The representation of coupling interactions in the Material Properties Open Database (MPOD)

International audience; The Material Properties Open Database (MPOD, http//mpod.cimav.edu.mx) is a functional element of the web-based open databases system linked with crystallography. MPOD delivers single-crystal tensor properties in several representations, ranging from numerical matrices to 3D printing. Longitudinal moduli surfaces can be displayed in computers as well as in smart cell phones. Properties are stored as '.mpod' files. IUCr formatting standards (CIF) are followed. The original published paper containing the data is cited. Structural and experimental information is also registered and linked. 'Coupling properties', say piezo-effects and magnetoelectricity, represent interactions linking different subsystems in a material. Currently, piezoelectricity occupies a significant fraction of cases in MPOD. The implications of crystal symmetry in piezoelectricity are systematically taken into account. Matrices' elements and longitudinal moduli surfaces are checked for consistency with the Neumann principle. The inclusion of magnetoelectric axial tensors introduces exciting features into MPOD

Concrete Durability Probed Using Compressive Strength, Chloride Penetration and Porosity Measurements on CEMII and CEMV Concretes Incorporating Mollusc Shell Spares in Artificial and Natural Seawaters

The purpose of this study is to improve the recruitment of flat oyster larvae, an endangered species, by means of a specific marine infrastructure made of concrete. This work aims to develop and optimize concrete formulations by varying the type of cement and introducing shellfish by-products into their composition and determine which concrete formulation is the most sustainable to marine organism colonization. Indeed, it is essential to obtain a sustainable concrete submitted to aggressive marine environment (chloride ions diffusion and bio-colonisation). Four concrete formulations were tested with two types of cements (CEMII and CEMV) and with or without the incorporation of shell aggregates. The durability of these materials was tested after 3 months of immersion in the Rance of Dinard (France). It appears from this study that the CEMII concrete exhibits a good mechanical resistance independently of the presence of shell, after immersion in situ. This concrete also shows better resistance to chloride ions diffusion than CEMV. However, CEMV possess larger compressive strengths than CEMII, and mollusc shells incorporation does not decrease this strength as much as for CEMII. Shell incorporation in the concretes has an effect on strength, chloride penetration and porosity which depend on the used cement and seawater

Combined XRF, XRD, SEM-EDS, and Raman Analyses on Serpentinized Harzburgite (Nickel Laterite Mine, New Caledonia): Implications for Exploration and Geometallurgy

International audienceDifferent techniques have been combined to determine the crystallography and the chemical composition of serpentinized harzburgite sampled in a drill core coming from the lower part of the New Caledonia ophiolite. Specifically, this serpentinized harzburgite is the common bedrock of most of the nickel laterite mines in New Caledonia. Most of the minerals present in serpentinized harzburgite were analyzed by Raman spectroscopy and XRD. In this study, Raman spectroscopy has been applied for the first time to estimate the nickel content in lizardite, forsterite, talc, and goethite. The analyses confirm that the major serpentine minerals show two varieties: (1) Ni-bearing lizardite and (2) Ni-free lizardite. Furthermore, Ni-rich forsterite, enstatite, Ni-rich talc, sepiolite, periclase (MgO), and quartz were detected. Additionally, Raman spectroscopy evidence minor phases not detected by XRD: anatase, rutile, pyrite, hematite, chromite, magnesiochromite, and Ni-rich goethite. Our results show that the Ni substitution is only present in lizardite exhibiting turbostratic-stacking disorder. This finding has potential for being used as an exploration tool using short-wave-infrared spectroscopy online or as a portable instrument, and for defining geometallurgical parameters for processing these complex ores

Crystallography Open Database – an open-access collection of crystal structures

The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files

PREDON Scientific Data Preservation 2014

LPSC14037Scientific data collected with modern sensors or dedicated detectors exceed very often the perimeter of the initial scientific design. These data are obtained more and more frequently with large material and human efforts. A large class of scientific experiments are in fact unique because of their large scale, with very small chances to be repeated and to superseded by new experiments in the same domain: for instance high energy physics and astrophysics experiments involve multi-annual developments and a simple duplication of efforts in order to reproduce old data is simply not affordable. Other scientific experiments are in fact unique by nature: earth science, medical sciences etc. since the collected data is "time-stamped" and thereby non-reproducible by new experiments or observations. In addition, scientific data collection increased dramatically in the recent years, participating to the so-called "data deluge" and inviting for common reflection in the context of "big data" investigations. The new knowledge obtained using these data should be preserved long term such that the access and the re-use are made possible and lead to an enhancement of the initial investment. Data observatories, based on open access policies and coupled with multi-disciplinary techniques for indexing and mining may lead to truly new paradigms in science. It is therefore of outmost importance to pursue a coherent and vigorous approach to preserve the scientific data at long term. The preservation remains nevertheless a challenge due to the complexity of the data structure, the fragility of the custom-made software environments as well as the lack of rigorous approaches in workflows and algorithms. To address this challenge, the PREDON project has been initiated in France in 2012 within the MASTODONS program: a Big Data scientific challenge, initiated and supported by the Interdisciplinary Mission of the National Centre for Scientific Research (CNRS). PREDON is a study group formed by researchers from different disciplines and institutes. Several meetings and workshops lead to a rich exchange in ideas, paradigms and methods. The present document includes contributions of the participants to the PREDON Study Group, as well as invited papers, related to the scientific case, methodology and technology. This document should be read as a "facts finding" resource pointing to a concrete and significant scientific interest for long term research data preservation, as well as to cutting edge methods and technologies to achieve this goal. A sustained, coherent and long term action in the area of scientific data preservation would be highly beneficial

Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides also added at specific sites. The existence of insertional editing makes gene identification difficult and localization of editing sites has relied upon characterization of individual cDNAs. We have now determined the complete mitochondrial transcriptome of Physarum using Illumina deep sequencing of purified mitochondrial RNA. We report the first instances of A and G insertions and sites of partial and extragenic editing in Physarum mitochondrial RNAs, as well as an additional 772 C, U and dinucleotide insertions. The notable lack of antisense RNAs in our non-size selected, directional library argues strongly against an RNA-guided editing mechanism. Also of interest are our findings that sites of C to U changes are unedited at a significantly higher frequency than insertional editing sites and that substitutional editing of neighboring sites appears to be coupled. Finally, in addition to the characterization of RNAs from 17 predicted genes, our data identified nine new mitochondrial genes, four of which encode proteins that do not resemble other proteins in the database. Curiously, one of the latter mRNAs contains no editing sites

Challenges in coupled on-line-on-mine-real time mineralogical and chemical analyses on drill cores

The SOLSA project aims to develop an innovative on-line-on-mine-real-time expert system, combining sonic drilling, mineralogical and chemical characterization and data treatment. Ideally, this combination, highly demanded by mining and metallurgical companies, will speed up exploration, mining and processing. In order to evaluate the instrumental parameters for the SOLSA expert system, portable and laboratory analyses have been performed on four samples with contrasting lithologies: siliceous breccia, serpentinized harzburgite, sandstone and granite. More precisely, we evaluated the influence of the surface state of the sample on the signals obtained by portable X-Ray Fluorescence (pXRF) for chemistry and portable Infra-Red spectroscopy (pIR) for mineralogy. In addition, laboratory Raman spectroscopy, X-Ray Diffraction (XRD), XRF and ICP-OES laboratory analyses were performed to compare surface bulk mineralogical and chemical analyses. This presentation highlights (1) the importance of coupling chemical and mineralogical analytical technologies to obtain most complete information on samples, (2) the effect of the sample surface state on the XRF and IR signals from portable instruments. The last point is crucial for combined instrumental on-line sensor design and the calibration of the different instruments, especially in the case of pXRF

Photochemical solution processing of films of metastable phases for flexible devices: the beta-Bi2O3 polymorph

The potential of UV-light for the photochemical synthesis and stabilization of non-equilibrium crystalline phases in thin films is demonstrated for the beta-Bi2O3 polymorph. The pure beta-Bi2O3 phase is thermodynamically stable at high temperature (450-667 degrees C), which limits its applications in devices. Here, a tailored UV-absorbing bismuth(III)-N-methyldiethanolamine complex is selected as an ideal precursor for this phase, in order to induce under UV-light the formation of a -Bi-O-Bi- continuous network in the deposited layers and the further conversion into the beta-Bi2O3 polymorph at a temperature as low as 250 degrees C. The stabilization of the beta-Bi2O3 films is confirmed by their conductivity behavior and a thorough characterization of their crystal structure. This is also supported by their remarkable photocatalytic activity. Besides, this processing method has allowed us for the first time the preparation of beta-Bi2O3 films on flexible plastic substrates, which opens new opportunities for using these materials in potential applications not available until now (e.g., flexible photocatalytic reactors, self-cleaning surfaces or wearable antimicrobial fabrics). Therefore, photochemical solution deposition (PCSD) demonstrates to be not only an efficient approach for the low temperature processing of oxide films, but also an excellent alternative for the stabilization of metastable phases

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

The angiosperm genus Silene exhibits some of the most extreme and rapid divergence ever identified in mitochondrial genome architecture and nucleotide substitution rates. These patterns have been considered mitochondrial specific based on the absence of correlated changes in the small number of available nuclear and plastid gene sequences. To better assess the relationship between mitochondrial and plastid evolution, we sequenced the plastid genomes from four Silene species with fully sequenced mitochondrial genomes. We found that two species with fast-evolving mitochondrial genomes, S. noctiflora and S. conica, also exhibit accelerated rates of sequence and structural evolution in their plastid genomes. The nature of these changes, however, is markedly different from those in the mitochondrial genome. For example, in contrast to the mitochondrial pattern, which appears to be genome wide and mutationally driven, the plastid substitution rate accelerations are restricted to a subset of genes and preferentially affect nonsynonymous sites, indicating that altered selection pressures are acting on specific plastid-encoded functions in these species. Indeed, some plastid genes in S. noctiflora and S. conica show strong evidence of positive selection. In contrast, two species with more slowly evolving mitochondrial genomes, S. latifolia and S. vulgaris, have correspondingly low rates of nucleotide substitution in plastid genes as well as a plastid genome structure that has remained essentially unchanged since the origin of angiosperms. These results raise the possibility that common evolutionary forces could be shaping the extreme but distinct patterns of divergence in both organelle genomes within this genus