Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis

Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.

Volumetric modulated arc therapy and breath-hold in image-guided locoregional left-sided breast irradiation

PURPOSE: To investigate the effects of using volumetric modulated arc therapy (VMAT) and/or voluntary moderate deep inspiration breath-hold (vmDIBH) in the radiation therapy (RT) of left-sided breast cancer including the regional lymph nodes.

MATERIALS AND METHODS: For 13 patients, four treatment combinations were compared; 3D-conformal RT (i.e., forward IMRT) in free-breathing 3D-CRT(FB), 3D-CRT(vmDIBH), 2 partial arcs VMAT(FB), and VMAT(vmDIBH). Prescribed dose was 42.56 Gy in 16 fractions. For 10 additional patients, 3D-CRT and VMAT in vmDIBH only were also compared.

RESULTS: Dose conformity, PTV coverage, ipsilateral and total lung doses were significantly better for VMAT plans compared to 3D-CRT. Mean heart dose (D(mean,heart)) reduction in 3D-CRT(vmDIBH) was between 0.9 and 8.6 Gy, depending on initial D(mean,heart) (in 3D-CRT(FB) plans). VMAT(vmDIBH) reduced the D(mean,heart) further when D(mean,heart) was still >3.2 Gy in 3D-CRT(vmDIBH). Mean contralateral breast dose was higher for VMAT plans (2.7 Gy) compared to 3DCRT plans (0.7 Gy).

CONCLUSIONS: VMAT and 3D-CRT(vmDIBH) significantly reduced heart dose for patients treated with locoregional RT of left-sided breast cancer. When Dmean,heart exceeded 3.2 Gy in 3D-CRT(vmDIBH) plans, VMAT(vmDIBH) resulted in a cumulative heart dose reduction. VMAT also provided better target coverage and reduced ipsilateral lung dose, at the expense of a small increase in the dose to the contralateral breast.

ELM-induced transient tungsten melting in the JET divertor

The original goals of the JET ITER-like wall included the study of the impact of an all W divertor on plasma operation (Coenen et al 2013 Nucl. Fusion 53 073043) and fuel retention (Brezinsek et al 2013 Nucl. Fusion 53 083023). ITER has recently decided to install a full-tungsten (W) divertor from the start of operations. One of the key inputs required in support of this decision was the study of the possibility of W melting and melt splashing during transients. Damage of this type can lead to modifications of surface topology which could lead to higher disruption frequency or compromise subsequent plasma operation. Although every effort will be made to avoid leading edges, ITER plasma stored energies are sufficient that transients can drive shallow melting on the top surfaces of components. JET is able to produce ELMs large enough to allow access to transient melting in a regime of relevance to ITER.

Transient W melt experiments were performed in JET using a dedicated divertor module and a sequence of I-P = 3.0 MA/B-T = 2.9 T H-mode pulses with an input power of P-IN = 23 MW, a stored energy of similar to 6 MJ and regular type I ELMs at Delta W-ELM = 0.3 MJ and f(ELM) similar to 30 Hz. By moving the outer strike point onto a dedicated leading edge in the W divertor the base temperature was raised within similar to 1 s to a level allowing transient, ELM-driven melting during the subsequent 0.5 s. Such ELMs (delta W similar to 300 kJ per ELM) are comparable to mitigated ELMs expected in ITER (Pitts et al 2011 J. Nucl. Mater. 415 (Suppl.) S957-64).

Although significant material losses in terms of ejections into the plasma were not observed, there is indirect evidence that some small droplets (similar to 80 mu m) were released. Almost 1 mm (similar to 6 mm(3)) of W was moved by similar to 150 ELMs within 7 subsequent discharges. The impact on the main plasma parameters was minor and no disruptions occurred. The W-melt gradually moved along the leading edge towards the high-field side, driven by j x B forces. The evaporation rate determined from spectroscopy is 100 times less than expected from steady state melting and is thus consistent only with transient melting during the individual ELMs. Analysis of IR data and spectroscopy together with modelling using the MEMOS code Bazylev et al 2009 J. Nucl. Mater. 390-391 810-13 point to transient melting as the main process. 3D MEMOS simulations on the consequences of multiple ELMs on damage of tungsten castellated armour have been performed.

These experiments provide the first experimental evidence for the absence of significant melt splashing at transient events resembling mitigated ELMs on ITER and establish a key experimental benchmark for the MEMOS code.

The Reliability of the Arc-Length Method in the Analysis of Mode-Jumping Problems

The Arc-Length Method is a solution procedure that enables a generic non-linear problem to pass limit points. Some examples are provided of mode-jumping problems solutions using a commercial nite element package, and other investigations are carried out on a simple structure of which the numerical solution can be compared with an analytical one. It is shown that Arc-Length Method is not reliable when bifurcations are present in the primary equilibrium path; also the presence of very sharp snap-backs or special boundary conditions may cause convergence diÆculty at limit points. An improvement to the predictor used in the incremental procedure is suggested, together with a reliable criteria for selecting either solution of the quadratic arc-length constraint. The gap that is sometimes observed between the experimantal load level of mode-jumping and its arc-length prediction is explained through an example.

Comparative Raman Study of Carbon Nanotubes Prepared by D.C. Arc Discharge and Catalytic Methods

The Raman spectra of carbon nanotubes prepared by catalytic (C-CNT) and d.c. arc discharge (D-CNT) methods are reported. A previously unnoticed third-order Raman peak at ca. 4248 cm-1 was observed in the Raman spectrum of D-CNT. The Raman features of D-CNT and C-CNT are similar to those of highly oriented pyrolytic graphite (HOPG) and active carbon, respectively. The data also suggest that the increase in disorder in D-CNT compared with HOPG is due to structural defects in D-CNT. © 1997 by John Wiley & Sons, Ltd.