VictorJuiz/thesis huggingface dataset:
Camera design optimization using image systems simulation [electronic resource]
Keywords: Electrical Engineering.

In this thesis I use physically accurate, end-to-end camera simulation environment to explore different imaging system architectures and to co-optimize the acquisition hardware with computational imaging and computer vision algorithms. The simulation tools use 3D modeling to create different scene models. Scene images that are projected onto the sensor are computed with ray tracing tools. Finally, realistic sensor and camera pipeline simulators compute pixel values that can be used by subsequent computational photography or vision algorithms. I use the simulation tools to optimize the spectral characteristics of cameras and lights used to collect data for inverse estimation methods that characterize surface spectral properties. I show that appropriately selected narrowband lights improve the performance of pixel based surface classification. I also propose a new algorithm that extends beyond narrowband light selection by computing the spectral power distribution of light that is optimal for such classification tasks. I further use simulations to guide and optimize the design of a system that characterizes fluorescent materials which interact with incident light in more complex ways than simple reflection. Spectral illuminant optimization is also useful in consumer photography. I describe a spectrally tunable flash and computational algorithms that can be used to efficiently estimate the ambient illuminant spectrum and to improve the color reproduction of captured images. Such flash is particularly useful when capturing images under extreme ambient lights, for example in underwater photography. The end-to-end nature of the simulation tools makes it possible to explore how viewing conditions (e.g. light level, spectral content, depth), hardware components of an imaging system (e.g. optics, sensor QE, filters, pixel and noise properties) and image processing pipelines affect both the perceived image quality of camera images and the ability of machine learning algorithms to detect and classify objects. I use simulation to render large collections of images in order to evaluate the object detection performance of convolutional neural networks (CNNs) . I demonstrate that the performance of CNNs trained using images that are generated by simplified image processing pipelines (ISP) is similar to the performance of CNNs trained using images generated by more complex and time-consuming ISPs optimized for consumer photography. I also explore and quantify the robustness and performance bounds of detection methods against fundamental algorithms controlling camera exposure and focus.
Capoeira and Community in Grupo Besouro
Keywords: Capoeira
Culturally Sustaining Pedagogies
Brazil
Rio de Janeiro
CSRE
Comparative Studies for Race and Ethnicity
Stanford University
IDA
Institute for Diversity in the Arts
Thesis

Capoeira is seen as a martial art, a dance, a game, and a music. Shaped by slavery and official repression throughout the 19th and early 20th century in Brazil, it is uniquely Brazilian, but at the same time, many capoeiristas acknowledge its afro-centricity. Often called a jogo, or game, two players use kicks, evasive maneuvers, leg sweeps, counterattacks and balances on their hands and head to resist the other’s advances while an instrument ensemble plays capoeira music and sings around them. Through my thesis, I argue that Capoeira Besouro, a capoeira school in Rio de Janeiro, Brazil, functions as a For Us, By Us community center that strengthens the surrounding community and creates community leaders. Furthermore, the capoeira school serves as an grassroots alternative educational space that passes on a black-centric narrative, passing on Afro-Brazilian musical, cultural, and artistic traditions. For my Senior Thesis in CSRE, I will be using the framework of Django Paris and H. Samy Alim’s theory of Culturally Sustaining Pedagogies to explore and offer insights into the community practices of Grupo de Capoeira Besouro.
Carlo: Harnessing the Power of Teacher Feedback Through Improving the Writing Cycle
Keywords: Graduate School of Education
Learning Design &amp; Technology
Julia Rubin
formative assessment
feedback
writing development
literacy
learning sciences
Thesis

Students often struggle to implement teacher feedback on their writing, and teachers report that they provide the same feedback time and again. In order to successfully teach the craft of writing, teachers must both provide meaningful feedback to their students and assist them in implementing the feedback they’ve provided. Carlo is an online feedback tool that collects teacher annotations on student writing and generates powerful data visualizations about an individual’s or a class’s areas of strength and growth over time. With Carlo, teachers are able to guide their students in implementing feedback and students are provided the necessary tools to improve their craft and build positive self-identification as writers.
Catalytic enantioselective dihalogenation of allylic alcohols [electronic resource]
Keywords: Chemistry.

Enantioselective dihalogenation is an important method for the total synthesis of stereocomplex polyhalogenated natural products, but only a few methods with significant limitations currently exist for this transformation. In 2015, we developed the chemo-, regio- and enantioselective bromochlorination of allylic alcohols featuring a titanium half-salen catalyst to help address this problem. The utility of this method has been demonstrated by the enantioselective total syntheses of 11 halogenated natural products to date by our lab, each of which was directly enabled by this method. Following development, we applied the enantioselective bromochlorination to various new substrates including homoallylic alcohols, which resulted in the total synthesis of (--)-anverene, a polyhalogenated marine natural product with modest but selective antibiotic activity. Computational and experimental mechanistic work was undertaken to better understand the catalytic enantioselective bromochlorination, as well as the enantiospecific solvolysis of resulting enantioenriched bromochlorides. The enantioselective dihalogenation catalyst system has also been extended to new reactions using other electrophile-nucleophile pairs, including haloazidation, which uses TMSN3 as the nucleophilic azide source.
Channel power and rate optimization of nonlinear optical fiber networks
Keywords: Electrical Engineering.

Channel power and rate optimization objectives are examined in nonlinear long-haul optical communication networks. Problems of maximizing the minimum channel margin and maximizing fiber capacity are found to have convex forms. The Kerr nonlinear inter- and intra-channel nonlinear interference is initially modelled via the Gaussian noise nonlinearity model. Valuable performance benefits are obtained in inhomogeneous scenarios including mesh networks. The inhomogeneity introduced by the additional nonlinear impairment of stimulated Raman scattering makes the optimization objective non-convex, but also provides inherent inhomogeneity that supports performance benefits from power optimization. The discrete-rate optimization objective is formulated for maximizing the real-world capacity of optical communication systems with discrete code rates. Efficient heuristic methods are proposed that make use of a sequence of calls to solve the minimum-margin channel power optimization problem. Lastly, the channel power optimization problem is generalized with a model that applies beyond the dispersion-uncompensated domain of the Gaussian noise model. A first-order perturbation-based approach is used for the nonlinear interference modelling.
Characterization of a Novel p53-Mettl3 Protein-Protein Interaction
Keywords:  Department of Biology
Biology
Cancer Biology
Thesis

The transcription factor p53, which can activate or repress gene expression, is known to be critical for suppressing tumorigenesis in humans and mice. Known as the guardian of the genome, p53 responds to DNA damage by inducing apoptosis, cell cycle arrest and senescence. p53 is a well characterized transcription factor involved in diverse cellular pathways, but its full protein interactome remains undefined. The Attardi lab has performed dual affinity purification and mass spectrometry to identify novel binding partners of mouse p53 and has developed a protein interactome for p53. One of the proteins identified in this interactome is Mettl3, which is a methyltransferase enzyme involved in the modification of RNA. It has been implicated in cellular differentiation, cell self-renewal and DNA-damage responses. We validated the interaction of p53 and Mettl3 by performing co-immunoprecipitation assays. Our data indicate that p53 does indeed co-immunoprecipitate with Mettl3 and corroborate the interaction between them as shown by affinity purification and mass spectrometry studies. We have shown that Mettl3 plays an important role in modulating p53 stability, and that Mettl3 deficiency results in decreased expression of several key p53 target genes in response to DNA damage. The findings in this study validate that Mettl3 interacts with p53 and that this interaction may have important implications in p53 biology.
Characterization of arterial-venous cell fate plasticity during coronary vessel development
Keywords: Biology.

Understanding arterial-venous fate plasticity is important for innovating and improving vascular regenerative therapies. During coronary vessel development in the mouse, coronary arteries originate from a venous vessel. In this study, single-cell RNA-seq was used to investigate the characteristics of the arterial-venous fate switch during coronary vessel development. Results showed that instead of rapidly losing all arterial-venous identity as soon as they exit the vein, nascent coronary cells coexisted in a continuum of gradual venous fate loss and arterial fate gain. A rare subpopulation of surprisingly mature pre-artery cells within this continuum crossed a transcriptional threshold to resemble mature arterial cells. These pre-artery cells were specified at an unexpectedly early developmental stage, and they were necessary for coronary arteriogenesis. Modulations of the cell cycle was found to be an important regulator of arterial-venous plasticity: activation of the cell cycle correlated with the loss of venous identity, while inhibition of cell cycle was necessary for arterial redifferentiation. The transcription factor COUP-TF2 inhibited the development of the pre-artery cells by activating the cell cycle.
Characterization of functional nucleic acid structure in translation, reverse transcription, and electronics applications
Keywords: Chemistry.

Ribonucleic acid (RNA) actively regulates all stages of genetic expression from transcription to translation. Actions performed by RNA molecules are made possible by the ability of RNA to fold into unique tertiary structures. Messenger RNA (mRNA) structure enables alternative translational pathways, such as frameshifting and bypassing, that recode the protein sequence. Transfer RNA (tRNA) structure is highly evolved for interfacing with the ribosome to maximize translational fidelity, but can be repurposed by retroviruses to act as a primer during reverse transcription. Ribosomal RNA (rRNA) is a majority component of the ribosome by mass and catalyzes amide bond formation between amino acids in a peptide chain. This work examines RNA structure in four systems: Escherichia coli rRNA, T4 bacteriophage mRNA, human tRNA, and synthetic conductive nanowires. Mutations in E. coli rRNA structure, as well as the effects of treatment with macrolide antibiotics, were probed by a novel quantitative fluorescent translation assay using the SNAPf reporter protein to evaluate changes in ribosomal processivity. The solution NMR structure of the T4 bacteriophage Gene 60 mRNA 5' stem-loop was solved, and the terminal loop sequence was determined to be important for the mechanism of translational bypassing. Human tRNALys3 in complex with HIV genomic RNA was also studied by solution NMR to reveal a unique structure adopted by the complex during HIV reverse transcription initiation. Finally, the thermal and chemical stability of Ag(I)-intercalated polycytosine nanowire structures was evaluated by enzymatic, spectrophotometric, and biophysical assays. These projects not only reflect the deep importance of RNA structure to all aspects of genetic expression but also highlight some of the applications of nucleic acid structure in bioengineering.
Characterization of greenhouse gas impacts of unconventional oil and natural gas resources : analysis and field study
Keywords: Energy Resources Engineering.

As the need for addressing the impacts of climate change has become more urgent, the primary focus in the scientific and engineering disciplines has been on reducing the combustion of fossil fuels through clean energy technology development. Simultaneously, there has been rapid development of unconventional fossil fuels such as tight oil and oil sands, especially in the United States and Canada. The development of these resources raises considerable obstacles to the challenge of reducing emissions. As nations realize the need for climate action and begin to transition a low-carbon energy sources, there is considerable inertia in the legacy fossil-fuel-reliant energy infrastructure. In the near-to medium-term a climate-conscious approach is needed to reduce emissions from existing infrastructure. Toward this end, this work investigates the greenhouse gas impacts of unconventional fossil fuel production. We first investigate the Alberta oil sands where we examine the historical trends in life-cycle greenhouse gas intensity of production utilizing industrial data. We show that the emissions intensity for oil sands production decreased from being close to two times greater than a modern conventional crude oil to roughly twenty percent greater. From this initial work, we utilized this operator-provided data to develop a life-cycle energy intensity model for the four most common fuel pathways in modern oil sands production. This model is both more comprehensive and more robust than prior work on oil sands emissions intensity, largely due to innovations we make in leveraging government-reported data to estimate emissions. We show that the energy intensity of oil sands production ranges from 0.08 to 0.41 GJ fuel consumed/GJ oil produced, varying by pathway. This work was integrated into the US Federal Greenhouse Gases, Regulated Emissions, and Energy use in Transportation Model (GREET) developed by Argonne National Laboratory. Next, we examine vented and fugitive emissions of hydrocarbon gas from production facilities in the Bakken oil field of North Dakota. These emissions, due to the high global warming potential (GWP) of methane (CH¬4) -- the primary component of produced gas -- are a large source of uncertainty for quantifying the greenhouse gas intensity of these resources. We conducted two studies which utilize Optical Gas Imaging (OGI) to evaluate the persistence of hydrocarbon emissions over time: 1) a helicopter survey which follows up on a previous study and examines the year-to-year trends in emissions-emitting sites, and 2) a ground-based survey where > 100 sites were visited regularly over the course of a year. Both of these studies demonstrate very high rates of persistence of emitting (as well as non-emitting) sites over the course of the study time-frame. These results strongly suggest that emissions are not random or intermittent, but instead due to long-term operational or design problems in the production, gathering, or transportation infrastructure.
Characterization of Premixed Flames Using High Energy X-Ray Absorption
Keywords:  Department of Mechanical Engineering
X-ray computed tomography
XCT
Pourous media burners
PMBs
combustion
Thesis

Experimental and numerical studies have shown that porous media burners (PMBs) can reduce many of the adverse effects of combustion. However, studying the porous microstructure of PMBs and the flames that stabilize within can be a difficult task. Recent advances in X-ray computed tomography (XCT) offer a non-invasive, high resolution technique that enables the investigation of three-dimensional (3D) fields such as temperature and density, which can be used to quantify the complex processes that occur within PMBs. The objective of this thesis work is to calibrate X-ray diagnostics and quantify uncertainties using well-characterized, stable flames, where temperature, gas concentrations, and flow velocities can be predictably controlled. A laboratory burner was designed and operated with a premixed methane/air/krypton flame. Flame characteristics for different setups and a range of equivalence ratios were studied using a tabletop X-ray system in the Stanford Medical School. The results obtained in this study demonstrate the usefulness of XCT in obtaining both quantitative and qualitative information about combustion experiments. Although this study focuses on simple systems that are optically accessible, the diagnostics developed can also be applied to other systems of interest that are optically inaccessible. This work furthers the recent development of XCT as a novel combustion diagnostic tool, capable of yielding non-intrusive 3D datasets in optically inaccessible environments.
A characterization of the neural stem cell niche and lineage at single cell resolution during aging
Keywords: Stem Cell Biology and Regenerative Medicine.

The mammalian brain contains select neurogenic niches composed of neural stem cells (NSCs) and several other cell types, including microglia, and endothelial cells. Neurogenic niches become less functional with increasing age, and this decline could underlie cognitive and sensory deterioration. This functional deterioration could underlie cognitive and sensory restriction with age, although the exact age at which it occurs is still debated in humans. How the neurogenic niche changes with age, and whether new cell types arise in older individuals, is not known. Here we perform single cell RNA-sequencing of the young and old neurogenic niche in mice. We first show that cells in the youthful NSC lineage exist on a continuum through the processes of activation and differentiation. Interestingly, rare intermediate states with distinct molecular profiles can be identified and experimentally validated, and our analysis identifies putative surface markers and key intracellular regulators for these new subpopulations of NSCs. We also utilize the power of single cell profiling to conduct meta-analysis to compare in vivo NSCs and in vitro cultures, distinct fluorescent-activated cell sorting strategies, and different neurogenic niches. We go on to analyze the transcriptomes of 8993 single cells isolated in an unbiased fashion from the youthful and aged neurogenic niche. We identify clear age-dependent changes in the neurogenic niche, with a decrease in activated NSCs, changes in endothelial cells and microglia transcriptomes, and the striking appearance of T cells in old niches. T cells invading the old neurogenic niche exhibit characteristics of cytotoxic effector memory T cells. Surprisingly, T cells from old brains are clonally expanded, and express different T cell receptors than those from old blood, suggesting they experienced specific antigens. Furthermore, unlike their counterparts in old blood, old brain T cells express interferon γ (IFNγ) and immune checkpoint genes. Analysis of the response to IFNγ at the single cell level in the old neurogenic niche shows that several cell types, including NSCs, endothelial cells, and microglia, respond to IFNγ. The response of NSCs to IFNγ is heterogeneous, and the subset of NSCs experiencing a high IFN response shows decreased proliferation in vivo. Furthermore, IFNγ expressed by T cells was sufficient to inhibit NSC proliferation in co-cultures. Our study provides a system-level understanding of the old neurogenic niche and reveals the infiltration of T cells in old neurogenic niches. Our results also provide a possible cause for the decline of NSC during aging and could identify immune- or antigen-based strategies to ameliorate this decline.
Characterization of thermal systems using low level resistance measurements and the development and validation of a high-stability ALD platinum thermal accelerometer
Keywords: Mechanical Engineering.

The thermal properties of the materials used in microelectromechanical systems (MEMS) are of increasing concern as devices progressively miniaturize with improved fabrication technologies. Temperature sensitivity (or insensitivity) is often a major consideration for MEMS sensors, as many components of a sensor's output drift with and depend on temperature. Thus, thermal characterization should be a necessary step for any sensor material. This thesis begins with thermal conductivity measurements for size-limited highly-doped silicon and ALD platinum. Though these results were mainly internal to lab-group needs, the methods used are widely applicable to other studies. As MEMS manufacturing techniques and technologies advance and mature, previously encountered limitations should no longer be assumed. The thermal accelerometer is a device that has found limited use within the MEMS community, thanks to its high power consumption and notably low bandwidth. However, with new fabrication techniques the thermal accelerometer's performance can be pushed in new and exciting ways, potentially expanding its usability for a larger variety of applications. Here we present the results from the first thermal accelerometer fabricated using Plasma Enhanced Atomic Layer Deposition (PEALD). PEALD allows for ultra-thin, low defect, high-density platinum films that deliver excellent stability and accuracy. We offer a 100× cross-section reduction relative to previous thermal accelerometers, thereby increasing the heating efficiency and decreasing thermal time constants. The suspended resistance thermometers and heaters capitalize on the properties provided by PEALD and Pt: pronounced stability, high resistivity, and linear temperature coefficient of resistance (TcR), giving our device tractable and consistent results. For a heater temperature rise of 150 degrees C and acceleration between +/- 1g, this device has a raw sensitivity of 54e-3 C/g, excellent cross-axis isolation, high-linearity, and remarkably low drift.
Characterizing Temperature Variations in the Large Synoptic Survey Telescope Camera
Keywords:  Department of Physics
LSST
Large Synoptic Survey Telecope
Astronomy
Astronomical Instrumentation
CCD
Thesis

We have measured how the temperature varies on a science raft for the Large Synoptic Survey Telescope (LSST) Camera, and have made preparations to repeat this test on the full Camera focal plane. Such tests are important in order to ensure that the LSST Camera behaves as expected in response to temperature changes, and in particular that spurious spatial patterns are not introduced into near-IR observations due to a spatially varying temperature profile. We describe first the construction of a Flat Field Projector that will be used to conduct a wide array of tests on the LSST Camera Focal Plane, including a test of temperature variation. Then we proceed to describe a pilot version of this test, in which a single LSST science raft was illuminated with flat fields at several temperatures and wavelengths. After developing several methods of removing fringe artifacts from these images we calculate the temperature variation, and find that the variation of the spatial pattern of temperature on a single raft is less than 0.25K when the bulk temperature is changed 10K, somewhat better than the specification of 0.5K variation.