Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC)-5-mC's oxidation product-in cardiac biology and disease is unknown. Here we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethy...

This paper introduces a novel way of adapting the Hybrid Monte Carlo (HMC) algorithm using parametric bandits with nonlinear features. HMC is a powerful Markov chain Monte Carlo (MCMC) method, but it requires careful tuning of its hyper-parameters. We propose a Bayesian parametric bandit approach to carry out the adaptation of the hyper-parameters while the Markov chain progresses. We also intr...

We investigate numerical integration of ordinary differential equations (ODEs) for Hamiltonian Monte Carlo (HMC). High-quality integration is crucial for designing efficient and effective proposals for HMC. While the standard method is leapfrog (Störmer-Verlet) integration, we propose the use of an exponential integrator, which is robust to stiff ODEs with highly-oscillatory components. This os...

In this paper, we develop the self-learning Monte-Carlo (SLMC) algorithm for non-Abelian gauge theory with dynamical fermions in four dimensions to resolve autocorrelation problem lattice QCD. We perform simulations staggered and plaquette action by both hybrid (HMC) SLMC zero finite temperature examine validity of SLMC. confirm that can reduce time reproduce results from HMC. For runs, reprodu...

Recent data suggest that mast cells (MC) are involved in the regulation of leukocyte accumulation in inflammatory reactions. In this study, expression of leukocyte-chemotactic peptides (chemokines) in purified human lung MC (n = 16) and a human mast cell line, HMC-1, was analyzed. Northern blotting and reverse transcriptase-polymerase chain reaction (RT-PCR) showed baseline expression of monocy...

Lipid abnormalities and dysregulation of the plasminogen activator (PA)/plasmin system may be involved in the development of glomerulosclerosis. We investigated the effects of low-density lipoprotein (LDL) on PA inhibitor-1 (PAI-1), urokinase-type PA (uPA), and tissue-type PA (tPA) in relationship to protein kinase C (PKC) in cultured human mesangial cells (HMC). LDL (200 microg/ml) induced two...

Neutrophil gelatinase-associated lipocalin (NGAL), one of the most promising next-generation biomarkers in clinical nephrology, has received extensive attention. However, the basic role of its receptor (NGALR) remains unclear. Here, we have assessed the expression pattern of NGALR in injured glomeruli and explored the possible mechanism of the NGALR involvement in inflammation in human mesangia...

Nerve growth factor (NGF) can influence mast cell development and function in murine rodents by interacting with its receptors on mast cells. We now report the identification of mRNA transcripts of full-length tyrosine kinase-containing trkA, trkB, and trkC neurotrophin receptor genes in HMC-1 human mast cell leukemia cells. Although HMC-1 cells lacked p75 mRNA, they expressed transcripts for t...