Performance of three-photon PET imaging: Monte Carlo simulations

We have recently introduced the idea of making use of three-photon positron annihilations in positron emission tomography. In this paper the basic characteristics of the three-gamma imaging in PET are studied by means of Monte Carlo simulations and analytical computations. Two typical configurations of human and small animal scanners are considered. Three-photon imaging requires high energy resolution detectors. Parameters currently attainable by CdZnTe semiconductor detectors, the technology of choice for the future development of radiation imaging, are assumed. Spatial resolution is calculated as a function of detector energy resolution and size, position in the field of view, scanner size, and the energies of the three gamma annihilation photons. Possible ways to improve the spatial resolution obtained for nominal parameters: 1.5 cm and 3.2 mm FWHM for human and small animal scanners, respectively, are indicated. Counting rates of true and random three-photon events for typical human and small animal scanning configurations are assessed. A simple formula for minimum size of lesions detectable in the three-gamma based images is derived. Depending on the contrast and total number of registered counts, lesions of a few mm size for human and sub mm for small animal scanners can be detected

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments

Investigation of the possibility of improving spatial resolution in SPECT with the combination of LaBr3:Ce-based detector and 3D-OSEM reconstruction algorithms

This study investigates the potential of improving spatial resolution in SPECT imaging using a combination of LaBr(3):Ce detectors and 3D-OSEM image reconstruction algorithms. Potential spatial resolution improvement was assessed intrinsically and extrinsically using GATE Monte Carlo simulation. Significantly improved MTF of LaBr(3):Ce detectors suggests better resolution performance at all spatial frequencies. In comparison to conventional Nal(Tl) scintillators, a combination of the LaBr(3):Ce crystal and 3D-OSEM incorporating resolution recovery could significantly improve the extrinsic spatial resolution of SPECT images. (C) 2010 Elsevier B.V. All rights reserved