Coherent Heteroepitaxy of Bi2Se3 on GaAs (111)B

We report the heteroepitaxy of single crystal thin films of Bi2Se3 on the (111)B surface of GaAs by molecular beam epitaxy. We find that Bi2Se3 grows highly c-axis oriented, with an atomically sharp interface with the GaAs substrate. By optimizing the growth of a very thin GaAs buffer layer before growing the Bi2Se3, we demonstrate the growth of thin films with atomically flat terraces over hundreds of nanometers. Initial time-resolved Kerr rotation measurements herald opportunities for probing coherent spin dynamics at the interface between a candidate topological insulator and a large class of GaAs-based heterostructures.Comment: To appear in Applied Physics Letter

Gene3D: comprehensive structural and functional annotation of genomes

Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein–protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk

The occupation of a box as a toy model for the seismic cycle of a fault

We illustrate how a simple statistical model can describe the quasiperiodic occurrence of large earthquakes. The model idealizes the loading of elastic energy in a seismic fault by the stochastic filling of a box. The emptying of the box after it is full is analogous to the generation of a large earthquake in which the fault relaxes after having been loaded to its failure threshold. The duration of the filling process is analogous to the seismic cycle, the time interval between two successive large earthquakes in a particular fault. The simplicity of the model enables us to derive the statistical distribution of its seismic cycle. We use this distribution to fit the series of earthquakes with magnitude around 6 that occurred at the Parkfield segment of the San Andreas fault in California. Using this fit, we estimate the probability of the next large earthquake at Parkfield and devise a simple forecasting strategy.Comment: Final version of the published paper, with an erratum and an unpublished appendix with some proof

A comprehensive assessment of the applicability of available and proposed offshore mooring and foundation technologies and design tools for array applications

PublishedThe function and type of mooring and/or foundation system are determined by a number of factors including: cost, site characteristics, expected environmental loading and environmental or legislative constraints. The design of the device and its mode of operation will also influence the decision making process. It is the role of DTOcean Work Package 4 to produce a decision making tool which has the capability to assess a range of technologies for the design and selection of mooring and foundation systems for marine renewable energy (MRE) device arrays. In this first deliverable report, criteria are introduced which can be used to appraise technologies and approaches relevant to MRE devices. Existing mooring and foundation technologies used in the offshore industry are summarised with examples given of MRE device deployments. A general overview of the design tools which are currently used for mooring and foundation design in the offshore and MRE industries is provided, along with a list of the capabilities of several commercially available software packages.European Commission’s 7th Framework; Grant agreement number: 60859

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch.

As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones

Who Produces for Whom in the World Economy?

International audienceFor two decades, the share of trade in inputs, also called vertical trade, has been dramatically increasing. In reallocating trade flows to their original input-producing industries and countries, this paper suggests a new measure of international trade: "value-added trade" and makes it possible to answer the question "who produces for whom?". In 2004, 27% of international trade was vertical trade. The industrial and geographic patterns of value-added trade are very different from those of standard trade. Value-added trade is relatively less important in regional trade but the difference is not more important for Asia than for AmericaLa part du commerce en produits intermédiaires dans le commerce international, appelé aussi "commerce vertical", n'a cessé d'augmenter depuis vingt ans. Cet article propose une nouvelle mesure du commerce international "le commerce en valeur ajoutée" qui réalloue les flux commerciaux aux pays et aux secteurs produisant les intrants. Les répartitions géographique et sectorielle du commerce en valeur ajoutée sont très différentes de celles du commerce " standard ". La différence entre le commerce en valeur ajoutée et le commerce standard est plus importante dans le cas du commerce régional mais ce n'est pas plus le cas en Asie qu'en Amérique