No abstract

Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.

A new method of capacitance measurement for electrical capacitance tomography is presented. A single-shot excitation is used to accelerate measurement. A high-voltage pulse and oversampling of received signal are applied to obtain an acceptable signal-to-noise ratio. The results of measurements of standard capacitors and mutual capacitance of electrodes in 16 electrode tomographic sensors are presented. The elaborated circuit is stray-immune. It can measure capacitance in a range from about 1 fF to 1 pF at one gain setting with good linearity and precision at the rate of 20 000 samples per second.

An electric field solver based on a finite volume method using refined structural mesh is proposed to implement a quadtree structure and estimate the electric flux in the mesh cell. Numerical experiments were carried out using uniform and non-uniform meshes to assess quality of numerical modeling. The proposed method of verification of the quality of numerical calculations based on circular symmetry of the electrical capacitance tomography (ECT) probe allows to assess the effectiveness of mesh refinement and to reduce the number of mesh elements. Experiments showed that even a moderate level of mesh refinement is sufficient to significantly reduce the simulation error that occurs in modeling of cylindrical probes. The reduced number of mesh elements and applied implementation of the quadtree ensures high speed of forward problem calculations.

Electrical capacitance tomography (ECT) is a technique of imaging the distribution of permittivity inside an object under test. Capacitance is measured between the electrodes surrounding the object, and the image is reconstructed from these data by solving the inverse problem. Although both sinusoidal excitation and pulse excitation are used in the sensing circuit, only the AC method is used to measure both components of complex capacitance. In this article, a novel method of complex capacitance measurement using pulse excitation is proposed for ECT. The real and imaginary components are calculated from digital samples of the integrator response. A pulse shape in the front-end circuit was analyzed using the Laplace transform. The numerical simulations of the electric field inside the imaging volume as well as simulations of a pulse excitation in the front-end circuit were performed. The calculation of real and imaginary components using digital samples of the output signal was verified. The permittivity and conductivity images reconstructed for the test object were presented. The method enables imaging of permittivity and conductivity spatial distributions using capacitively coupled electrodes and may be an alternative measurement method for ECT as well as for electrical impedance tomography.