Unbiased taxonomic annotation of metagenomic samples

The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under thereceiver operating characteristic (ROC) curve andF-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample.Peer ReviewedPostprint (published version

Detector Description and Performance for the First Coincidence Observations between LIGO and GEO

For 17 days in August and September 2002, the LIGO and GEO interferometer gravitational wave detectors were operated in coincidence to produce their first data for scientific analysis. Although the detectors were still far from their design sensitivity levels, the data can be used to place better upper limits on the flux of gravitational waves incident on the earth than previous direct measurements. This paper describes the instruments and the data in some detail, as a companion to analysis papers based on the first data.Comment: 41 pages, 9 figures 17 Sept 03: author list amended, minor editorial change

A First Search for coincident Gravitational Waves and High Energy Neutrinos using LIGO, Virgo and ANTARES data from 2007

We present the results of the first search for gravitational wave bursts associated with high energy neutrinos. Together, these messengers could reveal new, hidden sources that are not observed by conventional photon astronomy, particularly at high energy. Our search uses neutrinos detected by the underwater neutrino telescope ANTARES in its 5 line configuration during the period January - September 2007, which coincided with the fifth and first science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed for candidate gravitational-wave signals coincident in time and direction with the neutrino events. No significant coincident events were observed. We place limits on the density of joint high energy neutrino - gravitational wave emission events in the local universe, and compare them with densities of merger and core-collapse events.Comment: 19 pages, 8 figures, science summary page at http://www.ligo.org/science/Publication-S5LV_ANTARES/index.php. Public access area to figures, tables at https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p120000

The effects of social TV on television advertising effectiveness

Social TV is the use of communication devices to connect with family and friends watching other TV screens. Plausible arguments suggest both positive and negative effects of social TV viewing on ad-effectiveness. This study contributes by providing evidence for the direction of social TV's effects. The results of a controlled laboratory experiment suggest that the benefits of social TV, principally its association with live TV and therefore less ad-avoidance, come at the cost of negative distraction effects. Like normal coviewing, social TV viewing distracts from ad-processing, reducing unaided recall and brand attitude favorability, compared to individual (solus) viewing. However, social TV messaging about ads improved brand attitude. Perceived creativity increased the likelihood of ad-related messaging. Social TV also has an additional source of distraction, multitasking, but in this study, multitasking did not further reduce ad-effectiveness compared to coviewing. The paper concludes with implications for advertisers and future research

Scale Dependence of Soil Permeability to Air: Measurement Method and Field Investigation

This work investigates the dependence soil air-permeability on sampling scale in near-surface unsaturated soils. A new dual-probe dynamic pressure technique was developed to measure permeability in situ over different length scales and different spatial orientations in the soil. Soils at three sites were studied using the new technique. Each soil was found to have higher horizontal than vertical permeability. Significant scale dependence of permeability was also observed at each site. Permeability increased by a factor of 20 as sampling scale increased from 0.1 to 2 m in a sand soil vegetated with dry grass, and by a factor of 15 as sampling scale increased from 0.1 to 3.5 m in a sandy loam with mature Coast Live Oak trees (Quercus agrifolia). The results indicate that standard methods of permeability assessment can grossly underestimate advective transport of gas-phase contaminants through soils