Magnetostructural effects and phase transition in Cr_2O_3 under pressure

We have successfully calculated the electronic and structural properties of chromia (Cr_2O_3) in the Local Spin Density Approximation (LSDA). We predict a transformation from the corundum to the Rh_2O_3(II) structure around 15 GPa in the anti-ferromagnetic (AFM) phase as well as in the paramagnetic (PM) insulating state which occurs above the Neel temperature (T_N). This transition is relevant to interpreting the optical anomalies observed in the absorption spectrum of ruby under pressure. We have modeled the structural properties of the PM state using a Landau-like expansion of the magnetostriction energy. This treatment correctly describes the structural anomalies across T_N in the corundum phase and indicates that the AFM and PM insulating states should have distinct compressive behaviors.Comment: 4 pages, 3 figure

Nanostructured exchange coupled hard / soft composites: from the local magnetization profile to an extended 3D simple model

In nanocomposite magnetic materials the exchange coupling between phases plays a central role in the determination of the extrinsic magnetic properties of the material: coercive field, remanence magnetization. Exchange coupling is therefore of crucial importance in composite systems made of magnetically hard and soft grains or in partially crystallized media including nanosized crystallites in a soft matrix. It has been shown also to be a key point in the control of stratified hard / soft media coercive field in the research for optimized recording media. A signature of the exchange coupling due to the nanostructure is generally obtained on the magnetization curve $M(H)$ with a plateau characteristic of the domain wall compression at the hard/soft interface ending at the depinning of the wall inside the hard phase. This compression / depinning behavior is clearly evidenced through one dimensional description of the interface, which is rigorously possible only in stratified media. Starting from a local description of the hard/soft interface in a model for nanocomposite system we show that one can extend this kind of behavior for system of hard crystallites embedded in a soft matrix.Comment: 18 pages, 8 figures. To be published in the Journal of Magnetism and Magnetic Materials. (To be found at http://www.sciencedirect.com/science/journal/03048853

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Many Eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications, and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5'-complete cDNA sequencing with an integrated data analysis workflow to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first available developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1,300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes

Exchange Field Induced Magnetoresistance in Colossal Magnetoresistance Manganites

The effect of an exchange field on electrical transport in thin films of metallic ferromagnetic manganites has been investigated. The exchange field was induced both by direct exchange coupling in a ferromagnet/antiferromagnet multilayer and by indirect exchange interaction in a ferromagnet/paramagnet superlattice. The electrical resistance of the manganite layers was found to be determined by the absolute value of the vector sum of the effective exchange field and the external magnetic field.Comment: 5 pages, 4 figure

Mass Azithromycin Distribution and Community Microbiome: A Cluster-Randomized Trial.

BackgroundMass distributions of oral azithromycin have long been used to eliminate trachoma, and they are now being proposed to reduce childhood mortality. The observed benefit appears to be augmented with each additional treatment, suggesting a possible community-level effect. Here, we assess whether 2 biannual mass treatments of preschool children affect the community's gut microbiome at 6 months after the last distribution.MethodsIn this cluster-randomized controlled trial, children aged 1-60 months in the Dossa region of Niger were randomized at the village level to receive a single dose of azithromycin or placebo every 6 months. Fecal samples were collected 6 months after the second treatment for metagenomic deep sequencing. The prespecified primary outcome was the Euclidean PERMANOVA of the gut microbiome, or effectively the distance between the genus-level centroid at the community level, with the secondary outcome being the Simpson's α diversity.ResultsIn the azithromycin arm, the gut microbial structures were significantly different than in the placebo arm (Euclidean PERMANOVA, P < .001). Further, the diversity of the gut microbiome in the azithromycin arm was significantly lower than in the placebo arm (inverse Simpson's index, P = .005).ConclusionsTwo mass azithromycin administrations, 6 months apart, in preschool children led to long-term alterations of the gut microbiome structure and community diversity. Here, long-term microbial alterations in the community did not imply disease but were associated with an improvement in childhood mortality.Clinical trials registrationNCT02048007

Exchange coupled perpendicular media

The potential of exchange spring bilayers and graded media is reviewed. An analytical model for the optimization of graded media gives an optimal value of the magnetic polarization of Js = 0.8 T. The optimum design allows for thermally stable grains with grain diameters in the order of 3.3 nm, which supports ultra high density up to 5 to 10 Tbit per inch2. The switching field distribution is significantly reduced in bilayer media and graded media compared to single phase media. For the graded media the switching field distribution is reduced by about a factor of two. For bilayer media the minimum switching field distribution is obtained for soft layer anisotropies about one fifth of the hard layer anisotropy. The influence of precessional switching on the reversal time and the reversal field is investigated in detail for magnetic bilayers. Exchange spring bilayers can be reversed with field pulses of 20 ps.Comment: submitted to JMMM, 'Current Perspectives; Perpendicular recording

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.

The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs. Building on this regulatory map, we explored GWAS signals for 4083 traits, detecting colocalization for 180 disease loci with eQTLs. We show that eQTL analyses taking HLA type haplotypes into account have substantially greater power compared with only using single variants. We examined the association between the 8.1 ancestral haplotype and delayed colonization in Cystic Fibrosis, postulating that downregulation of RNF5 expression is the likely causal mechanism. Our study provides insights into the genetic architecture of the MHC region and pinpoints disease associations that are due to differential expression of HLA genes and non-HLA genes

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure