How to compute Green's Functions for entire Mass Trajectories within Krylov Solvers

The availability of efficient Krylov subspace solvers play a vital role for the solution of a variety of numerical problems in computational science. Here we consider lattice field theory. We present a new general numerical method to compute many Green's functions for complex non-singular matrices within one iteration process. Our procedure applies to matrices of structure $A=D-m$, with $m$ proportional to the unit matrix, and can be integrated within any Krylov subspace solver. We can compute the derivatives $x^{(n)}$ of the solution vector $x$ with respect to the parameter $m$ and construct the Taylor expansion of $x$ around $m$. We demonstrate the advantages of our method using a minimal residual solver. Here the procedure requires $1$ intermediate vector for each Green's function to compute. As real life example, we determine a mass trajectory of the Wilson fermion matrix for lattice QCD. Here we find that we can obtain Green's functions at all masses $\geq m$ at the price of one inversion at mass $m$.Comment: 11 pages, 2 eps-figures, needs epsf.st

A Parallel SSOR Preconditioner for Lattice QCD

A parallelizable SSOR preconditioning scheme for Krylov subspace iterative solvers in lattice QCD applications involving Wilson fermions is presented. In actual Hybrid Monte Carlo and quark propagator calculations it helps to reduce the number of iterations by a factor of 2 compared to conventional odd-even preconditioning. This corresponds to a gain in cpu-time of 30\% - 70\% over odd-even preconditioning.Comment: Talk presented at LATTICE96(algorithms), 3 pages, LaTeX file, 3 epsf-files include

SESAM and TXL Results for Wilson Action--A Status Report

Results from two studies of full QCD with two flavours of dynamical Wilson fermions are presented. At beta=5.6, the region 0.83 > m_pi/m_rho > 0.56 at m_pia > 0.23 L^{-1} is explored. The SESAM collaboration has generated ensembles of about 200 statistically independent configurations on a 16^3 x 32-lattice at three different kappa-values and is entering the final phase of data analysis. The TXL simulation on a 24^3 x 40-lattice at two kappa-values has reached half statistics and data analysis has started recently, hence most results presented here are preliminary. The focus of this report is fourfold: we demonstrate that algorithmic improvements like fast Krylov solvers and parallel preconditioning recently introduced can be put into practise in full QCD simulations, we present encouraging observations as to the critical dynamics of the Hybrid Monte Carlo algorithm in the approach to the chiral limit, we mention signal improvements of noisy estimator techniques for disconnected diagrams to the pi-N sigma term, and we report on SESAM's results for light hadron spectrum, light quark masses, and heavy quarkonia.Comment: 24 pages, tex + postscript figures, to appear in Proceedings of Int. Workshop "Lattice QCD on Parallel Computers", University of Tsukuba, Japa

Critical Dynamics of the Hybrid Monte Carlo Algorithm

We investigate the critical dynamics of the Hybrid Monte Carlo algorithm approaching the chiral limit of standard Wilson fermions. Our observations are based on time series of lengths O(5000) for a variety of observables. The lattice sizes are 16^3 x 32 and 24^3 x 40. We work at beta=5.6, and kappa=0.156, 0.157, 0.1575, 0.158, with 0.83 > m_pi/m_rho > 0.55. We find surprisingly small integrated autocorrelation times for local and extended observables. The dynamical critical exponent $z$ of the exponential autocorrelation time is compatible with 2. We estimate the total computational effort to scale between V^2 and V^2.25 towards the chiral limit.Comment: 3 pages, Latex with espcrc2.sty and postscript figures, Talk given at Lattice 9

GPU-Accelerated Asynchronous Error Correction for Mixed Precision Iterative Refinement

In hardware-aware high performance computing, block-asynchronous iteration and mixed precision iterative refinement are two techniques that may be used to leverage the computing power of SIMD accelerators like GPUs in the iterative solution of linear equation systems. although they use a very different approach for this purpose, they share the basic idea of compensating the convergence properties of an inferior numerical algorithm by a more efficient usage of the provided computing power. In this paper, we analyze the potential of combining both techniques. Therefore, we derive a mixed precision iterative refinement algorithm using a block-asynchronous iteration as an error correction solver, and compare its performance with a pure implementation of a block-asynchronous iteration and an iterative refinement method using double precision for the error correction solver. For matrices from the University of Florida Matrix collection, we report the convergence behaviour and provide the total solver runtime using different GPU architectures

Moments of Nucleon Light Cone Quark Distributions Calculated in Full Lattice QCD

Moments of the quark density, helicity, and transversity distributions are calculated in unquenched lattice QCD. Calculations of proton matrix elements of operators corresponding to these moments through the operator product expansion have been performed on $16^3 \times 32$ lattices for Wilson fermions at $\beta = 5.6$ using configurations from the SESAM collaboration and at $\beta = 5.5$ using configurations from SCRI. One-loop perturbative renormalization corrections are included. At quark masses accessible in present calculations, there is no statistically significant difference between quenched and full QCD results, indicating that the contributions of quark-antiquark excitations from the Dirac Sea are small. Close agreement between calculations with cooled configurations containing essentially only instantons and the full gluon configurations indicates that quark zero modes associated with instantons play a dominant role. Naive linear extrapolation of the full QCD calculation to the physical pion mass yields results inconsistent with experiment. Extrapolation to the chiral limit including the physics of the pion cloud can resolve this discrepancy and the requirements for a definitive chiral extrapolation are described.Comment: 53 Pages Revtex, 26 Figures, 9 Tables. Added additional reference and updated referenced data in Table I

Papillary carcinoma of the thyroid: methylation is not involved in the regulation of MET expression

Hypomethylation has been reported to be responsible for the activation of several oncogenes. The possibility that hypomethylation is involved in the regulation of MET transcription was investigated through the analysis of the methylation status of one CpG island containing 43 CpGs in six cases of papillary carcinoma, in the corresponding normal thyroid tissue, and in two cases of hyperplastic goitre. Evidence of methylation was not found in any of the analysed CpG. © 2004 Cancer Research UK

Influence of extracellular rnas, released by rheumatoid arthritis synovial fibroblasts, on their adhesive and invasive properties

© 2016 by The American Association of Immunologists, Inc.Extracellular RNA (exRNA) has been characterized as a molecular alarm signal upon cellular stress or tissue injury and to exert biological functions as a proinflammatory, prothrombotic, and vessel permeability-regulating factor. In this study, we investigated the contribution of exRNA and its antagonist RNase1 in a chronic inflammatory joint disease, rheumatoid arthritis (RA). Upon immunohistochemical inspection of RA, osteoarthritis (OA), and psoriatic arthritis synovium, exRNA was detectable only in the RA synovial lining layer, whereas extracellular DNAwas detectable in various areas of synovial tissue. In vitro, exRNA (150-5000 nt) was released by RA synovial fibroblasts (RASF) under hypoxic conditions but not under normoxia or TNF-A treatment. RNase activity was increased in synovial fluid from RA and OA patients compared with psoriatic arthritis patients, whereas RNase activity of RASF and OASF cultures was not altered by hypoxia. Reduction of exRNA by RNase1 treatment decreased adhesion of RASF to cartilage, but it had no influence on their cell proliferation or adhesion to endothelial cells. In vivo, treatment with RNase1 reduced RASF invasion into coimplanted cartilage in the SCID mouse model of RA. We also analyzed the expression of neuropilins in synovial tissue and SF, as they may interact with vascular endothelial growth factor signaling and exRNA. The data support the concepts that the exRNA/RNase1 system participates in RA pathophysiology and that RASF are influenced by exRNA in a prodestructive manner. The Journal of Immunology, 2016, 197: 2589-2597

Long-term efficacy, tolerability and overall survival in patients with platinum-sensitive, recurrent high-grade serous ovarian cancer treated with maintenance olaparib capsules following response to chemotherapy

BACKGROUND: In Study 19, maintenance monotherapy with olaparib significantly prolonged progression-free survival vs placebo in patients with platinum-sensitive, recurrent high-grade serous ovarian cancer. METHODS: Study 19 was a randomised, placebo-controlled, Phase II trial enrolling 265 patients who had received at least two platinum-based chemotherapy regimens and were in complete or partial response to their most recent regimen. Patients were randomised to olaparib (capsules; 400 mg bid) or placebo. We present long-term safety and final mature overall survival (OS; 79% maturity) data, from the last data cut-off (9 May 2016). RESULTS: Thirty-two patients (24%) received maintenance olaparib for over 2 years; 15 (11%) did so for over 6 years. No new tolerability signals were identified with long-term treatment and adverse events were generally low grade. The incidence of discontinuations due to adverse events was low (6%). An apparent OS advantage was observed with olaparib vs placebo (hazard ratio 0.73, 95% confidence interval 0.55‒0.95, P = 0.02138) irrespective of BRCA1/2 mutation status, although the predefined threshold for statistical significance was not met. CONCLUSIONS: Study 19 showed a favourable final OS result irrespective of BRCA1/2 mutation status and unprecedented long-term benefit with maintenance olaparib for a subset of platinum-sensitive, recurrent ovarian cancer patients