leeHom: adaptor trimming and merging for Illumina sequencing reads

The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate identification of the adaptor sequence and accurate reconstruction of the original sequence most likely to have given rise to the observed read(s). We introduce an algorithm that removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and is freely available from: https://bioinf.eva.mpg.de/leehom

Matching NLLA+NNLO for event shape distributions

We study the matching of the next-to-leading logarithmic approximation (NLLA) onto the fixed next-to-next-to-leading order (NNLO) calculation for event shape distributions in electron-positron annihilation. The resulting theoretical predictions combine all precision QCD knowledge on the distributions, and are theoretically reliable over an extended kinematical range. Compared to previously available matched NLLA+NLO and fixed order NNLO results, we observe that the effects of the combined NLLA+NNLO are small in the three-jet region, relevant for precision physics.Comment: 14 pages, 18 figures; typos corrected, published versio

Separation of lymphocytes by electrophoresis under terrestrial conditions and at zero gravity, phase 3

Electrophoretic mobilities (EPM) of peripheral lymphocytes were studied from normal subjects, chronic hemodialysis patients and kidney transplant recipients. A technique to separate B lymphocytes and null cells from non-T lymphocyte preparation was developed. The experiments were designed to determine which subpopulation of the non-T lymphocytes is primarily affected and shows a decreased EPM in chronic hemodialysis patients and kidney transplant recipients

freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers

Motivation: The conversion of the raw intensities obtained from next-generation sequencing platforms into nucleotide sequences with well-calibrated quality scores is a critical step in the generation of good sequence data. While recent model-based approaches can yield highly accurate calls, they require a substantial amount of processing time and/or computational resources. We previously introduced Ibis, a fast and accurate basecaller for the Illumina platform. We have continued active development of Ibis to take into account developments in the Illumina technology, as well as to make Ibis fully open source. Results: We introduce here freeIbis, which offers significant improvements in sequence accuracy owing to the use of a novel multiclass support vector machine (SVM) algorithm. Sequence quality scores are now calibrated based on empirically observed scores, thus providing a high correlation to their respective error rates. These improvements result in downstream advantages including improved genotyping accuracy. Availability and implementation: FreeIbis is freely available for use under the GPL (http://bioinf.eva.mpg.de/freeibis/). It requires a Python interpreter and a C++ compiler. Tailored versions of LIBOCAS and LIBLINEAR are distributed along with the package. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Fluctuations of g-factors in metal nanoparticles: Effects of electron-electron interaction and spin-orbit scattering

We investigate the combined effect of spin-orbit scattering and electron-electron interactions on the probability distribution of $g$-factors of metal nanoparticles. Using random matrix theory, we find that even a relatively small interaction strength %(ratio of exchange constant $J$ and mean level %spacing \spacing $\simeq 0.3$) significantly increases $g$-factor fluctuations for not-too-strong spin-orbit scattering (ratio of spin-orbit rate and single-electron level spacing 1/\tau_{\rm so} \spacing \lesssim 1), and leads to the possibility to observe $g$-factors larger than two.Comment: RevTex, 2 figures inserte

QCD studies with e+e−e^+ e^- annihilation data from 130 to 172 GeV

Hadronic events produced at LEP at centre-of-mass energies of 130, 136, 161 and 172 GeV have been studied and compared with QCD predictions. Distributions of event-shape observables, jet rates, momentum spectra and multiplicities are presented and compared to the predictions of several Monte Carlo models and analytic QCD calculations. From a fit of O(alpha_s^2)+NLLA QCD calculations to the differential two-jet rate, alpha_s has been determined at various energies. The mean charged particle multiplicities and the peak positions xi_star in the xi = ln(1/x_p) distribution have also been determined. These results have been compared to lower energy data and to analytic QCD or Monte Carlo predictions for their energy evolution

The photon‐induced reactions of chemisorbed CH₃Br on Pt{111}

The photochemistry of chemisorbed CH3Br on Pt{111} has been investigated using high resolution electron energy loss spectroscopy (HREELS) and thermal desorption. The primary photon‐induced reaction involves the cleavage of the C–Br bond, giving rise to chemisorbed CH3 and Br, both of which can be identified in HREELS. From the angular dependence of the loss peaks, the symmetry of the CH3 surface complex is shown to be C3v. HBr can also be identified in subsequent thermal desorption. Experiments performed directly with HBr on Pt{111} indicate that molecular HBr adsorbs dissociatively on this surface. This result, in combination with observations of the C–H vibrational mode as a function of temperature, shows that the production of HBr arises from a secondary surface reaction between Br and CHx fragments. Based on the wavelength dependence of the fragmentation cross section and the photoemission spectrum of adsorbed CH3Br the primary photon‐induced reaction to a charge transfer excitation is ascribed

Organic modification of layered silicates for use as barrier pigments in coating systems

Functional coatings and the barrier pigments they contain are an indispensable part of corrosion or product protection. The frequently used layered silicates in their pure form often do not achieve a sufficient protection of the components or products. The barrier effect of the silicates can be significantly improved through targeted organic modification. The general use of commercial (unmodified) silicates leads to an improvement in the barrier of about 20 %. In contrast, the use of modified silicates achieves an improvement of up to 80 % [1], due to the extent of the diffusion path [2]. Decisive for the diffusion path and therefore for the subsequent functionality of the barrier is the exfoliation and orientation of the silicates, which depends on the compatibility with the coating system. Due to the large number of coating systems and the associated binder classes, the silicates should be specifically adapted to the respective polymer by being modified with reactive groups, which represents the main focus of this work. As a first polymer system an epoxy matrix was chosen. Thus, commercial silicates were modified by an epoxy-oligomer matrix based on 1,4-butanediol diglycidyl ether. The produced silicates were examined with the aid of scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The expansion of the layers and the attachment of the organic molecules were investigated using X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS)

Cross-game Learning and Cognitive Ability in Auctions

Overbidding in sealed-bid second-price auctions (SPAs) has been shown to be persistent and associated with cognitive ability. We study experimentally to what extent cross-game learning can reduce overbidding in SPAs, taking into account cognitive skills. Employing an order-balanced design, we use first-price auctions (FPAs) to expose participants to an auction format in which losses from high bids are more salient than in SPAs. Experience in FPAs causes substantial cross-game learning for cognitively less able participants but does not affect overbidding for the cognitively more able. Vice versa, experiencing SPAs before bidding in an FPA does not substantially affect bidding behavior by the cognitively less able but, somewhat surprisingly, reduces bid shading by cognitively more able participants, resulting in lower profits in FPAs. Thus, 'cross-game learning' may rather be understood as 'cross-game transfer', as it has the potential to benefit bidders with lower cognitive ability whereas it has little or even adverse effects for higher-ability bidders