VictorJuiz/thesis huggingface dataset:
IgE antibody dynamics and its role in receptor binding and inhibition [electronic resource]
Keywords: Structural Biology.

IgE antibodies interact with the high affinity IgE Fc receptor (Fc [epsilon] RI) expressed on mast cells and basophils, and the low affinity IgE Fc receptor (CD23) on B cells. These interactions are directly involved in triggering the allergen-specific activation of inflammatory responses. The IgE-Fc region, comprising the C-terminal domains of the IgE heavy chain, binds Fc [epsilon] RI and the crystal structures of the human IgE-Fc alone and IgE-Fc complexes exhibited IgE-Fc conformational flexibility. In addition, the crystal structure of IgE-Fc bound to CD23 indicated a preference of CD23 for a closed conformation of the IgE-Fc incompatible with Fc [epsilon] RI binding. These observations suggested the importance of IgE conformational dynamics for its receptor binding mechanism and the potential to identify non-classical or allosteric inhibitors for IgE-receptor interactions. To investigate IgE dynamics and its role in receptor binding and inhibition, I have employed 5 experimental approaches: 1) IgE-Fc mutants trapped by an engineered disulfide bond, blocking Fc [epsilon] RI but not IgE inhibitor binding, 2) a fluorescence assay for IgE-Fc:Fc [epsilon] RI binding and inhibition that can distinguish IgE-inhibitors based on their proximity to the Fc [epsilon] RI binding site, 3) the determination of the E2_79 crystal structure showing that the IgE inhibitor E2_79 binds IgE-Fc outside the Fc [epsilon] RI-binding site and acts through a facilitated dissociation mechanism to block receptor binding, 4) the development of a TR-FRET assay suitable for high-throughput screening for small molecule inhibitors of IgE-receptor binding, and 5) a single-molecule FRET approach to characterize the conformational states of the IgE-Fc3-4 and observe changes upon Fc [epsilon] RI, CD23, and E2_79. These experiments revealed different conformational requirements for IgE binding, identified a disruptive inhibitor that actively dissociates preformed receptor complexes, and provided direct observation of receptor binding-induced IgE-Fc conformational changes. This work provides a new perspective on the role of IgE dynamics in receptor binding and inhibition, and makes possible the development of new disruptive inhibitors for IgE-receptor binding acting through non-classical or allosteric mechanisms.
Illuminating the universe [electronic resource] : using the cosmic microwave background to probe structure at intermediate redshift
Keywords: Physics.

The cosmic microwave background (CMB) provides a backlight that allows us to probe structure out to the last scattering surface. We exploit observations of the sky at microwave and sub-mm wavelengths to measure properties of galaxies and galaxy clusters, as well as to search for possible pre-inflationary signals. In Chapters 2--4 we measure the correlation between the dark matter distribution and the microwave and sub-mm emission from galaxies to probe the connection between dark and luminous matter at redshifts ~1-3. CMB photons are gravitationally deflected by dark matter overdensities, with the majority of the ~3 arcminute RMS deflection occurring between redshift 2 and 3. The dark matter structures that lens the CMB are traced by dusty star-forming galaxies that emit strongly in the infrared, and have a redshift distribution that peaks between redshift 1 and 3. We use observations of the CMB from the Planck satellite to reconstruct the deflection angles with statistical estimators, and we correlate the deflections with observations of the infrared background light at 100-850 GHz. We find that the two signals are strongly correlated, with a correlation coefficient of approximately 0.8, and we use the measured cross spectrum to estimate the minimum mass scale at which dark matter halos host a CIB source, as well as the star formation rate density in three redshift bins between redshift 1 and 7. In Chapter 5 we use the Doppler shift of CMB light scattered by moving galaxy clusters, known as the kinetic Sunyaev-Zeldovich (kSZ) effect, to put a limit on the large-scale velocity distribution of a sample of galaxy clusters observed in WMAP CMB data. On 100 Mpc scales cluster velocities relative to the CMB are expected to be small, originating from gravitational instabilities. Larger motions could be generated by pre-inflationary inhomogeneities that leave a "tilt" across our horizon, resulting in a uniform matter flow across the horizon. The kSZ effect is sensitive to such a flow, and we use it to constrain the radial and dipole velocity of a sample of 736 clusters with mean redshift 0.12, finding no evidence for either. In Chapters 6 and 7 we search for a possible pre-inflationary signal in CMB data. Models of inflation suggest that our current patch of the universe could have been created as a nucleation bubble from a phase of false vacuum eternal inflation. If additional bubbles are produced, then it is possible that one of them intersected our past lightcone at the time of decoupling, imprinting a disk-shaped signal in the CMB. We have searched for this signal in the WMAP data using optimal algorithms that evaluate the exact posterior likelihood in an efficient and computationally fast way. We find no evidence for the signal, and place limits on the curvature perturbation generated by a collision intersecting the last scattering surface.
Image artifact reduction for fast magnetic resonance imaging [electronic resource]
Keywords: Electrical Engineering.

Magnetic resonance imaging (MRI) is a rich source for diagnostic information. It has the ability to obtain excellent soft-tissue contrast at a very high spatial resolution. The imaging process of this modality can be conveniently described as a linear system with Fourier encoding. However, to increase flexibility and robustness, imaging techniques are used that cause basic assumptions of this model to fall apart. As a result, image artifacts arise, decreasing the clinical quality of the scans. More sophisticated methods that take these effects into account must be considered. Many of the errors reside in both the spatial and frequency domain, so simple linear solutions do not suffice. Two sources of image artifacts are investigated: (1) concomitant gradient field and field inhomogeneity and (2) nonrigid motion in free-breathing acquisitions. Each image-artifact source has specific effects which are dependent on the application. For real-time cardiac imaging with spiral k-space trajectories, concomitant gradient field and field inhomogeneity errors result in image blurring. Two fast and practical solutions are developed and applied to real-time cardiac studies and high-resolution cardiac studies. MRI is also a compelling choice for imaging pediatric patients as they are highly susceptible to risks of ionizing radiation of computed tomography and nuclear scintigraphy studies. However, this imaging modality is highly sensitive to motion. The motion can result in destructive image artifacts. To enable free-breathing volumetric exams, novel data acquisition strategies and image reconstruction techniques are developed to compensate for nonrigid respiratory motion. These methods are demonstrated in select pediatric patient studies. Image artifacts fromrespiratory motion are reduced from the free-breathing abdominal scans.
Image webs [electronic resource] : discovering and using object-manifold structure in large-scale image collections
Keywords: Electrical Engineering.

This dissertation explores a method for data-mining in large image collections with applications to object recognition and dataset visualization. The method builds graphs that preserve the local metric structure of the ideal object-manifolds by linking instances of the same object in different scenes using local image feature matching techniques. A range of image matching techniques are evaluated resulting in a design optimized for the task of preserving local metric structure. Benchmark evaluations on a large dataset show the proposed graph representation is useful for fine-grained semi-supervised object discovery, localization, and annotation tasks. These findings are interesting because fine-grained object recognition for a large number of objects is beyond the reach of the current state-of-the art computer vision algorithms. This work suggests promising directions for data-driven computer vision techniques for automatically organizing massive image collections in which the size of the dataset becomes an advantage rather than a limiting factor.
Imaging nanoscale electronic inhomogeneity with microwave impedance microscopy [electronic resource]
Keywords: Applied Physics.

Ability to measure local dielectric constant and conductivity at nanoscale is desir- able for many research disciplines. Traditional transport measurements and many scanning probe techniques require ohmic contacts to the sample, which further com- plicates the sample preparation and is a low throughput process. Techniques based on high-frequency coupling is advantageous over these techniques since the measure- ments rely on the capacitive coupling between the tip and the sample. Among the high-frequency probes, near-field microwave microscopy sits on the sweet spot with the advantages from the high frequency coupling, but still maintains high contrast between metal and insulator. Implementing microwave microscopy technique is no trivial task. The first part of this thesis describes various engineering aspects during the developmental stage of our microwave microscopy, which we call microwave impedance microscope (MIM). We will begin with introduction to the principle of near-field microscopy, and follow by describing various components of MIIM. The second part of the thesis devotes to the study of nanoscale electronic inhomogeneity both at room temperature and low temperature. The room temperature works provide examples of application of MIM for nanoscale electrical characterization in nano graphene and semiconductor devices. The low temperature studies focus on the phase transition in pervoskite manganites and edge states of two-dimensional electron gas. In pervoskite manganites, we provide direct observation of the phase-separation and the glassy behavior of manganites. In the two-dimensional systems, we study the formation edge states during quantum Hall and quantum spin Hall effects. Finally, we concludes the thesis with plans for future developments and scientific problems.
Immediate mediation [electronic resource] : a narrative of the newsreel and the film
Keywords: Art and Art History.

This dissertation examines the ways in which newsreels were central to modes of reportage and visual display in the interwar years. Drawing from primary and archival sources, and looking directly to the films themselves, this study imparts a new understanding of newsreels' unique, compiled, nonfiction narrative style. This dissertation uses the visual and phenomenological experience of the cinema to understand how interwar newsreels were not simply ephemeral (and literally disposable) documents of the mundane, but were a true vernacular—a common language of contemporary history. At their most basic level, newsreels were formal groupings of eight to ten "stories" designed to bring the outside world into the film theatre; they were instruments both of journalism and cinema and are now forgotten examples of the inherent hybridity of motion pictures. Newsreels' compilation structure, a relic of cinema's earliest years, and their content, a highly mediated refraction of contemporary experience, together represent a singular mode of historical documentation and narration. Discussing newsreels' relationship to contemporary reportage media, their place in cinema history, and the implications of their status as compilation films underlines newsreels' kaleidoscopic form and function. Widely consumed and eagerly anticipated, interwar newsreels were documents constructed in a medium whose burgeoning popularity and ubiquity has become emblematic of its specific historical moment.
Impact of metal gate work function variability and reliability on MOSFETs and theory and application of topological insulators [electronic resource]
Keywords: Electrical Engineering.

For almost half a century, IC technology development has been successfully guided under the Moore's Law. However, as transistor has to scale further down for further integration, a number of of parasitic effects, such as variability, reliability and power dissipation start to impede the benefit of scaling. Under such situation, we need to study these obstacles and overcome them by using new material, new processing and technology. In the first part of this thesis, the metal gate work function variability problem and also reliability problem of MOS transistor are discussed. Modeling and experimental study suggest that gate work function induced threshold voltage variability is going to become the dominating variability factor beyond the 22nm technology node at both device and circuits level. Also discussed is a new negative bias temperature instability (NBTI) model for the recoverable part (RNBTI). This model is able to cover the full range of various experimental data in the different stress/recovery phases. In the second part of this thesis, the study on a newly discovered class of material, so called topological insulators is reported, including the search for strong interacting topological insulators and their potential applications in interconnects and optoelectronics.
Impulsive alignment in dense molecular gasses [electronic resource] : high temperatures and new directions
Keywords: Applied Physics.

A molecular ensemble which is aligned to a laboratory-fixed axis can be useful in any number of structure determination experiments including spectroscopy, x-ray scattering, and high harmonic generation. To date, the majority of techniques aimed at achieving and measuring alignment have been developed for low-density ensembles commonly found in vacuum chambers. In this work, I explore the application of one technique, impulsive alignment, in particular, to samples at densities and pressures approaching one atmosphere. This regime is shown to represent opportunities for new measurement techniques based on optical absorption and measurements of refractive index. Specific experimental demonstrations covered within this work include alignment of a sample of molecular iodine at 425 degrees Kelvin in which centrifugal distortion and vibrational population are shown to have a significant effect on alignment. The creation and measurement of a wavepacket exhibiting both transient and static alignment along the axis of beam propagation is demonstrated as well, allowing for alignment of a symmetric top molecule along all three lab-fixed axes. Measurement techniques developed and discussed in this work include forms of both spectroscopy and interferometry. Herein, spectroscopic detection methods are demonstrated to be effective at measuring alignment at near-atmospheric densities, while revealing additional effects of driving fields, such as ionization and dissociation. A novel interferometric measurement technique is also explored and shown to be effective for nonresonant measurements of alignment. It is additionally useful in that it is capable of measuring the temporally changing refractive index of an impulsively aligned ensemble without the need for an associated birefringence.
Incentives and Manipulation in Large Market Matching with Substitutes
Keywords:  Department of Economics
Stanford Department of Economics
Law of Aggregate Demand
large market matching
Thesis

The analysis of large two-sided many-to-one matching markets available to date focuses on the class of responsive preferences. This paper gives the first thorough analysis of large market matching under the wider class of substitutable preferences satisfying the Law of Aggregate Demand. We show that the central results of Kojima and Pathak (2009) establishing vanishing incentives to misreport hold under these more general preferences. In doing so, we apply the characterization of stable matchings developed in Hateld and Milgrom (2005) to extend the foundational large market matching theorems not only to more general preferences, but also to arbitrary stable mechanisms. This analysis culminates in the first proof that truthful reporting constitutes an epsilon Nash equilibrium in large markets for all agents under any stable mechanism.
Inducing process models from spatio-temporal scientific data [electronic resource]
Keywords: Aeronautics and Astronautics.

Research on automation of system modeling has focused on the construction of models from measured continuous data. However, the data were generally time series; thus, it has been difficult to induce models from spatio-temporal data. We offer a way to discover models that involve spatial dynamics in the form of partial differential equations. We review an earlier system for inductive process modeling and present our approaches to constructing models from spatio-temporal data. Although the system generally induces reasonable models, the parameter estimation component of the system may not find plausible parameter values for true models since the search space can be very large. In response, we introduce a technique for reducing the ranges of parameters and show the advantage of transferring the revised parameter ranges to other similar modeling tasks. In addition, we develop a method to improve execution time for inducing process models by reducing the size of the search space for model structures. The system takes more computation time for constructing models from spatio-temporal data than time series since execution time increases exponentially with the number of dimensions considered. To tackle this challenge, we integrate a third-level search component, which is based on inductive logic programming, into the modeling system. The component dynamically alters the structural search space to rule out large classes of models unlikely to explain a given data set. We present the details of the method and show how it benefits computation time.
Inequality and discrimination in historical and modern labor markets [electronic resource]
Keywords: Economics.

This dissertation uses two disparate settings to investigate sources of racial and ethnic inequality in labor markets. In the first setting we study the effect of race on economic outcomes using unique data from the first half of the twentieth century, a period in which skin color was explicitly coded in population censuses as "White, " "Black, " or "Mulatto." We construct a panel of siblings by digitizing and matching records across the 1910 and 1940 censuses and identifying all 12,000 African-American families in which enumerators classified some children as light-skinned ("Mulatto") and others as dark-skinned ("Black"). Siblings coded "Mulatto" when they were children (in 1910) earned similar wages as adults (in 1940) relative to their Black siblings. This within-family earnings difference is substantially lower than the Black-Mulatto earnings difference in the general population, suggesting that skin color in itself played only a small role in the racial earnings gap. To explore the role of the more social aspect that might be associated with being Black, we then focus on individuals who "passed for White, " an important social phenomenon at the time. To do so, we identify individuals coded "Mulatto" as children but "White" as adults. Passing for White meant that individuals changed their racial affiliation by changing their social ties, while skin color remained unchanged. We compare passers to their siblings who did not pass. Passing was associated with substantially higher earnings, suggesting that race in its social form could have significant consequences for economic outcomes. The second setting is an online employer-freelancer matching platform freelancer.com. I study the effect of a freelancer's country-of-origin on the employer's decision of whether to hire them. Having to rely on a relatively small number of characteristics, employers use the freelancer's country of origin and reputation scores to infer the expected service quality. I find that freelancers from developing countries are less likely to be hired when they have no individual reputation, and as individual reputation becomes better this country effect disappears. This setting also allows me to study how employers' experience in past hires affects their behavior in current hires. I show that following a good match with a freelancer, employers are more likely to hire freelancers from the good match's country. I discuss how these findings contributes to our understanding of matching, learning, and discrimination in online settings.
Inferring protein structure and dynamics from simulation and experiment [electronic resource]
Keywords: Biophysics.

An atomic-scale understanding of biological molecules remains a grand challenge for the physical and biological sciences. Here, I describe how molecular dynamics simulations can be used to directly connect to biophysical experiments. I first describe the use of Markov state models to connect simulated and measured protein kinetics, allowing studies of protein folding at the atomic scale. I then introduce the use of NMR measurements, such as chemical shifts and scalar couplings, for the evaluation of molecular dynamics force field quality. Finally, I propose a new statistical technique that can be used to combine both simulation and experiment into accurate models of conformational ensembles. Such models are shown to be free of force field bias and can be used to investigate the structural and equilibrium properties of biomolecules. In sum, the present work demonstrates how statistically-sound methods of inference can forge a direct connection between simulation and experiment.
Inhibitory projection neurons in olfactory information processing [electronic resource]
Keywords: Applied Physics.

Inhibition occurs throughout the nervous system and impacts diverse neuronal processes. In this dissertation, I focus on an inhibitory circuit motif in the Drosophila olfactory system, parallel inhibition, which differs from the classical feed-forward or feedback inhibition. The Drosophila excitatory and GABAergic inhibitory projection neurons (ePNs and iPNs) each receive input from antennal lobe glomeruli and send parallel output to the lateral horn, a higher-order brain center implicated in regulating innate olfactory behavior. By incorporating in vivo two-photon calcium imaging, advanced fly genetics and optogenetic methods to manipulate and record neuronal activity, we find that iPNs selectively suppress food-related odorant responses but spare signals from pheromone channel stimulation when using specific lateral horn neurons as an olfactory readout. Co-applying food odorant does not affect pheromone signal transmission, suggesting that the differential effects likely result from connection specificity of iPNs, rather than a generalized inhibitory tone. Calcium responses in the ePN axon terminals show no detectable suppression by iPNs, arguing against presynaptic inhibition as a primary mechanism. The parallel inhibition motif may provide specificity in inhibition to funnel specific olfactory information, such as food and pheromone, into distinct downstream circuits.