Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection)

For use in routine prenatal diagnostics, we developed software and methods for automatic aneuploidy detection based on a commercial multiplex ligation-dependent probe amplification (MLPA) kit. Software and methods ensure a reliable, objective, and fast workflow, and may be applied to other types of MLPA kits. Following CE of MLPA amplification products, the software automatically identified the peak area for each probe, normalized it in relation to the neighboring peak areas of the test sample, computed the ratio relative to a reference created from normal samples, and compensated the ratio for a side effect of the normalization procedure that scaled all chromosomally normal DNA peak areas slightly up or down depending on the kind of aneuploidy present. For the chromosomes 13, 18, 21, X, and Y, probe reliability weighted mean ratio values and corresponding SDs were calculated, and the significance for being outside a reference interval around ratio 1.0 was tested. p < or = 1% suggested aneuploidy and 1 < p < or = 5% suggested potential aneuploidy. Individual peaks, where the normalized area was situated more than 4 SD from the corresponding reference, suggested possible partial deletion or gain. Sample quality was automatically assessed. Control probes were not required. Having used the software and methods for two years, we conclude that a reliable, objective, and fast workflow is obtained.     

Partially reduced graphite oxide as an electrode material for electrochemical double-layer capacitors

Partially reduced graphite oxide was prepared from graphite oxide by using synthetic graphite as precursor. The reduction of graphite oxide with a layer distance of 0.57?nm resulted in a reduction of the layer distance depending on the degree of reduction. Simultaneously the amount of oxygen functionalities in the graphite oxide was reduced, which was corroborated by elemental analysis and EDX. The electrochemical activation of the partially reduced graphite oxide was investigated for tetraethylammonium tetrafluoroborate in acetonitrile and in propylene carbonate. The activation potential depends significantly on the degree of reduction, that is, on the graphene-layer distance and on the solvent used. The activation potential decreased with increasing layer distance for both positive and negative activation. The resulting capacitance after activation was found to be affected by the layer distance, the oxygen functionalities and the used electrolyte. For a layer distance of 0.43?nm and with acetonitrile as the solvent, a differential capacitance of 220?Fg(-1) was achieved for the discharge of the positive electrode near the open-circuit potential and 195?Fg(-1) in a symmetric full-cell assembly.     

A stationary iterative pseudoinverse algorithm

Iterative methods applied to the normal equationsA ^T Ax=A ^T b are sometimes used for solving large sparse linear least squares problems. However, when the matrix is rank-deficient many methods, although convergent, fail to produce the unique solution of minimal Euclidean norm. Examples of such methods are the Jacobi and SOR methods as well as the preconditioned conjugate gradient algorithm. We analyze here an iterative scheme that overcomes this difficulty for the case of stationary iterative methods. The scheme combines two stationary iterative methods. The first method produces any least squares solution whereas the second produces the minimum norm solution to a consistent system. This work was supported by the Swedish Research Council for Engineering Sciences, TFR.     

Magnetic Flux Lines in Complex Geometry Type-II Superconductors Studied by the Time Dependent Ginzburg-Landau Equation

The time-dependent Ginzburg-Landau equation is solved numerically for type-II superconductors of complex geometry using the finite element method. The geometry has a marked influence on the magnetic vortex distribution and the vortex dynamics. We have observed generation of giant vortices at boundary defects, suppressing the superconducting state far into the superconductor.     

Structure-activity relationships for apomorphine congeners. Conformational energies vs. biological activities

Summary A series of apomorphine congeners has been studied with respect to their ability to mimic the structural requirements of the dopamine pharmacophore in the potent and stereoselective dopamine receptor agonist (R)-apomorphine. Conformational energies of the mimicking structures calculated by molecular mechanics (MMP2) correlate well with the observed biological activities.     

Thermolysis reaction of 2-acetyl-1-oxo-five-, six-, and seven-membered ring

The rates of gas-phase thermolysis reactions of 2-acetylcyclopentanone 1,2-acetylcyclohexanone 2, N-acetylcaprolactam 3,2-acetylbutyrolactone 4,2-acetyl-2-methylbutyrolactone 5, and 3-acetyl-2-oxazolidinone 6 have been measured over a temperature range of 50 K. They undergo unimolecular first-order elimination reactions for which log A = 11.7, 11.7, 11.2, 11.4, 11.5, and 11.1 s^?1 and E_a = 193.4, 189.5, 153.2, 201.0, 206.8, and 176.1 kJ mol^?1, respectively. The effect of the ring size together with the effect of a heteroatom in the ring on the rate of thermolysis reactions for compound 1–6 is the subject of this work. © 1995 John Wiley & Sons, Inc.     

Running of neutrino parameters and the Higgs self-coupling in a six-dimensional UED model

We investigate a six-dimensional universal extra-dimensional model in the extension of an effective neutrino mass operator. We derive the β  -functions and renormalization group equations for the Yukawa couplings, the Higgs self-coupling, and the effective neutrino mass operator in this model. Especially, we focus on the renormalization group running of physical parameters such as the Higgs self-coupling and the leptonic mixing angles. The recent measurements of the Higgs boson mass by the ATLAS and CMS Collaborations at the LHC as well as the current three-flavor global fits of neutrino oscillation data have been taken into account. We set a bound on the six-dimensional model, using the vacuum stability criterion, that allows five Kaluza–Klein modes only, which leads to a strong limit on the cutoff scale. Furthermore, we find that the leptonic mixing angle _θ12${\theta }_{12}$ shows the most sizeable running, and that the running of the angles _θ13${\theta }_{13}$ and _θ23${\theta }_{23}$ are negligible. Finally, it turns out that the findings in this six-dimensional model are comparable with what is achieved in the corresponding five-dimensional model, but the cutoff scale is significantly smaller, which means that it could be detectable in a closer future.