Histoire d'une famille de deux générations atteinte par la forme dominante de la maladie de Stargardt, due à une mutation sur le gène ELOVL4 : Case report

Un patient de 22 ans et les membres de sa famille se soumettent à un examen ophtalmique complet, comprenant un examen du fond d'oeil, une autofluorescence, une tomographie à cohérence optique (OCT), un champ visuel et un électrorétinogramme (ERG). De l'ADN génomique est extrait du sang périphérique de ces patients afin de subir une analyse IROme, un « séquençage à haut débit » de 120 gènes, connus pour être impliqués dans diverses maladies rétiniennes héréditaires. Les résultats de cette analyse génétique ont été validés par un séquençage selon Sanger

Phylogenetic Analysis of Cell Types using Histone Modifications

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We propose new data representation techniques and new distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful trees that indicate how diverse types of cells are related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13 types of cells respectively, using the dataset to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. The promising results we obtain point the way to a new approach to the study of cell differentiation.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Summary: TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, through rearrangement operations, is modelled by the uniform Double-Cut-and-Join model. Using a true distance estimate under this model and simple distance-based methods, TIBA reconstructs a phylogeny of the input genomes. Unlike any previous tool for inferring phylogenies from rearrangement data, TIBA uses novel methods of robustness estimation to provide support values for the edges in the inferred tree. Availability: http://lcbb.epfl.ch/softwares/tiba.html. Contact: [email protected]

A Taxonomy-Based Usability Study of an Intelligent Speed Adaptation Device

This is an Accepted Manuscript of an article published by Taylor & Francis in International Journal of Human–Computer Interaction on 04 Apr 2014, available online: http://dx.doi.org/10.1080/10447318.2014.907463[Abstract] Usability studies are often based on ad hoc definitions of usability. These studies can be difficult to generalize, they might have a steep learning curve, and there is always the danger of being inconsistent with the concept of usability as defined in standards and the literature. This alternative approach involves comprehensive, general-purpose, and hierarchically structured taxonomies that follow closely the main usability literature. These taxonomies are then instantiated for a specific product. To illustrate this approach, a usability study for a prototype of an Intelligent Speed Adaptation device is described. The usability study consists of usability requirements analysis, heuristic evaluation, and subjective analysis, which helped identify problems of clarity, operability, robustness, safety, and aesthetics. As a context-specific usability taxonomy for this particular field of application happened to exist, the way that real-world usability results can be mapped to that taxonomy compared to the taxonomy in this article is examined, with the argument that this study’s taxonomy is more complete and generalizable.Xunta de Galicia; CN2011/007Xunta de Galicia; CN2012/211European Global Navigation Satellite Systems Agency; Nº. 22835

Answering Conjunctive Queries under Updates

We consider the task of enumerating and counting answers to $k$-ary conjunctive queries against relational databases that may be updated by inserting or deleting tuples. We exhibit a new notion of q-hierarchical conjunctive queries and show that these can be maintained efficiently in the following sense. During a linear time preprocessing phase, we can build a data structure that enables constant delay enumeration of the query results; and when the database is updated, we can update the data structure and restart the enumeration phase within constant time. For the special case of self-join free conjunctive queries we obtain a dichotomy: if a query is not q-hierarchical, then query enumeration with sublinear$^\ast$ delay and sublinear update time (and arbitrary preprocessing time) is impossible. For answering Boolean conjunctive queries and for the more general problem of counting the number of solutions of k-ary queries we obtain complete dichotomies: if the query's homomorphic core is q-hierarchical, then size of the the query result can be computed in linear time and maintained with constant update time. Otherwise, the size of the query result cannot be maintained with sublinear update time. All our lower bounds rely on the OMv-conjecture, a conjecture on the hardness of online matrix-vector multiplication that has recently emerged in the field of fine-grained complexity to characterise the hardness of dynamic problems. The lower bound for the counting problem additionally relies on the orthogonal vectors conjecture, which in turn is implied by the strong exponential time hypothesis. $^\ast)$ By sublinear we mean $O(n^{1-\varepsilon})$ for some $\varepsilon>0$, where $n$ is the size of the active domain of the current database