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

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.

Keywords: Biology.
Advisor: Gordon Deborah (Film producer) primary advisor. Thesis advisor
Dirzo Rodolfo advisor. Thesis advisor
Greene Michael
Watt Ward B. advisor. Thesis advisor
The role of M18BP1 in the propagation of centromeric chromatin [electronic resource]

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.

Keywords: Biochemistry
Advisor: Straight Aaron
Herschlag Daniel advisor. Thesis advisor
Theriot Julie advisor. Thesis advisor
The role of the frontal eye field in gating and maintaining object signals in short-term memory [electronic resource]

Spatial attention is known to gate entry into short-term memory, and some evidence suggests that spatial signals may also play a role in binding features or protecting object representations during memory maintenance. To examine a potential role for spatial signals in maintaining object short-term memory, the activity of neurons in the Frontal Eye Field (FEF) of macaque monkeys was recorded during an object-based delayed match-to-sample (DMS) task. In this task monkeys were trained to remember an object identity over a brief delay, irrespective of the locations of the sample or target presentation. FEF neurons exhibited visual, delay, and target period activity, including selectivity for sample location and target location. Delay period activity represented the sample location throughout the delay, despite the irrelevance of spatial information for successful task completion. Furthermore, neurons continued to encode sample position in a variant of the task in which the matching stimulus never appeared in their response field. FEF neurons also exhibited target-position-dependent anticipatory activity immediately prior to target onset, suggesting that the monkeys can predict target position within blocks. These results show that FEF neurons maintain spatial information during short-term memory, even when that information is irrelevant for task performance. Despite the robust delay period activity we observed in FEF during the DMS task, we found little further evidence to support the theory that this activity contributes to object memory maintenance. Noise correlations were present between pairs of simultaneously recorded FEF and IT neurons during the sample and early delay periods, but did not persist into the second half of the delay period, despite the continued elevation of firing rates in both regions throughout the delay. The most direct method of assessing the contribution of the FEF delay period activity observed during the DMS task to object memory was the pharmacological elimination of that activity and evaluation of the impact on task performance. Inactivation of FEF with muscimol produced spatially localized deficits on the memory guided saccade task, but did not selectively impair object memory performance for sample stimuli appearing in the mnemonic scotoma.

Advisor: Moore Tirin
Knudsen Eric I. advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Wagner Anthony David advisor. Thesis advisor
The rule of law [electronic resource] : a philosophical investigation of law and liberty

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.

Keywords: Philosophy
Advisor: Cohen Joshua
Hussain Nadeem J. Z. advisor. Thesis advisor
Satz Debra advisor. Thesis advisor
A rule-based dialog management system for integration of unmanned aerial systems into the national airspace system [electronic resource]

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.

Keywords: Aeronautics and Astronautics
Advisor: Alonso Juan José
Erzberger Heinz advisor. Thesis advisor
Pavone Marco
The rules of the few [electronic resource] : institutions and the struggle for political order in classical Greek oligarchies

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.

Keywords: Classics
Advisor: Ober Josiah primary advisor. Thesis advisor
Morris Ian
Nightingale Andrea Wilson advisor. Thesis advisor
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

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 (

Keywords: Education.
Advisor: Loeb Susanna primary advisor. Thesis advisor
McFarland Daniel (Daniel A.) advisor. Thesis advisor
Plank David N. (David Nathan)
Schwann cell migration and myelination in zebrafish peripheral nerves [electronic resource]

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.

Keywords: Developmental Biology.
Advisor: Talbot William
Barres Ben
Kingsley David M. (David Mark) advisor. Thesis advisor
Krasnow Mark
Search for new superconductors and novel physical properties in thin films and interfaces [electronic resource]

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.

Keywords: Applied Physics
Advisor: Beasley Malcolm primary advisor. Thesis advisor
Kapitulnik Aharon primary advisor. Thesis advisor
Geballe Theodore H. advisor. Thesis advisor
The search for zero neutrino double beta decay in 136-Xe with EXO-200 [electronic resource]

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.

Keywords: Physics
Advisor: Gratta Giorgio primary advisor. Thesis advisor
Blandford Roger D. advisor. Thesis advisor
Cabrera Blas advisor. Thesis advisor
Searches for natural supersymmetry in Hadronic final states with heavy flavor at ATLAS [electronic resource]

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.

Keywords: Physics
Advisor: Su Dong
Macfarlane David
Peskin Michael Edward