VictorJuiz/thesis huggingface dataset:
Immunological factors in healthy individuals that lead to different disease risks : influenza susceptibility and sex differences

Current technology cannot fully predict a healthy person's disease susceptibilities. This is particularly true of immune-mediated disease, such as infection and autoimmunity, which are caused by both genetic and environmental factors. If we could predict an individual's disease risks, we could start treatment earlier and potentially prevent disease entirely. We propose using the blood transcriptome as a measure of disease risk, because it reflects an individual's immune state through cellular phenotypes and immune cell proportions. We pursued this idea through two projects: influenza susceptibility and sex differences. First, using influenza challenge studies we identified a gene, KLRD1, that could predict who would become sick upon challenge with influenza. Second, as females are at higher risk for autoimmune disease and males are at higher risk for infection and cancer, we examined sex differences in the healthy transcriptome. We identified an autosomal gene signature that consistently separated males and females 18-40 years old, changed with age, and predicted male, but not female, antibody responses to influenza infection. Our work demonstrates that the blood transcriptome reflects population variation in our immune systems, and can even predict disease outcomes.

Advisor: Khatri Purvesh
Utz Paul 
Mallick Parag
Stefanick Marcia Lynn
The impact of climate change and land use change on species population dynamics

Two of the most important drivers of species loss are climate change and land use change. Although climate change and land use change are widely studied, we know little about the interaction of changing climate and habitat degradation on a population's dynamics or how a population will respond to increasing environmental variability. To understand how both of these factors affect species population dynamics, I use a variety of methods, including simulation-based and theoretical approaches, and the application of empirical data. In this thesis, I (1) downscale extreme event modeling to an ecologically-relevant spatial scale using generalized extreme value theory and apply this method to a hurricane-disturbed subtropical understory shrub in Southeast Florida, (2) analyze the sensitivity of the stochastic growth rate to changes in transitions between environmental states, and (3) use a simulation-based study of the interaction of climate change and habitat degradation on a population's time to extinction.

Keywords: Biology.
Advisor: Tuljapurkar Shripad
Dirzo Rodolfo 
Fukami Tadashi
Horvitz Carol Cecile
Imperial refuge : resettlement of Muslims from Russia in the Ottoman Empire, 1860-1914

Imperial Refuge revisits late Ottoman history through the lens of migration, holding the resettlement of Muslim refugees as critical to the making of the modern Balkans, Turkey, and the Levant. In the half-century before World War I, about one million Muslims from Russia's North Caucasus region arrived in the Ottoman Empire. Most of them came as refugees fleeing war and persecution. This dissertation investigates the political economy of refugee resettlement in the Ottoman provinces of Danube, Sivas, and Damascus and traces refugee networks throughout the empire and beyond. The ability of refugees to tap into local economies underpinned Ottoman regional and imperial stability. State support, whether in financial aid, legal infrastructure, or transportation, was paramount to the economic success of agricultural refugee settlements. In the northern Balkans, for example, insufficient state subsidies and scarcity of land for refugees contributed to the outbreak of Muslim-Christian clashes and then to the 1877-78 Russo-Ottoman War, which ultimately ejected the Ottomans from much of the Balkans. In central Anatolia, a lack of state investment hindered the development of refugee villages, which led to economic stagnation of the region. In contrast, in the Levant, Circassian and Chechen refugees took advantage of the state-built Hejaz Railway and land reforms to create booming settlements. The refugees founded three of the four largest cities in modern Jordan, including the capital city of Amman. This bottom-up history of refugee migration and resettlement is based on archival materials from Turkey, Jordan, Bulgaria, Russia, Georgia, and the United Kingdom, including previously unknown private letters and refugee petitions.

Keywords: History.
Advisor: Beinin Joel
Crews Robert D.
Naimark Norman M. 
Yaycioglu Ali
Improved discrimination for neutrinoless double beta decay searches with EXO-200 and nEXO [electronic resource]

Neutrinos have been shown to have non-zero mass, however how they generate their minuscule masses is an open question. One well motivated possibility is that neutrinos have Majorana masses, for which the most sensitive test is the observation of neutrinoless double-beta decay. The half-life of this neutrinoless mode is much slower than that of the observed two-neutrino mode of double-beta decay, which is many orders longer than the age of the universe, thus searches are heavily background dominated. In this work discusses two, completely distinct, methods to improve discrimination of neutrinoless double-beta decay, of xenon-136, from backgrounds. The first method is through training new discriminators to more fully exploit the observed topological information in EXO-200 to distinguish neutrinoless double-beta decay from the most common backgrounds. The second method is to enable the observation of barium-136 resulting from double-beta decay for a future generation detector via a hardware-centric approach. One path requires extraction from high pressure gas to vacuum of heavy ions from similarly heavy medium with high efficiency. Work on a prototype extraction apparatus for the nEXO collaboration and lessons learned are presented here.

Keywords: Physics.
Advisor: Gratta Giorgio primary advisor. Thesis advisor
Akerib Daniel S. advisor. Thesis advisor
Tompkins Lauren Alexandra
Improved methodologies for seismic collapse risk estimation [electronic resource]

Avoiding structural collapse is the most important objective in earthquake resistant design because it is typically the main contributor to fatalities and serious injuries. Therefore, it is extremely important to adequately assess its probability of occurrence.In the context of Performance-Based Earthquake Engineering, an intensity measure (IM) is a parameter that quantifies the severity of an earthquake ground motion and serves as a link between probabilistic seismic hazard analysis (PSHA) and probabilistic structural response analysis. The choice of which parameter is used as an IM in nonlinear response history analyses has important consequences not only on the reliability of the estimated structural collapse capacity but also on the computational effort involved in conducting the collapse risk assessment. This study aims to provide improved estimations of structural collapse risk in low- and intermediate-rise moment frame structures. The main contributions are: (1) A new method, termed Enhanced-2-Stripe-Analysis (E2SA), to accurately estimate the structural collapse risk using the most commonly used IM, Sa(T1); (2) A thorough evaluation of the possible bias in the probability of collapse introduced from record scaling when Sa(T1) is used as the IM. It is shown that the bias is very important and persists even when taking into account spectral shape; (3) A new intensity measure, FIV3, which outperforms the efficiency, sufficiency, scale factor robustness, and predictability of several traditional and recently proposed IMs. More importantly, this IM is equally applicable to pulse- and non-pulse-like ground motions and greatly simplifies the ground motion selection process without significantly introducing a bias on collapse risk results; and (4) Ground motion prediction models for the recently proposed IM, Sa_avg, and for the IM proposed in this dissertation, FIV3. These two models will enable practitioners to use these two IMs in PSHA as well as in ground motion selection procedures.

Advisor: Miranda Eduardo (Miranda Mijares) primary advisor. Thesis advisor
Deierlein Gregory G. (Gregory Gerard)
Kiremidjian Anne S. (Anne Setian) advisor. Thesis advisor
Improving and applying atomistic simulation to study biophysical conformational dynamics

Models are tools used to interpret and draw conclusions from nature. Molecular dynamics (MD) simulation is a powerful technique for modeling complex atomistic systems such as biomolecules. In this dissertation, I discuss how one can improve and apply MD simulation in order to learn about biophysical phenomena. I first discuss how to improve the representation of the underlying physical interactions in a simulation. Chapter 2 discusses the optimization method, and 3 discusses how to rigorously characterize a resultant potential function. I then discuss how to use Markov state modeling to derive an interpretable mechanistic characterization of a simulation dataset. Chapters 4 and 5 apply this framework to study the conformational dynamics of the TREK-2 and CLC-2 ion channels, respectively. A brief introduction to the topics of MD simulation, force field optimization, and Markov state modeling is given in chapter 1. There remains a lot of work to be done before simulations are able to mimic reality with high fidelity. However, I am optimistic that with increasing data availability and improvements in optimization methodology, simulation will prove itself progressively more useful for studying dynamics at atomic resolution.

Keywords: Chemistry.
Advisor: Maduke Merritt C.
Pande Vijay 
Markland Thomas E.
Martinez Todd J. (Todd Joseph)
Improving dark energy measurements by controlling systematics in the point spread function and redshift distribution

Most of the universe is made up of dark energy, but we are unsure of its fundamental nature. Large, wide-field optical galaxy surveys such as the Dark Energy Survey (DES) seek to measure any time variation in dark energy through its impact on the growth of large scale structure. Among the many features that must be controlled in order to achieve this measurement are the point spread function (PSF) and redshift distribution. In the first half of my thesis I will present a physically motivated model for the optical and atmospheric portions of the PSF and apply them to DES data. In the second half of my thesis I will turn to the measurement and calibration of redshift distributions. First, I present `clustering redshifts, ' a novel method of calibrating the redshift distributions of an ensemble of galaxies using their correlations with quasi-spectroscopic tracers of large scale structure, such as galaxy clusters. Then, I present a calibration of the DES Year 1 source redshift distributions using these clustering redshifts. Finally, I present a scheme for calibrating redshift distributions using self-organizing maps and overlapping infrared data. Both threads of this thesis will be useful for future cosmological galaxy surveys like the Large Synoptic Survey Telescope, Euclid, and the Wide Field Infrared Survey Telescope.

Keywords: Physics.
Advisor: Roodman Aaron J. (Aaron Jay)
Burchat P. (Patricia) 
Wechsler Risa H. (Risa Heyrman)
Improving problem-solving through reflection

Effective science and engineering education goes beyond teaching content knowledge, and encompasses training problem-solvers who can use their knowledge to solve complex problems. Over the past decade, the science and engineering education community (NRC 2012, NGSS) has acknowledged the significance of training good scientific problem-solvers, and called for including teaching science and engineering practices in the curriculum, but there remain essential questions to be addressed: "What are the characteristics of good scientific problem-solving?", "how should we assess scientific problem-solving?", and "how should we teach scientific problem-solving?" In a series of three studies, we have addressed these questions. In the first study, we studied problem-solvers working to solve novel, complex problems. We identified eight major practices used in solving such problems. Based on the identified practices, we designed a problem-solving framework to assess students' level of performance in each of these practices. We showed that performance as measured by this framework was a better predictor than the level of content knowledge for success in problem solving. Based on the identified practices in the first study, for the second and third study, we designed a problem-solving training. We first showed that this training indeed improved students' problem-solving (study 2 & 3); second, this improvement transcended specific content area, and students' problem-solving improved in a content area different than the content area of their training (study 2). Last but not least, the improvement from the problem-solving training exceeded the improvement produced by the learner attempting multiple problems and receiving feedback only about the accuracy of answers; the conventional method for teaching problem solving. (study 3). In summary, in these three studies, we used empirical data to characterize problem-solving practices. Based on this characterization, we developed a framework to assess students' problem-solving. Further, based on the developed framework, we designed a training program that successfully taught students to become better problem-solvers.

Keywords: Education.
Advisor: Wieman C. E. (Carl Edwin) 
Kenny Thomas William 
Schwartz Daniel L.
Improving the quality of urban stormwater with innovative treatment technologies from the lab to watershed scale

Urban runoff, or stormwater, poses engineering challenges including increased flood risk and water quality impairment. Stormwater control measures (SCMs) are increasingly used to both mitigate the negative effects of stormwater and capitalize on stormwater as a valuable water resource. SCMs have been shown to provide water quantity benefits such as decreased peak flow and increased groundwater recharge. But the ability of SCMs to reduce pollutants is variable, prompting researchers and practitioners to develop enhanced SCMs with modified geomedia, plant and fungal processes, or hydraulic conditions to provide increased and more reliable pollutant removal. Examples of enhanced SCMs include open surface wetlands, biochar-amended biofilters, and detention ponds with real-time controls. This dissertation focuses on how these next generation SCMs can provide laboratory- and watershed-scale benefits. Chapter 2 investigates the use of wood-decay fungi to enhance biodegradation processes in stormwater at the laboratory scale. Batch studies indicate that the wood-decay fungi are capable of degrading the urban-use pesticide fipronil. Chapters 3 and 4 investigate the impacts of enhanced SCMs on stormwater quality at the watershed scale. Chapter 3 examines effects of implementing enhanced SCMs on fecal indicator bacteria (FIB) pollution in the Ballona Creek Watershed (Los Angeles County, CA). Chapter 4 examines urban-use pesticide occurrence in runoff and subsequent watershed-scale management of pesticides with SCMs in the San Diego River (San Diego County, CA). This work reveals enhanced SCMs provide water quality benefits in the laboratory that are scalable to the watershed level. Further, water managers should consider water quality and quantity goals concurrently when designing SCM networks.

Advisor: Luthy Richard G. 
Boehm Alexandria 
Hogue Terri
Improving urological diagnostics : designing a low-cost screening tool and developing tools for bladder cancer detection

Urological diseases, including urinary tract infections, kidney stones, prostate cancer, and bladder cancer, represent a major financial burden on our healthcare system. I aimed to reduce these costs in several ways: 1) by reducing the cost of currently used screening tools; 2) by fabricating test targets for various bladder conditions, which will decrease the cost of and time needed to develop new diagnostic tools; and 3) by building bladder cancer detection tools to aid in early disease diagnosis. To reduce the cost of currently used screening tools, I designed and fabricated a low-power, low-cost, portable device capable of running the standard "Routine Urinalysis and Microscopy" (RUM) protocol. RUM, which involves chemical analysis via a semi-quantitative dipstick and review of the microscopic contents (e.g., red blood cells, white blood cells, crystals, and casts), is often the first step in diagnosing any urological disease. My device is designed to remove the many sources of user error that often plague dipstick testing and inhibit robust and accurate analysis. The dipstick testing is coupled with a low-cost microscope based on power-free filtration and oblique illumination, which enables visualization and quantification of microscopic components. Because the device is low cost and user friendly, it opens the door for urinalysis testing both at home and in low-resource environments. For test targets of various bladder conditions, I developed a multi-modal, disease-mimicking bladder phantom, which provides a realistic imaging environment for testing various aspects of optical systems and image processing algorithms before validation in real tissue. This access to a realistic imaging environment in the lab decreases the cost and time of development for new bladder-related diagnostic tools. Last, for bladder cancer detection, I designed a method for quantifying the local attenuation coefficient of tissue using optical coherence tomography, which has been shown to be an important parameter for many diagnostic, classification, and surveillance applications (including bladder cancer diagnosis). Due to constraints in the data collection process, the current method is only clinically applicable in ophthalmology. However, there is a clear path moving forward, which will expand the utility of the method for use in other organs, including the bladder.

Keywords: Electrical Engineering.
Advisor: Bowden Audrey
Liao Joseph
Pauly John (John M.)
In the Air: Examining the Historical, Legal, and Social Dimensions of Drone Domestication

Drones are a revolutionary and disruptive technology that has already affected and will continue to influence existing legislation, programs, and infrastructure in the United States. Drones were created as a military tool, but they have been repurposed for civilian and commercial applications in nonmilitary contexts. As drones have been adopted in the civilian realm for nonmilitary purposes, new actors have shaped and molded drones by changing how drones are viewed and used. Thus, drones have evolved due to repeated alterations and transformations by different audiences. Drones are becoming more commonplace in society, and while drone usage offers numerous benefits, there is also a multitude of issues and challenges associated with their widespread adoption. However, there is still a lack of federal legislation on drones. This thesis explores the historical military origins, as well as the current roles and implications, of drones in order to answer the questions: what are the historical, legal, and social dimensions of drones? Even though drones have been repurposed for nonmilitary functions, how does the military narrative of drones affect the legal and social aspects of domestic drone use? How should that information, framed through an STS paradigm, be employed in order to impact drone policy? This thesis is a historical and theoretical discussion on drones that examines when and why were drones created, how drones have changed and evolved, what are the new capabilities of drones, and for what purposes are drones now used. Because a comprehensive legal framework does not yet exist, this thesis offers a 5-step model that is informed by science and technology studies for drone policy considerations. The 5 steps of the model are: 1) Identify actor(s), 2) Identify and disaggregate possible applications, 3) Identify threats and vulnerabilities, 4) Analyze and evaluate potential risks, and 5) Rank priorities for policy considerations.

Keywords: unmanned aerial systems
drones
military
nonmilitary
civilian
society
legal
policy considerations
model
legislation
science and technology studies
history
theory
Stanford University
Thesis
In the name of the home : the politics of gender, race, and reconstruction in nineteenth-century America

In the Name of the Home is a history of the central concept of the nineteenth-century United States: the American home. It explores how the home lay at the center of efforts to first connect and then reconstruct the expanding nation according to a single vision of American citizenship. The home served as a moral blueprint for the reconstruction efforts of government officials, politicians, social reformers, and cultural purveyors attempting to integrate both the defeated South and the still largely unincorporated West. However, when applied to the nation's "problem" groups—freedpeople, Native peoples, Chinese immigrants, and Mormons—the home failed to create the inclusive, homogenous society that they had imagined. Instead, by the end of the century, the home had been wielded to exclude, terrorize, and enforce assimilation. By connecting the experiences of southern and western minority groups together through home politics and policies, this project reveals how ultimately the home became an illiberal form of coercion in a new liberal order.

Keywords: History.
Advisor: Freedman Estelle B.
White Richard
Winterer Caroline
Increasing Efficacy in social behavior analyses using Astatotilapia burtoni

The African cichlid Astatotilapia burtoni is an extensively used model organism for social behavior due to the males’ ability to rapidly change in social status. Upon achieving social dominance, males perform distinctive aggressive and courtship behaviors. As in any kind of behavior analysis, these behaviors can be recorded by observers for further study. However, no set standard currently exists for determining the length of the timeframe necessary for analyzing behavior of A. burtoni or of other behavioral models, which can make comparisons between studies of even the same species difficult. We analyzed data from males of this species, using the list of behaviors they performed and the time at which they were performed. We then sampled random minutes within logs in order to determine how much time is truly needed to accurately construct an individual’s behavioral repertoire. Furthermore, we calculated mean behavior performed and coefficient of variation of behaviors to determine how they influence the required time. We found that mean rate of a behavior positively correlates with time needed to score a behavior, while coefficient of variation of behavior has a negative correlation. By determining how different factors can influence the amount of time needed to observe an animal to adequately represent its behavior, we can improve the efficiency of behavioral analysis of A. burtoni and identify principles of behavior that may be used to study other species.

Keywords:  Department of Biology
Biology
Astatotilapia burtoni
aggression
sampling interval
social behavior
behavioral analysis
Thesis
Advisor: Fernald Russell
Heller H Craig