BAT AGN Spectroscopic Survey-III. An observed link between AGN Eddington ratio and narrow emission line ratios

We investigate the observed relationship between black hole mass ($M_{\rm BH}$), bolometric luminosity ($L_{\rm bol}$), and Eddington ratio (${\lambda}_{\rm Edd}$) with optical emission line ratios ([NII] {\lambda}6583/H{\alpha}, [SII] {\lambda}{\lambda}6716,6731/H{\alpha}, [OI] {\lambda}6300/H{\alpha}, [OIII] {\lambda}5007/H{\beta}, [NeIII] {\lambda}3869/H{\beta}, and HeII {\lambda}4686/H{\beta}) of hard X-ray-selected AGN from the BAT AGN Spectroscopic Survey (BASS). We show that the [NII] {\lambda}6583/H{\alpha} ratio exhibits a significant correlation with ${\lambda}_{\rm Edd}$ ($R_{\rm Pear}$ = -0.44, $p$-value=$3\times10^{-13}$, {\sigma} = 0.28 dex), and the correlation is not solely driven by $M_{\rm BH}$ or $L_{\rm bol}$. The observed correlation between [NII] {\lambda}6583/H{\alpha} ratio and $M_{\rm BH}$ is stronger than the correlation with $L_{\rm bol}$, but both are weaker than the ${\lambda}_{\rm Edd}$ correlation. This implies that the large-scale narrow lines of AGN host galaxies carry information about the accretion state of the AGN central engine. We propose that the [NII] {\lambda}6583/H{\alpha} is a useful indicator of Eddington ratio with 0.6 dex of rms scatter, and that it can be used to measure ${\lambda}_{\rm Edd}$ and thus $M_{\rm BH}$ from the measured $L_{\rm bol}$, even for high redshift obscured AGN. We briefly discuss possible physical mechanisms behind this correlation, such as the mass-metallicity relation, X-ray heating, and radiatively driven outflows.Comment: Accepted for publication in MNRAS, 9 pages, 5 figures, 1 tabl

BAT AGN Spectroscopic Survey I: Spectral Measurements, Derived Quantities, and AGN Demographics

We present the first catalog and data release of the Swift-BAT AGN Spectroscopic Survey (BASS). We analyze optical spectra of the majority of AGN (77%, 641/836) detected based on their 14-195 keV emission in the 70-month Swift BAT all-sky catalog. This includes redshift determination, absorption and emission line measurements, and black hole mass and accretion rate estimates for the majority of obscured and un-obscured AGN (74%, 473/641) with 340 measured for the first time. With ~90% of sources at z<0.2, the survey represents a significant census of hard-X-ray selected AGN in the local universe. In this first catalog paper, we describe the spectroscopic observations and datasets, and our initial spectral analysis. The FWHM of the emission lines show broad agreement with the X-ray obscuration (~94%), such that Sy 1-1.8 have NH10^21.9 cm^-2. Seyfert 1.9 show a range of column densities. Compared to narrow line AGN in the SDSS, the X-ray selected AGN have a larger fraction of dusty host galaxies suggesting these types of AGN are missed in optical surveys. Using the most sensitive [OIII]/Hbeta and [NII]/Halpha emission line diagnostic, about half of the sources are classified as Seyferts, ~15% reside in dusty galaxies that lack an Hbeta detection, but for which the line upper limits imply either a Seyfert or LINER, ~15% are in galaxies with weak or no emission lines despite high quality spectra, and a few percent each are LINERS, composite galaxies, HII regions, or in known beamed AGN.Comment: Accepted ApJ, see www.bass-survey.com for dat

BAT AGN spectroscopic survey–II. X-ray emission and high-ionization optical emission lines

We investigate the relationship between X-ray and optical line emission in 340 nearby (z ≃ 0.04) AGN selected above 10 keV using Swift BAT. We find a weak correlation between the extinction corrected [O iii] and hard X-ray luminosity (L^(int)_([OIII])∝L_(14-195) with a large scatter (R_(Pear) = 0.64, σ = 0.62 dex) and a similarly large scatter with the intrinsic 2–10 keV to [O iii] luminosities (R_(Pear) = 0.63, σ = 0.63 dex). Correlations of the hard X-ray fluxes with the fluxes of high-ionization narrow lines ([O iii], He ii, [Ne iii] and [Ne v]) are not significantly better than with the low-ionization lines (H α, [S ii]). Factors like obscuration or physical slit size are not found to be a significant part of the large scatter. In contrast, the optical emission lines show much better correlations with each other (σ = 0.3 dex) than with the X-ray flux. The inherent large scatter questions the common usage of narrow emission lines as AGN bolometric luminosity indicators and suggests that other issues such as geometrical differences in the scattering of the ionized gas or long-term AGN variability are important

The immune gene repertoire encoded in the purple sea urchin genome

Echinoderms occupy a critical and largely unexplored phylogenetic vantage point from which to infer both the early evolution of bilaterian immunity and the underpinnings of the vertebrate adaptive immune system. Here we present an initial survey of the purple sea urchin genome for genes associated with immunity. An elaborate repertoire of potential immune receptors, regulators and effectors is present, including unprecedented expansions of innate pathogen recognition genes. These include a diverse array of 222 Toll-like receptor (TLR) genes and a coordinate expansion of directly associated signaling adaptors. Notably, a subset of sea urchin TLR genes encodes receptors with structural characteristics previously identified only in protostomes. A similarly expanded set of 203 NOD/NALP-like cytoplasmic recognition proteins is present. These genes have previously been identified only in vertebrates where they are represented in much lower numbers. Genes that mediate the alternative and lectin complement pathways are described, while gene homologues of the terminal pathway are not present. We have also identified several homologues of genes that function in jawed vertebrate adaptive immunity. The most striking of these is a gene cluster with similarity to the jawed vertebrate Recombination Activating Genes 1 and 2 (RAG1/2). Sea urchins are long-lived, complex organisms and these findings reveal an innate immune system of unprecedented complexity. Whether the presumably intense selective processes that molded these gene families also gave rise to novel immune mechanisms akin to adaptive systems remains to be seen. The genome sequence provides immediate opportunities to apply the advantages of the sea urchin model toward problems in developmental and evolutionary immunobiology

Exploring evolution of maximum growth rates in plankton

Evolution has direct and indirect consequences on species–species interactions and the environment. However, Earth systems models describing planktonic activity invariably fail to explicitly consider organism evolution. Here we simulate the evolution of the single most important physiological characteristic of any organism as described in models—its maximum growth rate (μm). Using a low-computational-cost approach, we incorporate the evolution of μm for each of the plankton components in a simple Nutrient-Phytoplankton-Zooplankton -style model such that the fitness advantages and disadvantages in possessing a high μm evolve to become balanced. The model allows an exploration of parameter ranges leading to stresses, which drive the evolution of μm. In applications of the method we show that simulations of climate change give very different projections when the evolution of μm is considered. Thus, production may decline as evolution reshapes growth and trophic dynamics. Additionally, predictions of extinction of species may be overstated in simulations lacking evolution as the ability to evolve under changing environmental conditions supports evolutionary rescue. The model explains why organisms evolved for mature ecosystems (e.g. temperate summer, reliant on local nutrient recycling or mixotrophy), express lower maximum growth rates than do organisms evolved for immature ecosystems (e.g. temperate spring, high resource availability)

The Genome of the Sea Urchin Strongylocentrotus purpuratus

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Generation of insulin-secreting organoids: a step toward engineering and transplanting the bioartificial pancreas

Diabetes is a major health issue of increasing prevalence. ß-cell replacement, by pancreas or islet transplantation, is the only long-term curative option for patients with insulin-dependent diabetes. Despite good functional results, pancreas transplantation remains a major surgery with potentially severe complications. Islet transplantation is a minimally invasive alternative that can widen the indications in view of its lower morbidity. However, the islet isolation procedure disrupts their vasculature and connection to the surrounding extracellular matrix, exposing them to ischemia and anoikis. Implanted islets are also the target of innate and adaptive immune attacks, thus preventing robust engraftment and prolonged full function. Generation of organoids, defined as functional 3D structures assembled with cell types from different sources, is a strategy increasingly used in regenerative medicine for tissue replacement or repair, in a variety of inflammatory or degenerative disorders. Applied to ß-cell replacement, it offers the possibility to control the size and composition of islet-like structures (pseudo-islets), and to include cells with anti-inflammatory or immunomodulatory properties. In this review, we will present approaches to generate islet cell organoids and discuss how these strategies can be applied to the generation of a bioartificial pancreas for the treatment of type 1 diabetes