On Clustering and Evaluation of Narrow Domain Short-Test Corpora

En este trabajo de tesis doctoral se investiga el problema del agrupamiento de conjuntos especiales de documentos llamados textos cortos de dominios restringidos. Para llevar a cabo esta tarea, se han analizados diversos corpora y métodos de agrupamiento. Mas aún, se han introducido algunas medidas de evaluación de corpus, técnicas de selección de términos y medidas para la validez de agrupamiento con la finalidad de estudiar los siguientes problemas: -Determinar la relativa dificultad de un corpus para ser agrupado y estudiar algunas de sus características como longitud de los textos, amplitud del dominio, estilometría, desequilibrio de clases y estructura. -Contribuir en el estado del arte sobre el agrupamiento de corpora compuesto de textos cortos de dominios restringidos El trabajo de investigación que se ha llevado a cabo se encuentra parcialmente enfocado en el "agrupamiento de textos cortos". Este tema se considera relevante dado el modo actual y futuro en que las personas tienden a usar un "lenguaje reducido" constituidos por textos cortos (por ejemplo, blogs, snippets, noticias y generación de mensajes de textos como el correo electrónico y el chat). Adicionalmente, se estudia la amplitud del dominio de corpora. En este sentido, un corpus puede ser considerado como restringido o amplio si el grado de traslape de vocabulario es alto o bajo, respectivamente. En la tarea de categorización, es bastante complejo lidiar con corpora de dominio restringido tales como artículos científicos, reportes técnicos, patentes, etc. El objetivo principal de este trabajo consiste en estudiar las posibles estrategias para tratar con los siguientes dos problemas: a) las bajas frecuencias de los términos del vocabulario en textos cortos, y b) el alto traslape de vocabulario asociado a dominios restringidos. Si bien, cada uno de los problemas anteriores es un reto suficientemente alto, cuando se trata con textos cortos de dominios restringidos, la complejidad del problema se incrPinto Avendaño, DE. (2008). On Clustering and Evaluation of Narrow Domain Short-Test Corpora [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/2641Palanci

Multiomic Hypotheses Underlying Behavioral Manipulation of Camponotus floridanus ants by Ophiocordyceps camponoti-floridani fungi

Parasitic manipulation of host behavior lies at the intersection of disease, animal behavior, and coevolutionary processes. In many of these interactions, the underpinning biology is brought into sharp focus as they are obligate relationships, under strong selection to bring about specific changes in host behavior that determine if the parasite will transmit or die. However, experimental and molecular techniques to understand these interactions are still developing and identification of the mechanisms of manipulation is a primary goal in the field. As such, we investigated host-parasite interactions between Camponotus floridanus (Florida carpenter ant) and Ophiocordyceps camponoti-floridani (Florida zombie ant fungus) from multiple molecular perspectives. By combining genome, gene expression, protein-interaction, and metabolite data from multiple experiments, we analyzed parasitic manipulation in a multiomic framework. We considered the most robust hypotheses of how parasitic manipulation occurs to be those supported by multiomic data. Two major avenues of parasitic influence on host behavior appear to be direct interference with neurotransmission and dysregulation of core cellular pathways that affect behaviors. For example, heightened expression of host dopamine synthesis enzyme genes, predicted binding of secreted parasite proteins to dopamine receptors, and reduced dopamine precursor abundance during displays of manipulated behavior all correlate the dysregulation of dopaminergic processes to manipulation phenotypes. We discuss numerous possible hypotheses, many with multiomic support, some without. We predict that modification of host behavior is a complex and multi-layered process that integrates multiple mechanisms we propose here

Mechanisms of Nestmate Recognition Cue Production in the European Honey Bee, Apis mellifera.

Social insects are some of the world’s most ecologically successful animal groups, and their complex societies are considered one of the pinnacles of animal evolution. Since these organisms live in colonies composed of many individuals and stored resources, they are a target for intruders, such as parasites, predators and conspecific robbers. Therefore, many social insect species have evolved mechanisms for nest defense, including nestmate recognition, where guarding individuals at the entrance of the colony use cues on incoming individuals to determine whether they are nestmates or intruders. Although nestmate recognition is incredibly important for maintaining colony integrity and fitness, the behavioral and physiological mechanisms that underlie this behavior remain unknown for most species. My dissertation work focused on elucidating the mechanisms of colony-specific nestmate recognition cue production in the economically important honey bee. Previously, it was assumed that the colony-specific chemical signatures used for nestmate recognition are acquired by individual workers through the homogenization of cuticular chemicals, called cuticular hydrocarbons (CHCs), via interactions with other colony members or hive materials. Although this mechanism seems to be used by few ant species, my dissertation work shows that in honey bee colonies, the CHC profiles of workers develop through a sequence of stereotypic qualitative and quantitative chemical transitions driven by environmentally-sensitive biosynthetic pathways, which result in the final mature colony-specific nestmate recognition cue in forager bees, independent of their genetic background (Chapter 2). These data suggest that, rather than acquiring cues via CHC homogenization mechanisms, honey bees intrinsically produce colony specific CHC profiles via environmentally-sensitive mechanisms. To further understand how hive-specific environmental factors might define the colony-level specificity of the nestmate recognition cue, independent of the bee’s genetics, I subsequently show that colony-specific gut microbial communities contribute to the development and perception of nestmate recognition cues in honey bee colonies (Chapter 3). My work highlights the link between gut microbial community and cue production in honey bees, but also remarkably suggests a link between gut microbial community and cue perception, implying a pleiotropic role of the gut microbiome in this recognition behavior. Overall, my dissertation work supports the model that colony-specific gut microbial communities drive the intrinsic production of colony-specific nestmate recognition cues across foragers of the same colony, as well as the ability to identify colony-specific cues in guard bees

An Effort Prediction Framework for Software Defect Correction

Developers apply changes and updates to software systems to adapt to emerging environments and address new requirements. In turn, these changes introduce additional software defects, usually caused by our inability to comprehend the full scope of the modi ed code. As a result, software practitioners have developed tools to aid in the detection and prediction of imminent software defects, in addition to the eort required to correct them. Although software development eort prediction has been in use for many years, research into defect-correction eort prediction is relatively new. The increasing complexity, integration and ubiquitous nature of current software systems has sparked renewed interest in this eld. Eort prediction now plays a critical role in the planning activities of managers. Accurate predictions help corporations budget, plan and distribute available resources eectively and e ciently. In particular, early defect-correction eort predictions could be used by testers to set schedules, and by managers to plan costs and provide earlier feedback to customers about future releases. In this work, we address the problem of predicting the eort needed to resolve a software defect. More speci cally, our study is concerned with defects or issues that are reported on an Issue Tracking System or any other defect repository. Current approaches use one prediction method or technique to produce eort predictions. This approach usually suers from the weaknesses of the chosen prediction method, and consequently the accuracy of the predictions are aected. To address this problem, we present a composite prediction framework. Rather than using one prediction approach for all defects, we propose the use of multiple integrated methods which complement the weaknesses of one another. Our framework is divided into two sub-categories, Similarity-Score Dependent and Similarity-Score Independent. The Similarity-Score Dependent method utilizes the power of Case-Based Reasoning, also known as Instance-Based Reasoning, to compute predictions. It relies on matching target issues to similar historical cases, then combines their known eort for an informed estimate. On the other hand, the Similarity-Score Independent method makes use of other defect-related information with some statistical manipulation to produce the required estimate. To measure similarity between defects, some method of distance calculation must be used. In some cases, this method might produce misleading results due to observed inconsistencies in history, and the fact that current similarity-scoring techniques cannot account for all the variability in the data. In this case, the Similarity-Score Independent method can be used to estimate the eort, where the eect of such inconsistencies can be reduced. We have performed a number of experimental studies on the proposed framework to assess the eectiveness of the presented techniques. We extracted the data sets from an operational Issue Tracking System in order to test the validity of the model on real project data. These studies involved the development of multiple tools in both the Java programming language and PHP, each for a certain stage of data analysis and manipulation. The results show that our proposed approach produces signi cant improvements when compared to current methods

Role of biological clocks in ant behavioral plasticity and parasitic manipulation of ant behavior

Living organisms exhibit daily rhythms as a way to anticipate predictable fluctuations in their environment. Such daily rhythmicity is the phenotypic outcome of oscillating genes and proteins, driven by an endogenous biological clock. Clock-controlled behavioral rhythms are inherently flexible since their phase, amplitude, and period can change throughout an animal\u27s life hallmarked by changes in so-called chronotype. How this inherent plasticity of clock-controlled rhythms is linked to plasticity of behavior is still an open question in biology. Characterizing the various mechanistic links between plasticity of the animal clock and behavioral state will not only shed light on the molecular underpinnings of animal behavior, but also lead to novel chronotherapeutic interventions to treat human disorders that affect the behavioral state such as bipolar disorder and Alzheimer\u27s. While clock-controlled behavioral plasticity is crucial to a species\u27 survival and fitness, it has also been hypothesized to be a target for manipulative parasites that need to induce timely changes in host behavior to facilitate growth and transmission. Using the Florida carpenter ant Camponotus floridanus as a model, this dissertation attempts to bridge some of the existing knowledge gaps in sociobiology, chronobiology, and parasitology. In the first chapter, we have identified a mechanistic link between plasticity of the C. floridanus clock and its behavioral state. Subsequently, in chapter two, we have provided evidence showing that Ophiocordyceps camponoti-floridani, a fungal parasite that induces timely changes in C. floridanus behavior targets the pre-existing links between host behavior and chronobiological plasticity we have found in chapter one. In the final chapter, we characterize how the clock of O. camponoti-floridani functionally differs from the clock of a non-manipulating fungal parasite, Beauveria bassiana, and put forward a regulatory mechanism via which the manipulating parasite\u27s clock might be inducing timely changes in host behavior

Against remediation

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