CI-Miner: semantically enhancing scientific processes

The realization of an international cyberinfrastructure of shared resources to overcome time and space limitations is challenging scientists to rethink how to document their processes. Many known scientific process requirements that would normally be considered impossible to implement a few years ago are close to becoming a reality for scientists, such as large scale integration and data reuse, data sharing across distinct scientific domains, comprehensive support for explaining process results, and full search capability for scientific products across domains. This article introduces the CI-Miner approach that can be used to aggregate knowledge about scientific processes and their products through the use of semantic annotations. The article shows how this aggregated knowledge is used to benefit scientists during the development of their research activities. The discussion is grounded on lessons learned through the use of CI-Miner to semantically annotate scientific processes in the areas of geo-sciences, environmental sciences and solar physics: A use case in the field of geo-science illustrates the CI-Miner approach in action.     

Numerical analysis of an embankment built on soft soil reinforced with deep mixing columns: Parametric study

The behaviour of an embankment built on normally consolidated soft soil reinforced with deep mixing columns is studied using a coupled soil–water formulation. The numerical predictions are analysed in terms of settlements, increments in vertical effective stresses and excess pore pressures. Firstly, the effectiveness of the use of deep mixing columns is studied. Afterwards, a parametric analysis is performed to study the influence on the soil-columns system of the replacement ratio (columns’ spacing), the deformability of the embankment and columns, and the coefficient of vertical permeability of the columns.     

Efforts to reduce sea turtle bycatch in the shrimp fishery in Northeastern Brazil through a co-management process

The neritic waters of the state of Sergipe in Northeastern Brazil is adjacent to the main nesting area of the olive ridley sea turtles (Lepidochelys olivacea) in the Western Atlantic Ocean and an important area for shrimp trawl fishery. To address the problem of incidental mortality of sea turtles captured during trawling and reduce the risk of overexploitation of shrimp stocks, Projeto TAMAR/ICMBio, a Brazilian sea turtle conservation program, has adopted two main strategies: (1) the implementation of a marine monitoring program and (2) active participation in local forums. This paper describes the conflicts among stakeholders, the arrangements and established mechanisms of negotiation aimed to protect sea turtles and shrimp grounds, and strategies to reduce conflicts between user groups. The analysis of this co-management process highlights the importance of stakeholder participation in resource management decision-making through a cooperative process, the role assumed by non-governmental organizations as mediators, and the factors that influence this system. The key factors and actions learnt from the current study include clear identification of the conflicts, identification of stakeholders – both local and external, and local leaders, encouragement of actors and leaders to participate, support and strengthening of local groups, legitimization of the discussion forums through involvement with government, formalization of decisions taken through legislation, and monitoring of the management efficacy.     

Wind-Speed Controls on Scalar Gradients,Fluxes, and Cospectra in the Stable Boundary Layer

Boundary-Layer Meteorology - Vertical profiles of temperature, water vapour, and carbon dioxide ( $$\mathrm {CO}_{2}\,$$ ) densities are analyzed, together with the respective turbulent fluxes of...     

Study of the influence of different organic pollutants on Cu accumulation by Halimione portulacoides

The influence of each of four organic pollutants selected from among those commonly found in coastal areas, 1,1-dichloro-2,2-bis(p-chlorophenyl) ethylene (DDE), monobutyltin (MBT), Triton X-100 and polycyclic aromatic hydrocarbons (PAHs), on Cu accumulation by Halimione portulacoides was investigated. Experiments were carried out in a laboratory setting, either in hydroponics (sediment elutriate) or in a salt marsh sediment (Cávado River, NW Portugal) soaked in elutriate. Groups of H. portulacoides were exposed to media for 6 days spiked with 10 mg/L Cu(II) and with one of the selected pollutants, at an environmentally realistic concentration. DDE and MBT did not cause any major change on Cu accumulation by H. portulacoides, whereas PAHs slightly increased accumulation only in hydroponics i.e. in the absence of sediment. On the other hand, the non-ionic surfactant Triton X-100 markedly favoured Cu accumulation on plant roots both in the presence and absence of sediment. The addition of DDE, MBT and Triton X-100 also favoured Cu solubility from sediments. Therefore, the simultaneous presence of pollutants from different nature (inorganic and organic) in the estuarine environment may result in a composition of water column, pore water, sediment or biota different of that expected considering the effect of each individual pollutant.     

Can PAHs influence Cu accumulation by salt marsh plants?

The presence of polycyclic aromatic hydrocarbons (PAHs) may change the mechanisms of metal uptake, thus influencing kinetics and extent of metal phytoextraction. Studies on the subject are scarce, particularly for salt marsh plants. The aim of this work was to investigate the effect of PAHs on the uptake of Cu by Halimione portulacoides, a plant commonly found in salt marshes. Experiments were carried out in the laboratory, either in hydroponics (sediment elutriate) or in sediment soaked in elutriate, which were prepared with sediment and water from a salt marsh of the Cavado river estuary (NW Portugal). Groups of H. portulacoides (grown in a greenhouse) were exposed to those media during six days. Cu(2+) (as Cu(NO(3))(2)), 10(2) and 10(4)mugl(-1), was added to the media as well as 1.6mugl(-1) of the sixteen EPA priority PAHs (0.1mugl(-1) of each PAHs). Cu was assayed in solutions, sediments and different plant tissues before and after experiments. After exposure, photosynthetic efficiency and levels of chlorophylls were also measured, indicating that plant stress indicators were identical in all plants independently of the media to which the plants were exposed. PAHs influenced both the soluble Cu fraction and Cu uptake by plants. The amounts of metal accumulated in both roots and stems were significantly higher when the 10(4)mugl(-1) of Cu enriched elutriate was amended with PAHs. Thus, results suggest that PAHs may modify Cu solubility, the Cu sorption by plants and/or the passive penetration of Cu into the root cells. Therefore, the combined effects of different types of pollutants should be taken in consideration when studying the remediation potential of plants, namely in terms of phytoextraction.     

Modélisation glacio-hydrologique et gestion des ressources en eau dans les Andes équatoriennes : l’exemple de Quito

La forte croissance socio-économique de Quito a conduit à d’importants projets de transferts interbassins, intensifiant la mobilisation des ressources d’altitude situées dans des zones écologiques sensibles et connaissant une fonte accélérée des glaciers. Afin d’étudier divers scénarios d’évolutions, nous proposons une modélisation du continuum climat/glacier/hydrologie/gestion des ressources en eau. Utilisant l’outil Water Evaluation and Planning (WEAP), nous avons développé : (1) une modélisation hydro-climatologique semi-distribuée avec des données mensuelles homogénéisées par vectorisation régionale ; (2) une modélisation de la production en eau des glaciers et de leur évolution interannuelle ; (3) une modélisation en unités hydrologiques distinguant différentes couvertures de sols ; et (4) une modélisation de la gestion distinguant droits, allocation et usages de l’eau. Nous présentons les résultats du calage hydrologique mensuel (1963–2006), en étudiant particulièrement l’équifinalité de diverses paramétrisations. Nous montrons la souplesse, la robustesse et les limites de la modélisation proposée, contribuant à cerner différentes incertitudes dans l’évaluation de scénarios prospectifs.     

Transgressive dunefield landforms and vegetation associations,Doña Juana,Veracruz, Mexico

Transgressive dune fields often comprise a multiplicity of landforms where vegetation processes largely affect landform dynamics, which in turn, also affect vegetation processes. These associations have seldom been studied in detail. This paper examines four separate landform types in a complex coastal transgressive dunefield located in the central Gulf of Mexico, in order to assess the relationships between dunefield habitat, local environmental factors, vegetation associations and landform evolution. Topographic surveys using tape and clinometer were conducted in conjunction with vegetation survey transects at four locations across the Doña Juana dunefield. Vegetation surveys allowed the estimation of relative plant cover of each plant species found along the transects. A large variety of landforms were found at the Doña Juana Dunefield: deflation plains, gegenwalle (counter) ridges, transverse dune trailing ridges, blowouts and parabolic dunes, aklé (fish‐scale shaped) dunefields and precipitation ridges, with plant species associations developing on these different landforms equally variable. Flood tolerant species were located in the lower parts (deflation plain and gegenwalle ridges) whereas the older and dryer parts were covered by coastal matorral shrubs. Burial‐tolerant species were dominant in the most mobile areas (blowouts and aklé dunefield and margin). The dune trailing ridge, with relatively milder conditions, showed the highest richness, with no dominant species. A dual interaction was found such that colonizing species both create and affect topography, and in turn, topography determines vegetation association and succession patterns. In coastal dunes, the vegetation and abiotic environment (namely the different landforms and the inherent micronevironmental variability) interact tightly and generate a complex and highly dynamic biogeomorphic system where substrate mobility and colonization processes reinforce one another in positive feedback. Copyright © 2010 John Wiley & Sons, Ltd.     

The earth system model of intermediate complexity CLIMBER-3α. Part I: description and performance for present-day conditions

We herein present the CLIMBER-3α Earth System Model of Intermediate Complexity (EMIC), which has evolved from the CLIMBER-2 EMIC. The main difference with respect to CLIMBER-2 is its oceanic component, which has been replaced by a state-of-the-art ocean model, which includes an ocean general circulation model (GCM), a biogeochemistry module, and a state-of-the-art sea-ice model. Thus, CLIMBER-3α includes modules describing the atmosphere, land-surface scheme, terrestrial vegetation, ocean, sea ice, and ocean biogeochemistry. Owing to its relatively simple atmospheric component, it is approximately two orders of magnitude faster than coupled GCMs, allowing the performance of a much larger number of integrations and sensitivity studies as well as longer ones. At the same time its oceanic component confers on it a larger degree of realism compared to those EMICs which include simpler oceanic components. The coupling does not include heat or freshwater flux corrections. The comparison against the climatologies shows that CLIMBER-3α satisfactorily describes the large-scale characteristics of the atmosphere, ocean and sea ice on seasonal timescales. As a result of the tracer advection scheme employed, the ocean component satisfactorily simulates the large-scale oceanic circulation with very little numerical and explicit vertical diffusion. The model is thus suited for the study of the large-scale climate and large-scale ocean dynamics. We herein describe its performance for present-day boundary conditions. In a companion paper (Part II), the sensitivity of the model to variations in the external forcing, as well as the role of certain model parameterisations and internal parameters, will be analysed.