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

Le cœur alcalin du complexe du Messum, Namibie : Description pétrologique, interprétation de l'évolution minéralogique et relations roches sous- et sur-saturées en silice.

The anorogenic annular Messum complex, associated with the basaltic province of Etendeka (Namibia), show the coexistence of silica under- and over-saturated rocks. A petrological detailed study is necessary to understand the mineralogical evolution of these two groups of rocks. In the first one, all the observations allowed us to propose a path of crystallization involving peritectic lines and explaining the late development of nepheline at the expense of the primary phases (olivine, plagioclase, aluminous clinopyroxene) and the intermediate meaning of pargasite. Not yet indicated significant minerals are described: spinels in the basic rocks, wohlérite and hiortdahlite in the most evolved syénites, as well as pyrochlores considered as potential indicators of the presence of cabonatitic material. Quartz-syenites appears as a composite set with several comings differently evolved. Paragenesis are more or less peralcalines, with fayalite, acmitic hedenbergite, and late development of riebeckite. The chevkinite, rare titano-silicate, is described in relatively plentiful quantity as a magmatic mineral. No mineralogical link exists between these two groups of rocks and its make difficult to pass from one to another by crustal contamination.Le complexe anorogénique annulaire du Messum, associé à la province basaltique de l'Etendeka (Namibie), montre la coexistence de roches sous- et sur-saturées en silice. Une étude pétrologique détaillée est nécessaire pour comprendre l'évolution minéralogique de ces deux ensembles de roches. Dans le premier, l'ensemble des observations a permis de proposer une route de cristallisation mettant en jeu des lignes péritectiques et expliquant le développement de la néphéline tardivement aux dépens des phases précoces (olivine, plagioclase, clinopyroxène alumineux) et la signification intermédiaire de la pargasite. Des minéraux significatifs non encore signalés sont décrits : spinelles dans les roches basiques, wohlérite et hiortdahlite dans les syénites les plus évoluées, ainsi que des pyrochlores considérés comme des indices potentiels de la présence de matériaux à affinités carbonatitique. Les syénites à quartz apparaissent comme un ensemble composite avec plusieurs venues différemment évoluées. Les paragenèses sont plus ou moins peralcalines, avec fayalite, hédenbergite acmitique, et développement tardif de riebéckite. La chevkinite, titano-silicate rare, y est décrit en quantité relativement abondante comme un minéral magmatique. Aucun lien minéralogique entre ces deux ensembles ne peut être établi ce qui rend peut crédible l'hypothèse du passage de l'un à l'autre par contamination crustale

Le cœur alcalin du complexe du Messum, Namibie (description pétrologique, interprétation de l évolution minéralogique et relations roches sous- et sur-saturées en silice)

Le complexe anorogénique annulaire du Messum, associé à la province basaltique de l Etendeka (Namibie), montre la coexistence de roches sous- et sur-saturées en silice. Une étude pétrologique détaillée est nécessaire pour comprendre l évolution minéralogique de ces deux ensembles de roches. Dans le premier, l ensemble des observations a permis de proposer une route de cristallisation mettant en jeu des lignes (ou surfaces) péritectiques et expliquant le développement de la néphéline tardivement aux dépens des phases précoces (olivine, plagioclase, clinopyroxène alumineux) et la signification intermédiaire de la pargasite. Des minéraux significatifs non encore signalés sont décrits : spinelles dans les roches basiques, wohlérite et hiortdahlite dans les syénites les plus évoluées, ainsi que des pyrochlores considérés comme des indices potentiels de la présence de matériaux à affinités carbonatitique. Les syénites à quartz apparaissent comme un ensemble composite avec plusieurs venues différemment évoluées. Les paragenèses sont plus ou moins peralcalines, avec fayalite, hédenbergite acmitique, et développement tardif de riebéckite. La chevkinite, titano-silicate rare, y est décrit en quantité relativement abondante comme un minéral magmatique. Aucun lien minéralogique entre ces deux ensembles ne peut être établi ce qui rend peut crédible l hypothèse du passage de l un à l autre par contamination crustale.PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Sci.Terre recherche (751052114) / SudocSudocFranceF

Physical property changes of Fe-Ti oxides along their alteration: a geometallurgical study to improve the yield of a mineralurgical plant

International audienc

Characterization of Weda Bay nickel laterite ore from Indonesia

International audienceThe association of fine grained MgeNi silicates with oxy-hydroxides in laterites and saprolites representschallenges for ore processing, in particular, in nickel enrichment. The Weda Bay nickel deposit in Indonesia is atypical example of these complex ores, where clays such as nontronites develop on polyphase serpentinite asprotolith. Thus, ores at Weda Bay have a very fine textured and complex mineralogy, which requires a comprehensivemineralogical identification through the use of a series of different types of analytical approaches (i.e.macroscopic and microscopic methods including SEM equipped with energy dispersive X-ray spectrometry(EDS), Raman spectroscopy, Infrared and X-ray fluorescence spectroscopy, and QEMSCAN® mapping). Nickelrich saprolites were found to be principally composed of several types of MgeNi serpentines, quartz, clays(nontronite in particular) and little amounts of iron hydroxides. Besides, some parts of the deposit were characterizedby the development of nontronites at the interface between the saprolite and the limonite zone. Abovethis zone, the limonite zone is dominated by iron hydroxides as expected, which replace all earlier silicatesincluding serpentine, and contains a significant amount of nickel. The representative composite ore samplecontains several nickel bearers with variable nickel grade of 2 to 3%. Exceptionally richer phases such aspolygonal Fe (Ni)-rich serpentine were also found with nickel grade of 5 to 10%. Serpentine types as well asother newly formed silicates such as Fe-Mg-(Ni) smectites, are intimately mixed, preventing any mineral separation.Therefore, the only phases which can be separated are quartz and magnetite. This complicates theupgrading of nickel in Weda Bay laterite ore

Binder-free tableting experiments on manganese oxides and industrial mineral powders

International audienceCold, binder-free tableting experiments under controlled pressure (0-450 MPa), water addition (0-10 wt.%) and pH (4, 11) were performed on powder of pyrolusite ore concentrates, refined hausmannite, bentonite, kaolinite, as well as blends of those materials. It has been shown that increased pressure was beneficial for agglomeration of oxide materials, but pressure > 250 MPa triggered an elastic recovery in the clay minerals. Water addition up to 4 wt.% improved tabletability, increasing diametral resistance and reducing elastic recovery and fines generation. Amounts above 6 wt.% decreased diametral resistance. The presence of layered-structure minerals (such as montmorillonite, kaolinite, lithiophorite) appeared to be key to determine the agglomeration potential of a sample. This study also showed that tableting provides good performances for recycling industrial manganese oxide fines by obtaining industrial-grade resistance for tablets made with an 80/20 pyrolusite concentrate/hausmannite blends and 4 wt.% H2O

Building a Hyperspectral Library and its Incorporation into Sparse Unmixing for Mineral Identification

International audienceThe objective of the SOLSA project (EU-H2020) is to develop an analytical expert system for on-line-on-mine-real-time mineralogical and geochemical analyses on sonic drill cores. As one aspect of the system, this paper presents the building of the hyperspectral library and its incorporation into sparse unmixing techniques for mineral identification. Twenty seven spectra representing 14 minerals have been collected for the library. Three sparse unmixing techniques have been investigated and evaluated using simulated data generated from our hyperspectral library, and real hyperspectral data acquired from a serpentinized harzburgite sample. Among the three techniques, the collaborative sparse unmixing by variable splitting and augmented Lagrangian (CLSUnSAL) method provided the best accurate results on the simulated data. In addition, the results of the CLSUnSAL method show high correlation with that of the QEMSCAN® analysis on the harzburgite hyperspectral data

Building a Hyperspectral Library and its Incorporation into Sparse Unmixing for Mineral Identification

International audienceThe objective of the SOLSA project (EU-H2020) is to develop an analytical expert system for on-line-on-mine-real-time mineralogical and geochemical analyses on sonic drill cores. As one aspect of the system, this paper presents the building of the hyperspectral library and its incorporation into sparse unmixing techniques for mineral identification. Twenty seven spectra representing 14 minerals have been collected for the library. Three sparse unmixing techniques have been investigated and evaluated using simulated data generated from our hyperspectral library, and real hyperspectral data acquired from a serpentinized harzburgite sample. Among the three techniques, the collaborative sparse unmixing by variable splitting and augmented Lagrangian (CLSUnSAL) method provided the best accurate results on the simulated data. In addition, the results of the CLSUnSAL method show high correlation with that of the QEMSCAN® analysis on the harzburgite hyperspectral data

Nest and nest-site reuse within and between breeding seasons by three neotropical flycatchers (Tyrannidae)

Nest and or nest site reuse within and between breeding seasons was reported by the Euler's Flycatcher (Lathrotriccus euleri), the Sepia-capped Flycatcher (Leptopogon amaurocephalus) and the Gray-hooded Flycatcher (Mionectes -rufiventris) in forest fragments from southeastern Brazil. Nest and or nest site reuse between some years was frequent within a single breeding season by the Sepia-capped Flycatcher. Nest reuse, however, was not related to nesting success in the previous breeding attempt. Nest turnover rates (movement to a new site between years) were low for L. amaurocephalus, intermediate for L. euleri and high for M. rufiventris