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

Use of cylindrical artefacts for AFM vertical calibration

Scanning probe microscopes are widely used for the surface analysis of micro- and nano-devices. In particular, the blow-up of miniaturization calls for the fine and traceable characterization of micro- topographies with the highest resolutions. This is at the basis of an increasing demand for easy and fast calibration procedures for such instruments. A number of artefacts are available on the market, intended prevalently for the calibration of SPM horizontal and vertical axes, in terms of scaling factors, linearity and squareness. The present paper focuses, in particular, on vertical calibration. New cylindrical artefacts that offer advantages in terms of instrument control are presented here. In particular, we discuss the possibility of calibrating the instrument all over the scanned range in terms of first-, second- and third-order vertical calibration coefficients (respectively C-zz', C-zz'2 and C-zz'beta). Two artefacts with different diameters were measured and compared in the investigations

Acoustic Scanning Probe Microscopy

This comprehensive presentation of a powerful new technology deals with everything from basic theoretical explanations to calibration, enhancement, and applications. It also compares the advantages of the process to more established scanning probe methods