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There are many clinical and topographic classifications of keratoconus but only one, proposed by Sandali et al., used optical coherence tomography (OCT) to evaluate the corneal structure. The purpose of this study was to evaluate the classification in clinical practice.Methode: we performed a retrospective analysis of all patients with keratoconus who consulted at Montpellier University Hospital between July 2018 and July 2020. The diagnosis of keratoconus was based on a range of clinical and topographic features. Exclusion criteria were a history of ocular surgery. Patients with keratoconus were classified according to 5 stages of increasing severity based on the appearance of corneal OCT. We analyzed the functional, clinical and topographic characteristics according to the stages. We also analyzed the error of corneal thickness measurement by topography and described the proposed treatments by stage.Results: we included 143 eyes in 143 patients with keratoconus and 35 eyes in 35 healthy patients. Of the keratoconus patients, 116, 8, 9, 6, and 4 were at stage 1, 2, 3, 4, and 5 of the classification, respectively. The severity of structural damage on OCT was associated with greater severity of functional, anatomic and topographic damage. The difference in corneal thickness measurement between OCT and topography was higher with more severe stage. The proposed treatments for the more severe stages were more invasive.Conclusion: the structural classification examined seems able to classify keratoconus severity. We found similar results to the study of Sandali et al. The classification is not well known by practitioners but could find increasing interest for keratoconus with improvement and wider use of anterior segment OCT.; Il existe de nombreuses classifications cliniques et topographiques du kératocône mais une seule, proposée par Sandali et al. utilise la tomographie en cohérence optique (OCT) pour évaluer la structure cornéenne. L’objectif de cette étude est d’évaluer cette classification en pratique clinique.Matériel et méthode : nous avons effectué une analyse rétrospective de tous les patients atteints de kératocône ayant consulté au CHU de Montpellier entre juillet 2018 et juillet 2020. Le diagnostic de kératocône était posé sur un faisceau d’arguments cliniques et topographiques. Les critères d’exclusion étaient les antécédents de chirurgie oculaire. Les patients atteints de kératocône ont été classé d’après la classification utilisée en 5 stades de sévérité croissante en fonction de l’aspect de leur OCT cornéen. Nous avons analysé les caractéristiques fonctionnelles, clinique et topographique en fonction des stades. Nous avons analysé l’erreur de mesure d’épaisseur cornéenne par la topographie et décrit les traitements proposés en fonction du stade.Résultats : nous avons inclus 143 yeux de 143 patients atteints de kératocône et 35 yeux de 35 patients sains. Parmi les patients atteints de kératocône, 116, 8, 9, 6, 4 ont été classés respectivement en stade 1, 2, 3, 4, 5 de la classification. La sévérité de l’atteinte structurelle en OCT était associée à une plus grande sévérité de l’atteinte fonctionnelle, anatomique et topographique. La différence de mesure d’épaisseur cornéenne entre l’OCT et la topographie était plus élevée pour les stades plus sévères. Les traitements proposés étaient plus invasifs pour les stades plus sévères.Conclusion : cette classification structurelle semble bien être un marqueur de sévérité du kératocône. Nous avons retrouvé des résultats similaires à l’étude de Sandali et al. Elle est peu connue des praticiens et semble peu adaptée aux kératocônes modérés. Elle pourrait trouver un intérêt croissant avec le perfectionnement et l’usage plus large de l’OCT de segment antérieur dans le kératocône.

International audience; This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.

Les carcinomes de l'oropharynx induits par les papillomavirus oncogènes (COP HPV+) représentent une entité distincte au sein des cancers des VADS. La 7ème classification TNM de l'American Joint Committee on Cancer / Union for International Cancer Control (AJCC/UICC) est devenue insuffisante pour rendre compte de leur pronostic, bien plus favorable que celui des COP HPV- . Plusieurs classifications spécifiques aux COP HPV+ ont été publiées mais certaines n'ont jamais été validées de façon indépendante. Celle qui a été retenue en tant que 8ème édition de la TNM a été mise au point par un consortium international (ICON-S). Les stades T et N y sont refondés et regroupés en 3 stades (I/II/III), rendant mieux compte du pronostic des patients. Cette nouvelle édition doit entrer en vigueur en 2018, bien que peu d’équipes aient évalué ses performances. De plus, elle est basée uniquement sur des critères anatomiques ; le tabagisme n'y figure pas bien que son impact sur la survie soit désormais établi. Dans notre étude, la 8ème TNM a permis de mieux stratifier les COP HPV + que la 7ème TNM mais n'a pas surpassé certaines classifications « concurrentes ». De plus, le pronostic des stades I et II était comparable, seul le stade III avait une survie significativement moins favorable. Le tabagisme au-delà de 20 paquets-années a significativement majoré le risque de décès, en particulier pour les stades "avancés" T4/N2c/N3. Nos résultats suggèrent que la 8ème TNM pourrait être améliorée pour pouvoir s'appliquer à l'ensemble les COP HPV+. L'intégration de critères non-anatomiques, permettant de mieux rendre compte de l’individualité de chaque patient, peut constituer l’une des pistes pour la mise au point de classifications ultérieures.

International audience; This special issue of Systematic Biology contains review articles contributed by keynote speakers at the “Mathematical and Computational EvolutionaryBiology” conference (MCEB; see web sites below), held in 2015. This is the seventh conference in this series, the first being held in Paris in 2003 with keynote addresses from such notables as Joe Felsenstein, Ziheng Yang, and Walter Fitch. Oxford University Press published two books based on the 2003 and 2005 Paris meetings (Gascuel 2005; Gascuel and Steel 2007).

International audience; Satellite viruses encode structural proteins required for the formation of infectious particles but depend on helper viruses for completing their replication cycles. Because of this unique property, satellite viruses that infect plants, arthropods, or mammals, as well as the more recently discovered satellite-like viruses that infect protists (virophages), have been grouped with other, so-called "sub-viral agents." For the most part, satellite viruses are therefore not classified. We argue that possession of a coat-protein-encoding gene and the ability to form virions are the defining features of a bona fide virus. Accordingly, all satellite viruses and virophages should be consistently classified within appropriate taxa. We propose to create four new genera - Albetovirus, Aumaivirus, Papanivirus, and Virtovirus - for positive-sense single-stranded (+) RNA satellite viruses that infect plants and the family Sarthroviridae, including the genus Macronovirus, for (+)RNA satellite viruses that infect arthopods. For double-stranded DNA virophages, we propose to establish the family Lavidaviridae, including two genera, Sputnikvirus and Mavirus.

International audience; Fossil-based estimates of diversity and evolutionary dynamics mainly rely on the study of morphological variation. Unfortunately, organism remains are often altered by post-mortem taphonomic processes such as weathering or distortion. Such a loss of information often prevents quantitative multivariate description and statistically-controlled comparisons of extinct species based on morphometric data. A common way to deal with missing data involves imputation methods that directly fill the missing cases with model estimates. Over the last years, several empirically-determined thresholds for the maximum acceptable proportion of missing values have been proposed in the literature, whereas other studies showed that this limit actually depends on various properties of the study data set and of the selected imputation method, and is by no way generalizable. We evaluate the relative performances of seven multiple imputation (MI) techniques through a simulation-based analysis under three distinct patterns of missing data distribution. Overall, Fully Conditional Specification and Expectation-Maximization algorithms provide the best compromises between imputation accuracy and coverage probability. MI techniques appear remarkably robust to the violation of basic assumptions such as the occurrence of taxonomically or anatomically biased patterns of missing data distribution, making differences in simulation results between the three patterns of missing data distribution much smaller than differences between the individual MI techniques. Based on these results, rather than proposing a new (set of) threshold value(s), we develop an approach combining the use of MIs with procrustean superimposition of principal component analysis results, in order to directly visualize the effect of individual missing data imputation on an ordinated space. We provide an R function for users to implement the proposed procedure.

The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.

International audience; Recently, several theoretical and applied studies have shown that unsupervised Bayesian classification systems are of particular relevance for biological studies. However, these systems have not yet fully reached the biological community mainly because there are few freely available dedicated computer programs, and Bayesian clustering algorithms are known to be time consuming, which limits their usefulness when using personal computers. To overcome these limitations, we developed AutoClass@IJM, a computational resource with a web interface to AutoClass, a powerful unsupervised Bayesian classification system developed by the Ames Research Center at N.A.S.A. AutoClass has many powerful features with broad applications in biological sciences: (i) it determines the number of classes automatically, (ii) it allows the user to mix discrete and real valued data, (iii) it handles missing values. End users upload their data sets through our web interface; computations are then queued in our cluster server. When the clustering is completed, an URL to the results is sent back to the user by e-mail. AutoClass@IJM is freely available at: http://ytat2.ijm.univ-paris-diderot.fr/AutoclassAtIJM.html.

International audience; Wolbachia are endosymbiotic bacteria that may alter the reproductive mechanisms of arthropod hosts. Eusocial termites provide considerable scope for Wolbachia studies owing to their ancient origin, their great diversity and their considerable ecological, biological and behavioral plasticity. This article describes the phylogenetic distribution of Wolbachia infecting termites of the Cubitermes genus, which are particularly abundant soil-feeders in equatorial Africa. Fourteen colonies of the Cubitermes sp. affinis subarquatus complex of species were screened using five bacterial genes (wsp, ftsZ, coxA, fbpA and 16S rRNA genes) and a striking diversity of Wolbachia strains was identified within these closely related species. In the host complex, three Wolbachia variants were found that were not in the super groups usually reported for termites (F and H), each infecting one or two Cubitermes species.

International audience; The taxonomic and phylogenetic status of Echinococcus granulosus strains are still controversial and under discussion. In the present study, we investigated the genetic polymorphism of E. granulosus isolates originating from three countries of Africa, including a region of Algeria, where the common G1 sheep and the camel G6 strains coexist sympatrically. Seventy-one hydatid cysts were collected from sheep, cattle, camels, and humans. Two mitochondrial markers (cox1 and nad1) were used for strain identification. Two nuclear markers (actII and hbx2) were used to study the possible occurrence of cross-fertilization. Despite the heterogeneity observed among the G1 isolates, they were all localized within one robust cluster. A second strong cluster was also observed containing all of the G6 isolates. Both strains appeared as two distinct groups, and no cases of interbreeding were found. Thus, the attribution of a species rank can be suggested. We also found the Tasmanian sheep G2 strain for the first time in Africa. Because of the slight variations observed between the common sheep and the Tasmanian sheep strains, further studies should be carried out to elucidate the epidemiological relevance of this genetic discrimination.

International audience; Four male Long-Evans rats were trained to discriminate between synthetic vowel sounds using a GO/NOGO response choice task. The vowels were characterized by an increase in fundamental frequency correlated with an upward shift in formant frequencies. In an initial phase we trained the subjects to discriminate between two vowel categories using two exemplars from each category. In a subsequent phase the ability of the rats to generalize the discrimination between the two categories was tested. To test whether rats might exploit the fact that attributes of training stimuli covaried, we used non-standard stimuli with a reversed relation between fundamental frequency and formants. The overall results demonstrate that rats are able to generalize the discrimination to new instances of the same vowels. We present evidence that the performance of the subjects depended on the relation between fundamental and formant frequencies that they had previously been exposed to. Simple simulation results with artificial neural networks could reproduce most of the behavioral results and support the hypothesis that equivalence classes for vowels are associated with an experience-driven process based on general properties of peripheral auditory coding mixed with elementary learning mechanisms. These results suggest that rats use spectral and temporal cues similarly to humans despite differences in basic auditory capabilities.