Probing the physics of narrow-line regions of Seyfert galaxies I: The case of NGC 5427

We have used the Wide Field Spectrograph (WiFeS) on the ANU 2.3m telescope at Siding Spring to observe the nearby, nearly face-on, Seyfert 2 galaxy, NGC 5427. We have obtained integral field spectroscopy of both the nuclear regions and the HII regions in the spiral arms. We have constrained the chemical abundance in the interstellar medium of the extended narrow line region (ENLR) by measuring the abundance gradient in the circum-nuclear \ion{H}{ii} regions to determine the nuclear chemical abundances, and to use these to in turn determine the EUV spectral energy distribution for comparison with theoretical models. We find a very high nuclear abundance, $\sim 3.0$ times solar, with clear evidence of a nuclear enhancement of N and He, possibly caused by massive star formation in the extended ($\sim 100$pc) central disk structure. The circum-nuclear narrow-line region spectrum is fit by a radiation pressure dominated photoionisation model model with an input EUV spectrum from a Black Hole with mass $5\times10^7 M_{\odot}$ radiating at $\sim 0.1$ of its Eddington luminosity. The bolometric luminosity is closely constrained to be $\log L_{\mathrm bol.} = 44.3\pm 0.1$ erg s$^{-1}$. The EUV spectrum characterised by a soft accretion disk and a harder component extending to above 15keV. The ENLR region is extended in the NW-SE direction. The line ratio variation in circum-nuclear spaxels can be understood as the result of mixing \ion{H}{ii} regions with an ENLR having a radius-invariant spectrum.Comment: Accepted for publication in Astronomy and Astrophysics, 14 pages, 13 figure

Probing the Physics of Narrow Line Regions in Active Galaxies II: The Siding Spring Southern Seyfert Spectroscopic Snapshot Survey (S7)

Here we describe the \emph{Siding Spring Southern Seyfert Spectroscopic Snapshot Survey} (S7) and present results on 64 galaxies drawn from the first data release. The S7 uses the Wide Field Spectrograph (WiFeS) mounted on the ANU 2.3m telescope located at the Siding Spring Observatory to deliver an integral field of $38\times25$~ arcsec at a spectral resolution of $R=7000$ in the red ($530-710$nm), and $R=3000$ in the blue ($340-560$nm). {From these data cubes we have extracted the Narrow Line Region (NLR) spectra from a 4 arc sec aperture centred on the nucleus. We also determine the H$\beta$ and [OIII]~$\lambda$5007 fluxes in the narrow lines, the nuclear reddening, the reddening-corrected relative intensities of the observed emission lines, and the H$\beta$ and \lOIII\ luminosities {determined from spectra for which the stellar continuum has been removed.} We present a set of images of the galaxies in [OIII]~$\lambda$5007, [NII]~$\lambda$6584 and H$\alpha$ which serve to delineate the spatial extent of the extended narrow line region (ENLR) and {\bf also to} reveal the structure and morphology of the surrounding \HII\ regions. Finally, we provide a preliminary discussion of those Seyfert~1 and Seyfert~2 galaxies which display coronal emission lines in order to explore the origin of these lines.Comment: Accepted for publication 9 Jan 2015, Astrophysical Journal Supplements. 49pages, 8 figure

S7 : Probing the physics of Seyfert Galaxies through their ENLR & HII Regions

Here we present the first results from the Siding Spring Southern Seyfert Spectroscopic Snapshot Survey (S7) which aims to investigate the physics of ~140 radio-detected southern active Galaxies with z<0.02 through Integral Field Spectroscopy using the Wide Field Spectrograph (WiFeS). This instrument provides data cubes of the central 38 x 25 arc sec. of the target galaxies in the waveband 340-710nm with the unusually high resolution of R=7000 in the red (530-710nm), and R=3000 in the blue (340-560nm). These data provide the morphology, kinematics and the excitation structure of the extended narrow-line region, probe relationships with the black hole characteristics and the host galaxy, measures host galaxy abundance gradients and the determination of nuclear abundances from the HII regions. From photoionisation modelling, we may determine the shape of the ionising spectrum of the AGN, discover whether AGN metallicities differ from nuclear abundances determined from HII regions, and probe grain destruction in the vicinity of the AGN. Here we present some preliminary results and modelling of both Seyfert galaxies observed as part of the survey.Comment: 6 pages, 2 figures, Invited Talk at the IAU symposium 30

Probing the Physics of Narrow Line Regions in Active Galaxies III: Accretion and Cocoon Shocks in the LINER NGC1052

We present Wide Field Spectrograph (WiFeS) integral field spectroscopy and HST FOS spectroscopy for the LINER galaxy NGC 1052. We infer the presence of a turbulent accretion flow forming a small-scale accretion disk. We find a large-scale outflow and ionisation cone along the minor axis of the galaxy. Part of this outflow region is photoionised by the AGN, and shares properties with the ENLR of Seyfert galaxies, but the inner ($R \lesssim 1.0$~arcsec) accretion disk and the region around the radio jet appear shock excited. The emission line properties can be modelled by a "double shock" model in which the accretion flow first passes through an accretion shock in the presence of a hard X-ray radiation, and the accretion disk is then processed through a cocoon shock driven by the overpressure of the radio jets. This model explains the observation of two distinct densities ($\sim10^4$ and $\sim10^6$ cm$^{-3}$), and provides a good fit to the observed emission line spectrum. We derive estimates for the velocities of the two shock components and their mixing fractions, the black hole mass, the accretion rate needed to sustain the LINER emission and derive an estimate for the jet power. Our emission line model is remarkably robust against variation of input parameters, and so offers a generic explanation for the excitation of LINER galaxies, including those of spiral type such as NGC 3031 (M81).Comment: Accepted for publication in Astrophysical Journal. 16 pages, 12 figure

Prognostic modeling studies of the Keweenaw Current in Lake Superior. Part II: Simulation,

ABSTRACT The formation and evolution of the Keweenaw Current in Lake Superior were examined using a nonorthogonalcoordinate primitive equation numerical model. The model was initialized by the monthly averaged temperature field observed in June and September 1973 and run prognostically under different forcing conditions with and without winds. As a Rossby adjustment problem, the model predicted the formation of a well-defined coastal current jet within an inertial period of 16.4 h after the current field adjusted to the initial temperature field. The magnitude and direction of this current jet varied with the cross-shelf temperature gradient and wind velocity. It tended to intensify during northeastward (downwelling favorable) winds, and to lessen, or even reverse, during southwestward to northwestward (upwelling favorable) or southeastward (downwelling favorable) winds. In a case with strong stratification and without external atmospheric forcings, a well-defined clockwise warm-core eddy formed near the northeastern coast of the Keweenaw Peninsula as a result of baroclinic instability. A warmcore eddy was detected recently from satellite surface temperature images, the shape and location of which were very similar to those of the model-predicted eddy. The energy budget analysis suggested that the eddy kinetic energy grew exponentially over a timescale of 7 days. Growth was due to a rapid energy transfer from available eddy potential energy. The subsequent decline of the eddy kinetic energy was the result of turbulent diffusion, transfer from the eddy kinetic energy to mean kinetic energy, and outward net energy flux

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone

Fifteen years of the Australian imaging, biomarkers and lifestyle (AIBL) study: Progress and observations from 2,359 older adults spanning the spectrum from cognitive normality to Alzheimer\u27s disease

Background: The Australian Imaging, Biomarkers and Lifestyle (AIBL) Study commenced in 2006 as a prospective study of 1,112 individuals (768 cognitively normal (CN), 133 with mild cognitive impairment (MCI), and 211 with Alzheimer\u27s disease dementia (AD)) as an \u27Inception cohort\u27 who underwent detailed ssessments every 18 months. Over the past decade, an additional 1247 subjects have been added as an \u27Enrichment cohort\u27 (as of 10 April 2019). Objective: Here we provide an overview of these Inception and Enrichment cohorts of more than 8,500 person-years of investigation. Methods: Participants underwent reassessment every 18 months including comprehensive cognitive testing, neuroimaging (magnetic resonance imaging, MRI; positron emission tomography, PET), biofluid biomarkers and lifestyle evaluations. Results: AIBL has made major contributions to the understanding of the natural history of AD, with cognitive and biological definitions of its three major stages: preclinical, prodromal and clinical. Early deployment of Aβ-amyloid and tau molecular PET imaging and the development of more sensitive and specific blood tests have facilitated the assessment of genetic and environmental factors which affect age at onset and rates of progression. Conclusion: This fifteen-year study provides a large database of highly characterized individuals with longitudinal cognitive, imaging and lifestyle data and biofluid collections, to aid in the development of interventions to delay onset, prevent or treat AD. Harmonization with similar large longitudinal cohort studies is underway to further these aims

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe