VictorJuiz/thesis huggingface dataset:
Targeting TYMS as a Therapeutic Strategy for Aggressive Prostate Cancers

In the modern-day United States, prostate cancer (PC) remains the most common non-skin cancer in men. While the 5-year survival for localized prostate cancer is greater than 99%, patients with aggressive, metastatic prostate cancer subtypes experience worse prognostics and a 5-year survival of only 31%. This suggests that aggressive, metastatic prostate cancer subtypes are responsible for the majority of prostate cancer-driven deaths and underscores the need to develop novel therapies for these aggressive PCs. The DNA replication and repair pathway is a common target in cancer therapies since DNA de-regulation is a well-identified cancer hallmark. Thymidylate synthase (TYMS), an enzyme that is an important component of DNA synthesis, replication, and repair due to its synthesis of thymidylate, has been identified as a potential therapeutic target for aggressive PCs since TYMS is highly expressed in invasive PC subtypes and exert anti-cancer activities in vitro and in vivo. Our result indicates a positive association between TYMS expression and PC progression since TYMS is elevated in metastatic patient tumors relative to benign and localized samples, and TYMS is also up-regulated in AR-independent castration resistant prostate cancer (CRPC) and neuroendocrine prostate cancer (NEPC) relative to localized and normal prostate tissues in patient tissue microarray (TMA). Results from in vitro cell viability and colony formation assays also indicate that TYMS inhibition exerts anti-cancer activities in the reduction of PC cell viability, colony-forming ability, and tumor growth. Thus, we propose TYMS as a novel therapeutic target against metastatic, invasive PC subtypes.

Keywords: Bioengineering
Prostate > Cancer > Treatment
Raltitrexed
Pemetrexed
Thymidylate synthase
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Thesis
Advisor: Stoyanova Tanya
Bintu Lacramioara
Liu Shiqin
Teachers, Headscarves, and German Integration Policies: An Argument for Neutrality through Diversity

Natassia Walley’s capstone project examined the impact of German state-by-state Neutralitätsgesetzes (neutrality laws) on public schools. To varying degrees, these laws prohibit employees in offices of the court, the police force and in state-funded educational institutes from displaying their religious affiliation through accessories and clothing. Utilizing a 2003 German Federal Constitutional Court ruling on individual freedom of religion and a 2015 case of a Muslim elementary school teacher in the state of Rheinland-Westfallen who was denied employment because she wore a headscarf, Natassia took a closer look at how neutrality laws and headscarf bans are applied differently across German states. Contextualizing these differences within the religious history of Germany, and the history of immigration in Germany in the 20th century, Natassia explored the contemporary implication of these laws for immigrant and refugee empowerment and integration.

Keywords: Neutrality Law
Germany
Emigration and immigration law
Text
Thesis
Teaching Students How to Sing: Choral Teachers' Conception of Vocal Pedagogy

There is little existing literature that collects the various experiences of high school choral teachers in their backgrounds with and navigation of vocal pedagogy; in other words, there is little published documentation of how teachers go about teaching singing to a large group of primarily inexperienced, untrained high school students. This research looks at how vocal pedagogy impacts the objectives and instructional methods of high school choral teachers as it pertains to their classroom. In order to collect these experiences and opinions, ten high school choral teachers were interviewed and were asked open-ended questions followed by hypothetical situations. All participants agreed that having knowledge of and implementing vocal pedagogy are beneficial; for some participants, vocal pedagogy was the top priority in job qualifications, aiming to provide a daily group voice lesson to their students using age-appropriate vernacular. In framing and implementing vocal pedagogy to affect other classroom objectives, vocal pedagogy was utilized as a way of enhancing inclusivity and accessibility, creating safe spaces and encouraging teamwork. That said, participants also discussed the necessity to expand the narrow Western scope of vocal pedagogy to match the diversifying demographics of their students; to do so, they recommend music teacher preparation programs incorporate non-Eurocentric pedagogical methods into their programs. While vocal pedagogy was unanimously viewed to be important, three participants stated that having complete mastery over vocal pedagogy is secondary to establishing teacher-student connections, creating interpersonal relationships, and listening to larger community needs, especially after the impacts of the COVID-19 pandemic.

Keywords: Music
Choral music
Choral conductors
Music in education
Voice teachers
Vocal pedagogy
Choral pedagogy
Graduate School of Education
Honors Thesis in Education
Interdisciplinary approach in education
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Thesis
Advisor: Williamson Peter
Willinsky John
Kelman Ari
Smith Daniel
Techniques for efficient and responsible operation of mobility systems

Transportation is a necessary resource for many societies around the world. While advances in data science provide promising tools for personalized, adaptive and more efficient mobility services, they also bring new challenges in equal measure. In this dissertation I will discuss algorithm design for two such challenges faced by modern mobility services. First, I will discuss techniques for operating ridehailing and ridesharing systems in settings with incomplete information, which often arise due to the on-demand nature of such services. In particular, I will show both in theory and in practice how ideas from model predictive control, online optimization and machine learning can be used to effective serve existing customers while also adequately preparing for unknown future demand. Second, I will highlight some privacy concerns that arise from the sharing of mobility data that is often required for modern data-driven algorithms. To address some of these concerns, I present techniques based on multiparty computation and differential privacy to effectively use location data to improve routing services in a privacy-preserving way

Keywords: Electrical Engineering.
Advisor: Pavone Marco
Boyd Stephen P. 
Sadigh Dorsa
Technoeconomic Analysis of Decarbonization Options for California's Industrial Sector

Climate change is one of the leading problems of today with devastating consequences if left unaddressed. This project analyzes the technoeconomics of decarbonizing California’s industrial sector. The industrial sector is the 2nd largest emitting sector in the state, emitting approximately 100 Mt of CO2e in 2019. California’s industry sector can be broken down to multiple subsectors. The cement, oil and gas, and refinery and hydrogen subsectors are industrial subsectors that require intense heat to operate their production process which leads to large amounts of energy requirements and emissions in comparison to other industrial subsectors.
Carbon capture and sequestration (CCS), fuel switching options, and electrification were the main pathways for decarbonization that were considered throughout the study; however, other pathways such as energy efficiency and feedstock changes are also potential decarbonization options. Limitations of decarbonization using the pathways considered were dependent on each subsectors’ operations and processes.
The decarbonization pathways for each subsector showed economic and environmental favorable outcomes for CCS. Some subsectors had technical limitations due to the nature of their operations; however, the economic favorability was clearly due to the ability to implement incentives such as 45Q tax credit ($50 per ton of CO2e) or California’s Low Carbon Fuel Standard (LCFS) credit (assumed to be $100 per ton of CO2e). Though the study was able to identify a key technology for each of the subsector for decarbonization while maintaining the best economic outcome, the technologies that were determined to be most economically viable were not always the technologies with the largest amount of emissions abatable.

Keywords: California State Building and Construction Trades Council
Decarbonization
Technoeconomics
California's Industrial Sector
Text
Thesis
Advisor: Brandt Adam
Saltzer Sarah
Temperature coupling effects in radiatively heated particle-laden flows

Turbulent particle-laden flows are common in many natural phenomena and engineering applications. While particle-laden turbulence is a relatively well-studied subject, not many studies address the concurrent effect of an radiative heat transfer on the multiphase system. Understanding such an interaction can be key to designing effective spray combustors, fire suppression systems, and particle solar receivers. Using the particle solar receiver as a test bed for investigation, this work aims to experimentally investigate the coupling between radiation, turbulence, and particles in such a system using two different flow configurations of a duct flow and an isokinetic co-flowing jet. The goals of the work are to examine the effects of preferential concentration on the behavior of the radiation transport through the disperse medium and the convective heat transfer between the carrier and disperse phase. In addition, it also aims to study the converse effect of how the radiative heating can effect the clustering behavior of the particles by examining measures of preferential concentration of particles in the flow in the presence of radiative heating. The study finds that the preferential concentration of particles can cause the radiation transmission to deviate from a classical Beer's Law extinction behavior, due to increased line of sight distances in the medium. Measurements of the carrier phase temperature statistics show that large coherent particles clusters dominate the modulation of the gas phase temperature, especially in the boundary layer in wall-bounded flows. Measurements of the radial distribution function, clustering index, and Voronoi cell area PDFs all indicated a reduction of preferential concentration within clusters, particularly in denser clusters with smaller associated separation length scales, which correspond to the most intensely heated regions of the flow. Particle velocity statistics showed evidence of bulk turbulence modification by radiative heating, as particle velocity fluctuations were dampened. This was likely caused by variable property effects from temperature-dependent properties, specifically from the increase in fluid kinematic viscosity. Buoyancy and dilatation effects were identified as possible mechanisms for turbulence modification at the smaller cluster scales, supported by scaling analyses and directional measures of preferential concentration

Keywords: Mechanical Engineering.
Advisor: Eaton John K.
Iaccarino Gianluca
Mani Ali (Professor of mechanical engineering)
Temperature dependence of mosquitoes: comparing mechanistic and machine learning approaches

Mosquitoes that can transmit viral pathogens of humans (e.g., Aedes, Anopheles, and Culex genera) are of increasing concern for global public health. These vectors not only cause a rapidly growing infectious disease burden (e.g., malaria, dengue, Zika, chikungunya, yellow fever), but are also spreading in geographic range under climate change. As small-bodied ectotherms, mosquitoes are strongly affected by temperature, and prior laboratory research has demonstrated nonlinear and unimodal relationships between temperature and mosquito life history traits, with upper and lower thermal limits and intermediate thermal optima as predicted by first principles of enzyme kinetics and the metabolic theory of ecology. However, it remains unknown how mosquito thermal responses measured in laboratory experiments relate to the realized thermal responses of mosquitoes in the field.
To address these questions, we leverage thousands of global mosquito occurrences and geospatial satellite rasters at high temporal and spatial resolution to construct machine-learning based species distribution models. We apply new methods to restrict models to the temporally-relevant mosquito activity season and to ecologically-relevant spatial background sampling for comparison to mosquito occurrence records. Thermal response signatures from these ‘top-down’ statistical models supported the nonlinear temperature responses apparent in the laboratory-derived mosquito abundance estimates. Further, we found that, across mosquitoes, thermal minima estimated from laboratory studies were highly correlated with those estimated from field-based models. However, we could not estimate thermal maxima from field occurrence records due to inherent limitations in background sampling, and comparisons of thermal optima were inconclusive. Together, the current evidence suggests that laboratory studies have the potential to be highly transportable to real-world mosquito inferences for thermal minima, while other key temperature dependence metrics merit further investigation.

Keywords:  Department of Biology
Childs, Marissa
Biology
Ecology
Mosquitoes
Temperature
Species distribution modeling
Machine learning
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Thesis
Advisor: De Leo Giulio
Mordecai Erin
Temporality of political content exposure via smartphone screens : a computational description of rapidity and idiosyncrasy

This dissertation provides a computational description of the rapid and idiosyncratic nature of exposure to political content in the smartphone environment, in order to critically address implicit conceptual and methodological assumptions common in computational political communication research. The data used are hyper-rich longitudinal screen-recordings collected from 115 Americans' smartphones for up to two weeks each in late 2019, amounting to over four years of natural screen usage. Drawing on theoretical temporal foundations of empirical research, I discuss the importance of timescale explication in political communication research and the temporally fragmented nature of smartphone usage. I then discuss how political content fits into the smartphone environment, in terms of format, sequencing, psychological processing, and especially information retention. Tying together these considerations, I demonstrate measurement validity concerns that arise from (1) aggregating unique encounters with political content as commensurable units, (2) aggregating durations of exposure to political content as commensurable units, and (3) utilizing singular formats or sources (including the news format) as proxies for measuring political content exposure. I also find connections between political content exposure durations and idiosyncratic content sequencing as afforded by the smartphone's flexibility. Throughout, I illustrate and quantify high variance in core measures both across and within subjects, and I show that the risk of ecological fallacy in this domain is similar interindividually and intraindividually. I conclude with an assessment of current research practices, suggestions for the field, reflection on limitations, and directions for future research

Keywords: Communication.
Advisor: Reeves Byron
Hancock Jeff
Pan Jennifer
Willer Robert Bartley
Texture and object representation for human visual perception

Human visual object perception occurs in service of behavior. The behaviors which rely on object vision are numerous and varied, from object categorization to visual search to face recognition to novel pattern discrimination. The format of brain representations which underlie visual perception must therefore be sufficiently generalizable as to support this wide variety of behaviors. The visual cortex of humans, especially the ventral visual cortex, contains neural populations which encode information about objects. For example, neurons in primary visual cortex (V1) respond more to lines of some orientations than others, neurons in area V2 respond more to naturalistic textures than to noise patterns, and neurons in the fusiform gyrus respond more to faces than to other objects. Despite decades of research characterizing such neural selectivities, much remains to be understood about how these visual feature representations give rise to perception. In this dissertation, I aim to characterize the format of visual object and texture representations in human ventral visual cortex as well as the downstream cortical computations which select and integrate such representations in support of behavior. I present evidence that human visual cortex encodes information about objects but does not directly support object perception. Rather than explicitly encoding a fixed set of familiar stimuli, visual cortex provides a configurable basis of complex texture-like feature representations. Further, I show that attention is necessary to transform these texture-like representations into a format better suited to support object perception. Finally, I demonstrate that depending on task demands, visual perception must be able to flexibly access feature representations from different visual cortical regions. I conclude by discussing the implications of this work on future modeling efforts for computer vision and cognitive neuroscience. Taken in sum, this dissertation suggests that human visual cortex extracts a complex basis set of features which describe the visual world, and attention and task engagement select and integrate those visual features to support perception

Keywords: Psychology.
Advisor: Gardner Justin
Grill-Spector Kalanit
Norcia Anthony Matthew
Yamins Daniel
The Ads that Slip Through the Cracks: Undisclosed Political Ads on Facebook

In response to widespread criticism for rampant misinformation on their platform, in 2018 Facebook created an online ‘Ad Library’ intended to serve as a meaningful mechanism of transparency to the public. However, in reality, there have been a number of issues and criticisms with the Ad Library that undercut its ability to truly be an effective tool of accountability and transparency. One such issue is that some political ads are able to slip through Facebook’s automated filters without the required disclosure that details who paid for the ad. This project aims to investigate what kinds of political ads tend to slip through Facebook’s automated filters. Specifically, this paper explores why some undisclosed political ads garner a greater number of impressions than others, with a focus on the impact of the political-leaning and sentiment of the ad. Ultimately, I find that undisclosed political ads that take a strong political stance and utilize rhetoric that evokes a negative sentiment seem to be relatively successful at garnering more impressions than non-political, positive-sentiment ads.

Keywords: Public Policy Program
Political ads
Misinformation
Online ads
Facebook (Electronic resource)
Sentiment analysis
Facebook (Firm)
Stanford University
Humanities and Sciences
Public Policy Program
Text
Thesis
Advisor: Bonica Adam
The Blob and the Blues: Analyzing the Impact of a Marine Heatwave on Blue Whale Behavioral Patterns Between Two Foraging Hotspots Along the California Current - Monterey Bay and Cordell Bank

Between 2013 and 2016, the California Current Large Marine Ecosystem experienced the longest marine heatwave event ever recorded in this region. Nicknamed The Blob, this extended period of abnormally high sea surface temperatures had detrimental impacts on many of the species that inhabit this ecosystem. Through a combined analysis of oceanographic and acoustic data collected from 2015 – 2018, this study aimed to determine how The Blob marine heatwave event impacted the largest species on the planet – the blue whale (Balaenoptera musculus). An endangered species, blue whales feed selectively on krill and conduct an annual migration between breeding locations in the south and foraging hotspots in the north. Two of these foraging hotspots, Monterey Bay and Cordell Bank, both within the California Current, were considered within this study. These hotspots were chosen because they are each home to a hydrophone (underwater microphone), which were used to determine blue whale acoustic presence. I found that blue whale acoustic presence did not vary significantly as a result of The Blob marine heatwave event, and that blue whales were more consistently present in Cordell Bank than Monterey Bay. Using a combination of environmental oceanographic data sources, I also found that The Blob marine heatwave event impacted both sea surface height and upwelling conditions similarly in Monterey Bay and Cordell Bank. These findings suggest that rather than be considered as distinct foraging hotspots, the region encompassing Monterey Bay and Cordell Bank should be thought of as one continuous foraging hotspot in the context of the blue whale. This region is subdivided by various human-created boundaries, including three marine sanctuaries and heavily trafficked shipping vessel lanes, and therefore the suggestion that it is all one large foraging hotspot points to a need for interconnectedness within the differing management schemes of this region. Additionally, marine heatwave events have been projected to increase in both frequency and intensity as a result of anthropogenic climate change. Therefore, the additional layer this study adds to our collective understanding of blue whale behavior and adaptation to environmental change is essential now more than ever before to ensure the protection of these gentle giants.

Keywords: Ryan, John
Blue whale
Pacific Ocean > California Current
Marine ecology
California > Monterey Bay National Marine Sanctuary
California > Cordell Bank National Marine Sanctuary
Animals > Food
Marine heatwave
Text
Thesis
The Effect of California's Local Control Funding Formula on School-Level Resources for English Language Learners

Since the 1990s, state school finance reforms have progressively allocated funds to disadvantaged students with the goal of narrowing academic achievement gaps. In 2013, California Governor Jerry Brown signed into law the Local Control Funding Formula (LCFF) to target supplemental and concentration funds to districts with larger shares of low-income students, foster youth, and English Language Learners (ELL). Studies have shown that LCFF has increased total school resources in high-need districts, as the policy intended. However, LCFF does not guarantee additional district funds are spent on school-level resources for target students, such as ELLs. To investigate the effect of LCFF on ELLs’ access to resources, this paper analyzes the pre- and post-LCFF trends in the between-district, within-district, and statewide resource disparities for ELLs relative to their non-ELL peers. My primary focus is the within-district resource disparity, as less is known about LCFF’s impact on resources for ELLs among schools within the same district. Consistent with previous research, I find that between-district resource disparities for ELLs increased in progressivity post LCFF. In contribution to the literature, I find that the within-district resource allocation for ELLs maintained similar levels of progressivity. I find no evidence that LCFF worsened resource allocation patterns at any organizational level for ELLs.

Keywords: Public Policy Program
Reardon, Sean
California
English learner
School resources
Intradistrict
Stanford University
Humanities and Sciences
Public Policy Program
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Thesis