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

Aerodynamic performance of the feathered dinosaur Microraptor and the evolution of feathered flight

Understanding the aerodynamic performance of feathered, non-avialan dinosaurs is critical to reconstructing the evolution of bird flight. Here we show that the Early Cretaceous five-winged paravian Microraptor is most stable when gliding at high-lift coefficients (low lift/drag ratios). Wind tunnel experiments and flight simulations show that sustaining a high-lift coefficient at the expense of high drag would have been the most efficient strategy for Microraptor when gliding from, and between, low elevations. Analyses also demonstrate that anatomically plausible changes in wing configuration and leg position would have made little difference to aerodynamic performance. Significant to the evolution of flight, we show that Microraptor did not require a sophisticated, ‘modern’ wing morphology to undertake effective glides. This is congruent with the fossil record and also with the hypothesis that symmetric ‘flight’ feathers first evolved in dinosaurs for non-aerodynamic functions, later being adapted to form lifting surface

The effects of scaling on age, sex and size relationships in Red-legged Partridges

Wild birds differ in size according to their age and sex, adult birds being larger than juveniles. In the galliforms, males are larger than females, in contrast to some groups, such as the raptors, in which the females are larger. Size generally influences the rank hierarchy within a group of birds, although the age, sex, temperament and behaviour of an individual may override its size related rank order. The scaled size of birds according to age and sex affects their physiology and behaviour. Precise details of body-size differences by age and sex are poorly known in most partridge species. We measured 13,814 wild partridges in a homogenous population over 14 years of study to evaluate size differences within a uniform habitat and population management regime. We show that wild Red-legged Partridges have scaled mass, and body- and wing-lengths consistent with age/sex classes. Power functions between mass and body-length (as a proxy for walking efficiency), and between mass and wing-length (for flight efficiency) differ between juvenile females and males, and adult females and males. We discuss these findings and their physiological, behavioural and ecological implications.A.M. was supported by a Ramón y Cajal research contract by the Ministry of Economy and Competitiveness (RYC-2012-11867).Peer reviewe