energy Resources Engineering

Chemical reactions occur in a number of subsurface flow processes. Numerical modeling is an essential tool for understanding and optimizing complex reactive flows in a variety of application areas. In this work, we propose and implement chemical reaction modeling capabilities in Stanford's General Purpose Research Simulator (GPRS). The formulations developed include a procedure based on species conservation equations and an approach based on element conservation equations. The species-based formulation is suitable for solving reactive flow problems characterized by kinetic reactions only. In the element-based formulation, by contrast, both equilibrium and kinetic reactions can be treated consistently in the fully coupled system. This procedure represents a new treatment for reactive flow modeling. Additionally, in both formulations, a new generic representation of reaction terms is developed, which allows simultaneous modeling of homogeneous and heterogeneous reactions within or among phases (i.e., gas, liquid, water and solid phases). We apply the species-based formulation to model the in-situ upgrading of oil shale. Oil shale is a highly abundant but difficult to produce energy resource. The in-situ upgrading process entails heating the oil shale to about 700 F, at which point the kerogens decompose to gas and liquid hydrocarbons through a series of chemical reactions. After adjusting a few uncertain parameters (within physical ranges), our simulation results show relatively close agreement with available field data. The other application considered in this work is the modeling of carbon storage in deep saline aquifers. Detailed results are presented for a fine-grid model of a benchmark study. For this case, chemical reactions are not considered. Carbon mineralization reactions are then modeled using the element-based reactive flow formulation. Coarse-grid models are used for these simulations. Because the chemistry data relevant to carbon mineralization are, to date, not fully defined, we provide simulation results using available chemistry parameters. We discuss the remaining challenges that must be overcome before mineralization reactions can be simulated on fine-grid models. We note finally that the chemical reaction modeling capabilities in GPRS can be extended to other subsurface reactive flow processes (e.g., enhanced coalbed methane recovery).
Choreography in conversation [electronic resource] : the imperial ballet and Russian literature, 1851-1905
Keywords: Slavic Languages and Literatures

In "Choreography in Conversation: The Imperial Ballet and Russian Literature, 1851-1905, " I argue that the simultaneous incorporation of cosmopolitan influences and promotion of national themes in Russian literature and ballet in the second half of the nineteenth century participated in the construction of identity through performance. The emergence of a professional cadre of writers alongside an imperial system of ballet patronage led to a perceived division between the "progressive" realm of realist prose and the "retrograde" world of ballet. Yet I show how, contrary to contemporary criticism and subsequent scholarly interpretations, these two cultural spheres developed along similar artistic lines and in lively conversation, with attention to folkloric sources and concerns about authenticity and in anticipation of modernist experiments with form. Drawing on the historical production of Jules Perrot's 1851 ballet "The Naiad and the Fisherman, " I first consider the fetishization of ballet in the case of Lev Tolstoy and his lifelong polemic with dance: in his early story "The Tale of How Another Girl Named Varenka Quickly Grew Up, " his novels "War and Peace" and "Anna Karenina, " and his aesthetic manifesto "What is Art?." I then examine Arthur Saint-Léon's adaptation of fairytales by Peter Ershov and Alexander Pushkin into "national ballets, " which were popularly lauded as "authentically" Russian yet parodied by the prominent radical writer Mikhail Saltykov-Shchedrin as ballet travesties. I next propose that Nikolai Nekrasov's long poem "Ballet" mirrors Marius Petipa's "Florida" in a poetic pastiche of peasants, pirates, and patrons. Finally, I posit a shared provenance in the fin-de-siècle fugues of Peter Tchaikovsky, Lev Ivanov, and Petipa's "Swan Lake" and Anton Chekhov's "The Seagull." In my dissertation, I offer a new understanding of the relationship between text and spectacle, in which ballet evolved from a space for discourse on Russian identity to an integral part of the Russian national narrative and one of its most celebrated cultural commodities.
Chromatin remodeling and dendrite wiring specificity in the Drosophila olfactory system [electronic resource]
Keywords: Neurosciences.

The human brain is an extraordinarily complex organ containing billions of neurons forming trillions of connections. The functionality of the brain lies in this intricate circuit wiring. How do the neurons form proper connections during development? The Drosophila olfactory system exhibits very precise and stereotyped neuronal connectivity that is specified predominantly by genetic programming. The dendrites of second-order olfactory projection neurons (PNs) pattern the developing antennal lobe prior to first-order olfactory receptor neuron (ORN) axon arrival, indicating an intrinsic wiring mechanism for PN dendrites. The antennal lobe is formed of ~50 glomeruli, each of which represents a very specific gathering of axons and dendrites; ORNs expressing the same odorant receptor and PNs of the same class converge onto single glomeruli. In this thesis, I present work furthering our understanding of intrinsic PN wiring specificity. First, I examine the role of histone deacetylase Rpd3 in PNs and show that it acts largely through the transcription factor Prospero. Second, I show the actin-related protein Bap55 acts as part of the TIP60 ATP-dependent chromatin remodeling complex in PNs. My thesis shows that chromatin remodeling factors, previously believed to be involved in general housekeeping, actually play important postmitotic roles and contribute to PN dendrite wiring specificity.