VictorJuiz/thesis huggingface dataset:
The evolution of genetic and epigenetic diversity in changing environments [electronic resource]
Keywords: Biology.

The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection has been a major focus of study in population genetics for more than five decades. In this thesis, I use analytical and computational models to gain insight into the relative roles of genetic and epigenetic diversity in adaptation to changing selection. The different chapters provide complimentary perspectives on the signatures of environmental volatility in the patterns of variation. Chapter 2 explores the evolution of epigenetic variation and its role in adaptation under changing selection pressures. Chapter 3 investigates the effect of recombination on the geometric mean principle under different environmental regimens and fitness landscapes. Two chapters of this thesis, Chapter 4 and Chapter 5 explore the evolution of phenotypic switching, a phenomenon widely documented in viruses, yeast and bacteria, where offspring can express a phenotype different from those of their parents. These chapters highlight the interplay of spatial and temporal environmental variability, offering new insights into how migration can influence the evolution of stochastic switching rates, epigenetic inheritance, and sources of phenotypic variation. Chapter 6 compares and contrasts how fluctuating selection shapes the rates of recombination, mutation and migration, highlighting surprising similarities in their evolutionary dynamics to changing selection. This chapter offers new insights into the role of the environmental duration, shape and randomness in predicting the long-term evolutionary advantage of the forces of recombination, mutation and migration. The models and analyses presented here provide a more complete understanding of the role of genetic and epigenetic diversity in adaptation to changing selection pressures.
Exact simulation of jump-diffusions [electronic resource]
Keywords: Management Science and Engineering.

This thesis treats the problems of exact simulation and parameter inference for jump-diffusion processes. It has two parts. The first part develops a method for the exact simulation of a skeleton, a hitting time and other functionals of a one-dimensional jump-diffusion with state-dependent drift, volatility, jump intensity and jump size. The method requires the drift function to be C1, the volatility function to be C2, and the jump intensity function to be locally bounded. No further structure is imposed on these functions. The method leads to unbiased simulation estimators of security prices, transition densities, hitting probabilities, and other quantities. Numerical results illustrate its features. The second part develops and analyzes likelihood estimators for the parameters of a discretely-observed jump diffusion. We consider the case when the transition density of the process admits an expansion in terms of an infinite series. A randomization technique leads to an unbiased Monte Carlo estimator of the transition density and the likelihood function. We provide conditions under which resulting likelihood estimators are consistent and asymptotically normal. The method avoids the second-order bias of conventional discretization-based estimators. Unlike the estimators based directly on the density expansion, we do not require high-frequency observations. Numerical results confirm the method's properties.
Exploiting geometric information in camera networks [electronic resource]
Keywords: Electrical Engineering.

Ubiquitous cameras have been widely deployed on smart phones and in smart environments. Because of the richness of the visual data that they provide, the key challenges are organizing and extracting useful information from the cameras. This dissertation explores different applications utilizing geometric information in camera networks to understand the visual data. These applications include image retrieval, image organization, tracking and detection. We first present a key point selection algorithm based on geometric consistency across images. Using selected key points can significantly reduce the length of the inverted index without hurting retrieval performance. Then we show a new compact image descriptor for large scale image search. Our proposed descriptor is an extension of Vector of Locally Aggregated Descriptors (VLAD) that incorporates weak geometry information into the current framework. We demonstrate the efficiency of our method where we achieve the state-of-the-art performance on existing benchmarks. We then propose an image organization algorithm based on constraints across two domains. By solving the co-clustering problem using the alternative optimization, the algorithm exhibits the state-of-the art performance on two datasets. After that we present a real time non-rigid face tracking system deployed in smart offices based on geometric constraints on facial landmarks, which analyzes behaviors of the computer user and helps avoid potential health issues. At last, we present an occupancy detection system deployed in a smart environment which utilizes a set of filters and the geometric consistency from multiple cameras to improve the accuracy of detections.
Exploration of the regulatory networks of hybrid two-component systems in the model gut symbiont Bacteroides thetaiotaomicron [electronic resource]
Keywords: Microbiology and Immunology.

This dissertation describes the regulatory capabilities of hybrid two-component systems in the model gut bacteria Bacteroides thetaiotaomicron. These unique proteins are important for carbohydrate sensing and consumption in the Bacteroides, but the full extent of their regulatory networks has not been previously explored. We created a chimeric hybrid two-component system that fused the well-characterized sensing domain of one, BT1754, to the uncharacterized regulatory domain of another, BT0366. We then used the BT1754 ligand, fructose, to functionally activate BT0366. Using genome-wide transcriptional profiling, we discovered that BT0366 both upregulates adjacent genes associated with the degradation of the plant polysaccharide arabinan, but also downregulates distal genes involved in mucin consumption. Using Chromatin Immunoprecipitation with high throughput sequencing, we then found that BT0366 binds directly to the genomic loci it helps regulate. Next, we developed tools for live-cell fluorescent microscopy of Bacteroides thetaiotaomicron in order to allow us to describe the physical positioning of hybrid two-component systems and their partnering molecules. This dissertation both describes regulatory activities of hybrid two-component systems in this common gut microbe and also provides tools for further study of subcellular localization in Bacteroides species.
Exploring abstract interfaces in system-on-chip integration [electronic resource]
Keywords: Electrical Engineering.

Modern mobile devices are marvels of computation. They can encode high-definition video, processing and compressing over 350MB/s of image data in real time. They have no trouble driving displays with as much resolution as a full laptop, and smart-phone manufacturers boast of running games with ``console quality'' graphics. Mobile devices pack all of this computational power into a 1-2W hand-held package by integrating a number of specialized hardware accelerators (IP) along with conventional CPU and GPUs in a system-on-chip (SoC). Unfortunately, creating these specialized systems is becoming increasingly expensive. Since hardware accelerators come from a number of different sources and design cycles, different accelerator blocks will often contain incompatible hardware interfaces. Therefore, a large portion of SoC design cost comes in the form of designers manually interfacing each accelerator into a system. This work includes everything from building custom logic to wire up a block, to developing the drivers and API needed to take advantage of the hardware. My research focuses on generating these interfaces, including the physical hardware used to tie IP blocks into a system and the associated software collateral. Leveraging recent trends such as High Level Synthesis and other hardware ``generator'' methodologies, I propose an IP interface abstraction and parameterization designed to describe the interface of most current IP blocks. By encoding this knowledge at a higher-level of abstraction, I am able to construct and demonstrate a hardware generator that maps an interface protocol description into synthesizable register transfer language (RTL), and that can automatically create hardware bridges between different interconnect standards. To ease the integration of the next generation of IP blocks---blocks that are automatically generated based off of user specification---I propose a set of interface primitives. When integrated into an IP generator, these primitives can automatically generate an interface that my interface system can tie to the rest of the system. I also demonstrate how the information stored in these types of primitives can be used to automatically generate a low-level software driver that manages access to the IP blocks. Finally, I show how the simulation environment provided with an IP generator can be used to provide a domain appropriate application programming interface (API) to drive the software. Using an image signal processor generator as my platform, I demonstrate the construction of a map between the simulation software and hardware driver that enables a full one-button flow from algorithm development to applications running on specialized hardware within a working system.
Exploring the complexity of pathway-level evolution [electronic resource]
Keywords: Biology.

This thesis explores how genes evolve together as integrated systems. In Chapter 1, I present conceptual background on the field of complexity and its relevance to this topic. Chapter 2 discusses theoretical work analyzing expected levels of divergence and polymorphism in the simple case of a linear metabolic pathway. Chapters 3 through 5 are gene-specific evolutionary studies in which I analyze the glycolytic enzymes phosphofructokinase, aldolase, and enolase in molecular functional terms. These gene-specific studies will contribute to a forthcoming empirical analysis of glycolysis at the pathway level.
Extensions of Bayesian sequential partitioning for multivariate density estimation [electronic resource]
Keywords: Electrical Engineering.

Density estimation is a fundamental problem in statistic, which can be used as a building block in statistical methods such as classification. Traditional approaches, such as the kernel method, have yielded accurate results when dealing with a moderate amount of data in a low dimensional space, but may perform poorly in higher dimension. Bayesian sequential partitioning (BSP) was proposed to overcome the drawback of traditional methods by applying scalable algorithms to estimate the probability density in higher dimension. The resulting estimate is a piecewise constant function supported on a partition that is learned from the data. In this work, two extensions/enhancements of BSP are proposed to broaden the area of its application. First, a smoothed version of the estimate is obtained by optimizing over a tensor-spline expansion of the log-density condition on the partition learned by BSP. Second, we develop a version of BSP that uses oriented cuts to produce non-rectangular partitions. By allowing more options to build the partition, our estimate is made invariant to the direction of data point distribution. Our numerical experiments show that the resulting estimate can achieve better approximation to the true density compared to standard BSP.
Fabrication of synthetic nanoparticles for cell manipulation, water purification and plasmonic applications [electronic resource]
Keywords: Materials Science and Engineering.

A major challenge in nanoparticle synthesis is to achieve monodispersity, excellent shape and composition control and high throughput simultaneously. Here, a new template-based method to fabricate monodisperse, multi-layered, anisotropic nanoparticles is established, which involves nanoimprinting lithography. These particles are so-called synthetic nanoparticles. Particles with different shapes are fabricated using this method at wafer-scale and are explored for different applications. In this dessertation, four different topics are covered. First, high-moment synthetic antiferromagnetic (SAF) nanoparticles are used for cell manipulations. They are covalently bound with streptavidin and therefore ready for specific binding to H1650 lung cancer cells, which are conjugated with biotin. Once coated with particles, these cells can be easily manipulated under external magnetic field and be 'identified' and 'picked-up' using a magnetic sifter when spiked into blood sample. Second, a point-of-use water purification device is proposed based on novel magnetically ultraresponsive nanoscavengers. The nanoscavengers are disk-shaped, with SAF core layers and functional capping layers. Specifically, Ag-capped SAF nanoscavengers are fabricated for water disinfection. These nanoscavengers are very efficient in disinfecting bacteria and can be collected with a permanent magnet within 5 min. A collision based model is established to explain the high disinfection efficiency using Monte-Carlo simulation. The cyclic performance of these nanoscavengers is also demonstrated with a high disinfection efficiency up to 9 cycles. Third, high-density Ag/Au dimer arrays are patterned on a whole wafer using a novel shadow evaporation method. By controlling the deposition angle, dimers with sub-10-nm gaps with universal orientation throughout the wafer are achieved. The plasmon modes of Au-Au and Au-Ag dimers are studied, where dimers are fabricated on 50-nm-thin Si3N4 films for Electron Energy-Loss Spectrum (EELS) measurements. Several resonance peaks are identified for the different dimer structures. Fourth, an orthogonal double exposure method, incorporating both normal photo-lithography and edge photo-lithography, is developed to fabricate templates of nanorod arrays. These templates are then used for making monodisperse nanorods with different aspect ratios. Specifically, novel synthetic magnetic multilayered nanorods are fabricated and the magnetic properties of these novel nanorods are characterized, with anisotropic hysteresis loops when the external magnetic field is applied along different directions. A model is established to explain that both shape anisotropy and interlayer interaction play a role in the magnetic response of these nanorods. The theoretically calculated saturation fields in the transverse direction match well with the experimentally measured values for all different geometries of nanorods.
False discovery rate control for spatial data [electronic resource]
Keywords: Statistics.

In many modern applications the aim of the statistical analysis is to identify `interesting' or `differentially behaved' regions from noisy spatial measurements. From a statistical standpoint the task is both to identify a collection of regions which are likely to be non-null, and to associate to this collection a measure of uncertainty. Viewing this task as a large scale multiple testing problem, we present methods for controlling the clusterwise false discovery rate, defined as the expected fraction of reported regions that are in truth null. Our methods extend the recent work of Siegmund, Zhang, and Yakir (2011), and can be applied whenever the high level excursions of the noise process are well approximated by a (potentially inhomogeneous) Poisson process. Borrowing ideas from the Poisson clumping heuristic literature, we show that the widely used pointwise procedure generally fails to control the clusterwise FDR. We also present a general framework for incorporating various measures of cluster significance into the clusterwise false discovery control procedure. We show that incorporating cluster size can result in a significant increase in power.
Far From Black and White: The role of Race on Mother’s views of Emotional Intelligence Development in Children
Keywords: emotional intelligence
culture
race
children
Thesis

This study aims to discover whether parental views of appropriate emotional expression and management development in children are affected by subculture within the US. Currently, many public and private educational institutions are devoting resources towards creating and implementing emotional intelligence curricula. Since the norms for emotional expression vary among cultures, it important to identify possible inconsistencies between curricula used at school and parental teachings in children’s homes. An understanding of whether racial or cultural backgrounds are a pertinent factor could be used to ensure compatibility between school and home. Data were collected through in-depth structured in person interviews with eighteen parents of children from two distinct self-identified cultural groups, Black parents of Black children age five to twelve and White parents of White children age five to twelve. Commonalities and differences were found between the two groups. Both groups of parents believed that children must learn to control their emotions just as they must learn to control their behavior, valued the emotional comfortableness of their children and viewed the ability to identify emotions in his or her self and in others as essential for their children to develop. It was also found that parents of Black children preferred their children to manage and express emotions in a more limited manner. This was in contrast to the views of parents of White children. Therefore, this study found a correlation between culture and parental views of appropriate emotional expression and management development in children.
Far-from-equilibrium phenomena in protein dynamics [electronic resource]
Keywords: Chemistry.

The diverse physical principles that govern living things conform to one common precept: all biological processes operate, to some extent, out-of equilibrium. As our understanding of biological pathways advances at the nanoscale, theoretical and simulation techniques that function under non-equilibrium conditions will play an important role in elucidating the working environment of the cell. In this research, large-scale molecular dynamics simulations, discrete dynamical network models, and sophisticated non-equilibrium theories are synthesized to study glassy and dissipative processes facilitated by protein molecules. Leveraging atomistic molecular dynamics data derived from the Folding@home distributed computing project, a number of detailed biophysical systems are examined. I first describe glassy solvent structures that emerge as functional components of a protein chaperone, and I connect such observations to the theory of disordered systems. By coupling Folding@home data, Markov state models of biomolecular dynamics, and the theory of large deviations, I go on to characterize [beta] sheet-rich, amyloid-like misfolded states that appear on protein folding landscapes; I explore the relationship between these misfolded states and so-called dynamical glass transitions. Applying theory related to the Crooks fluctuation theorem, I next explicate the dissipative dynamics in detailed models of signaling proteins, and I illustrate how the input of external energy harmonizes with equilibrium fluctuations to yield functional signaling components. Lastly, I discuss methods by which protein landscapes can be sampled in an adaptive fashion and means for recovering equilibrium kinetics from biased, non-equilibrium simulation data.
Fault reactivation potential and stress path due to severe depletion and subsequent injection in Paleogene (Lower Tertiary) reservoirs of the Gulf of Mexico [electronic resource]
Keywords: Geophysics.

This thesis applies the principles of geomechanics to model and better understand the implications of production in a new and prolific oil province in ultra-deepwater Gulf of Mexico. The larger problem at hand is to characterize the geomechanics of the Paleogene in order to understand how the change in stress can affect wellbore stability, production-related fault slip, injection-related fault slip, and reservoir deformation leading to rock failure. We determine depletion and subsequent injection reservoir stress paths, the potential for fault reactivation, and depletion-related compaction in order to aid in future reservoir management and planning.
A flow reactor study of pyrolysis and oxidation characteristics of N-dodecane [electronic resource]
Keywords: Mechanical Engineering.

The design of the next generation of energy efficient and fuel flexible air breathing propulsion systems requires the development of increasingly sophisticated turbulent combustion models that incorporate reduced but realistic finite-rate chemical kinetic mechanisms for fuel oxidation and pyrolysis. N-dodecane (n-C12H26) is a straight chain alkane that is often recommended as an important constituent of the 3-5 component surrogate blends that are used for modeling the combustion characteristics of aviation fuels like JP-8 or Jet-A. Therefore, an experimental investigation of n-dodecane oxidation and pyrolysis kinetics under engine relevant conditions is necessary for the development and validation of chemical mechanisms that seek to predict the combustion characteristics of jet fuels. In the current work, the Stanford Variable Pressure Flow Reactor (VPFR) facility was used to investigate n-dodecane pyrolysis and oxidation at the less studied intermediate temperature regime (950K - 1250 K) in a vitiated environment and at 1 atmosphere pressure. The initial stages of fuel decomposition were investigated in a 1000 K pyrolysis run and a 1050 K rich oxidation run, while the final oxidation and heat generation stages were investigated in 1170 K lean oxidation and 1220 K rich oxidation runs. The species time history data for n-dodecane and oxygen, as well as for 12 intermediate product species including C2H4, CH4, H2, C3H6, C2H2, CO, CO2, CH2O and several of the higher 1-alkenes, were measured using online Gas Chromatography over a 1-40 ms residence time. The experimental data were used to validate an optimized version of the detailed JetSurf 1.0 mechanism as well as to compare against several other detailed models that are used in the combustion community. The optimized JetSurf model performed relatively well against the flow reactor measurements, though the selected detailed mechanisms were observed to diverge significantly from each other in their species time history predictions. The cause of these divergences was identified to be uncertainties in several of the C1- C3 reaction rates and thermochemistry values that are responsible for radical build up and for ethylene generation and oxidation kinetics. The experimental results also pointed to a temporal scale separation between the initial stages of fuel breakdown that occur through essentially pyrolytic reactions into a mix of 1-alkenes, and the later stages where the alkenes undergo oxidation to form CO and CO2. A new methodology of kinetic mechanism reduction was proposed that lumped the pyrolysis stages into a small set of one-step reactions that directly convert the fuel into the final cracked products. An initial proof of concept validation of the new lumping scheme was done by comparing the predictions from a lumped version of the JetSurf mechanism with the flow reactor measurements. The results were found to be promising enough to warrant the further development of the lumping methodology in future investigations.