VictorJuiz/thesis huggingface dataset:
Surface water-groundwater interactions during extreme floods : hydrologic and biogeochemical controls on water quality

In both natural and human-impacted ecosystems, floods play a pivotal role in shaping our environment. In natural systems, floods replenish groundwater and support riparian habitats. In intensively managed environments, engineered floods have become a valuable tool for mitigating the effects of global change. During flood managed aquifer recharge (flood-MAR), for example, water managers intentionally inundate working landscapes in order to replenish depleted aquifers. Both natural and engineered floods deliver an influx of water and reactive species into the subsurface, triggering a complex web of hydrologic and biogeochemical processes that can mobilize nutrients and contaminants, impacting water quality. Through a combination of modeling and data science approaches, my research sifts through this complexity and seeks to understand the fundamental drivers of surface and groundwater quality during extreme floods. In my first chapter, I examine the impact of seasonal floods on redox cycling in heterogeneous floodplain aquifers. Through stochastic reactive transport simulations, I show that the hydrogeologic properties of a floodplain often exert a stronger control on redox conditions than do biogeochemical reaction rates. In subsequent chapters, I identify controls on the movement of water and solutes through the subsurface during flood-MAR. Using high-resolution hydrogeophysical data and hydrologic simulations, I find that tension-driven flow within the vadose zone draws recharge water away from coarse-grained flow paths and traps it in lenses of fine-grained sediment. These fine-grained sediments can take years to drain following inundation, limiting recharge efficiency. In my final chapter, I pair hydrologic simulations with Lagrangian particle tracking to investigate contaminant transport during flood-MAR. Results reveal that recharge water applied at the surface takes decades to reach the water table, during which time some contaminants may be removed through biogeochemical reactions. Overall, my work deepens our understanding of subsurface hydrologic and biogeochemical processes during inundation and provides actionable insights for sustainable water resource management in a changing climate.

Keywords: Sustainability.
Earth System Science.
Advisor: Maher Katharine
Gorelick Steven M.
Kitanidis P. K. (Peter K.)
Survival after Hospital Admission in Adults with Liver Cirrhosis in California

Cirrhosis of the liver currently ranks 9th amongst all causes of death in the United States, with a prevalence of 0.27%. In the world, with a prevalence of about 1.4%, it caused around 1.32 million or 2.4% of the total deaths in 2017. Cirrhosis is characterized by widespread fibrosis and regeneration of liver tissue, which is in response to irreversible and usually prolonged damage to the liver. The continued presence of the inciting factor causes progression to end-stage liver disease with or without hepatocellular carcinoma or liver cancer. The commonest cause in the US is chronic viral hepatitis by Hepatitis C or Hepatitis B virus, while alcohol-associated liver disease is more common worldwide. Currently, cirrhosis due to hepatitis is on a downward trend because of newer, more effective therapeutic options, whereas a lifestyle disorder called non-alcoholic fatty liver disease, as a cause of cirrhosis, is on the rise.
Survival with compensated liver cirrhosis is estimated to be around 12 years, while it is only 2 years with the decompensated form of the disease. There has not been any major population-based study in the United States providing us with recent survival estimates. Hence, to obtain current estimates, we used the Health Care Access and Information (HCAI) Patient Discharge Database of the Government of California to obtain a cohort of all California adults with diagnosed liver cirrhosis from 2005 to 2013. This database is linked to the California Comprehensive Master Death File via a unique Record Linkage Number, which allowed us to perform a time-to-death analysis. Using Kaplan-Meier methods, we estimated the median survival time for the sample overall, and stratified by variables like age, sex, race, ethnicity, payment type, and decompensation status. We used Cox proportional hazards regression to estimate hazard ratios for the outcome of death.
Our sample size consisted of 193,127 adults with an average age of 59.4 and a standard deviation of 13.1 years. 63.5% of our sample was male, 70.2% were white, and 30.7% were of Hispanic ethnicity. 39.3% were decompensated at baseline, and 39.1% of the sample used Medicare to pay for the services received. The median survival time for the overall sample was 4.16 (95% CI 4.09-4.24) years, with age more than 68 years and decompensated disease increasing the risk of death by 99% (95% CI 95%-104%) and 53% (95% CI 51%-55%), respectively. Belonging to the Asian race decreased the risk by 7% (95% CI 5%-10%), and the female sex had a 14% (95% CI 13%-16%) lower risk. The median survival for compensated liver disease was 5.37 (95% CI 5.25-5.48) years while it was 2.77 (95% CI 2.71-2.83) years for those decompensated at baseline.

Keywords: Proportional hazards models
Liver cirrhosis- survival
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Thesis
Advisor: Nguyen Mindie
Popat Rita
Synthesis and applications of flower-like polyacrylonitrile (PAN) and PAN-derived carbon superstructures

Polyacrylonitrile (PAN) and PAN-derived carbon materials have diverse applications in areas such as adsorption, separation, energy storage, and biomedical applications. However, synthesizing nanostructured PAN is challenging, often requiring complex, multi-step processes like sacrificial templating. Recently, researchers have reported a simple, one-pot free radical polymerization method for synthesizing flower-like PAN superstructures. This method has drawn increasing interest in recent years due to the unique morphology of the resulting structures. The flower-like shape of the PAN superstructures offers many benefits, including open-pore structures that are well suited for applications such as sensors, separation, catalysis, and energy storage. Additionally, the simple synthesis procedure allows for scalability in industrial production, making it easier to produce large quantities of nanostructured PAN. However, the formation process for the complex flower-like structures in the one-step polymerization reaction remains unclear, and the advantages of the flower-like morphology are still under-explored. This thesis aims to contribute to our understanding of the flower-like PAN superstructures and their potential uses in various fields. The thesis consists of four main parts. The first part provides a comprehensive review summarizing recent progress in developing similar flower-like superstructures, including their synthesis, formation mechanism, and existing applications. The second part focuses on investigating the formation mechanism of flower-like PAN particles using various in situ and ex situ characterization techniques, such as in-situ ultra-small-angle x-ray scattering (USAXS). The third part of the thesis focuses on fine-tuning and developing more advanced PAN and PAN-derived carbon superstructures. This includes tuning and designing sub-particle level, particle level, and device-level superstructures. The fourth part of the thesis focuses on demonstrating the potential of flower-like PAN and PAN-derived carbon particles (carbon flower) in various applications, including lithium metal anodes, sulfur cathodes, supercapacitors, and flexible pressure sensors. This thesis provides a fundamental understanding of the formation mechanism of flower-like PAN superstructures and demonstrates their advantages in a range of applications

Keywords: Engineering.
Chemical Engineering.
Advisor: Bao Zhenan
Cargnello Matteo
Cui Yi
Synthesis and evaluation of novel tiglianes for PKC-related therapeutic indications

EBC-46 (aka tigilanol tiglate), has emerged as an exciting anti-cancer agent for the treatment of solid tumors. Intratumoral injection leads to activation of its primary target protein kinase C (PKC), causing increased permeability of tumor endothelial cells and subsequent inflammation to lead to tumor death. Currently, EBC-46 is obtained via extraction of blushwood tree berries, a potentially unsustainable supply tree found only in Queensland, Australia. To ensure a sustainable supply and enable further research into EBC-46, my research has focused on the development of a semi-synthesis of EBC-46 from phorbol, an abundantly available starting material. This work was since been published in Nature Chemistry and a patent has been filed. To obtain phorbol, Croton tiglium seeds are subjected to a robust extraction process that affords upwards of 10 grams of phorbol from 3 kg of seeds. With phorbol in hand, the molecule is walked though a unique oxidation sequence that yields EBC-46 in 12 % overall yield and 12 steps (> 2 grams synthesized). With a sustainable supply of EBC-46, several analogs have been synthesized to probe its structure-activity relationship with PKC. Ongoing efforts continue to elucidate how structural changes to EBC-46 influence its PKC isoform selectivity, potency, and therapeutic potential

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Wender Paul A.
Du Bois Justin
Kanan Matthew William
Synthesis, evaluation, and mechanistic analysis of ruthenium(II) precatalysts for C-H hydroxylation

Current efforts to improve C--H oxidation methodologies are constrained by the limited set of structurally flexible metal-ligand complexes capable of effecting such transformations. We describe the development of a synthetic route towards novel heteroleptic Ru(II) complexes bound to both a 2,2'-bipyridine ligand and a strong σ-donating bidentate group. The selective and convenient synthesis of these complexes is possible under mild conditions that promote Ru- cymene ligand substitution. Evaluation of these heteroleptic complexes as precatalysts for C--H oxidation resulted in the discovery of an efficient precatalyst that displays excellent stability and turnover numbers. In efforts to further develop this technology, mechanistic studies to identify catalyst speciation and decomposition pathways were undertaken. A combination of reaction kinetics analysis, isotopic labeling, mass spectrometry, and electrochemical measurements have revealed that ligand oxidation is critical for generating an active catalyst, and highlight reactivity and stability differences between homo- and heteroleptic Ru complexes. Insights gained from these studies should inform development of next-generation C--H oxidation catalysts.

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Du Bois Justin
Burns Noah
Stack T. (T. Daniel P.)
Synthesizing high-quality and controllable tennis animation from real-world video collections

Demonstrations of human performance are important for creating realistic virtual characters. However, collecting high-quality demonstrations via motion capture can be costly in both time and monetary cost, because it requires expensive environment setup and skilled performers to be present at the capture location. In contrast, there is an abundance of video capturing expert-level human performances. Given this observation, this thesis seeks to answer the question: how can we harvest information from internet videos to create realistic virtual human characters? In particular, online videos of athletic events provide a rich sampling of in-activity motion data which encompass the full spectrum of skills an athlete must perform in a sport. The challenge is that compared to the high quality of motion capture data, demonstrations extracted from monocular real-world videos will exhibit errors due to limitations of current machine perception algorithms, and source video deficiencies like occlusions and motion blur. This thesis centers its focus on a specific sports domain: tennis, and demonstrates that it is possible to use large-scale observations of athlete performance obtained from real-world video collections to create controllable, high-quality tennis animations of virtual characters playing singles tennis points. These characters successfully conduct tennis rallies, carry out realistic decision-making, and appear photorealistic. Specifically, this thesis shows that a fairly simple state machine designed given the domain knowledge of tennis, is sufficient to provide structure for building complicated tennis controllers from unstructured video demonstrations. Next, this thesis contributes a system for learning a motion controller from real-world video demonstrations that is capable of precisely controlling a physically simulated character to play tennis points using a diverse set of skills. Finally, this thesis shows that macro-level behavior and player appearance information can be extracted from videos to enhance the realism of synthesized virtual characters. Overall, this thesis creates realistic virtual characters that can be effectively controlled to play singles tennis points involving a diverse array of strokes (serves, forehands, and backhands), spins (topspins and slices), and playing styles (one hand vs. two hand, left hand vs. right hand), as well as macro level behavioral choices that reflect player specific styles, such as shot selection choices. In the limited case of 2D sprite animation generation, it also demonstrates that appearance data from the videos can be employed to yield characters that are photorealistic in their appearance.

Keywords: Engineering.
Advisor: Fatahalian Kayvon
Fedkiw Ron
Liu Karen
Synthetic polyelectrolyte models for understanding partitioning in polyelectrolyte complex coacervates

Polyelectrolyte complex coacervates (PECs) are liquid-like droplets that are formed from mixing oppositely charged polyelectrolytes and are important in biology, food science, and personal care products. Since the first observation of coacervation almost a century ago, there have been several efforts to understand what molecular features affect coacervate stability. However, the physical rules for how PECs selectively partition species remains an unresolved question. In this thesis, I used dye-labeled polyelectrolytes prepared by RAFT polymerization and ICP-MS to understand the partitioning of added divalent salt and its effect on polyelectrolyte partitioning. In the third chapter, I used dye-labeled polyelectrolytes prepared from ATRP, RAFT, and NCA ring-opening polymerizations to understand how the molecular weight of polyelectrolytes affects their partitioning in the coacervate phase. I also used fluorescence microscopy to understand the replacement dynamics of PECs and PECs with an added enzyme. These studies shed light on our understanding of the physical rules for partitioning of components in PECs.

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Xia Yan
Kool Eric T.
Qin Jian (Professor of Chemical Engineering)
Systematic characterization of gene regulatory interactions with high-throughput CRISPR screens

Chapter 1: Hundreds of thousands of cis-regulatory elements (CREs) have been identified across a myriad of cell types and conditions, but relatively few have been empirically characterized. Here, we present a scalable, phenotype-driven CRISPR screen to identify hundreds of essential regulatory elements in K562 cells by perturbing 7,500 DNase hypersensitive sites (DHS) around the top 400 essential genes in K562. In addition to distal enhancers, we identify promoter-overlapping enhancers that selectively regulate multiple genes. Using orthogonal CRISPR systems with narrow or broad perturbative windows, we demonstrate that fine-mapping screens can resolve and characterize core transcription factor binding sites (TFBSs) within enhancers, highlighting the advantages of complementary CRISPR systems to investigate CREs. Lastly, we use our results to further interrogate how transcription factor binding sites hierarchically interact to drive enhancer function at the CBFA2T3 locus. This study demonstrates a scalable CRISPR screening framework for identifying and dissecting CREs that regulate selectable phenotypes. Chapter 2: The ENCODE consortium's encyclopaedia, containing millions of non-coding CREs has advanced our understanding of gene regulatory landscapes. Nonetheless, few CREs have been functionally characterized directly; determining the regulatory effects on gene expression is a critical next step, and pooled, non-coding CRISPR screens have emerged as a valuable tool to endogenously characterize the function of CREs. However, these screens' design, execution, and analysis have been highly heterogeneous. Here, we present the ENCODE CRISPR screen database: the largest, multi-center, standardized collection of non-coding screens to date. We evaluated the most common design and analysis platforms and observed that functional elements are enriched at DHS/H3K27ac sites, while the strongest sgRNAs target the DHS summit. Additionally, we discovered a subtle, previously undescribed target DNA strand-bias for CRISPRi in transcribed regions. Our dataset represents a broad resource for the community, establishes a standardized data format, provides guidelines for screen implementation, and uncovers fundamental insights into gene regulation

Keywords: Medicine.
Genetics.
Advisor: Bassik Michael
Engreitz Jesse
Greenleaf William James
Kundaje Anshul
A systematic study of GaN static induction transistors (a.k.a. vertical FinFETs) for RF applications

Silicon has played a crucial role in the advancement of electronics, but it has limitations in high-power, high-temperature, and high-frequency applications. These limitations have led to the emergence of wide-bandgap semiconductors such as gallium nitride (GaN) as alternative materials. GaN, particularly in the form of AlGaN/GaN high electron mobility transistors (HEMTs), is now commercially utilized. Despite their excellent high-frequency and high-power performance, GaN HEMTs face inherent issues associated with their lateral device structure, including DC-RF dispersion, due to its horizontal channel with electrons confined to a thin sheet near the interface. In recent years, there have been efforts to replace GaN HEMTs with vertical transistor structures for applications where the weaknesses of GaN HEMTs become more pronounced than their strengths. One such structure is the static induction transistor (SIT), which is also called the vertical FinFET. During my time as a Ph.D. student in Professor Srabanti Chowdhury's group, my primary objective was to demonstrate the advantages of this device over HEMTs. To achieve this, I developed a TCAD model to design, analyze, and comprehend the device. The major focus of my work was establishing the complete fabrication process at Stanford. Throughout this phase, numerous challenges arose, stemming from the unique nature of the device structure as well as practical issues encountered in the cleanroom. However, I tackled these challenges systematically, addressing them one by one. Notably, I developed and refined various fabrication techniques, including an accurate sidewall patterning technique, etching of the high aspect-ratio fin structure using alternative mask materials, and plasma-based ohmic contact for low thermal budget processing. The fabricated devices exhibited desirable characteristics such as DC-RF dispersion-free behavior and hysteresis-free operation. The implementation of the new ohmic contact technique resulted in the achievement of the lowest on-resistance in published GaN SIT devices. These achievements represent significant strides towards the realization of next-generation RF electronics.

Keywords: Engineering.
Electrical Engineering.
Advisor: Chowdhury Srabanti
Plummer Jim
Saraswat Krishna
Systems approach to unravel lymphoid development in human bone marrow

Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow (BM) are the source of life-long replenish of immune cells in the humans. Among multiple lineages, T cell, B cell, NK cell, and Innate lymphoid cell (ILC) are classified as lymphoid cells, based on their morphology and developmental origin. However, mainly due to the limited experimental manipulations for human hematopoiesis studies, lymphopoiesis in human bone marrow still remains elusive. To overcome the experimental limitations, we leveraged the systems approach to analyze healthy human BM HSPCs. We conducted a highly multiplexed single-cell proteomic screen to construct a comprehensive protein expression map of human BM HSPCs. From there, we identified several lymphoid progenitor populations by their lymphoid specific functional protein markers. The target populations were assessed for their epigenetic priming for lymphoid lineages by chromatin accessibility. Furthermore, we utilized the protein expression information to identify surface markers to enrich for the target population, prospectively isolated, and functionally validated their lymphoid potentials ex vivo. This multi-omic study exemplifies the integration of a high-dimensional single-cell study with experimental validations. Moreover, we provide a fine-mapped human lymphopoiesis landscape in human hematopoiesis.

Keywords: Medicine.
Microbiology and Immunology.
Advisor: Bendall Sean
Greenleaf William
Davis Mark
Majeti Ravindra
TaleStream: Supporting Story Ideation with Trope Knowledge

Story ideation is a critical and creative part of the story-writing process. It is challenging to support it computationally due to its exploratory and subjective nature. Tropes, which are narrative elements recurring across stories, are essential in stories as they shape the structure of narratives and our understanding of them. In this paper, we propose to use tropes as an intermediate representation of stories to approach narrative design. We present TaleStream, a canvas system that uses tropes as building blocks of stories and provides steerable suggestions of story ideas in the form of tropes. Our suggestion methods leverage data from the tvtropes.org wiki. We find that 97% of the time, trope suggestions generated by our methods provide better story materials than random tropes. Our system evaluation suggests that TaleStream can support writers’ creative flow and greatly facilitates developing stories. Tropes, as a rich lexicon of narratives with available examples, play a key role in TaleStream and hold promise for story ideation.

Keywords: Siu, Alexa
Dernoncourt, Franck
Storytelling
Tropes
Recommender systems
Knowledge graph
Creativity Support Tool
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Thesis