Species abundance information improves sequence taxonomy classification accuracy.

Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments

Urinary Catheters: What Type Do Men and Their Nurses Prefer?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111067/1/j.1532-5415.1999.tb01567.x.pd

Strong Lensing Model of SPT-CLJ0356-5337, a Major Merger Candidate at Redshift 1.0359

We present an analysis of the mass distribution inferred from strong lensing by SPT-CL J0356-5337, a cluster of galaxies at redshift z = 1.0359 revealed in the follow-up of the SPT-SZ clusters. The cluster has an Einstein radius of Erad=14 for a source at z = 3 and a mass within 500 kpc of M_500kpc = 4.0+-0.8x10^14Msol. Our spectroscopic identification of three multiply-imaged systems (z = 2.363, z = 2.364, and z = 3.048), combined with HST F606W-band imaging allows us to build a strong lensing model for this cluster with an rms of <0.3'' between the predicted and measured positions of the multiple images. Our modeling reveals a two-component mass distribution in the cluster. One mass component is dominated by the brightest cluster galaxy and the other component, separated by ~170 kpc, contains a group of eight red elliptical galaxies confined in a ~9'' (~70 kpc) diameter circle. We estimate the mass ratio between the two components to be between 1:1.25 and 1:1.58. In addition, spectroscopic data reveal that these two near-equal mass cores have only a small velocity difference of 300 km/s between the two components. This small radial velocity difference suggests that most of the relative velocity takes place in the plane of the sky, and implies that SPT-CL J0356-5337 is a major merger with a small impact parameter seen face-on. We also assess the relative contributions of galaxy-scale halos to the overall mass of the core of the cluster and find that within 800 kpc from the brightest cluster galaxy about 27% of the total mass can be attributed to visible and dark matter associated with galaxies, whereas only 73% of the total mass in the core comes from cluster-scale dark matter halos.Comment: 19 pages, 11 figures. Submitted to Ap

Comparing the Mechanical Response of Di-, Tri-, and Tetra-functional Resin Epoxies with Reactive Molecular Dynamics

The influence of monomer functionality on the mechanical properties of epoxies is studied using Molecular Dynamics (MD) with the Reax Force Field (ReaxFF). From deformation simulations, the Youngs modulus, yield point, and Poissons ratio are calculated and analyzed. The results demonstrate an increase in stiffness and yield strength with increasing resin functionality. Comparison between the network structures of distinct epoxies is further advanced by the Monomeric Degree Index (MDI). Experimental validation demonstrates the MD results correctly predict the relationship in Youngs moduli. Therefore, ReaxFF is confirmed to be a useful tool for studying the mechanical behavior of epoxies

A Search for Oxygen in the Low-Density Lyman-alpha Forest Using the Sloan Digital Sky Survey

We use 2167 Sloan Digital Sky Survey (SDSS) quasar spectra to search for low-density oxygen in the Intergalactic Medium (IGM). Oxygen absorption is detected on a pixel-by-pixel basis by its correlation with Lyman-alpha forest absorption. We have developed a novel Locally Calibrated Pixel (LCP) search method that uses adjacent regions of the spectrum to calibrate interlopers and spectral artifacts, which would otherwise limit the measurement of OVI absorption. Despite the challenges presented by searching for weak OVI within the Lyman-alpha forest in spectra of moderate resolution and signal-to-noise, we find a highly significant detection of absorption by oxygen at 2.7 < z < 3.2 (the null hypothesis has a chi^2=80 for 9 data points). We interpret our results using synthetic spectra generated from a lognormal density field assuming a mixed quasar-galaxy photoionizing background (Haardt & Madau 2001) and that it dominates the ionization fraction of detected OVI. The LCP search data can be fit by a constant metallicity model with [O/H] = -2.15_(-0.09)^(+0.07), but also by models in which low-density regions are unenriched and higher density regions have a higher metallicity. The density-dependent enrichment model by Aguirre et al. (2008) is also an acceptable fit. All our successful models have similar mass-weighted oxygen abundance, corresponding to [_MW] = -2.45+-0.06. This result can be used to find the cosmic oxygen density in the Lyman-alpha forest, Omega_(Oxy, IGM) = 1.4(+-0.2)x10^(-6) = 3x10^(-4) Omega_b. This is the tightest constraint on the mass-weighted mean oxygen abundance and the cosmic oxygen density in the Lyman-alpha forest to date and indicates that it contains approximately 16% of metals produced by star formation (Bouch\'e et al. 2008) up to z = 3.Comment: 12 pages, 9 figures. Accepted by ApJ (minor changes

A first application of the Alcock-Paczynski test to stacked cosmic voids

We report on the first application of the Alcock-Paczynski test to stacked voids in spectroscopic galaxy redshift surveys.We use voids from the Sutter et al. (2012) void catalog, which was derived from the Sloan Digital Sky Survey Data Release 7 main sample and luminous red galaxy catalogs. The construction of that void catalog removes potential shape measurement bias by using a modified version of the ZOBOV algorithm and by removing voids near survey boundaries and masks. We apply the shape-fitting procedure presented in Lavaux & Wandelt (2012) to ten void stacks out to redshift z=0.36. Combining these measurements, we determine the mean cosmologically induced "stretch" of voids in three redshift bins, with 1-sigma errors of 5-15%. The mean stretch is consistent with unity, providing no indication of a distortion induced by peculiar velocities. While the statistical errors are too large to detect the Alcock-Paczynski effect over our limited redshift range, this proof-of-concept analysis defines procedures that can be applied to larger spectroscopic galaxy surveys at higher redshifts to constrain dark energy using the expected statistical isotropy of structures that are minimally affected by uncertainties in galaxy velocity bias.Comment: 11 pages, 8 figures, 1 table, minor revisions from referee comments, ApJ accepte

An autonomous, in situ light-dark bottle device for determining community respiration and net community production

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography-Methods 16 (2018): 323-338, doi:10.1002/lom3.10247.We describe a new, autonomous, incubation-based instrument that is deployed in situ to determine rates of gross community respiration and net community production in marine and aquatic ecosystems. During deployments at a coastal pier and in the open ocean, the PHORCYS (PHOtosynthesis and Respiration Comparison-Yielding System) captured dissolved oxygen fluxes over hourly timescales that were missed by traditional methods. The instrument uses fluorescence-quenching optodes fitted into separate light and dark chambers; these are opened and closed with piston-like actuators, allowing the instrument to make multiple, independent rate estimates in the course of each deployment. Consistent with other studies in which methods purporting to measure the same metabolic processes have yielded divergent results, respiration rate estimates from the PHORCYS were systematically higher than those calculated for the same waters using a traditional two-point Winkler titration technique. However, PHORCYS estimates of gross respiration agreed generally with separate incubations in bottles fitted with optode sensor spots. An Appendix describes a new method for estimating uncertainties in metabolic rates calculated from continuous dissolved oxygen data. Multiple successful, unattended deployments of the PHORCYS represent a small step toward fully autonomous observations of community metabolism. Yet the persistence of unexplained disagreements among aquatic metabolic rate estimates — such as those we observed between rates calculated with the PHORCYS and two existing, widely-accepted bottle-based methods — suggests that a new community intercalibration effort is warranted to address lingering sources of error in these critical measurements.This research was supported by the U.S. National Science Foundation (awards OCE-1155438 to B.A.S.V.M., J.R.V., and R.G.K., and OCE- 1059884 to B.A.S.V.M.), the Woods Hole Oceanographic Institution through a Cecil and Ida Green Foundation Innovative Technology Award and an Interdisciplinary Science Award, and a U.S. Environmental Protection Agency (EPA) STAR Graduate Fellowship to J.R.C. under Fellowship Assistance Agreement no. FP-91744301-0

Low-Intrusion Techniques and Sensitive Information Management for Warhead Counting and Verification: FY2012 Annual Report

Progress in the second year of this project is described by the series of technical reports and manuscripts that make up the content of this report. These documents summarize successes in our goals to develop our robust image-hash templating and material-discrimination techniques and apply them to test image data

A negative feedback loop mediated by the Bcl6-cullin 3 complex limits Tfh cell differentiation

Induction of Bcl6 (B cell lymphoma 6) is essential for T follicular helper (Tfh) cell differentiation of antigen-stimulated CD4(+) T cells. Intriguingly, we found that Bcl6 was also highly and transiently expressed during the CD4(+)CD8(+) (double positive [DP]) stage of T cell development, in association with the E3 ligase cullin 3 (Cul3), a novel binding partner of Bcl6 which ubiquitinates histone proteins. DP stage-specific deletion of the E3 ligase Cul3, or of Bcl6, induced the derepression of the Bcl6 target genes Batf (basic leucine zipper transcription factor, ATF-like) and Bcl6, in part through epigenetic modifications of CD4(+) single-positive thymocytes. Although they maintained an apparently normal phenotype after emigration, they expressed increased amounts of Batf and Bcl6 at basal state and produced explosive and prolonged Tfh responses upon subsequent antigen encounter. Ablation of Cul3 in mature CD4(+) splenocytes also resulted in dramatically exaggerated Tfh responses. Thus, although previous studies have emphasized the essential role of Bcl6 in inducing Tfh responses, our findings reveal that Bcl6-Cul3 complexes also provide essential negative feedback regulation during both thymocyte development and T cell activation to restrain excessive Tfh responses