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Though this current study was initiated independently and was not a test laboratory for the taxonomic sub-committee's evaluative program, the problem outlined in this treatise was also designed in an effort to test certain characteristics of the actinomycetes of both a biochemical and morphological nature. This problem employed methods that might absolve or establish certain criteria for taxonomic use in the group of actinomycetes.

Comunidades microbianas possuem papéis importantes em processos que ocorrem em diversos ambientes, tais como solos, oceanos e o trato gastrointestinal dos seres humanos. Portanto, é de interesse a compreensão da estrutura e do funcionamento dessas comunidades. A estrutura dessas comunidades, em termos de organismos componentes, pode ser determinada com o uso do sequenciamento de nova geração em conjunto com as técnicas meta-ômicas e pela análise taxonômica das sequências obtidas com programas de classificação taxonômica. Se por um lado diversos programas estão disponíveis, por outro lado eles cometem erros, como a identificação parcial dos organismos presentes na amostra e a identificação de organismos que não estão presentes na amostra (os falsos positivos - FPs). Algumas abordagens foram propostas para a melhoria das classificações taxonômicas obtidas por esses programas com a redução desses FPs, porém elas abordam apenas um tipo de meta-ômica, a metagenômica. Neste trabalho, propomos uma nova abordagem através da integração de diferentes meta-ômicas - metagenômicas shotgun e de amplicons de 16S, e metatranscritômica. Exploramos os resultados de classificações de dados simulados e mocks para a extração de variáveis e desenvolvemos modelos de classificação para discriminação de predições de espécies de bactérias classificadas como corretas ou incorretas. Comparamos o desempenho dos resultados obtidos entre as meta-ômicas individuais e os obtidos através da integração observando o balanceamento entre a precisão e a sensibilidade. De acordo com as medidas calculadas com nossos conjuntos de dados, nossa abordagem demonstrou melhorias na classificação com a redução de FPs e aumentos para a medida F1, quando comparada com abordagens não integrativas, inclusive com o uso de métodos de combinação de classificadores. Para facilitar seu uso, desenvolvemos o Gunga, uma ferramenta que incorpora a abordagem desenvolvida em formato de pacote do R, com funcionalidades para a integração de dados de classificação taxonômica com diferentes meta-ômicas e a classificação das predições incorretas. / Microbial communities play important roles in processes that occur in diverse environments, such as soils, oceans, and the gastrointestinal tract of humans. Therefore, it is of interest to understand the structure and functioning of these communities. The structure of these communities, in terms of component organisms, can be determined by the use of the next generation sequencing in conjunction with the meta-omics techniques and by the taxonomic analysis of the sequences obtained with taxonomic classification programs. If on the one hand several programs are available, on the other hand they make mistakes, such as the partial identification of the organisms present in the sample and the identification of organisms that are not present in the sample (the false positives - FPs). Some approaches have been proposed to improve the taxonomic classifications obtained by these programs with the reduction of these FPs, but they address only one type of meta-omics, the metagenomics. In this work, we propose a new approach by integrating different meta-omics - shotgun and 16S amplicon metagenomics, and metatranscriptomics. We explored the classifications results of simulated data and mocks for variable extraction and developed classification models for discriminating predictions of bacterial species classified as correct or incorrect. We compared the performance of the results obtained between the individual meta-omics and the obtained through the integration observing the balance between precision and sensitivity. According to the measures calculated with our data sets, our approach has shown improvements in the classification with the reduction of the FPs and increases for the F1 measure, when compared to non-integrative approaches, including the use of classifiers combination methods. To facilitate its use, we developed the Gunga, a tool that incorporates the developed approach in R package format, with features for the integration of taxonomic classification data with different meta-omics and the classification of the incorrect predictions.

Seasonality estimates based on archaeological shellfish remains have been an important component of settlement pattern reconstruction. Investigations of this nature allow researchers to place prehistoric people on the landscape at points in space at different times of the year. Many of the previous seasonality studies, however, have focused on marine species from coastal sites, with little attention given to freshwater locales, especially ones in the Mississippi Delta. To address that disparity, this study examines freshwater mussel “season of capture” via analysis of stable oxygen isotope ratios in specimens recovered from two Late Woodland sites located along the Yazoo River, Mississippi. As freshwater mussel shells are composed of aragonite, a metastable form of calcium carbonate (CaCO3), they can suffer greatly from the impact of meteoric diagenesis. Because of this, samples must be evaluated for diagenesis prior to any geochemical analysis taking place. Archaeological shell samples were examined via thin-section petrography and scanning electron microscopy (SEM). Visual analysis indicated pristine aragonite microstructure and crystallography in all archaeological shell samples, and confirmed their suitability for isotope analysis. Vetted shells were then micromilled across accretionary growth bands, and analyzed for their oxygen isotope signatures. Isotope profiles were then interpreted for their individual “season of capture”, and oscillation patterns for 22 shell specimens indicated mussels were being collected in all four seasons. These data support the view that at least some portion of the human population at both sites engaged in shellfishing activities year-round, indicating sedentary populations at both locales. The shell assemblages were also investigated for the purpose of informing modern conservation efforts (i.e., “applied zooarchaeology”). Nearly 24,000 valves were analyzed taxonomically, yielding the presence of 37 species, of which 24 represented new river records for the Yazoo River. These data provide a valuable historical perspective, cataloging communities as they existed prior to extensive modern impacts, thus representing an ecological baseline to be compared with modern populations. Though modern data are extremely limited for the river, the study revealed it once supported a diverse mussel community containing numerous species currently considered rare, endangered, or extinct in Mississippi.

This thesis presents the Multiple Modelling Quality Evaluation Framework method (hereinafter MMQEF), which is a conceptual, methodological, and technological framework for evaluating quality issues in modelling languages and modelling elements by the application of a taxonomic analysis. It derives some analytic procedures that support the detection of quality issues in model-driven projects, such as the suitability of modelling languages, traces between abstraction levels, specification for model transformations, and integration between modelling proposals. MMQEF also suggests metrics to perform analytic procedures based on the classification obtained for the modelling languages and artifacts under evaluation. MMQEF uses a taxonomy that is extracted from the Zachman framework for Information Systems (Zachman, 1987; Sowa and Zachman, 1992), which proposed a visual language to classify elements that are part of an Information System (IS). These elements can be from organizational to technical artifacts. The visual language contains a bi-dimensional matrix for classifying IS elements (generally expressed as models) and a set of seven rules to perform the classification. As an evaluation method, MMQEF defines activities in order to derive quality analytics based on the classification applied on modelling languages and elements. The Zachman framework was chosen because it was one of the first and most precise proposals for a reference architecture for IS, which is recognized by important standards such as the ISO 42010 (612, 2011). This thesis presents the conceptual foundation of the evaluation framework, which is based on the definition of quality for model-driven engineering (MDE). The methodological and technological support of MMQEF is also described. Finally, some validations for MMQEF are reported. / Esta tesis presenta el método MMQEF (Multiple Modelling Quality Evaluation Framework), el cual es un marco de trabajo conceptual, metodológico y tecnológico para evaluar aspectos de calidad sobre lenguajes y elementos de modelado mediante la aplicación de análisis taxonómico. El método deriva procedimientos analíticos que soportan la detección de aspectos de calidad en proyectos model-driven tales como: idoneidad de lenguajes de modelado, trazabilidad entre niveles de abstracción, especificación de transformación de modelos, e integración de propuestas de modelado. MMQEF también sugiere métricas para ejecutar procedimientos analíticos basados en la clasificación obtenida para los lenguajes y artefactos de modelado bajo evaluación. MMQEF usa una taxonomía para Sistemas de Información basada en el framework Zachman (Zachman, 1987; Sowa and Zachman, 1992). Dicha taxonomía propone un lenguaje visual para clasificar elementos que hacen parte de un Sistema de Información. Los elementos pueden ser artefactos asociados a niveles desde organizacionales hasta técnicos. El lenguaje visual contiene una matriz bidimensional para clasificar elementos de Sistemas de Información, y un conjunto de siete reglas para ejecutar la clasificación. Como método de evaluación MMEQF define actividades para derivar analíticas de calidad basadas en la clasificación aplicada sobre lenguajes y elementos de modelado. El marco Zachman fue seleccionado debido a que éste fue una de las primeras y más precisas propuestas de arquitectura de referencia para Sistemas de Información, siendo ésto reconocido por destacados estándares como ISO 42010 (612, 2011). Esta tesis presenta los fundamentos conceptuales del método de evaluación basado en el análisis de la definición de calidad en la ingeniería dirigida por modelos (MDE). Posteriormente se describe el soporte metodológico y tecnológico de MMQEF, y finalmente se reportan validaciones. / Aquesta tesi presenta el mètode MMQEF (Multiple Modelling Quality Evaluation Framework), el qual és un marc de treball conceptual, metodològic i tecnològic per avaluar aspectes de qualitat sobre llenguatges i elements de modelatge mitjançant l'aplicació d'anàlisi taxonòmic. El mètode deriva procediments analítics que suporten la detecció d'aspectes de qualitat en projectes model-driven com ara: idoneïtat de llenguatges de modelatge, traçabilitat entre nivells d'abstracció, especificació de transformació de models, i integració de propostes de modelatge. MMQEF també suggereix mètriques per executar procediments analítics basats en la classificació obtinguda pels llenguatges i artefactes de mode-lat avaluats. MMQEF fa servir una taxonomia per a Sistemes d'Informació basada en el framework Zachman (Zachman, 1987; Sowa and Zachman, 1992). Aquesta taxonomia proposa un llenguatge visual per classificar elements que fan part d'un Sistema d'Informació. Els elements poden ser artefactes associats a nivells des organitzacionals fins tècnics. El llenguatge visual conté una matriu bidimensional per classificar elements de Sistemes d'Informació, i un conjunt de set regles per executar la classificació. Com a mètode d'avaluació MMEQF defineix activitats per derivar analítiques de qualitat basades en la classificació aplicada sobre llenguatges i elements de modelatge. El marc Zachman va ser seleccionat a causa de que aquest va ser una de les primeres i més precises propostes d'arquitectura de referència per a Sistemes d'Informació, sent això reconegut per destacats estàndards com ISO 42010 (612, 2011). Aquesta tesi presenta els fonaments conceptuals del mètode d'avaluació basat en l'anàlisi de la definició de qualitat en l'enginyeria dirigida per models (MDE). Posteriorment es descriu el suport metodològic i tecnològic de MMQEF, i finalment es reporten validacions. / Giraldo Velásquez, FD. (2017). A framework for evaluating the quality of modelling languages in MDE environments [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90628

Submitted by (edna.saturno@ufrpe.br) on 2016-06-29T15:52:10Z No. of bitstreams: 1 Nisia Karine C Vasconcelos Aragao.pdf: 3206270 bytes, checksum: e88b27fe7c6732478bbfce0177933804 (MD5) / Made available in DSpace on 2016-06-29T15:52:10Z (GMT). No. of bitstreams: 1 Nisia Karine C Vasconcelos Aragao.pdf: 3206270 bytes, checksum: e88b27fe7c6732478bbfce0177933804 (MD5) Previous issue date: 2011-02-07 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Cyanobacteria occur in aquatic ecosystems in Brazil, especially in the semiarid region, are mostly responsible for the formation of blooms, and thus the increase of this phenomenon has been increasing concern because of its potential to release toxins. These organisms show a great morphological variability that reflect the taxonomic difficulties. This study aimed to perform a taxonomic study of cyanobacteria in 19 reservoirs of Pernambuco state, describing their morphological characteristics, with illustrations and geographical distribution, and quantify the population. Were 42 samples in the period between February 2009 and January 2010. The samples for qualitative and quantitative analysis of cyanobacteria were collected with a van Dorn bottle at a single point in the environment near the shore and in the subsurface. For the taxonomic study, samples were analyzed by optical microscope and was used identification keys in articles and specialized books. The quantitative analysis was performed using an inverted microscope by the method of Utermöhl. The count was performed on random fields, and the results expressed as densities (cel.mL-1), and from these, certain biomass of cyanobacteria. There were 23 taxa, distributed in Chroococcales, and Oscillatoriales Nostocales these, 11 were cited for the first time for the state of Pernambuco. In Alagoinha, Carpina Ingazeira were recorded and the highest species richness (10 spp.). Cylindrospermopsis raciborskii (Woloszynska) Seenaya & Subba Raju and Geitlerinema amphibium (Agardh ex Gomont) Anagnostidis were the only taxa with more occurrence (84.21% and 68.42%, respectively). The highest cell density was about 5x1010 cel.mL-1, registered in Venturosa. 14 reservoirs in the densities of cyanobacteria were above 106 cel.mL-1, while the reservoirs Bitury, Jazigo, Pastora, Saco I and Santo Antonio dos Palmares densities were between 104 and 105cel.mL-1. Two Unas fortunate and had the highest biomass recorded by Merismopedia tenuissima Lemmermann (74x103 mg.L-1) and Microcystis sp. (42x103 mg.L-1), respectively. / As cianobactérias ocorrentes nos ecossistemas aquáticos do Brasil, principalmente na região semiárida, são em sua maioria, responsáveis pelas formações de florações, e desta forma, o aumento deste fenômeno tem sido cada vez mais preocupante devido ao seu potencial em liberar toxinas. Tais organismos apresentam grande variabilidade morfológica que refletem dificuldades aos estudos taxonômicos. O presente trabalho objetivou realizar um estudo taxonômico das cianobactérias em 19 reservatórios do estado de Pernambuco, descrevendo suas características morfológicas, apresentando ilustrações e distribuição geográfica, além de quantificar as populações. Foram realizadas 42 amostragens no período entre fevereiro de 2009 e janeiro de 2010. As amostras para análises quali-quantitativas das cianobactérias foram coletadas com garrafa de van Dorn, em um único ponto do ambiente, próximo à margem e na subsuperfície. Para o estudo taxonômico, as amostras foram analisadas em microscópio óptico e foram utilizadas chaves de identificação em artigos e livros especializados. A análise quantitativa foi realizada em microscópio invertido através do método de Utermöhl. A contagem foi procedida em campos aleatórios, e os resultados expressos em densidades (cel.mL-1), e a partir destas, determinadas as biomassas das cianobactérias. Foram identificados 23 táxons, distribuídos em Chroococcales, Oscillatoriales e Nostocales, destes, 11 foram citados pela primeira vez para o estado de Pernambuco. Em Alagoinha, Carpina e Ingazeira foram registradas as maiores riquezas de espécies (10 spp.). Cylindrospermopsis raciborskii (Woloszynska) Seenaya & Subba Raju e Geitlerinema amphibium (Agardh ex Gomont) Anagnostidis foram os únicos táxons com maior número de ocorrência (84.21% e 68.42%, respectivamente). A maior densidade celular foi cerca de 5x1010 cel.mL-1, registrada em Venturosa. Em 14 reservatórios estudados as densidades de cianobactérias estiveram acima de 106 cel.mL-1, enquanto que nos reservatórios Bitury, Jazigo, Pastora, Saco I e Santo Antonio dos Palmares as densidades estiveram entre 104 e 105cel.mL-1. Venturosa e Duas Unas apresentaram as maiores biomassas registradas por Merismopedia tenuissima Lemmermann (74x103 mg.L-1) e Microcystis sp. (42x103 mg.L-1), respectivamente.