Agricolae - Ten years of an open source statistical tool for experiments in breeding, agriculture and biology.

Plant breeders and educators working with the International Potato Center (CIP) needed freely available statistical tools. In response, we created first a set of scripts for specific tasks using the open source statistical software R. Based on this we eventually compiled the R package agricolae as it covered a niche. Here we describe for the first time its main functions in the form of an article. We also review its reception using download statistics, citation data, and feedback from a user survey. We highlight usage in our extended network of collaborators. The package has found applications beyond agriculture in fields like aquaculture, ecology, biodiversity, conservation biology and cancer research. In summary, the package agricolae is a well established statistical toolbox based on R with a broad range of applications in design and analyses of experiments also in the wider biological community

Evaluacion de la estabilidad de resistencia de clones avanzados del CIP a la marchitez bacteriana usando diferentes variantes de Ralstonia solanacearum.

La marchitez bacteriana (MB) o pudricion parda causada por Ralstonia solanacearum es una de las enfermedades bacterianas mas destructivas en el cultivo de la papa. La resistencia de las plantas es el medio mas efectivo para controlar esta enfermedad. Sin embargo, la resistencia a la MB es a menudo superada debido a la gran variabilidad del patogeno. En el presente trabajo se evaluo la reaccion de 10 clones avanzados del CIP (seleccionados previamente por su resistencia al BV2A) contra 5 cepas correspondientes a los biovares 1, 2a, 2T y 3, de R. solanacearum bajo condiciones de invernadero. 15 plantas por clon de aproximadamente 15 cm de altura fueron inoculadas vertiendo en el suelo una suspension de 150 ml de la bacteria para obtener una concentracion final de 10 7 ufc/g suelo. Las variedades de papa Revolucion y CIP -01149 fueron utilizadas como control susceptible y moderadamente resistente, respectivamente. Las evaluaciones de la presencia de los sintomas de marchitez se realizaron semanalmente hasta 10 dias antes de la cosecha de los tuberculos. En plantas sin sintomas, los tallos y tuberculos fueron analizados mediante ELISA-NCM post-enriquecimiento para detectar infeccion latente. El analisis estadistico del porcentaje de plantas infectadas muestra diferencias significativas entre clones y cepas de R. solanacearum. No se observo resistencia completa (0% de infeccion) en ninguno de los clones evaluados a todas las cepas -de R. solanacearum. Sin embargo, el clon 394895.7 fue el mas resistente, mostrando un maximo de 13 % de infeccion cuando fue inoculado con la cepa mas virulenta (CIP-204). La resistencia a todas las cepas de R. solanacearum detectada en el clon 394895.7 muestra su alto potencial como una fuentes genetica de la resistencia a la marchitez bacterian

Regularized logistic regression and multi-objective variable selection for classifying MEG data

This paper addresses the question of maximizing classifier accuracy for classifying task-related mental activity from Magnetoencelophalography (MEG) data. We propose the use of different sources of information and introduce an automatic channel selection procedure. To determine an informative set of channels, our approach combines a variety of machine learning algorithms: feature subset selection methods, classifiers based on regularized logistic regression, information fusion, and multiobjective optimization based on probabilistic modeling of the search space. The experimental results show that our proposal is able to improve classification accuracy compared to approaches whose classifiers use only one type of MEG information or for which the set of channels is fixed a priori

Final NOMAD results on nu_mu->nu_tau and nu_e->nu_tau oscillations including a new search for nu_tau appearance using hadronic tau decays

Results from the nu_tau appearance search in a neutrino beam using the full NOMAD data sample are reported. A new analysis unifies all the hadronic tau decays, significantly improving the overall sensitivity of the experiment to oscillations. The "blind analysis" of all topologies yields no evidence for an oscillation signal. In the two-family oscillation scenario, this sets a 90% C.L. allowed region in the sin^2(2theta)-Delta m^2 plane which includes sin^2(2theta)<3.3 x 10^{-4} at large Delta m^2 and Delta m^2 < 0.7 eV^2/c^4 at sin^2(2theta)=1. The corresponding contour in the nu_e->nu_tau oscillation hypothesis results in sin^2(2theta)<1.5 x 10^{-2} at large Delta m^2 and Delta m^2 < 5.9 eV^2/c^4 at sin^2(2theta)=1. We also derive limits on effective couplings of the tau lepton to nu_mu or nu_e.Comment: 46 pages, 16 figures, Latex, to appear on Nucl. Phys.