A simple way to evaluate self-designed probes for tumor specific Multiplex Ligation-dependent Probe Amplification (MLPA)

<p>Abstract</p> <p>Background</p> <p>The Multiplex Ligation-dependent Probe Amplification (MLPA) is widely used for analysis of copy number variations (CNVs) in single or multiple loci. MLPA is a versatile methodology and important tool in cancer research; it provides precise information on increased or decreased copy number at specific loci as opposed to loss of heterozygosity (LOH) studies based upon microsatellite analysis. Pre-designed MLPA kits and software are commercially available to analyze multiple exons, genes, and genomic regions. However, an increasing demand for new gene specific assays makes it necessary to self-design new MLPA probes for which the available software may not be applicable. During evaluation of new self-designed reference probes, we encountered a number of problems, especially when applying the MLPA methodology to tumor samples.</p> <p>Findings</p> <p>DNA samples from 48 unaffected individuals and 145 breast cancer patients were used to evaluate 11 self-designed MLPA probes and determine the cut-off values for CNV, before applying the MLPA probes to normalize the target probes in a cohort of affected individuals. To test the calculation strategy, three probes were designed to cover regions in Regulator of G-protein Signaling 8 (<it>RGS8</it>), which we previously have identified as being affected by allelic imbalance by LOH analysis across <it>RGS8 </it>in the cohort comprising 145 breast tumors. Agreement between the LOH results and the results obtained by each of the three MLPA probes in <it>RGS8 </it>was found for 64%, 73%, and 91%, of the analyzed samples, respectively.</p> <p>Conclusion</p> <p>Here, we present a straightforward method, based upon the normalization pattern in both unaffected and affected individuals, to evaluate self-designed reference probes and to calculate CNV for the MLPA assay with specific focus on the difficulties when analyzing tumor DNA.</p

Overview of the JET ITER-like wall divertor

The work presented draws on new analysis of components removed following the second JET ITER-like wall campaign 2013–14 concentrating on the upper inner divertor, inner and outer divertor corners, life- time issues relating to tungsten coatings on JET carbon fibre composite divertor tiles and dust/particulate generation. The results show that the upper inner divertor remains the region of highest deposition in the JET-ILW. Variations in plasma configurations between the first and second campaign have altered ma- terial migration to the corners of the inner and outer divertor. Net deposition is shown to be beneficial in the sense that it reduces W coating erosion, covers small areas of exposed carbon surfaces and even encapsulates particles.EURATOM 633053RCUK Energy Programme EP/I50104

Assessment of erosion, deposition and fuel retention in the JET-ILW divertor from ion beam analysis data

Proceedings of the 22nd International Conference on Plasma Surface Interactions 2016, 22nd PSI.Post-mortem analyses of individual components provide relevant information on plasma-surface interactions like tungsten erosion, beryllium deposition and plasma fuel retention with divertor tiles via implantation or co-deposition. Ion Beam techniques are ideal tools for such purposes and have been extensively used for post-mortem analyses of selected tiles from JET following each campaign. In this contribution results from tiles removed from the JET ITER-Like Wall (JET-ILW) divertor following the 2013–2014 campaign are presented. The results summarize erosion, deposition and fuel retention along the poloidal cross section of the divertor surface and provide data for comparison with the first JET-ILW campaign, showing a similar pattern of material migration with the exception of Tile 6 where the strike point time on the tile was ∼ 4 times longer in 2013–2014 than in 2011–2012, which is likely to account for more material migration to this region. The W deposition on top of the Mo marker coating of Tile 4 shows that the enrichment takes place at the strike point location.Peer reviewe

Deposition of impurity metals during campaigns with the JET ITER-like Wall

Post mortem analysis shows that mid and high atomic number metallic impurities are present in deposits on JET plasma facing components with the highest amount of Ni and W, and therefore the largest sink, being found at the top of the inner divertor. Sources are defined as "continuous" or "specific", in that "continuous" sources arise from ongoing erosion from plasma facing surfaces and specific" are linked with specific events which decrease over time until they no longer act as a source. This contribution evaluates the sinks and estimates sources and the balance gives an indication of the dominating processes. Charge exchange neutral erosion is found to be the main source of nickel, whereas erosion of divertor plasma facing components is the main source of tungsten. Specific sources are shown to have little influence over the global mid- and high-Z impurity concentrations in deposits.EURATOM 633053RCUK Energy Programme EP/I50104

Deuterium retention on the tungsten-coated divertor tiles of JET ITER-like wall in 2015-2016 campaign

Tungsten-coated divertor files exposed during the third JET ITER-Like Wall (ILW) campaign in 2015-2016 (ILW-3) were studied with Secondary Ion Mass Spectrometry (SIMS). ILW-3 campaign contained more high-power plasma discharges and longer plasma time than the earlier ILW campaigns. Measurements showed increased beryllium (Be) deposition on the upper inner divertor, whereas on the outer divertor, Be deposition was lower than during the second campaign in 2013-2014 (ILW-2). Increased intensifies of nickel, molybdenum and tungsten were observed at the surface layer of the inner divertor Be dominated deposits. These layers are probably formed during the high-power plasma discharge phase near the end of the ILW-3 campaign. Compared to the earlier campaigns, D retention on the upper inner divertor was observed to on a similar level than after ILW-2, whereas at the lower inner divertor and most parts of the outer divertor, D retention was lower for ILW-3 than ILW-2. D retention was increased at lower part of outer divertor Tile 7, where Be deposition was slightly increased. Probable reason for the reduction is the higher surface temperature of the files due to higher powers used.Peer reviewe

Thermal desorption spectrometry of beryllium plasma facing tiles exposed in the JET tokamak

Corrigendum: 10.1016/j.fusengdes.2018.08.007.The phenomena of retention and de-trapping of deuterium (D) and tritium (T) in plasma facing components (PFC) and supporting structures must be understood in order to limit or control total T inventory in larger future fusion devices such as ITER, DEMO and commercial machines. The goal of this paper is to present details of the thermal desorption spectrometry (TDS) system applied in total fuel retention assessment of PFC at the Joint European Torus (JET). Examples of TDS results from beryllium (Be) wall tile samples exposed to JET plasma in PFC configuration mirroring the planned ITER PFC is shown for the first time. The method for quantifying D by comparison of results from a sample of known D content was confirmed acceptable. The D inventory calculations obtained from Ion Beam Analysis (IBA) and TDS agree well within an error associated with the extrapolation from very few data points to a large surface area.Peer reviewe

Surface analysis of tiles and samples exposed to the first JET campaigns with the ITER-Like Wall

This paper reports on the first post-mortem analyses of tiles removed from JET after the first campaigns with the ITER-like Wall (ILW) during 2011-2 [1]. Tiles from the divertor have been analysed by the Ion Beam Analysis (IBA) techniques Rutherford Backscattering Spectroscopy (RBS) and Nuclear Reaction Analysis (NRA) and by Secondary Ion Mass Spectrometry (SIMS) to determine the amount of beryllium deposition and deuterium retention in the tiles exposed to the scrape-off layer. Films 10-20 microns thick were present at the top of Tile 1, but only very thin films (<1 micron) were found in the shadowed areas and on other divertor tiles. The total amount of Be found in the divertor following the ILW campaign was a factor of ~9 less that the material deposited in the 2007-9 carbon campaign, after allowing for the longer operations in 2007-9.Comment: 10 pages, 5 figures. This is an author-created, un-copyedited version of an article accepted for publication in Physica Scripta. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from i

Overview of the JET ITER-like wall divertor

The work presented draws on new analysis of components removed following the second JET ITER-like wall campaign 2013–14 concentrating on the upper inner divertor, inner and outer divertor corners, lifetime issues relating to tungsten coatings on JET carbon fibre composite divertor tiles and dust/particulate generation. The results show that the upper inner divertor remains the region of highest deposition in the JET-ILW. Variations in plasma configurations between the first and second campaign have altered material migration to the corners of the inner and outer divertor. Net deposition is shown to be beneficial in the sense that it reduces W coating erosion, covers small areas of exposed carbon surfaces and even encapsulates particles.The work presented draws on new analysis of components removed following the second JET ITER-like wall campaign 2013–14 concentrating on the upper inner divertor, inner and outer divertor corners, lifetime issues relating to tungsten coatings on JET carbon fibre composite divertor tiles and dust/particulate generation. The results show that the upper inner divertor remains the region of highest deposition in the JET-ILW. Variations in plasma configurations between the first and second campaign have altered material migration to the corners of the inner and outer divertor. Net deposition is shown to be beneficial in the sense that it reduces W coating erosion, covers small areas of exposed carbon surfaces and even encapsulates particles.Peer reviewe

The possible effect of high magnetic fields on the aqueous corrosion behaviour of Eurofer

In defining the corrosion control requirements for DEMO, the impact of the mixed Eurofer-97/AISI 316 steel system and plant specific effects should be considered throughout, in particular, the effect of the intense magnetic fields present. A substantial amount of data related to corrosion resistance of structural materials is available for industrial applications in fission, but applies to different materials and neutronic conditions. Experimental work is being carried out under the DEMO Breeding Blanket Project of the EUROfusion programme, which will further develop the understanding of irradiation effects. However, there is very limited information regarding magnetic field-assisted corrosion under conditions relevant for the fusion environment readily available in the literature. This work reviews current knowledge and progress in establishing the possible influence of the intense magnetic field on corrosion behaviour of the main structural material, Eurofer-97, in the breeding blanket. To support the relevance of this problem statement, preliminary corrosion experimental results of Eurofer-97 coupons, obtained by using a simple apparatus that allows exposure to a magnetic field intensity of 0.88 T and temperatures up to 80 °C in water at atmospheric pressure, are presented as an initial qualitative investigation of possible magnetic field related effects

Comparative study of deuterium retention and vacancy content of self-ion irradiated tungsten

Self-ion irradiation of pure tungsten with 2 MeV W ions provides a way of simulating microstructures generated by neutron irradiation in tungsten components of a fusion reactor. Transmission electron microscopy (TEM) has been used to characterize defects formed in tungsten samples by ion irradiation. It was found that tungsten irradiated to 0.85 dpa at relatively low temperatures develops a characteristic microstructure dominated by dislocation loops and black dots. The density and size distribution of these defects were estimated. Some of the samples exposed to self-ion irradiation were then implanted with deuterium. Thermal Desorption Spectrometry (TDS) analysis was performed to estimate the deuterium inventory as a function of irradiation damage and deuterium release as a function of temperature. Increase of inventory with increasing irradiation dose followed by slight decrease above 0.1 dpa was found. Application of Positron Annihilation Spectroscopy (PAS) to self-irradiated but not deuterium implanted samples enabled an assessment of the density of irradiation defects as a function of exposure to highenergy ions. The PAS results show that the density of defects saturates at doses in the interval from 0.085 to 0.425 displacements per atom (dpa). These results are discussed in the context of recent theoretical simulations exhibiting the saturation of defect microstructure in the high irradiation exposure limit. The saturation of damage found in PAS agrees with the simulation data described in the paper. (c) 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )Peer reviewe