Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40), and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P < 0.0001) and SCAs (P < 0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility

On the net reproduction rate of continuous structured populations with distributed states at birth

We consider a nonlinear structured population model with a distributed recruitment term. The question of the existence of non-trivial steady states can be treated (at least!) in three different ways. One approach is to study spectral properties of a parametrized family of unbounded operators. The alternative approach, on which we focus here, is based on the reformulation of the problem as an integral equation. In this context we introduce a density dependent net reproduction rate and discuss its relationship to a biologically meaningful quantity. Finally, we briefly discuss a third approach, which is based on the finite rank approximation of the recruitment operator.Comment: To appear in Computers and Mathematics with Application

Dust-trapping Rossby vortices in protoplanetary disks

One of the most challenging steps in planet formation theory is the one leading to the formation of planetesimals of kilometre size. A promising scenario involves the existence of vortices able to concentrate a large amount of dust and grains in their centres. Up to now this scenario has been studied mostly in 2D razor thin disks. A 3D study including, simultaneously, the formation and resulting dust concentration of the vortices with vertical settling, was still missing. The Rossby wave instability self-consistently forms 3D vortices, which have the unique quality of presenting a large scale vertical velocity in their centre. Here we aim to study how this newly discovered effect can alter the dynamic evolution of the dust. We perform global 3D simulations of the RWI in a radially and vertically stratified disk using the code MPI-AMRVAC. After the growth phase of the instability, the gas and solid phases are modelled by a bi-fluid approach, where the dust is considered as a fluid without pressure. Both the drag force of the gas on the dust and the back-reaction of the dust on the gas are included. Multiple grain sizes from 1mm to 5cm are used with a constant density distribution. We obtain in a short timescale a high concentration of the largest grains in the vortices. Indeed, in 3 rotations the dust-to-gas density ratio grows from 10^-2 to unity leading to a concentration of mass up to that of Mars in one vortex. The presence of the radial drift is also at the origin of a dust pile-up at the radius of the vortices. Lastly, the vertical velocity of the gas in the vortex causes the sedimentation process to be reversed, the mm size dust is lifted and higher concentrations are obtained in the upper layer than in the mid-plane.Comment: Accepted for publication in Astronomy and Astrophysic

Metal-insulator transition in the two-orbital Hubbard model at fractional band fillings: Self-energy functional approach

We investigate the infinite-dimensional two-orbital Hubbard model at arbitrary band fillings. By means of the self-energy functional approach, we discuss the stability of the metallic state in the systems with same and different bandwidths. It is found that the Mott insulating phases are realized at commensurate band fillings. Furthermore, it is clarified that the orbital selective Mott phase with one orbital localized and the other itinerant is stabilized even at fractional band fillings in the system with different bandwidths.Comment: 7 pages, 10 figure

Ginzburg-Landau Equations for Coexistent States of Superconductivity and Antiferromagnetism in t-J model

Ginzburg-Landau (GL) equations for the coexistent state of superconductivity and antiferromagnetism are derived microscopically from the t-J model with extended transfer integrals. GL equations and the GL free energy, which are obtained based on the slave-boson mean-field approximation, reflect the electronic structure of the microscopic model, especially the evolution of the Fermi surface due to the change of the doping rate. Thus they are suitable for studying the material dependence of the coexistent states in high-$T_C$ cuprate superconductors.Comment: 12 page

Spag16, an Axonemal Central Apparatus Gene, Encodes a Male Germ Cell Nuclear Speckle Protein that Regulates SPAG16 mRNA Expression

Spag16 is the murine orthologue of Chlamydomonas reinhardtii PF20, a protein known to be essential to the structure and function of the “9+2” axoneme. In Chlamydomonas, the PF20 gene encodes a single protein present in the central pair of the axoneme. Loss of PF20 prevents central pair assembly/integrity and results in flagellar paralysis. Here we demonstrate that the murine Spag16 gene encodes two proteins: 71 kDa SPAG16L, which is found in all murine cells with motile cilia or flagella, and 35 kDa SPAG16S, representing the C terminus of SPAG16L, which is expressed only in male germ cells, and is predominantly found in specific regions within the nucleus that also contain SC35, a known marker of nuclear speckles enriched in pre-mRNA splicing factors. SPAG16S expression precedes expression of SPAG16L. Mice homozygous for a knockout of SPAG16L alone are infertile, but show no abnormalities in spermatogenesis. Mice chimeric for a mutation deleting the transcripts for both SPAG16L and SPAG16S have a profound defect in spermatogenesis. We show here that transduction of SPAG16S into cultured dispersed mouse male germ cells and BEAS-2B human bronchial epithelial cells increases SPAG16L expression, but has no effect on the expression of several other axoneme components. We also demonstrate that the Spag16L promoter shows increased activity in the presence of SPAG16S. The distinct nuclear localization of SPAG16S and its ability to modulate Spag16L mRNA expression suggest that SPAG16S plays an important role in the gene expression machinery of male germ cells. This is a unique example of a highly conserved axonemal protein gene that encodes two protein products with different functions

Nonperturbative transverse-momentum-dependent effects in dihadron and direct photon-hadron angular correlations in p+p collisions at s =200 GeV

Dihadron and isolated direct photon-hadron angular correlations are measured in p+p collisions at s=200 GeV. The correlations are sensitive to nonperturbative initial-state and final-state transverse momenta kT and jT in the azimuthal nearly back-to-back region Δφ∼π. To have sensitivity to small transverse momentum scales, nonperturbative momentum widths of pout, the out-of-plane transverse-momentum component perpendicular to the trigger particle, are measured. In this region, the evolution of pout can be studied when several different hard scales are measured. These widths are used to investigate possible effects from transverse-momentum-dependent factorization breaking. When accounting for the longitudinal-momentum fraction of the away-side hadron with respect to the near-side trigger particle, the widths are found to increase with the hard scale; this is qualitatively similar to the observed behavior in Drell-Yan and semi-inclusive deep-inelastic scattering interactions, where factorization is predicted to hold. The momentum widths are also studied as a function of center-of-mass energy by comparing to previous measurements at s=510 GeV. The nonperturbative jet widths also appear to increase with s at a similar xT, which is qualitatively consistent to similar measurements in Drell-Yan interactions. Future detailed global comparisons between measurements of processes where transverse-momentum-dependent factorization is predicted to hold and be broken will provide further insight into the role of color in hadronic interactions

Nonperturbative-transverse-momentum broadening in dihadron angular correlations in sNN =200 GeV proton-nucleus collisions

The PHENIX collaboration has measured high-pT dihadron correlations in p+p, p+Al, and p+Au collisions at sNN=200 GeV. The correlations arise from inter- and intrajet correlations and thus have sensitivity to nonperturbative effects in both the initial and final states. The distributions of pout, the transverse-momentum component of the associated hadron perpendicular to the trigger hadron, are sensitive to initial- and final-state transverse momenta. These distributions are measured multidifferentially as a function of xE, the longitudinal momentum fraction of the associated hadron with respect to the trigger hadron. The near-side pout widths, sensitive to fragmentation transverse momentum, show no significant broadening between p+Au, p+Al, and p+p. The away-side nonperturbative pout widths are found to be broadened in p+Au when compared to p+p; however, there is no significant broadening in p+Al compared to p+p collisions. The data also suggest that the away-side pout broadening is a function of Ncoll, the number of binary nucleon-nucleon collisions, in the interaction. The potential implications of these results with regard to initial- and final-state transverse-momentum broadening and energy loss of partons in a nucleus, among other nuclear effects, are discussed

Measurements of μμ pairs from open heavy flavor and Drell-Yan in p+p collisions at s =200 GeV

PHENIX reports differential cross sections of μμ pairs from semileptonic heavy-flavor decays and the Drell-Yan production mechanism measured in p+p collisions at s=200 GeV at forward and backward rapidity (1.2<|η|<2.2). The μμ pairs from cc, bb, and Drell-Yan are separated using a template fit to unlike- and like-sign muon pair spectra in mass and pT. The azimuthal opening angle correlation between the muons from cc and bb decays and the pair-pT distributions are compared to distributions generated using pythia and powheg models, which both include next-to-leading order processes. The measured distributions for pairs from cc are consistent with pythia calculations. The cc data present narrower azimuthal correlations and softer pT distributions compared to distributions generated from powheg. The bb data are well described by both models. The extrapolated total cross section for bottom production is 3.75±0.24(stat)±0.500.35(syst)±0.45(global) [μb], which is consistent with previous measurements at the Relativistic Heavy Ion Collider in the same system at the same collision energy and is approximately a factor of 2 higher than the central value calculated with theoretical models. The measured Drell-Yan cross section is in good agreement with next-to-leading-order quantum-chromodynamics calculations