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

The Devonian-Carboniferous Boundary in South Africa and the age of the earliest episode of the Dwyka Glaciation : new palynological result.

peer reviewe

Reconstruction of the ordovician pakhuis ice sheet, South Africa

This reconstruction of the Late Ordovician, glacigenic Pakhuis Formation of the Table Mountain Group is based on a variety of diverse datasets. Field observations were made over the full 300 km extent of exposure in a north-south direction. The thin glacigenic package constitutes a minor interlude in the development of a subcontinental, Palaeozoic, siliciclastic basin. The Pakhuis Formation is of special interest because it includes features like the extensive penecontemporaneous folding, an erosional unconformity and the uniform lithological character of the sandy diamictites. A model is presented by which an unusual concurrence of circumstances produced the special features of the Pakhuis glacigenics. These are the ice invasion of a developing basin, an onset zone within basin and a deep trough harboring an ice-stream. Subglacial, grounding zone and iceberg facies associations with their lateral variations are developed. The temperate, glaciation of relative short duration, comprised one major and a second minor advance. During the first advance the grounded ice sheet with slow-moving sheet-flow reached ice-stream characteristics along at least part of a trough. The occurrence of an ice-stream within a slow-moving, low-profile ice sheet provides the glaciological environment for ice-stream draw-down, flanking infill of ice, resulting in compressional ice-flow from the sides. The fundamental requirement for buckling (i.e. the development of the Fold Zone) is layer parallel shortening achieved by the compressional ice-flow. Ice-bed interface features like deforming-bed structures are developed, as well as outsize flutes for which an alternative bulk strain model is proposed. The glacial retreat was rapid, interrupted only by the second, minor advance. A marine environment is attested by the postglacial fauna of a black shale. © 2010 September Geological Society of South Africa.Articl

Reply to the discussion by C.D. Roweand N.R. Backeberg on the paper "reconstruction of the Ordovician Pakhuis ice sheet, South Africa" by H.J. Blignault and J.N. Theron (SAJG, 113, 335-360, 2010)

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Spherical and columnar, septarian,18 O-depleted, calcite concretions from Middle-Upper Permian lacustrine siltstones in northern Mozambique : evidence for very early diagenesis and multiple fluids

Calcite septarian concretions from the Permian Beaufort Group in the Maniamba Graben (NW Mozambique) allow controls on the composition and nature of diagenetic fluids to be investigated.The concretions formedinlacustrine siltstones, where they occur in spherical (1 to 70 cm in diameter) and columnar (up to 50 cm long) forms within three closely spaced, discrete beds totalling 2Æ5 min thickness. Cementation began at an early stage of diagenesis and entrapped non-compacted burrows and calcified plant roots. The cylindrical concretions overgrew calcified vertical plant roots, which experienced shrinkage cracking after entrapment. Two generations of concretionary body cement and two generations of septarian crack infill are distinguished. The early generation in both cases is a low-Mn, Mg-rich calcite, whereas the later generation is a low-Mg, Mn-rich calcite. The change in chemistry is broadly consistent with a time (burial)-related transition from oxic to sub-oxic/anoxic conditions close to the sediment–water interface. Geochemical features of all types of cement were controlled by the sulphate-poor environment and by the absence of bacterial sulphate reduction. All types of cement present have d13C ranging between 0&and )15&(Vienna Peedee Belemnite, V-PDB), and highly variable and highly depleted d18O (down to 14& Vienna Standard Mean Ocean Water, V-SMOW). The late generation of cement is most depleted in both 13C and 18O. The geochemical and isotopic patterns are best explained by interaction between surface oxic waters, pore waters and underground, 18Odepleted, reducing, ice-meltwaters accumulated in the underlying coal-bearing sediments during the Permian deglaciation. The invariant d13C distribution across core-to-rim transects for each individual concretion is consistent with rapid lithification and involvement of a limited range of carbon sources derived via oxidation of buried plant material and from dissolved clastic carbonates. Syneresis of the cement during an advanced stage of lithification at early diagenesis is considered to be the cause of development of the septarian cracks. After cracking, the concretions retained a small volume of porosity, allowing infiltration of anoxic, Ba-bearing fluids, resulting in the formation of barite. The results obtained contribute to a better understanding of diagenetic processes at the shallow burial depths occurring in rift-bound, lacustrine depositional systems