VictorJuiz/thesis huggingface dataset:
Rational and combinatorial engineering of the met and axl receptor systems [electronic resource]
Keywords: Bioengineering.

Ligand-receptor interactions govern nearly all cellular processes, and dysregulation leads to a range of diseases including cancer, autoimmune diseases, and regenerative disorders. As such, new strategies to target ligand-receptor interactions for therapeutic applications are an important area of research. To develop enhanced agonists and antagonists of the Met receptor, a critical target in cancer therapy and regenerative medicine, we engineered a fragment of the natural activating ligand (termed NK1). First, NK1 was evolved for improved stability using directed evolution. Then, using the activation mechanism of Met by NK1, the resulting enhanced stability mutants were rationally engineered for either agonistic or antagonistic activity. Next, the rationally engineered mutants were used as 'molecular tools' to provide further insights into NK1 structure and function. Finally, these insights supported additional rational engineering to generate further enhanced agonistic proteins. The antagonistic and agonistic proteins developed in this thesis hold promise as cancer therapeutics and diagnostics or for regenerative medicine applications, respectively. This work also supports native ligands as a promising starting point for development of therapeutic proteins.
Realism between metaphysics and science [electronic resource]
Keywords: Philosophy

The aim of my dissertation is to understand what realism debates in philosophy of science should be about. To achieve this goal, a number of questions need to be addressed: What is the target of realism and antirealism in the philosophy of science, and what does it mean to be a realist or an antirealist? Does only realism in this debate imply a commitment to metaphysics, or are both realism and antirealism equally metaphysical positions? Is there really anything to be debated, or should we just be quietists about realism debates in philosophy of science? My answer is that, in its current form, the realism debate in philosophy of science is a skeptical debate, that is, antirealism is offered exclusively as an epistemic challenge to realism. This leads to an unsatisfactory stalemate between realism and antirealism, which often prompts a kind of quietism about these debates. While I reject this quietism as insufficiently supported by argument, I concede that the debate in its current shape is not satisfactory either. Instead I propose to change the target of realism debates away from claims about unobservables towards modal claims made in the sciences. Debates about the latter, I argue, can go beyond skeptical challenges to include semantic and metaphysical questions as well. Switching the target in this way makes the debate about realism in the philosophy of science more like realism debates in other fields.
Realized GARCH [electronic resource] : a joint modeling framework of return and realized measures of volatility
Keywords: Economics

GARCH models have been successful in modeling financial returns. Still, much is to be gained by incorporating a realized measure of volatility in these models. In this thesis, we introduce a new framework for the joint modeling of returns and realized measures of volatility. A key feature of the Realized GARCH framework is a measurement equation that relates the observed realized measure to latent volatility. The new framework fills the gap between two lines of research on volatility modeling: GARCH and high frequency data. There are three major advantages of the Realized GARCH framework. First, the new framework nests most GARCH models as special cases and is, in many ways, a natural extension of standard GARCH models. The models with linear and log-linear specifications retain the simplicity and tractability of the classical GARCH framework; they imply an ARMA structure for the conditional variance and for the realized measures of volatility; and models in this class are parsimonious and simple to estimate. The measurement equation facilitates a simple modeling of the dependence between returns and future volatility that is commonly referred to as the leverage effect. Second, by incorporating the realized measures into the model, which are based on high frequency data and are much more accurate measurements for integrated volatility than daily squared returns, the Realized GARCH models provide a better performance in modeling and forecasting volatility. An empirical application with DJIA stocks and an exchange traded index fund shows that a simple Realized GARCH structure leads to substantial improvements in the empirical fit over to the standard GARCH model. This is true in-sample as well as out-of-sample. Moreover, the point estimates are remarkably similar across the different time series. Third, the measurement equation enables us to obtain additional insights on the bias and variance of different realized measures. Realized EGARCH model further extends the Realized GARCH model by reparameterizing the model and allowing different impacts of the leverage effect and residual measurement error on the conditional variance. The empirical results are in general consistent with the theoretical results in high frequency data literature and give practical guidance about how to use realized measures directly. The Realized EGARCH model is also applied to the exchange traded fund S& P500 index to study the volatility shocks during the financial crisis. We use this model to zoom into the events during the 2007-2009 period, and the model produces a daily series of volatility shocks. We link the announcements of events to large positive and negative volatility shocks.
Regulation of mast cell function by the membrane trafficking proteins RabGEF1 and Rabaptin-5 [electronic resource]
Keywords: Immunology.

Cell surface receptor regulation maintains proper responses to external signals and disregulation of receptors can have drastic effects. We found that RabGEF1, a guanine exchange factor (GEF) for the endocytic regulating small GTPase Rab5, regulates IgE+antigen (Ag)-induced Ras signaling in mast cells and skin homeostasis in vivo. To further understand RabGEF1's role in mast cell function we investigated if RabGEF1 generally regulates mast cell signaling by examining a number of modes of mast cell activation. Like IgE+Ag stimulation, RabGEF1 deficient (-/-) mast cells demonstrated enhanced activation after exposure to stem cell factor (SCF), the ligand for the receptor tyrosine kinase c-kit. Enhanced responses correlated with delayed c-kit and IgE receptor (Fc[epsilon]RI) internalization suggesting a proximal role of RabGEF1 in regulating mast cell signaling events. To dissect the roles of RabGEF1 and its domains in regulating mast cell biology we lentivirally expressed a panel of RabGEF1 mutants in RabGEF1-/- mast cells. We found that RabGEF1 (1) harbors ubiquitin (Ub) ligase activity within an N-terminal A20 zinc finger domain, (2) binds to Ub and localizes to membranes through amino acids 1-150, (3) interacts with Rabaptin-5, a Rab5 effector, through a C-terminal coiled coil (CC) domain and, (4) activates Rab5 with a central VPS9 domain. Despite containing a number of domains, only the VPS9 was crucial to restore wildtype activation of RabGEF1-/- cells after IgE+Ag stimulation. Moreover, lack of the VPS9 or CC domain diminished Rabaptin-5 levels and reduced surface Fc[epsilon]RI and [beta]1 expression on mast cells suggesting that these domains are important for receptor homeostasis. Using shRNA knockdown of Rabaptin-5 we identified a novel role for Rabaptin-5 in maintaining Fc[epsilon]RI and [beta]1 surface expression by increasing surface stability and receptor half-life. The reduced Fc[epsilon]RI and [beta]1 surface levels in Rabaptin-5 deficient cells attenuated sensitivity to antigen induced adhesion, migration, and cytokine production in these cells. Despite Rabaptin-5's in vitro documented role as a Rab5 effector, Rab5 dependant processes (i.e., receptor internalization or endosome fusion) were unaffected by Rabaptin-5 deficiency and challenge the current thoughts of Rab5 processes in intact cells. These data show the importance of receptor trafficking in regulating mast cell activation.
Regulation of motility in helicobacter pylori and the epsilon proteobacteria [electronic resource]
Keywords: Microbiology and Immunology

Microbes can colonize harsh and dynamic environments. Often, this ability depends on rapid responses through directed motility. Members of the Epsilon proteobacteria are found in many 'extreme' environments, including the human stomach1. We discovered that Helicobacter pylori establish bacterial colonies deep in the gastric glands, and identified a novel protein, ChePep, necessary to colonize this niche. By tracking the movement of single bacteria we found that mutants lacking ChePep cannot control the rotation of their flagella and swim with abnormally frequent reversals and even sustain bursts of movement backwards. Genetic experiments show that ChePep regulates flagellar rotation through the chemotaxis signaling system. By examining H. pylori within a microscopic pH gradient, we determined that ChePep is critical for normal chemotactic behavior. We expressed ChePep from the zoonotic pathogen Campylobacter jejuni, and the deep sea hydrothermal vent inhabitant Caminibacter mediatlanticus in H. pylori and found that ChePep is functionally conserved across the [Epsilon]-proteobacteria. ChePep represents a new family of chemotaxis regulators unique to the [Epsilon]-proteobacteria, and illustrates the differing strategies that microbes have evolved to control motility.
Regulation of neuronal survival and CREB-dependent transcription by CaV1.2 L-type calcium channels [electronic resource]
Keywords: Neurosciences.

Electrical activity is a potent trophic factor that promotes the survival of many populations of neurons. L-type calcium channels (LTCs) are particularly effective at promoting survival of neurons during development, in part by activating transcription factors such as CREB. Mutation of the LTC CaV1.2 causes Timothy Syndrome (TS), a disorder characterized by cardiac arrhythmias, webbing of fingers and toes, and autism. The TS mutation leads to loss of voltage-dependent inactivation (VDI) of the channel. Although it is known that VDI is critical for the transition between the open and resting states of the channel, the role that channel inactivation plays in cell signaling and neuronal development is poorly understood. The work in this dissertation shows that the TS mutation impairs CaV1.2-dependent neuronal survival and prevents activation of the transcription factor CREB. By using TS channels that contain pore mutations that prevent Ca2+ flux, we found that the ability of TS channels to cause apoptosis is independent of Ca2+ flux through the channel. Conversely, a novel leucine to proline mutation at position 1368 restores VDI to TS channels and prevents TS-dependent apoptosis and inhibition of CREB. These findings support the idea that CaV1.2 conveys two signals that together regulate activity-dependent neuronal survival and activation of CREB: a signal that depends on the channel conformation and a signal that depends on calcium influx through the channel. These results provide new insights into the mechanisms by which the L-type calcium channels activate transcription and regulate neuronal survival during development.
The regulation of p53 function by lysine methylation [electronic resource]
Keywords: Biology.

The human p53 tumor suppressor is the most widely studied gene and protein in cellular biology. An open question in the field relates to the regulatory mechanism(s) that manage the complex functions of an essential tumor suppressor protein. Recently, a number of the protein lysine methyltrasferases (PKMTs) that mediate histone lysine methylation have also been identified as having activity on non-histone substrates. Reversible covalent methylation of lysine residues on histone or non-histone proteins constitutes a principal molecular mechanism that guides substrate proteins to diverse biological outcomes. The goal of this work was to 1) expand the understanding of lysine methylation and methyllysine recognition in the context of non-histone tumor suppressor proteins, and 2) elucidate the molecular mechanisms of such events. A handful of studies characterizing lysine methyation events on four distinct lysines in the C-terminal regulatory region of p53, have lead to the emergence of p53 as a model for non-histone lysine methylation. We contributed to this body of work by demonstrating that the lysine methyltransferase enzyme SET8/PR-Set7 is a novel regulator of p53. SET8 monomethylates p53 at lysine 382 (p53K382me1), resulting in reduced transactivation of highly responsive target genes. We used biochemical and crystallographic studies to identify the triple malignant brain tumor (MBT) domain containing chromatin compaction factor L3MBTL1 as the second know p53-effector protein. We demonstrated that SET8-mediated methylation of p53 at K382 promotes the interaction between L3MBTL1 and p53 in cells, and the chromatin occupancy of L3MBTL1 at p53 target promoters, thus providing a molecular explanation for the mechanism by which p53K382me1 is transduced to regulate p53 activity. Additionally we demonstrated that retinoblastomal tumor suppressor (RB) can be mono-methylated in vivo by SMYD2 at lysine 860, and that this methylation provides a direct binding site for L3MBTL1, helping to guide its functions in mammalian cells. In summary, we identified SET8 as a novel p53-modifying enzyme that mediates the regulatory post-translational modification at lysine 382; and, we identified L3MBTL1 a novel methyllysine effector protein for that mark. In a collaborative study we demonstrated that methylation of RB by Smyd2 promotes interaction with L3MBTL1. Together these results suggest that regulation by lysine methylation represents a broader paradigm for modulation of non-histone protein activity.
Regulatory controls of microRNA genes beyond the mature microRNAs [electronic resource]
Keywords: Microbiology and Immunology.

MicroRNA (miRNA) genes, which encode an abundant class of ~22-nucleotide (nt), evolutionarily conserved small RNAs, control a fundamental layer of genetic programs at the post-transcriptional level. However, little is known about how the activity of miRNA genes is regulated and how the regulatory information controlling their activity is encoded. Interestingly, mature miRNAs can often be classified into large families consisting of members with identical seeds (nucleotides 2 through 8 of the mature miRNAs) and highly homologous ~22-nt mature miRNA sequences, but with divergent sequences and structural elements beyond their mature miRNAs. Here we investigated whether members of a miRNA gene family that encode identical or nearly identical mature miRNAs are functionally interchangeable in vivo and if not, why? We compare the activities of the mir-181 gene family in promoting double positive T cell development and show that miRNA genes that encode identical to nearly identical mature miRNAs can have distinct activities. The differences in activity between mir-181a-1 and mir-181c are largely determined by their unique primary/precursor-miRNA (pri/pre-miRNA) loop nucleotides, and the differences in activity between mir-181a-1 and mir-181b-1 are determined by both the pri/pre-miRNA loop and stem. Furthermore, the organization of mir-181a-1/b-1 in a cluster is important for its full activity. We also show that mir-181 family members can differentially regulate target genes quantitatively, and that some target genes can be upregulated. Taken together, we have demonstrated that regulatory information encoded in a miRNA gene beyond the mature miRNA plays a critical role in controlling the activity of the miRNA gene, suggesting that miRNA family members could have evolved different functions through their divergent miRNA gene sequences and structural elements beyond their mature miRNAs. Although, proteins may have evolved to recognize the structural and sequence elements of the pri/pre-miRNAs, we suggest that the regulatory information encoded in the structured pri/pre-miRNA may be directly interpreted through target and pri/pre-miRNA interactions.
Relating time series in data to spatial variation in the reservoir using wavelets [electronic resource]
Keywords: Energy Resources Engineering

An important issue in reservoir parameter estimation is to develop methods that are computationally efficient and reliable. Furthermore, in history matching, one of the challenges in the use of gradient-based Newton algorithms such as Gauss-Newton and Levenberg-Marquardt in solving the inverse problem is the huge cost associated with the computation of sensitivity matrix. Although the Newton type of algorithm gives faster convergence than most other gradient-based inverse solution algorithms, its use is limited to small and medium-scale problems in which the sensitivity coefficients are easily and quickly computed. Modelers often use less efficient algorithms such as conjugate-gradient and quasi-Newton to model large-scale problems because these algorithms avoid the direct computation of sensitivity coefficients. To find a direction of descent, such algorithms often use less precise curvature information that would be contained in the gradient of the objective function. Using a sensitivity matrix gives more detailed information about the curvature of the function; however this comes with a significant computational cost for large-scale problems. We present a multiresolution wavelet approach to estimate the spatial distribution of reservoir parameters, by performing the nonlinear least squares regression in the wavelet domains of both time and space. Wavelet transforms have the ability to reveal important events in time signals or spatial images. Thus we transformed both the model space and the time series pressure data into spatial wavelet and time wavelet domains and used a thresholding to select a subset of wavelet coefficients from each of the transformed domains. These subsets were used subsequently in nonlinear regression to estimate the appropriate description of reservoir parameters. The appropriate subset is not only smaller; the problem is also reduced to the consideration of only the important components of the measured data and only the part of the reservoir description that depends on them. Furthermore, the approach developed in this research improves parameter estimation by reducing the dimension of the inverse problem without significant loss in accuracy. We transformed the inverse problem into reduced wavelet spaces and subsequently coupled the transformation with adjoint sensitivity formulation to reduce the cost associated with computing sensitivity coefficients. The improved adjoint sensitivity formulation presented in this work exploits the reduction in observation (data) space to enforce a reduction in the adjoint linear system of equations thus leading to a reduction in the memory and time required to compute sensitivities. We were able to achieve up to 20 times reduction in computational requirements in some example cases.
Replacing the "teacher-proof" curriculum with the "curriculum-proof" teacher [electronic resource] : toward a more systematic way for mathematics teachers to interact with their textbooks
Keywords: Education.

This research examines when and how secondary mathematics teachers adapt textbook curricula within "typical" cycles of planning and teaching over the course of a school year. The curriculum use of four middle and high school teachers was examined before (September) and after (December, March) engagement in a form of professional development called the Mathematics Curriculum Assessment and Adaptation (MCAA) process. Classroom materials were collected from teachers at three distinct points in the school year, at which time teachers were observed and interviewed about their planning and teaching practices. Overall, the number of textbook materials teachers used as-is dropped dramatically while the number of materials they adapted increased. This finding was true regardless of teaching experience, teaching context, textbook used or content taught, and was reflected in changes in teachers' commentaries about their planning and teaching and changes in classroom practice. Furthermore, the types of adaptations teachers made to their curricula were more reflective of the MCAA process in March than they were in the beginning of the school year. This dissertation research sits within the broader domain of understanding how mathematics teachers use curriculum and raises new questions about how, when and why teachers make changes to textbook materials.
Reproduction and early life of the Humboldt squid [electronic resource]
Keywords: Biological Sciences.

Dosidicus gigas, the Humboldt squid, is endemic to the eastern Pacific, and its range has been expanding poleward in recent years. It is a voracious predator of small fish and invertebrates and prominent prey for large fish and mammals, including humans. Very little is known about Humboldt squid reproduction, development, and early life stages. To study the behavior, including dispersal capabilities, of paralarval D. gigas, I analyzed video of animals swimming in the laboratory, and determined that paralarvae are active swimmers that engage in hop-and-sink behavior. Control of the mantle aperture allows them to engage in slow swimming, in which water is leaked through the mantle aperture, and fast jetting, in which the mantle aperture is tightly closed and all water is expelled through the siphon--as is typical of adult jetting. A theoretical model of squid swimming was built to study the importance of aperture control during the jet cycle. This model predicts that active reduction of the aperture during jetting increases hydrodynamic efficiency, and that squid of large sizes can constrain the risk of embolism by increasing aperture size and decreasing jet frequency to values comparable to empirical measurements. Connectivity among populations of D. gigas throughout the range of this species was assessed with a population genetic approach, in which D. gigas was compared to the co-occurring squid Sthenoteuthis oualaniensis. In D. gigas, only two weakly differentiated populations were evident, with a biogeographic break at 5-6° N. I uncovered four deeply divergent clades in S. oualaniensis, including one which aligns with previous descriptions in the literature of Sthenoteuthis sp. nov. Breaks between clades of S. oualaniensis also occurred at 5-6° N. Range overlap between these two species occurs in the eastern tropical Pacific (ETP), a region both are believed to use as spawning grounds. I looked for paralarvae of D. gigas and S. oualaniensis in surface and subsurface net tows taken in the ETP from 1998 to 2006, and found that abundance was much greater in surface than subsurface tows. I then used a Generalized Linear Model approach to assess the importance of in situ oceanographic variables as predictors of paralarval incidence. Sea surface temperature was found to be a strong predictor of incidence in both surface and subsurface tows, with the probability of paralarval capture rising monotonically from near zero at 15 °C to 0.9 at 30 °C. The apparent lack of paralarvae at surface temperatures below 15 °C raises a question of whether D. gigas can spawn in the temperate and even subpolar waters of its expanded range. I conducted in vitro fertilization studies and found the optimal temperature range for successful laboratory development of D. gigas is 15-25° C.