Simulation based estimation of branching models for LTR retrotransposons

Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows to take into account both positions and degradations of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results: Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we show that an accurate estimation of the parameters of this propagation model can be performed. We applied this method to the study of the spread of the transposable elements ROO, GYPSY, and DM412 on a chromosome of \textit{Drosophila melanogaster}. Availability: Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread.Comment: 7 pages, 3 figures, 7 tables. Submit to "Bioiformatics" on March 1, 201

Faune arachnologique de quatre carrières et éboulis en Valais, avec une nouvelle espèce pour la Suisse

Pierriers étudiés à Charrat, Martigny et Dorénaz

Quantification and Modeling of Broken Links Prevalence in Hyper Traffic Websites Homepages

Broken links in websites external resources pose a serious threat to cybersecurity and the credibility of websites. They can be hijacked to eavesdrop user traffic or to inject malicious software. In this paper, we present the first result of an ongoing research. We focus on the prevalence of broken links in external resources on home pages of the most visited websites in the world. The analysis was conducted on the top 88 000 homepages extracted from the Majestic Million rankings. 35,2% of them have at least one broken link. We also identify the common causes of these broken links and highlight improper implementation of testing phases to prevent such errors. We provide a formal model for the distribution of external links. At the next research step, we are exploring the potential impact on privacy of broken links by analyzing inherited traffic of purchasable expired domains.Comment: 4 pages, 3 tables, 1 figur

Reduction of Cadmium Availability to Tobacco ( Nicotiana tabacum ) Plants using Soil Amendments in Low Cadmium-contaminated Agricultural Soils: A Pot Experiment

Cadmium (Cd) concentration in field-grown tobacco leaves usually ranges from < 0.5 to 5mgCdkg-1 dry matter (DM). Reducing bioavailability of soil Cd by adding amendments to the soil could be suitable to mitigate Cd uptake by tobacco plants. However, little is known on the effect of inorganic amendments on agricultural soils with low Cd concentrations. Therefore, we performed a pot experiment with tobacco plants that were grown during 56days in two neutral to alkaline agricultural soils with low total Cd concentrations (soil 1=0.4, soil 2=0.7mgkg-1). Both soils were amended or not with 1 or 5% of sepiolite, zeolite, hydroxyapatite and apatite II™. Major and trace elements were measured in mid-stalk position leaves. Soil metals were measured in a DTPA soil extraction to assess the effect of the amendments on metal bioavailability. Some amendments significantly reduced Cd concentration in tobacco leaves, but the effect differed between the two soils tested. In soil 1, the use of zeolite at the 1% dose was the most efficient, reducing the average Cd concentration from 0.6 to 0.4mgkg-1. In soil 2, the 5% hydroxyapatite treatment led to the maximal reduction in Cd concentration (50%), with an average final Cd concentration in leaves of 0.7mgkg-1 (control: 1.5mgkg-1). There was a dose effect for some amendments in soil 2 (containing more Cd), suggesting a reduced efficiency of the amendment at the lowest addition rate. DTPA extractable Cd and Zn measured at the end of the pot experiment were correlated to the metal concentrations in tobacco leaves suggesting that (1) the reduction in leaf Cd concentration was due to a reduction in metal availability to tobacco and (2) DTPA may be a suitable extractant to estimate Cd availability to tobacco plants in these two soils. In addition, a batch experiment was performed with the same soils to test a larger number of amendments, including the four tested in the pot experiment. Results were compared to those of the pot experiment to assess whether a batch experiment may predict the efficiency of an amendment on a given soil. It gave results compatible with those from the pot experiment except for the sepiolite and highlighted the broad range of potential amendments available for heavy metal remediation in crop plant

Coupling multiphysics problems in transient regimes: application to liquid resin infusion process

Liquid resin infusion (LRI) process is widely considered in the aeronautics, due to its benefits (low void content and production of large parts), for high performance composite material forming. The main objective of the present work is to simulate nu- merically the LRI process, in a high performance computing framework, which consists in coupling fluid-solid mechanics. Hence, two fluid flow regimes are coupled with an ef- ficient ASGS stabilized monolithic finite element formulations: the resin flow in both a highly permeable distribution medium (Stokes) and low permeability fibrous orthotropic preforms (Darcy). Moreover, weak coupling algorithms are used along for coupling solid / fluid mechanics, solid / level-set problems and fluid / level-set problems; where the level-set method is used to capture the moving flow front and the Stokes-Darcy interface. To transfer the different physical variables between the above coupled problems, Message Passing Interface (MPI) library is chosen, to ensure the best data transfer performances

Happiness, Health and Well-Being in a Life Course Perspective : Quantitative Data Collection and Analysis of Sequences of Subjective Indicators

MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2014-2018)Forming a Social Well-being Research Consortium in AsiaSubjective information has recently made a remarkable breakthrough into quantitative data collection and analysis in demography. Seen as a complement to hard statistics, the new perspective it opens seems promising. In the study of life-event histories, pioneering sociologists have developed the qualitative analysis of turning-points based on qualitative life-course narratives; we here present quantitative surveys which recorded factual individual life-event histories together with perceptions of subjective well-being, self-rated health indicators and financial situation over the life course. The interest of this approach is to explore variations in the subjective indicators along individual life courses rather than their absolute level at any point in time; and to confront facts and perceptions in order to better grasp the interpretation of social, familial, health transitions that take place along the life course. We here present how demographers collect such data and how they validate the subjective information against factual data. Some examples of the analysis of individual histories of subjective well-being are then presented and discussed

Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex

<p>Abstract</p> <p>Background</p> <p>Influenza A viruses are well characterized to antagonize type I IFN induction in infected mammalian cells. However, limited information is available for avian cells. It was hypothesised that avian influenza viruses (AIV) with distinct virulence may interact differently with the avian innate immune system. Therefore, the type I IFN responses induced by highly virulent and low virulent H5N1 AIV and reassortants thereof were analysed in chicken cells.</p> <p>Results</p> <p>The highly pathogenic (HP) AIV A/chicken/Yamaguchi/7/04 (H5N1) (Yama) did not induce type I IFN in infected chicken HD-11 macrophage-like cells. This contrasted with an NS1 mutant Yama virus (Yama-NS1^A144V) and with the attenuated H5N1 AIV A/duck/Hokkaido/Vac-1/04 (Vac) carrying the haemagglutinin (HA) of the Yama virus (Vac-Yama/HA), that both induced type I IFN in these cells. The substitution of the NS segment from Yama with that from Vac in the Yama backbone resulted in induction of type I IFN secretion in HD-11 cells. However, vice versa, the Yama NS segment did not prevent type I IFN induction by the Vac-Yama/HA virus. This was different with the PB1/PB2/PA segment reassortant Yama and Vac-Yama/HA viruses. Whereas the Yama virus with the Vac PB1/PB2/PA segments induced type I IFN in HD-11 cells, the Vac-Yama/HA virus with the Yama PB1/PB2/PA segments did not. As reported for mammalian cells, the expression of H5N1 PB2 inhibited the activation of the IFN-β promoter in chicken DF-1 fibroblast cells. Importantly, the Yama PB2 was more potent at inhibiting the IFN-β promoter than the Vac PB2.</p> <p>Conclusions</p> <p>The present study demonstrates that the NS1 protein and the polymerase complex of the HPAIV Yama act in concert to antagonize chicken type I IFN secretion in HD-11 cells. PB2 alone can also exert a partial inhibitory effect on type I IFN induction. In conclusion, the control of type I IFN induction by H5N1 HPAIV represents a complex phenotype that involves a particular viral gene constellation rather than a single viral protein. Collectively, these findings contribute to understand the high virulence of HPAIV H5N1 viruses observed in the chicken host.</p