Standardization of Computed Tomography Images by Means of a Material-Selective Beam Hardening Correction

Polychromaticity of the X-rays used in computed tomography (CT) has made it difficult to establish an absolute scale for CT values and has made quantitative comparisons between patients unreliable. The spectral shift of the X-rays depends on the material distribution within the structure measured and is significant if substantial amounts of bone, fat, or injected contrast material are present. A material-selective beam hardening correction procedure has been developed that allows the reconstruction of good approximations of linear attenuation coefficients with respect to a reference energy. With the aid of mathematical simulations and measurements on a physical phantom, the feasibility of the procedure and its insensitivity with regard to energy settings and other machine parameters are documented

Standardization of Computed Tomography Images by Means of a Material-Selective Beam Hardening Correction

Polychromaticity of the X-rays used in computed tomography (CT) has made it difficult to establish an absolute scale for CT values and has made quantitative comparisons between patients unreliable. The spectral shift of the X-rays depends on the material distribution within the structure measured and is significant if substantial amounts of bone, fat, or injected contrast material are present. A material-selective beam hardening correction procedure has been developed that allows the reconstruction of good approximations of linear attenuation coefficients with respect to a reference energy. With the aid of mathematical simulations and measurements on a physical phantom, the feasibility of the procedure and its insensitivity with regard to energy settings and other machine parameters are documented

Position-dependent inhibition of the cleavage step of pre-mRNA 3'-end processing by U1 snRNP.

The 3' ends of most eukaryotic pre-mRNAs are generated by 3' endonucleolytic cleavage and subsequent polyadenylation. 3'-end formation can be influenced positively or negatively by various factors. In particular, U1 snRNP acts as an inhibitor when bound to a 5' splice site located either upstream of the 3'-end formation signals of bovine papilloma virus (BPV) late transcripts or downstream of the 3'-end processing signals in the 5' LTR of the HIV-1 provirus. Previous work showed that in BPV it is not the first step, 3' cleavage, that is affected by U1 snRNP, but rather the second step, polyadenylation, that is inhibited. Since in HIV-1 the biological requirement is to produce transcripts that read through the 5' LTR cleavage site rather than being cleaved there, this mechanism seemed unlikely to apply. The obvious difference between the two examples was the relative orientation of the 3'-end formation signals and the U1 snRNP-binding site. In vitro assays were therefore used to assess the effect of U1 snRNP bound at various locations relative to a cleavage/polyadenylation site on the 3' cleavage reaction. U1 snRNP was found to inhibit cleavage when bound to a 5' splice site downstream of the cleavage/polyadenylation site, as in the HIV-1 LTR. U1 snRNP binding at this location was shown not to affect the recruitment of multiple cleavage/polyadenylation factors to the cleavage substrate, indicating that inhibition is unlikely to be due to steric hindrance. Interactions between U1A, U1 70K, and poly(A) polymerase, which mediate the effect of U1 snRNP on polyadenylation of other pre-mRNAs, were shown not to be required for cleavage inhibition. Therefore, U1 snRNP bound to a 5' splice site can inhibit cleavage and polyadenylation in two mechanistically different ways depending on whether the 5' splice site is located upstream or downstream of the cleavage site

Structural basis of pre-mRNA recognition by the human cleavage factor Im complex

The cleavage factor Im (CF Im), consists of a 25 kDa subunit (CF Im25) and one of three larger subunits (CF Im59, CF Im68, CF Im72), and is an essential protein complex for pre-mRNA 3′-end cleavage and polyadenylation. It recognizes the upstream sequence of the poly(A) site in a sequence-dependent manner. Here we report the crystal structure of human CF Im, comprising CF Im25 and the RNA recognition motif domain of CF Im68 (CF Im68RRM), and the crystal structure of the CF Im-RNA complex. These structures show that two CF Im68RRM molecules bind to the CF Im25 dimer via a novel RRM-protein interaction mode forming a heterotetramer. The RNA-bound structure shows that two UGUAA RNA sequences, with anti-parallel orientation, bind to one CF Im25-CF Im68RRM heterotetramer, providing structural basis for the mechanism by which CF Im binds two UGUAA elements within one molecule of pre-mRNA simultaneously. Point mutation and kinetic analyses demonstrate that CF Im68RRM can bind the immediately flanking upstream region of the UGUAA element, and CF Im68RRM binding significantly increases the RNA-binding affinity of the complex, suggesting that CF Im68 makes an essential contribution to pre-mRNA binding