Observation of coherent oxide precipitates in polycrystalline MgB2

Here we describe the results of an atomic resolution study of oxygen incorporation into bulk MgB2. We find that ~20-100 nm sized precipitates are formed by ordered substitution of oxygen atoms onto boron lattice sites, while the basic bulk MgB2 crystal structure and orientation is preserved. The periodicity of the oxygen ordering is dictated by the oxygen concentration in the precipitates and primarily occurs in the (010) plane. The presence of these precipitates correlates well with an improved critical current density and superconducting transition behavior, implying that they act as pinning centers.Comment: Submitted to Applied Physics Letters, 6 pages, 3 figure

Giant two-phonon Raman scattering from nanoscale NbC precipitates in Nb

High purity niobium (Nb), subjected to the processing methods used in the fabrication of superconducting RF cavities, displays micron-sized surface patches containing excess carbon. High-resolution transmission electron microscopy and electron energy-loss spectroscopy measurements are presented which reveal the presence of nanoscale NbC coherent precipitates in such regions. Raman backscatter spectroscopy on similar surface regions exhibit spectra consistent with the literature results on bulk NbC but with significantly enhanced two-phonon scattering. The unprecedented strength and sharpness of the two-phonon signal has prompted a theoretical analysis, using density functional theory (DFT), of phonon modes in NbC for two different interface models of the coherent precipitate. One model leads to overall compressive strain and a comparison to ab-initio calculations of phonon dispersion curves under uniform compression of the NbC shows that the measured two-phonon peaks are linked directly to phonon anomalies arising from strong electron-phonon interaction. Another model of the extended interface between Nb and NbC, studied by DFT, gives insight into the frequency shifts of the acoustic and optical mode density of states measured by first order Raman. The exact origin of the stronger two-phonon response is not known at present but it suggests the possibility of enhanced electron-phonon coupling in transition metal carbides under strain found either in the bulk NbC inclusions or at their interfaces with Nb metal. Preliminary tunneling studies using a point contact method show some energy gaps larger than expected for bulk NbC.Comment: Phys. Rev. B, accepte

Disorder induced collapse of the electron phonon coupling in MgB2_{2} observed by Raman Spectroscopy

The Raman spectrum of the superconductor MgB$_{2}$ has been measured as a function of the Tc of the film. A striking correlation is observed between the $T_{c}$ onset and the frequency of the $E_{2g}$ mode. Analysis of the data with the McMillan formula provides clear experimental evidence for the collapse of the electron phonon coupling at the temperature predicted for the convergence of two superconducting gaps into one observable gap. This gives indirect evidence of the convergence of the two gaps and direct evidence of a transition to an isotropic state at 19 K. The value of the electron phonon coupling constant is found to be 1.22 for films with T$_{c}$ 39K and 0.80 for films with T$_{c}\leq$19K.Comment: 5 pages, 4 figure

Two-bands superconductivity with intra- and interband pairing for synthetic superlattices

We consider a model for superconductivity in a two-band superconductor, having an anisotropic electronic structure made of two partially overlapping bands with a first hole-like and a second electron-like fermi surface. In this pairing scenario, driven by the interplay between interband $V_{i,j}$ and intraband $V_{i,i}$ pairing terms, we have solved the two gap equations at the critical temperature $T = T_c$ and calculate $T_c$ and the chemical potential $\mu$ as a function of the number of carriers $n$ for various values of pairing interactions, $V_{1,1}$, $V_{2,2}$, and $V_{1,2}$. The results show the complexity of the physics of condensates with multiple order parameters with the chemical potential near band edges.Comment: 6 pages, 2 figure

Formation of MgB2 at low temperatures by reaction of Mg with B6Si

Formation of MgB2 by reactions of Mg with B6Si and Mg with B were compared, the former also producing Mg2Si as a major product. Compared to the binary system, the ternary reactions for identical time and temperature were more complete at 750 C and below, as indicated by higher diamagnetic shielding and larger x-ray diffraction peak intensities relative to those of Mg. MgB2 could be produced at temperatures as low as 450 C by the ternary reaction. Analyses by electron microscopy, x-ray diffraction, and of the upper critical field show that Si does not enter the MgB2 phase.Comment: Submitted to Supercond. Sci. Techno

Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses (Rosa hybrida)

<p>Abstract</p> <p>Background</p> <p>Gene expression studies are a prerequisite for understanding the biological function of genes. Because of its high sensitivity and easy use, quantitative PCR (qPCR) has become the gold standard for gene expression quantification. To normalise qPCR measurements between samples, the most prominent technique is the use of stably expressed endogenous control genes, the so called reference genes. However, recent studies show there is no universal reference gene for all biological questions. Roses are important ornamental plants for which there has been no evaluation of useful reference genes for gene expression studies.</p> <p>Results</p> <p>We used three different algorithms (BestKeeper, geNorm and NormFinder) to validate the expression stability of nine candidate reference genes in different rose tissues from three different genotypes of <it>Rosa hybrida </it>and in leaves treated with various stress factors. The candidate genes comprised the classical "housekeeping genes" (<it>Actin, EF-1α, GAPDH</it>, <it>Tubulin </it>and <it>Ubiquitin</it>), and genes showing stable expression in studies in <it>Arabidopsis </it>(<it>PP2A, SAND, TIP </it>and <it>UBC</it>). The programs identified no single gene that showed stable expression under all of the conditions tested, and the individual rankings of the genes differed between the algorithms. Nevertheless the new candidate genes, specifically, <it>PP2A </it>and <it>UBC</it>, were ranked higher as compared to the other traditional reference genes. In general, <it>Tubulin </it>showed the most variable expression and should be avoided as a reference gene.</p> <p>Conclusions</p> <p>Reference genes evaluated as suitable in experiments with <it>Arabidopsis thaliana </it>were stably expressed in roses under various experimental conditions. In most cases, these genes outperformed conventional reference genes, such as <it>EF1-α </it>and <it>Tubulin</it>. We identified <it>PP2A</it>, <it>SAND </it>and <it>UBC </it>as suitable reference genes, which in different combinations may be used for normalisation in expression analyses via qPCR for different rose tissues and stress treatments. However, the vast genetic variation found within the genus <it>Rosa</it>, including differences in ploidy levels, might also influence expression stability of reference genes, so that future research should also consider different genotypes and ploidy levels.</p

Speeding up the Consensus Clustering methodology for microarray data analysis

<p>Abstract</p> <p>Background</p> <p>The inference of the number of clusters in a dataset, a fundamental problem in Statistics, Data Analysis and Classification, is usually addressed via internal validation measures. The stated problem is quite difficult, in particular for microarrays, since the inferred prediction must be sensible enough to capture the inherent biological structure in a dataset, e.g., functionally related genes. Despite the rich literature present in that area, the identification of an internal validation measure that is both fast and precise has proved to be elusive. In order to partially fill this gap, we propose a speed-up of <monospace>Consensus</monospace> (Consensus Clustering), a methodology whose purpose is the provision of a prediction of the number of clusters in a dataset, together with a dissimilarity matrix (the consensus matrix) that can be used by clustering algorithms. As detailed in the remainder of the paper, <monospace>Consensus</monospace> is a natural candidate for a speed-up.</p> <p>Results</p> <p>Since the time-precision performance of <monospace>Consensus</monospace> depends on two parameters, our first task is to show that a simple adjustment of the parameters is not enough to obtain a good precision-time trade-off. Our second task is to provide a fast approximation algorithm for <monospace>Consensus</monospace>. That is, the closely related algorithm <monospace>FC</monospace> (Fast Consensus) that would have the same precision as <monospace>Consensus</monospace> with a substantially better time performance. The performance of <monospace>FC</monospace> has been assessed via extensive experiments on twelve benchmark datasets that summarize key features of microarray applications, such as cancer studies, gene expression with up and down patterns, and a full spectrum of dimensionality up to over a thousand. Based on their outcome, compared with previous benchmarking results available in the literature, <monospace>FC</monospace> turns out to be among the fastest internal validation methods, while retaining the same outstanding precision of <monospace>Consensus</monospace>. Moreover, it also provides a consensus matrix that can be used as a dissimilarity matrix, guaranteeing the same performance as the corresponding matrix produced by <monospace>Consensus</monospace>. We have also experimented with the use of <monospace>Consensus</monospace> and <monospace>FC</monospace> in conjunction with <monospace>NMF</monospace> (Nonnegative Matrix Factorization), in order to identify the correct number of clusters in a dataset. Although <monospace>NMF</monospace> is an increasingly popular technique for biological data mining, our results are somewhat disappointing and complement quite well the state of the art about <monospace>NMF</monospace>, shedding further light on its merits and limitations.</p> <p>Conclusions</p> <p>In summary, <monospace>FC</monospace> with a parameter setting that makes it robust with respect to small and medium-sized datasets, i.e, number of items to cluster in the hundreds and number of conditions up to a thousand, seems to be the internal validation measure of choice. Moreover, the technique we have developed here can be used in other contexts, in particular for the speed-up of stability-based validation measures.</p