Multiwavelength observations of the M15 intermediate velocity cloud

We present Westerbork Synthesis Radio Telescope HI images, Lovell Telescope multibeam HI wide-field mapping, Wisconsin H-alpha Mapper facility images, William Herschel Telescope longslit echelle CaII observations, and IRAS ISSA 60 and 100 micron coadded images towards the intermediate velocity cloud located in the general direction of the M15 globular cluster. When combined with previously-published Arecibo data, the HI gas in the IVC is found to be clumpy, with peak HI column density of 1.5x10^(20) cm^(-2), inferred volume density (assuming spherical symmetry) of 24 cm^(-3)/(D kpc), and maximum brightness temperature at a resolution of 81x14 arcsec of 14 K. The HI gas in the cloud is warm, with a minimum FWHM value of 5 km/s, corresponding to a kinetic temperature, in the absence of turbulence, of 540 K. There are indications in the HI data of 2-component velocity structure in the IVC, indicative of cloudlets. This velocity structure is also tentatively seen in the CaK spectra, although the SNR is low. The main IVC condensation is detected by WHAM in H-alpha with intensities uncorrected for Galactic absorption of upto 1.3 Rayleigh, indicating that the cloud is partially ionised. The FWHM of the ionised component, at a resolution of 1 degree, exceeds 30 km/s. The spatial and velocity coincidence of the H-alpha and HI peaks in emission is qualitatively good. Finally, the 100 and 60 micron IRAS images show spatial coincidence over a 0.7 degree field, with low and intermediate-velocity gas, respectively, indicating that the IVC may contain dust.Comment: MNRAS, in pres

ROPS: A New Search for Habitable Earths in the Southern Sky

We present the first results from our Red Optical Planet Survey (ROPS) to search for low mass planets orbiting late type dwarfs (M5.5V - M9V) in their habitable zones (HZ). Our observations, with the red arm of the MIKE spectrograph (0.5 - 0.9 microns) at the 6.5 m Magellan Clay telescope at Las Campanas Observatory indicate that >= 92 per cent of the flux lies beyond 0.7 microns. We use a novel approach that is essentially a hybrid of the simultaneous iodine and ThAr methods for determining precision radial velocities. We apply least squares deconvolution to obtain a single high S/N ratio stellar line for each spectrum and cross correlate against the simultaneously observed telluric line profile, which we derive in the same way. Utilising the 0.62 - 0.90 micron region, we have achieved an r.m.s. precision of 10 m/s for an M5.5V spectral type star with spectral S/N ~160 on 5 minute timescales. By M8V spectral type, a precision of ~30 m/s at S/N = 25 is suggested, although more observations are needed. An assessment of our errors and scatter in the radial velocity points hints at the presence of stellar radial velocity variations. Of our sample of 7 stars, 2 show radial velocity signals at 6-sigma and 10-sigma of the cross correlation uncertainties. If the signals are planetary in origin, our findings are consistent with estimates of Neptune mass planets that predict a frequency of 13 - 27 per cent for early M dwarfs.Our current analysis indicates the we can achieve a sensitivity that is equivalent to the amplitude induced by a 6 M_Earth planet orbiting in the habitable zone. Based on simulations, we estimate that <10 M_Earth habitable zone planets will be detected in a new stellar mass regime, with <=20 epochs of observations.Comment: MNRAS accepted: 14 pages, 8 figures, 3 table

Dust and the type II-Plateau supernova 2004dj

We present mid-infrared (MIR) spectroscopy of a Type II-plateau supernova, SN 2004dj, obtained with the Spitzer Space Telescope, spanning 106--1393 d after explosion. MIR photometry plus optical/near-IR observations are also reported. An early-time MIR excess is attributed to emission from non-silicate dust formed within a cool dense shell (CDS). Most of the CDS dust condensed between 50 d and 165 d, reaching a mass of 0.3 x 10^{-5} Msun. Throughout the observations much of the longer wavelength (>10 microns) part of the continuum is explained as an IR echo from interstellar dust. The MIR excess strengthened at later times. We show that this was due to thermal emission from warm, non-silicate dust formed in the ejecta. Using optical/near-IR line-profiles and the MIR continua, we show that the dust was distributed as a disk whose radius appeared to be slowly shrinking. The disk radius may correspond to a grain destruction zone caused by a reverse shock which also heated the dust. The dust-disk lay nearly face-on, had high opacities in the optical/near-IR regions, but remained optically thin in the MIR over much of the period studied. Assuming a uniform dust density, the ejecta dust mass by 996 d was 0.5 +/- 0.1) x 10^{-4} Msun, and exceeded 10^{-4}Msun by 1393 d. For a dust density rising toward the center the limit is higher. Nevertheless, this study suggests that the amount of freshly-synthesized dust in the SN 2004dj ejecta is consistent with that found from previous studies, and adds further weight to the claim that such events could not have been major contributors to the cosmic dust budget.Comment: ApJ in press; minor changes c.f. v

Transmission of Avian Influenza A Viruses among Species in an Artificial Barnyard

Waterfowl and shorebirds harbor and shed all hemagglutinin and neuraminidase subtypes of influenza A viruses and interact in nature with a broad range of other avian and mammalian species to which they might transmit such viruses. Estimating the efficiency and importance of such cross-species transmission using epidemiological approaches is difficult. We therefore addressed this question by studying transmission of low pathogenic H5 and H7 viruses from infected ducks to other common animals in a quasi-natural laboratory environment designed to mimic a common barnyard. Mallards (Anas platyrhynchos) recently infected with H5N2 or H7N3 viruses were introduced into a room housing other mallards plus chickens, blackbirds, rats and pigeons, and transmission was assessed by monitoring virus shedding (ducks) or seroconversion (other species) over the following 4 weeks. Additional animals of each species were directly inoculated with virus to characterize the effect of a known exposure. In both barnyard experiments, virus accumulated to high titers in the shared water pool. The H5N2 virus was transmitted from infected ducks to other ducks and chickens in the room either directly or through environmental contamination, but not to rats or blackbirds. Ducks infected with the H7N2 virus transmitted directly or indirectly to all other species present. Chickens and blackbirds directly inoculated with these viruses shed significant amounts of virus and seroconverted; rats and pigeons developed antiviral antibodies, but, except for one pigeon, failed to shed virus

Optical and infrared observations of the Type IIP SN2002hh from day 3 to 397

We present optical and infrared (IR) observations of the type IIP SN2002hh from 3 to 397 days after explosion. The optical spectroscopic (4-397d) and photometric (3-278d) data are complemented by spectroscopic (137-381d) and photometric (137-314d) data acquired at IR wavelengths. This is the first time L-band spectra have ever been successfully obtained for a supernova at a distance beyond the Local Group. The VRI light curves in the first 40 days reveal SN2002hh to be a SN IIP (plateau) - the most common of all core-collapse supernovae. SN2002hh is one of the most highly extinguished supernovae ever investigated. To provide a good match between its early-time spectrum and a coeval spectrum of the Type IIP SN1999em, as well as maintaining consistency with KI interstellar absorption, we invoke a 2-component extinction model. One component is due to the combined effect of the interstellar medium of our Milky Way Galaxy and the SN host galaxy, while the other component is due to a "dust pocket" where the grains have a mean size smaller than in the interstellar medium. The early-time optical light curves of SNe 1999em and 2002hh are generally well-matched, as are the radioactive tails of these two SNe and SN1987A. The late-time similarity of the SN2002hh optical light curves to those of SN1987A, together with measurements of the optical/IR luminosity and [FeII] 1.257mu emission indicate that 0.07 +- 0.02 Msun of Ni 56 was ejected by SN2002hh. [... ABRIDGED...] From the [OI] 6300,6364 A doublet luminosity we infer a 16-18 Msun main-sequence progenitor star. The progenitor of SN2002hh was probably a red supergiant with a substantial, dusty wind.Comment: 32 pages, 30 figures, accepted for publication in MNRA

Evaluation of geospatial methods to generate subnational HIV prevalence estimates for local level planning

Objective: There is evidence of substantial subnational variation in the HIV epidemic. However, robust spatial HIV data are often only available at high levels of geographic aggregation and not at the finer resolution needed for decision making. Therefore, spatial analysis methods that leverage available data to provide local estimates of HIV prevalence may be useful. Such methods exist but have not been formally compared when applied to HIV. Design/methods: Six candidate methods – including those used by the Joint United Nations Programme on HIV/AIDS to generate maps and a Bayesian geostatistical approach applied to other diseases – were used to generate maps and subnational estimates of HIV prevalence across three countries using cluster level data from household surveys. Two approaches were used to assess the accuracy of predictions: internal validation, whereby a proportion of input data is held back (test dataset) to challenge predictions; and comparison with location-specific data from household surveys in earlier years. Results: Each of the methods can generate usefully accurate predictions of prevalence at unsampled locations, with the magnitude of the error in predictions similar across approaches. However, the Bayesian geostatistical approach consistently gave marginally the strongest statistical performance across countries and validation procedures. Conclusions: Available methods may be able to furnish estimates of HIV prevalence at finer spatial scales than the data currently allow. The subnational variation revealed can be integrated into planning to ensure responsiveness to the spatial features of the epidemic. The Bayesian geostatistical approach is a promising strategy for integrating HIV data to generate robust local estimates

Searching the protein structure database for ligand-binding site similarities using CPASS v.2

<p>Abstract</p> <p>Background</p> <p>A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function.</p> <p>Findings</p> <p>We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG) to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated.</p> <p>Conclusions</p> <p>CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores for false positives by ~30%, while leaving true positives unaffected. Importantly, receiver operating characteristics (ROC) curves demonstrate the high correlation between CPASS similarity scores and an accurate functional assignment. As indicated by distribution curves, scores ≥ 30% infer a functional similarity. Software URL: <url>http://cpass.unl.edu</url>.</p

Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006)

BACKGROUND: The underlying basis for the seasonality of influenza A viruses is still uncertain. Phylogenetic studies investigated this phenomenon but have lacked sequences from more subtropical and tropical regions, particularly from Southeast Asia. METHODOLOGY/PRINCIPAL FINDINGS: 281 complete hemagglutinin (HA) and neuraminidase (NA) sequences were obtained from influenza A(H3N2) viruses, collected over 10 years (1997-2006) from Hong Kong. These dated sequences were analyzed with influenza A(H3N2) vaccine strain sequences (Syd/5/97, Mos/10/99, Fuj/411/02, Cal/7/04) and 315 other publicly available dated sequences from elsewhere, worldwide. In addition, the NA sequence alignment was inspected for the presence of any naturally occurring, known, neuraminidase inhibitor (NAI) resistance-associated amino acid mutations (R292K and E119V). Before 2001, the Hong Kong HA and NA sequences clustered more closely with the older vaccine sequences (Syd/5/97, Mos/10/99) than did sequences from elsewhere. After 2001, this trend reversed with significant clusters containing HA and NA sequences from different locations, isolated at different times, suggesting that viral migration may account for much of the influenza A(H3N2) seasonality during this 10-year period. However, at least one example from Hong Kong was found suggesting that in some years, influenza A(H3N2) viruses may persist in the same location, perhaps continuing to circulate, sub-clinically, at low levels between seasons, to re-emerge in the influenza season the following year, relatively unchanged. None of these Hong Kong influenza A(H3N2) NA sequences contained any of the known NAI-resistance associated mutations. CONCLUSIONS/SIGNIFICANCE: The seasonality of influenza A(H3N2) may be largely due to global migration, with similar viruses appearing in different countries at different times. However, occasionally, some viruses may remain within a single location and continue to circulate within that population, to re-emerge during the next influenza season, with relatively little genetic change. Naturally occurring NAI resistance mutations were absent or, at least, very rare in this population

Comparative Pathogenesis of an Avian H5N2 and a Swine H1N1 Influenza Virus in Pigs

Pigs are considered intermediate hosts for the transmission of avian influenza viruses (AIVs) to humans but the basic organ pathogenesis of AIVs in pigs has been barely studied. We have used 42 four-week-old influenza naive pigs and two different inoculation routes (intranasal and intratracheal) to compare the pathogenesis of a low pathogenic (LP) H5N2 AIV with that of an H1N1 swine influenza virus. The respiratory tract and selected extra-respiratory tissues were examined for virus replication by titration, immunofluorescence and RT-PCR throughout the course of infection. Both viruses caused a productive infection of the entire respiratory tract and epithelial cells in the lungs were the major target. Compared to the swine virus, the AIV produced lower virus titers and fewer antigen positive cells at all levels of the respiratory tract. The respiratory part of the nasal mucosa in particular showed only rare AIV positive cells and this was associated with reduced nasal shedding of the avian compared to the swine virus. The titers and distribution of the AIV varied extremely between individual pigs and were strongly affected by the route of inoculation. Gross lung lesions and clinical signs were milder with the avian than with the swine virus, corresponding with lower viral loads in the lungs. The brainstem was the single extra-respiratory tissue found positive for virus and viral RNA with both viruses. Our data do not reject the theory of the pig as an intermediate host for AIVs, but they suggest that AIVs need to undergo genetic changes to establish full replication potential in pigs. From a biomedical perspective, experimental LP H5 AIV infection of pigs may be useful to examine heterologous protection provided by H5 vaccines or other immunization strategies, as well as for further studies on the molecular pathogenesis and neurotropism of AIVs in mammals

Experimental Infection of Mice with Avian Paramyxovirus Serotypes 1 to 9

The nine serotypes of avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds worldwide. APMV-1, also called Newcastle disease virus, was shown to be attenuated in non-avian species and is being developed as a potential vector for human vaccines. In the present study, we extended this evaluation to the other eight serotypes by evaluating infection in BALB/c mice. Mice were inoculated intranasally with a prototype strain of each of the nine serotypes and monitored for clinical disease, gross pathology, histopathology, virus replication and viral antigen distribution, and seroconversion. On the basis of multiple criteria, each of the APMV serotypes except serotype 5 was found to replicate in mice. Five of the serotypes produced clinical disease and significant weight loss in the following order of severity: 1, 2>6, 9>7. However, disease was short-lived. The other serotypes produced no evident clinical disease. Replication of all of the APMVs except APMV-5 in the nasal turbinates and lungs was confirmed by the recovery of infectious virus and by substantial expression of viral antigen in the epithelial lining detected by immunohistochemistry. Trace levels of infectious APMV-4 and -9 were detected in the brain of some animals; otherwise, no virus was detected in the brain, small intestine, kidney, or spleen. Histologically, infection with the APMVs resulted in lung lesions consistent with broncho-interstitial pneumonia of varying severity that were completely resolved at 14 days post infection. All of the mice infected with the APMVs except APMV-5 produced serotype-specific HI serum antibodies, confirming a lack of replication of APMV-5. Taken together, these results demonstrate that all APMV serotypes except APMV-5 are capable of replicating in mice with minimal disease and pathology