VictorJuiz/thesis huggingface dataset:
Reactivity of a trans-dioxo complex towards carbon dioxide and its incorportation into a new Prussian blue framework [electronic resource]

The use of well-defined molecular building blocks as a strategy to try to design the properties of a resulting extended framework has been previously employed with success in the field of metal-organic frameworks in the attempt to obtain highly porous structures. Similarly, molecular cyanide complexes have been incorporated as building units in extended frameworks in the quest for room temperature magnets, owing to the ability of cyanide ligands to form polymeric structures. In this thesis, I describe our efforts to confirm the reactivity of a molecular cyanide complex, trans-tetracyanomolybdate, with atmospheric CO2, as well as those undertaken to characterize the extended framework obtained using this complex as a building unit. The characterization of the resulting Prussian blue analogue showed that this material undergoes a rare example of partial linkage isomerism as well as several electron transfers during its synthesis. Although the reactivity of the molecule was not translated into the framework, the material reversibly adsorbs CO2 at room temperature and can be regenerated without appreciable capacity loss. The variability of the material resulted in the variability of its gas sorption properties.

Keywords: Chemistry.
Advisor: Karunadasa Hemamala
Kanan Matthew William
Stack T. (T. Daniel P.)
Read Cloud Sequencing Elucidates Microbiome Dynamics in a Stem Cell Transplant Patient

Low intestinal microbial diversity, often leading to domination of the intestine by a single organism, is associated with poor outcomes following stem cell transplantation. However, the process by which certain organisms achieve domination over others is not well-understood. Previously, it has been difficult to obtain genetic clues as to why the dominating organism has such high fitness in a given circumstance. This is because it has been nearly impossible to obtain near complete genome drafts of the dominating organism without isolation and culturing. Recently, we developed a metagenomic read cloud sequencing approach, which provides significantly improved genome drafts for individual organisms compared to commonly used alternative sequencing methods. Here, we apply read cloud sequencing to stool samples collected longitudinally from a stem cell transplant patient before and after heavy antibiotic exposure across four time points, during which the patient experienced a period of gut domination by E. coli as well as an E. coli bloodstream infection. Comparative genomic analysis reveals that the E. coli strain present in the gut and the E. coli strain isolated from the bloodstream infection are nearly identical (~99.97 nucleotide identity with a difference of 169 SNPs), indicating that the infection likely originated from the gut. Alignment of the pre-transplant E. coli draft genome to the Comprehensive Antibiotic Resistance Database reveals that the pre-transplant E. coli strain (prior to any antibiotic exposure) harbored 55 known resistance genes, including fluoroquinolone resistance and a multitude of multidrug efflux pumps. All other draft genomes from the pre-transplant time point contained <5 resistance genes, suggesting that the E. coli outgrowth was a result of selection after heavy antibiotic exposure. This case study highlights the application of metagenomic read cloud sequencing in a clinical context to investigate microbiome dynamics under extreme selective pressures.

Keywords:  Department of Computer Science
Metagenomics
read cloud sequencing
genome assembly
microbiome
antibiotic resistance
stem cell transplantation
Computer Science
Thesis
Advisor: Bhatt Ami S.
Kundaje Anshul B.
Readability, profitability, and discretionary MD&A text

This study examines the relation between profitability and disclosure readability. Prior research finds that less profitable firms have less readable disclosures, which is consistent with obfuscation. However, this research does not distinguish text that is non-discretionary, i.e., required disclosure or standard language given the economic environment, from text that is discretionary, i.e., voluntary disclosure or required disclosure written in a non-standard way. I measure discretion in Management Discussion & Analysis (MD&A) sentences based on their commonness relative to sentences from firms with similar profitability. I assume that sentences that are less (more) common among firms with similar profitability contain more (less) discretion. I find that less profitable firms have less readable non-discretionary text but more readable discretionary text, and this discretionary text is even more readable when firms have stronger incentives to garner a reputation for clear disclosure. My results imply that less profitable firms have less readable disclosures because of their economic environment, yet exercise discretion by increasing readability, rather than obfuscating.

Keywords: Business.
Advisor: Barth Mary E. 
Blankespoor Elizabeth
Kasznik Ron
Reading for the anthropocene : humanimality as resilience

In this dissertation, I investigate what role literary thinking can have in helping to cultivate human resilience during the geological era known as the Anthropocene, a concept that designates the global environmental devastation that human systems have wrought. My particular focus is anthropogenic global warming, which I conceive of as a philosophical and physical existential crisis that demands a human response. My research participates in a multidisciplinary conversation that considers how to find ways to adapt to life and death on a changing planet. Literary thinking encompasses both a textual mode of creative production and a way of reading. I develop an ecologically attuned hermeneutic that decenters the human and pays attention to the ethical dimensions of scale and of the materiality of the humanimal body. I practice this hermeneutic, what I refer to in the title as "Reading for the Anthropocene, " on texts produced during what the environmental journalist Elizabeth Kolbert suggests we call the Age of the Emissions. My corpus begins in the Global North, with Friedrich Nietzsche's The Birth of Tragedy (1872) and Louis-Ferdinand Céline's Voyage au bout de la nuit (1932), and then moves to the Global South, with Cronwell Jara's Montacerdos (1981-2006) and Junot Díaz's The Brief Wondrous Life of Oscar (2007). Although diverse in their genres, languages, and times and places of production, these texts all register a crisis of the human and respond to that upheaval in different ways. On one end, there is a denial of new relationality with more-than-human life because of the changes that relationality would require of and in the human; on the other end, there is an acceptance of material intra-action with more-than-human life accompanied by the cultivation of multispecies flourishing. Motivated by the belief that it matters how we tell ourselves the multidimensional stories of our past and future environmental impacts, the goal of this dissertation is to examine the way humanimality and other-than-human animalities have been described from the inception of modernity-coloniality and global warming to the twenty-first century. Utilizing decolonial, feminist materialist, and environmental humanities methodologies, I contend that literary thinking can teach us resilience by displaying how to reimagine the narratives of what humanimals can be and what humanimals can do in relation to our shared planet and our more-than-human neighbors who also live on it.

Keywords: Comparative Literature.
Advisor: Gumbrecht Hans Ulrich 
Hoyos Ayala Héctor 
Briceño Ximena
Saldívar José David 
Saldívar Ramón
Reading nature : empiricism and literary imagination in Friedrich Schelling's naturphilosophie, 1797-1800

Concepts of reading and literary interpretation pervade Friedrich Schelling's Naturphilosophie (1797-1801). Schelling sees objects and systems in nature, such as eddies in a river, thunderstorms, the geomorphology of mountains and volcanoes, and (especially) the diachronic development of animal physiology, as susceptible to a particularly literary kind of interpretation. All of these systems, Schelling holds, arise from moments of radical novelty and are expressions of nature's own freedom. Natural objects, then, cannot be explained merely by analyzing and recreating a chain of causal events. In order to understand the appearance of radically new levels of complexity, natural evolutions on vast time scales, and their relationship to the symbolic representations that govern human life we need the tools of the reader. A particular sensitivity to metaphor, metonymy, and narrative was, Schelling thought, essential for the Naturphilosoph. By way of close reading, the Naturphilosoph could discover complex interactions of literary, symbolic and aesthetic forms with the material forms of nature. Schelling's account of nature is an explicitly relational account: the diachronic and synchronic forms of the physical world are always in communication with the symbolic representations of human thought. Moments of radical novelty in nature, such as the arising of self-sustaining life forms from general chemical processes, , introduce the need for a type of interpretation that is not exclusively empirical, because empirical descriptions are designed to establish continuous chains of causality. Schelling's claim that nature is a text to be "read" challenges standard views of nature, including the budding empirical life sciences of the late eighteenth century. It also calls into question ideas of reading as a purely internal endeavor that is passive, detached, and without material consequences. He takes up a Romantic discourse around hermeneutics, which holds interpretation to be balanced grasping the whole of a symbolic representation and relating it to detailed analysis of its parts, and extends this style of interpretation to the natural world. In a bold departure from Kantian transcendental philosophy as well as the empirical sciences, Schelling charts a path for "reading nature" that requires us to rethink "reading" as a creative—and potentially destructive—activity, deeply tied to body as well as mind.

Keywords: German Studies.
Advisor: Berman Russell A.
Smith Matthew
Starkey Kathryn
Reading skills : the politics of literacy in the nineteenth and twenty-first centuries

"Reading Skills: The Politics of Literacy in the Nineteenth and Twenty-First Centuries" is committed to uniting teaching and research in the same conversation. The project interweaves three elements: extensive nineteenth-century archival records from British working-class and pre-professional reading communities, close readings of Victorian novels, and reflections on the experience of teaching those novels in the diverse landscape of the twenty-first-century American classroom. Droge argues that the work of Charles Dickens and George Eliot enabled their readers to navigate social and academic systems of increasingly specialized literacies. She first analyzes the literacy networks formed in over sixty Mutual Improvement Societies (small informal reading groups often hosted by churches) in London and northwestern England from the 1830s-90s, with particular attention to the way these societies read Dickens. Droge activates this reception history to perform her own analyses of The Pickwick Papers, Oliver Twist, and Our Mutual Friend and argues that Dickens's novels allowed readers to adopt flexibly-literate personas to foster social ties across communities with varied levels of education. She then recovers the importance of George Eliot's novels for first-generation college students at the Mason Science College in 1880s Birmingham and claims that Eliot resonated with students because of her refusal to specialize. Through readings of The Mill on the Floss and Impressions of Theophrastus Such, Droge demonstrates that Eliot's literary use of evolutionary discourse provided a model for students seeking to evade the strict boundaries of emergent academic disciplines, even while extracurricular literary culture effectively enabled a specialized system of scientific education to cohere. Droge closes each section of the dissertation with a lesson plan, using her teaching experiences to pivot between the nineteenth and twenty-first centuries and reflect on the continued affordances of Victorian texts to confront specialization in today's reading communities.

Advisor: Woloch Alex
Gumbrecht Hans Ulrich 
Jarvis Claire
Moretti Franco
Recommendation systems on social networks [electronic resource]

Recommendation systems have great power to know and shape who we are. First, we discuss how Twitter's feed-recommendation system exposes sensitive and uniquely identifying information, and explain how this knowledge can be used to identify anonymous visitors on social-media sites. Next, we describe a randomized controlled experiment we ran on Twitter's Who-To-Follow recommendation system that drastically influenced the social networks of individual Twitter users. Finally, we use a natural experiment to quantify the effect of the Who-To-Follow system on the global structure of the Twitter follow graph, and discuss its implications for large-scale social dynamics.

Advisor: Goel Sharad
Leskovec Jurij primary advisor. Thesis advisor
Ullman Jeffrey D.
(Re)creating Mexico in the US: How grandchildren of Mexican immigrants develop diasporic subjectivities

US Mexican subjectivities and diasporization are markedly different from European immigrants’ path toward assimilation. According to scholars, this difference is explained by the sustained flow of new immigrants replenishes the strength of community identification with Mexicanness. While continued immigration accounts for some aspects of how identity is maintained, such as Spanish language use, it does not account for other aspects of identity. In fact, US Mexican identity formation may be a different process entirely. As such, a better framework for understanding subjectivities among grandchildren of Mexican immigrants is that of the creation of diasporic subjectivities rather than identities that are slowly becoming more “American.” The US Mexicans I interviewed are invested in constructing a diasporic Mexicanness in the United States. This group attempts to bring closer that which is expected to be distant from them, and from which they are expected to feel alienated. In some ways, they successfully bridge temporal and spatial distances, but they cannot bridge all distances. Instead, they redefine what makes up categories of belonging, and they enact these alternative subjectivities through the terms they use to define themselves, their language practices, and the ways in which they bring their families’ past into the present.

Keywords: Mexican immigration
diaspora
identity formation
migration narratives
diasporic subjectivities
Thesis
Advisor: Rosa Jonathan
Jiménez Tomás
Rectifying the Curve: Deformity in Early Modern Drama

“Rectifying the Curve: Deformity in Early Modern Drama” explores the dramatization of disfigured characters in late medieval and Renaissance English drama. Situated in the context of disability studies, this thesis aims to dispense with the tendency to render Shakespeare’s Richard III in an anachronistic and idealist light. Aiming to “listen to the whispers of lived experience that permeate every representation of ‘deformed’ individuals in early modern drama,” this thesis provides an analysis of four major instances: William Jordan’s Creation of the World, Thomas Lupton’s All for Money, George Peele’s Arraignment of Paris, and Shakespeare’s tetralogy that culminates with Richard III.

Keywords:  Department of English
early modern drama
disability studies
Richard III
William Shakespeare
Thomas Lupton
George Peele
William Jordan
medieval drama
hunchback
deformity
Department of English
Thesis
Advisor: Greene Roland
Redefining Consumer Engagement for Social Media Marketing

Brands have leveraged the power of Facebook, Instagram and Twitter in an attempt to create relationships with their consumers by sharing product information, promotions, and brand content online. While social media brand marketing is necessary for companies looking to thrive in today’s advertising landscape, it is difficult to quantify the return on investment of social media marketing. What is the value of a ‘like’? How does gaining a ‘follower’ benefit a company? Marketers try to measure this benefit through consumer engagement, a multifaceted term that scholars have attempted to clearly define for years. The following literature review seeks to concisely define consumer engagement, and show that the amalgamation of likes and comments on social networking sites are not sufficient metrics of consumer engagement for social media marketing.

Keywords:  Department of Communication
Department of Communication
Coterminal MA in Communication
Media Studies Track
Consumer Engagement
Customer Engagement
Social Media Marketing
Thesis
Advisor: Reeves Byron
Re-examining the Leaky Pre-med Pipeline: An Updated Survey on Female and Minority Undergraduate Perspectives on Pre-medical Preparation at Stanford University

The goal of the study was to determine how the pre-medical preparation at Stanford is affecting student interest levels in pursuing medicine as a career, with a specific focus on the perspectives of women and Underrepresented Minority (URM) students. The study also examines the ways in which women and URM students perceive the effectiveness strategies that either encouraged, maintained, or discouraged their interest in pursuing medicine to identify the specific types of resources, forms of support, and experiences that facilitate successful premedical preparation. During the 2017-2018 Winter quarter, rated their interest in pursuing premedical studies on a Likert Scale of 1 to 4 at the time they completed the survey. They were asked to recall and rate their interest levels in pursuing premedical studies at the beginning of their freshman year when they matriculated to Stanford University. The difference between ratings were taken to be the change in interest levels. Students’ sense of belongingness in their premedical studies was assessed as well. Responses to open-ended questions regarding the factors that lead to change of interest were identified and categorized with emergent coding. The responses of males to females and URM to non-URM students were compared. The principal positive influencers on student interest include physician mentorship and peer and familial support. Negative influencers include excessive peer competition, and perceived lack of preparedness in premed classes. Three areas of improvement were identified: 1) Alternative Introductory Science Sequences, 2) Expansion of Dedicated Pre-Med Advising, 3) Expansion of Social Support Groups and Mentoring. Longitudinal studies need to be conducted to obtain a more accurate view of the degree to which students’ interest levels changed over the course of their undergraduate career and to determine whether the key factors identified at Stanford apply to a larger, more diverse sample. Data from this study suggest that more specific attention and support must be allocated to URM students aspiring to enter a career in medicine.

Keywords: Stanford University
Department of Mechanical Engineering
Graduate School of Education
Interdisciplinary honors thesis
medical education
education
undergraduate
pre-med
premedical
interest levels
medical school
medical career pipeline
sense of belonging
women
minority students
URM students
Underrepresented minority
chemistry
biology
pursuing medicine
Leaky Pre-Med Pipeline
physician mentorship
peer support
peer competition
preparedness
Thesis
Advisor: Barr Donald
Regeneration and functional recovery of the adult mouse utricle

Utricular hair cells (HC) are mechanoreceptors required for vestibular function. After damage, the mammalian utricle only marginally regenerates; thus, loss of vestibular function is presumed irreversible. Whether mammalian HC regeneration restores function is unclear. Here, we found partial HC replacement and functional recovery in the spontaneously regenerating mature mouse utricle, both enhanced by overexpressing the transcription factor Atoh1. Following toxin-induced HC death and vestibular dysfunction, long-term fate-mapping revealed that extrastriolar supporting cells non-mitotically and modestly regenerated HCs displaying nascent bundles. In the damaged but not undamaged utricle, constitutive Atoh1 overexpression stimulated proliferation and widespread regeneration of HCs (~80%) exhibiting elongated bundles, patent mechanotransduction channels, and synaptic connections. Finally, significantly more animals recovered vestibular function with Atoh1 overexpression than with damage only. Therefore, the mature, damaged utricle harbors a previously unrecognized Atoh1-responsive regenerative potential leading to functional recovery, underscoring the promise of a reprogramming approach to sensory regeneration.

Keywords: Cheng, Alan (Alan G.), degree supervisor.
Advisor: Heller Stefan
Nusse Roel
Raymond Jennifer L.
A regularized deconvolution method for large-eddy simulations of multiphase reacting flows

In Large-eddy simulations (LES) for turbulent multiphase and reacting flows, sub-grid scale (SGS) models are required to represent the interaction between turbulence, combustion, and the dispersed phase. Different approaches have been proposed in the literature to represent these unresolved terms, such as gradient diffusion models for turbulent scalar fluxes, presumed-PDF and artificially thickened flame models for turbulence-chemistry interactions, and random walk and stochastic Langevin models for turbulence-spray interactions. Although these modeling approaches show good performance in application to a wide range of problems, it is also observed that different combinations of models lead to different results for the same simulation configuration, and the performance of these models depends highly on flow and flame configurations. This model behavior is a consequence of the inconsistency between closure models and LES formulations. To address this inconsistency, closure models in coherence with the LES formulation need to be developed. In this work, a regularized deconvolution method (RDM) for the SGS closure models is developed. This method is based on an approximate inversion of the filtering operation in LES, which is consistent with the LES formulation. The method is formulated as an optimization problem. To ensure the properties of boundedness and conservation for reactive scalars, which are not considered in existing deconvolution methods, constraints are introduced in the formulation of RDM. The framework of RDM is developed in the context of both explicitly and implicitly filtered LES. For explicitly-filtered LES, RDM reconstructs the flow structures that are under-resolved. In this context, the deconvolution is formulated as a solution to a Wiener filtering. To account for the boundedness and conservation of reactive scalars, a constrained minimum mean square error problem is solved on a subset of the deconvolution solution that violates these properties. In an implicitly-filtered LES, the unresolved flow structures require modeling. To provide a correct description of these sub-grid fluctuations, an additional constraint is enforced in the RDM framework to regularize the sub-grid scale energy. The performance of RDM is examined for the closure of turbulence-flame interaction, turbulent scalar transport, and sub-grid dispersion through both \emph{a priori} and \emph{a posteriori} analysis of multiple LES configurations. Improved predictability is observed with RDM compared to other SGS closures model combinations.

Keywords: Mechanical Engineering.
Advisor: Ihme Matthias
Lele Sanjiva K. (Sanjiva Keshava)
Moin Parviz