VictorJuiz/thesis huggingface dataset:
Host-centric proteomics : laying the foundation to use human stool proteins as biomarkers of gastrointestinal disease
Keywords: Chemical and Systems Biology.

It is common practice for a physician to request a blood draw at a doctor's visit in order to determine the levels of key molecules in our blood as proxy's for a healthy or diseased state. Though this is a common practice, establishing these molecules' usefulness as diagnostic agents often takes many years. First, it is necessary to determine what molecules are present in blood. Then, extraction protocols for these molecules need to be established in order to ensure reproducible and measurable results. Next, it is necessary to establish the variability of these molecules across healthy people. Finally, it is necessary to ascertain whether these molecules can distinguish states of health or disease based on their abundance or presence in each phenotype. While these steps have been taken countless times in establishing blood biomarkers, thus far human stool has seen limited use as a source of biomarkers. However, new biological discoveries have brought a renewed interest to human stool. In 2013, microbiome sequencing became cheap and high-throughput. The development of this technology allowed researchers to study the microbiome under a multitude of conditions, including how the microbiome changed in the gut. However, these microbes are not living in isolation and constantly interact with and influence the human gut. One avenue through which microbes and their hosts interact is through the use of proteins secreted by cells in the epithelium. Several protein classes are prevalent in stool including structural, immune, and digestion-related proteins. Given the functional importance of gut-related proteins and their relation to the microbiome, it is important to understand their temporal and insult-related changes. The Elias lab has developed a protocol to enrich and purify these proteins from stool and characterize their abundance using mass-spectrometry-based proteomics. Using a mass spectrometer as a diagnostic approach offers the user many excellent attributes in a diagnostic. This host-centric proteomics approach is quantitative, non-invasive, multi-dimensional, and directly gastrointestinally targeted. The goal of this thesis is to further establish the use of human stool proteins as diagnostic markers of gastrointestinal health using mass spectrometry-based proteomics. First, I optimized a protocol focused on human stool that reliably and reproducibly extracts proteins from stool and enables their quantitation on proteomics platform. Next, I describe how these proteins and their relative abundances vary in healthy people. From this study I found that the largest source of variability of human stool protein abundance was between people. This allows us to control for this variability in the future by studying many people to determine "healthy" protein abundance ranges. Finally, I report stool proteins distinguish states of flare or remission in inflammatory bowel disease patients.
How Agricultural Technologies' Development Might Impact U.S. Agricultural Subsidy Policies
Keywords:  Public Policy Program
Stanford University
Humanities and Sciences
Public Policy Program
farms subsidy policy
agricultural technologies
cost-benefit analysis
USDA
farming
agriculture
agricultural commodities
food security
data
artificial intelligence
Thesis

In 2017, U.S. farmers received more than $16 billion in subsidies. Critics often point out that these subsidies disproportionately benefit farmers with larger farms. The Food and Agriculture Organization (FAO) predicts that the global population will reach 10 billion by 2050. Experts estimate that the world will need to produce 70% more food to feed this population and that Agricultural Technologies will play a prominent role in increasing production. Besides disrupting the value chain, this shift in technology will also provide a tremendous amount of information and transparency in agri-food production systems. This thesis attempts to answer the following question: how can the information provided by the new technologies change the way the Government subsidizes agricultural commodities?
How do wildfires affect recreation patterns?
Keywords: wildfires
Flickr
social media
Stanford Economics
thesis
econometrics
recreation
Thesis

The occurrence of large wildfires is an increasing feature of the American West. Despite this, little is known about how these fires affect welfare-relevant outcomes like recreation demand because of the cost of conducting such analyses at a large scale. In this paper, I use the number of photos uploaded to Flickr between 2006-2013 as a costless and scalable proxy for visits to National Parks and Forests in California. Using this dataset, I examine the effect of fires of different sizes, severities, and ages on recreation demand in forests with different types of vegetation over a 30-year period. I find that a fire of average size and severity causes a 9.9% reduction in visits in the long run. Second, the response function of recreation demand to fire occurrence over time is non-monotonic; results suggest that visits drop in response to fires initially, gradually increase, and then drop again towards the end of the 30-year period. Third, while the number of visitors drops in response to fires of all severity levels momentarily, it recovers faster in sites that were burned more severely relative to sites that had milder fires. Lastly, the effect of a wildfire on recreation varies dramatically depending on the vegetation type of a site.
How to design and analyze online A/B tests within decentralized organizations
Keywords: Statistics.

From e-commerce to digital media to social networks, essentially any company that does business online is using A/B tests -- randomized experiments on its customers -- in order to optimize its service. A standard approach to designing and analyzing these experiments, based on classical statistical theory, is ubiquitous in industrial practice. Namely, a sample size for each test should be set in advance, and the data collected should be analyzed in isolation through p-values and confidence intervals that are computed based on a 2-sample t-test of means. This thesis investigates four ways that this default approach proves insufficient, due to the decentralized manner in which A/B tests at these companies are run. For each of the four, we empower experimenters to continue their current behavior, while we offer novel methodology that is simple to implement and ensures inferential reliability. Some of our methods are now in use in industry. We supplement our theoretical results with empirical data from these industrial deployments.
Human-computer conflicts in partially-automated driving
Keywords: Communication.

Computer systems with independent agency that directly act on the environment or influence behaviors and beliefs now mediate our interactions with the ambient environment—influencing what we believe, and what we can do. We will increasingly come in to conflict with such systems, even if they are helping us pursue our superordinate desires. Moral conflicts, without an objectively correct solution, present a complex challenge and demand empirical investigation as to how people will cope with a human-computer moral conflict, so to inform the design of such systems. To study human-computer moral conflicts, a full-vehicle driving simulator was used to elicit naturalistic driver responses in a set of moral conflict situations, where the computer would steer the participant towards greater danger to self, or would protect them by steering towards vulnerable others. Participants fought more strongly against the computer when it pushed participants towards greater danger to themselves and less when it steered them towards vulnerable others when collisions were impossible and time was available to evaluate the situation and act against the computer's actions. In a time-pressured situation where a collision was inevitable, participants fought more strongly against the system when it steered them to strike a person, and less when it pushed them towards a barrier that would injure them. Ultimately, the circumstances of the situation, time available, and level of perceived threat greatly influence fighting against a computer's actions in the moment, and thus systems need to be designed carefully, as supervisory control may be difficult or impossible in critical situations.
Hunting for Special Solutions in Calabi-Yau Compactifications
Keywords:  Department of Physics
string theory
Calabi-Yau manifolds
moduli stabilization
Thesis

In this thesis, we discuss approaches to various problems in the field of geometric moduli stabilization in type IIB string theory. We introduce the physics and mathematics of Calabi-Yau compactifications, flux compactifications, and attractor black holes. With these tools we investigate the construction of explicit, analytical flux solutions that generate vacua with small and nonvanishing superpotential and connect these solutions to old ideas in number theory about approximations of irrational numbers. Finally, we detail the statistical theory of vacua in moduli space and cite some new and old results as they pertain to non-supersymmetric vacua and non-BPS attractor black holes.
Hydrodynamics of condensed matter
Keywords: Physics.

Symmetries control the late time physics of classical and quantum systems that thermalize; hydrodynamics is the framework that describes this physics. The first part of this thesis establishes the hydrodynamic description of several archetypal systems of modern condensed matter physics: anomalous metals, Wigner crystals and fractional quantum Hall materials. A hydrodynamic theory describing the elusive bad metallic phase of high temperature superconductors is proposed. The second part of this thesis lays out several developments in the theoretical framework itself. It is shown that the symmetry algebra alone (as opposed to how it is realized) determines the hydrodynamic description of a system. A systematic theory of hydrodynamic fluctuations is presented and used to determine universal corrections to diffusion. Finally, bounds on transport coefficients are derived from microscopic positivity conditions.
Hydrogen bond dynamics and directional interactions in nanostructured condensed phases
Keywords: Chemistry.

The hydrogen bond is a key intermolecular interaction in chemistry, biology, geology, and materials science, with its energy tuned for a perfect balance between structural rigidity and rapid dynamic rearrangements around ambient conditions. Ultrafast infrared spectroscopic methods are described that can interrogate the dynamics and intermolecular interactions of the hydroxyl stretch mode, a sensitive reporter of hydrogen bonding environments, of water and alcohols in complex environments far removed from the bulk liquids. New methodology for conducting noncollinear two-dimensional infrared experiments in a rotating frame to accelerate data acquisition is described. Water confined in polyacrylamide hydrogels is found to slow as one population as the size of the water pool decreases. The lack of any water with bulk-like dynamics is surprising and attributed to the continuity of hydrogen bond network between the water pool and confining polymer. Room temperature ionic liquids, a family of tunable, non-volatile, and non-flammable solvents composed entirely of cations and anions, are structured at the nanoscale by charge ordering as well as the possibility of other motifs, such as segregation of polar and apolar groups. Water and alcohols isolated in ionic liquids, as representative solutes or cosolvents, experience hydrogen bond interactions with the solvating ions. A rich hierarchy of dynamical processes in the randomization of their orientations and intermolecular interactions is observed, ranging from less than 100 femtoseconds to sometimes over 100 picoseconds. The hydrogen bond interactions are highly directional, leading to distinct forms in the polarization dependence of ultrafast IR measurements of structural dynamics (spectral diffusion), particularly in ionic liquids. Theory is developed to characterize these directional interactions and dynamics quantitatively and separate the reorientation-induced spectral diffusion (RISD) processes, arising through rotation of the tracer, from spectral diffusion that is due to the randomization of the surroundings. Related theories of RISD are presented that are appropriate for carbon dioxide, a highly symmetrical vibrational probe, as well as fluorescent probe molecules undergoing time-dependent Stokes shift with highly directional interactions that determine the absorption and emission frequencies. Measurements of the dynamics of water confined in the nanoscale pores of amorphous silica are presented. Several techniques to overcome the inherent scatter from silica particles (sand) were combined, including phase cycling, polarization control, and spatial filtering, and their individual merits are discussed. The slowdown in dynamics of water in the silica pore are compared to previous measurements of the dynamics of selenocyanate, an anion that H-bonds to the surrounding water in the pore.
Hydrologic change and muskrat population dynamics in the Peace-Athabasca Delta, Canada
Keywords: Earth System Science.

Empirical and anecdotal reports suggest that muskrat are in decline across North America, including in the 5500 square km Peace-Athabasca Delta ("Delta"), Canada, part of a World Heritage Site with 'in Danger' status pending. This dissertation is concerned with the effects of rapid hydrologic change on the Delta's muskrat population. Analysis of a Landsat-derived record of inundation for the Delta (1972-2017), together with 21 years of muskrat survey records, show that the catastrophic decline in the Delta's muskrat population is synchronous with loss of critical habitat. Results suggest that loss of wetland habitat could be the cause of the observed, but as yet unexplained, decline of muskrat across North America. Conceptual and quantitative agent models of the muskrat population at a model floodplain lake region of the Delta illustrate mechanisms controlling muskrat abundance. Model results show that shoreline habitat and muskrat intensive herbivory are key mechanisms controlling muskrat abundance, while trapping intensity is not a primary factor. This is a key finding as muskrat trapping continues to be an important practice for Indigenous communities with traditional territory in the Delta. Ecological agent modeling, dynamic habitat maps driven by hydrologic change, and landscape genetic analysis are brought together to assess spatio-temporal characteristics of population dynamics for muskrat on the Delta floodplain. Results show that the Delta undergoes dramatic transitions from a network of population sources, to a network of population sinks, on an interannual basis in years following floodwater inputs. Notably, this network of sources and sinks is less prominent following the most recent flood in 2014, suggesting a reduced footprint of the muskrat population on the Delta floodplain, a change with broad implications for the ecological integrity of the Delta ecosystem. Together, the findings from this dissertation lay the groundwork for use of muskrat as an indicator species for the impacts of hydrologic change on wetland ecosystems, particularly in subarctic and arctic delta regions where the hydrologic effects of climate change are pronounced.
Identification of genetic regulators of antibody-drug conjugate toxicity using CRISPR-Cas9 screens
Keywords: Genetics.

Antibody-drug conjugates (ADCs) selectively deliver highly toxic chemotherapeutic agents to target antigen-expressing cells and have become an important cancer treatment in recent years. However, the molecular mechanisms by which ADCs are internalized and activated within cells remain unclear. Here we use CRISPR-Cas9 screens to identify genes that control the toxicity of ADCs targeting different cancer antigens and cell types. Our results demonstrate critical roles for a range of known and novel intracellular trafficking regulators in ADC toxicity. We identify and characterize C18orf8/RMC1 as a regulator of ADC toxicity through its role in endosomal maturation. Through comparative analysis of CRISPR screens with ADCs bearing a noncleavable linker versus a cleavable valine-citrulline (VC) linker, we show that a subset of late endo/lysosomal and retrograde trafficking regulators selectively influence toxicity of noncleavable linker ADCs. We further show that cleavable VC linkers are rapidly processed upon internalization and therefore surprisingly appear to bypass the requirement of lysosomal delivery. Lastly, we show that depletion of sialic acids sensitizes cells to anti-CD22 and anti-Her2 ADCs by increasing the rate of ADC lysosomal delivery. In contrast, deletion of sialic acid biosynthesis genes protects cells from anti-CD30 ADCs, suggesting that proper sialylation is required for CD30 cell surface-expression. Together, these results reveal novel regulators of endolysosomal trafficking, provide important insights to guide future ADC design, and identify candidate combination therapy targets as well as potential mechanisms of ADC resistance.
Identifying cell types and cellular contexts relevant for complex traits
Keywords: Biomedical Informatics.

We now know of many thousand genetic mutations associated with human phenotypes, and yet the process of translating this information into an understanding of biology has lagged. A crucial step forward is to identify trait-relevant cellular states or contexts, which when disrupted have a significant effect on a phenotype. With knowledge of the specific pathological contexts, one can develop model systems required for in-depth mechanistic study and further biological insights. Thus, in this thesis I investigated approaches of aggregating the many effects of variants associated with gene expression regulatory networks to identify trait-relevant cell types and cellular contexts. Through this work I demonstrate that to realize the lofty -- albeit achievable -- goals of human genetics, we must rethink strategies of producing biological knowledge from genetic studies.
Identity and Self-Presentation in Computer Mediated Environments
Keywords:  Department of Communication
Communication
Media Studies
online identity
social media identity
digital media identity
online self-presentation
online self perception
Thesis

Identity and self-presentation have been prominent areas of study in the fields of communication and psychology for decades. Despite this lengthy history of study, interpretations of the two concepts are varied. With the introduction of computer mediated environments such as social media, scholars’ understanding of these concepts have been put to the test. This paper analyzes, categorizes, and synthesizes leading research in the area of identity and self-presentation in computer mediated environments. This literature review is guided by two overarching research questions: (1) How does identity influence self presentation online? and (2) How does self presentation online influence identity? Similarities and differences between theories as well as gaps in the literature and societal implications are discussed.
Image descriptor aggregation for efficient retrieval
Keywords: Electrical Engineering.

As more and more visual content is created every day, it is critical to make sense of large image databases. Searching such databases using a query image is the goal of content-based image retrieval, or visual search. At the core of this task is the trade-off between search speed and accuracy. This work proposes to use aggregation to improve this trade-off. By aggregating information across images we can directly compare a query image with sets of images represented by a single descriptor. We show that this can make the search considerably faster with a very limited loss of accuracy. The main questions explored in this work relate to how to best perform this aggregation: how to choose which images should be aggregated, how to represent a set of images with a single descriptor, and finally how to index these descriptors so as to maximize the search speed. We show that it is beneficial to aggregate images that share similar characteristics, such as images captured from nearby viewpoints, and that the higher level of abstraction achieved by searching aggregated descriptors instead of original images allows for considerable speed gains by reducing the size of the database. Our next contribution is to show that improving the representation of a given set of image descriptors can lead to additional gains: the representation using generalized max pooling is much better for retrieval tasks. More complex parametric methods do not seem to show additional benefits compared to simple pooling of optimized image descriptors. Finally, we show the importance of indexing the aggregated descriptors into a well-chosen hierarchical structure that combines the benefits of a coarse database search at the higher levels of the hierarchy with the benefits of a fine database search at the lower levels. All these contributions jointly combine to drastically improve retrieval speed without degrading the accuracy. This study is rooted in a theoretical framework that we develop as a basis for aggregation, and we then show that the insights learned from this framework carry on to a wide range of real-world applications such as 3D object retrieval, indoor localization and person re-identification.
Imaging diagnostics for in situ measurements within challenging environments
Keywords: Mechanical Engineering.

The development, validation, and deployment of imaging diagnostic systems and corresponding image processing algorithms are presented that enable in situ measurements within two challenging environments: aquatic environments and high temperature, high pressure reactive gas environments. Image processing algorithms for a single-camera defocusing digital particle image velocimetry (DDPIV) imaging system were developed to perform three-dimensional tracking of natural particulate and organisms in the water column within a 10 cm x 10 cm x 20 cm volume at 60 Hz. The developed underwater imaging system was deployed at the Marine Biological Laboratory (Woods Hole, MA), and measurements of Mnemiopsis leidyi ctene rows are presented to demonstrate the measurement capabilities of the developed system. An imaging diagnostic was developed to image the structure of combustion events behind reflected shock waves. An intensified high-repetition-rate imaging system was used to acquire images of OH* chemiluminescence (near 308 nm) through a fused quartz shock tube end-wall window at 10-33 kHz during the combustion of n-heptane. The imaging technique enabled observation (12 cm x 12 cm) of the main ignition event in the core of the shock tube, that corresponds to typical markers of ignition (e.g., pressure rise).