VictorJuiz/thesis huggingface dataset:
Insurgency formation and civil war onset

Why do civil wars begin? Since the end of the Cold War, civil conflict has become the most prevalent formed of armed conflict, but too little is known about the causes and evolution of these conflicts. Extant scholarship focuses on country-level conditions to explain variation in conflict onset, but this often misses pre-war mobilization and within-state variation in armed group campaigns. To address these gaps, I develop an original dataset on 1,582 armed groups operating around the world between 1970 and 2012. I collect new data on organizational characteristics and the timing of three distinct campaign stages. The dataset establishes several new sources of variation in the organization and evolution of armed groups to guide future research. I argue that existing explanations for civil war are relatively time-invariant and so poorly explain the timing of different campaign stages. As a result, I argue scholars must consider the strategic interactions between the state and an armed group to better understand the causes and evolution of these conflicts. I develop and test two separate explanations for rebel group formation and civil war onset using a combination of fieldwork interviews, supervised learning algorithms, and regression analysis. The first theory focuses on how poor economic conditions and ongoing conflict affect the probability of rebel group formation by lowering opportunity costs and shifting the state's relative capacity to detect emerging threats. The second theory focuses on how states condition their responses to emerging threats based and under what conditions miscalculations are more likely to lead to civil war. The results advance theoretical understanding about why civil wars erupt and provide a new dataset on armed groups for future terrorism and insurgency research.

Keywords: Political Science.
Advisor: Fearon James D. 
Crenshaw Martha
Schultz Kenneth A. 
Tomz Michael
Integrated motion planning and control for automated vehicles up to the limits of handling

In order to keep self-driving cars safe, it is important that these vehicles can plan safe trajectories through their environment and have the ability to robustly use their full tire-force potential. Racing at the limits of handling provides a purposefully challenging scenario for the development of reliable vehicle-motion planning and control techniques, as race cars are constantly pushed to their physical limits. With a common trajectory-tracking architecture for automated vehicle control, steering provides path-tracking control, and the throttle and brakes are used to track a desired speed profile. For the specific application of racing, this speed profile can be designed to fully use the tire-force potential. Experimental data show that a preexisting control framework based on this approach can match the lap time of an amateur race-car driver, but a professional race-car driver proves to be slightly faster. It is demonstrated with both experimental results and an analytical method that with this decoupled path-tracking and speed-tracking controller, an automated vehicle is prone to either under-utilize the tires or lose control over the path-tracking dynamics when unintentionally operating beyond the limit. Furthermore, a professional race-car driver successfully operates the vehicle with a control strategy that seems fundamentally different from trajectory tracking. Namely, he shows significant lap-to-lap variations in both speed and path, but he is consistently faster than automated trajectory-tracking control. This inspires new strategies for automated vehicle control. In this context, two novel feedback-control strategies are presented, which employ slip-angle control to robustly use the vehicle's full tire-force potential, while speed control provides the path-tracking functionality. Subsequently, in order to have the ability to also adjust the vehicle's path, a Nonlinear Model Predictive Control (NMPC) framework is presented which can trade-off longitudinal and lateral control inputs. Experimental results demonstrate that this controller successfully coordinates the inputs at the limits of handling. However, the computational burden of this NMPC framework limits the length of the planning horizon for real-time control, which in turn inhibits its ability to adjust the vehicle's path and speed. To address this issue, a new NMPC framework is developed, which serially cascades vehicle models of different levels of complexity in the planning horizon. Experimental results on an automated race car demonstrate the benefits of this new concept, with a high quality of control provided by a high-fidelity vehicle model in the near-term planning horizon, and significant extension of the planning horizon with a low-fidelity model.

Keywords: Mechanical Engineering.
Advisor: Gerdes J. Christian 
Pavone Marco
Schwager Mac
Interactive simulation and design of yarn-level cloth patterns

Modern design tools for yarn-level cloth patterns struggle to predict the final shape of knit or woven fabrics. My work describes an interactive design tool for authoring, simulating, and adjusting yarn-level patterns for knit and woven cloth. To achieve interactive performance for notoriously slow yarn-level simulations, I use two acceleration schemes: (a) yarn-level periodic boundary conditions that enable the simulation of only small periodic patches, thereby exploiting the spatial repetition of many cloth patterns in cardinal directions, and (b) a highly parallel GPU solver for efficient yarn-level simulation of the small patch. My system supports interactive pattern editing and simulation, and runtime modification of parameters. To adjust the amount of material used (yarn take-up) I support "on the fly" modification of (a) local yarn rest-length adjustments for pattern specific edits, e.g., to tighten slip stitches, and (b) global yarn length by way of a novel yarn-radius similarity transformation. I demonstrate the tool's ability to support interactive modeling, by novice users, of a wide variety of yarn-level knit and woven patterns. To validate this approach, I compare dozens of generated patterns against reference images of actual woven or knitted cloth samples, and I released this corpus of digital patterns and simulated models as a public dataset to support future comparisons. This work has served as the foundation for two other collaborative projects, including improving yarn-level cloth renderings via macro-fibers simulations, and a design tool for 3D woven materials. Finally, to avoid regenerating yarn curves for each pattern edit, I provide a method for live pattern updates in order to support interactive design of complex fabrics.

Keywords: Electrical Engineering.
Advisor: James Doug L. 
Horowitz Mark (Mark Alan) 
Wetzstein Gordon
Interface circuits for affinity-free, label-free molecular detection platform

The field of molecular diagnostics is dominated by affinity-based techniques (e.g., ELISA) where the critical signal processing steps are implemented in the chemical domain. This makes affinity-based techniques time consuming, expensive, and difficult to execute reliably outside of a laboratory environment. Affinity-free techniques address these problems by implementing the critical signal processing steps in the digital domain, where computation is more flexible and efficient. In this thesis we describe the development and implementation of electronic instrumentation for an affinity-free molecular sensing platform that records the vibrational signatures of proteins in blood using a nanoscale electrochemical interface. The sensing mechanism relies on coherent interference of electron wave functions at the interface between a nanoscale working electrode and a liquid electrolyte. Coherence at the sensing interface is enabled by low-noise potentiostatic feedback, which reduces the effective temperature of the electrons.

Keywords: Electrical Engineering.
Advisor: Murmann Boris 
Arbabian Amin 
Howe Roger Thomas
Interplay between mechanotransduction and force generation underlies cancer cell division in three dimensionally confining viscoelastic microenvironments

In physiological tissues, such as growing tumor spheroids, cells are surrounded by adjacent cells and viscoelastic extracellular matrices (ECMs). This confining microenvironment can mechanically constrain the growth of cells and the morphological changes required for mitosis. However, little is known about how the viscoelastic properties of ECM influence cell cycle progression, and how cells overcome the mechanical constraints to undergo mitosis. Here we probed the viscoelasticity of ECM and its impact on cancer cell division. First, we investigated the viscoelastic and viscoplastic properties of collagen gels, a primary component in ECM. Gels of collagen were found to exhibit remarkable viscoelastic properties; at greater deformations, they become stiffer but then flow more rapidly to relax this increase in stiffness, a behavior named strain-enhanced stress relaxion. We found that this behavior arises from force-dependent unbinding of weak bonds between collagen fibers. Collagen gels also exhibit mechanical plasticity, a property that leads to permanent deformation in response to a mechanical stress. The plastic properties of collagen gels allow cells to mechanical remodel the collagen. Next, we examined cell division in confining viscoelastic hydrogels. In confining hydrogels, cells are able to sense when growth is sufficient for division to proceed via a growth responsive TRPV4-PI3K/Akt-p27Kip1 signaling axis. When cells do progress to mitosis in the confining hydrogels, they are able to generate substantial protrusive forces that deform the microenvironment along the mitotic axis, clearing space for mitotic elongation to proceed. These forces result from interpolar spindle elongation and lateral contraction of the actomyosin ring, which drives expansion along the mitotic axis through volume conservation. Finally, we developed a new materials approach to tuning viscoelasticity of alginate-PEG hydrogels. Together, these findings shed light on the mechanical interactions between cells and their confining viscoelastic microenvironments during cell division.

Keywords: Mechanical Engineering.
Advisor: Chaudhuri Ovijit 
Huang Kerwyn Casey
Levenston Marc Elliot
Intertwined orders and their dynamical properties in strongly correlated systems

Strongly correlated quantum materials are of interest for both their exotic phases, often harboring multiple intertwined orders, and their unconventional normal states. This thesis investigates these topics from the perspective of numerical simulations of strongly correlated toy model Hamiltonians. First, I present large scale determinantal quantum Monte Carlo calculations demonstrating fluctuating spin stripes in both the Emery and Hubbard models on a 2d square lattice. These results suggest the pervasiveness and importance of density wave ordering in the phase diagram of high-Tc cuprate superconductors. Furthermore, they shed new light on interpreting previous numerical results for the Hubbard model. Second, I discuss transport properties of the 2d Hubbard model evaluated by analytic continuation of DQMC data. Our data, extending to temperatures around an order of magnitude below the Fermi temperature, show features reminiscent of the strange metal phase observed in unconventional superconductors, including resistivity with linear-T dependence and in violation of the Mott-Ioffe-Regel limit. I conclude with a survey of possible ideas that might enable one to go beyond the results in this thesis.

Keywords: Physics.
Advisor: Devereaux Thomas Peter
Kivelson Steven 
Shen Zhi-Xun
Intestinal enteroids as a novel model system for studying MHC class II regulation and function in intestinal epithelial cells

The intestinal epithelium is a vast surface where dietary antigens, enteric microbes, and the mucosal immune system interact. The intestinal immune system faces a considerable challenge: mediating the timely clearance of pathogens while maintaining tolerance to harmless commensals and dietary antigens. Dysregulation of tolerance leads to disorders such as celiac disease and inflammatory bowel disease. Major Histocompatibility Complex II (MHC-II) plays a critical role in regulating adaptive immunity through the presentation of fragment fragments to CD4 T cells. Small intestinal epithelial cells (IECs) constitutively express MHC-II, though the precise role of epithelial MHC-II in tolerance and immunity is poorly understood. A major obstacle to elucidating the role of IEC MHC-II is the lack of a tractable, physiologically relevant model system. We present a method for inducing MHC class II (MHC-II) in human enteroids, "mini-guts" derived from small intestinal crypt stem cells. The cytokine interferon gamma, typically found at low levels in healthy epithelium, induces MHC-II when provided to IECs along their basolateral surface. We analyzed the intracellular MHC-II peptide-pathway and show that MHC-II molecules in IECs undergo peptide editing before trafficking to the cell surface. We then used a novel polarity reversal approach to demonstrate that MHC-II-expressing enteroids could be reversed such that their apical surface faces outward. This allows for apical antigens and microbes to be added to enteroids in a physiological manner. Our method enables human enteroids to be used for novel in vitro studies into IEC MHC-II regulation and function during health and disease.

Keywords: Immunology.
Advisor: Amieva Manuel 
Mellins Elizabeth 
Habtezion Aida
Khosla Chaitan
Investigating contrary phenotypes in TSO/SOL mutants of Arabidopsis and Brachypodium

Stomata, gas-exchange valves in the epidermis of plants, provide a useful developmental model for regulation of cell division and differentiation. The TSO/SOL protein family members play key roles in certain division steps and fate transitions within the stomatal lineage, which can drastically affect plant physiological fitness via stomatal shape and patterning. Recent work in the dicot plant Arabidopsis thaliana found that mutants with SOL1 and SOL2 deletions display increased small cells and instances of stomatal clustering, which both indicate extra cell divisions in stomatal precursor cells. However, deletion of SOL2 in the monocot species Brachypodium distachyon leads to incomplete divisions in stomatal guard cells. To determine the functional similarity between these homologous proteins, we cloned the Brachypodium SOL2 gene into Arabidopsis sol1;sol2 double mutants expressed under Arabidopsis SOL, TSO1, and overexpression promoters. The transformed Arabidopsis sol1;sol2 mutants displayed a lack of expression of Brachypodium SOL2 protein despite confirmed presence of the BdSOL2 gene. If the expression of BdSOL2 in Arabidopsis is substantially different from AtSOL1 and AtSOL2 expression, this result could imply a diversification of roles within the TSO/SOL gene family. The specialization of homologous proteins could contribute to the developmental differences of the stomatal lineage between the two species. These findings are a start towards further understanding of the stomatal lineage as a model for species-specific cellular development and of functional roles for TSO/SOL proteins in general cell cycle control.

Keywords:  Department of Biology
Biology
Plant Biology
Molecular Genetics
Thesis
Advisor: Dominique Bergmann
Sharon R. Long
Investigating distributed brain circuits in vivo with multi-axis calcium imaging

A major technological goal in neuroscience is to enable the interrogation of neural populations throughout the living brain. Calcium imaging allows monitoring of neural activity at sub-cellular resolution, but has typically been restricted to single fields-of-views per subject and hence limited to studies of local neural dynamics in isolated brain regions. Here, by combining computer-aided surgical planning for rodents, custom miniaturized optics, and specialized imaging instrumentation, we expand the capability of optical physiology to address distributed brain circuits in individual subjects. We first present the "Crystal Skull", a curved glass replacement to the dorsal mouse cranium yielding an estimated > 1 million neurons (albeit not concurrently) over > 30 neocortical areas. Next, we introduce the "multi-axis" approach for optically accessing multiple brain regions---deep or superficial---by way of a dual-axis two-photon microscope. With this apparatus, we performed, for the first time, chronic studies of the corticocerebellar pathway at single-cell resolution as mice learned a forelimb movement planning task. Concurrent optogenetic manipulation demonstrated the necessity of specific anatomical pathways for the observed corticocerebellar dynamics. This study highlights the potency of the multi-axis approach for discovering new insights for how distributed brain networks communicate and interact. From the initial dual area experiments, we identify the key optomechanical principles necessary to extend our approach to four or more regions in a single subject. Namely, scaling of the multi-axis concept requires: (1) an efficient use of the space above the animal's head by optimizing the surgical placement of optical ports (e.g. microendoscopes) on the animal itself; (2) miniaturization of each optical instrument using elements such as millimeter-scale gradient index lenses and specialized micro-prisms; and, (3) enhanced instrument maneuverability, attained by incorporating concepts such as remote center of motion from the field of surgical robotics. We design and implement a novel two-photon microscope based on these principles, which will enable the optical investigation of 4--8 brain areas simultaneously from behaving mice.

Keywords: Electrical Engineering.
Advisor: Schnitzer Mark Jacob
Nishimura Dwight George 
Wetzstein Gordon
Investigating molybdenum disulfide as a protective catalyst for solar-water splitting devices

Generating hydrogen by using solar energy to split water molecules is an appealing idea due to the renewable and sustainable nature of the inputs: sunlight and water. This idea can be achieved with photoelectrochemical hydrogen evolution in which a photoactive semiconductor is paired with an electrocatalyst. The field of unassisted, solar-driven water-splitting for hydrogen production has made remarkable progress in the past few decades. Solar to hydrogen (STH) efficiencies have increased from low single digits in the 1970s to 19% in 2018 -- rivaling the typical efficiencies of "off the shelf" solar cells. While efficiencies have become competitive, durabilities have not. The average commercial solar panel comes with a 25 year "lifetime guarantee", but the longest an unassisted water-splitting device of any efficiency has lasted to date is only 100 hours. This stability gap has remained largely unchanged these past few decades primarily due to the complex challenge of preventing semiconductor corrosion in aqueous environments. In this dissertation, we explore whether Molybdenum Disulfide nanomaterials can serve as protection layers and catalysts for solar water-splitting devices. We found that a very thin, conformal coating of MoS2 can improve the stability of GaInP2 by over 500 times as measured by light-limited current density. Furthermore, we found that our MoS2 protection layers were excellent catalysts for hydrogen evolution, rivaling a state-of-the-art Pt-based catalyst, and our MoS2 protected device was among the most active and stable single-absorber photocathodes to date. We further probed the interfacial energetics with transient photon reflectance and revealed that a conformal MoS2 catalyst interface imparts improved electron transfer in addition to catalytic activity compared to a nonconformal PtRu catalyst. This insight into the semiconductor-catalyst interface is potentially relevant to catalytically protected photoectrodes across the field. We also found that our Molybdenum Disulfide nanomaterials can be used to stabilize high-efficiency GaAs/GaInAsP tandem water-splitting devices and demonstrated the first-ever unassisted water splitting device that uses Molybdenum Disulfide protective catalysts. We compared these devices to the best unassisted water-splitting devices to date and revealed a two orders of magnitude "stability gap" between where the field currently is and where the field needs to be for feasible commercialization. This dissertation explores the field of photoelectrochemical water-splitting at multiple levels. We dive into the stability challenges facing the field and present detailed and novel strategies for overcoming them. We also put our results into a greater context, revealing important field-wide trends, and discussing the challenges that must be solved to enable this sustainable technology to change how we produce and consume energy.

Keywords: Chemical Engineering.
Advisor: Jaramillo Thomas Francisco 
Bao Zhenan 
Deutsch Todd
Investigating neural stem cell function in an Alzheimer's disease model

Alzheimer's disease is a progressive neurodegenerative disease characterized by dementia and amyloid plaques. In a mouse model of Alzheimer's disease harboring mutant amyloid precursor protein, we show elevated expression of Cdkn2a, a gene linked to brain aging, apoptosis, and neural precursor cell long-term proliferation defects. Genetic reduction of USP16, a critical up-regulator of Cdkn2a, led to decreased astrogliosis and neuronal apoptosis, reduced neural precursor cell proliferation defects, and improved memory. In combination with agents targeting classical Alzheimer's disease pathologies, we identify USP16 as a potential therapeutic target that may help to ameliorate the cognitive deficits in some cases of Alzheimer's disease.

Keywords: Stem Cell Biology and Regenerative Medicine.
Advisor: Clarke Michael F.
Heller H. Craig
Monje-Deisseroth Michelle
Investigating Pain Modulation by the Descending Pathway from the Locus Coeruleus To the Spinal Cord

Pain sensation, also known as nociception, involves a complex system of neural connections that balance inhibition and excitation. Although the mechanisms that determine the level of nociception at the peripheral nervous system have been extensively studied, similar pathways in the central nervous system are not as well defined. Moreover, our understanding of how sustained inflammation, often found in chronic pain diseases, affects these pathways is not complete. Descending control circuits from the brainstem to the spinal cord are strong candidates for the modulation of nociception. The locus coeruleus (LC) is a nucleus in the pons of the brain stem that broadly innervates cortical areas involved in arousal, cognition, and memory. The LC descends down to the spinal cord and has been suggested to play an important role in modulating pain transmission in the spinal cord. In this study, we explored the possible influence of the noradrenergic descending projections from the LC to the dorsal horn on pain sensation. Combining a novel retrograde tracing strategy with Dbh-Cre mice, we achieved specific targeting of the spinal cord projecting neurons in the LC (LC→SC). This approach enabled us to use targeted chemogenetic manipulation to activate the LC→SC neurons and test the effect of this descending pathway on pain sensation. Our preliminary results indicated that activation of the LC→SC neurons decreased pain sensitivity, revealing an inhibitory role in nociception. We also found that LC inhibition of pain decreases in intensity in the presence of chronic inflammation, suggesting a possible connection between LC activity and chronic pain. Moreover, we employed a novel retrograde tracing method, named cTRIO, to identify brain wide monosynaptic inputs onto the LC→SC neurons. Together, results of this study advanced our understanding of the role of the locus coeruleus in nociception and may provide insights for developing novel pain treating strategies that do not have the addictive characteristics of currently used opiates.

Keywords:  Department of Biology
Biology
neurobiology
nociception
locus coeruleus
central nervous system
DREADD
cTRIO
Thesis
Advisor: Chen Xiaoke
Heller Craig