BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature

<p>Abstract</p> <p>Background</p> <p>The rapid evolution of Internet technologies and the collaborative approaches that dominate the field have stimulated the development of numerous bioinformatics resources. To address this new framework, several initiatives have tried to organize these services and resources. In this paper, we present the BioInformatics Resource Inventory (BIRI), a new approach for automatically discovering and indexing available public bioinformatics resources using information extracted from the scientific literature. The index generated can be automatically updated by adding additional manuscripts describing new resources. We have developed web services and applications to test and validate our approach. It has not been designed to replace current indexes but to extend their capabilities with richer functionalities.</p> <p>Results</p> <p>We developed a web service to provide a set of high-level query primitives to access the index. The web service can be used by third-party web services or web-based applications. To test the web service, we created a pilot web application to access a preliminary knowledge base of resources. We tested our tool using an initial set of 400 abstracts. Almost 90% of the resources described in the abstracts were correctly classified. More than 500 descriptions of functionalities were extracted.</p> <p>Conclusion</p> <p>These experiments suggest the feasibility of our approach for automatically discovering and indexing current and future bioinformatics resources. Given the domain-independent characteristics of this tool, it is currently being applied by the authors in other areas, such as medical nanoinformatics. BIRI is available at <url>http://edelman.dia.fi.upm.es/biri/</url>.</p

Accuracy of a method based on atomic absorption spectrometry to determine inorganic arsenic in food : Outcome of the collaborative trial IMEP-41

Peer reviewedPublisher PD

e-MIR2: a public online inventory of medical informatics resources

Background. Over the last years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for Medical Informatics (MI) field, so that locating and accessing them currently remains a hard and time-consuming task. Description. We have created a repository of MI resources from the scientific literature, providing free access to its contents through a web-based service. Relevant information describing the resources is automatically extracted from manuscripts published in top-ranked MI journals. We used a pattern matching approach to detect the resources? names and their main features. Detected resources are classified according to three different criteria: functionality, resource type and domain. To facilitate these tasks, we have built three different taxonomies by following a novel approach based on folksonomies and social tagging. We adopted the terminology most frequently used by MI researchers in their publications to create the concepts and hierarchical relationships belonging to the taxonomies. The classification algorithm identifies the categories associated to resources and annotates them accordingly. The database is then populated with this data after manual curation and validation. Conclusions. We have created an online repository of MI resources to assist researchers in locating and accessing the most suitable resources to perform specific tasks. The database contained 282 resources at the time of writing. We are continuing to expand the number of available resources by taking into account further publications as well as suggestions from users and resource developers

A Search for Dark Matter Annihilation with the Whipple 10m Telescope

We present observations of the dwarf galaxies Draco and Ursa Minor, the local group galaxies M32 and M33, and the globular cluster M15 conducted with the Whipple 10m gamma-ray telescope to search for the gamma-ray signature of self-annihilating weakly interacting massive particles (WIMPs) which may constitute astrophysical dark matter (DM). We review the motivations for selecting these sources based on their unique astrophysical environments and report the results of the data analysis which produced upper limits on excess rate of gamma rays for each source. We consider models for the DM distribution in each source based on the available observational constraints and discuss possible scenarios for the enhancement of the gamma-ray luminosity. Limits on the thermally averaged product of the total self-annihilation cross section and velocity of the WIMP, , are derived using conservative estimates for the magnitude of the astrophysical contribution to the gamma-ray flux. Although these limits do not constrain predictions from the currently favored theoretical models of supersymmetry (SUSY), future observations with VERITAS will probe a larger region of the WIMP parameter phase space, and WIMP particle mass (m_\chi).Comment: 33 pages, 12 figures, accepted for publication in the Astrophysical Journa

Multiwavelength Observations of the Gamma-Ray Blazar PKS 0528+134 in Quiescence

We present multiwavelength observations of the ultraluminous blazar-type radio loud quasar PKS 0528+134 in quiescence during the period July to December 2009. Significant flux variability on a time scale of several hours was found in the optical regime, accompanied by a weak trend of spectral softening with increasing flux. We suggest that this might be the signature of a contribution from the accretion disk at the blue end of the optical spectrum. The optical flux is weakly polarized with rapid variations of the degree and direction of polarization, while the polarization of the 43 GHz radio core remains steady. Optical spectropolarimetry suggests a trend of increasing degree of polarization with increasing wavelength, providing additional evidence for an accretion disc contribution towards the blue end of the optical spectrum. We constructed four SEDs indicating that even in the quiescent state, the bolometric luminosity of PKS 0528+134 is dominated by its gamma-ray emission. A leptonic single-zone jet model produced acceptable fits to the SEDs with contributions to the high-energy emission from synchrotron self-Compton radiation and Comptonization of direct accretion disk emission. Fit parameters close to equipartition were obtained. The moderate variability on long time scales implies the existence of on-going particle acceleration, while the observed optical polarization variability seems to point towards a turbulent acceleration process. Turbulent particle acceleration at stationary features along the jet therefore appears to be a viable possibility for the quiescent state of PKS 0528+134.Comment: Accepted for Publication in The Astrophysical Journal. - Acknowledgement adde

Accuracy of a method based on atomic absorption spectrometry to determine inorganic arsenic in food: outcome of the collaborative trial IMEP-41

A collaborative trial was conducted to determine the performance characteristics of an analytical method for the quantification of inorganic arsenic (iAs) in food. The method is based on (i) solubilisation of the protein matrix with concentrated hydrochloric acid to denature proteins and allow the release of all arsenic species into solution, and (ii) subsequent extraction of the inorganic arsenic present in the acid medium using chloroform followed by back-extraction to acidic medium. The final detection and quantification is done by flow injection hydride generation atomic absorption spectrometry (FI-HG-AAS). The seven test items used in this exercise were reference materials covering a broad range of matrices: mussels, cabbage, seaweed (hijiki), fish protein, rice, wheat, mushrooms, with concentrations ranging from 0.074 to 7.55 mg kg(-1). The relative standard deviation for repeatability (RSDr) ranged from 4.1 to 10.3%, while the relative standard deviation for reproducibility (RSDR) ranged from 6.1 to 22.8%. (C) 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

The TeV spectrum of H1426+428

The BL Lac object H1426+428 was recently detected as a high energy gamma-ray source by the VERITAS collaboration (Horan et al. 2002). We have reanalyzed the 2001 portion of the data used in the detection in order to examine the spectrum of H1426+428 above 250 GeV. We find that the time-averaged spectrum agrees with a power law of the shape dF/dE = 10^(-7.31 +- 0.15(stat) +- 0.16(syst)) x E^(-3.50 +- 0.35(stat) +- 0.05(syst)) m^(-2)s^(-1)TeV^(-1) The statistical evidence from our data for emission above 2.5 TeV is 2.6 sigma. With 95% c.l., the integral flux of H1426+428 above 2.5 TeV is larger than 3% of the corresponding flux from the Crab Nebula. The spectrum is consistent with the (non-contemporaneous) measurement by Aharonian et al. (2002) both in shape and in normalization. Below 800 GeV, the data clearly favours a spectrum steeper than that of any other TeV Blazar observed so far indicating a difference in the processes involved either at the source or in the intervening space.Comment: LaTeX, 8 pages, 4 figures, accepted for publication in Ap

FERO: Finding Extreme Relativistic Objects. I. Statistics of Relativistic Fe Kalpha lines in Radio-Quiet Type 1 AGN

Accretion models predict that fluorescence lines broadened by relativistic effects should arise from reflection of X-ray emission onto the inner region of the accretion disc surrounding the central black hole of active galactic nuclei (AGN). The theory behind the origin of relativistic lines is well established, and observational evidence from a moderate number of sources seems to support the existence of these lines. The aim of this work is to establish the fraction of AGN with relativistic Fe Kalpha lines, and study possible correlations with source physical properties. An XMM-Newton collection of 149 radio-quiet Type 1 AGN has been systematically and uniformly analyzed in order to search for significant evidence of a relativistically broadened Fe Kalpha line. To enable statistical studies, an almost complete, flux-limited subsample of 31 sources has been defined. The 2-10 keV spectra of the FERO sources have been compared with a complex model including most of the physical components observed in the X-ray spectra of Seyfert galaxies: a power law primary continuum modified by non-relativistic Compton reflection and warm absorption, plus a series of narrow Fe line reflection features. The observed fraction of sources in the flux-limited sample that show significant evidence of a relativistic Fe Kalpha line is 36%. The average line Equivalent Width (EW) is of the order of 100 eV, while the average disc inclination angle is 28+/-5 deg and the average power-law index of the radial disc emissivity law is 2.4+/-0.4. The spin value is well constrained only in 2 cases (MCG-6-30-15 and MRK509), and in the rest of the cases, whenever a constraint can be placed, it always implies the rejection of the static black hole solution. The Fe Kalpha line EW does not correlate with disc parameters or with system physical properties, such as black hole mass, accretion rate and hard X-ray luminosity.Comment: 22 pages, 7 figures. Accepted for publication in A&