VictorJuiz/thesis huggingface dataset:
Spatiotemporal dynamics from interlinked positive-and-negative feedback loops [electronic resource]
Keywords: Chemical and Systems Biology.

Positive and negative feedback loops are two of the most ubiquitous network motifs in biological systems. When a positive feedback loop and a negative feedback loop are coupled together, rich dynamics can emerge. Among these, oscillations in time and space, and pulses of protein activity are some of the commonly observed phenomena in a biological system. In this thesis, we started by computationally study the benefit of a positive feedback in an oscillator, and concluded that oscillators running on interlinked positive-and-negative feedback loops are more robust and tunable in period than the oscillators with only the negative feedback. We then focused on the Xenopus laevis embryonic cell cycle oscillator, a well characterized biochemical oscillator that runs on interlinked positive-and-negative feedback loops. We identified a transition of oscillator topology during Xenopus early development, from the long first cell cycle that depends critically on Wee1/Cdc25 mediated positive feedback, to the short subsequent cell cycles in which the positive feedback is dispensable. Using the human neutrophil-like HL60 cells, we studied the spatiotemporal dynamics of cytoskeleton proteins. We identified a perfect coupling between the protruding front and the retracting rear of a migrating HL60 cells. Myosin exhibits dynamic flashes at the rear of the cell, and the time scale of the flashes depends on local positive and negative feedback loops. When the duration of the myosin flashes is perturbed, the cell exhibits difficulties in turning and has inefficient chemotaxis. We also performed a statistical study comparing the shape and migration dynamics of HL60 cells, and provided evidence of a close correlation between the two phenotypes. Our results showed that the spatiotemporal protein dynamics allowed by proper regulation of interlinked positive-and-negative feedback loops is important in many examples in biology.
Specifying and validating memory protocols for chip generators [electronic resource]
Keywords: Electrical Engineering.

Shared memory protocols are a complex and active area of research. A memory protocol describes the way in which multiple processing entities communicate in order to achieve a consistent view of a hierarchical shared memory system. From a research perspective, it is easiest to specify a protocol at a high level, to emphasize what is new and interesting about the protocol. With only this specification it is a challenge to evaluate these solutions in hardware, because creating an entire hardware chip multiprocessor platform is a complex and error prone task. This thesis presents Specification Language for Advanced Memory Models (SLAMM), a language for specifying protocols at a high level in a C-like language. A SLAMM specification is compiled to configure a hardware template which can implement the memory protocol. This overall system template is composed of a number of independent controllers, and we present in detail the template for one such controller and the microblocks which compose it. We also describe a technique for verifying the resulting hardware system using a Relaxed Scoreboard, which allows either random testing of the system or monitored directed tests. These parts taken together provide a flexible memory platform that is easy to program and validate to evaluate new protocols in hardware.
Spectroscopic characterization of binuclear non-heme iron and MN/FE active sites [electronic resource] : correlation of geometric and electronic structure with reactivity
Keywords: Chemistry.

Binuclear non-heme iron enzymes catalyze various reactions including H-atom abstraction, desaturation, hydroxylation, and electrophilic aromatic substitution through O2 activation. In addition, they protect cells from oxidative stress and regulate iron levels in the cell. These enzymes utilize two irons and have common structural motif of 2-His / 4-carboxylate. Despite the enzymes' structural similarities, subtle changes at their active sites allow these enzymes to have different reactivities. Understanding the active site structures of these enzymes and the key mechanistic features related to these structures can provide a basis for potential applications: they could be drug inhibition targets to treat cancer, diabetes, and pathogenic diseases; they could work as biocatalysts; and they could carry out bioremediation reactions. In this dissertation, studies that examine three binuclear non-heme iron and Mn/Fe enzyme active sites (class Ic ribonucleotide reductase, ferritin variants, and bacterioferritin) and peroxo-bridged biferric model complexes are described. A combined spectroscopic methodology of nuclear resonance vibrational spectroscopy (NRVS), circular dichroism (CD), magnetic circular dichroism (MCD), and variable temperature, variable field (VTVH) MCD is used to probe geometric and electronic structures of Mn and Fe centers in protein active site and in model complexes.
A statistical analysis correlating controllable factors identified by the integration-VDC-lean method and project outcome metrics for MEP coordination [electronic resource]
Keywords: Civil and Environmental Engineering.

MEP coordination has become an important step in construction project delivery. It bridges the gap between design and construction, facilitating communication between the different stakeholders involved and resolving issues before they are encountered in the field. Successful MEP coordination has been tied to successful project outcomes (Khanzode, Fischer, & Reed, 2005; Korman, Fischer, & Tatum, 2003; Staub-French & Khanzode, 2007), resulting in fewer field conflicts. Khanzode et al. (2011) developed the IVL method for MEP coordination with fifty factors project managers can control to make the coordination successful. However, guidelines that help managers prioritize these factors do not exist. For example, is identifying the strategic goals and specific objectives for the coordination of MEP systems more important for successful MEP coordination than having the team co-located during MEP coordination? Until now, managers have relied on their personal experience and lessons learned from past projects to guide their efforts during coordination. This has led to wide variations in project outcomes across projects (even within the same organization) and a lack of consistency during coordination. With the support of Professor Martin Fischer from Stanford University, and Dr. Atul Khanzode and Stephane Denerolle from DPR Construction, I carried out a survey inquiring 65 construction projects about their MEP coordination methods and correlated them with their project outcomes. This allowed the development of a thorough analysis correlating the different controllable factors to the different project outcomes to uncover which are the most important controllable factors that influence project outcomes during MEP coordination. This research uncovered the most critical controllable factors related to each project outcome. In particular, we were able to identify that fifteen controllable factors (out of the fifty identified by Khanzode et al. (2011)) that have the greatest influence on the fourteen outcome metrics for MEP coordination. Using this methodology, teams can to focus their attention on manageable controllable factors which are directly correlated to MEP outcomes which are critical for the project.
Statistical and computational methods for credit portfolio loss and financial state-space models [electronic resource]
Keywords: Management Science and Engineering.

Financial institutions are often exposed to credit sensitive assets such as loans and corporate bonds. Positions involving these securities could be entered into for hedging, speculation, or diversification purposes. An important consideration in the design and risk management of these credit-linked portfolios is the distribution of the portfolio loss. In the first part of this thesis, we develop an analytical approximation for the distribution of the portfolio loss due to defaults in a loan portfolio at a fixed time horizon. Our method is generic in that it can handle a large class of models of default timing, and addresses other important features of corporate loan portfolios, including stochastic volatility, and state-dependent jumps at and between defaults. A related problem which has been studied extensively in the recent filtering literature is that of joint online parameter estimation and latent state filtering in frailty models for credit risk, and other state-space models. In the second part of this thesis, we discuss a new methodological advancement. We introduce an adaptive particle filter that uses a computationally efficient Markov Chain Monte Carlo estimate of the posterior distribution of the state-space model parameters in conjunction with sequential state estimation. Our method can be widely applied to state-space models in economics, finance, engineering, and biostatistics to name a few. The superior numerical performance of our adaptive filter makes it a practical alternative to estimate parameters in a large class of dynamic state-space models in financial econometrics. We discuss one such application and develop an efficient sequential Monte Carlo method which updates market microstructure parameter estimates at each new quote or trade transaction for high-frequency transaction data. We introduce a dynamic non-linear microstructure model for the latent efficient price, which incorporates price discreteness and live market information from the limit order book.
Statistical methods for dynamic panel data and their applications [electronic resource]
Keywords: Statistics.

Dynamic panel data models are widely studied in econometrics and in biostatistics. We propose a unified approach based on the empirical Bayes methodology to provide a computationally efficient framework for the analysis and prediction of the dynamic panel data with many individuals. In the econometrics literature, an alternative approach to dynamic panel data is to use moment restrictions. How to choose the combination of model and moment restrictions that yields the proper balance between bias and variance of the GMM or the GEL estimator is a fundamental problem in moment restriction models. We propose a new two-stage model and moment selection procedure and derive new asymptotic properties of maximum empirical likelihood estimators. We apply our proposed methods to simulation studies and empirical analysis of dynamic panel data. Related applications include modeling joint default probabilities of multiple firms and empirical study of subprime mortgage loans.
Statistics and probability in criminal trials [electronic resource] : the good, the bad, and the ugly
Keywords: Philosophy.

Is a high probability of guilt, in and of itself, enough to convict? I answer in the negative. The prosecutor's burden of proof does not only consist in establishing the high probability of the defendant's guilt; it also consists in offering a reasonably specific narrative of the crime. This can explain, among other things, the nuances of using statistical evidence in criminal trials. Taking DNA evidence as a case study, I argue that statistical evidence can be particularly problematic whenever it fails to support a reasonably specific narrative of the crime.
Status processes and organizational inequality [electronic resource] : the social psychology of inclusion
Keywords: Sociology.

Building on Status Characteristics Theory (SCT), this dissertation provides new insight into how macro and meso-level structural forces, such as legal environment, organizational context and cultural beliefs about race influence micro dynamics in group processes, attitudes, and behavior within organizations. This study breaks new ground by extending SCT propositions with critical insights from institutional and intergroup attitude theories. Guided by this theoretical extension, several hypotheses are investigated to clarify the effects of competing diversity logics on productive organizational outcomes. Organizations increasingly endorse inclusive diversity values, yet broader societal bias and discrimination continue to limit opportunity for racial/ethnic minorities and women. While intended to be unifying, inclusive diversity values can generate informal resistance and backlash because they challenge culturally-based status hierarchies that are deeply ingrained in society. This experimental study investigates several hypotheses to further clarify the conditions under which inclusive diversity values are most successful in promoting productive outcomes, such as equitable management decisions and reduced bias. Both laboratory (n=63) and survey-based (n=220) experiments support the basic SCT hypothesis that formal organizational diversity logics endorsing a value of low status group members can often lead to informal resistance that exacerbates existing status effects and inequalities. An especially surprising experimental finding supports the efficacy of the "legal compliance case" over the "business case" in contrast to a growing literature on both detrimental effects of legal compliance and benefits of business rationales. Despite the perceived legitimacy of profit-based rationales for diversity endorsed by Corporate America, results indicate that a "business case" for diversity elicited more negative behavior toward minority group members and a weaker value of diversity and inclusion than rationales emphasizing antidiscrimination law. As a legitimate and authoritative social institution with historical, political, and moral grounding, civil rights law appears to have a normative influence that other strategies do not. Additional multivariate analyses also suggest that future research on these effects need to further clarify rather complex social psychological mediating and moderating processes. Beyond theoretical benefits, findings can inform organizational leaders seeking to better understand effects of alternative policies, structural arrangements, and training strategies to institutionalize the value of diversity. Findings should also help raise awareness for managers, employees, attorneys, judges, and numerous other stakeholders investing in diversity and inclusion or evaluating such efforts within the context of color-blind ideological debates.
Sticky attunements [electronic resource] : on the relationship between organisms and their environments
Keywords: Philosophy.

In this dissertation I make a case, and provide tools for, an approach to cognition that takes seriously the human mind's evolved nature. Specifically, I argue that interaction with the environment in ways that are biologically beneficial to an organism is a central feature of cognition. I capture this phenomenon in the theoretical notion of attunement that I define in its passive and active form. I argue that theories of cognition that attempt to explain how the mind works must be compatible with capacities that feature in a `dealing with' of the environment---a phenomenon I call environmentally-oriented competence. Moreover, I make the case for the gradual evolution of cognitive capacities from our nonhuman ancestors to us humans, and I argue that as a result we should be highly parsimonious in positing cognitive mechanisms to explain cognitive phenomena.
Stochastic acceleration of electrons by turbulence in solar flares [electronic resource]
Keywords: Physics.

Solar flares are among the most powerful explosions and most efficient particle accelerators in the solar system. The model of stochastic acceleration by plasma turbulence has been very instrumental in explaining the observed high-energy radiations and particles from solar flares. In this thesis, we aim to better constrain the electron acceleration and scattering processes by turbulence from hard X-ray imaging spectroscopic observations of solar flares. By utilizing the leaky box Fokker-Planck equation and the thick target equation describing particle acceleration and transport, we derive analytical formulas for the stochastic acceleration model quantities directly in terms of the accelerated and escaping particle spectra. Based on the hard X-ray radiating electron flux spectral images via regularized inversion, we determine the timescales for electron escape, pitch angle scattering, energy diffusion, and direct acceleration in two intense solar flares with a high-energy loop-top coronal source observed by the RHESSI mission. The existence of distinct coronal hard X-ray sources up to 100-150 keV in the impulsive phase indicates efficient confinement of high-energy electrons in the corona. The results that the electron escape time increases with energy and the acceleration time and scattering time exhibit very different energy dependences contradict existing predictions for stochastic acceleration due to wave-particle resonant interactions. The discrepancy between the observations and the acceleration model could be alleviated if the turbulence spectrum is much steeper than commonly assumed. A more plausible explanation for such events is that the escape of electrons from the loop-top acceleration region is not diffusive in nature due to scattering, but is affected by magnetic mirroring.
Strained germanium technology for on-chip optical interconnects [electronic resource]
Keywords: Electrical Engineering.

Since the invention of the first transistor over half a century ago, transistor scaling has led the semiconductor industry to blossom. Despite the improved performance of scaled transistors, however, the computational speed of integrated circuits (IC) has now become limited by their electrical interconnects. To alleviate this performance bottleneck in ICs, optical interconnects, which have already revolutionized long-haul communications, have recently gained much attention for on-chip applications. Over the past decade many of the key constituents of an on-chip optical interconnect system, such as high-performance photodetectors and modulators, have been demonstrated on a silicon-compatible platform. However, an efficient light source remains particularly challenging: silicon and silicon-compatible materials such as germanium (Ge) are not readily suitable for light emission because their band gaps are indirect. It has been proposed to use tensile strain to make Ge's band gap direct and therefore suitable for light emission, however experimental realization has thus far been lacking. In this dissertation, we focus on developing an efficient silicon-compatible light emitter based on strained Ge technology. Starting from theoretical calculations showing how tensile strain can improve the light emission efficiency of Ge, we present several approaches for enhancing light emission from highly strained Ge on a CMOS-compatible platform. In the first part, we describe a thin film membrane technique in which a large residual stress in a tungsten layer is used as a stressor to induce a biaxial strain in a Ge membrane, upon which we have fabricated optoelectronic devices. In the second part, we introduce an approach to induce uniaxial strain that can potentially create a direct band gap in Ge wire using geometrical amplification of a small pre-existing strain. Lastly, we present a novel way to mimic double-heterostructure behavior within a single material, further enhancing light emission from Ge by capturing photo-generated carriers within a strain-induced potential well. Throughout this dissertation, we discuss the implications of these experimental achievements towards creating an efficient Ge laser for use in silicon-compatible optical interconnects.
Strategic elite rhetoric, manipulation of electoral institutions and voter decision-making [electronic resource]
Keywords: Political Science.

This manuscript analyzes how two prominent means of elite influence -- political advertisements and election administration policies -- shape the composition of the American electorate. Separate chapters utilize observational and experimental methods and examine the influence of Voter Identification statutes, Polling Place hours and Televised Political Advertising on voter turnout. The study demonstrates that election administration policies and strategic elite rhetoric can influence voter turnout and affect the composition of the American electorate.
Stratigraphic architecture and flow dynamics of deep-water turbidite deposits [electronic resource] : the miocene lower Mount Messenger Formation in the Taranaki Basin in New Zealand, and the Oligocene Puchkirchen Formation in the Molasse Basin in Austria
Keywords: Geological and Environmental Sciences.

This dissertation focuses on the architecture, depositional setting, fluid dynamics, and stratigraphic evolution of deep-water deposits in the Taranaki and Molasse Basins. This dissertation consists of three chapters: two of them are studies of the Mount Messenger Formation in the Taranaki Basin, New Zealand, and the third is the study of the Puchkirchen Formation in the Molasse Basin, Austria. Chapter 1 is a field-based outcrop study of the channel-lobe complex in New Zealand which documents the terminal destination of the siliciclastic deposits on the basin floor. Chapter 1 gives a more precise and polished picture to timing of filling and deposition of the channel and lobe complexes, and a larger picture of the paleogeography of the eastern Taranaki Basin. The subsurface study of Chapter 2 explores the interplay between submarine channel belt and overbank deposits in the Molasse Basin in Austria. This chapter describes the interaction between turbidity currents and debris flows within the channel as well as documents in more detail the slope of the foreland basin and gullies developed on it. Chapter 3 explores the hydrodynamics of formation of dune-size ripples under high-density turbidity currents.
Structural and biochemical analysis of phosphorylation events during Wnt signal transduction [electronic resource]
Keywords: Molecular and Cellular Physiology.

A great deal is known about elements of the Wnt signal transduction cascade and the [beta]-catenin destruction complex, but a complete molecular understanding of their function has remained elusive. Many of the proteins that are necessary for [beta]-catenin destruction, including GSK-3, CK1, Axin, and APC, also have roles in stabilizing [beta]-catenin on Wnt stimulation, thus confounding genetic analyses and cell culture overexpression studies in difficult-to-predict ways. In addition, Wnt signal transduction proteins such as GSK-3, CK1, and APC play critical roles in other signal transduction and metabolic cascades within cells, including such diverse pathways as glycogen regulation, circadian rhythm, spindle formation during mitosis, and microtubule stability. In order to carefully dissect Wnt signal transduction in the absence of these confounding factors, biochemical and structural studies were carried out on proteins from the destruction complex and the Wnt signaling cascade, with emphasis placed on the role of phosphorylation events on the APC, [beta]-catenin, and LRP5/6 proteins during the transition from [beta]-catenin destruction to activation.