Flame: A Flexible Data Reduction Pipeline for Near-Infrared and Optical Spectroscopy

We present flame, a pipeline for reducing spectroscopic observations obtained with multi-slit near-infrared and optical instruments. Because of its flexible design, flame can be easily applied to data obtained with a wide variety of spectrographs. The flexibility is due to a modular architecture, which allows changes and customizations to the pipeline, and relegates the instrument-specific parts to a single module. At the core of the data reduction is the transformation from observed pixel coordinates (x, y) to rectified coordinates (lambda, gamma). This transformation consists in the polynomial functions lambda(x,y) and gamma(x,y) that are derived from arc or sky emission lines and slit edge tracing, respectively. The use of 2D transformations allows one to wavelength calibrate and rectify the data using just one interpolation step. Furthermore, the gamma(x,y) transformation includes also the spatial misalignment between frames, which can be measured from a reference star observed simultaneously with the science targets. The misalignment can then be fully corrected during the rectification, without having to further resample the data. Sky subtraction can be performed via nodding and/or modeling of the sky spectrum; the combination of the two methods typically yields the best results. We illustrate the pipeline by showing examples of data reduction for a near-infrared instrument (LUCI at the Large Binocular Telescope) and an optical one (LRIS at the Keck telescope).Comment: 17 pages, 10 figures, published in MNRAS. The pipeline is available at https://github.com/siriobelli/flam

Star Formation in the Circumnuclear Environment of NGC1068

We present near-infrared emission line images of the circumnuclear ring in NGC1068. We have measured the Br_gamma fluxes in a number of star forming complexes and derived extinctions for each of these by comparison with H_alpha. We investigate the star forming histories of these regions and find that a short burst of star formation occured co-evally throughout the ring within the last 30-40 Myr, and perhaps as recently as 4-7 Myr ago. The 1-0 S(1) flux and S(1)/Br_gamma ratios indicate that as well as fluorescence, shock excited H_2 emission contributes to the total flux. There is excess H_2 flux to the North-West where the ionisation cone crosses the ring, and we have shown it is possible that the non-stellar continuum from the Seyfert nucleus which produces the high excitation lines could also be causing fluorescence at the edges of molecular clouds in the ring. The nuclear 1-0 S(1) is more extended than previously realised but only along the bar's major axis, and we consider mechanisms for its excitation.Comment: 10 pages, 4 figures, LaTeX (mn.sty & psfig.sty). Accepted for publication in MNRA

A Multiwavelength Study of the Starburst Galaxy NGC 7771

We present a multiwavelength study of the interacting starburst galaxy NGC 7771, including new optical and ultra-violet spectra and a previously unpublished soft X-ray ROSAT image and spectrum. The far-infrared, radio, and X-ray fluxes suggest that a massive burst of star-formation is currently in progress but the small equivalent width of the Balmer emission lines (equivalent width H(alpha approximately equals 100 A), the weak UV flux, the low abundance of ionised oxygen, and the shape of the optical spectrum lead us to conclude that there are few 0 stars. This might normally suggest that star-formation has ceased but the galaxy's barred gravitational potential and large gas reserves imply that this should not be so, and we therefore consider other explanations. We argue that the observations cannot be due to effects of geometry, density bounded nebulae, or dust within the nebulae, and conclude that a truncated IMF is required. The dwarf galaxy NGC 7770 appears to be in the initial stages of a merger with NGC 7771, and the resulting tidal perturbations may have induced the apparent two-armed spiral pattern, and driven a substantial fraction of the disk gas inwards. The presence of a bulge in NGC 7771 may be moderating the starburst so that, while still occuring on a large scale with a supernova rate of 0.8-1/yr, it is less violent and the IMF has a relatively low upper mass limit. We find that there is a cluster of stars obscuring part of the starburst region, and we offer an explanation of its origin

A diversity of dusty AGN tori: Data release for the VLTI/MIDI AGN Large Program and first results for 23 galaxies

The AGN-heated dust distribution (the "torus") is increasingly recognized not only as the absorber required in unifying models, but as a tracer for the reservoir that feeds the nuclear Super-Massive Black Hole. Yet, even its most basic structural properties (such as its extent, geometry and elongation) are unknown for all but a few archetypal objects. Since most AGNs are unresolved in the mid-infrared, we utilize the MID-infrared interferometric Instrument (MIDI) at the Very Large Telescope Interferometer (VLTI) that is sensitive to structures as small as a few milli-arcseconds (mas). We present here an extensive amount of new interferometric observations from the MIDI AGN Large Program (2009 - 2011) and add data from the archive to give a complete view of the existing MIDI observations of AGNs. Additionally, we have obtained high-quality mid-infrared spectra from VLT/VISIR. We present correlated and total flux spectra for 23 AGNs and derive flux and size estimates at 12 micron using simple axisymmetric geometrical models. Perhaps the most surprising result is the relatively high level of unresolved flux and its large scatter: The median "point source fraction" is 70 % for type 1 and 47 % for type 2 AGNs meaning that a large part of the flux is concentrated on scales smaller than about 5 mas (0.1 - 10 pc). Among sources observed with similar spatial resolution, it varies from 20 % - 100 %. For 18 of the sources, two nuclear components can be distinguished in the radial fits. While these models provide good fits to all but the brightest sources, significant elongations are detected in eight sources. The half-light radii of the fainter sources are smaller than expected from the size ~ L^0.5 scaling of the bright sources and show a large scatter, especially when compared to the relatively tight size--luminosity relation in the near-infrared.Comment: A&A in press; 93 pages, 63 figures, 39 tables; data available only via CD

Jellyfish on the menu: mtDNA assay reveals scyphozoan predation in the Irish Sea

Localized outbreaks of jellyfish, known as blooms, cause a variety of adverse ecological and economic effects. However, fundamental aspects of their ecology remain unknown. Notably, there is scant information on the role jellyfish occupy in food webs: in many ecosystems, few or no predators are known. To identify jellyfish consumers in the Irish Sea, we conducted a molecular gut content assessment of 50 potential predators using cnidarian-specific mtDNA primers and sequencing. We show that jellyfish predation may be more common than previously acknowledged: uncovering many previously unknown jellyfish predators. A substantial proportion of herring and whiting were found to have consumed jellyfish. Rare ingestion was also detected in a variety of other species. Given the phenology of jellyfish in the region, we suggest that the predation was probably targeting juvenile stages of the jellyfish life cycle

How quantitative is metabarcoding: a meta-analytical approach

Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis, and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ±0.34, p<0.01), albeit it with a large degree of uncertainty. None of the tested moderators: sequencing platform type, the number of species used in a trial, or the source of DNA were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilised for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study

HST/WFC3 Observations of an Off-Nuclear Superbubble in Arp 220

We present a high spatial resolution optical and infrared study of the circumnuclear region in Arp 220, a late-stage galaxy merger. Narrowband imaging using HST/WFC3 has resolved the previously observed peak in H$\alpha$+[NII] emission into a bubble-shaped feature. This feature measures 1.6" in diameter, or 600 pc, and is only 1" northwest of the western nucleus. The bubble is aligned with the western nucleus and the large-scale outflow axis seen in X-rays. We explore several possibilities for the bubble origin, including a jet or outflow from a hidden active galactic nucleus (AGN), outflows from high levels of star formation within the few hundred pc nuclear gas disk, or an ultraluminous X-ray source. An obscured AGN or high levels of star formation within the inner $\sim$100 pc of the nuclei are favored based on the alignment of the bubble and energetics arguments.Comment: Accepted for publication in ApJ. 12 pages, 10 figure

Mass of the Southern Black Hole in NGC 6240 from Laser Guide Star Adaptive Optics

NGC 6240 is a pair of colliding disk galaxies, each with a black hole in its core. We have used laser guide star adaptive optics on the Keck II telescope to obtain high-resolution ($\sim 0.06$") near-infrared integral-field spectra of the region surrounding the supermassive black hole in the south nucleus of this galaxy merger. We use the K-band CO absorption bandheads to trace stellar kinematics. We obtain a spatial resolution of about 20 pc and thus directly resolve the sphere of gravitational influence of the massive black hole. We explore two different methods to measure the black hole mass. Using a Jeans Axisymmetric Multi-Gaussian mass model, we investigate the limit that a relaxed mass distribution produces all of the measured velocity dispersion, and find an upper limit on the black hole mass at 2.0 \pm 0.2 \times 10^9 M_{\sun}. When assuming the young stars whose spectra we observe remain in a thin disk, we compare Keplerian velocity fields to the measured two-dimensional velocity field measured and fit for a mass profile containing a black hole point mass plus a radially-varying spherical component, which suggests a lower limit for the black hole mass of 8.7 \pm 0.3 \times 10^8 M_{\sun}. Our measurements of the stellar velocity dispersion place this AGN within the scatter of the $M_{BH}$-$\sigma_{*}$ relation. As NGC 6240 is a merging system, this may indicate that the relation is preserved during a merger at least until the final coalescence of the two nuclei.Comment: 10 pages, 12 figures; accepted to Ap

Mergers and Mass Accretion Rates in Galaxy Assembly: The Millennium Simulation Compared to Observations of z~2 Galaxies

Recent observations of UV-/optically selected, massive star forming galaxies at z~2 indicate that the baryonic mass assembly and star formation history is dominated by continuous rapid accretion of gas and internal secular evolution, rather than by major mergers. We use the Millennium Simulation to build new halo merger trees, and extract halo merger fractions and mass accretion rates. We find that even for halos not undergoing major mergers the mass accretion rates are plausibly sufficient to account for the high star formation rates observed in z~2 disks. On the other hand, the fraction of major mergers in the Millennium Simulation is sufficient to account for the number counts of submillimeter galaxies (SMGs), in support of observational evidence that these are major mergers. When following the fate of these two populations in the Millennium Simulation to z=0, we find that subsequent mergers are not frequent enough to convert all z~2 turbulent disks into elliptical galaxies at z=0. Similarly, mergers cannot transform the compact SMGs/red sequence galaxies at z~2 into observed massive cluster ellipticals at z=0. We argue therefore, that secular and internal evolution must play an important role in the evolution of a significant fraction of z~2 UV-/optically and submillimeter selected galaxy populations.Comment: 5 pages, 4 figures, Accepted for publication in Ap