The circumgalactic medium (CGM) is fed by galaxy outflows and accretion of intergalactic gas, but its mass, heavy element enrichment, and relation to galaxy properties are poorly constrained by ...observations. In a survey of the outskirts of 42 galaxies with the Cosmic Origins Spectrograph onboard the Hubble Space Telescope, we detected ubiquitous, large (150-kiloparsec) halos of ionized oxygen surrounding star-forming galaxies; we found much less ionized oxygen around galaxies with little or no star formation. This ionized CGM contains a substantial mass of heavy elements and gas, perhaps far exceeding the reservoirs of gas in the galaxies themselves. Our data indicate that it is a basic component of nearly all star-forming galaxies that is removed or transformed during the quenching of star formation and the transition to passive evolution.
We describe the design and performance of the near-infrared (1.51-1.70 m), fiber-fed, multi-object (300 fibers), high resolution (R = λ/Δλ ∼ 22,500) spectrograph built for the Apache Point ...Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ∼105 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 to 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ∼400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.
The first objective of this study was to examine effects of adding Escherichia coli O157:H7 with or without chemical or microbial additives on the bacterial diversity and composition of alfalfa ...silage. The second objective was to examine associations between the relative abundance of known and unknown bacterial species and indices of silage fermentation quality. Alfalfa forage was harvested at 54% dry matter, chopped to a theoretical length of cut of 19 mm, and ensiled in quadruplicate in laboratory silos for 100 d after the following treatments were applied: (1) distilled water (control); (2) 1 × 105 cfu/g of E. coli O157:H7 (EC); (3) EC and 1 × 106 cfu/g of Lactobacillus plantarum (EC+LP); (4) EC and 1 × 106 cfu/g of Lactobacillus buchneri (EC+LB); and (5) EC and 0.22% propionic acid (EC+PA). After 100 d of ensiling, the silage samples were analyzed for bacterial diversity and composition via the Illumina MiSeq platform (Illumina Inc., San Diego, CA) and chemically characterized. Overall, Firmicutes (74.1 ± 4.86%) was the most predominant phylum followed by Proteobacteria (20.4 ± 3.80%). Relative to the control, adding E. coli O157:H7 alone at ensiling did not affect bacterial diversity or composition but adding EC+LP or EC+LB reduced the Shannon index, a measure of diversity (3.21 vs. 2.63 or 2.80, respectively). The relative abundance of Firmicutes (69.2 and 68.8%) was reduced, whereas that of Proteobacteria (24.0 and 24.9%) was increased by EC+LP and EC+PA treatments, relative to those of the control (79.5 and 16.5%) and EC+LB (77.4 and 18.5%) silages, respectively. Compared with the control, treatment with EC+LP increased the relative abundance of Lactobacillus, Sphingomonas, Pantoea, Pseudomonas, and Erwinia by 426, 157, 200, 194, and 163%, respectively, but reduced those of Pediococcus, Weissella, and Methylobacterium by 5,436, 763, and 250%, respectively. Relative abundance of Weissella (9.19%) and Methylobacterium (0.94%) were also reduced in the EC+LB silage compared with the control (29.7 and 1.50%, respectively). Application of propionic acid did not affect the relative abundance of Lactobacillus, Weissella, or Pediococcus. Lactate concentration correlated positively (r = 0.56) with relative abundance of Lactobacillus and negatively (r = −0.41) with relative abundance of Pediococcus. Negative correlations were detected between ammonia-N concentration and relative abundance of Sphingomonas (r = −0.51), Pantoea (r = −0.46), Pseudomonas (r = −0.45), and Stenotrophomonas (r = −0.38). Silage pH was negatively correlated with relative abundance of Lactobacillus (r = −0.59), Sphingomonas (r = −0.66), Pantoea (r = −0.69), Pseudomonas (r = −0.69), and Stenotrophomonas (r = −0.50). Future studies should aim to speciate, culture, and determine the functions of the unknown bacteria detected in this study to elucidate their roles in silage fermentation.
The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial ...phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.
We examine the dependence of the mass-to-light (M/L) ratio of large-scale structure on cosmological parameters, in models that are constrained to match observations of the projected galaxy ...correlation function w sub(p) (r sub(p)) and the galaxy luminosity function. For a sequence of cosmological models with a fixed, observationally motivated power spectrum shape and increasing normalization s sub(8), we find parameters of the galaxy halo occupation distribution (HOD) that reproduce w sub(p)(r sub(p)) measurements as a function of luminosity from the Sloan Digital Sky Survey (SDSS). From these HOD models we calculate the r-band conditional luminosity function (L\M sub(h)), and from this the mean M/L ratio as a function of halo mass M sub(h). We also use (L\M sub(h)) to populate halos of N-body simulations with galaxies and thereby compute M/L in a range of large-scale environments, including cluster infall regions. For all cosmological models, the M/L ratio in high-mass halos or high-density regions is approximately independent of halo mass or smoothing scale. However, the "plateau" value of M/L depends on s sub(8) in addition to the obvious proportionality with the matter density parameter sub(m), and it represents the universal value (M/L) = sub(m)r sub(crit)/r sub(lum) only for models in which the galaxy correlation function is approximately unbiased, i.e., with s sub(8) - s sub(8g). Our results for cluster mass halos follow the trend (M/L) sub(cl) = 577 ( sub(m)/0.3)(s sub(8)/0.9) super(1.7) h M sub(z)/L sub(z). Combined with the mean M/L ratio for CNOC galaxy clusters, this relation implies (s sub(8)/0.9)( sub(m)/0.3) super(0.6) = 0.75 c 0.06. M/L estimates for SDSS clusters and the virial regions of clusters in the CAIRNS survey imply a similar value of s sub(8) sub(m) super(0.6), while the CAIRNS estimates for cluster infall regions imply a lower value. These results are inconsistent with parameter values sub(m) - 0.3, s sub(8) - 0.9 favored by recent joint analyses of cosmic microwave background measurements and other large-scale structure data, although they agree with values inferred from the van den Bosch et al. analysis of the 2dF Galaxy Redshift Survey. We discuss possible resolutions of this discrepancy, none of which seems entirely satisfactory. In appendices we present an improved formula for halo bias factors calibrated on our 360 super(3) N-body simulations and an improved analytic technique for calculating the galaxy correlation function from a given cosmological model and HOD.
The halo occupation distribution (HOD) describes the relation between galaxies and dark matter at the level of individual dark matter halos. The properties of galaxies residing at the centers of ...halos differ from those of satellite galaxies because of differences in their formation histories. Using a smoothed particle hydrodynamics (SPH) simulation and a semianalytic (SA) galaxy formation model, we examine the separate contributions of central and satellite galaxies to the HOD, more specifically to the probability P(N"M) that a halo of virial mass M contains N galaxies of a particular class. In agreement with earlier results for dark matter subhalos, we find that the mean occupation function < N > sub(M) for galaxies above a baryonic mass threshold can be approximated by a step function for central galaxies plus a power law for satellites and that the distribution of satellite numbers is close to Poisson at fixed halo mass. Since the number of central galaxies is always zero or one, the width of P(N"M) is narrower than a Poisson distribution at low N and approaches Poisson at high N. For galaxy samples defined by different baryonic mass thresholds, there is a nearly linear relation between the minimum halo mass M sub(min) required to host a central galaxy and the mass M sub(1) at which an average halo hosts one satellite, with M sub(1) - 14M sub(min) (SPH) or M sub(1) - 18M sub(min) (SA). The stellar population age of central galaxies correlates with halo mass, and this correlation explains much of the age dependence of the galaxy HOD. The mean occupation number of young galaxies exhibits a local minimum at M 6 10M sub(min) where halos are too massive to host a young central galaxy but not massive enough to host satellites. Using the SA model, we show that the conditional galaxy mass function at fixed halo mass cannot be described by a Schechter function because central galaxies produce a "bump" at high masses. We suggest parameterizations for the HOD and the conditional luminosity function that can be used to model observed galaxy clustering. Many of our predictions are in good agreement with recent results inferred from clustering in the Sloan Digital Sky Survey.
Inhibiting the growth of Escherichia coli O157:H7 (EC) in feeds may prevent the transmission or cycling of the pathogen on farms. The first objective of this study was to examine if addition of ...propionic acid or microbial inoculants would inhibit the growth of EC during ensiling, at silo opening, or after aerobic exposure. The second objective was to examine how additives affected the bacterial community composition in corn silage. Corn forage was harvested at approximately 35% dry matter, chopped to a theoretical length of cut of 10 mm, and ensiled after treatment with one of the following: (1) distilled water (control); (2) 1 × 105 cfu/g of EC (ECCH); (3) EC and 1 × 106 cfu/g of Lactobacillus plantarum (ECLP); (4) EC and 1 × 106 cfu/g of Lactobacillus buchneri (ECLB); and (5) EC and 2.2 g/kg (fresh weight basis) of propionic acid, containing 99.5% of the acid (ECA). Each treatment was ensiled in quadruplicate in laboratory silos for 0, 3, 7, and 120 d and analyzed for EC, pH, and organic acids. Samples from d 0 and 120 were also analyzed for chemical composition. Furthermore, samples from d 120 were analyzed for ammonia N, yeasts and molds, lactic acid bacteria, bacterial community composition, and aerobic stability. The pH of silages from all treatments decreased below 4 within 3 d of ensiling. Escherichia coli O157:H7 counts were below the detection limit in all silages after 7 d of ensiling. Treatment with L. buchneri and propionic acid resulted in fewer yeasts and greater aerobic stability compared with control, ECCH, and ECLP silages. Compared with the control, the diversity analysis revealed a less diverse bacterial community in the ECLP silage and greater abundance of Lactobacillus in the ECLP and ECA silages. The ECLB silage also contained greater abundance of Acinetobacter and Weissella than other silages. Subsamples of silages were reinoculated with 5 × 105 cfu/g of EC either immediately after silo opening or after 168 h of aerobic exposure, and EC were enumerated after 6 or 24 h, respectively. All silages reinoculated with EC immediately after silo opening (120 h) had similar low pH values (<4.0) and EC counts were below the detection limit. The ECCH and ECLP silages reinoculated with EC after 168 h of aerobic exposure had relatively high pH values (>5.0) and EC counts (5.39 and 5.30 log cfu/g, respectively) 24 h later. However, those treated with L. buchneri or propionic acid had lower pH values (4.24 or 3.96, respectively) and lower EC counts (1.32 log cfu/g or none, respectively). During ensiling, EC was eliminated from all silages at pH below 4.0. During aerobic exposure, the growth of EC was reduced or prevented in silages that had been treated with L. buchneri or propionic acid at ensiling, respectively.
We study the luminosity and color dependence of the galaxy two-point correlation function in the Sloan Digital Sky Survey, starting from a sample of 6200,000 galaxies over 2500 deg super(2). We ...concentrate our analysis on volume-limited subsamples of specified luminosity ranges, for which we measure the projected correlation function w sub(p)(r sub(p)), which is directly related to the real-space correlation function y(r). The amplitude of w sub(p)(r sub(p)) rises continuously with luminosity from M sub(r) - -17.5 to M sub(r) - -22.5, with the most rapid increase occurring above the characteristic luminosity L sub(*) (M sub(r) - -20.5). Over the scales 0.1 h super(-1) Mpc < r sub(p) < 10 h super(-1) Mpc, the measurements for samples with M sub(r) > -22 can be approximated, imperfectly, by power-law three-dimensional correlation functions y(r) = (r/r sub(0)) super(-g) with g - 1.8 and r sub(0)(L sub(*)) - 5.0 h super(-1) Mpc. The brightest subsample, -23 < M sub(r) < -22, has a significantly steeper y(r). When we divide samples by color, redder galaxies exhibit a higher amplitude and steeper correlation function at all luminosities. The correlation amplitude of blue galaxies increases continuously with luminosity, but the luminosity dependence for red galaxies is less regular, with bright red galaxies exhibiting the strongest clustering at large scales and faint red galaxies exhibiting the strongest clustering at small scales. We interpret these results using halo occupation distribution (HOD) models assuming concordance cosmological parameters. For most samples, an HOD model with two adjustable parameters fits the w sub(p)(r sub(p)) data better than a power law, explaining inflections at r sub(p) 6 1-3 h super(-1) Mpc as the transition between the one-halo and two-halo regimes of y(r). The implied minimum mass for a halo hosting a central galaxy more luminous than L grows steadily, with M sub(min) 8 L at low luminosities and a steeper dependence above L sub(*). The mass at which a halo has, on average, one satellite galaxy brighter than L is M sub(1) - 23M sub(min) (L), at all luminosities. These results imply a conditional luminosity function (at fixed halo mass) in which central galaxies lie far above a Schechter function extrapolation of the satellite population. The HOD model fits nicely explain the color dependence of w sub(p)(r sub(p)) and the cross correlation between red and blue galaxies. For galaxies with M sub(r) < -21, halos slightly above M sub(min) have blue central galaxies, while more massive halos have red central galaxies and predominantly red satellite populations. The fraction of blue central galaxies increases steadily with decreasing luminosity and host halo mass. The strong clustering of faint red galaxies follows from the fact that nearly all of them are satellite systems in high-mass halos. The HOD fitting results are in good qualitative agreement with the predictions of numerical and semianalytic models of galaxy formation.
Abstract
The APOGEE Open Cluster Chemical Abundances and Mapping survey is used to probe the chemical evolution of the s-process element cerium in the Galactic disk. Cerium abundances were derived ...from measurements of Ce
ii
lines in the APOGEE spectra using the Brussels Automatic Code for Characterizing High Accuracy Spectra in 218 stars belonging to 42 open clusters. Our results indicate that, in general, for ages < 4 Gyr, younger open clusters have higher Ce/Fe and Ce/
α
-element ratios than older clusters. In addition, metallicity segregates open clusters in the Ce/X–age plane (where X can be H, Fe, or the
α
-elements O, Mg, Si, or Ca). These metallicity-dependent relations result in Ce/Fe and Ce/
α
ratios with ages that are not universal clocks. Radial gradients of Ce/H and Ce/Fe ratios in open clusters, binned by age, were derived for the first time, with
d
Ce/H/
d
R
GC
being negative, while
d
Ce/Fe/
d
R
GC
is positive. Ce/H and Ce/Fe gradients are approximately constant over time, with the Ce/Fe gradient becoming slightly steeper, changing by ∼+0.009 dex kpc
−1
Gyr
−1
. Both the Ce/H and Ce/Fe gradients are shifted to lower values of Ce/H and Ce/Fe for older open clusters. The chemical pattern of Ce in open clusters across the Galactic disk is discussed within the context of s-process yields from asymptotic giant branch (AGB) stars, gigayear time delays in Ce enrichment of the interstellar medium, and the strong dependence of Ce nucleosynthesis on the metallicity of its AGB stellar sources.
Recent advances in machine learning have enabled image-based prediction of local tissue pathology in gliomas, but the clinical usefulness of these predictions is unknown. We aimed to evaluate the ...prognostic ability of imaging-based estimates of cellular density for patients with gliomas, with comparison to the gold standard reference of World Health Organization grading.
Data from 1181 (207 grade II, 246 grade III, 728 grade IV) previously untreated patients with gliomas from a single institution were analyzed. A pretrained random forest model estimated voxelwise tumor cellularity using MR imaging data. Maximum cellular density was correlated with the World Health Organization grade and actual survival, correcting for covariates of age and performance status.
A maximum estimated cellular density of >7681 nuclei/mm
was associated with a worse prognosis and a univariate hazard ratio of 4.21 (
< .001); the multivariate hazard ratio after adjusting for covariates of age and performance status was 2.91 (
< .001). The concordance index between maximum cellular density (adjusted for covariates) and survival was 0.734. The hazard ratio for a high World Health Organization grade (IV) was 7.57 univariate (
< .001) and 5.25 multivariate (
< .001). The concordance index for World Health Organization grading (adjusted for covariates) was 0.761. The maximum cellular density was an independent predictor of overall survival, and a Cox model using World Health Organization grade, maximum cellular density, age, and Karnofsky performance status had a higher concordance (C = 0.764; range 0.748-0.781) than the component predictors.
Image-based estimation of glioma cellularity is a promising biomarker for predicting survival, approaching the prognostic power of World Health Organization grading, with added values of early availability, low risk, and low cost.
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