D3.2 Cost Concept Model and Gateway Specification

This document introduces a Framework supporting the implementation of a cost concept model against which current and future cost models for curating digital assets can be benchmarked. The value built into this cost concept model leverages the comprehensive engagement by the 4C project with various user communities and builds upon our understanding of the requirements, drivers, obstacles and objectives that various stakeholder groups have relating to digital curation. Ultimately, this concept model should provide a critical input to the development and refinement of cost models as well as helping to ensure that the curation and preservation solutions and services that will inevitably arise from the commercial sector as ‘supply’ respond to a much better understood ‘demand’ for cost-effective and relevant tools. To meet acknowledged gaps in current provision, a nested model of curation which addresses both costs and benefits is provided. The goal of this task was not to create a single, functionally implementable cost modelling application; but rather to design a model based on common concepts and to develop a generic gateway specification that can be used by future model developers, service and solution providers, and by researchers in follow-up research and development projects.<p></p> The Framework includes:<p></p> • A Cost Concept Model—which defines the core concepts that should be included in curation costs models;<p></p> • An Implementation Guide—for the cost concept model that provides guidance and proposes questions that should be considered when developing new cost models and refining existing cost models;<p></p> • A Gateway Specification Template—which provides standard metadata for each of the core cost concepts and is intended for use by future model developers, model users, and service and solution providers to promote interoperability;<p></p> • A Nested Model for Digital Curation—that visualises the core concepts, demonstrates how they interact and places them into context visually by linking them to A Cost and Benefit Model for Curation.<p></p> This Framework provides guidance for data collection and associated calculations in an operational context but will also provide a critical foundation for more strategic thinking around curation such as the Economic Sustainability Reference Model (ESRM).<p></p> Where appropriate, definitions of terms are provided, recommendations are made, and examples from existing models are used to illustrate the principles of the framework

GeMprospector—online design of cross-species genetic marker candidates in legumes and grasses

The web program GeMprospector (URL: ) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses

A large population-based investigation into the genetics of susceptibility to gastrointestinal infections and the link between gastrointestinal infections and mental illness.

Gastrointestinal infections can be life threatening, but not much is known about the host's genetic contribution to susceptibility to gastrointestinal infections or the latter's association with psychiatric disorders. We utilized iPSYCH, a genotyped population-based sample of individuals born between 1981 and 2005 comprising 65,534 unrelated Danish individuals (45,889 diagnosed with mental disorders and 19,645 controls from a random population sample) in which all individuals were linked utilizing nationwide population-based registers to estimate the genetic contribution to susceptibility to gastrointestinal infections, identify genetic variants associated with gastrointestinal infections, and examine the link between gastrointestinal infections and psychiatric and neurodevelopmental disorders. The SNP heritability of susceptibility to gastrointestinal infections ranged from 3.7% to 6.4% on the liability scale. Significant correlations were found between gastrointestinal infections and the combined group of mental disorders (OR = 2.09; 95% CI: 1.82-2.4, P = 1.87 × 10-25). Correlations with autism spectrum disorder, attention deficit hyperactivity disorder, and depression were also significant. We identified a genome-wide significant locus associated with susceptibility to gastrointestinal infections (OR = 1.13; 95% CI: 1.08-1.18, P = 2.9 × 10-8), where the top SNP was an eQTL for the ABO gene. The risk allele was associated with reduced ABO expression, providing, for the first time, genetic evidence to support previous studies linking the O blood group to gastrointestinal infections. This study also highlights the importance of integrative work in genetics, psychiatry, infection, and epidemiology on the road to translational medicine

Influences of the Common FTO rs9939609 Variant on Inflammatory Markers Throughout a Broad Range of Body Mass Index

A recent study reported that the fatness associated A-allele of FTO rs9939609 increased plasma high sensitivity C-reactive protein (hs-CRP) levels independent of fatness. We aimed to investigate if this gene variant had fatness-independent effects on plasma hs-CRP and 10 additional circulating obesity-related adipokines throughout a broad range of body mass index (BMI) among Danish men.In a population of 362,200 young men, examined for military service between 1943 and 1977, two groups were identified: 1) a random 1% sample and 2) all obese men (BMI = 31.0 kg/m(2), all of whom were above the 99(th) percentile of this population). At an average age of 49 years (range: 39 through 65 years), 551 men, hereof 231 of the obese, were re-examined, including genotyping and measurement of the fasting circulating inflammatory markers hs-CRP, IL-1β, IL-6, IL-10, IL-18, mip1α, mip1β, sTNFα-R1, TGF-β, TNF-α and leptin. Men with known disease were excluded from the examination. All the inflammatory markers were log-transformed to approximate a normal distribution. Genotype-phenotype relationships were studied using linear regression analyses with the inflammatory markers as the response variable. Significant positive associations between hs-CRP, leptin and a broad range of BMI were observed, but the associations did not significantly differ across FTO rs9939609 genotype. There were no significant associations between the other inflammatory markers, FTO rs9939609 genotype or BMI, respectively.No fatness-independent effects of the FTO rs9939609 A-allele on a series of inflammatory markers were observed in this cohort of healthy middle-aged men representing a broad range of fatness

Systemic and local inflammatory response in women with preterm prelabor rupture of membranes

Objective:To evaluate the inflammatory pattern in maternal circulation, amniotic cavity, cervix and vagina from women with preterm prelabor rupture of membranes (PPROM) considering the occurrence of microbial invasion of the amniotic cavity (MIAC). Methodology: A prospective study was performed in 58 women with PPROM before 34+0 weeks of gestational age. Twenty-six proteins were analyzed by a multiple immunoassay in samples of amniotic fluid, serum, cervix and vagina. Association of an inflammatory response in the invasive and non-invasive samples with MIAC was investigated. Results: The rate of MIAC was 36.2% (21/58). Both amniotic fluid IL-6 and cervical C-reactive protein (CRP) showed to be independent predictors of MIAC. A cut-off level of cervical CRP≥1836 pg/mL showed a detection rate of 75%, false positive rate of 19% and positive and negative predictive values to predict MIAC of 67% and 87%, respectively. There were no independent biomarkers of MIAC either in the serum or vaginal compartment. Conclusion: A cervical inflammatory response mediated by CRP was observed in PPROM women with MIAC. Evaluation of serum or vaginal samples did not add valuable information regarding the outcome evaluated

Intra-amniotic inflammatory response in subgroups of women with preterm prelabor rupture of the membranes

Background To evaluate the influence of microbial invasion of the amniotic cavity (MIAC) and histological chorioamnionitis (HCA) on the magnitude of intra-amniotic inflammatory response in preterm prelabor rupture of membranes (PPROM). Methodology/Principal Finding A prospective cohort study was performed in 107 women with PPROM between 23.0 and 36.6 weeks of gestational age. Twenty-six proteins were assayed by multiple immunoassay in amniotic fluid. The policy for PPROM in Czech Republic is active, and 90% of the women were delivered within 96 hours of membrane rupture. Histopathological placental findings were evaluated based on the Salafia classification. Data were analyzed in four subgroups of population according to the presence of MIAC and/or HCA. Results were stratified by gestational age at PPROM (< or ≥34.0 weeks). The rates of MIAC and HCA were 44% and 57%, respectively. Regardless of gestational age at PPROM, intra-amniotic inflammatory response was higher when MIAC and HCA were both present. There were no differences in the intra-amniotic inflammatory response between women with MIAC or HCA alone and women without infection. Conclusion A higher intra-amniotic inflammatory response was identified when both HCA and MIAC were detected

SIP Draft Specification

A Submission Information Package (SIP) is defined in the OAIS standard1 as an Information Package that is delivered by the Producer to the OAIS for use in the construction or update of one or more AIPs and/or the associated Descriptive Information. Many different SIP formats are used all over the world and unfortunately there is currently no central format for a SIP which would cover all individual national and business needs identified in the E-ARK Report on Available Best Practices. Therefore, the main objective of this report is to describe a draft SIP specification for the E-ARK project – give an overview of the structure and main metadata elements for E-ARK SIP and provide initial input for the technical implementations of E-ARK ingest tools. The target group of this work are E-ARK project partners as well as all other archival institutions and software providers creating or updating their SIP format specifications. This report provides an overview of: • The general structure for submission information packages. This report explains how the E-ARK SIP is constructed by following the common rules for all other (archival, dissemination) information packages. • The SIP METS Profile. We provide a detailed overview of metadata sections and the metadata elements in these sections. The table with all metadata elements could possibly be of interest to technical stakeholders who wish to continue with the more detailed work of the E-ARK SIP implementation later. Two examples with different kinds of content (MoReq2010, SIARD-E) following the common structure for EARK submission information package can be found in the appendixes to this report