38,742 research outputs found

    Evolution of foot-and-mouth disease virus intra-sample sequence diversity during serial transmission in bovine hosts

    Get PDF
    RNA virus populations within samples are highly heterogeneous, containing a large number of minority sequence variants which can potentially be transmitted to other susceptible hosts. Consequently, consensus genome sequences provide an incomplete picture of the within- and between-host viral evolutionary dynamics during transmission. Foot-and-mouth disease virus (FMDV) is an RNA virus that can spread from primary sites of replication, via the systemic circulation, to found distinct sites of local infection at epithelial surfaces. Viral evolution in these different tissues occurs independently, each of them potentially providing a source of virus to seed subsequent transmission events. This study employed the Illumina Genome Analyzer platform to sequence 18 FMDV samples collected from a chain of sequentially infected cattle. These data generated snap-shots of the evolving viral population structures within different animals and tissues. Analyses of the mutation spectra revealed polymorphisms at frequencies >0.5% at between 21 and 146 sites across the genome for these samples, while 13 sites acquired mutations in excess of consensus frequency (50%). Analysis of polymorphism frequency revealed that a number of minority variants were transmitted during host-to-host infection events, while the size of the intra-host founder populations appeared to be smaller. These data indicate that viral population complexity is influenced by small intra-host bottlenecks and relatively large inter-host bottlenecks. The dynamics of minority variants are consistent with the actions of genetic drift rather than strong selection. These results provide novel insights into the evolution of FMDV that can be applied to reconstruct both intra- and inter-host transmission routes

    The prospects for mathematical logic in the twenty-first century

    Get PDF
    The four authors present their speculations about the future developments of mathematical logic in the twenty-first century. The areas of recursion theory, proof theory and logic for computer science, model theory, and set theory are discussed independently.Comment: Association for Symbolic Logi

    Memoization for Unary Logic Programming: Characterizing PTIME

    Full text link
    We give a characterization of deterministic polynomial time computation based on an algebraic structure called the resolution semiring, whose elements can be understood as logic programs or sets of rewriting rules over first-order terms. More precisely, we study the restriction of this framework to terms (and logic programs, rewriting rules) using only unary symbols. We prove it is complete for polynomial time computation, using an encoding of pushdown automata. We then introduce an algebraic counterpart of the memoization technique in order to show its PTIME soundness. We finally relate our approach and complexity results to complexity of logic programming. As an application of our techniques, we show a PTIME-completeness result for a class of logic programming queries which use only unary function symbols.Comment: Soumis {\`a} LICS 201

    A cookbook for temporal conceptual data modelling with description logic

    Get PDF
    We design temporal description logics suitable for reasoning about temporal conceptual data models and investigate their computational complexity. Our formalisms are based on DL-Lite logics with three types of concept inclusions (ranging from atomic concept inclusions and disjointness to the full Booleans), as well as cardinality constraints and role inclusions. In the temporal dimension, they capture future and past temporal operators on concepts, flexible and rigid roles, the operators `always' and `some time' on roles, data assertions for particular moments of time and global concept inclusions. The logics are interpreted over the Cartesian products of object domains and the flow of time (Z,<), satisfying the constant domain assumption. We prove that the most expressive of our temporal description logics (which can capture lifespan cardinalities and either qualitative or quantitative evolution constraints) turn out to be undecidable. However, by omitting some of the temporal operators on concepts/roles or by restricting the form of concept inclusions we obtain logics whose complexity ranges between PSpace and NLogSpace. These positive results were obtained by reduction to various clausal fragments of propositional temporal logic, which opens a way to employ propositional or first-order temporal provers for reasoning about temporal data models
    • ā€¦
    corecore