VictorJuiz/thesis huggingface dataset:
Transcriptional Network Analysis During Early Differentiation Reveals a Role for Polycomb-like 2 in Mouse Embryonic Stem Cell Commitment
Keywords: embryonic stem cell
gene regulatory network
polycomb

We used mouse embryonic stem cells (ESCs) as a model to study the mechanisms that regulate stem cell fate. Using gene expression analysis during a time course of differentiation, we identified 281 candidate regulators of ESC fate. To integrate these candidate regulators into the known ESC transcriptional network, we incorporated promoter occupancy data for OCT4, NANOG and SOX2. We used shRNA knockdown studies followed by a high-content fluorescence imaging assay to test the requirement of our predicted regulators in maintaining self-renewal. We further integrated promoter occupancy data for Polycomb group (PcG) proteins, EED and PHC1 to identify 43 transcriptional networks in which we predict that OCT4 and NANOG co-operate with EED and PHC1 to influence the expression of multiple developmental regulators. Next, we turned our focus to the PcG protein PCL2 which we identified as being bound by both OCT4 and NANOG and down-regulated during differentiation. PcG proteins are conserved epigenetic transcriptional repressors that control numerous developmental gene expression programs. Using multiple biochemical strategies, we demonstrated that PCL2 associates with Polycomb Repressive Complex 2 (PRC2) in mouse ESCs, a complex that exerts its effect on gene expression through H3K27me3. Although PCL2 was not required for global histone methylation, it was required at specific target regions to maintain proper levels of H3K27me3. Knockdown of Pcl2 in ESCs resulted in heightened self-renewal characteristics and defects in differentiation. Integration of global gene expression and promoter occupancy analyses allowed us to identify PCL2 and PRC2 transcriptional targets and draft regulatory networks. We describe the role of PCL2 in both modulating transcription of ESC self-renewal genes in undifferentiated ESCs as well as developmental regulators during early commitment and differentiation.
Loewner Theory in Several Complex Variables and Related Problems
Keywords: Loewner chains
several complex variables
extreme points
Caratheodory mappings
spirallike mappings
Loewner chain equation
resonances
parametric representation

The first part of the thesis deals with aspects of Loewner theory in several complex variables. First we show that a Loewner chain with minimal regularity assumptions (Df(0,t) of local bounded variation) satisfies an associated Loewner equation. Next we give a way of renormalizing a general Loewner chain so that it corresponds to the same increasing family of domains. To do this we will prove a generalization of the converse of Carathéodory's kernel convergence theorem. Next we address the problem of finding a Loewner chain solution to a given Loewner chain equation. The main result is a complete solution in the case when the infinitesimal generator satisfies Dh(0,t)=A where inf {Re<Az,z>: ||z| =1}> 0. We will see that the existence of a bounded solution depends on the real resonances of A, but there always exists a polynomially bounded solution. Finally we discuss some properties of classes of biholomorphic mappings associated to A-normalized Loewner chains. In particular we give a characterization of the compactness of the class of spirallike mappings in terms of the resonance of A. The second part of the thesis deals with the problem of finding examples of extreme points for some classes of mappings. We see that straightforward generalizations of one dimensional extreme functions give examples of extreme Carathéodory mappings and extreme starlike mappings on the polydisc, but not on the ball. We also find examples of extreme Carathéodory mappings on the ball starting from a known example of extreme Carathéodory function in higher dimensions.
Regulation of the Dopamine D1-D2 Receptor Heterooligomer
Keywords: Dopamine Receptor
Heterooligomer

Dopamine receptors are members of the G protein-coupled receptor superfamily and play important roles in neuronal transmission. A D1-D2 receptor heterooligomer generating a G-protein linked PLC-dependent intracellular calcium signal was previously identified. The discovery of this dopamine mediated calcium signal implicated a direct link between dopamine receptors and calcium generation, but its regulation remained to be elucidated. By measuring calcium signaling with Fluo-4 fluorescence or cameleon FRET, rapid desensitization of the calcium signal in heterologous cells and striatal neurons was demonstrated by pre-treatment with SKF 83959, which selectively activates D1-D2 receptor heteromers, or SKF 83822 which only activates D1 receptor homooligomers. Although SKF 83822 was unable to activate D1-D2 receptor heteromers, it still permitted desensitization of the calcium signal. This suggested that occupancy of the D1 receptor binding pocket by SKF 83822 resulted in conformational changes sufficient for desensitization without activation of the heteromer. BRET and co-immunoprecipitation studies indicated an agonist induced interaction between the D1-D2 receptor heteromer and GRK2. Increased expression of GRK2 led to a decrease in the calcium signal and decreased expression of GRK2 led to an increased calcium signal. Expression of the catalytically inactive and RGS mutated GRK2 constructs each led to a partial recovery of the GRK2-attenuated calcium signal. These results indicated that desensitization of the D1-D2 receptor heteromer mediated calcium signal can occur by agonist occupancy even without activation and is regulated by two distinct functions of GRK2. Immunocytochemistry and calcium assays demonstrated that recycling of internalized D1 and D2 receptors and resensitization of the desensitized calcium signal occurred after dopamine pre-treatment but not SKF 83959, suggesting that the trafficking and resensitization response associated with the D1-D2 receptor heteromer is differentially regulated by specific ligands. Overall, these results suggest that D1-D2 receptor heterooligomers are uniquely regulated from their constituent receptors which are not coupled to Gq.
Eighty-eight Drums: The Piano as Percussion Instrument in Jazz
Keywords: piano
drumming
jazz

Evidence of a link between piano and drumming performance practices in western music dates back to at least the mid-nineteenth century. The modern construction of the piano had yet to be fully standardized when percussive techniques were being applied to its keyboard. Since that time, pianists and drummers (especially those involved with the creation of groove-based music) have grown closer and closer, participating in what remains a richly symbiotic relationship. This study examines parallels between piano and drumming performance practices in jazz. In this context, drumming is acknowledged as an important inspiration guiding the expression of rhythm and percussive attack by non-drummers, pianists in particular. Historical connections between pianism and drumming in jazz are addressed through an examination of those legacies that are widely believed to derive from West African drumming, European march and dance traditions, and various aspects of the so-called "Latin tinge" from the Caribbean and South America. Playing techniques are compared in part based on the premise that similarities in musical output flow naturally from congruencies in instrumental architecture. Percussive action unites pianists and drummers, as do shared abilities to create rhythmic layers through the independent functioning of multiple limbs. A discussion of ensemble roles reveals conceptual links, especially with regard to time-keeping, "comping," and mutual approaches to the creation of groove and swing. Transcriptions are employed to illustrate instances of widely adopted drumming-like gestures from the history of jazz with special attention paid to rhythmic counterpoint, complementation, and rudimental sticking patterns used by jazz pianists since the 1960's. Though a statistically small sample, interviews with ten professional jazz pianists support the essential findings of the study. Questions are raised throughout regarding the effectiveness of traditional jazz pedagogy in emphasizing the importance of drumming to non-drummer instrumental praxis.
A Double-blinded Randomized Controlled Trial on the Effect of Distant Reiki on Pain after Non-emergency Caesarean Section and the Effect of CYP2D6 Variation on Codeine Analgesia
Keywords: CAM
Codeine
Reiki
CYP2D6

Codeine-containing medication is commonly used for pain after c-section. In most people, 10% of codeine is biotransformed into morphine by the Cytochrome P450 enzyme 2D6 (CYP2D6). Individuals who convert up to 50 fold more codeine into morphine, ultrarapid metaboizers, are at a greater risk for adverse effects. Conversely poor metabolizers, individuals who convert almost no codeine into morphine, are at risk for untreated pain. The pharmacodynamic relationship between codeine-analgesia and CYP2D6 genotype is studied for possible development of a titration model. To minimize these treatment risks, alternatives to opioids are sought. Reiki, an ancient Japanese form of healing used to treat pain and depression, has not been systematically reviewed for its efficacy in treating pain. My systematic review of Reiki literature (n=12) showed that while most trials yielded a positive result on primary outcomes, all existing Reiki studies lacked in one of the three key areas of proper patient allocation concealment, randomization or blinding which can lead to the introduction of bias. We designed a randomized controlled trial using distant Reiki for postpartum pain, taking careful steps to control for each of those three key areas. Eighty pregnant women scheduled for an elective c-section where recruited and randomly allocated to one of the two arms (n=40 Reiki and n=40 control). Women were monitored in hospital for up to three days. Visual Analogue Scores (VAS) for pain were recorded 4 times per day; and all pain medication, adverse effects and milestone recovery rates after c-section were recorded. Blood samples were taken to determine CYP2D6 genotype. We determined that distant Reiki did not reduce women’s pain; neither the measured pain nor the cumulative dose of pain medication differed between groups. Moreover, rates of recovery after c-section were also not different between the two groups. This led to the conclusion that distant Reiki was not suitable as a primary method of controlling pain after c-section. Our second study (n=45) looked for correlation between CYP2D6 genotype and effectiveness of codeine analgesia. Only a small sample of the women were genetic extremes (n=2 poor metabolizers and n=3 ultrarapid metabolizers), while most were, as expected, extensive or intermediate metabolizers. An individual examination of each of these cases provided valuable insight into patients where CYP2D6 polymorphism is clinically relevant. Two of the three ultrarapid metabolizers stopped opioid analgesia due to adverse effects, while both poor metabolizers complained that the codeine-containing medication was not providing analgesia (i.e. ineffective pain treatment). Healthcare providers need to be aware of patient response to pharmacotherapy and use this information to individualize postpartum opioid analgesia.
Toric Varieties Associated with Moduli Spaces
Keywords: Symplectic Geometry
Toric Geometry

Any genus g surface, Σg,n with n boundary components may be given a trinion decomposition: a realization of the surface as a union of 2g – 2 + n trinions glued together along 3g – 3 + n of their boundary circles. Together with the flows of Goldman, Jeffrey and Weitsman use the trinion boundary circles in a decomposition of Σg,n to obtain a Hamiltonian action of a compact torus (S1)3 g-3+n' on an open dense subset of the moduli space of certain gauge equivalence classes of flat SU(2)-connections on Σg,n. Jeffrey and Weitsman also provide a complete description of the moment polytopes for these torus actions, and we make use of this description to study the cohomology of associated toric varieties. While we are able to make use of the work of Danilov to obtain the integral (rational) cohomology ring in the smooth (orbifold) case, we show that the aforementioned toric varieties almost always possess singularities worse than those of an orbifold. In these cases we use an algorithm of Bressler and Lunts to recover the intersection cohomology Betti numbers using the combinatorial information provided by the corresponding moment polytopes. The main contribution of this thesis is a computation of the intersection cohomology Betti numbers for the toric varieties associated to trinion decomposed surfaces Σ2,0, Σ 2,1, Σ3,0, Σ3,1, Σ4,0, and Σ4,1.
Spray Combustion Characteristics and Emissions of a Wood derived Fast Pyrolysis Liquid-ethanol Blend in a Pilot Stabilized Swirl Burner
Keywords: spray combustion
fast pyrolysis liquid
pyrolysis oil
bio-oil
swirl burner
CO emissions
NOx emissions
particulate emissions

Biomass fast pyrolysis liquid (bio-oil) is a cellulose based alternative fuel with the potential to displace fossil fuels in stationary heat and power applications. To better understand the combustion behavior and emissions of bio-oil, a 10 kW spray burner was designed and constructed. The effect of swirl, atomization quality, ignition source (pilot) energy, air/fuel preheat and equivalence ratio on the stability and emissions of bio-oil spray flames was investigated. A blend of 80% pyrolysis liquid and 20% ethanol by volume was used during the tests and the results were compared to burner operation with diesel. It is important to have good atomization, thorough mixing and high swirl in order to stabilize ignition, promote the burnout of bio-oil and decrease CO, hydrocarbon and particulate matter emissions. The total amount of primary air and atomizing air that can be used to improve turbulence, mixing, droplet burnout and overall combustion quality is limited by the distillable fraction and narrow lean blow-out limit associated with pyrolysis liquid. Air and fuel preheat are important for reducing hydrocarbon and CO emissions, although subsequent fuel boiling should be avoided in order to maintain flame stability. The NOx produced in bio-oil flames is dominated by the conversion of fuel bound nitrogen. The particulate matter collected during bio-oil combustion is composed of both carbonaceous cenosphere residues and ash. Under good burning conditions, the majority consists of ash. Pilot flame energy and air/fuel preheat have a weak effect on the total particulate matter in the exhaust. Generally, these results suggest that available burner parameters can be adjusted in order to achieve low hydrocarbon, CO and carbonaceous particulate matter emissions when using pyrolysis liquid. Total particulates can be further mitigated by reducing the inherent ash content in bio-oil. Comparative burner tests with diesel reveal much lower emissions for this fuel at most of the operating points considered. This is due to the fully distillable nature, better atomization and improved spray ignition characteristics associated with diesel. Because of its superior volatility, diesel can also operate over a much wider range of primary air and atomizing air flow rates compared to bio-oil.
Structural Change and Income Differences
Keywords: Structural Change
International Trade
Food Problem
Convergence

Economic growth and development is intimately related to the decline of agriculture’s share of output and employment. This process of structural change has important implications for income and productivity differences between regions within a country or between countries themselves. Agriculture typically has low productivity relative to other sectors and this is particularly true in poor areas. So, as labour switches to nonagricultural activities or as agricultural productivity increases, poor agriculturallyintensive areas will benefit the most. In this thesis, I contribute to a recent and growing line of research and incorporate a separate role for agriculture, both into modeling frameworks and data analysis, to examine income and productivity differences. I first demonstrate that restrictions on trade in agricultural goods, which support inefficient domestic producers, inhibit structural change and lower productivity in poor countries. To do this, I incorporate multiple sectors, non-homothetic preferences, and labour mobility costs into an Eaton-Kortum trade model. With the model, I estimate productivity from trade data (avoiding problematic data for poor countries that typical estimates require) and perform a variety of counterfactual exercises. I find import barriers and labour mobility costs account for one-third of the aggregate labour productivity gap between rich and poor countries and for nearly half the gap in agriculture. Second, moving away from international income differences, I use a general equilibrium model of structural transformation to show a large labour migration cost between regions of the US magnifies the impact improved labour markets have on regional convergence. Finally, I estimate the influence of structural change on convergence between Canadian regions. I construct a unique dataset of census-division level wage and employment levels in both agriculture and nonagriculture between 1901 and 1981. I find convergence is primarily due to region-specific factors with structural change playing little role.
Understanding the Mechanisms of Motor Learning in the Vestibulo-ocular Reflex
Keywords: VOR
cerebellum
motor learning
vestibulo-ocular reflex

The vestibulo-ocular reflex (VOR) is a simple reflex that stabilizes gaze by moving the eyes in the opposite direction to the head. The gain of the VOR (ratio of head to eye velocity) can be increased or decreased during motor learning. It is thought that the memory for learned changes in the VOR gain is initially encoded within the cerebellar flocculus. Furthermore, these learned gain changes can be disrupted or consolidated into a long-term memory. In this thesis we describe novel results that show that consolidation of the VOR can take place rapidly, within 1 hour after learning has stopped. Furthermore, we demonstrated that unlike learning, which has been shown to have frequency selectivity, disruption and rapid consolidation generalize across the range of frequencies. We suggest that disruption and rapid consolidation in the VOR are local mechanisms within the cerebellar cortex, and do not require new learning. This thesis also provides additional evidence for the idea that learned gain increases and decreases are the result of separate mechanisms, most likely long-term depression and potentiation respectively, at the parallel fibre-Purkinje cell synapses. We demonstrate that learned gain increases, but not decreases, require the activation of type 1 metabotropic glutamate receptors (mGluR1) and B type γ-aminobutyric acid (GABAB) receptors. Blocking one or both of these receptors with an antagonist inverts gain-up learning, while the agonist augments gain-up learning. Furthermore, we provide novel evidence that these receptors are co-activated during gain-up learning.
The Cuntz Semigrop of C(X,A)
Keywords: C*-algebras
the Cuntz semigroup

The Cuntz semigroup is an isomorphism invariant for C*-algebras consisting of a semigroup with a compatible (though not algebraic) ordering. Its construction is similar to that of the Murray-von Neumann semigroup (from which the ordered K_0-group arises by the Grothendieck construction), but using positive elements in place of projections. Both rich in structure and sensitive to subtleties of the C*-algebra, the Cuntz semigroup promises to be a useful tool in the classification program for nuclear C*-algebras. It has already delivered on this promise, particularly in the study of regularity properties and the classification of nonsimple C*-algebras. The first part of this thesis introduces the Cuntz semigroup, highlights structural properties, and outlines some applications. The main result of this thesis, however, contributes to the understanding of what the Cuntz semigroup looks like for particular examples of (nonsimple) C*-algebras. We consider separable C*-algebras given as the tensor product of a commutative C*-algebra C_0(X) with a simple, approximately subhomogeneous algebra A, under the regularity hypothesis that A is Z-stable. (The Z-stability hypothesis is needed even to describe of the Cuntz semigroup of A.) For these algebras, the Cuntz semigroup is described in terms of the Cuntz semigroup of A and the Murray-von Neumann semigroups of C(K,A) for compact subsets K of X. This result is a marginal improvement over one proven by the author in [Tikuisis, A. "The Cuntz semigroup of continuous functions into certain simple C*-algebras." Internat. J. Math., to appear] (there, A is assumed to be unital), although improvements have been made to the techniques used. The second part of this thesis provides the basic theory of approximately subhomogeneous algebras, including the important computational concept of recursive subhomogeneous algebras. Theory to handle nonunital approximately subhomogeneous algebras is novel here. In the third part of this thesis lies the main result. The Cuntz semigroup computation is achieved by defining a Cuntz-equivalence invariant I(.) on the positive elements of the C*-algebra, picking out certain data from a positive element which obviously contribute to determining its Cuntz class. The proof of the main result has two parts: showing that the invariant I(.) is (order-)complete, and describing its range.
Slice Sampling with Multivariate Steps
Keywords: adaptive Markov chain Monte Carlo
adaptive MCMC
slice sampling
crumb framework

Markov chain Monte Carlo (MCMC) allows statisticians to sample from a wide variety of multidimensional probability distributions. Unfortunately, MCMC is often difficult to use when components of the target distribution are highly correlated or have disparate variances. This thesis presents three results that attempt to address this problem. First, it demonstrates a means for graphical comparison of MCMC methods, which allows researchers to compare the behavior of a variety of samplers on a variety of distributions. Second, it presents a collection of new slice-sampling MCMC methods. These methods either adapt globally or use the adaptive crumb framework for sampling with multivariate steps. They perform well with minimal tuning on distributions when popular methods do not. Methods in the first group learn an approximation to the covariance of the target distribution and use its eigendecomposition to take non-axis-aligned steps. Methods in the second group use the gradients at rejected proposed moves to approximate the local shape of the target distribution so that subsequent proposals move more efficiently through the state space. Finally, this thesis explores the scaling of slice sampling with multivariate steps with respect to dimension, resulting in a formula for optimally choosing scale tuning parameters. It shows that the scaling of untransformed methods can sometimes be improved by alternating steps from those methods with radial steps based on those of the polar slice sampler.