Fast and accurate read mapping with approximate seeds and multiple backtracking

We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2-4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai

The Sequence of the Human Genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective cov- erage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additiona

Temperature dependence of the Kondo resonance and its satellites in CeCu_2Si_2

We present high-resolution photoemission spectroscopy studies on the Kondo resonance of the strongly-correlated Ce system CeCu$_2$Si$_2$. Exploiting the thermal broadening of the Fermi edge we analyze position, spectral weight, and temperature dependence of the low-energy 4f spectral features, whose major weight lies above the Fermi level $E_F$. We also present theoretical predictions based on the single-impurity Anderson model using an extended non-crossing approximation (NCA), including all spin-orbit and crystal field splittings of the 4f states. The excellent agreement between theory and experiment provides strong evidence that the spectral properties of CeCu$_2$Si$_2$ can be described by single-impurity Kondo physics down to $T \approx 5$ K.Comment: 4 pages, 3 figure

Comprehensive investigation of the symmetric space-star configuration in the nucleon-deuteron breakup

We examine a description of available cross section data for symmetric space star (SST) configurations in the neutron-deuteron (nd) and proton-deuteron (pd) breakup reaction using numerically exact solutions of the three-nucleon (3N) Faddeev equation based on two- and three-nucleon (semi)phenomenological and chiral forces. The predicted SST cross sections are very stable with respect to the underlying dynamics for incoming nucleon laboratory energies below $\approx 25$ MeV. We discuss possible origins of the surprising discrepancies between theory and data found in low-energy nd and pd SST breakup measurements.Comment: 30 pages, 12 figure

Systematics of electronic and magnetic properties in the transition metal doped Sb2_2Te3_3 quantum anomalous Hall platform

The quantum anomalous Hall effect (QAHE) has recently been reported to emerge in magnetically-doped topological insulators. Although its general phenomenology is well established, the microscopic origin is far from being properly understood and controlled. Here we report on a detailed and systematic investigation of transition-metal (TM)-doped Sb$_2$Te$_3$. By combining density functional theory (DFT) calculations with complementary experimental techniques, i.e., scanning tunneling microscopy (STM), resonant photoemission (resPES), and x-ray magnetic circular dichroism (XMCD), we provide a complete spectroscopic characterization of both electronic and magnetic properties. Our results reveal that the TM dopants not only affect the magnetic state of the host material, but also significantly alter the electronic structure by generating impurity-derived energy bands. Our findings demonstrate the existence of a delicate interplay between electronic and magnetic properties in TM-doped TIs. In particular, we find that the fate of the topological surface states critically depends on the specific character of the TM impurity: while V- and Fe-doped Sb$_2$Te$_3$ display resonant impurity states in the vicinity of the Dirac point, Cr and Mn impurities leave the energy gap unaffected. The single-ion magnetic anisotropy energy and easy axis, which control the magnetic gap opening and its stability, are also found to be strongly TM impurity-dependent and can vary from in-plane to out-of-plane depending on the impurity and its distance from the surface. Overall, our results provide general guidelines for the realization of a robust QAHE in TM-doped Sb$_2$Te$_3$ in the ferromagnetic state.Comment: 40 pages, 13 figure

Spin-orbit splitting of image states

We quantify the effect of the spin-orbit interaction on the Rydberg-like series of image state electrons at the (111) and (001) surface of Ir, Pt and Au. Using relativistic multiple-scattering methods we find Rashba-like dispersions with Delta E(K)=gamma K with values of gamma for n=1 states in the range 38-88 meV Angstrom. Extending the phase-accumulation model to include spin-orbit scattering we find that the splittings vary like 1/(n+a)^3 where a is the quantum defect and that they are related to the probability of spin-flip scattering at the surface. The splittings should be observable experimentally being larger in magnitude than some exchange-splittings that have been resolved by inverse photoemission, and are comparable to linewidths from inelastic lifetimes.Comment: 10 pages, 4 figure

Towards high-order calculations of three-nucleon scattering in chiral effective field theory

We discuss the current status of chiral effective field theory in the three-nucleon sector and present selected results for nucleon–deuteron scattering observables based on semilocal momentum-space-regularized chiral two-nucleon potentials together with consistently regularized three-nucleon forces up to third chiral order. Using a Bayesian model for estimating truncation errors, the obtained results are found to provide a good description of the experimental data. We confirm our earlier findings that a high-precision description of nucleon–deuteron scattering data below pion production threshold will require the theory to be pushed to fifth chiral order. This conclusion is substantiated by an exploratory study of selected short-range contributions to the three-nucleon force at that order, which, as expected, are found to have significant effects on polarization observables at intermediate and high energies. We also outline the challenges that will need to be addressed in order to push the chiral expansion of three-nucleon scattering observables to higher orders

Twisted exchange interaction between localized spins embedded in a one- or two-dimensional electron gas with Rashba spin-orbit coupling

We study theoretically the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction in one- and two-dimensions in presence of a Rashba spin-orbit (SO) coupling. We show that rotation of the spin of conduction electrons due to SO coupling causes a twisted RKKY interaction between localized spins which consists of three different terms: Heisenberg, Dzyaloshinsky-Moriya, and Ising interactions. We also show that the effective spin Hamiltonian reduces to the usual RKKY interaction Hamiltonian in the twisted spin space where the spin quantization axis of one localized spin is rotated.Comment: 4pages, no figur

Cell specific quantitative iron mapping on brain slices by immuno-µPIXE in healthy elderly and Parkinson’s disease

Iron is essential for neurons and glial cells, playing key roles in neurotransmitter synthesis, energy production and myelination. In contrast, high concentrations of free iron can be detrimental and contribute to neurodegeneration, through promotion of oxidative stress. Particularly in Parkinson's disease (PD) changes in iron concentrations in the substantia nigra (SN) was suggested to play a key role in degeneration of dopaminergic neurons in nigrosome 1. However, the cellular iron pathways and the mechanisms of the pathogenic role of iron in PD are not well understood, mainly due to the lack of quantitative analytical techniques for iron quantification with subcellular resolution. Here, we quantified cellular iron concentrations and subcellular iron distributions in dopaminergic neurons and different types of glial cells in the SN both in brains of PD patients and in non-neurodegenerative control brains (Co). To this end, we combined spatially resolved quantitative element mapping using micro particle induced X-ray emission (mu PIXE) with nickel-enhanced immunocytochemical detection of cell type-specific antigens allowing to allocate element-related signals to specific cell types. Distinct patterns of iron accumulation were observed across different cell populations. In the control (Co) SNc, oligodendroglial and astroglial cells hold the highest cellular iron concentration whereas in PD, the iron concentration was increased in most cell types in the substantia nigra except for astroglial cells and ferritin-positive oligodendroglial cells. While iron levels in astroglial cells remain unchanged, ferritin in oligodendroglial cells seems to be depleted by almost half in PD. The highest cellular iron levels in neurons were located in the cytoplasm, which might increase the source of non-chelated Fe3+, implicating a critical increase in the labile iron pool. Indeed, neuromelanin is characterised by a significantly higher loading of iron including most probable the occupancy of low-affinity iron binding sites. Quantitative trace element analysis is essential to characterise iron in oxidative processes in PD. The quantification of iron provides deeper insights into changes of cellular iron levels in PD and may contribute to the research in iron-chelating disease-modifying drugs

Cell specific quantitative iron mapping on brain slices by immuno-μPIXE in healthy elderly and Parkinson’s disease

Iron is essential for neurons and glial cells, playing key roles in neurotransmitter synthesis, energy production and myelination. In contrast, high concentrations of free iron can be detrimental and contribute to neurodegeneration, through promotion of oxidative stress. Particularly in Parkinson’s disease (PD) changes in iron concentrations in the substantia nigra (SN) was suggested to play a key role in degeneration of dopaminergic neurons in nigrosome 1. However, the cellular iron pathways and the mechanisms of the pathogenic role of iron in PD are not well understood, mainly due to the lack of quantitative analytical techniques for iron quantification with subcellular resolution. Here, we quantified cellular iron concentrations and subcellular iron distribution in dopaminergic neurons and different types of glial cells in the SN both in brains of PD patients and in non-neurodegenerative control brains (Co). To this end, we combined spatially resolved quantitative element mapping using micro particle induced X-ray emission (μPIXE) with nickel-enhanced immunocytochemical detection of cell type-specific antigens allowing to allocate element-related signals to specific cell types. Distinct patterns of iron accumulation were observed across different cell populations. In the control (Co) SNc, oligodendroglial and astroglial cells hold the highest cellular iron concentration whereas in PD, the iron concentration was increased in most cell types in the substantia nigra except for astroglial cells and ferritin-positive oligodendroglial cells. While iron levels in astroglial cells remain unchanged, ferritin in oligodendroglial cells seems to be depleted by almost half in PD. The highest cellular iron levels in neurons were located in the cytoplasm, which might increase the source of non-chelated Fe3+, implicating a critical increase in the labile iron pool. Indeed, neuromelanin is characterised by a significantly higher loading of iron including most probable the occupancy of low-affinity iron binding sites. Quantitative trace element analysis is essential to characterise iron in oxidative processes in PD. The quantification of iron provides deeper insights into changes of cellular iron levels in PD and may contribute to the research in iron-chelating disease-modifying drugs