Two flavors of dynamical quarks on anisotropic lattices

We report on our study of two-flavor full QCD on anisotropic lattices using $O(a)$-improved Wilson quarks coupled with an RG-improved glue. The bare gauge and quark anisotropies corresponding to the renormalized anisotropy $\xi=a_s/a_t = 2$ are determined as functions of $\beta$ and $\kappa$, which covers the region of spatial lattice spacings $a_s\approx 0.28$--0.16 fm and $m_{PS}/m_V\approx 0.6$--0.9. The calibrations of the bare anisotropies are performed with the Wilson loop and the meson dispersion relation at 4 lattice cutoffs and 5--6 quark masses. Using the calibration results we calculate the meson mass spectrum and the Sommer scale $r_0$. We confirm that the values of $r_0$ calculated for the calibration using pseudo scalar and vector meson energy momentum dispersion relation coincide in the continuum limit within errors. This work serves to lay ground toward studies of heavy quark systems and thermodynamics of QCD including the extraction of the equation of state in the continuum limit using Wilson-type quark actions.Comment: 16 pages, 23 figures, Version accepted for publication in Physical Review

Light hadron spectroscopy in two-flavor QCD with small sea quark masses

We extend the study of the light hadron spectrum and the quark mass in two-flavor QCD to smaller sea quark mass, corresponding to $m_{PS}/m_{V}=0.60$--0.35. Numerical simulations are carried out using the RG-improved gauge action and the meanfield-improved clover quark action at $\beta=1.8$ ($a = 0.2$ fm from $\rho$ meson mass). We observe that the light hadron spectrum for small sea quark mass does not follow the expectation from chiral extrapolations with quadratic functions made from the region of $m_{PS}/m_{V}=0.80$--0.55. Whereas fits with either polynomial or continuum chiral perturbation theory (ChPT) fails, the Wilson ChPT (WChPT) that includes $a^2$ effects associated with explicit chiral symmetry breaking successfully fits the whole data: In particular, WChPT correctly predicts the light quark mass spectrum from simulations for medium heavy quark mass, such as m_{PS}/m_V \simgt 0.5. Reanalyzing the previous data %at $m_{PS}/m_{V}=0.80$--0.55 with the use of WChPT, we find the mean up and down quark mass being smaller than the previous result from quadratic chiral extrapolation by approximately 10%, $m_{ud}^{\bar{\rm MS}}(\mu=2 {GeV}) = 3.11(17)$ [MeV] in the continuum limit.Comment: 33 page

Thermodynamics of SU(3) gauge theory on anisotropic lattices

Finite temperature SU(3) gauge theory is studied on anisotropic lattices using the standard plaquette gauge action. The equation of state is calculated on $16^{3} \times 8$, $20^{3} \times 10$ and $24^{3} \times 12$ lattices with the anisotropy $\xi \equiv a_s / a_t = 2$, where $a_s$ and $a_t$ are the spatial and temporal lattice spacings. Unlike the case of the isotropic lattice on which $N_t=4$ data deviate significantly from the leading scaling behavior, the pressure and energy density on an anisotropic lattice are found to satisfy well the leading $1/N_t^2$ scaling from our coarsest lattice, $N_t/\xi=4$. With three data points at $N_t/\xi=4$, 5 and 6, we perform a well controlled continuum extrapolation of the equation of state. Our results in the continuum limit agree with a previous result from isotropic lattices using the same action, but have smaller and more reliable errors.Comment: RevTeX, 21 pages, 17 PS figures. A quantitative test about the benefit of anisotropic lattices added, minor errors corrected. Final version for PR

Transport Properties of the Quark-Gluon Plasma -- A Lattice QCD Perspective

Transport properties of a thermal medium determine how its conserved charge densities (for instance the electric charge, energy or momentum) evolve as a function of time and eventually relax back to their equilibrium values. Here the transport properties of the quark-gluon plasma are reviewed from a theoretical perspective. The latter play a key role in the description of heavy-ion collisions, and are an important ingredient in constraining particle production processes in the early universe. We place particular emphasis on lattice QCD calculations of conserved current correlators. These Euclidean correlators are related by an integral transform to spectral functions, whose small-frequency form determines the transport properties via Kubo formulae. The universal hydrodynamic predictions for the small-frequency pole structure of spectral functions are summarized. The viability of a quasiparticle description implies the presence of additional characteristic features in the spectral functions. These features are in stark contrast with the functional form that is found in strongly coupled plasmas via the gauge/gravity duality. A central goal is therefore to determine which of these dynamical regimes the quark-gluon plasma is qualitatively closer to as a function of temperature. We review the analysis of lattice correlators in relation to transport properties, and tentatively estimate what computational effort is required to make decisive progress in this field.Comment: 54 pages, 37 figures, review written for EPJA and APPN; one parag. added end of section 3.4, and one at the end of section 3.2.2; some Refs. added, and some other minor change

Adult-onset Alexander disease with typical "tadpole" brainstem atrophy and unusual bilateral basal ganglia involvement: a case report and review of the literature

<p>Abstract</p> <p>Background</p> <p>Alexander disease (ALX) is a rare neurological disorder characterized by white matter degeneration and cytoplasmic inclusions in astrocytes called Rosenthal fibers, labeled by antibodies against glial fibrillary acidic protein (GFAP). Three subtypes are distinguished according to age at onset: infantile (under age 2), juvenile (age 2 to 12) and adult (over age 12). Following the identification of heterozygous mutations in <it>GFAP </it>that cause this disease, cases of adult-onset ALX have been increasingly reported.</p> <p>Case Presentation</p> <p>We present a 60-year-old Japanese man with an unremarkable past and no family history of ALX. After head trauma in a traffic accident at the age of 46, his character changed, and dementia and dysarthria developed, but he remained independent. Spastic paresis and dysphagia were observed at age 57 and 59, respectively, and worsened progressively. Neurological examination at the age of 60 revealed dementia, pseudobulbar palsy, left-side predominant spastic tetraparesis, axial rigidity, bradykinesia and gaze-evoked nystagmus. Brain MRI showed tadpole-like atrophy of the brainstem, caused by marked atrophy of the medulla oblongata, cervical spinal cord and midbrain tegmentum, with an intact pontine base. Analysis of the <it>GFAP </it>gene revealed a heterozygous missense mutation, c.827G>T, p.R276L, which was already shown to be pathogenic in a case of pathologically proven hereditary adult-onset ALX.</p> <p>Conclusion</p> <p>The typical tadpole-like appearance of the brainstem is strongly suggestive of adult-onset ALX, and should lead to a genetic investigation of the <it>GFAP </it>gene. The unusual feature of this patient is the symmetrical involvement of the basal ganglia, which is rarely observed in the adult form of the disease. More patients must be examined to confirm, clinically and neuroradiologically, extrapyramidal involvement of the basal ganglia in adult-onset ALX.</p

Heavy quarkonium: progress, puzzles, and opportunities

A golden age for heavy quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the $B$-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations. The plethora of newly-found quarkonium-like states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c\bar{c}, b\bar{b}, and b\bar{c} bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.Comment: 182 pages, 112 figures. Editors: N. Brambilla, S. Eidelman, B. K. Heltsley, R. Vogt. Section Coordinators: G. T. Bodwin, E. Eichten, A. D. Frawley, A. B. Meyer, R. E. Mitchell, V. Papadimitriou, P. Petreczky, A. A. Petrov, P. Robbe, A. Vair

Genetically enhanced asynapsis of autosomal chromatin promotes transcriptional dysregulation and meiotic failure

During meiosis, pairing of homologous chromosomes and their synapsis are essential prerequisites for normal male gametogenesis. Even limited autosomal asynapsis often leads to spermatogenic impairment, the mechanism of which is not fully understood. The present study was aimed at deliberately increasing the size of partial autosomal asynapsis and analysis of its impact on male meiosis. For this purpose, we studied the effect of t12 haplotype encompassing four inversions on chromosome 17 on mouse autosomal translocation T(16;17)43H (abbreviated T43H). The T43H/T43H homozygotes were fully fertile in both sexes, while +/T43H heterozygous males, but not females, were sterile with meiotic arrest at late pachynema. Inclusion of the t12 haplotype in trans to the T43H translocation resulted in enhanced asynapsis of the translocated autosome, ectopic phosphorylation of histone H2AX, persistence of RAD51 foci, and increased gene silencing around the translocation break. Increase was also on colocalization of unsynapsed chromatin with sex body. Remarkably, we found that transcriptional silencing of the unsynapsed autosomal chromatin precedes silencing of sex chromosomes. Based on the present knowledge, we conclude that interference of meiotic silencing of unsynapsed autosomes with meiotic sex chromosome inactivation is the most likely cause of asynapsis-related male sterility

Error-Prone ZW Pairing and No Evidence for Meiotic Sex Chromosome Inactivation in the Chicken Germ Line

In the male mouse the X and Y chromosomes pair and recombine within the small pseudoautosomal region. Genes located on the unsynapsed segments of the X and Y are transcriptionally silenced at pachytene by Meiotic Sex Chromosome Inactivation (MSCI). The degree to which MSCI is conserved in other vertebrates is currently unclear. In the female chicken the ZW bivalent is thought to undergo a transient phase of full synapsis at pachytene, starting from the homologous ends and spreading through the heterologous regions. It has been proposed that the repair of the ZW DNA double-strand breaks (DSBs) is postponed until diplotene and that the ZW bivalent is subject to MSCI, which is independent of its synaptic status. Here we present a distinct model of meiotic pairing and silencing of the ZW pair during chicken oogenesis. We show that, in most oocytes, DNA DSB foci on the ZW are resolved by the end of pachytene and that the ZW desynapses in broad synchrony with the autosomes. We unexpectedly find that ZW pairing is highly error prone, with many oocytes failing to engage in ZW synapsis and crossover formation. Oocytes with unsynapsed Z and W chromosomes nevertheless progress to the diplotene stage, suggesting that a checkpoint does not operate during pachytene in the chicken germ line. Using a combination of epigenetic profiling and RNA–FISH analysis, we find no evidence for MSCI, associated with neither the asynaptic ZW, as described in mammals, nor the synaptic ZW. The lack of conservation of MSCI in the chicken reopens the debate about the evolution of MSCI and its driving forces