Characterization of Posidonia Oceanica Seagrass Aerenchyma through Whole Slide Imaging: A Pilot Study

Characterizing the tissue morphology and anatomy of seagrasses is essential to predicting their acoustic behavior. In this pilot study, we use histology techniques and whole slide imaging (WSI) to describe the composition and topology of the aerenchyma of an entire leaf blade in an automatic way combining the advantages of X-ray microtomography and optical microscopy. Paraffin blocks are prepared in such a way that microtome slices contain an arbitrarily large number of cross sections distributed along the full length of a blade. The sample organization in the paraffin block coupled with whole slide image analysis allows high throughput data extraction and an exhaustive characterization along the whole blade length. The core of the work are image processing algorithms that can identify cells and air lacunae (or void) from fiber strand, epidermis, mesophyll and vascular system. A set of specific features is developed to adequately describe the convexity of cells and voids where standard descriptors fail. The features scrutinize the local curvature of the object borders to allow an accurate discrimination between void and cell through machine learning. The algorithm allows to reconstruct the cells and cell membrane features that are relevant to tissue density, compressibility and rigidity. Size distribution of the different cell types and gas spaces, total biomass and total void volume fraction are then extracted from the high resolution slices to provide a complete characterization of the tissue along the leave from its base to the apex

Induction of α1-tubulin gene expression during development and regeneration of the fish central nervous system

The α1- and α2-tubulin encoding genes were cloned from a goldfish genomic DNA library. α1- and α2-tubulin RNA expression was examined in developing and adult retinas. These studies demonstrated increased α1-tubulin RNA in presumptive ganglion cells that grow axons early in retinal development and in adult retinal ganglion cells whose optic axons had been damaged. The α2-tubulin RNA was undetectable in developing retina and constitutively expressed in adult retinal ganglion cells regardless of optic nerve crush. To determine if these changes in α1-tubulin RNA reflected changes in α1-tubulin promoter activity, we introduced into zebrafish embryos and adult goldfish retinal explants expression vectors harboring the α1-tubulin gene's promoter. These studies showed that the α1-tubulin promoter confers a developmentally regulated, neuron-restricted pattern of reporter gene expression in vivo and its activity is increased in adult retinal neurons induced to regenerate their axons. Promoter deletions defined regions of α1-tubulin DNA necessary for this pattern of expression. These results suggest that DNA sequences necessary for α1-tubulin gene induction during central nervous system development and regeneration are contained within the α1-tubulin gene's 5′-flanking DNA and that this promoter will be useful for identifying these elements and their DNA binding proteins. © 1998 John Wiley & Sons, Inc. J Neurobiol 37: 429–440, 1998Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34478/1/8_ftp.pd

A New Method to Address Unmet Needs for Extracting Individual Cell Migration Features from a Large Number of Cells Embedded in 3D Volumes

Background: In vitro cell observation has been widely used by biologists and pharmacologists for screening molecule-induced effects on cancer cells. Computer-assisted time-lapse microscopy enables automated live cell imaging in vitro, enabling cell behavior characterization through image analysis, in particular regarding cell migration. In this context, 3D cell assays in transparent matrix gels have been developed to provide more realistic in vitro 3D environments for monitoring cell migration (fundamentally different from cell motility behavior observed in 2D), which is related to the spread of cancer and metastases. Methodology/Principal Findings: In this paper we propose an improved automated tracking method that is designed to robustly and individually follow a large number of unlabeled cells observed under phase-contrast microscopy in 3D gels. The method automatically detects and tracks individual cells across a sequence of acquired volumes, using a template matching filtering method that in turn allows for robust detection and mean-shift tracking. The robustness of the method results from detecting and managing the cases where two cell (mean-shift) trackers converge to the same point. The resulting trajectories quantify cell migration through statistical analysis of 3D trajectory descriptors. We manually validated the method and observed efficient cell detection and a low tracking error rate (6%). We also applied the method in a real biological experiment where the pro-migratory effects of hyaluronic acid (HA) were analyzed on brain cancer cells. Using collagen gels with increased HA proportions, we were able to evidence a dose-response effect on cell migration abilities. Conclusions/Significance: The developed method enables biomedical researchers to automatically and robustly quantify the pro- or anti-migratory effects of different experimental conditions on unlabeled cell cultures in a 3D environment. © 2011 Adanja et al.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Combined analysis of HPV DNA, p16, p21 and p53 to predict prognosis in patients with stage IV hypopharyngeal carcinoma

We examined p16, p21 and p53 expression in combination with the presence of human papillomavirus (HPV) DNA as molecular markers to predict survival in patients with stage IV hypopharyngeal squamous cell carcinoma (HSCC).Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Incremental concept formation via a suitability criterion

info:eu-repo/semantics/publishe

Formation incrémentale de concepts par un critère d'adéquation

info:eu-repo/semantics/publishe

Finding prototypes for nearest neighbour classification by means of gradient descent and deterministic annealing

info:eu-repo/semantics/publishe

Incremental Classification, a Multidisciplinary Viewpoint

info:eu-repo/semantics/publishe

Statistical Strategies in Incremental Conceptual Classification

info:eu-repo/semantics/publishe

Formation de concepts en intelligence artificielle: Comparaison avec l'analyse relationnelle

Des des travaux précédents ([Decaes89 a,b][Decaes90]), l'auteure a étudié des mécanismes incrémentaux de "Formation de Concepts", et a développé ADECLU, un système incrémental de "Conceptual Clustering". Dans cet article, l'auteure présente les différentes version de ADECLU et les compare, du point de vue conceptuel et des performances, aux méthodes développées en Analyse Relationnelle (Agrégation et Bloc Sériation) [Marc81, 87][Mich87]info:eu-repo/semantics/publishe