The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)

Biodiversity recovery of Neotropical secondary forests

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes. Copyright © 2019 The Authors, some rights reserved

Etude des mécanismes d'altération par l'eau du verre R7T7 en milieu confiné (compréhension et modélisation de la cinétique résiduelle)

MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Deciphering the reaction mechanisms of photothermal hydrogen production using H/D kinetic isotope effect

International audienceH/D kinetic isotope effect has been employed to study the mechanism of the thermally assisted photocatalytic hydrogen production over noble metal-free Ti@TiO2 core–shell nanoparticles. We have found that the observed large H/D isotope separation factor (αH = 11.3 ± 1.7–6.2 ± 0.9) is due to the electron hole-mediated cleavage of OH bond. It was concluded that strong H/D isotopic selectivity is associated with significant photothermal effect

Insights into the Photothermal Hydrogen Production from Glycerol Aqueous Solutions over Noble Metal-Free Ti@TiO 2 Core-Shell Nanoparticles

International audiencePhotocatalytic production of hydrogen from renewable sources with platinum group metal‐free catalysts is of great importance for environmentally friendly energetics. Herein, Ti@TiO2 core–shell nanoparticles prepared by sonohydrothermal treatment of titanium metal nanoparticles are examined for hydrogen generation from aqueous glycerol solutions under vis/NIR light irradiation. It is shown that photocatalytic reforming of glycerol in the presence of Ti@TiO2 exhibits strong photothermal effect allowing more efficient use of solar energy. Apparent activation energy equal to E act = 27 ± 2 kJ mol−1 indicates that the thermal effect is related to the diffusion of reaction intermediates at catalyst surface rather than to the activation of chemical bonds. The photoexcitation mechanism of Ti@TiO2 particles involves interband transitions in nonplasmonic Ti metal core followed by nonradiative Landau damping. Effective electron–hole separation between Ti core and nanocrystalline TiO2 anatase shell in Ti@TiO2 nanoparticles is confirmed by photoluminescence spectroscopy. In studied system, photothermal hydrogen production is not accompanied by CO2 emission indicating that glycerol is oxidized to glyceric acid without further decarboxylation

Sonochemical reactions with mesoporous alumina

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Sonocatalytic degradation of EDTA in the presence of Ti and Ti@TiO2 nanoparticles

International audienceThe sonocatalytic degradation of EDTA (C0 = 5 10−3 M) in aqueous solutions was studied under 345 kHz (Pac = 0.25 W mL−1) ultrasound at 22–51 °C, Ar/20%O2, Ar or air, and in the presence of metallic titanium (Ti0) or core-shell Ti@TiO2 nanoparticles (NPs). Ti@TiO2 NPs have been obtained using simultaneous action of hydrothermal conditions (100–214 °C, autogenic pressure P = 1.0–19.0 bar) and 20 kHz ultrasound, called sonohydrothermal (SHT) treatment, on Ti0 NPs in pure water. Ti0 is composed of quasi-spherical particles (30–150 nm) of metallic titanium coated with a metastable titanium suboxide Ti3O. SHT treatment at 150–214 °C leads to the oxidation of Ti3O and partial oxidation of Ti0 and formation of nanocrystalline shell (10–20 nm) composed of TiO2 anatase. It was found that Ti0 NPs do not exhibit catalytic activity in the absence of ultrasound. Moreover, Ti0 NPs remain inactive under ultrasound in the absence of oxygen. However, significant acceleration of EDTA degradation was achieved during sonication in the presence of Ti0 NPs and Ar/20%O2 gas mixture. Coating of Ti0 with TiO2 nanocrystalline shell reduces sonocatalytic activity. Pristine TiO2 anatase nanoparticles do not show a sonocatalytic activity in studied system. Suggested mechanism of EDTA sonocatalytic degradation involves two reaction pathways: (i) sonochemical oxidation of EDTA by OHradical dot/HO2radical dot radicals in solution and (ii) EDTA oxidation at the surface of Ti0 NPs in the presence of oxygen activated by cavitation event. Ultrasonic activation most probably occurs due to the local heating of Ti0/O2 species at cavitation bubble/solution interfac

Glass–water interphase reactivity with calcium rich solutions

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Mechanism of PtIV Sonochemical Reduction in Formic Acid Media and Pure Water

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Photocatalytic and Sonocatalytic Degradation of EDTA and Rhodamine B over Ti0 and Ti@TiO2 Nanoparticles

International audienceHerein, we report a comparative study of photocatalytic (Xe-lamp) and sonocatalytic (345 kHz power ultrasound) degradation of Ethylenediaminetetraacetic acid (EDTA) and Rhodamine B (RhB) in the presence of Ti0 and Ti@TiO2 core-shell nanoparticles (NPs). Ti@TiO2 NPs have been obtained by sonohydrothermal treatment (20 kHz, 200 °C) of commercially available Ti0 NPs in pure water. The obtained material is composed of quasi-spherical Ti0 particles (30–150 nm) coated by 5–15 nm crystals of anatase. In contrast to pristine TiO2, the Ti@TiO2 NPs exhibit the extend photo response from UV to NIR light region due to the light absorption by nonplasmonic Ti core. EDTA can be oxidized effectively by photocatalysis in the presence of Ti@TiO2 NPs. By contrast, air passivated Ti0 nanoparticles was found to be inactive in the photocatalytic process for both EDTA and RhB. Photocatalytic degradation of EDTA over Ti@TiO2 NPs exhibits strong photothermal effect, which has been attributed to the higher yield of oxidizing radicals produced by light at higher bulk temperature. The efficiency of RhB photocatalytic degradation depends strongly on RhB concentration. At [RhB] ≥ 1 × 10−3 M, its photocatalytic degradation is not feasible due to a strong self-absorption. At lower concentrations, RhB photocatalytic degradation is observed, but at lower efficiency compared to EDTA. We found that the efficient sonochemical degradation of RhB does not require the presence of any catalysts. For both processes, EDTA and RhB, sonochemical and photocatalytic processes are more effective in the presence of Ar/O2 gas mixture compared to pure Ar. The obtained results suggest that the choice of the optimal technology for organic pollutants degradation can be determined by their optical and complexing properties