VictorJuiz/thesis huggingface dataset:
Beclin-1 mediated protein sorting in neurodegeneration [electronic resource]
Keywords: Biology.

Protein sorting coordinates membrane dynamics with the clustering and isolation of proteins into discrete membrane domains. Proper protein sorting not only mediates intracellular homeostasis, for example, through the delivery of hydrolase enzymes to the lysosome or through degradation of long-lived proteins in autophagy. It also facilitates the communication between a cell and its environment (the extracellular milieu or neighboring cells) by regulating both ligand secretion as well as the availability of receptors at the plasma membrane by balancing receptor degradation with receptor recycling. Disruption of protein sorting pathways can therefore interfere with intracellular processes and prevent the interactions between cells necessary for the maintenance of tissue homeostasis. The nervous system, in particular, is sensitive to disruption of protein sorting pathways, as evidenced by the growing number of reports linking polymorphisms in protein sorting machinery to neurological disease, such as Alzheimer's Disease (AD). It is therefore necessary to elucidate the mechanisms controlling protein sorting so that we may better understand the normal biology underlying these processes and the consequences of their disruption in pathogenesis. Previous work has established that levels of beclin 1, a protein that functions in multiple membrane trafficking pathways, are decreased in the brains of Alzheimer's Disease patients. We show that, in addition to it's well-known function in regulating autophagy, beclin 1 regulates receptor recycling in two systems relevant to neurodegeneration: phagocytosis in microglia and TGF-[beta] signaling in neurons. We use immunocytochemistry, confocal microscopy, and live-cell imaging to demonstrate beclin 1 regulates receptor recycling through production of phosphatidylinositol-3-phosphate at vesicle membranes and recruitment of the retromer complex. We also use a combination of biochemical techniques, flow cytometry, and immunohistochemistry to show the functional consequence of disrupted receptor recycling in phagocytosis and the TGF-[beta] signaling pathway using both in vitro and in vivo models. In light of our findings, we discuss the implications of impaired beclin 1-mediated protein sorting in neurological disease.
Behavioral Determinants of Exercise Maintenance Lessons From Past & Current Rowers
Keywords:  Department of Economics
Stanford Department of Economics
Rowing
Crew
Exercise Maintenance
Time-inconsistent Preferences
Intrinsic Motivation
Extrinsic Motivation
Participation Motivation
Self-Efficacy
Physical Activity
Behavioral Economics
Thesis

This paper examines the determinants of exercise maintenance through the lens of behavioral economics. I aim to explain the motivational differences between those who successfully maintain healthy exercise habits and those who do not. The implications of this paper inform rowers, athletes and non-athletes alike how toapproach exercise from a perspective of long-term maintenance and health. Additionally, I briefly discuss policy implications addressed in some of the existing literature. Using an anonymous self-report survey, I collected data on numerous incentives for exercise maintenance (primary activity type, intrinsic and extrinsic motivations), and, primarily, their impact on hours of weekly exercise. I sampled 294 past and current university rowers (distinguishing between those who currently belong to a team with coached or compulsory practices) from the United States and the United Kingdom. I provide evidence that shows rowers differ from individuals described in the existing literature. Incentives for current exercise maintenance among both current and past rowers are primarily extrinsic. However, regression and ordered logit analyses indicate that parental influence at initiation has a persistent negative effect on current exercise levels, despite rigorous physical activity in the interim, among both current and past rowers.
Beyond answer choice B [electronic resource] : the development of an assessment of argumentation in ecology
Keywords: Education.

The Next Generation Science Standards describe students' proficiency in science in three dimensions: disciplinary core ideas (content), scientific practices, and crosscutting concepts. However, the field currently lacks high quality assessments that measure students' progress toward mastering scientific practices. In this dissertation, I developed a set of tasks that assess students' competence with one of these practices in a particular content domain: argument from evidence in ecology. I administered the tasks to a sample of high school biology students and conducted cognitive "think aloud" interviews with a subset of students. Conclusions about what worked (and what did not work) in these tasks are offered, as well as implications for future work in assessment design. In addition, this work investigated the extent to which students relied on specific ecological content knowledge to construct and critique arguments. Findings indicate that content knowledge was necessary, but not sufficient, for high performance in argumentation. Ideas are offered about what, in addition to content knowledge, may improve students' argumentation in science.
Beyond 'Because I Like It': Emergent Readers' Picture Book Selection and Interaction
Keywords:  Graduate School of Education
emergent readers
early childhood
literacy
picture books
Stanford Graduate School of Education
Thesis

This study examined the book selections of a population of emergent readers (n = 32; 15 male) and asked them to reflect upon their choices with the intention of cultivating a deeper understanding of what matters to children in their early reading experiences. The hypothesis tested was that ethnicity would emerge as a significant predictor of book selection and duration of interaction. Participants sat with an experimenter who showed them three books each featuring characters from diverse backgrounds (African-American, Hispanic, Caucasian). Children received brief summaries of each book (presented in counterbalanced order) and were instructed to choose the one they most wanted to look at. The experimenter was silent and recorded the child’s total time with the book as well as his or her total independent interaction times. Once finished children were asked and answered a series of questions evaluating what they found most important. No differences in selection based on ethnic background were observed. Agentive factors emerged as the most significant justifications for selecting books, and children routinely made connections to their personal lives (e.g. family, experiences, preferences), and children regularly used text as a substrate for reflection on experience and revelation-of-self. As children in early childhood are in the early stages of ethnic identity development it was likely that ethnicity was deemed irrelevant or at least secondary to immediate lived experiences in children’s literary engagement. Implications for authors, teachers, and parents are considered.
Beyond language [electronic resource] : Viktor Shklovsky, estrangement, and the search for meaning in art
Keywords: Slavic Languages and Literatures.

The key concept of Viktor Shklovsky's (1893-1984) understanding of literature is estrangement, a literary device the twofold purpose of which is to make a text strange and to restore one's perception of life. While previous scholarship has focused on the first of these purposes, this dissertation focuses on the second. Shklovsky, far from arguing for a vision of literature in which the meaning of a text is either nonexistent or located strictly in its language or formal features, in fact puts forth a theory of creativity as an existential enterprise, intimately connected with and even inseparable from deep human experiences such as alienation, love, transcendence, and the search for meaning. These experiences may be invoked or self-consciously created by language employed in specific, formally complex ways, but they can never finally be reduced to language. Particular attention is given to the way in which Shklovsky develops these ideas by engaging with the work of Roman Jakobson (1896-1982), Lev Tolstoy (1828-1910), and Vladimir Mayakovsky (1893-1930).
Beyond the empire [electronic resource] : living in Cerro de Oro
Keywords: Anthropology.

Between ca. AD 500-900, Cerro de Oro, a large monumental settlement located in the lower Cañete valley of coastal Peru, saw the construction of adobe compounds, structures and platforms across an area of 140ha. The traces left by the people who constructed, used, abandoned (ca. AD 500-800), and finally reused (ca. AD 800-900) this settlement form the focus of this investigation. By centering on the inextricable relationships between social practices, inhabited spaces and the things of daily life, I aim to better understand the making and remaking of the Cerro de Oro community. Social practices (encompassing the activities that people engage in every moment of the day: moving, eating, working, playing, and others) are inherently material practices (Voss 2010:4). These practices are fundamentally entwined with their relation with things (Hodder 2012). I propose to study the remains and fragments of the things used by Cerro de Oro people within their own situated social contexts of production, use and discard as a way to understand the entanglements that underpinned daily life. Moreover, the highly constructed nature of the Cerro de Oro landscape has led to an emphasis on space. This built environment was shaped by tall constructions with limited access and restrictive visibility. It is proposed that people made sense of this landscape through their participation in its organization, use, remodeling, abandonment, and reuse. Importantly, the study of the spatial organization and practices people engaged will allow us to understand how the social practices of everyday life articulated with centralized coordination; thus emphasizing the role of daily events in the formation of local historical trajectories. This view highlights a multi-scalar approach that moves beyond the conceptualization of elites as the sole movers behind monumental construction and cultural change; posing its attention on the collective actions of people. Understanding how people lived at Cerro de Oro also entails contextualizing the settlement and its residents within the socially dynamic period that characterized the central and south-central coast during the end of the Early Intermediate Period and the beginning of the Middle Horizon (ca. AD 500-800). The interactions of people, objects, and ideas that characterized this period generated a particularly interactive social sphere which is reflected in a hybridized set of objects that blend regional styles with those of the Wari society. I suggest, exploring this scenario from the ¨local perspective¨ of Cerro de Oro will allow us to avoid reducing local settlements to its relations with larger social groups. Thus, drawing on the results from Cerro de Oro, I consider this culturally dynamic period should be studied from the perspective of the site by focusing on how foreign elements, ceramics and other, were adopted and reconfigured by the people of Cerro de Oro.
BICEP3 and CMB-S4 [electronic resource] : current and future CMB polarization experiments to probe fundamental physics
Keywords: Physics.

Cosmic Microwave Background (CMB) polarization is a powerful probe of fundamental physics -- from the physics of inflation to the sum of neutrino masses. BICEP3 is a new 95GHz receiver in the BICEP/Keck Array series of inflationary probes at the South Pole sensitive to the CMB polarization at degree-angular scales. The goal of the BICEP/Keck program is to test one of inflation's prediction: generation of stochastic gravitational wave background. This gravitational wave background imprints B-mode polarization patterns on the CMB which peaks at 2 degrees in the power spectrum. BICEP3 advances per-receiver sensitivity, while maintaining the advantages of a compact refractor with degree-angular resolution. BICEP3 doubles the aperture of BICEP2/Keck receivers, has faster optics, and can house 1280 dual-polarization pixels on its focal plane. This thesis details the instrument design of BICEP3, with discussions on initial performance from instrument characterization measurements and preliminary maps made from the first 3 months of observations in 2015. Together with multi-frequency observation data from Planck, BICEP2, and the Keck Array, BICEP3 is projected to be able to set upper limits on the tensor-to-scalar ratio to $ $\lesssim$ 0.03 at 95\% C.L.. CMB-S4 is a future ground-based CMB polarization experiment, planned to observe large fractions of the sky (> 50%), have high resolution (less than 3') focusing on the arc-minute scale B-mode spectrum generated by lensing, and orders of magnitude more detectors than current generation of experiments (200,000+). The high signal-to-noise measurement of E-modes and B-modes of the CMB enables delensing through the E-to-B channel and reconstructing the lensing potential. We can therefore study 1) the gravitational wave generated B-modes with lensing removal, 2) physics that changes the shape of the lensing potential, and 3) further constraint and verify cosmological parameters through the E-modes. This thesis focuses on investigating how a wider range of input experiment configurations (sky fraction, detector count, beam sizes) for CMB-S4 changes the constraints on physics parameters of interests. With unprecedented sensitivity, CMB-S4 is projected to place competitive constraints on these areas of physics: cosmic neutrino background, dark matter, dark energy, and inflation.
Biochemical analysis of engineered TAL effector nuclease at on and novel off target sites [electronic resource]
Keywords: Biology.

Genome editing is a process that entails precise manipulation of a DNA sequence. To achieve this, a define stretch of nucleotides is replaced by a new, exogenously provided, DNA template using the cellular DNA repair machinery as a mean to promote the exchange. By taking this approach, we not only can repair alterations that impede gene functions but we can also expand our knowledge of basic biological processes driven by genes. Different classes of site-specific hybrid nucleases have been engineered precisely for the purpose of deleting a DNA sequence in a targeted manner. There are three main supporting platforms, Zinc Finger Nucleases (ZFNs), Transcription Activator Like Effector Nucleases (TALENs) and Cluster Regulatory Interspaced Short Palindromic Repeats/Cas9 Nucleases (CRISPR/Cas9). Of these three, TALENs have the highest targeting range, the flexibility of modifying different genomes and cell types with the lowest off-target activity, features that promote TALENs as potential powerful therapeutic tools. To further characterize them, I have employed a biochemical approach that allowed me to determine their specificity, affinities and kinetics at both cognate and novel OFF target DNA binding sites. From this study it became apparent that TALENs' kinetic signature is the missing link that connects their in vitro behavior with in vivo activity.
Biochemical insights into the evolution of alpha-catenin function in metazoan epithelia [electronic resource]
Keywords: Molecular and Cellular Physiology.

Alpha-catenin is a multi-functional adhesion protein that links cadherin and beta-catenin at the adherens junction to the underlying cortical actin cytoskeleton, and regulates actin dynamics in the cytoplasm. Alpha-catenin is essential for the formation of stable cell-cell contacts, and depletion results in gross developmental defects and cancer. While all animals have homologs of alpha-catenin, previous work from the Nelson and Weis labs demonstrated surprising functional differences between alpha-catenin homologs from M. musculus, C.elegans, and D. discoideum. These studies lacked sufficient phylogenetic coverage to make broad interpretations about the evolution of the cadherin-catenin complex and epithelial tissues. To address this gap in the literature, I reviewed previous data about the evolution of alpha-catenin and performed sequence analysis on animals and their near ancestors to make hypotheses about how the cadherin-catenin complex may have evolved (Chapter 1). I then investigated the biochemical properties of alpha-catenin homologs from three phylogenetic groups crucial to our understanding of the evolution of the cadherin-catenin complex but not before studied. Namely, an α-catenin homolog from a close outgroup to mammals (the zebrafish Danio rerio; Chapter 2), the closest outgroup to bilaterians (the sea anemone Nematostella vectensis; Chapter 3), and one of the earliest branching animal lineages (the marine sponge Oscarella carmela; Chapter 4) were characterized biochemically. This study reinforces the importance of biochemical characterization in studies of protein evolution as all three homologs possess distinct biochemical profiles from previously annotated alpha-catenins. Most importantly, this study provides a framework for future discussion about the evolution of the cadherin-catenin complex in animals and its role in the development of organized epithelial tissues (Chapter 5).
Biogeography of nitrogen-cycling microbial communities in San Francisco Bay [electronic resource]
Keywords: Environmental Earth System Science.

Nitrogen is an essential element to all of life on earth, and its bioavailability in the environment is governed by the activities of microorganisms that transform nitrogen species through redox processes such as denitrification, nitrification, and anammox. In this study, we survey the nitrogen-cycling microbial populations in the sediments of San Francisco Bay, using diverse DNA-based methods to address questions about microbial population dynamics across space, time, and the environmental gradients typical of an estuary. Our results include: a comparison of the abundance and community structures of nirK-type and nirS-type denitrifying bacteria; a novel use of next-generation sequencing for surveying functional gene diversity in the environment and a demonstration of machine-learning techniques for identifying ecological trends in that sequence data; and finally, deep sequencing of the 16S rRNA gene to survey and compare several N-cycling functional communities at once. Overall, we observe strong spatial structure in each nitrogen-cycling functional group as well as in the total microbial community, a strong response of all groups to salinity and to sediment nitrogen content, and marked differences in the temporal variability of communities in different sites. This survey of microbial diversity in San Francisco Bay contributes to our understanding of the processes influencing sediment biota in the estuary, and forms a foundation for future studies in the functioning of these nitrogen-cycling communities.
Biomechanical barrier function of human stratum corneum [electronic resource]
Keywords: Materials Science and Engineering.

The outermost layer of skin, the stratum corneum (SC), provides mechanical protection and acts as a controlled permeable barrier to the external environment while subject to highly variable conditions. The mechanical integrity of the skin is a critical and often overlooked component of overall skin health, and is vital for not only the feel and appearance of skin, but also for wound care, scar formation, biosensing, drug delivery, and technologies that interface with the skin, such as electronic tattoos. The effects of ubiquitous physiological and environmental conditions, including aging, solar ultraviolet (UV) exposure, and humidity, on the biomechanical barrier function of SC were examined, along with strategies for mitigating these effects and preserving the native biomechanical properties. Our results indicate that the combination of structural and mechanical property changes that occur with age and UV exposure, including changes to SC stiffness, cellular cohesion, and drying stress development, are quite significant and may contribute to the prevalence of skin disorders among the elderly. In addition, the hydration level of the SC is crucial for the barrier function and physical appearance of skin. Water loss causes the development of drying stresses, which provide a driving force for damage in the form of chapping and cracking. Emollient molecules are commonly used to alleviate dry skin conditions and some cause a significant alteration in the drying stress behavior of the SC. We characterized and modeled the SC's water loss profile with changes in humidity and applied emollient molecule composition. Engineering a suitable combination of emollient molecules has the potential to significantly reduce dry skin damage by removing the driving force for damage altogether.
Black conceptualism and the atmospheric turn, 1968-2008 [electronic resource]
Keywords: Art History.

This dissertation analyzes the work of six African American conceptual artists from the late twentieth century and early twenty-first century who explored the problem of race and representation in the wake of what I term "the atmospheric turn." Although African American art is often connected to visual representations of racialized experience and Conceptual art is regularly positioned as disinterested in political content, an analysis of artistic practices since the late 1960s reveals that artists, both black and white, regularly investigated race as a site of conceptual significance. Throughout the last half of the twentieth century, transformations in race discourse shifted the idea of race from an embodied essence to a social force, in a kind of "dematerialization." I focus on Black conceptual artists who, despite prevailing expectations that their work reflect the black experience, responded through the critique of representation itself, troubling the role of the visual field as the guarantor of racial expression. Their purposeful denaturing of blackness as a visual signifier of race yielded two possibilities: the mobilization of blackness as a conceptual strategy and the embrace of the extravisual dimensions of racial meaning, such as sound, voice, performance, and proprioception. Over the course of four chapters, I examine the artistic practices and theories of African American artists from the Civil Rights generation—David Hammons, Charles Gaines, and performance artist Lorraine O'Grady—and post-Civil Rights generation—photographer Lorna Simpson and sound artists Nadine Robinson and Jennie C. Jones—as they engaged the legacies of Conceptual art to interrogate and challenge the insistent materialization of race. By situating their practices in relation to historical debates on Conceptual art and African American art, and combining formal analysis of artworks with theories of racialization, this project offers an inquiry into the complex intersections of American art, Conceptual art, and African American art that posit the racial self, and blackness, as a productive site of artistic meaning.