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

Helium isotope ratios in mafic phenocrysts and geothermal fluids from La Palma, the Canary Islands (Spain): Implications for HIMU mantle sources

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No slab-derived CO₂ in Mariana Trough back-arc basalts: Implications for carbon subduction and for temporary storage of CO₂ beneath slow spreading ridges

[1] The Southern Mariana Trough is particularly well suited to study mass balance in subduction zones because the flux of material recycled from the subducted slab has been shown to diminish to negligible levels in the southernmost part of the area. We present new He and Ar concentration and isotopic data for 16 back-arc basaltic glasses and combine these with previously published CO2 and H2O concentration and δ13C data to explore the recycling of carbon and light noble gases in the Mariana back arc. Degassing has affected all samples and is particularly extensive in more water-rich samples, i.e., those containing the largest recycled component. The degassing history features three stages: (1) deep degassing which commenced when the melt reached saturation of CO2 and noble gases in the mantle, (2) preeruptive degassing during storage in the crust-mantle transition zone which involved addition of extraneous CO2 to the vapor phase, and (3) eruption. CO2 released during stage 1 was, at least partially, incorporated into wall rock and subsequently remobilized during stage 2 degassing of later magma batches. Reconstructed parental values for 3He/4He, δ13C, CO2/3He, and CO2/40Ar* are indistinguishable from those of mid-ocean ridge basalt. This implies that there is negligible recycling of subducted carbon, helium, or argon into the source of Mariana Trough basalt

Sources, degassing, and contamination of CO₂, H₂O, He, Ne and Ar in basaltic glasses from Kolbeinsey Ridge, North Atlantic

New volatile data (CO₂, H₂O, He, Ne, and Ar) are presented for 24 submarine basaltic glasses from the Kolbeinsey Ridge, Tjörnes Fracture Zone and Mohns Ridge, North Atlantic. Low CO₂ and He contents indicate that magmas were strongly outgassed with the extent of degassing increasing toward the south, as expected from shallower ridge depths. Ne and Ar are significantly more abundant in the southernmost glasses than predicted for degassed melt. The strong atmospheric isotopic signal associated with this excess Ne and Ar suggests syn- or posteruptive contamination by air. Degassing, by itself, cannot generate the large variations in δ13C values of dissolved CO₂ or coupled CO₂-Ar variations. This suggests that δ13C values were also affected by some other processes, most probably melt-crust interaction. Modelling indicates that degassing had a negligible influence on water owing to its higher solubility in basaltic melt than the other volatiles. Low H₂O contents in the glasses reflect melting of a mantle source that is not water-rich relative to the source of N-MORB. Before eruption, Kolbeinsey Ridge melts contained ~400 ppm CO₂ with δ13C of -6‰, 0.1 to 0.35 wt.% H₂O, 3He/4He ~ 11 RA, and CO₂/3He of ~2 x 10⁹. We model restored volatile characteristics and find homogeneous compositions in the source of Kolbeinsey Ridge magmas. Relative to the MORB-source, He and Ne are mildly fractionated while the 40Ar/36Ar may be low. The 3He/4He ratios in Tjörnes Fracture Zone glasses are slightly higher (13.6 RA) than on Kolbeinsey Ridge, suggesting a greater contribution of Icelandic mantle from the south, but the lack of 3He/4He variation along the Kolbeinsey Ridge is inconsistent with active dispersal of Icelandic mantle beyond the Tjörnes Fracture Zone

Extreme ³He/⁴He ratios in northwest Iceland: constraining the common component in mantle plumes

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High ³He/⁴He ratios in the Manus Back-Arc Basin: implications for mantle mixing and the origin of plumes in the western Pacific Ocean.Basin.

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Nucleogenic neon in high ³He/⁴He lavas from the Manus back-arc basin: a new perspective on He-Ne decoupling.

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CO₂, ¹³C/¹²C and H₂O variability in natural basaltic

no abstrac