VictorJuiz/thesis huggingface dataset:
Towards a Systems Understanding in Biology: Data and Modeling

Breast cancer signaling pathways and neural systems are composed of networks of mutually dependent and thus interconnected genes or neurons. Systems biology is an emerging interdisciplinary field of study that focuses on understanding these complex interactions using a systematic approach. The main goal is transforming biology into a fully quantitative, theory-rich science to understand complex behavior and produce effective predictions. However, since often only incomplete abstracted hypotheses exist to explain observed complex behavior and functions, new techniques for identifying breast cancer signaling pathways and neural systems need to be able to incorporate different types of experimental data and varying levels of prior knowledge./nThis dissertation describes several efforts aimed towards an understanding of these systems by developing system identification tools and computational analysis techniques to facilitate these studies. In systems biology, models may focus on different features, different aspects and different objectives, so there can exist several model classes./nThe first class of tools that we present includes the hybrid Boolean framework and optimization-based inference, and is developed in conjunction with existing mathematical tools. For example, the former is a combination of ordinary differential equations (ODEs) and Boolean networks (BNs), and the latter is that of graph models and linear time-varying systems. These tools take advantage of existing mathematical models and compensate for their limitations or disadvantages. The second class of tools that we present includes data-driven graph reconstruction using compressive sensing, discrete mode identification via sparse subspace clustering, and low-rank representation of neural activity. These adopt a data-driven approach using little prior knowledge which has its origin in the computer vision literature. Case studies of Human Epidermal growth factor Receptor 2 overexpressed breast cancer and neural systems for a Brain Machine Interface are given./nSince the challenge in systems biology has become to show that the identified networks and corresponding mathematical models are enough to represent the underlying system, these tools are developed both for identifying models and also suggesting experimental directions to better understand the systems. The ultimate goal of the work presented is to create a framework to broaden the spectrum of different modeling approaches since each model can be described through a different perspective and may highlight different aspects of the system.

Advisor: Tomlin, Claire
Inertial and Aerodynamic Tail Steering of a Meso-scale Legged Robot

Legged robots have excellent potential for all-terrain mobility, and are capable of many behaviors wheeled and tracked robots are unable to perform. However, legged robots have difficulty turning rapidly, or turning while running forward. For maximum maneuverability, terrestrial robots need to be able to turn precisely, quickly, and with a small radius. Previous efforts at turning in legged robots primarily have used leg force or velocity modulation. This work presents two novel methods of legged robot turning./nThe first of these methods is inertial tail turning, or using a rapidly actuated, weighted tail to cause a sudden change in angular momentum, turning the body of the robot. The tailed robot presented here is able to make rapid, precise turns. By rapidly rotating the tail as the robot runs forward, the robot was able to make sudden 90 degree turns at 360 degrees per second, making it the fastest turning legged robot known to the author at the time of this publication. Unlike other turning methods, this turn is performed with almost no change in forward running speed. The dynamics of this maneuver have also been modeled, to examine how features, such as tail length and mass, affect the robot's turning ability. This approach has produced turns with a radius of 0.4 body lengths at 3.2 body lengths per second running speed. Using a nonlinear feedback controller, turns with an accuracy of 5 degrees for a 60 degree turn have been achieved./nThe second method of turning presented here allows a legged robot to turn continuously while running at high speeds. This remains a difficult task for legged robots, but is crucial for maneuvering quickly in a real-world environment. SailRoACH is the first running robot that uses aerodynamic forces to turn. A flat plate serves as an aerodynamic surface, and depending on its position, can be used to impart positive or negative aerodynamic yaw torques on the robot as it runs forward, causing turns of up to 70 degrees per second at a radius of 1.2 meters and a running speed of 1.8 meters per second. A scale analysis of aerodynamic steering is also presented, showing this method is most effective for small robots. Comparisons to other steering methods are made, showing that inertial and aerodynamic steering are superior for high speed turns at high forward velocity, compared to existing methods.

Advisor: Fearing, Ronald S
O'Reilly, Oliver M
Color, Bodily Capital, and Ethnoracial Division in the U.S. and Brazil

This dissertation is the first comparative, mixed-methods study of the social and economic significance of skin tone and hair type as markers of ethnoracial division among African Americans in the U.S. and the Brazilian population as a whole. Using an extended concept of "bodily capital" to capture salient and consequential phenotypical properties, it combines a quantitative analysis of several nationally representative data sets in the U.S. and Brazil with 100 in-depth interviews (50 in each country) (Part III, forthcoming) to show that (1) skin tone is as powerful a basis of intraracial classification and stratification among African Americans as it is within the Brazilian population at large; (2) skin tone and hair type are both powerful markers of social experience and widely perceived to determine differential treatment in intimate, commercial and public spheres alike. These findings are mined to contribute to current debates on the foundations and lived reality of ethnoracial inequality in the two Americas, colorism in global perspective, and theories of group formation.

Advisor: Wacquant, Loïc
Early Care and Education Classrooms as Ecological Systems: Predictors and Implications of Classroom Quality Profiles

Early care and education quality is a complex, multi-faceted construct consisting of multiple dimensions, such as: 1) emotional climate, 2) instructional supports, 3) learning formats, 4) assessment practices, and 5) support for families (e.g., Bulotsky-Shearer, Wen, Faria, Hahs-Vaughn, & Korfmacher, 2012; Copple & Bredekamp, 2009; LoCasale-Crouch, et al., 2007). Each of these dimensions represents separate but interrelated aspects of classroom quality that exist as part of an ecological system. Individual teachers may vary widely in the levels of support they provide across domains (Curby, Rimm-Kaufman, & Ponitz, 2009). The present study used profile analysis to identify distinct patterns of quality across multiple dimensions in a national sample of early care and education settings (N = 283 classrooms). Five distinct profiles emerged, which were differentially related to teacher/program background characteristics such as teacher education, beliefs, self-efficacy, salary, and program type. Profile membership was also predictive of child outcomes (N = 2,604) at the end of the preschool and kindergarten year. For academic outcomes, the most optimal gains were seen in the profile with high levels of quality overall, particularly in the area of instructional supports. For social-emotional outcomes, this profile was statistically similar to other profiles with above average levels of quality in emotional climate and support for families. These findings are discussed within the context of implications for policy and practice.

Advisor: Cunningham, Anne E
Controlling the Nanostructure of Solution-Processed Thin-Film Organic Electronics

Organic semiconductors hold the promise of electronic devices whose manufacturing scalability and form factor versatility could disrupt the existing electronics market. From a commercial feasibility standpoint, however, the technology is still in its relative infancy. To date, significant research effort has been directed toward developing polymers and small molecules for use in solution-processed thin-film bulk heterojunction organic photovoltaics (BHJ OPVs) and field-effect transistors (OFETs). A key goal of this research is to better understand the structure-property relationships that govern material performance. Molecular structure has been shown to influence material properties such as light absorption, intermolecular electronic compatibility, charge transport characteristics, thin-film morphology, and molecular packing. Similarly, processing steps such as the use of certain electronic interlayers or the incorporation of solvent additives can have a dramatic improvement on device performance./nIn this work, polymer and small molecule systems are used to investigate such structure-property relationships, particularly ones governing solid-state nanostructure. Seemingly small changes in structure are shown to have a significant and systematic impact on OPV and OFET device performance. We investigate how a solution-processed organic semiconductor's π-conjugated backbone, end-capping groups, and solubilizing aliphatic side-chains can have a profound impact on nanostructure and device performance. In addition, we study how the processing conditions of polymers used in OPV and OFET devices affect solution-phase thermodynamics, as well as the dynamics of spin-coating and film formation. In both polymer and small molecule systems, we have demonstrated forward-looking design and processing principles that can inform the development of the next generation of ever higher-performing OPV and OFET materials.

Advisor: Frechet, Jean M
A Computational Light Field Display for Correcting Visual Aberrations

Vision problems such as near-sightedness, far-sightedness, as well as others, are due to optical aberrations in the human eye. These conditions are prevalent, and the population is growing rapidly. Correcting optical aberrations is traditionally done optically using eyeglasses, contact lenses, or refractive surgeries; these are sometime not convenient or not always available to everyone. Furthermore, higher order aberrations are not correctable with eyeglasses./nIn this work, we introduce a new computation based aberration-correcting light field display: by incorporating the persons own optical aberration into the computation, we alter the content shown on the display, such that he or she will be able to see it in sharp focus without wearing eyewear. We analyze the image formation models; through the retinal light field projection, we find it is possible to compensate for the optical blurring on the target image by prefiltering with the inverse blur./nUsing off-the-shelf components, we built a light field display prototype that supports our desired inverse light field prefiltering. The results show a significant contrast improvement and resolution/nenhancement over prior approaches. Finally, we also demonstrate the capability to correct for higher order aberrations.

Advisor: Barsky, Brian A
Probing large-scale structure with intrinsic alignments and galaxy clustering

The study of large-scale structure aims to describe the distribution of matter in the universe. This thesis examines two important topics in this field: intrinsic alignments and anisotropic galaxy clustering. Intrinsic alignments of galaxies are correlations between galaxy shapes and the surrounding density field and are a significant systematic uncertainty in weak gravitational lensing measurements. We examine intrinsic alignments from both theoretical and observational perspectives. First, the most commonly used model for intrinsic alignments, the tidal (linear) alignment model, is tested and developed in the context of recent measurements. The model is found to provide a reasonably accurate description of observations on large scales, particularly for luminous red galaxies. We raise unresolved issues with the model and explore several ways in which it could be improved and expanded. Second, we develop a technique to separate intrinsic alignments from galaxy-galaxy lensing measurements. This technique allows the removal of contamination from the desired lensing signal while also providing a probe of intrinsic alignments in different galaxy populations. Using data from the Sloan Digital Sky Survey (SDSS), we use this method to place the tightest current constraints on intrinsic alignment strength for the SDSS lensing sample, finding that it is a subdominant source of uncertainty at the current level of statistical precision./nThe measured galaxy clustering signal in redshift surveys is anisotropic due to both geometric and dynamic distortions. We discuss the nature of these distortions and examine their information content in the context of future redshift surveys. We employ a model for the galaxy power spectrum in redshift space, based on an expansion in velocity moments of the phase-space distribution function of matter. This model includes nonlinear treatment of matter clustering, galaxy bias, shot noise, and redshift-space distortions. Comparing with numerical simulations, we find that this model is able to describe halo clustering with sufficient accuracy to allow the inclusion of broadband information on small scales, thus significantly improving constraints on both geometry and growth of structure in the universe.

Advisor: Seljak, Uros
Towards engineering nanobioreactors: characterization of bacterial microcompartment stability, regulation, and protein encapsulation

Compartmentalization of biological processes is an optimization strategy found throughout the biological world. On the cellular level, organelles act as compartments that allow for spatial and temporal control of biochemical reactions, as well as provide controlled microenvironments for these reactions. Bacteria generally lack the traditional membrane-enclosed organelles associated with eukaryotes. However, recent studies found that many bacterial species utilize microcompartments (MCPs) to carry out metabolic processes./nBacterial MCPs have been suggested as scaffolds for nanobioreactors, in which biochemical pathways are targeted to the lumen of MCPs. The advantages of such an encapsulated pathway are many, including enhanced kinetics, sequestration of toxic intermediates, and insulation of internalized pathways from side reactions. MCPs may also prove to be an attractive protein cage for drug delivery. However, several challenges remain to be overcome to successfully repurpose naturally occurring MCPs into biotechnological tools./nHere, we first demonstrate that the propanediol utilization (Pdu) MCP of Salmonella enterica has the structural stability required for use as a nanobioreactor or in drug delivery applications. Transmission electron microscopy shows that the Pdu MCP is remarkably stable over time and is able to retain its structural integrity for several weeks at 4°C. The Pdu MCP is also able to maintain its structural integrity at temperatures up to 60°C, although aggregation of MCPs is observed above 50°C. On the other hand, the Pdu MCP is sensitive to pH and high salt, and denatures outside the range of pH 6 to pH 10, and in 1 M NaCl and 1 M urea./nWe then investigate regulation of Pdu MCP formation. We find that PocR is a transcriptional activator of the pdu operon, and heterologous expression of PocR results in MCP formation in the absence of the natural inducer 1,2-propanediol. Next, we report the first instance of heterologous expression of the Pdu shell proteins in Escherichia coli in which MCPs form without morphological aberrations when compared to MCPs from the native host S. enterica./nFinally, we investigate the rules that govern the encapsulation of proteins within the Pdu MCP--a critical component for many of the proposed applications. Due to the time consuming process of MCP purification and subsequent western blot for detecting protein encapsulation using current methods, we first develop a rapid flow cytometry assay for quantifying the relative amount of protein encapsulated within MCPs based on fluorescence. Using this assay, we then characterize various MCP-targeting signal sequence mutants for their ability to encapsulate proteins and identify mutants that encapsulate a greater amount of protein than the wild type signal sequence. We demonstrate that this assay is a powerful tool for reporting protein encapsulation./nThe studies presented here show that the Pdu MCP is a promising scaffold for nanobioreactors and drug delivery systems.

Advisor: Tullman-Ercek, Danielle
Smooth Interface Reconstruction from Volume Fraction Data Using Variational Techniques and Level Set Methods

The volume fraction data structure describes the location of a given material within space. It partitions a domain into a set of discrete cells, and for each cell stores the ratio of material contained within it to the total volume of the cell. The task of transforming a grid of volume fractions into a surface representation of the boundary is called the Material Interface Reconstruction Problem. We investigate a variational formulation to this problem, implemented via a level set method, that produces a surface representation of the boundary. We start with an initial guess and iteratively refine the surface by computing a surface-area minimizing curvature flow, followed by an approximate L2 projection of that flow onto a volume-preserving space. We find that the method yields satisfactory results for both two-phase and multiphase data. In the cases where there are C0 but not C1 boundaries between only two materials, the exact solution produces oscillations with period equal to the volume fraction grid size, and amplitude exponentially decreasing away from the location of the loss of smoothness. To reduce oscillations, an alternative method is proposed where in place of the volume fraction constraint, we minimize a weighted sum of the total surface area, plus the sum of squared error in reconstruction. We discuss the results and compare with the projection algorithm.

Advisor: Sethian, James A
Probing Mechanical Flexibility and Discrete Stepping of an Ultra-Fast Ring ATPase

DNA translocation is a fundamental process in biology, required for essential cellular processes including recombination, replication, and chromosome segregation. The SpoIIIE motor is a homo-hexameric dsDNA translocase, part of the ASCE [Additional Strand Conserved E (glutamate)] superfamily of oligomeric ring NTPases. SpoIIIE is found in the bacterium Bacillus subtilis, its biological role is to actively translocate DNA to ensure the proper segregation of sister chromatids. SpoIIIE accomplishes this task by coupling the chemical energy provided by ATP to generate mechanical work, pumping the DNA across a cellular membrane at a rate of 4 kbp/s. While generating mechanical work is a common function of ring NTPases, the timing and order of individual power strokes applies this work in a nuanced manner to better suit particular biological tasks. Understanding the mechanical aspects of fast DNA translocation provides a unique insight into the diverse mechanical strategies employed by these large class of ring NTPases./nUsing single-molecule optical trapping techniques, I present real-time measurements of SpoIIIE DNA translocation. By challenging the motor with different lengths of modified DNA substrates, I have determined that SpoIIIE makes critical phosphate contacts with the DNA backbone during translocation and characterized the periodicity of motor-DNA interactions, suggesting a fundamental step size of 2 bp. Furthermore, velocity dependence on an applied external load and various concentrations of ATP, ADP and Pi have demonstrated that translocation is coupled to phosphate release. Finally, ATP analogue experiments are presenting an emerging model of a unique, partially coordinated mechanism of hydrolysis between the individual subunits of SpoIIIE.

Advisor: Bustamante, Carlos J
Mediating Global Filipinos: The Filipino Channel and the Filipino Diaspora

Mediating Global Filipinos: The Filipino Channel and the Filipino Diaspora examines the notion of the "global Filipino" as imagined and constructed vis-à-vis television programs on The Filipino Channel (TFC). This study contends that transnational Philippine media broadly construct the notion of "global Filipinos" as diverse, productive, multicultural citizens, which in effect establishes a unified overseas Filipino citizenry for Philippine economic welfare and global cultural capital. Despite the network's attempts at representing difference and inclusion, what the notion of "global Filipinos" does not address are the structural and social inequities that affect the everyday lives Filipino diasporans and the ways in which immigrants and second generation Filipino Americans alike carefully negotiate family ties and the politics of their changing identities and commitments. Taking into account TFC's impact on audiences, interviews with first- and second-generation Filipino Americans in San Diego revealed that while they were aware of the global span of Filipino communities, even touting Filipino success, diligence, and adaptability that is often featured in ethnic television media, Filipino American immigrants continued to identify with their regional affiliations even as they gravitated to Philippine-based television media. Furthermore, although there are efforts to expand U.S.-based production to address local issues and broaden its reach across different segments of Filipino American audiences, second generation Filipino Americans sought to understand and express their ethnic identities outside of Philippine-based mediums.

Advisor: Choy, Catherine Ceniza
The embedded contact homology of toric contact manifolds

Embedded contact homology (ECH) is an invariant of a contact three-manifold. In Part I of this thesis, we provide a combinatorial description of the ECH chain complex of certain ``toric'' contact manifolds. This is an extension of the combinatorial description appearing in Hutchings-Sullivan. ECH capacities are invariants of a symplectic four-manifold with boundary, which give obstructions to symplectically embedding one symplectic four-manifold with boundary into another. In Part II of this thesis, we compute the ECH capacities of a large family of symplectic four-manifolds with boundary, called ``concave toric domains''. Examples include the (nondisjoint) union of two ellipsoids in $\R^4$. We use these calculations to find sharp obstructions to certain symplectic embeddings involving concave toric domains. This is a joint work with D. Cristofaro-Gardiner, D. Frenkel, M. Hutchings and V. G. B. Ramos.

Advisor: Hutchings, Michael