VictorJuiz/thesis huggingface dataset:
The role of cuticular hydrocarbons in the behavioral ecology of the red harvester ant, Pogonomyrmex barbatus [electronic resource]
Keywords: Biology.

Sociality has evolved several times in different species over thousands of years. There are no social organisms more interesting than social insects. Social insects form colonies composed of hundreds to millions of individuals known as nestmates. Workers in social insect colonies discriminate between nestmates and non-nestmates in a process called nestmate recognition. Nestmate recognition is based on differences in cuticular hydrocarbons, recognition cues found on the cuticle of social insects. In this dissertation, I investigate how the behavioral ecology of the red harvester ant, Pogonomyrmex barbatus, influences nestmate recognition behavior and the cuticular hydrocarbon profiles of workers. In P. barbatus, nestmate recognition behavior is task-dependent and not based on differences in cuticular hydrocarbon profiles. Cuticular hydrocarbons change according to the task of workers, and hydrocarbons are better predictors of a workers task than of its colony of origin. Task-specific hydrocarbon profiles reflect the influence of task environment on worker profiles. Task-specific profiles influence both worker and colony behavior. Because knowing the task of a nestmate is more important than smelling more like you nestmates, our findings fit well with the behavioral ecology of this species. Placing nestmate recognition in the proper ecological context will help gain a better understanding of nestmate recognition behavior for all social insects.
The role of M18BP1 in the propagation of centromeric chromatin [electronic resource]
Keywords: Biochemistry

Accurate chromosome segregation is essential for the viability of all organisms. During mitosis, each chromosome attaches to microtubules of the mitotic spindle through a chromosomal microtubule-binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant centromere protein A (CENP-A). Understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segregation. The assembly of CENP-A into centromeric chromatin requires the activities of the Mis18 complex and the CENP-A chaperone HJURP, however how these proteins are recruited to centromeric chromatin is not known. In this work, we use an in vitro CENP-A assembly assay in Xenopus extract to examine the role of Mis18BP1, a component of the Mis18 complex, in CENP-A nucleosome assembly. We show that depletion of CENP-C prevents M18BP1 recruitment to centromeres and inhibits CENP-A chromatin assembly. We find that the recruitment of M18BP1 to centromeres occurs through a direct interaction with conserved domains in CENP-C. These findings suggest that the factors required for CENP-A assembly are recruited by the existing centromeric chromatin to ensure the assembly of new CENP-A nucleosomes at the site of the current centromere. In a separate set of experiments, we use an in vitro degradation assay in Xenopus extract to identify substrates of the Anaphase Promoting Complex or Cyclosome (APC/C) whose degradation regulates CENP-A assembly. We screen a collection of 20 centromere proteins and find that only M18BP1 is an APC/C substrate. We show that depletion of the APC/C from extract or mutation of the conserved destruction motifs prevented the degradation of M18BP1 in vitro. We also show that M18BP1 is degraded in vivo in a manner consistent with APC/C substrates. We find that the expression of a non-degradable M18BP1 mutant does not alter CENP-A assembly over the course of a single cell cycle, suggesting that there are multiple mechanisms in place to ensure the stable propagation of centromeric chromatin. In summary, we have identified a mechanism by which M18BP1 is recruited to centromeres to promote new CENP-A assembly. In addition, we have also demonstrated a novel role for the APC/C in regulating the activity of M18BP1. This work has furthered our understanding of how centromere chromatin is propagated and suggests a possible model in which CENP-C recruits M18BP1 to centromeres to promote new CENP-A assembly and that upon completion, M18BP1 is degraded by the APC/C to restrict CENP-A nucleosome assembly to a specific window in the cell cycle.
The rule of law [electronic resource] : a philosophical investigation of law and liberty
Keywords: Philosophy

This dissertation assesses justifications of the political ideal of the rule of law in virtue of its contribution to individual liberty. The main arguments supporting these justifications are investigated and shown to be effective only with respect to a narrow conception of liberty. A different conception of individual liberty is then developed, which, it is argued, plays an important role in many social contexts, particularly those involving personal relations, and with respect to which the rule of law is often sub-optimal. The aim of this work is to provide an argument based on the value of individual liberty for non-legalistic means of social organization and regulation.
A rule-based dialog management system for integration of unmanned aerial systems into the national airspace system [electronic resource]
Keywords: Aeronautics and Astronautics

Unmanned Aerial Systems (UAS) are one of the fastest growing segments of the aviation industry with the U.S. UAS market projected to nearly double by 2020. UAS have been used extensively overseas in military roles, but there are many civilian missions that could be performed by UAS operating domestically such as law enforcement, homeland security, wildfire suppression, air-freight, and aerial-survey. However, despite these potential markets, UAS are currently banned from flying within the U.S. National Airspace System (NAS) by federal regulation. This ban is due primarily to reasons related to operational safety of flight, among them the inability of UAS to respond to and engage in the spoken Air Traffic Control (ATC) instructions that govern the use of the NAS. In this thesis an Autonomous Communication System (AutoComm System) and Dialog Management System (DMS) are developed that enables UAS to autonomously communicate with ATC using spoken natural language speech. The AutoComm System uses probabilistic techniques to automatically learn the rules of ATC communications and models the dialog as a Bayesian network. In order to implement the AutoComm System several novel contributions were developed. These include: a novel scheme for part of speech tagging for ATC dialog; a central sliding window algorithm for determining the most probable part-of-speech tagging in the presence of noise and transcription errors in the sentence being labeled; and a robust hybrid method for enabling a DMS to automatically learn rule-based dialog trees while accounting for non-deterministic dialog and variance in accepted phraseology. The approach discussed in this thesis is formulated to run on the potentially limited computing power found on smaller UAS while still enabling them to speak with the very high accuracy necessary for operation in the NAS. The results of flying the AutoComm System through simulated and real-world ATC scenarios show that the AutoComm System can correctly respond to ATC communications with an accuracy of 88.5%. This lags the observed 98.9% accuracy rate of human pilots. However, this performance gap is caused almost entirely by scenarios where ATC failed to properly self-identify their transmissions as required by the FAA. It is possible for the AutoComm System developed in this thesis to approach a human-equivalent level of performance with more rigorous ATC adherence to FAA phraseology and a more extensive training corpus. Further, in its current form, the AutoComm System can outperform human pilots in a few key areas such as the ability to not interrupt inappropriately and proper phrasing of messages. These results show that it is possible to develop and implement a high-accuracy system that enables UAS to autonomously communicate with ATC in order to better integrate UAS into the NAS for a wide variety of missions.
The rules of the few [electronic resource] : institutions and the struggle for political order in classical Greek oligarchies
Keywords: Classics

This dissertation presents an analysis of the rise and fall of oligarchy (Greek: oligarchia) as a constitutional form in the Greek Classical period. Confining myself to the period when the actual term "oligarchia" begins to be used, I show (Chapter Three) that it emerged as a reaction to democracy (demokratia) on the part of the wealthy elite. Contrary to accounts that treat oligarchy as the default form of human political organization, this study shows that Greek oligarchia was from its inception unpopular and actively resisted by the mass of the free adult male citizenry, the demos. But neither was oligarchy forced upon the people through raw coercion. In my alternative account, I show (Chapter Four) that oligarchic stability can be explained on institutional grounds, through an examination of the specifically oligarchic political and social institutions that successful oligarchs used to maintain equality of power and privilege among themselves while keeping the demos divided and weak through a combination of targeted repression, co-optation, and clientelism. In categorizing and analyzing these practices I adapt theoretical frameworks developed in the "new institutionalism" in social science, which takes a particular view of the origin and function of institutions in society. By introducing to Classics ideas from comparative Political Science I am able to shed new light on an important but understudied topic of Classical Greek political history.
Salary incentives and teacher quality [electronic resource] : the effect of a compensation increase on teacher recruitment and retention in the San Francisco Unified School District
Keywords: Education.

Research consistently shows that teacher quality is a powerful determinant of student achievement gains. It has also been shown that urban school districts serving low-performing, low-income, and/or minority students have a less-qualified teacher workforce. This disparity can be traced back to both teacher recruitment and retention; urban school districts have a harder time recruiting teachers, and their retention rates are much lower than surrounding districts in the labor market. In order to improve teacher recruitment and retention, an increasingly popular intervention for urban school districts is raising teacher salaries, often in targeted areas. While there is evidence to suggest that teachers respond to compensation in deciding to become or remain teachers, there is little empirical research studying the effectiveness of compensation increases in recruiting or retaining high-quality teachers in high-need schools and districts. To address this gap, this dissertation assesses the effect of a salary increase on teacher recruitment and retention in the San Francisco Unified School District (SFUSD). Specifically, I examine the effect of the Quality Teacher and Education Act of 2008 (QTEA), which introduced an overall salary increase (
Schwann cell migration and myelination in zebrafish peripheral nerves [electronic resource]
Keywords: Developmental Biology.

The nervous system connects cells throughout the body to coordinate actions and transmit signals. Critical to the nervous system are the neurons that extend axons to their targets and the glial cells that interact with these axons. Oligodendrocytes in the central nervous system and Schwann cells in the peripheral nervous system wrap axons to make the myelin sheath. Myelin is critical for enhancing the speed of action potentials as well as providing support to axons. Myelin was a critical adaptation that has allowed vertebrates to increase in size, precision of movement, and complexity. Insults to myelin cause devastating diseases, and a better understanding of the normal development of myelinating glia is necessary for improving treatment of human neuropathies. In this dissertation I investigate both well-known and novel signaling pathways and their roles in Schwann cell migration and myelination in zebrafish peripheral nerves. Before making myelin, Schwann cells must migrate along and cover the surface of a bundle of axons. Here, I demonstrate that Neuregulin 1 type III (Nrg 1 type III) is required in neurons to signal through ErbB receptors in Schwann cells for Schwann cell migration along the posterior lateral line nerve, a mechanosensory nerve. Further, ectopic expression of this signal in all neurons is sufficient to attract peripheral Schwann cells into the spinal cord. There appears to be distinct regulation of Schwann cell migration in different nerves of the peripheral nervous system, as migration of Schwann cells in motor nerves requires ErbB receptors but not the Nrg 1 type III ligand. Nrg1 type III does, however, control myelination in both sensory and motor nerves. Schwann cell migration is not only important to properly localize Schwann cells, but also to localize the lateral line nerve itself, which begins in the epidermis but then transitions across a basement membrane to the subepidermal space. As they migrate, Schwann cells degrade the basement membrane beneath the skin, which allows the nerve to transition out of the epidermis, and then rebuild the basement membrane after the nerve has been repositioned and protected from the disorganization that otherwise would take place if it remained in the epidermis. Finally, through analysis of a mutation that was found in a forward genetic screen for genes essential in myelination, I also identify a novel regulator of Schwann cell myelination. Together this work elucidates new roles of known genes in Schwann cell and nerve development and also identifies a novel gene required for peripheral myelination.
Search for new superconductors and novel physical properties in thin films and interfaces [electronic resource]
Keywords: Applied Physics

This dissertation describes our unique experimental attempts to search for new high temperature superconductors. In this thesis, we focus on three different materials systems (graphite-sulfur composites, copper (Cu) / copper monoxide (CuO) bilayers and doped tungsten oxides), all of which have been reported in the literature to exhibit trace very high temperature superconductivity. Without simply trying to reproduce the reported results by exactly following the synthesis procedure in the original reports, however, we first consider what theoretical insights might have relevance to possible superconductivity in these systems. Suitable model systems based on such theoretical considerations are then designed, synthesized, and examined in order to study the physical properties in a carefully controlled way. For the case of graphite-sulfur composites, based on experimental convenience (selenium is easier to deposit than sulfur) as well as theoretical considerations, the interface of selenium and epitaxial graphene thin films was selected as the model system. Clean graphene thin films were successfully synthesized, and then a Se layer was deposited on the graphene by pulsed laser deposition in a carefully controlled way. On the basis of photoemission spectroscopy and transport measurements, however, no superconductivity was found, and it is suggested that the Se overlayer merely increases disorder for the electrons in graphene. For the case of Cu/CuO, based on transport measurements no superconductivity was detected in our experiments using clean bilayer interfaces between copper (Cu) and copper monoxide (CuO). However, by careful magnetotransport measurements and theoretical considerations, this model system was found to exhibit a novel interface phenomenon (in which antiferromagnetic spin correlations are induced into the Cu layer due to the adjacent antiferromagnetic CuO) that has not been observed previously. We term this phenomenon an "antiferromagnetic proximity effect". For the case of doped tungsten oxides, we first synthesized single-layer potassium tungsten oxide thin films and characterized the physical properties as a function of the temperatures used in a vacuum annealing process, which presumably controls the carrier density. The films show a number of interesting superconducting properties, including a strange curvature of upper critical fields as a function of temperature and an anomalously high transition temperature in one sample. Motivated by these observations and theoretical considerations, we also synthesized bilayer structures in an attempt to enhance superconducting transition temperature. In some cases, it was found that such bilayers in fact have significantly higher transition temperatures than the monolayer films.
The search for zero neutrino double beta decay in 136-Xe with EXO-200 [electronic resource]
Keywords: Physics

This analysis reports a search for the neutrinoless double decay (0[nu][beta][beta]) of 136-Xe with the EXO-200 detector. 0[nu][beta][beta] is a hypothetical nuclear process which only occurs if neutrinos are so called Majorana particles, which are there own anti-particles, as opposed to Dirac particles which have separate anti-particles. The search for 0[nu][beta][beta] is currently the most experimentally viable technique to address the Dirac or Majorana nature of neutrinos. The EXO-200 experiment is a liquid xenon time projection cham- ber operating 655 meters underground at the Waste Isolation Pilot Plant (WIPP) with 200 kg of xenon enriched to 80.6% in the isotope 136-Xe. A total of one event in the one sigma region of interest is observed with background of (1.5 ± .1) × 10^−3 counts/keV/kg/yr. This places a limit on the 0[nu][beta][beta] half-life of 136Xe is of 1.59×10^25.
Searches for natural supersymmetry in Hadronic final states with heavy flavor at ATLAS [electronic resource]
Keywords: Physics

This thesis presents the hadronic-channel supersymmetric searches for direct sbottom and gluino-mediated sbottom and stop production performed on 4.71 integrated femtobarns of 7 TeV center-of-mass energy data collected by the ATLAS detector at the Large Hadron Collider. These signatures are characterized by final states with multiple b-tagged jets and missing transverse energy and the analysis strategy is chosen accordingly. Particular emphasis is placed on the utilization of the simplified models approach in signal characterization, optimization, and interpretation of results. No significant excess is observed resulting in limits set at 95% confidence level. Relative to the previous versions of the analyses, this iteration represents a several-fold increase in sensitivity to the new physics signatures considered. This is largely due to the use of three b-tag signal regions as well as signal regions based on initial state radiation.
Searching for genomic events contributing to brain expansion in the human lineage [electronic resource]
Keywords: Neurosciences.

Understanding the genetic changes responsible for the evolution of human traits is a major goal of biology. One of the most distinctive human traits is the dramatic expansion of the forebrain that has occurred over the last six million years. Whole genome sequencing projects have identified millions of genomic differences that separate human and chimpanzee (Chimpanzee Sequencing and Analysis Consortium, 2005). However, connecting particular mutations to evolved human traits such as brain size remains challenging due to the vast number of mutations that have accumulated (Varki and Altheide 2005; Sikela, 2006). Nonetheless, recent evolutionary genetic studies are identifying the most prevalent types of genetic mechanisms contributing to evolved traits in natural populations, and studies of comparative and molecular development are providing an emerging picture for mechanisms by which human brain expansion could have occurred. By combining insights from evolutionary genetics and developmental neurobiology, this thesis aims to identify genomic differences that are particularly likely to have contributed to the evolutionary expansion of the human brain. First, this thesis provides evidence for the role of cis-regulatory mutations in the evolution of natural populations of stickleback fish. Next, this thesis describes a genomic screen we conducted identifying 510 deletions likely to remove cis-regulatory enhancers from the human genome. One of these deletions removes a developmental ventral forebrain enhancer near the tumor suppressor gene GADD45g, the loss of which may release a brake on cell division in particular regions of the brain during neurogenesis. A second deletion removes a developmental dorsolateral neocortex enhancer demonstrating the specificity by which evolution can affect particular regions of the brain. Finally, this thesis identifies a human enhancer near the gene BDNF that drives expression in the nail bed of the digit tips and the stomach, and could influence the distribution and function of mechanoreceptors.
Searching for structured interactions in and between datasets [electronic resource]
Keywords: Statistics

This dissertation considers two problems related to finding structured interactions in and between datasets. The first problem is to estimate interaction terms in a regression where the interaction coefficients are assumed to have a particular low-rank structure. The second problem is to identify relationships between datasets using extensions of recent work on regularized canonical correlation analysis. We propose methodologies and computational strategies based on regularized regression techniques that are well-suited to modern datasets where the number of features may be much larger than the number of observations. The final chapter provides a theoretical result on the performance of a low-rank interaction estimation procedure that motivates its use in large-scale problems.
Self-calibrating on-chip interconnects [electronic resource]
Keywords: Electrical Engineering

This dissertation covers the conception, design and evaluation of the self-calibrating interconnect, a new type of capacitively-driven on-chip interconnect that uses feedback and charge-pumps to automatically neutralize receiver offsets caused by device mismatch. It can operate with extremely low signal swings, which minimizes energy, without compromising reliability. A 2 mm long prototype built in a 90 nm low-power CMOS process consumes 77 fJ/bit of energy at 1.5 GHz, and sustains a bit-error rate (BER) below 10^-30 with just 32 mV of swing. We also present a new way to reduce the noise level of comparators by adjusting the size of the precharge devices. For a given energy budget, we demonstrate that by upsizing the precharge devices we can reduce the input-referred thermal noise of the popular StrongARM latch by up to 30% over previously known sizing techniques.