Biopax and Semantics

Biopax community is producing sets of data in RDF files, but most of them are not available through query interfaces. The publication of SPARQL endpoints is feasible with current sets of data, but the use of reasoning in these interfaces is unfeasible in many cases. The use of large scale reasoners is a need to take advantage of these data sets

Doctor of Philosophy

dissertationModern medicine would benefi t from the pursuit of new, more speci fic and easier to implement diagnosis tools. In recent years, Raman scattering, surface-enhanced Raman scattering and fluorescence spectroscopy have proven to be successful diagnostic techniques for a wide range of diseases including atherosclerosis, kidney stones, bone diseases, diabetes, and a wide collection of neoplasms. Optical spectroscopy has several advantages over more traditional diagnostic methods (i.e., histopathology, quantitative PCR, etc.) such as faster data analysis, nonspecifi c sample preparation, nonspecifi c labels/reagents/antibodies usage requirements, and immediate on-site implementation. In the present work, label-free in vitro fluorescence and surface enhanced Raman scattering (SERS) spectroscopy have been used to di fferentiate between blood cells of patients aff ected with myeloproliferative neoplasms (MPN) and those of healthy subjects. The SERS technique has also been applied to hemoglobin variants as well as to serum obtained from patients affected with chronic heart failure who positively or negatively responded to the seasonal influenza vaccine. We found that spectral ratios of the background fluorescence intensity that accompanies the SERS spectra of granulocytes serve as excellent markers for the presence of MPNs. In addition, we also found expression dysregulation of two hypoxia induced factor regulated genes, which correlates with our results obtained by SERS spectroscopy assay in MPN patients and supports the presence of the Warburg e ffect in MPNs. We hypothesize that SERS measures metabolic change in granulocytes through two possible mechanisms: (i) Changes in dielectric properties of the environment surrounding the silver-cell interface; and (ii) changes in flavinadenine dinucleotide concentrations, which in turn changes the relative contribution of the auto uorescence to the emission spectrum. These hypotheses are supported by SERS measurement of 2-deoxy-D-glucose incubated granulocytes, where the emission spectra show a similar behavior as observed in the SERS spectra of controls and patients. Using SERS spectroscopy in combination with multivariate analysis (e.g., principal component analysis) and classi fication algorithms (e.g., support vector machines), we are able to distinguish among hemoglobin variants S, C and E and traits FS and FE, as well as seasonal infuenza vaccine responders and nonresponders within a population of patients su ffering from chronic heart failure. The results presented here may have an extraordinary impact on the diagnostics of patients having Myeloproliferative Neoplasms, as well as on the health care management of patients aff ected with hemoglobinopathies and chronic heart failure

3D hydrodynamic model as a tool for more efficient port management and operations.

Ports have been attempting to increase their competitiveness by enhancing their productivity and operate in a more environmentally friendly way. The Port of Seville is located in the Guadalquivir River in the south of Spain and it is the unique Spanish inland port. The estuary has generated and is still generating conflicts of interests. The access channel to the port is being periodically dredged, the natural course has been anthropologically modified several times, original salt marshes have been transformed to grow rice and approximately one-fourth of the total surface of the estuary is now part of two protected areas, one of them is a UNESCO_MAB Biosphere Reserve. Despite its socio-economic and environmental significance there is a surprising lack of scientific and technical information about the environmental interactions between the port activities and the Guadalquivir estuary stakeholders. A 3D hydrodynamic model has been developed to study the tidal regime, water circulation, temperature and salinity distributions, flooding areas and the sediment dynamics in the estuary. The model output has been validated with in situ current speed, direction, water elevation and also with temperature and salinity measurements. Good agreement between modeled and real measurements have been obtained. Our preliminary results show that the vessel traffic management could be improved by using the tidal elevations and currents calculated by the model in the whole estuary. The interactions among the port activities (mainly due of changes in the sediments dynamics), the watershed management and the saline intrusion evolution will be studied in detail. 3D Hydrodynamic Modelling provide spatially explicit information on the key variables governing the dynamics of estuarine areas. The numerical model is a powerful tool to effectively guide the management and operations of ports located in a complex socio-ecological systems.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Bioqueries: a collaborative environment to create, explore and share SPARQL queries in Life Sciences

Bioqueries provides a collaborative environment to create, explore, execute, clone and share SPARQL queries (including Federated Queries). Federated SPARQL queries can retrieve information from more than one data source.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Heat fluxes between the Guadalquivir river and the Gulf of Cádiz Continental Shelf

An 18-year time series of daily sea surface temperature of Gulf of Cadiz and an 18-month time series of temperature collected in the vicinity of the Guadalquivir estuary mouth have been analyzed to investigate the heat exchange between the estuary and the adjacent continental shelf. The first time identifies a continental shelf area where seasonal thermal oscillation signal (amplitudes and phase) changes abruptly. In order to explain this anomaly, the second data set allows a description of thermal fluctuations in a wide range of frequencies and an estimation of the upstream heat budget of the Guadalquivir estuary. Results show that high frequency thermal signal, diurnal and semidiurnal, and water flux signal through Guadalquivir mouth, mainly semidiurnal, apparently interact randomly to give a small exchange of thermal energy at high frequency. There is no trace, at the estuary's mouth, of daily heat exchanges with intertidal mudflats probably because it tends to cancel on daily time scales. Results also show that fluctuations of estimated air-sea fluxes force fluctuations of temperature in a quite homogeneous estuarine, with a delay of 20 days. The along-channel thermal energy gradient reaches magnitudes of 300-400 J m-4 near the mouth during the summer and winter and drives the estuary-shelf exchange of thermal energy at seasonal scale. Particularly, the thermal heat imported by the estuary from the shelf area during late fall-winter-early spring of 2008/2009 is balanced by the thermal heat that the estuary exports to the shelf area during late spring-summer of 2008. In summary, Guadalquivir river removes/imports excess of thermal energy towards/from the continental shelf seasonally, as a mechanism to accommodate excess of heat from one side respect to the other side.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Autoridad Portuaria de Sevilla (APS

LA INTEGRACION REGIONAL DESDE LAS COMPETENCIAS COMO ESTRATEGIA DE ARMONIZACION DE LAS PROPUESTAS CURRICULARES CASO DOCTORADOS EN EDUCACIÓN REGION ANDINA

Partiendo del conocimiento de las bondades de armonizar e integrar regiones, países, instituciones y programas, Tomando como referente experiencias europeas caso tuning; experiencias en el ámbito Iberoamericano como la creación del Espacio Iberoamericano del Conocimiento (EIC) y latinoamericanas como la conformación del Mercosur educativo y el proyecto Tuning-América Latina 2004-2006, éste trabajo se planteo como objetivo identificar las competencias que debe tener un doctor en educación desde las dimensiones del ser, convivir, conocer y hacer en forma tal que responda a las necesidades de la emergente y actual sociedad del conocimiento. Este grupo de competencias se constituye en el corazón de las propuestas de formación doctoral en educación en la región andina como armonizador de ellas. Para el logro del objetivo se empleo, la técnica Delphi para hallar el consenso acerca del grupo de competencias, parámetros estadísticos para su verificación y respectiva comprobación. Se realizó un diagnostico de las competencias que actualmente se promueven desde las 22 propuestas ofertadas en la región por las diferentes universidades de los países miembros de la misma, encontrándose una tendencia a privilegiar las competencias del saber y del hacer; y por ultimo se hace un recorrido por lo que en este tema se ha avanzado en países de la unión europea y los estados unidos, para que sirvan como referentes internacionales concluyendo en la conformación de cinco grupos específicos de competencias a promocionar desde los doctorados en educación que van a servir como elementos de integración y armonización de dichas propuestas asegurando su pertinencia en el ámbito internacional

Physical characterization of the Guadiana Estuary using a 3D model

Guadiana estuary is an intertidal estuary situated in SW of Iberian Península, the latest 50 Km of which constitutes the natural border between Spain and Portugal. Tidal influence extends to about 80 Km upstream. The Guadiana River presents a high seasonal irregularity with wet winters and dry summers. A 3D hydrodynamic model based on the MOHID System has been developed to study the hydrodynamics of the Guadiana Estuary. The model has been validated by comparison the output with in situ data measurements in several points along the estuary.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech