VictorJuiz/thesis huggingface dataset:
Shared vehicle control using safe driving envelopes for obstacle avoidance and stability [electronic resource]
Keywords: Mechanical Engineering.

Recent trends in automotive crash statistics suggest a dual role of technology in both saving and threatening the lives of American drivers. Advancements in automotive safety like Anti-Lock Braking Systems and Electronic Stability Control have led to a significant reduction in automotive fatalities over the last decade. However, the ubiquity of technology, mainly the cellular phone, has led to a dramatic increase in fatalities attributed to distracted driving. To address this challenge, auto manufacturers are empowering modern vehicles with even more technology. Advanced sensors provide real-time information about the surrounding environment. By-wire actuators, which allow drivers indirect command of the vehicle through an electronic pathway, enable vehicle safety systems to share control with a driver through augmentation of the driver's commands. This technology combination gives safety systems an unprecedented amount of authority to react to the vehicle's newly perceived world. Leveraging these advancements in vehicle actuation and sensing, this dissertation presents a shared control framework for obstacle avoidance and stability control using safe driving envelopes. One of these envelopes is defined by the vehicle handling limits while the other is defined by spatial limitations imposed by lane boundaries and obstacles. A Model Predictive Control (MPC) scheme determines at each time step if the current driver command allows for a safe vehicle trajectory within these two envelopes, intervening only when such a trajectory does not exist. A sparsity seeking objective in the MPC formulation serves as a simple and effective approach to shared control between a human driver and an automated machine. In this way, the controller seeks to identically match the driver's commands whenever possible while avoiding obstacles and preventing loss of control. Computationally efficient models of the environment, the vehicle, and the handling limits allow for real-time prediction of dangerous scenarios over a 4 (s) horizon. This advanced warning enables the use of brake actuation to ensure safe vehicle trajectories that adhere to both safe envelopes, providing an envelope of protection through augmentation of a driver's steering, braking, and throttle commands. The optimal control problem underlying the controller is inherently non-convex but is solved as a set of convex problems allowing for reliable, real-time implementation that is executed at 100 (Hz). This approach is validated on an experimental vehicle working with human drivers to negotiate obstacles in low friction environments.
Sharing costs to optimize network equilibria [electronic resource]
Keywords: Management Science and Engineering.

Congestion games are a fundamental class of applications in the study of strategic behavior in large systems. In congestion games, selfish individuals act as consumers of resources at local parts of the system. These individuals typically obey their own self-interests and will not necessarily adhere to the prescriptions of a socially optimal solution. Imposing centralized control upon these individuals is infeasible, but the deployment of simple rules at a local level can limit the discrepancy between the individual goals of the system users and the global optimization objectives of the system designer. Such rules can be abstracted as cost sharing methods that distribute the joint cost on a resource among those who generate it. This thesis aims to present a comprehensive study of cost sharing as a means of decentralized control in congestion games and their generalizations.
Simulation of hypersonic flow within electromagnetic fields [electronic resource]
Keywords: Aeronautics and Astronautics.

Space vehicles that enter the atmosphere require the use of a Thermal Protection System (TPS) to protect them from aerodynamic heating. The TPS currently in use is composed of a heat-resistant material to protect the inner part of the vehicle, and it adds tremendously to the cost of a space mission. In contrast, it has been pointed out that such a high enthalpy gas flow, which is partially ionized, could be controlled through an electromagnetic effect, and as a result, the high convective heat could be reduced, and furthermore, the aerodynamic force acting on the vehicle could be controlled. A lot of research has been carried out, not only theoretically but also experimentally, to understand the electromagnetic effect. However, numerical accuracy in predicting these effects, especially for heat flux mitigation, has not been satisfactory. Accurate simulation of such flows requires the solution of the Navier-Stokes equations for compressible viscous flow, and for the equations describing the state of the high temperature gas containing many species in chemical and thermal equilibrium or non-equilibrium. In addition, Maxwell's equations for including the effects of electromagnetic fields upon an ionized hypersonic flow through Lorentz forces and Joule heating need to be solved in order to realize flow control advantages. Inclusion of these three sets of equations in the numerical simulation of hypersonic flow is computationally intensive and stiff to solve. Therefore, many researchers have made a number of simplifications based on certain assumptions to reduce the size of the governing equations. However, these simplifications and assumptions are not valid under certain flight regimes and can lead to inaccurate estimates of heat flux to the vehicle. In this thesis, the full magneto fluid dynamics (MFD) equations, including multi-species, chemical reactions, and Maxwell's equations, have been solved. The approach includes formulation of the full governing equations, the boundary conditions including catalytic, cold wall boundaries, and the numerical procedure for solving the governing equations. The solver is verified and validated with experimental data provided by Ziemer for shock stand-off distance, by Gulhan et al. and Kawamura et al. for heat flux mitigation. The numerical results show an excellent match with previously published experimental data.
Simultaneous dual-beam optical trap and sm-fret probing long-range tertiary interactions in tpp riboswitch [electronic resource]
Keywords: Biophysics.

RNAs are ubiquitous in virtually all biological processes and its function is based on their 3D structures. From sequence to 3D structure, its ability to carry genetic information and function like proteins shows remnants of a RNA world (Breaker, 2012). Riboswitches are evidence of a RNA world as they are cis-regulatory elements formed in mRNA that can modify gene expression in response to environmental cues. A well-known example is the thiamine pyrophosphate (TPP) riboswitch, whose specificity for TPP is dependent upon conformational changes that take place within its ligand-binding aptamer region. Here, the role of tertiary interactions in ligand binding is studied at the single-molecule level by combined force spectroscopy and Fӧrster resonance energy transfer (smFRET), using a dual-beam optical trapping apparatus equipped for simultaneous, spatially coincident smFRET. Detailed calibrations and optimization of the "Force-FRET" technique are performed using several well-characterized DNA hairpins by force spectroscopy. Extending this approach, we directly probe secondary and tertiary structural changes during TPP aptamer folding, including key events associated with ligand binding. The concurrent transitions observed in smFRET signals and RNA length changes revealed differences in helix arm orientation between two previously-identified ligand-binding states that were undetectable by force spectroscopy alone. With our Force-FRET technique, we can resolve the structural details of the weaker binding state when fully bind to TPP, and identify the mechanism behind its inability to form the tertiary interaction that completes the TPP binding process. This powerful single-molecule technique enhances our understanding of how tertiary interactions play a crucial role in stabilizing global riboswitch structure and, ultimately, in increasing ligand specificity. Further investigation of these multidimensional energy landscape for RNA folding require development of techniques, such as Force-FRET, that can probe this landscape with more than one reaction coordinate. This development enables us to ask more complicated questions such as coupling transcription-translation and observing both processivity and conformational changes of these proteins.
Single cell expression analysis of human cellular reprogramming [electronic resource]
Keywords: Genetics.

The ability to reprogram adult human cells into induced pluripotent stem cells (iPSCs) has allowed us to study development like never before. By studying the reprogramming process, we are able to dissect molecular and developmental events that give rise to all cells of the human body. Despite intense interest and research into the molecular mechanisms of reprogramming, we still lack full understand the reprogramming process itself and downstream effects on the resulting cells. What we do know is that there is a significant amount of heterogeneity in the cells that result from reprogramming and in the way that individual, otherwise homogenous, cells respond to reprogramming factors. In order to better understand the reprogramming process, I used an mRNA reprogramming technique to modulate the types and numbers of mRNAs used in an attempt to identify novel reprogramming factors. I generated a large dataset of gene expression data from single iPSCs and parental fibroblasts to uncover some of the expression patterns that define different developmental time points. This dataset includes two cell lines (fetal and adult), four developmental time points (fibroblasts, passage 0, passage 3, and passage 20 iPSCs), as well as two growth conditions (5 or 20% oxygen). Using this dataset, I was able to address critical questions about the effects of reprogramming on female cells. Female cells have a unique biology linked to X chromosome inactivation, which is required to equalize the gene expression between males and females. As this X chromosome-based epigenetic regulation is set up in early development, there has been much interest in the state of the X chromosome during the reprogramming process. Here, I show that passage 0 iPSCs maintain XCI but that these cells lose XIST expression, which is the non-coding RNA that regulated the silencing, by passage 20. These results have significant implications for the clinical translation of stem cell therapies into clinics, especially for women.
Single-molecule whole genome reconstruction and haplotype phasing [electronic resource]
Keywords: Physics.

Recent advances in DNA sequencing technologies improved the scale and cost of reading DNA by multiple orders of magnitude enabling new ways to study evolution, genetic variation and genome-related diseases. This dissertation focuses on developing experimental and computational techniques to address clinically and scientifically relevant applications of high throughput DNA sequencing. Firstly, we started by examining single molecule DNA sequencing by synthesis (SBS) -- a method that allows reading DNA sequence by incorporating fluorescently labeled nucleotides into short strands of DNA attached to a flow cell surface. We demonstrated the feasibility of measuring whole human genome variation and accurate detection of copy number changes. We further applied this technique to study clonal evolution in acute myeloid leukemia and found that the CD34+ 38- leukemia stem cells and CD34- blasts have a genome that is clearly distinct from the normal cells, yet no significant differences are observed between the blast and LSC genomes. However, current technologies are insufficient in resolving complex genome structure to produce consistent genome assembly similar to reference genome assemblies typically obtained from sequencing fosmid or BAC libraries. To address the shortcomings associated with assembling short read sequences from complex genomes, we described a novel experimental method of molecular barcoding that allows accurate sequencing of long contiguous strands of DNA and its applications to assembling repeat-rich genomes for which a reference is not available. We applied this method to assemble the Botryllus schlosseri genome to study the genetics of histocompatibility. We further presented a computational method, the statistically aided long-read haplotyping (SLRH), that extends this technique to measure haplotype information of the human genome to provide a high resolution haplotype map of the NA12878 trio. Since SLRH requires a substantial amount of input material up to 1microgram of HMW DNA which may not be always possible to obtain, we presented another experimental approach to human genome haplotyping based on contiguity preserving transposition with the Tn5 transposase and combinatorial indexing. We demonstrated accurate megabase scale human genome haplotyping using less than 1 nanogram of input DNA material. We introduced a simple, fast and reliable approach for genome-wide, haplotyping based on sequencing of nearly 10,000 "virtual partitions" generated by contiguity preserving transposition and combinatorial indexing. With as little as 40 - 60 Gb of sequencing data ~94 - 96% of SNPs in individual human genomes can be phased. Haplotyping blocks are in the megabase range with long switch error rate on the order of 1 - 2 per 10 Mb assuring accurate phasing across the genome. The method uses readily available equipment, requires minimal hands-on time, and can potentially be integrated with microfluidic, droplet and flow cell platforms.
Solitude in postwar Italian and French cinema [electronic resource]
Keywords: Art and Art History.

This dissertation examines solitude in Italian and French films of the 1950s, '60s, and '70s. Through close analyses of the canonical oeuvres of four preeminent directors -- Roberto Rossellini, Robert Bresson, Jean-Luc Godard, and Michelangelo Antonioni -- I provide a new theory for the development of film aesthetics in Italian and French cinema during the postwar era. I argue that the shift from the apparent cohesion and transparency of realism to the narrative ambiguity and audio-visual fragmentation of modernist film form in their work is principally determined by the representation of solitude.
Solution deposition of semiconductor thin films for photovoltaics [electronic resource]
Keywords: Chemistry.

Thin film photovoltaics are among the most promising clean, renewable energy technologies and have the potential to meet future world energy demand by covering only a small fraction of the earth's surface. To meet this challenge, annual production of photovoltaic modules, despite recent escalation, must still increase several orders of magnitude, and the development of inexpensive and scalable thin film deposition methods is of crucial importance to this effort. The cost and scalability limitations of the standard high-vacuum thin film deposition methods may be overcome by using solution-based methods. Furthermore, the transition from photovoltaic materials containing cadmium, indium, and tellurium to materials comprised of earth-abundant, non-toxic elements is expected to accelerate their large-scale deployment. Here, I present several strategies for the improvement of inorganic thin films synthesized by solution deposition. In this work, two low-cost, solution-based methods (chemical bath deposition and nanocrystal inks) were applied to the deposition of thin films of ZnS, SnS, and Cu2ZnSnS4 (CZTS), all potential earth-abundant non-toxic materials for photovoltaics. First, through the chemical bath deposition of SnS, I show how film quality is a function of deposition kinetics and can be manipulated through control of bath compositions and post-annealing parameters to improve film properties In the same SnS system, using nanocrystal inks, I show that control over nanocrystal morphology can be used as a strategy for improving thin film quality. A selective synthesis was developed for the production of high-aspect ratio sheet-like nanocrystals. Nanocrystal inks formulated from these crystals were capable of producing extremely highly-oriented thin films through the lamellar stacking of SnS sheets, which yielded favorable optical and electronic properties. The second major study in nanocrystal inks examined the efficacy of inorganic ligand exchanges and the resulting effect on film formation. Ammonium polysulfides were demonstrated as a novel species for ligand exchange on cubic ZnS nanocrystals, where they were shown to remove native ligands with high efficacy and improve film quality. Finally, this ligand exchange was applied to CZTS nanocrystal inks with promising implications for the deposition solar absorber layers. The use of these ligands has the potential to improve efficiency and lower costs in the production of CZTS photovoltaics and other chalcogenide thin films.
Spatiotemporal resolution of T-box function in early mesoderm patterning [electronic resource] : an optochemical approach
Keywords: Chemical and Systems Biology.

Zebrafish mesoderm development is largely regulated by a network of T-box transcription factors comprised of the Brachyury ortholog no tail a (ntla), spadetail (spt), and tbx6-like (tbx6l). Conventional genetic mutant analyses have demonstrated the importance of these factors in mesoderm patterning; however, the non-conditionality of these perturbations have limited our understanding of how these genes function in space and time. Exploiting the optical transparency of early zebrafish embryos, our lab has developed photoactivatable caged morpholinos (cMO) that permit light-inducible gene silencing with spatiotemporal precision. The focus of this dissertation is on the application of these optochemical probes to resolve the function of the T-box gene spt in two distinct developmental contexts: 1) paraxial mesoderm patterning and 2) posterior medial floor plate (MFP) formation. In Chapter 1, I provide a brief survey of zebrafish mesoderm development, describe the dynamics of T-box gene expression during gastrulation, and detail the mesodermal phenotypes observed upon loss or gain of function of these factors. In Chapter 2, I apply a cMO targeting spt with photoactivatable lineage tracers, fluorescence-activated cell sorting, and RNA-sequencing to reveal 124 transcripts that are differentially expressed within a population of cells enriched for paraxial mesoderm progenitors upon loss of Spt function. Furthermore, I uncover a novel Spt-dependent regulation of collinear hox gene activation in these cells. In Chapter 3, I combine the spt cMO with a conventional ntla MO to characterize the temporal and spatial requirements of these genes in posterior MFP development. These studies indicate that ntla and spt act specifically within lateral margin derived progenitors during gastrulation to promote posterior morphogenetic movement of MFP progenitors in the midline without affecting Nodal-dependent MFP fate specification. This dissertation highlights the advantages of light-activated technologies to spatiotemporally characterize gene function during early vertebrate development.
Speech, variation, and meaning [electronic resource] : the effects of emotional prosody on word recognition
Keywords: Linguistics.

This dissertation investigates the effect of phonetically cued emotional information (i.e., emotional prosody) on spoken word recognition. Even words whose meanings are not emotionally laden (e.g., pineapple) can be uttered in a way that conveys anger, happiness, or sadness through phonetic modulation, and the current work investigates how this phonetic variation in the speech signal affects the way spoken words are perceived, recognized, and ultimately understood. Based on the results from five cross-modal priming experiments, I claim that social information from speech is available early and influences spoken word recognition, that all linguistic experience is not equal in that two atypical forms prompt different listener behavior, and that a full explanation of spoken language understanding must include an attentional mechanism. I argue for a new approach to spoken word understanding based on a recent proposal made by my colleagues and me (Sumner, Kim, King and McGowan, 2014). This approach is grounded in existing theories of exemplar dynamics, but expands on the notions of socioacoustic encoding and social weighting. The speech signal is simultaneously mapped to social representations (via socioacoustic encoding) and linguistic representations. The socioacoustic encoding activates social features and categories (e.g., information about the speaker's age, gender, and emotional state) from the speech signal early in lexical processing. Once activated, the social features and categories interact with other social or linguistic representations and they modulate the allocation of cognitive resources (i.e., attention) to the linguistic signal, effectively weighting the significance of each linguistic experience differently (social weighting). This dissertation significantly broadens the current understanding of spoken word recognition by demonstrating the crucial influence of phonetically cued emotional information, offering a new approach that embraces the rich informational contribution contained in phonetic variation.