Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity

BACKGROUND The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this work a broad phylogenetic study has been undertaken which, considered in the context of the functional characteristics of some fully characterised CDF transporters, has aimed at identifying molecular determinants of substrate selectivity and at suggesting metal specificity for newly identified CDF transporters. RESULTS Representative CDF members from all three kingdoms of life (Archaea, Eubacteria, Eukaryotes) were retrieved from genomic databases. Protein sequence alignment has allowed detection of a modified signature that can be used to identify new hypothetical CDF members. Phylogenetic reconstruction has classified the majority of CDF family members into three groups, each containing characterised members that share the same specificity towards the principally-transported metal, i.e. Zn, Fe/Zn or Mn. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The function of some conserved amino acids was assessed by site-directed mutagenesis in the poplar Zn2+ transporter PtdMTP1 and compared with similar experiments performed in prokaryotic members. An essential structural role can be assigned to a widely conserved glycine residue, while aspartate and histidine residues, highly conserved in putative transmembrane domains, might be involved in metal transport. The potential role of group-conserved amino acid residues in metal specificity is discussed. CONCLUSION In the present study phylogenetic and functional analyses have allowed the identification of three major substrate-specific CDF groups. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The modified signature sequence proposed in this work can be used to identify new hypothetical CDF members

New Results from a Near-Infrared Search for Hidden Broad-Line Regions in Ultraluminous Infrared Galaxies

This paper reports the latest results from a near-infrared search for hidden broad-line regions (BLRs: FWHM >~ 2,000 km/s) in ultraluminous infrared galaxies (ULIGs). The new sample contains thirty-nine ULIGs from the 1-Jy sample selected for their lack of BLRs at optical wavelengths. The results from this new study are combined with those from our previous optical and near-infrared surveys to derive the fraction of all ULIGs with optical or near-infrared signs of genuine AGN activity (either a BLR or [Si VI] emission). Comparisons of the dereddened emission-line luminosities of the optical or obscured BLRs detected in the ULIGs of the 1-Jy sample with those of optical quasars indicate that the obscured AGN/quasar in ULIGs is the main source of energy in at least 15 -- 25% of all ULIGs in the 1-Jy sample. This fraction is 30 -- 50% among ULIGs with L_ir > 10^{12.3} L_sun. These results are compatible with those from recent mid-infrared spectroscopic surveys carried out with ISO. (abridged)Comment: 40 pages including 10 figures and 3 tables (Table 3 should be printed in landscape mode

Major Galaxy Mergers and the Growth of Supermassive Black Holes in Quasars

Despite observed strong correlations between central supermassive black holes (SMBHs) and star-formation in galactic nuclei, uncertainties exist in our understanding of their coupling. We present observations of the ratio of heavily-obscured to unobscured quasars as a function of cosmic epoch up to z~3, and show that a simple physical model describing mergers of massive, gas-rich galaxies matches these observations. In the context of this model, every obscured and unobscured quasar represent two distinct phases that result from a massive galaxy merger event. Much of the mass growth of the SMBH occurs during the heavily-obscured phase. These observations provide additional evidence for a causal link between gas-rich galaxy mergers, accretion onto the nuclear SMBH and coeval star formation.Comment: Accepted for publication in Science. Published by Science Express on March 25th. 17 pages, 5 figures, including supplemental online materia

Stating Appointment Costs in SMS Reminders Reduces Missed Hospital Appointments: Findings from Two Randomised Controlled Trials

BACKGROUND: Missed hospital appointments are a major cause of inefficiency worldwide. Healthcare providers are increasingly using Short Message Service reminders to reduce 'Did Not Attend' (DNA) rates. Systematic reviews show that sending such reminders is effective, but there is no evidence on whether their impact is affected by their content. Accordingly, we undertook two randomised controlled trials that tested the impact of rephrasing appointment reminders on DNA rates in the United Kingdom. TRIAL METHODS: Participants were outpatients with a valid mobile telephone number and an outpatient appointment between November 2013 and January 2014 (Trial One, 10,111 participants) or March and May 2014 (Trial Two, 9,848 participants). Appointments were randomly allocated to one of four reminder messages, which were issued five days in advance. Message assignment was then compared against appointment outcomes (appointment attendance, DNA, cancellation by patient). RESULTS: In Trial One, a message including the cost of a missed appointment to the health system produced a DNA rate of 8.4%, compared to 11.1% for the existing message (OR 0.74, 95% CI 0.61-0.89, P<0.01). Trial Two replicated this effect (DNA rate 8.2%), but also found that expressing the same concept in general terms was significantly less effective (DNA rate 9.9%, OR 1.22, 95% CI 1.00-1.48, P<0.05). Moving from the existing reminder to the more effective costs message would result in 5,800 fewer missed appointments per year in the National Health Service Trust in question, at no additional cost. The study's main limitations are that it took place in a single location in England, and that it required accurate phone records, which were only obtained for 20% of eligible patients. We conclude that missed appointments can be reduced, for no additional cost, by introducing persuasive messages to appointment reminders. Future studies could examine the impact of varying reminder messages in other health systems. TRIAL REGISTRATION: Controlled-Trials.com 49432571

Optical Spectroscopy of the IRAS 1-Jy Sample of Ultraluminous Infrared Galaxies

This paper discusses the optical spectroscopic properties of the IRAS 1-Jy sample of ultraluminous infrared galaxies (ULIGs). One hundred and eight of the 118 1-Jy ULIGs have been observed at dlambda = 8.3 AA resolution over the wavelength range ~4500 A -- 8900 A. These data are combined with large, previously published sets of optical spectroscopic data of lower luminosity infrared galaxies to look for systematic trends with infrared luminosity over the luminosity range L_ir ~ 10^{10.5}-10^{13} L_sun. As found in previous studies, the fraction of Seyfert galaxies among luminous infrared galaxies increases abruptly above L_ir ~ 10^{12.3} L_sun --- about 50% of the galaxies with L_ir > 10^{12.3} L_sun present Seyfert characteristics. Many of the optical and infrared spectroscopic properties of the Seyfert galaxies are consistent with the presence of a genuine active galactic nucleus (AGN). About 30% of these galaxies are Seyfert 1s with broad-line regions similar to those of optical quasars. The percentage of Seyfert 1 ULIGs increases with infrared luminosity, contrary to the predictions of the standard unification model for Seyfert galaxies. Comparisons of the broad-line luminosities of optical and obscured Seyfert 1 ULIGs with those of optically selected quasars of comparable bolometric luminosity suggest that the dominant energy source in most of these ULIGs is the same as in optical quasars, namely mass accretion onto a supermassive black hole, rather than a starburst. These results are consistent with recently published ISO, ASCA, and VLBI data. (abridged)Comment: Text and 23 figures (45 pages), Tables 1 - 6 (16 pages

An IRAS High Resolution Image Restoration (HIRES) Atlas of All Interacting Galaxies in the IRAS Revised Bright Galaxy Sample

We present high-resolution (30"-1') 12, 25, 60, and 100 micron images of 106 interacting galaxy systems contained in the IRAS Revised Bright Galaxy Sample (RBGS, Sanders et al. 2003), a complete sample of all galaxies having a 60 micron flux density greater than 5.24 Jy. These systems were selected to have at least two distinguishable galaxies separated by less than three average galactic diameters, and thus we have excluded very widely separated systems and very advanced mergers. The new complete survey has the same properties as the prototype survey of Surace et al. 1993. We find no increased tendency for infrared-bright galaxies to be associated with other infrared bright galaxies among the widely separated pairs studied here. We find small enhancements in far-infrared activity in multiple galaxy systems relative to RBGS non-interacting galaxies with the same blue luminosity distribution. We also find no differences in infrared activity (as measured by infrared color and luminosity) between late and early-type spiral galaxies.Comment: 49 pages, 13 figures. To appear in the Astronomical Journal. Figures have been degraded due to space considerations. A PDF version with higher quality figures is available at http://humu.ipac.caltech.edu/~jason/pubs/surace_hires.pd

Multi-Terabyte EIDE Disk Arrays running Linux RAID5

High-energy physics experiments are currently recording large amounts of data and in a few years will be recording prodigious quantities of data. New methods must be developed to handle this data and make analysis at universities possible. Grid Computing is one method; however, the data must be cached at the various Grid nodes. We examine some storage techniques that exploit recent developments in commodity hardware. Disk arrays using RAID level 5 (RAID-5) include both parity and striping. The striping improves access speed. The parity protects data in the event of a single disk failure, but not in the case of multiple disk failures. We report on tests of dual-processor Linux Software RAID-5 arrays and Hardware RAID-5 arrays using a 12-disk 3ware controller, in conjunction with 250 and 300 GB disks, for use in offline high-energy physics data analysis. The price of IDE disks is now less than $1/GB. These RAID-5 disk arrays can be scaled to sizes affordable to small institutions and used when fast random access at low cost is important.Comment: Talk from the 2004 Computing in High Energy and Nuclear Physics (CHEP04), Interlaken, Switzerland, 27th September - 1st October 2004, 4 pages, LaTeX, uses CHEP2004.cls. ID 47, Poster Session 2, Track

Galactic metric, dark radiation, dark pressure and gravitational lensing in brane world models

In the braneworld scenario, the four dimensional effective Einstein equation has extra terms which arise from the embedding of the 3-brane in the bulk. These non-local effects, generated by the free gravitational field of the bulk, may provide an explanation for the dynamics of the neutral hydrogen clouds at large distances from the galactic center, which is usually explained by postulating the existence of the dark matter. We obtain the exact galactic metric, the dark radiation and the dark pressure in the flat rotation curves region in the brane world scenario. Due to the presence of the bulk effects, the flat rotation curves could extend several hundred kpc. The limiting radius for which bulk effects are important is estimated and compared with the numerical values of the truncation parameter of the dark matter halos, obtained from weak lensing observations. There is a relatively good agreement between the predictions of the model and observations. The deflection of photons is also considered and the bending angle of light is computed. The bending angle predicted by the brane world models is much larger than that predicted by standard general relativistic and dark matter models. The angular radii of the Einstein rings are obtained in the small angles approximation. The predictions of the brane world model for the tangential shear are compared with the observational data obtained in the weak lensing of galaxies in the Red-Sequence Cluster Survey. Therefore the study of the light deflection by galaxies and the gravitational lensing could discriminate between the different dynamical laws proposed to model the motion of particles at the galactic level and the standard dark matter models.Comment: 33 pages, 3 figures, accepted for publication in Ap

Representations of the Weyl group and Wigner functions for SU(3)

Bases for SU(3) irreps are constructed on a space of three-particle tensor products of two-dimensional harmonic oscillator wave functions. The Weyl group is represented as the symmetric group of permutations of the particle coordinates of these space. Wigner functions for SU(3) are expressed as products of SU(2) Wigner functions and matrix elements of Weyl transformations. The constructions make explicit use of dual reductive pairs which are shown to be particularly relevant to problems in optics and quantum interferometry.Comment: : RevTex file, 11 pages with 2 figure