ASCA observations of type-2 Seyfert galaxies: II. The Importance of X-ray Scattering and Reflection

We discuss the importance of X-ray scattering and Compton reflection in type-2 Seyfert galaxies, based upon the analysis of ASCA observations of 25 such sources. Consideration of the iron Kalpha, [O III] line and X-ray variability suggest that NGC 1068, NGC 4945, NGC 2992, Mrk 3, Mrk 463E and Mrk 273 are dominated by reprocessed X-rays. We examine the properties of these sources in more detail. We find that the iron Kalpha complex contains significant contributions from neutral and high-ionization species of iron. Compton reflection, hot gas and starburst emission all appear to make significant contributions to the observed X-ray spectra. Mrk 3 is the only source in this subsample which does not have a significant starburst contamination. The ASCA spectrum below 3 keV is dominated by hot scattering gas with U_X ~ 5, N_H ~ 4 x 10^23 cm^-2. This material is more highly ionized than the zone of material comprising the warm absorber seen in Seyfert~1 galaxies, but may contain a contribution from shock-heated gas associated with the jet. Estimates of the X-ray scattering fraction cover 0.25 - 5%. The spectrum above 3 keV appears to be dominated by a Compton reflection component although there is evidence that the primary continuum component becomes visible close to 10 keV.Comment: 27 pages, 6 figures. LaTeX with encapsulated postscript. To appear in the Astrophysical Journal. Also available via http://lheawww.gsfc.nasa.gov/~george/papers/gnt_s2p2/abstract.htm

The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi

Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population-level RAD-seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome-level specialization for life at depth as an important process in cichlid radiation

Elemental Abundances in NGC 3516

We present RGS data from an XMM-Newton observation of the Seyfert 1 galaxy NGC 3516, taken while the continuum source was in an extreme low state. The spectrum shows numerous emission lines including the H-like lines of C, N and O and the He-like lines of N, O and Ne. These data show that the N lines are far stronger than would be expected from gas of solar abundances. Based on our photoionization models, we find that N is overabundant compared to C, O and Ne by at least a factor of 2.5. We suggest this is the result of secondary production of N in intermediate mass stars, and indicative of the history of star formation in NGC 3516.Comment: 19 pages, 3 color figures. ApJ in pres

Statistical Algorithms for Ontology-based Annotation of Scientific Literature

Background: Ontologies encode relationships within a domain in robust data structures that can be used to annotate data objects, including scientific papers, in ways that ease tasks such as search and meta-analysis. However, the annotation process requires significant time and effort when performed by humans. Text mining algorithms can facilitate this process, but they render an analysis mainly based upon keyword, synonym and semantic matching. They do not leverage information embedded in an ontology’s structure. Methods: We present a probabilistic framework that facilitates the automatic annotation of literature by indirectly modeling the restrictions among the different classes in the ontology. Our research focuses on annotating human functional neuroimaging literature within the Cognitive Paradigm Ontology (CogPO). We use an approach that combines the stochastic simplicity of naïve Bayes with the formal transparency of decision trees. Our data structure is easily modifiable to reflect changing domain knowledge. Results: We compare our results across naïve Bayes, Bayesian Decision Trees, and Constrained Decision Tree classifiers that keep a human expert in the loop, in terms of the quality measure of the F1-mirco score. Conclusions: Unlike traditional text mining algorithms, our framework can model the knowledge encoded by the dependencies in an ontology, albeit indirectly. We successfully exploit the fact that CogPO has explicitly stated restrictions, and implicit dependencies in the form of patterns in the expert curated annotations

The X-ray Emission from the Nucleus of the Dwarf Elliptical Galaxy NGC 3226

We present the first high resolution X-ray image of the dwarf elliptical galaxy NGC 3226. The data were obtained during an observation of the nearby Seyfert Galaxy NGC 3227 using the Chandra X-ray Observatory. We detect a point X-ray source spatially consistent with the optical nucleus of NGC 3226 and a recently-detected, compact, flat-spectrum, radio source. The X-ray spectrum can be measured up to ~10 keV and is consistent with a power law with a photon index 1.7 <~ Gamma <~ 2.2, or thermal bremmstrahlung emission with 4 <~ kT <~ 10 keV. In both cases the luminosity in the 2--10 keV band ~10^{40} h_{75}^{-1} erg/s. We find marginal evidence that the nucleus varies within the observation. These characteristics support evidence from other wavebands that NGC 3226 harbors a low-luminosity, active nucleus. We also comment on two previously-unknown, fainter X-ray sources <~ 15 arcsec from the nucleus of NGC 3226. Their proximity to the nucleus (with projected distances <~ 1.3/h_{75} kpc) suggests both are within NGC 3226, and thus have luminosities (~few x 10^{38} -- few x 10^{39} erg/s) consistent with black-hole binary systems.Comment: Accepted for publication in ApJ. Figures in colo