VictorJuiz/thesis huggingface dataset:
Under doctors' eyes [electronic resource] : private life in Russian literature in the first half of the nineteenth century
Keywords: Slavic Languages and Literatures

My dissertation deals with the figure of the doctor in early Russian nineteenth-century prose, which manifests a shift in the way literature depicts human physicality and the characters' everyday life. My major source is 1820s-1840s prose, mostly published in the literary and cultural journals Biblioteka dlia Chtenia, Syn Otechestva, and others. My sources reflect the impressive expansion in Russian literature and medicine in the first quarter of the nineteenth century. Using documentary and literary sources, I demonstrate that the artistic representation of physicians in Romantic and Realist prose contributes to the introduction of previously unknown themes into literature: medical perspectives on physical suffering, the private everyday lives of ordinary people, and even the mystical view of other worlds. The combination of medical and mystical discourses in the vocabulary of real doctors in the first half of the nineteenth century gave them the authority to judge human bodies, lives, and, they believed, souls: they seemed to observe from inside and outside at the same time. By including a doctor among their characters, fiction writers thus could use a powerful instrument that let them introduce new topics. As I show, through the mid nineteenth century, the fictional doctors situated at the margin of literary plots performed the role of an important textual device: they served as go-betweens among other characters, mediating, connecting or splitting them. They affected the relationship between characters, the plot's trajectory, and the readers' perception. The situation shifts in mid century; with the gradual separation of doctor from his instrumental function, this character moves to the center of the plot and loses his structural power.
Understanding and predicting RNA structure [electronic resource]
Keywords: Applied Physics

RNA is an important biological macromolecule that carries out a variety of roles in the cell. To function, RNA needs to fold into precise three-dimensional structures. Different physical forces like entropy, base-pairing and stacking interactions, tertiary contacts and electrostatics affect this folding process. In the first part of this thesis, we focus on nucleic acid electrostatics; RNA molecules have negatively charged backbones that require counterions to neutralize charge-repulsion and facilitate folding. We discuss the ion conditions necessary for a riboswitch (gene-regulating RNA found on 5' or 3' ends of messenger RNA) folding, studied how the flexibility of single stranded DNA is affected by the presence of different amounts of counterions and present a benchmark experimental dataset that can be used for direct comparison to electrostatic theories. The second part of the thesis deals with computational and analysis tools developed to model and understand nucleic acid systems with the ultimate goal of being able to predict RNA structure. Since RNA typically folds hierarchically, we devised a general hierarchical sampling protocol that naturally explores RNA three-dimensional conformational space efficiently and can be used in concert with any force field, such as an RNA knowledgebased potential that we also discuss in this thesis. Additionally, we examined a clustering method that can assist analysis of structural models. Lastly, we applied our modeling techniques to study simple two-way RNA junctions with all-atom representation, and probed the modeled effects of sterics, chain connectivity and sequence on dynamic RNA behavior.
Understanding Current Trends and Outcomes in Generic Drug Patent Litigation: An Empirical Investigation
Keywords: ANDA
Pharmaceuticals
Hatch-Waxman
Paragraph IV Certifications
Text
Thesis

This thesis examines the role of patent litigation in the generic drug approval process.
Generic drug companies wishing to enter a brand-name drug market early may challenge
a brand-name’s patents by filing for an Abbreviated New Drug Application (ANDA) with a
paragraph IV certification. While anecdotal evidence on the characteristics of paragraph IV
lawsuits abound, there has yet to be a comprehensive study on these unique cases. Leveraging
a new dataset of district court cases, this thesis presents an empirical investigation
into some of the current trends in generic drug litigation from January 1, 2006 to August 1,
2011. Using several basic econometric specifications, I study the determinants of settlement
and other outcomes in these cases, observing that factors such as declaratory judgment, the
size of a pioneer company, the level of patent protection, and remaining exclusivity may be
significant factors.
Understanding spacecraft electrical anomalies [electronic resource] : theory and experiments characterizing hypervelocity impact plasma dynamics
Keywords: Aeronautics and Astronautics

Small meteoroids, with masses less than a microgram, are common within the solar system and routinely impact spacecraft. In Earth orbit, human-made debris also presents a risk of impact. This thesis provides the first characterization of the threat of electrical damage from these hypervelocity impacts. When an impactor encounters a spacecraft (typically at 60 km/s for meteoroids or 10 km/s for debris), its kinetic energy is converted over a very short timescale into energy of vaporization and ionization, resulting in a small, dense plasma. This plasma can produce radio frequency (RF) emission, causing electrical anomalies within the spacecraft. The behavior of hypervelocity impact plasmas was studied through ground-based experiments and a corresponding plasma expansion model to interpret the data. The experiments were conducted using a Van de Graaff dust accelerator at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany. Impacts of iron projectiles ranging from 0.1 fg to 10 pg at speeds of up to 70 km/s were studied using a variety of target materials. Novel plasma sensors were designed and built to characterize the plasma expansion from impacts on these targets under a range of surface charging conditions representative of space environment effects. Impact plasmas associated with bare metal targets as well as spacecraft materials were studied. The expansion behavior of the impact plasma was found to depend strongly on the surface charge of the target. From a correlation of experimental measurements with theoretical models, the dependence of plasma composition and temperature on target material, impact speed, and surface charge was analyzed. This work includes three major results. First, the initial temperature of the impact plasma is at least an order of magnitude lower than previously reported, providing conditions more favorable for sustained RF emission. Second, the composition of impact plasmas from glass targets, unlike that of impact plasmas from tungsten, has low dependence on impact speed, indicating a charge production mechanism that is significant down to orbital debris speeds. Finally, negative ion formation has a strong dependence on target material. These new results can inform the design and operation of satellites in order to prevent impact-related electrical anomalies. Since spacecraft charging is strongly dependent on orientation and surface material, deleterious electrical effects of hypervelocity impacts can be mitigated through design and operational practices that account for the influence of spacecraft geometry and the space environment on the behavior of impact plasmas.
Understanding the interaction of organic functional groups with single-walled carbon nanotubes (SWNTS) for solution processable electronics [electronic resource]
Keywords: Chemical Engineering

Single-walled carbon nanotubes (SWNTs) have shown impressive electrical properties but are synthesized in mixtures of metallic and semiconducting tubes that prove difficult to separate. However, we have recently discovered that different organic functional groups, when confined to surfaces, can efficiently separate SWNTs. Amine surfaces yield semiconducting (sc) nanotube networks, while aromatic surfaces yield metallic (met) networks. It is proposed that aromatics interact preferably with met-CNTs via [pi]-[pi] stacking, but the effect on the amine surface is more difficult to interpret. Explanations for this interaction include charge polarization, electrostatic forces, or the influence of defect sites. In my presentation, I present a series of experiments used to elucidate the exact nature of the amine / sc-SWNT interaction. The electrostatic influence on the amine-SWNT interaction was studied by altering the pH of the environment around the amine. Subsequently, by altering the density of the amine on the surface, the ideal structure of an amine surface to optimize the SWNT sorting was under analysis. Finally, alternate functional groups were considered to further optimize the sorting and remove the need of amine silanes, which were typically difficult to handle. Once the interaction is better understood, it can be controlled and used to optimize conditions for high quality nanotube network transistors and sensors.
Understanding the mechanis of mammalian damage tolerance proteins in suppressing damage-specific mutagenesis [electronic resource]
Keywords: Chemical and Systems Biology.

Post-replication repair (PRR) pathways play important roles in restarting stalled replication forks and regulating mutagenesis. In yeast, Rad5-mediated damage avoidance and Rad18-mediated translesion synthesis (TLS) are two forms of PRR. Two Rad5-related proteins, SHPRH and HLTF, have been identified in mammalian cells, but their specific roles in PRR are unclear. Here, we show that HLTF and SHPRH suppress mutagenesis in a damage-specific manner, preventing mutations induced by UV and MMS, respectively. Following UV, HLTF enhances PCNA monoubiquitination and recruitment of TLS polymerase eta, while also inhibiting SHPRH function. In contrast, MMS promotes the degradation of HLTF and the interactions of SHPRH with Rad18 and polymerase kappa. Our data not only suggest that cells differentially utilize HLTF and SHPRH for different forms of DNA damage, but also, surprisingly, that HLTF and SHPRH may coordinate the two main branches of PRR to choose the proper bypass mechanism for minimizing mutagenesis. Though the degradation of HLTF is required for the SHPRH-Rad18 interaction in MMS-damaged cells, knockdown of HLTF is not sufficient to induce SHPRH-Rad18 binding in undamaged cells. Thus, an unidentified factor, in addition to HLTF degradation, is required to fully activate SHPRH and Rad18 upon MMS damage. We have noticed that Rad18 is deubiquitinated after MMS treatment, and that this de-ubiquitination is correlated with the degree of Rad18-SHPRH interaction. Moreover, we show that promoting the ubiquitination of Rad18 has an inverse effect on the interaction with SHPRH both in vitro and in cells. Surprisingly, though, the ubiquitinated Rad18 shows a stronger self-interaction than the wild-type Rad18, opposite from the SHPRH binding results. As the zinc-finger motif of Rad18 has been previously shown to bind ubiquitin, this may be a logical mechanism to control the switch between Rad18 dimerization and its interaction with other proteins. Interestingly, ubiquitinated Rad18 appears to be inactive, not only from loss of its ability to interact with SHPRH, but also through the inability to form damage foci and suppress MMS-induced mutagenesis. Altogether, our data reveal a unique regulation of Rad18 through self-ubiquitination and dimerization. In summary, our studies have revealed a number of new mechanistic insights into the post-replication repair pathways in human cells, including the interesting conclusion that protein degradation, deubiquitination, and other key cell processes may be controlled in a DNA damage-specific manner.
Unified tracking and recognition with rotation-invariant fast features [electronic resource]
Keywords: Electrical Engineering

Mobile Augmented Reality (MAR) systems overlay virtual content on a live video stream of real-world content. These systems rely on content recognition and tracking to generate this overlay. Typically, these two components use disjoint image processing pipelines, which complicates and slows the system. We propose a new keypoint detector and local feature descriptor that enables the unification of tracking and recognition. This Rotation-Invariant Fast Feature (RIFF) is fast enough to track in real-time on a mobile device, and accurate enough for large-scale image recognition. We propose a tracking algorithm that efficiently matches RIFF descriptors between consecutive frames. This tracker operates with state-of-the-art accuracy at 30 fps on a 1 GHz mobile phone. The same descriptors used for tracking can be matched against a database for image recognition without the need for a separate descriptor pipeline. We evaluate the retrieval performance of RIFF on a challenging, real-world database of 1 million images. By using the same features for largescale image retrieval and video tracking, we have shown that these two tasks can be unified, providing particular benefit to MAR applications.
Using conflicting information and holistic judgments in diagnostic computer models [electronic resource]
Keywords: Management Science and Engineering

Diagnostic computer models use observable variables, referred to as features, to generate predictions. Experts often identify feature observations as the input for diagnostic computer models. In addition to these feature observations, I propose obtaining those experts' holistic judgments about the diagnosis to improve the overall system diagnostic performance. I develop what I call the Holistic Feature Integration (HFI) framework, which allows a decision maker to integrate the holistic judgments of multiple experts along with their (possibly conflicting) feature observations into an overall diagnosis. To resolve expert disagreement I need to model the accuracy of each expert; because the HFI framework only requires one such assessment for each expert, it can be easily implemented in practice. In those situations where the experts can be calibrated on test cases, I develop a statistical procedure for estimating accuracy parameters. Through a case study of medical diagnosis with thyroid sonograms, I demonstrate that the HFI framework substantially improves prediction quality by incorporating experts' holistic judgments. Some of this benefit can be obtained by a simple mixture model of the diagnostic computer model with the expert judgments, especially when there is only one expert. In my case study, the holistic judgments alone in the HFI framework are more beneficial than the diagnostic computer model alone. However, using both holistic judgments and the diagnostic computer model yields even better performance in the HFI framework. I see increasing marginal benefit as additional experts were included. I also develop a new technique for eliciting experts' holistic judgments, which are valuable in the HFI framework. I introduce a new class of strictly proper scoring rules parameterized by a simple tradeoff significant to the decision maker and the risk attitude of the expert. I prove that my new scoring rule incentivizes experts to report their risk attitudes and assessments honestly.
A vacuum encapsulated resonator for humidity measurement [electronic resource]
Keywords: Electrical Engineering

Relative humidity sensing is everywhere. Current applications include home appliances, semiconductor manufacturing, air conditioning, medical, automotive, and meteorology. Various technologies are being used to measure relative humidity, including capacitive, resistive and resonant gravimetric sensors. In resonant gravimetric sensors, the quality factor is limited by air damping because the resonator must be exposed to the ambient. The sensor presented in this work decouples the ambient of the resonator from the monitored ambient. Therefore, the sensor achieves a high quality factor (~10,000). This study uses surface resistance of silicon dioxide and a charge-biased, microshell encapsulated, single-anchored double-ended tuning fork resonator (DETF) to measure relative humidity. The vacuum encapsulated resonator is charge biased and electrically connected to a metal bond pad on the surface silicon dioxide, which is exposed to the ambient. The surface resistance of the silicon dioxide decreases as relative humidity increases. Smaller surface resistance leads to faster decay from the resonator. This variation in decay is monitored by measuring the shift in the resonant frequency. As the charge decays, the resonant frequency increases because of the electrostatic spring softening. The relative humidity is determined by the time constant of the decay, or the initial slope. The time constant and the initial slope depend on the relative humidity. In summary, variation in surface resistance causes changes in the charge decay characteristic of the resonator and ultimately, the resonant frequency of the resonator. The sensing principal of this new sensor is expanded upon. The variation of surface resistance with respect to relative humidity and temperature is discussed. Additionally, analytical models are derived for the steady state and transient surface resistance. A charge biased resonator is compared to a voltage bias resonator. The charge biased resonator is more linear than the voltage biased resonator. However, the charge biased resonator has internal feedthrough. The noise sources in the sensor are explored. Equations are developed to convert Allan deviation to limit of detection of relative humidity. Scaling laws are also derived to improve the limit of detection of the sensor. To characterize the sensor, a custom experimental test setup, including environmental chamber and oscillator board, was built. The effect of relative humidity and temperature on the surface resistance was measured. The limit of detection was 1.3·10^-3 % RH when slope fitting is used. Additionally, the limit of detection was 1.4·10^-4 % RH when exponential fitting is used. The rise time of the sensor was one third of the rise time of the commercial capacitive sensor. The measured hysteresis of the sensor was less than 0.15% relative humidity. This is significantly less than the hysteresis of the commercial capacitive sensor. In conclusion, a new relative humidity sensor was developed.
Validation of non-invasive standing arterial stiffness measurements using ballistocardriography and photoplethysmography [electronic resource]
Keywords: Bioengineering.

More than 76 million Americans have hypertension, or high blood pressure, which can shorten life by 10 15 years if left untreated. Hypertension increases the risk of developing cardiovascular diseases (CVD) such as stroke, heart attack, congestive heart failure, or kidney failure that are often debilitating and impact quality of life. Prevention is the key to minimize CVD risk and increase longevity, but accurate prognosis of a future disease is difficult. Elevated blood pressure (BP) is generally the first sign of risk, but measuring pressure alone does not provide insight to where in the body problems may exist. Therefore, other screening tests are needed to more specifically isolate the underlying cause, which would improve the selection process of prescribing medications, or diet and exercise changes. And similar to BP measurements, such hypertensive screening tests may need to be performed at home to improve accuracy, since doctor's visits often trigger physiological responses that falsely elevate and lower BP. To address these concerns this work describes the design and validation of a home based noninvasive system (a bathroom scale) to measure aortic pulse wave velocity (PWV), to assess arterial stiffness, which is a clinical risk factor for certain CV diseases. The purpose of this work was four-fold: to develop a home monitoring device with simple user operation; to develop biomechanical theories as to why forces in the aortic arch can be sensed synchronously at the feet; clinically validate the biomechanical theory; and to demonstrate potential clinical utility of standing PWV measurements for trending and prognosis. The PWV scale is comprised of two different sensing technologies, ballistocardiography and photoplethysmography, which are embedded in the scale to measure pulse arrival times in the aortic arch and the foot—simply by standing on the scale. Using this system, PWV can be routinely determined in less than 30-seconds—significantly faster than commercial systems using trained operators. To validate this PWV system, a novel biomechanical theory was developed called Central Aortic Forces (CAF) to explain how the cardiovascular forces inside the body can be synchronously sensed outside the body. The computational models accurately predicted the amplitude of forces in the aortic arch (2-3 Newtons at rest), which were empirically confirmed in a clinical study; the empirical results agreed within 10% of the theory. To demonstrate trending abilities, a longitudinal PWV study was also performed over a four month duration, with results highly correlated to the applanation methods. Finally, an age study was conducted to characterize arterial aging, which matched well (p< 0.01) in slope and intercept major clinical trials published in the literature using applanation PWV (clinical gold standard). Examples are given on how such a system may improve prognosis to detect early vascular aging in young adults, otherwise masked in standard blood pressure measurements.
Virtual imposters [electronic resource] : responses to avatars that do not look like their controllers
Keywords: Communication

The norm that individuals should truthfully portray themselves to others is frequently violated in computer-mediated interactions. Even in the early days of the internet, scholars documented crimes in cyberspace where individuals would take on the identities of others to commit virtual crimes. Today, crime reports warn of the ease of identity disguise and the associated dangers. For example, sexual predators use computer code names to disguise their real identities and pretend to be the same age as their juvenile victims, and perpetrators use created email addresses to send sexually explicit or derogatory messages under the cover of other individuals or companies. Additionally, sometimes individuals utilize identity disguise while behaving anti-socially, even if this behavior wouldn't be categorized as a crime. Bullying others using a created social media identity, or aggressing against other players in an online game using an avatar that disguises one's true identity would be examples of such anti-social behavior. Does the fact that these individuals disguised their identities while committing these acts make their actions even more despicable? This research examines that question.