Cement stratigraphy: image probes of cathodoluminescent facies

Cement stratigraphy of carbonates aims to establish the chronology of processes involved in the rock diagenesis. Regional cement stratigraphy allows correlations and understanding of the petrological heterogeneities in reservoirs and aquifers, but is a long and rigorous approach. This article exposes a methodology of image analysis that facilitates the spatial correlation of diagenetic events in carbonate rocks. Based on the statistical comparison of signals extracted from the red spectrum emission of cathodoluminescence digital images, it gives via crosscorrelation a measure of similarity (values scaled from minimum −1 to maximum 1) between two cathodoluminescence facies. Cementation events and diagenetic chronologies can thus be quickly correlated without the support of a full chronology, the model normally established on cement morphologies, petrological analyses and cathodoluminescence zonation sequences. A case study from two Upper Kimmeridgian Mount Salève outcrops (France) illustrates this methodology. Their diagenetic sequences recorded in cathodoluminescent cements are presented and being compared. The final statistical similarity between the two outcrops reaches an index of R=0.78. This result is sustained by petrological and geochemical analyses such as alizarine-ferricyanure stained thin sections, X microfluorescence mapping of elements, and microthermometry of fluid inclusion

Real time correlation-based stereo: algorithm, implementations and applications

This paper describes some of the work on stereo that has been going on at INRIA in the last four years. The work has concentrated on obtaining dense, accurate and reliable range maps of the environment at rates compatible with the real-time constraints of such applications as the navigation of mobile vehicles in man-made or natural environments. The class of algorithms which has been selected among several is the class of algorithms which has been selected among several is the class of correlation-based stereo algorithms because they are the only ones that can produce sufficiently dense range maps with an algoritmic structure which lends itself nicely to fast implementations because of the simplicity of the underlying computation. We describe the various improvements that we have brought to the original idea, including validation and characterization of the quality of the matches, a recursive implementation of the score computation which makes the method independent of the size of the correlation window and a calibration method which does not require the use of a calibration pattern. We then describe two implementations of this algorithm on two very different pieces of hardware. The first implementation is on a board with four digital signal processors designed jointly with Matra MSII. This implementation can produce 64x64 range maps at rate varying between 200 and 400 ms, depending upon the range of disparities. The second implementation is on a board developed by DEC-PRL and can perform the cross-correlation of two 256X256 images in 140 ms. The first implementation has been integrated in the navigation system of the INRIA cart and used to correct for inertial and odometric errors in navigation experiments both indoors and outdoors on road. This is the first application of our correlation-based algorithm which is described in the paper. The second application has been done jointly with people from the french national space agence (CNES) to study the possibility of using stereo on a future planetary rover for the construction of digital elevation maps. We have shown that real time stereo is possible today at low-cost and can be applied in real applications. The algorithm that has been described is not the most sophisticated available but we have made it robust and reliable thanks to a number of improvements. Evan though each of these improvements is not earth-shattering from the pure research point of view, altogether they have allowed us to go beyond a very important threshold. This threshold measures the difference between a program that runs in the laboratory on a few images and one that works continuously for hours on a sequence of stereo pairs and produces results at such rates and of such quality that they can be used to guide a real vehicle or to produce discrete elevation maps. We believe that this threshold has only been reached in a very small number of cases

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction

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

Application of total internal reflexion fluorescence microscopy for studying pH changes in an occluded electrochemical cell: Development of a waveguide sensor

A device for pH mapping derived from optical sensors similar to total internal reflection fluorescence microscopy (TIRFM) has been developed for future possible applications in the field of localized corrosion. The sensing principle is the increase of the fluorescent yield of the fluorescein with the pH of the medium. The basic principle of this sensor is based on the excitation of a fluorescent silica polymer film of nanometre dimensions, deposited by sol–gel method on a waveguiding layer. The total internal reflexion conditions creates an evanescent wave which interacts with the molecules trapped in the silica layer. A conventional microscope located above the sample collects the fluorescence emitted by this sensing layer. An original application of this type of sensor is proposed for studying the concentration profile of chemical species in an occluded electrochemical cell using a very simple type of waveguide. This method takes advantages of the confinement and strong intensity of the field over a few hundred nanometres below the surface of the waveguide thus allowing local analysis and imaging of the concentration profiles of chemical species in this volume. Keywords: Fluorescence, pH mapping, Microscopy, Waveguide, TIRFM, Crevice corrosio

Copper-uptake mediated by an ecofriendly zwitterionic ionic liquid: A new challenge for a cleaner bioeconomy

This study aims to investigate the ability of an imidazolium biobased Zwitterionic Ionic Liquids (ZILs) in enhancing the phytoavailability of copper from garden (G) and vineyard (V) soils using the model plant ryegrass. Uncontaminated and artificially contaminated CuSO4 soils, unamended and ZIL-amended soil modalities were designed. The copper/ZIL mo-lar ratio (1/4) introduced was rationally established based on molecular modeling and on the maximal copper concentration in artificially contaminated soil. Higher accumulation of copper in the shoots was detected for the uncontaminated and copper contaminated ZIL amended V soils (18.9 and 23.3 mg/kg, respectively) contrary to G soils together with a ZIL concentration of around 3% (W/W) detected by LC-MS analyses. These data evidenced a Cu-accumulation improvement of 38% and 66% compared to non-amended V soils (13.6 and 13.9 mg/kg respectively). ZIL would be mainly present under Cu(II)-ZIL4 complexes in the shoots. The impact on the chemical composition of shoot was also studied. The results show that depending on the soils modalitity, the presence of free copper and/or ZIL led to different chemical compositions in lignin and monomeric sugar contents. In the biorefinery context, performances of enzymatic hydrolysis of shoots were also related to the presence of both ZIL and copper under free or complex forms. Ecotoxicity assessment of the vineyard soil samples indicated that the quantity of copper and ZIL remaining in the soils had no sig-nificant toxicity. ZIL amendment in a copper-contaminated soil was demonstrated as being a promising way to promote the valorization of phytoremediation plants

Real time correlation-based stereo: algorithm, implementations and applications

This paper describes some of the work on stereo that has been going on at INRIA in the last four years. The work has concentrated on obtaining dense, accurate and reliable range maps of the environment at rates compatible with the real-time constraints of such applications as the navigation of mobile vehicles in man-made or natural environments. The class of algorithms which has been selected among several is the class of algorithms which has been selected among several is the class of correlation-based stereo algorithms because they are the only ones that can produce sufficiently dense range maps with an algoritmic structure which lends itself nicely to fast implementations because of the simplicity of the underlying computation. We describe the various improvements that we have brought to the original idea, including validation and characterization of the quality of the matches, a recursive implementation of the score computation which makes the method independent of the size of the correlation window and a calibration method which does not require the use of a calibration pattern. We then describe two implementations of this algorithm on two very different pieces of hardware. The first implementation is on a board with four digital signal processors designed jointly with Matra MSII. This implementation can produce 64x64 range maps at rate varying between 200 and 400 ms, depending upon the range of disparities. The second implementation is on a board developed by DEC-PRL and can perform the cross-correlation of two 256X256 images in 140 ms. The first implementation has been integrated in the navigation system of the INRIA cart and used to correct for inertial and odometric errors in navigation experiments both indoors and outdoors on road. This is the first application of our correlation-based algorithm which is described in the paper. The second application has been done jointly with people from the french national space agence (CNES) to study the possibility of using stereo on a future planetary rover for the construction of digital elevation maps. We have shown that real time stereo is possible today at low-cost and can be applied in real applications. The algorithm that has been described is not the most sophisticated available but we have made it robust and reliable thanks to a number of improvements. Evan though each of these improvements is not earth-shattering from the pure research point of view, altogether they have allowed us to go beyond a very important threshold. This threshold measures the difference between a program that runs in the laboratory on a few images and one that works continuously for hours on a sequence of stereo pairs and produces results at such rates and of such quality that they can be used to guide a real vehicle or to produce discrete elevation maps. We believe that this threshold has only been reached in a very small number of cases

Combining Phytoremediation and Biorefinery Strategies Assisted by an Ecofriendly Zwitterionic Ionic Liquid: A New Challenge for a Cleaner Bioeconomy

International audienceThis study aims to investigate the ability of an imidazolium biobased Zwitterionic Ionic Liquids (ZILs) in enhancing the phytoextraction of copper from garden and vineyard soils using the model plant ryegrass (Lolium perenne L.). The copper/ZIL molar ratio (1/4) introduced was rationally established based on molecular modeling and on the maximal copper concentration in artificially contaminated soil. Higher accumulation of copper in the shoots was detected for the uncontaminated and copper contaminated ZIL amended soils (18.9 and 23.3 mg.kg-1, respectively) together with a similar ZIL concentration of around 3% w/w detected by LC-MS analyses. These data evidenced a phytoextraction improvement of 38 and 66% compared to non-amended soils. ZIL would be mainly present under Cu(II)-ZIL4 complexes in the shoots. However depending on the soil modalities, the presence of free copper and/or free ZIL led to different chemical compositions in lignin and monomeric sugar contents. In the biorefinery context, performances of enzymatic hydrolysis of shoots were related to the presence of both ZIL and copper under free or complex forms. Ecotoxicity of the different soils indicated that the quantity of copper and ZIL remaining in the soils had no significant toxicity. ZIL amendment in a copper-contaminated soil was demonstrated as being a promising way to promote the valorization of phytoremediation plants