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.

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.

The benefits of one-dimensional detectors for high-pressure powder X-ray diffraction

High-pressure powder X-ray diffraction is a fundamental technique for investigating structural responses to externally applied force. Synchrotron sources and two-dimensional detectors are required. In contrast to this conventional setup, high-resolution beamlines equipped with one-dimensional detectors could offer much better resolved peaks but cannot deliver accurate structure factors because they only sample a small portion of the Debye rings, which are usually inhomogeneous and spotty because of the small amount of sample. In this study, a simple method to overcome this problem is presented and successfully applied to solving the structure of an L-serine polymorph from powder data. A comparison of the obtained high-resolution high-pressure data with conventional data shows that this technique, providing up to ten times better angular resolution, can be of advantage for indexing, for lattice parameter refinement, and even for structure refinement and solution in special cases.

Reference values for digital X-ray radiogrammetry parameters in children and adolescents in comparison to estimates in patients with distal radius fractures.

The first objective of this study was to determine normative digital X-ray radiogrammetry (DXR) values, based on original digital images, in a pediatric population (aged 6-18 years). The second aim was to compare these reference data with patients suffering from distal radius fractures, whereas both cohorts originated from the same geographical region and were evaluated using the same technical parameters as well as inclusion and exclusion criteria. DXR-BMD and DXR-MCI of the metacarpal bones II-IV were assessed on standardized digital hand radiographs, without printing or scanning procedures. DXR parameters were estimated separately by gender and among six age groups; values in the fracture group were compared to age- and gender-matched normative data using Student's t tests and Z scores. In the reference cohort (150 boys, 138 girls), gender differences were found in bone mineral density (DXR-BMD), with higher values for girls from 11 to 14 years and for boys from 15 to 18 years (p < 0.05). Girls had higher normative metacarpal index (DXR-MCI) values than boys, with significant differences at 11-14 years (p < 0.05). In the case-control investigation, the fracture group (95 boys, 69 girls) presented lower DXR-BMD at 15-18 years in boys and 13-16 years in girls vs. the reference cohort (p < 0.05); DXR-MCI was lower at 11-18 years in boys and 11-16 years in girls (p < 0.05). Mean Z scores in the fracture group for DXR-BMD were -0.42 (boys) and -0.46 (girls), and for DXR-MCI were -0.51 (boys) and -0.53 (girls). These findings indicate that the fully digital DXR technique can be accurately applied in pediatric populations ≥ 6 years of age. The lower DXR-BMD and DXR-MCI values in the fracture group suggest promising early identification of individuals with increased fracture risk, without the need for additional radiation exposure, enabling the initiation of prevention strategies to possibly reduce the incidence of osteoporosis later in life.

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.

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. ^

X-ray fluorescence (XRF) scannings and grain size analysis at sites in the Gulf of Cádiz

Contourites in the Gulf of Cádiz preserve a unique archive of Mediterranean Outflow Water (MOW) variability over the past 5.3 Ma. In our study we investigate the potential of geochemical data obtained by XRF scanning to decipher bottom current processes and paleoclimatic evolution at two different sites drilled through contourite deposits in the northern Gulf of Cadiz: Site U1387, which is bathed by the upper MOW core, and Site U1389, located more proximal to the Straits of Gibraltar. The lack of major downslope transport at both locations during the Pleistocene makes them ideal locations for the purpose of our study. The results indicate that the Zr/Al ratio, representing the relative enrichment of heavy minerals (zircon) over less dense alumosilicates under strong bottom current flow, is the most useful indicator for a semi-quantitative assessment of current strength. While most elements are biased by current-related processes, the bromine record, representing organic content, preserves the most pristine climate signal rather independent of grain size changes. Hence, Br can be used for chronostratigraphy and site-to-site correlation in addition to stable isotope stratigraphy. Based on these findings we reconstructed MOW variability for Marine Isotope Stages 1-5 using the Zr/Al ratio from Site U1387. The results reveal abrupt, millennial-scale variations of MOW strength during Greenland Stadials (GS) and Interstadials (GI) with strong MOW during GS and glacial Terminations and a complex behavior during Heinrich Stadials. Millennial-scale variability persisting during periods of poorly expressed GS/GI cyclicities implies a strong internal oscillation of the Mediterranean/North Atlantic climate system.

Non-Maxwellian electron distributions in time-dependent simulations of low-Z materials illuminated by a high-intensity X-ray laser

The interaction of high intensity X-ray lasers with matter is modeled. A collisional-radiative timedependent module is implemented to study radiation transport in matter from ultrashort and ultraintense X-ray bursts. Inverse bremsstrahlung absorption by free electrons, electron conduction or hydrodynamic effects are not considered. The collisional-radiative system is coupled with the electron distribution evolution treated with a Fokker-Planck approach with additional inelastic terms. The model includes spontaneous emission, resonant photoabsorption, collisional excitation and de-excitation, radiative recombination, photoionization, collisional ionization, three-body recombination, autoionization and dielectronic capture. It is found that for high densities, but still below solid, collisions play an important role and thermalization times are not short enough to ensure a thermal electron distribution. At these densities Maxwellian and non-Maxwellian electron distribution models yield substantial differences in collisional rates, modifying the atomic population dynamics.

Geometrical characterization of undisturbed soil samples using X-ray computed tomography image analysis. Effect of soil management on soil structure

El estudio de la estructura del suelo es de vital importancia en diferentes campos de la ciencia y la tecnología. La estructura del suelo controla procesos físicos y biológicos importantes en los sistemas suelo-planta-microorganismos. Estos procesos están dominados por la geometría de la estructura del suelo, y una caracterización cuantitativa de la heterogeneidad de la geometría del espacio poroso es beneficiosa para la predicción de propiedades físicas del suelo. La tecnología de la tomografía computerizada de rayos-X (CT) nos permite obtener imágenes digitales tridimensionales del interior de una muestra de suelo, proporcionando información de la geometría de los poros del suelo y permitiendo el estudio de los poros sin destruir las muestras. Las técnicas de la geometría fractal y de la morfología matemática se han propuesto como una poderosa herramienta para analizar y cuantificar características geométricas. Las dimensiones fractales del espacio poroso, de la interfaz poro-sólido y de la distribución de tamaños de poros son indicadores de la complejidad de la estructura del suelo. Los funcionales de Minkowski y las funciones morfológicas proporcionan medios para medir características geométricas fundamentales de los objetos geométricos tridimensionales. Esto es, volumen, superficie, curvatura media de la superficie y conectividad. Las características del suelo como la distribución de tamaños de poros, el volumen del espacio poroso o la superficie poro-solido pueden ser alteradas por diferentes practicas de manejo de suelo. En este trabajo analizamos imágenes tomográficas de muestras de suelo de dos zonas cercanas con practicas de manejo diferentes. Obtenemos un conjunto de medidas geométricas, para evaluar y cuantificar posibles diferencias que el laboreo pueda haber causado en el suelo. ABSTRACT The study of soil structure is of vital importance in different fields of science and technology. Soil structure controls important physical and biological processes in soil-plant-microbial systems. Those processes are dominated by the geometry of soil pore structure, and a quantitative characterization of the spatial heterogeneity of the pore space geometry is beneficial for prediction of soil physical properties. The technology of X-ray computed tomography (CT) allows us to obtain three-dimensional digital images of the inside of a soil sample providing information on soil pore geometry and enabling the study of the pores without disturbing the samples. Fractal geometry and mathematical morphological techniques have been proposed as powerful tools to analyze and quantify geometrical features. Fractal dimensions of pore space, pore-solid interface and pore size distribution are indicators of soil structure complexity. Minkowski functionals and morphological functions provide means to measure fundamental geometrical features of three-dimensional geometrical objects, that is, volume, boundary surface, mean boundary surface curvature, and connectivity. Soil features such as pore-size distribution, pore space volume or pore-solid surface can be altered by different soil management practices. In this work we analyze CT images of soil samples from two nearby areas with contrasting management practices. We performed a set of geometrical measures, some of them from mathematical morphology, to assess and quantify any possible difference that tillage may have caused on the soil.

Structural features of the γ subunit of the Escherichia coli F1 ATPase revealed by a 4.4-Å resolution map obtained by x-ray crystallography

The F1 part of the F1FO ATP synthase from Escherichia coli has been crystallized and its structure determined to 4.4-Å resolution by using molecular replacement based on the structure of the beef-heart mitochondrial enzyme. The bacterial F1 consists of five subunits with stoichiometry α3, β3, γ, δ, and ɛ. δ was removed before crystallization. In agreement with the structure of the beef-heart mitochondrial enzyme, although not that from rat liver, the present study suggests that the α and β subunits are arranged in a hexagonal barrel but depart from exact 3-fold symmetry. In the structures of both beef heart and rat-liver mitochondrial F1, less than half of the structure of the γ subunit was seen because of presumed disorder in the crystals. The present electron-density map includes a number of rod-shaped features which appear to correspond to additional α-helical regions within the γ subunit. These suggest that the γ subunit traverses the full length of the stalk that links the F1 and FO parts and makes significant contacts with the c subunit ring of FO.

Repair of x-ray-induced DNA double-strand breaks in specific Not I restriction fragments in human fibroblasts: joining of correct and incorrect ends.

An assay that allows measurement of absolute induction frequencies for DNA double-strand breaks (dsbs) in defined regions of the genome and that quantitates rejoining of correct DNA ends has been used to study repair of dsbs in normal human fibroblasts after x-irradiation. The approach involves hybridization of single-copy DNA probes to Not I restriction fragments separated according to size by pulsed-field gel electrophoresis. Induction of dsbs is quantitated from the decrease in the intensity of the hybridizing restriction fragment and an accumulation of a smear below the band. Rejoining of dsbs results in reconstitution of the intact restriction fragment only if correct DNA ends are joined. By comparing results from this technique with results from a conventional electrophoresis assay that detects all rejoining events, it is possible to quantitate the misrejoining frequency. Three Not I fragments on the long arm of chromosome 21 were investigated with regard to dsb induction, yielding an identical induction rate of 5.8 X 10(-3) break per megabase pair per Gy. Correct dsb rejoining was measured for two of these Not I fragments after initial doses of 80 and 160 Gy. The misrejoining frequency was about 25% for both fragments and was independent of dose. This result appears to be representative for the whole genome as shown by analysis of the entire Not I fragment distribution. The correct rejoining events primarily occurred within the first 2 h, while the misrejoining kinetics included a much slower component, with about half of the events occurring between 2 and 24 h. These misrejoining kinetics are similar to those previously reported for production of exchange aberrations in interphase chromosomes.

Circumstellar emission in Be/X-ray binaries of the Magellanic Clouds and the Milky Way

Aims. We study the optical and near-infrared colour excesses produced by circumstellar emission in a sample of Be/X-ray binaries. Our main goals are exploring whether previously published relations, valid for isolated Be stars, are applicable to Be/X-ray binaries and computing the distance to these systems after correcting for the effects of the circumstellar contamination. Methods. Simultaneous UBVRI photometry and spectra in the 3500−7000 Å spectral range were obtained for 11 optical counterparts to Be/X-ray binaries in the LMC, 5 in the SMC and 12 in the Milky Way. As a measure of the amount of circumstellar emission we used the Hα equivalent width corrected for photospheric absorption. Results. We find a linear relationship between the strength of the Hα emission line and the component of E(B − V) originating from the circumstellar disk. This relationship is valid for stars with emission lines weaker than EW ≈ −15   Å. Beyond this point, the circumstellar contribution to E(B − V) saturates at a value ≈0.17   mag. A similar relationship is found for the (V − I) near infrared colour excess, albeit with a steeper slope and saturation level. The circumstellar excess in (B − V) is found to be about five times higher for Be/X-ray binaries than for isolated Be stars with the same equivalent width EW(Hα), implying significant differences in the physical properties of their circumstellar envelopes. The distance to Be/X-ray binaries (with non-shell Be star companions) can only be correctly estimated by taking into account the excess emission in the V band produced by free-free and free-bound transitions in the circumstellar envelope. We provide a simple method to determine the distances that includes this effect.