OpenReq-DD: A requirements dependency detection tool

Requirements Engineering (RE) is one of the most critical phases insoftware development. Analyzing requirements data is a laborious taskperformed by expert stakeholders using manual processes, as there areno standard automatic tools to handle this issue in a more efficientway. The purpose of this paper is to summarize the approach of theOpenReq-DD dependency detection tool developed at the OpenReqproject, which allows an automatic requirement dependency detectionapproach. The core of this proposal is based on an ontology whichdefines dependency relations between specific terminologies related tothe domain of the requirements. Using this information, it is possible toapply Natural Language Processing techniques to extract meaning fromthese requirements and relations, and Machine Learning techniques toapply conceptual clustering, with the major purpose of classifying theserequirements into the defined ontology.Peer ReviewedPostprint (published version

Horizontal and Vertical Distributions of Transparent Exopolymer Particles (TEP) in the NW Mediterranean Sea Are Linked to Chlorophyll a and O2 Variability

12 pages, 6 figures, 3 tables, supplementary material http://journal.frontiersin.org/article/10.3389/fmicb.2016.02159/full#supplementary-materialTransparent Exopolymer Particles (TEP) are relevant in particle and carbon fluxes in the ocean, and have economic impact in the desalination industry affecting reverse osmosis membrane fouling. However, general models of their occurrence and dynamics are not yet possible because of the poorly known co-variations with other physical and biological variables. Here, we describe TEP distributions in the NW Mediterranean Sea during late spring 2012, along perpendicular and parallel transects to the Catalan coast. The stations in the parallel transect were sampled at the surface, while the stations in the perpendicular transect were sampled from the surface to the bathypelagic, including the bottom nepheloid layers. We also followed the short-term TEP dynamics along a 2-day cycle in offshore waters. TEP concentrations in the area ranged from 4.9 to 122.8 and averaged 31.4 ± 12.0 μg XG eq L−1. The distribution of TEP measured in transects parallel to the Catalan Coast correlated those of chlorophyll a (Chla) in May but not in June, when higher TEP-values with respect to Chla were observed. TEP horizontal variability in epipelagic waters from the coast to the open sea also correlated to that of Chla, O2 (that we interpret as a proxy of primary production) and bacterial production (BP). In contrast, the TEP vertical distributions in epipelagic waters were uncoupled from those of Chla, as TEP maxima were located above the deep chlorophyll maxima. The vertical distribution of TEP in the epipelagic zone was correlated with O2 and BP, suggesting combined phytoplankton (through primary production) and bacterial (through carbon reprocessing) TEP sources. However, no clear temporal patterns arose during the 2-day cycle. In meso- and bathypelagic waters, where phytoplanktonic sources are minor, TEP concentrations (10.1 ± 4.3 μg XG eq l−1) were half those in the epipelagic, but we observed relative TEP increments coinciding with the presence of nepheloid layers. These TEP increases were not paralleled by increases in particulate organic carbon, indicating that TEP are likely to act as aggregating agents of the mostly inorganic particles present in these bottom nepheloid layersThis work was funded by projects funded by the Spanish Ministry of Science STORM (CTM2009-09352/MAR), SUMMER (CTM2008-03309/MAR), DOREMI (CTM2012-34294), REMEI (CTM2015-70340-R), ANIMA (CTM2015-65720-R), PEGASO (CTM2012-37615), and Grup consolidat de Recerca de la Generalitat de Catalunya (2014SGR/1179)Peer Reviewe

On-line applet-based optics course for undergraduate students

We present an educational resource based in a virtual optical laboratory for undergraduate students. It consists in a web-based textbook with several applets to illustrate the theory and simplify the teaching tasks in the classroom. These programs can also be used as a method for self-learning in an on-line environment. Applets are written in Java language using the Java Network Launching Protocol (JNPL) for avoiding problems related with the use of specific browsers or Java interpreters versions

FICARAM-15 Cruise Report 20th March – 22nd May 2013 on board BIO Hespérides by the Group FICARAM

54 páginas, 19 figuras, 3 anexosThe FICARAM-15 is the fifteenth repetition of a section conducted in 1994. This section is part of the international program GOSHIP (http://www.go-ship.org/CruisePlans.html) to develop a globally coordinated network of sustained hydrographic sections as part of the global ocean/climate observing system. The objective of the FICARAM-15 cruise is to investigate the temporal evolution of the anthropogenic carbon and evaluate the CO2 absorption capacity of the South Atlantic region, the Equatorial zone, and the subtropical region of Azores-Gibraltar in the North Atlantic. This cruise is supported by the CATARINA project funded by the Ministry of Economy and Competitiveness (CTM2010-17141) and is part of the European Union FP7 project CARBOCHANGE (http://carbochange.b.uib.no/). The objective of FICARAM-15 cruise is framed in the CATARINA project conducted by the tasks I.2.1 (air-sea CO2 exchange) I.3 (ventilation of water masses), I.4.1 (zonal variability of N2O and CH4), I.4.2 (anthropogenic carbon storage), I.4.4 (saturation horizon of calcium carbonate along the section) and I.5.4 (evolution of the acidification rates). Another component of the FICARAM-15 cruise aims to examine the biological and biogeochemical mechanisms that hinder total dissolved organic carbon (DOC) remineralisation in marine systems, taking a multidisciplinary perspective and applying many different approaches. This is the global objective of the Spanish project DOREMI (CTM2012-34294) that joins this FICARAM-15 cruise.During the FICARAM cruise the physical oceanography group was responsible for collecting the following data sets: CTD and XBT data; vessel-mounted ADCP and lowered ADCP; continuous thermosalinograph. Physical oceanographers participated in the cruise financed through Project “Tipping Corners in the Meridional Overturning Circulation” (TIC-MOC), CTM2011-28867. The FICARAM-15 cruise was organized in two phases with a common sampling. LEG 1: From Punta Arenas (Chile) to Recife (Brazil): 62 stations. Chief Scientist: Aida F. Ríos, PI of CATARINA project LEG 2: From Recife (Brazil) to Cartagena (Spain): 46 stations Chief Scientist: Celia Marrasé, PI of DOREMI project This report contains the sampling of all the variables at each station along the FICARAM section, as well as the analysis of the biogeochemical variables and the preliminary results. The principal investigator of the DOREMI project produced another report with the common sampling section, showing the analysis and results of the experiments on dissolved organic matter carried out on board.This cruise is supported by the CATARINA project funded by the Ministry of Economy and Competitiveness (CTM2010-17141) and is part of the European Union FP7 project CARBOCHANGE (http://carbochange.b.uib.no/)Peer reviewe

Phylogenetic and functional diversity of the bacterial community associated to blooms of toxic phytobenthos

Trabajo final presentado por Encarna Borrull Francesch para el Máster en Ciencias del Mar: Oceanografía y Gestión del Medio Marino de la Universitat de Barcelona (UB) y la Universitat Politècnica de Catalunya (UPC), realizado bajo la dirección de la Dra. Maria Montserrat Sala del Institut de Ciències del Mar (ICM-CSIC).-- 43 pages, 12 figures, 4 tablesBlooms of the benthic dinoflagellate Ostreopsis have been associated with respiratory disorders in humans and mass mortalities in fish. A bloom of Ostreopsis sp. appears regularly in summer in Sant Andreu de Llavaneres beach. The bloom has been associated with respiratory symptoms, rhinitis and skin irritation in bath users. Although several studies have shown the contribution of bacteria to harmful dinoflagellate blooms, the composition and activity of the bacterial community associated to blooms of Ostreopsis in situ has not been assessed. For this reason, a two-year sampling was carried out in Sant Andreu de Llavaneres. The main aims of this study were 1) to characterize the bacterial community to assess their possible contribution to the toxicity of the bloom and 2) to evaluate the effects of the bloom, and the mucilage associated, for the activity of the bacteria. The results of this study have brought three main conclusions: 1. Epiphytic bacteria on macrophytes are significantly more active than bacteria in the water. During periods of blooms, epiphytic bacteria are significantly more active than during periods when Ostreopsis was not present. 2. The bacterial community in the macrophyte shows higher activities of most of the extracellular enzyme activities during the blooms and a significantly higher utilization of carboxylic acids and carbohydrates, suggesting their major contribution in the composition of the mucilage. 3. The epiphytic bacterial community associated to the bloom appears to have a higher diversity than the community in the water or in non-bloom periods. 4. The DNA sequences obtained from the DGGE gels show the presence of several bacterial strains (mainly Vibrio) which contain tetradotoxin and may very likely contribute to the toxicity of the bloom

Review of approaches to study bacterial activity and diversity along the organic matter continuum

2nd International Workshop on Marine Aggregates from Molecular principles to Biochemical Impact (IWOMA), 15-17 August 2012, Bremen, GermanyThis study is possible thanks to the financial support of the project STORM (CTM2009-09352)Peer Reviewe

Determinación de la diversidad funcional del bacterioplancton marino

Peer Reviewe

Viral abundance and size-fractionated viral mediated bacterial mortality in the NW Mediterranean

Symposium on Integrating New Advances in Mediterranean Oceanography and Marine Biology, 26-29 November 2013, Institut de Ciències del Mar (CSIC), Barcelona, Catalunya, SpainSuspended organic aggregates are hotspots for bacterial growth but do not offer a refuge from protistan grazing. Concerning another mortality agent, i.e. viral lysis, published results are ambiguous: High viral abundance on transparent exopolymer particles, different stages of marine snow and mucilage and riverine aggregates suggest high viral infection of attached bacteria. However, inactivation of viruses attached to particles has also been reported. From freshwater studies, there is some speculation of decreased viral lysis of attached bacteria inferred from lower viral infectivity in freshwater benthic habitats compared to the upper water column. However, to our best knowledge viral production associated to particles has never been assessed directly. In the present study viral abundance as well as lytic and lysogenic production was determined along with the viral induced mortality of attached bacteria and compared to viral infection of the free-living bacteria through 0.8 μm and 3.0 μm fractionation of surface, deep chlorophyll maximum (DCM) and deep water samples from the NW Mediterranean. Samples were taken during two cruises, labeled NEMO-1 and NEMO-2 in May and June 2012, respectively, from a transect perpendicular to the coast between Blanes and Majorca. Profiles of viral abundance showed a pronounced peak at the DCM and a sharp decrease by one order of magnitude at 200m. Viral production, the fraction of infected cells and viral mediated mortality of bacteria was significantly higher in the total than in the size fraction in the DCM and deep water samples. The latter were found to originate from a moderate benthic nepheloid layer. These preliminary data suggest that (1) viral mediated mortality of bacteria is important in deep waters and (2) the attached fraction of bacteria was found especially prone to viral lysisPeer Reviewe

OpenReq-DD: A requirements dependency detection tool

Requirements Engineering (RE) is one of the most critical phases insoftware development. Analyzing requirements data is a laborious taskperformed by expert stakeholders using manual processes, as there areno standard automatic tools to handle this issue in a more efficientway. The purpose of this paper is to summarize the approach of theOpenReq-DD dependency detection tool developed at the OpenReqproject, which allows an automatic requirement dependency detectionapproach. The core of this proposal is based on an ontology whichdefines dependency relations between specific terminologies related tothe domain of the requirements. Using this information, it is possible toapply Natural Language Processing techniques to extract meaning fromthese requirements and relations, and Machine Learning techniques toapply conceptual clustering, with the major purpose of classifying theserequirements into the defined ontology.Peer Reviewe

Seasonal patterns of free-living and attached bacterial activity in the coastal NW Mediterranean

Aquatic Sciences Meeting, Aquatic Sciences: Global And Regional Perspectives - North Meets South, 22-27 February 2015, Granada, SpainMatter in the ocean has traditionally been divided into dissolved or particulate fractions and associated to these, the life-style of bacteria can be classified as free-living (FL) or particle-attached (PA). We followed the size structure of bacterioplankton from September 2010 to June 2013 in a NW Mediterranean Sea coastal site (Blanes Bay Microbial Observatory, BBMO). A monthly sampling was performed in surface waters following bulk seawater, but also size fractionating through 5 different filters: 0.2 – 0.8 – 3.0 – 5.0 – 10.0 µm pore size. Bacterial abundance and production, extracellular enzyme activities, and utilization of sole carbon sources (95 substrates) were determined in these fractions. We observed different patterns of activity in different size fractions. Our results also suggest an important role of meteorological events, such as precipitation, and environmental factors such as temperature, nutrients and chlorophyll a in determining the seasonal patterns of fractionated bacterial activityPeer Reviewe