VictorJuiz/thesis huggingface dataset:
Towards low-cost spatial haptics : brake-based shape displays and automatic content authoring

Haptic technology can significantly enhance the richness and realism of user interaction by providing the experience of physical touch. It is broadly used in various application scenarios including game controllers, surgical robots, design and modeling tools, and accessibility for Blind people. Tactile displays are a class of haptic devices that can render tactile effects to the users, for example reproducing the skin deformation of a user when in contact with a real object, allowing the user to feel vibration, pressure, touch, and texture. However, key challenges currently limit the widespread use of tactile displays including cost, spatial resolution, fabrication complexity, shape rendering flexibility, and refresh rate. Beyond these hardware limitations, authoring of rich tactile content is another challenge. Although manual authoring methods have been developed, methods that can automatically translate vast amounts of information into meaningful tactile stimuli are highly desirable. In this thesis, I present my work on addressing the hardware and content authoring challenges of the tactile displays. The first part of my thesis work focuses on the use of electrostatic brakes and clutches to enable low-cost tactile displays. I investigated the use of low-cost electrostatic adhesion in the context of high-resolution, refreshable 2.5D tactile shape display. I modeled, fabricated, and characterized the contact force, refresh rate and robustness of the brakes. A user study conducted using an integrated 4×2 tactile shape display based on the brakes showed similar user shape recognition performance using our device and the 3D printed shapes. In addition to the bed-of-nails tactile displays mentioned above, I also explored the formable-crust 2.5D tactile shape displays using auxetic materials. A simulation model and algorithms were developed to investigate the characteristics of the shape display and render a target shape. An experimental prototype was constructed to verify the simulation results. The auxetic 2.5D tactile shape display has the advantages of low cost, large displacement range, and roll-to-roll fabrication compatibility. In the second part of my thesis, I investigated methods to address the content authoring challenges of tactile displays. A pipeline was built to automatically generate spatial tactile effects by analyzing cross-modality features in a video. We believe the above results help to improve the accessibility of the haptic technology to a broader audience

Keywords: Electrical Engineering.
Advisor: Follmer Sean 
Rivas-Davila Juan 
Wetzstein Gordon
Training computers to read human faces : what artificial intelligence can teach us about first impressions

First impressions, such as a job interview or a meeting with a new client, involve making two kinds of inferences about the mind of a stranger. On the one hand, you may want to know what this new person is like, and on the other hand, you might be wondering how this individual sees you. In this dissertation, I demonstrate that artificial intelligence can make both of these social inferences more accurately than people can and explore how such developments may advance our scientific understanding

Keywords: Business.
Advisor: Kosinski Michal 
Halevy Nir
Miller D. A. B.
Transatlantic Turmoil: Populist Parties and NATO Membership in the European Union

For the past few years, scholars, politicians, and journalists on both sides of the Atlantic Ocean have been ringing alarm bells about the rise of anti-institutional populism in Europe bringing about the fall of the bulwark institutions of the liberal international order. Although there is a lot of literature on the antagonistic relationship between populist parties and the European Union (EU), there is little on how these parties view the North Atlantic Treaty Organization (NATO), another bastion of the internationalist post-war order. Seeking to close this gap, thesis asks the following question: what are the attitudes of populist parties in the EU towards NATO membership and why?
Interestingly, a majority of EU populist parties support NATO membership. This work uses party platforms and secondary sources to examine this counterintuitive variation in populist party stances on NATO membership. It assesses domestic and international explanations of this variation and concludes that the latter have more explanatory power than the former. Specifically, this thesis posits that domestic party competition does not parallel party stances on NATO membership, while numerous international positions do. Foreign policy positions related to support for NATO membership include not being Euroskeptic and holding a positive view of the United States, while those that are correlated with opposition to NATO membership are a negative view of the United States and opposition to EU membership. A party’s view of Russia, its support of EU membership, and Euroskepticism are inconsequential. Furthermore, this thesis argues that there is no such thing as a “populist foreign policy,” at least in the realm of NATO- related affairs, since populist parties have a diverse range of stances on these matters. As such, it stresses that EU populist parties should not be treated as a homogenous group and notes that while we can take some comfort in knowing that NATO is not threatened by populism to the same extent that the EU is, we should not rest easy: the unpredictability and influence of these parties means that if they make severing ties with NATO their core issue, they may get their way.

Keywords:  Fisher Family Honors Program in Democracy
CDDRL
International Relations
Center on Democracy Development and the Rule of Law
NATO
Populism
Europe
European Union
EU
North Atlantic Treaty Organization
Security
Thesis
Advisor: Grzymala-Busse Anna
Transcriptional and position effect contributions to recombinant adeno-associated virus-mediated homologous recombination

Recombinant AAV vectors have the unique ability to promote targeted integration of transgenes via homologous integration at specified genomic sites reaching frequencies of 0.1-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions, finding that targeting efficiency was enhanced by target site transcription. Chromatin states associated with transcription and epigenetic measures reflecting accessible chromatin and a depletion of heterochromatin were also predictive of higher targeting efficiency. Furthermore, there was a positive effect on the amenability of a site to targeting due to other factors such as the level of endogenous transcription from intersecting genes and, in the absence of target site transcription, intersecting LINE-1 elements and accessible chromatin. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination

Keywords: Genetics.
Advisor: Kay Mark Allan 
Fire Andrew Zachary
Winslow Monte 
Wysocka Joanna
Transcriptional dynamics of a large family of surface protein genes in toxoplasma gondii

Toxoplasma gondii is a eukaryotic intracellular parasite that has evolved numerous large, paralogous gene families. These families are critical for supporting Toxoplasma's unparalleled host range which consists of nearly any nucleated cell in almost any warm-blooded animal. The SRS (SAG1-related sequence) gene family encodes over 100 surface proteins, some of which are involved in parasite attachment and evading the immune response of a host. For most SRS genes, however, little is understood about their function and expression profile. Additionally, Toxoplasma undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. In chapter 1, I review the current literature on the SRS family and present novel analyses on how SRS gene expression changes across the life stages of Toxoplasma. In chapter 2, I describe efforts to apply single-cell RNA-sequencing to Toxoplasma parasites to create a comprehensive atlas of cell cycle and asexual development based on data from over 5,400 parasites. This data reveals unexpected heterogeneity in SRS gene expression among individual parasites: in a population of the rapidly growing tachyzoite stage nearly all > 100+ SRS genes are detected despite only an average of 7 SRS genes being "on" in any individual tachyzoite at a given time. From this dataset, AP2IX-1 is identified as a parasite transcription factor that triggers downregulation of SAG1, a ubiquitous surface antigen and SRS, and upregulation of transcripts typically only expressed in the sexual stages of Toxoplasma's lifecycle. In chapter 3, I describe efforts to determine whether heterogeneous SRS expression signatures are inherited over generations of parasite replication by comparing transcriptomics from clonally derived parasites. Preliminary data from these studies suggests that SRS expression patterns are not strongly inherited by progeny and that heterogeneity of SRS expression arises within 10 generations between subcloned parasites. In chapter 4, I present work that identified new parasite factors involved in the secretion of Toxoplasma effector proteins into the host cell during infection. In chapter 5, I conclude with remarks on future directions for the study of the SRS gene family and understanding heterogeneity in expression patterns in Toxoplasma

Keywords: Microbiology and Immunology.
Advisor: Boothroyd John C.
Amieva Manuel
Fordyce Polly
Monack Denise M.
Pringle John R.
Transcriptional dysregulation in diffuse intrinsic pontine glioma

Diffuse intrinsic pontine glioma (DIPG) is a fatal pediatric cancer with limited therapeutic options. The majority of cases of DIPG exhibit a mutation in histone-3 (H3K27M) that results in oncogenic transcriptional aberrancies. In this work, we study the mechanisms by which the H3K27M mutation reprograms the epigenome of DIPG, identifying core dysregulations driving its malignant state and novel strategies for treating this cancer. We show that DIPG is vulnerable to transcriptional disruption using bromodomain inhibition or CDK7 blockade and these targets may help overcome resistance to other forms of therapy. We additionally demonstrate that H3K27M chromatin remodeling and the resultant oncogenic state depend upon both the variant of histone-3 and the cell-context in which the mutation occurs. These studies allow for identification and validation of both shared and subgroup-specific pathophysiology of DIPG tumors, advancing the possibility of personalized therapy for this disease. Altogether, the work here provides a detailed characterization of the molecular profile of DIPG and identifies previously unknown pathophysiology important for future therapeutic development

Advisor: Monje-Deisseroth Michelle
Chang Howard Y. (Howard Yuan-Hao)
Wysocka Joanna
Transcriptomic-informed rare variants in common and rare disease diagnosis

Rare genetic variants are abundant in the human genome and can have large effects on the expression of proximal genes and downstream risk for common and rare diseases, but are difficult to characterize due to annotation and sample size constraints. In recent years, RNA-sequencing (RNA-seq) has emerged as a useful tool in interpreting the molecular and phenotypic effects of rare variants. Using new methods for data de-noising, summarizing genome-wide burden of large-effect rare variants, and aggregation of a large-scale reference set of pluripotent cells, in this dissertation I present research that extends current applications of RNA-seq in rare and common disease diagnosis. In chapter 2, I present work that assesses the utility of RNA-seq of blood as a diagnostic tool among 94 individuals with undiagnosed rare diseases across 16 diverse disease categories. In chapter 3, I discuss research on mapping rare variant effects in induced pluripotent stem cells (iPSCs) as part of a systematic, expansive analysis of both common and rare variation within the "Integrated iPSC QTL" (i2QTL) consortium. Finally, in chapter 4, I present research on integrating rare, large-effect expression variants to assess the deviation in phenotypes as predicted by polygenic risk scores (PRS)

Advisor: Montgomery Stephen
Pritchard Jonathan (Jonathan K.) 
Rivas Manuel (Manuel A.)
Tibshirani Robert
Transition metal oxides for photoelectrochemical water-splitting and superconductivity

Transition metal oxide materials have garnered significant research interest over the past decades due to their diverse chemical and physical properties, ranging from electrochemistry and superconductivity. Moreover, the capability to access vastly different properties with similar crystal structures by controlling the stoichiometry provides a powerful additional degree of freedom in materials engineering for applications. By using pulsed laser deposition, we obtained epitaxial thin films providing a solid platform to investigate and engineer the properties of these oxides. We will first discuss a transition metal oxide, known as pseudobrookite (Fe2TiO5), for photoelectrochemical (PEC) water-splitting. Recently, Fe2TiO5 has emerged as a photoanode for water oxidation due to its chemical stability, scalability, and suitable bandgap. Based on our successful fabrication of epitaxial thin films, we will present our comprehensive characterization of the intrinsic PEC properties. We discovered that Fe2TiO5 exhibits highly efficient charge transfer at the Fe2TiO5-electrolyte interface and deduce a long minority carrier diffusion length of 19 nm, far exceeding that of α-Fe2O3. Furthermore, by forming heterostructures, PEC performance of α-Fe2O3 is enhanced significantly, where photocurrent density increases by one order of magnitude, and the onset potential improves by ∼300 mV. In the second topic, we discuss the infinite layer nickelates, RENiO2 (RE: rare-earth element). Ever since their discovery, superconductivity in cuprates has motivated the search for materials with analogous electronic or atomic structure. Here we present how soft chemistry approaches can be used to synthesize superconducting infinite layer nickelates from their perovskite precursor phase, using topotactic reactions. Following the discovery of superconductivity in Nd1−xSrxNiO2, we find superconductivity in Pr1−xSrxNiO2 and La1−xSrxNiO2

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.)
Hwang Harold Yoonsung
Cui Yi
Transnational Senegal River development, 1920-2000

Environmental bodies, such as rivers, rebel against political frontiers, and seldom conform to man-made borders. Transnational Senegal River Development, 1920-2000 reveals that regional-level coordination and collaboration between postcolonial African nations in the Senegal River basin was an important strategy for the development and management of the river. Drawing on research in France, Mali, Senegal, and the United States, this research tells a new story of environmental governance in Africa. Chapter 1 looks at French colonial development activities in the Senegal basin. The long afterlife of colonial-era Senegal River development plans calls into question whether a timeline focusing on decolonization is the only salient way to look at West African history, as do continuities in engineering expertise between the colonial and postcolonial eras. Chapter 2 analyzes the appeal of regional and pan-African political organizations during decolonization. It also focuses on the failure of transnational organizations centered on the Senegal River to provide broad regional unification and explicates the formation of an organization named the Organisation pour la Mise en Valeur de Fleuve Sénégal (Senegal River Development Authority or OMVS) in 1972. Beginning in the late-1960s, severe drought and famine ravaged the Sahel. Environmental crisis provided an opportunity for the OMVS. It mobilized concerns about famine to pitch its river development scheme as a long-term solution to food insecurity, and Chapter 3 explains how the OMVS obtained financing for dam projects during the 1970s. Case studies of the construction and consequences of two major dams, Manantali and Diama illustrate gaps between the OMVS' development rhetoric and actual practices, as well as unintended consequences of river management. Chapter 4 focuses on the planning and construction of Manantali Dam and town, the largest and most complex project the OMVS executed. Chapters 5 and 6 investigate the consequences of the integrated Senegal River management plan put forward by the OMVS for river basin populations. Chapter 5 looks at the Manantali Resettlement Program, while Chapter 6 considers downstream effects. The dissertation concludes by explaining how, during the 1990s, the OMVS decentralized due to funder pressures, losing much of its power to shape riverine sovereignty. Nonetheless, it remained a force for transnational river management in West Africa and a global model

Keywords: History.
Advisor: Roberts Richard L.
Ferguson James
Hanretta Sean
Hecht Gabrielle
Trends in heavy drinking behaviors and hepatitis C virus infection in China : a mathematical modeling study

Population health has drastically changed over time, especially in countries like China where rapid economic and social growth has occurred in the past decades. Economic development in China was paralleled with increase alcohol consumption and an increasing burden of chronic diseases. Empirical studies provide observations on the trends and patterns in health risk behaviors and diseases. Mathematical modelling can further describe dynamics underlying the observed epidemiology and explore evolving disease epidemiology in the population with or without potential interventions. In this dissertation, I apply mathematical models to better understand what drove past trends in high-risk drinking behaviors, hepatitis C virus (HCV) infections, and their interactions among Chinese men in order to project future burden of diseases and potential policy effects. The first chapter of this dissertation shows that inclusion of cohort trends when modeling disease results in different model outcomes and projections than when cohort trend are not included. In Chapter 2, I identify age patterns and cohort trends in high-risk drinking behaviors among Chinese men by applying a model calibration technique to longitudinal data. The constructed model predicts a declining trend in future prevalence of heavy drinking and estimates significant future health benefits of mitigating heavy drinking behaviors among the subpopulation at high risk of heavy drinking. I incorporate the model of heavy drinking behavior into Chapter 3 where I develop a natural history model of HCV infection among Chinese men. By combining sparse data on HCV and HCV-related liver diseases in China, the calibrated model identifies the variation in HCV infection rates by birth cohorts whose risk of infection has changed in response to prior regulations on HCV transmission in China

Keywords: Medicine.
Advisor: Goldhaber-Fiebert Jeremy D.
Brandeau Margaret L. 
Salomon Joshua A.
Two sides of the same coin : separable inhibitory action against GLI and ALDH1B1 activity

Small molecules are powerful tools that enable the interrogation of complex biological questions and provide insights into routes for modulating these processes. Furthermore, small molecules often provide a framework for the design of novel therapeutics with relevant disease targets. In this dissertation, I present my work employing a family of bicyclic imidazolium compounds towards the inhibition of the Hedgehog (Hh) signaling pathway and the aldehyde dehydrogenase ALDH1B1. These studies have enhanced our understanding of specific molecular mechanisms that drive cancer, and potential routes to mitigate tumorigenicity driven by GLI or ALDH1B1

Keywords: Chemical and Systems Biology.
Advisor: Chen James Kenneth
Dixon Scott James
Meyer Tobias
Mochly-Rosen Daria
Two-pulse x-ray photon correlation spectroscopy at Linac coherent light source

Nearly fully transversely coherent femtosecond x-ray pulses produced by x-ray free electron laser sources opened up the possibilities of direct measurement of atomic scale dynamics of complex systems at their native timescales. One area of particular interest is the investigation of noncrystalline matter such as liquids, glasses, amorphous and disordered systems, and holds the promises of unlocking the mysteries behind the glass transition, liquid-liquid phase transitions, fragile-to-strong transitions, etc. A primary methodology with the potential to extend dynamic light scattering to angstrom and femto- to nanosecond timescale is the so-called two-pulse x-ray photon correlation spectroscopy (XPCS) technique, where the dynamics of the scattering object are imprinted onto the fluctuations of coherent scattering intensity distribution. This dissertation focuses on the instrumentation and methodology of two-pulse XPCS, highlighting the challenges and efforts to establish it as a robust technique at x-ray free electron laser facilities towards measuring ultrafast dynamics in complex matter

Keywords: Physics.
Advisor: Bucksbaum Philip H. 
Dunne Anthony Michael 
Reis David A.
Sutton Mark (Professor of physics)
Ultra low power oven controlled MEMS resonator timing reference

The main goal of this dissertation is to provide readers with some insights of how silicon MEMS based resonators can be a viable option in making an OCXO-level timing references. We will take a look into the fabrication of such devices using wafer-scale encapsulation techniques, simulation and design of the oven-controlled MEMS resonators, followed by the full characterization

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Howe Roger Thomas
Solgaard Olav
Ultrafast infrared spectroscopy reveals the structural and dynamical heterogeneity of glassy materials

The remarkable properties of glassy materials arise from their complex amorphous structures and dynamics. The heterogeneity of these materials was studied on molecular length scales and picosecond time scales using a combination of polarization-selective IR pump-probe and 2D IR experiments and a vibrational chromophore that is sensitive to local chemical and electrical environments. By monitoring the restricted orientational motion of the chromophore in a polymer, the distribution of sub-nanometer pores could be explored. The same chromophore in a hydrogen-bonding system showed extreme polarization dependence in the 2D line shape, providing evidence for significant dynamical heterogeneity in the supercooled liquid phase

Keywords: Chemistry.
Advisor: Fayer Michael D.
Moerner W. E. (William Esco)
Zare Richard N.