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

Rare earth element fractionation in heterogenite (CoOOH): Implication for cobalt oxidized ore in the Katanga Copperbelt (Democratic Republic of Congo)

International audienceHeterogenite (CoOOH) is the most abundant cobalt oxide mineral in the Katanga Copperbelt, which hosts around half of the world's known reserves of mineable cobalt. Heterogenite formed by the oxidation of Co-sulfides and accumulated as residual deposits during a Pliocene weathering event. Bulk analysis samples of oxidized cobalt ore samples containing with variable heterogenite concentration display two rare earth element (REE) patterns: (i) Type 1 is enriched in middle REE, with a negative cerium anomaly and a relatively low REE content; (ii) Type 2 is variably enriched in light REE (LREE), without a cerium anomaly and with higher REE content. However, in situ LA-ICP-MS reveals that the Type 2 patterns are due to the mixing of heterogenite with a LREE-rich mineral.Weathering processes leading to heterogenite formation mainly consist of water–rock interactions at high Co activity, in the near-surface environment. These result in the formation of a lateritic deposit. Heterogenite precipitates at near-neutral pH conditions together with manganese oxides. REE are mainly fractionated between these Co- and Mn-oxide minerals. In the deeper part of the oxidized profile, cobalt activity decreases and the heterogenite stability field shifts to alkaline pH conditions due to the dissolution of dolostone in the bedrock. In such an alkaline environment, REE speciation is mainly driven by carbonate complexation/precipitation. This environment would be favorable for the formation of REE-rich carbonate which is intimately associated with heterogenite (LREE-rich Type 2 patterns).The combined whole-rock and in situ geochemical analyses presented here clearly help (1) to distinguish the REE signature of the Co oxidized ore (mineral paragenesis comprising heterogenite) and of heterogenite itself, and subsequently (2) to highlight two different chemical environments for the formation of heterogenite in supergene ores. This study therefore improves the understanding of REE behavior and metal mobility in near-surface environments, and more particularly in environments where the supergene ores form. In the future, the approach developed here can be applied to other Co–Ni–Mn lateritic deposits such as those in New Caledonia and Cameroon

Fluid circulations and iron oxides associated on cataclastic deformation Bands in porous sandstones, Bassin du Sud-Est, Provence, France: new insights from rare earth elements geochemistry

International audience5. Rare Earth Elements proxy of elemental mobility Conclusion The oxidation fronts underline preferential pathways for the ground water, localized along the CDBs (fig. 3). CDBs seem to constitute a trap where the oxides, contained in the fluid, are accumulated. Fluid circulations have print specific rare earth element (REE) pattern in sandstone host rocks, clays and oxides (fig.5). They particularly print heavy REE enrichment patterns, the light REE remain in fluids and are carried downstream. Further analysis have to be performed on groundwater to verify this hypothesis. BDs are both pipes and barriers to the fluid circulations along the fault zone

Bracing in adult with scoliosis: experience in diagnosis and classification from a 15 year prospective study of 739 patients

Abstract Background Despite the frequency of adult scoliosis, very few publications concern the conservative orthopaedic treatments. The indications have not been defined to date. The experience of a department specialized in rigid bracing allows us to consolidate and clarify diagnosis and indications as well. Methods Individual observational prospective cohort study from a database started in 1998, with selection of all 739 adult scoliosis patients for which conservative orthopaedic treatment has been proposed to, even in case of drop-out. Scoliosis treated during adolescence and monitored in adulthood are included if a new brace is prescribed. A first descriptive study of the main parameters was performed: gender, age, Cobb angle. A tentative classification according to aetiology, age and angulation is proposed. Results 1) Descriptive Data: The Ratio Female/Male is 88 %, the mean age: 56.97 ± 15.82, the mean Cobb angle: 35.58 ± 17.35. The rate of non-adherent patients not wearing the brace is 17 % (but the plaster cast before bracing was routinely proposed at the time). 2) All patients can be grouped into five diagnoses, all statistically different, according to the age and the initial Cobb angle: Rotatory dislocation: 361 cases, age: 59.73 ± 13.52 (p = 0.05), (Cobb 39.08 ± 16.59 (p = 0.02)* Instability and disc disease: 150 cases, age: 46.03 ± 15.49 (p = 0.00)*, Cobb: 25.29 ± 12.29 (p = 0.00)* Camptocormia: 68 cases, age: 69.78 ± 12.19 (p = 0.00)*), Cobb: 38.09 ± 14.23 (p = 0.25) Kyphosis TL or T: 62 cases, age: 60.73 ± 15.51 (p = 0.07), Cobb: 43.34 ± (21.48 (p = 0.00)* Disabling pain: 33 cases, age: 48.36 ± 13.73 (p = 0.02)*, Cobb: 36.45 ± 25.21 (p = 0.78) Treatment after surgery and in the context of a lumbar stenosis and spondylolisthesis are independent groups. Despite the wide variety of etiologies, nearly 2/3 of patients have a discal pathology like rotatory dislocation and disc instability. For these patients a short brace can be used. Other patients usually have high kyphotic pathology as Kyphosis or camptocormia. They need a long brace. Conclusions The wide variety of adult scoliosis makes any objective classification difficult. This first approach is intended to specify the best indications of bracing in adulthood. 1. The female ratio is slightly higher than that of the adolescent. 2. The dropout rate is high and justify improvements with adaptation of bracing to adults. 3. All proposed etiological groups are statistically significantly different

Prospective study of 158 adult scoliosis treated by a bivalve polyethylene overlapping brace and reviewed at least 5 years after brace fitting

Abstract Background The conservative orthopaedic treatment of adult scoliosis is very disappointing. In a series of 144 patients; only 25 % (33 cases) were monitored at 2 years of treatment. (Papadopoulos 2013). Thereby the literature typically focuses on a small number of patients, which limits the usefulness and relevance of its results. The brace effect on pain has been systematically described, but there is no publication on the effect of treatment on the Cobb angle and main clinical parameters. Methods From a prospective database started in 1998, we selected all 158 consecutive patients effectively treated conservatively with the Lyon management treatment and controlled five years after brace fitting. Lyon management includes a lordosing bivalve polyethylene overlapping brace in association with specific physiotherapy. The brace can either be short with anterior support under the chest or long with sterno-clavicular support when there is a high thoracic kyphosis. Results 1. For the rate of scoliosis controlled after 5 years, the follow-up was 24 % of the 661 patients accepting the treatment. Pain is almost the main reason for the medical consultation, generally correlating with an increase of the scoliotic angulation. 2. The descriptive data can be superimposed on general group with age (m=56 years, SD=13) but initial Cobb angulation is significantly higher (m=40°, SD=17). Ratio Female/Male=0.91. Generally, the scoliosis is stabilized at (m=39.74 °, SD=19.40), 8 years after the beginning of the treatment. 38 improvements of more than 5°= 24 %; 88 stable = 56 %; 32 worsening of more than 5° = 20 % The rib hump is improved of by 3 mm, (modelling effect of the brace). The occipital axis is improved by more than 6 mm. But the T1 plumb line distance is worsening by 7 mm (most braces are short without sterno-clavicular support). Conclusions For the first time, the number of records and follow up after 8 years allows to study the radiological progression of adult scoliosis rigid bracing. Stability or improvement of more than 5° in 80 % of cases justify rigid bracing in adults. The accentuation of the thoracic kyphosis is the only negative element and a modified ARTbrace will soon be used

Additional file 1: of Prospective study of 158 adult scoliosis treated by a bivalve polyethylene overlapping brace and reviewed at least 5Â years after brace fitting

Excel spreadsheet with results of 158 patients. Data from the prospective database (age, Cobb, balance, follow up at the Beginning and last follow-up). (XLSX 24 kb

Additional file 1: of Bracing in adult with scoliosis: experience in diagnosis and classification from a 15 year prospective study of 739 patients

Excel spreadsheet: Spreadsheet used for the diagnostic comparison of average according to the age and angulation. (XLSX 80 kb