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

Characteristics of internal solitary waves in the Maluku Sea, Indonesia

International audienc

Characteristics of internal solitary waves in the Maluku Sea, Indonesia

International audienc

Characteristics of internal solitary waves in the Maluku Sea, Indonesia

International audienc

Characteristics of internal solitary waves in the Maluku Sea, Indonesia

International audienc

Response to "Comment on the Paper "Characteristic Time Scales of Decadal to Centennial Changes in Global Surface Temperatures Over the Past 150 years" by J. L. Le Mouël, F. Lopes and V. Courtillot"

International audienceWe thank the authors (hereafter referred to as CCC) for providing us an opportunity to clarify some points of our original paper. CCC list in their abstract three "key points"that we respond to in this Reply. The first comment is the central one and the most developed. It deals mainly with discussion of features of methods of spectral analysis, mainly SSA. We have quoted the sub parts of that comment as items 1a to 1k. The replies to comments/key points 2 and 3 are shorter. We disagree with most of the comments by CCC and explain why. We conclude that we have successfully countered CCC's criticism and shown many of their points to be unsubstantiated. The main problem seems to reside in differences concerning the literature on Singular Spectral Analysis and our use of it. Much of our response to the comments can be found in textbooks and review papers on SSA and time series analysis; we quote extensively, both in our original paper and in this response to CCC, Golyandina and Zhigljavsky (2013)

Turbulence produite par l'explosion d'un vortex

PARIS7-Bibliothèque centrale (751132105) / SudocPARIS-BIUSJ-Lab.Mécanique the (751055218) / SudocPARIS-BIUSJ-Mathématiques rech (751052111) / SudocSudocFranceF

Observation of internal tides, nonlinear internal waves and mixing in the Lombok Strait, Indonesia

International audienceLombok Strait is one of the main exit passages of the Indonesian throughflow (ITF), connecting the interior Indonesian seas with the Indian Ocean. Satellite images have shown that this strait is also the most remarkable zone of the Indonesian seas for the generation of internal tides, which frequently evolve into internal solitary waves (ISWs). Here we present the first comprehensive high-frequency observations of the internal tide in the strait. The observations were carried out at a fixed position around 8 km from the western coast of Lombok Island at a depth of ~300 m. We confirmed the appearance of the non-linear internal tide with an amplitude of ~90 m at a fairly close distance (~30 km) from its generation site in the Nusa Penida Sills (NPS), with a dominant M2 tidal frequency. High-frequency internal waves associated with vertical velocities reaching 20 cm s-1 were observed within the internal tidal trough. We estimated the turbulent kinetic energy dissipation rate using Thorpe and Ellison scales and found a mean dissipation rate of the order of ~ [10-6-10-7] m2 s-3, with enhanced values in the thermocline layer, possibly driven by shear instabilities. We underlined that the use of the Ellison scale is a promising alternative for indirectly estimating the dissipation rate from high-resolution time-series data sets