Identity in research infrastructure and scientific communication: Report from the 1st IRISC workshop, Helsinki Sep 12-13, 2011

Motivation for the IRISC workshop came from the observation that identity and digital identification are increasingly important factors in modern scientific research, especially with the now near-ubiquitous use of the Internet as a global medium for dissemination and debate of scientific knowledge and data, and as a platform for scientific collaborations and large-scale e-science activities.

The 1 1/2 day IRISC2011 workshop sought to explore a series of interrelated topics under two main themes: i) unambiguously identifying authors/creators & attributing their scholarly works, and ii) individual identification and access management in the context of identity federations. Specific aims of the workshop included:

• Raising overall awareness of key technical and non-technical challenges, opportunities and developments.
• Facilitating a dialogue, cross-pollination of ideas, collaboration and coordination between diverse – and largely unconnected – communities.
• Identifying & discussing existing/emerging technologies, best practices and requirements for researcher identification.

This report provides background information on key identification-related concepts & projects, describes workshop proceedings and summarizes key workshop findings

Pesticide residues in boreal arable soils: Countrywide study of occurrence and risks

Large volumes of pesticides are applied every year to support agricultural production. The intensive use of pesticides affects soil quality and health, but soil surveys on pesticide residues are scarce, especially for northern Europe. We investigated the occurrence of 198 pesticide residues, including both banned and currently used substances in 148 field sites in Finland. Results highlight that pesticide residues are common in the agricultural soils of Finland. A least one residue was found in 82% of the soils, and of those 32% contained five or more residues. Maximum total residue concentration among the conventionally farmed soils was 3043 μg/kg, of which AMPA and glyphosate contributed the most. Pesticide residues were also found from organically farmed soils, although at 75–90% lower concentrations than in the conventionally farmed fields. Thus, despite the application rates of pesticides in Finland being generally much lower than in most parts of central and southern Europe, the total residue concentrations in the soils occurred at similar or at higher levels. We also established that AMPA and glyphosate residues in soil are significantly higher in fields with cereal dominated rotations than in grass dominated or cereal–grass rotations. However, risk analyses for individual substances indicated low ecological risk for most of the fields. Furthermore, the total ecological risk associated with the mixtures of residues was mostly low except for 21% of cereal dominated fields with medium risk. The results showed that the presence of mixtures of pesticide residues in soils is a rule rather than an exception also in boreal soils. In highly chemicalized modern agriculture, the follow-up of the residues of currently used pesticides in national and international soil monitoring programs is imperative to maintain soil quality and support sustainable environment policies

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leadingmostly tomonogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnicmutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FIND-base, as a key resource for Genomic Medicine applications

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

Peer reviewe

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

Peer reviewe

A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy

Temporal lobe epilepsy is the most common drug-resistant form of epilepsy in adults. The reorganization of neural networks and the gene expression landscape underlying pathophysiologic network behavior in brain structures such as the hippocampus has been suggested to be controlled, in part, by microRNAs. To systematically assess their significance, we sequenced Argonaute-loaded microRNAs to define functionally engaged microRNAs in the hippocampus of three different animal models in two species and at six time points between the initial precipitating insult through to the establishment of chronic epilepsy. We then selected commonly up-regulated microRNAs for a functional in vivo therapeutic screen using oligonucleotide inhibitors. Argonaute sequencing generated 1.44 billion small RNA reads of which up to 82% were microRNAs, with over 400 unique microRNAs detected per model. Approximately half of the detected microRNAs were dysregulated in each epilepsy model. We prioritized commonly up-regulated microRNAs that were fully conserved in humans and designed custom antisense oligonucleotides for these candidate targets. Antiseizure phenotypes were observed upon knockdown of miR-10a-5p, miR-21a-5p, and miR-142a-5p and electrophysiological analyses indicated broad safety of this approach. Combined inhibition of these three microRNAs reduced spontaneous seizures in epileptic mice. Proteomic data, RNA sequencing, and pathway analysis on predicted and validated targets of these microRNAs implicated derepressed TGF-\u3b2 signaling as a shared seizure-modifying mechanism. Correspondingly, inhibition of TGF-\u3b2 signaling occluded the antiseizure effects of the antagomirs. Together, these results identify shared, dysregulated, and functionally active microRNAs during the pathogenesis of epilepsy which represent therapeutic antiseizure targets

Bioenergy entrepreneurship as a tool for rural development in Northern Finland

This paper aims at analyzing business services in bioenergy investments and innovations on farms in the Northern Ostrobothnia region in Finland. Finance into research of bioenergy has strongly increased during the last years both in Finland and Europe. Primary focus of this research has been so far on the technical and economic problems, like production, processing and combustion techniques of biofuels and environmental effects of bioenergy production. Energy resources of farms and their possibilities to act as bioenergy entrepreneurs has been paid attention to only lately. Research focusing on the background factors, support services and regional conditions effecting farm level bioenergy entrepreneurship has been minor in Finland. The number of Finnish farm enterprises is assumed to decrease from 70,000 to about 50,000 by the year 2013 and the decline is especially drastic in marginal rural areas like Northern Finland. This trend fosters the depopulation of rural areas and weakens the well-being there. New business opportunities are important in keeping up agricultural enterprises in business. High hopes have been put on the production and use of domestic bioenergy as one of the farm businesses, which is at the same time seen as one of the solutions for reacting to the demands of climate change. In here, governmental and other business services have an important role, but the Finnish business services are scattered in numerous organizations. The research emphasis is put on local/regional actors, who make fi nal energy decisions. Empirically this paper is based on questioning (150 farmers) and structural interviews (39 farmers) for farms directed to bioenergy production in the province of Northern Ostrobothnia, Finland. The data was collected in 2006 and 2007. Three groups of farmers were categorized according to their attitudes to bioenergy production on their farms: investors, entrepreneurs and hobbyist. The results will help to develop future business services, increase bioenergy use, and bring in information about the factors and causalities behind bioenergy decisions

Conservation of human alternative splice events in mouse

Human and mouse genomes share similar long-range sequence organization, and have most of their genes being homologous. As alternative splicing is a frequent and important aspect of gene regulation, it is of interest to assess the level of conservation of alternative splicing. We examined mouse transcript data sets (EST and mRNA) for the presence of transcripts that both make spliced-alignment with the draft mouse genome sequence and demonstrate conservation of human transcript-confirmed alternative and constitutive splice junctions. This revealed 15% of alternative and 67% of constitutive splice junctions as conserved; however, these numbers are patently dependent on the extent of transcript coverage. Transcript coverage of conserved splice patterns is found to correlate well between human and mouse. A model, which extrapolates from observed levels of conservation at increasing levels of transcript support, estimates overall conservation of 61% of alternative and 74% of constitutive splice junctions, albeit with broad confidence intervals. Observed numbers of conserved alternative splicing events agreed with those expected on the basis of the model. Thus, it is apparent that many, and probably most, alternative splicing events are conserved between human and mouse. This, combined with the preservation of alternative frame stop codons in conserved frame breaking events, indicates a high level of commonality in patterns of gene expression between these two species

GBuilder—An Application for the Visualization and Integration of EST Cluster Data

This paper presents a network-centric DNA sequence visualization and analysis tool called GBuilder. The tool is an easy-to-use Java application that can be used to analyze DNA sequence clusters and assemblies. The emphasis is on the analysis of EST data, where these highly redundant collections of low-quality and often alternatively spliced or chimeric sequence data are difficult to explore. The tool has the capacity to visualize similarities or dissimilarities between sequences at the level of the nucleotide base or annotation in many ways. Sequences may also be edited manually. The novel feature of GBuilder is its ability to access different data sources and analysis applications available on the Internet and to integrate these results and functionality back into itself. External resources such as EST cluster databases and conventional command-line analysis applications are integrated and accessed using CORBA (Common Object Request Broker Architecture), which provides a standard implementation independent protocol for integration. New CORBA services can be integrated immediately if they use a known interface described using the Interface Definition Language

Bioenergy decision making of farms in Northern Finland: combining bottom-up and top-down perspectives

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