VictorJuiz/thesis huggingface dataset:
Dry well performance analysis : efficiency of stormwater capture and emerging contaminant removal

Dry wells are vadose zone infiltration wells that are deeper than their widest surface dimension. Dry wells are promising for urban stormwater capture and recharge because of their high infiltration capacity, low cost, and small footprint. However, little is known about how much stormwater can be captured by dry wells. Furthermore, since dry wells bypass the natural contaminant attenuation processes in topsoil, concerns have been raised about potential groundwater contamination by dry wells especially for hydrophilic organic compounds. This study applies field monitoring, mathematical modeling, and laboratory testing to address the abovementioned concerns about dry wells. In the first part of the study, a hydrologic model was constructed using Storm Water Management Model to estimate the stormwater capture efficiency of dry wells under various climate conditions and evaluate different dry well deployment strategies. In the second part of the study, four pilot-scale stormwater treatment systems [i.e., biochar-amended filters, regenerated activated carbon (RAC)-amended filters, UV/H2O2 + biochar-amended filters, UV/H2O2 + RAC-amended filters] were developed and their performance for removal of hydrophilic contaminants of emerging concern (CECs) was tested under high flow rates and continuous CEC dosing. The field lifespan of the developed systems was estimated for a demonstration case study in a Los Angeles neighborhood using a contaminant transport model. Results from this work show that dry wells can be configured to capture about 20% of annual rainfall in Southern California. However, this efficiency will decrease because of climate change and thus better deployment strategies need to be employed. UV light coupled with black carbon-amended filters are cost-effective stormwater treatment systems for the removal of hydrophilic CECs in dry wells. Adopting these systems in dry wells can effectively increase public acceptance for stormwater capture and facilitate future deployment of dry wells.

Keywords: Engineering.
Advisor: Luthy Richard G.
Fendorf Scott
Fletcher Sarah (Sarah Marie)
Efficient learning from 3D molecular structures using equivariant neural networks

Deep learning methods operating on three-dimensional (3D) molecular structures show promise in addressing vital challenges in biology and chemistry. The scarcity of experimentally determined structures, however, poses a significant hurdle in many machine learning applications. The incorporation of equivariance into deep learning models, leveraging inherent symmetries in structural biology problems, is essential for efficient learning from limited data. This dissertation delves into the utilization of rotationally and translationally equivariant neural networks in various structural biology problems. These include protein model quality assessment, the development of a machine learning--based scoring function for protein-ligand docking that considers protein flexibility, and the implementation of pocket-aware 3D fragment-based ligand optimization.

Keywords: Engineering.
Advisor: Dror Ron
Feng Liang
Kundaje Anshul
Maduke Merritt C.
Electrochemical sulfur recovery from sulfide-containing wastewaters

Shifting paradigms from wastewater treatment to resource recovery requires innovative processes for converting contaminants to products to address water scarcity, combat resource depletion, and promote circular economies. Sulfide, a contaminant in wastewater, can be recovered as sulfur-containing products that add value to various industrial manufacturing processes. Electrochemical sulfur recovery from wastewaters exhibits advantages in terms of modularity and tunability, but further insights are required to transform this opportunity into a robust and stable practice that yields a diverse portfolio of recovered sulfur products from wastewaters. Therefore, this dissertation explores mechanistic- and process- level understanding of both bulk and interfacial reactions during electrochemical sulfur recovery to guide the design and optimization of process with enhanced performance and feasibility. Specifically, the rate-limiting steps and reaction barriers of electrochemical sulfide oxidation were identified by product quantification and electrode characterization. Then, the performance of electrochemical sulfate production was evaluated in a broad range of sulfide-containing wastewaters. Integration of sulfate production and nitrogen recovery was also demonstrated via electrochemical stripping. Finally, gas evolution reactions at electrode-electrolyte interfaces were probed using scanning electrochemical microscopy to inform electrode design for electrochemical sulfur recovery and, more broadly, for electrochemical water treatment. The insights from this dissertation will advance water reuse and a circular sulfur economy by enabling sulfur recovery and informing the incorporation of electrochemical unit processes into wastewater treatment trains.

Keywords: Engineering.
Advisor: Tarpeh William
Criddle Craig
Mitch William A.
Enabling agile hardware development with the PEak programming language

Domain-specific languages for hardware can significantly enhance designer productivity, but sometimes at the cost of ease of verification. On the other hand, ISA specification languages are too static to be used during early stage design space exploration. This dissertation presents PEak, an open-source hardware design and specification language, which aims to improve both design productivity and verification capability. PEak does this by providing a single source of truth for functional models, formal specifications, and RTL. PEak has been used in several academic projects, and PEak-generated RTL has been included in multiple fabricated hardware accelerators. In these projects, the formal capabilities of PEak were crucial for enabling both novel design space exploration techniques and automated compiler synthesis.

Keywords: Engineering.
Computer Science.
Advisor: Barrett Clark
Hanrahan P. M. (Patrick Matthew)
Horowitz Mark (Mark Alan)
Engineered proteins to NKp46 for cancer therapeutics

NKp46 (NCR1, CD335) is an activating receptor expressed on the surface of natural killer (NK) cells in the immune system. NKp46 has been the target of NK cell engaging bispecific antibodies in recent years, with multiple studies demonstrating the potential of engaging NKp46 for antitumor responses in cancer. In this thesis, I discuss the discovery and engineering of antibodies and fibronectin domain proteins that bind to either human NKp46, mouse NKp46, or both using phage display and yeast surface display. One species cross-reactive antibody was epitope mapped to conserved mouse and human amino acid residues and could induce NK cell proliferation and activation. A panel of NK cell engager (NKCE) bispecific antibody constructs was created from binders of both NKp46 and the tumor antigen CD20 to explore NCKE configurations, valency, and Fc effector functions. NKp46 engagement with the bispecific antibodies was shown to increase NK cell cytotoxicity against tumor cells as compared to the anti-CD20 antibody alone in an Fc-independent manner. This thesis contributes to a body of work related to NKp46, NCKEs, and cancer therapeutics, and provides a number of proteins as useful tools for basic science and translational applications.

Keywords: Engineering.
Chemical Engineering.
Advisor: Cochran Jennifer R.
Swartz James R.
Sunwoo John B.
Engineering catalyst interfaces for carbon dioxide utilization

CO2 hydrogenation provides the unique opportunity of valorizing this greenhouse gas to a variety of chemicals, and the selectivity towards a specific product relies in first place on the heterogeneous catalysts used to accelerate the rate of the reactions, whose properties are further dictated by their structure. Conventional heterogeneous catalysts consist of multiple elements in their metal and/or oxide form supported on oxide materials, and the interface between the metal(s) and the supporting oxide has been identified as a crucial aspect in achieving reactivity and selectivity beyond what can be obtained with individual components. This dissertation focuses on three types of catalyst interfaces, and the impact of their structure on CO2 hydrogenation reactions. This knowledge acquired during my PhD was utilized to design novel catalyst structures that achieved unprecedented activity and selectivity for CO2 hydrogenation towards valuable products.

Keywords: Engineering.
Chemical Engineering.
Advisor: Cargnello Matteo
Bao Zhenan
Mai Danielle
Engineering self-assembling superantigen as cancer immunotherapy

Superantigens are the most potent immune activating molecules known in nature. As such, they hold unique potential in the field of cancer immunotherapy, where treatments demand vigorous stimulation of the immune system. Studies in immunotherapy point to a tension between two opposing factors: the need to increase effectiveness while decreasing adverse reactions. Superantigens provide an avenue for a magnified boosting of the immune system, but likewise necessitate greater molecular control and precision to leverage this capacity. This thesis focuses on utilizing computational tools to propose a novel method for introducing molecular logic gate control into an existing superantigen, and consequently harness the unique ability of these proteins while providing a mechanism for control. In the first chapter, we begin with a review of the molecular interactions and strategies behind existing superantigen therapies. We then leverage the computational protein design program RosettaRemodel in chapter two in order to design the molecular logic gates AND and NOT into a superantigen through creating a novel fusion protein between the Mycoplasma Arthritidis Mitogen superantigen and the TIM (triose-phosphate isomerase) barrel. Next, in chapter three we express a focused library of computational solutions and identify the optimal conditions for production and characterization of an ideal design. Finally, in chapter four we experimentally test and quantify the anti-tumor activity of our designed superantigen through both in vitro and in vivo studies, ending with conclusion of our work in chapter five.

Keywords: Engineering.
Bioengineering.
Advisor: Cochran Jennifer R.
Huang Possu
Engleman Edgar G.
Enhancing machine learning with data-efficient methods

Supervised deep learning techniques have made a tremendous and unprecedented impact in all segments of our lives, including finance, healthcare, social networks, and more. However, the progress is hindered by a substantial challenge: the dependence on large, high-quality labeled datasets. This issue is particularly acute in areas such as biomedicine, where the procurement and annotation of data are not only costly but also intricate. In response to these challenges, this thesis introduces innovative machine learning strategies that are data-efficient, aiming to reduce the dependence on extensive labeled datasets while either preserving or improving the efficacy of deep learning models. The thesis is systematically divided into two primary sections, each targeting key aspects of data-efficient machine learning. Part I is dedicated to the development of advanced algorithms optimized for existing datasets, particularly under the constraint of limited labeling. This section introduces a novel machine learning setting for enhancing generalization and robustness in low-label scenarios, proposes an innovative open-world semi-supervised learning framework, and adapts this framework to real-world applications. Part II focuses on augmenting training resources by incorporating supplementary knowledge. It explores the integration of auxiliary tasks to enhance training, examines the use of historical data to improve AutoML search efficiency, and introduces methods for including large datasets that were previously unmanageable due to memory constraints.

Keywords: Engineering.
Advisor: Leskovec Jurij
Koyejo Oluwasanmi
Ma Tengyu
Essays in political economy : status perceptions and survey experiments

This dissertation contains three chapters each of which addresses topics related to status perceptions and survey experiments. The first chapter provides a new theory that clarifies the mechanism through which low perceptions of subjective status can lead to increased support for populist and populist-right candidates. The second chapter is the experimental extension of the first chapter, and it implements a survey experiment with a treatment that induces respondents to hold lower perceptions of their socioeconomic status. The last chapter is a methodological investigation of adaptive algorithms' relative performance in efficiently identifying the best arm compared to uniform randomization, the most widely adopted experimental design in social science, in a setting with multiple treatments and a limited budget.

Keywords: Business.
Advisor: Shotts Kenneth W.
Broockman David E.
Malhotra Neil Ankur
Ethics without moralism : an essay on agency, reason, and responsibility

In this dissertation I appeal to a substantive moral ideal of autonomy to defend "constitutivism in ethics", i.e. the view that there are constitutive standards of action which inform the range of morally legitimate answers to the question of how one should live. I first argue that a minimally satisfactory theory of action must recognize the exercise of practical rationality to be constitutive of the exercise of agency, at least for agents who are persons. It follows that there are constitutive standards of action, namely the standards of practical rationality. From here I contextualize contemporary constitutivism within a larger philosophical tradition. According to what I call "the generalized guise of the good thesis", the exercise of person-guided agency constitutively involves the exercise of practical reason. Although it is articulated using different concepts than the previously-established claim - talk of "practical rationality" concerns foremost the guidance of action, but talk of "practical reason" concerns its justification -, to endorse the generalized guise of the good thesis is to hold the distinction to be shallow: both pick out what is fundamentally the same agential capacity, necessarily exercised whenever a person exercises her agency. Finally I argue that the antithesis of constitutivism, a view I call "separatism about agency and practical reason", embroils one in a dubious form of moralism quite at odds with the ideal of autonomy. In particular I argue that the separatist does not do enough to relate her agent-directed moral judgments to the agent's own practical rationality; in this way she repeats the mistake embedded within more concrete forms of moralizing, only at a higher level of abstraction.

Keywords: Humanities and Sciences.
Philosophy.
Advisor: Lawlor Krista
Schapiro Tamar
Bratman Michael
Dannenberg Jorah
Hills David James
Evolved and engineered molecular force sensors in the brain

Mechanical force plays an integral role in biological processes ranging from tissue development to cancer metastasis, but the ways by which forces are transduced remain largely unknown. In particular, force has emerged as a potentially important driver of processes involved in the formation and function of the nervous system and brain. In the first portion of this work, I discuss two ways in which mechanical force can regulate important physiological processes in the brain at the molecular and cellular scales. First, I describe our efforts to characterize the mechanosensitivity of latrophilins, a class of adhesion G-protein coupled receptors (aGPCRs) that are implicated in multiple neuropsychiatric diseases and control excitatory synapse formation. These molecules were hypothesized to function as mechanosensors at the synapse, but the physiological plausibility of such a hypothesis was unknown. Using magnetic tweezers, we demonstrate that forces of 1-10 pN, well within the physiological range of forces, are sufficient to accelerate the rate of a key conformational change in the latrophilin-3 receptor by 10000-fold compared to the rate in the absence of force. Thus, mechanical force may be a driver of latrophilin signaling during synapse formation, suggesting a physiological mechanism by which aGPCRs may mediate mechanically induced signal transduction. As a second example, I discuss our work exploring changes in the force generation capabilities of neural stem cells in the aging brain. ATAC-seq of activated neural stem cells (aNSCs) from mouse brains reveals that chromatin accessibility is enhanced at loci associated with cell-substrate adhesion in older brains compared to younger brains. We use FRET-based force sensors to measure forces associated with cell-ECM adhesion in aNSCs and demonstrate that these adhesive forces are heightened in aNSCs from older brains. In the second portion of this work, I describe a new class of molecular tension sensors that we have engineered to increase the accessibility of force measurements in biological systems. These tension sensors are derived from the human muscle protein titin and can be used in fixed or live cells to provide either fluorescent or bioluminescent readout of the spatiotemporal dynamics of force transmission. We use magnetic tweezers to demonstrate that our sensor responds to forces > 2 pN and apply our sensor to living systems to visualize physiological, cell-generated adhesive forces. These results illustrate the utility of our tools for measuring molecular-scale forces in biological systems, which may facilitate a better understanding of mechanical forces in the brain and in biology more broadly. Taken together, these studies highlight several mechanisms that nature has evolved for force sensing in the brain and outline ways in which force sensors can be engineered to uncover new insights about mechanotransduction.

Keywords: Engineering.
Chemical Engineering.
Advisor: Dunn Alexander Robert
Khosla Chaitan
Südhof Thomas C.
Exploration and analysis of a blind hydrogen system in western California, USA

This work presents a comprehensive exploration and analysis of a “blind hydrogen system” in Western California. Previous discoveries of natural hydrogen accumulations in various global locations suggest that hydrogen can form in geological settings, often indicated by surface features like "fairy circles". This study pioneers the concept of exploring for "blind hydrogen systems" - areas where geological configurations conducive to hydrogen formation exist, but without surface indications like fairy circles. The hypothesis is that certain geological settings conducive to hydrogen formation exist beyond areas marked by fairy circles. The research involves the assessment of several geological settings, including the presence of ultramafic rocks, aquifers, faults, and serpentinized rocks, to identify potential hydrogen systems. Field studies were conducted in Jasper Ridge Biological Preserve and Portola Valley, California, utilizing soil gas sampling to detect hydrogen presence. Laboratory analyses included measurements of hydrogen, carbon dioxide, methane, and other associated gasses. Results indicated hydrogen concentrations up to 20.32 ppmv in Jasper Ridge and 17.32 ppmv in Portola Valley, with significant seasonal and diurnal variations observed. The study also noted
anomalous concentrations of carbon dioxide and methane, suggesting possible abiotic origins. This work contributes to the understanding of natural hydrogen occurrence and proposes a methodical exploration approach for identifying 'blind hydrogen systems'. It demonstrates the potential for discovering natural hydrogen resources in areas without apparent surficial indicators and underscores the importance of developing systematic methodologies for their identification and exploration.

Keywords: Earth and Planetary Sciences
Blind hydrogen system
Fairy circles
Serpentine
Ultramafic
Hydrogen
Basin Processes and Subsurface Modeling
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Thesis
Advisor: Graham Stephan
Mukerji Tapan
Exploring connections at the mammalian cell surface

Monoclonal antibodies have become powerful tools for biomedical research and cancer therapy. However, identifying the precise molecular targets of monoclonal antibodies can be challenging. This thesis leverages emerging techniques in proteomics and genome editing to elucidate the targets of two clinically relevant monoclonal antibodies. First, we re-evaluate putative RNA binding by galectin-3 using CRISPR-mediated gene knockouts and endogenous epitope tagging. We demonstrate that previously reported RNA interactions are likely an artifact resulting from cross-reactivity with the RNA-binding protein hnRNPA2B1. Our findings refute direct RNA binding by galectin-3 in HeLa, underscoring the need for stringent controls when characterizing antibody targets. Next, we uncover the molecular identity of the cryptic tumor-associated antigen TAG-72 after decades of uncertainty. We identify the mucin protein MUC2 as a dominant TAG-72 carrier in colon cancer cells. Further analysis defines TAG-72 as aberrantly glycosylated sialyl-Tn pattern on select mucin-like domains. By integrating cutting-edge proteomic and genomic techniques, this thesis provides molecular insight into two clinically important monoclonal antibody targets. Our strategy of leveraging emerging technologies to characterize antibody epitopes could be widely applied to clarify other enigmatic biomarker interactions relevant to medicine and biology.

Keywords: Medicine.
Chemical and Systems Biology.
Advisor: Bertozzi Carolyn R.
Long Jonathan Z.
Martinez Nicole M.
Wysocka Joanna
For the Nations or Against the Nations: Wang Jingwei’s and Kawashima Yoshiko’s Rationales for Collaborating with Japan

Traditional mainland Chinese historiography emphasizes Japan’s brutality during World War II and utilizes the “myth of resistance” to attribute political legitimacy to the Chinese Communist government for defeating the Japanese invading forces during the Second Sino-Japanese War (1931–1945). As indicated by the terminology used in China to refer to the conflict, the “War of Resistance against Japanese Aggression,” the prevailing narrative insists that the only acceptable response to Japan was resistance. Collaboration with Japan, viewed as an act of moral failure, is condemned, as collaborators witnessed Japanese atrocities yet chose to assist Japan in exploiting their compatriots. In China, collaborators are labeled as hanjian (traitors to the Han nation) or maiguozei (thieves who sell out their country), implying that they supported Japan in exchange for personal gain at the expense of the Chinese nation’s existence. Through the examination of two case studies of Chinese collaborators—Wang Jingwei (1883–1944) and Kawashima Yoshiko (1906?–1948)—this thesis argues that collaboration and nationalism were not necessarily mutually exclusive. Contrary to being traitors to their nation, they espoused nationalism and even cited it as their rationale to collaborate with Japan.

Keywords:  Stanford Global Studies
Collaboration
Sino-Japanese War (1937-1945)
Wang, Jingwei, 1883-1944
Kawashima, Yoshiko, 1906?-1948
Resistance
Historiography
Traitor
Nationalism
Transnationalism
Text
Thesis
Advisor: Wang Ban