Correcting the optimally selected resampling-based error rate: A smooth analytical alternative to nested cross-validation

High-dimensional binary classification tasks, e.g. the classification of microarray samples into normal and cancer tissues, usually involve a tuning parameter adjusting the complexity of the applied method to the examined data set. By reporting the performance of the best tuning parameter value only, over-optimistic prediction errors are published. The contribution of this paper is two-fold. Firstly, we develop a new method for tuning bias correction which can be motivated by decision theoretic considerations. The method is based on the decomposition of the unconditional error rate involving the tuning procedure. Our corrected error estimator can be written as a weighted mean of the errors obtained using the different tuning parameter values. It can be interpreted as a smooth version of nested cross-validation (NCV) which is the standard approach for avoiding tuning bias. In contrast to NCV, the weighting scheme of our method guarantees intuitive bounds for the corrected error. Secondly, we suggest to use bias correction methods also to address the bias resulting from the optimal choice of the classification method among several competitors. This method selection bias is particularly relevant to prediction problems in high-dimensional data. In the absence of standards, it is common practice to try several methods successively, which can lead to an optimistic bias similar to the tuning bias. We demonstrate the performance of our method to address both types of bias based on microarray data sets and compare it to existing methods. This study confirms that our approach yields estimates competitive to NCV at a much lower computational price

Unbiased split selection for classification trees based on the Gini Index

The Gini gain is one of the most common variable selection criteria in machine learning. We derive the exact distribution of the maximally selected Gini gain in the context of binary classification using continuous predictors by means of a combinatorial approach. This distribution provides a formal support for variable selection bias in favor of variables with a high amount of missing values when the Gini gain is used as split selection criterion, and we suggest to use the resulting p-value as an unbiased split selection criterion in recursive partitioning algorithms. We demonstrate the efficiency of our novel method in simulation- and real data- studies from veterinary gynecology in the context of binary classification and continuous predictor variables with different numbers of missing values. Our method is extendible to categorical and ordinal predictor variables and to other split selection criteria such as the cross-entropy criterion

Toxicity of Pb and of Pb/Cd combination on the springtail Folsomia candida in natural soils: Reproduction, growth and bioaccumulation as indicators

The toxicity of Pb and Cd+Pb was assessed on the Collembola F. candida in two cultivated soils (SV and AU) with low organic matter (OM) content and circumneutral to basic pH, and an acid forested soil (EPC) with high OM content. Collembola reproduction and growth as well as metal content in Collembola body, in soil, exchangeable fraction and soil solutions, pH and DOC were investigated. Pb and Cd+Pb were the highest in exchangeable fraction and soil solution of the acidic soils. Soil solution pH decreased after metal spiking in every soil due to metal adsorption, which was similar for Cd and the highest in AU for Pb. With increasing Pb and Cd+Pb, the most important reproduction decrease was in EPC soil. The LOEC for reproduction after metal addition was 2400 (Pb) and 200/2400 (Cd/Pb), 1200 and 100/1200, 300 and 100/1200 μg g−1 for AU, SV and EPC, respectively. The highest and the lowest Pb toxicity was observed for EPC and AU bulk soil, respectively. The metal in Collembola increased with increasing soil concentration, except in AU, but the decreasing BFsolution with increasing concentrations indicates a limited metal transfer to Collembola or an increased metal removal. Loading high Pb concentrations decreases Cd absorption by the Collembola, but the reverse was not true. The highest Pb toxicity in EPC can be explained by pH and OM content. Because of metal complexation, OM might have a protective role but its ingestion by Collembola lead to higher toxicity. Metal bioavailability in Collembola differs from soil solution indicating that soil solution is not sufficient to evaluate toxicity in soil organisms. The toxicity as a whole decreased when metals were combined, except for Pb in AU, due to adsorption competition between Cd and Pb on clay particles and OM sites in AU and EPC soils, respectively

Determining cadmium critical concentrations in natural soils by assessing Collembola mortality, reproduction and growth

The toxicity of cadmium for the Collembola Folsomia candida was studied by determining the effects of increasing Cd concentrations on growth, survival and reproduction in three cultivated and forested soils with different pH (4.5–8.2) and organic matter content (1.6–16.5%). The Cd concentration in soil CaCl2 exchangeable fraction, in soil solution and in Collembola body was determined. At similar total soil concentrations, the Cd concentration in soil solutions strongly decreased with increasing pH. Reproduction was the most sensitive parameter. Low organic matter content was a limiting factor for reproduction. Effect of Cd on reproduction was better described by soil or body concentrations than by soil solution concentration. Values of EC50-Repro expressed on the basis of nominal soil concentration were 182, 111 and 107 μg g−1, respectively, for a carbonated cultivated soil (AU), an acid forested soil with high organic matter (EPC) and a circumneutral cultivated soil with low organic content (SV). Sensitivity to Cd was enhanced for low OM content and acidic pH. The effect of Cd on reproduction is not directly related to Cd concentration in soil solution for carbonated soil: a very low value is found for EC50-Repro (0.17) based on soil solution for the soil with the highest pH (AU; pH=8.2). Chronic toxicity cannot be predicted on the basis of soluble fractions. Critical concentrations were 8×10−5, 1.1, 0.3 μg mL−1, respectively, for AU, EPC and SV soils

World Health Organisation test applied on Culicoides: a multicentric study

The aim of this work is to organize a multicentric assay to compare susceptibilities of Culicoides populations to insecticides (i.e. C. imicola and C. obsoletus sensu stricto). The base line of the World Health Organisation test kit (WHO/VBC81.805) is to expose mosquitoes to papers impregnated with insecticides to detect the resistance of Anopheles (paludism vector) in the field. In a novel approach, the WHO test can be used on Culicoides to assess midges' susceptibility to insecticides. Information on the intrinsic susceptibilities to insecticides is required to assess correctly the existing (or new) formulations of insecticide. This multicentric assay will improve our capacity to experiment by networking and assess the population variability by comparing susceptibilities between different populations of Culicoides. Field-collected midges are trapped alive using an ultraviolet light trap (OVI model, South Africa) and replacing the collection jar with a fine mesh cage. To prevent desiccation, cages are covered with wet papers, wrapped in aluminium foil and retrieved at dawn. It is important to choose the site and period with abundant target species to improve robustness with more individuals. Experiments should be carried out in an insecticide-free environment with constant temperature and humidity, and started a few hours after collection. Insecticide-impregnated papers are rolled and fastened into the WHO kit test tube. About 30 Culicoides (approximately 20 nulliparous females) are collected and transferred to the tube. Tubes are maintained horizontally for an hour (exposure to insecticide). Mortalities are recorded 1 h and 24 h after exposure. One control is performed without insecticide to validate the test. Mortalities are analysed by probit regression to obtain LC50 and LC90 for each population. The test has to be run at least with four concentrations of insecticide, one control and four replicates with samples from the same population. Only nulliparous females are recorded. Insecticide concentrations are given in percentages (WHO standard). In this WHO test, the target species are C. imicola and C. obsoletus s.s., and the active ingredient used is deltamethrin at doses 0.005, 0.001, 0.0005 and 0.0001%. Data will be centralized and analysed by EID-Méditerranée (France), and results will be given back to the partners and published. Future studies could focus on comparing the four deltamethrin concentrations on other species and testing Culicoides susceptibility to other components. (Texte intégral

Evolution and relationships of the conifer seed cone telemachus: Evidence from the triassic of antarctica

The seed cone Telemachus is known from several Triassic localities in Gondwana. New specimens from two localities in Antarctica provide additional information about the type species, Telemachus elongatus, based on details of morphology and anatomy revealed by using a modified transfer technique on the compressed plants. Seed cones of T. elongatus are up to 6.0 cm long and characterized by conspicuous, elongate bracts. A second Antarctic species, described here as Telemachus antarcticus, is segregated, based on a shorter bract and differences in cone size. Newly recognized features of the genus include the shape, size, and disposition of the ovules; vascularization of the ovuliferous complex; and scale and bract histology. As a result of this new information, it is now possible to compare Telemachus with the permineralized Middle Triassic conifer seed cone Parasciadopitys from the Central Transantarctic Mountains. The similarities between the two genera make it possible to relate organs in different preservational modes and to develop a more complete concept for this widely distributed Gondwana conifer. Placing the Telemachus plant within a phylogenetic context makes it possible to evaluate the relationship with other so-called transitional conifers, an informal group that has been interpreted as intermediate between Paleozoic and modern conifers.Fil: Escapa, Ignacio Hernán. University of Kansas; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Decombeix, Anne-Laure. University of Kansas; Estados UnidosFil: Taylor, Edith L.. University of Kansas; Estados UnidosFil: Taylor, Thomas N.. University of Kansas; Estados Unido

Cartographie des zones humides de montagne par télédétection. Potentialités à très haute résolution spatiale

International audienceSuite aux lois Grenelle 1 et 2, la mise en place des schémas régionaux de cohérence écologique (SRCE) devra s'appuyer sur des outils cartographiques pour aider à la définition des trames verte et bleue. En raison de leurs multiples intérêts, les zones humides constituent des entités essentielles à intégrer. La télédétection fait preuve de potentialités et d'efficience quant à la détection et à la caractérisation de ces milieux, bien qu'ils restent difficiles à délimiter. Les zones humides de montagne sont particulièrement bien représentatives de cette problématique. Elles revêtent à la fois un fort intérêt écologique (richesse floristique et faunistique) mais sont potentiellement difficiles à détecter (petite taille, recouvertes par la neige de l'automne au printemps, ombres portées des crêtes, etc.). L'émergence de futures données à très haute résolution spatiale (THRS) et à forte répétitivité, qui seront produites par les missions spatiales Pléiades ou Venµs, offrent ainsi de nouvelles perspectives. L'objectif de cet article vise à déterminer si la THRS apporte une plus-value pour la caractérisation des petites zones humides de montagne, comparativement à des données HRS qui présentent une résolution spectrale plus riche. Les résultats obtenus démontrent ainsi que 1) des images THRS (Quickbird) permettent de compenser la richesse spectrale d'images HRS (Spot-5), 2) les méthodes orientées objets présentent de meilleurs résultats que des méthodes orientées pixels bien que 3) ces milieux restent difficiles à détecter (53 % de détection correcte)

Evidence of Springwater Acidification in the Vosges Mountains (North-East of France): Influence of Bedrock Buffering Capacity

Investigations on springwater acidity were carried out in the Vosges mountains (north-eastern France). Acid or poorly buffered spring and streamwaters were detected in the same area. The proportion of acid springwaters (pH < 5.6) is about 20% among 220 springs. The springwater pH on granite are equally spread between 5.0 and 6.8 whereas on sandstone a majority of springs is in the range 5.6 to 6.2. As a whole, but mainly on sandstone, from the 1960's to 1990's, the shape of the pH distributions shifts toward greater acidity. In the sandstone area, trends in pH, alkalinity, total hardness (corresponding to divalent cations), sulfate and nitrate were considered over the 30 yr period (1963-1996) in relation to the bedrock chemical composition. Kendall seasonal tau coefficients indicate that decreasing trends were significant for the first three parameters. Linear regression on the smoothed mean value revealed 18 and 90% decrease for pH and alkalinity respectively, for springwaters draining poor-base cation sandstone whereas only 8 and 30% decrease respectively, was observed on clay-enriched sandstone. On silica-enriched sandstone, alkalinity began to decrease in the early 70's as well as pH. Loss of alkalinity only occurred in the early 80's for springs draining clay enriched sandstone. This can be interpreted as a titration process by acid atmospheric inputs of the buffering capacity of weathering and exchange processes in the soils and the catchment bedrock. The nitrate presents an increasing step in the early seventies but possibly as a result of change in analytical technics and/or increase in atmospheric inputs mainly resulting from increase in fertiliser inputs in agricultural areas or in car traffic. Surprisingly no change in sulfate was noticed in any groups of springs probably as a result of the adsorption/mobilisation in the soils. These long-term trends in spring waters (1963-1996) confirmed the soil and streamwater acidification trends already mentioned in this region, in relation to acid atmospheric inputs since no climate nor forestry practice changes have been detected over the period. Moreover, in spite of acid atmospheric input reductions, no recovery can presently be detected