Search results for "Cripto"

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

2019

AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…

A Dual Taxonomy for Defects in Digitized Historical Photos

2009

Old photos may be affected by several types of defects. Manual restorers use their own taxonomy to classify damages by which a photo is affected, in order to apply the proper restoration techniques for a specific defect. Once a photo is digitally acquired, defects become part of the image, and their aspect change. This paper wants to be a first attempt to correlate real defects of printed photos, and digital defects of their digitized versions. A dual taxonomy is proposed, for real and digital defects, and used to classify an image dataset, for a posteriori comparative study. Furthermore, a set of digital features is analyzed for digitized images, to identify which of them could be useful f…

Advances in the statistical methodology for the selection of image descriptors for visual pattern representation and classification

1995

Recent advances in the statistical methodology for selecting optimal subsets of features (image descriptors) for visual pattern representation and classification are presented. The paper attempts to provide a guideline about which approach to choose with respect to the a priori knowledge of the problem. Two basic approaches are reviewed and the conditions under which they should be used are specified. References to more detailed material about each one of the methods are given and experimental results supporting the main conclusions are briefly outlined.

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data …

2013

Abstract Background Clustering is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from statistics to computer science. Following Handl et al., it can be summarized as a three step process: (1) choice of a distance function; (2) choice of a clustering algorithm; (3) choice of a validation method. Although such a purist approach to clustering is hardly seen in many areas of science, genomic data require that level of attention, if inferences made from cluster analysis have to be of some relevance to biomedical research. Results A procedure is proposed for the assessment of the discriminative ability of a distance functi…

Statistical Reconstruction of Microstructures Using Entropic Descriptors

2018

We report a multiscale approach of broad applicability to stochastic reconstruction of multiphase materials, including porous ones. The approach devised uses an optimization method, such as the simulated annealing (SA) and the so-called entropic descriptors (EDs). For a binary pattern, they quantify spatial inhomogeneity or statistical complexity at discrete length-scales. The EDs extract dissimilar structural information to that given by two-point correlation functions (CFs). Within the SA, we use an appropriate cost function consisting of EDs or comprised of EDs and CFs. It was found that the stochastic reconstruction is computationally efficient when we begin with a preliminary synthetic…

Set Descriptors for Visual Evaluation of Human Corneal Endothelia

2001

Images of corneal endothelium obtained from specular microscopy are of great importance in the evaluation of the corneal endothelium status. Several commercial tools provide some numerical descriptors to characterize these images in terms of cell density, hexagonality, and some descriptive statistics of the cell areas. However, it is a too simple analysis that only detects severe abnormal endothelia with many irregular and large cells. Detection of subtle abnormalities needs a more refined analysis. This paper proposes a shape-size descriptor based on some modified versions of the geometric covariogram. This descriptor is presented as a valid alternative to the classical analysis that provi…

Multivariate analysis in the identification of biological targets for designed molecular structures: The BIOTA protocol

2013

In this work the new protocol BIOlogical Target Assignation (BIOTA) for the prediction of the biological target from molecular structures is proposed. BIOTA is based on the Principal Components Analysis (PCA) application on a matrix of ligands versus molecular descriptors. The application of BIOTA could allow to hypothesize the mechanism of action of a candidate drug prior to its biological evaluation or to repurpose old drugs. The protocol can be fine-tuned by choosing opportune targets (biological or not) and molecular descriptors, and it can be useful in every fields in with it is possible to collect set of compounds with known properties. The robustness of the protocol depends from diff…

Influence du court noué sur la diversité fonctionnelle des champignons mycorhiziens à arbuscules dans des racines et du sol de vigne

2022

Le court-noué (CN) correspond à un dépérissement infectieux (népovirus) qui apparaît par taches au sein des parcelles. Cette maladie entraîne une dégénérescence progressive de la vigne qui conduit in fine à la mort des ceps. A l’heure actuelle, environ 60% du vignoble national serait touché, dont 30% de façon importante. Seize népovirus sont responsables de dégénérescence ou de dépérissement de la vigne. Cependant, le Grapevine FanLeaf Virus (GFLV) est le principal agent responsable. Il est transmis spécifiquement de plante à plante par un nématode ectoparasite du sol, Xiphinema index. Les nématodes, en piquant successivement deux ceps voisins dont les racines sont proches, inoculent le vir…

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Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease.

2016

Background Huanglongbing (HLB) disease is still the greatest threat to citriculture worldwide. Although there is not any resistance source in the Citrus germplasm, a certain level of moderated tolerance is present. A large-scale analysis of proteomic responses of Citrus may help: 1) clarifying physiological and molecular effects of disease progression, 2) validating previous data at transcriptomic level, and 3) identifying biomarkers for development of early diagnostics, short-term therapeutics and long-term genetic resistance. Results In this work we have conducted a proteomic analysis of mature leaves of two Citrus genotypes with well-known differing tolerances to HLB: Navel orange (highl…