VictorJuiz/thesis huggingface dataset:
Spatiotemporal Dynamics of Working Memory in Humans

Working memory (WM) is the ability to hold information for online processing. As the basis of long-term memory formation and a fundamental construct of thinking, it is paramount that we understand how WM works. Distributed network models posit that the prefrontal cortex (PFC) supports WM by coordinating top-down control over other regions involved in sensory representation and long-term memory. We utilized an episodic memory paradigm that probes WM for identity, spatial, and temporal information to examine the PFC dependent model of WM. In two studies, multimodal electrophysiology data reveal that PFC control over WM is fundamentally dynamic in nature, and that WM is dependent on activity distributed across anterior and posterior cortical regions. Results challenge the simple PFC model of WM./nCh. 1 presents evidence from intracranial recordings that frontal and medial temporal lobe (MTL) theta rhythms carry WM-related activity, and uncovers two WM systems. The PFC-MTL system exhibits bidirectional interaction that shifts with msec precision in response to task demands. In contrast, MTL rhythms direct activity in the orbitofrontal cortex via theta rhythms that do not vary with task demands. These findings support a bidirectional PFC-MTL system in humans – in which theta rhythms subserve executive control during episodic memory formation. Ch. 2 presents evidence from patients with unilateral PFC damage, which shows that a posteriorly-sourced alpha-beta network provides adequate resources for well above-chance WM accuracy. However, when the PFC is intact, PFC low theta activity increases commensurate with executive demand, and PFC-sourced slow rhythms and posteriorly-sourced alpha-beta rhythms travel in opposite directions to support optimal WM./nCh. 3 reviews 15 years of intracranial research on human memory, and considers the potential of intracranial electrophysiology as a technique to address unresolved questions in the neuroscience of human memory. Ch. 4 presents key themes from this work for younger readers; specifically, it introduces the concepts of cross-frequency coupling between theta rhythms and fast activities in the MTL, and inter-regional PFC-MTL synchrony for memory formation. In a second public outreach piece, appendix 1 introduces the logic of neuropsychology to younger readers to understand why memories of music are resilient to the deleterious effects of amnesia and dementia. Appendix 2 shows that WM develops in children along with increases in sustained attention, and appendix 3 reviews evidence that executive control develops commensurate with PFC connectivity across distributed neural networks. Finally, appendices 4-5 present applications of research on WM and control, together delineating behavioral and neural underpinnings of optimal relational reasoning in neurologically healthy adults.

Advisor: Knight, Robert
Rethinking the Status of Animals in the French Renaissance Culture: from Pierre Belon to Michel de Montaigne

This dissertation discusses the status of animals in sixteenth century French texts of various literary and non-literary genres. It aims at demonstrating the significant shift from the Middle Ages to the Renaissance with regards to the literary portrayal of animals, which were no longer regarded in the allegorical tradition but rather as a subject matter. These changes in philosophers’ perceptions of animals were conditioned by the intersection of two major phenomena taking place at the time – geographical explorations exposing new knowledge about unknown animals and species, and a rediscovery of classical texts that challenged the Aristotelian vision of a hierarchy of species. As a result, scholars were urged to break the old tradition of animals’ representation as a vehicle of human flaws and social differences, and created instead a new role for animals for the first time in the history of Western civilization./nThe main goal of this dissertation goes beyond simply introducing the animal as subject in French Renaissance texts, but it ambitiously seeks to demonstrate that, despite modern scholars’ belief that the Renaissance was a period of all-embracing anthropocentrism when Aristotelian ideas regarding the hierarchy of species flourished and freed man from all moral obligations towards animals, there was a significant cluster of French texts from various authors, such as Des Périers and Montaigne, that raised the question of animal equality, or even superiority, and called upon man to take responsibility for the treatment of animals. The careful examination of these texts surprisingly reveals that modern ideas regarding animal rights and species equality were already addressed, or at least touched on, in French Renaissance literature.

Advisor: Hampton, Timothy
Vector AC Stark shift in 133Cs atomic magnetometers with antirelaraxion coated cells

The main focus of this dissertation is investigation of vector AC Stark shifts (light shifts) in evacuated 133Cs paraffin-coated cells. Although light shifts in alkali atoms have been investigated since 1960s, the effect of laser-induced vector light shifts (VLS) in paraffin-coated cells is little explored in literature. The works considering light shift effects primarily focus on transitions relevant for atomic clocks, or magnetometers using buffer gas cells, or magnetometers using broad-spectrum alkali metal lamps. This work, on the other hand, focuses on light shifts in a setup shared by finite-field optical magnetometers that use paraffin-coated sensor cells, as well as on their impact on sensitivity and accuracy of these devices./nAlong with describing the light shifts, this work presents several techniques that take advantage of the VLS to improve atomic magnetometers as a tool. The proposed techniques eliminate the need for oscillating radio-frequency magnetic fields and replace them with well contained laser beams. This can benefit applications where non-magnetic sensors are needed and stray fields are highly undesirable, such as the search for a permanent electric dipole moment of the neutron./nThis dissertation includes two such projects, the all-optical vector magnetometer and the rf magnetometer driven by a fictitious magnetic field. In the first project a finite-field optical magnetometer, which is normally a scalar sensor, is augmented with two power-modulated orthogonal laser beams that provide the directional sensitivity. The sensor exhibits a demonstrated rms noise floor of 50 fT/√Hz in measurement of the field magnitude and 0.5 mrad/√Hz in the field direction. Elimination of technical noise would improve these sensitivities to 12 fT/√Hz and 5 μrad/√Hz, respectively. In the second project, the atomic precession in a scalar 133Cs magnetometer is driven by an effective oscillating magnetic field provided by the AC Stark shift of an intensity-modulated laser beam. The demonstrated sensitivity of this magnetometer is 40 fT/√Hz rms, which is equivalent to the conventional coil-driven scalar magnetometer we built sharing the same setup./nThe Appendix includes documentation on the custom-built polarimeter used in the experiments and the frequency response of the magnetic sensor head.

Advisor: Budker, Dmitry
Resonant Interactions of Surface and Internal Waves with Seabed Topography

This dissertation provides a fundamental understanding of water-wave transformations over seabed corrugations in the homogeneous as well as in the stratified ocean. Contrary to a flat or mildly sloped seabed, over which water waves can travel long distances undisturbed, a seabed with small periodic variations can strongly affect the propagation of water waves due to resonant wave-seabed interactions--a phenomenon with many potential applications./nHere, we investigate theoretically and with direct simulations several new types of wave transformations within the context of inviscid fluid theory, which are different than the classical wave Bragg reflection. Specifically, we show that surface waves traveling over seabed corrugations can become trapped and amplified, or deflected at a large angle ($\sim 90\degree$) relative to the incident direction of propagation. Wave trapping is obtained between two sets of parallel corrugations, and we demonstrate that the amplification mechanism is akin to the Fabry-Perot resonance of light waves in optics. Wave deflection requires three-dimensional and bi-chromatic corrugations and is obtained when the surface and corrugation wavenumber vectors satisfy a newly found class I$_2$ Bragg resonance condition. Internal waves propagating over seabed topography in a stratified fluid can exhibit similar wave trapping and deflection behaviors, but more surprising and intricate internal wave dynamics can also be obtained. Unlike surface waves, internal waves interacting with monochromatic seabed corrugations can simultaneously generate many new waves with different wavenumbers and directions of propagation--a phenomenon which we call chain resonance. Here, we demonstrate that the chain resonance leads to significant energy transfer from long internal waves to short internal waves for almost all angles of the incident waves relative to the orientation of the oblique seabed corrugations. Since short internal waves are prone to breaking, the resonance mechanism, therefore, may have important consequences on the spatial variability of ocean mixing and energy dissipation. Potential applications of the theory of resonant wave-seabed interactions for wave energy extraction and coastal protection are also discussed.

Advisor: Alam, Mohammad-Reza
Essays on Platform Markets

This dissertation is comprised of three studies investigating how the provision of public information facilitates matching in online marketplaces./nThe first study examines how employers on oDesk.com, the world’s largest online marketplace, use public information in hiring. I show that when employers are searching for someone low-skilled the provision of coarse information is sufficient. When employers are looking for someone high-skilled they will pay fixed screening costs to acquire information beyond what is provided by the platform. When information is not provided by the market- place all employers will pay to acquire more information. This leads to more matches and hiring quality workers at a lower price. However, the cost savings from hiring these low-cost, but high-quality workers does not outweigh the upfront cost of information acquisition./nThe second study investigates how employers on oDesk.com alter their hiring behavior when some applicants, who were selected to be of higher quality by a machine learning algorithm, are covered by a money-back guarantee (MBG). The MBG increases the probability of transacting for employers looking for high-expertise talent. However, conditional on hir- ing, these employers do not substitute to observably different employees. Employers that are looking for lower expertise applicants substitute to higher quality applicants who are backed by the money-back guarantee. A follow-up experiment found that, given some reasonable assumptions, employers found the MBG to be more useful as a signal of applicant quality than as a risk-shifting mechanism./nThe third study uses a series of empirical tests to isolate the mechanism through which the weather affects bidders’ willingness to pay (WTP) on eBay. I find that some variation in bidders’ WTP across multiple auctions can be explained by weather affecting mood. Changes in mood can alter WTP through two channels. Mood can directly alter the perceived value of the item or mood can influence cognitive processes, changing bidding strategies and indirectly changing the bid amount. I concluded that rain alters mood, which alters bidders’ perceived value of an item on eBay leading to bidders increasing their bids.

Advisor: Morgan, John
Tadelis, Steven
Be Our Guest: 129Xe Detection in Macrocycles and Oriented Environments

Nuclear Magnetic Resonance (NMR) is an extrememly powerful technique for determin- ing chemical structure, which can look in opaque samples. Using 129Xe as our detected nucleus we can synthesize molecualar cages that interact with their chemical environment or molecular target, which is observed through the chemical shift of the xenon in the molecular cage. The use of spin exchange optical pumping (SEOP) the pool of xenon can be hy- perpolarized to give signal enhancement that makes it on par with proton NMR techniques. Further using chemical exchnge saturation transfer (CEST) we can use the exchange of xenon in and out of the molecualr cage to detect concentrations in the nanomolar range. In chapter 3 we will look at a cryptophane-A based sensor and how the chemical shift changes when the cage is chelated to different metal ions. In chapter 4 we looked at using a relaxation based detection method for cryptophane sensors showing a decrease in relaxation time when bound to the protein Avidin. In chapter 5 we look at cucurbituril based xenon detection with a base activated sensor using a rotaxane backbone. In chapter 6 we further develop the rotaxane to include a peptide sequence recognizable by the enzyme MMP2. In chapter 7 we explore a new device that allows for xenon to dissolve directly into ordered media without disturbing the local structure, and in chapter 8 we show preliminary results and discuss the future of xenon based sensors.

Advisor: Pines, Alex
Data-Driven Cyber-Physical Systems via Real-Time Stream Analytics and Machine Learning

Emerging distributed cyber-physical systems (CPSs) integrate a wide range of heterogeneous components that need to be orchestrated in a dynamic environment. While model-based techniques are commonly used in CPS design, they be- come inadequate in capturing the complexity as systems become larger and extremely dynamic. The adaptive nature of the systems makes data-driven approaches highly desirable, if not necessary./nTraditionally, data-driven systems utilize large volumes of static data sets to extract models and predictions of physical processes. However, in emerging CPS, networked sensors provide continually streaming data, creating an essentially infinite source of information. Processing data in batches is no longer a viable option: streams are most valuable when processed on-line, allowing actionable information to be gathered just as the data becomes available. This fundamental shift from big data to infinite data, while having great potential to enable smarter systems, also poses unique challenges. Computation models that capture the integration of streaming data into CPS design become a key requirement for systems to learn, adapt, and evolve in real-time./nThis thesis explores methodologies for developing data-driven CPSs that integrate model-based design and real-time stream analytics in a modular way. The key modeling framework to be introduced is the aspect-oriented modeling (AOM) paradigm, which leverages the principle of separation-of-concerns in actor-oriented de- sign. Aspects are useful for representing cross-cutting concerns in complex system architectures, as first introduced by the aspect-oriented programming paradigm in object-oriented design. AOM applies this idea to actor-oriented design, creating aspects that enable representation of modular concerns in a complex system model. In data-driven CPS, the introduced aspects can be leveraged to process streaming data, extract actionable information, and incorporate these into the system workflow in a way that preserves model semantics and modularity. To address information extraction from streaming data, we propose the use of aspects that implement Dynamic Bayesian Network based algorithms for machine learning and optimization. Specifically, we introduce an actor-oriented toolkit that enables dynamics and sensing models to be composed with inference, Bayesian learning, and optimization algorithms, and present comprehensive case studies on cooperative mobile robot control. We additionally study the use of streaming data for control of dynamic networked CPS in the context of home automation, and present an overview of the use cases of aspects in actor-oriented CPS development.

Advisor: Lee, Edward A
Uniformization of semistable bundles on elliptic curves

Let $G$ be a connected reductive complex algebraic group, and $E$ a complex elliptic curve. Let $G_E$ denote the connected component of the trivial bundle in the stack of semistable $G$-bundles on $E$. We introduce a complex analytic uniformization of $G_E$ by adjoint quotients of reductive subgroups of the loop group of $G$. This can be viewed as a nonabelian version of the classical complex analytic uniformization $ E \simeq \mathbb{C}^*/q^{\mathbb{Z}}$. We similarly construct a complex analytic uniformization of $G$ itself via the exponential map, providing a nonabelian version of the standard isomorphism $\C^* \simeq \C/\Z$, and a complex analytic uniformization of $G_E$ generalizing the standard presentation $E = \C/(\Z \oplus \Z \tau )$. Finally, we apply these results to the study of sheaves with nilpotent singular support.

Advisor: Nadler, David
Expanding Merit Through Communitarianism: Racial and Ethnic Implications

Abstract/nExpanding Merit Through Communitarianism: Racial and Ethnic Implications/nby Jerlena Denise Griffin/nDoctor of Philosophy in Education University of California, Berkeley Professor David Stern, Chair/nLow-income students and some racial minorities, in particular African Americans, have been chronically under-represented in higher education. In the ongoing debate about affirmative action, conceptions of merit based on test scores and grades have been viewed as conflicting with the goal of more equitable representation. However, some previous researchers have proposed that a broader conception of merit, based on the mission of the higher educational institution, could be more consistent with equity goals. In particular, the public-serving mission of a public university would warrant greater emphasis on community service achievements in selecting among applicants. In the University of California (UC) system, high school community service already is one of the qualifications considered in the comprehensive review of freshman applications./nThis study explores the possible implications of giving greater consideration to high school community service in the admission process. Data from UC applications for fall/n2013 are used to compare the average amount of time spent in high school volunteer/nactivities among applicants, admitted students, and enrolled freshman by race/ethnicity, gender, and other characteristics. Among other findings, African American and Asian students reported the highest average hours of community service in high school. Increasing consideration of high school community service would result in admitting slightly larger numbers of students in these groups./nData on community service from the spring 2014 UC Undergraduate Experience Survey also were used to compare the amount of hours per week spent in community service by students in their freshman year. Among other findings, high school service was a strong predictor of college service, and African American students were the most likely to participate in community service as freshmen. A regression in which high school community service and student characteristics were used to predict hours of community service in college revealed that African American freshmen actually contributed more hours of community service than would have been predicted by their high school service and other characteristics.

Advisor: Stern, David
Investigating Meningeal Dissemination in B-Cell Acute Lymphoblastic Leukemia

Leptomeningeal dissemination (LMD) is frequently observed in patients with B-cell acute lymphoblastic leukemia (B-ALL), particularly those that carry the Philadelphia chromosome (Ph+). To prevent disease relapse from B-ALL cells in the meninges, patients are treated prophylactically with intrathecal chemotherapy, which is often accompanied by deleterious side effects such as neuropathy. Using a mouse model of B-ALL that recapitulates the genetic lesions commonly found in Ph+ B-ALL (expression of Ph and loss of tumor suppressor Arf), I characterized the molecular and cellular defects during meningeal dissemination, and explored the underlying mechanism through which B-ALL cells promote meningeal dissemination. In this Ph+ B-ALL model, meningeal dissemination was found in conjunction with extensive osteoclast-mediated osteolysis in the skull, caused by the expansion and activation of osteoclasts. Repression of osteoclast differentiation and activation in the Ph+ B-ALL model, either by RANK-Fc or bisphosphonate treatment, significantly delayed the onset of meningeal dissemination, suggesting the osteolysis of the skull provides a favorable stromal environment for meningeal tumor growth. I also found that the Ph+ B-ALL tumors exhibited a high level of Rankl and Tnfα, at least in part, through aberrant STAT5A signaling downstream of inappropriate activation of the ABL kinase component of the BCR-ABL fusion protein. Rankl and Tnfα both promote osteoclast differentiation and osteolysis, and hence, early colonization and expansion of Ph+ B-ALL cells in the meninges. Taken together, my studies reveal an unexpected connection between meningeal dissemination and osteolysis, and will likely provide important insights into patient stratification and LMD prevention in human B-ALL patients.

Advisor: H, Lin
Optimizing Nanophotonics: from Photoreceivers to Waveguides

Optical communication systems are replacing electrical interconnects on shorter and shorter scales, thanks to the large bandwidth they can provide and their better energy efficiency over long distances. Optical circuit boards or even on-chip interconnects are becoming an increasingly attractive possibility, thanks to tighter integration of photonics and electronics in technology platforms such as Silicon photonics. Nevertheless in order for optical links to become competitive with their electrical counterparts at these very short length scales, their energy efficiency must still be drastically improved. State of the art systems today consume ~1pJ/bit of energy to communicate information, which is orders of magnitude above theoretical bounds./nIn this thesis, the discrepancies between the theoretical limits and real world perfor- mance are explored, with a focus on the photoreceiver, which dictates the sensitivity and therefore much of the energy used by the link./nA thorough modeling of optical links is performed, leading to the determination of optimal receiver circuit topologies to improve the sensitivity and reduce the power con- sumption of photoreceiver systems. This enables the identification of crucial performance bottlenecks and the establishment of a technological roadmap for future generations of optical interconnects./nAdditionally an extremely efficient shape optimization technique using the adjoint method for passive nanophotonics is presented, in order to provide lower loss components thereby also offering a path to improve the performance of optical links.

Advisor: Yablonovitch, Eli