Hamiltonian Monte Carlo (HMC) exploits Hamiltonian dynamics to construct efficient proposals for Markov chain Monte Carlo (MCMC). In this paper, we present a generalization of HMC which exploits non-canonical Hamiltonian dynamics. We refer to this algorithm as magnetic HMC, since in 3 dimensions a subset of the dynamics map onto the mechanics of a charged particle coupled to a magnetic field. W...

5-hydroxymethylcytosine (5-hmC) is an extensively studied DNA epigenetic modification. Here we present a novel tool which combined with next generation sequencing offers new ways of analyzing 5-hmC at the genomic level. We demonstrate that the Thermo ScientificTM EpiJETTM 5-hmC Enrichment Kit is highly specific for different DNA samples containing 5-hmC modifications. Our data shows that this t...

The Jacobi metric introduced in mathematical physics can be used to analyze Hamiltonian Monte Carlo (HMC). In a geometrical setting, each step of HMC corresponds to a geodesic on a Riemannian manifold with a Jacobi metric. Our calculation of the sectional curvature of this HMC manifold allows us to see that it is positive in cases such as sampling from a high dimensional multivariate Gaussian. ...

Received: July 11, 2016 Revised: February 20, 2017 Accepted: March 02, 2017 Abstract: Background: Domestic medical waste from Home Medical Care (HMC) is a concern in Japan. In 2005, the Japanese government provided that HMC waste is collected by municipalities. HMC waste includes infectious or sharps, thus such waste should be collected by doctor or nurse. Nevertheless, no studies have examined...

The Hybrid Monte Carlo (HMC) algorithm[1] is now the standard method to simulate dynamical fermions. However the cost of the algorithm is substantial. It is therefore desirable to improve the efficiency of the HMC algorithm. First, we examine the possibility of changing the step size adaptively[2,3]. Second, we implement the HMC algorithm with approximate Hamiltonians. Lastly, we precondition t...

The aim of our study was to analyze the presence of 5-methyl-cytosine (5-mC) and 5-hydroxymethyl-cytosine (5-hmC) in the genome of crustacean Daphnia pulex. First, the presence of 5-mC and 5-hmC in genomic DNA was demonstrated by using antibodies specific to either 5-mC or 5-hmC. Then, analysis of 5-mC and 5-hmC using pairs of restriction enzymes with different sensitivity to methylation and hy...

Mast cells (MC) are stem cell factor-dependent tissue-based hematopoietic cells with substantial functional heterogeneity. Cord blood-derived human MC (hMC) express functional receptors for IL-5, and IL-5 mediates stem cell factor-dependent comitogenesis of hMC in vitro. Although IL-5 is not required for normal hMC development, we considered that it might prime hMC for their high-affinity Fc re...

The formation of differentiated cell types from pluripotent progenitors involves epigenetic regulation of gene expression. DNA hydroxymethylation results from the enzymatic oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) 5-mC dioxygenase enzymes. Previous work has mapped changes in 5-mC during differentiation of intestinal stem cells...

To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross...

Accumulating evidences suggest that large-scale loss of 5-hydroxymethylcytosine (5-hmC) is an epigenetic hallmark in different cancers. However, the levels of 5-hmC in laryngeal squamous cell carcinoma (LSCC) and its prognostic value in this cancer remain largely unknown. Using dot-blot and quantitative RT-PCR assays, we investigate 5-hmC levels and expression of TET-1, -2 and -3 in LSCCs and e...