Towards a North Sea ecosystem component of GOOS for assessment and management: report from a strategic workshop in Bergen 5-7 September 2001

ICES and IOC have established a joint Steering Group on GOOS (SGGOOS), which also involves the European component of GOOS (EuroGOOS). To increase the efficiency and effectiveness of the use of data products from current relevant national and international monitoring of the North Sea, the workshop invited the national agencies responsible for monitoring of the North Sea to: - establish a coordinated mechanism that could add value to existing activities by integrating data from various sources (physical, chemical, biological) to aid development of an ecosystem approach, - collaborate by means of a pilot project sponsored by ICES and EuroGOOS to demonstrate the usefulness of this approach by integrating data on oceanography and fisheries

Temporal differences in food abundance promote coexistence between two congeneric passerines

Many related species share the same environment and utilize similar resources. This is surprising because based on the principle of competitive exclusion one would predict that the superior competitor would drive the other species to extinction; coexistence is only predicted if interspecific competition is weaker than intraspecific competition. Interspecific competition is frequently reduced by differential resource use, resulting in habitat segregation. In this paper, we use the closely related collared and pied flycatcher to assess the potential of habitat differences to affect interspecific competition through a different mechanism, namely by generating temporal differences in availability of similar food resources between the two species. We found that the tree species composition of the breeding territories of the two species differed, mainly by a higher abundance of coniferous species around nest-boxes occupied by pied flycatchers. The temporal availability of caterpillars was measured using frass traps under four deciduous and two coniferous tree species. Deciduous tree species showed an early and narrow peak in abundance, which contrasted with the steady increase in caterpillar abundance in the coniferous tree species through the season. We subsequently calculated the predicted total caterpillar biomass available in each flycatcher territory. This differed between the species, with biomass decreasing more slowly in pied flycatcher territories. Caterpillar biomass is strongly correlated with the reproductive success of collared flycatchers, but much less so with pied flycatchers. However, caterpillar availability can only partly explain the differences in seasonal decline of reproductive success between the two species; we discuss additional factors that may contribute to this species difference. Overall, our results are consistent with the suggestion that minor habitat differences between these two species may contribute to promoting their coexistence

Evaluation of antibody response to an adjuvanted hapten-protein vaccine as a potential inhibitor of sexual maturation for farmed Atlantic salmon

An experimental contraceptive vaccine was evaluated in Atlantic salmon (Salmo salar). A peptide derived from the beta subunit of luteinizing hormone (LH) was conjugated to two different carrier proteins, bovine serum albumin (BSA) and keyhole limpet hemocyanin (KLH), and formulated with one of four immunostimulants in a water-in-oil emulsion. Specific antibody responses to the peptide and each carrier protein were evaluated. While the antibody response to KLH was stronger than the response to BSA, both carrier proteins stimulated comparable antibody responses to the LH peptide. The immunostimulant proved to be more important for enhancing the LH peptide antibody response than the carrier protein selection; vaccines containing a combination of Aeromonas salmonicida and Vibrio anguillarum stimulated significantly greater LH peptide antibody production than any of the other three immunostimulants evaluated at 12 weeks post-vaccination. This study provides proof-of-concept for specific antibody production against a hapten-carrier protein antigen in Atlantic salmon and reinforces the importance of vaccine immunostimulant selection

A realistic assessment of methods for extracting gene/protein interactions from free text

Background: The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger. Results: Our results show: that performance across different evaluation corpora is extremely variable; that the use of tagged (as opposed to gold standard) gene and protein names has a significant impact on performance, with a drop in F-score of over 20 percentage points being commonplace; and that a simple keyword-based benchmark algorithm when coupled with a named entity tagger outperforms two of the tools most widely used to extract gene/protein interactions. Conclusion: In terms of availability, ease of use and performance, the potential non-specialist user community interested in automatically extracting gene and/or protein interactions from free text is poorly served by current tools and systems. The public release of extraction tools that are easy to install and use, and that achieve state-of-art levels of performance should be treated as a high priority by the biomedical text mining community

Insight into real-world complexities is required to enable effective response from the aquaculture sector to climate change

This study demonstrates how a comprehensive knowledge base can be used by the aquaculture industry, researchers, and policymakers as a foundation for more targeted and detailed climate change impact analysis, risk assessments and adaptation planning. Atlantic salmon (Salmo salar) production in Norway was used as a case study and to illustrate the need to consider impacts from multiple stressors across different production stages and the wider supply chain. Based on literature searches and industry news, a total of 45 impacts and 101 adaptation responses were identified. Almost all impacts were linked to multiple climate stressors, and many adaptation responses can be used for a range of impacts. Based on the research, a move towards more targeted and detailed assessments is recommended. This can be facilitated through a strong knowledge base, further research to address complexities, and better communication between all stakeholders. The results also demonstrate the need for more climate change research that reflects the challenges that the aquaculture sector faces, where multiple stressors and the range of impacts across production stages and the wider supply chain are included. Highlighting the wide range of stressors, impacts and adaptation responses provides a more holistic understanding of the real-world complexities that aquaculture producers face. This again could facilitate adoption of more effective responses to climate change needed to maintain or increase production sustainably

Climate change with increasing seawater temperature will challenge the health of farmed Atlantic Cod (Gadus morhua L.)

Aquaculture is one of the fastest growing food production sectors in the world and further expansion is expected throughout the 21st century. However, climate change is threatening the development of the sector and action is needed to prepare the industry for the coming challenges. Using downscaled temperature projections based on the Intergovernmental Panel on Climate Change (IPCC) climate projection (Shared Socioeconomic Pathway, SSP2-4.5), we analysed potential future temperatures at a selected Atlantic cod (Gadus morhua L.) farm site in Northern Norway. Results showed that the farming area may experience increased temperatures the next 10–15 years, including more days with temperatures above 17°C. Based on the predicted future conditions, we designed a study with Atlantic cod (Gadus morhua L.) to evaluate effects from high temperature alone and in combination with Fransicella noatunensis infection. Fish were kept at 12°C and 17°C for eight weeks and samples of skin and spleen collected at different timepoints were analysed with transcriptomics, histology, scanning electron microscopy and immunohistochemistry. Results showed that high temperature had a stronger effect on the barrier functions of skin than the infection. Increased temperature induced gene expression changes in skin and spleen, heat shock protein 47 and cold inducible RNA binding protein were identified as potential gene markers for thermal stress. The effect of bacterial challenge was small at 12°C. At high temperature, the development of severe pathology in spleen coincided with a significant decrease of immunoglobulins transcripts, which contrasted with the activation of multiple immune genes. In addition, we used an in vitro model of skin biopsies and scale explants exposed to hydrogen peroxide (H2O2) to assess the effects of thermal and oxidative stress. High temperature and H2O2 reduced proliferation and migration of keratocytes, and increased expression of stress markers, and compounding effects were observed with combined stressors. Results suggest that the projected increased seawater temperature will pose a significant threat to Norwegian cod farming, affecting various biological processes and making fish more vulnerable to stressors and pathogens. Cod farming needs high attention to temperature changes, and special precautions should be taken if the temperature increases beyond cods’ thermal optimum

A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents

<p>Abstract</p> <p>Background</p> <p>A drug-drug interaction (DDI) occurs when one drug influences the level or activity of another drug. The increasing volume of the scientific literature overwhelms health care professionals trying to be kept up-to-date with all published studies on DDI.</p> <p>Methods</p> <p>This paper describes a hybrid linguistic approach to DDI extraction that combines shallow parsing and syntactic simplification with pattern matching. Appositions and coordinate structures are interpreted based on shallow syntactic parsing provided by the UMLS MetaMap tool (MMTx). Subsequently, complex and compound sentences are broken down into clauses from which simple sentences are generated by a set of simplification rules. A pharmacist defined a set of domain-specific lexical patterns to capture the most common expressions of DDI in texts. These lexical patterns are matched with the generated sentences in order to extract DDIs.</p> <p>Results</p> <p>We have performed different experiments to analyze the performance of the different processes. The lexical patterns achieve a reasonable precision (67.30%), but very low recall (14.07%). The inclusion of appositions and coordinate structures helps to improve the recall (25.70%), however, precision is lower (48.69%). The detection of clauses does not improve the performance.</p> <p>Conclusions</p> <p>Information Extraction (IE) techniques can provide an interesting way of reducing the time spent by health care professionals on reviewing the literature. Nevertheless, no approach has been carried out to extract DDI from texts. To the best of our knowledge, this work proposes the first integral solution for the automatic extraction of DDI from biomedical texts.</p