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This does not exclude the possibility, that larger structural fragments (such as tetra-mers and pentamers) can also contribute to the low-frequency vibrational spectrum around the boson peak. On the basis of these results, the following model of the glass transition of glycerol can be proposed. At temperatures far above Tg (186 K), the lifetime of the MRO(More)
We have identified a series of 1H-imidazo-[4,5-c]quinolines as selective allosteric enhancers of human A3 adenosine receptors. Several of these compounds potentiated both the potency and maximal efficacy of agonist-induced responses and selectively decreased the dissociation of the agonist N6-(4-amino-3-[125I]iodobenzyl)-5'-N-methylcarboxamidoadenosine from(More)
1. We recently reported that the activation by UDP of rat P2Y6 nucleotide receptors expressed in 1321N1 astrocytoma cells protected them from TNFalpha-induced apoptosis by suppressing activation of caspase 3 and 8. This study aims to characterize the involvement of intracellular signaling pathways, including kinases involved in the antiapoptotic effect of(More)
We propose a catalytic growth mechanism of single-wall carbon nanotubes based on density functional total energy calculations. Our results indicate nanotubes with an " armchair " edge to be energetically favored over " zigzag " nanotubes. We also suggest that highly mobile Ni catalyst atoms adsorb at the growing edge of the nanotube, where they catalyze the(More)
The field of genomics has seen a glorious explosion of high-quality data, with tremendous strides having been made in genomic sequencing instruments and computational genomics applications meant to make sense of the data. A common use case for genomics data is to answer the question if a specific genetic signature is correlated with some disease(More)
We use Monte Carlo simulations to investigate the thermodynamical behavior of aggregates consisting of few superparamagnetic particles in a colloidal suspension. The potential energy surface of this classical two-isomer system with a stable and a metastable ''ring'' and ''chain'' configuration is tunable by an external magnetic field and temperature. We(More)
—Enhancers are short DNA sequences that modulate gene expression patterns. Recent studies have shown that enhancer elements could be enriched for certain histone modification combinatorial codes, leading to interest in developing computational models to predict enhancer locations. Here we present EP-DNN, a protocol for predicting enhancers based on(More)
We use Monte Carlo and quaternion molecular dynamics simulations to study the self-assembly of intriguing structures which form in colloidal suspensions of small magnetite particles. We show that the only stable isomers with few particles, a ring and a chain, can be efficiently interconverted using a magnetizable tip. We propose to use the oscillating(More)
Gene expression is mediated by specialized cis-regulatory modules (CRMs), the most prominent of which are called enhancers. Early experiments indicated that enhancers located far from the gene promoters are often responsible for mediating gene transcription. Knowing their properties, regulatory activity, and genomic targets is crucial to the functional(More)
We present EP-DNN, a protocol for predicting enhancers based on chromatin features, in different cell types. Specifically, we use a deep neural network (DNN)-based architecture to extract enhancer signatures in a representative human embryonic stem cell type (H1) and a differentiated lung cell type (IMR90). We train EP-DNN using p300 binding sites, as(More)