نتایج جستجو برای: hmc
تعداد نتایج: 1106 فیلتر نتایج به سال:
DNA methylation is an important epigenetic modification and is frequently altered in cancer. Convert of 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5 hmC) by ten-eleven translocation (TET) family enzymes plays important biological functions in embryonic stem cells, development, aging and disease. Recent reports showed that level of 5 hmC was altered in various types of cancers. However,...
DNA methylation is an important epigenetic modification as a hallmark in cancer. Conversion of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by ten-eleven translocation (TET) family enzymes plays an important biological role in embryonic stem cells, development, aging and disease. Lymphoid specific helicase (LSH), a chromatin remodeling factor, is regarded as a reader of 5-hmC. Rec...
This paper presents a fully non-Gaussian version of the Hamiltonian Monte Carlo (HMC) sampling filter. The Gaussian prior assumption in the original HMC filter is relaxed. Specifically, a clustering step is introduced after the forecast phase of the filter, and the prior density function is estimated by fitting a Gaussian Mixture Model (GMM) to the prior ensemble. Using the data likelihood func...
Limousin-cross steers (n=135; 258+/-26 kg) were used to compare forage vs grain feeding on carcass composition and palatability attributes of beef when time on feed was controlled. Diets included a 95% alfalfa silage ration (AS) or a 68% high-moisture corn, 25% alfalfa silage ration (HMC). These were incorporated into six treatments to allow comparisons of end points based on similar days on fe...
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...
Prior to 2009, 5-methylcytosine (5-mC) was thought to be the only biologically significant cytosine modification in mammalian DNA. With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), however, intense interest has emerged in determining the biological function of 5-hmC. Here, we review the techniques used to study 5-hmC and evidence th...
Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the...
DNA methylation has been proven to be a critical epigenetic mark important for various cellular processes. Here, we report that redox-active quinones, a ubiquitous class of chemicals found in natural products, cancer therapeutics and environment, stimulate the conversion of 5 mC to 5 hmC in vivo, and increase 5 hmC in 5751 genes in cells. 5 hmC increase is associated with significantly altered ...
5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA modification in mammalian genomes. This protocol is to be a highly efficient and selective chemical approach to label and capture 5-hmC, taking advantage of a bacteriophage enzyme that adds a glucose moiety to 5-hmC specifically, which could in turn be used for high-throughput mapping via next-generation sequencing.
In this thesis we look at the design and development of a Probabilistic Programming Language (PPL) in Julia named Turing and the challenges of implementing the Hamiltonian Monte Carlo (HMC) sampler inside the Turing framework. This dissertation starts with a review of three important fields behind the project, which are Bayesian inference, general inference algorithms and probabilistic programm...
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