VictorJuiz/thesis huggingface dataset:
Parasite Diversity of Carnivores at Jasper Ridge Biological Preserve
Keywords:  Department of Biology
Biology
ecology
parasite
carnivore
Thesis

Anthropogenic stressors such as urbanization can cause physiological stress, which may impair the immune system response of wild animal populations and lead to dysfunction in wildlife communities. Animals with weakened immune systems are thus more susceptible to parasites and pathogens, which healthy animals might successfully eliminate or control. One way to measure the health of a population is to monitor parasite abundance and diversity within a population of wild animals. Yet few studies have directly documented the parasite load of wild animals in urban environments. The goals of this study were to (1) determine the parasite presence and diversity in four predator species at Jasper Ridge Biological Preserve: puma (Puma concolor), bobcat (Lynx rufus), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus); (2) examine seasonal variation in numbers of infected animals and diversity of parasites; and (3) compare parasite identification methods (flotations vs DNA metabarcoding). Both morphological identification (72/113) and genetic identification (92/143) found 64% of samples tested to be positive for parasitic presence. Parasite prevalence amongst the species ranged from 40% (coyote) to 76% (bobcat) according to morphological data and from 50% (puma) to 69% (grey fox) according to genetic data. Seventeen morphologically distinct parasite species were discovered from fecal floatation which were conservatively grouped into eight separate morphotypes. Morphological data found higher parasite presence in the dry season, but there was no seasonal effect according to genetic data. Understanding the parasite load of wildlife populations will, in turn, help to protect domesticated animals as parasite spillover poses a threat to all animals in human-dominated systems.
Parsing Through Predictions
Keywords:  Program in Science Technology and Society
risk assessment tools
risk assessment scores
pretrial decisions
judges
predictive algorithms
courts
justice
judicial discretion
Science Technology and Society
Thesis

Can algorithms send us to jail? This research analyzes the role predictive algorithms play in sorting defendants in and out of custody. Specifically, it investigates the Santa Clara County pretrial risk assessment instrument and how judges and legal professionals interpret its scores to make pretrial decisions. Are risk assessment scores the primary determinants of pretrial decisions or just consulted as supplementary information? Moreover, how much do judges trust the information from risk assessment tools given their history of racially prejudiced training data and scores? 14 interviews with legal professionals in Santa Clara County and Orange County were conducted to tackle these questions. After the analysis, a hierarchy of information became apparent whereby some forms of information had more bearing on a judge's decision than risk assessment scores. Judges prioritize information in the following order: 1) Swing facts or improvements to a defendant's behavior or lifestyle had the most bearing on pretrial decisions. They have the potential for judges to go against pretrial services recommendations. 2) Simple facts about a defendant's case such as, how many failures to appear, were very indicative of a defendant's future behavior for a judge. They are the most reliant forms of information for judges. 3) Lastly, risk assessment scores or indicators that aggregate the aforementioned facts into a number or score are consulted. These are treated as supplemental and somewhat nebulous forms of information on which to base a decision. Overall, the risk assessment score was not the determining factor for pretrial custody decisions. I make a call for algorithmic literacy, weeding out factors and algorithmic transparency to make risk assessment scores more useful for pretrial decisions.
Part I: development of dirhodium-catalyzed intermolecular C-H amination; part II: synthesis and applications of sulfamate esters
Keywords: Chemistry.

Catalytic methods for C(sp3)--H amination are enabling technologies for both the synthesis and late-stage diversification of myriad organic molecules. Contemporary challenges that propel future development of such processes are presented by complex substrates approximating the architectures found in natural products along with polar, functional group-rich active pharmaceutical and agrochemical ingredients. In our efforts to address these limitations, we have established a catalytic system for C--H amination that markedly advances the ability of chemists to efficiently introduce nitrogen into molecules of different structural types. The discovery of pivalonitrile (t-BuCN) as a differential solvent for Rh-catalyzed intermolecular amination of C(sp3)--H bonds and phenyl sulfamate (PhsNH2) as a nitrene precursor has enabled efficient functionalization of a wide variety of complex molecule substrates including natural products and active pharmaceutical ingredients (APIs). Although limitations remain with oxidatively labile functional groups, including basic amines, our disclosure represents a definitive leap forward in the state-of-the-art for C--H bond oxidation. Mechanistic data strongly implicate a pathway for catalyst decomposition that initiates with solvent oxidation, thus providing rationale for the marked influence of pivalonitrile on this reaction process. The phenyl sulfamate nitrogen source can be unmasked under mild conditions using pyridine and water to unveil the corresponding primary amine products. Additionally, through amination of bromoalkane and mesyloxalkane substrates, SN2 cyclization can afford azetidines and other saturated azacycles in good to excellent yield. In pursuit of alternative, modular methods for the installation of sulfamate and sulfamide groups, we have developed pentafluorophenyl sulfamate (PfpsNH2) and trichlorphenyl sulfmatate (TcpsNH2) as bench-stable, versatile reagents for sulfamoylation of alcohol and amine nucleophiles to generate N-unsubstituted sulfamates and sulfamides. This type of 'click' reaction should find widespread use in academic and industrial labs.
Partial Symmetry Detection in Large-Scale 3D Data Collections
Keywords:  Department of Computer Science
symmetry
ShapeNetCore
computer science
discrete symmetries
graphics
component-level
Thesis

This thesis describes a component-level discrete symmetry detection algorithm that detects translation, reflection, and rotation symmetry in pairs of parts of a whole shape. The dataset used is ShapeNetCore, a large-scale dataset of man-made 3D shapes of everyday objects. Currently, ShapeNet only provides information on pre-segmentation of the shapes. We are interested in improving ShapeNet by annotating the shapes with information on the symmetries within the models. In addition to the three partial symmetries listed before, the algorithm also detects global self-reflection as well as symmetry groups of pairs of parts. The results show the partial symmetry detection algorithm at around 99% accuracy for detecting reflection and rotation symmetries and around 95% for translation symmetries on the dataset of chair shapes. Future work includes evaluating the algorithm on other kinds of shapes, as well as improving the current partial symmetry detection to reduce errors. Future uses of the partial symmetry detection algorithm include helping with 3D shape completion from partial shapes.
Party Over Reality: The Impact of Partisanship on Perceptions of Political Disinformation
Keywords:  Dept. of Communication
political disinformation
partisanship
polarization
Communication Masters Thesis
Thesis

The present study seeks to investigate three questions: (1) Does partisanship influence an individual’s belief of true and false political information? (2) Does partisanship influence an individual’s desire to share true and false political information?, and (3) Does the order in which information is processed influence the effect size of partisanship on belief of true and false political information? 149 Amazon MTurk participants completed a Qualtrics survey consisting of 8 “filler” (nonpolitical, clickbait-style) headlines and 8 political headlines (4 pro-Trump and 4 anti-Trump) of varying levels of accuracy (1: real headline, more plausible; 2: real headline, less plausible; 3: fake headline, more plausible; 4: fake headline, less plausible). For each headline, they were asked five question, including “How likely is it that the events described in this headline are true?” and “How likely is it that you would share this article with friends or family?” Participants were randomly assigned to one of three conditions: foot-in-the-door (most real headlines first), door-in-the-face (most fake headlines first), and random. Across all participants, believability ratings of partisan-affirming headlines were significantly higher than the ratings of partisan-contradicting headlines (Levels 1-3, p < 0.001; Level 4, p < 0.05). Interestingly, Trump supporters’ ratings of belief in the most fake, friendly, Level 4 headlines were not significantly different from ratings of belief in either of the real, antagonistic Levels 1 and 2 headlines, suggesting that partisanship plays a more influential role than accuracy when assessing believability amongst Trump supporters (Level 4:1, p = 0.103; Level 4:2, p = 0.576). As far as likelihood of sharing, both Trump supporters and Trump opposers partisanship were more likely to share headlines that affirmed their beliefs than headlines that contradicted their beliefs, for all levels of headline believability. Lastly, there were no effects for order of headline presentation.
Patterns of diversity in the indigenous microbiota of marine mammals
Keywords: Microbiology and Immunology.

This thesis describes patterns of microbial diversity in the digestive tracts of a variety of marine mammal species to better understand how host-driven and external factors affect these indigenous bacterial communities. In chapter one, the distal gut microbiota from representatives of each extant taxonomic order of marine mammals was characterized and compared to that of terrestrial mammals. The goal was to parse out the influence of intrinsic and extrinsic variables that shape the mammalian microbiome structure, specifically the relative impact of host phylogeny versus life in the sea on the marine mammal distal gut microbiota. Results revealed that marine mammals, despite their divergent evolutionary history, harbor distal gut microbiota that bears similarity across taxonomic orders, presumably due to environmental filtering from their marine environment. However, signals of phylosymbiosis are also observed among this group, the strength of which appears to be host-lineage dependent. In chapter two, we explored a scenario in which knowledge of a microbial baseline could yield clinical value for a specific marine mammal species, the harbor seal (Phoca vitulina). The assembly of the oral and distal gut microbiome of neonatal seal pups was characterized longitudinally as they aged at a rehabilitation center. Since some seals received prophylactic antibiotics, this was also an opportunity to determine the effect of antibiotic-treatment on the developing microbiome of these healthy growing seals. Results revealed a transient perturbation in the indigenous gut microbiota to which the seal pup host demonstrated resilience. This study has clinical implications for the prophylactic antibiotic protocol used in this age group. The aim of this thesis was to better characterize the marine mammal microbiome to improve the husbandry, therapeutic and preventative care of marine mammals in the future.
Patterns of the world : Chinese fashion and cosmopolitan ideas in late Imperial Russia
Keywords: Slavic Languages and Literatures.

This dissertation examines Russian interactions with Chinese texts, artifacts, and migrants in intellectual and everyday life from the 1870s to the 1910s, when China was becoming increasingly visible in Russian literature, art, journalism, and daily life. It argues that writing about China became an indispensable means for Russians in the late imperial period to disseminate a variety of cosmopolitan and anti-cosmopolitan ideas and to address urgent cultural and political issues of the emerging global interconnectivity. "Cosmopolitanism, " for them, described two opposing but linked concepts: in a critical mode, the new material life created by the political economy of globlaization, and in an idealistic mode, a voluntary spiritual affilation to world culture. This discourse coincided with a shift in political relations between Russia and China, from bilateral antagonism to Russian rivalry with other world powers in the imperial partition of Asia. I analyze how writers mobilized modernist forms to explore aesthetic diversity, question ethical and political norms, especially narratives of western versus eastern civilizations. This dissertation challenges the widely-held view that Russians, monolithically, see the East through the prism of an age-old ambivalence about their identity between Europe and Asia. My chapters, which are roughly chronological, address both thematic and generic perspectives. The first chapter interrogates how Russia's "China" emerged in everyday consumer culture and political polemics; it describes the world my writers inhabited. Chapter two shows that as Lev Tolstoy translated the aphorisms of the Chinese philosopher Laozi, he constructed Laozi as a global philosophical ancestor, not an exotic Oriental sage. Chapter three rereads four major modernist poets, Maksimalian Voloshin, Innokentii Annenskii, Nikolai Gumilev, and Andrei Bely, and argues that in incorporating Chinese aesthetics into Russian poetry, they worked to denaturalize the universal status of European tradition. I reexamine the familiar association of exoticism in Russian modernist poetry with defamiliarization. In the fourth chapter, I show that Aleksei Remizov explores the translatability of cultural experience in his adaptations of Chinese ghost stories and his depictions of Chinese migrants. The dissertation situates the Russian Silver Age in the global context by examining Russians' understudied connections to European writers on China, such as Stanislas Julien, Judith Gautier, and Ezra Pound. Drawing on archival research in Russia, China, France, and United States, I hope to provide a newly detailed and nuanced intellectual history of Russia's place in global networks at the end of the imperial period.
Perovskite tandem solar cells
Keywords: Materials Science and Engineering.

Solar cells are an energy source of the future - clean, renewable, and with the promise of increasing energy access globally. A promising way to speed up the shift of global energy production toward renewable sources is to make highly efficient and inexpensive solar cells. Ten years ago, a new family of semiconductors was discovered to work well as solar cell absorbers - organic-inorganic metal halide perovskites. These materials absorb light strongly and have long carrier lifetimes and diffusion lengths. They can be processed quickly and inexpensively into high-performing solar cells. Perovskite band gaps can be tuned by simple compositional substitution - and this enables them to be used in two-junction tandem solar cells, which get past theoretical efficiency limits on single junction solar cells. This thesis begins with an overview of the main materials properties of perovskites that are relevant to their use in efficient solar cells. We then present a study identifying the chemical mechanisms band gap tuning in halide perovskites, based on molecular orbital theory and measurements of absorption spectra, X-ray diffraction and photoelectron spectroscopy across a range of perovskite compositions. This work helps identify a mixed tin-lead perovskite whose band gap is appropriate for the rear subcell in a two-junction tandem solar cell. A persistent concern with tin-containing perovskites has been that they are unstable to oxidation - this has hampered the development of all-perovskite tandems. We describe our study of the chemistry of how this oxidation occurs. The conclusions of this study lead to a chemical strategy to suppress oxidation in low band gap perovskite semiconductors. Practically building an efficient tandem solar cell requires designing perovskite compositions, contact and electrode layers, and a recombination layer to connect the subcells together and protect the first cell while fabricating the second cell on top of it. The fourth chapter shows our work that led to a monolithic tandem solar cell whose efficiency is a record for all-perovskite tandems. Finally, tin-lead perovskites present unique challenges to stability when integrated into full solar cells. The last chapter presents work on understanding how these solar cells degrade, and strategies that we developed to ensure that tin-lead perovskite solar cells, which are critical to high-efficiency all-perovskite tandems, can be designed to successfully retain their performance through 1000-hour tests under heat, light, and atmospheric exposure.
Persistent cities : creative ruination in Latin America and Europe
Keywords: Comparative Literature.

This work explores the concept and manifestations of urban ruination in Rio de Janeiro, Lisbon and Bucharest over a period of more than a century. My analysis focuses on the ways in which ruination is creative rather than destructive. Material decay is often associated with negative phenomena, but in this work I show how ruination, a very specific, protean type of decay, is a process that opens up spaces for artistic creativity. In these case studies, ruination emerges in fiction and street art, and it has three different faces. In the novel "Dom Casmurro" (1899) by Machado de Assis, ruination produces relics that saturate the protagonist's homes and the text he is writing. In "Livro do Desassossego" (1982) by Fernando Pessoa, ruination happens at the level of the semi-heteronym's self and exists on the same spectrum as the ruins of Carmo Convent and contemporary street art in Lisbon. Finally, in the trilogy "Blinding" (1996-2007) by Romanian novelist Mircea Cărtărescu, ruination is what connects the city of Bucharest and the identity of the protagonist as a writer. Street art in the Romanian capital similarly derives its power from buildings in ruination, where their materiality serves as the canvas and medium for a rich variety of works.
Petroleum system modeling of heterogeneous organic-rich mudrocks
Keywords: Energy Resources Engineering.

A successful characterization of a petroleum system involves understanding the potential and thermal maturity of the source rock, which can be done using basin and petroleum system modeling. Estimating the lateral and vertical heterogeneity of organic rich mudrocks is important to obtain accurate simulation results. Well penetrations in emerging plays are sparse and so data-oriented approaches to estimate the heterogeneity will not yield accurate results. In the case where data-based interpolation is not feasible, quantitative seismic interpretation (QSI) is helpful in estimating the desired properties. In this dissertation, we show how to apply the QSI workflow on organic-rich mudrocks by combining rock physics, basin and petroleum system modeling concepts, and statistical analysis.
Phosphoethanolamine cellulose : discovery, biosynthesis, and importance in e. coli biofilms
Keywords: Chemistry.

Biofilms are multicellular communities of cells embedded in a self-secreted extracellular matrix (ECM), a complex polymeric mixture that protects cells from harsh environments including antibiotic treatments. Our solid-state NMR analysis of the ECM material produced by uropathogenic E. coli, the most common causative agent of urinary tract infections, led to an unanticipated discovery that E. coli naturally produces a modified form of cellulose— phosphoethanolamine (pEtN) cellulose. Cellulose is the most abundant biopolymer on Earth and this discovery provided the first example of a chemically modified cellulose in nature. We investigated the biosynthesis of pEtN cellulose and determined the unknown functions of bcsEFG genes to be involved in the modification of cellulose. BcsG was identified as the necessary phosphoethanolamine transferase that installs the pEtN functionality on the cellulose via a BcsE-BcsF-BcsG transmembrane signaling pathway. To facilitate further investigation of pEtN cellulose, we developed new approaches to identify and study pEtN cellulose. These include: (1) a Congo red fluorescence method to distinguish pEtN cellulose from unmodified cellulose, (2) the 15N-serine biosynthetic labelling strategy to incorporate 15N into pEtN cellulose, and (3) the use of Closantel to suppress curli production in biofilms and enable facile detection of the cellulosic material. We employed each of these new approaches to evaluate uropathogenic E. coli clinical isolates for their abilities to produce pEtN cellulose. Our findings demonstrate the importance of the pEtN modification of cellulose in E. coli biofilm formation. They will be of value in ongoing studies of new strains and conditions that might affect pEtN cellulose production in bacteria. Our study of pEtN cellulose has implications for developing novel materials biosynthetically and alternative strategies to treat bacterial infections. Since the pEtN modification of cellulose contributes to biofilm formation, it provides a promising therapeutic target for anti-infective treatments to avoid the use of traditional antibiotics which can lead to antibiotic resistance.
Physical Modeling of Chromatin with Heterogeneous Nucleosome Spacings
Keywords:  Program in Engineering Physics
biophysics
chromatin
DNA
polymer physics
epigenetics
Thesis

The spatial organization of chromatin — genomic DNA and its associated proteins — underpins key biological processes from controlling gene expression to facilitating DNA damage repair. At the most basic level of organization, 147bp segments of DNA wrap histone proteins to form nucleosomes, which create heterogeneously spaced kinks in an otherwise semiflexible double-helix. This geometrical effect has not previously been included in analytical treatments of chromosomal DNA. As a result, the relative contributions of this structural heterogeneity and the thermal fluctuations in the DNA on chromatin organization is currently unknown. To address this gap, we present an analytical model of chromatin, treating nucleosomes as arbitrarily spaced, rigid kinks, in a wormlike chain backbone. We demonstrate that changing the positions of nucleosomes between two genomic loci can affect their probability of contact by up to six orders of magnitude. We also show that averaging over these heterogeneous binding configurations leads to chromatin tracing out an effective wormlike chain that is drastically more elastic than bare DNA. Since chromatin must bend back on itself in order for enhancers to bind their targets, this change in elasticity has a profound influence on transcriptional regulation. In particular, we examine the effects of nucleosome positioning around gene promoters on the spreading of epigenetic modifications through transient chromatin looping. Collectively, our work demonstrates that heterogeneity in nucleosome spacing dominates both local and global chromatin organization.