Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

An Empirical Analysis of the Spanish Gas Price Structure

We can say without hesitation that in energy markets a throughout data analysis is crucial when designing sophisticated models that are able to capture most of the critical market drivers. In this study we will attempt to investigate into Spanish natural gas prices structure to improve understanding of the role they play in the determination of electricity prices and decide in the future about price modelling aspects. To further understand the potential for modelling, this study will focus on the nature and characteristics of the different gas price data available. The fact that the existing gas market in Spain does not incorporate enough liquidity of trade makes it even more critical to analyze in detail available gas price data information that in the end will provide relevant information to understand how electricity prices are affected by natural gas markets. In this sense representative Spanish gas prices are typically difficult to explore given the fact that there is not a transparent gas market yet and all the gas imported in the country is negotiated and purchased by private companies at confidential terms.

Methods for the analysis of multi-scale cell dynamics from fluorescence microscopy images

La embriogénesis es el proceso mediante el cual una célula se convierte en un ser un vivo. A lo largo de diferentes etapas de desarrollo, la población de células va proliferando a la vez que el embrión va tomando forma y se configura. Esto es posible gracias a la acción de varios procesos genéticos, bioquímicos y mecánicos que interaccionan y se regulan entre ellos formando un sistema complejo que se organiza a diferentes escalas espaciales y temporales. Este proceso ocurre de manera robusta y reproducible, pero también con cierta variabilidad que permite la diversidad de individuos de una misma especie. La aparición de la microscopía de fluorescencia, posible gracias a proteínas fluorescentes que pueden ser adheridas a las cadenas de expresión de las células, y los avances en la física óptica de los microscopios han permitido observar este proceso de embriogénesis in-vivo y generar secuencias de imágenes tridimensionales de alta resolución espacio-temporal. Estas imágenes permiten el estudio de los procesos de desarrollo embrionario con técnicas de análisis de imagen y de datos, reconstruyendo dichos procesos para crear la representación de un embrión digital. Una de las más actuales problemáticas en este campo es entender los procesos mecánicos, de manera aislada y en interacción con otros factores como la expresión genética, para que el embrión se desarrolle. Debido a la complejidad de estos procesos, estos problemas se afrontan mediante diferentes técnicas y escalas específicas donde, a través de experimentos, pueden hacerse y confrontarse hipótesis, obteniendo conclusiones sobre el funcionamiento de los mecanismos estudiados. Esta tesis doctoral se ha enfocado sobre esta problemática intentando mejorar las metodologías del estado del arte y con un objetivo específico: estudiar patrones de deformación que emergen del movimiento organizado de las células durante diferentes estados del desarrollo del embrión, de manera global o en tejidos concretos. Estudios se han centrado en la mecánica en relación con procesos de señalización o interacciones a nivel celular o de tejido. En este trabajo, se propone un esquema para generalizar el estudio del movimiento y las interacciones mecánicas que se desprenden del mismo a diferentes escalas espaciales y temporales. Esto permitiría no sólo estudios locales, si no estudios sistemáticos de las escalas de interacción mecánica dentro de un embrión. Por tanto, el esquema propuesto obvia las causas de generación de movimiento (fuerzas) y se centra en la cuantificación de la cinemática (deformación y esfuerzos) a partir de imágenes de forma no invasiva. Hoy en día las dificultades experimentales y metodológicas y la complejidad de los sistemas biológicos impiden una descripción mecánica completa de manera sistemática. Sin embargo, patrones de deformación muestran el resultado de diferentes factores mecánicos en interacción con otros elementos dando lugar a una organización mecánica, necesaria para el desarrollo, que puede ser cuantificado a partir de la metodología propuesta en esta tesis. La metodología asume un medio continuo descrito de forma Lagrangiana (en función de las trayectorias de puntos materiales que se mueven en el sistema en lugar de puntos espaciales) de la dinámica del movimiento, estimado a partir de las imágenes mediante métodos de seguimiento de células o de técnicas de registro de imagen. Gracias a este esquema es posible describir la deformación instantánea y acumulada respecto a un estado inicial para cualquier dominio del embrión. La aplicación de esta metodología a imágenes 3D + t del pez zebra sirvió para desvelar estructuras mecánicas que tienden a estabilizarse a lo largo del tiempo en dicho embrión, y que se organizan a una escala semejante al del mapa de diferenciación celular y con indicios de correlación con patrones de expresión genética. También se aplicó la metodología al estudio del tejido amnioserosa de la Drosophila (mosca de la fruta) durante el cierre dorsal, obteniendo indicios de un acoplamiento entre escalas subcelulares, celulares y supracelulares, que genera patrones complejos en respuesta a la fuerza generada por los esqueletos de acto-myosina. En definitiva, esta tesis doctoral propone una estrategia novedosa de análisis de la dinámica celular multi-escala que permite cuantificar patrones de manera inmediata y que además ofrece una representación que reconstruye la evolución de los procesos como los ven las células, en lugar de como son observados desde el microscopio. Esta metodología por tanto permite nuevas formas de análisis y comparación de embriones y tejidos durante la embriogénesis a partir de imágenes in-vivo. ABSTRACT The embryogenesis is the process from which a single cell turns into a living organism. Through several stages of development, the cell population proliferates at the same time the embryo shapes and the organs develop gaining their functionality. This is possible through genetic, biochemical and mechanical factors that are involved in a complex interaction of processes organized in different levels and in different spatio-temporal scales. The embryogenesis, through this complexity, develops in a robust and reproducible way, but allowing variability that makes possible the diversity of living specimens. The advances in physics of microscopes and the appearance of fluorescent proteins that can be attached to expression chains, reporting about structural and functional elements of the cell, have enabled for the in-vivo observation of embryogenesis. The imaging process results in sequences of high spatio-temporal resolution 3D+time data of the embryogenesis as a digital representation of the embryos that can be further analyzed, provided new image processing and data analysis techniques are developed. One of the most relevant and challenging lines of research in the field is the quantification of the mechanical factors and processes involved in the shaping process of the embryo and their interactions with other embryogenesis factors such as genetics. Due to the complexity of the processes, studies have focused on specific problems and scales controlled in the experiments, posing and testing hypothesis to gain new biological insight. However, methodologies are often difficult to be exported to study other biological phenomena or specimens. This PhD Thesis is framed within this paradigm of research and tries to propose a systematic methodology to quantify the emergent deformation patterns from the motion estimated in in-vivo images of embryogenesis. Thanks to this strategy it would be possible to quantify not only local mechanisms, but to discover and characterize the scales of mechanical organization within the embryo. The framework focuses on the quantification of the motion kinematics (deformation and strains), neglecting the causes of the motion (forces), from images in a non-invasive way. Experimental and methodological challenges hamper the quantification of exerted forces and the mechanical properties of tissues. However, a descriptive framework of deformation patterns provides valuable insight about the organization and scales of the mechanical interactions, along the embryo development. Such a characterization would help to improve mechanical models and progressively understand the complexity of embryogenesis. This framework relies on a Lagrangian representation of the cell dynamics system based on the trajectories of points moving along the deformation. This approach of analysis enables the reconstruction of the mechanical patterning as experienced by the cells and tissues. Thus, we can build temporal profiles of deformation along stages of development, comprising both the instantaneous events and the cumulative deformation history. The application of this framework to 3D + time data of zebrafish embryogenesis allowed us to discover mechanical profiles that stabilized through time forming structures that organize in a scale comparable to the map of cell differentiation (fate map), and also suggesting correlation with genetic patterns. The framework was also applied to the analysis of the amnioserosa tissue in the drosophila’s dorsal closure, revealing that the oscillatory contraction triggered by the acto-myosin network organized complexly coupling different scales: local force generation foci, cellular morphology control mechanisms and tissue geometrical constraints. In summary, this PhD Thesis proposes a theoretical framework for the analysis of multi-scale cell dynamics that enables to quantify automatically mechanical patterns and also offers a new representation of the embryo dynamics as experienced by cells instead of how the microscope captures instantaneously the processes. Therefore, this framework enables for new strategies of quantitative analysis and comparison between embryos and tissues during embryogenesis from in-vivo images.

Nuevos Esquemas de Visualizaciones para Mejorar la Comprensibilidad de Modelos de Data Mining

La gran cantidad de datos que se registran diariamente en los sistemas de base de datos de las organizaciones ha generado la necesidad de analizarla. Sin embargo, se enfrentan a la complejidad de procesar enormes volúmenes de datos a través de métodos tradicionales de análisis. Además, dentro de un contexto globalizado y competitivo las organizaciones se mantienen en la búsqueda constante de mejorar sus procesos, para lo cual requieren herramientas que les permitan tomar mejores decisiones. Esto implica estar mejor informado y conocer su historia digital para describir sus procesos y poder anticipar (predecir) eventos no previstos. Estos nuevos requerimientos de análisis de datos ha motivado el desarrollo creciente de proyectos de minería de datos. El proceso de minería de datos busca obtener desde un conjunto masivo de datos, modelos que permitan describir los datos o predecir nuevas instancias en el conjunto. Implica etapas de: preparación de los datos, procesamiento parcial o totalmente automatizado para identificar modelos en los datos, para luego obtener como salida patrones, relaciones o reglas. Esta salida debe significar un nuevo conocimiento para la organización, útil y comprensible para los usuarios finales, y que pueda ser integrado a los procesos para apoyar la toma de decisiones. Sin embargo, la mayor dificultad es justamente lograr que el analista de datos, que interviene en todo este proceso, pueda identificar modelos lo cual es una tarea compleja y muchas veces requiere de la experiencia, no sólo del analista de datos, sino que también del experto en el dominio del problema. Una forma de apoyar el análisis de datos, modelos y patrones es a través de su representación visual, utilizando las capacidades de percepción visual del ser humano, la cual puede detectar patrones con mayor facilidad. Bajo este enfoque, la visualización ha sido utilizada en minería datos, mayormente en el análisis descriptivo de los datos (entrada) y en la presentación de los patrones (salida), dejando limitado este paradigma para el análisis de modelos. El presente documento describe el desarrollo de la Tesis Doctoral denominada “Nuevos Esquemas de Visualizaciones para Mejorar la Comprensibilidad de Modelos de Data Mining”. Esta investigación busca aportar con un enfoque de visualización para apoyar la comprensión de modelos minería de datos, para esto propone la metáfora de modelos visualmente aumentados. ABSTRACT The large amount of data to be recorded daily in the systems database of organizations has generated the need to analyze it. However, faced with the complexity of processing huge volumes of data over traditional methods of analysis. Moreover, in a globalized and competitive environment organizations are kept constantly looking to improve their processes, which require tools that allow them to make better decisions. This involves being bettered informed and knows your digital story to describe its processes and to anticipate (predict) unanticipated events. These new requirements of data analysis, has led to the increasing development of data-mining projects. The data-mining process seeks to obtain from a massive data set, models to describe the data or predict new instances in the set. It involves steps of data preparation, partially or fully automated processing to identify patterns in the data, and then get output patterns, relationships or rules. This output must mean new knowledge for the organization, useful and understandable for end users, and can be integrated into the process to support decision-making. However, the biggest challenge is just getting the data analyst involved in this process, which can identify models is complex and often requires experience not only of the data analyst, but also the expert in the problem domain. One way to support the analysis of the data, models and patterns, is through its visual representation, i.e., using the capabilities of human visual perception, which can detect patterns easily in any context. Under this approach, the visualization has been used in data mining, mostly in exploratory data analysis (input) and the presentation of the patterns (output), leaving limited this paradigm for analyzing models. This document describes the development of the doctoral thesis entitled "New Visualizations Schemes to Improve Understandability of Data-Mining Models". This research aims to provide a visualization approach to support understanding of data mining models for this proposed metaphor visually enhanced models.

Detection of Biological CO2 and 1,3-Pentadiene Using Non-refrigerated Low-Cost MWIR Detectors

The early detection of spoiling metabolic products in contaminated food is a very important tool to control quality. Some volatile compounds produce unpleasant odours at very low concentrations, making their early detection very challenging. This is the case of 1,3-pentadiene produced by microorganisms through decarboxylation of the preservative sorbate. In this work, we have developed a methodology to use the data produced by a low-cost, compact MWIR (Mid-Wave IR) spectrometry device without moving parts, which is based on a linear array of 128 elements of VPD PbSe coupled to a linear variable filter (LVF) working in the spectral range between 3 and 4.6 ?m. This device is able to analyze food headspace gases through dedicated sample presentation setup. This methodology enables the detection of CO2 and the volatile compound 1,3-pentadiene, as compared to synthetic patrons. Data analysis is based on an automated multidimensional dynamic processing of the MWIR spectra. Principal component and discriminant analysis allow segregating between four yeast strains including producers and no producers. The segregation power is accounted as a measure of the discrimination quality.

Gaia-ESO Survey: Analysis of pre-main sequence stellar spectra

Context. The Gaia-ESO Public Spectroscopic Survey is obtaining high-quality spectroscopy of some 100 000 Milky Way stars using the FLAMES spectrograph at the VLT, down to V = 19 mag, systematically covering all the main components of the Milky Way and providing the first homogeneous overview of the distributions of kinematics and chemical element abundances in the Galaxy. Observations of young open clusters, in particular, are giving new insights into their initial structure, kinematics, and their subsequent evolution. Aims. This paper describes the analysis of UVES and GIRAFFE spectra acquired in the fields of young clusters whose population includes pre-main sequence (PMS) stars. The analysis is applied to all stars in such fields, regardless of any prior information on membership, and provides fundamental stellar atmospheric parameters, elemental abundances, and PMS-specific parameters such as veiling, accretion, and chromospheric activity. Methods. When feasible, different methods were used to derive raw parameters (e.g. line equivalent widths) fundamental atmospheric parameters and derived parameters (e.g. abundances). To derive some of these parameters, we used methods that have been extensively used in the past and new ones developed in the context of the Gaia-ESO survey enterprise. The internal precision of these quantities was estimated by inter-comparing the results obtained by these different methods, while the accuracy was estimated by comparison with independent external data, such as effective temperature and surface gravity derived from angular diameter measurements, on a sample of benchmarks stars. A validation procedure based on these comparisons was applied to discard spurious or doubtful results and produce recommended parameters. Specific strategies were implemented to resolve problems of fast rotation, accretion signatures, chromospheric activity, and veiling. Results. The analysis carried out on spectra acquired in young cluster fields during the first 18 months of observations, up to June 2013, is presented in preparation of the first release of advanced data products. These include targets in the fields of the ρ Oph, Cha I, NGC 2264, γ Vel, and NGC 2547 clusters. Stellar parameters obtained with the higher resolution and larger wavelength coverage from UVES are reproduced with comparable accuracy and precision using the smaller wavelength range and lower resolution of the GIRAFFE setup adopted for young stars, which allows us to provide stellar parameters with confidence for the much larger GIRAFFE sample. Precisions are estimated to be ≈120 K rms in Teff, ≈0.3 dex rms in log g, and ≈0.15 dex rms in [Fe/H] for the UVES and GIRAFFE setups.

The Gaia-ESO Survey: The analysis of high-resolution UVES spectra of FGK-type stars

Context. The ongoing Gaia-ESO Public Spectroscopic Survey is using FLAMES at the VLT to obtain high-quality medium-resolution Giraffe spectra for about 105 stars and high-resolution UVES spectra for about 5000 stars. With UVES, the Survey has already observed 1447 FGK-type stars. Aims. These UVES spectra are analyzed in parallel by several state-of-the-art methodologies. Our aim is to present how these analyses were implemented, to discuss their results, and to describe how a final recommended parameter scale is defined. We also discuss the precision (method-to-method dispersion) and accuracy (biases with respect to the reference values) of the final parameters. These results are part of the Gaia-ESO second internal release and will be part of its first public release of advanced data products. Methods. The final parameter scale is tied to the scale defined by the Gaia benchmark stars, a set of stars with fundamental atmospheric parameters. In addition, a set of open and globular clusters is used to evaluate the physical soundness of the results. Each of the implemented methodologies is judged against the benchmark stars to define weights in three different regions of the parameter space. The final recommended results are the weighted medians of those from the individual methods. Results. The recommended results successfully reproduce the atmospheric parameters of the benchmark stars and the expected Teff-log  g relation of the calibrating clusters. Atmospheric parameters and abundances have been determined for 1301 FGK-type stars observed with UVES. The median of the method-to-method dispersion of the atmospheric parameters is 55 K for Teff, 0.13 dex for log  g and 0.07 dex for [Fe/H]. Systematic biases are estimated to be between 50−100 K for Teff, 0.10−0.25 dex for log  g and 0.05−0.10 dex for [Fe/H]. Abundances for 24 elements were derived: C, N, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, Nd, and Eu. The typical method-to-method dispersion of the abundances varies between 0.10 and 0.20 dex. Conclusions. The Gaia-ESO sample of high-resolution spectra of FGK-type stars will be among the largest of its kind analyzed in a homogeneous way. The extensive list of elemental abundances derived in these stars will enable significant advances in the areas of stellar evolution and Milky Way formation and evolution.

Involvement and detachment in David Cameron and Ed Miliband’s political discourse. An analysis of deictic shields on the pronoun ‘I’ in UK 2015 General Election news interviews

The goal of my study is to investigate the relationship between selected deictic shields on the pronoun ‘I’ and the involvement/detachment dichotomy in a sample of television news interviews. I focus on the use of personal pronouns in political discourse. Drawing upon Caffi’s (2007) classification of mitigating devices into bushes, hedges and shields, I focus on deictic shields on the pronoun ‘I’: I examine the way a selection of ‘I’-related deictic shields is employed in a collection of news interviews broadcast during the electoral campaign prior to the UK 2015 General Election. My purpose is to uncover the frequencies of each of the linguistic items selected and the pragmatic functions of those linguistic items in the involvement/detachment dichotomy. The research is structured as follows. Chapter 1 provides an account of previous studies on the three main areas of research: speech event analysis, institutional interaction and the news interview, and the UK 2015 General Election television programmes. Chapter 2 is centred on the involvement/detachment dichotomy: I provide an overview of nonlinguistic and linguistic features of involvement and detachment at all levels of sentence structure. Chapter 3 contains a detailed account of the data collection and data analysis process. Chapter 4 provides an accurate description of results in three steps: quantitative analysis, qualitative analysis and discussion of the pragmatic functions of the selected linguistic features of involvement and detachment. Chapter 5 includes a brief summary of the investigation, reviews the main findings, and indicates limitations of the study and possible inputs for further research. The results of the analysis confirm that, while some of the linguistic items examined point toward involvement, others have a detaching effect. I therefore conclude that deictic shields on the pronoun ‘I’ permit the realisation of the involvement/detachment dichotomy in the speech genre of the news interview.

Le sentiment d'appartenance à l'école : un regard conceptuel, psychométrique et théorique

Parce qu’il est notamment lié à des facteurs de réussite scolaire et d’adaptation sociale (Eccles & Roeser, 2009; Finn, 1989; Janosz, Georges, & Parent, 1998), le sentiment d’appartenance des élèves est considéré comme étant un élément de première instance qui doit d’être développé et maintenu par les professionnels de l’éducation (MELS, 2012). L'objectif général visait à approfondir notre compréhension du sentiment d’appartenance à l’école. Pour répondre à cet objectif général, trois articles de recherche distincts ont été élaborés. Le premier article présente une analyse conceptuelle visant à clarifier la compréhension du concept de sentiment d’appartenance à l’école. La méthode conceptuelle privilégiée dans cet article est celle de Walker et Avant (2011). La recension des écrits et les référents empiriques répertoriés indiquent que ce concept est de nature multidimensionnelle. L’analyse des données indique quatre attributs définitionnels. L’élève doit : (1) ressentir une émotion positive à l’égard du milieu scolaire; (2) entretenir des relations sociales de qualité avec les membres du milieu scolaire; (3) s’impliquer activement dans les activités de la classe ou celles de l’école; (4) percevoir une certaine synergie (harmonisation), voir même une similarité, avec les membres de son groupe. À la suite de cette étude permettant de mieux comprendre le sentiment d’appartenance à l’école, le deuxième article visait à examiner la structure factorielle et l'invariance de l’instrument de mesure du sentiment d’appartenance Psychological Sense of School Membership (PSSM) au regard du sexe des élèves. Cette étude a été menée chez un échantillon composé de 766 filles et de 391 garçons de troisième secondaire. Les analyses factorielles confirmatoires ont indiqué une structure à trois facteurs : (1) la qualité des relations entre les élèves; (2) la qualité des relations entre les élèves et l’enseignant; ainsi que (3) le sentiment d’acceptation par le milieu. Les analyses factorielles multigroupes ont indiqué pour leur part que le PSSM est un instrument invariant chez les filles et les garçons de troisième secondaire. Finalement, le troisième article a été mené chez un échantillon de 4166 élèves de niveau secondaire afin d’examiner les processus psychologiques complexes s’opérant entre le sentiment d’appartenance et le rendement scolaire (Anderman & Freeman, 2004; Connell & et al., 1994; Roeser et al., 1996). Afin d’examiner ces processus psychologiques, quatre hypothèses issues du modèle de Freeman-Anderman ont été validées par le biais d’analyses acheminatoires : H1 Les affects positifs médiatisent partiellement et positivement l’effet du sentiment d’appartenance sur l’engagement comportemental; H2 Les affects positifs médiatisent partiellement et positivement l’effet du sentiment d’appartenance sur l’engagement affectif; H3 Les affects positifs médiatisent partiellement et positivement l’effet du sentiment d’appartenance sur l’engagement cognitif; H4 Les engagements affectif, cognitif et comportemental médiatisent partiellement et positivement l’effet du sentiment d’appartenance sur le rendement scolaire. Nos résultats appuient partiellement la première hypothèse de recherche tout en soutenant les hypothèses deux, trois et quatre. Spécifiquement, la relation entre le sentiment d’appartenance et l’engagement émotionnel montre davantage un effet direct qu’un effet indirect (H2). L’étude a produit des résultats similaires pour l’engagement cognitif (H3). Finalement, la relation entre le sentiment d’appartenance et le rendement scolaire indique un effet indirect plus grand qu’un effet direct (H4). À la lumière de ces résultats, des recommandations à l’intention des professionnels de l’éducation sont offertes en guise de conclusion.

Expert systems for crash data collection.

Federal Highway Administration, Office of Safety and Traffic Operations, Washington, D.C.

Using linked data to evaluate medical and financial outcomes of motor vehicle crashes in Connecticut.

Federal Highway Administration, Washington, D.C.

Using linked data to evaluate severity and outcome of injury by type of object struck (first object struck only) for motor vehicle crashes in Connecticut.

Federal Highway Administration, Washington, D.C.

Test site instrumentation study. Volume II: Crash 1 and Crash 2 "raw" data. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Control charts as a tool in data quality improvement.

Mode of access: Internet.

Solid state data acquisition and processing system (SSDAPS). Volume III: description, installation, calibration, and operating procedures. Final report.

National Highway Traffic Safety Administration, Washington, D.C.