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

Experimental investigation of deformation mechanisms during shear-enhanced compaction in poorly lithified sandstone and sand

Shear-enhanced compaction in shallow sandstone reservoirs has been investigated in laboratory experiments using high-pressure triaxial testing of poorly lithified sandstone and sand. We have studied the deformation mechanism involved during shear-enhanced compaction and controlling parameters for yield stress at varying confining pressures for sandstone/sand with different grain sizes, porosities, and packing. Experimental testing provides insights into the deformation mechanism during hydrostatic and axial compression of coarse- and fine-grained sands with different packing including (1) natural coarse-grained sandstone, (2) densely packed fine-grained sand, and (3) loosely packed fine-grained sand. Monitoring of deformation and ultrasonic velocity during deformation indicates porosity loss, compaction, and strain hardening for most of the samples. Visualization of deformation using pretest and posttest X-ray imaging and thin sections demonstrates localized deformation fabrics and grain damage. The results show grain rearrangement as the controlling deformation mechanism for material at low stress and high porosity, whereas for lower porosity and higher stress, grain fracturing controlled the deformation. The most pronounced localization of deformation was observed for the coarse-grained, low-porosity material. A Cam-Clay cap model was used to describe the porosity loss during compaction and shear-enhanced compaction, demonstrating large inelastic compaction with increasing confining pressure. Yield stress and end caps for poorly lithified sandstone are observed for various porosities and stress conditions and found to be lower than predicted using empirical relationships for sandstone

Provenance characteristics of the Brumunddal sandstone in the Oslo Rift derived from U-Pb, Lu-Hf and trace element analyses of detrital zircons by laser ablation ICMPS

The 800 m thick Brumunddal sandstone is partly an eolian, partly a fluvial sandstone deposited in a fault-bounded basin in the northern part of the Oslo Rift in Permian time.The sandstone is the youngest rift-related deposit in the northern part of the Oslo Rift. Well rounded detrital zircons are common accessory mineral grains in the sandstone. U-Pb dating of detrital zircon from a sample of the Brumunddal sandstone by LAM-ICPMS gives a range of ages from (rare) late Archaean ages to Permian (283±4 Ma). The age and initial εHf pattern of zircons in the sediment match the main rockforming events in Fennoscandia from Archaean to Phanerozoic time. This kind of diverse provenance was most likely obtained by repeated recycling of clastic sediments of Fennoscandian origin, with Silurian, continental sandstones as the most probable direct precursors. Trace element distributions show a conspicuous absence of patterns with the high level of U and Th enrichment typical of zircon from granitic rocks. This is consistent with a complex transport and redepositional history: High U-Th, metamict zircons were selectively removed by abrasion during repeatedtransport-deposition-erosion cycles. In addition to recycled material, Caledonian syn-orogenic intrusions and Permian intermediate to felsic plutonic rocks in the Oslo Rift itself were minor, but still significant sources of detrital zircon.18 page(s

Architecture of the evaporite accumulation and salt structures dynamics in Tiddlybanken Basin, southeastern Norwegian Barents Sea

An extensive, reprocessed two‐dimensional (2D) seismic data set was utilized together with available well data to study the Tiddlybanken Basin in the southeastern Norwegian Barents Sea, which is revealed to be an excellent example of base salt rift structures, evaporite accumulations and evolution of salt structures. Late Devonian–early Carboniferous NE‐SW regional extensional stress affected the study area and gave rise to three half‐grabens that are separated by a NW‐SE to NNW‐SSE trending horst and an affiliated interference transfer zone. The arcuate nature of the horst is believed to be the effect of pre‐existing Timanian basement grain, whereas the interference zone formed due to the combined effect of a Timanian (basement) lineament and the geometrical arrangement of the opposing master faults. The interference transfer zone acted as a physical barrier, controlling the facies distribution and sedimentary thickness of three‐layered evaporitic sequences (LES). During the late Triassic, the northwestern part of a salt wall was developed due to passive diapirism and its evolution was influenced by halite lithology between the three‐LES. The central and southeastern parts of the salt wall did not progress beyond the pedestal stage due to lack of halite in the deepest evaporitic sequence. During the Triassic–Jurassic transition, far‐field stresses from the Novaya Zemlya fold‐and‐thrust belt reactivated the pre‐salt Carboniferous rift structures. The reactivation led to the development of the Signalhorn Dome, rejuvenated the northwestern part of the salt wall and affected the sedimentation rates in the southeastern broad basin. The salt wall together with the Signalhorn Dome and the Carboniferous pre‐salt structures were again reactivated during post‐Early Cretaceous, in response to regional compressional stresses. During this main tectonic inversion phase, the northwestern and southeastern parts of the salt wall were rejuvenated; however, salt reactivation was minimized towards the interference transfer zone beneath the centre of the salt wall

Zircon U–Pb age for the Orkney lamprophyre dyke swarm, Scotland, and relations to Permo-Carboniferous magmatism in northwestern Europe

<p>Magmatic zircon in the syenite (bostonite) part of a composite NE–SW-trending cogenetic bostonite–camptonite dyke in Orkney, Scotland, yields a laser ablation inductively coupled plasma mass spectrometry age of 313 ± 4 Ma and <em>ε</em>Hf_{(313 Ma)} values of +6 to +11. This suggests that the NE–SW-, east–west- and NW–SE-trending Scottish lamprophyre dyke swarms were emplaced during one late Carboniferous magmatic event, contrasting with published K–Ar dates ranging between <em>c</em>. 325 and 250 Ma. This magmatism is interpreted as a response to late Variscan regional extension or an early response to the Skagerrak mantle plume. Lamprophyre magmatism was initiated some 10 Ma earlier in Scotland than in the Oslo Rift. </p