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

Urinary tract effects of HPSE2 mutations

Urofacial syndrome (UFS) is an autosomal recessive congenital disease featuring grimacing and incomplete bladder emptying. Mutations of HPSE2, encoding heparanase 2, a heparanase 1 inhibitor, occur in UFS, but knowledge about the HPSE2 mutation spectrum is limited. Here, seven UFS kindreds with HPSE2 mutations are presented, including one with deleted asparagine 254, suggesting a role for this amino acid, which is conserved in vertebrate orthologs. HPSE2 mutations were absent in 23 non-neurogenic neurogenic bladder probands and, of 439 families with nonsyndromic vesicoureteric reflux, only one carried a putative pathogenic HPSE2 variant. Homozygous Hpse2 mutant mouse bladders contained urine more often than did wild-type organs, phenocopying human UFS. Pelvic ganglia neural cell bodies contained heparanase 1, heparanase 2, and leucine-rich repeats and immunoglobulin-like domains-2 (LRIG2), which is mutated in certain UFS families. In conclusion, heparanase 2 is an autonomic neural protein implicated in bladder emptying, but HPSE2 variants are uncommon in urinary diseases resembling UFS

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&

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