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

NEW DEVELOPMENT IN CONFOCAL SCANNING OPTICAL MICROSCOPY AND ITS APPLICATION TO THE STUDY OF ELECTRICALLY ACTIVE DEFECTS IN SEMICONDUCTORS

A description is given of the design and some early results from a new confocal scanning optical microscope. It is designed for the study of Photoluminescence but has a broad range of potential applications in materials science. The optical system is integrated with a helium cryostat to permit control of specimen temperature from ambient to 2K. Servomechanisms control the position of the specimen with respect to the focal point of the objective, to eliminate the effects of vibration and drift

Growth of crustose lichens : a review

Crustose species are the slowest growing of all lichens. Their slow growth and longevity, especially of the yellow-green Rhizocarpon group, has made them important for surface-exposure dating (lichenometry). This review considers various aspects of the growth of crustose lichens revealed by direct measurement including: 1) early growth and development; 2) radial growth rates (RGR, mm yr−1); 3) the growth rate–size curve; and 4) the influence of environmental factors. Many crustose species comprise discrete areolae that contain the algal partner growing on the surface of a non-lichenized fungal hypothallus. Recent data suggest that 'primary' areolae may develop from free-living algal cells on the substratum while 'secondary' areolae develop from zoospores produced within the thallus. In more extreme environments, the RGR of crustose species may be exceptionally slow but considerably faster rates of growth have been recorded under more favourable conditions. The growth curves of crustose lichens with a marginal hypothallus may differ from the 'asymptotic' type of curve recorded in foliose and placodioid species; the latter are characterized by a phase of increasing RGR to a maximum and may be followed by a phase of decreasing growth. The decline in RGR in larger thalli may be attributable to a reduction in the efficiency of translocation of carbohydrate to the thallus margin or to an increased allocation of carbon to support mature 'reproductive' areolae. Crustose species have a low RGR accompanied by a low demand for nutrients and an increased allocation of carbon for stress resistance; therefore enabling colonization of more extreme environments