A New End-User Composition Model to Empower Knowledge Workers to Develop Rich Internet Applications

Enabling real end-user programming development is the next logical stage in the evolution of Internetwide service-based applications. Even so, the vision of end users programming their own web-based solutions has not yet materialized. This will continue to be so unless both industry and the research community rise to the ambitious challenge of devising an end-to-end compositional model for developing a new age of end-user web application development tools. This paper describes a new composition model designed to empower programming-illiterate end users to create and share their own off-the-shelf rich Internet applications in a fully visual fashion. This paper presents the main insights and outcomes of our research and development efforts as part of a number of successful European Union research projects. A framework implementing this model was developed as part of the European Seventh Framework Programme FAST Project and the Spanish EzWeb Project and allowed us to validate the rationale behind our approach.

Small-scale variation of vegetation in a mixed forest understorey is partly controlled by the effect of overstory composition on litter accumulation

We investigated how richness and composition of vascular plant species in the understory of a mixed hardwood forest stand varied with respect to the abundance and composition of the overstory. The stand is in central Spain and represents the southernmost range of distribution of several tree and herbaceous species in Europe. Understory species were identified in 46 quadrats (0.25 m2) where variables litter depth and light availability were measured. In addition, we estimated tree density, basal area, and percent basal area by tree species within 6-m-radius areas around each plot. Species richness and composition were studied using path analysis and scale-dependent geostatistical methods, respectively. We found that the relative abundance of certain trees species in the overstory was more important than total overstory abundance in explaining understory species richness. Richness decreased as soil litter depth increased, and soil litter increased as the relative proportion of Fagus sylvatica in the overstory increased, which accounted for a negative, indirect effect of Fagus sylvatica on richness. Regarding understory species composition, we found that some species distributed preferentially below certain tree species. For example, Melica uniflora was most frequent below Fagus sylvatica and Quercus petraea while the increasing proportion of Q. pyrenaica in the overstory favored the presence of Cruciata glabra, Arenaria montana, Prunus avium, Conopodium bourgaei, Holcus mollis, Stellaria media and Galium aparine in the understory. Overall, these results emphasize the importance of individual tree species in controlling the assemblage and richness of understory species in mixed stands. We conclude that soil litter accumulation is one way through which overstory composition shapes the understory community.

Supporting End-User Development through a New Composition Model: An Empirical Study

End-user development (EUD) is much hyped, and its impact has outstripped even the most optimistic forecasts. Even so, the vision of end users programming their own solutions has not yet materialized. This will continue to be so unless we in both industry and the research community set ourselves the ambitious challenge of devising end to end an end-user application development model for developing a new age of EUD tools. We have embarked on this venture, and this paper presents the main insights and outcomes of our research and development efforts as part of a number of successful EU research projects. Our proposal not only aims to reshape software engineering to meet the needs of EUD but also to refashion its components as solution building blocks instead of programs and software developments. This way, end users will really be empowered to build solutions based on artefacts akin to their expertise and understanding of ideal solutions

Microbes as engines of ecosystem function : When does community structure enhance predictions of ecosystem processes?

Peer reviewed

The Comprehensive Microbial Resource

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.

Fisiologia e formação de partículas lipídicas durante o crescimento da levedura Yarrowia lipolytica IMUFRJ 50682.

A levedura Yarrowia lipolytica tem sido muito investigada, especialmente por ser um microrganismo oleaginoso, ou seja, capaz de acumular grandes quantidades de lipídios, o que ocorre majoritariamente em organelas denominadas partículas lipídicas. Estes lipídios apresentam várias potenciais aplicações biotecnológicas, como por exemplo na produção de óleo microbiano (single cell oil) e na produção de biodiesel. Durante este projeto de mestrado, objetivou-se estudar a fisiologia de duas linhagens da levedura Y. lipolytica, sendo uma tradicionalmente estudada pela comunidade científica internacional (linhagem w29) e outra isolada da Baía da Guanabara, no Rio de Janeiro (linhagem IMUFRJ 50682). Foram realizados cultivos em frascos agitados tipo Erlenmeyer com defletores tampados com algodão (volume total 500 mL, volume de meio 100 mL, 28 oC e 200 rotações por minuto), durante os quais foi possível: 1) escolher um meio de cultivo de composição totalmente definida, com tiamina como único fator de crescimento, adequado a estudos de fisiologia quantitativa com esta levedura; 2) verificar que Y. lipolytica não é capaz de crescer com sacarose ou xilose como única fonte de carbono; 3) verificar que Y. lipolytica cresce com velocidade específica de crescimento máxima (Máx) de 0,49 h-1 num meio complexo contendo glicose, extrato de levedura e peptona (meio YPD), 0,31 h-1 em meio definido com glicose como única fonte de carbono e 0,35 h-1 no mesmo meio, mas com glicerol como única fonte de carbono, sem excreção de metabólitos para o meio de cultivo; 4) verificar que ocorreu limitação por oxigênio nos cultivos em frasco agitado, sendo este o motivo pelo qual as células deixaram de crescer exponencialmente; 5) verificar que o uso de ureia, em vez de sulfato de amônio, como fonte de nitrogênio, contribui para uma variação menor do pH durante os cultivos, sem prejuízo ao crescimento da levedura; 6) observar que, ao se restringir a oferta de nitrogênio à levedura (aumento da relação C/N inicial no meio de 12,6 para 126), as células têm sua morfologia alterada e apresentam maior quantidade de partículas lipídicas; 7) determinar uma composição elementar para a biomassa de Y. lipolytica (CH1,98O0,58N0,13), em que os átomos de carbono encontram-se em média mais reduzidos do que na biomassa de leveduras como Saccharomyces cerevisiae e Dekkera bruxellensis. Foram também realizados cultivos em biorreator em batelada (1 L de volume útil, 28 oC, aerobiose plena e pH controlado em 5,0), durante os quais foi possível: a) estabelecer um protocolo de cultivo para Y. lipolytica em biorreator (que envolvem agitação mecânica, aeração e uso de anti-espumante, entre outras diferenças em relação aos cultivos em frasco); b) confirmar os valores dos principais parâmetros fisiológicos apresentados por esta levedura, anteriormente obtidos a partir de cultivos em frasco; c) confirmar que o fator de conversão de substrato a células (Yx/s) é maior para cultivos realizados com glicerol como fonte única de carbono (0,53 g/g para a linhagem IMUFRJ 50682), do que com glicose (0,48 g/g para a mesma linhagem). Finalmente, cultivos realizados em quimiostato com glicerol como fonte de carbono e energia, limitados por amônio (fonte de nitrogênio, relação C/N 126), às vazões específicas de 0,25 h-1 e 0,15 h-1, permitiram observar que o número de partículas lipídicas por célula de Y. lipolytica permaneceu em torno de 2 em ambas as situações e houve uma diminuição no teor de nitrogênio nas células quando a velocidade específica de crescimento diminuiu de 0,25 para 0,15 h-1.

Biogas from MSW landfill: Composition and determination of chlorine content with the AOX (adsorbable organically bound halogens) technique

An exhaustive characterization of the biogas from some waste disposal facilities has been carried out. The analysis includes the main components (methane, carbon dioxide, nitrogen and oxygen) as well as trace components such as hydrogen sulphide, ammonia and VOCs (volatile organic compounds) including siloxanes and halogenated compounds. VOCs were measured by GC/MS (Gas Chromatography/Mass Spectrometry) using two different procedures: thermal desorption of the Tenax TA and Carbotrap 349 tubes and SPME (Solid Phase Micro-Extraction). A method has been established to measure the total halogen content of the biogas with the AOX (adsorbable organically bound halogens) technique. The equipment used to analyze the samples was a Total Organic Halogen Analyzer (TOX-100). Similar results were obtained when comparing the TOX (Total Organic Halogen) values with those obtained by GC/MS. The halogen content in all the samples was under 22 mg Cl/Nm3 which is below the limit of 150 mg/Nm3 proposed in the Spanish Regulations for any use of the biogas. The low chlorine content in the biogas studied, as well as the low content of other trace compounds, makes it suitable for use as a fuel for electricity generating engines.

Community attributes determine facilitation potential in a semi-arid steppe

Studies on positive plant–plant relations have traditionally focused on pair-wise interactions. Conversely, the interaction with other co-occurring species has scarcely been addressed, despite the fact that the entire community may affect plant performance. We used woody vegetation patches as models to evaluate community facilitation in semi-arid steppes. We characterized biotic and physical attributes of 53 woody patches (patch size, litter accumulation, canopy density, vegetation cover, species number and identity, and phylogenetic distance), and soil fertility (organic C and total N), and evaluated their relative importance for the performance of seedlings of Pistacia lentiscus, a keystone woody species in western Mediterranean steppes. Seedlings were planted underneath the patches, and on their northern and southern edges. Woody patches positively affected seedling survival but not seedling growth. Soil fertility was higher underneath the patches than elsewhere. Physical and biotic attributes of woody patches affected seedling survival, but these effects depended on microsite conditions. The composition of the community of small shrubs and perennial grasses growing underneath the patches controlled seedling performance. An increase in Stipa tenacissima and a decrease in Brachypodium retusum increased the probability of survival. The cover of these species and other small shrubs, litter depth and community phylogenetic distance, were also related to seedling survival. Seedlings planted on the northern edge of the patches were mostly affected by attributes of the biotic community. These traits were of lesser importance in seedlings planted underneath and in the southern edge of patches, suggesting that constraints to seedling establishment differed within the patches. Our study highlights the importance of taking into consideration community attributes over pair-wise interactions when evaluating the outcome of ecological interactions in multi-specific communities, as they have profound implications in the composition, function and management of semi-arid steppes.

Variations in coastal fish species composition captured by traps in Romsdalsfjord, Western Norway

Fish traps are widely used in Norwegian fjords, especially those designed for monitoring salmonid populations in the marine environment, although many other marine fish species are also captured. The composition and spatio-temporal variations of fish species captured by fish traps were monitored in five different coastal locations throughout the Romsdalsfjord region, Western Norway, from May to August during the three consecutive years (2011–2013). Twenty-three fish species were captured by traps in coastal waters, both resident and migratory fishes. The most common fish and with greater catchability were saithe (Pollachis virens) and sea trout (Salmo trutta), followed by cod (Gadus morhua), pollack (P. pollachius), herring (Clupea harengus) and mackerels (Trachurus trachurus and Scomber scombrus). However, the captured assemblage presented great spatial and seasonal variations, in terms of mean daily catch, probably associated with hydrographical conditions and migrational patterns. Information obtained in this study will help us to better understand the compositions and dynamic of coastal fish populations inhabiting Norwegian coastal waters. In addition, traps are highly recommended as a management tool for fish research (e.g. fish-tagging experiments, mark and recapture) and conservation purposes (coastal use and fisheries studies).

Potential Shifts in Canadian High Arctic Sedimentary Organic Matter Composition With Permafrost Active Layer Detachments

Increased temperature and precipitation in Arctic regions have led to deeper thawing and structural instability in permafrost soil. The resulting localized disturbances, referred to as active layer detachments (ALDs), may transport organic matter (OM) to more biogeochemically active zones. To examine this further, solid state cross polarization magic angle spinning 13C nuclear magnetic resonance (CPMAS NMR) and biomarker analysis were used to evaluate potential shifts in riverine sediment OM composition due to nearby ALDs within the Cape Bounty Arctic Watershed Observatory, Nunavut, Canada. In sedimentary OM near ALDs, NMR analysis revealed signals indicative of unaltered plant-derived material, likely derived from permafrost. Long chain acyclic aliphatic lipids, steroids, cutin, suberin and lignin occurred in the sediments, consistent with a dominance of plant-derived compounds, some of which may have originated from permafrost-derived OM released by ALDs. OM degradation proxies for sediments near ALDs revealed less alteration in acyclic aliphatic lipids, while constituents such as steroids, cutin, suberin and lignin were found at a relatively advanced stage of degradation. Phospholipid fatty acid analysis indicated that microbial activity was higher near ALDs than downstream but microbial substrate limitation was prevalent within disturbed regions. Our study suggests that, as these systems recover from disturbance, ALDs likely provide permafrost-derived OM to sedimentary environments. This source of OM, which is enriched in labile OM, may alter biogeochemical patterns and enhance microbial respiration within these ecosystems.

Limitations of microbial hydrocarbon degradation at the Amon Mud Volcano (Nile Deep Sea Fan)

The Amon mud volcano (MV), located at 1250 m water depth on the Nile Deep Sea Fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulphate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition and microbial activities over three years, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulphide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. Furthermore, within three years, cell numbers and hydrocarbon degrading activity increased at the gas-seeping sites. The low microbial activity in the hydrocarbon-vented areas of Amon mud volcano is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer mud volcano area is limited by hydrocarbon transport.

Mesocosm experiment on warming and acidification effects on phytoplankton composition and cell size

While the isolated responses of marine phytoplankton to climate warming and to ocean acidification have been studies intensively, studies on the combined effect of both aspects of Global Change are still scarce. Therefore, we performed a mesocosm experiment with a factorial combination of temperature (9 and 15°C) and pCO2 (560 ppm and 1400 ppm) with a natural autumn plankton community from the western Baltic Sea. Temporal trajectories of total biomass and of the biomass of the most important higher taxa followed similar patterns in all treatments. When averaging over the entire time course, phytoplankton biomass decreased with warming and increased with CO2 under warm conditions. The contribution of the two dominant higher phytoplankton taxa (diatoms and cryptophytes) and of the 4 most important species (3 diatoms, 1 cryptophyte) did not respond to the experimental treatments. Taxonomic composition of phytoplankton showed only responses at the level of subdominant and rare species. Phytoplankton cell sizes increased with CO2 addition and decreased with warming. Both effects were stronger for larger species. Warming effects were stronger than CO2 effects and tended to counteract each other. Phytoplankton communities without calcifying species and exposed to short-term variation of COO2 seem to be rather resistant to ocean acidification.