VictorJuiz/thesis huggingface dataset:
Identification of novel regulators of the long interspersed nuclear element-1 retrotransposon in humans
Keywords: genetics) degree committee member.
Genetics.

First identified by Barbara McClintock in Zea mays, transposable elements are now recognized not only as parasitic DNA, the spread of which in the genome must be controlled by the host, but also as major players in genome evolution and regulation. The most abundant and only currently autonomously active transposable element in the human genome, LINE-1, contributes to inter- and intragenic variation within the human population. In addition, LINE-1 sequences can regulate transcriptional programs in cis and trans as well as lead to the mobilization of other cellular mRNAs, including other transposons. Here I address how cells defend against LINE-1 mobile activity, as well as explore the extent to which LINE-1 sequences are transcribed in adult human somatic tissues. Chapter 1 provides a short historical introduction to the identification of transposable elements and the biology of the LINE-1 transposon. In chapter 2, I describe our high-throughput screening approaches to identify key regulators of LINE-1 transposition. In addition to classifying regulators as acting through sequence dependent or independent mechanisms, we also identify the HUSH complex as a major regulator of LINE-1 activity in human cancer cells. In chapter 3, I use adult somatic tissue expression measurements from GTEx consortium to identify and describe somatic LINE-1 expression. We find tissue specific L1 expression, and further leverage publicly available ENCODE data to identify potential regulators of L1 transcription. In chapter 4 I discuss our findings from our screen and tissue-level expression analysis, with a focus on remaining unanswered questions. Taken together, these chapters improve our understanding host/LINE-1 interactions in human cells and tissues.
Identifying the Role of Early Sex Hormone Exposure in the Development of Social Behavior in Astatotilapia burtoni
Keywords:  Department of Biology
Biology
Astatotilapia burtoni
Testosterone
Estradiol
Shoaling
Aggression
Development
Organizational Effect
Thesis

Far from simply mediating sexual development and reproduction, steroid sex hormones play a large role in the regulation of complex social behaviors across species. Several studies have elucidated how sex steroid hormones (i.e., androgens and estrogens) can increase adult male sexual and aggressive behaviors. But just how sex steroid hormones influence the onset of social behavior in both sexes during early ontogeny remains to be established. Here, we use the African cichlid fish Astatotilapia burtoni, to investigate how early sex hormone exposure influences the transition from gregarious shoaling behavior to aggressive chasing behavior in juveniles. Three equally sized groups of eggs from the same brood were separated and immersed into aquarium water containing a known concentration of androgen, estrogen, or control (dimethyl sulfoxide or DMSO) shortly after fertilization. At three time points up to two months after fertilization, the movements of six fish from each treatment group were video recorded to map their individual positions over time. We found that fish in the androgen-treated group shoaled (measured by the mean similarity between trajectories) significantly less than those in the estrogen- and DMSO-treated groups at the latter two time points, suggesting that early androgen exposure has an organizational effect in the brain that facilitates a premature transition to aggressive behavior from shoaling behavior. As all vertebrates—including humans—share many of the same sex hormones and associated receptors with A. burtoni, these results might inform our understanding of how differential prenatal sex hormone exposure could influence social behavior later in life.
Ignition delay time measurements for distillate and synthetic jet fuels
Keywords: Mechanical Engineering.

As alternatives to traditional petroleum-based fuels are increasingly sought after, the National Jet Fuel Combustion Program (NJFCP) was established to streamline the evaluation and certification of these fuels. The current mandate is for the replacements of traditional fuels to be equally safe and to provide better environmental performance [1]. These so-called "drop-in" jet fuels refer to hydrocarbon fuels that deliver identical combustion performance and are produced from non-petroleum sources [2]. Following the mandate delivered by the NJFCP for alternative fuels, this study aims to improve the traditionally phenomenological understanding of combustion performance by making connections between fuel properties and the chemical composition of fuels. The ignition delay time is an important measure of the combustion performance of fuels, as it is an integrated measure of the fuels' physical and chemical properties, such as volatility, diffusivity, and chemical reactivity. Consequently, it is a very useful validation target in chemical kinetic modeling and has implications in practical aviation phenomena such as, among others, lean blowout, cold-start ignition and altitude relight. Shock tubes are well-suited for ignition delay time measurements, as they provide a well-defined time zero and a quasi-constant temperature and pressure test region behind the reflected shocks. All experiments in this thesis were performed on the Stanford Flexible Application Shock Tube (FAST). Reactive gas mixtures were prepared with equivalence ratios of 1 ± 0.05, and mixed in the shock tube driven section to avoid fuel loss attributed to non-idealities in the jet fuel vapor. Changes in the fuel mole fraction during mixing and ignition were monitored using laser absorption diagnosis at 3.39 µm. The ignition delay time is defined in this study by the onset of emission from electronically excited OH radicals at 306 nm. Ignition delay times were measured in the temperature range of 1200-1500 K and at 4 atm pressure for five distillate jet fuels from refineries around the US (termed geographical fuels), and for six synthetic jet fuels with varying cetane numbers ranging from 30-55 (termed CN fuels). The ignition delay times for A1-3 and C1-9 jet fuels were also measured at 1300 K and at 4 atm. The dependence of combustion properties on fuel chemical composition were investigated using the ignition delay times for these fuels. In particular, the key role that the degree of branching in the jet fuel molecular structure plays in the combustion kinetics and performance is discussed.
Imagining, building, and understanding the next-generation battery
Keywords: Materials Science and Engineering.

Harnessing electricity marked the beginning of the industrial revolution; making it portable completely transformed modern society. Battery technology has largely enabled the conveniences of social connectivity and mobile services we enjoy today. However, current batteries are rapidly approaching their fundamental limits. To make a lasting impact in emerging applications such as electric vehicles and grid-scale energy storage, better batteries that can store more energy in a safe manner need to be developed. Innovations and breakthroughs in such technologies require a synergistic and interdisciplinary combination of materials design (chemistry, engineering) and fundamental characterization (materials science, physics). In my Ph.D., I demonstrate successful examples within these two major thrusts, which will not only bring practical applications in the short-term, but also establish fundamental insights that are necessary to facilitate long-term solutions. Chapters 1, 2, and 3 focus on the first major thrust of this dissertation: materials design. Chapters 1 and 2 are an introduction to batteries. In chapter 1, I detail the history, working mechanisms, and limitations of the current state-of-the-art batteries based on lithium chemistry. In chapter 2, I provide an overview of the two most relevant candidates for next-generation battery anode materials: silicon and lithium metal. Intrinsic failure modes, previous solutions, and remaining challenges will be discussed. Chapter 3 summarizes my graphene cage design to stabilize the silicon anode. With such a design (patent pending), the long-standing obstacles have been addressed. Chapters 4, 5, and 6 explore the second major thrust of this dissertation: fundamental discovery. In chapter 4, I explain the key fundamental working principles of the transmission electron microscope (TEM), a powerful characterization technique that can enable atomic-level observations with both structural and chemical information. In chapter 5, I discuss the in situ TEM studies that revealed the nanoscale corrosion and passivation mechanisms of lithium metal. In chapter 6, I highlight the breakthrough cryogenic electron microscopy technique I pioneered for use in battery materials. Finally in chapter 7, I conclude with the implications of my Ph.D. work and comment on the exciting future directions that can be pursued in the future.
The impact of climate change and land use change on species population dynamics
Keywords: Biology.

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.
Imperial refuge : resettlement of Muslims from Russia in the Ottoman Empire, 1860-1914
Keywords: History.

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.
Improved discrimination for neutrinoless double beta decay searches with EXO-200 and nEXO [electronic resource]
Keywords: Physics.

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.
Improving and applying atomistic simulation to study biophysical conformational dynamics
Keywords: Chemistry.

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.
Improving dark energy measurements by controlling systematics in the point spread function and redshift distribution
Keywords: Physics.

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.
Improving problem-solving through reflection
Keywords: Education.

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.
Improving urological diagnostics : designing a low-cost screening tool and developing tools for bladder cancer detection
Keywords: Electrical Engineering.

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.
In the Air: Examining the Historical, Legal, and Social Dimensions of Drone Domestication
Keywords: unmanned aerial systems
drones
military
nonmilitary
civilian
society
legal
policy considerations
model
legislation
science and technology studies
history
theory
Stanford University
Thesis

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.