924 research outputs found

    Detecting Beyond-Einstein Polarizations of Continuous Gravitational Waves

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    The direct detection of gravitational waves with the next generation detectors, like Advanced LIGO, provides the opportunity to measure deviations from the predictions of General Relativity. One such departure would be the existence of alternative polarizations. To measure these, we study a single detector measurement of a continuous gravitational wave from a triaxial pulsar source. We develop methods to detect signals of any polarization content and distinguish between them in a model independent way. We present LIGO S5 sensitivity estimates for 115 pulsars.Comment: submitted to PR

    BamView: visualizing and interpretation of next-generation sequencing read alignments.

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    So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user

    Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

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    MOTIVATION: High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids. RESULTS: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation. AVAILABILITY: Artemis is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute websites: http://www.sanger.ac.uk/resources/software/artemis/

    Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

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    Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences

    Software-Enabled Smallsat Autonomy: Discussion with Examples

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    Smallsat missions using cooperating constellations offer significant benefits compared to traditional space missions. These benefits include lower unit costs, better robustness to failures, and the ability to collect data in a distributed fashion. Significant commercial smallsat missions are active in low Earth orbit, and spacecraft operators have expressed interest in smallsat constellations operating both at higher altitudes and in proximity operations missions. Autonomy plays a significant role in extending smallsat missions to these more challenging domains. Autonomy in a broad sense refers to a spacecraft\u27s or constellation\u27s ability to operate independently of ground systems, and affects every part of a typical mission. For example, onboard processing of data can significantly reduce the frequency and expense of communications to a terrestrial ground station link. Onboard safety and health management is critical in proximity operations with fast dynamics, or in remote operations where offboard monitoring is available infrequently. Onboard monitoring of mission objectives enables remote operations and reduces the required operator workload. Emergent Space Technologies has developed flight software products to enable future missions with greater autonomy. Navigator is a standalone application for cooperative absolute and relative navigation within a cluster of space vehicles. The Autopilot software suite enables routine orbit maintenance and satellite maneuvers to be monitored and executed onboard, increasing safety and reducing reliance on ground systems. Guardian is a suite of applications thatenable fault detection, isolation, and recovery on modules within a distributed mission. The Cirrus cloud computing framework enables distributed computing tasks within a fleet of cooperating platforms, allowing complex data processing algorithms to be executed onboard and distributed among vehicles according to their computational availability. Finally, Commander is a set of applications for autonomous execution of a planned mission on a distributed group of platforms. Critically, Commander enables autonomous coordination of the actions of Navigator, Autopilot, Guardian, and Cirrus, providing a significantly greater level of autonomy than the suites provide individually. In this paper, we describe the capabilities of the flight software and demonstrate how coordination using Commander enables desired operator missions. The following missions are considered: (1) autonomous lunar injection; (2) rendezvous and proximity operations; (3) constellation intelligence, surveillance, and reconnaissance. Discussion is informed by use case diagrams and simulation results using Emergent\u27s Ascent simulation environment

    The interaction of unfolding α-lactalbumin and malate dehydrogenase with the molecular chaperone αB-crystallin: a light and X-ray scattering investigation

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    Purpose: The molecular chaperone αB-crystallin is found in high concentrations in the lens and is present in all major body tissues. Its structure and the mechanism by which it protects its target protein from aggregating and precipitating are not known. Methods: Dynamic light scattering and X-ray solution scattering techniques were used to investigate structural features of the αB-crystallin oligomer when complexed with target proteins under mild stress conditions, i.e., reduction of α- lactalbumin at 37 °C and malate dehydrogenase when heated at 42 °C. In this investigation, the size, shape and particle distribution of the complexes were determined in real-time following the induction of stress. Results: Overall, it is observed that the mass distribution, hydrodynamic radius, and spherical shape of the αB-crystallin oligomer do not alter significantly when it complexes with its target protein. Conclusions: The data are consistent with the target protein being located in the outer protein shell of the αB-crystallin oligomer where it is readily accessible for possible refolding via the action of other molecular chaperones. © 2010 Molecular Vision