Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972

Escherichia coli strains are the major cause of urinary tract infections in humans. Such strains can be divided into virulent, UPEC strains causing symptomatic infections, and asymptomatic, commensal-like strains causing asymptomatic bacteriuria, ABU. The best-characterized ABU strain is strain 83972. Global gene expression profiling of strain 83972 has been carried out under seven different sets of environmental conditions ranging from laboratory minimal medium to human bladders. The data reveal highly specific gene expression responses to different conditions. A number of potential fitness factors for the human urinary tract could be identified. Also, presence/absence data of the gene expression was used as an adaptive genomics tool to model the gene pool of 83972 using primarily UPEC strain CFT073 as a scaffold. In our analysis, 96% of the transcripts filtered present in strain 83972 can be found in CFT073, and genes on six of the seven pathogenicity islands were expressed in 83972. Despite the very different patient symptom profiles, the two strains seem to be very similar. Genes expressed in CFT073 but not in 83972 were identified and can be considered as virulence factor candidates. Strain 83972 is a deconstructed pathogen rather than a commensal strain that has acquired fitness properties

Overview of JET results for optimising ITER operation

The JET 2019–2020 scientific and technological programme exploited the results of years of concerted scientific and engineering work, including the ITER-like wall (ILW: Be wall and W divertor) installed in 2010, improved diagnostic capabilities now fully available, a major neutral beam injection upgrade providing record power in 2019–2020, and tested the technical and procedural preparation for safe operation with tritium. Research along three complementary axes yielded a wealth of new results. Firstly, the JET plasma programme delivered scenarios suitable for high fusion power and alpha particle (α) physics in the coming D–T campaign (DTE2), with record sustained neutron rates, as well as plasmas for clarifying the impact of isotope mass on plasma core, edge and plasma-wall interactions, and for ITER pre-fusion power operation. The efficacy of the newly installed shattered pellet injector for mitigating disruption forces and runaway electrons was demonstrated. Secondly, research on the consequences of long-term exposure to JET-ILW plasma was completed, with emphasis on wall damage and fuel retention, and with analyses of wall materials and dust particles that will help validate assumptions and codes for design and operation of ITER and DEMO. Thirdly, the nuclear technology programme aiming to deliver maximum technological return from operations in D, T and D–T benefited from the highest D–D neutron yield in years, securing results for validating radiation transport and activation codes, and nuclear data for ITER

EUROfusion Integrated Modelling (EU-IM) capabilities and selected physics applications

International audienceRecent developments and achievements of the EUROfusion Code Development for Integrated Modelling project (WPCD), which aim is to provide a validated integrated modelling suite for the simulation and prediction of complete plasma discharges in any tokamak, are presented. WPCD develops generic complex integrated simulations, workflows, for physics applications, using the standardized European Integrated Modelling (EU-IM) framework. Selected physics applications of EU-IM workflows are illustrated in this paper

Investigation into the formation of the scrape-off layer density shoulder in JET ITER-like wall L-mode and H-mode plasmas

The low temperature boundary layer plasma (Scrape-Off-Layer or SOL) between the hot core and the surrounding vessel determines the level of power-loading, erosion and implantation of material surfaces, and thus the viability of tokamak-based fusion as an energy source. This study explores mechanisms affecting the formation of flattened density profiles, so-called ‘density shoulders’, in the low-field side (LFS) SOL, which modify ion and neutral fluxes to surfaces – and subsequent erosion. There is evidence against local enhancement of ionization inducing shoulder formation. We find that increases in SOL parallel resistivity, Λdiv (=[L||νei Ωi ]/cs Ωe), postulated to lead to shoulder growth through changes in SOL turbulence characteristics, correlates with increases in upstream SOL shoulder amplitude, As only under a subset of conditions (D2-fuelled L-mode density scans with outer strike point on the horizontal target). Λdiv fails to correlate with As for cases of N2 seeding or during sweeping of the strike point across the horizontal target. The limited correlation of Λdiv with As was also found for H-mode discharges. Thus, while Λdiv above a threshold of ~1 may be necessary for shoulder formation and/or growth, another shoulder mechanism is required. More significantly we find that in contrast to parallel resistivity, outer divertor recycling as quantified by the total outer divertor Balmer Dα emission, I-Dα, does scale with shoulder amplitude where Λdiv does and even where Λdiv fails. Divertor recycling could lead to SOL density shoulder formation through: a) reducing the parallel to the field flow (loss) of ions out of the SOL to the divertor; and b) changes in radial electric fields which lead to ExB poloidal flows as well as potentially affecting the SOL turbulence birth characteristics. Thus changes in divertor recycling may be the sole process in bringing about SOL density shoulders or in tandem with parallel resistivity

Neutral pathways and heat flux widths in vertical- and horizontal-target EDGE2D-EIRENE simulations of JET

This paper further analyses the EDGE2D-EIRENE simulations presented by Chankin et al (2017 Nucl. Mater. Energy 12 273), of L-mode JET plasmas in vertical-vertical (VV) and Vertical-horizontal (VH) divertor configurations. As expected, the simulated outer divertor ionisation source peaks near the separatrix in VV and radially further out in VH. We identify the reflections of recycled neutrals from lower divertor tiles as the primary mechanism by which ionisation is concentrated on the outer divertor separatrix in the VV configuration. These lower tile reflection pathways (of neutrals from the outer divertor, and to an even greater extent from the inner divertor) dominate the outer divertor separatrix ionisation. In contrast, the lower-tile-reflection pathways are much weaker in the VH simulation and its outer divertor ionisation is dominated by neutrals which do not reflect from any surfaces. Interestingly, these differences in neutral pathways give rise to strong differences in the heat flux density width λq at the outer divertor entrance: λq = 3.2 mm in VH compared to λq = 11.8 mm in VV. In VH, a narrow channel exists in the near scrape-off-layer (SOL) where the convected heat flux, driven by strong Er × B flow and thermoelectric current, dominates over the conducted heat flux. The width of this channel sets λq and is determined by the radial distance between the separatrix and the ionisation peak in the outer divertor

Observations and modelling of ion cyclotron emission observed in JET plasmas using a sub-harmonic arc detection system during ion cyclotron resonance heating

Peer reviewe