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

Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations

Osteoarthritis affects over 300 million people worldwide. Here, we conduct a genome-wide association study meta-analysis across 826,690 individuals (177,517 with osteoarthritis) and identify 100 independently associated risk variants across 11 osteoarthritis phenotypes, 52 of which have not been associated with the disease before. We report thumb and spine osteoarthritis risk variants and identify differences in genetic effects between weight-bearing and non-weight-bearing joints. We identify sex-specific and early age-at-onset osteoarthritis risk loci. We integrate functional genomics data from primary patient tissues (including articular cartilage, subchondral bone, and osteophytic cartilage) and identify high-confidence effector genes. We provide evidence for genetic correlation with phenotypes related to pain, the main disease symptom, and identify likely causal genes linked to neuronal processes. Our results provide insights into key molecular players in disease processes and highlight attractive drug targets to accelerate translation

Reliability of non-invasive cardiac output measurement in individuals with tetraplegia

Study design:The study is conducted on the basis of comparative-repeated measures.Objectives:The objective of this study is to assess the reliability of non-invasive cardiac output (CO) measurements in individuals with tetraplegia (TP) at rest and during exercise using Innocor, and to test the hypothesis that CO measurements are less reliable in TP than in able-bodied (AB) individuals.Setting:Ambulatory volunteers, Switzerland.Methods:Nine male motor-complete TP (C5-C7) and nine pair-matched AB performed repeated CO measurements at rest and during submaximal arm-crank and wheelchair exercises in four different test sessions. Within- and between-day reliabilities were compared between TP and AB.Results:Mean differences between measurements at rest (TP vs AB, within-day: 0.1±0.5 vs 0.2±0.6 l min(-1), between-day: -0.7±0.6 vs -0.1±0.8 l min(-1)), during arm-crank (TP vs AB, within-day: 0.1±0.9 vs 0.5±0.7 l min(-1), between-day: -0.3±1.1 vs 0.0±1.1 l min(-1)) and wheelchair exercises (TP vs AB, within-day: 0.3±1.2 vs -0.1±0.8 l min(-1), between-day: 0.1±1.1 vs 0.5±0.9 l min(-1)) were not significantly different between TP and AB (all P>0.05). Coefficients of variation in TP (within-day, rest: 6.8%, arm-crank: 9.6% and wheelchair: 10.8%; between-day, rest: 11.9%, arm-crank: 11.2% and wheelchair: 10.3%) and in AB (within-day, rest: 7.7%, arm crank: 6.8% and wheelchair: 6.0%; between-day, rest: 9.2%, arm crank: 8.5% and wheelchair: 8.0%) indicated acceptable reliability.Conclusion:In contrast to our hypothesis, we found non-invasive CO measurements using Innocor to be as reliable in TP as they are in AB. Consequently, Innocor can be recommended for repeated assessments of CO in TP within routine diagnostics or for evaluation of training progress.Sponsorship:The study was supported by the Swiss National Science Foundation (Grant no. 32-116777).Spinal Cord advance online publication, 21 December 2010; doi:10.1038/sc.2010.173