Fundamental Physical Processes in Coronae: Waves, Turbulence, Reconnection, and Particle Acceleration

Our understanding of fundamental processes in the solar corona has been greatly progressed based on the space observations of SMM, Yohkoh, Compton GRO, SOHO, TRACE, RHESSI, and STEREO. We observe now acoustic waves, MHD oscillations, turbulence-related line broadening, magnetic configurations related to reconnection processes, and radiation from high-energy particles on a routine basis. We review a number of key observations in EUV, soft X-rays, and hard X-rays that innovated our physical understanding of the solar corona, in terms of hydrodynamics, MHD, plasma heating, and particle acceleration processes.Comment: Proc. IAU Symp. 247, Waves and Oscillations in the Solar Atmosphere: Heating and Magneto-Seismology, (ed. R. Erdelyi

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex’s entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that upregulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype

Death or survival from invasive pneumococcal disease in Scotland: associations with serogroups and multilocus sequence types

We describe associations between death from invasive pneumococcal disease (IPD) and particular serogroups and sequence types (STs) determined by multilocus sequence typing (MLST) using data from Scotland. All IPD episodes where blood or cerebrospinal fluid (CSF) culture isolates were referred to the Scottish Haemophilus, Legionella, Meningococcal and Pneumococcal Reference Laboratory (SHLMPRL) from January 1992 to February 2007 were matched to death certification records by the General Register Office for Scotland. This represented 5959 patients. The median number of IPD cases in Scotland each year was 292. Deaths, from any cause, within 30 days of pneumococcal culture from blood or CSF were considered to have IPD as a contributing factor. Eight hundred and thirty-three patients died within 30 days of culture of Streptococcus pneumoniae from blood or CSF [13.95%; 95% confidence interval (13.10, 14.80)]. The highest death rates were in patients over the age of 75. Serotyping data exist for all years but MLST data were only available from 2001 onward. The risk ratio of dying from infection due to particular serogroups or STs compared to dying from IPD due to all other serogroups or STs was calculated. Fisher's exact test with Bonferroni adjustment for multiple testing was used. Age adjustment was accomplished using the Cochran-Mantel-Haenszel test and 95% confidence intervals were reported. Serogroups 3, 11 and 16 have increased probability of causing fatal IPD in Scotland while serogroup 1 IPD has a reduced probability of causing death. None of the 20 most common STs were significantly associated with death within 30 days of pneumococcal culture, after age adjustment. We conclude that there is a stronger association between a fatal outcome and pneumococcal capsular serogroup than there is between a fatal outcome and ST

Trends in serotypes and sequence types among cases of invasive pneumococcal disease in Scotland, 1999-2010.

INTRODUCTION: The 7-valent pneumococcal conjugate vaccine (Prevenar(®), Wyeth; PCV7) was introduced to the UK paediatric immunisation schedule in 2006. This study investigates trends in serotypes and multi locus sequence types (STs) among cases of invasive pneumococcal disease (IPD) in Scotland prior to, and following, the introduction of PCV7. METHODS: Scottish Invasive Pneumococcal Disease Enhanced Surveillance has records of all cases of IPD in Scotland since 1999. Cases diagnosed from blood or cerebrospinal fluid isolates until 2010 were analysed. Logistic and poisson regression modelling was used to assess trends prior to and following the introduction of PCV7. RESULTS: Prior to PCV7 use, on average 650 cases of IPD were reported each year; 12% occurred in those aged <5 years and 35% affected those aged over 65 years. Serotypes in PCV7 represented 47% of cases (68% in <5 year olds). The serotype and ST distribution was relatively stable with only serotype 1 and associated ST 306 showing an increasing trend. PCV7 introduction was associated with a 69% (95% CI: 50%, 80%) reduction in the incidence of IPD among those aged <5 years, a 57% (95% CI: 47%, 66%) reduction among those aged 5-64 years but no significant change among those aged 65 years and over where increases in non-PCV7 serotypes were observed. Serotypes which became more prevalent post-PCV7 are those which were associated with STs related to the PCV7 serotypes. CONCLUSIONS: Routine serotyping and sequence typing in Scotland allowed the assessment of the relationship between the capsule and the clones in the post vaccination era. Changes in the distribution of serotypes post PCV7 introduction appear to be driven by associations between serotypes and STs prior to PCV7 introduction. This has implications for the possible effects of the introduction of higher valency vaccines and could aid in predicting replacement serotypes in IPD

On Solving the Coronal Heating Problem

This article assesses the current state of understanding of coronal heating, outlines the key elements of a comprehensive strategy for solving the problem, and warns of obstacles that must be overcome along the way.Comment: Accepted by Solar Physics; Published by Solar Physic

Staphylococcus aureus endocarditis associated with injecting new psychoactive substances

Background Staphylococcus aureus infective endocarditis (IE) associated with injection of new psychoactive substances (NPS) in Edinburgh from 2014 to 2016 was observed. We compared these infections with a series of S. aureus IE cases in a non-injecting population within Edinburgh. Methods NPS-associated S. aureus IE diagnosed between 1 January 2014 and 31 May 2016 in persons who inject drugs (PWID) were compared with a series of S. aureus IE cases from non-PWID. Results There was a fourfold increase in the annual incidence of S. aureus IE, mainly due to NPS use in PWID. A larger vegetation diameter was seen on echocardiogram in PWID vs non-PWID (median 1.7 cm vs 0.65 cm; p = 0.009) with more embolic complications in PWID (15 PWID vs 1 non-PWID; p = 2.1 x 10-7) but no difference in 90-day mortality (2 PWID vs 4 non-PWID; p = 0.39). Conclusions NPS-associated S. aureus IE correlated with complications, such as deep organ embolic abscesses, that were different from non-PWID S. aureus IE. The alarming increase in incidence resolved with targeted public health and legislative measures

Is null-point reconnection important for solar flux emergence?

The role of null-point reconnection in a 3D numerical MHD model of solar emerging flux is investigated. The model consists of a twisted magnetic flux tube rising through a stratified convection zone and atmosphere to interact and reconnect with a horizontal overlying magnetic field in the atmosphere. Null points appear as the reconnection begins and persist throughout the rest of the emergence, where they can be found mostly in the model photosphere and transition region, forming two loose clusters on either side of the emerging flux tube. Up to 26 nulls are present at any one time, and tracking in time shows that there is a total of 305 overall, despite the initial simplicity of the magnetic field configuration. We find evidence for the reality of the nulls in terms of their methods of creation and destruction, their balance of signs, their long lifetimes, and their geometrical stability. We then show that due to the low parallel electric fields associated with the nulls, null-point reconnection is not the main type of magnetic reconnection involved in the interaction of the newly emerged flux with the overlying field. However, the large number of nulls implies that the topological structure of the magnetic field must be very complex and the importance of reconnection along separators or separatrix surfaces for flux emergence cannot be ruled out.Comment: 26 pages, 12 figures. Added one referenc

First 3D Reconstructions of Coronal Loops with the STEREO A+B Spacecraft: IV. Magnetic Modeling with Twisted Force-Free Fields

The three-dimensional (3D) coordinates of stereoscopically triangulated loops provide strong constraints for magnetic field models of active regions in the solar corona. Here we use STEREO/A and B data from some 500 stereoscopically triangulated loops observed in four active regions (2007 Apr 30, May 9, May 19, Dec 11), together with SOHO/MDI line-of-sight magnetograms. We measure the average misalignment angle between the stereoscopic loops and theoretical magnetic field models, finding a mismatch of $\mu=19^\circ-46^\circ$ for a potential field model, which is reduced to $\mu=14^\circ-19^\circ$ for a non-potential field model parameterized by twist parameters. The residual error is commensurable with stereoscopic measurement errors ($\mu_{SE} \approx 8^\circ-12^\circ$). We developed a potential field code that deconvolves a line-of-sight magnetogram into three magnetic field components $(B_x, B_y, B_z)$, as well as a non-potential field forward-fitting code that determines the full length of twisted loops ($L \approx 50-300$ Mm), the number of twist turns (median $N_{twist}=0.06$), the nonlinear force-free $\alpha$-parameter (median $\alpha \approx 4 \times 10^{-11}$ cm$^{-1}$), and the current density (median $j_z \approx 1500$ Mx cm$^{-2}$ s$^{-1}$). All twisted loops are found to be far below the critical value for kink instability, and Joule dissipation of their currents is found be be far below the coronal heating requirement. The algorithm developed here, based on an analytical solution of nonlinear force-free fields that is accurate to second order (in the force-free parameter $\alpha$), represents the first code that enables fast forward-fitting to photospheric magnetograms and stereoscopically triangulated loops in the solar corona.Comment: The Astrophysical Journal (in press), 37 pages, 14 Figure

Effects of clarithromycin at sub-minimum inhibitory concentrations on early ermB gene expression, metabolic activity and growth of an erm(B)-expressing macrolide-resistant strain of Streptococcus pneumoniae

AIM: To investigate the effects of exposure of a macrolide-resistant [erm(B)-expressing] strain of Streptococcus pneumo- niae (strain 2507) to clarithromycin (0.5 and 5 mg/L) added at the outset and 6 hours after initiation of culture on early gene expression, energy metabolism, and growth. METHODS: Bacterial growth was determined by turbidometric and colony counting procedures, energy metabolism by measurement of ATP, while analysis of gene expression was per- formed using reverse transcription-PCR and sequencing. RESULTS: Addition of clarithromycin, at either concentration, at the outset of culture, caused transient suppression of growth of 10 - 12 hours duration, while delayed addition of antibi-otic (during the logarithmic phase) resulted in an abrupt halt in growth followed by recovery. These inhibitory effects of clarithromycin on bacterial growth were associated with up-regulation of expression of erm(B), decreased ATP and protein synthesis, and were unaffected by inclusion of either catalase (500 and 1000 kunits/L), or compe- tence-stimulating peptide (CSP-1, 0.5 mg/L). The inhibitory effects could, however, be overcome by pre-exposure of the bacteria to the antibiotic. Moreover, clarithromycin appeared to potentiate the antimicrobial actions of ceftriaxone, at sub-MIC concentrations, for strain 2507. CONCLUSIONS: Unlike several other common bacterial pathogens, the full expression of erm(B)-mediated macrolide resistance by the pneumococcus has a slow onset, which is associated with transient susceptibility to macrolides and inhibition of growth.CF is supported by the National Research Foundation of South Africa.http://www.SciRP.org/journal/ojr

The Met Office Forecast Ocean Assimilation Model (FOAM) using a 1/12‐degree grid for global forecasts

The Met Office Forecast Ocean Assimilation Model (FOAM) ocean–sea-ice analysis and forecasting operational system has been using an ORCA tripolar grid with 1/4° horizontal grid spacing since December 2008. Surface boundary forcing is provided by numerical weather prediction fields from the operational global atmosphere Met Office Unified Model. We present results from a 2-year simulation using a 1/12° global ocean–sea-ice model configuration while keeping a 1/4° data assimilation (DA) set-up. We also describe recent operational data assimilation enhancements that are included in our 1/4° control and 1/12° simulations: a new bias-correction term for sea-level anomaly assimilation and a revised pressure correction algorithm. The primary effect of the first is to decrease the mean and variability of sea-level anomaly increments at high latitudes, whereas the second significantly reduces the vertical velocity standard deviation in the tropical Pacific. The level of improvement achieved with the higher resolution configuration is moderate but consistently satisfactory when measured using neighbourhood verification metrics that provide fairer quantitative comparisons between gridded model fields at different spatial resolutions than traditional root-mean-square metrics. A comparison of the eddy kinetic energy from each configuration and an observation-based product highlights the regions where further system developments are most needed