Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Optical properties of tungsten thin films perforated with a bidimensional array of subwavelength holes

We present a theorical investigation of the optical transmission of a dielectric grating carved in a tungsten layer. For appropriate wavelengths tungsten shows indeed a dielectric behaviour. Our numerical simulations leads to theoretical results similar to those found with metallic systems studied in earlier works. The interpretation of our results rests on the idea that the transmission is correlated with the resonant response of eigenmodes coupled to evanescent diffraction orders.Comment: 4 pages, 3 figure

The effect of pressure on statics, dynamics and stability of multielectron bubbles

The effect of pressure and negative pressure on the modes of oscillation of a multi-electron bubble in liquid helium is calculated. Already at low pressures of the order of 10-100 mbar, these effects are found to significantly modify the frequencies of oscillation of the bubble. Stabilization of the bubble is shown to occur in the presence of a small negative pressure, which expands the bubble radius. Above a threshold negative pressure, the bubble is unstable.Comment: 4 pages, 2 figures, accepted for publication in Physical Review Letter

Cultural basis of social ‘deficits’ in autism spectrum disorders

There is very little research that specifically looks at how autism spectrum disorders are perceived in various communities. This qualitative research was conducted with parents who had children on the autistic spectrum belonging to four different ethnic communities (White British, Somali, West African and South Asian- 63 in total) and living in the UK. The study found that the importance that the parents give to various social skills varied on the basis of their cultural background and the gender of the parent. This is an important aspect to consider while providing support and services to individuals on the autism spectrum and their family members if the services have to be appropriate for their needs. This consideration would also enable the individuals on the autism spectrum to develop appropriate social skills required within their cultural groups. This is a preliminary study and further research on the topic is required

Mid-Infrared Spectral Diagnostics of Luminous Infrared Galaxies

We present a statistical analysis of the mid-infrared (MIR) spectra of 248 luminous infrared (IR) galaxies (LIRGs) which comprise the Great Observatories All-sky LIRG Survey (GOALS) observed with the Infrared Spectrograph (IRS) on-board the Spitzer Space Telescope. The GOALS sample enables a direct measurement of the relative contributions of star-formation and active galactic nuclei (AGN) to the total IR emission from a large sample of local LIRGs. The AGN contribution to the MIR emission (f-AGN) is estimated by employing several diagnostics based on the properties of the [NeV], [OIV] and [NeII] fine structure gas emission lines, the 6.2 microns PAH and the shape of the MIR continuum. We find that 18% of all LIRGs contain an AGN and that in 10% of all sources the AGN contributes more than 50% of the total IR luminosity. Summing up the total IR luminosity contributed by AGN in all our sources suggests that AGN supply ~12% of the total energy emitted by LIRGs. The average spectrum of sources with an AGN looks similar to the average spectrum of sources without an AGN, but it has lower PAH emission and a flatter MIR continuum. AGN dominated LIRGs have higher IR luminosities, warmer MIR colors and are found in interacting systems more often than pure starbursts LIRGs. However we find no linear correlations between these properties and f-AGN. We used the IRAC colors of LIRGs to confirm that finding AGN on the basis of their MIR colors may miss ~40% of AGN dominated (U)LIRGsComment: accepted for publication in ApJ, 34 pages, 12 figure

Crystalline Assemblies and Densest Packings of a Family of Truncated Tetrahedra and the Role of Directional Entropic Forces

Polyhedra and their arrangements have intrigued humankind since the ancient Greeks and are today important motifs in condensed matter, with application to many classes of liquids and solids. Yet, little is known about the thermodynamically stable phases of polyhedrally-shaped building blocks, such as faceted nanoparticles and colloids. Although hard particles are known to organize due to entropy alone, and some unusual phases are reported in the literature, the role of entropic forces in connection with polyhedral shape is not well understood. Here, we study thermodynamic self-assembly of a family of truncated tetrahedra and report several atomic crystal isostructures, including diamond, {\beta}-tin, and high- pressure lithium, as the polyhedron shape varies from tetrahedral to octahedral. We compare our findings with the densest packings of the truncated tetrahedron family obtained by numerical compression and report a new space filling polyhedron, which has been overlooked in previous searches. Interestingly, the self-assembled structures differ from the densest packings. We show that the self-assembled crystal structures can be understood as a tendency for polyhedra to maximize face-to-face alignment, which can be generalized as directional entropic forces.Comment: Article + supplementary information. 23 pages, 10 figures, 2 table

Investigation of Dual Active Nuclei, Outflows, Shock-Heated Gas, and Young Star Clusters in Markarian 266

Results of observations with the Spitzer, Hubble, GALEX, Chandra, and XMM-Newton space telescopes are presented for the Luminous Infrared Galaxy (LIRG) merger Mrk 266. The SW (Seyfert 2) and NE (LINER) nuclei reside in galaxies with Hubble types SBb (pec) and S0/a (pec), respectively. Both galaxies have L > L*, and they are inferred to each contain a ~2.5x10^8 M_sun black hole. Mrk 266 SW is likely the primary source of a bright Fe K-alpha line detected from the system, consistent with the reflection-dominated X-ray spectrum of a heavily obscured AGN. Optical knots embedded in an arc with aligned radio continuum radiation, combined with luminous H_2 line emission, provide evidence for a radiative bow shock in an AGN-driven outflow surrounding the NE nucleus. Soft X-ray emission modeled as shock-heated plasma is co-spatial with radio continuum emission between the galaxies. Mid-IR diagnostics indicate roughly equal contributions of AGN and starburst radiation powering the bolometric luminosity. Approximately 120 star clusters have been detected, with most having estimated ages < 50 Myr. Detection of 24 micron emission extending ~34 arcsec (20 kpc) north of the galaxies is interpreted as ~2x10^7 M_sun of dust entrained in an outflowing superwind; at optical wavelengths this region is resolved into a fragmented morphology indicative of Rayleigh-Taylor instabilities in an expanding shell of ionized gas. Mrk 266 demonstrates that the dust "blow-out" phase can begin in a LIRG well before the galaxies fully coalesce during a subsequent ULIRG phase, and rapid gas consumption in luminous dual AGNs (kpc scale separations) early in the merger process may explain the paucity of detected binary QSOs (sub-pc scale orbits) in large surveys. An evolutionary sequence is proposed representing a progression from dual to binary AGNs, accompanied by an increase in observed L_x/L_ir ratios by 10^4 or more.Comment: Accepted for publication in the Astronomical Journal, 40 pages, 31 figures, 15 table

Do adults with high functioning autism or Asperger Syndrome differ in empathy and emotion recognition?

The present study examined whether adults with high functioning autism (HFA) showed greater difficulties in (i) their self-reported ability to empathise with others and/or (ii) their ability to read mental states in others’ eyes than adults with Asperger syndrome (AS). The Empathy Quotient (EQ) and ‘Reading the Mind in the Eyes’ Test (Eyes Test) were compared in 43 adults with AS and 43 adults with HFA. No significant difference was observed on EQ score between groups, while adults with AS performed significantly better on the Eyes Test than those with HFA. This suggests that adults with HFA may need more support, particularly in mentalizing and complex emotion recognition, and raises questions about the existence of subgroups within autism spectrum conditions

Theory of extraordinary optical transmission through subwavelength hole arrays

We present a fully three-dimensional theoretical study of the extraordinary transmission of light through subwavelength hole arrays in optically thick metal films. Good agreement is obtained with experimental data. An analytical minimal model is also developed, which conclusively shows that the enhancement of transmission is due to tunneling through surface plasmons formed on each metal-dielectric interfaces. Different regimes of tunneling (resonant through a ''surface plasmon molecule", or sequential through two isolated surface plasmons) are found depending on the geometrical parameters defining the system.Comment: 4 pages, 4 figure

The Buried Starburst in the Interacting Galaxy II Zw 096 as Revealed by the Spitzer Space Telescope

An analysis of data from the Spitzer Space Telescope, Hubble Space Telescope, Chandra X-ray Observatory, and AKARI Infrared Astronomy Satellite is presented for the z = 0.036 merging galaxy system II Zw 096 (CGCG 448-020). Because II Zw 096 has an infrared luminosity of log(L_(IR)/L_☉) = 11.94, it is classified as a Luminous Infrared Galaxy (LIRG), and was observed as part of the Great Observatories All-sky LIRG Survey (GOALS). The Spitzer data suggest that 80% of the total infrared luminosity comes from an extremely compact, red source not associated with the nuclei of the merging galaxies. The Spitzer mid-infrared spectra indicate no high-ionization lines from a buried active galactic nucleus in this source. The strong detection of the 3.3 μm and 6.2 μm polycyclic aromatic hydrocarbon emission features in the AKARI and Spitzer spectra also implies that the energy source of II Zw 096 is a starburst. Based on Spitzer infrared imaging and AKARI near-infrared spectroscopy, the star formation rate is estimated to be 120 M_☉ yr^(-1) and >45 M_☉ yr^(-1), respectively. Finally, the high-resolution B-, I-, and H-band images show many star clusters in the interacting system. The colors of these clusters suggest at least two populations—one with an age of 1-5 Myr and one with an age of 20-500 Myr, reddened by 0-2 mag of visual extinction. The masses of these clusters span a range between 10^6 and 10^8 M_☉. This starburst source is reminiscent of the extranuclear starburst seen in NGC 4038/9 (the Antennae Galaxies) and Arp 299 but approximately an order of magnitude more luminous than the Antennae. The source is remarkable in that the off-nuclear infrared luminosity dominates the entire system