A Bayesian method for evaluating and discovering disease loci associations

Background: A genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analyze multi-SNP associations. Techniques for handling so many hypotheses include the Bonferroni correction and recently developed Bayesian methods. These methods can encounter problems. Most importantly, they are not applicable to a complex multi-locus hypothesis which has several competing hypotheses rather than only a null hypothesis. A method that computes the posterior probability of complex hypotheses is a pressing need. Methodology/Findings: We introduce the Bayesian network posterior probability (BNPP) method which addresses the difficulties. The method represents the relationship between a disease and SNPs using a directed acyclic graph (DAG) model, and computes the likelihood of such models using a Bayesian network scoring criterion. The posterior probability of a hypothesis is computed based on the likelihoods of all competing hypotheses. The BNPP can not only be used to evaluate a hypothesis that has previously been discovered or suspected, but also to discover new disease loci associations. The results of experiments using simulated and real data sets are presented. Our results concerning simulated data sets indicate that the BNPP exhibits both better evaluation and discovery performance than does a p-value based method. For the real data sets, previous findings in the literature are confirmed and additional findings are found. Conclusions/Significance: We conclude that the BNPP resolves a pressing problem by providing a way to compute the posterior probability of complex multi-locus hypotheses. A researcher can use the BNPP to determine the expected utility of investigating a hypothesis further. Furthermore, we conclude that the BNPP is a promising method for discovering disease loci associations. © 2011 Jiang et al

Faint recombination lines in Galactic PNe with [WC] nucleus

We present spatially resolved high-resolution spectrophotometric data for the planetary nebulae PB8, NGC2867, and PB6. We have analyzed two knots in NGC2867 and PB6 and one in PB8. The three nebulae are ionized by [WC] type nuclei: early [WO] for PB6 and NGC2867 and [WC 5-6] in the case of PB8. Our aim is to study the behavior of the abundance discrepancy problem (ADF) in this type of PNe. We measured a large number of optical recombination (ORL) and collisionally excited lines (CEL), from different ionization stages (many more than in any previous work), thus, we were able to derive physical conditions from many different diagnostic procedures. We determined ionic abundances from the available collisionally excited lines and recombination lines. Based on both sets of ionic abundances, we derived total chemical abundances in the nebulae using suitable ionization correction factors. From CELs, we have found abundances typical of Galactic disk planetary nebulae. Moderate ADF(O++) were found for PB8 (2.57) and NGC2867 (1.63). For NGC2867, abundances from ORLs are higher but still consistent with Galactic disk planetary nebulae. On the contrary, PB8 presents a very high O/H ratio from ORLs. A high C/O was obtained from ORLs for NGC2867; this ratio is similar to C/O obtained from CELs and with the chemical composition of the wind of the central star, indicating that there was no further C-enrichment in the star, relative to O, after the nebular material ejection. On the contrary, we found C/O<1 in PB8. Interestingly, we obtain (C/O)ORLs/(C/O)CELs < 1 in PB8 and NGC2867; this added to the similarity between the heliocentric velocities measured in [OIII] and OII lines for our three objects, argue against the presence of H-deficient metal-rich knots coming from a late thermal pulse event.Comment: 25 pages, 13 Tables, 4 Figures Accepted for publication in A&A. First page is blank for obscure latex reason

Near-infrared studies of the 2010 outburst of the recurrent nova U Scorpii

We present near-infrared (near-IR) observations of the 2010 outburst of U Sco. JHK photometry is presented on 10 consecutive days starting from 0.59 d after outburst. Such photometry can gainfully be integrated into a larger data base of other multiwavelength data which aim to comprehensively study the evolution of U Sco. Early near-IR spectra, starting from 0.56 d after outburst, are presented and their general characteristics discussed. Early in the eruption, we see very broad wings in several spectral lines, with tails extending up to ∼10 000 km s−1 along the line of sight; it is unexpected to have a nova with ejection velocities equal to those usually thought to be exclusive to supernovae. From recombination analysis, we estimate an upper limit of [inline image] for the ejected mass

One-dimensional modelling of air injection into abandoned oil fields for heat generation

With the global drive for net-zero emissions, it has never been more important to find clean energy sources. There are thousands of abandoned oilfields worldwide with the potential to be reactivated to produce clean energy with air injection and subsequent waste fluid sequestration. Air injection, and the development of a fire-front, may be used with enhanced geothermal systems by taking ad-vantage of the inherent increase in heat and pressure. Conventionally used as an enhanced oil re-covery technique, air injection has gained the reputation of being a high-risk intervention due to the many failures in its history. Knowledge of how petrophysical rock properties and oil physical and chemical properties control the consequences of air injection is key to optimising the selection of late-life, or even abandoned oilfields for use in such systems. Here we use one-dimensional model-ling to test the effect of varying porosity, permeability, oil viscosity and API gravity on the success of air injection. Modelling shows that the most important factor controlling temperature is the po-rosity of the reservoir, followed by the API gravity and then the viscosity of the oil. The most im-portant factors controlling velocity of the fire-front are API gravity followed by oil viscosity. We show that reservoirs with high porosity and low permeability with high viscosity and low API gravi-ty oil reach the highest fire-front temperatures. The significance of this work is that it provides sev-eral geoscience-related criteria to rank possible candidate reservoirs for reactivation and clean energy generation via air injection: the best candidates will have the highest total porosity, relatively low permeability, highest oil viscosity and lowest API gravity, such fields can then move on to bespoke and more complex simulations.</jats:p

A study of the neglected Galactic HII region NGC 2579 and its companion ESO 370-9

The Galactic HII region NGC 2579 has stayed undeservedly unexplored due to identification problems which persisted until recently. Both NGC 2579 and its companion ESO 370-9 have been misclassified as planetary or reflection nebula, confused with each other and with other objects. Due to its high surface brightness, high excitation, angular size of few arcminutes and relatively low interstellar extinction, NGC 2579 is an ideal object for investigations in the optical range. Located in the outer Galaxy, NGC 2579 is an excellent object for studying the Galactic chemical abundance gradients. In this paper we present the first comprehensive observational study on the nebular and stellar properties of NGC 2579 and ESO 370-9, including the determination of electron temperature, density structure, chemical composition, kinematics, distance, and the identification and spectral classification of the ionizing stars, and discuss the nature of ESO 370-9. Long slit spectrophotometric data in the optical range were used to derive the nebular electron temperature, density and chemical abundances and for the spectral classification of the ionizing star candidates. Halpha and UBV CCD photometry was carried out to derive stellar distances from spectroscopic parallax and to measure the ionizing photon flux.Comment: To be published in Astronomy & Astrophysic

Chemical abundances in the protoplanetary disk LV2 (Orion): clues to the causes of the abundance anomaly in HII regions

Optical integral field spectroscopy of the archetype protoplanetary disk LV2 in the Orion Nebula is presented, taken with the VLT FLAMES/Argus fibre array. The detection of recombination lines of CII and OII from this class of objects is reported, and the lines are utilized as abundance diagnostics. The study is complemented with the analysis of HST Faint Object Spectrograph ultraviolet and optical spectra of the target contained within the Argus field of view. By subtracting the local nebula background the intrinsic spectrum of the proplyd is obtained and its elemental composition is derived for the first time. The proplyd is found to be overabundant in carbon, oxygen and neon compared to the Orion Nebula and the sun. The simultaneous coverage over LV2 of the CIII] 1908-A and [OIII] 5007-A collisionally excited lines (CELs) and CII and OII recombination lines (RLs) has enabled us to measure the abundances of C++ and O++ for LV2 with both sets of lines. The two methods yield consistent results for the intrinsic proplyd spectrum, but not for the proplyd spectrum contaminated by the generic nebula spectrum, thus providing one example where the long-standing abundance anomaly plaguing metallicity studies of HII regions has been resolved. These results would indicate that the standard forbidden-line methods used in the derivation of light metal abundances in HII regions in our own and other galaxies underestimate the true gas metallicity.Comment: Accepted by MNRAS November 8; 16 pages, 9 figs; typos corrected, error in FWHMs in table 4 corrected in this versio

Evidence for binarity in the bipolar planetary nebulae A79, He2-428 and M1-91

We present low and high resolution long-slit spectra of three bipolar planetary nebulae (PNe) with bright central cores: A79, He2-428 and M1-91. He2-428 and M1-91 have high density (from 10^3.3 to 10^6.5 cm^-3) unresolved nebular cores that indicate that strong mass loss/exchange phenomena are occurring close to their central stars. An F0 star is found at the centre of symmetry of A79; its reddening and distance are consistent with the association of the star with the nebula. The spectrum of the core of He2-428 shows indications of the presence of a hot star with red excess emission, probably arising in a late-type companion. A79 is one of the richest PNe in N and He, the abundances of M1-91 are at the lower end of the range spanned by bipolar PNe, and He2-428 shows very low abundances, similar to those measured for halo PNe. The extended nebulae of A79 and He2-428 have inclined equatorial rings expanding at a velocity of approx. 15 km/s, with kinematical ages 10^4 yr. The association of these aged, extended nebulae with a dense nebular core (He2-428) or a relatively late type star (A79) is interpreted as evidence for the binarity of their nuclei.Comment: 13 pages including 8 tables. A&A accepted; also available at http://www.iac.es/publicaciones/preprints.htm

WR bubbles and HeII emission

We present the very first high quality images of the HeII 4686 emission in three high excitation nebulae of the Magellanic Clouds. A fourth high excitation nebula, situated around the WR star BAT99-2, was analysed in a previous letter. Using VLT FORS data, we investigate the morphology of the ring nebulae around the early-type WN stars BAT99-49 & AB7. We derive the total HeII fluxes for each object and compare them with the most recent theoretical WR models. Using Halpha, [OIII] and HeI 5876 images along with long-slit spectroscopy, we investigate the physical properties of these ring nebulae and find only moderate chemical enrichment. We also surveyed seven other LMC WR stars but we failed to detect any HeII emission but note that the nebula around BAT99-11 shows a N/O ratio and an oxygen abundance slightly lower than the LMC values, while the nebula around BAT99-134 presents moderate chemical enrichment similar to the one seen near BAT99-2, 49 and AB7. The third high excitation nebula presented in this paper, N44C, does not harbor stars hotter than mid-O main sequence stars. It was suggested to be a fossil X-ray nebula ionized but our observations of N44C reveal no substantial changes in the excitation compared to previous results reported in the literature.Comment: 13 pages, 8 figures (7 in jpg), accepted by A&A, also available from http://vela.astro.ulg.ac.be/Preprints/P81/index.htm

The Iron abundance in Galactic Planetary Nebulae

We constrain the iron abundance in a sample of 33 low-ionization Galactic planetary nebulae (PNe) using [Fe III] lines and correcting for the contribution of higher ionization states with ionization correction factors (ICFs) that take into account uncertainties in the atomic data. We find very low iron abundances in all the objects, suggesting that more than 90% of their iron atoms are condensed onto dust grains. This number is based on the solar iron abundance and implies a lower limit on the dust-to-gas mass ratio, due solely to iron, of M_dust/M_gas>1.3x10^{-3} for our sample. The depletion factors of different PNe cover about two orders of magnitude, probably reflecting differences in the formation, growth, or destruction of their dust grains. However, we do not find any systematic difference between the gaseous iron abundances calculated for C-rich and O-rich PNe, suggesting similar iron depletion efficiencies in both environments. The iron abundances of our sample PNe are similar to those derived following the same procedure for a group of 10 Galactic H II regions. These high depletion factors argue for high depletion efficiencies of refractory elements onto dust grains both in molecular clouds and AGB stars, and low dust destruction efficiencies both in interstellar and circumstellar ionized gas.Comment: Accepted for publication in ApJ. 15 pages, 4 Postscript figures, corrected typos, Tables 2 and 3 correcte

Improving Predictions for Helium Emission Lines

We have combined the detailed He I recombination model of Smits with the collisional transitions of Sawey & Berrington in order to produce new accurate helium emissivities that include the effects of collisional excitation from both the 2 (3)S and 2 (1) S levels. We present a grid of emissivities for a range of temperature and densities along with analytical fits and error estimates. Fits accurate to within 1% are given for the emissivities of the brightest lines over a restricted range for estimates of primordial helium abundance. We characterize the analysis uncertainties associated with uncertainties in temperature, density, fitting functions, and input atomic data. We estimate that atomic data uncertainties alone may limit abundance estimates to an accuracy of 1.5%; systematic errors may be greater than this. This analysis uncertainty must be incorporated when attempting to make high accuracy estimates of the helium abundance. For example, in recent determinations of the primordial helium abundance, uncertainties in the input atomic data have been neglected.Comment: ApJ, accepte