MutationDistiller: user-driven identification of pathogenic DNA variants

MutationDistiller is a freely available online tool for user-driven analyses of Whole Exome Sequencing data. It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines Mutation- Taster’s pathogenicity predictions with a phenotypebased approach. Phenotypic information is not limited to symptoms included in the Human Phenotype Ontology (HPO), but may also comprise clinical diagnoses and the suspected mode of inheritance. The search can be restricted to lists of candidate genes (e.g. virtual gene panels) and by tissue-specific gene expression. The inclusion of GeneOntology (GO) and metabolic pathways facilitates the discovery of hitherto unknown disease genes. In a novel approach, we trained MutationDistiller’s HPO-based prioritization on authentic genotype–phenotype sets obtained from ClinVar and found it to match or outcompete current prioritization tools in terms of accuracy. In the output, the program provides a list of potential disease mutations ordered by the likelihood of the affected genes to cause the phenotype. MutationDistiller provides links to gene-related information from various resources. It has been extensively tested by clinicians and their suggestions have been valued in many iterative cycles of revisions. The tool, a comprehensive documentation and examples are freely available at https://www.mutationdistiller.org

New information on a juvenile sauropod specimen from the Morrison Formation and the reassessment of its systematic position

Morphological changes in the ontogeny of sauropods are poorly known, making difficult to establish the systematic affinities of very young individuals. New information on an almost complete juvenile sauropod (SMA 0009) with an estimated total length of about 2m is here presented. The specimen was described as a diplodocid owing to the presence of some putative synapomorphies of this group. However, recent further preparation revealed the absence of diplodocid characters and the presence of macronarian derived characters. To test the affinities of this specimen, a phylogenetic analysis was conducted. The strict consensus tree recovers the specimen as a basal titanosauriform, in an unresolved relation with Brachiosaurus and Giraffatitan. Nevertheless, a brachiosaurid assignment is here suggested in base of the widely accepted monophyly of this group (only recovered when SMA 0009 is placed within this group). Although the existence of a new taxon cannot be completely ruled out, the combination of derived and plesiomorphic characters in the specimen suggests its assignment to Brachiosaurus. Sixteen extra steps are needed to place this specimen within Diplodocidae. The high cost to place this specimen within this group is owing to the fact that several diplodocid characters are absent in SMA 0009, such as the absence of divided centroprezygapophyseal lamina in cervical vertebrae, procoelous anterior caudal centra, composed lateral lamina in anterior caudal vertebrae, elongated middle caudal vertebrae, short cervical ribs and caudolateral projection of distal condyle of metatarsal I. Finally, the systematic position reveals few major ontogenetic transformations. These affect the pneumatic structures (e.g. change from simple pleurocoels in the cervical vertebrae to complex pleurocoels and the development of lateral excavations in the dorsal vertebrae) but also include unrecorded transformations of the neural spine (e.g. the development of the spinodiapophyseal lamina, the widening of the neural spines in the dorsal vertebrae) and allometric growth in some limb bones.Fil: Carballido, José Luis. Provincia del Chubut. Fundación Egidio Feruglio. Museo Paleontológico ; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Marpmann, Jean S.. Universitat Bonn; AlemaniaFil: Schwarz Wings, Daniela. Humboldt-Universität zu Berlin; AlemaniaFil: Pabst, Ben. No especifíca

Non abelian N=2 supersymmetric Born Infeld action

We present a N=2 supersymmetric action for the Born Infeld theory in the non abelian case. We quantize the theory in N=1 superspace and compute divergences at one-loop. The result is discussed in the N=4 case.Comment: reference adde

Periódicos Científicos da Ciência da Informação: os títulos indexados na WoS

This article studies the journals in the subject area of Information Science indexed in the Web of Science (WoS). The specific objectives are to: a) describe the publishing characteristics of information science journals indexed in the Web of Science database; b) indicate the type of access; c) identify which titles are indexed in DOAJ. The methodology is based on descriptive and exploratory research. The results identify 84 journals indexed in the Web of Science database in 2012, 9 of which are open access but, of these, only 6 are indexed in DOAJ. The predominant publishing model is that of commercial publishers with 56 titles (67% of total), and the most common frequency is quarterly. The majority (62.1%) of the journals has an impact factor of between 0 and 0.999; only 2 titles –published in the US and the Netherlands-- have an impact factor greater than 4,999. The study also reflects on the fact that Information Science is the discipline with the greatest perception on the issues of access to, and cost of, scientific journals. Likewise this area presents a representative quantity of titles from commercial publishers equivalent to that of publishers in general and there is a higher proportion of open access titles coming from Brazil.Este artículo estudia las revistas en el campo de Ciencias de la Información indexadas en la Web of Science (WoS). Los objetivos específicos son: a) describir las características editoriales de las revistas indexadas en la Web of Science (WoS). b) indicar el tipo de acceso; c) identificar qué títulos están indexados en DOAJ. El método utilizado se basea en la investigación descriptiva y exploratoria. Los resultados muestran 84 revistas indexadas en la WoS en 2012, 9 títulos de libre acceso, pero sólo 6 indexadas en DOAJ. La entidad editorial predominante son los editores comerciales, con 56 títulos (67% del total), y la publicación trimestral es la más común. La mayoría (62,1%) de las revistas tienen un factor de impacto entre 0 a 0,999 y sólo 2 títulos tienen factor de impacto superior a 4,999, y sus editores son de los Estados Unidos y de los Países Bajos. Reflexiona sobre la condición de Ciencias de la Información de ser el área de conocimiento con la percepción más evidente de la cuestión del acceso y el costo de las revistas científicas, y presentar una cantidad muy representativa de títulos de editoras comerciales, equivalente de las entidades editoriales en el escenario general, en la que los títulos de acceso abierto se deben a una condición geográfica, con una proporción mayor en Brasil. [pt] Este artigo estuda os periódicos da área da Ciência da Informação indexados na Web of Science (WoS). Os objetivos específicos são: a) descrever as características editoriais dos periódicos da Ciência da Informação indexados na base Web of Science; b) apontar o tipo de acesso; e c) identificar quais títulos estão indexados no DOAJ. A metodologia é pesquisa descritiva e exploratória. Os resultados mostram 84 periódicos indexados na base Web of Science, no ano de 2012, 9 títulos de acesso aberto, estando apenas 6 indexados no DOAJ. O tipo de entidade editorial predominante são as editoras comerciais, com 56 títulos (67% do total), e a periodicidade trimestral é a que fica em evidência. A maioria (62,1%) dos periódicos possui fator de impacto entre 0 a 0,999; apenas 2 títulos apresentam fator de impacto acima de 4,999, e seus editores são dos Estados Unidos e da Holanda. Reflete ainda sobre a condição da Ciência da Informação ser a área do conhecimento com a percepção mais evidente da questão do acesso e dos custos de periódicos científicos e apresentar uma quantidade muito significativa de títulos de editoras comerciais, equivalente ao cenário geral, na qual os títulos em acesso aberto se devem a uma condição geográfica, com uma proporção maior no Brasil

Analysis of Coastal Areas Using SAR Images: A Case Study of the Dutch Wadden Sea Region

The increased availability of civil synthetic aperture radar (SAR) satellite images with different resolution allows us to compare the imaging capabilities of these instruments, to assess the quality of the available data and to investigate different areas (e.g., the Wadden Sea region). In our investigation, we propose to explore the content of TerraSAR-X and Sentinel-1A satellite images via a data mining approach in which the main steps are patch tiling, feature extraction, classification, semantic annotation and visual-statistical analytics. Once all the extracted categories are mapped and quantified, then the next step is to interpret them from an environmental point of view. The objective of our study is the application of semi-automated SAR image interpretation. Its novelty is the automated multiclass categorisation of coastal areas. We found out that the north-west of the Netherlands can be interpreted routinely as land surfaces by our satellite image analyses, while for the Wadden Sea, we can discriminate the different water levels and their impact on the visibility of the tidal flats. This necessitates a selection of time series data spanning a full tidal cycle

Macrophage Polarization is Deregulated in Haemophilia

Macrophages make important contributions to inflammation and wound healing. We show here that macrophage polarization is deregulated in haemophilia in response to macrophage colony-stimulating factor (M-CSF) and partially in response to granulocyte-macrophage colony-stimulating factor (GM-CSF). As a result, haemophilia macrophages exhibit a specific impairment of M-CSF-mediated functions involved in wound healing such as clot invasion and phagocytosis. Haemophilia monocytes express reduced amounts of the receptors for M-CSF and GM-CSF, which correlates with a failure to express tumour necrosis factor α (TNFα) and CD163 in M-CSF-treated haemophilia macrophages and reduced expression of TNFα and CD206 after treatment with GM-CSF. Protein expression in response to M-CSF was regained with respect to CD163 and CD206 after embedding haemophilia monocytes in clotted plasma suggesting that a functioning coagulation system has positive effects on macrophage M2 polarization. Mimicking the functional deficits of haemophilia macrophages in normal macrophages was possible by adding leptin, which we found to be elevated in the blood of haemophilia patients, to a monocyte cell line. The increase of leptin occurred in conjunction with C-reactive protein in a body mass index-controlled cohort suggesting that haemophilia patients harbour chronic low-grade inflammation. Together, our data indicate that impaired clotting in haemophilia patients leads to increased inflammation and a deregulation in macrophage differentiation, which may explain the commonly observed deficits in wound healing and tissue regeneration

Very-High-Resolution SAR Images and Linked Open Data Analytics Based on Ontologies

In this paper, we deal with the integration of multiple sources of information such as Earth observation (EO) synthetic aperture radar (SAR) images and their metadata, semantic descriptors of the image content, as well as other publicly available geospatial data sources expressed as linked open data for posing complex queries in order to support geospatial data analytics. Our approach lays the foundations for the development of richer tools and applications that focus on EO image analytics using ontologies and linked open data. We introduce a system architecture where a common satellite image product is transformed from its initial format into to actionable intelligence information, which includes image descriptors, metadata, image tiles, and semantic labels resulting in an EO-data model. We also create a SAR image ontology based on our EO-data model and a two-level taxonomy classification scheme of the image content. We demonstrate our approach by linking high-resolution TerraSAR-X images with information from CORINE Land Cover (CLC), Urban Atlas (UA), GeoNames, and OpenStreetMap (OSM), which are represented in the standard triple model of the resource description frameworks (RDFs)