VictorJuiz/thesis huggingface dataset:
Timing of discrete musical air-gestures [electronic resource]
Keywords: Music.

Motion sensing technologies enable musical interfaces where a performer can control sound by moving their body ``in the air, '' without manipulating or contacting a physical object. These interfaces work well when the movement and resulting sound are smooth and continuous. However, it has proven difficult to design a system which triggers discrete sounds with precision that feels natural to the performer and allows them to play complex rhythmic music. This thesis presents a study into "air-drumming" gestures. Participants performed drumming-like gestures in time to simple recorded rhythmic drum sounds. These movements are recorded and then examined to look for aspects of the movement that correspond to the timing of the drum sounds. The goal of this research is to understand what we do with our bodies when we gesture in the air to trigger a sound, with the hope that the results can be used to design more accurate and responsive air-gesture-controlled instruments. It is assumed that when we gesture in the air to generate a sound, we do something with our bodies to create a sensation of a moment in time and that we intend the sound to occur at this time. Eight movement features are extracted from the movement data, and it is hypothesized that one or more of these movement features correspond to this body sensation. Four of the movement features are based on tracking the location of the hand and wrist. Hits are moments where the hand or wrist suddenly change direction at the end of a strike gesture, and a novel algorithm for detecting hits is presented. And acceleration peaks are peaks in the magnitude acceleration of the hand or wrist as they suddenly decelerate at the end of the gesture . The remaining four movement features are based on the angles of the elbow and wrist joints. Extrema in joint angle are detected, as are sudden peaks in angular acceleration of the joint. The timing of these movement events is analyzed with respect to the timing of the drum sounds. Analysis is also performed comparing how the timing of movement events changes when speed at which notes are repeated changes. In general it is found that features based on acceleration peaks occur earlier, closer to the audio event, and with less noise, and that these features vary less with respect to note speed. It is also shown that timing differences between hand and wrist features can be used to study individual differences and group performers according to movement style.
To stake a claim [electronic resource] : the making of rabbinic agricultural spaces in the Roman contryside
Keywords: Religious Studies.

This dissertation argues that the prescriptions for Jewish practice and the boundaries of Jewish space in the Late Antique countryside may be considered a call by the rabbis for the transformation of a landscape filled with many different neighbors, from non-rabbinic Jews to Roman conquerors. The rabbinic sources set forth the vision for an idealized Jewish landscape filled with rabbinic Jews who manage their estates in accordance with God's will. In modern scholarship, agricultural rituals and spaces in the Mishnah and the Tosefta are often set aside in favor of consideration of urban life and society. By interrogating the importance of these spaces and their rituals, this dissertation shows that the authors of Jewish literature adopt Roman ideals of rural life but subvert those ideals to impose a specifically Jewish vernacular upon the landscape. The commitment to Biblical laws of agriculture, even in light of profound changes to the landscape wrought by Roman imperial domination, serves to challenge that domination through the assertion of distinctly Jewish agricultural spaces. In this dissertation, the halakhic reasoning and argumentation found in early rabbinic literature is analyzed through textual, literary, and spatial analysis to reveal the cultural and spatial ideals of the creators of these texts. These legal texts describe a world filled with outsiders, from Roman conquerors to Jews with different interpretations of scripture and practice: the laws of Jewish farming serve to differentiate normative Jewish practice and social structures from those others. It is the spatial aspect of agricultural life, from its fences to its regimented rows of crops that serve to physically and visually mark a Jewish space as distinct. This dissertation offers tools for spatial analysis of legal texts in rabbinic Judaism specifically and imperial spaces more broadly.
To Starve a Fever or Feed a Cold? How Food Intake Modifies an Immune Response
Keywords:  Department of Biology
diet restriction
AMPs
gene expression profiles
immunity
Drosophila
anorexia
Biology
Thesis

In many organisms, including humans and mice, diet-restriction is one of the most common immune responses. In mice, long-term diet restriction has been shown to decrease the age-associated reduction in immune function, effectively increasing the capacity of the immune response. Despite this, long-term diet restriction decreased mouse survival from Influenza infections. In Drosophila, anorexia can alter both host tolerance and resistance in response to microbial infection, and can be beneficial or detrimental to host survival rates, depending upon the pathogen. This suggests that diet has the ability to modulate expression of genes of the innate immune system. Although anorexia is a commonly-induced immune response, its mechanism of action is unclear. Further research into the mechanism and effects of infection-induced diet restriction on the immune system is necessary because previous research has focused mostly on long-term diet restriction. We seek to determine how infection-induced anorexia, and subsequently diet restriction, alters gene expression profiles in order to modulate an immune response.
The effectiveness of an immune response is shaped by the genes that are activated to fight the infection and their degree of activation at different times during the infection. Diet restricted flies that are infected with Listeria monocytogenes show decreased survival when compared to non-diet restricted flies. We hypothesized that diet-restriction could affect survival
of infected flies by changing the dynamics of the immune response.
Recent work from our lab has shown that many immune responsive genes, including antimicrobial peptide (AMP) genes, are expressed at levels directly dependent upon microbe number in the fly. Analyzing complete gene expression profiles for immune genes allows us to more precisely describe changes in gene induction by measuring not only maximal induction levels but the rate of gene induction. Here we show that for several AMP genes, diet restriction causes gene induction at a lower microbe concentration, thereby increasing the sensitivity of the fly to infection and reducing survival. We conclude that diet is an important factor during infection that can cause shifts in the expression of many immune genes, a fact that was
previously unnoticed due to the way in which gene expression was measured.
Topics in matrix inference [electronic resource]
Keywords: Statistics.

Two topics in matrix inference are considered: matrix denoising and matrix organization. In matrix denoising, one attempts to recover an unknown matrix $X$ from a single noisy observation $Y=X+Z$, where $Z$ is a noise matrix with independent, identically distributed entries. It is shown that random matrix theory delivers simple, convincing answers to a range of fundamental questions, such as the minimax risk of matrix denoising by singular value soft thresholding, the location of the optimal singular value threshold and the shape of the optimal singular value shrinker. In matrix organization, one attempts to recover the latent structure of the row set of the column set of a matrix, such that matrix entries can be reliably predicted from close-by entries. We propose a self-contained framework for matrix organization and subsequent sampling, approximation and compression.
Topics in quantum information and string theory [electronic resource]
Keywords: Physics.

There are many aspects of the Ads/CFT correspondence that end up having rather direct applications to condensed matter physics. While some of these applications are rather straightforward and expected from parallel results in the condensed matter literature, some of the results are rather interesting and new, and sometimes derive from entirely unexpected aspects of the gravitational theory proposed to be dual to the condensed matter eld theory. In this thesis, I will explore several such examples that I have had the honor to study. This thesis is based on the papers [75], [2], [3] and [4] written with Xi Dong, Sarah Harrison, Shamit Kachru, Eva Silverstein, Subir Sachdev, and Gonzalo Torroba, or some subset thereof. It should not be cited without also referencing those papers.
Toxoplasma gondii reduces innate fear to predator urine by altering the brain of its rodent host [electronic resource]
Keywords: Neuroscience.

The protozoan parasite Toxoplasma gondii is known to dampen fear responses to cat urine in infected rodent hosts. Such manipulation is likely advantageous to the parasite in the wild, possibly increasing predation by the definitive host of Toxoplasma, the cat. Here we report that in infected rats, Toxoplasma modifies limbic structures responsive to appetitive, sexual stimuli, converting ensembles of neural activity in regions of sexual attraction to respond to cat urine. Understanding how Toxoplasma is inspiring these behavioral changes in the host brain requires knowledge of the precise anatomical location of the parasite in the host brain. For this reason, we used a genetically-engineered Toxoplasma in a mouse that allowed us to track, at single-neuron resolution, the location of the parasite and the location of any neuron it invaded or tried to invade ("Toxoplasma-interacted neurons"). We report high individual variation in loss-of-aversion to cat urine in infected mice and that numbers of Toxoplasma-interacted neurons in the total brain did not explain this variation. However, variation in number of Toxoplasma-interacted neurons in the corpus striatum predicted response to the dopamine D2 receptor antagonist haloperidol, providing evidence that Toxoplasma is interacting with dopamine in the infected host brain.
Trafficking and axodendritic transcytosis of BDNF in hippocampal neurons [electronic resource]
Keywords: Chemistry.

Brain derived neurotrophic factor (BDNF) plays a key role in the growth, development and maintenance of the central and peripheral nervous systems. Exogenous BDNF activates its membrane receptors at the axon terminal, and subsequently sends regulation signals to the cell body. To understand how BDNF signal propagates in neurons, it is important to follow the trafficking of BDNF after it is internalized at the axon terminal. Here we labeled BDNF with bright, photostable quantum dot (QD-BDNF) and followed the axonal transport of QD-BDNF in real time in hippocampal neurons. We showed that QD-BDNF was able to bind BDNF receptors and activate downstream signaling pathways. When QD-BDNF was applied to the distal axons of hippocampal neurons, it was observed to be actively transported toward the cell body at an average speed of 1.11 ± 0.05 [mu] m/s. A closer examination revealed that QD-BDNF was transported by both discrete endosomes and multivesicular body-like structures. Our results showed that QD-BDNF could be used to track the movement of exogenous BDNF in neurons over long distances and to study the signaling organelles that contain BDNF. Surprisingly, not all QD-BDNF ended up in lysosomes in the cell body for degradation. Instead, some BDNF was transported to dendrites possibly for signaling purposes. BDNF transcytosis challenges the model that neurotrophic action is terminated by rapid degradation of the neurotrophin molecule after delivery of the trophic signal. It is postulated that BDNF as well as other neurotrophic factors might be recycled and targeted to dendrites as endogenous neurotrophins for the purpose of releasing. To develop a comprehensive understanding of the molecular mechanisms of BDNF transcytosis, it is important to follow BDNF retrograde transport in axons toward the cell body, axodendritic translocation, properties of the BDNF endosomes transcytosed into dendrites, and study whether these processes are activity dependent. Using QD for monitoring BDNF transcytosis through neurons requires that the labeling method does not perturb the biological function of BDNF. Meanwhile, to observe the trafficking of QD-BDNF internalized from the axon terminal, it is necessary to polarize the growth of axons into a fluidic isolated environment and separate from cell body and dendrites. With modifications and coating with neurite guidance molecules in the channels, the microfluidic platform can be improved to fit the purpose of observing BDNF transcytosis in a more controlled environment. By combining fluorescent labeled BDNF, microfluidic neuron culture platform and dual-color imaging, we found that (1) After BDNF internalized from axon terminal transport retrogradely into soma, most goes to degradation but some enters dendrites and ends up at different locations with its receptor TrkB; (2) Cargos transcytosed from axon terminal can be directed into dendrites and transport in similar manner as endogenous protein cargos.
Transmit array concepts for improved safety in magnetic resonance imaging [electronic resource]
Keywords: Electrical Engineering.

Magnetic resonance imaging (MRI) is a powerful medical imaging modality that can generate high-resolution diagnostic images with excellent soft-tissue contrast. Unlike x-ray and CT, MRI does not use any ionizing radiation and consequently is considered a safe imaging modality for most patients. However, for patients with implanted medical devices, MRI presents significant safety hazards. The transmit radiofrequency (RF) fields used in MRI can induce current in elongated conductors, such as neurostimulator and cardiac pacemaker leads, potentially causing dangerous heating of surrounding tissues. This safety hazard prevents many patients with implanted medical devices from receiving MRI exams, and it also presents challenges for MRI-guided interventional procedures. Much of the RF safety work to date has focused on modifying implanted devices to be safer in the MRI environment. This dissertation presents a different approach to the RF safety problem. Instead of modifying devices for the MRI environment, this work explores how transmit array technology can be used to make the MRI environment itself safer for existing devices by controlling the induced RF current levels that are responsible for heating. A novel toroidal transmit-receive coil for safely visualizing conductive interventional guidewires is presented. This coil transforms conductive guidewires and catheters into controllable elements of a transmit array and allows device visualization using only milliwatts of transmit power. Successful device visualization is demonstrated at 1.5T and 3T. Fluoroptic temperature probe measurements indicate that the low power levels required for device visualization are orders of magnitude below the levels that induce heating in a tissue-mimicking phantom. It is then shown that an array of independently-controllable transmit coils (parallel transmit) can be used to induce minimal RF current in elongated conductors, thereby reducing the RF heating risk, while still allowing visualization of the surrounding volume. Feasibility is demonstrated on a four-channel parallel transmit system at 1.5T, and the current reduction performance is quantified with current sensor measurements and image-based current estimates. Fluoroptic temperature probe measurements confirm that the reduction in current results in the reduction of wire tip heating.
Trapping ultracold gases near cryogenic materials with rapid reconfigurability [electronic resource]
Keywords: Applied Physics.

We demonstrate an atom chip trapping system that allows the placement and high-resolution imaging of ultracold atoms within microns of any 100 µm-thin, UHV-compatible material, while also allowing sample exchange with minimal experimental downtime. The sample is not connected to the atom chip, allowing rapid exchange without perturbing the atom chip or laser cooling apparatus. Exchange of the sample and retrapping of atoms has been performed within a week turnaround, limited only by chamber baking. Moreover, the decoupling of sample and atom chip provides the ability to independently tune the sample temperature and its position with respect to the trapped ultracold gas, which itself may remain in the focus of a high-resolution imaging system. As a first demonstration of this system, we have confined a 200-nK cloud of 10,000 rubidium 87 atoms within 100 µm of a gold-mirrored 100-µm-thick silicon substrate. The substrate was cooled to 35 K without use of a heat shield, while the atom chip, 100 µm away, remained at room temperature. Atoms may be imaged and retrapped every 16 s, allowing rapid data collection.
Turbulent wake interaction LES and aeroacoustic predictions [electronic resource]
Keywords: Aeronautics and Astronautics.

As increased scrutiny and regulation is placed on the environmental impact of air transportation, tools and methods which enable design of lower footprint next generation aircraft become critical. One of the major environmental obstacles to air travel is noise impact on communities during departure and arrival. Jet noise, dominant during take off, has been studied extensively and as the field has matured, attention has turned to airframe noise - a significant fraction of the total noise signature during approach to landing. As a result, the development of accurate prediction tools for noise generated by complex airframe systems is necessary. Since direct simulation of aerodynamic noise, particularly when realistic geometries and Reynolds numbers are considered, is prohibitively expensive, hybrid methods have become the de-facto standard. In such methods, the near flow field is computed by a given Computational Fluid Dynamics (CFD) simulation while the far-field noise is predicted by a separate acoustic analogy. In this dissertation, we first demonstrate the advantages and challenges of Large Eddy Simulation for the prediction of the near flow field using a simple tandem cylinder geometry. This configuration has been identified by the computational aeroacoustic (CAA) community as a benchmark problem, representative of airframe components such as landing gear struts and hydraulic lines. Since realistic engineering problems typically occur in high Reynolds number flow regimes, forced transition trips are often employed in experiments which are used as benchmarks for simulation results. This was the case in the tandem cylinder problem, and it was found that a naively applied numerical transition trip resulted in significant extraneous noise generation. In the second part of this work, we develop an improved numerical trip which reduces the acoustic impact on the far field. The bulk of this work concentrates on the prediction of noise generated by a model airfoil-cylinder interaction problem. The objective of this portion is twofold: first, common industry practice in the noise prediction of complicated geometries is to exclude the effect of volume noise source terms ("quadrupole sources") due to the prohibitive cost of including them. This is based on the commonly held assumption that their effect is minimal compared to that of surface fluctuation source terms ("dipole sources") in low Mach number conditions. The goal here is to determine if this is still a valid assumption when turbulent flow interaction between two or more bodies is present. Additionally, if volume sources are necessary for accurate prediction, our goal is to examine when they may be important to include (based on Mach number and variation in geometry) and what the volume sources physically represent. The second objective is to compare the results of three separate acoustic prediction methods to explore possible generation of erroneous numerical noise when using common porous-surface Ffowcs Williams & Hawkings (FWH) integration predictions.
Ultrafast photoemission studies of the topological insulator Bi2Se3 [electronic resource]
Keywords: Physics.

Most macroscopic properties of a material (electrical, thermal, and optical) can be understood on the basis of its band structure and the dynamical behavior of its electrons. However, resolving electron dynamics directly is difficult using conventional techniques because the underlying interactions typically occur on a femtosecond timescale. Ultrafast photoemission spectroscopy is an experimental technique which can probe electronic band structure with femtosecond time resolution. This dissertation presents work using this technique to study dynamic phenomena in the topological insulator Bi2Se3, a fascinating material due to the coexistence of its insulating bulk and metallic surface electronic structures. It will demonstrate three types of novel measurements that can be performed with ultrafast photoemission spectroscopy which are unattainable by other methods: (1) By performing two-photon photoemission (2PPE) spectroscopy, it is possible to resolve unoccupied band structure above the Fermi level. In Bi2Se3 this reveals a second, topologically protected surface state. (2) Time-resolved 2PPE (tr2PPE) is used to record real-time "movies" of the electron relaxation which follows optical excitation. This allows for the identification of intra- and inter- band electron scattering pathways in the material. Temperature-dependent tr2PPE measurements are performed on the conduction band to help understand the role of electron-phonon coupling. A model of fundamental electron-phonon scattering processes is implemented to describe the results. (3) In a time- and angle- resolved photoemission spectroscopy (trARPES) experiment, intense optical excitation is used to drive coherent motion of A1g optical phonon modes in Bi2Se3. These modes lead to periodic binding energy shifts in the bulk conduction band and surface state. A slight red-shift of the phonon frequency is observed in the surface state, which is used to deduce a softening of the phonon due to the abrupt termination of the crystal at its surface.
Ultrafast X-ray tomography of breathing mode excitations in semiconductor nanocrystals [electronic resource]
Keywords: Chemistry.

Femtosecond x-ray scattering techniques are used to directly visualize ultrafast strains and changes in atomic-scale structure in nanoscale CdSe and CdS spheres and rods. We construct a tomographic view of photo-induced lattice displacements and nanoscale shape changes by measuring multiple lattice reflections. Large amplitude tensile strains at the percent level are observed, associated with a rapid expansion followed by contraction along the nanocrystal radial direction. These morphological changes occur simultaneously with the first steps in the melting transition on hundreds of femtosecond time-scales. This work represents the first direct, real-time probe of the dynamics of these strains in few-nanometer scale particles, with bulk thermodynamic elastic constants remaining sufficient to describe their response despite the extreme excitation conditions.