Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: David A. Kendrick. Vita. Includes bibliographical references.

Os dados do Plano Nacional de Controle de Resíduos e Contaminantes (PNCRC) foram utilizados para identificação de áreas geográficas de ocorrência preferencial de níveis baixos de metais pesados em bovinos abatidos, no período 2002 a 2010. Critérios de inclusão definiram o período 2006 a 2010 como base para identificação de fatores de risco, ao que a distribuição de contaminações registradas pelo PNCRC é apresentada em mapas temáticos individuais para cada ano. Avaliou- se o efeito de risco das concentrações reduzidas (detecções) na ocorrência de extrapolação aos limites legais máximos (violações) no estado de São Paulo. Foram estabelecidos modelos de tendência para detecções de metais pesados nas unidades federativas e no conjunto nacional. As categorias de resultados de cada bovino amostrado (resultado negativo, detecção, violação) foram utilizadas para dividir o banco de dados em áreas de ocorrência e não ocorrência mutuamente exclusiva de arsênio (detecções) e também de chumbo e cádmio (detecções+ violações) no estado de São Paulo. Gerou-se um estudo ecológico considerando cada município como unidade de análise, utilizando-se as categorias de resultados do PNCRC como variável \"doença\" e como fator de exposição as categorias (mediana ou tercis) dos fatores produtivos do Levantamento das Unidades de Produção Agropecuária, fornecidos pela Secretaria de Agricultura do estado de São Paulo. A modelagem de regressão logística múltipla permitiu identificar variáveis que aumentam o risco de contaminações no contexto ecológico, demonstrando ser possível integrar dados do PNCRC com outras bases de dados públicas. Os fatores identificados devem ser utilizados por novos estudos com delineamento propício a avaliar o efeito de risco em propriedades individuais antes que se proponham ações preventivas específicas aos animais e seus locais de criação. Propõe-se a implantação de um sistema de vigilância epidemiológica para o PNCRC como maneira de definir metodologia objetiva para acompanhar seus resultados juntamente com o do monitoramento de fatores produtivos das propriedades rurais. Esta proposta pretende fornecer um formato de subsídios baseado na ciência, no sentido de municiar as decisões de gerenciamento de risco. Enfatiza-se a necessidade de sistemas informatizados para integração de dados que possam ser estudados como fator de exposição aos achados do PNCRC, o que se prevê como vanguarda aos sistemas de inspeção baseada em risco e que poderão habilitar os governos a darem foco à antecipação/resolução de crises de saúde pública e de comércio internacional. Reitera-se a necessidade de definir escopo objetivo de fatores produtivos a serem monitorados pelos serviços de defesa agropecuária, no âmbito dos programas de boas práticas agrícolas. Tendo-se em vista o destaque do Brasil no cenário global de fornecimento de alimentos de origem animal e a relevância crescente da demonstração de controle dos quesitos técnicos com contexto em potenciais barreiras sanitárias, abordagens no âmbito deste trabalho são promissoras em respaldar a sustentabilidade do agronegócio nacional, uma vez que se relacionam com a atualização da plataforma de gerenciamento dos controles técnicos necessários às etapas do continuum produtivo. / The National Control Plan for Residues and Contaminants (PNCRC) was searched to identify preferential geographic areas for occurrence of low levels of heavy metals in cattle slaughtered in the period 2002-2010. Period 2006-2010 enables the identification of risk factors and presents the contamination distribution by means of thematic maps for each individual year. Trend analysis was carried out for heavy metals in federative units and in the National setting. The category of results for each sampled animal (negative, detection, violation) ensures database division into mutually exclusive areas with occurrence and non-occurrence of arsenic (detections) and also of lead and cadmium (detections+violations). The effect of the low concentrations (detections) on the risk of extrapolation to the maximum legal limits (violations) was evaluated in the state of São Paulo. An ecological study was done considering each county as an analysis unit: PNCRC results depict the \"disease status\" variable while the productive factors (tertiles or median) the exposure ones. The crude variables for the latter were provided by the Secretariat of Agriculture of São Paulo state. Multiple logistic regression modeling allowed to recognition of variables that increase the risk of contamination in the ecological context, demonstrating that PNCRC integration with other public databases is in fact possible. The \"clues\" of ecological risk factors should be used as a direction to further studies to evaluate the effect on individual farms before specific preventive measures can be made for animals and their rearing sites. There is a surveillance system proposal for PNCRC as way of defining objective methodology to track their results along with the monitoring of performance in the rearing procedures at the farm, thus entailing a framework based on science as a guide for risk management decisions. This study emphasizes the need of computerized systems for data integration and as a tool for evaluate the findings of PNCRC in the light of exposure factors, which is expected by the vanguard inspection systems based on risk with reliance in anticipation / resolution of public health crisis and international trade contentions by governments. There is a need to define the scope of objective production factors to be monitored by animal health services under the programs intending good agricultural practices. The approach of this study is suitable for enhance Brazilian position in terms of agribusiness sustainability by means of an update in the platform for control management relevant in the technical barriers context on each step of the productive continuum.

Os dados do Plano Nacional de Controle de Resíduos e Contaminantes (PNCRC) foram utilizados para identificação de áreas geográficas de ocorrência preferencial de níveis baixos de metais pesados em bovinos abatidos, no período 2002 a 2010. Critérios de inclusão definiram o período 2006 a 2010 como base para identificação de fatores de risco, ao que a distribuição de contaminações registradas pelo PNCRC é apresentada em mapas temáticos individuais para cada ano. Avaliou- se o efeito de risco das concentrações reduzidas (detecções) na ocorrência de extrapolação aos limites legais máximos (violações) no estado de São Paulo. Foram estabelecidos modelos de tendência para detecções de metais pesados nas unidades federativas e no conjunto nacional. As categorias de resultados de cada bovino amostrado (resultado negativo, detecção, violação) foram utilizadas para dividir o banco de dados em áreas de ocorrência e não ocorrência mutuamente exclusiva de arsênio (detecções) e também de chumbo e cádmio (detecções+ violações) no estado de São Paulo. Gerou-se um estudo ecológico considerando cada município como unidade de análise, utilizando-se as categorias de resultados do PNCRC como variável \"doença\" e como fator de exposição as categorias (mediana ou tercis) dos fatores produtivos do Levantamento das Unidades de Produção Agropecuária, fornecidos pela Secretaria de Agricultura do estado de São Paulo. A modelagem de regressão logística múltipla permitiu identificar variáveis que aumentam o risco de contaminações no contexto ecológico, demonstrando ser possível integrar dados do PNCRC com outras bases de dados públicas. Os fatores identificados devem ser utilizados por novos estudos com delineamento propício a avaliar o efeito de risco em propriedades individuais antes que se proponham ações preventivas específicas aos animais e seus locais de criação. Propõe-se a implantação de um sistema de vigilância epidemiológica para o PNCRC como maneira de definir metodologia objetiva para acompanhar seus resultados juntamente com o do monitoramento de fatores produtivos das propriedades rurais. Esta proposta pretende fornecer um formato de subsídios baseado na ciência, no sentido de municiar as decisões de gerenciamento de risco. Enfatiza-se a necessidade de sistemas informatizados para integração de dados que possam ser estudados como fator de exposição aos achados do PNCRC, o que se prevê como vanguarda aos sistemas de inspeção baseada em risco e que poderão habilitar os governos a darem foco à antecipação/resolução de crises de saúde pública e de comércio internacional. Reitera-se a necessidade de definir escopo objetivo de fatores produtivos a serem monitorados pelos serviços de defesa agropecuária, no âmbito dos programas de boas práticas agrícolas. Tendo-se em vista o destaque do Brasil no cenário global de fornecimento de alimentos de origem animal e a relevância crescente da demonstração de controle dos quesitos técnicos com contexto em potenciais barreiras sanitárias, abordagens no âmbito deste trabalho são promissoras em respaldar a sustentabilidade do agronegócio nacional, uma vez que se relacionam com a atualização da plataforma de gerenciamento dos controles técnicos necessários às etapas do continuum produtivo. / The National Control Plan for Residues and Contaminants (PNCRC) was searched to identify preferential geographic areas for occurrence of low levels of heavy metals in cattle slaughtered in the period 2002-2010. Period 2006-2010 enables the identification of risk factors and presents the contamination distribution by means of thematic maps for each individual year. Trend analysis was carried out for heavy metals in federative units and in the National setting. The category of results for each sampled animal (negative, detection, violation) ensures database division into mutually exclusive areas with occurrence and non-occurrence of arsenic (detections) and also of lead and cadmium (detections+violations). The effect of the low concentrations (detections) on the risk of extrapolation to the maximum legal limits (violations) was evaluated in the state of São Paulo. An ecological study was done considering each county as an analysis unit: PNCRC results depict the \"disease status\" variable while the productive factors (tertiles or median) the exposure ones. The crude variables for the latter were provided by the Secretariat of Agriculture of São Paulo state. Multiple logistic regression modeling allowed to recognition of variables that increase the risk of contamination in the ecological context, demonstrating that PNCRC integration with other public databases is in fact possible. The \"clues\" of ecological risk factors should be used as a direction to further studies to evaluate the effect on individual farms before specific preventive measures can be made for animals and their rearing sites. There is a surveillance system proposal for PNCRC as way of defining objective methodology to track their results along with the monitoring of performance in the rearing procedures at the farm, thus entailing a framework based on science as a guide for risk management decisions. This study emphasizes the need of computerized systems for data integration and as a tool for evaluate the findings of PNCRC in the light of exposure factors, which is expected by the vanguard inspection systems based on risk with reliance in anticipation / resolution of public health crisis and international trade contentions by governments. There is a need to define the scope of objective production factors to be monitored by animal health services under the programs intending good agricultural practices. The approach of this study is suitable for enhance Brazilian position in terms of agribusiness sustainability by means of an update in the platform for control management relevant in the technical barriers context on each step of the productive continuum.

Metabolomics is the study of metabolites and metabolic processes. Due to the diversity of structures and polarities of metabolites, no single analytical technique is able to measure the entire metabolome - instead a varied set of experimental designs and instrumental technologies are used to measure specific portions. This has led to the development of many distinct data analysis and processing methods and software. There is hope that metabolomics can be utilized for clinical applications, in toxicology and to measure the exposome. However, for these applications to be realised data must be high quality, sufficiently standardised and annotated, and FAIR (Findable, Accessible, Interoperable and Reproducible). For this purpose, it is also important that standardised, FAIR software workflows are available. There has also recently been much concern over the reproducibility of scientific research, which FAIR and open data, and workflows can help to address. To this end, this thesis aims to assess current practices and standards of sharing data within the field of metabolomics, using metascientific approaches. The types of functions of software for processing and analysing metabolomics data is also assessed. Reporting standards are designed to ensure that the minimum information required to un- derstand and interpret the results of analysis are reported. However, poor reporting standards are ignored and not complied with. Compliance to the biological context Metabolomics Standards Initiative (MSI) guidelines was examined, in order to investigate their timeliness. The state of open data within the metabolomics community was examined by investigating how much publicly available metabolomics data there is and where has it been deposited. To explore whether journal data sharing policies are driving open metabolomics data, which journals publish articles that have their underlying data made open was also examined. However, open data alone is not inherently useful: if data is incomplete, lacking in quality or missing crucial metadata, it is not valuable. Conversely, if data are reused, this can demonstrate the worth of public data archiving. Levels of reuse of public metabolomics data were therefore examined. With greater than 250 software tools specific for metabolomics, practitioners are faced with a daunting task to select the best tools for data collection and analysis. To help educate researchers about what software is available, a taxonomy of metabolomics software tools and a GitHub pages wiki, which provides extensive details about all included software, have been developed.

Alors que plus de cinquante pays dans le monde ont entrepris une démarche d’ouverture des données publiques, la thèse enquête sur l’émergence et la mise en oeuvre des politiques d’open data. Elle repose sur l’analyse de sources publiques et sur une enquête ethnographique conduite dans sept collectivités locales et institutions françaises. Revenant sur six moments de définition de grands « principes » de l’open data et leur traduction en politique publique par une institution française, Etalab, ce travail montre comment la catégorisation par l’open data a porté l’attention sur les données, en particulier sous leur forme « brute », considérées comme une ressource inexploitée, le « nouveau pétrole » gisant sous les organisations. L’enquête montre que le processus de l’ouverture débute généralement par une phase d’identification marquée par des explorations progressives et incertaines. Elle permet de comprendre que l’identification constitue un geste d’instauration qui transforme progressivement les fichiers de gestion de l’administration en données. Leur mise en circulation provoque des frictions : pour sortir des réseaux sociotechniques de l’organisation, les données doivent généralement passer à travers des circuits de validation et des chaînes de traitement. Par ailleurs, les données doivent souvent subir d’importantes transformations avant leur ouverture pour devenir intelligibles à la fois par les machines et par les humains. Cette thèse montre enfin que l’instauration concerne aussi les publics dont il est attendu qu’ils visualisent, inspectent et exploitent les données ouvertes. L’instauration des publics par des instruments très divers constitue un autre pan du travail invisible des politiques d’open data. Il ressort enfin de cette thèse que l’obligation à l’ouverture des données publiques, une suite possible des politiques d’open data, pose de manière saillante une question fondamentale « qu’est-ce qu’une donnée ? » Plutôt que de réduire la donnée à une catégorie relative, qui s’appliquerait à toutes sortes de matériaux informationnels, les cas étudiés montrent qu’elle est généralement attribuée dès lors que les données sont le point de départ de réseauxsociotechniques dédiés à leur circulation, leur exploitation et leur mise en visibilité. / As more than fifty countries have launched an open data policy, this doctoral dissertation investigates on the emergence and implementation of such policies. It is based on the analysis of public sources and an ethnographic inquiry conducted in seven French local authorities and institutions. By retracing six moments of definitions of the “open data principles” and their implementation by a French institution, Etalab, this work shows how open data has brought attention to data, particularly in their raw form, considered as an untapped resource, the “new oil” lying under the organisations. The inquiry shows that the process of opening generally begins by a phase of identification marked by progressive and uncertain explorations. It allows to understand that data are progressively instantiated from management files into data. Their circulation provoke frictions: to leave the sociotechnical network of organisations, data generally go through validation circuits and chains of treatment. Besides, data must often undergo important treatments before their opening in order to become intelligible by machines as well as humans. This thesis shows eventually that data publics are also instantiated as they are expected to visualize, inspect and process the data. Data publics are instantiated through various tools, which compose another area of the invisible work of open data projects. Finally, it appears from this work that the possible legal requirement to open data asks a fundamental question, “what is data?” Instead of reducing data to a relational category, which would apply to any informational material, studied cases show that they generally are applied when data are a starting point of sociotechnical networks dedicated to their circulation, their exploitation and their visibility.

Le service public a éprouvé une ouverture massive de données publiques dite "Open Data". Ce phénomène s'est développé avec l'émergence des nouvelles technologies d’information dans les administrations publiques, devenant un facteur important dans le renouveau et la modernisation du service public. Cette nouvelle tendance que le monde explore depuis quelques années, vise à partager et à réutiliser les données publiques détenues par le service public. L’objectif de l’Open Data étant la transparence démocratique en réponse à l’exigence de rendre des comptes aux citoyens, pour lutter contre la corruption et promouvoir un gouvernement ouvert en faveur de la participation citoyenne. À cet égard, le concept Open Data mène à nous interroger sur l'importance de l'ouverture des données du service public, sur le degré de l'obligation de s'adapter à cette ouverture, sur les conséquences de l'intrusion d’Open Data dans la sphère du service public et sur les limites imposées à l'Open Data. Pour répondre à ces interrogations, on s’intéressera à l’apparition et au développement de l’Open Data dans le service public, tout en illustrant son impact sur l'évolution de la démocratie et son rôle éminent dans la création de nouveaux services publics, avec notamment le cas du service public de la donnée en France. Ainsi, le meilleur angle pour étudier l'ouverture des données publiques dans le service public sera le droit public comparé, cela nous permettra d'analyser la pratique d'Open Data dans les pays pionniers dans ce domaine et les pays du Maghreb qui intègrent, depuis peu, cette nouvelle méthode de travail. Cette étude a pour but aussi de démontrer ce que l'Open Data peu apporter concrètement à l'administration et au citoyen. / The public service has experienced a massive opening of public data known as "Open Data". This phenomenon has developed with the emergence of new information technologies in public administrations, becoming then an important factor in the renewal and modernization of the public service. This new trend that the world has been exploring for a few years aims to share and reuse the public data held by the public service, while keeping as objective the democratic transparency in response to the requirement to be accountable to citizens to fight against corruption and promote Open Government in favor of citizen involvement.In this respect, the Open Data concept leads us to question ourselves about the importance of opening up data in the public service, about the degree of obligation to adapt to this opening, also about the consequences of the Open Data’s intrusion into the sphere of the public service and the limits that Open Data may encounter.To answer these questions, we will focus on the emergence and development of Open Data in the public service, with a depiction of its impact on democracy evolution and its eminent role in the creation of new public services, such as the case of data public service in France. Thus, the best angle to study the opening of public data in the public service is the comparative public law, this allows us to analyze the practice of Open Data in the pioneer countries in this field and the Maghreb countries who recently integrated this new way of work. This study also aims to prove what are the benefits of Open Data for the administration and the citizen.