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Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.
BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades
ArborZ: Photometric Redshifts Using Boosted Decision Trees
Precision photometric redshifts will be essential for extracting cosmological
parameters from the next generation of wide-area imaging surveys. In this paper
we introduce a photometric redshift algorithm, ArborZ, based on the
machine-learning technique of Boosted Decision Trees. We study the algorithm
using galaxies from the Sloan Digital Sky Survey and from mock catalogs
intended to simulate both the SDSS and the upcoming Dark Energy Survey. We show
that it improves upon the performance of existing algorithms. Moreover, the
method naturally leads to the reconstruction of a full probability density
function (PDF) for the photometric redshift of each galaxy, not merely a single
"best estimate" and error, and also provides a photo-z quality figure-of-merit
for each galaxy that can be used to reject outliers. We show that the stacked
PDFs yield a more accurate reconstruction of the redshift distribution N(z). We
discuss limitations of the current algorithm and ideas for future work.Comment: 10 pages, 13 figures, submitted to Ap
Cosmological Constraints from Galaxy Clustering and the Mass-to-Number Ratio of Galaxy Clusters
We place constraints on the average density (Omega_m) and clustering
amplitude (sigma_8) of matter using a combination of two measurements from the
Sloan Digital Sky Survey: the galaxy two-point correlation function, w_p, and
the mass-to-galaxy-number ratio within galaxy clusters, M/N, analogous to
cluster M/L ratios. Our w_p measurements are obtained from DR7 while the sample
of clusters is the maxBCG sample, with cluster masses derived from weak
gravitational lensing. We construct non-linear galaxy bias models using the
Halo Occupation Distribution (HOD) to fit both w_p and M/N for different
cosmological parameters. HOD models that match the same two-point clustering
predict different numbers of galaxies in massive halos when Omega_m or sigma_8
is varied, thereby breaking the degeneracy between cosmology and bias. We
demonstrate that this technique yields constraints that are consistent and
competitive with current results from cluster abundance studies, even though
this technique does not use abundance information. Using w_p and M/N alone, we
find Omega_m^0.5*sigma_8=0.465+/-0.026, with individual constraints of
Omega_m=0.29+/-0.03 and sigma_8=0.85+/-0.06. Combined with current CMB data,
these constraints are Omega_m=0.290+/-0.016 and sigma_8=0.826+/-0.020. All
errors are 1-sigma. The systematic uncertainties that the M/N technique are
most sensitive to are the amplitude of the bias function of dark matter halos
and the possibility of redshift evolution between the SDSS Main sample and the
maxBCG sample. Our derived constraints are insensitive to the current level of
uncertainties in the halo mass function and in the mass-richness relation of
clusters and its scatter, making the M/N technique complementary to cluster
abundances as a method for constraining cosmology with future galaxy surveys.Comment: 23 pages, submitted to Ap
Element abundance patterns in stars indicate fission of nuclei heavier than uranium
The heaviest chemical elements are naturally produced by the rapid
neutron-capture process (r-process) during neutron star mergers or supernovae.
The r-process production of elements heavier than uranium (transuranic nuclei)
is poorly understood and inaccessible to experiments, so must be extrapolated
using nucleosynthesis models. We examine element abundances in a sample of
stars that are enhanced in r-process elements. The abundances of elements Ru,
Rh, Pd, and Ag (atomic numbers Z = 44 to 47, mass numbers A = 99 to 110)
correlate with those of heavier elements (63 150). There is no
correlation for neighboring elements (34 <= Z <= 42 and 48 <= Z <= 62). We
interpret this as evidence that fission fragments of transuranic nuclei
contribute to the abundances. Our results indicate that neutron-rich nuclei
with mass numbers >260 are produced in r-process events.Comment: Authors' version of manuscript published in Science on December 07,
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Common carotid intima media thickness and ankle-brachial pressure index correlate with local but not global atheroma burden:a cross sectional study using whole body magnetic resonance angiography
Common carotid intima media thickness (CIMT) and ankle brachial pressure index (ABPI) are used as surrogate marker of atherosclerosis, and have been shown to correlate with arterial stiffness, however their correlation with global atherosclerotic burden has not been previously assessed. We compare CIMT and ABPI with atheroma burden as measured by whole body magnetic resonance angiography (WB-MRA).50 patients with symptomatic peripheral arterial disease were recruited. CIMT was measured using ultrasound while rest and exercise ABPI were performed. WB-MRA was performed in a 1.5T MRI scanner using 4 volume acquisitions with a divided dose of intravenous gadolinium gadoterate meglumine (Dotarem, Guerbet, FR). The WB-MRA data was divided into 31 anatomical arterial segments with each scored according to degree of luminal narrowing: 0 = normal, 1 = <50%, 2 = 50-70%, 3 = 70-99%, 4 = vessel occlusion. The segment scores were summed and from this a standardized atheroma score was calculated.The atherosclerotic burden was high with a standardised atheroma score of 39.5±11. Common CIMT showed a positive correlation with the whole body atheroma score (β 0.32, p = 0.045), however this was due to its strong correlation with the neck and thoracic segments (β 0.42 p = 0.01) with no correlation with the rest of the body. ABPI correlated with the whole body atheroma score (β -0.39, p = 0.012), which was due to a strong correlation with the ilio-femoral vessels with no correlation with the thoracic or neck vessels. On multiple linear regression, no correlation between CIMT and global atheroma burden was present (β 0.13 p = 0.45), while the correlation between ABPI and atheroma burden persisted (β -0.45 p = 0.005).ABPI but not CIMT correlates with global atheroma burden as measured by whole body contrast enhanced magnetic resonance angiography in a population with symptomatic peripheral arterial disease. However this is primarily due to a strong correlation with ilio-femoral atheroma burden
Cosmological Constraints from the SDSS maxBCG Cluster Catalog
We use the abundance and weak lensing mass measurements of the SDSS maxBCG
cluster catalog to simultaneously constrain cosmology and the richness--mass
relation of the clusters. Assuming a flat \LambdaCDM cosmology, we find
\sigma_8(\Omega_m/0.25)^{0.41} = 0.832\pm 0.033 after marginalization over all
systematics. In common with previous studies, our error budget is dominated by
systematic uncertainties, the primary two being the absolute mass scale of the
weak lensing masses of the maxBCG clusters, and uncertainty in the scatter of
the richness--mass relation. Our constraints are fully consistent with the WMAP
five-year data, and in a joint analysis we find \sigma_8=0.807\pm 0.020 and
\Omega_m=0.265\pm 0.016, an improvement of nearly a factor of two relative to
WMAP5 alone. Our results are also in excellent agreement with and comparable in
precision to the latest cosmological constraints from X-ray cluster abundances.
The remarkable consistency among these results demonstrates that cluster
abundance constraints are not only tight but also robust, and highlight the
power of optically-selected cluster samples to produce precision constraints on
cosmological parameters.Comment: comments welcom
Can sacrificial feeding areas protect aquatic plants from herbivore grazing? Using behavioural ecology to inform wildlife management
Effective wildlife management is needed for conservation, economic and human well-being objectives. However, traditional population control methods are frequently ineffective, unpopular with stakeholders, may affect non-target species, and can be both expensive and impractical to implement. New methods which address these issues and offer effective wildlife management are required. We used an individual-based model to predict the efficacy of a sacrificial feeding area in preventing grazing damage by mute swans (Cygnus olor) to adjacent river vegetation of high conservation and economic value. The accuracy of model predictions was assessed by a comparison with observed field data, whilst prediction robustness was evaluated using a sensitivity analysis. We used repeated simulations to evaluate how the efficacy of the sacrificial feeding area was regulated by (i) food quantity, (ii) food quality, and (iii) the functional response of the forager. Our model gave accurate predictions of aquatic plant biomass, carrying capacity, swan mortality, swan foraging effort, and river use. Our model predicted that increased sacrificial feeding area food quantity and quality would prevent the depletion of aquatic plant biomass by swans. When the functional response for vegetation in the sacrificial feeding area was increased, the food quantity and quality in the sacrificial feeding area required to protect adjacent aquatic plants were reduced. Our study demonstrates how the insights of behavioural ecology can be used to inform wildlife management. The principles that underpin our model predictions are likely to be valid across a range of different resource-consumer interactions, emphasising the generality of our approach to the evaluation of strategies for resolving wildlife management problems
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