VictorJuiz/thesis huggingface dataset:
Characterizing Toxin-Induced Neuronal Cell Death in Zebrafish
Keywords: Stanford University
Chemical Engineering
ChEM-H
Chemical &amp; Systems Biology
Developmental Biology
Zebrafish
Model Organism
SCI
CNS
M2
NTR
Apoptosis
Necrosis
In situ hybridization
Honors Thesis
Thesis

Zebrafish larvae are an ideal model organism for modeling spinal cord injury (SCI) and the subsequent biochemical response because of the unique ability to regenerate. Current methods to model injury suffer from a lack of cell specificity and reproducibility. By combining chemical and genetic tools, we can ablate cells in a spatiotemporal specific manner to model injury in the organism, as well as study regeneration. We developed a genetic method of neural ablation where SCI in zebra sh is initiated using encoded toxins, speci cally viral protein M2(H37A) and Nitroreductase (NTR), that are expressed within the CNS during development. Characterization of these toxins show that M2(H37A) kills more rapidly that NTR and leads to tissue loss throughout the CNS. Based on the speed and damaged caused by M2(H37A) we believe the viral toxin kills through necrosis, inducing apoptotic death in the surrounding cells due to activated Caspase-3 and TUNEL staining. A complete death and regeneration pro le following expression of M2(H37A) and NTR will develop a powerful model of SCI that can be applied widely. Transgenic zebra sh serve as a resource for studies investigating cell death and regeneration; and due to the severe and rapid ablation of M2(H37A) through a compound death mechanism, the toxic protein can be a tool of choice in injury modeling studies in a variety of model organisms.
Chemical approaches to the study of N-glycanase 1 : understanding NGLY1 deficiency and implications in cancer therapy
Keywords: Chemistry.

N-Glycanase 1 (NGLY1) is the human cytosolic protein N-glycosidase. The relationship between NGLY1 and the transcription factor Nrf1 is examined, particularly observing cellular response to proteasomal stress in healthy, NGLY1 deficient, and cancer model systems using genetic and chemical tools. Additionally, the role of NGLY1 in innate immunological signaling and other stress-response pathways that are regulated by the ERAD pathway is explored. Finally, the further development of the Quadricyclane (QC) ligation, a bioorthogonal reaction between QC and nickel bis(dithiolene) is described.
Chemical inhibition of apicoplast biogenesis
Keywords: Microbiology and Immunology.

Malaria infections caused by Plasmodium spp. parasites are a serious public health problem that disproportionately affects the poorest and youngest people in the world. With 216 million infections occurring annually and growing resistance to all front-line drugs, we are in desperate need of new antimalarials with novel mechanisms-of-action. Plasmodium and other Apicomplexan parasites contain an essential, non-photosynthetic plastid organelle, called the apicoplast, which is a key antimalarial target. While the apicoplast was derived from a secondary endosymbiosis of a red alga, it is no longer photosynthetic and instead it participates in anabolic metabolism such as fatty acid, heme, iron-sulfur cluster, and isoprenoid biosynthesis. Apicoplast biogenesis depends on novel, but largely cryptic, mechanisms for the maintenance, replication, and inheritance of the organelle during parasite replication. These critical pathways present untapped opportunities to discover new parasite-specific drug targets. To discover novel factors involved in apicoplast biogenesis, we designed a chemical screen in Plasmodium falciparum to identify specific inhibitors of apicoplast biogenesis. This screen revealed the natural product antibiotic, actinonin, as a first-in-class antimalarial compound inhibiting apicoplast biogenesis. We further demonstrate that the unexpected target of actinonin in both P. falciparum and the related parasite Toxoplasma gondii is FtsH1, a AAA+ ATPase membrane metalloprotease. These findings provide an important proof-of-concept for inhibitors of apicoplast biogenesis, and lay a foundation for future studies on the role of FtsH1 in apicoplast biogenesis. Next, we provide a comparative characterization of the downstream cellular effects of the three major classes of apicoplast inhibitors in T. gondii. In contrast with P. falciparum, treatment of T. gondii with apicoplast inhibitors leads to loss of the apicoplast prior to growth defects. We find evidence that this surprising discrepancy is partially due to T. gondii's ability to scavenge host metabolites that are similar to apicoplast metabolites. Our results as whole demonstrate apicoplast biogenesis as an important and productive source of antimalarial drug targets that lead to complex downstream cellular effects that depend on the host cell environment.
Chicha, Carporales y Charangos: Towards Building a "Soundscape of Migration" in Buenos Aires
Keywords: Stanford University Center for Latin American Studies
Thesis

This interdisciplinary exploration of aural cultures in Buenos Aires posits different genres of cumbia as comprising a “soundscape” of migration for Paraguayan, Bolivian and Peruvian immigrants residing in the porteño city. By close-reading two
films produced in the 2000s that have key scenes with cumbia soundtracks/performances (Bolivia and El niño pez) as well as formulating a proof-of-concept, temporal visualization of the movement of this aural culture across a city, I aimed to move towards theorizing on a soundscape of migration as itself a moving, migrating subject.
Children's information seeking during signed and spoken language processing
Keywords: Psychology.

How do children comprehend and learn language despite noisy input and limits on their information processing capabilities? Social learning theories argue for the importance of acquiring language from more knowledgeable adults who can constrain the learning task. Statistical learning accounts emphasize the role of children's pattern detection abilities that can take advantage of the structure available in the input. Finally, active learning explanations focus on children's capacity to gather useful information to support their learning. This thesis presents an integrative explanation that brings together ideas from these theoretical accounts to investigate how children's information seeking adapts to learning within social contexts. I use the formalization of Optimal Experiment Design (OED) as a conceptual tool to bring together ideas from social and active learning. Then, I present a series of empirical studies motivated by the integrative account that ask how children's information seeking adapts during language processing across a diverse set of contexts: signed vs. spoken language (Chapters 2 and 3), (2) speech in clear vs. noisy environments (Chapter 3), and (3) novel words with or without an accompanied social cue to reference (Chapters 4 and 5). The upshot of the empirical work is that children are quite capable of flexibly seeking information from their communicative partners to support language processing.
China's Security Cooperation: A Hidden Policy Dimension of the Belt and Road Initiative?
Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
China
Central Asia
Security
Belt and Road Initiative
Security Cooperation
Thesis

The modernization and increasing employment of the People’s Liberation Army (PLA) around the world lead many scholars to generate assumptions on the nature of the security policy of the People’s Republic of China (PRC). This thesis analyzes the historical development of PRC security concerns and their resultant security cooperation activities from. It explores the relationship between China’s security cooperation policies and the development of the Belt and Road Initiative (BRI) in Central Asia. In its early history, PRC security cooperation reflected the greater dynamics of the Cold War. The PRC conducted security cooperation and entered into conflict to support its ideological allies and balance against regional or global threats. Changing assessments of China’s security environment by Deng Xiaoping and subsequent leaders allowed the PRC to shift the focus of its security cooperation from preparation for imminent great-power conflict to supporting and enabling economic development and modernization. These new outlooks prompted evolution in PRC security cooperation activity. In some instances, PRC security considerations drove other policy priorities; security cooperation activity pioneered diplomatic or economic relationships. In other settings however, security cooperation quickly became an integral part, or even a consequence, of China’s greater development and engagement strategy. In the case of BRI development in Central and South Asian countries, PRC security cooperation addresses long-term, security-oriented relationship, fails to correlate with China’s investment activity, or is essentially non-existent. This thesis refutes monocausal characterizations of PRC security cooperation and finds a wide variance in its nature, motivation and conduct. This thesis also identifies a general trend of secular commercialization within PRC security cooperation that will aid in understanding China’s future security cooperation activity.
Choice and Pro-Social Behavior: The Effect of Choosing Your Hands in a Virtual Reality Perspective-Taking Task
Keywords:  Department of Communication
virtual reality
empathy
Stanford University Department of Communication
Thesis

A 2017 study demonstrated taking the perspective of a homeless person in virtual reality (VR) is more effective at increasing empathy and pro-social behavior toward the homeless than other forms of perspective taking tasks. The present study aimed to replicate the results of the aforementioned study, as well as explore the difference in effects when participants chose the skin tone of their virtual hands, had hands assigned to them, or had no hands at all. Furthermore, this study looked at the variation in participants’ physical interaction with the virtual environment in the three conditions and whether tracking data could be used to predict if participants performed pro-social behavior toward the homeless. There was no significant difference in pro-social behavior between participants in the VR perspective taking conditions and participants in the control. Analysis of the tracking data showed no statistically significant differences in movement between the four conditions. Results also did not show a correlation between participant tracking data and whether or not participants performed pro-social behavior toward the homeless.
Cinematic languages and the unrealized film projects of Sergei Eisenstein
Keywords: Slavic Languages and Literatures.

This dissertation investigates a series of incomplete film projects initiated by Soviet director Sergei Eisenstein between the years 1927 and 1933. Its purpose is to consider the value, both aesthetically and theoretically, of the materials used by Eisenstein in the generation, elaboration, communication, and exploitation of cinematic ideas that for a variety of reasons were never able to be filmed. Through a thorough analysis of archival materials, Eisenstein's published works, and secondary literature, I suggest that these incomplete films, far from being failures, instead represent a glimpse into a creative process yet unbounded by the practical considerations of actual film production, and can be read as utopian attempts to further develop Eisenstein's personal cinema aesthetic as well as that of the medium in general. In Chapter One, I analyze the external similarities of the Capital (1928--29) and Glass House (1927--30) projects and their shared film-theoretical mandate to develop the possibilities of intellectual cinema—in the domains of vision and cognition. I demonstrate here how their cinematic execution would have required new, and ultimately impossible, film languages for both camera and page. In Chapter Two, I consider the evolution of Eisenstein's theoretical assumptions about the sound film and development of the ideas of audiovisual counterpoint and the internal monologue. I analyze the two resulting "American" screenplays and the novels from which they were adapted: Sutter's Gold (1930), based on the novel L'Or by Blaise Cendrars, and Theodore Dreiser's An American Tragedy (1930). Eisenstein reworks the ideological fabric of these literary works and uses audio to both deepen the sensual atmosphere of the action and complicate the psychology of the central characters. In Chapter Three, I address the demand from above for a new form of Soviet comedy and its influence on the origins of the incomplete project MMM (1932--33), analyzing the strange textual structure, verse form, and content of the script. An unbounded plasticity of bodily boundaries and shapes arises in the script and leads to a climax in which Eisenstein uses the mechanical devices of cinema production to penetrate into the human body. The intention of this study is to formulate an approach to the unfinished Eisenstein work, modeled as an opportunity to look deeply into the process of cinema creation. In introducing new information on this canonical Russian artist and thinker, I argue for an understanding of the cinematic work as a syncretic collection of evolving written and visual forms and demonstrate the value of what is produced around the cinema—its literary apparatuses and graphic generators. I propose that such a view of cinema as a multiform process, segmented into many stages, can allow the part—the unrealized film—to stand in for the illusory whole of the completed work.
CO₂ utilization via carbonate-promoted C--H carboxylation and CO₂ hydrogenation
Keywords: Chemistry.

With the CO2 level in the atmosphere at 400 ppm and rising, finding new and efficient ways to recycle this greenhouse gas is of paramount importance. Most previous efforts have focused on converting CO2 to low-value C1 compounds such as CO, formic acid, methanol and methane. The use of CO2 as a feedstock for the synthesis of multi-carbon compounds is advantageous because these targets generally have higher value and greater energy density. The key chemical challenge is to form C--C bonds to CO2 without using energy-intensive reagents. Here we describe a novel carboxylation reaction in which a C--H bond and CO2 are transformed into a carboxylate (C--CO2--) using alkali carbonates as a promoter, in absence of any catalyst or solvent. Alkali carbonate salts are capable of deprotonating C--H bonds that are ordinarily weak acids (pKa> 40 in organic solvent) to generate carbanions (C--) at intermediate temperatures (200-360 °C). In the presence of CO2, the carbanions react rapidly to form carboxylates. The chemistry has been applied in the synthesis of 2,5-furandicarboxylic acid (FDCA) from 2-furoic acid, which can readily be made from lignocellulose. FDCA is an attractive green replacement for fossil fuel-derived terephthalic acid, used in polyethylene terephthalate (PET) polymer synthesis. Based on the above-described approach of C--C bond formation, we also demonstrate that a mixture of alkali carbonate, CO2 and H2 can be readily converted to formate, oxalate and other C2+ carboxylates like acetate, propionate and succinate. The reaction occurs at intermediate temperature and pressure and requires H2O vapor for hydrating the carbonate salt. Isotopic labelling studies are consistent with a mechanism that proceeds by a series of H2 and C--H deprotonations to form H-- and C-centred nucleophiles that undergo H--C and C--C bond formations.
Coherent pattern identification in fluid flows
Keywords: Mechanical Engineering.

The motion of complex fluid flows, and material advection in them, can be understood though the identification and analysis of persistent transport features in the flow. These features, often referred to as coherent structures, act as a robust framework of material surfaces that separate the flow into distinct regions which resist mixing with surrounding regions. Understanding the evolution of these structures is a critical step in identifying the mechanisms underlying fluid transport. Material transport is central to many geophysical flow phenomena, such as the development of marine ecosystems, and the spread of pollutants including volcanic ash and oil. However, many of the techniques currently available for measuring such flows, including tracking arrays of Lagrangian drifters (e.g. ocean surface drifters and weather balloons), result in sparse and spatially irregular velocity data. This is insufficient for the use of many coherent structure detection algorithms, which rely on an assumption of initially closely-spaced fluid tracers. Additionally, current methods often focus on determination of the full boundaries of coherent sets, whereas in practice, it is often more valuable and practical to identify the complete set of trajectories that are coherent with an individual trajectory of interest. Motivated by the successes in using coherent structure analysis to study transport, and considering the limitations of measuring large-scale geophysical flows, this work details the development of an algorithm for detecting coherent patterns from potentially sparse Lagrangian flow trajectories. The method, based on principles from graph coloring and unsupervised machine learning, groups trajectories based on a measure of pairwise dissimilarity between their displacement patterns. Through the use of several analytical and experimental validation cases, this method detects coherent flow patterns using significantly less data than is required by existing techniques. Consideration of less optimal groupings of trajectories also allows for the detection of all trajectories coherent with a chosen trajectory of interest. Due to the robustness of the coherent patterns to effects such as chaotic advection, the flow structures identified prove useful in the assimilation of Lagrangian trajectory data into models of geophysical flows. Importantly, although the method is demonstrated here in the context of fluid flow kinematics, the generality of the approach allows for its potential application to other unsupervised clustering problems in dynamical systems.
College of Last Chance: Latinx Students and the Community College System
Keywords: Community college
Latinx
Latinos
Higher education
Disparities
Low-income
Disenfranchised
Meritocracy
Barriers
Family
Illinois
Free education
Focus groups
Embodied knowledge
System justification
Thesis

Growing up, the local community college, notoriously re-named “College of Last Chance,” was never any of my peer’s dream school, but by decision day, most high school seniors were enrolled. The Latinx community college experience is one that is highly stigmatized through existing literature and quantitative data on attendance and retention rates, and even through misconceptions about the institution that are unaware of its history and place in communities. Very often, community college is seen as the final opportunity for students to change their life trajectory a Last Chance. While this framing highlights the overall disparity that exists within the community college system, it does not fully encapsulate the complexities of the Latinx community college student experience. In my thesis, I argue that educational outcomes that are often framed as products of individual behaviors, such as working hard and following the rules, must be understood as institutionalized phenomena, such that our theory of change should focus on restructuring institutions rather than simply modifying individual behaviors. Through my methodology, I highlight the need to center this type of research on those that are most influenced and affected: Latinx students, both past and present. My research takes into account the lived experiences of 10 Latinx community college students that have attended, left, or transferred out of the College of Last Chance, and also considers their ideas to improve the system that most affects them. Through my analysis, I conclude that Latinx students must be understood in the context of their historical disposition, rather than individuals separate from outside influences. Furthermore, community colleges, like the College of Last Chance, are building a space for students to succeed through their social equity efforts, but cannot do it alone. The responsibility lies in the institutions extending from community colleges to four-year institutions, local cities or townships, and beyond.
Colonial pasts, future cities : urban heritage advocacy in post-authoritarian Indonesia
Keywords: Anthropology.

In cities across Indonesia, the tangible traces of Dutch colonial rule are drawing the attention of an eclectic group of academics, activists, and artists, who now advocate vigorously for these crumbling buildings and aging infrastructures to be treasured as "heritage." This dissertation explores this emergent phenomenon, which I term "urban heritage advocacy, " as one that can offer critical insights into wider debates regarding colonialism and postcolonialism, urban development and urban governance, and the political and social sea-changes that post-Reformasi Indonesia has undergone since the fall of authoritarian rule in 1998. Drawing upon extensive ethnographic fieldwork in Semarang, Central Java, urban heritage advocacy is shown here to shape not only the material fabric of the neighborhoods now designated as heritage sites, but also to produce new forms of citizenship, re-negotiate the relationship between civil society and state authority, and profoundly impact the lives of the city's most marginalized inhabitants. Throughout, I argue that heritage furnishes Indonesia's newly-energized middle-classes with the opportunity and means to order and re-order the world around them, while also constraining the lives and livelihoods of the urban poor with whom they share this rapidly-changing cityscape.
Comics as a Literary Resource
Keywords: Multimedia
comics
ELA
English language arts
high school students
Graduate School of Education
survey
Thesis

The English Language Arts (ELA) classroom has evolved from a space for students to not only learn about general reading and writing skills, but to also gain prowess in articulating and backing up claims with textual evidence. With the recent adoption of the Common Core State Standards Initiatives by California (CCSSI), evidence-based claim-writing has become an essential component of the modern day ELA class. The adoption of CCSSI also comes at a time where student consumption of visual media outside of the classroom is at an extreme high-point. As a result of developments in technology and increasing access to a proliferation of media platforms, visual media consumption is leading to an increase in potential for visual literacy development for students. In order to engage students of this visually immersed generation, the employment of multimedia texts will be important in acknowledging the skills in visual literacy that students have developed outside of the classroom to be bridged towards evidence-based claim-writing. I am proposing that comics, as a genre of multimedia text, can bridge this gap between budding visual literacy and relevance towards the skills emphasized by the CCSSI for modern day ELA classrooms.
In order to see what effects comics have on student engagement, and whether comics can viably be integrated into a CCSSI classroom in order to improve claim-based evidence writing, I conducted a field study at Sequoia High School in Redwood City, California, in conjunction with an english teacher in a 9th grade English II Support Classroom. Over the course of two months, I made weekly visits to the classroom, creating comics-based assignments and lesson plans for students in conjunction with their classroom teacher to aid them in developing claim-writing skills for their final semester essay, which was to prove a claim about a group of characters in John Steinbeck’s Of Mice and Men. I found that the use of comics as text allowed for a quantitative and qualitative increase in student textual engagement, and was conducive in aiding students generate original claim ideas and opinions about the text as well.