Ultrasensitive detection and identification of BRAF V600 mutations in fresh frozen,FFPE, and plasma samples of melanoma patients by E-ice-COLD-PCR

A number of molecular diagnostic methods have been developed for the detection and identification of mutations in tumor samples, which are important for the choice of treatment in the context of personalized medicine. For the treatment of metastatic melanoma, Vemurafenib is recommended for patients with BRAF V600 activating mutations. However, the different assays developed to date for the detection of these mutations lack sensitivity or specificity or do not allow a sequencing-based identification or validation of the mutation. Recently, enhanced improved and complete enrichment co-amplification at lower denaturation temperature-polymerase chain reaction (E-ice-COLD-PCR) has been developed as a sensitive method for the detection and identification of mutations in KRAS codons 12/13. Here, we present the first E-ice-COLD-PCR assay for the detection and identification of BRAF codon 600 mutations, which has a large dynamic range, as 25 pg to 25 ng can be used as DNA input without any reduction in mutation enrichment efficiency, and which can detect down to 0.01 % of mutated alleles in a wild-type background. The assay has been validated on fresh frozen, formalin-fixed paraffin-embedded (FFPE), and plasma samples of melanoma patients and has allowed the detection and identification of BRAF mutations present in samples appearing as wild type using standard pyrosequencing, endpoint genotyping, or Sanger sequencing. Thus, the BRAF V600 E-ice-COLD-PCR assay is currently one of the most powerful molecular diagnostic tools for the ultrasensitive detection and identification of BRAF codon 600 mutations.     

Electrochemically deposited palladium as a substrate for self-assembled monolayers

The vast majority of reports of self-assembled monolayers (SAMs) on metals focus on the use of gold. However, other metals, such as palladium, platinum, and silver offer advantages over gold as a substrate. In this work, palladium is electrochemically deposited from PdCl2 solutions on glassy carbon electrodes to form a substrate for alkanethiol SAMs. The conditions for deposition are optimized with respect to the electrolyte, pH, and electrochemical parameters. The palladium surfaces have been characterized by scanning electron microscopy (SEM) and the surface roughness has been estimated by chronocoulometry. SAMs of alkane thiols have been formed on the palladium surfaces, and their ability to suppress a Faradaic process is used as an indication for palladium coverage on the glassy carbon. The morphology of the Pd deposit as characterized by SEM and the blocking behavior of the SAM formed on deposited Pd delivers a consistent picture of the Pd surface. It has been clearly demonstrated that, via selection of experimental conditions for the electrochemical deposition, the morphology of the palladium surface and its ability to support SAMs can be controlled. The work will be applied to create a mixed monolayer of metals, which can subsequently be used to create a mixed SAM of a biocomponent and an alkanethiol for biosensing applications.     

Fracture and cavitation in a constrained thin metal layer under a scale effect in layered materials

Dislocation activities are confined within a thin metal layer. Therefore instead of continuum plasticity theory, individual dislocation activities are considered in order to analyse their effects on fracture, especially interface fracture. Three failure modes may occur in the thin ductile layer: interface fracture, metal fracture and metal cavitation. These failure modes are studied and the competition between them is examined. It seems that interface fracture occurs prior to metal fracture provided that the cohesive strengths of the interface and the metal are similar. In general, the fracture toughness of the thin layer will increase with increasing layer thickness. However, at a layer thickness of about 10 mm, the layer is more likely to fail by interface debonding, prior to any failure by ductile cavitation. Finally, using material and geometric parameters, a relation is given which determines the competition between crack fracture and cavity instability.     

Gas-phase structures of neutral silicon clusters

Vibrational spectra of neutral silicon clusters Si(n), in the size range of n = 6-10 and for n = 15, have been measured in the gas phase by two fundamentally different IR spectroscopic methods. Silicon clusters composed of 8, 9, and 15 atoms have been studied by IR multiple photon dissociation spectroscopy of a cluster-xenon complex, while clusters containing 6, 7, 9, and 10 atoms have been studied by a tunable IR-UV two-color ionization scheme. Comparison of both methods is possible for the Si(9) cluster. By using density functional theory, an identification of the experimentally observed neutral cluster structures is possible, and the effect of charge on the structure of neutrals and cations, which have been previously studied via IR multiple photon dissociation, can be investigated. Whereas the structures of small clusters are based on bipyramidal motifs, a trigonal prism as central unit is found in larger clusters. Bond weakening due to the loss of an electron leads to a major structural change between neutral and cationic Si(8).     

Crystalline morphology in polymer blends via competition with spinodal decomposition

Miscible polymer blends containing one crystallizable component and exhibiting liquid-liquid phase separation at elevated temperatures [lower critical solution temperature (LCST) behavior] offer an excellent possibility of controlling morphology and thus mechanical properties. For instance, if a homogeneous mixture of dissimilar polymers is allowed to undergo a rapid temperature jump from below LCST to above LCST, spinodal decomposition takes place and a highly interconnected two-phase morphology with uniform domain size (so-called modulated structure) develops. By quenching the phase-separated system below the glass transition temperature after an appropriate time of phase separation, one is able to fix this characteristic morphology [1]. By quenching the phase-separated blend below the melting point of the crystallizable component to different supercooling depths, it is possible to control the number of nuclei and thus the spherulite's size, creating more or less ordered structures.     

Choosing Strategies to Deal with Artifactual EEG Data in Children with Cognitive Impairment

Rett syndrome is a disease that involves acute cognitive impairment and, consequently, a complex and varied symptomatology. This study evaluates the EEG signals of twenty-nine patients and classify them according to the level of movement artifact. The main goal is to achieve an artifact rejection strategy that performs well in all signals, regardless of the artifact level. Two different methods have been studied: one based on the data distribution and the other based on the energy function, with entropy as its main component. The method based on the data distribution shows poor performance with signals containing high amplitude outliers. On the contrary, the method based on the energy function is more robust to outliers. As it does not depend on the data distribution, it is not affected by artifactual events. A double rejection strategy has been chosen, first on a motion signal (accelerometer or EEG low-pass filtered between 1 and 10 Hz) and then on the EEG signal. The results showed a higher performance when working combining both artifact rejection methods. The energy-based method, to isolate motion artifacts, and the data-distribution-based method, to eliminate the remaining lower amplitude artifacts were used. In conclusion, a new method that proves to be robust for all types of signals is designed.     

Surface activity and fluorite flotation with myristic acid derivatives containing oxygen and sulphur atoms

Surface tension isotherms and fluorite flotation were studied in systems containing myristic acid derivatives in which carbon atoms in the hydrocarbon skeleton were partly replaced by oxygen and/or sulphur atoms. The location of the oxygen and sulphur atoms affects significantly compound hydrophobicity, adsorption at the air/water interface and fluorite flotation. The most effective collectors were the compounds with one oxygen or sulphur atom close to the carboxylic group.     

Diffusive dynamics of water in tert-butyl alcohol/water mixtures

Quasielastic neutron scattering has been used to investigate the dynamical behavior of H(2)O in water/tert-butyl alcohol solutions. The measurements were made at fixed temperature (293 K) as a function of tert-butyl alcohol molar fraction, x, in the range 0-0.042. The data have been compared to those of pure water in the temperature range 269-293 K. The effect of tert-butyl alcohol addition on water dynamics is equivalent to that obtained by lowering the temperature of pure water by an amount proportional to the alcohol concentration. The temperature dependence of the diffusivity parameters in pure water and their concentration dependence in tert-butyl alcohol/water solutions can be rescaled to a common curve attributing to each solution a concentration-dependent "structural temperature" lower than the actual thermodynamic one. These results can be understood in terms of Stillinger's picture of water structuring and of other more recent theoretical pictures that emphasize the influence of the geometrical properties of hydrogen bond networks on water mobility.     

Electrodeless dielectrophoresis: Impact of geometry and material on obstacle polarization

Insulator‐based (electrodeless) dielectrophoresis (iDEP) is a promising particle manipulation technique, based on movement of matter in inhomogeneous fields. The inhomogeneity of the field arises because the excitatory field distorts at obstacles (posts). This effect is caused by accumulation of polarization charges at material interfaces. In this study, we utilize a multipole expansion method to investigate the influence of geometry and material on field distortion of posts with arbitrary cross‐sections in homogeneous electric fields applied perpendicular to the longitudinal axis of the post. The post then develops a multipole parallel or anti parallel to the excitatory field. The multipoles intensity is defined by the post's structure and material properties and directly influences the DEP particle trapping potential. We analyzed posts with circular and rhombus‐shaped cross‐sections with different cross‐sectional width‐to‐height ratios and permittivities for their polarization intensity, multipole position, and their particle trapping behavior. A trade‐off between high maximum field gradient and high coverage range of the gradient is presented, which is determined by the sharpness of the post's edges. We contribute to the overall understanding of the post polarization mechanism and expect that the results presented will help optimizing the structure of microchannels with arrays of posts for electrodeless DEP application.     

(Eco)toxicity of fluoro-organic and cyano-based ionic liquid anions

The (eco)toxicity of the most common ionic liquid anions like [N(CN)(2)](-), [C(CN)(3)](-), [B(CN)(4)](-), [(CF(3)SO(2))(2)N](-), [(C(2)F(5))(3)PF(3)](-) was investigated in test systems of different trophic level. In the same order, and thus with increasing hydrophobicity, a trend of higher toxicity was found. Especially the [(C(2)F(5))(3)PF(3)](-) moiety poses a significant hazard towards aquatic organisms.