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STEP is a spherical tokamak prototype power plant that is being designed to demonstrate net electric power. The design phase involves the exploitation of plasma models to optimise fusion performance subject to satisfying various physics and engineering constraints. A modelling workflow, including integrated core plasma modelling, MHD stability analysis, SOL and pedestal modelling, coil set and free boundary equilibrium solvers, and whole plant design, has been developed to specify the design parameters and to develop viable scenarios. The integrated core plasma model JETTO is used to develop individual flat-top operating points that satisfy imposed criteria for fusion power performance within operational constraints. Key plasma parameters such as normalised beta, Greenwald density fraction, auxiliary power and radiated power have been scanned to scope the operational space and to derive a collection of candidate non-inductive flat-top points. The assumed auxiliary heating and current drive is either from electron cyclotron systems only or a combination of electron cyclotron and electron Bernstein waves. At present stages of transport modelling, there is a large uncertainty in overall confinement for relevant parameter regimes. For each of the two auxiliary heating and current drive systems scenarios, two candidate flat-top points have been developed based on different confinement assumptions, totalling to four operating points. A lower confinement assumption generally suggests operating points in high-density, high auxiliary power regimes, whereas higher confinement would allow access to a broader parameter regime in density and power while maintaining target fusion power performance.

In Hybrid plasma operation in JET with its ITER-like wall (JET-ILW) it is found that n>1 tearing activity can significantly enhance the rate of on-axis peaking of tungsten impurities, which in turn significantly degrades discharge performance. Core n=1 instabilities can be beneficial in removing tungsten impurities from the plasma core (e.g. sawteeth or fishbones), but can conversely also degrade core confinement (particularly in combination with simultaneous n=3 activity). The nature of MHD instabilities in JET Hybrid discharges, with both its previous Carbon wall and subsequent JET-ILW, is surveyed statistically and the character of the instabilities is examined. Possible qualitative models for how the n>1 islands can enhance on-axis tungsten transport accumulation processes are presented.

Calculations of tearing mode stability in tokamaks split conveniently into an external region, where marginally stable ideal MHD is applicable, and a resonant layer around the rational surface where sophisticated kinetic physics is needed. These two regions are coupled by the stability parameter. Pressure and current perturbations localized around the rational surface alter the stability of tearing modes. Equations governing the changes in the external solution and - are derived for arbitrary perturbations in axisymmetric toroidal geometry. The relationship of - with and without pressure flattening is obtained analytically for four pressure flattening functions. Resistive MHD codes do not contain the appropriate layer physics and therefore cannot predict stability directly. They can, however, be used to calculate -. Existing methods (Ham et al. 2012 Plasma Phys. Control. Fusion 54 025009) for extracting - from resistive codes are unsatisfactory when there is a finite pressure gradient at the rational surface and favourable average curvature because of the Glasser stabilizing effect. To overcome this difficulty we introduce a specific pressure flattening function that allows the earlier approach to be used. The technique is first tested numerically in cylindrical geometry with an artificial favourable curvature. Its application to toroidal geometry is then demonstrated using the toroidal tokamak tearing mode stability code T7 (Fitzpatrick et al. 1993 Nucl. Fusion 33 1533) which uses an approximate analytic equilibrium. The prospects for applying this approach to resistive MHD codes such as MARS-F (Liu et al. 2000 Phys. Plasmas 7 3681) which utilize a fully toroidal equilibrium are discussed.

Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for bla CTX-M-15 , bla NDM , bla KPC and bla OXA-48 -like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates’ rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers’ rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli , Klebsiella pneumoniae and Enterobacter cloacae / E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes. Analysis of gut microbiota of mothers and its neonates—as part of the BARNARDS study—reveals associations between β-lactamase gene carriage and neonatal sepsis risk in low-income settings.

There is a vital need for authentic COVID-19 animal models to enable the pre-clinical evaluation of candidate vaccines and therapeutics. Here we report a dose titration study of SARS-CoV-2 in the ferret model. After a high (5 × 10 6  pfu) and medium (5 × 10 4  pfu) dose of virus is delivered, intranasally, viral RNA shedding in the upper respiratory tract (URT) is observed in 6/6 animals, however, only 1/6 ferrets show similar signs after low dose (5 × 10 2  pfu) challenge. Following sequential culls pathological signs of mild multifocal bronchopneumonia in approximately 5–15% of the lung is seen on day 3, in high and medium dosed groups. Ferrets re-challenged, after virus shedding ceased, are fully protected from acute lung pathology. The endpoints of URT viral RNA replication & distinct lung pathology are observed most consistently in the high dose group. This ferret model of SARS-CoV-2 infection presents a mild clinical disease. SARS-CoV-2 induces mild infection in ferret model. Here, Ryan et al. characterise optimal infection dosage inducing upper respiratory tract (UTR) viral shedding, progression time of viral shedding, and pathology in ferrets and finally provide evidence for protection after re-challenge.

Recent epidemiological evidence supports the hypothesis that health effects from inhalation of ambient particulate matter (PM) are governed by more than just the mass of PM inhaled. Both specific chemical components and sources have been identified as important contributors to mortality and hospital admissions, even when these end points are unrelated to PM mass. Sources may cause adverse health effects via their ability to produce reactive oxygen species in the body, possibly due to the transition metal content of the PM. Our goal is to quantify the oxidative potential of ambient particle sources collected during two seasons in Fresno, CA, using the dithiothreitol (DTT) assay. We collected PM from different sources or source combinations into different ChemVol (CV) samplers in real time using a novel source-oriented sampling technique based on single-particle mass spectrometry. We segregated the particles from each source-oriented mixture into two size fractions – ultrafine Dp ≤ 0.17 μm) and submicron fine (0.17 μm ≤ Dp ≤ 1.0 μm) – and measured metals and the rate of DTT loss in each PM extract. We find that the mass-normalized oxidative potential of different sources varies by up to a factor of 8 and that submicron fine PM typically has a larger mass-normalized oxidative potential than ultrafine PM from the same source. Vehicular emissions, regional source mix, commute hours, daytime mixed layer, and nighttime inversion sources exhibit the highest mass-normalized oxidative potential. When we apportion DTT activity for total PM sampled to specific chemical compounds, soluble copper accounts for roughly 50% of total air-volume-normalized oxidative potential, soluble manganese accounts for 20%, and other unknown species, likely including quinones and other organics, account for 30%. During nighttime, soluble copper and manganese largely explain the oxidative potential of PM, while daytime has a larger contribution from unknown (likely organic) species.

Radium has four naturally occurring isotopes that have proven useful in constraining water mass source, age, and mixing rates in the coastal and open ocean. In this study, we used radium isotopes to determine the fate and flux of runoff-derived cesium from the Fukushima Dai-ichi Nuclear Power Plant (FNPP). During a June 2011 cruise, the highest cesium (Cs) concentrations were found along the eastern shelf of northern Japan, from Fukushima south, to the edge of the Kuroshio Current, and in an eddy ~ 130 km from the FNPP site. Locations with the highest cesium also had some of the highest radium activities, suggesting much of the direct ocean discharges of Cs remained in the coastal zone 2–3 months after the accident. We used a short-lived Ra isotope (223Ra, t1/2 = 11.4 d) to derive an average water mass age (Tr) in the coastal zone of 32 days. To ground-truth the Ra age model, we conducted a direct, station-by-station comparison of water mass ages with a numerical oceanographic model and found them to be in excellent agreement (model avg. Tr = 27 days). From these independent Tr values and the inventory of Cs within the water column at the time of our cruise, we were able to calculate an offshore 134Cs flux of 3.9–4.6 × 1013 Bq d−1. Radium-228 (t1/2 = 5.75 yr) was used to derive a vertical eddy diffusivity (Kz) of 0.7 m2 d−1 (0.1 cm2 s−1); from this Kz and 134Cs inventory, we estimated a 134Cs flux across the pycnocline of 1.8 × 104 Bq d−1 for the same time period. On average, our results show that horizontal mixing loss of Cs from the coastal zone was ~ 109 greater than vertical exchange below the surface mixed layer. Finally, a mixing/dilution model that utilized our Ra-based and oceanographic model water mass ages produced a direct ocean discharge of 134Cs from the FNPP of 11–16 PBq at the time of the peak release in early April 2011. Our results can be used to calculate discharge of other water-soluble radionuclides that were released to the ocean directly from the Fukushima NPP.

Fast Repetition Rate fluorometry (FRRf) measurements of phytoplankton photophysiology from an across-basin South Atlantic cruise (as part of the GEOTRACES programme) characterised two dominant ecophysiological regimes which were interpreted on the basis of nutrient limitation. South of the South Subtropical Convergence (SSTC) in the northern sub-Antarctic sector of the Antarctic Circumpolar Current (ACC) in the Eastern Atlantic Basin, waters are characterised by elevated chlorophyll concentrations, a dominance by larger phytoplankton cells, and low apparent photochemical efficiency (Fv / Fm). Shipboard 24 h iron (Fe) addition incubation experiments confirmed that Fe stress was primarily responsible for the low Fv / Fm, with Fe addition to these waters, either within the artificial bottle additions or naturally occurring downstream enrichment from Gough Island, significantly increasing Fv / Fm values. To the north of the SSTC at the southern boundary of the South Atlantic Gyre, phytoplankton are characterised by high values of Fv / Fm which, coupled with the low macronutrient concentrations and increased presence of picocyanobacteria, are interpreted as conditions of Fe replete, balanced macronutrient-limited growth. Spatial correlation was found between Fv / Fm and Fe:nitrate ratios, supporting the suggestion that the relative supply ratios of these two nutrients can control patterns of limitation and consequently the ecophysiology of phytoplankton in subtropical gyre and ACC regimes.

Rising ocean temperatures will likely increase stratification of the water column and reduce nutrient input into the photic zone. This will increase the likelihood of nutrient limitation in marine microalgae, leading to changes in the abundance and composition of phytoplankton communities, which in turn will affect global biogeochemical cycles. Calcifying algae, such as coccolithophores, influence the carbon cycle by fixing CO2 into particulate organic carbon through photosynthesis (POC production) and into particulate inorganic carbon through calcification (PIC production). As calcification produces a net release of CO2, the ratio of PIC to POC production determines whether coccolithophores act as a source (high PIC / POC) or a sink (low PIC / POC) of atmospheric CO2. We studied the effect of phosphorus (P-) limitation and high temperature on the physiology and the PIC / POC ratio of two subspecies of Coccolithus pelagicus. This large and heavily calcified species is a major contributor to calcite export from the photic zone into deep-sea reservoirs. Phosphorus limitation did not influence exponential growth rates in either subspecies, but P-limited cells had significantly lower cellular P-content. One of the subspecies was subjected to a 5 °C temperature increase from 10 °C to 15 °C, which did not affect exponential growth rates either, but nearly doubled cellular P-content under both high and low phosphate availability. This temperature increase reduced the PIC / POC ratio by 40–60%, whereas the PIC / POC ratio did not differ between P-limited and nutrient-replete cultures when the subspecies were grown near their respective isolation temperature. Both P-limitation and elevated temperature significantly increased coccolith malformations. Our results suggest that a temperature increase may intensify P-limitation due to a higher P-requirement to maintain growth and POC production rates, possibly reducing abundances in a warmer ocean. Under such a scenario C. pelagicus may decrease its calcification rate relative to photosynthesis, thus favouring CO2 sequestration over release. It seems unlikely that P-limitation by itself causes changes in the PIC / POC ratio in this species.

Regional and global chemical transport models underpredict NOx (NO + NO2) in the upper troposphere where it is a precursor to the greenhouse gas ozone. The NOx bias has been shown in model evaluations using aircraft data (Singh et al., 2007) and total column NO2 (molecules cm−2) from satellite observations (Napelenok et al., 2008). The causes of NOx underpredictions have yet to be fully understood due to the interconnected nature of simulated emission, transport, and chemistry processes. Recent observation-based studies, in the upper troposphere, identify chemical rate coefficients as a potential source of error (Olson et al., 2006; Ren et al., 2008). Since typical chemistry evaluation techniques are not available for upper tropospheric conditions, this study develops an evaluation platform from in situ observations, stochastic convection, and deterministic chemistry. We derive a stochastic convection model and optimize it using two simulated datasets of time since convection, one based on meteorology, and the other on chemistry. The chemistry surrogate for time since convection is calculated using seven different chemical mechanisms, all of which predict shorter time since convection than our meteorological analysis. We evaluate chemical simulations by inter-comparison and by pairing results with observations based on NOx:HNO3, a photochemical aging indicator. Inter-comparison reveals individual chemical mechanism biases and recommended updates. Evaluation against observations shows that all chemical mechanisms overpredict NOx removal relative to long-lived methanol and carbon monoxide. All chemical mechanisms underpredict observed NOx by at least 30%, and further evaluation is necessary to refine simulation sensitivities to initial conditions and chemical rate uncertainties.