REAPR: a universal tool for genome assembly evaluation.

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/

The movement of Indian Monsoon Depressions by interaction with image vortices near the Himalayan Wall

It is argued that a simple explanation for the westward propagation of Indian monsoon depressions (IMDs) is the interaction of the depression vortex with the Himalayan ‘wall’. This interaction can be modelled by simulating an IMD as a point vortex in a horizontal plane (at 850 hPa) and invoking image vortices behind the barrier. Solenoidal flows associated with the image vortices allow the boundary conditions at the Himalayas to be met, and cause the IMD vortex to propagate parallel to the barrier, toward the west. This simple model is tested against propagation speeds for observed IMDs. The histogram of observed propagation speed, normalised by the point-vortex model prediction, has a mean of 1.08 and standard deviation of 0.68. The model also explains the observed intensification of flow on the Himalayan side of the IMD which is a key process in enhancing rainfall to the Indo-Gangetic Plain in the monsoon season

A controlled evaluation of an enhanced self-directed behavioural family intervention for parents of children with conduct problems in rural and remote areas.

Few studies have examined the impact of parenting interventions for families in rural and isolated areas who have children with conduct problems, where-access to professional services can be difficult. The present investigation compared the effects of three conditions, two levels of self-directed behavioral family intervention: an enhanced self-directed program that combined a self-help program using written materials and a weekly telephone consultation (ESD), a self-help program (SD) and a waitlist control group (WL). At postintervention the ESD group reported significantly lower levels of disruptive behaviour, and lower levels of dysfunctional parenting than the SD and WL controls, and higher levels of consumer satisfaction. At 6 months follow-up the main effects for the ESD group had been maintained. The SD group continued to evidence improvement from postintervention to follow-up such that 65% of children in the ESD condition and 57% of children in the SD condition showed clinical reliable change on measures of disruptive behaviour. Implications of findings and directions for future research are discussed

Imaging Carbon Monoxide Emission in the Starburst Galaxy NGC 6000

We present measurements of carbon monoxide emission in the central region of the nearby starburst NGC 6000 taken with the Submillimeter Array. The J=2-1 transition of 12CO, 13CO, and C18O were imaged at a resolution of ~3''x2'' (450x300 pc). We accurately determine the dynamical center of NGC 6000 at R.A(J2000.0)=15h49m49.5s and dec(J2000.0)=-29d23'13'' which agrees with the peak of molecular emission position. The observed CO dynamics could be explained in the context of the presence of a bar potential affecting the molecular material, likely responsible for the strong nuclear concentration where more than 85% of the gas is located. We detect a kinematically detached component of dense molecular gas at relatively high velocity which might be fueling the star formation. A total nuclear dynamical mass of 7x10^9 Msun is derived and a total mass of gas of 4.6x10^8 Msun, yielding a Mgas/Mdyn~6%, similar to other previously studied barred galaxies with central starbursts. We determined the mass of molecular gas with the optically thin isotopologue C18O and we estimate a CO-to-H2 conversion factor X(CO)=0.4x10^20 cm-2/(K km s-1) in agreement with that determined in other starburst galaxies.Comment: 31 pages, 7 figures. Accepted for publication in Astronomical Journal

The infrared compactness-temperature relation for quiescent and starburst galaxies

IRAS observations show the existence of a correlation between the infrared luminosity Lir and dust temperature Td in star-forming galaxies, in which larger Lir leads to higher dust temperature. The Lir-Td relation is commonly seen as reflecting the increase in dust temperature in galaxies with higher star formation rate. Even though the correlation shows a significant amount of dispersion, a unique relation has been commonly used to construct spectral energy distributions of galaxies in distant universe studies, such as source number counting or photometric redshift determination. In this work, we introduce a new parameter, namely the size of the star-forming region Rir and lay out the empirical and modelled relation between the global parameters Lir, Td and Rir of IR-bright non-AGN galaxies. IRAS 60-to-100um color is used as a proxy for the dust temperature and the 1.4GHz radio contiuum emission for the infrared spatial distribution. The analysis has been carried out on two samples. The first one is made of the galaxies from the 60um flux-limited IRAS Revised Bright Galaxy Samples which have a reliable RC size estimate from the VLA follow-ups of the IRAS Bright Galaxy Samples. The second is made of the sources from the 170um ISOPHOT Serendipity Sky Survey which are resolved by the NVSS or FIRST surveys. We show that the dispersion in the Lir-Td diagram can be reduced to a relation between the infrared surface brightness and the dust temperature, a relation that spans 5 orders of magnitude in surface brightness. We explored the physical processes giving rise to the Sir-Td relation, and show that it can be derived from the Schmidt law, which relates the star formation rate to the gas surface density.Comment: 13 pages, 7 figures, accepted for publication in A&

Discovery of two infrared supernovae: a new window on the SN search

We report the discovery of two supernovae (SN 1999gw and SN 2001db) obtained within the framework of an infrared monitoring campaign of Luminous Infrared Galaxies, aimed at detecting obscured supernovae. SN 2001db, extinguished by Av~5.5 mag, is the first supernova discovered in the infrared which has received the spectroscopic confirmation. This result highlights the power of infrared monitoring in detecting obscured SNe and indicates that optical surveys are probably missing a significant fraction of SNe, especially in obscured systems such as starburst galaxies. The preliminary estimate of SN rate in LIRG galaxies is about an order of magnitude higher than that expected from optical surveys.Comment: 9 pages, 7 figures, accepted for publication in A&

Black Hole Mass, Host galaxy classification and AGN activity

We investigate the role of host galaxy classification and black hole mass in a heterogeneous sample of 276 mostly nearby (z<0.1) X-ray and IR selected AGN. Around 90% of Seyfert 1 AGN in bulge-dominated host galaxies (without disk contamination) span a very narrow range in the observed 12um to 2-10keV luminosity ratio (1<R_{IR/X}<7). This narrow dispersion incorporates all possible variations among AGN central engines, including accretion mechanism and efficiency, disk opening angle, orientation to sightline, covering fraction of absorbing material, patchiness of X-ray corona and measured variability. As a result, all models of X-ray and IR production in AGN are very strongly constrained. Among Seyfert 1 AGN, median X-ray and IR luminosities increase with black hole mass at >99% confidence. Using ring morphology of the host galaxy as a proxy for lack of tidal interaction, we find that AGN luminosity in host galaxies within 70Mpc is independent of host galaxy interaction for $\sim$ Gyrs, suggesting that the timescale of AGN activity due to secular evolution is much shorter than that due to tidal interactions. We find that LINER hosts have lower 12um luminosity than the median 12um luminosity of normal disk- and bulge-dominated galaxies which may represent observational evidence for past epochs of feedback that supressed star formation in LINER host galaxies. We propose that nuclear ULXs may account for the X-ray emission from LINER 2s without flat-spectrum, compact radio cores. We confirmed the robustness of our results in X-rays by comparing them with the 14-195keV 22-month BAT survey of AGN, which is all-sky and unbiased by photoelectric absorption.Comment: MNRAS accepted. 14 pages, 11 figures, complete Table 1 in online journa

Supermassive Black Hole Mass Regulated by Host Galaxy Morphology

We investigated the relationship between supermassive black hole (SMBH) mass and host starburst luminosity in Seyfert galaxies and Palomar-Green QSOs, focusing on the host galaxy morphology. Host starburst luminosity was derived from the 11.3 micron polycyclic aromatic hydrocarbon luminosity. We found that the SMBH masses of elliptical-dominated host galaxies are more massive than those of disk-dominated host galaxies statistically. We also found that the SMBH masses of disk-dominated host galaxies seem to be suppressed even under increasing starburst luminosity. These findings imply that final SMBH mass is strongly regulated by host galaxy morphology. This can be understood by considering the radiation drag model as the SMBH growth mechanism, taking into account the radiation efficiency of the host galaxy.Comment: 6 pages, 1 figure; accepted for publication in MNRA

The infrared supernova rate in starburst galaxies

We report the results of our ongoing search for extincted supernovae (SNe) at near-infrared wavelengths. We have monitored at 2.2 micron a sample of 46 Luminous Infrared Galaxies and detected 4 SNe. The number of detections is still small but sufficient to provide the first estimate of supernova rate at near-infrared wavelengths. We measure a SN rate ofv 7.6+/-3.8 SNu which is an order of magnitude larger than observed in quiescent galaxies. On the other hand, the observed near-infrared rate is still a factor 3-10 smaller than that estimated from the far-infrared luminosity of the galaxies. Among various possibilities, the most likely scenario is that dust extinction is so high (Av>30) to obscure most SNe even in the near-IR. The role of type Ia SNe is also discussed within this context. We derive the type Ia SN rate as a function of the stellar mass of the galaxy and find a sharp increase toward galaxies with higher activity of star formation. This suggests that a significant fraction of type Ia SNe are associated with young stellar populations. Finally, as a by-product, we give the average K-band light curve of core-collapse SNe based on all the existing data, and review the relation between SN rate and far-infrared luminosity.Comment: A&A, in press, 13 page