scholarly journals CT-guided bone biopsy using electron density maps from dual-energy CT

2021 ◽  
Vol 16 (9) ◽  
pp. 2343-2346
Author(s):  
Shota Yamamoto ◽  
Shunsuke Kamei ◽  
Kosuke Tomita ◽  
Chikara Fujita ◽  
Kazuyuki Endo ◽  
...  
Keyword(s):  
Electron Density ◽  
Bone Biopsy ◽  
Dual Energy ◽  
Dual Energy Ct ◽  
Ct Guided ◽  
Density Maps

A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement

1998 ◽  
Vol 54 (1) ◽  
pp. 81-85 ◽  
Author(s):  
F. M. D. Vellieux
Keyword(s):  
Electron Density ◽  
Initial Density ◽  
Acta Cryst ◽  
Density Maps ◽  
Resolution Electron ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Ornithine Transcarbamoylase ◽  
Electron Density Map ◽  
Pseudo Atom

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

scholarly journals σ2 R , a reciprocal-space measure of the quality of macromolecular electron-density maps

1999 ◽  
Vol 55 (6) ◽  
pp. 1174-1178 ◽  
Author(s):  
Thomas C. Terwilliger
Keyword(s):  
Standard Deviation ◽  
Ab Initio ◽  
Electron Density ◽  
Reciprocal Space ◽  
Rapid Evaluation ◽  
Reliable Measure ◽  
Similar Measure ◽  
Acta Cryst ◽  
Density Maps

It has previously been shown that the presence of distinct regions of solvent and protein in macromolecular crystals leads to a high value of the standard deviation of local r.m.s. electron density and that this can in turn be used as a reliable measure of the quality of macromolecular electron-density maps [Terwilliger & Berendzen (1999a). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a similar measure, \sigma_{R}^{2}, the variance of the local roughness of the electron density, can be calculated in reciprocal space. The formulation is suitable for rapid evaluation of macromolecular crystallographic phases, for phase improvement and for ab initio phasing procedures.

scholarly journals Thermal History of Matrix Forsterite Grains from Murchison Based on High-resolution Tomography

2021 ◽  
Vol 922 (2) ◽  
pp. 256
Author(s):  
Giulia Perotti ◽  
Henning O. Sørensen ◽  
Henning Haack ◽  
Anja C. Andersen ◽  
Dario Ferreira Sanchez ◽  
...  
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Chemical Compositions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Maps ◽  
Thermally Processed ◽  
The Matrix ◽  
History Of ◽  
Chondrule Formation

Abstract Protoplanetary disks are dust- and gas-rich structures surrounding protostars. Depending on the distance from the protostar, this dust is thermally processed to different degrees and accreted to form bodies of varying chemical compositions. The primordial accretion processes occurring in the early protoplanetary disk such as chondrule formation and metal segregation are not well understood. One way to constrain them is to study the morphology and composition of forsteritic grains from the matrix of carbonaceous chondrites. Here, we present high-resolution ptychographic X-ray nanotomography and multimodal chemical microtomography (X-ray diffraction and X-ray fluorescence) to reveal the early history of forsteritic grains extracted from the matrix of the Murchison CM2.5 chondrite. The 3D electron density maps revealed, at unprecedented resolution (64 nm), spherical inclusions containing Fe–Ni, very little silica-rich glass and void caps (i.e., volumes where the electron density is consistent with conditions close to vacuum) trapped in forsterite. The presence of the voids along with the overall composition, petrological textures, and shrinkage calculations is consistent with the grains experiencing one or more heating events with peak temperatures close to the melting point of forsterite (∼2100 K), and subsequently cooled and contracted, in agreement with chondrule-forming conditions.

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