XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry

XMapTools is a MATLAB©-based graphical user interface program for electron microprobe X-ray image processing, which can be used to estimate the pressure–temperature conditions of crystallization of minerals in metamorphic rocks. This program (available online at http://www.xmaptools.com) provides a method to standardize raw electron microprobe data and includes functions to calculate the oxide weight percent compositions for various minerals. A set of external functions is provided to calculate structural formulae from the standardized analyses as well as to estimate pressure–temperature conditions of crystallization, using empirical and semi-empirical thermobarometers from the literature. Two graphical user interface modules, Chem2D and Triplot3D, are used to plot mineral compositions into binary and ternary diagrams. As an example, the software is used to study a high-pressure Himalayan eclogite sample from the Stak massif in Pakistan. The high-pressure paragenesis consisting of omphacite and garnet has been retrogressed to a symplectitic assemblage of amphibole, plagioclase and clinopyroxene. Mineral compositions corresponding to ~165,000 analyses yield estimates for the eclogitic pressure–temperature retrograde path from 25 kbar to 9 kbar. Corresponding pressure–temperature maps were plotted and used to interpret the link between the equilibrium conditions of crystallization and the symplectitic microstructures. This example illustrates the usefulness of XMapTools for studying variations of the chemical composition of minerals and for retrieving information on metamorphic conditions on a microscale, towards computation of continuous pressure–temperature-and relative time path in zoned metamorphic minerals not affected by post-crystallization diffusion.

Dehydration of the zeolite merlinoite from the Khibiny massif, Russia: an in situ temperature-dependent single-crystal X-ray study

Dehydration behaviour of the zeolite merlinoite, NaK11[Al12Si20O64]·15H2O, from the Khibiny massif (Russia) was studied by means of single-crystal X-ray diffraction conjoined with step-wise heating to 225 C. At room temperature merlinoite has the space group Immm with a = 14.0312(5), b = 14.2675(6), c = 10.0874(4) Å, and V = 2019.40(14) Å3. At 75 °C the merlinoite structure undergoes pronounced dehydration accompanied by a phase transition to a structure that has the space group P42/nmc and remains consistent at elevated temperature. A fully dehydrated phase occurs at 200 °C (at 225 °C: a = 13.341(4), b = 13.341(4), c = 9.707(4) Å, V = 1727.7(12) Å3). Dehydration-induced framework distortion and symmetry were found to be different from those observed for synthetic potassium merlinoite with the K11.5[Al11.5Si20.5O64]·15H2O composition.

Experimental Characterization and Quantification of Cement-Bentonite Interaction using Core Infiltration Techniques Coupled with X-ray Tomography

Deep geological storage of radioactive waste foresees cementitious materials as reinforcement of tunnels and as backfill. Bentonite is proposed to enclose spent fuel canisters and as drift seals. Sand/bentonite (s/b) is foreseen as backfill material of access galleries or as drift seals. The emplacement of cementitious material next to clay material generates an enormous chemical gradient in pore-water composition that drives diffusive solute transport. Laboratory studies and reactive transport modeling predicted significant mineral alteration at and near interfaces, mainly resulting in a decrease of porosity in bentonite. The goal of this thesis was to characterize and quantify the cement/bentonite interactions both spatially and temporally in laboratory experiments. A newly developed mobile X-ray transparent core infiltration device was used to perform X-ray computed tomography (CT) scans without interruption of running experiments. CT scans allowed tracking the evolution of the reaction plume and changes in core volume/diameter/density during the experiments. In total 4 core infiltration experiments were carried out for this study with the compacted and saturated cores consisting of MX-80 bentonite and sand/MX-80 bentonite mixture (s/b; 65/35%). Two different high-pH cementitious pore-fluids were infiltrated: a young (early) ordinary Portland cement pore-fluid (APWOPC; K+–Na+–OH-; pH 13.4; ionic strength 0.28 mol/kg) and a young ‘low-pH’ ESDRED shotcrete pore-fluid (APWESDRED; Ca2+–Na+–K+–formate; pH 11.4; ionic strength 0.11 mol/kg). The experiments lasted between 1 and 2 years. In both bentonite experiments, the hydraulic conductivity was strongly reduced after switching to high-pH fluids, changing eventually from an advective to a diffusion-dominated transport regime. The reduction was mainly induced by mineral precipitation and possibly partly also by high ionic strength pore-fluids. Both bentonite cores showed a volume reduction and a resulting transient flow in which pore-water was squeezed out during high-pH infiltration. The outflow chemistry was characterized by a high ionic strength, while chloride in the initial pore water got replaced as main anionic charge carrier by sulfate, originating from gypsum dissolution. The chemistry of the high-pH fluids got strongly buffered by the bentonite, consuming hydroxide and in case of APWESDRED also formate. Hydroxide got consumed by mineral reactions (saponite and possibly talc and brucite precipitation), while formate being affected by bacterial degradation. Post-mortem analysis showed reaction zones near the inlet of the bentonite core, characterized by calcium and magnesium enrichment, consisting predominately of calcite and saponite, respectively. Silica got enriched in the outflow, indicating dissolution of silicate-minerals, identified as preferentially cristobalite. In s/b, infiltration of APWOPC reduced the hydraulic conductivity strongly, while APWESDRED infiltration had no effect. The reduction was mainly induced by mineral precipitation and probably partly also by high ionic strength pore-fluids. Not clear is why the observed mineral precipitates in the APWESDRED experiment had no effect on the fluid flow. Both s/b cores showed a volume expansion along with decreasing ionic strengths of the outflow, due to mineral reactions or in case of APWESDRED infiltration also mediated by microbiological activity, consuming hydroxide and formate, respectively. The chemistry of the high-pH fluids got strongly buffered by the s/b. In the case of APWESDRED infiltration, formate reached the outflow only for a short time, followed by enrichment in acetate, indicating most likely biological activity. This was in agreement to post-mortem analysis of the core, observing black spots on the inflow surface, while the sample had a rotten-egg smell indicative of some sulfate reduction. Post-mortem analysis showed further in both cores a Ca-enrichment in the first 10 mm of the core due to calcite precipitation. Mg-enrichment was only observed in the APWOPC experiment, originating from newly formed saponite. Silica got enriched in the outflow of both experiments, indicating dissolution of silicate-minerals, identified in the OPC experiment as cristobalite. The experiments attested an effective buffering capacity for bentonite and s/b, a progressing coupled hydraulic-chemical sealing process and also the preservation of the physical integrity of the interface region in this setup with a total pressure boundary condition on the core sample. No complete pore-clogging was observed but the hydraulic conductivity got rather strongly reduced in 3 experiments, explained by clogging of the intergranular porosity (macroporosity). Such a drop in hydraulic conductivity may impact the saturation time of the buffer in a nuclear waste repository, although the processes and geometry will be more complex in repository situation.

Molecular-Based Magnetism in Bimetallic Two-Dimensional Oxalate-Bridged Networks. An X-ray and Neutron Diffraction Study

Bimetallic, oxalate-bridged compounds with bi- and trivalent transition metals comprise a class of layered materials which express a large variety in their molecular-based magnetic behavior. Because of this, the availability of the corresponding single-crystal structural data is essential to the successful interpretation of the experimental magnetic results. We report in this paper the crystal structure and magnetic properties of the ferromagnetic compound {[N(n-C3H7)4][MnIICrIII(C2O4)3]}n (1), the crystal structure of the antiferromagnetic compound {[N(n-C4H9)4][MnIIFeIII(C2O4)3]}n (2), and the results of a neutron diffraction study of a polycrystalline sample of the ferromagnetic compound {[P(C6D5)4][MnIICrIII(C2O4)3]}n (3). Crystal data:  1, rhombohedral, R3c, a = 9.363(3) Å, c = 49.207(27) Å, Z = 6; 2, hexagonal, P63, a = 9.482(2) Å, c = 17.827(8) Å, Z = 2. The structures consist of anionic, two-dimensional, honeycomb networks formed by the oxalate-bridged metal ions, interleaved by the templating cations. Single-crystal field dependent magnetization measurements as well as elastic neutron scattering experiments on the manganese(II)−chromium(III) samples show the existence of long-range ferromagnetic ordering behavior below Tc = 6 K. The magnetic structure corresponds to an alignment of the spins perpendicular to the network layers. In contrast, the manganese(II)−iron(III) compound expresses a two-dimensional antiferromagnetic ordering.

Diagnostic Accuracy of Full-Body Linear X-Ray Scanning in Multiple Trauma Patients in Comparison to Computed Tomography

Purpose: The purpose of this study was to evaluate the diagnostic accuracy of full-body linear X-ray scanning (LS) in multiple trauma patients in comparison to 128-multislice computed tomography (MSCT). Materials and Methods: 106 multiple trauma patients (female: 33; male: 73) were retrospectively included in this study. All patients underwent LS of the whole body, including extremities, and MSCT covering the neck, thorax, abdomen, and pelvis. The diagnostic accuracy of LS for the detection of fractures of the truncal skeleton and pneumothoraces was evaluated in comparison to MSCT by two observers in consensus. Extremity fractures detected by LS were documented. Results: The overall sensitivity of LS was 49.2 %, the specificity was 93.3 %, the positive predictive value was 91 %, and the negative predictive value was 57.5 %. The overall sensitivity for vertebral fractures was 16.7 %, and the specificity was 100 %. The sensitivity was 48.7 % and the specificity 98.2 % for all other fractures. Pneumothoraces were detected in 12 patients by CT, but not by LS. 40 extremity fractures were detected by LS, of which 4 fractures were dislocated, and 2 were fully covered by MSCT. Conclusion: The diagnostic accuracy of LS is limited in the evaluation of acute trauma of the truncal skeleton. LS allows fast whole-body X-ray imaging, and may be valuable for detecting extremity fractures in trauma patients in addition to MSCT. Key Points: • The overall sensitivity of LS for truncal skeleton injuries in multiple-trauma patients was < 50 %.• The diagnostic reference standard MSCT is the preferred and reliable imaging modality.• LS may be valuable for quick detection of extremity fractures. Citation Format: • Jöres APW., Heverhagen JT, Bonél H et al. Diagnostic Accuracy of Full-Body Linear X-Ray Scanning in Multiple Trauma Patients in Comparison to Computed Tomography. Fortschr Röntgenstr 2016; 188: 163 - 171.

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair

DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties. Herein we report the first X-ray structure of a duplex containing a phen-pair in the center of the double helix in a zipper like stacking arrangement.

A LAPLACE TRANSFORM PAIR MODEL TO DETERMINE BREMSSTRAHLUNG SPECTRA FROM ATTENUATION DATA (RADIATION, X-RAY, SPECTRAL MODELING)

Every x-ray attenuation curve inherently contains all the information necessary to extract the complete energy spectrum of a beam. To date, attempts to obtain accurate spectral information from attenuation data have been inadequate.^ This investigation presents a mathematical pair model, grounded in physical reality by the Laplace Transformation, to describe the attenuation of a photon beam and the corresponding bremsstrahlung spectral distribution. In addition the Laplace model has been mathematically extended to include characteristic radiation in a physically meaningful way. A method to determine the fraction of characteristic radiation in any diagnostic x-ray beam was introduced for use with the extended model.^ This work has examined the reconstructive capability of the Laplace pair model for a photon beam range of from 50 kVp to 25 MV, using both theoretical and experimental methods.^ In the diagnostic region, excellent agreement between a wide variety of experimental spectra and those reconstructed with the Laplace model was obtained when the atomic composition of the attenuators was accurately known. The model successfully reproduced a 2 MV spectrum but demonstrated difficulty in accurately reconstructing orthovoltage and 6 MV spectra. The 25 MV spectrum was successfully reconstructed although poor agreement with the spectrum obtained by Levy was found.^ The analysis of errors, performed with diagnostic energy data, demonstrated the relative insensitivity of the model to typical experimental errors and confirmed that the model can be successfully used to theoretically derive accurate spectral information from experimental attenuation data. ^

Electron intensity modulation for mixed-beam radiation therapy with an x-ray multi-leaf collimator

The current standard treatment for head and neck cancer at our institution uses intensity-modulated x-ray therapy (IMRT), which improves target coverage and sparing of critical structures by delivering complex fluence patterns from a variety of beam directions to conform dose distributions to the shape of the target volume. The standard treatment for breast patients is field-in-field forward-planned IMRT, with initial tangential fields and additional reduced-weight tangents with blocking to minimize hot spots. For these treatment sites, the addition of electrons has the potential of improving target coverage and sparing of critical structures due to rapid dose falloff with depth and reduced exit dose. In this work, the use of mixed-beam therapy (MBT), i.e., combined intensity-modulated electron and x-ray beams using the x-ray multi-leaf collimator (MLC), was explored. The hypothesis of this study was that addition of intensity-modulated electron beams to existing clinical IMRT plans would produce MBT plans that were superior to the original IMRT plans for at least 50% of selected head and neck and 50% of breast cases. Dose calculations for electron beams collimated by the MLC were performed with Monte Carlo methods. An automation system was created to facilitate communication between the dose calculation engine and the treatment planning system. Energy and intensity modulation of the electron beams was accomplished by dividing the electron beams into 2x2-cm2 beamlets, which were then beam-weight optimized along with intensity-modulated x-ray beams. Treatment plans were optimized to obtain equivalent target dose coverage, and then compared with the original treatment plans. MBT treatment plans were evaluated by participating physicians with respect to target coverage, normal structure dose, and overall plan quality in comparison with original clinical plans. The physician evaluations did not support the hypothesis for either site, with MBT selected as superior in 1 out of the 15 head and neck cases (p=1) and 6 out of 18 breast cases (p=0.95). While MBT was not shown to be superior to IMRT, reductions were observed in doses to critical structures distal to the target along the electron beam direction and to non-target tissues, at the expense of target coverage and dose homogeneity. ^

Proton therapy versus intensity modulated x-ray therapy in the treatment of prostate cancer: Estimating secondary cancer risks

External beam radiation therapy is used to treat nearly half of the more than 200,000 new cases of prostate cancer diagnosed in the United States each year. During a radiation therapy treatment, healthy tissues in the path of the therapeutic beam are exposed to high doses. In addition, the whole body is exposed to a low-dose bath of unwanted scatter radiation from the pelvis and leakage radiation from the treatment unit. As a result, survivors of radiation therapy for prostate cancer face an elevated risk of developing a radiogenic second cancer. Recently, proton therapy has been shown to reduce the dose delivered by the therapeutic beam to normal tissues during treatment compared to intensity modulated x-ray therapy (IMXT, the current standard of care). However, the magnitude of stray radiation doses from proton therapy, and their impact on this incidence of radiogenic second cancers, was not known. ^ The risk of a radiogenic second cancer following proton therapy for prostate cancer relative to IMXT was determined for 3 patients of large, median, and small anatomical stature. Doses delivered to healthy tissues from the therapeutic beam were obtained from treatment planning system calculations. Stray doses from IMXT were taken from the literature, while stray doses from proton therapy were simulated using a Monte Carlo model of a passive scattering treatment unit and an anthropomorphic phantom. Baseline risk models were taken from the Biological Effects of Ionizing Radiation VII report. A sensitivity analysis was conducted to characterize the uncertainty of risk calculations to uncertainties in the risk model, the relative biological effectiveness (RBE) of neutrons for carcinogenesis, and inter-patient anatomical variations. ^ The risk projections revealed that proton therapy carries a lower risk for radiogenic second cancer incidence following prostate irradiation compared to IMXT. The sensitivity analysis revealed that the results of the risk analysis depended only weakly on uncertainties in the risk model and inter-patient variations. Second cancer risks were sensitive to changes in the RBE of neutrons. However, the findings of the study were qualitatively consistent for all patient sizes and risk models considered, and for all neutron RBE values less than 100. ^