Workflow-centric research objects: First class citizens in scholarly discourse.

A workflow-centric research object bundles a workflow, the provenance of the results obtained by its enactment, other digital objects that are relevant for the experiment (papers, datasets, etc.), and annotations that semantically describe all these objects. In this paper, we propose a model to specify workflow-centric research objects, and show how the model can be grounded using semantic technologies and existing vocabularies, in particular the Object Reuse and Exchange (ORE) model and the Annotation Ontology (AO).We describe the life-cycle of a research object, which resembles the life-cycle of a scienti?c experiment

A dp53-Dependent Mechanism Involved in Coordinating Tissue Growth in Drosophila

A study in the Drosophila wing suggests a crucial role of p53 in the coordination of growth between adjacent cell populations to maintain organ proportions and shape

Trends and outcome of neoadjuvant treatment for rectal cancer: A retrospective analysis and critical assessment of a 10-year prospective national registry on behalf of the Spanish Rectal Cancer Project

Introduction: Preoperative treatment and adequate surgery increase local control in rectal cancer. However, modalities and indications for neoadjuvant treatment may be controversial. Aim of this study was to assess the trends of preoperative treatment and outcomes in patients with rectal cancer included in the Rectal Cancer Registry of the Spanish Associations of Surgeons. Method: This is a STROBE-compliant retrospective analysis of a prospective database. All patients operated on with curative intention included in the Rectal Cancer Registry were included. Analyses were performed to compare the use of neoadjuvant/adjuvant treatment in three timeframes: I)2006–2009; II)2010–2013; III)2014–2017. Survival analyses were run for 3-year survival in timeframes I-II. Results: Out of 14, 391 patients, 8871 (61.6%) received neoadjuvant treatment. Long-course chemo/radiotherapy was the most used approach (79.9%), followed by short-course radiotherapy ± chemotherapy (7.6%). The use of neoadjuvant treatment for cancer of the upper third (15-11 cm) increased over time (31.5%vs 34.5%vs 38.6%, p = 0.0018). The complete regression rate slightly increased over time (15.6% vs 16% vs 18.5%; p = 0.0093); the proportion of patients with involved circumferential resection margins (CRM) went down from 8.2% to 7.3%and 5.5% (p = 0.0004). Neoadjuvant treatment significantly decreased positive CRM in lower third tumors (OR 0.71, 0.59–0.87, Cochrane-Mantel-Haenszel P = 0.0008). Most ypN0 patients also received adjuvant therapy. In MR-defined stage III patients, preoperative treatment was associated with significantly longer local-recurrence-free survival (p < 0.0001), and cancer-specific survival (p < 0.0001). The survival benefit was smaller in upper third cancers. Conclusion: There was an increasing trend and a potential overuse of neoadjuvant treatment in cancer of the upper rectum. Most ypN0 patients received postoperative treatment. Involvement of CRM in lower third tumors was reduced after neoadjuvant treatment. Stage III and MRcN + benefited the most

Spatial and Temporal Variations in the Annual Pollen Index Recorded by Sites Belonging to the Portuguese Aerobiology Network

This study presents the findings of a 10-year survey carried out by the Portuguese Aerobiology Network (RPA) at seven pollen-monitoring stations: five mainland stations (Oporto, Coimbra, Lisbon, Évora and Portimão) and two insular stations [Funchal (Madeira archipelago) and Ponta Delgada (Azores archipelago)]. The main aim of the study was to examine spatial and temporal variations in the Annual Pollen Index (API) with particular focus on the most frequently recorded pollen types. Pollen monitoring (2003–2012) was carried out using Hirst-type volumetric spore traps, following the minimum recommendations proposed by the European Aerobiology Society Working Group on Quality Control. Daily pollen data were examined for similarities using the Kruskal–Wallis nonparametric test and multivariate regression trees. Simple linear regression analysis was used to describe trends in API. The airborne pollen spectrum at RPA stations is dominated by important allergenic pollen types such as Poaceae, Olea and Urticaceae. Statistically significant differences were witnessed in the API recorded at the seven stations. Mean API is higher in the southern mainland cities, e.g. Évora, Lisbon and Portimão, and lower in insular and littoral cities. There were also a number of significant trends in API during the 10-year study. This report identifies spatial and temporal variations in the amount of airborne pollen recorded annually in the Portuguese territory. There were also a number of significant changes in API, but no general increases in the amount of airborne pollen

Influence of oak origin and ageing conditions on wine spoilage by Brettanomyces yeasts

© 2015 Elsevier Ltd. The use of oak wood is a common practice for the maturation of higher quality wines, but this practice also has been occasionally related with the spoilage of wines with ethylphenols produced by Brettanomyces/Dekkera yeasts. This work studied the presence of these yeasts and ethylphenol production in the same wine aged in different conditions: aerobic/anaerobic, sulfur dioxide additions, and oak origin of the casks used (American, French, Russian and Chinese), with the aim of characterizing factors affecting the development and production of volatile phenols by Brettanomyces. Results obtained indicated the spoilage risk exists when Brettanomyces cells are present, even at a low level, in wines subjected to ageing, both in the cask and the bottle. Brettanomyces presence (cfu/ml and strains) and ethylphenol production during ageing, is affected more by the ageing conditions (aerobic/anaerobic and sulfiting) than by the origin of the oak.This study has been undertaken with a grant from the Government of La Rioja, Spain (Project PR-11-11).Peer Reviewe

Influence des conditions de vieillisement sur l'alteration de vins par levures brettanomyces

Póster presentado en el 38th World Congress of Vine and Wine (OIV), celebrado en Mainz (Alemania) del 5 al 10 de julio de 2015.[EN] This work studied the presence of Brettanomyces/ Dekkera yeast strains and ethylphenol production in the same wine aged in different conditions: aerobic/ anaerobic, sulfur dioxide additions, and oak origin of the casks used (American, French, Russian and Chinese), with the aim of characterizing factors affecting the development and production of volatile phenols by Brettanomyces. Results obtained indicated the spoilage risk exists when Brettanomyces cells are present, even at a low level, in wines subjected to ageing, both in the cask and the bottle. Brettanomyces presence (cfu/ml and strains) and ethylphenol production during ageing, is affected more by the ageing conditions (aerobic/anaerobic and sulfiting) than by the origin of the oak.[ES] Este trabajo estudió la presencia de levaduras Brettanomyces/ Dekkera y la producción de etilfenoles en el mismo vino envejecido en diferentes condiciones: aerobiosis/ anaerobiosis, adición de anhídrido sulfuroso y origen de las barricas de roble empleadas (americano, francés, ruso y chino). El objetivo fue estudiar si dichos factores afectan al desarrollo de Brettanomyces y a la producción de fenoles volátiles en el vino. Los resultados obtenidos indicaron que el riesgo de alteración existe cuando las células de Brettanomyces están presentes en los vinos sometidos a envejecimiento, incluso en niveles bajos, y tanto en barrica como en botella. Las condiciones de envejecimiento (aerobiosis/ anaerobiosis y sulfitado), afectaron más al desarrollo de Brettanomyces (ufc/ ml y cepas) y a la producción de etilfenoles que el origen del roble empleado.[FR] Ce travail a étudié la présence de souches de levures Brettanomyces/ Dekkera et la production d’ éthylphénols dans le même vin vieilli dans des différentes conditions: aérobie/ anaérobie, ajouts de dioxyde de soufre, et l'origine de chêne des fûts utilisés (américaine, française, russe et chinois), avec le but d’étudier si ces facteurs influent sur le développement de Brettanomyces et la production de phénols volatils dans le vin. Les résultats obtenus ont montré que le risque d'altération existe lorsque les cellules de Brettanomyces sont présentes, même à un faible niveau, dans les vins soumis à un vieillissement, à la fois dans le fût et la bouteille. La présence de Brettanomyces (ufc/ ml et les souches) et la production d’ éthylphénols au cours du vieillissement est plus influencée par les conditions de vieillissement (aérobie/ anaérobie et sulfitage) que par l'origine du chêne.Peer Reviewe

Introducing Context and Context-awareness in Data Integration: Identifying the Problem and a Preliminary Case Study on Informed Consent

peer reviewe

Workflow-centric research objects:First class citizens in scholarly discourse

A workflow-centric research object bundles a workflow, the provenance of the results obtained by its enactment, other digital objects that are relevant for the experiment (papers, datasets, etc.), and annotations that semantically describe all these objects. In this paper, we propose a model to specify workflow-centric research objects, and show how the model can be grounded using semantic technologies and existing vocabularies, in particular the Object Reuse and Exchange (ORE) model and the Annotation Ontology (AO).We describe the life-cycle of a research object, which resembles the life-cycle of a scientific experiment.</p