Scenarios about the long-time damage of silicon as material and detectors operating beyond LHC collider conditions

For the new hadron collider LHC and some of its updates in luminosity and energy, as SLHC and VLHC, the silicon detectors could represent an important option, especially for the tracking system and calorimetry. The main goal of this paper is to analyse the expected long-time degradation in the bulk of the silicon as material and for silicon detectors, in continuous radiation field, in these hostile conditions. The behaviour of silicon in relation to various scenarios for upgrade in energy and luminosity is discussed in the frame a phenomenological model developed previously by the authors. Different silicon material parameters resulting from different technologies are considered to evaluate what materials are harder to radiation and consequently could minimise the degradation of device parameters in conditions of continuous long time operation.Comment: submitted to Physica Scripta Work in the frame of CERN RD-50 Collaboratio

Looking beyond forest cover: an analysis of landscape-scale predictors of forest degradation in the Brazilian Amazon.

While forest degradation rates and extent exceed deforestation in the Brazilian Amazon, less attention is given to the factors controlling its spatial distribution. No quantified correlation exists between changes of forest structure due to anthropogenic disturbances and dynamics of land use and cover change occurring at broader spatial levels. This study examines the influence of multi-scale landscape structure factors (i.e. spatial composition, configuration and dynamic of land use/cover) on primary forest's aboveground biomass (AGB), spanning from low to highly degraded, in Paragominas municipality (Pará state). We used random forest models to identify the most important landscape predictors of degradation and clustering methods to analyze their distribution and interactions. We found that 58% of the variance of AGB could be explained by metrics reflecting land use practices and agricultural dynamics around primary forest patches and that their spatial patterns were not randomly distributed. Forest degradation is mainly driven by fragmentation effects resulting from old deforestation and colonization events linked with cropland expansion (e.g. soybean and maize) coupled with high accessibility to market. To a lesser extent, degradation is driven by recent and ongoing (1985?2015) deforestation and fragmentation in slash-and-burn agricultural areas, characterized by heterogeneous mosaics of pastures and fallow lands combined with high use of fire. Our findings highlight the potential of landscape-level framework and remotely sensed land cover data for a thorough understanding of the distribution of forest degradation across human-modified landscapes. Addressing these spatial determinants by looking at agricultural dynamics beyond forest cover is necessary to improve forest management which has major implications for biodiversity, carbon and other ecosystem services

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

The repeatability of cognitive performance:A meta-analysis

This is the author accepted manuscript. The final version is available from The Royal Society via the DOI in this record.Behavioural and cognitive processes play important roles in mediating an individual's interactions with its environment. Yet, while there is a vast literature on repeatable individual differences in behaviour, relatively little is known about the repeatability of cognitive performance. To further our understanding of the evolution of cognition, we gathered 44 studies on individual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repeatable. We compared repeatability (R) in performance (1) on the same task presented at different times (temporal repeatability), and (2) on different tasks that measured the same putative cognitive ability (contextual repeatability). We also addressed whether R estimates were influenced by seven extrinsic factors (moderators): type of cognitive performance measurement, type of cognitive task, delay between tests, origin of the subjects, experimental context, taxonomic class and publication status. We found support for both temporal and contextual repeatability of cognitive performance, with mean R estimates ranging between 0.15 and 0.28. Repeatability estimates were mostly influenced by the type of cognitive performance measures and publication status. Our findings highlight the widespread occurrence of consistent inter-individual variation in cognition across a range of taxa which, like behaviour, may be associated with fitness outcomes.PKYC is supported by Japan Society for the Promotion of Science (PE1801); JOvH was funded by an ERC consolidator grant (616474). MC and this research was supported by a grant from the Human Frontier Science Program to ASC and JM-F (RGP0006/2015)

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer

Pancreatobiliary cancers have among the highest mortality rates of any cancer type. Discovering the full spectrum of molecular genetic alterations may suggest new avenues for therapy. To catalogue genomic alterations, we carried out array-based genomic profiling of 31 exocrine pancreatic cancers and 6 distal bile duct cancers, expanded as xenografts to enrich the tumor cell fraction. We identified numerous focal DNA amplifications and deletions, including in 19% of pancreatobiliary cases gain at cytoband 18q11.2, a locus uncommonly amplified in other tumor types. The smallest shared amplification at 18q11.2 included GATA6, a transcriptional regulator previously linked to normal pancreas development. When amplified, GATA6 was overexpressed at both the mRNA and protein levels, and strong immunostaining was observed in 25 of 54 (46%) primary pancreatic cancers compared to 0 of 33 normal pancreas specimens surveyed. GATA6 expression in xenografts was associated with specific microarray gene-expression patterns, enriched for GATA binding sites and mitochondrial oxidative phosphorylation activity. siRNA mediated knockdown of GATA6 in pancreatic cancer cell lines with amplification led to reduced cell proliferation, cell cycle progression, and colony formation. Our findings indicate that GATA6 amplification and overexpression contribute to the oncogenic phenotypes of pancreatic cancer cells, and identify GATA6 as a candidate lineage-specific oncogene in pancreatobiliary cancer, with implications for novel treatment strategies

The Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl

Comprehensive study of tellurium based glass ceramics for thermoelectric application

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