Design and multicriteria evaluation of regionalized test cases in organic crops without animal production

What are the performances of different stockless organic crops systems? And more specifically, are there rotations more efficient than other for economic, technical and / or environmental criteria? This work aims to present the method of co-construction of simulated cases for an evaluation of economic, environmental and technical performances, at rotation and production system scale. Fifteen «test cases» have been defined in the partner regions of CASDAR projects ROTAB and ProtéAB and evaluated with a set of quantitative and non-aggregated indicators (tool Systerre ®). The results provided many references at different scales. In the current context, profitability was ensured for all cases studied, but the production environment had a major impact on the overall performance. Long rotations with multiannual crop rotation (often alfalfa), sometimes less economically efficient, had strong advantages regarding agricultural sustainability. They also seemed to be less sensitive to changes in economic conditions and provided that the crop harvest was performed by a company, (it requires less work time). The typical cases are upgradeable tools to be adapted to different simulations or prospective studies

Human streptococcus agalactiae strains in aquatic mammals and fish

<p>Background: In humans, Streptococcus agalactiae or group B streptococcus (GBS) is a frequent coloniser of the rectovaginal tract, a major cause of neonatal infectious disease and an emerging cause of disease in non-pregnant adults. In addition, Streptococcus agalactiae causes invasive disease in fish, compromising food security and posing a zoonotic hazard. We studied the molecular epidemiology of S. agalactiae in fish and other aquatic species to assess potential for pathogen transmission between aquatic species and humans.</p> <p>Methods: Isolates from fish (n = 26), seals (n = 6), a dolphin and a frog were characterized by pulsed-field gel electrophoresis, multilocus sequence typing and standardized 3-set genotyping, i.e. molecular serotyping and profiling of surface protein genes and mobile genetic elements.</p> <p>Results: Four subpopulations of S. agalactiae were identified among aquatic isolates. Sequence type (ST) 283 serotype III-4 and its novel single locus variant ST491 were detected in fish from Southeast Asia and shared a 3-set genotype identical to that of an emerging ST283 clone associated with invasive disease of adult humans in Asia. The human pathogenic strain ST7 serotype Ia was also detected in fish from Asia. ST23 serotype Ia, a subpopulation that is normally associated with human carriage, was found in all grey seals, suggesting that human effluent may contribute to microbial pollution of surface water and exposure of sea mammals to human pathogens. The final subpopulation consisted of non-haemolytic ST260 and ST261 serotype Ib isolates, which belong to a fish-associated clonal complex that has never been reported from humans.</p> <p>Conclusions: The apparent association of the four subpopulations of S. agalactiae with specific groups of host species suggests that some strains of aquatic S. agalactiae may present a zoonotic or anthroponotic hazard. Furthermore, it provides a rational framework for exploration of pathogenesis and host-associated genome content of S. agalactiae strains.</p&gt

Alkemio: association of chemicals with biomedical topics by text and data mining

The PubMed(R) database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have implemented the Alkemio text mining web tool and SOAP web service to help in this task. The tool uses biomedical articles discussing chemicals (including drugs), predicts their relatedness to the query topic with a naïve Bayesian classifier and ranks all chemicals by P-values computed from random simulations. Benchmarks on seven human pathways showed good retrieval performance (areas under the receiver operating characteristic curves ranged from 73.6 to 94.5%). Comparison with existing tools to retrieve chemicals associated to eight diseases showed the higher precision and recall of Alkemio when considering the top 10 candidate chemicals. Alkemio is a high performing web tool ranking chemicals for any biomedical topics and it is free to non-commercial users. Availability: http://cbdm.mdc-berlin.de/∼medlineranker/cms/alkemio

KNOWING, CHARACTERIZING AND ASSESSING SYSTEMS OF ORGANIC CROP ROTATIONS

The choice of crop rotations in organic stockless cropping systems is the first leverage used to manage technical issues (to maintain soil fertility, to control pest and weeds) and economic issues (to insure income). The RotAB project (French Casdar funding 2008-2010) implemented complementary approaches to better knowing, characterizing and assessing arable crop rotations. Their conception depends on numerous factors such as the types of soil and climate (on which depend the types of crops, yield potential, possibility of mechanical weed control…) or the economic context (existence of outlets and continuity of markets). If nitrogen supply and weed control are the most important agronomic issues of organic farmers in stockless cropping systems, phosphorus availability appears to be the next important issue for soil fertility and system sustainability

OPTIMIZING AND PROMOTING MECHANICAL WEED CONTROL IN ARABLE CROPS

Within an overall strategy of weed flora management, mechanical weed control practices are complementary solutions to agronomic levers (crop rotation, tillage...) in weed control. Acquiring knowledge and communicating on the effectiveness of mechanical practices and tools appear essential. The "Mechanical Weed Control" project in France conducted between 2009 and 2012 made progress in this regard. The project shows that research activities are to be continued (experimentation, analysis of practices) and should be complemented by promotion that focuses on participatory approaches where farmers are involved in the implementation of these new practices

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Biomedical literature curation is the process of automatically and/or manually deriving knowledge from scientific publications and recording it into specialized databases for structured delivery to users. It is a slow, error-prone, complex, costly and, yet, highly important task. Previous experiences have proven that text mining can assist in its many phases, especially, in triage of relevant documents and extraction of named entities and biological events. Here, we present the curation pipeline of the CellFinder database, a repository of cell research, which includes data derived from literature curation and microarrays to identify cell types, cell lines, organs and so forth, and especially patterns in gene expression. The curation pipeline is based on freely available tools in all text mining steps, as well as the manual validation of extracted data. Preliminary results are presented for a data set of 2376 full texts from which >4500 gene expression events in cell or anatomical part have been extracted. Validation of half of this data resulted in a precision of ~50% of the extracted data, which indicates that we are on the right track with our pipeline for the proposed task. However, evaluation of the methods shows that there is still room for improvement in the named-entity recognition and that a larger and more robust corpus is needed to achieve a better performance for event extraction. Database URL: http://www.cellfinder.org

CXCL5 limits macrophage foam cell formation in atherosclerosis

The ELR+-CXCL chemokines have been described typically as potent chemoattractants and activators of neutrophils during the acute phase of inflammation. Their role in atherosclerosis, a chronic inflammatory vascular disease, has been largely unexplored. Using a mouse model of atherosclerosis, we found that CXCL5 expression was upregulated during disease progression, both locally and systemically, but was not associated with neutrophil infiltration. Unexpectedly, inhibition of CXCL5 was not beneficial but rather induced a significant macrophage foam cell accumulation in murine atherosclerotic plaques. Additionally, we demonstrated that CXCL5 modulated macrophage activation, increased expression of the cholesterol efflux regulatory protein ABCA1, and enhanced cholesterol efflux activity in macrophages. These findings reveal a protective role for CXCL5, in the context of atherosclerosis, centered on the regulation of macrophage foam cell formation

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

BACKGROUND: Biological knowledge is represented in scientific literature that often describes the function of genes/proteins (bioentities) in terms of their interactions (biointeractions). Such bioentities are often related to biological concepts of interest that are specific of a determined research field. Therefore, the study of the current literature about a selected topic deposited in public databases, facilitates the generation of novel hypotheses associating a set of bioentities to a common context. RESULTS: We created a text mining system (LAITOR: Literature Assistant for Identification of Terms co-Occurrences and Relationships) that analyses co-occurrences of bioentities, biointeractions, and other biological terms in MEDLINE abstracts. The method accounts for the position of the co-occurring terms within sentences or abstracts. The system detected abstracts mentioning protein-protein interactions in a standard test (BioCreative II IAS test data) with a precision of 0.82-0.89 and a recall of 0.48-0.70. We illustrate the application of LAITOR to the detection of plant response genes in a dataset of 1000 abstracts relevant to the topic. CONCLUSIONS: Text mining tools combining the extraction of interacting bioentities and biological concepts with network displays can be helpful in developing reasonable hypotheses in different scientific backgrounds