Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Diagnostic measures for sarcopenia and bone mineral density

Currently used diagnostic measures for sarcopenia utilize different measures of muscle mass, muscle strength, and physical performance. These diagnostic measures associate differently to bone mineral density (BMD), as an example of muscle-related clinical outcome. These differences should be taken into account when studying sarcopenia. Introduction: Diagnostic measures for sarcopenia utilize different measures of muscle mass, muscle strength, and physical performance. To understand differences between these measures, we determined the association with respect to whole body BMD, as an example of muscle-related clinical outcome. Methods: In the European cross-sectional study MYOAGE, 178 young (18-30 years) and 274 healthy old participants (69-81 years) were recruited. Body composition and BMD were evaluated using dual-energy X-ray densitometry. Diagnostic measures for sarcopenia were composed of lean mass as percentage of body mass, appendicular lean mass (ALM) as percentage of body mass, ALM divided by height squared (ALM/height2), knee extension torque, grip strength, walking speed, and Timed Up and Go test (TUG). Linear regression models were stratified for sex and age and adjusted for age and country, and body composition in separate models. Results: Lean mass and ALM/height2 were positively associated with BMD (P < 0.001). Significance remained in all sex and age subgroups after further adjustment for fat mass, except in old women. Lean mass percentage and ALM percentage were inversely associated with BMD in old women (P < 0.001). These inverse associations disappeared after adjustment for body mass. Knee extension torque and handgrip strength were positively associated with BMD in all subgroups (P < 0.01), except in old women. Walking speed and TUG were not related to BMD. Conclusions: The associations between diagnostic measures of sarcopenia and BMD as an example of muscle-related outcome vary widely. Differences between diagnostic measures should be taken into account when studying sarcopenia. \ua9 2013 International Osteoporosis Foundation and National Osteoporosis Foundation

MAGIC observations of the microquasar V404 Cygni during the 2015 outburst

146siThe microquasar V404 Cygni underwent a series of outbursts in 2015, June 15–31, during which its flux in hard X-rays (20–40 keV) reached about 40 times the Crab nebula flux. Because of the exceptional interest of the flaring activity from this source, observations at several wavelengths were conducted. The MAGIC telescopes, triggered by the INTEGRAL alerts, followed-up the flaring source for several nights during the period June 18–27, for more than 10 h. One hour of observation was simultaneously conducted on a giant 22 GHz radio flare and a hint of signal at GeV energies seen by Fermi-LAT. The MAGIC observations did not show significant emission in any of the analysed time intervals. The derived flux upper limit, in the energy range 200–1250 GeV, is 4.8 × 10−12 photons cm−2 s−1. We estimate the gamma-ray opacity during the flaring period, which along with our non-detection points to an inefficient acceleration in the V404 Cyg jets if a very high energy emitter is located further than 1 × 1010 cm from the compact object.openopenAhnen, M. L.; Ansoldi, S.; Antonelli, L. A.; Arcaro, C.; Babić, A.; Banerjee, B.; Bangale, P.; Barres de Almeida, U.; Barrio, J. A.; Becerra González, J.; Bednarek, W.; Bernardini, E.; Berti, A.; Biasuzzi, B.; Biland, A.; Blanch, O.; Bonnefoy, S.; Bonnoli, G.; Carosi, R.; Carosi, A.; Chatterjee, A.; Colin, P.; Colombo, E.; Contreras, J. L.; Cortina, J.; Covino, S.; Cumani, P.; Da Vela, P.; Dazzi, F.; De Angelis, A.; De Lotto, B.; de Oña Wilhelmi, E.; Di Pierro, F.; Doert, M.; Domínguez, A.; Dominis Prester, D.; Dorner, D.; Doro, M.; Einecke, S.; Eisenacher Glawion, D.; Elsaesser, D.; Engelkemeier, M.; Fallah Ramazani, V.; Fernández-Barral, A.; Fidalgo, D.; Fonseca, M. V.; Font, L.; Fruck, C.; Galindo, D.; García López, R. J.; Garczarczyk, M.; Gaug, M.; Giammaria, P.; Godinović, N.; Gora, D.; Griffiths, S.; Guberman, D.; Hadasch, D.; Hahn, A.; Hassan, T.; Hayashida, M.; Herrera, J.; Hose, J.; Hrupec, D.; Hughes, G.; Ishio, K.; Konno, Y.; Kubo, H.; Kushida, J.; Kuveždić, D.; Lelas, D.; Lindfors, E.; Lombardi, S.; Longo, F.; López, M.; Maggio, C.; Majumdar, P.; Makariev, M.; Maneva, G.; Manganaro, M.; Mannheim, K.; Maraschi, L.; Mariotti, M.; Martínez, M.; Mazin, D.; Menzel, U.; Minev, M.; Mirzoyan, R.; Moralejo, A.; Moreno, V.; Moretti, E.; Neustroev, V.; Niedzwiecki, A.; Nievas Rosillo, M.; Nilsson, K.; Ninci, D.; Nishijima, K.; Noda, K.; Nogués, L.; Paiano, S.; Palacio, J.; Paneque, D.; Paoletti, R.; Paredes, J. M.; Paredes-Fortuny, X.; Pedaletti, G.; Peresano, M.; Perri, L.; Persic, M.; Prada Moroni, P. G.; Prandini, E.; Puljak, I.; Garcia, J. R.; Reichardt, I.; Rhode, W.; Ribó, M.; Rico, J.; Saito, T.; Satalecka, K.; Schroeder, S.; Schweizer, T.; Sillanpää, A.; Sitarek, J.; Šnidarić, I.; Sobczynska, D.; Stamerra, A.; Strzys, M.; Surić, T.; Takalo, L.; Tavecchio, F.; Temnikov, P.; Terzić, T.; Tescaro, D.; Teshima, M.; Torres, D. F.; Torres-Albà, N.; Treves, A.; Vanzo, G.; Vazquez Acosta, M.; Vovk, I.; Ward, J. E.; Will, M.; Zarić, D.; Collaboration), (The MAGIC; Loh, A.; Rodriguez, J.Ahnen, M. L.; Ansoldi, S.; Antonelli, L. A.; Arcaro, C.; Babić, A.; Banerjee, B.; Bangale, P.; Barres de Almeida, U.; Barrio, J. A.; Becerra González, J.; Bednarek, W.; Bernardini, E.; Berti, Alessio; Biasuzzi, B.; Biland, A.; Blanch, O.; Bonnefoy, S.; Bonnoli, G.; Carosi, R.; Carosi, A.; Chatterjee, A.; Colin, P.; Colombo, E.; Contreras, J. L.; Cortina, J.; Covino, S.; Cumani, P.; Da Vela, P.; Dazzi, F.; De Angelis, A.; De Lotto, B.; de Oña Wilhelmi, E.; Di Pierro, F.; Doert, M.; Domínguez, A.; Dominis Prester, D.; Dorner, D.; Doro, M.; Einecke, S.; Eisenacher Glawion, D.; Elsaesser, D.; Engelkemeier, M.; Fallah Ramazani, V.; Fernández Barral, A.; Fidalgo, D.; Fonseca, M. V.; Font, L.; Fruck, C.; Galindo, D.; García López, R. J.; Garczarczyk, M.; Gaug, M.; Giammaria, P.; Godinović, N.; Gora, D.; Griffiths, S.; Guberman, D.; Hadasch, D.; Hahn, A.; Hassan, T.; Hayashida, M.; Herrera, J.; Hose, J.; Hrupec, D.; Hughes, G.; Ishio, K.; Konno, Y.; Kubo, H.; Kushida, J.; Kuveždić, D.; Lelas, D.; Lindfors, E.; Lombardi, S.; Longo, Francesco; López, M.; Maggio, C.; Majumdar, P.; Makariev, M.; Maneva, G.; Manganaro, M.; Mannheim, K.; Maraschi, L.; Mariotti, M.; Martínez, M.; Mazin, D.; Menzel, U.; Minev, M.; Mirzoyan, R.; Moralejo, A.; Moreno, V.; Moretti, E.; Neustroev, V.; Niedzwiecki, A.; Nievas Rosillo, M.; Nilsson, K.; Ninci, D.; Nishijima, K.; Noda, K.; Nogués, L.; Paiano, S.; Palacio, J.; Paneque, D.; Paoletti, R.; Paredes, J. M.; Paredes Fortuny, X.; Pedaletti, G.; Peresano, M.; Perri, L.; Persic, M.; Prada Moroni, P. G.; Prandini, E.; Puljak, I.; Garcia, J. R.; Reichardt, I.; Rhode, W.; Ribó, M.; Rico, J.; Saito, T.; Satalecka, K.; Schroeder, S.; Schweizer, T.; Sillanpää, A.; Sitarek, J.; Šnidarić, I.; Sobczynska, D.; Stamerra, A.; Strzys, M.; Surić, T.; Takalo, L.; Tavecchio, F.; Temnikov, P.; Terzić, T.; Tescaro, D.; Teshima, M.; Torres, D. F.; Torres Albà, N.; Treves, A.; Vanzo, G.; Vazquez Acosta, M.; Vovk, I.; Ward, J. E.; Will, M.; Zarić, D.; Collaboration), (The MAGIC; Loh, A.; Rodriguez, J

Discovery of VHE\u3b3-rays from the blazar 1ES\ua01215+303 with the MAGIC telescopes and simultaneous multi-wavelength observations

Context. We present the discovery of very high energy (VHE, E > 100GeV) gamma-ray emission from the BL Lac object 1ES 1215+303 by the MAGIC telescopes and simultaneous multi-wavelength data in a broad energy range from radio to gamma-rays. Aims. We study the VHE gamma-ray emission from 1ES 1215+303 and its relation to the emissions in other wavelengths. Methods. Triggered by an optical outburst, MAGIC observed the source in January-February 2011 for 20.3 hrs. The target was monitored in the optical R-band by the KVA telescope that also performed optical polarization measurements. We triggered target of opportunity observations with the Swift satellite and obtained simultaneous and quasi-simultaneous data from the Fermi Large Area Telescope and from the Mets\"ahovi radio telescope. We also present the analysis of older MAGIC data taken in 2010. Results. The MAGIC observations of 1ES 1215+303 carried out in January-February 2011 resulted in the first detection of the source at VHE with a statistical significance of 9.4 sigma. Simultaneously, the source was observed in a high optical and X-ray state. In 2010 the source was observed in a lower state in optical, X-ray, and VHE, while the GeV gamma-ray flux and the radio flux were comparable in 2010 and 2011. The spectral energy distribution obtained with the 2011 data can be modeled with a simple one zone SSC model, but it requires extreme values for the Doppler factor or the electron energy distribution.Comment: 10 pages, 8 figures, accepted to A&

Very-high-energy gamma rays from a distant quasar: How transparent is the universe?

The atmospheric Cherenkov gamma- ray telescope MAGIC, designed for a low- energy threshold, has detected very- high- energy gamma rays from a giant flare of the distant Quasi- Stellar Radio Source ( in short: radio quasar) 3C 279, at a distance of more than 5 billion light- years ( a redshift of 0.536). No quasar has been observed previously in very- high- energy gamma radiation, and this is also the most distant object detected emitting gamma rays above 50 gigaelectron volts. Because high- energy gamma rays may be stopped by interacting with the diffuse background light in the universe, the observations by MAGIC imply a low amount for such light, consistent with that known from galaxy counts

MAGIC discovery of Very High Energy Emission from the FSRQ PKS 1222+21

Very High Energy (VHE) gamma-ray emission from the flat spectrum radio quasar (FSRQ) PKS 1222+21 (4C 21.35, z=0.432) was detected with the MAGIC Cherenkov telescopes during a short observation (~0.5 hr) performed on 2010 June 17. The MAGIC detection coincides with high energy MeV/GeV gamma-ray activity measured by the Large Area Telescope (LAT) on board the Fermi satellite. The VHE spectrum measured by MAGIC extends from about 70 GeV up to at least 400 GeV and can be well described by a power law dN/dE \propto E^-Gamma with a photon index Gamma= 3.75+/-0.27stat +/-0.2syst. The averaged integral flux above 100 GeV is (4.56+/-0.46)x10^(-10) cm^-2 s^-1 (~1 Crab Nebula flux). The VHE flux measured by MAGIC varies significantly within the 30 min exposure implying a flux doubling time of about 10 min. The VHE and MeV/GeV spectra, corrected for the absorption by the extragalactic background light (EBL), can be described by a single power law with photon index 2.72+/-0.34 between 3 GeV and 400 GeV, and is consistent with emission belonging to a single component in the jet. The absence of a spectral cutoff constrains the gamma-ray emission region outside the Broad Line Region, which would otherwise absorb the VHE gamma-rays. Together with the detected fast variability, this challenges present emission models from jets in FSRQ. Moreover, the combined Fermi/LAT and MAGIC spectral data yield constraints on the density of the Extragalactic Background Light in the UV-optical to near-infrared range that are compatible with recent models.Comment: 6 pages, 5 figur

Prospects for Cherenkov Telescope Array Observations of the Young Supernova Remnant RX J1713.7 123946

We perform simulations for future Cherenkov Telescope Array (CTA) observations of RX J1713.7 123946, a young supernova remnant (SNR) and one of the brightest sources ever discovered in very high energy (VHE) gamma rays. Special attention is paid to exploring possible spatial (anti)correlations of gamma rays with emission at other wavelengths, in particular X-rays and CO/H i emission. We present a series of simulated images of RX J1713.7 123946 for CTA based on a set of observationally motivated models for the gamma-ray emission. In these models, VHE gamma rays produced by high-energy electrons are assumed to trace the nonthermal X-ray emission observed by XMM-Newton, whereas those originating from relativistic protons delineate the local gas distributions. The local atomic and molecular gas distributions are deduced by the NANTEN team from CO and H i observations. Our primary goal is to show how one can distinguish the emission mechanism(s) of the gamma rays (i.e., hadronic versus leptonic, or a mixture of the two) through information provided by their spatial distribution, spectra, and time variation. This work is the first attempt to quantitatively evaluate the capabilities of CTA to achieve various proposed scientific goals by observing this important cosmic particle accelerator