BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes

Microbes play an increasingly recognized role in determining host-associated phenotypes by producing small molecules that interact with other microorganisms or host cells. The production of these molecules is often encoded in syntenic genomic regions, also known as gene clusters.

Comparing different mass estimators for a large subsample of the Planck-ESZ clusters

Context. Total mass is arguably the most fundamental property for cosmological studies with galaxy clusters. The individual cluster masses can be obtained with different methods, each with its own biases and limitations. Systematic differences in mass measurements can strongly impact the determination of the hydrostatic bias and of the mass-observable relations, key requirements of many cluster abundance studies. Aims. We investigate the present differences in the mass estimates obtained through independent X-ray, weak-lensing, and dynamical studies using a large subsample of the Planck-ESZ clusters. We also discuss the implications for mass bias analyses. Methods. After assessing the systematic differences in the X-ray-derived masses reported by distinct groups, we examine the mass estimates obtained with independent methods and quantify the differences as the mean ratio 1-b = MHE/MWL, dyn, where HE refers to hydrostatic masses obtained from X-ray observations, WL refers to the results of weak-lensing measurements, and dyn refers to the mass estimates either from velocity dispersion or from the caustic technique. So defined, the 1-b parameter includes all possible astrophysical, observational, and methodological biases in one single value. Results. Recent X-ray masses reported by independent groups show average differences smaller than ∼10%, posing a strong limit on the systematics that can be ascribed to the differences in the X-ray analysis when studying the hydrostatic bias. The mean ratio between our X-ray masses and the weak-lensing masses in the LC2-single catalog is 1-b = 0.74 ± 0.06, which corresponds to a mass bias of 26 ± 6%, a value insufficient to reconcile the Planck cluster abundance and cosmic microwave background results. However, the mean mass ratios inferred from the WL masses of different projects vary by a large amount, with APEX-SZ showing a bias consistent with zero (1-b = 1.02 ± 0.12), LoCuSS and CCCP/MENeaCS showing a significant difference (1-b = 0.76 ± 0.09 and 1-b = 0.77 ± 0.10, respectively), and WtG pointing to the largest deviation (1-b = 0.61 ± 0.12), which would substantially reduce the tension between the Planck results. Because of small differences between our M − YX relation and the one used by the Planck collaboration, our X-ray masses are on average 7% lower (4% at the same physical radius) than the Planck masses and can further reduce the required bias. At odds with the WL results, the dynamical mass measurements show better agreement with the X-ray hydrostatic masses, although there are significant differences when relaxed or disturbed clusters are used. However, the comparison is currently limited by the small sample sizes. Conclisions. The systematic differences between total masses obtained with recent independent X-ray analyses are smaller than those found in previous studies. This shifts the focus to WL and dynamical studies for a better convergence of the level of mass bias. However, the ratios obtained using different mass estimators suggest that there are still systematics that are not accounted for in all the techniques used to recover cluster masses. This prevents the determination of firm constraints on the level of hydrostatic mass bias in galaxy clusters.

Beach restoration improves habitat quality for American horseshoe crabs and shorebirds in the Delaware Bay, USA

Beach nourishment is commonly conducted to protect human infrastructure but rarely for the primary purpose of improving wildlife habitat. To improve horseshoe crab spawning and shorebird feeding habitat in the Delaware Bay, New Jersey (USA), we removed 2000 t of shoreline rubble and placed sand on 16 ha of degraded shoreline spanning 8 beaches. Horseshoe crab egg cluster abundance varied annually, seasonally and spatially. Beaches restored using sand with grain size fractions similar to native sand had horseshoe crab egg cluster abundances matching or exceeding those of high-quality reference beaches. Deeper sand with a higher coarse-grain fraction resulted in the highest egg cluster abundance across all sites and beaches, while finer-grained sand used on a subset of restored beaches was associated with lower egg cluster abundances. These patterns were also reflected in shallow egg availability for shorebirds, with egg cluster abundance correlating positively with shallow egg abundance. Over time, sand placed on beaches moved cross-shore and longshore, and overwashed into marshes. Longshore sand movement nourished adjacent beaches and ebb shoals at creek mouths. Such shoals attract spawning horseshoe crabs and have high densities of surface eggs available for shorebird feeding, but experience high attrition of egg clusters. This study demonstrates that investments in beach restoration provide important benefits for horseshoe crabs and shorebirds. Outcomes can be further improved by expanding project scope and integrating other coastal restoration strategies. Restoration will be critical for the conservation of coastal species as sea levels rise and current and past coastal management practices continue to degrade habitats.

Cosmological implications of a modified galaxy cluster pressure profile using the Planck tSZ power spectrum

The mean pressure profile of the cluster population is a key element in cosmological analyses based on surveys of galaxy clusters observed through the Sunyaev-Zel’dovich (SZ) effect. A variation of both the shape and the amplitude of this profile could explain part of the discrepancy currently observed between the cosmological constraints obtained from the analyses of the CMB primary anisotropies and those from cluster abundance in SZ surveys for a fixed mass bias parameter. We study the cosmological implications of a modification of the mean pressure profile through the analysis of the SZ power spectrum measured by Planck. We define two mean pressure profiles on either side of the one obtained from the observation of nearby clusters by Planck. The parameters of these profiles are chosen to ensure their compatibility with the distributions of pressure and gas mass fraction profiles observed at low redshift. We find significant differences between the cosmological parameters obtained by using these two profiles to fit the Planck SZ power spectrum and those found in previous analyses. We conclude that a ∼15% decrease of the amplitude of the mean normalized pressure profile is sufficient to alleviate the discrepancy observed between the constraints of σ8 and Ωm from the CMB and cluster analyses.

Influence of Vitellaria Paradoxa Gaertn Depletion on the Incidence, Abundance and Distribution of Cirina Forda Westwood (Lepidoptera: Saturniidae) in Niger State, Nigeria

The pallid emperor moth, Cirina forda, is a prominent edible insect in Niger State but currently at great risk of extinction. The incidence, abundance and distribution of Cirina forda, was investigated for four consecutive seasons, i.e. May-June 2010, 2011, 2012 and 2013 to ascertain the effect of the depletion of its host plant, Shea butter trees, Vitellaria paradoxa. in Niger State, Nigeria. C. forda egg clusters located on the host plants were enumerated to ascertain the seasonal abundance by visual counting using hand lenses and binoculars (MARCO-model 750/8 m-988000 m). At each location, 100m2 land area in which three 10m2 portions were mapped as replicate sites, were investigated for host plant density, egg cluster abundance and distribution within three host plant canopy height ranges. The 41 locations in six Local Government Areas (LGAs) where C. forda occurred in Niger State in 2010 were investigated. The result indicated the GPS of each of the locations and showed that Niger state had a very rich but fast dwindling population of V. paradoxa. C. forda egg cluster abundance across the six LGAs showed Niger state as highly endowed but ephemeral and highly unpredictable, especially in terms of location where they occurred. The egg cluster abundance reduced drastically from 58.1± 12.1 and 56.1±24.1 egg cluster/host plant in 2010 and 2011, respectively to 41.3 ± 8.3 and 29.7 ±5.1 egg cluster/host plant in 2012 and 2013 cropping seasons, respectively. Locational similarities were observed in the trends of C. forda host plant density reduction and egg cluster abundance over the four cropping seasons and these were corroborated across the State. The decreasing densities of Shea butter trees was identified as posing serious threats to egg laying by C. forda. The possibility of the extinction of C. forda was identified as imminent and a conservation approach that stems the indiscriminate destruction of host tree, V. paradoxa (Shea butter trees) was proposed.

Halo exclusion criteria impacts halo statistics

ABSTRACT Every halo-finding algorithm must make a critical yet relatively arbitrary choice: it must decide which structures are parent haloes, and which structures are subhaloes of larger haloes. We refer to this choice as percolation. We demonstrate that the choice of percolation impacts the statistical properties of the resulting halo catalogue. Specifically, we modify the halo-finding algorithm rockstar to construct three different halo catalogues from the same simulation data, each with identical mass definitions, but different choice of percolation. The resulting haloes exhibit significant differences in both halo abundance and clustering properties. Differences in the halo mass function reach 6 per cent for haloes of mass $10^{13}\ h^{-1}\ {\rm {\rm M}_{\odot }}$, larger than the few per cent precision necessary for current cluster abundance experiments such as the Dark Energy Survey. Comparable differences are observed in the large-scale clustering bias, while differences in the halo–matter correlation function reach 30 per cent on translinear scales. These effects can bias weak-lensing estimates of cluster masses at a level comparable to the statistical precision of current state-of-the-art experiments.

Non-LTE chemical abundances in Galactic open and globular clusters

Aims. We study the effects of non-local thermodynamic equilibrium (NLTE) on the determination of stellar parameters and abundances of Fe, Mg, and Ti from the medium-resolution spectra of FGK stars. Methods. We extended the Payne fitting approach to draw on NLTE and LTE spectral models. These were used to analyse the spectra of the Gaia-ESO benchmark stars and the spectra of 742 stars in 13 open and globular clusters in the Milky Way: NGC 3532, NGC 5927, NGC 2243, NGC 104, NGC 1851, NGC 2808, NGC 362, M 2, NGC 6752, NGC 1904, NGC 4833, NGC 4372, and M15. Results. Our approach accurately recovers effective temperatures, surface gravities, and abundances of the benchmark stars and clusters members. The differences between NLTE and LTE are significant in the metal-poor regime, [Fe/H] ≲ −1. The NLTE [Fe/H] values are systematically higher, whereas the average NLTE [Mg/Fe] abundance ratios are ∼0.15 dex lower, compared to LTE. Our LTE measurements of metallicities and abundances of stars in Galactic clusters are in a good agreement with the literature. Though, for most clusters, our study yields the first estimates of NLTE abundances of Fe, Mg, and Ti. Conclusion. All clusters investigated in this work are homogeneous in Fe and Ti, with the intra-cluster abundance variations of less then 0.04 dex. NGC 2808, NGC 4833, M 2, and M 15 show significant dispersions in [Mg/Fe]. Contrary to common assumptions, the NLTE analysis changes the mean abundance ratios in the clusters, but it does not influence the intra-cluster abundance dispersions.