VictorJuiz/thesis huggingface dataset:
Diverse Patient Trajectories during Chemotherapy: Capturing Longitudinal Patient Reported Outcomes

Background
High-value cancer care balances effective treatment with preservation of quality of life. Chemotherapy is known to affect patients’ physical and psychological well-being negatively. Patient-reported outcomes (PROs) provide a means to monitor declines in a patients’ well-being during treatment.
Methods
We identified 741 oncology patients undergoing chemotherapy in our electronic health record (EHR) system who completed PROMIS surveys during treatment at a comprehensive cancer center, 2013-2018. PROMIS surveys were collected before, during, and after chemotherapy treatment. Linear mixed-effects models were performed to identify predictors of physical and mental health scores over time. A k-mean cluster analysis was used to group patient PROMIS score trajectories.
Results
Mean global physical health (GPH) scores were 48.7 (SD 9.3), 47.7 (8.8), and 48.6 (8.9) and global mental health (GMH) scores were 50.4 (8.6), 49.5 (8.8), and 50.6 (9.1) before, during, and after chemotherapy, respectively. Asian race, Hispanic ethnicity, public insurance, anxiety/depression, stage III cancer, and palliative care were predictors of GPH and GMH decline. The treatment time period was also a predictor of both GPH and GMH decline relative to pre-treatment. Trajectory clustering identified four distinct PRO clusters associated with chemotherapy treatment.
Conclusions
Patient-reported outcomes are increasingly used to help monitor cancer treatment and are now a part of care reimbursement. This study leveraged routinely collected PROMIS surveys linked to EHRs to identify novel patient trajectories of physical and mental well-being in oncology patients undergoing chemotherapy and potential predictors. Supportive care interventions in high-risk populations identified by our study may optimize resource deployment.

Keywords: Hernandez-Boussard, Tina
patient-reported outcomes
chemotherapy
PROMIS
quality-of-life
physical health
mental health
epidemiology
clinical research
Thesis
Advisor: Kurian Alison
Divided in Exile: Cooperation among Tajikistani Opposition Members in the EU

Theories in political sociology and migration studies point to a diaspora’s structural position in a host state as a factor promoting cooperative political behavior. However, these theories do not consider the transnational influence of authoritarian regimes. In this thesis, I examine cooperation among the EU-based exiles of different factions of Tajikistan’s political opposition. Based on the results of ten qualitative interviews with members of the Tajikistani opposition in four EU countries, I conclude that cooperation among these diasporans remains limited between the two largest opposition groups, the Islamic Renaissance Party of Tajikistan (IRPT) and Group 24. The Tajikistani government’s transnational repression tactics solidify the rift within the EU-based Tajikistani opposition. However, intergroup activism on behalf of individual human rights cases may provide a pathway to future joint efforts within the opposition. This thesis suggests that the political cooperation of diasporic populations is tied to conditions in both the home and host state. Where factors promoting cooperation exist, they may be eclipsed by the transnational influence of authoritarian host states.

Keywords: Center for Russian, East European and Eurasian Studies
Central Asia
Tajikistan
Text
Thesis
Advisor: Crews Robert
Asad Asad
Divided We Stand: The Role of Homophily in the Malleability of Social Networks

The influence of the structure of a society on the dynamics of coordination is a rich area of investigation. This structure, encoded by multitudes of influence networks and by the distribution of individual characteristics across these networks, constrains the degree of coordination in social activity. In this study, we explore the influence of homophily--the enhanced association between similar individuals--on the malleability of outcomes of social dynamics. In public discourse, the implicit assumption is that homophily has a negative effect on the flexibility or malleability of collective response to social challenges. In our model, we find the counterintuitive result that intermingling can enable one influential homogeneous subgroup to subordinate the response of another, negatively influencing overall malleability. The manner of the departure from perfect homophily ends up characterizing the exact nature of this reduction.

Keywords: Opinion Formation
Dynamics
Social Networks
Global Games
Homophily
Thesis
Advisor: Jackson Matthew
Dividing the Indivisible: A Study of the Views of the People of Azad Kashmir

Kashmir has been a cause of continuous strife between India and Pakistan and, consequently, a constant threat to regional peace and stability. Originating in the ambiguous decision of the British regarding the princely states of India, the dispute has led India and Pakistan, both of whom lay claim to the state, to wage several wars since partition. Several peace proposals have appeared over the decades. Yet, the views of Kashmiris, particularly from Pakistani-held Kashmir, are largely ignored and remain unknown. In this thesis, I utilize primary and secondary historical sources and an original survey to detail the views of Azad Kashmiris on both militancy and the proposals regarding the division of Kashmir and the creation of an independent, united Kashmir. I find that the majority of the surveyed respondents from Azad Kashmir oppose the division of Kashmir and support a proposed independent state. A majority are also divided on the question of the use of armed struggle/militancy as a plausible course of action. The thesis concludes that no peace process and settlement will be workable and ensure justice and fairness unless it involves and engages the people of Kashmir.

Keywords:  Department of International Relations
Program in International Relations
Stanford University
Human Rights
Political Rights
Kashmir
Self-determination
Militancy
Survey
Territorial Conflict
Indivisibility
Kashmir Dispute
India
Pakistan
Thesis
Advisor: Crews Robert D.
Do Accessory Dwelling Units (ADUs) live up to the hype?

The goal of this paper is to determine how an increase in Accessory Dwelling Unit (ADU) development impacts neighborhood heterogeneity. ADUs are secondary housing units established in conjunction with a primary housing unit. Examples include basement and attic apartments, garage additions, or small second housing units that share property with larger, primary units. ADUs have been considered as a way to ease the housing crisis in North American cities by increasing housing stock in areas where new development is otherwise restricted by geographic or zoning limitations. However, limited research has been done to determine the actual impact of ADU construction. This paper will seek to examine the neighborhood effects of detached ADU (DADUs) in Vancouver, Canada. It will consider how DADU construction impacts neighborhood race, income, and immigration status heterogeneity. Employing a construction that compares the exposure of different Vancouver neighborhoods to the DADU policy, this paper will aim to measure to what degree DADU construction increases heterogeneity. Ultimately, this paper finds that the construction of DADUs have a statistically significant impact on neighborhood racial heterogeneity, but does not impact income or immigration status heterogeneity.

Keywords: Economics Department
Stanford School of Humanities &amp; Sciences
Housing policy
planning and zoning
Accessory Dwelling Units
ADUs
Vancouver
Canada
Thesis
Advisor: Mark Duggan
Domestic Politics of Data Privacy Laws in Latin America: A Descriptive Analysis

The unharmonized protection of personal data presents risks to individuals’ privacy and poses economic costs to firms and nations by hampering the flow of data. If the regulation of data collection is a globalized issue that preserves individuals’ privacy while permitting economic innovation, why do some countries have data privacy laws while others do not? Why do we observe variations in these laws? In this thesis, I focused on the spread of data privacy laws in Latin America, where countries show variations in their level of economic development and regimes. The first part of my analysis describes the state of data privacy laws in Latin America, showing how countries rank across several categories. In the second part of my thesis, I study Chile, Uruguay, and Brazil and describe the domestic factors and stakeholders that were involved in the adoption of these laws. Through this research, I hope to provide a more nuanced understanding of how domestic factors shape data privacy laws in Latin America.

Keywords:  Program in International Relations
Data privacy laws
Latin America
Thesis
Advisor: Weinstein Jeremy
Doping and conformal non-planar growth of 2D semiconductors

To overcome the limitations of conventional transistor size scaling, recent proposals have been made to increase transistor density by vertically stacking transistors, in three dimensions (3D). However, conventional bulk semiconductors such as silicon are difficult to process in a vertical fashion due to their strong 3D bonding, and due to high-temperature growth required for high-quality films. To realize new scaling paradigms, new semiconductor materials are needed that can be easily processed for 3D heterogeneous integration, including on vertical sidewalls or trenches. While two-dimensional (2D) semiconductors offer promising properties for vertical scaling, 2D transistor performance has been insufficient and the deposition capabilities are not well understood. This thesis details my PhD work on improving 2D semiconductor transistor performance and demonstrating non-planar growth to realize the first vertical 2D transistor. First, I discuss analysis of experimental data on 2D transistors, highlighting key metrics and basic modeling. I then outline my efforts to standardize analysis and benchmarking of 2D transistors with the Python framework SemiPy and benchmarking website 2D Device Trends (http://2d.stanford.edu), introduced during this work. I also discuss the role of self-heating in 2D transistors and possible avenues to reduce their operating temperatures. Next, I present new doping techniques to increase the carrier concentration in n-type MoS2 and p-type WSe2 transistors, lowering their electrical contact resistance and increasing their on-state current. With modeling, I show that these doped 2D transistors are limited by thermal dissipation and could be comparable to state-of-the-art silicon transistors with improved heat sinking. Finally, I show that by utilizing van der Waals growth, 2D semiconductors can be conformally deposited on amorphous, non-planar features including sidewalls and high aspect ratio trenches. Such 2D semiconductor growth then enables vertical 2D transistors, which can have much smaller footprint than planar transistors, thereby offering higher transistor density. I then conclude with my own perspective on 2D semiconductor research and the necessary future work to enable commercial applications of 2D transistors

Keywords: Electrical Engineering.
Advisor: Pop Eric 
Saraswat Krishna
Wong Hon-Sum Philip
Dreaming in public : art, politics, and power in late medieval Rome

In the thirteenth century, the city of Rome was adorned with frescoes, mosaics, and sculptures of dreaming figures: images that frequently depicted a sleeping figure amidst an oneiric scene. This dissertation argues that these dream depictions were a powerful visual tool in the period, one that used the intimate qualities of dreaming to address its audience in profoundly personal terms. These dream images in medieval Rome assimilated scientific conceptions into the visual arts, drew on popular cultures of dream interpretation and divination, illustrated both contemporary and historical political aspirations as well as theology and eschatology. Ultimately this powerful medium, I argue, became a carefully crafted political tool, one that the papacy wielded to great effect in the thirteenth century to illustrate the extent of its role in the life of the faithful, a doctrine clearly espoused by the church beginning with the Fourth Lateran Council of 1215. The first chapter explores the roots of this visual phenomenon, examining the political context and history of how an image of Emperor Constantine dreaming became a central visual device in a small and heavily fortified papal chapel at the Basilica of Santi Quattro Coronati. The second chapter focusses on dream images in the public square: arguing that a scene of a dream depicted on the façade of the church of Santa Maria in Aracoeli served as an overt political statement precisely by appealing to popular practices of dream interpretation. The third chapter considers the city's most prominent dream image, the façade of the Basilica of Santa Maria Maggiore, within the intellectual and scientific culture of the period, arguing that the peculiar image functioned as a kind of diagram of cutting-edge dream science. The final chapter examines thirteenth-century conceptions of dream interpretation, reassessing now-lost frescoes of the Basilica of San Paolo fuori le mura as like a dream to be interpreted by its viewers. A further conclusion reflects on the ethics and politics of this kind of Art History, considering dream interpretation as fundamental part of art historical analysis and methodology. By considering these dreams images as the fundamentally visual nexus of scientific discovery, mass culture, popular religious practices, and political histories in the city I argue that these prominent images of the oneiric were a powerful and political visual medium in medieval Rome that has been largely overlooked in histories of the city

Keywords: Art and Art History.
Advisor: Pentcheva Bissera V. 
Derbes Anne
Lugli Emanuele
Drugs and the Black Panther Party: A Study in Contradiction. An Ideological and Intimate History, 1966-1972

This thesis uncovers the ideology of the Black Panther Party surrounding drugs alongside Party members' personal experiences with drug addiction as a further exploration of the founding concept of the Black Panther Party, contradiction, in its many manifestations and expressions.

Keywords:  Department of History
Stanford Department of History
drugs
Black Panther Party
contradiction
dialectical materialism
Huey Newton
violence
Thesis
Advisor: Olivarius Kathryn
Hobbs Allyson
Duration and intensity of end-Permian Marine Anoxia

Ocean anoxia was an important kill mechanism in the end-Permian mass extinction and uranium isotope data are among the most powerful tools for quantifying the global extent and duration of ocean deoxygenation. Although coherent stratigraphic variation in uranium isotope ratios (δ238U) and uranium concentrations ([U]) indicative of prolonged deoxygenation is well established, the precise extent of anoxia and associated uncertainty have yet to be quantified. Uncertainty arises from both noise in the data and imprecise knowledge of key parameters within the uranium cycle. In this study, we use the Monte Carlo method to explore a range of scenarios and their implications for the uranium cycle across the Permian-Triassic boundary and through the first 1.7 million years of the Triassic. We then compare model predictions against measured data using principal component analysis to identify model runs and associated parameter values most compatible with trends in the observed data. The best-fitting models indicate a pronounced increase in the extent of seafloor anoxia across the Permian/Triassic transition, reaching ~17.8% of the seafloor (95% CI: [10.9%, 47.1%]), lasting anywhere from 20 kyr to 1.2 Myr. There is an inverse relationship between the extent and duration of anoxia in the set of best-fitting models. This initial pulse of pronounced anoxia is followed by a prolonged aftermath, which continues through the remainder of the study interval, of less extensive, yet still expanded, anoxia covering 7.8% of the seafloor (95% CI: 1.6%, 48.9%]). Both expanded and protracted anoxia are required to fit existing data, with no indication of re-oxygenation during the study interval.

Keywords: Anoxia
Uranium > Isotopes
Uranium > Concentrations
end-Permian
Monte Carlo method
Text
Thesis
Dynamic introspection

In this dissertation, I study an under-appreciated type of introspection that helps explain how we can come to know the world around us. Much of today's epistemology, can be traced back to the work of Rene Descartes, and to the skeptical challenge he posed: what can we know beyond doubt? A longstanding response to Descartes' challenge is to locate the underlying assumptions that drove him, and others, to their skeptical conclusion; Descartes reached his skeptical position while assuming that subjects have clear and direct access to their own minds, that they have full introspection. During the last 70 years, philosophers have challenged these assumptions, developing tools in epistemology and philosophical logic to study the kind of ignorance subjects have about their own knowledge. Nevertheless, there is a type of introspection, which I call dynamic introspection, that has not caught the attention of epistemologists. This introspection is about, on the one hand, what we know about the way new experience will affect our future knowledge and on the other hand, what we know about the ways we got our current knowledge. Many epistemological debates either ignore such questions or implicitly assume that we are always certain about these matters. Do I need to have the prior certainty that my sources of information are trustworthy in order to gain knowledge from them? The answer to such questions depends on the dynamic introspective abilities we assume we have. Understanding the nature of dynamic introspection can vindicate our reliance on ordinary knowledge in the face of skeptical doubt. A subject might know that there is a tree in front of her (as a result of her perceptual experience) without having the ability to explain the exact source of her knowledge. I argue that this lack of dynamic introspection is natural, and does not lead to skeptical problems. In this dissertation, I introduce a new logical framework for analyzing and modeling dynamic introspection. After introducing the logical framework in Chapter 2, I use it to analyze important debates from the contemporary epistemological literature in which, I argue, dynamic introspection principles implicitly play a key role, and much can be learned by making them explicit. One debate concerns the skeptical challenge to the possibility of our perceptual knowledge about the external world: how can we answer the skeptic who doubts the possibility of perceptual knowledge? The second debate concerns the limits to which we can know and access our own internal mental world: what can we know about our own knowledge? By making the underlying dynamic introspection principles explicit in such debates, I hope to make a meaningful contribution to our understanding of our own knowledge

Keywords: Philosophy.
Advisor: Lawlor Krista
Briggs R. A.
Benthem Johan van
Dynamics in nanostructured liquids and surfaces probed with nonlinear infrared and optical spectroscopies

Many condensed phase systems with complex nanostructure are regularly being developed to address important technological problems. Although the systems may appear static on a macroscopic level, at the molecular level their structure is constantly evolving on ultrafast time scales. However, because these materials are new and more complex than the existing ones, much is still unknown about the local structures and dynamics that give rise to their function. Nonlinear infrared and optical spectroscopies are a powerful class of methods that measure the ultrafast dynamical fluctuations occurring in molecular systems. These methods use short femtosecond pulses of light to perturb and subsequently probe the optical properties of a material system through interactions with molecular properties such as vibrations or molecular polarizabilities. Polarization-selective pump-probe (PSPP) and two-dimensional infrared (2D IR) spectroscopies respectively measure the orientational dynamics and vibrational frequency dynamics of a vibrational probe molecule, which can serve as a reporter of the surrounding structure. Optical Kerr Effect (OKE) spectroscopy measures the collective polarizability dynamics of a molecular ensemble, providing information on collective orientational dynamics. Using these methods, the dynamics in three classes of molecular systems, an ionic liquid, mesoporous silica, and a dipolar liquid, were revealed

Keywords: Chemistry.
Advisor: Fayer Michael D.
Markland Thomas E.
Moerner W. E. (William Esco)
Effective mapping class group dynamics

We prove a quantitative estimate with a power saving error term for the number of filling closed geodesics of a given topological type and length at most L on an arbitrary closed, orientable, negatively curved surface. More generally, we prove estimates of the same kind for the number of free homotopy classes of filling closed curves of a given topological type on a closed, orientable surface whose geometric intersection number with respect to a given filling geodesic current is at most L. The proofs rely on recent progress made on the study of the effective dynamics of the mapping class group on Teichmüller space and the space of closed curves of a closed, orientable surface, and introduce a novel method for addressing counting problems of mapping class group orbits that naturally yields power saving error terms. This method is also applied to study counting problems of mapping class group orbits of Teichmüller space with respect to Thurston's asymmetric metric

Keywords: Mathematics.
Advisor: Kerckhoff Steve 
Wright Alexander
Trettel Steve J.
Effects of optical and environmental parameters on angle-resolved photoemission from materials

Studies in condensed matter physics have led to the discovery of a profusion of materials with interesting quantum properties, such as superconductors and topological insulators. The wide variety of material systems demands a wide variety of experimental techniques. I focus on two techniques: angle-resolved photoemission spectroscopy (ARPES), which measures electronic band structure in the energy and momentum domains; and time-resolved ARPES, which probes out-of-equilibrium phenomena by extending ARPES to the time domain. There are many parameters which can affect measurements of quantum materials. I show how varying nonlinear crystal thickness in an ultrafast laser setup allows for fine-tunable time and energy resolution in time-resolved photoemission. Achieving a high degree of control over resolutions is critical for enabling new experiments. I also investigate how Bi2Se3 surfaces change to bismuth upon exposure to air, potentially affecting results of surface-sensitive measurements in atmosphere. High control and understanding of temporal, spectroscopic, and sample composition properties, as well as the optical and environmental parameters which control them, are essential to performing successful experiments on quantum materials

Keywords: Applied Physics.
Advisor: Shen Zhi-Xun
Devereaux Thomas Peter
Heinz Tony F.
The effects of relatedness and population structure on patterns of genomic sharing

In this dissertation, I use several approaches to study patterns of genomic sharing. Chapters 2 and 3 take a theoretical approach, modeling the effect of consanguinity on patterns of genomic sharing. In Chapter 4, I describe a new method to detect IBD segments between closely related individuals. Lastly, in Chapter 5, I take a data-driven approach, analyzing levels of genomic segment sharing as well as genotype sharing to understand the genetic relationship between ancient and modern Indigenous individuals in North America

Keywords: Genetics.
Advisor: Rosenberg Noah
Montgomery Stephen
Pritchard Jonathan (Jonathan K.) 
Tang Hua (Geneticist)