73 research outputs found
Optimality Clue for Graph Coloring Problem
In this paper, we present a new approach which qualifies or not a solution
found by a heuristic as a potential optimal solution. Our approach is based on
the following observation: for a minimization problem, the number of admissible
solutions decreases with the value of the objective function. For the Graph
Coloring Problem (GCP), we confirm this observation and present a new way to
prove optimality. This proof is based on the counting of the number of
different k-colorings and the number of independent sets of a given graph G.
Exact solutions counting problems are difficult problems (\#P-complete).
However, we show that, using only randomized heuristics, it is possible to
define an estimation of the upper bound of the number of k-colorings. This
estimate has been calibrated on a large benchmark of graph instances for which
the exact number of optimal k-colorings is known. Our approach, called
optimality clue, build a sample of k-colorings of a given graph by running many
times one randomized heuristic on the same graph instance. We use the
evolutionary algorithm HEAD [Moalic et Gondran, 2018], which is one of the most
efficient heuristic for GCP. Optimality clue matches with the standard
definition of optimality on a wide number of instances of DIMACS and RBCII
benchmarks where the optimality is known. Then, we show the clue of optimality
for another set of graph instances. Optimality Metaheuristics Near-optimal
Persisting Mixed Cryoglobulinemia in Chikungunya Infection
Chikungunya virus is present in tropical Africa and Asia and is transmitted by mosquito bites. The disease is characterized by fever, headache, severe joint pain and transient skin rash for about a week. Most patients experience persisting joint pain and/or stiffness for months to years. In routine practice, diagnosis is based upon serology. Since 2004 there has been an ongoing giant outbreak of Chikungunya fever in East Africa, the Indian Ocean Islands, India and East Asia. In parallel, more than 1,000 travelers were diagnosed with imported Chikungunya infection in most developed countries. Considering the clinical features of our patients (joint pain), we hypothesized that cryoglobulins could be involved in the pathophysiology of the disease as observed in chronic hepatitis C infection. Cryoglobulins, which are immunoglobulins that precipitate when temperature is below 37°C, can induce rheumatic and vascular disorders. From April 2005 through May 2007, we screened all patients with possible imported Chikungunya infection for cryoglobulins. They were present in over 90% of patients, and possibly responsible for the unexpected false negativity of serological assays. Cryoglobulin frequency and levels decreased with time in recovering patients
Travelling in time with networks: revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis
Background: Hybridization or divergence between sympatric sister species provides a natural laboratory to study speciation processes. The shared polymorphism in sister species may either be ancestral or derive from hybridization, and the accuracy of analytic methods used thus far to derive convincing evidence for the occurrence of present day hybridization is largely debated.
Results: Here we propose the application of network analysis to test for the occurrence of present day hybridization between the two species of brown algae Fucus spiralis and F. vesiculosus. Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic. Two genetic distances integrating different time steps were used, the Rozenfeld (RD;
based on alleles divergence) and the Shared Allele (SAD; based on alleles identity) distances. A diagnostic level of genotype divergence and clustering of individuals from each species was obtained through RD while screening for exchanges through putative hybridization was facilitated using SAD. Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia. Conclusion: These results suggesting rare hybridization were confirmed by simulation of hybrids and F2 with directed backcrosses. Comparison with the Bayesian method STRUCTURE confirmed the usefulness of both approaches and emphasized the reliability of network analysis to unravel and study hybridization
Panmixia in a fragmented and unstable environment: the hydrothermal shrimp Rimicaris exoculata disperses extensively along the Mid-Atlantic ridge
Dispersal plays a fundamental role in the evolution and persistence of species, and especially for species inhabiting extreme,
ephemeral and highly fragmented habitats as hydrothermal vents. The Mid-Atlantic Ridge endemic shrimp species Rimicaris exoculata was studied using microsatellite markers to infer connectivity along the 7100-Km range encompassing the sampled sites. Astonishingly, no genetic differentiation was found between individuals from the different geographic origins, supporting a scenario of widespread large-scale dispersal despite the habitat distance and fragmentation. We hypothesize that delayed metamorphosis associated to temperature differences or even active directed migration
dependent on physical and/or chemical stimuli could explain these results and warrant further studies on adaptation and
dispersal mechanisms
On the general theory of the origins of retroviruses
<p>Abstract</p> <p>Background</p> <p>The order retroviridae comprises viruses based on ribonucleic acids (RNA). Some, such as HIV and HTLV, are human pathogens. Newly emerged human retroviruses have zoonotic origins. As far as has been established, both repeated infections (themselves possibly responsible for the evolution of viral mutations <b>(Vm) </b>and host adaptability <b>(Ha)</b>); along with interplay between <it>inhibitors </it>and <it>promoters </it>of cell tropism, are needed to effect retroviral cross-species transmissions. However, the exact <it>modus operadi </it>of intertwine between these factors at molecular level remains to be established. Knowledge of such intertwine could lead to a better understanding of retrovirology and possibly other infectious processes. This study was conducted to derive the mathematical equation of a general theory of the origins of retroviruses.</p> <p>Methods and results</p> <p>On the basis of an arbitrarily non-Euclidian geometrical "thought experiment" involving the cross-species transmission of simian foamy virus (sfv) from a non-primate species <it>Xy </it>to <it>Homo sapiens </it>(<it>Hs</it>), initially excluding all social factors, the following was derived. At the port of exit from <it>Xy </it>(where the species barrier, SB, is defined by the <it>Index of Origin</it>, IO), sfv shedding is (1) enhanced by two transmitting tensors <b>(Tt)</b>, (i) virus-specific immunity (VSI) and (ii) evolutionary defenses such as APOBEC, RNA interference pathways, and (when present) expedited therapeutics (denoted e<sup>2</sup>D); and (2) opposed by the five accepting scalars <b>(At)</b>: (a) genomic integration hot spots, gIHS, (b) nuclear envelope transit <b>(</b>NMt) vectors, (c) virus-specific cellular biochemistry, VSCB, (d) virus-specific cellular receptor repertoire, VSCR, and (e) pH-mediated cell membrane transit, (↓<sub>pH </sub>CMat). Assuming <b>As </b>and <b>Tt </b>to be independent variables, <b>IO = Tt/As</b>. The same forces acting in an opposing manner determine SB at the port of sfv entry (defined here by the <it>Index of Entry</it>, <b>IE = As/Tt</b>). Overall, If sfv encounters no unforeseen effects on transit between X<it>y </it>and <it>Hs</it>, then the square root of the combined index of sfv transmissibility (√<b>|RTI|) </b>is proportional to the product IO* IE (or ~Vm* Ha* ∑Tt*∑As*<b>Ω</b>), where <b>Ω </b>is the retrovirological constant and ∑ is a function of the ratio Tt/As or As/Tt for sfv transmission from <it>Xy </it>to <it>Hs</it>.</p> <p>Conclusions</p> <p>I present a mathematical formalism encapsulating the general theory of the origins of retroviruses. It summarizes the choreography for the intertwined interplay of factors influencing the probability of retroviral cross-species transmission: <b>Vm, Ha, Tt, As, </b>and <b>Ω</b>.</p
Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster
Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes
Deciphering the Code for Retroviral Integration Target Site Selection
Upon cell invasion, retroviruses generate a DNA copy of their RNA genome and integrate retroviral cDNA within host chromosomal DNA. Integration occurs throughout the host cell genome, but target site selection is not random. Each subgroup of retrovirus is distinguished from the others by attraction to particular features on chromosomes. Despite extensive efforts to identify host factors that interact with retrovirion components or chromosome features predictive of integration, little is known about how integration sites are selected. We attempted to identify markers predictive of retroviral integration by exploiting Precision-Recall methods for extracting information from highly skewed datasets to derive robust and discriminating measures of association. ChIPSeq datasets for more than 60 factors were compared with 14 retroviral integration datasets. When compared with MLV, PERV or XMRV integration sites, strong association was observed with STAT1, acetylation of H3 and H4 at several positions, and methylation of H2AZ, H3K4, and K9. By combining peaks from ChIPSeq datasets, a supermarker was identified that localized within 2 kB of 75% of MLV proviruses and detected differences in integration preferences among different cell types. The supermarker predicted the likelihood of integration within specific chromosomal regions in a cell-type specific manner, yielding probabilities for integration into proto-oncogene LMO2 identical to experimentally determined values. The supermarker thus identifies chromosomal features highly favored for retroviral integration, provides clues to the mechanism by which retrovirus integration sites are selected, and offers a tool for predicting cell-type specific proto-oncogene activation by retroviruses
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