VictorJuiz/thesis huggingface dataset:
Ge/SiGe quantum confined stark effect waveguide modulator for optical interconnects
Keywords: Electrical Engineering.

The improved performance of computer systems has been realized by downscaling the integrated circuit minimum feature sizes. However, interconnection through wires is becoming increasingly difficult such that the signal I/O rate cannot keep up with the growth of computational performance. Optical interconnects provide a promising solution to this on-chip interconnect bottleneck. To meet the energy requirement, a system with an off-chip laser and Si-compatible on-chip modulators and detectors appears to be the most probable approach. Among Si compatible modulators, Ge/SiGe quantum-confined Stark effect (QCSE) modulators are the best approach to meet both the speed and power targets. This thesis proposed and investigated a 3-dimensional (3D) taper design for Ge/SiGe quantum well waveguide modulators on a Si waveguide to improve the coupling efficiency between the Si bus waveguide and the SiGe devices. We showed by simulations the superiority of the 3D tapers for coupling due to its better maintenance of the fundamental mode. We then demonstrated the fabrication of 3D tapers through grayscale lithography using a Heidelberg Maskless Aligner. When comparing the performance of modulators coupled by 3D tapers and 2D tapers, we showed that 3D tapers can lead to a coupling enhancement by a factor of 4. These 3D tapers combined with the Ge/SiGe QCSE waveguide modulators pave the way to on-chip, integrated modulators and detectors for optical interconnects.
Getting cereus about roots: Tracking dynamic plant-microbe interactions in the A. thaliana root system
Keywords:  Department of Biology
Biology
rhizosphere
plant roots
Bacillus cereus
Bacillus subtilis
ICEBs1
photosynthesis mutations
Thesis

The symbiotic relationships that bacteria form with plant roots have far-reaching effects on plant physiology. Analysis of symbiotic interactions yield valuable information about the impact of bacteria in the rhizosphere, the interface of plant-soil interactions. Current research has focused on the location and interactions of specific plant and bacterial species to gain insights into effects of their association. My research uses an engineered integrative and conjugative element (ICE) to label bacteria isolated from the roots of the model plant Arabidopsis thaliana with a green fluorescent protein. Fluorescence imagining is then used to visualize bacterial colonization in the roots of wild type and mutant plants. Using this approach, we found that a soil isolate of Bacillus cereus stably colonizes the root tip of both wild type and mutant A. thaliana. Although the bacteria do not significantly affect plant growth, this strain may be useful as an engineered probiotic in the future because it stably colonizes of the root tip of A. thaliana.
Getting into the Weeds: Competition and Cheating in the Washington State Marijuana Market
Keywords:  Department of Economics
Department of Economics
Stanford University
Competition
Marijuana
Washington
Cheating
Difference-in-Differences
License
County
Regulation
Thesis

To sustain profitability, firms strive to gain any edge over their competitors: sometimes even acting illegally. This paper looks into the effect of the level of competition on the rates of license violations within the Washington State Recreational Marijuana Market. I exploit a 2016 policy change in which some counties received a bump in the amount of firms allowed to operate in the county, while others did not. Using a difference-in- differences approach around this competition shock, this paper finds that counties that received more licenses were correlated with significant, higher levels of license violations than those that did not.
The gilded renewal : capital, politics, and the re-fashioning of Marseille
Keywords: Anthropology.

By labeling Marseille's urban renewal gilded, this dissertation argues that the city's rehabilitation is inherently spectacular. Marseille's EuroMediterranean renovation participates in a profound mystification of the social relations of capital accumulation and state governance, visible in the limits of the discursive understandings of the changing city center. As the French State works to take Marseille from murder capital to fashion capital, the material and discursive spectacle of the transformation of urban space and cultural life obscures not only the city's entrenched poverty, ethnic divisions, and housing insecurity, but, even more disconcerting, the increasing imbrication of state and capital and the abandonment of the city's political sphere. In this quest for demystification, I uncover how the process of refashioning Marseille devolves into the production and circulation of spectacles of renewal by tracing the networks and social relations of a diverse cast of actors, including city and state officials, real estate developers, urban planners, business owners, and fashion designers. Finally, I question the possibility of the resuscitation of the political sphere by examining how several citizen-led associations and the networks they constitute articulate alternative ways of living together in the struggle over the meaning, image, and experience of urban space and the future of Marseille.
Going viral : printing disease in early modern Germany
Keywords: German Studies.

This dissertation traces the cultural history of virality to the turn of the sixteenth century and uncovers the pervasive notion that ideas can be transmitted analogously to diseases. I argue that a discourse of virality, which is commonplace in the digital age, arises in this period in response to the development of new forms of print media. By looking at the works of vernacular poets and Humanist scholars as well as medical professionals, both canonical and non-canonical, and by discussing three contagious diseases with different pathological and social profiles - plague, syphilis, and the English sweating sickness - this dissertation expands our picture of early print to include sources that have generally been excluded from print's history. This dissertation also contributes to the recent scholarly tendency to view print as a technological development whose introduction also included setbacks, continuities, and criticism, rather than as a phenomenon that revolutionized early modern Europe. Writers on these three diseases raise concerns that print spreads harmful or false information, stokes fears, and cannot be controlled. As such, these writers participate in a discourse of virality, suggesting that printed information on disease may be more dangerous than the disease itself.
Gratitude and compassion during adolescence
Keywords: Education.

Informed by recent research findings on the benefits of gratitude and compassion, an increasing number of schools are keen to implement education lessons to help youth cultivate gratitude and compassion. The available research literature reveals, however, that there are only a handful of studies that have investigated the nature of gratitude and compassion among children and adolescents. Given the growth in interest to foster gratitude and compassion in youth, more research on the nature of these character strengths in adolescents will bring important theoretical insights and educational implications. With this research objective in mind, I present the following three papers in this dissertation that shed light on the nature of gratitude and compassion in eighth- and ninth- graders, and show the positive associations between these two character strengths, students' affective engagement and sense of belonging at school.
The Greek face of Roman Egypt
Keywords: Classics.

"The Greek Face of Roman Egypt" offers two perspectives on cultural translation between Egypt, Greece, and Rome: one grounded in the Egyptian articulation of Egyptian culture under new forms of Roman imperial control, the other in the alternatively optimistic and world-weary Roman responses to a Principate whose contours were explored and explained through Egypt. The two halves of this dissertation are devoted to the explanatory power of two marginalized literary traditions: first, Egyptians' explanations of Egyptian culture, and, second, those Greek and Roman authors who looked to Egyptian space and Egyptian people to justify the new institutions of the Principate. Both traditions can enrich discussions of Egypt's presence in Roman literature and material culture, which have overemphasized Rome's tendency either to exoticize or marginalize Egypt.
Green in-space propellants : ignition chemistry of hypergolic ionic liquids
Keywords: Aeronautics and Astronautics.

This thesis focuses on a class of promising green propellants alternatives for bipropellant applications: ionic liquids. Ionic liquids have extremely low vapor pressures and other beneficial properties while reacting hypergolically (spontaneously igniting upon mixing) with select oxidizers. Although ionic liquids show a great amount of promise as future green propellant alternatives, there is still little understood about the chemistry occurring during hypergolic ignition with oxidizers and how ignition properties relate to the chemical structure of the fuel. The work presented here contributes to the understanding of hypergolic ionic liquids by (1) expanding the understanding of the ignition process through various droplet ignition testing, (2) providing valuable data on key thermal decomposition and hypergolic ignition chemical pathways by using in situ infrared spectroscopy coupled with computational quantum chemistry techniques, (3) exploring a novel hypergolic ionic liquid using spectroscopy and computational methods to highlight effects of fuel design and chemical structure on hypergolic reactivity, (4) examining the value of propellant additives through use of one fuel and one oxidizer additive, and (5) contributing high quality data to expand the capabilities of predictive algorithms to include hypergolic molecular liquids, providing ways to predict chemical and performance properties from chemical and electronic structure alone. All together, the contributions of this thesis provide a stronger basis upon which future green propellant development may occur. The experimental portion provides intuition for designing future fuels, using spectroscopy and computational quantum chemistry techniques to help relate fuel structure and composition to reactivity. Once there is an idea for a future fuel, the predictive methods expanded in this thesis may then provide preliminary performance metrics for potential fuel designs prior to synthesis and experimentation, saving time and money associated with trial-and-error experimentation. Utilizing predictive methods for propellant design will help expedite and streamline the implementation of safer, more cost-effective green propellant alternatives and ultimately provide a more accessible future for space exploration.
Growing Impact: Understanding Evaluation in Youth Programs in Urban Farming & Gardening
Keywords: urban agriculture
youth programs
evaluation
high school
experiential education
positive youth development
education
Thesis

Educational programs in an urban farm or garden setting can provide youth with opportunities for personal development, experiential learning, engaging in environmental behaviors and enhancing nutritional literacy. Evaluation tools and processes are used to measure program impact, report to funders, and promote the need for such programs. Therefore, it is important that program evaluations accurately convey the impacts and outcomes. In what ways do evaluations capture or fail to capture the extent of program impacts cited by staff and youth involved in the programs? This question was explored through a qualitative study of two paid summer youth programs in urban farming and gardening in Columbus, Ohio. Theoretical frameworks of place-based education (PBE) and positive youth development (PYD) were used to guide analysis of semi-structured interview data. Staff and youth alike felt that the program played a key role in developing youths’ sense of confidence, nutritional literacy, and vocational skills, but staff and youth perspectives differed in the way they characterized the role of youth in carrying out the program’s social impact goals. Staff tended to describe youth as the primary beneficiaries of the program’s social impact; youth described themselves as actors increasing food access in the community through their work in the program. More holistic evaluation tools and processes that amplify youth voices and take into account sense of ownership, autonomy, and community impact have the potential to demonstrate additional value of such programs in urban agriculture and within the field of youth development.
Hacking for Good: Leveraging HackerOne Data to Develop an Economic Model of Bug Bounties
Keywords: bug bounties
cybersecurity
crowdsourced cybersecurity
IT management
HackerOne
Thesis

I ran an empirical study on bug bounties, cybersecurity programs where ethical hackers are compensated for submitting reports to companies, detailing bugs which might be maliciously exploited. Leveraging instrumental variables, I eliminated many potential sources of endogenity, better establishing causality for what motivates hackers to submit reports to programs. Among other things, I rank industries by the number of reports they receive, find that new programs reduce the number of reports submitted to existing programs, compute a price elasticity between .1 and .2 at the median for hackers, and fail to validate the assumption that programs receive fewer reports as they age. This paper provides a snapshot of a rapidly changing––and increasingly important––industry.
Hardware acceleration and algorithms for genomic sequence alignment and its applications
Keywords: Electrical Engineering.

While genome sequencing data continues to rise exponentially (80%/year), transistor performance scaling has considerably slowed down (3%/year). Domain-specific acceleration (DSA), which uses specialized hardware for accelerating a narrow domain of applications, is one of the few remaining approaches in computer architecture to continue to scale compute performance and efficiency to enable the vast potential of genomics data. The entire domain of genomics relies heavily on one fundamental algorithm — genome sequence alignment — with wide-ranging applications in medicine and comparative genomics. The first part of this dissertation presents our work on hardware acceleration of genome sequence alignment, particularly for two emerging, compute-intensive applications in genomics — long read assembly (Darwin co-processor) and whole-genome alignments (Darwin-WGA co-processor). The accelerators are based on hardware-software co-design, which modifies an existing algorithm in a way that provides massive speedup (1,000-10,000x) in specialized hardware without compromising, and sometimes even enhancing, the results for a biologist. The second part of this dissertation focuses on the applications whole-genome alignments to make novel biological discoveries. It presents a novel algorithm (ORCHID) to confidently identify the orthologous region of a reference gene in the query genome. ORCHID is further used to develop a novel screen (hcoErosions) to discover hundreds of genes that are surprisingly lost in different mammals, some of which are considered indispensable in human and mouse. It also presents a novel screen we developed for testing the molecular basis of convergent evolution in mammals that also relied on our ORCHID algorithm.
Hardware development for wireless MRI receive arrays
Keywords: Electrical Engineering.

Magnetic resonance imaging (MRI) is an imaging modality effective for viewing soft tissue contrast that usually outperforms other modalities such as computed tomography (CT) or X-ray. However, while effective, MRI requires long scan times that can be onerous for patients and technicians. Considerable research has been done to decrease scan times, which would improve patient experience and scanning workflow. A major development that has improved scan times while maintaining good signal-to-noise ratio (SNR) is parallel imaging. This uses multiple receive coil elements and channels to collect spatial frequency data simultaneously before combining the data in the final image. The use of multi-coil receive arrays for parallel imaging can be cumbersome, due to bulky cables, baluns that heat up, and cable coupling. Hence, there has been a considerable push to develop wireless MRI receive coils that are easier for technicians to use and more comfortable for patients. The goal of this work is to develop low power system components and to study the challenges of wirelessly transmitting scanner state signals and phase correction information to an unconnected MRI receive coil, which would eliminate the cabling and associated issues with safety and convenience. My work begins with a focus on power reduction for MRI receive arrays. This is important since wireless coils are not connected to the scanner, so coils must be battery powered or harvest energy by wireless power transfer. One energy-intensive process is Q-spoiling, the process of decoupling receive array coil elements during MRI transmit. This is necessary to protect the receiver on-coil electronics and the patient. Q-spoiling conventionally uses PIN diodes for switching, drawing significant current. In my work, I applied Gallium Nitride (GaN) HEMT switches for Q-spoiling, which require negligible power and result in at least 100x in power savings. The use of GaN HEMT switches can provide sufficient decoupling at negligible power without affecting image quality. Finally, this work leads to wireless Q-spoil triggering and clock synchronization for wireless MRI receive arrays. Antennas used for wireless transmission must be constructed to operate within the MRI bore environment in the presence a patient. These antennas should not perturb the B1 transmit fields of the MRI scanner and must satisfy maximum path loss constraints. Using prototype shielded dipole antennas, I achieved wireless Q-spoiling with sub-microsecond delay, suitable for the majority of pulse sequences including extreme cases such as ultra-short TE. In addition, I implemented different wireless modulation schemes for use in clock synchronization between the on-coil receiver electronics and the scanner. MRI scans acquire phase sensitive data, and sampling of this data due to improper clock synchronization may appear as blurring or translational artifacts in the MRI image. These core technological components are key to enabling wireless coils for faster, safer, and more effective MRI scans that can benefit doctors, technicians, and patients.
Health and loan default risk analytics : prediction models and their evaluation
Keywords: Statistics.

Risk prediction of future events or other adverse outcomes is widely used in health and medicine, economics and finance, climate change and infrastructure reliability. How to evaluate the risk forecasts and forecasting models/methods and quantify the difference of the predictions from the true risks is an important but challenging problem in using the forecasts to guide regulatory, or policy, or treatment/intervention decisions. Lai et al (2011) review the literature on the evaluation of risk forecasts using scoring rules and associated loss functions in weather forecasting and econometric forecasts, and introduce a new approach that gives valid confidence intervals for the difference in average scores of two forecasts. It provides a martingale approach to analyzing the prediction accuracy for binary outcomes when the outcomes are not independent across time and space. In this thesis, we give some background of score statistics and concordance-type statistics, discuss their limitations and some challenges in the evaluation of risk models, and develop methods, more specifically, the martingale approach, to address these challenges. We also extend our approach to a) subgroup identification using multiple hypotheses testing framework and b) sequential test to find change point of model performance statistics. We demonstrate our methods with simulations and two real-world applications.
Health Behavior Change in Virtual Worlds: A Systematic Review
Keywords:  Department of Communication
Health behavior
behavior change
virtual worlds
virtual environments
avatars
Communications
Media Studies
Thesis

Internet and web based interventions have been utilized as effective tools for health behavior changes. Virtual worlds also hold a great deal of promise in the future of behavior change because of the affordances the medium has in supporting many types of health care. This paper provides an overview of literature for virtual worlds as agents of health behavior change in the period 2000-2019. 20 papers were selected for analysis. The findings of the selected literature are summarized according to 2 broad characterizations: health behavior change technique, and intention of virtual world design.
Health Insurance Expansion and Rural Hospital Finances: Evaluating the Impact of the Affordable Care Act in California
Keywords:  Public Policy Program
Affordable Care Act
Medicaid expansion
California
rural hospitals
financial distress
payer mix
Stanford University
Public Policy Program
Thesis

The Patient Protection and Affordable Care Act (ACA) extended health insurance coverage to previously uninsured individuals, thereby altering reimbursement patterns at the hospital level. Given the historical financial difficulties of rural hospitals, this paper focuses on the effect of this insurance expansion on hospital inpatient payer mix and financial outcomes in rural settings. Using hospital-level data from 2006-2017, this paper utilizes a fixed effects regression and difference-in-differences study design to determine the effect of the ACA on rural hospital financial performance in California. I find a statistically significant decline in Medicaid payer mix and increase in private payer mix for rural inpatient services after the ACA. I also find significant reductions in Medicaid income per bed and uncompensated care cost, particularly in uninsured rural areas. However, overall profitability improved in rural hospitals after the ACA, suggesting the financial importance of private shares of payer mix to cover losses incurred by increased expenses of Medicaid patients.