Exploration of phylogenetic data using a global sequence analysis method

BACKGROUND: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets. RESULTS: Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers. CONCLUSION: The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis

Detection of melanoma from dermoscopic images of naevi acquired under uncontrolled conditions.

International audienceBACKGROUND AND OBJECTIVE: Several systems for the diagnosis of melanoma from images of naevi obtained under controlled conditions have demonstrated comparable efficiency with dermatologists. However, their robustness to analyze daily routine images was sometimes questionable. The purpose of this work is to investigate to what extent the automatic melanoma diagnosis may be achieved from the analysis of uncontrolled images of pigmented skin lesions. MATERIALS AND METHODS: Images were acquired during regular practice by two dermatologists using Reflex 24 x 36 cameras combined with Heine Delta 10 dermascopes. The images were then digitalized using a scanner. In addition, five senior dermatologists were asked to give the diagnosis and therapeutic decision (exeresis) for 227 images of naevi, together with an opinion about the existence of malignancy-predictive features. Meanwhile, a learning by sample classifier for the diagnosis of melanoma was constructed, which combines image-processing with machine-learning techniques. After an automatic segmentation, geometric and colorimetric parameters were extracted from images and selected according to their efficiency in predicting malignancy features. A diagnosis was subsequently provided based on selected parameters. An extensive comparison of dermatologists' and computer results was subsequently performed. RESULTS AND CONCLUSION: The KL-PLS-based classifier shows comparable performances with respect to dermatologists (sensitivity: 95% and specificity: 60%). The algorithm provides an original insight into the clinical knowledge of pigmented skin lesions

Low-dose hyper-radiosensitivity of progressive and regressive cells isolated from a rat colon tumour: impact of DNA repair.

International audiencePURPOSE: To ask whether highly metastatic sublines show more marked low-dose hyper-radiosensitivity (HRS) response than poorly metastatic ones. MATERIALS AND METHODS: The progressive (PRO) subline showing tumourigenicity and metastatic potential and the regressive (REG) subline showing neither tumourigenicity nor metastatic potential were both isolated from a parental rat colon tumour. Clonogenic survival, micronuclei and apoptosis, cell cycle distribution, DNA single- (SSB) and double-strand breaks (DSB) induction and repair were examined. RESULTS: HRS phenomenon was demonstrated in PRO subline. Before irradiation, PRO cells show more spontaneous damage than REG cells. After 0.1 Gy, PRO cells displayed: (i) More DNA SSB 15 min post-irradiation, (ii) more unrepaired DNA DSB processed by the non-homologous end-joining (NHEJ) and by the RAD51-dependent recombination pathways, (iii) more micronuclei, than REG cells while neither apoptosis nor p53 phosphorylation nor cell cycle arrest was observed in both sublines. CONCLUSIONS: HRS response of PRO subline may be induced by impairments in NHEJ repair that targets G(1) cells and RAD51-dependent repair that targets S-G(2)/M cells. The cellular consequences of such impairments are a failure to arrest in cell cycle, the propagation of damage through cell cycle, mitotic death but not p53-dependent apoptosis. Tumourigenic cells with high metastatic potential may preferentially show HRS response

Automatic classification of skin lesions using geometrical measurements of adaptive neighborhoods and local binary patterns

ISBN:978-1-4799-8339-1International audienceThis paper introduces a method for characterizing and classifying skin lesions in dermoscopic color images with the goal of detecting which ones are melanoma (cancerous lesions). The images are described by means of the Local Binary Patterns (LBPs) computed on geometrical feature maps of each color component of the image. These maps are extracted from geometrical measurements of the General Adaptive Neighborhoods (GAN) of the pixels. The GAN of a pixel is a region surrounding it and fitting its local image spatial structure. The performance of the proposed texture descriptor has been evaluated by means of an Artificial Neural Network, and it has been compared with the classical LBPs. Experimental results using ROC curves show that the GAN-based method outperforms the classical one and the dermatologists' predictions

Automatic classification of skin lesions using color mathematical morphology-based texture descriptors

SPIE : Society of Photo-Optical Instrumentation EngineersInternational audienceIn this paper an automatic classification method of skin lesions from dermoscopic images is proposed. This method is based on color texture analysis based both on color mathematical morphology and Kohonen Self-Organizing Maps (SOM), and it does not need any previous segmentation process. More concretely, mathematical morphology is used to compute a local descriptor for each pixel of the image, while the SOM is used to cluster them and, thus, create the texture descriptor of the global image. Two approaches are proposed, depending on whether the pixel descriptor is computed using classical (i.e. spatially invariant) or adaptive (i.e. spatially variant) mathematical morphology by means of the Color Adaptive Neighborhoods (CANs) framework. Both approaches obtained similar areas under the ROC curve (AUC): 0.854 and 0.859 outperforming the AUC built upon dermatologists' predictions (0.792)

Texture descriptors based on adaptive neighborhoods for classification of pigmented skin lesions

art. 061104Se proponen diferentes descriptores de textura para la clasificación automática de lesiones cutáneas a partir de imágenes dermoscópicas. Se basan en el análisis de textura de color obtenido de (1) morfología matemática del color (MM) y mapas autoorganizativos de Kohonen (SOM) o (2) patrones binarios locales (LBP), calculados con el uso de barrios adaptativos locales de la imagen. Ninguno de estos dos enfoques necesita un proceso de segmentación anterior. En el primer descriptor propuesto, los barrios adaptativos se utilizan como elementos de estructuración para llevar a cabo operaciones MM adaptables que se combinan aún más mediante el uso de KOhonen SOM; esto se ha comparado con una versión no adaptativa. En la segunda, las vecindades adaptables permiten definir mapas de entidades geométricas, a partir de los cuales se calculan histogramas LBP. Esto también se ha comparado con un enfoque clásico de LBP. Un análisis de las características operativas del receptor de los resultados experimentales muestra que el enfoque adaptativo de LBP basado en la vecindad produce los mejores resultados. Supera a las versiones no adaptativas de los descriptores propuestos y las predicciones visuales de los dermatólogos.S

Position statement on classification of basal cell carcinomas. Part 1: unsupervised clustering of experts as a way to build an operational classification of advanced basal cell carcinoma based on pattern recognition

Background No simple classification system has emerged for 'advanced basal cell carcinomas', and more generally for all difficult-to-treat BCCs (DTT-BCCs), due to the heterogeneity of situations, TNM inappropriateness to BCCs, and different approaches of different specialists. Objective To generate an operational classification, using the unconscious ability of experts to simplify the great heterogeneity of the clinical situations into a few relevant groups, which drive their treatment decisions. Method Non-supervised independent and blinded clustering of real clinical cases of DTT-BCCs was used. Fourteen international experts from different specialties independently partitioned 199 patient cases considered 'difficult to treat' into as many clusters they want (<= 10), choosing their own criteria for partitioning. Convergences and divergences between the individual partitions were analyzed using the similarity matrix, K-mean approach, and average silhouette method. Results There was a rather consensual clustering of cases, regardless of the specialty and nationality of the experts. Mathematical analysis showed that consensus between experts was best represented by a partition of DTT-BCCs into five clusters, easily recognized a posteriori as five clear-cut patterns of clinical situations. The concept of 'locally advanced' did not appear consistent between experts. Conclusion Although convergence between experts was not granted, this experiment shows that clinicians dealing with BCCs all tend to work by a similar pattern recognition based on the overall analysis of the situation. This study thus provides the first consensual classification of DTT-BCCs. This experimental approach using mathematical analysis of independent and blinded clustering of cases by experts can probably be applied to many other situations in dermatology and oncology