RefXAS: an open access database of X-ray absorption spectra.

Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.

Absorption Correction for 3D Elemental Distributions of Dental Composite Materials Using Laboratory Confocal Micro-X-ray Fluorescence Spectroscopy.

Confocal micro-X-ray fluorescence (micro-XRF) spectroscopy facilitates three-dimensional (3D) elemental imaging of heterogeneous samples in the micrometer range. Laboratory setups using X-ray tube excitation render the method accessible for diverse research fields but interpretation of results and quantification remain challenging. The attenuation of X-rays in composites depends on the photon energy as well as on the composition and density of the material. For confocal micro-XRF, attenuation severely impacts elemental distribution information, as the signal from deeper layers is distorted by superficial layers. Absorption correction and quantification of fluorescence measurements in heterogeneous composite samples have so far not been reported. Here, an absorption correction approach for confocal micro-XRF combining density information from microcomputed tomography (micro-CT) data with laboratory X-ray absorption spectroscopy (XAS) and synchrotron transmission measurements is presented. The energy dependency of the probing volume is considered during the correction. The methodology is demonstrated on a model composite sample consisting of a bovine tooth with a clinically used restoration material.

Quantitative Analysis and 2D/3D Elemental Imaging of Cocoa Beans Using X-ray Fluorescence Techniques.

As an important raw material for the confectionery industry, the cocoa bean (Theobroma cacao L.) has to meet certain legal requirements in terms of food safety and maximum contaminant levels in order to enter the cocoa market. Understanding the enrichment and distribution of essential minerals but also toxic metals is of utmost importance for improving the nutritional quality of this economically important raw food material. We present three X-ray fluorescence (XRF) techniques for elemental bio-imaging of intact cocoa beans and one additional XRF technique for quantitative analysis of cocoa pellets. The interrelation of all the methods presented gives a detailed picture of the content and 3D-resolved distribution of elements in complete cocoa beans for the first time.

Scan-Free GEXRF in the Soft X-ray Range for the Investigation of Structured Nanosamples.

Scan-free grazing-emission X-ray fluorescence spectroscopy (GEXRF) is an established technique for the investigation of the elemental depth-profiles of various samples. Recently it has been applied to investigating structured nanosamples in the tender X-ray range. However, lighter elements such as oxygen, nitrogen or carbon cannot be efficiently investigated in this energy range, because of the ineffective excitation. Moreover, common CCD detectors are not able to discriminate between fluorescence lines below 1 keV. Oxygen and nitrogen are important components of insulation and passivation layers, for example, in silicon oxide or silicon nitride. In this work, scan-free GEXRF is applied in proof-of-concept measurements for the investigation of lateral ordered 2D nanostructures in the soft X-ray range. The sample investigated is a Si3N4 lamellar grating, which represents 2D periodic nanostructures as used in the semiconductor industry. The emerging two-dimensional fluorescence patterns are recorded with a CMOS detector. To this end, energy-dispersive spectra are obtained via single-photon event evaluation. In this way, spatial and therefore angular information is obtained, while discrimination between different photon energies is enabled. The results are compared to calculations of the sample model performed by a Maxwell solver based on the finite-elements method. A first measurement is carried out at the UE56-2 PGM-2 beamline at the BESSY II synchrotron radiation facility to demonstrate the feasibility of the method in the soft X-ray range. Furthermore, a laser-produced plasma source (LPP) is utilized to investigate the feasibility of this technique in the laboratory. The results from the BESSY II measurements are in good agreement with the simulations and prove the applicability of scan-free GEXRF in the soft X-ray range for quality control and process engineering of 2D nanostructures. The LPP results illustrate the chances and challenges concerning a transfer of the methodology to the laboratory.

Microfluidic-like fabrication of metal ion-cured bioadhesives by mussels.

To anchor in seashore habitats, mussels fabricate adhesive byssus fibers that are mechanically reinforced by protein-metal coordination mediated by 3,4-dihydroxyphenylalanine (DOPA). The mechanism by which metal ions are integrated during byssus formation remains unknown. In this study, we investigated the byssus formation process in the blue mussel, Mytilus edulis, combining traditional and advanced methods to identify how and when metals are incorporated. Mussels store iron and vanadium ions in intracellular metal storage particles (MSPs) complexed with previously unknown catechol-based biomolecules. During adhesive formation, stockpiled secretory vesicles containing concentrated fluid proteins are mixed with MSPs within a microfluidic-like network of interconnected channels where they coalesce, forming protein-metal bonds within the nascent byssus. These findings advance our understanding of metal use in biological materials with implications for next-generation metallopolymers and adhesives.

Selective mineral transport barriers at Cuscuta-host infection sites.

The uptake of inorganic nutrients by rootless parasitic plants, which depend on host connections for all nutrient supplies, is largely uncharted. Using X-ray fluorescence spectroscopy (XRF), we analyzed the element composition of macro- and micronutrients at infection sites of the parasitic angiosperm Cuscuta reflexa growing on hosts of the genus Pelargonium. Imaging methods combining XRF with 2-D or 3-D (confocal) microscopy show that most of the measured elements are present at similar concentrations in the parasite compared to the host. However, calcium and strontium levels drop pronouncedly at the host/parasite interface, and manganese appears to accumulate in the host tissue surrounding the interface. Chlorine is present in the haustorium at similar levels as in the host tissue but is decreased in the stem of the parasite. Thus, our observations indicate a restricted uptake of calcium, strontium, manganese and chlorine by the parasite. Xylem-mobile dyes, which can probe for xylem connectivity between host and parasite, provided evidence for an interspecies xylem flow, which in theory would be expected to carry all of the elements indiscriminately. We thus conclude that inorganic nutrient uptake by the parasite Cuscuta is regulated by specific selective barriers whose existence has evaded detection until now.