VictorJuiz/thesis huggingface dataset:
Densely integrated interface circuits for structural health monitoring [electronic resource]
Keywords: Electrical Engineering.

The field of aerospace structural health monitoring (SHM) has envisioned embedding piezoelectric sensors inside the airframe to actuate and sense ultrasounds for the detection of defects. This will bring tremendous safety and economic benefits. One technical improvement that will make the whole system embeddable and reliable is integrating the sensor interface electronics in a silicon chip to replace the current bulky solution. This can potentially enable mass deployment of SHM. The key challenge for implementing such an IC lies in the piezo actuation, due to the simultaneous requirements for high drive voltage (several tens of volts), relatively high excitation frequencies (several hundred kilohertz) and low-distortion continuous excitation waveform. This is beyond what existing IC products can achieve. This research investigates a piezo driving scheme in which the required wave-form is generated by a pulse width modulated (PWM) class-D power amplifier (PA) with off-chip filtering. The pulse transition times are pre-computed through a least square optimization problem, and stored digitally to take advantage of the a priori knowledge of the SHM excitation signal. A digital calibration technique is introduced to achieve sub-nanosecond timing accuracy and -40 dB signal dis-tortion spec. To evaluate this concept, a four-channel, ±36 V, 780 kHz piezo driver chip was designed and fabricated in a 0.25 [mu] m BCD process. The IC achieves output signal distortion of -40.5 dB after calibration, improved more than 13 dB from the uncalibrated performance. An SHM system based on Flex-PCB, which combines the IC and the piezos, was designed and built. The IC and the system were demonstrated using an SHM test bed.
Design and characterization of synthetic microRNA based gene expression circuits [electronic resource]
Keywords: Bioengineering.

The complexity of mammalian cells is largely due to the sophisticated control mechanisms employed to modulate the expression of endogenous genes. Various molecules in the cell are organized into circuits, which can respond to both changes in levels of intracellular molecules, as well as changes in the environment, by upregulating or downregulating the expression of any number of genes. The ability to interface with these endogenous programs to create novel molecular circuits would greatly advance our cellular engineering capabilities for a variety of applications. I first present a method to design and characterize synthetic circuits incorporating microRNAs (miRNAs). I derived and experimentally validated a model to capture the relationship between miRNA and target gene expression levels. I then extended the model to a more complex circuit incorporating an miRNA-based molecular switch to predict the impact of ligand levels on miRNA levels, and ultimately target gene expression levels, in the cell. Finally, I demonstrate the utility of this framework by using the model to inform the development of a synthetic circuit incorporating miRNAs responsive to intracellular protein levels, and show that this genetic circuit can serve as a sensitive, noninvasive sensor of nuclear protein concentration. Next, I extended the regulatory capabilities of synthetic miRNAs by developing a circuit that could perform OFF logic in response to levels of endogenous proteins within cells. This circuit was created by combining two different synthetic RNA-based regulators, a ligand-responsive ribozyme and a miRNA, to achieve the desired behavior. I developed a model that incorporates the component parameters and accurately described the behavior of this circuit. Finally, I combined a MS2-responsive ribozyme with a miRNA that targeted an MS2-dsRed fusion protein into this circuit architecture such that the system exerted negative feedback over MS2 levels within the cell. These powerful tools will enable the much more sophisticated engineering of biological systems as well as highlight the importance of methods for guiding the quantitative design of genetic circuits to achieve robust, reliable, and predictable systems-level behaviors.
Design of high-speed, high-resolution SAR A/D converters in nano-scale CMOS processes [electronic resource]
Keywords: Electrical Engineering.

This research investigates the design of high-speed SAR ADCs to identify circuit techniques that improve their conversion speed while maintaining low energy operation. In addition, it explores the limitations of pipelined-SAR ADCs, which recently have demonstrated high power efficiency at conversion rates of several tens of MS/s and SNDR > 65 dB. A modified pipelined-SAR architecture is proposed, which uses two switched-capacitor digital-to-analog converters (DACs) at the ADC frontend. This technique separates the high-speed SAR operation from the low noise residue computation and improves the conversion speed to over 150 MS/s while maintaining an SNDR > 65 dB with good power efficiency. Three prototype ICs were designed during this work. First, a test structure to extract mismatch information of small (~1fF) on-chip single-metal MOM capacitors was designed in the IBM 32 nm SOI CMOS process. Measurement results show very good matching characteristics with a matching coefficient of approximately 0.85%×1fF. Next, an 8-bit SAR ADC was designed in a 65 nm CMOS process. This design uses 0.75 fF unit capacitors in the DAC, top-plate sampling with symmetric DAC switching, SAR loop delay optimization, and a fast comparator optimized for regeneration and reset. Measured results show an SNDR of 47.3 dB (Nyquist input) at 450 MS/s with a Walden FOM of 72 fJ/conv-step. Lastly, to evaluate the proposed pipelined-SAR architecture, a prototype ADC was implemented in a 65 nm CMOS process. Measured results show an SNDR of 68.3/66 dB at low frequency/Nyquist inputs, respectively with a sampling frequency of 160 MS/s, which corresponds to a Schreier FOM of 167/164.7 dB respectively. These results validate the concept of the proposed two switched-capacitor DAC pipelined-SAR architecture, and the achieved performance compares favorably with the state of the art.
Design requirements for car-to-driver interaction in the context of semi-autonomous driving [electronic resource]
Keywords: Mechanical Engineering.

Autonomous driving at scale is approaching, yet human drivers are reluctant to relinquish control over their safety to a machine. Autonomous vehicle designers are thus challenged to mitigate user concern and promote trust—as well as to ensure safety under the new driving paradigm. If autonomous cars are to become commonplace, the car-to-driver interface must be designed around the user—driver and passenger. This research adopts a human-centered approach to interface design, studying the emotional responses and preferences of drivers in autonomous and semi-autonomous driving situations. The dissertation posits that the complex, rapid-response driving context calls for the car to provide advance, feed-forward information rather than just traditional feedback. This approach was tested in a set of four experiments: two involved semi-autonomous driving in a simulator environment using voice alerts, and two involved more fully autonomous driving in an actual car on public roadways using a visual display as the messaging medium. In all cases, drivers strongly preferred being kept in the information loop. Advance alerts, whether vocal or visual, alleviated anxiety, and increased the driver's alertness, sense of control, and trust in the technology. Messaging should be succinct; too much information overwhelmed drivers, who could not process multiple messages in the rapid-response driving context. Drivers considered the reasoning behind the car's autonomous action (e.g., "Obstacle ahead!") more salient than mere announcement of the car's action (e.g., "Car is braking"). Designers must beware that consumer preferences do not dictate the best (or safest) performance; study results anticipate potential tradeoffs between market appeal and safety. Beyond empirical results for specific message models, this work developed simulator and field research platforms that can be adapted for future investigations. The research culminates in core guidelines for designing an autonomous vehicle interface that satisfies driver needs.
Destabilizing the Photograph: The Process of Image-Making as a Discursive Exercise in Self-Making Through Photovoice Engagement With Children
Keywords:  Department of Anthropology
Stanford University Department of Anthropology
Public Service Scholars Program Haas Center for Public Service
Photovoice
photography
participatory research
children
case studies
child development
anthropology
engaged scholarship
memory
empathy
awareness
sharing
self-making
Thesis

This thesis examines questions about representation as they emerged from my fieldwork with children and youth ages 5 to 14-years-old who attended a farm-based education summer camp in Sunnyvale, CA, during the summer of 2013. I argue that the participatory and dialogic framework of Photovoice, a participatory photography methodology, allows for the empowerment and validation of research participants in the construction of their self-representation. Through an analysis of the participants’ transformative and exploratory responses to Photovoice, I highlight the experiences of five children as case studies in order to better understand what I call photographer persona as a concept for self-making, through which memory, empathy, awareness, sharing, and play emerge as extensions of the self and ways of being in the world. For this study, I draw upon the fields of child development, photography, anthropology, and engaged scholarship. I focus on the process of image-making as a conduit for self-making vis à vis the effects of participatory research on the empowerment of the self.
Determination of the S. Cerevisiae INO80 Chromatin-Remodeling Complex in Mitotic Stability Pathways
Keywords:  Department of Biology
mitosis
chromosome segregation
chromatin remodelers
INO80
ARP5
IES6
spindle assembly
microtubules
microtubule motor proteins
S. cerevisiae
Biology
Stanford
Thesis

The INO80 chromatin-remodeling complex was originally characterized as a transcriptional regulator that dynamically restructures chromatin, the packaging material of DNA. Recently, however, the complex has been implicated in chromosome segregation, as yeast deficient in INO80 subunits exhibit abnormal DNA ploidy. Currently, the precise mechanism by which the INO80 complex regulates mitotic stability remains unclear. This study sought to elucidate mechanisms for the INO80 complex in chromosome segregation by utilizing an integrative approach of genetics, molecular biology, and cell microscopy in S. cerevisiae. The hypothesis of this research is that the INO80 complex affects chromosome segregation by influencing microtubule dynamics. Through the assessment of genetic interactions between INO80 subunits and genes with characterized roles in mitosis, we find that INO80 subunits function in pathways related to kinesins, kinesin-like proteins, kinetochore-related, and cortical/microtubule associated proteins. Biochemical assays reveal a physical association between the INO80 complex and alpha-tubulin during G2/M-phase of the cell cycle. Cell microscopy provides further support for a role of the INO80 complex with microtubules, as fluorescently-labeled INO80 subunits localize to nuclear and cytoplasmic microtubules. Moreover, deletion of INO80 subunits results in an increased frequency of cells with shorter or undetectable cytoplasmic microtubules and non-elongated spindles. Interestingly, these results implicate the INO80 complex in microtubule function, which is important for kinesin (plus-end directed) and dynein (minus-end directed) motor proteins to generate the appropriate push/pull forces to separate sister chromatids, orient the spindle, and pull the nucleus into the daughter bud. This represents a novel mechanism by which INO80 regulates the critical mitotic machinery needed for chromosome segregation and to ensure accurate propagation of genetic materials into daughter cells.
Determining parentage in a population of harvester ants
Keywords:  Department of Biology
Department of Biology
Gordon Lab
ant colony population
Pogonomyrmex
parentage analysis
microsatellites
lineage ratio
Thesis

Reproduction in ant species takes place at the colony level, and daughter queens disperse after mating, two facts that make it difficult to track descent in ants. Genetic analysis can provide invaluable information about parent-offspring relationships in ants, making it possible to quantify reproductive success, a crucial measure for relating phenotype, fitness and environmental factors in ecology.
The Gordon Lab has been tracking a population of Pogonomyrmex barbatus colonies in a field site in the Chihuahuan desert in southeastern Arizona since 1985. Sequencing of the cox1 mitochondrial gene and five polymorphic microsatellite loci was performed on samples from 10 colonies, which were taken from the field in August 2013.
Like other harvester ant populations, the P. barbatus colonies on the site show an asymmetric ratio of two interbred but genetically distinct lineages. The ratio for the 10 colonies sampled in this project was not significantly different from samples taken in 1999 and 2010.
The sequencing data collected in this project will enable the lab to properly identify colonies that have relocated their nests or for which marking tags have been lost. Additionally, the lab will be able to determine if the colonies sampled have parent or offspring colonies living on the site.
Determining the role of gamma-glutamyl transferase 7 in glioblastoma tumorigenesis
Keywords:  Department of Biology
Biology
glioblastoma
gamma-glutamyl transferase 7
tumorigenesis
reactive oxygen species
Thesis

Glioblastoma (GBM) is the most malignant primary brain tumor in adults, with a median survival time of one and a half years. Traditional treatments including radiation, chemotherapy and surgery are not curative, and it is crucial to explore novel targets for therapeutic treatment. Gamma-glutamyl transferase (GGT) is a family of enzymes involved in the metabolism of glutathione, the cell’s main water-soluble antioxidant. GGT7 is a novel GGT family member whose function has not been fully determined and has not been previously studied in cancer. Recent reports have demonstrated that GBM patients have decreased expression of GGT7 but not GGT1 or GGT5, suggesting that loss of GGT7 may enhance glial tumor growth. We hypothesize that GGT7 could be acting as a tumor suppressor in GBM due to its role in pro-oxidation and detoxification. In this thesis project we sought out to determine if GGT7 plays a role in GBM tumorigenesis. To determine if GGT7 is involved in GBM tumorigenesis we transduced GBM cell lines with GGT7. We determined that an increase in GGT7 resulted in a minimal decrease in proliferation and 3-fold reduction in anchorage independent growth at normal serum conditions. Surprisingly, we observed a more pronounced reduction in GBM growth under starvation conditions, yielding a 2-fold decrease in proliferation and 3-fold decrease in anchorage independent growth. This suggests that when GBM cells undergo stressful situations GGT7 reduces tumorigenic phenotypes. Correspondingly, we reduced expression of GGT7 using both siRNAs and shRNA. We found that reducing GGT7 expression increased proliferation in the GBM cells. This was seen at both normal (1.5-fold increase) and low serum conditions (2-fold increase), with a greater increase at low serum conditions. GGT7 expression also modulated the activity of reactive oxygen species (ROS) in the cell. ROS levels were decreased by 14-15% at normal serum conditions and 11-33% at low serum conditions. Together, our study suggests that GGT7 may act as a tumor suppressor in glial tumorigenesis by protecting the cells from ROS damage and decreasing proliferation under stressful, low nutrient conditions. Further analysis will be conducted to determine if GGT7 can be used as a biomarker or therapeutic target for GBM.
Development of a low-temperature cavity ring-down spectrometer for the detection of carbon-14 [electronic resource]
Keywords: Mechanical Engineering.

This thesis covers the development and performance analysis of a cavity ring-down spectrometer (CRDS) prototype for the measurement of carbon-14. The overarching goal of the project was to build a prototype spectrometer using simple hardware to elucidate the hurdles in bringing a commercial carbon-14 CRDS analyzer to market. The development of the CRDS system is described. First, the theoretical analysis of the mid-IR spectra and line selection are presented. Then the hardware design choices that would enable measurements at low temperatures are discussed. Finally, the operation of the instrument is covered. This includes the experimental condition control systems and a model-based, closed-loop, PZT-creep-compensation, data-acquisition routine. Performance analysis of the spectrometer was conducted. Initial spectroscopic measurements characterized the interfering spectra surrounding the 14CO2 P(40) line candidate. This characterization was later used to quantify carbon-14 in room temperature carbon dioxide with a spectroscopic model. Finally, low-temperature trial measurements were made to elucidate any design flaws. The alpha prototype showed promise, but design flaws prevented measurements at the ideal temperature and wavelength. However, it demonstrated low-temperature measurement capabilities and resolved room temperature samples with a 14C/C concentration approximately 50 times contemporary atmospheric levels with 6.6% 1-sigma error. These results are reviewed, and possible options for moving forward are discussed.
Development of diamidophosphite ligands towards the palladium-catalyzed trimethylenemethane cycloaddition [electronic resource]
Keywords: Chemistry.

The synthesis of complex molecules in an efficient and selective fashion remains to be one of the driving forces in the development of the field of organic chemistry. Towards that end, the study of cycloaddition reactions has garnered much attention due to its ability to form multiple bonds in a single step while accessing complicated ring structures. Since its inception in 1979, the palladium-catalyzed trimethylenemethane (TMM) [3+2] cycloaddition has been heavily studied by the Trost group. It was found that the key zwitterionic palladium-TMM intermediate is capable of performing cycloaddition reactions with various coupling partners, forming cyclopentanes, tetrahydrofurans, and pyrrolidine rings, as well as seven- and nine-membered rings in good yields and selectivities. Additionally, substituents placed on the starting TMM-precursor, also known as the TMM donor, are also directly introduced onto the cycloadduct, allowing for the synthesis of highly-substituted ring systems. In 2006, the Trost group was able to perform the reaction in an enantioselective fashion through the development of BINOL-derived phosphoramidite ligands. While these cycloadducts were generated with high yields and enantioselectivities, the substitution on the TMM precursor was limited, owing to the reactivity of the phosphoramidite ligand employed. Herein, we describe the development of a new class of ligands, diamidophosphites, and their utility in the substituted-TMM cycloaddition. These ligands are easily accessed in a two-step procedure with high levels of modularity, allowing for the fine-tuning of the catalyst system. The effectiveness of these ligands will first be discussed in a vinyl-substituted TMM cycloaddition, where tetrasubstituted cyclopentanes bearing three contiguous stereocenters are synthesized in high yields, diastereo- and enantioselectivities. Additionally, a new disubstituted TMM donor was developed for the synthesis of pyrrolidine ring systems bearing a quaternary stereocenter. Finally, this method is applied towards the total synthesis of jogyamycin, where the core cyclopentane ring is accessed through the TMM cycloaddition.
The development of miniature Raman-based clinical imaging devices to detect targeted SERS nanoparticles [electronic resource]
Keywords: Mechanical Engineering.

Better screening strategies for early cancer detection and the identification of tumor boundaries during surgical resection are essential to improve patient care. The current standard relies on white-light visualization of tissue and the use of non-specific dyes to highlight the vasculature. As a result, lesions are often missed and the identification of the tumor boundaries during removal can be difficult, often resulting in the need for multiple random biopsies at the perimeter of the suspect tissue. Success in the detection and resection of malignant tissue is dependent on skilled and experienced surgeons and endoscopists. Sophisticated optical technologies that show biomarker-specific contrast are nearing clinical translation, and rapid detection of targeted surface enhanced Raman scattering (SERS) nanoparticles is a promising approach for sensitive detection of cancer. The advantages of SERS nanoparticles include multiplexing capabilities, high sensitivity, and consistent and stable signal over time. This thesis describes the development of miniature, highly sensitive fiber-optic-based Raman imaging devices that are capable of imaging a panel of SERS nanoparticles, which are being functionalized to target a multitude of cancer-specific biomarkers. The overreaching objective is to provide real-time diagnostic information during screening procedures by adding molecular specificity that complements white-light imaging. Here, I present two clinically translatable devices that I developed −a point-detection device and a circumferential scanning device− which were designed to be used in humans for detection of targeted SERS particles. The accomplishments of this work include the first clinically translatable Raman-based imaging device capable of simultaneously detecting mixtures of up to 10 distinct SERS nanoparticles. The non-contact nature of these designs enables them to scan large areas in short periods of time. The system is highly sensitive, rapid, and can be used in real-time. The techniques presented here open up new opportunities to significantly improve the detection and diagnosis of small and otherwise hard to detect lesions in a variety of clinical settings.