VictorJuiz/thesis huggingface dataset:
Lateral Diffusion of GABAARs Studied with a Novel Electrophysiological Technique: CREAP

GABAA receptors (GABAARs) mediate fast synaptic inhibition in the mammalian brain and are essential for balancing excitation and sharpening our sensory perceptions. GABAARs are plastic and respond to changes in neuronal activity by strengthening or weakening inhibitory neurotransmission. This inhibitory plasticity responds to many of the same signals that mediate glutamatergic excitatory plasticity and works in tandem with or in contraposition to excitation to form the cellular basis of memories. GABAARs are added to or dispersed from synapses to modulate synaptic strength, and this is achieved by lateral diffusion in the plane of the membrane. By tethering GABAARs with synaptic scaffold proteins, primarily gephyrin, the inhibitory synapse can accumulate GABAARs dependent on the potency of this interaction. The scaffolds themselves are highly plastic and can agglomerate or wash away in coordination with GABAARs. An additional element of this process is the availability of extrasynaptic GABAARs able to diffuse into synapses, a supply that is tightly controlled by endo- and exocytosis of receptors from internal endosomal reservoirs and which is important for both acute plasticity and long-term homeostasis. The result is inhibitory synapses that are able to respond to activity changes with structural rearrangements on the scale of minutes to days./nThus far, GABAAR mobility has been primarily interrogated with single particle tracking of quantum dots and FRAP in the context of neuronal cultures, where dendrite morphology and molecular composition have been radically altered from in vivo conditions. The rise of new optogenetic techniques, which provide great spatial and temporal precision, affords an opportunity to study mobility in more natural and intact conditions such as the acute slice preparation. Here we extend the optogenetic strategy to GABAARs, creating a light-regulated GABAAR (LiGABAR) by conjugating a photo-switchable tethered ligand (PTL) onto a mutant receptor containing a cysteine-substituted α1-subunit. The installed PTL can be advanced to or retracted from the GABA-binding pocket with 500-nm and 380-nm light, respectively, resulting in photo-switchable receptor antagonism. We created a transgenic knock-in α1 photoswitch-ready mouse (α1 PhoRM) to express the mutant receptor at endogenous levels and distributions./nWe make use of LiGABAR technology to pioneer a novel electrophysiological technique for measuring GABAAR mobility, which we call CREAP. We use this method to functionally probe GABAAR mobility in the context of acute brain slices and find that α1-containing receptors are a highly mobile population GABAARs that constitute a fluid portion of inhibitory synapses.

Advisor: Kramer, Richard
Time and the Other in the Anthropocene: Thoughts Towards our Non-Modern Future

Time and the Other in the Anthropocene is a reflection on the contemporary transformation of the figure of the human (anthropos) into a geological agent and the way this is linked to a pluralization of time, on the one hand, and a pluralization of ontology, on the other hand. Specifically, it examines the conceptual link between the disintegration of the notion of Nature in the contemporary and its connection to the new pluralism in anthropology which has arisen as a response to the climate crisis. I consider the way this new pluralism, associated with what has been dubbed “the ontological turn” in anthropology, is strikingly being formulated, no longer through the question of the relativity of cultures, but rather that of natures. This move towards an analysis of various ways of being or what could be called a pluralist realism, I suggest, is one of the most original and crucial responses to climate crisis in that it foregrounds the question of the multiplicity of the modes of composing worlds which the Anthropocene has made a matter of dire necessity to think today./nUsing the novel framework Philippe Descola and Bruno Latour’s comparative anthropology, I foreground the anthropologies of Amazonia and Melanesia as two examples of other modes of composing the world. I reflect on the manner in which the ontological predicates of the Amazonian (or Amerindian) and Melanesian world allow us to view fundamental modern concepts – nature and culture, subject and object – otherwise. As essentially anthropomorphic worlds, my implicit suggestion throughout is that Amazonia and Melanesia worlds stand in a stark counterpoint to anthropocentric ones with regard to the most basic principles of what counts as “being” and “human” being. By extending or attributing what we call “agency” and “subjectivity” to every other being in the world, Amazonians and Melanesians also turn these very categories from our point of view unrecognizable. Showing us that being and the world have been thought on entirely different premises and with entirely different concepts, the properly transcendental equivocation of these categories enables us to develop a new comparative vision and invites us to begin the collective work of imagining another mode of being human per se on the new Earth in which we live.

Advisor: Liu, Xin
“Property Owners and Not Proletarians”: Housing Policy and the Contested Production of Neoliberal Subjects in Chile and Brazil

In much of the world, neoliberal reforms since the 1970s have been associated with the market-driven dismantling of social housing and dispossession of the urban poor. In Latin America, however, the neoliberal era saw the rise of unprecedented state programs to subsidize private homeownership for poor city-dwellers. Examining the adoption of these housing programs in Chile and Brazil, this dissertation investigates their logics and socio-political consequences. Through a comparative ethnographic study of grassroots housing organizations in Santiago, Chile and São Paulo, Brazil, it asks how the privatized provision of social housing shapes state-citizen relations and the political subjectivities of poor city-dwellers in different urban contexts. It argues, first, that housing programs in both Chile and Brazil represent a new neoliberal state strategy for managing the urban poor, which I call accumulation by inclusion. By using subsidies to enable low-income families – and women in particular - to purchase homes built by the private sector, they sought foster profitable urban development while including the poor in private homeownership. Yet, these programs also entrenched urban inequalities by enabling developers to mass-produce segregated and low-quality homes for the poor. Second, I show this elicited similar kinds of contestations, as women in both Santiago and São Paulo organized to demand participatory processes and claim rights to “dignified housing.” However, shaped by different modes of organizing in each city, these contestations generated divergent dynamics and outcomes. Localized collective action by fragmented “homeless committees” in Santiago failed to wrest control from state and private actors, resulting in degraded housing and a shared sense of denigration as second-class citizens. In contrast, mass mobilization by broad-based housing movements in São Paulo led to the institutionalization of civil society participation in Brazil’s housing policy. This enabled grassroots movement associations to exercise direct control over their projects, and produce dignified housing that conferred a sense of inclusion as full citizens. Finally, in spite of these divergent outcomes, women in both Santiago and São Paulo came to act as similar kinds of neoliberal homeowner-citizens. Rather than continuing to make collective claims on the state, they learned to assume individual responsibility for improving and maintaining their homes. My findings reveal that neoliberalism operates not only though exclusion and dispossession of the poor, but also through their inclusion in market-oriented modes of citymaking and citizenship. They also show how different local configurations of civil society shape the possibilities and limits of claiming social inclusion in neoliberal cities.

Advisor: Ray, Raka
Methods for Earth System Analysis in the West African Sahel: Land Cover and Climate Through Computational and Applied Sciences

Precipitation and land cover in the West African Sahel have changed dramatically over the past 50 years. Region-wide data on land cover change in the Sahel, however, have been sparse or unreliable. I present a new 30 meter 2000-2016 annual resolution land cover dataset for the West African Sahel. The product is built from hand-classified land cover maps using random forest machine learning methods with Landsat, precipitation, and topography features. The resulting maps confirm the widespread extensification of agriculture in the region over this time period. Contrary to the common narrative of desertification, this increase in agriculture has not been accompanied by an increase in bare soil or sandy area. Land cover change volatility is shown to be spatially heterogeneous, both at local and regional scales. In addition to the new land cover dataset, I present spatial and temporal analyses of precipitation during the recent years of increased variability in the West African Sahel. I examine seasonal trends, interannual variability, and differences among datasets representing precipitation in the Sahel. Region-wide spatial organization of precipitation is identified using the self-organizing mapping pattern recognition technique. The number of days spent in the monsoon transition period is strongly negatively correlated with annual precipitation anomaly` indicating a tradeoff with the peak monsoon period, a result that supports the upped-ante hypothesis of precipitation in the Sahel.

Advisor: Larsen, Laurel G
Development of Chemical Probes for Studying Redox-Active Metals in Biology

Metals are necessary for sustaining life and play essential roles in each aspect of the central dogma of biology (DNA, RNA, and proteins). While many roles of redox-inactive metals in cellular signaling have been extensively characterized, the ability of redox-active transition metals like copper and iron to act as signals has been less explored. As these metals can aberrantly produce reactive oxygen species (ROS)1, most research has considered redox-active transition metals as cofactors sequestered within enzyme active sites, despite the intricate cellular machinery regulating their concentration in exchangeable forms. Recently, new roles for redox-active metals in their exchangeable (or labile) forms have been elucidated; however, visualizing redox-active metals in real-time (with spatial and temporal resolution) and identifying their protein binding partners remain formidable challenges. This dissertation chronicles the design and applications of novel imaging probes and chemoproteomic strategies for probing redox-active metals in biology. This work describes both the first fluorescence resonance energy transfer (FRET) probe for imaging cellular Fe2+ and the first bioluminescence probe for imaging iron in vivo; both probes utilize an adamantyl-endoperoxide as the iron-reactive moiety. Additionally, this work describes new metalloproteomic methods aimed at identifying novel metal-binding proteins. Taken as a whole, this dissertation describes the development and application of new chemical methods for probing redox-active metals in biology by imaging and/or proteomics.

Advisor: Chang, Christopher J.
Multiscale Crystal Defect Dynamics: A Crystal Plasticity Theory Based on Dislocation Pattern Dynamics

Understanding the mechanism of plasticity is of great significance in material science,/nstructure design as well as manufacture. For example, the mechanism of fatigue, one critical/norigin for mechanical failures, is governed by plastic deformation. In terms of simulating/nplasticity, multiscale methods have drawn a lot of attention by bridging simulations at different/nscales and yielding high-quality atomistic properties at affordable computational resources./nThe main limitation of some multiscale methods is that the accuracy in much of the continuum/nregion is inherently limited to the accuracy of the coarse-scale model, even though much/neffort has been made to improve the existing multiscale models by developing adaptive/nrefinement models. It is known that crystal defects play an important role in/ndetermining material properties at macroscale. Crystal defects have microstructure,/nand this microstructure should be related to the microstructure of the original/ncrystal. Hence each type of crystals may have similar defects due to the same failure/nmechanism originated from the same microstructure, if they are under the same loading/nconditions. In this dissertation, a multiscale crystal defect dynamics (MCDD) model/nis proposed that modelling defects by considering their intrinsic microstructure derived/nfrom the microstructure or dislocation patterns of the original perfect crystal. The main/nnovelties of present work are: (1) the discrete exterior calculus and algebraic topology/ntheory are used to construct a scale-up (coarse-grained) dual lattice model for crystal/ndefects, which may represent all possible defect modes inside a crystal; (2) a higher/norder Cauchy-Born rule (up to the fourth order) is adopted to construct atomistic-informed/nconstitutive relations for various defect process zones, and (3) an hierarchical strain/ngradient theory based finite element formulation is developed to support an hierarchical/nmultiscale process zone model for various defects in a unified formulation. The efficiency/nof MCDD computational algorithm allows us to simulate dynamic defect evolution at large/nscale while taking into account atomistic interaction. The MCDD model has been validated/nby comparing the results of MCDD simulations with that of molecular dynamics (MD)in the/ncases of nanoindentation, uniaxial tension and simple shear. Numerical simulations have/nshown that MCDD can capture not only material failure but also inelastic deformation in/na multiscale continuum simulation by considering the atomistic interaction./nIn addition, simulation of anisotropy demonstrates that MCDD is capable of capturing/nthe influence of loading axis orientation and the loading directionality on dislocation nucleation.

Advisor: Li, Shaofan
Understanding and Controlling the Optical Properties of Quasi Two-Dimensional Materials

In this thesis, I discuss the understanding and control of the optical properties of quasi-two-dimensional materials, an emerging field since the discovery of graphene. This thesis not only aims to understand and predict the distinct optical properties of quasi-two-dimensional materials from theoretical and numerical approaches, but also incorporates and quantitatively explains relevant experimental data when available. This thesis is organized as follows:/nIn the first chapter, I give a brief background overview on 1) research on excited states in general, 2) first-principles GW-BSE method that calculates the electron quasiparticle bands and exciton properties, and 3) recent progress on the optical properties of two-dimensional semiconductors and light-matter interactions in these materials./nIn the second chapter, I review the valley physics in transition metal dichalcogenide monolayers, which builds the foundation of the more advanced topics that we discuss in the next chapters./nIn the third chapter, I present several studies on the unusual optical properties of transition metal dichalcogenide monolayers arising from the novel exciton physics, including strongly-bound non-hydrogenic exciton series, light-like exciton dispersion, and magnetic brightening of the dark states. These results show the distinct optical properties of two-dimensional semiconductors compared with those in other dimensions./nIn the fourth chapter, I demonstrate some consequences of topological effects on optical transitions in two-dimensional semiconductors, which leads to a new set of optical selection rules dictated by the winding number of interband optical matrix elements. The new selection rules go beyond the selection rules for conventional semiconductors which have been used for over 6 decades, and explains the experimental results on the photo-current spectroscopy of gapped bilayer graphene./nIn the last chapter, I present materials engineering aspects of two-dimensional materials via van der Waals interfacial engineering. We show that by changing the interlayer stacking configurations and by applying out-of-plane electric fields, the electronic and optical properties of van der Waals layers can be rationally engineered and controlled.

Advisor: Louie, Steven G.
Institutional Determinants of Cyber Security Promotion Policies: Lessons from Japan, the U.S., and South Korea

Ensuring the cyber security of the private sector requires both the/nproduction of and consumption of cyber security technology./nStates vary in the degree to which they promote production and consumption./nTaking an institutionalist approach, I argue that the difference/nbetween states can be explained as the result of two policy/nlegacies. States with a policy legacy of maintaining strong/ntraditional national security capabilities have the instruments/nnecessary to promote production of cyber security technology, as well/nas actors---the military and intelligence agencies---who are motivated/nto do so. States with a policy legacy of economic guidance have the/ninstruments to promote the consumption of cyber security technology,/nand economically-oriented bureaucratic actors who see it as their/nresponsibility to do so./nTo provide evidence for my hypotheses, I do a comparative case study/nof Japan, the U.S., and South Korea. Japan, with a policy legacy of/nrestrained traditional security capabilities and a legacy of economic/nguidance, does little to promote production but is active in promoting/nconsumption. The U.S., with a legacy of maintaining strong traditional/nsecurity capabilities but without a legacy of economic guidance, is/nactive in promoting production but does little to promote/nconsumption. South Korea, which has a policy legacy of maintaining/nstrong traditional security capabilities and a legacy of economic/nguidance, promotes both./nThe key implication of this research is that a state's ability to/npromote cyber security in the private sector is heavily determined not/nonly by past policies, but past policies that were unrelated to cyber/nsecurity. States without the proper policy legacies will have to find/nways to build substituting institutions in order to promote both/nproduction and consumption of cyber security.

Advisor: Aggarwal, Vinod
Mapping nematic order in BaFe2(As,P)2

The discovery of the iron-based superconductors (Fe-SCs) has been a great boon to the continuing development of our understanding of high-Tc superconductivity, providing a wealth of new information and a valuable theoretical testbed. One of the most interesting developments has been the observation of nematic quantum criticality near optimal doping in several Fe-SCs. This, together with evidence of electronic nematicity in the cuprates, has fueled speculation that high-Tc superconductivity may be related to nematic physics at a fundamental level./nUsing ultrafast pump-probe reflectance as a photomodulation technique, we investigate superconducting and nematic order in the low-disorder BaFe2(As_{1−x}P_x)2 system, which contains a nematic quantum critical point. Our nonequilibrium approach is well-suited to the study of the onset and evolution of ordered phases, as the dominant effect of the pump pulse tends to be the suppression of the ordered phase. This yields a background-free probe of the order parameter, unlike measurements at equilibrium./nAt and above optimal doping x = 0.31 we observe nematic order manifested in a change in sign of the pump-probe response under polarization rotation. This nematic phase is observed above the superconducting critical temperature and competes with the superconducting phase, and it typically onsets sharply with decreasing temperature in a manner inconsistent with a Curie-Weiss divergence./nWe study the spatial variation of the nematic photomodulation response, and find that typical crystals have inhomogeneous nematicity on a length scale of 10−100 μm. In fact, the sign, magnitude, and onset temperature of the nematic response all vary significantly at optimal doping. The observation of this inhomogeneity helps resolve tension between localized probes that show evidence of nematicity, and bulk probes, which do not./nBy combining maps of strain obtained via spatially resolved Laue diffraction with photomodulation maps of nematicity at optimal doping, we test the hypothesis that a strong nematic susceptibility amplifies strain anisotropies intrinsic to the crystal in order to produce the observed nematic behavior. We find that local strain anisotropies cannot account for the nematic order we observe, although applying a tensile uniaxial strain of 0.1% to an optimally doped sample in the Fe−Fe frame does bias the population of nematic domains./nWe extend this multi-probe mapping analysis to the overdoped regime, and find that the nematic fraction of the samples studied decreased sharply for x > 0.39. However, each overdoped sample studied contains at least some regions of nematicity of both signs, with the same qualitative character as at optimal doping. Intriguingly, at the highest studied doping, x = 0.50, the apparent superconducting transition temperature in otherwise isotropic regions is found to change by 0.5 to 2.0 K under a π/2 rotation of the pump and probe polarization.

Advisor: Orenstein, Joseph
Learning to Navigate in Visual Environments

Artificially intelligent agents with some degree of autonomy in the real world must learn to complete visual navigation tasks. In this dissertation, we consider the learning problem of visual navigation, as well as implementation issues facing agents that utilize learned visual perception systems. We begin by formulating visual navigation tasks in the setting of deep reinforcement learning under partial observation. Previous approaches to deep reinforcement learning do not adequately address partial observation while remaining sample-efficient. Our first contribution is a novel deep reinforcement learning algorithm, advantage-based regret minimization (ARM), which learns robust policies in visual navigation tasks in the presence of partial observability. Next, we are motivated by performance bottlenecks arising from large scale supervised learning for training visual perception systems. Previous distributed training approaches are affected by synchronization or communication bottlenecks which limit their scaling to multiple compute nodes. Our second contribution is a distributed training algorithm, gossiping SGD, which avoids both synchronization and centralized communication. Finally, we consider how to train deep convolutional neural networks when inputs and activation tensors have high spatial resolution and do not easily fit in GPU memory. Previous approaches to reducing memory usage of deep convnets involve trading off between computation and memory usage. Our third and final contribution is an implementation of spatially parallel convolutions, which partition activation tensors along the spatial axes between multiple GPUs, and achieve practically linear strong scaling.

Advisor: Keutzer, Kurt
Gromov-Witten Axioms for Symplectic Manifolds via Polyfold Theory

Polyfold theory, as developed by Hofer, Wysocki, and Zehnder, is a relatively new approach to resolving transversality issues that arise in the study of J-holomorphic curves in symplectic geometry. This approach has recently led to a well-defined Gromov--Witten invariant for J-holomorphic curves of arbitrary genus, and for all closed symplectic manifolds. In this thesis we prove the Effective, Grading, Homology, Zero, Symmetry, Fundamental Class, and Divisor Gromov--Witten axioms for $J$-holomorphic curves of arbitrary genus, and for all closed symplectic manifolds.

Advisor: Wehrheim, Katrin