Classifying short genomic fragments from novel lineages using composition and homology

<p>Abstract</p> <p>Background</p> <p>The assignment of taxonomic attributions to DNA fragments recovered directly from the environment is a vital step in metagenomic data analysis. Assignments can be made using <it>rank-specific </it>classifiers, which assign reads to taxonomic labels from a predetermined level such as named species or strain, or <it>rank-flexible </it>classifiers, which choose an appropriate taxonomic rank for each sequence in a data set. The choice of rank typically depends on the optimal model for a given sequence and on the breadth of taxonomic groups seen in a set of close-to-optimal models. Homology-based (<it>e.g</it>., LCA) and composition-based (<it>e.g</it>., PhyloPythia, TACOA) rank-flexible classifiers have been proposed, but there is at present no hybrid approach that utilizes both homology and composition.</p> <p>Results</p> <p>We first develop a hybrid, rank-specific classifier based on BLAST and Naïve Bayes (NB) that has comparable accuracy and a faster running time than the current best approach, PhymmBL. By substituting LCA for BLAST or allowing the inclusion of suboptimal NB models, we obtain a rank-flexible classifier. This hybrid classifier outperforms established rank-flexible approaches on simulated metagenomic fragments of length 200 bp to 1000 bp and is able to assign taxonomic attributions to a subset of sequences with few misclassifications. We then demonstrate the performance of different classifiers on an enhanced biological phosphorous removal metagenome, illustrating the advantages of rank-flexible classifiers when representative genomes are absent from the set of reference genomes. Application to a glacier ice metagenome demonstrates that similar taxonomic profiles are obtained across a set of classifiers which are increasingly conservative in their classification.</p> <p>Conclusions</p> <p>Our NB-based classification scheme is faster than the current best composition-based algorithm, Phymm, while providing equally accurate predictions. The rank-flexible variant of NB, which we term ε-NB, is complementary to LCA and can be combined with it to yield conservative prediction sets of very high confidence. The simple parameterization of LCA and ε-NB allows for tuning of the balance between more predictions and increased precision, allowing the user to account for the sensitivity of downstream analyses to misclassified or unclassified sequences.</p

The Membership and Distance of the Open Cluster Collinder 419

The young open cluster Collinder 419 surrounds the massive O star, HD 193322, that is itself a remarkable multiple star system containing at least four components. Here we present a discussion of the cluster distance based upon new spectral classifications of the brighter members, UBV photometry, and an analysis of astrometric and photometric data from the UCAC3 and 2MASS catalogs. We determine an average cluster reddening of E(B-V)=0.37 +- 0.05 mag and a cluster distance of 741 +- 36 pc. The cluster probably contains some very young stars that may include a reddened M3 III star, IRAS~20161+4035

A Summary and Appraisal of Texas Real Property Tax Laws.

37 p

Periodic and Aperiodic Variability in the Molecular Cloud ρ Ophiuchus

Presented are the results of a near-IR photometric survey of 1678 stars in the direction of the ρ Ophiuchus (ρ Oph) star forming region using data from the 2MASS Calibration Database. For each target in this sample, up to 1584 individual J-, H-, and K_s-band photometric measurements with a cadence of ~1 day are obtained over three observing seasons spanning ~2.5 yr; it is the most intensive survey of stars in this region to date. This survey identifies 101 variable stars with ΔK_s-band amplitudes from 0.044 to 2.31 mag and Δ(J − K_s) color amplitudes ranging from 0.053 to 1.47 mag. Of the 72 young ρ Oph star cluster members included in this survey, 79% are variable; in addition, 22 variable stars are identified as candidate members. Based on the temporal behavior of the K_s time-series, the variability is distinguished as either periodic, long time-scale or irregular. This temporal behavior coupled with the behavior of stellar colors is used to assign a dominant variability mechanism. A new period-searching algorithm finds periodic signals in 32 variable stars with periods between 0.49 to 92 days. The chief mechanism driving the periodic variability for 18 stars is rotational modulation of cool starspots while 3 periodically vary due to accretion-induced hot spots. The time-series for six variable stars contains discrete periodic "eclipse-like" features with periods ranging from 3 to 8 days. These features may be asymmetries in the circumstellar disk, potentially sustained or driven by a proto-planet at or near the co-rotation radius. Aperiodic, long time-scale variations in stellar flux are identified in the time-series for 31 variable stars with time-scales ranging from 64 to 790 days. The chief mechanism driving long time-scale variability is variable extinction or mass accretion rates. The majority of the variable stars (40) exhibit sporadic, aperiodic variability over no discernable time-scale. No chief variability mechanism could be identified for these variable stars

Stellar Diameters and Temperatures. I. Main-Sequence A, F, and G Stars

We have executed a survey of nearby, main-sequence A-, F-, and G-type stars with the CHARA Array, successfully measuring the angular diameters of forty-four stars with an average precision of ~1.5%. We present new measures of the bolometric flux, which in turn leads to an empirical determination of the effective temperature for the stars observed. In addition, these CHARA-determined temperatures, radii, and luminosities are fit to Yonsei-Yale model isochrones to constrain the masses and ages of the stars. These results are compared to indirect estimates of these quantities obtained by collecting photometry of the stars and applying them to model atmospheres and evolutionary isochrones. We find that for most cases, the models overestimate the effective temperature by ~1.5%-4% when compared to our directly measured values. The overestimated temperatures and underestimated radii in these works appear to cause an additional offset in the star's surface gravity measurements, which consequently yield higher masses and younger ages, in particular for stars with masses greater than ~1.3 M_☉. Additionally, we compare our measurements to a large sample of eclipsing binary stars, and excellent agreement is seen within both data sets. Finally, we present temperature relations with respect to (B – V) and (V – K) colors as well as spectral type, showing that calibration of effective temperatures with errors ~1% is now possible from interferometric angular diameters of stars

WESTT (Workload, Error, Situational Awareness, Time and Teamwork): An analytical prototyping system for command and control

Modern developments in the use of information technology within command and control allow unprecedented scope for flexibility in the way teams deal with tasks. These developments, together with the increased recognition of the importance of knowledge management within teams present difficulties for the analyst in terms of evaluating the impacts of changes to task composition or team membership. In this paper an approach to this problem is presented that represents team behaviour in terms of three linked networks (representing task, social network structure and knowledge) within the integrative WESTT software tool. In addition, by automating analyses of workload and error based on the same data that generate the networks, WESTT allows the user to engage in the process of rapid and iterative “analytical prototyping”. For purposes of illustration an example of the use of this technique with regard to a simple tactical vignette is presented

Quantum interference experiments, modular variables and weak measurements

We address the problem of interference using the Heisenberg picture and highlight some new aspects through the use of pre-selection, post-selection, weak measurements, and modular variables, We present a physical explanation for the different behaviors of a single particle when the distant slit is open or closed: instead of having a quantum wave that passes through all slits, we have a localized particle with non-local interactions with the other slit(s). We introduce a Gedankenexperiment to measure this non-local exchange. While the Heisenberg picture and the Schrodinger pictures are equivalent formulations of quantum mechanics, nevertheless, the results discussed here support a new approach which has led to new insights, new intuitions, new experiments, and even the possibility of new devices that were missed from the old perspective

New Tetrahedral Global Minimum for the 98-atom Lennard-Jones Cluster

A new atomic cluster structure corresponding to the global minimum of the 98-atom Lennard-Jones cluster has been found using a variant of the basin-hopping global optimization algorithm. The new structure has an unusual tetrahedral symmetry with an energy of -543.665361, which is 0.022404 lower than the previous putative global minimum. The new LJ_98 structure is of particular interest because its tetrahedral symmetry establishes it as one of only three types of exceptions to the general pattern of icosahedral structural motifs for optimal LJ microclusters. Similar to the other exceptions the global minimum is difficult to find because it is at the bottom of a narrow funnel which only becomes thermodynamically most stable at low temperature.Comment: 3 pages, 2 figures, revte

Nutritional Skewing of Conceptus Sex in Sheep: Effects of a Maternal Diet Enriched in Rumen-Protected Polyunsaturated Fatty acids (PUFA)

doi:10.1186/1477-7827-6-21Evolutionary theory suggests that in polygynous mammalian species females in better body condition should produce more sons than daughters. Few controlled studies have however tested this hypothesis and controversy exists as to whether body condition score or maternal diet is in fact the determining factor of offspring sex. Here, we examined whether maternal diet, specifically increased n-6 polyunsaturated fatty acid(PUFA) intake, of ewes with a constant body condition score around the time of conception influenced sex ratio.The research was supported by USDA/CSREES/NRI Grant 2001-35203- 10693 (to RMR) and a Life Sciences Molecular Biology Fellowship, University of Missouri (partial salary support for MPG)