Development of FuGO: An ontology for functional genomics investigations

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans

Peculiarities of Ga and Te incorporation in glassy arsenic selenides

International audienceEffect of simultaneous Ga and Te addition on the structure of As2Se3 glasses is studied using X-ray photoelectron spectroscopy (XPS), extended X-ray absorption fine structure (EXAFS) and Raman techniques. It is shown that most of As, Se and Te atoms build a covalent network according to their main valences. Three-fold coordinated As atoms form pyramidal structural units, which are connected via bridges of two-fold coordinated chalcogen atoms (Se, Te). On the other hand, coordination of Ga in glassy samples is found to be greater than three, as expected from its valence, increasing with Te content. Some of the As atoms appear to be converted into four-fold coordinated state at low Te concentration, while a fraction of Te and, possibly, Se atoms are thought to exist in a singly-coordinated (terminal) state in the vicinity of Ga in the samples with higher Te concentration

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

Report of the study group on a superconducting proton linac as a PS Injector

A proposal was made at the end of 1996 to use the large inventory of RF hardware available after the decommissioning of LEP-2 for the construction of a 2 GeV Superconducting Proton Linac (SPL) to inject directly into the PS [1.1]. The brightness of the beam in the PS at low energy would double, helping the injector complex to satisfy the requirements of the LHC and benefiting the planned proton physics programme. Additional users could also be accommodated thanks to the capability of the SPL to operate at a much larger duty factor than that required for high-energy physics. Consequently, a small study group has been set up to analyse the major technical aspects of the SPL design as well as the processes of injection and capture in the PS. This report summarises the work done so far, and provides some information about the other possible uses of the SPL beam. The feasibility of such a cascade of accelerators is confirmed, although an in-depth design study is still required before the realistic performance and detailed design of that facility can be announced

The repeatability of cognitive performance: a meta-analysis

International audienceOne contribution of 15 to a theme issue 'Causes and consequences of individual differences in cognitive abilities'. 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 cogni-tion, we gathered 44 studies on individual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repea-table. We compared repeatability (R) in performance (1) on the same task presented at different times (temporal repeat-ability), 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 cog-nition across a range of taxa which, like behaviour, may be associated with fitness outcomes. This article is part of the theme issue 'Causes and consequences of individual differences in cognitive abilities'

The Stanford Microarray Database: implementation of new analysis tools and open source release of software

The Stanford Microarray Database (SMD; ) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release

The Stanford Microarray Database accommodates additional microarray platforms and data formats

The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD

Addition of Ag2O in Er3+doped oxyfluorophosphate glass to allow the drawing of optical fibers

Here, Ag2O containing glasses in the NaPO3–CaF2 glass network were prepared using standard melting process. The addition of Ag2O was found to increase the thermal stability of the glass due to the decrease in the Q2 units at the expense of Q1 units, to decrease the intensity of the upconversion under 980 nm pumping and to have a small impact on the nucleation and growth mechanism. Due to the thermal stability against crystallization of the glass prepared with 4 mol % of Ag2O, we demonstrate that fiber can be drawn from this glass. Despite the formation of Ag nanoparticles at the surface of the fiber although the drawing is a fast process, light can still be confined in the fiber. The fiber exhibits a large emission band centered at 1.5 μm under 980 nm pumping.Peer reviewe