Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster

textabstractNucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNasesensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/Trich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10?C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequencedependent models

Photonic Crystals: Physics and Practical Modeling

The great interest in photonic crystals and their applications in the past decade requires a thorough training of students and professionals who can practically apply the knowledge of physics of photonic crystals together with skills of independent calculation of basic characteristics of photonic crystals and modelling of various photonic crystal elements for application in all-optical communication systems. This book combines basic backgrounds in fiber and integrated optics with detailed analysis of mathematical models for 1D, 2D and 3D photonic crystals and microstructured fibers, as well as with descriptions of real algorithms and codes for practical realization of the models

Automatic Feature Selection for Stenosis Detection in X-ray Coronary Angiograms

The automatic detection of coronary stenosis is a very important task in computer aided diagnosis systems in the cardiology area. The main contribution of this paper is the identification of a suitable subset of 20 features that allows for the classification of stenosis cases in X-ray coronary images with a high performance overcoming different state-of-the-art classification techniques including deep learning strategies. The automatic feature selection stage was driven by the Univariate Marginal Distribution Algorithm and carried out by statistical comparison between five metaheuristics in order to explore the search space, which is O(249) computational complexity. Moreover, the proposed method is compared with six state-of-the-art classification methods, probing its effectiveness in terms of the Accuracy and Jaccard Index evaluation metrics. All the experiments were performed using two X-ray image databases of coronary angiograms. The first database contains 500 instances and the second one 250 images. In the experimental results, the proposed method achieved an Accuracy rate of 0.89 and 0.88 and Jaccard Index of 0.80 and 0.79, respectively. Finally, the average computational time of the proposed method to classify stenosis cases was ≈0.02 s, which made it highly suitable to be used in clinical practice