The data acquisition system for the Anglo-Australian Observatory 2-degree field project

The Anglo-Australian Observatory (AAO) is building a system that will provide a two-degree field of view at prime focus. A robot positioner will be used to locate up to 400 optical fibers at pre-determined positions in this field. While observations are being made using one set of 400 fibers, the robot will be positioning a second set of fibers in a background field that can be moved in to replace the first when the telescope is moved to a new position. The fibers feed two spectrographs each with a 1024 square CCD detector. The software system being produced to control this involves Vaxes for overall control and data recording, UNIX workstations for fiber configuration calculations and on-line data reduction, and VME systems running VxWorks for real-time control of critical parts such as the positioner robot. The system has to be able to interact with the observatory's present data acquisition systems, which use the ADAM system. As yet, the real-time parts of ADAM have not been ported to Unix, and so we are having to produce a smaller-scale system that is similar but inherently distributed (which ADAM is not). We are using this system as a testbed for ideas that we hope may eventually influence an ADAM II system. The system we are producing is based on a message system that is designed to be able to handle inter-process and inter-processor messages of any length, efficiently, and without ever requiring a task to block (i.e., be unresponsive to 'cancel' messages, enquiry messages), other than when deliberately waiting for external input - all of which will be through such messages. The essential requirement is that a message 'send' operation should never be able to block. The messages will be hierarchical, self-defining, machine-independent data structures. This allows us to provide very simple monitoring of messages for diagnostic purposes, and allows general purpose interface programs to be written without needing to share precise byte by byte message format definitions. Programs in this system have interfaces defined simply in terms of named actions and their parameters. Real-time control programs are required to be able to handle a number of such actions concurrently; data reduction programs will normally only need to handle one action at a time ('process an image', 'display a spectrum', etc)

Genetic analysis of porcine H3N2 viruses originating in southern China

From immunological and phylogenetic analyses of H3 influenza viruses isolated from pigs and ducks in the People's Republic of China (China), Hong Kong, Taiwan and Japan, between 1968 and 1982, we arrived at the following conclusions. The H3 haemagglutinin and N2 neuraminidase genes from swine isolates can be segregated into four mammalian lineages, including: (i) the earliest human strains; (ii) early swine strains including Hong Kong isolates from 1976-1977; (iii) an intermediate strain between the early swine and recent human strains; and (iv) recent human strains. In this study we found an unusual swine strain (sw/Hong Kong/127/82) belonging to the third lineage which behaved like those of the early swine-like lineage in the haemagglutination inhibition test; but neuraminidase inhibition profiles with monoclonal antibodies indicated that this virus is related to late human strains. On the basis of pairwise comparisons of complete or partial nucleotide sequences the genes encoding the three polymerase proteins (PB2, PB1, PA), the nucleoprotein, the membrane protein and possibly the nonstructural proteins of sw/Hong Kong/127/82 are of the swine H1N1 lineage, whereas genes encoding the two surface glycoproteins belong to the human H3N2 lineage. In contrast, all RNA segments of one swine isolate (sw/Hong Kong/81/78) are similar to those of recent human H3N2 viruses. This study indicated that frequent interspecies infections between human and swine hosts appeared to occur during 1976-82. Although the evolutionary rates of human (0.0122/site/year), swine (0.0127/site/year) and avian (0.0193/site/year) virus genes are similar when based upon synonymous substitutions, nonsynonymous substitutions indicated that viral genes derived from human and swine viruses evolved about three times faster (0.0026-0.0027/site/year) than those of avian viruses (0.0008/site/year). Furthermore, the evolutionary mechanism by which human and swine H3 haemagglutinin genes evolve at a similar rate, based on nonsynonymous substitutions, appeared to be quite different from previous evidence which showed that human H1 haemagglutinin genes evolved three times faster than those of swine viruses. However, comparison of the number of nonsynonymous substitutions in the antigenic sites (A-E) of haemagglutinin molecules demonstrated that swine viruses evolve at a rate that is about one fifth to one tenth that of human viruses, reflecting the conservative nature of the antigenic structure in the former.published_or_final_versio

Multi-Object Spectroscopy Field Configuration by Simulated Annealing

Multi-object spectroscopy (MOS) instruments, such as the Two-degree Field (2dF) facility of the Anglo-Australian Observatory (AAO), have facilitated large-scale redshift surveys. Yet despite their acclaim, instrument design has been suspected of introducing subtle selection effects into surveys. Investigation into these selection effects has been overshadowed by instrument complexity. We identify the field configuration algorithm (FCA) used to select targets for observation as mainly responsible for such effects. A FCA can imprint artificial structure on observed target distributions, which may accrue over large angular scales, potentially to the detriment of statistical analyses applied to such surveys. We present here a new FCA developed for 2dF that is based on simulated annealing (SA), a generic method commonly used to solve constrained optimisation problems. We generate synthetic fields and utilise mock 2dF volumes to contrast the behaviour of previous strategies with the SA FCA. The angular two-point correlation function and other sensitive techniques reveal that the new FCA achieves unprecedented sampling uniformity and target yield with improved target priority handling and observational flexibility over current FCAs. The SA FCA is generic enough to be used by current 2dF-like and potentially next-generation MOS instruments with little modification.Comment: 14 pages, 16 figures, accepted to MNRA

Characterization of H3N2 influenza viruses isolated from pigs in southern China

Poster Presentations: Animal Influenza EcologyHuman-like H3N2 influenza viruses have repeatedly transmitted to domestic pigs in different regions of the world, but it is still not certain whether any of those variants have become established in pig populations. The detection of different subtypes of avian influenza viruses from pigs makes it an ideal candidate for the genesis of a possible reassortant virus with both human and avian gene segments. However, whether pigs could act as a “mixing vessel” for a possible pandemic virus remains unanswered. Long-term influenza surveillance in pigs in southern China revealed that H3N2 influenza viruses were regularly detected from domestic pigs from 1998 to 2003. Antigenic analysis of representative strains revealed that two distinguishable groups of H3N2 influenza viruses were present in pigs during this period: a contemporary human-like viruses (represented by Sydney/5/97), and Port Chalmers/1/73-like (PC-like) viruses. Phylogenetic analysis of the representative strains confirmed those two groups. In general, the PC-like viruses were most closely related to those H3N2 reassortants recognized from European pigs since the mid-1980s, while the remaining isolates were most closely related to those contemporary human H3N2 viruses. It is interesting to note that one PC-like isolate contained a classical swine H1N1-like NP gene, Sw/HK/1197/02, suggesting that after introduction to pigs in southern China the European swine H3N2 virus further reassorted with local swine virus. The contemporary humanlike H3N2 viruses isolated from pig appeared to have resulted from repeated introduction from humans to pigs. Interestingly, one isolate (Sw/HK/NS1128/03) clustered with those human isolates detected in the early 1990s. These findings suggesting that some recent human H3N2 variants may be maintained long-term in pig populations in southern China. The present study provides updated information on the role of pigs in the interspecies transmission and genetic reassortment of influenza viruses in this region.postprin

Intersex in the clam Scrobicularia plana (Da Costa): Widespread occurrence in English Channel estuaries and surrounding areas

Estuarine clams Scrobicularia plana were sampled from 108 intertidal locations around the English Channel and adjacent areas. Although S. plana is believed to be a strict gonochorist, 58% of the populations sampled included intersexed individuals (described as male clams exhibiting ovotestis). Over the entire region, on average, 8.6% of male clams exhibited intersex, although proportions of affected males ranged from 0% to 53% depending on location. The severity of intersex was assessed using a simple classification scale, with the majority of individuals showing low levels of impact. Sex ratios were significantly skewed at some sites. There were no significant relationships between the incidence and severity of intersex; or of associations with size or parasitism of individual clams. Intersex in S. plana is a useful tool to assess endocrine disruptive effects in estuaries, although mechanisms of impact and causative agents remain uncertain

Workshop 1: Surveillance issues of pandemic influenza

published_or_final_versio

An Abundance Analysis for Five Red Horizontal Branch Stars in the Extremely Metal Rich Globular Cluster NGC 6553

We provide a high dispersion line-by-line abundance analysis of five red HB stars in the extremely metal rich galactic globular cluster NGC 6553. These red HB stars are significantly hotter than the very cool stars near the tip of the giant branch in such a metal rich globular cluster and hence their spectra are much more amenable to an abundance analysis than would be the case for red giants. We find that the mean [Fe/H] for NGC 6553 is -0.16 dex, comparable to the mean abundance in the galactic bulge found by McWilliam & Rich (1994) and considerably higher than that obtained from an analysis of two red giants in this cluster by Barbuy etal (1999). The relative abundance for the best determined alpha process element (Ca) indicates an excess of alpha process elements of about a factor of two. The metallicity of NGC 6553 reaches the average of the Galactic bulge and of the solar neighborhood.Comment: 29 pages, 6 figures, accepted for publication in the Ap

Suppression of the near-infrared OH night sky lines with fibre Bragg gratings - first results

The background noise between 1 and 1.8 microns in ground-based instruments is dominated by atmospheric emission from hydroxyl molecules. We have built and commissioned a new instrument, GNOSIS, which suppresses 103 OH doublets between 1.47 - 1.7 microns by a factor of ~1000 with a resolving power of ~10,000. We present the first results from the commissioning of GNOSIS using the IRIS2 spectrograph at the AAT. The combined throughput of the GNOSIS fore-optics, grating unit and relay optics is ~36 per cent, but this could be improved to ~46 per cent with a more optimal design. We measure strong suppression of the OH lines, confirming that OH suppression with fibre Bragg gratings will be a powerful technology for low resolution spectroscopy. The integrated OH suppressed background between 1.5 and 1.7 microns is reduced by a factor of 9 compared to a control spectrum using the same system without suppression. The potential of low resolution OH suppressed spectroscopy is illustrated with example observations. The GNOSIS background is dominated by detector dark current below 1.67 microns and by thermal emission above 1.67 microns. After subtracting these we detect an unidentified residual interline component of ~ 860 +/ 210 ph/s/m^2/micron/arcsec^2. This component is equally bright in the suppressed and control spectra. We have investigated the possible source of the interline component, but were unable to discriminate between a possible instrumental artifact and intrinsic atmospheric emission. Resolving the source of this emission is crucial for the design of fully optimised OH suppression spectrographs. The next generation OH suppression spectrograph will be focussed on resolving the source of the interline component, taking advantage of better optimisation for a FBG feed. We quantify the necessary improvements for an optimal OH suppressing fibre spectrograph design.Comment: Accepted for publication in MNRAS. 15 pages, 18 figure

Spatial Distribution and Risk Factors of Highly Pathogenic Avian Influenza (HPAI) H5N1 in China

Highly pathogenic avian influenza (HPAI) H5N1 was first encountered in 1996 in Guangdong province (China) and started spreading throughout Asia and the western Palearctic in 2004–2006. Compared to several other countries where the HPAI H5N1 distribution has been studied in some detail, little is known about the environmental correlates of the HPAI H5N1 distribution in China. HPAI H5N1 clinical disease outbreaks, and HPAI virus (HPAIV) H5N1 isolated from active risk-based surveillance sampling of domestic poultry (referred to as HPAIV H5N1 surveillance positives in this manuscript) were modeled separately using seven risk variables: chicken, domestic waterfowl population density, proportion of land covered by rice or surface water, cropping intensity, elevation, and human population density. We used bootstrapped logistic regression and boosted regression trees (BRT) with cross-validation to identify the weight of each variable, to assess the predictive power of the models, and to map the distribution of HPAI H5N1 risk. HPAI H5N1 clinical disease outbreak occurrence in domestic poultry was mainly associated with chicken density, human population density, and elevation. In contrast, HPAIV H5N1 infection identified by risk-based surveillance was associated with domestic waterfowl density, human population density, and the proportion of land covered by surface water. Both models had a high explanatory power (mean AUC ranging from 0.864 to 0.967). The map of HPAIV H5N1 risk distribution based on active surveillance data emphasized areas south of the Yangtze River, while the distribution of reported outbreak risk extended further North, where the density of poultry and humans is higher. We quantified the statistical association between HPAI H5N1 outbreak, HPAIV distribution and post-vaccination levels of seropositivity (percentage of effective post-vaccination seroconversion in vaccinated birds) and found that provinces with either outbreaks or HPAIV H5N1 surveillance positives in 2007–2009 appeared to have had lower antibody response to vaccination. The distribution of HPAI H5N1 risk in China appears more limited geographically than previously assessed, offering prospects for better targeted surveillance and control interventions

How do modern transportation projects impact on development of impervious surfaces via new urban area and urban intensification? Evidence from Hangzhou Bay Bridge, China

Many countries have been constructing modern ground transportation projects. This raises questions about the impacts of such projects on development of impervious surfaces, yet there have been few attempts to systematically analyze these impacts. This paper attempts to narrow this information gap using the Hangzhou Bay Bridge project, China, as an exploratory case study. Using remotely sensed data, we developed a framework based on statistical techniques, wavelet multi-resolution analysis and Theil-Sen slope analysis to measure the changes in impervious surfaces. The derived changes were then linked to the bridge project with respect to socio-economic factors and land use development activities. The findings highlight that the analytical framework could reliably quantify the area, pattern and form of new urban area and urban intensification. Change detection analysis showed that urban area, GDP and the length of highways increased moderately in the pre-Hangzhou Bay Bridge period (1995–2002) while all of these variables increased more substantially during (2002–2009) and after (2009–2013) the bridge construction. The results indicate that the development of impervious surfaces due to new urban area came at the expense of permeable surfaces in the urban fringe and within rural regions, while urban intensification occurred mainly in the form of the redevelopment of older structures to modern high-rise buildings within existing urban regions. In the context of improved transportation infrastructure, our findings suggest that new urban area and urban intensification can be attributed to consecutive events which act like a chain reaction: construction of improved transportation projects, their impacts on land use development policies, effects of both systems on socio-economic variables, and finally all these changes influence new urban area and urban intensification. However, more research is needed to better understand this sequential process and to examine the broader applicability of the concept in other developing regions