BioCIDER: a Contextualisation InDEx for biological Resources discovery

Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded

Water maser variability over 20 years in a large sample of star-forming regions: the complete database

Context. Water vapor emission at 22 GHz from masers associated with star-forming regions is highly variable. Aims. We present a database of up to 20 years of monitoring of a sample of 43 masers within star-forming regions. The sample covers a large range of luminosities of the associated IRAS source and is representative of the entire population of H2O masers of this type. The database forms a good starting point for any further study of H2O maser variability. Methods. The observations were obtained with the Medicina 32-m radiotelescope, at a rate of 4-5 observations per year. Results. To provide a database that can be easily accessed through the web, we give for each source: plots of the calibrated spectra, the velocity-time-flux density plot, the light curve of the integrated flux, the lower and upper envelopes of the maser emission, the mean spectrum, and the rate of the maser occurrence as a function of velocity. Figures for just one source are given in the text for representative purposes. Figures for all the sources are given in electronic form in the on-line appendix. A discussion of the main properties of the H2O variability in our sample will be presented in a forthcoming paper.Comment: 11 pages, 9 figures, to be published in Astronomy and Astrophysics; all plots in appendix (not included) can be downloaded from http://www.arcetri.astro.it/~starform/water_maser_v2.html or http://www.ira.inaf.it/papers/masers/water_maser_v2.htm

SPS’ Digest: the Swiss Proteomics Society selection of proteomics articles

Despite the consolidation of the specialized proteomics literature around a few established journals, such as Proteomics, Molecular and Cellular Proteomics, and the Journal of Proteome Research, a lot of information is still spread in many different publications from different fields, such as analytical sciences, MS, bioinformatics, etc. The purpose of SPS’ Digest is to gather a selection of proteomics articles, to categorize them, and to make the list available on a periodic basis through a web page and email alerts

VLA Observations of H2O Masers in the Class 0 Protostar S106 FIR: Evidence for a 10 AU-Scale Accelerating Jet-like Flow

We conducted VLA observations at 0".06 resolution of the 22 GHz water masers toward the Class 0 source S106 FIR (d=600 pc; 15" west of S106-IRS4) on two epochs separated by ~3 months. Two compact clusters of the maser spots were found in the center of the submillimeter core of S106 FIR. The separation of the clusters was ~80 mas (48 AU) along P. A. = 70 degrees and the size of each cluster was ~20 mas x 10 mas. The western cluster, which had three maser components, was 7.0 km/s redshifted with respect to the ambient cloud velocity. Each component was composed of a few spatially localized maser spots and was aligned on a line connecting the clusters. We found relative proper motions of the components with ~30 mas/yr (18 AU/yr) along the line. In addition, a series of single-dish observations show that the maser components drifted with a radial acceleration of ~1 km/s/yr. These facts indicate that the masers could be excited by a 10 AU-scale jet-like accelerating flow ejected from an assumed protostar located between the two clusters. The outflow size traced by the masers was 50 AU x 5 AU after correction for an inclination angle of 10 degrees which was derived from the relative proper motions and radial velocities of the maser components. The three-dimensional outflow velocity ranged from 40 to 70 km/s assuming symmetric motions for the blue and red components. Since no distinct CO molecular outflows have been detected so far, we suggest that S106 FIR is an extremely young protostar observed just after the onset of outflowing activity.Comment: 24 pages, 6 figures, No. 5 color. Accepted, Astrophysical Journa

Supersonic water masers in 30 Doradus

We report on extremely high velocity molecular gas, up to -80 km/s relative to the ambient medium, in the giant star-formation complex 30 Doradus in the Large Magellanic Cloud (LMC), as observed in new 22 GHz H2O maser emission spectra obtained with the Mopra radio telescope. The masers may trace the velocities of protostars, and the observed morphology and kinematics indicate that current star formation occurs near the interfaces of colliding stellar-wind blown bubbles. The large space velocities of the protostars and associated gas could result in efficient mixing of the LMC. A similar mechanism in the Milky Way could seed the galactic halo with relatively young stars and gas.Comment: 11 pages plus 1 PS and 1 EPS figure, uses AASTeX preprint style; accepted for publication in Astrophysical Journal Letter

A high-sensitivity 6.7 GHz methanol maser survey toward H2O sources

We present the results of a high sensitivity survey for 6.7 GHz methanol masers towards 22 GHz water maser using the 100 m Efflesberg telescope. A total of 89 sources were observed and 10 new methanol masers were detected. The new detections are relatively faint with peak flux densities between 0.5 and 4.0 Jy. A nil detection rate from low-mass star forming regions enhances the conclusion that the masers are only associated with massive star formation. Even the faintest methanol maser in our survey, with a luminosity of 1.1 $10^{-9} L_\odot$ is associated with massive stars as inferred from its infrared luminosity.Comment: Accepted for publication in A&

Sexual Signalling in Propithecus verreauxi: Male “Chest Badge” and Female Mate Choice

Communication, an essential prerequisite for sociality, involves the transmission of signals. A signal can be defined as any action or trait produced by one animal, the sender, that produces a change in the behaviour of another animal, the receiver. Secondary sexual signals are often used for mate choice because they may inform on a potential partner's quality. Verreaux's sifaka (Propithecus verreauxi) is characterized by the presence of two different morphs of males (bimorphism), which can show either a stained or clean chest. The chest becomes stained by secretions of the sternal gland during throat marking (rubbing throat and chest on a vertical substrate while smearing the scent deposition). The role of the chest staining in guiding female mate choice was previously hypothesized but never demonstrated probably due to the difficulty of observing sifaka copulations in the wild. Here we report that stained-chested males had a higher throat marking activity than clean-chested males during the mating season, but not during the birth season. We found that females copulated more frequently with stained-chested males than the clean-chested males. Finally, in agreement with the biological market theory, we found that clean-chested males, with a lower scent-releasing potential, offered more grooming to females. This “grooming for sex” tactic was not completely unsuccessful; in fact, half of the clean-chested males copulated with females, even though at low frequency. In conclusion, the chest stain, possibly correlated with different cues targeted by females, could be one of the parameters which help females in selecting mates

Severe Aortic Stenosis and Myocardial Function: Diagnostic and Prognostic Usefulness of Ultrasonic Integrated Backscatter Analysis

Background— The aim of this study was to assess the myocardial reflectivity pattern in severe aortic valve stenosis through the use of integrated backscatter (IBS) analysis. Patients with aortic stenosis (AS) were carefully selected in the Department of Cardiology. Methods and Results— Thirty-five subjects (AS: valve orifice ≤1 cm2; 12 female; mean age, 71.8±6.2 years) and 25 healthy subjects were studied. All subjects of the study had conventional 2D-Doppler echocardiography and IBS. Backscatter signal was sampled at the septum and posterior wall levels. Patients with AS were divided into 2 groups: 16 patients with initial signs of congestive heart failure and a depressed left ventricular systolic function (DSF) (ejection fraction [EF] range, 35% to 50%) and 19 asymptomatic patients with normal left ventricular systolic function (NSF) (EF >50%). Myocardial echo intensity (pericardium related) was significantly higher at the septum and posterior wall levels in DSF than in NSF and in control subjects. IBS variation, as an expression of variation of the signal, appeared to be significantly lower in AS with DSF than in NSF and in control subjects, at both the septum and posterior wall levels. Patients with DSF underwent aortic valve replacement, and, during surgical intervention, a septal myocardial biopsy was made for evaluation of myocardium/fibrosis ratio. Abnormally increased echo intensity was detected in left ventricular pressure overload by severe aortic stenosis and correlated with increase of myocardial collagen content (operating biopsy). Conclusions— One year after aortic valve replacement, we observed a significant reduction of left ventricular mass, and, only if pericardial indexed IBS value (reduction of interstitial fibrosis) decreased, it was possible to observe an improvement of EF and of IBS variation

Massive Stars: Their Environment and Formation

Cloud environment is thought to play a critical role in determining the mechanism of formation of massive stars. In this contribution we review the physical characteristics of the environment around recently formed massive stars. Particular emphasis is given to recent high angular resolution observations which have improved our knowledge of the physical conditions and kinematics of compact regions of ionized gas and of dense and hot molecular cores associated with luminous O and B stars. We will show that this large body of data, gathered during the last decade, has allowed significant progress in the understanding of the physical processes that take place during the formation and early evolution of massive stars.Comment: Pub. Astron. Soc. of Pacific (Invited Review), 95 pages (Latex), 5 pages (tables, Latex), 11 postscript or gif figure

The GOBLET training portal: A global repository of bioinformatics training materials, courses and trainers

Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide