VictorJuiz/thesis huggingface dataset:
Efficient Algorithms for Future Aircraft Design: Contributions to Aerodynamic Shape Optimization
Keywords: induced drag
shape optimization
aircraft design
computational fluid dynamics
b-spline volume
Newton Krylov
GMRES
GCROT
adjoint
summation-by-parts
simultaneous approximation terms

Advances in numerical optimization have raised the possibility that efficient and novel aircraft configurations may be ``discovered'' by an algorithm. To begin exploring this possibility, a fast and robust set of tools for aerodynamic shape optimization is developed. Parameterization and mesh-movement are integrated to accommodate large changes in the geometry. This integrated approach uses a coarse B-spline control grid to represent the geometry and move the computational mesh; consequently, the mesh-movement algorithm is two to three orders faster than a node-based linear elasticity approach, without compromising mesh quality. Aerodynamic analysis is performed using a flow solver for the Euler equations. The governing equations are discretized using summation-by-parts finite-difference operators and simultaneous approximation terms, which permit nonsmooth mesh continuity at block interfaces. The discretization results in a set of nonlinear algebraic equations, which are solved using an efficient parallel Newton-Krylov-Schur strategy. A gradient-based optimization algorithm is adopted. The gradient is evaluated using adjoint variables for the flow and mesh equations in a sequential approach. The flow adjoint equations are solved using a novel variant of the Krylov solver GCROT. This variant of GCROT is flexible to take advantage of non-stationary preconditioners and is shown to outperform restarted flexible GMRES. The aerodynamic optimizer is applied to several studies of induced-drag minimization. An elliptical lift distribution is recovered by varying spanwise twist, thereby validating the algorithm. Planform optimization based on the Euler equations produces a nonelliptical lift distribution, in contrast with the predictions of lifting-line theory. A study of spanwise vertical shape optimization confirms that a winglet-up configuration is more efficient than a winglet-down configuration. A split-tip geometry is used to explore nonlinear wake-wing interactions: the optimized split-tip demonstrates a significant reduction in induced drag relative to a single-tip wing. Finally, the optimal spanwise loading for a box-wing configuration is investigated.
Generation, Characterization and Applications of Femtosecond Electron Pulses
Keywords: Femtosecond Electron Diffraction
Femtosecond Electron Pulse Characterization
Plasma Dynamics

Ultrafast electron diffraction is a novel pump-probe technique which aims to determine transient structures during photoinduced chemical reactions and other structural transitions. This technique provides structural information at the atomic level of inspection by using an electron pulse as a diffractive probe. The atomic motions of interest happen on the 100 fs = 10^(−13) s time scale. To observe these atomic motions, a probe which matches this time scale is required. In this thesis, I describe the development of an electron diffractometer which is capable of 200 fs temporal resolution while maintaining high signal level per electron pulse. This was made possible by the construction of an ultra-compact photoactivated 60 keV femtosecond electron gun. Traditional electron pulse characterization methods are unsuitable for high number density femtosecond electron pulses such as the pulses produced by this electron gun. I developed two techniques based on the laser ponderomotive force to reliably determine the duration of femtosecond electron pulses into the sub-100 fs range. These techniques produce a direct cross-correlation trace between the electron pulse and a laser pulse. The results of these measurements conﬁrmed the temporal resolution of the newly developed femtosecond electron diffractometer. This cross-correlation technique was also used to calibrate a method for the determination of the temporal overlap of electron and laser pulses. These techniques provide the pulse diagnostics necessary to utilize the temporal resolution provided by femtosecond electron pulses. Owing to their high charge-to-mass ratio, electrons are a sensitive probe for electric ﬁelds. I used femtosecond electron pulses in an electron deﬂectometry experiment to directly observe the transient charge distributions produced during femtosecond laser ablation of a silicon (100) surface. We found an electric ﬁeld strength of 3.5 × 10^6 V/m produced by the emission of 5.3 × 10^11 electrons/cm^2 just 3 ps after an excitation pulse of 5.6 J/cm^2 . This observation allowed us to rule out Coulomb explosion as the mechanism for ablation under the conditions present in this experiment.
The Role of Vascular Matrix Metalloproteinase-2 and Heme Oxygenase-2 in Mediating the Response to Hypoxia
Keywords: hypoxia
endothelium
matrix metalloproteinase-2
heme oxygenase-2
apoptosis
protein translation
vascular reactivity

Systemic hypoxia frequently occurs in patients with cardiopulmonary diseases. Maintenance of vascular reactivity and endothelial viability is essential to preserving oxygen delivery in these patients. The role of matrix metalloproteinase-2 (MMP-2) and heme oxygenase-2 (HO-2) in the vascular response to hypoxia were investigated. In the first part of the thesis, the role of MMP-2 in regulating systemic arterial contraction after prolonged hypoxia was investigated. MMP-2 inhibition with cyclic peptide CTTHWGFTLC (CTT) reduced phenylephrine (PE)-induced contraction in aortae and mesenteric arteries harvested from rats exposed to hypoxia for 7 d. Responses to PE were reduced in MMP-2-/- mice exposed to hypoxia for 7 d compared to wild-type controls. CTT reduced contraction induced by big endothelin-1 (big ET-1) in aortae harvested from rats exposed to hypoxia. Increased contraction to big ET-1 after hypoxia was observed in wild-type controls, but not MMP-2-/- mice. Rat aortic MMP-2 and MT1-MMP protein levels and MMP activity were increased after 7 d of hypoxia. Rat aortic MMP-2 and MT1-MMP mRNA levels were increased in the deep medial vascular smooth muscle. These results suggest that hypoxic induction of MMP-2 activity potentiates contraction in systemic conduit and resistance arteries through proteolytic activation of big ET-1. The second part of the thesis investigated oxygen regulation of HO-2 protein and whether it plays a role in preserving endothelial cell viability during hypoxia. HO-2, but not HO-1, protein level was maintained during hypoxia in human endothelial cells through enhanced translation of HO-2 transcripts. Inhibition of HO-2 expression increased the production of reactive oxygen species, decreased mitochondrial membrane potential, and enhanced apoptotic cell death and activated caspases during hypoxia, but not during normoxia. These data indicate that HO-2 is translationally regulated and important in maintaining endothelial viability and function during hypoxia. In summary, the thesis demonstrates the importance of MMP-2 and HO-2 in preserving vascular function during prolonged systemic hypoxia. These enzymatic pathways may, therefore, represent novel therapeutic targets that may be exploited to ameliorate the effects of hypoxia in patients with cardiopulmonary disease.
The Performance of Critical History in Contemporary Irish Theatre and Film
Keywords: Contemporary Irish Theatre
Contemporary Irish Film
Drama
Cinema
Ireland
Irish History
Memory in theatre and film
Irish Identity
Marina Carr
Sebastian Barry
Goldfish Memory (2003)
Celtic Tiger
Dublin's Spire
Landscape in Film
Marginalized Characters
Myth in Drama
Cultural Transition

This dissertation examines theatre and film in Ireland between 1988 and 2005, focusing on the plays of Sebastian Barry and Marina Carr, as well as a select group of films from this period. Employing a method of analysis that couples close-readings with attention to socio-cultural context, aesthetic form, and issues of representation, the dissertation demonstrates how theatre and film work to complicate conventional Irish historical narratives and thereby encourages a reassessment of contemporary constructs of Irish identity. The introduction provides a contextual framework for significant contemporaneous social, cultural and economic changes in Ireland, and includes a case study of ‘The Spire,’ a monument unveiled on Dublin’s central boulevard in 2003, which I argue is the architectural metonym for the transitional nature of Celtic Tiger Ireland. The case study explores the aesthetics of the monument, as well as the politicised public debate that ensued, and thereby provides a snapshot of issues relevant to the readings pursued in dissertation’s remaining chapters. The discussion of Sebastian Barry’s ‘family plays’ reveals the playwright’s effort to refuse traditional binary conceptions of identity and to proffer, instead, a dramatic landscape that similarly refuses to allow conflict to dominate. Barry’s use of a non-conflictual dramatic form supports his narrative interest in compassion and peaceful resolution, and provides a model for living with otherness that could prove useful in an increasingly diverse and globalised Ireland. Marina Carr’s plays share Barry’s desire to represent aspects of Irish character anew, but they also dramatise how cultural transitions are difficult and never linear, and how the conventional pull of memory and the past has a residual presence in the ‘new’ Ireland. Taken together, these chapters reveal Barry’s hopefulness as an antidote to Carr’s tragic endings. The final chapter provides close readings of several ‘Celtic Tiger’ films, arguing that the representation of landscape is the key lens through which Irish film communicates shifting images of Irish identity. A cycle of films from the first years of the new millennium ekes out a space for new modes of representation through a critical dialogue with major tropes in Irish film history.
Use of Advanced Techniques to Estimate Zonal Level Safety Planning Models and Examine their Temporal Transferability
Keywords: Road Safety
Transportation Planning
Model Transferability
Safety Planning
Macro-level Collision Models
Collision Prediction Models

Historically, the traditional planning process has not given much attention to the road safety evaluation of development plans. To make an informed, defensible, and proactive choice between alternative plans and their safety implications, it is necessary to have a procedure for estimating and evaluating safety performance. A procedure is required for examining the influence of the urban network development on road safety, and in particular, determining the effects of the many variables that affect safety in urban planning. Safety planning models can provide a decision-support tool that facilitates the assessment of the safety implications of alternative network plans. The first objective of this research study is to develop safety planning models that are consistent with the regional models commonly used for urban transportation planning. Geographically weighted Poisson regression (GWPR), full-Bayesian semiparametric additive (FBSA), and traditional generalized linear modelling (GLM) techniques are used to develop the models. The study evaluates how well each model is able to handle spatial variations in the relationship between collision explanatory variables and the number of collisions in a zone. The evaluation uses measures of goodness of fit (GOF) and finds that the GWPR and FBSA models perform much better than the conventional GLM approach. There is little difference between the GOF values for the FBSA and GWPR models. The second objective of this research study is to examine the temporal transferability of the safety planning models and alternative updating methods. The updating procedures examine the Bayesian approach and application of calibration factors. The results show that the models are not temporally transferable in a strict statistical sense. However, relative measures of transferability indicate that the transferred models yield useful information in the application context. The results also show that the updated safety planning models using the Bayesian approach predict the number of collisions better than the calibration factor procedure.
The Use of Individual Participant Data (IPD) for Examining Heterogeneity in Meta-analysis of Observational Studies: An Application to Biomechanical Workplace Risk Factors and Low Back Pain
Keywords: low back pain
meta-analysis
heterogeneity
individual participant data

Background: The use of meta-analysis to combine the results of observational studies is controversial. Despite its common use, methodological work in this area is lacking. Because of the diversity of study designs, exposure and outcome measures, and differential adjustment for confounding variables, the identification of sources of heterogeneity among study effect estimates is particularly important when combining data from observational studies. This thesis presents the results of a study that examines the relative ability of individual participant data (IPD) meta-analysis (which was considered a “gold standard”) and traditional aggregate data (AD) meta-analysis to identify sources of heterogeneity among studies examining mechanical exposure and low back pain (LBP) in workers. Materials and Methods: A systematic literature search was conducted to identify relevant articles. The corresponding author of each article was contacted to request their individual-level data. Because the outcome definitions and exposure measures were not uniform across studies, two sub-studies were conducted 1) to identify sets of outcome definitions that could be combined in a meta-analysis and 2) to develop methods to translate mechanical exposure onto a common metric. IPD analyses were conducted using generalized estimating equation (GEE) regression to identify variables that acted as strong confounders and effect modifiers. Traditional AD meta-analysis was also conducted and potential sources of heterogeneity were tested using meta-regression. Key Findings: (1) Overall, we found an association between both forces and postures on LBP, although the magnitude varied depending on the exposure-outcome combination. Among the outcomes, the ORs tended to be highest for sick leave due to LBP. (2) There was very little evidence of strong confounders in the relationship between mechanical exposure and LBP; thus differential adjustment for confounders in studies would not likely be an important source of heterogeneity in an AD meta-analysis. (3) AD meta-analysis was able to identify the same study-level effect modifiers as IPD meta-analysis, but did not consistently identify individual-level effect modifiers. Both individual-level characteristics (older age and being male), and study-level characteristics (population-based studies and self-reported mechanical exposure), were associated with an increased OR for many of the LBP outcome and mechanical exposure combinations. Conclusion: AD meta-analysis is likely sufficient to detect heterogeneity for study-level factors but is not sufficient to identify individual-level effect modifiers. When the primary source of evidence in a research area is observational studies and when there is controversy despite several systematic reviews, IPD meta-analysis can be used to better understand sources of heterogeneity and provide context
Investigation of Rab34 and Munc13 In The Secretory Pathway: Potential Roles In Diabetic Nephropathy
Keywords: diabetic nephropathy
secretory pathway

Constitutive secretion is responsible for the targeting of transmembrane proteins to the plasma membrane, and for the secretion of extracellular matrix proteins, hormones, and other cellular products. The basic steps of secretion are well understood – proteins synthesized in the endoplasmic reticulum are transported in lipid-bound intermediates to the Golgi, and from the Golgi to the plasma membrane or cell exterior. Dysfunction of the secretory pathway – either constitutive or regulated – is involved in many disease states. One such state is diabetic nephropathy (DN). DN is characterized by renal hypertrophy and fibrosis, and is the leading cause of renal failure worldwide. Our lab had previously shown that munc13 is both upregulated and activated in the diabetic kidney, and that munc13 is an effector of rab34. Study of rab34 in HeLa cells revealed that rab34 is localized to the Golgi, and that it is required for the secretion of the Vesicular Stomatitis Virus glycoprotein. Colocalization experiments, as well as the use of Brefeldin A, localized the effect of rab34 to intra-Golgi transport. Further experiments indicated that glucose-induced upregulation of munc13 in rat mesangial cells increased the rate of constitutive secretion to the plasma membrane, and that this effect depended on its interaction with rab34. Finally, munc13 and rab34 were found to be required for the high glucose-mediated stimulation of Transforming Growth Factor-β secretion from mesangial cells, placing these two proteins at a key point in a pathway of physiological significance in the pathology of DN.
Molecular Mechanisms Regulating Fate Determination of Cerebral Cortex Precursors
Keywords: neural stem cells
SHP-2
Lfc
Tctex-1
neurogenesis
gliogenesis
symmetric divisions
asymmetric divisions

During development of the mammalian nervous system, neural stem cells generate neurons first and glia second, thereby allowing the initial establishment of neuronal circuitry, and subsequent matching of glial numbers and position to that circuitry. Multiple molecular mechanisms act in concert to control neural precursor expansion prior to neurogenesis, and to allow for an exponential generation of neurons while ensuring the maintenance of sufficient precursors to produce later-born neurons, glial cells and adult neural stem cells. Throughout cortical development, these processes are regulated in part by the precursors’ environment as well as intrinsic changes in precursors and their modes of division, which regulate the fate of daughter cells and the balance between self-renewal and differentiation. In the first part of this thesis, the protein tyrosine phosphatase SHP-2 was identified as a novel signaling protein that regulates the neurogenic to gliogenic switch by potentiating neurogenic signals and suppressing gliogenic signals until the appropriate developmental time point for astrogenesis, providing one mechanism whereby precursors integrate conflicting environmental cues. A Noonan Syndrome (NS)-associated activated SHP-2 mutation causes perturbations in neural cell genesis, which may contribute to the mild mental retardation and learning disabilities observed in NS patients. In the second part of this thesis, a novel Rho-regulatory pathway which includes the Rho-GEF Lfc and its negative regulator Tctex-1 were also found to regulate neurogenesis, potentially by directing mitotic spindle orientation during precursor divisions, thereby regulating the symmetric and asymmetric nature of radial precursor divisions.
D-brane Chan-Paton Factors and Orientifolds
Keywords: D-brane
Orientifold

In this thesis, we mainly study the structure of D 9-brane Chan-Paton factors in Type II orientifold [special characters omitted] theories. An explicit structure is found through a thorough and systematic derivation. For this purpose, we give a complete analysis of the worldsheet parity square action for all p-q open strings (i.e., the strings starting from Dp-branes and ending on Dq-branes), which is an extension of Gimon-Polchinski's work on the parity square action for p-q strings with p - q even. We also formulate the rules for computing the scattering amplitudes of open strings ending on D-branes. These are important to build phenomenological models in string theory. As an application to the mathematical aspects of string theory, we confirm the proposal that the D-brane charges in Type II orientifolds are classified by the KR-theory groups. All these results will appear in our paper [1]. We also show some preliminary results on the B-type D-branes in the orientifolds of linear sigma models. A typical linear sigma model has both a geometric phase and a Landau-Ginzberg phase over its K¨ahler moduli space. The B-type D-branes are described by suitable categories in a linear sigma model and its phases. The orientifold projection induces parity mappings on the various categories. By looking at the transportation of invariant branes in the moduli space, we find the relations among the parity mappings of different phases in the quintic model.
Monitoring the Generation and Execution of Optimal Plans
Keywords: artificial intelligence
automated planning
monitoring
execution

In dynamic domains, the state of the world may change in unexpected ways during the generation or execution of plans. Regardless of the cause of such changes, they raise the question of whether they interfere with ongoing planning efforts. Unexpected changes during plan generation may invalidate the current planning effort, while discrepancies between expected and actual state of the world during execution may render the executing plan invalid or sub-optimal, with respect to previously identified planning objectives. In this thesis we develop a general monitoring technique that can be used during both plan generation and plan execution to determine the relevance of unexpected changes and which supports recovery. This way, time intensive replanning from scratch in the new and unexpected state can often be avoided. The technique can be applied to a variety of objectives, including monitoring the optimality of plans, rather then just their validity. Intuitively, the technique operates in two steps: during planning the plan is annotated with additional information that is relevant to the achievement of the objective; then, when an unexpected change occurs, this information is used to determine the relevance of the discrepancy with respect to the objective. We substantiate the claim of broad applicability of this relevance-based technique by developing four concrete applications: generating optimal plans despite frequent, unexpected changes to the initial state of the world, monitoring plan optimality during execution, monitoring the execution of near-optimal policies in stochastic domains, and monitoring the generation and execution of plans with procedural hard constraints. In all cases, we use the formal notion of regression to identify what is relevant for achieving the objective. We prove the soundness of these concrete approaches and present empirical results demonstrating that in some contexts orders of magnitude speed-ups can be gained by our technique compared to replanning from scratch.