High order finite element calculations for the deterministic Cahn-Hilliard equation

In this work, we propose a numerical method based on high degree continuous nodal elements for the Cahn-Hilliard evolution. The use of the p-version of the finite element method proves to be very efficient and favorably compares with other existing strategies (C^1 elements, adaptive mesh refinement, multigrid resolution, etc). Beyond the classical benchmarks, a numerical study has been carried out to investigate the influence of a polynomial approximation of the logarithmic free energy and the bifurcations near the first eigenvalue of the Laplace operator

The Fruit Fly as a Meeting Place for Microbes

Many infectious diseases of humans are caused by polymicrobial communities, but there are few in vivo models to study such communities. In a recent issue of PLoS Pathogens, Sibley and colleagues (Sibley et al., 2008a) report the development of a fruit fly infection model to investigate polymicrobial interactions and their effects on the host

Rapid and Efficient Methods to Isolate, Type Strains and Determine Species of Agrobacterium spp. in Pure Culture and Complex Environments

International audienc

La pompe à efflux MexEF-OprN de pseudomonas aeruginosa exporte la molécule de communication intercellulaires 4-hydroxy-2-heptyliquinoline (HHQ)

La bactérie pathogène opportuniste Pseudomonas aeruginosa est la cause d’infections chroniques chez les personnes atteintes de la fibrose kystique (FK). De plus, P. aeruginosa est naturellement très résistante aux antimicrobiens, ce qui rend l’antibiothérapie souvent inefficace. Les pompes à efflux sont des déterminants majeurs de la résistance aux antibiotiques chez cette bactérie. Elles permettent la résistance simultanée à différentes classes d'antibiotiques. La pompe à efflux MexEF-OprN promeut la résistance au chloramphénicol, au triméthoprime, au triclosan et aux fluoroquinolones. L’expression continue de l’opéron mexEF-oprN est observée chez des mutants de mexS, gène dont la fonction est inconnue. Une mutation dans mexS affecte aussi les mécanismes de quorum sensing (QS), c’est-à-dire de communication intercellulaire. Le QS contrôle l’expression de facteurs de virulence et la formation de biofilms, observées dans les voies respiratoires des personnes atteintes de FK. Le QS est contrôlé par des régulateurs transcriptionnels qui, pour être actifs, doivent être couplés à de petites molécules signales nommées auto-inducteurs. Alors que la population bactérienne se densifie, les auto-inducteurs s’accumulent dans le milieu extracellulaire jusqu’à atteindre une concentration-seuil, à laquelle le "quorum" est atteint. MvfR est un régulateur du QS et contrôle l’expression de plusieurs gènes importants pour la virulence, dont ceux de l’opéron pqsABCDE, impliqués dans la biosynthèse des 4-hydroxy-2-alkylquinolines (HAQ). Un auto-inducteur associé à MvfR est le 3,4-dihydroxy-2- heptylquinoline (PQS; Pseudomonas Quinolone Signal). L’enzyme PqsH est responsable de la synthèse du PQS et utilise un HAQ, le 4-hydroxy-2-heptylquinoline (HHQ), comme substrat. Étrangement, la quantité de PQS produit par les mutants mexS est substantiellement réduite. Afin de mieux comprendre l’influence de cette mutation sur les HAQ, nous avons quantifié leurs concentrations par LC-MS/MS chez la souche parentale PA14 et son mutant isogénique mexS. Cette expérience fut effectuée en absence ou présence d’inhibiteurs des pompes à efflux. De plus, le niveau d’expression de plusieurs gènes du QS fût déterminé grâce à des fusions transcriptionnelles entre les régions promotrices des gènes à l’étude et le gène rapporteur lacZ. Mis ensemble, nos résultats démontrent que c’est l’exportation du HHQ par MexEF-OprN qui cause le déficit en PQS. Puisque des souches qui surexpriment mexEF-oprN sont défectueuses pour le QS et moins virulentes, il serait intéressant d’identifier de nouvelles molécules à potentiel thérapeutique qui permettrait de moduler l’activité de la pompe MexEF-OprN. Cela pourrait faciliter le traitement des infections pulmonaires à P. aeruginosa

Biochemical and molecular identification of a native Bacillus thuringiensis gv. cytolyticus isolate with insecticidal effect against the pod borer larvae (Helicoverpa armigera)

Bouslama, T., Laarif, A., Chattaoui, M., Vial, L., Lavire, C., and Doré, J., and Rhouma, A. 2023. Biochemical and molecular identification of a native Bacillus thuringiensis gv. cytolyticus isolate with insecticidal effect against the pod borer larvae (Helicoverpa armigera). Tunisian Journal of Plant Protection 18 (2): 71-91

Sea ice thickness and elastic properties from the analysis of multimodal guided wave propagation measured with a passive seismic array

Field data are needed for a better understanding of sea ice decline in the context of climate change. The rapid technological and methodological advances of the last decade have led to a reconsideration of seismic methods in this matter. In particular, passive seismology has filled an important gap by removing the need to use active sources. We present a seismic experiment where an array of 247 geophones was deployed on sea ice, in the Van Mijen fjord near Sveagruva (Svalbard). The array is a mix of 1C and 3C stations with sampling frequencies of 500 and 1000 Hz. They recorded continuously the ambient seismic field in sea ice between 28 February and 26 March 2019. Data also include active acquisitions on 1 and 26 March with a radar antenna, a shaker unit, impulsive sources, and artificial sources of seismic noise. This data set is of unprecedented quality regarding sea ice seismic monitoring, as it also includes thousands of microseismic events recorded each day. By combining passive seismology approaches with specific array processing methods, we demonstrate that the multimodal dispersion curves of sea ice can be calculated without an active source and then used to infer sea ice properties. We calculated an ice thickness, Young's modulus, and Poisson's ratio with values h=543 cm, E=3.90.15 GPa, and nu=0.340.02 on 1 March, and h=583 cm, E=4.4 +/- 0.15 GPa, and nu=0.32 +/- 0.02 on 5 March. These values are consistent with in situ field measurements and observations.Peer reviewe

Atmospheric radiative profiles during EUREC(4)A

The couplings among clouds, convection, and circulation in trade-wind regimes remain a fundamental puzzle that limits our ability to constrain future climate change. Radiative heating plays an important role in these couplings. Here we calculate clear-sky radiative profiles from 2580 in situ soundings (1068 dropsondes and 1512 radiosondes) collected during the field campaign EUREC4A (Elucidating the role of clouds&ndash;circulation coupling in climate). EUREC4A took place in the downstream trades of the western tropical Atlantic in January&ndash;February 2020. We describe the method used to calculate these cloud-free, aerosol-free radiative profiles. We then present preliminary results sampling variability at multiple scales, from the variability across all soundings to groupings by diurnal cycle and mesoscale organization, as well as individual soundings associated with elevated moisture layers. We also perform an uncertainty assessment and find that the errors resulting from uncertainties in observed sounding profiles and ERA5 reanalysis employed as upper and lower boundary conditions are small. The present radiative profile data set can provide important additional details missing from calculations based on passive remote sensing and aid in understanding the interplay of radiative heating with dynamic and thermodynamic variability in the trades. The data set can also be used to investigate the role of low-level radiative cooling gradients in generating shallow circulations. All data are archived and freely available for public access on AERIS (Albright et&nbsp;al.,&nbsp;2020a, https://doi.org/https://doi.org/10.25326/78). </div

Drosophila melanogaster as a Model Host for the Burkholderia cepacia Complex

Colonization with bacterial species from the Burkholderia cepacia complex (Bcc) is associated with fast health decline among individuals with cystic fibrosis. In order to investigate the virulence of the Bcc, several alternative infection models have been developed. To this end, the fruit fly is increasingly used as surrogate host, and its validity to enhance our understanding of host-pathogen relationships has been demonstrated with a variety of microorganisms. Moreover, its relevance as a suitable alternative to mammalian hosts has been confirmed with vertebrate organisms.The aim of this study was to establish Drosophila melanogaster as a surrogate host for species from the Bcc. While the feeding method proved unsuccessful at killing the flies, the pricking technique did generate mortality within the populations. Results obtained with the fruit fly model are comparable with results obtained using mammalian infection models. Furthermore, validity of the Drosophila infection model was confirmed with B. cenocepacia K56-2 mutants known to be less virulent in murine hosts or in other alternative models. Competitive index (CI) analyses were also performed using the fruit fly as host. Results of CI experiments agree with those obtained with mammalian models.We conclude that Drosophila is a useful alternative infection model for Bcc and that fly pricking assays and competition indices are two complementary methods for virulence testing. Moreover, CI results indicate that this method is more sensitive than mortality tests

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase&nbsp;1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation&nbsp;disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age&nbsp; 6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score&nbsp; 652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc&nbsp;= 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N&nbsp;= 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in&nbsp;Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in&nbsp;Asia&nbsp;and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701