VictorJuiz/thesis huggingface dataset:
Post-Paleozoic Trends in the Abundance of Benthic Marine Organisms: Increasing Skeletal Abundance in Shallow-Marine Environments over the past 250 million years
Keywords:  School of Earth
Singh, Pulkit
School of Earth Energy &amp; Environmental Science, Paleoecology, Post-Paleozoic, Marine Abundance
Text
Thesis

Variations in skeletal abundance through geological history, when combined with organismal body size, can provide a much-improved quantification of
animal abundance in marine environments, an important control on energy and nutrient flow through such systems. Increases in abundance have long been hypothesized to explain the increase in taxonomic diversity and mean animal body size in marine communities during the post-Paleozoic (252 Mya - Present) but total biomass has remained more poorly constrained than taxonomic diversity and body size due to the challenge of collecting relevant data. For this study, the abundance of skeletal fossils in marine limestones from the earliest Triassic through the Neogene (252 - 0 Mya) was evaluated in order to more directly quantify the absolute abundance of skeletal animals, algae, and foraminifera in marine carbonate environments. Absolute abundance data were collected from thirteen previously published papers reporting point count data for 1596 rock samples totaling to around 400,000 individual points. These data were recorded along with the geologic age, depositional environment, and standardized at the phylum and class level. An increase in the abundance of calcifying organisms across the post-Paleozoic was found, with the exception of a short-term decline following a major mass extinction event at the end of the Triassic period (201 Mya). These findings support the hypothesis that the abundance of marine biota has increased since the start of the Mesozoic, suggesting that increased trophic resources were at least one factor enabling the increases in taxonomic diversity. These and similar findings also have implications for modern conservation efforts. Conservationists can use these data as a deep-time baseline against which to compare changes in abundances within modern marine environments to identify ecosystems most in need of protection.
The practical point of view and constructivism : from transcendental idealism to metanormative constructivism
Keywords: Philosophy.

This project examines a family of views that can be seen as contemporary descendants of a tradition inspired by Immanuel Kant's transcendental idealism—a constructivism about human freedom and responsibility, and about values, reasons and normative truths in practical and moral philosophy. I investigate views that attempt to vindicate practical freedom by appeal to the so-called "practical point of view." Some views are designed to show that constructivism justifies that we are genuinely free and responsible for what we do. Other views concern the constitution of human agency in their accounts and explanations of normative entities. One fundamental issue I will investigate is whether "constitutivist constructivism" can be considered a distinctive general position in practical or moral philosophy about the nature of the normative. While I think they may have distinguished their views from, on one end, dispositionalism and, on the other end, robust realism, it is a challenge to explain just how an appeal to constitutive features of human agency figures into the accounts of normative entities, and in such a way that distinguishes constructivism from already existing general positions in practical or moral philosophy. I examine three constructivist views: compatibilist constructivism defended by Hilary Bok, and the constitutivist constructivism defended by Christine Korsgaard and by Sharon Street. What makes them all count as constructivist is a sort of procedural commitment, although as we will see the procedural dimensions of their views differ. And what makes Korsgaard and Street constructivist views count as constitutivists also differ in interesting ways. I argue that constitutivist versions of constructivism can be seen as a novel and distinctive form of antirealism in metaethics or metanormative studies. To do so, I ultimately return to Kant's works. I reject judgment-dependence as the primary way to understand Kant's own antirealism and as the best way to establish an antirealism for constitutivist constructivism as well, contrary to what the constitutivist constructivists that are the subject of this project argue. I argue that insofar as we accept Alexander Miller's three ways of being antirealist (2019), we can discern a novel fourth way: a non-error-theoretic, non-expressivist, non-idealist, and non-subjectivist style of non-realism that opposes robust realism in practical and moral philosophy by denying a rational will independence of normative truths, contra what Kant calls "heteronomy, " where the nature of normative truth must be understood in relation to the principles constitutive of the activities of the rational will
Practicing human rights in the Arab world : international law in 20th century advocacy
Keywords: History.

This dissertation explores how several Arab NGOs in Morocco, Palestine, Egypt and Kuwait practiced human rights from the late 1970s to the early 1990s. Drawing on institutional archives and interviews, it argues that these organizations provide new insights into the history of human rights both regionally and internationally. Located in a region battered by colonialism, foreign exploitation, and domestic autocracy, they are a valuable entry-point for considering the universality of rights and the extent to which Cold War politics shaped grassroots advocacy. The division between political and civil rights, and economic, cultural and social rights—so salient on the international level—was of minimal importance in shaping human rights advocacy on the ground. Instead, NGOs embraced those rights which most directly spoke to their particular political challenges and prioritized the most egregious state practices. Human rights activists found synergy between rights and nationalism, Socialism, democracy, and constitutional monarchy. Rights were not a single paradigm for how to organize political life, but part of several different visions that arose in response to the aftermath of the loss of the 1967 war with Israel. The 1970s and 1980s were period of both continuity, as advocates drew on the existing content of recent international treaties, and innovation, as they transformed the law from a text to a shared practice of resistance
Precision navigation of miniaturized distributed space systems using GNSS
Keywords: Aeronautics and Astronautics.

The way humans conduct spaceflight is being revolutionized by two key trends. The first trend is the distribution of payload tasks among multiple coordinated units, referred to as Distributed Space Systems (DSS), which allow for advances in planetary science, astronomy and astrophysics, and space infrastructure and development. The second is spacecraft miniaturization, where micro- and nanosatellites are transitioning from being merely educational tools to a viable scientific platform. Together, these pushes call for strict Guidance, Navigation, and Control (GNC) requirements while adhering to on-board constraints. In particular, advanced DSS require precise real-time knowledge of the relative orbits of each spacecraft in the system. Centimeter-level relative positioning precision can be obtained from Global Navigation Satellite Systems (GNSS), but this has only been demonstrated on ground through post-processing and only between two spacecraft. This research presents a methodology for nanosatellite swarms to provide on-board navigation solutions in real time using differential GNSS, combining the precision from ground-operated navigation systems with the timeliness of on-board payloads. To accomplish this task, a large swarm is divided into smaller subsets, within which differential GNSS provides centimeter-level relative positioning through successful carrier-phase integer ambiguity resolution. These precise subset estimates are then fused together to form a full swarm orbit estimate on each spacecraft. This system is validated in a new GNSS testbed at Stanford, designed to characterize and profile both hardware and software for GNC payloads. A hardware-in-the-loop experiment demonstrates that the new navigation system can provide precise navigation solutions to a swarm of six spacecraft, including the first demonstration of integer ambiguity resolution on CubeSat avionics. The payload is then applied to two upcoming science missions for which it is considered a mission-enabling technology: the Virtual Super-resolution Optics with Reconfigurable Swarms (VISORS) and the Miniaturized Distributed Occulter/Telescope (mDOT). These missions both present unique challenges, showing that the navigation system can meet strict mission requirements in the presence of frequent control maneuvers and large inter-spacecraft separations. In the latter case, a novel hybrid extended/unscented Kalman filter (KF) estimates the differential ionospheric path delay between GNSS receivers in the swarm, using an unscented KF measurement update to better handle nonlinearities while reducing computational load through an extended KF time update
Predicting Scalar Inference and Alternativehood With Neural Sentence Encoders
Keywords: neural network
BERT
alternatives
scalar inference
pragmatics
machine learning
NLP
Symbolic Systems
Thesis

Scalar inference is the interpretation of a less informative term to also mean the negation of a more informative alternative. The strength of these inferences is often sensitive to context and the presence of linguistic cues. Neural sentence encoders have been shown to successfully predict the strength of certain scalar inferences (in particular, from some to not all). In this work, we explore two topics: First, the extent of variability in scalar inference strength from or to not both, and whether this inference strength can be predicted by a neural sentence encoder; second, whether a BERT-based framing of lexical expectation can be used to model the availability of scalar alternatives to or. We find that a BERT-based LSTM predicts inference strength from or to not both with limited success (r = 0.45), due to the relative pragmatic complexity of or. We also find that a BERT- based language model successfully predicts the categorical availability of alternatives for or, indicating that BERT captures qualitative information about alternativehood, and that lexical expectation measures of alternativehood weakly predict inference strength.
The presence of Copley : animacy, magic, and afterlife in American painting, 1765-1925
Keywords: Art and Art History.

Between 1753 and 1774, John Singleton Copley (1738-1815) painted some 350 portraits depicting men, women, and children of the British-American colonies, where he lived. Though his portraits were painted two and a half centuries ago, still they strike contemporary viewers as compellingly immediate and eerily modern, somehow charged with energy despite the passing of time. While many have commented fleetingly on the uncanny realism of Copley's colonial canvases, the origins and implications of these aesthetic effects have never been questioned. This dissertation argues that the painter's portraits were made, viewed, and experienced as near-magical repositories of human presence, believed to carry some vital relic of their sitters into the future. Accordingly, the project explores the rich afterlives of Copley's portraits—canvases that have "lived on" because their pulsating lifelikeness anticipates a future in which the sitter has passed on but the painting has not. Contributing to a growing body of scholarship on the afterlives of art and the history of enchantment, I demonstrate how these portraits and their reception during the long nineteenth century are evidence of the widespread cultural inclination to attribute inanimate portraits with the force of animation
Principles of circular RNA translation and immunity
Keywords: Bioengineering.

The rapid development of Covid-19 mRNA therapeutics was enabled by an upfront investment in mRNA platform technology, built on a fundamental understanding of mRNA biology. Decades of mechanistic work have uncovered key drivers of mRNA translation such as the cap, untranslated regions, and poly(A) tail. Additionally, the use of nucleoside modifications such as N1-methylpseudouridine enabled in vivo translation by suppressing innate immune responses to mRNA. Circular RNAs (circRNAs) are single-stranded covalently-closed RNAs whose translation is driven by internal ribosome entry sites (IRESs) and whose structure confers stability advantages over mRNAs. My dissertation defense will describe the circRNA assembly platform I built, its use in uncovering principals behind circRNA translation, and the study of the mechanism of immune sensing of nucleoside modification N6-methyladenosine (m6A) on circRNAs. In order to elucidate principles for driving strong circRNA translation, I built a platform for rapid and robust assembly of vectors and subsequent synthesis of circRNAs. Using this modular system, I identified an optimum format for circRNAs and systematically tested sequence elements that enhanced circRNA translation. I screened 100 viral IRESs, discovered a set with greatly improved translation across cell types, then created novel synthetic IRESs through both rational engineering and random mutagenesis. Further, I characterized a set of nucleoside modifications that improve circRNA translation. We decided to focus on one such modification, m6A, the most abundant post-transcriptional RNA modification on endogenous RNAs. Investigating the interaction behind m6A and anti-circRNA innate immunity, I found that circRNAs without nucleoside modifications activate the antiviral RNA sensor RIG-I in the presence of lysine-63-linked polyubiquitin chains to trigger a downstream interferon response. m6A blunts this response in an m6A reader YTHDF2-dependent manner. Viewed broadly, my findings characterize a mechanism behind self versus non-self recognition of circRNAs. Taken together, my circRNA development platform and the numerous discoveries made with it have pushed circRNAs forward as a promising class of RNA therapeutics
Private Made Public: Women in Cinema in Post-Famine North Korea
Keywords:  Stanford Global Studies
east asian studies
Korea (North)
Women
Propaganda
private sphere
Public sphere
stanford global studies
Text
Thesis

This paper examines the evolution of the public and private sphere in North Korea before and after the paradigmatic social change caused by the famine of 1994-1998, also known as the Arduous March. Of particular interest is how depiction of the public and private spheres in state-produced films has adapted to respond to this social shift. Analysis draws upon six post-famine films with female leads: “A Mother’s Happiness” (2003), “A Schoolgirl’s Diary” (2006), “Kites Flying in the Sky” (2008), “A Flower in the Snow” (2011), “Comrade Kim Goes Flying” (2012), and “ The Story of Our Home” (2016). Compared with prior films, depictions of the public and private sphere appear to be intentionally blurred through two common narrative devices: the reframing of private aspirations as public affairs and the portrayal of motherhood and reproductive labor as service to the state. Two of the six films include the famine in their narratives, offering a revisionist interpretation of the famine that implies the markets were not necessary for survival. Taken together, these six films represent a propaganda campaign targeting the agents of the private sphere - North Korea’s housewives - with the end goal of convincing women to forego private market activity and dedicate their labor to serving the needs of the state.
The probabilistic method in combinatorics
Keywords: Mathematics.

The probabilistic method is the art of introducing probability to prove results that often do not involve randomness to begin with. In this thesis, we present four applications of this powerful technique, which has become one of the cornerstones of modern combinatorics. First, we prove a new lower bound for online Ramsey numbers, giving for the first time an exponential separation between the lower bounds for classical and online Ramsey numbers. Informally, this means that it is quite difficult to adaptively find a monochromatic clique in an edge-coloring of a large complete graph. Next, we determine the growth rate of a certain off-diagonal hypergraph Ramsey number, answering a question of Erdős and Hajnal from 1972. This is the first nontrivial hypergraph Ramsey number whose exponential order has been determined. The proof introduces a new random model for hypergraphs and relies heavily on the entropy method. Third, we apply the entropy method to extremal graph theory, proving Tomescu's graph-coloring conjecture from 1971. This determines the maximum number of proper k-colorings of any graph with chromatic number k and n vertices. In the proof we use an entropy inequality related to sequential importance sampling, an estimation technique from statistics. Finally, we present a result in probabilistic combinatorics outside graph theory. An n-permutation is called k-universal if it contains every k-permutation as a pattern, and it is known that the shortest k-universal permutation has length O(k^2). It was suggested by Alon that actually almost all n-permutations are k-universal for some n=O(k^2), and he proved that a random permutation of length O(k^2 logk) is k-universal with high probability. Using a structure-versus-randomness approach, we improve this bound to O(k^2 loglogk), almost closing the gap to the conjecture
Probability on groups : random walks and limit theorems
Keywords: Mathematics.

This thesis studies three problems in probability on groups and related structures. A variety of techniques are used, with the common thread connecting the various works being the interplay between the algebraic structure of the group and the probability within the problem being studied. The first problem concerns the mixing time of random walk on finite fields given by applying an almost rational bijection between steps of a random walk. It is shown that the mixing time is much faster than the random walk alone, using Cheeger's inequality and the Weil bounds. The second problem concerns a bi-invariant random walk on the symmetric space of symplectic forms over a finite field. Cutoff is established using spectral theory. An elementary argument is given for the eigenvalue computation, along with a proof through constructing a characteristic map relating the spherical functions to Macdonald symmetric functions. Other applications of this characteristic map are also given. The final problem concerns the distribution of descents in the symmetric group under the Mallows measure. A joint central limit theorem is established for descents of both the permutation and its inverse, as well as stronger results for their sum. The key tool is Stein's method with size-bias coupling
Probing force-dependent interactions between aE-catenin, vinculin and F-actin
Keywords: Structural Biology.

Classical cadherins are transmembrane proteins whose extracellular domains link neighboring cells, and whose intracellular domains connect to the actin cytoskeleton via β-catenin and α-catenin. The cadherin-catenin complex transmits forces that drive tissue morphogenesis and wound healing. αE-catenin binds directly to filamentous actin (F-actin) and displays catch bond behavior, such that force applied to the cadherin-catenin complex increases its lifetime on actin. Tension-dependent changes in αE-catenin conformation enable it to recruit the actin-binding protein vinculin to cell-cell junctions, where it contributes to junctional strengthening. Vinculin also plays a similar role at cell-matrix adhesions, where it is recruited to talin in a tension-dependent manner. I used single-molecule optical trap assays to probe the force-dependence of vinculin's interaction with F-actin. I found that vinculin's interaction with F-actin displays directional catch bond behavior -- that is, force directed towards the pointed (-) end of the F-actin results in mean binding lifetimes 3-fold longer than when load was applied towards the barbed (+) end. In a second set of experiments, I sought to assess whether vinculin might regulate the binding interaction between αE-catenin and F-actin. To do this, I measured force-dependent actin binding by a quaternary complex comprising the cadherin-catenin complex and the vinculin head region, which cannot itself bind actin. Binding lifetimes of this quaternary complex increased as additional complexes bound F-actin, but only when load was oriented toward the (-) end of the filament. In contrast, the cadherin-catenin complex alone did not show this form of cooperativity. Together, my findings reveal molecular mechanisms which may facilitate the higher-order cytoskeletal organization necessary for cellular functions such as cell-cell adhesion and cell mobility
Probing gut bacterial physiology and antibiotic action in complex environments
Keywords: Bioengineering.

For decades, research on bacterial physiology has been conducted in standardized conditions in monocultures, ignoring the natural community context of most species. As a result, predicting the effect of perturbations such as antibiotics on gut microbial communities remains highly challenging despite its paramount importance. Mechanistic understanding of human gut microbiota ecology has also been hampered by limited throughput and the fact that key parameters often cannot be precisely tuned or measured in animal models. During this PhD, I developed tools and systems to interrogate bacterial physiology in complex communities and within animal hosts, and used these tools to make seminal discoveries regarding how life in a community alters the behaviors of individuals. The gut microbiota of the laboratory fruit fly is a low diversity consortium with 5 bacterial species from the Lactobacillus and Acetobacter genera, all of which can be cultured in vitro. I leveraged the simplicity and manipulability of this microbiota to study the role of metabolic cross feeding on growth and antibiotic action. Using in vitro synthetic communities composed of Lactobacillus and Acetobacter species, I discovered non-canonical tolerance to rifampin and erythromycin that is induced by interspecies interactions and mediated by changes in pH due to metabolic cross-feeding. Additionally, I developed imaging techniques to visualize individual bacterial cells within live fruit flies, opening the door to studying single-cell bacterial physiology within intact hosts. To enable quantitative, systematic experimentation on the human gut microbiota, I developed culturing techniques to directly compare responses in vitro and in humanized mice. I compared the sensitivity of gut commensals in vitro and in humanized mice to explore the role of heterogeneous environments and community composition in antibiotic action. I then cultured hundreds of communities that resemble the human gut microbiota using fecal samples as inocula for high-throughput liquid culturing. In vitro antibiotic treatment of these communities recapitulated changes observed in vivo in mice, and uncovered different modes of recovery, highlighting the capabilities of this methodology.