VictorJuiz/thesis huggingface dataset:
Nearly-Kähler 6-manifolds of cohomogeneity two : local theory
Keywords: Mathematics.

We study nearly-Kahler 6-manifolds equipped with a cohomogeneity-two Lie group action for which each principal orbit is coisotropic. If the metric is complete, this last condition is automatically satisfied. We will show that the acting Lie group must be 4-dimensional and non-abelian. We partition the class of such nearly-Kahler structures into three types (called I, II, III) and prove a local existence and generality result for each type. Metrics of Types I and II are shown to be incomplete. We also derive a quasilinear elliptic PDE system on a Riemann surface that nearly-Kahler structures of Type I must satisfy. Finally, we remark on a relatively simple one-parameter family of Type III structures that turn out to be incomplete metrics cohomogeneity-one under the action of a larger group.
The needfinding machine
Keywords: Mechanical Engineering.

This thesis develops and evaluates a method for allowing designers to perform needfinding by remotely interacting with users in real-time through computer-enabled interactive devices. While interactive systems present new opportunities for creating intelligent products that adapt to their users, these devices may also help designers understand people's needs by providing a view into users' everyday experiences. This thesis asks: how can designers use interactive devices to connect with users to receive information and feedback about their in-context experiences with interactive products? To answer this question, I develop the Needfinding Machine. Using the Needfinding Machine method, a designer in-the-loop observes the user, asks questions through an interactive machine, and remotely performs the machine's behaviors in real-time as a way to conduct problem-space exploration in-context. This thesis has four major components. Part one gives an overview of the Needfinding Machine and situates the method among other design methods for understanding people and their needs. Part two presents a lab-based study exploring how we can use machines that speak to elicit meaningful information from people. I then move out of the lab and evaluate how practicing designers can use a needfinding machine to understand their users. Part three develops a needfinding machine for use in automobiles called WoZ Way. I then discuss a case study with designers from Renault using WoZ Way to understand driver experience with currently available advanced driving assistance features. Finally, part four presents a case study with an interaction research team from Spotify using a needfinding machine I developed, called DJ Bot, to explore people's experience with music in two contexts, the car and the home. These projects present a proof-of-concept for using interactive devices for real-time remote needfinding and describe how designers can engage with the Needfinding Machine method.
The neural basis of tactile attention
Keywords: Psychology.

Spatial tactile attention is the ability to improve the processing of tactile stimuli at particular, attended, parts of our body. In order to investigate the neural and behavioral characteristics of spatial tactile attention, we combined measurements of tactile sensory regions using functional magnetic resonance imaging, with a novel tactile behavioral paradigm that included an attentional manipulation. We find an improvement in amplitude discrimination performance when a cue directs attention to a particular hand, and a corresponding increment in neural activity in the primary and secondary somatosensory cortices contralateral to the attended hand. Taking inspiration from the literature on visual attention, we consider whether the observed behavioral and cortical changes are more likely to be caused by a change in processes to do with the selection of stimuli (operationalized as an offset in neural activity), or if they are instead the outcome of a change in sensitivity to stimuli (operationalized as a change in the gain of the stimulus drive). We find that both behavioral and neural data are most consistent with the selection (neural offset) hypothesis. This is consistent with findings with functional imaging in the visual attention literature, suggesting that mechanisms for allocating spatial attention in sensory regions of cortex might be similar across sensory modalities. The implications of these results are considered in light of previously documented inconsistencies between functional imaging and electrophysiological measurements in the visual attention literature.
Neural ensemble dynamics in behaving animals : computational approaches and applications in amygdala and striatum
Keywords: Biology.

The brain must integrate many sensory signals and decide appropriate actions to take given prior knowledge and the current state of the world. Many fundamental questions remain about how exactly neural circuits perform these critical functions. A confluence of novel technologies is allowing neuroscientists to address these old biological questions and ask new ones, but has also led to new challenges in handling and analyzing large-scale neural datasets. In this dissertation, I conducted a series of studies that give novel insights into the neural coding of pain, rewarded actions, and locomotion along with new and improved computational methods for analyzing large-scale calcium imaging datasets. First, I studied how the rodent amygdala codes for pain, demonstrating that a specific neural ensemble codes for noxious stimuli and that a subset of this ensemble is stable across days to weeks. I then show that heightened behavioral responses after nerve injury parallel alterations in the neural pain code and we find that this neural ensemble is necessary to produce certain pain behaviors. Next, I demonstrate enhanced analysis and development of methods for calcium imaging cell extraction and automated cell classification. Finally, in a pair of studies, we apply large-scale calcium imaging techniques in two genetically defined neuronal populations in the mammalian striatum to detail the ensemble neural codes used for action initiation in a learning paradigm and locomotion during spontaneous behavior. Taken together, this dissertation provides new insights into pain and action selection along with powerful examples of how large-scale optical and computational methods can broaden our understanding of neural circuits.
Neuronal Expression of the MHCI Qa-1 and Its Role in Activity-Dependent Plasticity
Keywords:  Department of Biology
synaptic plasticity
critical period
visual cortex
MHCI
Qa-1
HLA-E
neurobiology
biology
Thesis

During development, brain connectivity is modified by changes in experience and neural activity. These plastic modifications in the structure and function of synapses, the connections between neurons, are known as synaptic plasticity. Synaptic plasticity can alter the way neural circuits compute and ultimately lead to changes in behavior. In the visual system, vision is required for the refinement of connections in primary visual cortex (V1), especially during a developmental critical period. However, the molecular mechanisms by which changes in experience are translated into synapse modifications are unclear. This study describes a potential role for Qa-1, a mouse major histocompatibility complex protein, in visual cortical plasticity during the postnatal critical period. The role of Qa-1 in the immune system has been investigated, but we show that it may have a separate function in the brain that depends on neural activity. Multiplex in situ hybridization experiments showed that Qa-1 mRNA is specifically expressed in deep layer cortical excitatory neurons. This expression begins during the visual cortical critical period, correlating with a period of increased plasticity. Furthermore, Qa-1 mRNA in V1 is regulated by changes in visual experience. Exposure to darkness during the critical period resulted in lower expression of Qa-1 in mouse V1, and re-exposure to light restored Qa-1 expression to control levels. These results support a role for Qa-1 in transducing changes in neural activity into molecular signals for synaptic plasticity. Our results indicate that Qa-1 may be involved in activity-dependent plasticity and help clarify the molecular mechanisms by which synapses change in response to experience during development. Uncovering the molecular basis of synaptic plasticity in development will lead to a better understanding of neural developmental disorders and neurodegenerative disease.
New platforms for the generation and extraction of single photons
Keywords: Electrical Engineering.

At the core of next generation computing and communication paradigms lies the burgeoning field of quantum information science, which involves the encoding, communication, manipulation, and measurement of information using quantum-mechanical objects. One key example is quantum cryptography, which relies on quantum key distribution protocols to ensure secure communication channels. A vital enabling technology for this application is the single photon source. This thesis explores platforms for on-chip generation and extraction of single photons. First, we demonstrate a hybrid metal-dielectric nanocavity coupled to a single quantum dot that emits single photons directly into free space. In introducing this nanocavity, we conduct a detailed exploration of the design and subsequent nanofabrication of the device. Then, we introduce the design of a platform for high-purity single photon generation based on a waveguide with a partially transmitting element coupled to a photonic crystal cavity. This system generates single photons in an integrated fashion and without loss, allowing for further processing on a single chip. Finally, we test a method for angled fabrication of devices using a focused ion beam (FIB) system. We probe the feasibility of this technique in two ways: (a) undercutting of a nanobeam in 4H-SiC, and (b) angled milling of high-efficiency grating couplers using inverse design to convert from on-chip to free-space and vice versa. Taken together, we hope these individual advances provide a framework upon which to build in order to move closer to scalable, industry-ready single photon sources.
No escape: light waves in AdS
Keywords:  Department of Physics
Stanford Institute of Theoretical Physics
SITP
AdS
General Relativity
Klein-Gordon Equation
light waves
scalar fields
gravity
Thesis

The AdS/CFT correspondence represents a major advance in our understanding of string theory and quantum gravity. It provides a powerful toolkit for studying strongly coupled quantum field theories and understanding quantum gravity. To apply this framework effectively, it is important to understand AdS in the context of string theory. Calculations involving string theory in AdS rely heavily on the assumption that light starting from the center of Anti-de Sitter (AdS) cannot reach its boundary. However, it can be shown that light, if it follows null geodesics, will reach the boundary and then come back to the origin in finite time. How can we resolve this tension? This work proposes a simple resolution that involves modeling light as a massless scalar field instead of as rays. Using this new representation and applying some scattering theory, we show that light in AdS cannot be modelled as rays due to diffraction caused by the curvature of the spacetime. In other words, as the light wave travels up the gravitational potential of AdS, it is redshifted and its wavelength increases, which renders the geometric optics approximation inadequate after some finite distance. We then show how this implies that light does not reach the boundary of AdS.
Non-canonical roles for the E2F family in the survival and proliferation of stem and cancer cells
Keywords: Genetics.

The E2F family of transcription factors has a well-known, critical role in cell cycle regulation. At the G1/S checkpoint, the canonical "repressor" E2Fs inhibit the expression of cell cycle genes in conjunction with the RB family proteins, while the canonical "activator" E2Fs activate the expression of cell cycle genes in response to mitogenic cues. However, accumulating evidence points toward diverse functions for the E2F family outside of G1/S checkpoint regulation. For instance, loss-of-function studies suggest that specific E2F family members are required for cellular differentiation, self-renewal, and apoptosis in a context-dependent manner. In addition, the "repressor" and "activator" designations are based on in vitro studies in a few cell types, and the E2Fs may also have different molecular functions in physiological conditions, including in the cytoplasm. These non-canonical roles remain largely unexplored. Our work shows that E2F4, a canonical "repressor" E2F, can switch to an activator of cell cycle genes to promote the survival and proliferation of embryonic stem cells (ES cells). We demonstrate that E2F4 loss leads to cell cycle defects at the G1 and S phases, decreased cell viability, and global downregulation of cell cycle genes, and that rescue of E2F4 function relies on both its DNA binding and transactivation domains. We further demonstrate that the function of E2F4 in ES cells is RB family-independent, as E2F4 can translocate into the nucleus and bind to gene promoters in cells that completely lack RB family activity. Finally, we characterized the interactomes of E2F4 in ES cells and somatic cells, and found ES cell-specific interactors (e.g. components of the MLL methyltransferase complex) that may be critical for the activator function of E2F4. Our data reveal a non-canonical function for a well-known repressor E2F, and may lead to insights into the biology of other rapidly cycling cell types (e.g. cancer cells and progenitor cells) that lack RB family activity. Future work will be needed to examine the mechanisms driving gene activation by E2F4, the different protein complexes to which E2F4 contributes, and the plethora of cellular functions controlled by the E2F family members.
Nonmagnetic optical isolation and circulation with meta-surfaces and integrated photonics
Keywords: Electrical Engineering.

Nonreciprocal optical components, such as optical isolators and circulators, allow light to transmit in one direction but block its transmission in the opposite direction. Such devices play an indispensable role in photonic systems, as they provide lasers with feedback protection and mitigate multi-path interference in communication channels. Constructing nonreciprocal devices require the breaking of Lorentz reciprocity, which has traditionally been achieved with magneto-optical materials. This method, however, is incompatible with integrated photonics platforms, most notably silicon photonics, because most standard optoelectronic materials do not exhibit magneto-optical effects. As such, there has been a significant demand for achieving optical isolation without magneto-optic materials. In this Thesis, we present our recent advancements in using nonmagnetic approaches for constructing nonreciprocal optical devices. First, we discuss the use of nonlinear optics for optical isolation and highlight some of their fundamental limitations. Next, we focus on the use of dynamic modulation of refractive index to achieve nonreciprocal manipulation of light. In particular, we discuss our recent developments in the simulation of dynamically modulated optical devices, as well as the design and demonstration of optical isolators and circulators on both meta-surface and integrated photonics platforms. These elements provide the basis for robust photonic systems, improve the flexibility in optical designs, and expand the degrees of control over light propagation.
Non-negative matrix factorization and topic models
Keywords: Electrical Engineering.

Matrix factorization algorithms provide a powerful tool for data analysis and statistical inference. As an important class of these algorithms, nonnegative matrix factorization (NMF) suggests expressing a collection of data points as convex combinations of a small set of 'archetypes' with nonnegative entries. As a result, NMF enables us to extract the latent structure and underlying 'pure components' in a broad range of applications from chemometrics to image processing and topic modeling. In this thesis, we study the NMF problem from two different perspectives: 1. We consider the NMF problem under a deterministic model and propose a new estimator that robustly recovers the factors under a more general settings than the state-of-the-art estimators, with theoretical guarantees. 2. We analyze the NMF problem in a Bayesian setting under which the data is generated using an LDA model. We show negative results about variational inference in this problem, showing that it is not 'stable'. In particular, we show that in a certain region for signal-to-noise ratio, in which the underlying signal cannot be recovered, the variational method is randomly biased and outputs a non-trivial solution. This output, of course, is uncorrelated with the underlying truth. We also suggest a possible correction to remedy this issue.
Nonreciprocity and topology in dynamically modulated photonic systems [electronic resource]
Keywords: Applied Physics.

The propagation of light in linear, time-independent and non-magnetic media is governed by Lorentz reciprocity. As a result, nonreciprocal optical devices such as isolators and one-way waveguides traditionally rely on magneto-optical materials, which are hard to incorporate in an integrated photonics platform. Dynamic modulation of the refractive index breaks Lorentz reciprocity, and provides a CMOS-compatible and reconfigurable approach to optical nonreciprocity. Moreover, dynamically modulated photonic systems also provide a versatile platform for studying photonic topological states that support robust unidirectional photonic transport. Dynamic modulation also enables one to explore the synthetic dimension associated with the frequency axis in certain photonic resonator systems. With a synthetic dimension, one can access higher dimensional physics in a lower dimensional photonic structure. In this dissertation, we theoretically and numerically explore a rich set of nonreciprocal and topological photonic effects associated with dynamically modulated optical waveguides and resonators. Potential experimental realizations of our proposals are also discussed and evaluated. In the first part of this dissertation, I show that the phase of dynamic modulation creates an effective gauge field for photons, which is analogous to the vector potential for electrons in the sense that they both impart a direction-dependent propagation phase on the particles. Such a gauge field enables the creation of nonreciprocal photonic devices such as dynamic optical isolators and gauge-field one-way waveguides, as well as the realization of photonic quantum Hall effect in a nonreciprocal waveguide network. These results illustrate the power of the effective gauge field in manipulating the propagation of electromagnetic wave and enabling new designs for nonreciprocal photonic elements. In the second half of this dissertation, I show that the set of optical resonances supported in a ring resonator forms a synthetic dimension along the frequency axis, with dynamic modulation controlling the coupling between modes along the synthetic dimension. This synthetic dimension enables the realization of three-dimensional physics in a planar photonic structure, bypassing the complex three-dimensional geometries required by previous studies. I will demonstrate the creation of three-dimensional topological insulators and Weyl points in a two-dimensional array of ring resonators, which paves the way for experimental demonstration of three-dimensional topological effects that are difficult to study in other systems.
Non-uniform Fourier Analysis on Active Seismic Data recorded by 3-component Geophones and the Stanford Fiber Seismic Observatory
Keywords:  Department of Geophysics
School of Earth Energy &amp; Environmental Sciences
Geophysics
Seismic Processing
Thesis

A distributed acoustic sensing (DAS) system allows seismologists to record seismic data through optical fibers and provides denser spatial sampling than geophones. Optical fiber cables can be deployed in areas that are difficult to access with geophones, such as under the ocean and in urban areas. Pre-existing telecommunication cables can also be utilized, which can reduce the cost of a project. We conducted active-source seismic experiment on Stanford campus to test the performance of DAS with optical fiber cable installed along an existing conduit used for telecommunication cables. The data we collected are heavily contaminated by surface wave noises. To attenuate these noises, we analyzed filters that utilize two different techniques, regular and Non-equispaced Discrete Fourier Transform. Our study showed that overall the Non-equispaced Discrete Fourier Transform improves signal coherence better than regular Fourier Transform; however, the Non-equispaced Discrete Fourier Transform on DAS data can become unstable when offsets of the data cause instability in matrix inversion.
A novel enhancer near the Pitx1 gene influences vertebrate hindlimb development [electronic resource]
Keywords: Genetics.

The evolution and development of the vertebrate limb has long fascinated biologists. Vertebrates show a huge degree of diversity in limb form and function, ranging from the heavily modified forelimb of a bat which enables powered flight, to the partial loss of limbs in whales, or the complete loss of limbs in snakes. The mechanisms that produce such differences have been largely unknown. Studying limb modifications that have evolved recurrently can help reveal ecological and molecular factors that shape evolutionary outcomes. One classic example of repeated limb evolution is the loss of pelvic and hindlimb structures, a trait that has independently evolved in many clades, including fish, amphibians, reptiles, and mammals. To date, the molecular basis of hindlimb reduction is still poorly understood in most species. However, in threespine stickleback fish, a combination of genetic and genomic studies has previously identified the Pitx1 gene as a major locus controlling much of the variation in pelvic size in natural species. Recurrent deletion of a pelvic enhancer region upstream of the Pitx1 gene (PelA) is correlated with pelvic reduction in many independently evolved stickleback populations. Despite the widespread use of this enhancer in stickleback populations, the PelA enhancer is not well conserved outside of fish. In my Dissertation research, I have identified and characterized a second pelvic enhancer in the Pitx1 gene, PelB, which is functionally conserved from fish to mammals. The PelB enhancer drives robust reporter activity in the hindlimb autopod of a developing mouse embryo, and the orthologous stickleback sequence is able to drive robust activity in the pelvic spine of a developing fish. In mice, deletion of the PelB enhancer sequence leads to reductions in length of multiple bones in the hind feet. In addition, loss of the PelB enhancer on a genetic background with reduced Pitx1 expression results in complete loss of the patella (kneecap). These experiments confirm that PelB is required for normal hindlimb development, and suggest that mutations in this region might also contribute to evolutionary changes in limb size. To further test whether PelB is altered in species that show natural hindlimb reduction, I compared PelB sequences in pelvic complete and reduced species. While no obviously disabling lesions were observed in whales or manatees, partial loss of PelB was seen in several snake genomes. In addition, I identified one population of pelvic-reduced stickleback fish that has a complex insertion-deletion mutation in PelB. Using functional assays in transgenic sticklebacks, I showed that this naturally occurring mutation causes loss of PelB activity in the developing pelvis, while other expression domains remain intact. These experiments suggest that PelB is an important driver of evolutionary pelvic reduction in some species.