Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

General quantum theory of Thomson scattering

It is well known that the interaction of radiation with matter can be described using classical or quantum physics in relation to three systems: incoming radiation, matter, and scattered radiation. Currently, there is no general non-perturbative theory of electromagnetic wave scattering by free electrons, which describes the scattering process using quantum physics. In this paper, such a non-relativistic theory is presented, where statistics and the number of incoming photons is taken into account, and in scattering, statistics with the number of scattered photons is obtained. This theory is completely analytical, considering an arbitrary number of electrons in the system and, in a particular case, goes over into the previously known theory of scattering as the number of incident photons tends to infinity. It is shown that this theory can differ greatly from the previously known theory of Thomson scattering in the non-perturbative case and at relatively small numbers of incident photons. In addition, this theory is applicable to the scattering of ultrashort pulses by free electrons. This theory has good prospects for application in quantum optics, since it fully takes into account the quantum nature of the incident and scattered radiation when interacting with an arbitrary number of free electrons, including in the non-perturbative case

Defects in regular nanosystems and interference spectra at reemission of electromagnetic field attosecond pulses

The effect of defects in nanostructured targets on interference spectra at the reemission of attosecond electromagnetic pulses has been considered. General expressions have been obtained for calculations of spectral distributions for one-, two-, and three-dimensional multiatomic nanosystems consisting of identical complex atoms with defects such as bends, vacancies, and breaks. Changes in interference spectra by a linear chain with several removed atoms (chain with breaks) and by a linear chain with a bend have been calculated as examples allowing a simple analytical representation. Generalization to two- and three-dimensional nanosystems has been developed

Reemission spectra and inelastic processes at interaction of attosecond and shorter duration electromagnetic pulses with atoms

Inelastic processes and the reemission of attosecond and shorter electromagnetic pulses by atoms have been considered within the analytical solution of the Schrödinger equation in the sudden perturbation approximation. A method of calculations with the exact inclusion of spatial inhomogeneity of the field of an ultrashort pulse and the momenta of photons in the reemission processes has been developed. The probabilities of inelastic processes and spectra of reemission of ultrashort electromagnetic pulses by one- and many-electron atoms have been calculated. The results have been presented in the form of analytical formulas

Phosphorus removal from high-phosphorus hot metal in the converter

[No abstract available

Improving the quality of titanium-free corrosion-resistant steel sheet

[No abstract available

Reemission spectra and inelastic processes at interaction of attosecond and shorter duration electromagnetic pulses with atoms

Inelastic processes and the reemission of attosecond and shorter electromagnetic pulses by atoms have been considered within the analytical solution of the Schrödinger equation in the sudden perturbation approximation. A method of calculations with the exact inclusion of spatial inhomogeneity of the field of an ultrashort pulse and the momenta of photons in the reemission processes has been developed. The probabilities of inelastic processes and spectra of reemission of ultrashort electromagnetic pulses by one- and many-electron atoms have been calculated. The results have been presented in the form of analytical formulas