Modus D5.1 Definition of use cases

Within the Modus project, one of the main goals is to analyse how the performance of the overall European transport system can be optimized by considering the entire door-to-door journey holistically and considering air transport within an integrated, multimodal approach. In this regard, it is essential to identify the main barriers in achieving European (air) mobility goals and how air transport can evolve by efficiently connecting information and services with other transport modes to achieve a seamless journey experience for passengers. For this particular purposes, a set of use cases is identified and defined within this deliverable D5.1

A mesoscopic lattice model for morphology formation in ternary mixtures with evaporation

We develop a mesoscopic lattice model to study the morphology formation in interacting ternary mixtures with the evaporation of one component. As concrete potential application of our model, we wish to capture morphologies as they are typically arising during the fabrication of organic solar cells. In this context, we consider an evaporating solvent into which two other components are dissolved, as a model for a 2-component coating solution that is drying on a substrate. We propose a 3-spins dynamics to describe the evolution of the three interacting species. As main tool, we use a Monte Carlo Metropolis-based algorithm, with the possibility of varying the system's temperature, mixture composition, interaction strengths, and evaporation kinetics. The main novelty is the structure of the mesoscopic model – a bi-dimensional lattice with periodic boundary conditions, divided into square cells to encode a mesoscopic range interaction among the units. We investigate the effect of the model parameters on the structure of the resulting morphologies. Finally, we compare the results obtained with the mesoscopic model with corresponding ones based on an analogous lattice model with a short range interaction among the units, i.e. when the mesoscopic length scale coincides with the microscopic length scale of the lattice

Experimental infection of chickens by a flagellated motile strain of Salmonella enterica serovar Gallinarum biovar Gallinarum

Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum (SG) causes fowl typhoid (FT), a septicaemic disease which can result in high mortality in poultry flocks. The absence of flagella in SG is thought to favour systemic invasion, since bacterial recognition via Toll-like receptor (TLR)-5 does not take place during the early stages of FT. In the present study, chicks susceptible to FT were inoculated with a wild type SG (SG) or its flagellated motile derivative (SG Fla+). In experiment 1, mortality and clinical signs were assessed, whereas in experiment 2, gross pathology, histopathology, systemic invasion and immune responses were evaluated. SG Fla+ infection resulted in later development of clinical signs, lower mortality, lower bacterial numbers in the liver and spleen, and less severe pathological changes compared to SG. The CD8+ T lymphocyte population was higher in the livers of chicks infected with SG at 4 days post-inoculation (dpi). Chicks infected with SG had increased expression of interleukin (IL)-6 mRNA in the caecal tonsil at 1 dpi and increased expression of IL-18 mRNA in the spleen at 4 dpi. In contrast, the CD4+ T lymphocyte population was higher at 6 dpi in the livers of birds infected with SG Fla+. Therefore, flagella appeared to modulate the chicken immune response towards a CD4+ T profile, resulting in more efficient bacterial clearance from systemic sites and milder infection

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org

From the Trenches: A Cross-Sectional Study Applying the GRADE Tool in Systematic Reviews of Healthcare Interventions

Background: GRADE was developed to address shortcomings of tools to rate the quality of a body of evidence. While much has been published about GRADE, there are few empirical and systematic evaluations. Objective: To assess GRADE for systematic reviews (SRs) in terms of inter-rater agreement and identify areas of uncertainty. Design: Cross-sectional, descriptive study. Methods: We applied GRADE to three SRs (n = 48, 66, and 75 studies, respectively) with 29 comparisons and 12 outcomes overall. Two reviewers graded evidence independently for outcomes deemed clinically important a priori. Inter-rater reliability was assessed using kappas for four main domains (risk of bias, consistency, directness, and precision) and overall quality of evidence. Results: For the first review, reliability was: k = 0.41 for risk of bias; 0.84 consistency; 0.18 precision; and 0.44 overall quality. Kappa could not be calculated for directness as one rater assessed all items as direct; assessors agreed in 41 % of cases. For the second review reliability was: 0.37 consistency and 0.19 precision. Kappa could not be assessed for other items; assessors agreed in 33 % of cases for risk of bias; 100 % directness; and 58 % overall quality. For the third review, reliability was: 0.06 risk of bias; 0.79 consistency; 0.21 precision; and 0.18 overall quality. Assessors agreed in 100 % of cases for directness. Precision created the most uncertainty due to difficulties in identifying ‘‘optimal’ ’ information size and ‘‘clinica

Building The Sugarcane Genome For Biotechnology And Identifying Evolutionary Trends

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. 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