Local pre-processing for node classification in networks : application in protein-protein interaction

Network modelling provides an increasingly popular conceptualisation in a wide range of domains, including the analysis of protein structure. Typical approaches to analysis model parameter values at nodes within the network. The spherical locality around a node provides a microenvironment that can be used to characterise an area of a network rather than a particular point within it. Microenvironments that centre on the nodes in a protein chain can be used to quantify parameters that are related to protein functionality. They also permit particular patterns of such parameters in node-centred microenvironments to be used to locate sites of particular interest. This paper evaluates an approach to index generation that seeks to rapidly construct microenvironment data. The results show that index generation performs best when the radius of microenvironments matches the granularity of the index. Results are presented to show that such microenvironments improve the utility of protein chain parameters in classifying the structural characteristics of nodes using both support vector machines and neural networks

A non-LTE abundance analysis of the post-AGB star ROA 5701

An analysis of high-resolution Anglo-Australian Telescope (AAT)/ University College London Echelle Spectrograph (UCLES) optical spectra for the ultraviolet (UV)-bright star ROA 5701 in the globular cluster omega Cen (NGC 5139) is performed, using non-local thermodynamic equilibrium (non-LTE) model atmospheres to estimate stellar atmospheric parameters and chemical composition. Abundances are derived for C, N, O, Mg, Si and S, and compared with those found previously by Moehler et al. We find a general metal underabundance relative to young B-type stars, consistent with the average metallicity of the cluster. Our results indicate that ROA 5701 has not undergone a gas-dust separation scenario as previously suggested. However, its abundance pattern does imply that ROA 5701 has evolved off the AGB prior to the onset of the third dredge-up.Comment: 9 pages, 2 figures. Accepted for publication in MNRAS (Online Early

Fe XI emission lines in a high resolution extreme ultraviolet spectrum obtained by SERTS

New calculations of radiative rates and electron impact excitation cross sections for Fe XI are used to derive emission line intensity ratios involving 3s^23p^4 - 3s^23p^33d transitions in the 180-223 A wavelength range. These ratios are subsequently compared with observations of a solar active region, obtained during the 1995 flight Solar EUV Research Telescope and Spectrograph (SERTS). The version of SERTS flown in 1995 incorporated a multilayer grating that enhanced the instrumental sensitivity for features in the 170 - 225 A wavelength range, observed in second-order between 340 and 450 A. This enhancement led to the detection of many emission lines not seen on previous SERTS flights, which were measured with the highest spectral resolution (0.03 A) ever achieved for spatially resolved active region spectra in this wavelength range. However, even at this high spectral resolution, several of the Fe XI lines are found to be blended, although the sources of the blends are identified in the majority of cases. The most useful Fe XI electron density diagnostic line intensity ratio is I(184.80 A)/I(188.21 A). This ratio involves lines close in wavelength and free from blends, and which varies by a factor of 11.7 between N_e = 10^9 and 10^11 cm^-3, yet shows little temperature sensitivity. An unknown line in the SERTS spectrum at 189.00 A is found to be due to Fe XI, the first time (to our knowledge) this feature has been identified in the solar spectrum. Similarly, there are new identifications of the Fe XI 192.88, 198.56 and 202.42 A features, although the latter two are blended with S VIII/Fe XII and Fe XIII, respectively.Comment: 21 pages, 9 gigures, accepted for publication in the Astrophysical Journa

The Origin of B-Type Runaway Stars: Non-LTE Abundances as a Diagnostic

There are two accepted mechanisms to explain the origin of runaway OB-type stars: the Binary Supernova Scenario (BSS), and the Cluster Ejection Scenario (CES). In the former, a supernova explosion within a close binary ejects the secondary star, while in the latter close multi-body interactions in a dense cluster cause one or more of the stars to be ejected from the region at high velocity. Both mechanisms have the potential to affect the surface composition of the runaway star. TLUSTY non-LTE model atmosphere calculations have been used to determine atmospheric parameters and carbon, nitrogen, magnesium and silicon abundances for a sample of B-type runaways. These same analytical tools were used by Hunter et al. (2009) for their analysis of 50 B-type open cluster Galactic stars (i.e. non-runaways). Effective temperatures were deduced using the silicon-ionization balance technique, surface gravities from Balmer line profiles and microturbulent velocities derived using the Si spectrum. The runaways show no obvious abundance anomalies when compared with stars in the open clusters. The runaways do show a spread in composition which almost certainly reflects the Galactic abundance gradient and a range in the birthplaces of the runaways in the Galactic disk. Since the observed Galactic abundance gradients of C, N, Mg and Si are of a similar magnitude, the abundance ratios (e.g., N/Mg) are, as obtained, essentially uniform across the sample

Iron abundances from optical Fe III absorption lines in B-type stellar spectra

The role of optical Fe III absorption lines in B-type stars as iron abundance diagnostics is considered. To date, ultraviolet Fe lines have been widely used in B-type stars, although line blending can severely hinder their diagnostic power. Using optical spectra, covering a wavelength range ~ 3560 - 9200 A, a sample of Galactic B-type main-sequence and supergiant stars of spectral types B0.5 to B7 are investigated. A comparison of the observed Fe III spectra of supergiants, and those predicted from the model atmosphere codes TLUSTY (plane-parallel, non-LTE), with spectra generated using SYNSPEC (LTE), and CMFGEN (spherical, non-LTE), reveal that non-LTE effects appear small. In addition, a sample of main-sequence and supergiant objects, observed with FEROS, reveal LTE abundance estimates consistent with the Galactic environment and previous optical studies. Based on the present study, we list a number of Fe III transitions which we recommend for estimating the iron abundance from early B-type stellar spectra.Comment: 3 figures and 8 tables. Table 3 is to be published online only (included here on last page). Accepted for publication in MNRA

Emission lines of Fe XI in the 257--407 A wavelength region observed in solar spectra from EIS/Hinode and SERTS

Theoretical emission-line ratios involving Fe XI transitions in the 257-407 A wavelength range are derived using fully relativistic calculations of radiative rates and electron impact excitation cross sections. These are subsequently compared with both long wavelength channel Extreme-Ultraviolet Imaging Spectrometer (EIS) spectra from the Hinode satellite (covering 245-291 A), and first-order observations (235-449 A) obtained by the Solar Extreme-ultraviolet Research Telescope and Spectrograph (SERTS). The 266.39, 266.60 and 276.36 A lines of Fe XI are detected in two EIS spectra, confirming earlier identifications of these features, and 276.36 A is found to provide an electron density diagnostic when ratioed against the 257.55 A transition. Agreement between theory and observation is found to be generally good for the SERTS data sets, with discrepancies normally being due to known line blends, while the 257.55 A feature is detected for the first time in SERTS spectra. The most useful Fe XI electron density diagnostic is found to be the 308.54/352.67 intensity ratio, which varies by a factor of 8.4 between N_e = 10^8 and 10^11 cm^-3, while showing little temperature sensitivity. However, the 349.04/352.67 ratio potentially provides a superior diagnostic, as it involves lines which are closer in wavelength, and varies by a factor of 14.7 between N_e = 10^8 and 10^11 cm^-3. Unfortunately, the 349.04 A line is relatively weak, and also blended with the second-order Fe X 174.52 A feature, unless the first-order instrument response is enhanced.Comment: 9 pages, 5 figures, 13 tables; MNRAS in pres

The VLT-FLAMES Tarantula Survey V. The peculiar B[e]-like supergiant, VFTS698, in 30 Doradus

We present an analysis of a peculiar supergiant B-type star (VFTS698/Melnick 2/Parker 1797) in the 30 Doradus region of the Large Magellanic Cloud which exhibits characteristics similar to the broad class of B[e] stars. We analyse optical spectra from the VLT-FLAMES survey, together with archival optical and infrared photometry and X-ray imaging to characterise the system. We find radial velocity variations of around 400 km/s in the high excitation Si IV, N III and He II spectra, and photometric variability of ~0.6 mag with a period of 12.7 days. In addition, we detect long-term photometric variations of ~0.25 mag, which may be due to a longer-term variability with a period of ~400 days. We conclude that VFTS698 is likely an interacting binary comprising an early B-type star secondary orbiting a veiled, more massive companion. Spectral evidence suggests a mid-to-late B-type primary, but this may originate from an optically-thick accretion disc directly surrounding the primary.Comment: 18 pages, 14 figures and 8 tables. Table 8 to be published onlin

Early-type stars observed in the ESO UVES Paranal Observatory Project - V. Time-variable interstellar absorption

The structure and properties of the diffuse interstellar medium (ISM) on small scales, sub-au to 1 pc, are poorly understood. We compare interstellar absorption-lines, observed towards a selection of O- and B-type stars at two or more epochs, to search for variations over time caused by the transverse motion of each star combined with changes in the structure in the foreground ISM. Two sets of data were used: 83 VLT- UVES spectra with approximately 6 yr between epochs and 21 McDonald observatory 2.7m telescope echelle spectra with 6 - 20 yr between epochs, over a range of scales from 0 - 360 au. The interstellar absorption-lines observed at the two epochs were subtracted and searched for any residuals due to changes in the foreground ISM. Of the 104 sightlines investigated with typically five or more components in Na I D, possible temporal variation was identified in five UVES spectra (six components), in Ca II, Ca I and/or Na I absorption-lines. The variations detected range from 7\% to a factor of 3.6 in column density. No variation was found in any other interstellar species. Most sightlines show no variation, with 3{\sigma} upper limits to changes of the order 0.1 - 0.3 dex in Ca II and Na I. These variations observed imply that fine-scale structure is present in the ISM, but at the resolution available in this study, is not very common at visible wavelengths. A determination of the electron densities and lower limits to the total number density of a sample of the sightlines implies that there is no striking difference between these parameters in sightlines with, and sightlines without, varying components.Comment: 19 pages, 11 figures, accepted for publication in MNRA

Radiative transition rates and collision strengths for Si II

Aims. This work reports radiative transition rates and electron impact excitation collision strengths for levels of the 3s23p, 3s3p2, 3s24s, and 3s23d configurations of Siii. Methods. The radiative data were computed using the Thomas-Fermi-Dirac-Amaldi central potential, but with the modifications introduced by Bautista (2008) that account for the effects of electron-electron interactions. We also introduce new schemes for the optimization of the variational parameters of the potential. Additional calculations were carried out with the Relativistic Hartree-Fock and the multiconfiguration Dirac-Fock methods. Collision strengths in LS-coupling were calculated in the close coupling approximation with the R-matrix method. Then, fine structure collision strengths were obtained by means of the intermediate-coupling frame transformation (ICFT) method which accounts for spin-orbit coupling effects. Results. We present extensive comparisons between the results of different approximations and with the most recent calculations and experiment available in the literature. From these comparisons we derive a recommended set of gf- values and radiative transition rates with their corresponding estimated uncertainties. We also study the effects of different approximations in the representation of the target ion on the electron-impact collision strengths. Our most accurate set of collision strengths were integrated over a Maxwellian distribution of electron energies and the resulting effective collision strengths are given for a wide range of temperatures. Our results present significant differences from recent calculations with the B-spline non-orthogonal R-matrix method. We discuss the sources of the differences.Comment: 6 figures, 5 tables within text, 2 electronic table

Atmospheric parameters and rotational velocities for a sample of Galactic B-type supergiants

High resolution optical spectra of 57 Galactic B-type supergiant stars have been analyzed to determine their rotational and macroturbulent velocities. In addition, their atmospheric parameters (effective temperature, surface gravity and microturbulent velocity) and surface nitrogen abundances have been estimated using a non-LTE grid of model atmospheres. Comparisons of the projected rotational velocities have been made with the predictions of stellar evolutionary models and in general good agreement was found. However for a small number of targets, their observed rotational velocities were significantly larger than predicted, although their nitrogen abundances were consistent with the rest of the sample. We conclude that binarity may have played a role in generating their large rotational velocities. No correlation was found between nitrogen abundances and the current projected rotational velocities. However a correlation was found with the inferred projected rotational velocities of the main sequence precursors of our supergiant sample. This correlation is again in agreement with the predictions of single star evolutionary models that incorporate rotational mixing. The origin of the macroturbulent and microturbulent velocity fields is discussed and our results support previous theoretical studies that link the former to sub-photospheric convection and the latter to non-radial gravity mode oscillations. In addition, we have attempted to identify differential rotation in our most rapidly rotating targets.Comment: Submitted to MNRAS, 16 page