Host-linked soil viral ecology along a permafrost thaw gradient

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling

Fertility outcomes following obstetric fistula repair: a prospective cohort study

Abstract Background Obstetric fistula (OF) is a maternal morbidity associated with high rates of stillbirth, amenorrhea, and sexual dysfunction. Limited data exists on the reproductive outcomes of women in the years following a fistula repair. The objective of this study is to describe the fertility outcomes and family planning practices in a population of Malawian women 1–4 years after fistula repair. Methods Women who had enrolled into a clinical database of OF patients and undergone OF repair between January 1, 2012 and July 31, 2014 were recruited and enrolled to complete a home-based survey of their demographic and reproductive health data 1–4 years after their repair. Pregnancy, amenorrhea, and sexual function were described using frequency analysis, and we compared antimüllerian hormone (AMH) concentrations between women with menses or pregnancy with women with amenorrhea or no pregnancy using Wilcoxon rank sum tests. Results Of 297 women with a prior OF repair, 148 had reproductive potential and were included in this analysis. Overall 30 women of these women (21%) became pregnant since their fistula repair, with most pregnancies ending with cesarean delivery. Of the 32 women who were amenorrheic at the time of repair, 25 (78.1%) had resumption of menses. Only 11 (8.6%) of sexually active women reported dyspareunia, and among women who were not trying to conceive, 53.1% were currently using a method of family planning. No significant differences were found in AMH concentrations between those who were pregnant or had menses versus those without pregnancy or menses, respectively. Conclusions In this long-term follow-up study of women after OF repair, many women were able to achieve a pregnancy with a live birth, have normal menses, be sexually active, and access contraception. These achievements will further assist a population of women whose reintegration and restoration of dignity is closely tied to their ability to achieve their reproductive goals. Trial registration ClinicalTrials.gov Identifier: NCT02685878

Proline-rich tyrosine kinase 2 mediates gonadotropin-releasing hormone signaling to a specific extracellularly regulated kinase-sensitive transcriptional locus in the luteinizing hormone beta-subunit gene

G protein-coupled receptor regulation of gene transcription primarily occurs through the phosphorylation of transcription factors by MAPKs. This requires transduction of an activating signal via scaffold proteins that can ultimately determine the outcome by binding signaling kinases and adapter proteins with effects on the target transcription factor and locus of activation. By investigating these mechanisms, we have elucidated how pituitary gonadotrope cells decode an input GnRH signal into coherent transcriptional output from the LH β-subunit gene promoter. We show that GnRH activates c-Src and multiple members of the MAPK family, c-Jun NH(2)-terminal kinase 1/2, p38MAPK, and ERK1/2. Using dominant-negative point mutations and chemical inhibitors, we identified that calcium-dependent proline-rich tyrosine kinase 2 specifically acts as a scaffold for a focal adhesion/cytoskeleton-dependent complex comprised of c-Src, Grb2, and mSos that translocates an ERK-activating signal to the nucleus. The locus of action of ERK was specifically mapped to early growth response-1 (Egr-1) DNA binding sites within the LH β-subunit gene proximal promoter, which was also activated by p38MAPK, but not c-Jun NH(2)-terminal kinase 1/2. Egr-1 was confirmed as the transcription factor target of ERK and p38MAPK by blockade of protein expression, transcriptional activity, and DNA binding. We have identified a novel GnRH-activated proline-rich tyrosine kinase 2-dependent ERK-mediated signal transduction pathway that specifically regulates Egr-1 activation of the LH β-subunit proximal gene promoter, and thus provide insight into the molecular mechanisms required for differential regulation of gonadotropin gene expression

Comparison of alternative evidence summary and presentation formats in clinical guideline development: a mixed-method study.

BACKGROUND: Best formats for summarising and presenting evidence for use in clinical guideline development remain less well defined. We aimed to assess the effectiveness of different evidence summary formats to address this gap. METHODS: Healthcare professionals attending a one-week Kenyan, national guideline development workshop were randomly allocated to receive evidence packaged in three different formats: systematic reviews (SRs) alone, systematic reviews with summary-of-findings tables, and 'graded-entry' formats (a 'front-end' summary and a contextually framed narrative report plus the SR). The influence of format on the proportion of correct responses to key clinical questions, the primary outcome, was assessed using a written test. The secondary outcome was a composite endpoint, measured on a 5-point scale, of the clarity of presentation and ease of locating the quality of evidence for critical neonatal outcomes. Interviews conducted within two months following completion of trial data collection explored panel members' views on the evidence summary formats and experiences with appraisal and use of research information. RESULTS: 65 (93%) of 70 participants completed questions on the prespecified outcome measures. There were no differences between groups in the odds of correct responses to key clinical questions. 'Graded-entry' formats were associated with a higher mean composite score for clarity and accessibility of information about the quality of evidence for critical neonatal outcomes compared to systematic reviews alone (adjusted mean difference 0.52, 95% CI 0.06 to 0.99). There was no difference in the mean composite score between SR with SoF tables and SR alone. Findings from interviews with 16 panelists indicated that short narrative evidence reports were preferred for the improved clarity of information presentation and ease of use. CONCLUSIONS: Our findings suggest that 'graded-entry' evidence summary formats may improve clarity and accessibility of research evidence in clinical guideline development. TRIAL REGISTRATION: Controlled-Trials.com ISRCTN05154264

Effect of aerosol composition on the performance of low-cost optical particle counter correction factors

There is considerable interest in using low-cost optical particle counters (OPCs) to supplement existing routine air quality networks that monitor particle mass concentrations. In order to do this, low-cost OPC data need to be comparable with particle mass reference instrumentation; however, there is currently no widely agreed upon methodology to accomplish this. Aerosol hygroscopicity is known to be a key parameter to consider when correcting particle mass concentrations derived from low-cost OPCs, particularly at high ambient relative humidity (RH). Correction factors have been developed that apply κ-Köhler theory to correct for the influence of water uptake by hygroscopic aerosols. We have used datasets of co-located reference particle measurements and low-cost OPC (OPC-N2, Alphasense) measurements, collected in four cities on three continents, to explore the performance of this correction factor. We provide evidence that the elevated particle mass concentrations, reported by the low-cost OPC relative to reference instrumentation, are due to bulk aerosol hygroscopicity under different RH conditions, which is determined by aerosol composition and, in particular, the levels of hygroscopic aerosols (sulfate and nitrate). We exploit measurements made in volcanic plumes in Nicaragua, which are predominantly composed of sulfate aerosol, as a natural experiment to demonstrate this behaviour in the ambient atmosphere; the observed humidogram from these measurements closely resembles the calculated pure sulfuric acid humidogram. The results indicate that the particle mass concentrations derived from low-cost OPCs during periods of high RH (>60 %) need to be corrected for aerosol hygroscopic growth. We employed a correction factor based on κ-Köhler theory and observed that the corrected OPC-N2 PM2.5 mass concentrations were within 33 % of reference measurements at all sites. The results indicated that a κ value derived in situ (using suitable reference instrumentation) would lead to the most accurate correction relative to co-located reference instruments. Applying a κ values from the literature in the correction factor also resulted in improved OPC-N2 performance, with the measurements being within 50 % of the reference values. Therefore, for areas where suitable reference instrumentation for developing a local correction factor is lacking, using a literature κ value can result in a reasonable correction. For locations with low levels of hygroscopic aerosols and low RH values, a simple calibration against gravimetric measurements (using suitable reference instrumentation) would likely be sufficient. Whilst this study generated correction factors specific for the Alphasense OPC-N2 sensor, the calibration methodology developed is likely amenable to other low-cost PM sensors

The Fifth Data Release of the Sloan Digital Sky Survey

This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through June 2005 and represents the completion of the SDSS-I project (whose successor, SDSS-II will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 square degrees, and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 square degrees of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.Comment: ApJ Supp, in press, October 2007. This paper describes DR5. The SDSS Sixth Data Release (DR6) is now public, available from http://www.sdss.or

The Seventh Data Release of the Sloan Digital Sky Survey

This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11663 deg^2 of imaging data, with most of the roughly 2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry over 250 deg^2 along the Celestial Equator in the Southern Galactic Cap. A coaddition of these data goes roughly two magnitudes fainter than the main survey. The spectroscopy is now complete over a contiguous area of 7500 deg^2 in the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog (UCAC-2), reducing the rms statistical errors at the bright end to 45 milli-arcseconds per coordinate. A systematic error in bright galaxy photometr is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat-fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities. (Abridged)Comment: 20 pages, 10 embedded figures. Accepted to ApJS after minor correction

Sixty Years of Modern Human Origins in the American Anthropological Association

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65197/1/aa.2003.105.1.89.pd

CosmoDC2: A Synthetic Sky Catalog for Dark Energy Science with LSST

This paper introduces cosmoDC2, a large synthetic galaxy catalog designed to support precision dark energy science with the Large Synoptic Survey Telescope (LSST). CosmoDC2 is the starting point for the second data challenge (DC2) carried out by the LSST Dark Energy Science Collaboration (LSST DESC). The catalog is based on a trillion-particle, 4.225 Gpc^3 box cosmological N-body simulation, the `Outer Rim' run. It covers 440 deg^2 of sky area to a redshift of z=3 and is complete to a magnitude depth of 28 in the r-band. Each galaxy is characterized by a multitude of properties including stellar mass, morphology, spectral energy distributions, broadband filter magnitudes, host halo information and weak lensing shear. The size and complexity of cosmoDC2 requires an efficient catalog generation methodology; our approach is based on a new hybrid technique that combines data-driven empirical approaches with semi-analytic galaxy modeling. A wide range of observation-based validation tests has been implemented to ensure that cosmoDC2 enables the science goals of the planned LSST DESC DC2 analyses. This paper also represents the official release of the cosmoDC2 data set, including an efficient reader that facilitates interaction with the data