49 research outputs found

    The evolutionary signal in metagenome phyletic profiles predicts many gene functions

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    Background. The function of many genes is still not known even in model organisms. An increasing availability of microbiome DNA sequencing data provides an opportunity to infer gene function in a systematic manner. Results. We evaluated if the evolutionary signal contained in metagenome phyletic profiles (MPP) is predictive of a broad array of gene functions. The MPPs are an encoding of environmental DNA sequencing data that consists of relative abundances of gene families across metagenomes. We find that such MPPs can accurately predict 826 Gene Ontology functional categories, while drawing on human gut microbiomes, ocean metagenomes, and DNA sequences from various other engineered and natural environments. Overall, in this task, the MPPs are highly accurate, and moreover they provide coverage for a set of Gene Ontology terms largely complementary to standard phylogenetic profiles, derived from fully sequenced genomes. We also find that metagenomes approximated from taxon relative abundance obtained via 16S rRNA gene sequencing may provide surprisingly useful predictive models. Crucially, the MPPs derived from different types of environments can infer distinct, non-overlapping sets of gene functions and therefore complement each other. Consistently, simulations on > 5000 metagenomes indicate that the amount of data is not in itself critical for maximizing predictive accuracy, while the diversity of sampled environments appears to be the critical factor for obtaining robust models. Conclusions. In past work, metagenomics has provided invaluable insight into ecology of various habitats, into diversity of microbial life and also into human health and disease mechanisms. We propose that environmental DNA sequencing additionally constitutes a useful tool to predict biological roles of genes, yielding inferences out of reach for existing comparative genomics approaches

    Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

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    <p>Abstract</p> <p>Background</p> <p>While the number of newly sequenced genomes and genes is constantly increasing, elucidation of their function still is a laborious and time-consuming task. This has led to the development of a wide range of methods for predicting protein functions in silico. We report on a new method that predicts function based on a combination of information about protein interactions, orthology, and the conservation of protein networks in different species.</p> <p>Results</p> <p>We show that aggregation of these independent sources of evidence leads to a drastic increase in number and quality of predictions when compared to baselines and other methods reported in the literature. For instance, our method generates more than 12,000 novel protein functions for human with an estimated precision of ~76%, among which are 7,500 new functional annotations for 1,973 human proteins that previously had zero or only one function annotated. We also verified our predictions on a set of genes that play an important role in colorectal cancer (<it>MLH1</it>, <it>PMS2</it>, <it>EPHB4 </it>) and could confirm more than 73% of them based on evidence in the literature.</p> <p>Conclusions</p> <p>The combination of different methods into a single, comprehensive prediction method infers thousands of protein functions for every species included in the analysis at varying, yet always high levels of precision and very good coverage.</p

    The James Webb Space Telescope Mission

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    Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least 4m4m. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the 6.5m6.5m James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

    SIGN RETROREFLECTIVITY: COMPARING RESULTS OF NIGHTTIME VISUAL INSPECTIONS WITH APPLICATION OF MINIMUM RETROREFLECTIVITY VALUES

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    In 1993, the Federal Highway Administration (FHWA) published research recommendations for minimum levels of retroreflectivity for traffic signs. These values were later revised in a 1998 FHWA report. The minimum values were developed as part of a process to add end-of-service life retroreflectivity values to the Manual on Uniform Traffic Control Devices. There have been few or no comparisons between the use of minimum retroreflectivity values to define end-of-service life and the results of typical nighttime visual inspections. Researchers at the Texas Transportation Institute conducted such an evaluation as part of a Texas Department of Transportation (TxDOT) sign workshop. In the evaluation, TxDOT sign crews evaluated 49 signs on an 8-km (5-mi) closed course. Each sign was rated as acceptable, marginal, or unacceptable. Vehicle headlamp illuminance was also measured. The results of the evaluations were compared with the application of the FHWA minimum values. The results show that whereas one sign did not meet the low-speed FHWA minimum values, the average ratings for the TxDOT sign crews indicated that 26 signs were not acceptable. The researchers identified several factors that affected the average sign ratings. These factors included the uniformity of the sign face, the type of sheeting material, and the retroreflectivity. The findings indicate that among the TxDOT sign crews participating in the evaluation, visual nighttime inspections result in a higher failing rate than does the application of the FHWA research recommendations for minimum levels of retroreflectivity. This finding indicates that visual sign inspections should be an important component of assessing the nighttime visibility of traffic signs

    Research report (Austin, Tex.)

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    "This report catalogs several devices that were found to be effective at improving driver and worker safety at short-term work zones. The services include are: fluorescent yellow-green worker vests and hard hat covers, portable variable message signs, speed display trailers, fluorescent orange roll-up signs, radar drones, and retroreflective magnetic strips for work vehicles. The catalog provides a brief description of each treatment, along with a summary of the treatment's effectiveness, and recommendations for its use at short-term work zones.
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