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  • 1
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    Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low‐cost device is presented that functions as a cover for 96‐well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi‐crystal screening campaigns.
    Description: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Keywords: 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 2
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    Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple‐edge anomalous diffraction (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type.
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz‐kesterite structure type in contrast to the literature. image
    Keywords: 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 3
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    The copper(II)‐binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The growth of diffraction‐quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high‐affinity copper(II)‐binding tripeptide GHK was fused to the N‐terminus of a GFP variant and an MBP‐FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square‐pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S‐atom positions could also be located in log‐likelihood‐gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR‐SAD phasing.
    Description: A novel three‐residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described. image
    Keywords: 548 ; phasing ; crystallization ; GHK ; SAD
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  • 4
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    Determining paracrystallinity in mixed‐tacticity polyhydroxybutyrates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Recently, the authors reported on the development of crystallinity in mixed‐tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X‐ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.
    Description: A method to robustly determine paracrystalline contents from Rietveld‐refined powder X‐ray data is presented and discussed for the example of mixed‐tacticity polyhydroxybutyrates. image
    Keywords: 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 5
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    Concepts for nondestructive and depth‐resolved X‐ray residual stress analysis in the near‐surface region of nearly single crystalline materials with mosaic structure (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: Two evaluation concepts for nondestructive depth‐resolved X‐ray residual stress analysis in the near‐surface region of materials with cubic symmetry and nearly single crystalline structure are introduced by simulated examples. Both concepts are based on the same data acquisition strategy, which consists in the determination of lattice‐spacing depth profiles along the ⟨hkl⟩ poles by stepwise sample rotation around the scattering vector. Segmentation of these profiles parallel to the sample surface provides the lattice strain state as a function of depth. The first evaluation concept extends the crystallite group method developed for materials with pronounced crystallographic texture by the feature of depth resolution and can be applied to samples with arbitrary orientation. The second evaluation concept, which adapts the linear regression approach of the sin2ψ method for the case of single crystalline materials, is restricted to samples with (001) orientation. The influence of the strain‐free lattice parameter a0 on residual stress analysis using both evaluation concepts is discussed on the basis of explicitly derived relations.
    Description: Two data evaluation concepts are proposed for nondestructive and depth‐resolved X‐ray residual stress analysis by means of energy‐dispersive diffraction on materials featuring cubic symmetry and a nearly single crystalline structure. image
    Keywords: 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 6
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    X‐ray dichroism in polyimide caused by non‐resonant scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Dichroism is one of the most important optical effects in both the visible and the X‐ray range. Besides absorption, scattering can also contribute to dichroism. This paper demonstrates that, based on the example of polyimide, materials can show tiny dichroism even far from electronic resonances due to scattering. Although the effect is small, it can lead to a measurable polarization change and might have influence on highly sensitive polarimetric experiments.
    Description: Aligned molecules, for example in polyimide foils, lead to small dichroism even far from resonances, which can be revealed by high‐precision X‐ray polarimetry. image
    Keywords: 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 7
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    Elastic stiffness coefficients of thiourea from thermal diffuse scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high‐energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X‐ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high‐energy photons extends the applicability of the TDS‐based approach to organic compounds which would suffer from radiation damage at lower photon energies.
    Description: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Keywords: 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 8
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    Fast fitting of reflectivity data of growing thin films using neural networks (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-03
    Description: X‐ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α‐sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.
    Description: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Keywords: 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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  • 9
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    Numerically stable form factor of any polygon and polyhedron (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small‐angle scattering by nanocrystals.
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities. image
    Keywords: 548 ; form factors ; polyhedra ; Fourier shape transform
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  • 10
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    ROBL‐II at ESRF: a synchrotron toolbox for actinide research (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: ROBL‐II provides four different experimental stations to investigate actinide and other alpha‐ and beta‐emitting radionuclides at the new EBS storage ring of ESRF within an energy range of 3 to 35 keV. The XAFS station consists of a highly automatized, high sample throughput installation in a glovebox, to measure EXAFS and conventional XANES of samples routinely at temperatures down to 10 K, and with a detection limit in the sub‐p.p.m. range. The XES station with its five bent‐crystal analyzer, Johann‐type setup with Rowland circles of 1.0 and 0.5 m radii provides high‐energy resolution fluorescence detection (HERFD) for XANES, XES, and RIXS measurements, covering both actinide L and M edges together with other elements accessible in the 3 to 20 keV energy range. The six‐circle heavy duty goniometer of XRD‐1 is equipped for both high‐resolution powder diffraction as well as surface‐sensitive CTR and RAXR techniques. Single crystal diffraction, powder diffraction with high temporal resolution, as well as X‐ray tomography experiments can be performed at a Pilatus 2M detector stage (XRD‐2). Elaborate radioprotection features enable a safe and easy exchange of samples between the four different stations to allow the combination of several methods for an unprecedented level of information on radioactive samples for both fundamental and applied actinide and environmental research.
    Description: ROBL‐II at ESRF provides four experimental stations to investigate actinides with X‐ray absorption and emission spectroscopy, and with surface, high‐resolution powder, and single‐crystal X‐ray diffractometry.
    Keywords: 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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  • 11
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    ATSAS 3.0: expanded functionality and new tools for small‐angle scattering data analysis (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
    Description: ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems. image
    Keywords: 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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  • 12
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    XGANDALF – extended gradient descent algorithm for lattice finding (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real‐time feedback during serial crystallography experiments. It is implemented in an open‐source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
    Description: A description and evaluation are given of XGANDALF, extended gradient descent algorithm for lattice finding, an algorithm developed for fast and accurate indexing of snapshot diffraction patterns. image
    Keywords: 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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  • 13
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    pinkIndexer – a universal indexer for pink‐beam X‐ray and electron diffraction snapshots (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink‐beam X‐ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit‐cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink‐beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi‐monochromatic X‐rays and with electrons the algorithm indexed more patterns than other programs tested.
    Description: pinkIndexer, an algorithm developed for indexing of snapshot diffraction patterns recorded with pink‐beam X‐rays, monochromatic X‐rays and electrons, is described and its use evaluated. image
    Keywords: 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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  • 14
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    Crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-17
    Description: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal‐binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine‐dependent inhibitor compounds.
    Description: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Keywords: 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 15
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    Staircase array of inclined refractive multi‐lenses for large field of view pixel super‐resolution scanning transmission hard X‐ray microscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: Owing to the development of X‐ray focusing optics during the past decades, synchrotron‐based X‐ray microscopy techniques allow the study of specimens with unprecedented spatial resolution, down to 10 nm, using soft and medium X‐ray photon energies, though at the expense of the field of view (FOV). One of the approaches to increase the FOV to square millimetres is raster‐scanning of the specimen using a single nanoprobe; however, this results in a long data acquisition time. This work employs an array of inclined biconcave parabolic refractive multi‐lenses (RMLs), fabricated by deep X‐ray lithography and electroplating to generate a large number of long X‐ray foci. Since the FOV is limited by the pattern height if a single RML is used by impinging X‐rays parallel to the substrate, many RMLs at regular intervals in the orthogonal direction were fabricated by tilted exposure. By inclining the substrate correspondingly to the tilted exposure, 378000 X‐ray line foci were generated with a length in the centimetre range and constant intervals in the sub‐micrometre range. The capability of this new X‐ray focusing device was first confirmed using ray‐tracing simulations and then using synchrotron radiation at BL20B2 of SPring‐8, Japan. Taking account of the fact that the refractive lens is effective for focusing high‐energy X‐rays, the experiment was performed with 35 keV X‐rays. Next, by scanning a specimen through the line foci, this device was used to perform large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy (PSR‐STHXM) with a 780 ± 40 nm spatial resolution within an FOV of 1.64 cm × 1.64 cm (limited by the detector area) and a total scanning time of 4 min. Biomedical implant abutments fabricated via selective laser melting using Ti–6Al–4V medical alloy were measured by PSR‐STHXM, suggesting its unique potential for studying extended and thick specimens. Although the super‐resolution function was realized in one dimension in this study, it can be expanded to two dimensions by aligning a pair of presented devices orthogonally.
    Description: A new X‐ray focusing device generates hundreds of thousands of line foci, periodically spaced in the sub‐micrometre range, with centimetre length. It enables to achieve large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy. image
    Keywords: 502.82 ; inclined refractive X‐ray multi‐lens array ; pixel super‐resolution ; scanning transmission hard X‐ray microscopy ; deep X‐ray lithography and electroplating
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  • 16
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    A new concept for temporal gating of synchrotron X‐ray pulses (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-02
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented. First experimental tests of the concept yield a diffraction efficiency of 0.18%; however, the calculations indicate a theoretical efficiency and contrast of 〉30% and 10−5, respectively. The full efficiency of the pulse picker has not been reached yet due to a long‐range thermal deformation of the sample after absorption of the excitation laser. This method can be implemented in a broad spectral range (100 eV to 20 keV) and is only minimally invasive to an existing setup.
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Keywords: 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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  • 17
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    The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP at BESSY II (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-06
    Description: The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP for optical pump/X‐ray probe experiments at the electron storage ring BESSY II is dedicated to investigating the structural response of thin film samples and heterostructures after their excitation with ultrashort laser pulses and/or electric field pulses. It enables experiments with access to symmetric and asymmetric Bragg reflections via a four‐circle diffractometer and it is possible to keep the sample in high vacuum and vary the sample temperature between ∼15 K and 350 K. The femtosecond laser system permanently installed at the beamline allows for optical excitation of the sample at 1028 nm. A non‐linear optical setup enables the sample excitation also at 514 nm and 343 nm. A time‐resolution of 17 ps is achieved with the `low‐α' operation mode of the storage ring and an electronic variation of the delay between optical pump and hard X‐ray probe pulse conveniently accesses picosecond to microsecond timescales. Direct time‐resolved detection of the diffracted hard X‐ray synchrotron pulses use a gated area pixel detector or a fast point detector in single photon counting mode. The range of experiments that are reliably conducted at the endstation and that detect structural dynamics of samples excited by laser pulses or electric fields are presented.
    Description: The KMC‐3 XPP endstation of the synchrotron BESSY II is dedicated to time‐resolved studies of structural dynamics of matter upon optical and/or electrical excitation using hard X‐ray diffraction with an accessible time range from 17 ps to several microseconds. image
    Keywords: 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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  • 18
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    Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n‐propoxide (sodium n‐propanolate, NaOnPr), sodium n‐butoxide (sodium n‐butanolate, NaOnBu) and sodium n‐pentoxide (sodium n‐amylate, NaOnAm) were determined from powder X‐ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space‐group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti‐PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n‐propoxide n‐propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert‐amylate tert‐amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2‐methyl‐2‐butyl). Their crystal structures were determined by single‐crystal X‐ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen‐bond networks diverge widely among the solvate structures. The hydrogen‐bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
    Description: The crystal structures of NaOEt, NaOPr, NaOBu and NaOAm (Am = amyl = pentyl) were determined from powder data. These compounds crystallize in an anti‐PbO structure in the space groups P21m and P4/nmm. Additionally, solvates with the composition NaOEt·2EtOH, NaOPr·2PrOH, NaOiPr·5iPrOH and NaOtAm·tAmOH were synthesized, and their structures were determined from single crystals. They form interesting chain structures of different compositions and topologies. image
    Keywords: 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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  • 19
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    Small‐angle X‐ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Small‐angle X‐ray scattering from GaN nanowires grown on Si(111) is measured in the grazing‐incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X‐ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root‐mean‐square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre‐long facet, already gives rise to a strong intensity reduction.
    Description: The intensity of small‐angle X‐ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre‐long side facet notably changes the intensity curves. image
    Keywords: 548 ; nanowires ; Porod's law ; facet truncation rods ; small‐angle X‐ray scattering ; SAXS ; grazing‐incidence small‐angle X‐ray scattering ; GISAXS
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    The accuracy of protein models automatically built into cryo‐EM maps with ARP/wARP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Recent developments in cryogenic electron microscopy (cryo‐EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high‐resolution cryo‐EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo‐EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main‐chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo‐EM maps is comparable to that of X‐ray crystallographic models at similar local cryo‐EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
    Keywords: 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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    Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single‐crystal X‐ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
    Description: A new orthocarbonate, Sr2CO4, was synthesized under extreme pressure and temperature conditions of 92 GPa and 2500 K, respectively. The crystal structure of the compound s fully characterized in situ by synchrotron single‐crystal X‐ray diffraction and DFT calculations were employed to provide insight into its equation of state, Raman and IR spectra, and bonding. image
    Keywords: 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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  • 22
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    Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
    Keywords: 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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  • 23
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-27
    Description: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite‐type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower‐symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non‐existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 24
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    Comparison and evaluation of pair distribution functions, using a similarity measure based on cross‐correlation functions (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-20
    Description: An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross‐correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross‐correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product‐moment correlation coefficient, using polymorph IV of barbituric acid as an example.
    Description: A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross‐correlation functions is introduced and evaluated. image
    Keywords: 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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  • 25
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    Novel experimental setup for megahertz X‐ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser (EuXFEL) (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The high‐precision X‐ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X‐ray Free‐Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump–probe X‐ray diffraction experiments in the DAC are described and their implementation demonstrated during the First User Community Assisted Commissioning experiment. X‐ray heating and diffraction of Bi under pressure, obtained using 20 fs X‐ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in the DAC.
    Description: The high‐precision X‐ray diffraction (XRD) setup for work with diamond anvil cells (DACs) in Interaction Chamber 2 of the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser is described. image
    Keywords: 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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  • 26
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    The anisotropy in the optical constants of quartz crystals for soft X‐rays (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from orientation‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near‐edge regions.
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from polarization‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge. image
    Keywords: 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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  • 27
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    Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-05
    Description: Mixed ionic electronic conducting ceramics Nd6−yWO12−δ (δ is the oxygen deficiency) provide excellent stability in harsh environments containing strongly reactive gases such as CO2, CO, H2, H2O or H2S. Due to this chemical stability, they are promising and cost‐efficient candidate materials for gas separation, catalytic membrane reactors and protonic ceramic fuel cell technologies. As in La6−yWO12−δ, the ionic/electronic transport mechanism in Nd6−yWO12−δ is expected to be largely controlled by the crystal structure, the conclusive determination of which is still lacking. This work presents a crystallographic study of Nd5.8WO12−δ and molybdenum‐substituted Nd5.7W0.75Mo0.25O12−δ prepared by the citrate complexation route. High‐resolution synchrotron and neutron powder diffraction data were used in combined Rietveld refinements to unravel the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ. Both investigated samples crystallize in a defect fluorite crystal structure with space group Fm3m and doubled unit‐cell parameter due to cation ordering. Mo replaces W at both Wyckoff sites 4a and 48h and is evenly distributed, in contrast with La6−yWO12−δ. X‐ray absorption spectroscopy as a function of partial pressure pO2 in the near‐edge regions excludes oxidation state changes of Nd (Nd3+) and W (W6+) in reducing conditions: the enhanced hydrogen permeation, i.e. ambipolar conduction, observed in Mo‐substituted Nd6−yWO12−δ is therefore explained by the higher Mo reducibility and the creation of additional – disordered – oxygen vacancies.
    Description: The crystal structures of non‐substituted and Mo‐substituted neodymium tungstates are described in detail through neutron diffraction and high‐resolution X‐ray diffraction. Combined X‐ray and neutron diffraction refinements and electron probe micro‐analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X‐ray absorption spectroscopy in the near‐edge regions confirmed no changes in the oxidation states of Nd and W.
    Keywords: 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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  • 28
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    High‐temperature treatments of niobium under high vacuum, dilute air‐ and nitrogen‐atmospheres as investigated by in situ X‐ray absorption spectroscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: Niobium metal foils were heat‐treated at 900°C under different conditions and in situ investigated with time‐resolved X‐ray absorption fine‐structure (EXAFS and XANES) measurements. The present study aims to mimic the conditions usually applied for heat treatments of Nb materials used for superconducting radiofrequency cavities, in order to better understand the evolving processes during vacuum annealing as well as for heat treatments in controlled dilute gases. Annealing in vacuum in a commercially available cell showed a substantial amount of oxidation, so that a designated new cell was designed and realized, allowing treatments under clean high‐vacuum conditions as well as under well controllable gas atmospheres. The experiments performed under vacuum demonstrated that the original structure of the Nb foils is preserved, while a detailed evaluation of the X‐ray absorption fine‐structure data acquired during treatments in dilute air atmospheres (10−5 mbar to 10−3 mbar) revealed a linear oxidation with the time of the treatment, and an oxidation rate proportional to the oxygen (air) pressure. The structure of the oxide appears to be very similar to that of polycrystalline NbO. The cell also permits controlled exposures to other reactive gases at elevated temperatures; here the Nb foils were exposed to dilute nitrogen atmospheres after a pre‐conditioning of the studied Nb material for one hour under high‐vacuum conditions, in order to imitate typical conditions used for nitrogen doping of cavity materials. Clear structural changes induced by the N2 exposure were found; however, no evidence for the formation of niobium nitride could be derived from the EXAFS and XANES experiments. The presented results establish the feasibility to study the structural changes of the Nb materials in situ during heat treatments in reactive gases with temporal resolution, which are important to better understand the underlaying mechanisms and the dynamics of phase formation during those heat treatments in more detail.
    Keywords: 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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    Pressure‐induced Pb–Pb bonding and phase transition in Pb2SnO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: High‐pressure single‐crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator‐to‐semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory‐based calculations show that at ambient conditions the channels in the structure host the stereochemically‐active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
    Description: The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT‐based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb2+ ions with increasing pressure. image
    Keywords: 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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  • 30
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    A discussion on `Domain formation and phase transitions in the wurtzite‐based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front‐runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Description: A scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points. image
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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    X‐SPEC: a 70 eV to 15 keV undulator beamline for X‐ray and electron spectroscopies (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: X‐SPEC is a high‐flux spectroscopy beamline at the KIT (Karlsruhe Institute of Technology) Synchrotron for electron and X‐ray spectroscopy featuring a wide photon energy range. The beamline is equipped with a permanent magnet undulator with two magnetic structures of different period lengths, a focusing variable‐line‐space plane‐grating monochromator, a double‐crystal monochromator and three Kirkpatrick–Baez mirror pairs. By selectively moving these elements in or out of the beam, X‐SPEC is capable of covering an energy range from 70 eV up to 15 keV. The flux of the beamline is maximized by optimizing the magnetic design of the undulator, minimizing the number of optical elements and optimizing their parameters. The beam can be focused into two experimental stations while maintaining the same spot position throughout the entire energy range. The first experimental station is optimized for measuring solid samples under ultra‐high‐vacuum conditions, while the second experimental station allows in situ and operando studies under ambient conditions. Measurement techniques include X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS).
    Description: X‐SPEC is a high‐flux undulator beamline for electron and X‐ray spectroscopy with an energy range from 70 eV to 15 keV. It offers X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS) for in vacuo, in situ and operando sample environments. image
    Keywords: 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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    Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF‐Global‐Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross‐correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF‐Global‐Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF‐Global‐Fit is in excellent agreement with the published crystal structure data.
    Keywords: 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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    Structural basis of chitin utilization by a GH20 β‐N‐acetylglucosaminidase from Vibrio campbellii strain ATCC BAA‐1116 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-01
    Description: Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β‐N‐acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA‐1116. Crystal structures of wild‐type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N‐terminal carbohydrate‐binding domain linked to a small α+β domain and a C‐terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
    Description: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Keywords: 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-09-29
    Description: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Description: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Description: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Description: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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    Energy‐dispersive X‐ray stress analysis under geometric constraints: exploiting the material's inherent anisotropy (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-09-12
    Description: Two data evaluation concepts for X‐ray stress analysis based on energy‐dispersive diffraction on polycrystalline materials with cubic crystal structure, almost random crystallographic texture and strong single‐crystal elastic anisotropy are subjected to comparative assessment. The aim is the study of the residual stress state in hard‐to‐reach measurement points, for which the sin2ψ method is not applicable due to beam shadowing at larger sample tilting. This makes the approaches attractive for stress analysis in engineering parts with complex shapes, for example. Both approaches are based on the assumption of a biaxial stress state within the irradiated sample volume. They exploit in different ways the elastic anisotropy of individual crystallites acting at the microscopic scale and the anisotropy imposed on the material by the near‐surface stress state at the macroscopic scale. They therefore complement each other, in terms of both their preconditions and their results. The first approach is based on the evaluation of strain differences, which makes it less sensitive to variations in the strain‐free lattice parameter a0. Since it assumes a homogeneous stress state within the irradiated sample volume, it provides an average value of the in‐plane stresses. The second approach exploits the sensitivity of the lattice strain to changes in a0. Consequently, it assumes a homogeneous chemical composition but provides a stress profile within the information depth. Experimental examples from different fields in materials science, namely shot peening of austenitic steel and in situ stress analysis during welding, are presented to demonstrate the suitability of the proposed methods.
    Description: The single‐crystal elastic anisotropy and the anisotropy of the near‐surface (residual) stress state of polycrystalline materials with random texture are exploited in energy‐dispersive X‐ray stress analysis to study samples under constrained measurement conditions.
    Keywords: ddc:548 ; X‐ray stress analysis ; energy‐dispersive diffraction ; polycrystalline materials ; single‐crystal elastic anisotropy
    Language: English
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    Mapping the 3D position of battery cathode particles in Bragg coherent diffractive imaging (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-14
    Description: In Bragg coherent diffractive imaging, the precise location of the measured crystals in the interior of the sample is usually missing. Obtaining this information would help the study of the spatially dependent behavior of particles in the bulk of inhomogeneous samples, such as extra‐thick battery cathodes. This work presents an approach to determine the 3D position of particles by precisely aligning them at the instrument axis of rotation. In the test experiment reported here, with a 60 µm‐thick LiNi0.5Mn1.5O4 battery cathode, the particles were located with a precision of 20 µm in the out‐of‐plane direction, and the in‐plane coordinates were determined with a precision of 1 µm.
    Description: A method to determine the 3D position of particles in Bragg coherent diffractive imaging experiments is proposed. Test measurements demonstrate depth‐resolution with a precision of 20 µm along the beam. image
    Keywords: ddc:548 ; extra‐thick battery cathodes ; Bragg coherent X‐ray diffractive imaging ; battery cathodes ; Bragg diffraction ; sphere of confusion ; 3D mapping
    Language: English
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  • 39
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    The soft X‐ray and XUV split‐and‐delay unit at beamlines FL23/24 at FLASH2 (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-01-12
    Description: A split‐and‐delay unit for the extreme ultraviolet and soft X‐ray spectral regions has been built which enables time‐resolved experiments at beamlines FL23 and FL24 at the Free‐electron LASer in Hamburg (FLASH). Geometric wavefront splitting at a sharp edge of a beam splitting mirror is applied to split the incoming soft X‐ray pulse into two beams. Ni and Pt coatings at grazing incidence angles have been chosen in order to cover the whole spectral range of FLASH2 and beyond, up to hν = 1800 eV. In the variable beam path with a grazing incidence angle of ϑd = 1.8°, the total transmission (T) ranges are of the order of 0.48 〈 T 〈 0.84 for hν 〈 100 eV and T 〉 0.50 for 100 eV 〈 hν 〈 650 eV with the Ni coating, and T 〉 0.06 for hν 〈 1800 eV for the Pt coating. For a fixed beam path with a grazing incidence angle of ϑf = 1.3°, a transmission of T 〉 0.61 with the Ni coating and T 〉 0.23 with a Pt coating is achieved. Soft X‐ray pump/soft X‐ray probe experiments are possible within a delay range of −5 ps 〈 Δt 〈 +18 ps with a nominal time resolution of tr = 66 as and a measured timing jitter of tj = 121 ± 2 as. First experiments with the split‐and‐delay unit determined the averaged coherence time of FLASH2 to be τc = 1.75 fs at λ = 8 nm, measured at a purposely reduced coherence of the free‐electron laser.
    Description: The properties of the recently installed split‐and‐delay unit at beamlines FL23 and FL24 at FLASH2 are presented. Its operational range, performance parameters and results of a first experiment are described. image
    Keywords: ddc:550.724 ; time‐resolved pump–probe ; XUV ; soft X‐rays ; free‐electron laser
    Language: English
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  • 40
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    XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-01-12
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉XDSGUI〈/italic〉 is a lightweight graphical user interface (GUI) for the 〈italic〉XDS〈/italic〉, 〈italic〉SHELX〈/italic〉 and 〈italic〉ARCIMBOLDO〈/italic〉 program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X‐ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user‐modifiable and user‐extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉A customizable stateless graphical user interface simplifies the processing, analysis and phasing of diffraction data.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2yr5110:jcr2yr5110-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; X‐ray diffraction ; neutron diffraction ; electron diffraction ; data processing ; graphical user interfaces ; phasing ; XDS ; ARCIMBOLDO ; SHELX
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  • 41
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 3. Pseudosymmetry (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-20
    Description: A pseudosymmetric description of the crystal lattice derived from a single wide‐angle Kikuchi pattern can have several causes. The small size (〈15%) of the sector covered by an electron backscatter diffraction pattern, the limited precision of the projection centre position and the Kikuchi band definition are crucial. Inherent pseudosymmetries of the crystal lattice and/or structure also pose a challenge in the analysis of Kikuchi patterns. To eliminate experimental errors as much as possible, simulated Kikuchi patterns of 350 phases have been analysed using the software CALM [Nolze et al. (2021). J. Appl. Cryst.54, 1012–1022] in order to estimate the frequency of and reasons for pseudosymmetric crystal lattice descriptions. Misinterpretations occur in particular when the atomic scattering factors of non‐equivalent positions are too similar and reciprocal‐lattice points are systematically missing. As an example, a pseudosymmetry prediction depending on the elements involved is discussed for binary AB compounds with B1 and B2 structure types. However, since this is impossible for more complicated phases, this approach cannot be directly applied to compounds of arbitrary composition and structure.
    Description: Distinguishing between actual and apparent pseudosymmetry in electron backscatter diffraction patterns is nearly impossible, even for simulated patterns. However, the resulting lattice is always a superlattice as long as the signal is not a superposition of multiple patterns.
    Keywords: ddc:548 ; Bravais lattices ; pseudosymmetry ; lattice point density ; ordered/disordered structures ; lattice distortion ; electron backscatter diffraction ; backscattered Kikuchi diffraction patterns ; lattice parameters ; Funk transform
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  • 42
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    Crystal diffraction prediction and partiality estimation using Gaussian basis functions (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-04
    Description: The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
    Description: Reflection position, size and shape prediction and partiality estimation of crystal diffraction by integrating using a Gaussian basis are described.
    Keywords: ddc:548 ; partiality estimation ; diffraction prediction ; merging ; serial snapshot crystallography
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  • 43
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 2. Offset corrections (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-21
    Description: A band width determination using the first derivative of the band profile systematically underestimates the true Bragg angle. Corrections are proposed to compensate for the resulting offset Δa/a of the mean lattice parameters derived from as many Kikuchi band widths as possible. For dynamically simulated Kikuchi patterns, Δa/a can reach up to 8% for phases with a high mean atomic number Z, whereas for much more common low‐Z materials the offset decreases linearly. A predicted offset Δa/a = f(Z) is therefore proposed, which also includes the unit‐cell volume and thus takes into account the packing density of the scatterers in the material. Since Z is not always available for unknown phases, its substitution by Zmax, i.e. the atomic number of the heaviest element in the compound, is still acceptable for an approximate correction. For simulated Kikuchi patterns the offset‐corrected lattice parameter deviation is Δa/a 〈 1.5%. The lattice parameter ratios, and the angles α, β and γ between the basis vectors, are not affected at all.
    Description: Automatically determined band widths in simulated backscatter Kikuchi patterns exhibit differences from the double Bragg angles that correlate with the scatterer density. Corrections are proposed to compensate for this.
    Keywords: ddc:548 ; mean atomic number ; Kikuchi patterns ; lattice parameters ; automated Bragg angle determination ; lattice parameter determination ; dynamical theory of electron diffraction ; electron backscatter diffraction ; Funk transform
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  • 44
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    POWTEX visits POWGEN (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The high‐intensity time‐of‐flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world‐wide 〈sup〉3〈/sup〉He crisis in 2009, the authors promptly initiated the development of 〈sup〉3〈/sup〉He‐free detector alternatives that are tailor‐made for the requirements of large‐area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular‐ and wavelength‐dependent data from the POWTEX detector, unfortunately damaged by a 50〈italic〉g〈/italic〉 shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the 〈italic〉PowderReduceP2D〈/italic〉 algorithm implemented in 〈italic〉Mantid〈/italic〉 [Arnold 〈italic〉et al.〈/italic〉 (2014). 〈italic〉Nucl. Instrum. Methods Phys. Res. A〈/italic〉, 〈bold〉764〈/bold〉, 156–166]. The final part of the data treatment chain, namely a novel multi‐dimensional refinement using a modified version of the 〈italic〉GSAS‐II〈/italic〉 software suite [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?aj5212"〉Toby & Von Dreele (2013). 〈italic〉J. Appl. Cryst.〈/italic〉〈bold〉46〈/bold〉, 544–549〈/ext-link〉], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of 〈italic〉GSAS‐II〈/italic〉. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly‐user sample, BaZn(NCN)〈sub〉2〈/sub〉. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi‐dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the 〈italic〉a〈/italic〉 and 〈italic〉b〈/italic〉 lattice parameters of BaZn(NCN)〈sub〉2〈/sub〉 crystallizing in 〈italic〉Pbca〈/italic〉 as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, 〈italic〉e.g.〈/italic〉 the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large‐area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The first real‐world neutron diffraction data have been collected with one of the POWTEX detectors (FRM II, Garching, Germany) mounted for testing at the Spallation Neutron Source (Oak Ridge National Laboratory, USA). They allow for angular‐ and wavelength‐dispersive Rietveld refinement using a modified version of 〈italic〉GSAS‐II〈/italic〉.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2tu5033:jcr2tu5033-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; neutron detectors ; POWGEN beamline ; POWTEX detector ; DREAM beamline ; time‐of‐flight diffraction ; angular‐dispersive refinement ; wavelength‐dispersive refinement ; powder diffraction ; Rietveld refinement ; multi‐dimensional refinement
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  • 45
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    A note on the wedge reversion antisymmetry operation and 51 types of physical quantities in arbitrary dimensions (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The paper by Gopalan [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327〈/ext-link〉] presented an enumeration of the 41 physical quantity types in non‐relativistic physics, in arbitrary dimensions, based on the formalism of Clifford algebra. Gopalan considered three antisymmetries: spatial inversion, 〈overline〉1〈/overline〉, time reversal, 1′, and wedge reversion, 1〈sup〉†〈/sup〉. A consideration of the set of all seven antisymmetries (〈overline〉1〈/overline〉, 1′, 1〈sup〉†〈/sup〉, 1′〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉′, 〈overline〉1〈/overline〉′〈sup〉†〈/sup〉) leads to an extension of the results obtained by Gopalan. It is shown that there are 51 types of physical quantities with distinct symmetry properties in total.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉It is shown that there are 51 types of physical quantities in arbitrary dimensions with distinct transformations by wedge reversion symmetry. In the paper by 〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉Gopalan [(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327]〈/ext-link〉 only 41 types were enumerated.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:20532733:aya2ib5117:aya2ib5117-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; multivectors ; wedge reversion ; antisymmetry ; Clifford algebra
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  • 46
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 1. Where is the Bragg angle? (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-19
    Description: The derivation of a crystal structure and its phase‐specific parameters from a single wide‐angle backscattered Kikuchi diffraction pattern requires reliable extraction of the Bragg angles. By means of the first derivative of the lattice profile, an attempt is made to determine fully automatically and reproducibly the band widths in simulated Kikuchi patterns. Even under such ideal conditions (projection centre, wavelength and lattice plane traces are perfectly known), this leads to a lattice parameter distribution whose mean shows a linear offset that correlates with the mean atomic number Z of the pattern‐forming phase. The consideration of as many Kikuchi bands as possible reduces the errors that typically occur if only a single band is analysed. On the other hand, the width of the resulting distribution is such that higher image resolution of diffraction patterns, employing longer wavelengths to produce wider bands or the use of higher interference orders is less advantageous than commonly assumed.
    Description: The lattice parameters of more than 350 phases have been determined from simulated backscatter Kikuchi patterns. The deviations correlating with the mean atomic number correspond to those observed previously for experimental electron backscatter diffraction patterns.
    Keywords: ddc:548 ; Bragg angles ; Kikuchi bands ; Kikuchi patterns ; first derivative ; lattice parameters ; lattice parameter determination ; Bravais lattice type ; electron backscatter diffraction ; Radon transform
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  • 47
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    Data reduction for X‐ray serial crystallography using machine learning (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-19
    Description: Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large‐scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
    Description: A machine learning method for distinguishing good and bad images in serial crystallography is presented. To reduce the computational cost, this uses the oriented FAST and rotated BRIEF feature extraction method from computer vision to detect image features, followed by a multilayer perceptron (neural network) to classify the images.
    Keywords: ddc:548 ; serial crystallography ; data reduction ; machine learning ; feature extraction
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  • 48
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    Towards joint in situ determination of pressure and temperature in the large volume press exclusively from X‐ray diffraction (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-19
    Description: Since high‐pressure devices have been used at synchrotron facilities, accurate determination of pressure and temperature in the sample has been a crucial objective, particularly for experiments that simulate the Earth's interior. However, in some cases using a thermocouple may have a high likelihood of failure or is incompatible with a high‐pressure assembly. To address these challenges and similar issues, we aim to expand a previously proposed solution: to jointly estimate pressure and temperature (〈italic〉PT〈/italic〉) through 〈italic〉in situ〈/italic〉 X‐ray diffraction, to cover a wider range of internal 〈italic〉PT〈/italic〉 calibrants tested over larger 〈italic〉PT〈/italic〉 ranges. A modifiable Python‐based software is offered to quickly obtain results. To achieve these aims, 〈italic〉in situ〈/italic〉 large volume press experiments are performed on pellets of intimately mixed powders of a halide (NaCl, KCl, KBr, CsCl) or MgO and a metal (Pt, Re, Mo, W, Ni) in the pressure range 3–11 GPa and temperature range 300–1800 K. Although the pressure range was chosen for practical reasons, it also covers an equally important depth range in the Earth (down to 350 km) for geoscience studies. A thermocouple was used to validate the 〈italic〉PT〈/italic〉 conditions in the cell assemblies. The key results show that choosing the appropriate calibrant materials and using a joint 〈italic〉PT〈/italic〉 estimation can yield surprisingly small uncertainties (〈italic〉i.e.〈/italic〉 〈±0.1 GPa and 〈±50 K). This development is expected to benefit current and future research at extreme conditions, as other materials with high compressibility or high thermal pressure, stable over large 〈italic〉PT〈/italic〉 ranges, may be discovered and used as 〈italic〉PT〈/italic〉 calibrants.〈/p〉
    Description: Research in high‐pressure devices, such as the diamond anvil cell and the large volume press, requires knowledge of the pressure and temperature in the sample. Here, a large volume press and an internal resistive heater were used to generate high load and heat to various combinations of intimately mixed powders of materials. X‐ray diffraction and custom software were used to jointly estimate the pressures and temperatures in the samples and establish calibrants for 〈italic〉in situ〈/italic〉 experiments at extreme conditions.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2vl5008:jsy2vl5008-fig-0001"〉
    Description: https://gitlab.desy.de/robert.farla/eoscross
    Keywords: ddc:548 ; equations of state ; X‐ray diffraction ; large volume press ; high pressure ; resistive heating
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  • 49
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    In situ neutron diffraction for analysing complex coarse‐grained functional materials (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-10-24
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Complex functional materials play a crucial role in a broad range of energy‐related applications and in general for materials science. Revealing the structural mechanisms is challenging due to highly correlated coexisting phases and microstructures, especially for 〈italic〉in situ〈/italic〉 or 〈italic〉operando〈/italic〉 investigations. Since the grain sizes influence the properties, these microstructural features further complicate investigations at synchrotrons due to the limitations of illuminated sample volumes. In this study, it is demonstrated that such complex functional materials with highly correlated coexisting phases can be investigated under 〈italic〉in situ〈/italic〉 conditions with neutron diffraction. For large grain sizes, these experiments are valuable methods to reveal the structural mechanisms. For an example of 〈italic〉in situ〈/italic〉 experiments on barium titanate with an applied electric field, details of the electric‐field‐induced phase transformation depending on grain size and frequency are revealed. The results uncover the strain mechanisms in barium titanate and elucidate the complex interplay of stresses in relation to grain sizes as well as domain‐wall densities and mobilities.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉This work reports 〈italic〉in situ〈/italic〉 neutron diffraction experiments on a broad range of grain sizes of barium titanate. The study reveals the grain‐size‐dependent strain mechanisms and shows the competitiveness of neutron diffraction with high‐resolution synchrotron diffraction.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2vb5054:jcr2vb5054-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:550.724 ; ddc:548 ; neutron diffraction ; in situ ; applied electric fields ; barium titanate ; strain mechanisms ; grain sizes ; complex functional materials ; microstructures ; coexisting phases
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  • 50
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    Beam‐induced redox chemistry in iron oxide nanoparticle dispersions at ESRF–EBS (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2024-02-21
    Description: The storage ring upgrade of the European Synchrotron Radiation Facility makes ESRF–EBS the most brilliant high‐energy fourth‐generation light source, enabling in situ studies with unprecedented time resolution. While radiation damage is commonly associated with degradation of organic matter such as ionic liquids or polymers in the synchrotron beam, this study clearly shows that highly brilliant X‐ray beams readily induce structural changes and beam damage in inorganic matter, too. Here, the reduction of Fe3+ to Fe2+ in iron oxide nanoparticles by radicals in the brilliant ESRF–EBS beam, not observed before the upgrade, is reported. Radicals are created due to radiolysis of an EtOH–H2O mixture with low EtOH concentration (∼6 vol%). In light of extended irradiation times during insitu experiments in, for example, battery and catalysis research, beam‐induced redox chemistry needs to be understood for proper interpretation of insitu data.
    Description: With the increased brilliance at the European Research Facility–Extremely Brilliant Source (ESRF–EBS), a beam‐induced reduction of non‐stochiometric iron oxide nanoparticles (almost maghemite composition) to magnetite was observed in a mixture of ethanol and water with low ethanol concentration.
    Keywords: ddc:548 ; beam‐induced radiolysis ; radiation damage on inorganic materials ; ESRF–EBS
    Language: English
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  • 51
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    Machine learning for scattering data: strategies, perspectives and applications to surface scattering (2023)
    Hinderhofer, Alexander ; Greco, Alessandro ; Starostin, Vladimir ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-14
    Description: Machine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X‐ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing‐incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.
    Description: The status, opportunities, challenges and limitations of machine learning are discussed as applied to X‐ray and neutron scattering techniques, with an emphasis on surface scattering.
    Keywords: ddc:548 ; surface scattering ; X‐ray diffraction ; neutron scattering ; machine learning ; data analysis
    Language: English
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  • 52
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    Hard X‐ray full‐field nanoimaging using a direct photon‐counting detector (2023)
    Flenner, Silja ; Hagemann, Johannes ; Wittwer, Felix ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-03-05
    Description: Full‐field X‐ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low‐absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X‐ray microscopy with Zernike phase contrast, near‐field holography and near‐field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal‐to‐noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single‐photon‐counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz‐Zentrum Hereon. Thanks to the long sample‐to‐detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single‐photon‐counting detector in combination with a long sample‐to‐detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal‐to‐noise level.
    Description: A direct photon‐counting detector was used for different nanoimaging phase contrast techniques, increasing the temporal resolution.
    Keywords: ddc:548 ; nanotomography ; full‐field X‐ray microscopy ; near‐field holography ; near‐field ptychography ; Zernike phase contrast ; single‐photon‐counting detector ; phase contrast
    Language: English
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  • 53
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    Habitats of the Cap de Creus continental shelf and Cap de Creus Canyon, Northwestern Mediterranean (2012)
    Elsevier
    In:  In: Seafloor Geomorphology as Benthic Habitat. , ed. by Harris, P. T. and Baker, E. K. Elsevier, Amsterdam, pp. 457-469. ISBN 978-0-12-385140-6
    Details
    Publication Date: 2017-06-20
    Description: The Cap de Creus continental shelf and Cap de Creus canyon are located in the southern most sector of the Gulf of Lions, in the northwestern Mediterranean. The Cap de Creus continental shelf contains sandy and muddy sediments and an abrupt morpho­ logy, with rocky outcrops, relict bioherms, erosive features, and planar bedforms. The Cap de Creus canyon breaches the shelf at a depth of 110 m and denotes a marked dif­ ference in the morphology between the northern and the southern flank, reflecting a different depositional regime. The most common substrates correspond to coarse and medium sands (28%) and silty sediments (40%). The most common megabenthic assemblages of the shelf correspond to the communities of "offshore detritic" (31.95%) and "coastal terrigenous muds" (36.99%), mostly dominated by sea pens, alcyonaceans, and ceriantharians. The northern flank of the Cap de Creus canyon is predominantly depositional, whereas the southern flank is erosional. Rocky outcrops provide the sub­ stratum for cold­water coral (CWC) communities' development, in which the white coral Madrepora oculata is the most abundant species.
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  • 54
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    Isotopic, geophysical and biogeochemical investigation of submarine groundwater discharge: IAEA-UNESCO intercomparison exercise at Mauritius Island (2012)
    Elsevier
    In:  Journal of Environmental Radioactivity, 104 . pp. 24-45.
    Details
    Publication Date: 2018-03-08
    Description: Submarine groundwater discharge (SGD) into a shallow lagoon on the west coast of Mauritius Island (Flic-en-Flac) was investigated using radioactive (3H, 222Rn, 223Ra, 224Ra, 226Ra, 228Ra) and stable (2H, 18O) isotopes and nutrients. SGD intercomparison exercises were carried out to validate the various approaches used to measure SGD including radium and radon measurements, seepage rate measurements using manual and automated meters, sediment bulk conductivity and salinity surveys. SGD measurements using benthic chambers placed on the floor of the Flic-en-Flac Lagoon showed discharge rates up to 500 cm/day. Large variability in SGD was observed over distances of a few meters, which were attributed to different geomorphological features. Deployments of automated seepage meters captured the spatial and temporal variability of SGD with a mean seepage rate of 10 cm/day. The stable isotopic composition of submarine waters was characterized by significant variability and heavy isotope enrichment and was used to predict the contribution of fresh terrestrially derived groundwater to SGD (range from a few % to almost 100%). The integrated SGD flux, estimated from seepage meters placed parallel to the shoreline, was 35 m3/m day, which was in reasonable agreement with results obtained from a hydrologic water balance calculation (26 m3/m day). SGD calculated from the radon inventory method using in situ radon measurements were between 5 and 56 m3/m per day. Low concentrations of radium isotopes observed in the lagoon water reflected the low abundance of U and Th in the basalt that makes up the island. High SGD rates contribute to high nutrients loading to the lagoon, potentially leading to eutrophication. Each of the applied methods yielded unique information about the character and magnitude of SGD. The results of the intercomparison studies have resulted a better understanding of groundwater–seawater interactions in coastal regions. Such information is an important pre-requisite for the protection and management of coastal freshwater resources. Highlights ► Large fluctuations in SGD fluxes from 0 to 360 cm/day were observed. ► The integrated shoreline SGD fluxes were between 5 and 56 m3/m day. ► The groundwater contribution in SGD varied from a few % to almost 100%. ► The observed high SGD rates contributed to high nutrients loading to the lagoon.
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  • 55
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    Evaluation of boron isotope ratio as a pH proxy in the deep sea coral Desmophyllum dianthus: Evidence of physiological pH adjustment (2012)
    Elsevier
    In:  Earth and Planetary Science Letters, 349-350 . pp. 251-260.
    Details
    Publication Date: 2018-03-07
    Description: The boron isotope ratio (δ11B) of foraminifers and tropical corals has been proposed to record seawater pH. To test the veracity and practicality of this potential paleo-pH proxy in deep sea corals, samples of skeletal material from twelve archived modern Desmophyllum dianthus (D. dianthus) corals from a depth range of 274–1470 m in the Atlantic, Pacific, and Southern Oceans, ambient pH range 7.57–8.05, were analyzed for δ11B. The δ11B values for these corals, spanning a range from 23.56 to 27.88, are found to be related to seawater borate δ11B by the linear regression: δ11Bcoral=(0.76±0.28) δ11Bborate+(14.67±4.19) (1 standard error (SE)). The D. dianthus δ11B values are greater than those measured in tropical corals, and suggest substantial physiological modification of pH in the calcifying space by a value that is an inverse function of seawater pH. This mechanism partially compensates for the range of ocean pH and aragonite saturation at which this species grows, enhancing aragonite precipitation and suggesting an adaptation mechanism to low pH environments in intermediate and deep waters. Consistent with the findings of Trotter et al. (2011) for tropical surface corals, the data suggest an inverse correlation between the magnitude of a biologically driven pH offset recorded in the coral skeleton, and the seawater pH, described by the equation: ΔpH=pH recorded by coral−seawater pH=−(0.75±0.12) pHw+(6.88±0.93) (1 SE). Error analysis based on 95% confidence interval(CI) and the standard deviation of the regression residuals suggests that the uncertainty of seawater pH reconstructed from δ11Bcoral is ±0.07 to 0.12 pH units. This study demonstrates the applicability of δ11B in D. dianthus to record ambient seawater pH and holds promise for reconstructing oceanic pH distribution and history using fossil corals.
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  • 56
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    The Indus–Yarlung Zangbo ophiolites from Nanga Parbat to Namche Barwa syntaxes, southern Tibet: First synthesis of petrology, geochemistry, and geochronology with incidences on geodynamic reconstructions of Neo-Tethys (2012)
    Elsevier
    In:  Gondwana Research, 22 (2). pp. 377-397.
    Details
    Publication Date: 2017-12-13
    Description: The purpose of this first synthesis is to summarize findings on the Yarlung Zangbo Suture Zone (YZSZ) ophiolites and discuss still remaining problems. The YZSZ studied for almost 30 years and is the youngest of the sutures recognized on Tibet Plateau. It is now acknowledged that the YZSZ is a complex assemblage of sedimentary, metamorphic and igneous rocks created during and shortly after the collision between India and Eurasia. The ages of the various lithologies span a time interval from the Jurassic to the Middle Miocene, with some Permian and Devonian exotic blocks from mélange zone. The YZSZ is characterized by ophiolitic complexes and ophiolitic mélange. The ophiolites are of two types: non dismembered and dismembered sections. The non disturbed sections, although tectonically reworked, are observed along the segment from Dazhuqu to Jiding in Xigaze area and Spontang ophiolite. The dismembered sequences are found in various locations such as Nidar, Kiogar, Jungbwa, Saga, Sangsang, Xigugabu, and Luobusa. The incomplete stratigraphic log could be connected to intraoceanic or orogenetic origins. The ophiolites are distributed into two groups of ages: the Luobusa, Zedang and Kiogar sequences being Jurassic-Lower Cretaceous whereas all other sequences are of Lower Cretaceous age. Compilation of geochronological data suggest that some ophiolite sequences might have evolved for over more than 70 My from their initial genesis to obduction which occurred around 70–90 My ago. Ophiolites differ in terms of petrological and geochemical aspects however, they were all generated in suprasubduction zone and more specifically in arc (few fore-arc) and back-arc settings. Synthesis of more than 700 geochemical analyses show variable mixing of components from N-MORB-type to IAT-CAB and to OIB end-members. The Jurassic ophiolites show the maximum of arc component while the Lower Cretaceous ones show little to strong mixing. In addition, most ophiolites were created in short lived (30 My) basins and generated close to the Eurasiatic continental margin. We propose that Ladakh–Tibet ophiolites were generated in a suprasubduction context similar to Mariana arc, interarc and back-arc or Tonga–Lau system. The variable arc signature of these ophiolites is directly related to their initial position within the suprasubduction system.
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  • 57
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    Global analysis of satellite tracking data shows that adult green turtles are significantly aggregated in Marine Protected Areas (2012)
    Wiley
    In:  Global Ecology and Biogeography, 21 (11). pp. 1053-1061.
    Details
    Publication Date: 2017-12-14
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  • 58
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    Comparison of cyanobacterial and green algal growth rates at different temperatures (2012)
    Wiley
    In:  Freshwater Biology, 58 (3). pp. 552-559.
    Details
    Publication Date: 2018-01-29
    Description: 1. The hypothesis that cyanobacteria have higher optimum growth temperatures and higher growth rates at the optimum as compared to chlorophytes was tested by running a controlled experiment with eight cyanobacteria species and eight chlorophyte species at six different temperatures (20–35 °C) and by performing a literature survey. 2. In the experiment, all organisms except the chlorophyte Monoraphidium minutum grew well up to 35 °C. The chlorophyte Chlamydomonas reinhardtii was the fastest-growing organism over the entire temperature range (20–35 °C). 3. Mean optimum growth temperatures were similar for cyanobacteria (29.2 °C) and chlorophytes (29.2 °C). These results are concordant with published data, yielding slightly higher mean optimum growth temperatures for cyanobacteria (27.2 °C) than for chlorophytes (26.3 °C). 4. Mean growth rates of cyanobacteria at 20 °C (0.42 day−1) were significantly lower than those of chlorophytes at 20 °C (0.62 day−1). However, at all other temperatures, there were no differences between mean growth rates of cyanobacteria and chlorophytes. 5. Mean growth rates at the optimum temperature were similar for cyanobacteria (0.92 day−1) and chlorophytes (0.96 day−1). However, analysis of published data revealed that growth rates of cyanobacteria (0.65 day−1) were significantly lower than those of chlorophytes (0.93 day−1) at their optimum temperatures. 6. Although climate warming will probably lead to an intensification of cyanobacterial blooms, our results indicate that this might not be as a result of higher growth rates of cyanobacteria compared with their chlorophyte competitors. The competitive advantage of cyanobacteria can more likely be attributed to their ability to migrate vertically and prevent sedimentation in warmer and more strongly stratified waters and to their resistance to grazing, especially when warming reduces zooplankton body size.
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  • 59
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    Application of Tephrochronology in the Kurile-Kamchatka and Aleutean Marginal Sea-Island Arc Systems (KALMAR-Project) (2012)
    Elsevier
    In:  Quaternary International, 279-280 . p. 511.
    Details
    Publication Date: 2017-01-26
    Type: Article , NonPeerReviewed
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  • 60
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    Varying sediment sources (Hudson Strait, Cumberland Sound, Baffin Bay) to the NW Labrador Sea slope between and during Heinrich events 0 to 4 (2012)
    Wiley
    In:  Journal of Quaternary Science, 27 (5). pp. 475-484.
    Details
    Publication Date: 2020-07-20
    Description: Core HU97048-007PC was recovered from the continental Labrador Sea slope at a water depth of 945 m, 250km seaward from the mouth of Cumberland Sound, and 400km north of Hudson Strait. Cumberland Sound is a structural trough partly floored by Cretaceous mudstones and Paleozoic carbonates. The record extends from 10 to 58 ka. On-board logging revealed a complex series of lithofacies, including buff-colored detrital carbonate-rich sediments [Heinrich (H)-events] frequently bracketed by black facies. We investigate the provenance of these facies using quantitative X-ray diffraction on drill-core samples from Paleozoic and Cretaceous bedrock from the SE Baffin Island Shelf, and on the〈2-mm sediment fraction in a transect of five cores from Cumberland Sound to the NW Labrador Sea. A sediment unmixing program was used to discriminate between sediment sources, which included dolomite-rich sediments from Baffin Bay, calcite-rich sediments from Hudson Strait and discrete sources from Cumberland Sound. Results indicated that the bulk of the sediment was derived from Cumberland Sound, but Baffin Bay contributed to sediments coeval with H-0 (Younger Dryas), whereas Hudson Strait was the source during H-events 1–4. Contributions from the Cretaceous outcrops within Cumberland Sound bracket H-events, thus both leading and lagging Hudson Strait-sourced H-events.
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  • 61
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    The ecophysiology of Sprattus sprattus in the Baltic and North Seas (2012)
    Elsevier
    In:  Progress in Oceanography, 103 . pp. 42-57.
    Details
    Publication Date: 2020-10-16
    Description: The European sprat (Sprattus sprattus) was a main target species of the German GLOBEC program that investigated the trophodynamic structure and function of the Baltic and North Seas under the influence of physical forcing. This review summarizes literature on the ecophysiology of sprat with an emphasis on describing how environmental factors influence the life-history strategy of this small pelagic fish. Ontogenetic changes in feeding and growth, and the impacts of abiotic and biotic factors on vital rates are discussed with particular emphasis on the role of temperature as a constraint to life-history scheduling of this species in the Baltic Sea. A combination of field and laboratory data suggests that optimal thermal windows for growth and survival change during early life and are wider for eggs (5–17 °C) than in young (8- to 12-mm) early feeding larvae (5–12 °C). As larvae become able to successfully capture larger prey, thermal windows expand to include warmer waters. For example, 12- to 16-mm larvae can grow well at 16 °C and larger, transitional-larvae and early juveniles display the highest rates of feeding and growth at ∼18–22 °C. Gaps in knowledge are identified including the need for additional laboratory studies on the physiology and behavior of larvae (studies that will be particularly critical for biophysical modeling activities) and research addressing the role of overwinter survival as a factor shaping phenology and setting limits on the productivity of this species in areas located at the northern limits of its latitudinal range (such as the Baltic Sea). Based on stage- and temperature-specific mortality and growth potential of early life stages, our analysis suggests that young-of-the year sprat would benefit from inhabiting warmer, near-shore environments rather than the deeper-water spawning grounds such as the Bornholm Basin (central Baltic Sea). Utilization of warmer, nearshore waters (or a general increase in Baltic Sea temperatures) is expected to accelerate growth rates but also enhance the possibility for density-dependent regulation of recruitment (e.g., top-down control of zooplankton resources) acting during the late-larval and juvenile stages, particularly when sprat stocks are at high levels. Highlights ► Field, laboratory and modeling research on the ecophysiology of all sprat life stages is summarized. ► Environmental factors influencing growth and survival are revealed. ► Ontogenetic changes in thermal tolerance and prey requirements constrain life cycle scheduling. ► Gaps in knowledge are identified and future research efforts recommended on sprat recruitment dynamics. ► Exploring seasonal energy allocation will allow a mechanistic understanding of climate impacts.
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  • 62
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    The spatial dimension of climate-driven temperature change in the Baltic Sea and its implication for cod and sprat early life stage survival (2012)
    Elsevier
    In:  Journal of Marine Systems, 100-101 . pp. 1-8.
    Details
    Publication Date: 2019-09-23
    Description: Throughout the last decades there has been a world-wide, general warming trend. In this study, we use the example of the Baltic Sea to resolve the overall estimated temperature trend into smaller, meso-scale spatial units. Afterwards, we investigate the spatially resolved potential impact of the temperature trend on larval survival for two important fish species, cod and sprat. We used two different sets of hydrographic data: (i) long-term temporally and depth-resolved data measured in situ originating from one geographic position and (ii) long-term horizontally resolved data, originating from a circulation model. In contrast to basin-wide integrated results, our modelling approach revealed different results related to smaller spatial scales. In shallow and coastal areas non-significant long-term temperature trends were observed. In some cases even decreasing temperature trends were found. Average distribution maps (1973–2010) of cod and sprat eggs and larvae confirmed the higher importance of central, deep basins as nursery grounds. Applying the temperature trends when calculating cod larval window of opportunity values, resulted in decreased durations of 1–3 days (~ 3–13%) in most areas. Sprat larval window of opportunity values mainly increased up to 4 days (~ 45%), indicating a potential reproduction advantage of sprat over cod under anticipated future temperature increase. Highlights ► We resolve the overall positive temperature trend in the Baltic into meso-scale spatial units and investigate the impact on larval survival for two important fish species, cod and sprat. ► In shallow and coastal areas non-significant or even negative temperature trends occurred. ► Cod larval window of opportunity values decreased by 1–3 days (~ 3–13%). ► Sprat larval window of opportunity values increased up to 4 days (~ 45%). ► Sprat will have a reproduction advantage over cod under anticipated future temperature change.
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  • 63
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    Timing of trap formation and petroleum generation in the northern East China Sea Shelf Basin (2012)
    Elsevier
    In:  Marine and Petroleum Geology, 36 . pp. 154-163.
    Details
    Publication Date: 2017-07-26
    Description: Basin modeling and cross-section restoration from the northern East China Sea Shelf Basin reveal the timing of trap formation and petroleum generation. Cross-section restoration suggest that extension started in the Late Cretaceous and was interrupted by inversion at the end of Miocene that created large anticline structures, providing numerous petroleum traps. One-dimensional basin modeling of the JDZ-VII-I well show that the main phase of oil generation in the synrift fluvial shales in the Jeju Basin occurred during the Early Oligocene–middle Miocene period, predating the regional inversion. Thus, potential for large oil accumulations in the southern part of the basin is probably limited. Most of the petroleum are likely to have flowed toward the basin margin as well as basin center until the Late Miocene because no structures were available to capture them. The formation of anticline structures overlapped and/or postdated the main phase of gas generation in the Jeju Basin. This is probably why the JDZ-VII-1 is gas-prone with the gas trapped mainly in the anticlinal structures formed by the tectonic uplift. The source rocks in the southwestern part of the Domi Basin are immature for petroleum generation.
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  • 64
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    Reduced inflammatory response to Aeromonas salmonicida infection in common carp (Cyprinus carpio L.) fed with β-glucan supplements (2012)
    Elsevier
    In:  Fish & Shellfish Immunology, 32 (6). pp. 1051-1057.
    Details
    Publication Date: 2020-07-31
    Description: The objective of the present study was to determine the action of beta-glucans as feed additives on the gene expression profile of some inflammatory-related cytokines from common carp (Cyprinus carpio L) during the early stages of a non-lethal bacterial infection with Aeromonas salmonicida. beta-glucan (MacroGard (R)), was administered daily to carp (6 mg per kg body weight) in the form of supplemented commercial food pellets for 14 days prior to infection. Control and treated fish were then intraperitoneally injected with PBS or 4 x 10(8) bacteria per fish and were sampled at time 0 and 6 h, 12 h, I day, 3 days and 5 days post-injection. Head kidney and gut were collected and the gene expression patterns for tnf alpha 1, tnf alpha 2, il1 beta, il6 and il10 were analyzed by quantitative PCR. Results obtained showed that treatment with beta-glucans generally down-regulated the expression of all measured genes when compared to their corresponding controls. After injection, highest changes in the gene expression levels were obtained at 6 h: particularly, in head kidney there was higher up-regulation of tnfa1 and tnfa2 in infected fish fed beta-glucans in comparison to control feed: however, in gut there was a significant down-regulation of tnf alpha 1, tnf alpha 2, il1 beta and il6 in infected fish fed beta-glucans. Analysis of carp specific antibodies against A. salmonicida 30 days after injection revealed their levels were reduced in the infected beta-glucan group. In conclusion, a diet supplemented with beta-glucan (MacroGard (R)) reduced the gene expression levels of some inflammation-related cytokines in common carp. Such a response appears to be dependent of organ studied and therefore the immunostimulant may be preventing an acute and potential dangerous response in gut, whilst enhancing the inflammatory response in head kidney when exposed to A. salmonicida
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  • 65
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    Deformation and ultrafine dynamic recrystallization of quartz in pseudotachylyte-bearing brittle faults: A matter of a few seconds (2012)
    Elsevier
    In:  Journal of Structural Geology, 38 . pp. 21-38.
    Details
    Publication Date: 2016-03-03
    Description: Tectonic pseudotachylytes, i.e. quenched friction-induced silicate melts, record coseismic slip along faults and are mainly reported from the brittle crust in association with cataclasites. In this study, we document the occurrence of recrystallization of quartz to ultrafine-grained (grain size 1–2 μm) aggregates along microshear zones (50–150 μm thick) in the host rock adjacent to pseudotachylytes from two different faults within quartzite (Schneeberg Normal Fault Zone, Eastern Alps), and tonalite (Adamello fault, Southern Alps) in the brittle crust. The transition from the host quartz to microshear zone interior includes: (i) formation of high dislocation densities; (ii) fine (0.3–0.5 μm) polygonization to subgrains defined by disordered to well-ordered dislocation walls; (iii) development of a mosaic aggregate of dislocation-free new grains. The crystallographic preferred orientation (CPO) of quartz towards the microshear zone shows a progressive misorientation from the host grain, by subgrain rotation recrystallization, to a nearly random CPO possibly related to grain boundary sliding. These ultrafine aggregates appear to be typically associated with pseudotachylytes in nature. We refer the crystal plastic deformation of quartz accompanied by dramatic grain size refinement to the coseismic stages of fault slip due to high differential stress and temperature transients induced by frictional heating. Microshear zones localized on precursory fractures developed during the stages of earthquake rupture propagation and the very initial stages of fault slip. Thermal models indicate that the process of recrystallization, including recovery processes, occurred in a time lapse of a few tens of seconds.
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  • 66
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    How does dynamical spatial variability impact 234Th-derived estimates of organic export? (2012)
    Elsevier
    In:  Deep-Sea Research Part I-Oceanographic Research Papers, 68 . pp. 24-45.
    Details
    Publication Date: 2014-12-08
    Description: In this study we first evaluate the small-scale spatial variability of particulate export, using a set of synoptic thorium-234 activity observations sampled within a one-degree radius. These data show significant variability of surface thorium activity on scales of the order of 100 km (∼270–550 dpm m−3). This patchiness of export potentially affects the robustness of point observations and our interpretation of them. Motivated by these observations we subsequently couple an explicit model of thorium-234 dynamics to a coupled physical–biogeochemical basin model capable of resolving these small-scales. The model supports the observations in displaying marked thorium variability on spatial scales of the order of 100 km and smaller, with highest values in the regions of large eddy kinetic energy and large primary productivity. The model is also used to quantify the impact of small-scale variability on export estimates. Our model shows that the primary source of error associated with the presence of small-scale spatial variability is related to the standard assumptions of steady state and non-steady state (〉40% during bloom condition). The non-steady state method can misinterpret variations due to patchiness in thorium activity as temporal changes and lead to errors larger than those introduced by the simpler steady state approach. We show that the non-steady state approach could improve the flux estimates in some cases if the sampling was conducted in a Lagrangian framework. Undersampling the spatial variability results in further bias (〉20%) that can be reduced when the sampling density is increased. Finally, errors due to the dynamical transport of thorium associated with small-scale structures are relatively low (〈20%) except in regions of high eddy kinetic energy.
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  • 67
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    Tracing the effects of high-pressure metasomatic fluids and seawater alteration in blueschist-facies overprinted eclogites: Implications for subduction channel processes (2012)
    Elsevier
    In:  Chemical Geology, 292/293 . pp. 69-87.
    Details
    Publication Date: 2019-09-23
    Description: Eclogites from the Tian Shan high-pressure/low-temperature (HP/LT) metamorphic belt show evidence for successively increasing metasomatic alteration with increasing retrograde, blueschist-facies overprint. To constrain the source(s) of the metasomatizing fluid and to evaluate elemental and isotopic changes during this overprint, two sequences of eclogite-blueschist transitions were investigated: A layered transition from eclogite to blueschist (FTS 9–1 sequence) and blueschist-facies overprinted pillow metabasalts (FTS 4 samples). Geochemical trends based on the relationships of K, Ba, Rb and Th are consistent with HP metasomatism, but distinct from typical seafloor alteration trends. In contrast, oxygen isotope ratios in garnet (δ18OV-SMOW = 7.3–8.7‰) and omphacite (δ18OV-SMOW = 8.2–9.7‰) are similar to δ18OV-SMOW in bulk low-temperature altered oceanic crust (AOC), suggesting O isotopic preservation of a seafloor alteration signature. Carbonate crystallization related to the metasomatic overprint demonstrate CO2 mobility during subduction and potential C storage in HP metamorphic rocks. Carbon isotope ratios in the two sequences differ markedly: Disseminated calcite in the layered FTS 9–1 sequence has δ13CV-PDB = − 9.14 ± 0.19‰, whereas vein-forming ankerite in the pillow metabasalts has δ13CV-PDB = − 2.08 ± 0.12‰. The ankerite reflects an inorganic marine/hydrothermal signature, as observed in ophiolites, whereas the low δ13CV-PDB values from the calcite point to a contribution of organic carbon. The time when the metasomatic overprint occurred is estimated to be ~ 320 ± 11 Ma based on a Rb-Sr isochron age of six blueschist samples from the pillow metabasalts, which is in agreement with active subduction in this region. Initial (T = 320 Ma) 87Sr/86Sr ratios for all HP/LT rocks range from 0.7059 – 0.7085, and εNd320Ma varies from − 0.4 to + 10.9. Both eclogite-blueschist sequences have initial Sr isotope compositions (87Sr/86Sr ~ 0.707) that are significantly higher than those of typical oceanic mantle-derived basalts. They are thought to derive from a fluid that preserved the Sr isotopic signature of seawater by fluid-rock interaction with seawater-altered oceanic lithosphere in a subduction channel. Mixing models between eclogite and various fluids suggest that the contribution of a sediment-derived fluid was likely less than 20%. A fluid predominantly derived from seawater-altered oceanic lithosphere is also supported by the calculated O isotope composition of the fluids (10.2 – 11.2‰). It is thus evident that subduction channel fluids carry complex, mixed elemental and isotopic signatures, which reflect the composition of their source rocks modified by interaction with various other lithologies. Highlights ► Eclogites from the Tian Shan show blueschist-facies metasomatic overprint ► Fluid-induced metasomatism occurred at 320 ± 11 Ma ► Fluid predominantly derived from seawater-altered oceanic lithosphere ► Carbonates reflect C sequestration of mixture of organic and inorganic components
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    Upwelling events may cause cyanobacteria blooms in the Baltic Sea (2012)
    Elsevier
    In:  Journal of Marine Systems, 90 (1). pp. 67-76.
    Details
    Publication Date: 2015-09-25
    Description: Cyanobacteria blooms in the Baltic Sea appear after upwelling events, which transport phosphate-rich intermediate water to the surface. The growth potential of diazotrophic cyanobacteria in upwelled water was studied in a mesocosm (tank) experiment in summer 2007. An Anabaena bloom was only induced in the tanks filled with upwelled surface water but not in those filled with surface water from outside the upwelling cell and with intermediate water. The low initial cyanobacteria biomass in the intermediate water could not grow to bloom concentrations within three weeks. It is concluded that mixing of upwelled water with surrounding surface water forms a precondition for a cyanobacteria bloom. An additional mesocosm experiment conducted in 2009 revealed that mixing of intermediate water with surface water had the same stimulating effect on nitrogen fixation and cyanobacteria growth as artificial phosphate input. Phosphate input stimulates the growth of Nodularia and Anabaena more than that of Aphanizomenon. We suggest that the upwelled phosphate-rich intermediate water has to be mixed with the surface water containing physiologically “young” cyanobacteria biomass of at least 20 mg/m3 as an inoculum in order to initiate a cyanobacteria bloom.
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    Is growth of filamentous cyanobacteria supported by phosphate uptake below the thermocline? (2012)
    Elsevier
    In:  Estuarine, Coastal and Shelf Science, 99 . pp. 50-60.
    Details
    Publication Date: 2015-09-25
    Description: In the Baltic Sea, excess phosphorus after the spring bloom or phosphorus input from deeper layers e.g. by upwelling are nutrient sources for the development of filamentous cyanobacteria. The objective of this study was to investigate the ability of filamentous cyanobacteria to accumulate phosphate in depths within or below the thermocline under stratified conditions in the water column. Inorganic nutrient concentrations, as well as phytoplankton composition, chlorophyll a, POC, PON and POP and the ratios between them of water samples and of isolated filamentous cyanobacteria were estimated in five horizons of the upper 30 m surface layer together with phosphorus uptake and nitrogen fixation. During the investigation period, the water column was stratified with a surface temperature of 16 °C–18 °C in the eastern Gotland Basin. Cyanobacteria surface blooms occurred and constituted between 28 and 68% of the total phytoplankton biomass in the upper 5 m surface layer. Deduced from POC:POP ratios of 264–977, cyanobacteria were phosphorus depleted here. The POC:POP ratios became lower with increasing depth. In depths below 15 m, the cyanobacteria indicated phosphorus enrichment by POC:POP ratio declining down to 75 due to a forced gross uptake of 0.62 nmol P μg−1 Chla h−1compared to an uptake rate of 0.13 nmol P μg−1 Chla h−1 measured in the surface layer. Thus, filamentous cyanobacteria can acquire phosphate in deeper layers which enables further growth when they reach the surface. However, they occurred in low abundances there. In 30 m depth, cyanobacteria accounted for only 0.3–10% of their biomass in the surface layer. This contribution to bloom formation may therefore be of minor importance compared to other sources.
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    Changes in climate and weather extremes in the 21st century (2012)
    Wiley
    In:  Wiley Interdisciplinary Reviews: Climate Change, 3 (2). pp. 115-129.
    Details
    Publication Date: 2015-10-06
    Description: Climate and weather extremes are sporadically recurring events that may have major local or regional impacts on the society and the environment. These events are typically related to unusually high or low temperature, prolonged dry or wet conditions, heavy precipitation, or extreme winds. Extreme events are part of the overall climate and weather alongside average conditions and variability, and thus are not unexpected as such. Climate change is expected to affect not only means but also variability and extremes. Some inferences can be based on past and present observations, but analyses of especially rare events are hampered by the availability of long time series. Over time, depending on how far the on-going global warming takes us from the present and the past climate conditions, the weather and climate statistics may well come to shift in ways that are well outside observational data. This may lead to shifts in frequency, intensity and geographical distribution of different extremes. Indeed, projected changes in some extremes over the 21st century are quite robust, such as generally increasing warm and decreasing cold extremes. Possible changes in some other aspects, for example storms, remain much more uncertain. Science-based information both on robust findings and on relevant uncertainties on changing extremes can provide useful information for sectorial planning, disaster risk prevention and overall reduction of societal vulnerability related to climate and weather
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    Diagenetic barium cycling in Black Sea sediments – A case study for anoxic marine environments (2012)
    Elsevier
    In:  Geochimica et Cosmochimica Acta, 88 . pp. 88-105.
    Details
    Publication Date: 2015-11-24
    Description: High-resolution sedimentary records of major and minor elements (Al, Ba, Ca, Sr, Ti), total organic carbon (TOC), and profiles of pore water constituents (View the MathML sourceSO42-, CH4, Ca2+, Ba2+, Mg2+, alkalinity) were obtained for two gravity cores (core 755, 501 m water depth and core 214, 1686 m water depth) from the northwestern Black Sea. The records were examined in order to gain insight into the cycling of Ba in anoxic marine sediments characterized by a shallow sulfate–methane transition (SMT) as well as the applicability of barite as a primary productivity proxy in such a setting. The Ba records are strongly overprinted by diagenetic barite (BaSO4) precipitation and remobilization; authigenic Ba enrichments were found at both sites at and slightly above the current SMT. Transport reaction modeling was applied to simulate the migration of the SMT during the changing geochemical conditions after the Holocene seawater intrusion into the Black Sea. Based on this, sediment intervals affected by diagenetic Ba redistribution were identified. Results reveal that the intense overprint of Ba and Baxs (Ba excess above detrital average) strongly limits its correlation to primary productivity. These findings have implications for other modern and ancient anoxic basins, such as sections covering the Oceanic Anoxic Events which Ba is frequently used as a primary productivity indicator. Our study also demonstrates the limitations concerning the use of Baxs as a tracer for downward migrations of the SMT: due to high sedimentation rates at the investigated sites, diagenetic barite fronts are buried below the SMT within a relatively short period. Thus, ‘relict’ barite fronts would only be preserved for a few thousands of years, if at all.
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    Mass transport deposits and gas hydrate occurrences in the Ulleung Basin, East Sea – Part 1: Mapping sedimentation patterns using seismic coherency (2012)
    Elsevier
    In:  Marine and Petroleum Geology, 35 (1). pp. 91-104.
    Details
    Publication Date: 2020-07-08
    Description: Seismic coherency measures, such as similarity and dip of maximum similarity, were used to characterize mass transport deposits (MTDs) in the Ulleung Basin, East Sea, offshore Korea. Using 2-D and 3-D seismic data several slope failure masses have been identified near drill site UBGH1-4. The MTDs have a distinct seismic character and exhibit physical properties similar to gas hydrate bearing sediment: elevated electrical resistivity and P-wave velocity. Sediments recovered from within the MTDs show a reworked nature with chaotic assemblage of mud-clasts. Additionally, the reflection at the base of MTDs is polarity reversed relative to the seafloor, similarly to the bottom-simulating reflector commonly used to infer the presence of gas hydrates. The MTDs further show regional seismic blanking (absence of internal reflectivity), which is yet another signature often attributed to gas hydrate bearing sediments. At the drill site UBGH1-4, no gas hydrate was recovered in sediment-cores from inside a prominent MTD unit. Instead, pore-filling gas hydrate was recovered only within thin turbidite sand layers near the base of the gas hydrate stability zone. With the analysis of seismic attributes, the seismic character of the prominent MTD (Unit 3) was investigated. The base of the MTD unit exhibits deep grooves interpreted as gliding tracks from either outrunner blocks or large clasts that were dragged along the paleo-seafloor. Similar seismic features were identified on the seafloor although the length of the gliding tracks on the seafloor is much shorter (a few hundred meters to ∼1 km), compared to over 10 km long tracks at the base of the MTD. The seismic coherency attributes allowed to estimate the volume of the failed sediment as well as the direction of the flow of sediment. Tracking the MTD and extrapolating its spatial extent from the 3-D seismic volume to adjacent 2-D seismic profiles, a possible source region of this mass failure was defined ∼50 km upslope of Site UBGH1-4.
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    The effect of diagenesis and fluid migration on rare earth element distribution in pore fluids of the northern Cascadia accretionary margin (2012)
    Elsevier
    In:  Chemical Geology, 291 . pp. 152-165.
    Details
    Publication Date: 2017-10-24
    Description: Analytical challenges in obtaining high quality measurements of rare earth elements (REEs) from small pore fluid volumes have limited the application of REEs as deep fluid geochemical tracers. Using a recently developed analytical technique, we analyzed REEs from pore fluids collected from Sites U1325 and U1329, drilled on the northern Cascadia margin during the Integrated Ocean Drilling Program (IODP) Expedition 311, to investigate the REE behavior during diagenesis and their utility as tracers of deep fluid migration. These sites were selected because they represent contrasting settings on an accretionary margin: a ponded basin at the toe of the margin, and the landward Tofino Basin near the shelf's edge. REE concentrations of pore fluid in the methanogenic zone at Sites U1325 and U1329 correlate positively with concentrations of dissolved organic carbon (DOC) and alkalinity. Fractionations across the REE series are driven by preferential complexation of the heavy REEs. Simultaneous enrichment of diagenetic indicators (DOC and alkalinity) and of REEs (in particular the heavy elements Ho to Lu), suggests that the heavy REEs are released during particulate organic carbon (POC) degradation and are subsequently chelated by DOC. REE concentrations are greater at Site U1325, a site where shorter residence times of POC in sulfate-bearing redox zones may enhance REE burial efficiency within sulfidic and methanogenic sediment zones where REE release ensues. Cross-plots of La concentrations versus Cl, Li and Sr delineate a distinct field for the deep fluids (z 〉 75 mbsf) at Site U1329, and indicate the presence of a fluid not observed at the other sites drilled on the Cascadia margin. Changes in REE patterns, the presence of a positive Eu anomaly, and other available geochemical data for this site suggest a complex hydrology and possible interaction with the igneous Crescent Terrane, located east of the drilled transect.
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    Gas hydrate within the Winona Basin, offshore western Canada (2012)
    Elsevier
    In:  Marine and Petroleum Geology, 30 (1). pp. 66-80.
    Details
    Publication Date: 2015-11-17
    Description: In western Canada gas hydrates have been thought to exist primarily in the Cascadia accretionary prism off southern Vancouver Island, British Columbia (BC). We present evidence for the existence of gas hydrate in folds and ridges of the Winona Basin up to 40 km seaward from the foot of the continental slope off northern Vancouver Island. The occurrence of a bottom-simulating reflector (BSR) observed in a number of vintage seismic reflection profiles is strongly correlated to faulted, and folded sedimentary ridges and buried folds. The observed tectonic structures of the Winona Basin are within the rapidly evolving Juan de Fuca – Cascadia – Queen Charlotte triple junction off BC. Re-processing of multi-channel data imaged mildly to strongly deformed sediments; the BSR is confined to sediments with stronger deformation. Changes in the amplitude character of sediment-reflections above and below the depth of the base of gas hydrate stability zone were also used as an indicator for the presence of gas hydrate. Additionally, regional amplitude and frequency reduction below some strong BSR occurrences may indicate free gas accumulations. Gas hydrate formation in the Winona Basin appears strongly constrained to folds and ridges and thus correlated to deeper-routed fluid-advection regimes. Methane production from in situ microbial activities as a source of gas to form gas hydrates, as proposed to be a major contributor for gas hydrates within the accretionary prism to the south, appears to be insufficient to produce the widespread gas hydrate occurrences in the Winona Basin. Potential reasons for the lack of sufficient in situ gas production may be that sedimentation rates are 5–100 times higher than those in the accretionary prism so that available organic carbon moves too quickly through the gas hydrate stability field. The confinement of BSRs to ridges and folds within the Winona Basin results in an areal extent of gas hydrate occurrences that is a factor of five less than what is expected from regional gas hydrate stability field mapping using water-depth (pressure) as the only controlling factor only.
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    The Gibraltar subduction: A decade of new geophysical data (2012)
    Elsevier
    In:  Tectonophysics, 574-575 . pp. 72-91.
    Details
    Publication Date: 2015-01-27
    Description: The Gibraltar arc, spans a complex portion of the Africa-Eurasia plate boundary marked by slow oblique convergence and intermediate and deep focus seismicity. The seemingly contradictory observations of a young extensional marine basin surrounded by an arcuate fold-and-thrust belt, have led to competing geodynamic models (delamination and subduction). Geophysical data acquired in the past decade provide a test for these models and support a narrow east-dipping, subduction zone. Seismic refraction studies indicate oceanic crust below the western Gulf of Cadiz. Tomography of the upper mantle reveals a steep, east-dipping high P-wave velocity body, beneath Gibraltar. The anisotropic mantle fabric from SKS splitting shows arc-parallel "fast directions", consistent with toroidal flow around a narrow, westward retreating subducting slab. The accompanying WSW advance of the Rif-Betic mountain belt has constructed a thick pile of deformed sediments, an accretionary wedge, characterized by west-vergent thrust anticlines. Bathymetric swath-mapping images an asymmetric embayment at the deformation front where a 2 km high basement ridge has collided. Subduction has slowed significantly since 5 Ma, but deformation of recent sediments and abundant mud volcanoes suggest ongoing activity in the accretionary wedge. Three possible origins for this deformation are discussed; gravitational spreading, overall NW-SE convergence between Africa and Iberia and finally a WSW tectonic push from slow, but ongoing roll-back subduction. In the absence of arc volcanism and shallow dipping thrust type earthquakes, evidence in favor of present-day subduction can only be indirect and remains the object of debate. Continued activity of the subduction offers a possible explanation for great (M〉8.5) earthquakes known to affect the area, like the famous 1755 Great Lisbon earthquake. Recent GPS studies show SW motion of stations in N Morocco at velocities of 3-6 mm/yr indicating the presence of an independent block, a "Rif-Betic-Alboran" microplate, situated between Iberia and Africa
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    Mass-transport deposits and gas hydrate occurrences in the Ulleung Basin, East Sea – Part 2: Gas hydrate content and fracture-induced anisotropy (2012)
    Elsevier
    In:  Marine and Petroleum Geology, 35 (1). pp. 75-90.
    Details
    Publication Date: 2020-07-08
    Description: Mass-transport-deposits (MTDs) and hemipelagic mud interbedded with sandy turbidites are the main sedimentary facies in the Ulleung Basin, East Sea, offshore Korea. The MTDs show similar seismic reflection characteristics to gas-hydrate-bearing sediments such as regional seismic blanking (absence of internal reflectivity) and a polarity reversed base-reflection identical to the bottom-simulating reflector (BSR). Drilling in 2007 in the Ulleung Basin recovered sediments within the MTDs that exhibit elevated electrical resistivity and P-wave velocity, similar to gas hydrate-bearing sediments. In contrast, hemipelagic mud intercalated with sandy turbidites has much higher porosity and correspondingly lower electrical resistivity and P-wave velocity. At drill-site UBGH1-4 the bottom half of one prominent MTD unit shows two bands of parallel fractures on the resistivity log-images indicating a common dip-azimuth direction of about ∼230° (strike of ∼140°). This strike-direction is perpendicular to the seismically defined flow-path of the MTD to the north-east. At Site UBGH1-14, the log-data suggest two zones with preferred fracture orientations (top: ∼250°, bottom: ∼130°), indicating flow-directions to the north-east for the top zone, and north-west for the bottom zone. The fracture patterns may indicate post-depositional sedimentation that gave rise to a preferred fracturing possibly linked to dewatering pathways. Alternatively, fractures may be related to the formation of pressure-ridges common within MTD units. For the interval of observed MTD units, the resistivity and P-wave velocity log-data yield gas hydrate concentrations up to ∼10% at Site UBGH1-4 and ∼25% at Site UBGH1-14 calculated using traditional isotropic theories such as Archie's law or effective medium modeling. However, accounting for anisotropic effects in the calculation to honor observed fracture patterns, the gas hydrate concentration is overall reduced to less than 5%. In contrast, gas hydrate was recovered at Site UBGH1-4 near the base of gas hydrate stability zone (GHSZ). Log-data predict gas hydrate concentrations of 10–15% over an interval of 25 m above the base of GHSZ. The sediments of this interval are comprised of the hemipelagic mud and interbedded thin sandy turbidites, which did contain pore-filling gas hydrate as identified from pore-water freshening and core infra-red imaging. Seismically, this unit reveals a coherent parallel bedding character but has overall faint reflection amplitude. This gas-hydrate-bearing interval can be best mapped using a combination of regular seismic amplitude and seismic attributes such as Shale indicator, Parallel-bedding indicator, and Thin-bed indicator.
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    Maize Production in a Changing Climate (2012)
    Elsevier
    In:  Advances in Agronomy, 114 . pp. 1-65.
    Details
    Publication Date: 2020-04-23
    Description: Plant breeding and improved management options have made remarkable progress in increasing crop yields during the past century. However, climate change projections suggest that large yield losses will be occurring in many regions, particularly within sub-Saharan Africa. The development of climate-ready germplasm to offset these losses is of the upmost importance. Given the time lag between the development of improved germplasm and adoption in farmers’ fields, the development of improved breeding pipelines needs to be a high priority. Recent advances in molecular breeding provide powerful tools to accelerate breeding gains and dissect stress adaptation. This review focuses on achievements in stress tolerance breeding and physiology and presents future tools for quick and efficient germplasm development. Sustainable agronomic and resource management practices can effectively contribute to climate change mitigation. Management options to increase maize system resilience to climate-related stresses and mitigate the effects of future climate change are also discussed.
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    Combining impedance inversion and seismic similarity for robust gas hydrate concentration assessments – A case study from the Krishna–Godavari basin, East Coast of India (2012)
    Elsevier
    In:  Marine and Petroleum Geology, 36 (1). pp. 35-49.
    Details
    Publication Date: 2020-07-08
    Description: Gas hydrate saturations were calculated based on Archie's relation and rock-physics modeling utilizing log measurements of electrical resistivity and P-wave velocity through the gas hydrate stability zone (GHSZ) at two sites in the Krishna Godavari (KG) basin off the East Coast of India. Acoustic impedance inversion was then performed around the well sites for regional extrapolation of the borehole data. Well-log based gas hydrate concentration estimates and core data are in general agreement with the seismic impedance inversion results at the individual well sites. However, the correlation with seismic data and thus the confidence in the extrapolation decreases with distance from the well site. To address the general problem of unknown regional confidence limits in the extrapolation and aid in regional gas hydrate assessment analyses, a new approach is introduced by calculating the running-sum of the seismic similarity attribute across the gas hydrate stability zone. The running-sum of the similarity attribute can be used locally on a 2D seismic line or 3D seismic volume for defining the limit of well-data extrapolation around a given well site. By normalizing the running-sum of the similarity attribute from all available 2D seismic data in the KG basin, a regional map was generated yielding effective confidence limits for extrapolation of well-log data. Such maps of regional confidence limits can be used strategically in basin-wide gas hydrate assessments as they provide a measure of probability to find a given gas hydrate concentration, and may also offer a guide for defining a minimum regional spacing between well-sites to address the overall structural complexity of the basin (which is reflected in the similarity of the seismic data).
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    Benthic community changes at the North Siberian margin in response to Atlantic water mass variability since last deglacial times (2012)
    Elsevier
    In:  Marine Micropaleontology, 96-97 . pp. 13-28.
    Details
    Publication Date: 2017-06-21
    Description: The eastward penetration of Atlantic-derived water (ADW) into the Eurasian Basin of the Arctic Ocean was investigated at the western Laptev Sea continental margin for the time since c. 17.6 ka. Using a high-resolution investigation of the lithology, geochemistry, planktic and benthic foraminifers, and ostracods on a sediment core from 270 m water depth major steps in the environmental evolution of the region are recognized. In general, ADW was continuously present in the study area. Between 17.6 and 15.4 ka ADW manifested itself through open-water polynyas and associated upwelling events. Comparison between the Laptev Sea and northern Svalbard shelf using Cassidulina neoteretis allows assuming an unmodified subsurface inflow of ADW within its northern branch between 15.4 and 13.2, which was strongest after 14.7-ka and in line with the overall climate amelioration. A local freshwater event at 13 ka followed by shelf flooding and the establishment of a freshened shelf water mass resulted in an off-shelf displacement of ADW from the studied site as suggested by the disappearance of C. neoteretis between 12 and 7 ka. As evidenced by an abundance peak in Nonion labradoricum, the sea-ice marginal zone was located at the site around 12–11 ka but then shifted northward during the early Holocene warming. Enhanced ADW inflow since 7 ka correlated with climate cooling and southward retreat of the seasonal drift-ice margin. The inflow of ADW during mid–late Holocene differed from deglacial times because of the combined influence of northern and eastern ADW branches.
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    Cyclodysidins A–D, cyclic lipopeptides from the marine sponge-derived Streptomyces strain RV15 (2012)
    Elsevier
    In:  Tetrahedron Letters, 53 (1). pp. 23-29.
    Details
    Publication Date: 2015-07-03
    Description: Four new cyclic lipopeptides, cyclo-(AFA-Ser-Gln-Asn-Tyr-Asn-Ser-Thr), named cyclodysidins A–D, were isolated from the broth culture of Streptomyces strain RV15 associated with the marine sponge Dysidea tupha. The sequences of the amino acid building blocks in the compounds and their structures were determined by 1D- and 2D-NMR techniques and CID-MS/MS experiments. The absolute configurations of all α-amino acids were determined by HPLC analysis after derivatization with Marfey’s reagent and comparison with commercially available reference samples, while those two of the β-amino fatty acids were determined by using racemic and enantiopure reference samples synthetically prepared.
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    On the spatial scale of dispersal in coral reef fishes (2012)
    Wiley
    In:  Molecular Ecology, 21 (23). pp. 5675-5688.
    Details
    Publication Date: 2015-09-14
    Description: Marine biologists have gone through a paradigm shift, from the assumption that marine populations are largely ‘open’ owing to extensive larval dispersal to the realization that marine dispersal is ‘more restricted than previously thought’. Yet, population genetic studies often reveal low levels of genetic structure across large geographic areas. On the other side, more direct approaches such as mark-recapture provide evidence of localized dispersal. To what extent can direct and indirect studies of marine dispersal be reconciled? One approach consists in applying genetic methods that have been validated with direct estimates of dispersal. Here, we use such an approach—genetic isolation by distance between individuals in continuous populations—to estimate the spatial scale of dispersal in five species of coral reef fish presenting low levels of genetic structure across the Caribbean. Individuals were sampled continuously along a 220-km transect following the Mesoamerican Barrier Reef, population densities were estimated from surveys covering 17 200 m2 of reef, and samples were genotyped at a total of 58 microsatellite loci. A small but positive isolation-by-distance slope was observed in the five species, providing mean parent-offspring dispersal estimates ranging between 7 and 42 km (CI 1–113 km) and suggesting that there might be a correlation between minimum/maximum pelagic larval duration and dispersal in coral reef fishes. Coalescent-based simulations indicate that these results are robust to a variety of dispersal distributions and sampling designs. We conclude that low levels of genetic structure across large geographic areas are not necessarily indicative of extensive dispersal at ecological timescales.
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    An (U-Th)/He age for the shallow-marine Wetumpka impact structure, Alabama, USA (2012)
    Wiley
    In:  Meteoritics & Planetary Science, 47 (8). pp. 1243-1255.
    Details
    Publication Date: 2020-07-01
    Description: Single crystal (U-Th)/He dating was applied to 24 apatite and 23 zircon grains from the Wetumpka impact structure, Alabama, USA. This small approximately 5–7.6 km impact crater was formed in a shallow marine environment, with no known preserved impact melt, thus offering a challenge to common geochronological techniques. A mean (U-Th)/He apatite and zircon age of 84.4 ± 1.4 Ma (2σ) was obtained, which is within error of the previously estimated Late Cretaceous impact age of approximately 83.5 Ma. In addition, helium diffusion modeling of apatite and zircon grains during fireball/contact, shock metamorphism, and hydrothermal events was undertaken, to show the influence of these individual thermal processes on resetting (U-Th)/He ages in the Wetumpka samples. This study has shown that the (U-Th)/He geochronological technique has real potential for dating impact structures, especially smaller and eroded impact structures that lack impact melt lithologies.
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    Using the 87Sr/86Sr of modern and paleoseep carbonates from northern Cascadia to link modern fluid flow to the past (2012)
    Elsevier
    In:  Chemical Geology, 334 . pp. 122-130.
    Details
    Publication Date: 2016-01-06
    Description: Most authigenic carbonates previously recovered from the Cascadia slope have 87Sr/86Sr signatures that reflect shallow precipitation in equilibrium with coeval seawater. There is also evidence for carbonate formation supported by fluids that have been modified by reactions with the incoming Juan de Fuca plate (87Sr/86Sr = 0.7071; Teichert et al., 2005) or with terrigenous turbidites (87Sr/86Sr = 0.70975 to 0.71279; Sample et al., 1993). We report on the strontium isotopic composition of carbonates and fluids from IODP Site U1329 and nearby Barkley Canyon (offshore Vancouver Island), which have strontium isotope ratios as low as 0.70539. Whereas the strontium and oxygen isotopic compositions of carbonates from paleoseeps in the uplifted Coast Range forearc indicate formation in ambient bottom seawater, several samples from the Pysht/Sooke Fm. show a 87Sr-depleted signal (87Sr/86Sr = 0.70494 and 0.70511) similar to that of the anomalous Site U1329 and Barkley Canyon carbonates. Our data, when analyzed in the context of published elemental and isotopic composition of these carbonates (Joseph et al., 2012), point to two formation mechanisms: 1) shallow precipitation driven by the anaerobic oxidation of methane (AOM) with δ13C values as low as − 50‰ and contemporaneous 87Sr/86Sr seawater ratios, and 2) carbonate precipitation driven by fluids that have circulated through the oceanic crust, which are depleted in 87Sr. Carbonates formed from the second mechanism precipitate both at depth and at sites of deep-sourced fluid seepage on the seafloor. The 87Sr-depleted carbonates and pore fluids found at Barkley Canyon represent migration of a deep, exotic fluid similar to that found in high permeability conglomerate layers at 188 mbsf of Site U1329, and which may have fed paleoseeps in the Pysht/Sooke Fm. These exotic fluids likely reflect interaction with the 52–57 Ma igneous Crescent Terrane, which supplies fluids with high calcium, manganese and strontium enriched in the non-radiogenic nucleide. Tectonic compression and dehydration reactions then force these fluids updip, where they pick up the thermogenic hydrocarbons and 13C-enriched dissolved inorganic carbon that are manifested in fluids and carbonates sampled at Barkley Canyon and at Site U1329. The Crescent Terrane may have sourced cold seeps in this margin since at least the late Oligocene.
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    Climatic Variability on Decadal to Century Time-Scales (2012)
    Elsevier
    In:  In: The Future of the World’s Climate. , ed. by Henderson-Sellers, A. and McGuffie, K. Elsevier, Amsterdam, The Netherlands, pp. 167-195. ISBN 978-0-12-386917-3
    Details
    Publication Date: 2012-12-05
    Type: Book chapter , NonPeerReviewed
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  • 85
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    The influence of dietary β-glucan, PAMP exposure and Aeromonas salmonicida on apoptosis modulation in common carp (Cyprinus carpio) (2012)
    Elsevier
    In:  Fish & Shellfish Immunology, 33 (4). pp. 846-856.
    Details
    Publication Date: 2020-07-31
    Description: The association between beta-glucan (MacroGard (R)) supplemented feed and apoptosis in immune-related organs of common carp (Cyprinus carpio) was studied using fluorescence microscopy and real-time PCR. In addition the effect of Aeromonas salmonicida, LPS and Poly(I:C) injections on this relationship was evaluated. Whilst acridine orange staining revealed that apoptosis levels were independent of MacroGard (R) and LPS/Poly(1:C) administration or their combination, it was shown that injection with A. salmonicida increased the percentage of apoptotic cells irrespective of the feeding regime. It was apparent that in all the treatments gene expression profiles displayed organ and time dependency. For example no effect was observed at 7 days of MacroGard (R) administration while 25 days of feeding led to increased iNOS expression and differential up-regulation of anti- or pro-apoptotic genes depending on organ. This may indicate differences in NO sensitivity. MacroGard (R) also led to an elevation of pro- as well as anti-apoptotic genes in LPS or Poly(1:C) injected fish, while LPS/Poly(I:C) alone had little effect. A. salmonicida caused enhanced iNOS expression and it is possible that the type of apoptosis pathway induced is organ dependent as Caspase 9 is induced in mid-gut but not in pronephros. These results indicate that MacroGard (R) feeding alone or in combination with other pathogenic factors did not induce significant apoptosis in immune organs
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  • 86
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    Ocean acidification weakens the structural integrity of coralline algae (2012)
    Wiley
    In:  Global Change Biology, 18 (9). pp. 2804-2812.
    Details
    Publication Date: 2018-05-17
    Description: The uptake of anthropogenic emission of carbon dioxide is resulting in a lowering of the carbonate saturation state and a drop in ocean pH. Understanding how marine calcifying organisms such as coralline algae may acclimatize to ocean acidification is important to understand their survival over the coming century. We present the first long-term perturbation experiment on the cold-water coralline algae, which are important marine calcifiers in the benthic ecosystems particularly at the higher latitudes. Lithothamnion glaciale, after three months incubation, continued to calcify even in undersaturated conditions with a significant trend towards lower growth rates with increasing pCO2. However, the major changes in the ultra-structure occur by 589 μatm (i.e. in saturated waters). Finite element models of the algae grown at these heightened levels show an increase in the total strain energy of nearly an order of magnitude and an uneven distribution of the stress inside the skeleton when subjected to similar loads as algae grown at ambient levels. This weakening of the structure is likely to reduce the ability of the alga to resist boring by predators and wave energy with severe consequences to the benthic community structure in the immediate future (50 years).
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  • 87
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    Holocene cooling culminates in sea ice oscillations in Fram Strait (2012)
    Elsevier
    In:  Quaternary Science Reviews, 47 . pp. 1-14.
    Details
    Publication Date: 2019-09-23
    Description: A reconstruction of Holocene sea ice conditions in the Fram Strait provides insight into the palaeoenvironmental and palaeoceanographic development of this climate sensitive area during the past 8500 years BP. Organic geochemical analyses of sediment cores from eastern and western Fram Strait enable the identification of variations in the ice coverage that can be linked to changes in the oceanic (and atmospheric) circulation system. By means of the sea ice proxy IP25, phytoplankton-derived biomarkers and ice rafted detritus (IRD) increasing sea ice occurrences are traced along the western continental margin of Spitsbergen throughout the Holocene, which supports previous palaeoenvironmental reconstructions that document a general cooling. A further significant ice advance during the Neoglacial is accompanied by distinct sea ice fluctuations, which point to short-term perturbations in either the Atlantic Water advection or Arctic Water outflow at this site. At the continental shelf of East Greenland, the general Holocene cooling, however, seems to be less pronounced and sea ice conditions remained rather stable. Here, a major Neoglacial increase in sea ice coverage did not occur before 1000 years BP. Phytoplankton-IP25 indices (“PIP25-Index”) are used for more explicit sea ice estimates and display a Mid Holocene shift from a minor sea ice coverage to stable ice margin conditions in eastern Fram Strait, while the inner East Greenland shelf experienced less severe to marginal sea ice occurrences throughout the entire Holocene. Highlights ► Biomarker and IRD data give insight into Holocene sea ice conditions in Fram Strait. ► We find increasing sea ice coverage off West Spitsbergen throughout the Holocene. ► Oceanic/atmospheric variability caused Neoglacial sea ice fluctuations. ► Ice conditions along East Greenland shelf remain rather stable until 1000 years BP.
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  • 88
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    Impacts of natural and anthropogenic climate variations on North Pacific plankton in an Earth System Model (2012)
    Elsevier
    In:  Ecological Modelling, 244 . pp. 132-147.
    Details
    Publication Date: 2019-09-23
    Description: The impacts of natural atmospheric variability and anthropogenic climate change on the spatial distribution, seasonality, structure, and productivity of North Pacific plankton groups are investigated by means of an Earth System Model (ESM) that contains a plankton model with variable stoichiometry. The ESM is forced with observed greenhouse gases for the 20th century and with the Intergovernmental Panel on Climate Change A1B Emission Scenario for the 21st century. The impacts of the two main modes of variability – connected with the Aleutian Low (AL) strength and with the North Pacific Oscillation (NPO) – are considered. When the AL is strong, primary productivity and chlorophyll concentrations are higher in the central Pacific, the seasonality of plankton is enhanced, and the classical grazing chain is stimulated, whereas in the Alaskan Gyre the model simulates a chlorophyll decrease and a shift toward smaller phytoplankton species. A stronger NPO increases productivity and chlorophyll concentration at ∼45°N. In the anthropogenic climate change scenario, simulated sea surface temperature is 4 °C higher with respect to contemporary conditions, leading to reduced mixing and nutrient supply at middle-subpolar latitudes. The seasonal phytoplankton bloom is reduced and occurs one month earlier, the flow of carbon to the microbial loop is enhanced, and phytoplanktonic stoichiometry is nutrient-depleted. Primary productivity is enhanced at subpolar latitudes, due to increased ice-free regions and possibly to temperature-related photosynthesis stimulation. This study highlights that natural climate variability may act alternatively to strengthen or to weaken the human-induced impacts, and that in the next decades it will be difficult to distinguish between internal and external climate forcing on North Pacific plankton groups. Highlights ► A plankton model with variable stoichiometry has been used in a coupled climate study. ► Natural climate variations modify North Pacific plankton biomass by 10–30% while a warming scenario decreases primary production up to 50%. ► DOC production and the microbial foodweb will be favored in a warmer North Pacific. ► Positive phases of natural fluctuations counteract the impacts of global warming. ► Natural and anthropogenic impacts are distinguishable only in the second part of the 21st century.
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  • 89
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    Assessing the effect of food and light on Calanus sinicus swimming behavior through video-recording experiments (2012)
    Elsevier
    In:  Journal of Experimental Marine Biology and Ecology, 422-423 . pp. 14-19.
    Details
    Publication Date: 2017-07-11
    Description: The copepod Calanus sinicus is a common and abundant species in the shelf waters of the western North Pacific from Japan to Vietnam, and is a main food source for crucial fish species. This study examined the effect of food and light on the swimming behavior of this species. The swimming activity was assessed by using 2 approaches that focused on the dynamics of swimming states and the statistical properties of their trajectories. We discovered that the complexity of swimming paths was reduced under illuminated conditions, and intensified in the absence of food. The swimming activity in such conditions was characterized by a less tortuous shape of trajectories, a lower instantaneous swimming velocity, and a lower recurrence of extreme events. In addition, the entropy of swimming paths decreased when food was included, and the minimal entropy was reached in dark conditions and presence of food, indicating predictable behavior. A general increase in swimming activity was dominated by the slow swimming state. The variations in the swimming activity of adult females exhibited an adaptive pattern that allowed maximizing the exploitation of the three-dimensional, and generally diluted environment that the copepods inhabit, as well as limiting the risk of the predation. ⺠We used robust numerical techniques to identify behavioral patterns of C. sinicus. ⺠The light and food availability plays key role in C. sinicus. ⺠C. Sinicus exhibits an adaptive strategy for feeding success and minimize risk. ⺠Mechanistic understanding of Calanus sinicus feeding ecology.
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  • 90
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    Impacts of ocean warming and acidification on the larval development of the barnacle Amphibalanus improvisus (2012)
    Elsevier
    In:  Journal of Experimental Marine Biology and Ecology, 420-421 . pp. 48-55.
    Details
    Publication Date: 2019-09-23
    Description: The world's oceans are warming and becoming more acidic. Both stressors, singly or in combination, impact marine species, and ensuing effects might be particularly serious for early life stages. To date most studies have focused on ocean acidification (OA) effects in fully marine environments, while little attention has been devoted to more variable coastal ecosystems, such as the Western Baltic Sea. Since natural spatial and temporal variability of environmental conditions such as salinity, temperature or pCO(2) impose more complex stresses upon organisms inhabiting these habitats, species can be expected to be more tolerant to OA (or warming) than fully marine taxa. We present data on the variability of salinity, temperature and pH within the Kiel Fjord and on the responses of the barnacle Amphibalanus improvisus from this habitat to simulated warming and OA during its early development. Nauplii and cyprids were exposed to different temperature (12, 20 and 27 degrees C) and pCO(2) (nominally 400, 1250 and 3250 mu atm) treatments for 8 and 4 weeks, respectively. Survival, larval duration and settlement success were monitored. Warming affected larval responses more strongly than OA. Increased temperatures favored survival and development of nauplii but decreased survival of cyprids. OA had no effect upon survival of nauplii but enhanced their development at low (12 degrees C) and high (27 degrees C) temperatures. In contrast, at the intermediate temperature (20 degrees C), nauplii were not affected even by 3250 mu atm pCO(2). None of the treatments significantly affected settlement success of cyprids. These experiments show a remarkable tolerance of A. improvisus larvae to 1250 mu atm pCO(2), the level of OA predicted for the end of the century
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  • 91
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    Fishing industry borrows from natural capital at high shadow interest rates (2012)
    Elsevier
    In:  Ecological Economics, 82 . pp. 45-52.
    Details
    Publication Date: 2019-09-23
    Description: Fish stocks can be considered as natural capital stocks providing harvestable fish. Fishing at low stock sizes means borrowing from the natural asset. While fishing a particular quantity generates immediate profits and income, an interest rate has to be paid in terms of foregone future fishing income, as the fish stock's reproductive capacity remains low and fishing costs stay high. In this paper we propose to apply the concept of shadowinterest rate to quantify the degree of overfishing. It incorporates the relevant biological and economic information and compares across fish stocks.We calculate the shadow interest rates for 13major European fish stocks and find these rates to range from10% tomore than 200%. The concept of the shadow interest rate can be used to make the economic consequences of overfishing transparent and to evaluate the profitability of shortterm catch reductions as investments in natural capital stocks.
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  • 92
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    Shallow anatomy of a continent–ocean transition zone in the northern South China Sea from multichannel seismic data (2012)
    Elsevier
    In:  Tectonophysics, 554-557 . pp. 18-29.
    Details
    Publication Date: 2019-09-23
    Description: The Cenozoic tectonic evolution of the South China Sea is reflected in diverse tectonic processes including continental rifting, seafloor spreading, subduction, terrane collision and strike-slip fault movement. A continent-ocean transition zone in the northern South China Sea caused by the lithospheric extension when the continent underwent break-up, rifting and later seafloor spreading, is clearly imaged in the multi-channel seismic data presented in this study. The morphological units of the continent-ocean transition zone are the rift-depression, the volcanic zone and tilted fault blocks. The volcanic zone represents a highest extension zone within the continent-ocean transition zone and is mainly distributed in the southern slope uplift zone along the northern passive margin of the South China Sea. The large listric-normal faults bounding the Dongsha Rise and Baiyun Sag are evidenced in the seismic image. The passive margin in the northern South China Sea underwent the wide-rift to narrow-rift process in the transition zone as inferred from the relation between the surface heat flow and initial rifted crustal thickness. The continent-ocean transition zone in the continental margin of the South China Sea is consistent with high heat flow zone (average 90 mW.m(-2)) observed in the previous heat flow measurements and at ODP Site 1148, and is manifested in a sharp change of the P-wave velocity. The rifted margin of the South China Sea is a non-typical magma poor passive margin or an intermediary form between the Iberian-type non-volcanic and the Greenland-type volcanic margin compared to the world's typical passive margins
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  • 93
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    Controls on organic carbon and molybdenum accumulation in Cretaceous marine sediments from the Cenomanian–Turonian interval including Oceanic Anoxic Event 2 (2012)
    Elsevier
    In:  Chemical Geology, 324-325 . pp. 28-45.
    Details
    Publication Date: 2019-09-24
    Description: This study investigates the controls on organic carbon and molybdenum (Mo) accumulation in sediments deposited within the Western Interior Seaway across the Cenomanian–Turonian boundary interval (94.34–93.04 Ma) including Oceanic Anoxic Event 2 (OAE2). Carbon fluxes to the sediment–water interface (reflecting changes in primary productivity) and bottom-water oxygen concentrations (reflecting preservation effects) are reconstructed from field data and used to constrain a benthic model that simulates the geochemistry of unconsolidated sediments as they were deposited. The results show that increased availability of reactive iron prevents Mo sequestration as thiomolybdate (MoS42 −) during OAE2 (O2 ~ 105 μM) by (i) inhibiting sulfate reduction, and (ii) buffering any free sulfide that becomes available. In the post-OAE2 period (O2 ~ 50 μM), Mo accumulation is favored by a large reduction in iron flux. Importantly, this occurs in parallel with oxygenated bottom waters and high rates of aerobic carbon degradation in the surface sediments, implying that elevated Mo burial fluxes in ancient marine facies do not necessarily reflect euxinic or even anoxic conditions within the water column. Our findings suggest that both an increase in production and preservation lead to enrichment in organic carbon in the Western Interior Seaway. More generally, the results demonstrate that a careful consideration of the coupling between iron, carbon and oxygen cycles during the early stages of diagenesis is critical for interpreting geochemical proxies in modern and ancient settings.
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  • 94
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    Synergistic effects of ocean acidification and warming on overwintering pteropods in the Arctic (2012)
    Wiley
    In:  Global Change Biology, 18 (12). pp. 3517-3528.
    Details
    Publication Date: 2018-05-17
    Description: Ocean acidification and warming will be most pronounced in the Arctic Ocean. Aragonite shell-bearing pteropods in the Arctic are expected to be among the first species to suffer from ocean acidification. Carbonate undersaturation in the Arctic will first occur in winter and because this period is also characterized by low food availability, the overwintering stages of polar pteropods may develop into a bottleneck in their life cycle. The impacts of ocean acidification and warming on growth, shell degradation (dissolution), and mortality of two thecosome pteropods, the polar Limacina helicina and the boreal L. retroversa, were studied for the first time during the Arctic winter in the Kongsfjord (Svalbard). The abundance of L. helicina and L. retroversa varied from 23.5 to 120 ind m−2 and 12 to 38 ind m−2, and the mean shell size ranged from 920 to 981 μm and 810 to 823 μm, respectively. Seawater was aragonite-undersaturated at the overwintering depths of pteropods on two out of ten days of our observations. A 7-day experiment [temperature levels: 2 and 7 °C, pCO2 levels: 350, 650 (only for L. helicina) and 880 μatm] revealed a significant pCO2 effect on shell degradation in both species, and synergistic effects between temperature and pCO2 for L. helicina. A comparison of live and dead specimens kept under the same experimental conditions indicated that both species were capable of actively reducing the impacts of acidification on shell dissolution. A higher vulnerability to increasing pCO2 and temperature during the winter season is indicated compared with a similar study from fall 2009. Considering the species winter phenology and the seasonal changes in carbonate chemistry in Arctic waters, negative climate change effects on Arctic thecosomes are likely to show up first during winter, possibly well before ocean acidification effects become detectable during the summer season.
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  • 95
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    Changes in N:P stoichiometry influence taxonomic composition and nutritional quality of phytoplankton in the Peruvian upwelling (2012)
    Elsevier
    In:  Journal of Sea Research, 73 . pp. 74-85.
    Details
    Publication Date: 2020-10-16
    Description: Inorganic dissolved macronutrient (nitrogen, N, and phosphorus, P) supply to surface waters in the eastern tropical South Pacific is influenced by expanding oxygen minimum zones, since N loss occurs due to microbial processes under anoxic conditions while P is increasingly released from the shelf sediments. To investigate the impact of decreasing N:P supply ratios in the Peruvian Upwelling, we conducted nutrient manipulation experiments using a shipboard mesocosm setup with a natural phytoplankton community. In a first experiment, either N or P or no nutrients were added with mesozooplankton present or absent. In a second experiment, initial nutrient concentrations were adjusted to four N:P ratios ranging from 2.5 to 16 using two "high N" and two "high P" levels in combination (i.e., +N, +P, +N and P, no addition). Over six and seven days, respectively, microalgal biomass development as well as nutrient uptake was monitored. Phytoplankton biomass strongly responded to N addition, in both mesozooplankton-grazed and not grazed treatments. The developing diatom bloom in the "high N" exceeded that in the "low N" treatments by a factor of two. No modulation of the total biomass by P-addition was observed, however, species-specific responses were more variable. Notably, some organisms were able to benefit from low N:P fertilization ratios, especially Heterosigma sp. and Phaeocystis globosa which are notorious for forming blooms that are toxic or inadequate for mesozooplankton nutrition. After the decline of the diatom bloom, the relative contribution of unsaturated fatty acid to the lipid content of seston was positively correlated to diatom biomass in the peak bloom, indicating that positive effects of diatom blooms on food quality of the protist community to higher trophic levels remain even after the phytoplankton biomass was incorporated by grazers. Our results indicate an overall N-limitation of the system, especially in the case of dominating diatoms, which were able to immediately utilize the available nitrate (within two days) and develop a biomass maximum within three days of incubation. After the decline of diatom biomass, detection of the cyanobacterial marker pigment aphanizophyll indicated the occurrence of diazotrophs, especially in those enclosures initially provided with high N supply. This was surprising, as diazotrophs are thought to play a role in compensating to some extent the N deficit above OMZs in the succession of phytoplankton after an upwelling event
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  • 96
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    Hydrocarbon leakage through focused fluid flow systems in continental margins (2012)
    Elsevier
    In:  Marine Geology, 332/334 . pp. 1-3.
    Details
    Publication Date: 2019-09-23
    Description: Transport of liquid and gaseous hydrocarbons through focused fluid flow systems is a widespread process in continental margins and sedimentary basins, which is gaining increased attention in the assessment of geohazards, environment conservation, and securing fossil energy resources. Studying the abundance, distribution and drivers for this process is crucial for understanding its role in 1) the dynamics of gas hydrate accumulation and destabilization, 2) submarine slope stability and related tsunamis, 3) the plethora of chemosynthetic benthic ecosystems that develop in deep seep sites, and 4) the input of greenhouse gases (e.g. methane) into the ocean/atmosphere system, which may influence the atmospheric carbon budget and Earth's paleo- and present climate. New ocean exploration tools provide ever more data and improve our understanding of these systems. However, the subject still suffers from a lack of interdisciplinary knowledge dissemination. The ongoing international debate about the timing and the processes that control fluid expulsion in sedimentary basins is fuelled by their implications for structural and petroleum geology. Because fluids expelled at cold seeps originate at depth they represent open windows into the underlying petroleum systems and are valuable indicators for the reservoir systems. They may also help in deciphering past and predicting future climate change because worldwide release of large amounts of fluids may have an impact on the chemistry of the ocean and atmosphere. Highlights ► Special issue on hydrocarbon leakage through focused fluid flow systems. ► Imaging and interpretation of gas migration and flow structures. ► Polygonal fault systems and their implications on fluid and hydrocarbon migration. ► Ecosystems, methane-derived carbonates and geochemistry of seeps. ► Petroleum systems, thermogenic gas release, and Cenozoic hyper-thermal events.
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  • 97
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    Resource allocation and extracellular acid–base status in the sea urchin Strongylocentrotus droebachiensis in response to CO2 induced seawater acidification (2012)
    Elsevier
    In:  Aquatic Toxicology, 110-111 . pp. 194-207.
    Details
    Publication Date: 2017-12-12
    Description: Anthropogenic CO2 emission will lead to an increase in seawater pCO(2) of up to 80-100 Pa (800-1000 mu atm) within this century and to an acidification of the oceans. Green sea urchins (Strongylocentrotus droebachiensis) occurring in Kattegat experience seasonal hypercapnic and hypoxic conditions already today. Thus, anthropogenic CO2 emissions will add up to existing values and will lead to even higher pCO(2) values 〉200 Pa (〉2000 mu atm). To estimate the green sea urchins' potential to acclimate to acidified seawater, we calculated an energy budget and determined the extracellular acid base status of adult S. droebachiensis exposed to moderately (102-145 Pa, 1007-1431 mu atm) and highly (284-385 Pa, 2800-3800 mu atm) elevated seawater pCO(2) for 10 and 45 days. A 45-day exposure to elevated pCO(2) resulted in a shift in energy budgets, leading to reduced somatic and reproductive growth. Metabolic rates were not significantly affected, but ammonium excretion increased in response to elevated pCO(2). This led to decreased O:N ratios. These findings suggest that protein metabolism is possibly enhanced under elevated pCO(2) in order to support ion homeostasis by increasing net acid extrusion. The perivisceral coelomic fluid acid-base status revealed that S. droebachiensis is able to fully (intermediate pCO(2)) or partially (high pCO(2)) compensate extracellular pH (pH(e)) changes by accumulation of bicarbonate (maximum increases 2.5 mM), albeit at a slower rate than typically observed in other taxa (10-day duration for full pH(e) compensation). At intermediate pCO(2), sea urchins were able to maintain fully compensated pH(e) for 45 days. Sea urchins from the higher pCO(2) treatment could be divided into two groups following medium-term acclimation: one group of experimental animals (29%) contained remnants of food in their digestive system and maintained partially compensated pH(e) (+2.3 mM HCO3-), while the other group (71%) exhibited an empty digestive system and a severe metabolic acidosis (-0.5 pH units, -2.4 mM HCO3-). There was no difference in mortality between the three pCO(2) treatments. The results of this study suggest that S. droebachiensis occurring in the Kattegat might be pre-adapted to hypercapnia due to natural variability in pCO(2) in its habitat. We show for the first time that some echinoderm species can actively compensate extracellular pH. Seawater pCO(2) values of 〉200 Pa, which will occur in the Kattegat within this century during seasonal hypoxic events, can possibly only be endured for a short time period of a few weeks. Increases in anthropogenic CO2 emissions and leakages from potential sub-seabed CO2 storage (CCS) sites thus impose a threat to the ecologically and economically important species S. droebachiensis.
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    Rebuilding fish stocks and changing fisheries management, a major challenge for the Common Fisheries Policy reform in Europe (2012)
    Elsevier
    In:  Ocean & Coastal Management, 70 . pp. 1-3.
    Details
    Publication Date: 2019-09-23
    Description: In the European Union (EU), subsidies to the fishing industry and lack of compliance and enforcement of fishing regulations have led to a chronic overcapacity and a general decline of commercial fish stocks. The entire fisheries sector (extractive fishing, fish canning and commercialization subsectors) is still affected, with all directly and indirectly employed people being impacted by the overfishing problem. However, fish populations could strongly increase and generate more economic output if they were left for only a few years under less fishing pressure. The papers published in this Special Issue are the products of recent research conducted by European fisheries scientists, economists, and lawyers. A window of opportunity for change is currently open under the current Common Fisheries Policy (CFP) reform. This Special Issue is an attempt to stimulate the debate by providing new findings and formulating new proposals to rebuild stocks, strengthen ecosystems resilience and better manage EU fisheries. The Special Issue consists of eight papers dealing with relevant biological and economic aspects of the management of European fisheries. Together these papers show that the EU fish stocks are under high fishing pressure and that their recovery will generate not only environmental or ecosystem benefits but also greater profitability for the fisheries sector. Highlights: ► Subsidies, lack of compliance and enforcement have lead to a decline of fish stocks. ► The fisheries sector is affected by the overfishing problem. ► The Special Issue provides valuable papers for the next Common Fisheries Policy reform.
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    Crustal constraint through complete model space screening for diverse geophysical datasets facilitated by emulation (2012)
    Elsevier
    In:  Tectonophysics, 572/573 . pp. 47-63.
    Details
    Publication Date: 2019-09-23
    Description: Deep crustal constraint is often carried out using deterministic inverse methods, sometimes using seismic refraction, gravity and electromagnetic datasets in a complementary or "joint" scheme. With increasingly powerful parallel computer systems it is now possible to apply joint inversion schemes to derive an optimum model from diverse input data. These methods are highly effective where the uncertainty in the system is small. However, given the complex nature of these schemes it is often difficult to discern the uniqueness of the output model given the noise in the data, and the application of necessary regularization and weighting in the inversion process means that the extent of user prejudice pertaining to the final result may be unclear. We can rigorously address the subject of uncertainty using standard statistical tools but these methods also become less feasible if the prior model space is large or the forward simulations are computationally expensive. We present a simple Monte Carlo scheme to screen model space in a fully joint fashion, in which we replace the forward simulation with a fast and uncertainty-calibrated mathematical function, or emulator. This emulator is used as a proxy to run the very large number of models necessary to fully explore the plausible model space. We develop the method using a simple synthetic dataset then demonstrate its use on a joint data set comprising first-arrival seismic refraction. MT and scalar gravity data over a diapiric salt body. This study demonstrates both the value of a forward Monte Carlo approach (as distinct from a search-based or conventional inverse approach) in incorporating all kinds of uncertainty in the modelling process, exploring the entire model space, and shows the potential value of applying emulator technology throughout geophysics. Though the target here is relatively shallow, the methodology can be readily extended to address the whole crust.
    Type: Article , PeerReviewed
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    Thermochronological record of thrusting and strike-slip faulting along the Giudicarie fault system (Alps, Northern Italy) (2012)
    Elsevier
    In:  Tectonophysics, 579 . pp. 118-130.
    Details
    Publication Date: 2016-06-15
    Description: The Giudicarie fault system represents the central, approximately NE–SW-trending segment of the Periadriatic fault system. Based on new fission track data the near surface evolution of the units bordering the Giudicarie fault system (GFS) is analysed. New and published zircon fission track (ZFT) data are compiled in an age-contour map of the area, and depict some first order features of cooling and exhumation pattern. Out of the three main Permian plutons located in the footwall of the GFS, the northern (Brixen pluton) and southernmost (Kreuzberg pluton) yielded ZFT ages of about 100 Ma, while the intermediate Ifinger pluton cooled through the zircon partial annealing zone only in the Miocene. The Ifinger granodiorite overthrusts the Southalpine basement and the Permian rocks of the Athesian Volcanic District along the NW dipping brittle Naif fault. Across this thrust an important age jump from Miocene to Permian ZFT ages is observed, suggesting that the deformation has jumped towards the southeast, thus deactivating the related segment of the GFS. The most eye-catching feature of the age-contour map is the corridor of young, Miocene ZFT ages from small tonalitic intrusions along the Northern Giudicarie fault. This corridor connects Early Miocene (17–23 Ma) ZFT ages of the NE-Adamello with the Middle–Late Miocene (19–9 Ma) ZFT ages of the Meran–Mauls basement and the western Tauern window and provides evidence for a polyphase deformation along the GFS. A three-step evolution model is proposed for the GFS: (a) shearing of the northern rim of the Adamello batholith along the dextral strike slip Periadriatic fault system; (b) bending of the central part of the fault to a NE direction together with the adjacent intrusive rocks; (c) Dissection of the bend part (Meran–Mauls fault) by the sinistral transpressive Northern Giudicarie fault and exhumation of small tonalitic bodies along this structure. Highlights ► Different exhumation history for Permian intrusions along the Giudicarie fault system. ► Very consistent ZFT ages of ~ 15 Ma for the entire Meran–Mauls basement. ► Corridor of Miocene zircon fission track ages along the Giudicarie fault system. ► Evidence for a polyphase deformation along the Giudicarie fault system.
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