VictorJuiz/thesis huggingface dataset:
Oxygen activation by mononuclear non-heme iron enzymes

Non-heme iron (NHFe) enzymes are in critical in Nature, playing significant roles in bioremediation, the biosynthesis of natural products, DNA repair and human health. These metalloenzymes utilize an Fe cofactor to activate dioxygen for reaction with organic substrates in a wide variety of chemical transformations including: H-atom abstraction, hydroxylation, halogentation, aromatic ring cleavage, aliphatic ring expansion/formation, electrophilic aromatic substitution and sulfur oxygenation/oxidation. Elucidating the mechanisms of these diverse catalysts requires defining the geometric and electronic structure of key Fe-O2 intermediates along the reaction cycle. An ideal tool for the interrogation of these Fe-O2 intermediates is nuclear resonance vibrational spectroscopy (NRVS), a synchrotron-based technique that observes the vibrational side-bands of the Fe-57 Mossbauer transition, making it a site-selective probe of all normal modes containing Fe displacement. Interpretation and analysis of NRVS spectra by correlation to quantum mechanical simulations (via density functional theory), allows for assignment of Fe vibrations and crucially geometric structure. In this thesis, NRVS is applied to the Fe-O2 intermediates in the extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase (HPCD-HPCA-Int-1) and the intradiol dioxygenase, protocatechuate 3,4-dioxygenase (PCD-4FC-Int-1), the pre-Fe(IV)=O intermediate in the pterin-dependent hydroxylase, tryptophan hydroxylase, and intermediate Q in methane monooxygenase (included in the appendix), while the ETHE1 sulfur oxidase versus oxygenase and the alpha-KG-dependent DAOCS concerted versus sequential DAOCS mechanistic studies utilize a combination of spectroscopic methods

Keywords: Chemistry.
Advisor: Solomon Edward I.
Fayer Michael D.
Kanan Matthew William
Ozone oxidation of emerging contaminants in RO concentrate and reductive dehalogenation of halogenated contaminants using activated carbon-based electrolysis

Society has adapted to increased water stress by expanding drinking water portfolios to include unconventional water sources containing an array of pollutants. For example, potable reuse of municipal wastewater has become increasingly important to meet drinking water demand in arid regions. Full advanced treatment systems employ reverse osmosis (RO) to remove recalcitrant chemicals in conventional wastewater (e.g., home-use pesticides and chelated metals) to produce a clean permeate at ~85% water recovery. However, the remaining ~15% (RO concentrate) contains elevated concentrations of these contaminants that pose a risk to receiving water ecosystems. Meanwhile, halogenated organics are a different set of contaminants that occur in groundwater (e.g., trichloroethylene) and during the disinfection stage of drinking water treatment (e.g., trihalomethanes). These chemicals exhibit diverse structures, complicating their removal. This dissertation therefore investigated two methods to treat evolving waters: 1) Ozone to degrade contaminants of particular concern in RO concentrate, and 2) Electrochemical reduction of halogenated alkanes and alkenes using granular activated carbon (GAC) cathodes

Advisor: Mitch William A. 
Luthy Richard G.
Tarpeh William
A p53 super tumor suppressor reveals fundamental roles of p53 in lung cancer and regeneration

p53 is critical for tumor suppression. This is evidenced by (1) the fact that the TP53 gene is the most frequently mutated gene in human cancer, (2) patients with Li-Fraumeni syndrome, who inherit a copy of mutant TP53 nearly all develop cancer in their lifetimes, and (3) mice that lack the Trp53 gene develop cancer with complete penetrance. p53 is especially important for suppression of lung adenocarcinoma (LUAD), a deadly cancer in that originates from alveolar type 2 (AT2) cells in the lung in which TP53 is mutated in almost half of cases and is correlated with a worse prognosis. However, we have a limited understanding of the downstream gene expression programs and functions regulated by p53 that are critical for LUAD suppression. In this dissertation, I describe the work that led to the discovery that a p53-directed alveolar regeneration program underlies lung tumor suppression. Using genetically engineered mouse models of LUAD with an allelic series of p53, including loss-of-function and gain-of-function alleles, I first deciphered the contribution of p53 at different stages of LUAD development and uncovered dual roles for p53 in suppressing LUAD initiation and progression. Using transcriptomic and epigenomic approaches, I then identified that p53 promotes the presence of a lung and alveolar cell program in LUAD. Specifically, I discovered that p53 induces an alveolar type 1 (AT1) differentiation program in both mouse and human LUAD. Moreover, this program is directly induced by p53, with p53 expression leading to the binding, opening of chromatin, and transcriptional activation of numerous AT1 genes. This induction occurs after p53 is activated in a high-plasticity, transitional cancer cell state. p53 limits the expansion of these transitional cells through restricting gene expression programs that promote tumor progression and instead promoting an AT1 differentiation program. This AT2-to-AT1 switch through a transitional intermediary is reminiscent of an alveolar regeneration program in which AT2 cells enter into a transitional state en route to AT1 differentiation. I found that the similarities extend beyond this to include a p53-directed AT2-to-AT1 program, in which, after alveolar injury, p53 restrains initial AT2 self-renewal and, after cells enter the transitional state, p53 promotes their differentiation to AT1 cells. These studies show a p53 functions in regeneration underlie tumor suppressive programs. Finally, I analyze the contribution of p53 transactivation domains to gene expression programs and functions in LUAD suppression using a system with temporal control of p53 activation. I find that p53 transactivation function is required for tumor suppression and define the unique programs and cellular phenotypes associated with each transactivation domain. Together, this thesis work identifies new p53 programs active in tumor suppression and regeneration and fill the gap our gap in our understanding of p53-mediated LUAD suppression

Advisor: Attardi Laura
Bassik Michael
Krasnow Mark
Winslow Monte
Parched plants to flaming forests : understanding tree mortality and wildfires with microwave remote sensing of vegetation water stress

Vegetation water stress is a key driver of several critical processes in the Earth system. The amount of water stress an ecosystem can tolerate affects stomatal closure and thus its ability to sequester carbon dioxide (including anthropogenic emissions), and transpire water vapour. High amounts of vegetation water stress can also deplete water stored in vegetation, leaving them flammable and vulnerable to wildfires. Further, prolonged water stress in vegetation can lead to hydraulic failure in the xylem, eventually leading to drought-driven mortality. Both mortality and wildfires can lead to permanent changes in vegetation cover, and also impact ecosystem services such as air and water quality, recreation, and timber. However, despite its importance, we lack accurate, real-time, scalable measurements of vegetation water stress. In this dissertation, I first introduce three methods to estimate vegetation water stress with microwave observations ranging from plot-scale to global scale. I then show that vegetation water stress can predict drought-driven tree mortality in California, and wildfire hazard in the western US. In Chapter 2, I introduce a P-band side-facing radar measurement system to measure vegetation water stress in $\approx$ 100 m scales. In Chapter 3, I derive a new method to estimate vegetation water stress using an X-band satellite radiometer, and show that it is the best predictor of drought-driven forest mortality in California as compared to all existing metrics. In Chapter 4, I design a physics-guided deep learning algorithm to map live fuel moisture content- the percentage of vegetation water per unit dry biomass across the western US using several satellite measurements, including a C-band synthetic aperture radar. Using the resulting live fuel moisture content maps, in Chapter 5, I show that plant sensitivity to water limitation regulates the rise in burned area under a warming climate. In Chapter 6, I use the same maps to quantify the effect of live fuel moisture content on wildfire ignition probability using a causal inference framework. Together, this research provides the tools and data to estimate vegetation water stress across scales, and also shows its impacts on tree mortality and wildfire hazard

Keywords: Earth System Science.
Advisor: Konings Alexandra
Diffenbaugh Noah S.
Schroeder Dustin
Williams Park
Parking system : sensors, deployment, and evaluation

Parking is a headache in urban areas during busy hours. In this thesis, we propose and deploy an intelligent framework, based on wireless sensing networks, to provide both historical and real-time parking information to better help drivers find available parking spots. Utilizing the data collected by wireless sensors, we can further predict the parking occupancy rate to help commuters plan their daily trips to avoid parking congestion. More precisely, we first describe a system that senses the parking and provides parking availability information for users in a cost-effective and efficient manner. The hardware framework, in addition to being highly scalable, is built on advanced wireless sensor networks and cloud service over the Internet. The parking information provided to the users is set in the form of occupancy rates and expected searching time. Both are obtained from our analytical algorithm processing both historical and real-time data, and are thereafter visualized in a color theme. The entire parking system is deployed and extensively evaluated at Stanford University Parking Structure-1. After building the system and collecting data, we then develop an intuitive and accurate way to interpret parking availability by selecting an efficient algorithm to predict parking occupancy through an aggregation approach. The proposed Adaptive Autoregressive model yields better results than other predictors. Additionally, we disclose a simple empirical error curve that describes prediction performance against the aggregation level to understand the trade-off between estimation accuracy and spots spatial granularity. Finally, our parking information system matches well with real scenarios. Our pipeline of deploying sensing hardware, collecting data, and using analytical tools opens new opportunities for drivers to plan trips strategically and for urban planners to design policies (e.g., dynamic pricing or new parking constructions) comprehensively to balance the mobility demand in cities

Advisor: Rajagopal Ram
Partial reprogramming of the aging neurogenic niche as a potential rejuvenation strategy

Aging is associated with a decline in function of cells and tissues, accompanied by a dramatic increase in the incidence of many diseases including neurodegenerative diseases and cancers. Importantly, the accumulation of age-associated changes is not inevitable. Understanding how to slow down or potentially even reverse the process of aging in different cell types is critical to the goal of preserving tissue function and organism health during aging. One interesting strategy to reverse aging is reprogramming, through the forced expression of the Yamanaka reprogramming factors OCT4, SOX2, KLF4, and c-MYC (OSKM). Reprogramming of somatic cells by constant expression of OSKM results in embryonic stem cell-like cells and erases many hallmarks of aging in vitro. However, the impact of OSKM expression on cell function and heterogeneity in specific cell types in old animals is not fully known. In this dissertation, I present my work on aging and reprogramming. First, I discuss several categories of rejuvenation strategies that have recently been studied in mice, including soluble blood factors, manipulation of diet and metabolism, killing of senescent cells, and reprogramming. Next, I explore how partial reprogramming affects the subventricular zone (SVZ), a conserved neurogenic niche in mammalian brains. Partial reprogramming, achieved by expression OSKM in a time- or cell-restricted manner, has been shown to improve function in a variety of cell types from aging mice without permanent loss of cell identity. But the impact of partial reprogramming on the aging brain is largely unknown. I focus on the SVZ, a neurogenic niche which holds intrinsic regenerative potential, as neural stem cells from the SVZ can give rise to newborn neurons and astrocytes throughout adulthood. Lastly, I examine the impact of aging and heterogeneity on reprogramming of fibroblasts, the most commonly used cell type for reprogramming to pluripotency. Together, these studies demonstrate the complex interplay between aging and reprogramming, and the potential for reprogramming to be applied as a tool to counteract age-related decline

Keywords: Biology.
Advisor: Brunet Anne
Dixon Scott James
Nakauchi Hiromitsu
Shen Kang
Wyss-Coray Anton
Partitioning solidarity : Palestine and the British left, 1923-48

"Partitioning Solidarity" reconstructs the debate over Palestine among the British left between 1923 and 1948, the years of the British Empire's Mandate for Palestine. it reveals that contrary to the standard narrative—that the British left at first supported Zionism before "divorcing" Israel after the 1967 Arab-Israeli—in truth the "problem of Palestine" was a source of conflict within the British left from the very beginning. There was no clear "leftist position" in these formative years; rather, individual leftists debated, negotiated, and agonized over which group in Palestine to stand in solidarity with. Driven by the particularity of events in Palestine, and of Palestine's place in the British cultural imagination, these leftists presented new possibilities for solidarity, both between the metropole and the Empire and within the British left itself. By the end of Britain's Mandate for Palestine, however, this moment had closed. This dissertation thus provides a new "origin story" for the Arab-Israeli Conflict's divisive place in the history of the British left. At the theoretical level, it argues for a renewed engagement with solidarity as an analytic historical category. Recent research on the culture of the British Empire has focused on the pervasive power of Empire in shaping the minds of Britons to view colonial subjects as "Others." While important, this body of work has made imperial power seem impenetrable and resistance to it futile. Examining how some Britons were able to form international bonds of solidarity with people whom their culture declared unknowable Others, even in the face of the culture of imperialism, allows us to probe the weaknesses of imperial discourse rather than emphasize only its power

Keywords: History.
Advisor: Satia Priya
Barakat Nora Elizabeth 
Como David R.
Pediatricians’ Knowledge, Practice Patterns, and Barriers in Treating Lower Urinary Tract Symptoms: A Qualitative Study

Importance: Pediatric lower urinary tract symptoms (LUTS) are common experiences among school-aged children, with prevalence rates reaching as high as 20%. Pediatricians are first-line stakeholders in providing treatment for these bothersome symptoms, yet little knowledge exists about the treatment of LUTS by primary care providers. Evaluating pediatricians’ knowledge, beliefs, and practice patterns toward LUTS is an important step in developing resources to help clinicians treat LUTS and facilitate LUTS treatment at the primary care setting instead of the subspecialty care setting.
Objective: To explore pediatricians’ perspectives on the barriers and facilitators to providing care for children with LUTS and to identify their practices, knowledge, and beliefs about LUTS.
Design: This qualitative study was conducted using semi-structured key informant focus groups of pediatricians from Northern and Central California. A moderator guide was developed based on the social-ecological model, previous literature, and feedback from pediatricians and urology providers. Thematic analysis was performed using deductive and inductive approaches.
Participants: English-speaking pediatricians from Northern and Central California caring for children with or without LUTS.
Results: 15 pediatricians were interviewed. Participants were between the ages of 30-69 years and two were men. Practice types included general outpatient settings, hospital-based/inpatient, and subspecialty. Pediatricians believe pediatric LUTS is a common problem that can significantly impact a child’s well-being. In practice, pediatricians do not actively screen for LUTS beyond the potty training period due to limited clinic visit time and competing healthcare demands. Pediatricians feel limited in their ability to influence behavioral change in the home setting. Referrals to subspecialists are driven by parental mistrust and expectations. School-level factors are identified as barriers to bladder health. Pediatricians wish they had clear guidelines and additional residency education. They also recommend the development of resources for parents and teachers.
Conclusion and Relevance: This information may help develop and implement education tools for the primary care setting, which can be used prior to the onset of LUTS, shifting the focus from treatment to prevention.

Keywords: Medicine
Pediatricians
Lower urinary tract symptoms
Bowel and bladder training
Urotherapy
Urinary incontinence in children
Urinary incontinence
Primary care (Medicine)
Pediatrics
Barriers and Facilitators
Pediatricians' beliefs
Pediatricians > Attitudes
Qualitative research
Focus groups
Community Health and Prevention Research
Text
Thesis
Advisor: Kan Kathleen M.
Sharma Aditi
Brown-Johnson Cati
A penny-sized wearable wireless EEG recorder

Electroencephalography (EEG) is a test to record electrical activity in the brain by small electrodes through signals on the scalp. Due to its non-invasiveness, EEG recording has been widely used in a variety of applications, including sleep study, mental health monitoring, brain-computer interface, etc. However, mainstream clinical recording systems are still tethered with wet electrodes that require special preparation, limiting the setup to well-equipped labs and preventing the collection of longitudinal data. In this thesis, we summarized the special characteristics of EEG signals and presented a distributed recording system based on a penny-sized 1.2-gram (battery included) wearable wireless EEG recorder for long-term non-intrusive mental health monitoring. The core of the wearable EEG recorder is a custom designed chip, each with two signal-acquisition front-ends and a frequency-division multi-access (FDMA) transmitter. The signal-acquisition circuit is based on a direct recording 2nd-order ΣΔ ADC, which has an input-referred noise of 0.82 μVrms, a peak ENOB of 9.4 bits and an auto-ranging and fast-settling algorithm to cope with large instantaneous artifacts and interferences. The FDMA transmitter uses OOK modulation and supports in total 32 concurrent data telemetry channels, 12 of which are in the 915-MHz ISM band. This enables in total 24 concurrent recording sites in ISM band, and 64 sites if the experiment is in an isolated environment outside of FCC regulation. System functionality is also validated by comparing it to a clinical-grade instrument in two common EEG experiments, eye-closed alpha wave test and visual event-related potential (ERP) measurement. Similar performance has been observed between the two setups, proving our new system's potential to transform EEG measurement from uncomfortable tethered setup in the clinic, to non-intrusive long-term mental health monitoring at home

Keywords: Electrical Engineering.
Advisor: Poon Ada Shuk Yan
Pauly John (John M.)
Wong S. Simon
People and the sea in the Mascarenes : social-ecological impacts of disaster

Coastal communities face increasing risks in the Anthropocene, including a multitude of climatic and non-climatic stressors, which threaten livelihoods and wellbeing. Local environmental stewardship, which encompasses environmental conservation actions, active restoration activities, and the sustainable use and management of resources, is fundamental to responding to these growing stressors. In this dissertation, I draw on a community-engaged approach with a social-ecological lens to highlight the environmental and social justice implications of these threats for vulnerable coastal communities.   Across three studies, I examine how coastal communities are impacted by and respond to two compounding disasters: COVID-19, and an oil spill in the Republic of Mauritius. Through the first study, I explore how historical social-ecological context shapes local environmental stewardship. The second study demonstrates how we can integrate measures of pro-ecological behavior into the future planning of marine protected areas, an example of environmental stewardship action. In my third study, I present a comparative case study of how multiple stakeholder groups responded to the 2020 Wakashio oil spill in Mauritius and the 2021 Huntington Beach oil spill in California, to improve social learning for future disasters. Collectively, the results shed light on factors influencing environmental attitudes and behaviors, how that, in turn, can influence better planning and success of local environmental stewardship efforts such as protected areas, and the need for multi-stakeholder collaboration in pre-disaster management plans. Together, these findings contribute to our understanding of how intrinsic and extrinsic factors at a localized level can improve community inclusion and equity for local environmental stewardship actions and disaster preparedness

Advisor: Crowder Larry B.
Seetah Krish
Dunbar Robert B.
O'Leary Jennifer K.
Performance optimization of MEMS gyroscopes and their shock survivability

In recent times, MEMS gyroscopes have become more integral to the way we perceive the world. Recent MEMS gyroscopes address the size, cost, and power consumption considerations that have previously limited gyroscope applications. Of particular interest to this work is the MEMS version of the Disc Resonating Gyroscope (DRG). This design is compatible with wafer-scale manufacturing while also offering improvements such as reduced drift and high signal/noise. If this device is going to be used in wider applications, the quality factor and shock performance need to be examined. In this work, we show that the performance of DRGs can be improved if we alter the traditional structure into a serpentine ring structure. This serpentine ring structure or springy DRG (SRG) shows great potential to have a higher quality factor. We see improvements on the order of 2.5X as well as interesting opportunities for further improvement once the design is parameterized. We find DRG designs that depart from the "Zener curve" for ring resonators, showing greater potential for high-performance applications. On the flip side is that these new applications may also be subject to strong shocks. As MEMS gyroscopes are being used in more applications, understanding their survivability is of paramount performance. We explored the shock survivability profile of over ten DRGs and determined consistent survivability over 50,000g. Even more interesting is the variety of responses to the shocks of the devices. As expected, we see that the quality factor and resonant frequency are affected for some of these devices at these high shock levels. We also see that the frequency tuning curve of these devices had an unpredictable response to great shock. In this work, we find that through shock testing of these devices and parametric optimization of disc resonating gyroscopes, we can have a path to improved performance and gain a more in-depth understanding of shock survivability

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William
Howe Roger
Senesky Debbie