VictorJuiz/thesis huggingface dataset:
Flower of Dreams: Longing and Loss in Yosano Akiko's Man-Mō yūki
Keywords:  Stanford Global Studies
Yosano Akiko
Wu Yousheng
1928
South Manchurian Railway Company
Japanese Poetry
Tanka
Travel Writing
Manchuria
Japanese Imperialism
Stanford Global Studies
Stanford East Asian Studies
Thesis

In 1928, Japanese feminist poet Yosano Akiko traveled to Manchuria at the invitation of the Japanese-operated South Manchurian Railway Company. She recorded the six-week journey in a travelogue, Man-Mō yūki, which is notable for its organization in two parts: prose followed by poetry. English language scholarship on the travelogue has centered on the prose account, discounting the poetry or ignoring it entirely. This scholarship has largely converged around the point of Akiko’s complicity with Japanese imperialism. In this thesis, I examine Akiko’s poetry composed on the journey and show how it reveals ambivalences in Akiko’s position that resist easy categorization. In particular, I examine Akiko’s poetry related to a young Chinese noblewoman she meets on the journey, Wu Yousheng. For Akiko, Wu is a pivotal figure – one who stands at the intersection of literature and politics within the imperial context. Akiko’s poetry related to Wu reveals an emotional narrative of love and loss untold in the prose. Her grief is both personal and political, fueled by a commitment to a Sino-Japanese tradition of poetic exchange that she views as threatened by the violence of imperialism. Lamenting violence without rejecting imperialism itself, Akiko’s position is ultimately ambiguous, eluding a definitive political stance while in the end remaining loyal only to her core vision for poetry as a pure space for the free expression of emotion.
Fluorescence-based R-loop detection : characterization of cellular RNA-DNA hybrid signals
Keywords: Biology.

In this work, we present an improved fluorescence-based R-loop detection method that is more accurate and specific compared to the current standard practice of using the S9.6 antibody in immunofluorescence applications. We used this new procedure to characterize and provide novel insights on cellular RNA-DNA hybrid signals. Additionally, we investigated the nucleotide excision repair (NER)-mediated R-loop processing and explored the mechanisms underlying its impact on genome stability.
Focal adhesion architecture and composition regulate adhesion and traction generation
Keywords: Chemical Engineering.

Biological systems can sense and respond to a range of mechanical forces that can profoundly affect the forms of developing tissues and the progression of diseases. Even individual cells can recognize mechanical inputs that drive changes in cellular behavior and coordinate cell adhesion and migration. Cells use focal adhesion protein complexes to link the extracellular matrix (ECM) to the actomyosin cytoskeleton, the force bearing and generating network within the cell, allowing for both force sensing and active remodeling of their environment. These complexes include integrins, which are heterodimeric transmembrane proteins that bind to the ECM and recruit focal adhesion proteins that connect to the actin cytoskeleton. However, how force is transmitted through integrins and how cells regulate those forces is not fully understood. We used Förster resonance energy transfer (FRET)-based molecular tension sensors to determine the magnitude and origins of the forces experienced by individual integrins in living cells. These measurements revealed a functional modularity where the number and nature of connections to actin set the force per integrin, while different integrin classes independently controlled adhesion size and ECM ligand specificity. Our single-molecule measurements also revealed the dynamics of force transmission at individual integrins within cellular adhesion complexes. These observations provided a direct test of the predictions of the molecular clutch model, which is commonly used to describe how force is transmitted from the actin cytoskeleton through cellular adhesion complexes. Surprisingly, only a small subset of tension sensors exhibited dynamic loading in contrast to the predications of the clutch model. Instead, we found that the majority of sensors reported constant force magnitudes. We developed a modified model which incorporates the dynamics of the actin cytoskeleton and could reproduce the force plateaus we observe. In total, our observations support a general model for how cells create regulated and dynamic adhesions to the extracellular matrix.
Food, the body, and experience in Boccaccio's Decameron
Keywords: French & Italian.

This dissertation explores the connection between food and the body in Boccaccio's Decameron. I show how representations of food relate to the larger problem of embodiment and how Boccaccio uses food as a privileged material and vehicle through which to discuss such issues. While Boccaccio inherited a tradition that generally sought to abstract the body, he engages with a poetics that is human and embodied as he recognizes embodiment as a condition of human existence. I read food's representation in the Decameron in terms of Boccaccio's notions of corporeality, epistemology, and socio-ethical concerns. Boccaccio presents and links literal and metaphorical meanings of the body and its nourishment in the opening pages of his work, establishing food as one of the vehicles through which he will explore questions of corporeality and human experience. Through his effective application of language, presenting both the body and food items in both literal and metaphorical ways throughout the work, Boccaccio challenges already established notions surrounding class, nobility, gender, and knowledge to create new meanings and establish new paradigms out of the ambiguity that is inherent in his language. The first chapter examines two specific food items, bread and wine, which are, not coincidentally, Eucharistic items, to illustrate how both Cisti the baker (in novella VI.2) and Ghino di Tacco (in X.2) both strategically control and continually offer these Eucharistic elements in order to not only rehabilitate the higher-class individual with whom they are interacting, but more importantly to enact their own elevation and social transformation. The second chapter juxtaposes novella IV.1, the story of Tancredi and Ghismonda, with V.9, Federigo degli Alberighi, to show how Boccaccio uses items traditionally associated with nobility, the heart and the falcon, and turns them into food in order to construct a new way of conceiving of nobility. In the final core chapter, I explore Boccaccio's representation of food in terms of the pursuit of knowledge as well as how it relates to gender issues. I examine Calandrino's character in all four novelle of his saga (VIII.3, the story of the heliotrope; VIII.6, the story of the stolen pig; IX.3, Calandrino thinks that he is pregnant; and IX.5, Calandrino falls in love with Niccolosa) to investigate how Boccaccio uses food to champion a form of knowledge that is no longer abstracted from the body and the senses and how he employs the language of food to undermine ideas regarding disembodied knowledge in order to argue for and defend the body, and to champion the female's virtue, her practical knowledge, and her dominance in the domestic space.
The foundation of the forest : function and maintenance of symbiosis between ectomycorrhizal plants and fungi
Keywords: Biology.

Temperate and boreal forests can extend across thousands of kilometers, but some of the key forces shaping their ecology and evolution act on a micron scale. Roots alone often are not small enough to penetrate resource-rich soil pores, but fungal hyphae are: Many trees in these forests rely on symbiosis with ectomycorrhizal fungi to access soil nutrients. This dissertation explores the fine-scale mechanisms that make this symbiosis possible over ecological and evolutionary time, using physiology and gene expression as lenses to examine what happens when a hypha meets a root. The symbiosis itself is based around a cooperative exchange of resources, in which the plant provides carbon in exchange for nitrogen, phosphorous, and water scavenged by the fungus. In this dissertation, I treat this exchange as a resource economy, using stable isotope enrichment to examine trading dynamics and link them to symbiotic function. I also explore how biochemical negotiation, regulated at a transcriptomic level, affects the outcomes of these belowground exchanges, mediating the compatibility of plants and fungi across ecological and evolutionary time. Although a hypha and a root may only exchange a handful of molecules in a soil pore a few microns wide, it is these tiny interactions on which evolution acts to stabilize cooperation and produce the diversity of the forests that we see. Using genomic and physiological techniques, my dissertation highlights the power of micro-scale interactions to affect macro-scale outcomes.
Free, Open-Source, and Anonymous: Why deep learning regulators are in deep water
Keywords: deep learning
ai
computer science
stanford
center for international security and cooperation
cisac
proliferation
adversarial learning
national security
Thesis

Deep learning models have been instrumental in driving recent breakthroughs in artificial intelligence. Beyond autonomous navigation and game-playing, some deep learning applications, such as facial recognition and deep fakes, or counterfeit audio and video created by algorithms, pose challenges to individual privacy and US national security. The Director of National Intelligence's 2019 Worldwide Threat Assessment explicitly mentions the growing threat from deep fakes and machine learning systems. Yet, as most deep learning software, datasets, and academic papers are publicly accessible, individuals can effortlessly access the technical prerequisites required to develop deep learning models, build surveillance systems, and access instruments of mass deception. Thousands of deep fakes of politicians and celebrities have already been shared on the internet. The first step towards combating this threat is understanding how deep learning spreads and how its proliferation process differs from other dual-use technologies, or technologies with both civilian and military applications. This thesis seeks to fill this crucial gap by examining how all three critical components of deep learning - data, software, and hardware - have become accessible to internet users. We analyze how existing approaches to mitigating risks from dual-use technology, including establishing norms, limiting supply, and controlling exports, may fail to effectively delay or prevent deep learning threats. After examining how deep fake technology spread from academia to individuals, we present an original experimental study of how technical countermeasures could confuse a facial recognition deep learning model and be used to mitigate risks from deep fakes. Our experiments indicate how US policymakers could leverage both technical and policy mechanisms to delay or undermine malicious deep learning systems.
From G1 to S : understanding cell-cycle entry through single-cell microscopy techniques
Keywords: Chemical and Systems Biology.

Tight regulation of the cell cycle is critical for development and tissue homeostasis, and misregulation can lead to development defect, cancer, and degenerative diseases. While most of the individual components have been mapped out, our knowledge of the cell cycle remains incomplete. This is in part due to the popularity of bulk-cell assays in classical studies, where timing and kinetic measurements can be obscured by heterogeneity on a population level. In this thesis, we present two studies that take advantage of live, single-cell microscopy techniques. In the first study, we reveal how cells can proliferate without the kinase cyclin D-CDK4/6, a common target for cancer therapy. We found that in the start of this "alternate" pathway, the ordering of two critical events is inverted. We further demonstrate that in mice small intestinal crypt cells, this inverted sequence of events can be found alongside the canonical pathway that relies on cyclin D-CDK4/6. Our data thus suggests that wild-type, non-cancer cells can use two different paths to start the cell cycle. In the second study, we demonstrate how unperturbed cells use the kinase ATR, which detects DNA replication stress, to control CDK2 activity to rapidly modulate DNA synthesis rate. Besides fundamental characterizations, the two studies contribute to our understanding on how cells safeguard DNA replication. Cells need to achieve irreversibility prior to starting S phase to prevent reversion back to G1 (reversion results in over-replicated DNA). Once started, cells also must faithfully complete DNA replication. In the first study, we demonstrate that without CDK4/6 activity, cells have a different point of no return due to the inversion of signaling events. In the second study, we demonstrate that inevitable replication stress slows down DNA synthesis rate via an ATR-mediated negative feedback loop, thus preventing further accumulation of stress. Both studies enhance our knowledge on how cells maintain genome integrity. The studies also have potential clinical implications. An alternate pathway can at least partially explain how patients tolerate CDK4/6 inhibitors, and also explain how cancer cells bypass CDK4/6 inhibition. Finally, since many cancers have increased replication stress, understanding how cells resolve this stress may reveal synthetic lethal vulnerabilities in the future.
From Malinaltenango to Waukegan: A Case Study on Non-migrant Identity
Keywords: identity
transborder
transborder migrants
migration
migrants
State of Mexico
Estado de Mexico
Malinaltenango
Waukegan
Mexico
Tonatico
undocumented
poverty
NAFTA
bracero program
Illinois
Stanford University
Center for Latin American Studies
Thesis

This research explores complex identities rooted in displacement, poverty, and migration. It provides a historical overview of the relationship between two distinct places that are tied together by its people. Malinaltenango, Mexico is a small town tucked away in the valley of the State of Mexico. It is also my parent’s hometown, and a place I have only recently started to consider part of my own identity. In this essay, I provide a historical overview of the town and its relationship with a place I have always known to be home: Waukegan, Illinois. I began to ask myself, why is it that identity is rooted in the birthplace? Who has a stake in this identity, and how does this identity change through migration? In addition to understanding places like Waukegan as an extension of Malinaltenango, I argue that we should understand Malinaltenango identity as a byproduct of migrant lives in Waukegan. I provided an analysis of interviews conducted in the summer of 2018. Ultimately, I hope that my work shines light on non-traditional migrant groups typically explored by U.S. scholars, and births new understandings of identity and transborder relationships between the U.S. and Mexico.
From metagenomes to genomes : new tools for complex bacterial communities
Keywords: Genetics.

Characterizing the individual genomes of organisms within the human gut microbiome is a critical first step toward understanding this complex community as a whole and its impact on many aspects of human health. Thus far, efforts to characterize the genome sequences of gut microbiome bacteria have been largely based on short read sequencing and reference-based tools. Although these have benefited from advances in short read assembly and binning approaches as well as large-scale sequencing efforts, they face fundamental limitations that necessitate improved methods for metagenomic sequencing and assembly. This dissertation details some of the molecular and informatic challenges facing the field of metagenomic research within the gut microbiome, explores the limits of the existing methodologies, offers novel technological solutions, and applies those solutions to uncover novel biological insights into the gut microbiome. Chapter 2 describes the application of existing short read-based approaches to the gut microbiomes of cancer patients receiving fecal microbial transplant. Chapter 3 describes a new approach using read cloud sequencing to improve metagenomic assembly. Chapter 4 applies this read cloud approach to study insertion sequence mobilization within bacterial strains over the course of a patient's treatment for a hematological malignancy. Finally, chapter 5 describes a second new approach using nanopore long read sequencing to assemble full-length genomes directly from human gut metagenomes. Together, these chapters provide a deeper understanding of the challenges facing metagenomic assembly of the human gut microbiome, two new approaches to solve them, and new biological insights they have revealed.
From sad salad tweets to twisted carrots and dynamite beets : leveraging tasty and enjoyable attributes of healthy foods to promote a culture of healthy eating
Keywords: Crum, Alia degree supervisor.
Psychology.

Rising rates of obesity, diabetes, and cardiovascular disease call for interventions that promote healthier dietary intake. Many approaches have aimed to improve dietary intake by emphasizing the long-term importance of eating healthily and highlighting the nutritional benefits of healthier food choices, but these health-focused approaches have had limited success. In this dissertation, I draw on theory of cultural cycles of mutual constitution ("culture cycles"), mindsets and implicit theories, and insights from wise interventions to propose an integrated theoretical framework for analyzing this problem. I use this integrated theoretical framework to understand why Americans make unhealthy food choices, despite knowing what constitutes a healthy diet and wanting to live a healthy life. Studies 1-7 present evidence that the descriptive language used in popular American culture perpetuates and reinforces negative mindsets about healthy foods, both at the institutional and interactions levels of the culture cycle. In Studies 8-11, I use this framework to design and test a new solution, a taste-focused promotional approach for healthy foods that counteracts prevalent negative mindsets. I show that taste-focused labeling increases healthy food choices across a range of healthy foods and settings, concluding with a multi-site replication. Studies 12-15 further explore the psychological mechanisms by which these changes occur. Together, this research shows that a culturally informed theoretical framework of how particular mindsets are formed and reinforced can aid design of wiser intervention approaches. This research represents one small step towards changing a culture of negative mindsets surrounding healthy eating.
From Scribbles to Shapes: Measuring Developmental Changes of Visuomotor Abilities in Drawings
Keywords: Visuomotor Ability
Drawing Development
Symbolic Systems Program Thesis
Thesis

How do infants who can barely control their limbs grow into children who can produce richly meaningful drawings that express what they are learning about the world? One plausible contributor to this developmental change might be enhanced visuomotor control with age. In order to evaluate the developmental change of children’s visuomotor ability, we designed a set of tablet-based tasks to trace and copy primitive geometric shapes and recruited 4880 children, whose age ranges from two to ten, to complete these tasks. To evaluate the 9967 tracing and copying images from children, we then developed an automatic procedure to quantify children’s performance and collected adult ratings on a subset of the data to train and validate the model’s evaluation. The model is able to reproduce similar evaluations as human raters. Using the model on the full dataset, we found an age-related increase in children’s visuomotor ability in drawing.
From time-resolved to frequency-resolved x-ray scattering
Keywords: Physics.

Gas-phase time-resolved x-ray scattering (TRXS) measures internuclear separations in a molecule following laser-induced photoexcitation. TRXS constitutes an indirect measurement of the molecular motion because it captures information in reciprocal-space and real-time, which then must be inverted to recover the charge density as it changes in time. The spatial resolution of the recovered charge density is fundamentally restricted by the x-ray wavelength used in the experiment. There is no corresponding technical restriction on the ability to scan the delay between the pump-laser pulse and the x-ray-probe pulses, and thus no lower limit on the ability to resolve beat frequencies from TRXS measurements. This observation motivates transforming the measured TRXS in reciprocal-space and real-time into its reciprocal-space and reciprocal-time representation through a temporal Fourier transform. This representation is called frequency-resolved x-ray scattering (FRXS). The novel aspect of this approach is that an interpretable and compact representation of the experimental measurement may be obtained in reciprocal-space and reciprocal-time without the difficulty of inverting the measurement to the traditional real-space and time representation, and thus FRXS presents an alternative to traditional analyses of TRXS. The traditional approach based on pair correlation functions is limited by the range of momentum transfer, Q, that is accessible at x-ray free electron lasers (FELs). FRXS does not suffer this limitation, and in fact, FRXS leverages the strengths of FELs, namely fine time resolution and (relatively) fast data accumulation. This enables a long range of pump-probe delays to be measured in an experiment, thus improving the frequency resolution of an experiment, while maintaining sufficient temporal resolution to measure high beat frequencies. These advantages have been used to obtain compact representations of bound states and dissociations along lines in reciprocal-space and reciprocal-time, demonstrating an alternative to traditional analyses of time-resolved x-ray scattering for gas-phase photochemistry.
Functional Divergence of Plexin B Structural Motifs in Distinct Steps of Drosophila Olfactory Circuit Assembly
Keywords:  Department of Biology
Biology
Plexin
Neurodevelopment
Structure-to-Function
Drosophila
Thesis

Plexins are evolutionarily conserved receptors for Semaphorin signaling that carry out diverse and multitudinous neurodevelopmental processes. However, the molecular mechanisms behind how such proteins employ their structural architecture in vivo to perform distinct roles in neural circuit wiring remain unknown. Here, we systematically mutagenized structural motifs of Plexin B (PlexB), generating nine transgenic fly lines carrying mutant PlexB constructs expressed from the same genomic locus. We then assayed the efficacy of these variants at executing known PlexB-mediated neurodevelopmental processes in olfactory circuit assembly, namely axon fasciculation, trajectory choice, and synaptic partner selection. We found that certain structural motifs were involved in some processes but not in others. Furthermore, we report the first in vivo functional study of PlexB cleavage, revealing its regulatory role in multiple processes. Thus, PlexB differentially engages its signaling architecture in distinct wiring steps, allowing it to play varied roles in neural circuit assembly.
Fundamental Fractures: Children and Gendered Difference in Hisaye Yamamoto’s Seventeen Syllables
Keywords:  Department of English
Department of English
Asian-American Literature
Japanese-American
Short Story
Hisaye Yamamoto
Feminist Critical Theory
Thesis

For all its thematic complexity and literary prowess, Asian-American literature continues to be categorized and dismissed as cultural artifact. Unfortunately, the application of critical literary theory within the context of Asian-American works remains largely incomplete. In this thesis, I approach three stories from Hisaye Yamamoto's anthology "Seventeen Syllables" through the lens of critical feminist and historicist theory.