{"title":"Abducens nerve avulsion sustained by traumatic brain injury: A lesion not to be underestimated.","authors":"Rayan Fawaz, Mohamed Hedjoudje, Bruno Law-Ye","doi":"10.25259/JNRP_226_2023","DOIUrl":"10.25259/JNRP_226_2023","url":null,"abstract":"","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"9 1","pages":"591-592"},"PeriodicalIF":1.4,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10696310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84086060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
James Birch, Tristan O C Kwan, Peter J Judge, Danny Axford, Pierre Aller, Agata Butryn, Rosana I Reis, Juan F Bada Juarez, Javier Vinals, Robin L Owen, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Tomoyuki Tanaka, Shigeki Owada, Michihiro Sugahara, So Iwata, Allen M Orville, Anthony Watts, Isabel Moraes
{"title":"A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography.","authors":"James Birch, Tristan O C Kwan, Peter J Judge, Danny Axford, Pierre Aller, Agata Butryn, Rosana I Reis, Juan F Bada Juarez, Javier Vinals, Robin L Owen, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Tomoyuki Tanaka, Shigeki Owada, Michihiro Sugahara, So Iwata, Allen M Orville, Anthony Watts, Isabel Moraes","doi":"10.1107/S1600576723006428","DOIUrl":"10.1107/S1600576723006428","url":null,"abstract":"<p><p>Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates <i>in situ</i> crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A<sub>2A</sub> adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 5","pages":"1361-1370"},"PeriodicalIF":6.1,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10543674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41132287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Denys Naumenko, Max Burian, Benedetta Marmiroli, Richard Haider, Andrea Radeticchio, Lucas Wagner, Luca Piazza, Lisa Glatt, Stefan Brandstetter, Simone Dal Zilio, Giorgio Biasiol, Heinz Amenitsch
{"title":"Implication of the double-gating mode in a hybrid photon counting detector for measurements of transient heat conduction in GaAs/AlAs superlattice structures.","authors":"Denys Naumenko, Max Burian, Benedetta Marmiroli, Richard Haider, Andrea Radeticchio, Lucas Wagner, Luca Piazza, Lisa Glatt, Stefan Brandstetter, Simone Dal Zilio, Giorgio Biasiol, Heinz Amenitsch","doi":"10.1107/S1600576723004302","DOIUrl":"https://doi.org/10.1107/S1600576723004302","url":null,"abstract":"Use of the double-gating mode implemented on the modern hybrid photon counting system EIGER2 helps to suppress the influence of beam fluctuations in pump–probe experiments at synchrotron radiation facilities and provides better data quality.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 4","pages":"961-966"},"PeriodicalIF":6.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10405594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9957260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andreas Houben, Yannick Meinerzhagen, Noah Nachtigall, Philipp Jacobs, Richard Dronskowski
{"title":"POWTEX visits POWGEN.","authors":"Andreas Houben, Yannick Meinerzhagen, Noah Nachtigall, Philipp Jacobs, Richard Dronskowski","doi":"10.1107/S1600576723002819","DOIUrl":"https://doi.org/10.1107/S1600576723002819","url":null,"abstract":"<p><p>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<i>g</i> 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 <i>PowderReduceP2D</i> algorithm implemented in <i>Mantid</i> [Arnold <i>et al.</i> (2014). <i>Nucl. Instrum. Methods Phys. Res. A</i>, <b>764</b>, 156-166]. The final part of the data treatment chain, namely a novel multi-dimensional refinement using a modified version of the <i>GSAS-II</i> software suite [Toby & Von Dreele (2013). <i>J. Appl. Cryst.</i><b>46</b>, 544-549], 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 <i>GSAS-II</i>. 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 <i>a</i> and <i>b</i> lattice parameters of BaZn(NCN)<sub>2</sub> crystallizing in <i>Pbca</i> 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, <i>e.g.</i> 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>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 3","pages":"633-642"},"PeriodicalIF":6.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9595272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ricardo Fernández, Gizo Bokuchava, Giovanni Bruno, Itziar Serrano-Muñoz, Gaspar González-Doncel
{"title":"On the dependence of creep-induced dislocation configurations on crystallographic orientation in pure Al and Al-Mg.","authors":"Ricardo Fernández, Gizo Bokuchava, Giovanni Bruno, Itziar Serrano-Muñoz, Gaspar González-Doncel","doi":"10.1107/S1600576723003771","DOIUrl":"https://doi.org/10.1107/S1600576723003771","url":null,"abstract":"<p><p>The peak broadening in neutron diffraction experiments on tensile specimens of pure Al (99.8%) and an Al-Mg alloy pre-deformed at different creep strains is analysed. These results are combined with the kernel angular misorientation of electron backscatter diffraction data from the creep-deformed microstructures. It is found that differently oriented grains possess different microstrains. These microstrains vary with creep strain in pure Al, but not in the Al-Mg alloy. It is proposed that this behaviour can explain the power-law breakdown in pure Al and the large creep strain observed in Al-Mg. The present findings further corroborate a description of the creep-induced dislocation structure as a fractal, predicated on previous work.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 3","pages":"764-775"},"PeriodicalIF":6.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9595269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Three-phase material mapping with incomplete X-ray diffraction spectral information.","authors":"Xuyang Chang, Karine Lavernhe-Taillard, Stéphane Roux, Olivier Hubert","doi":"10.1107/S160057672300331X","DOIUrl":"https://doi.org/10.1107/S160057672300331X","url":null,"abstract":"<p><p>An equiatomic nickel-titanium shape-memory alloy specimen subjected to a uniaxial tensile load undergoes a two-step phase transformation under stress, from austenite (A) to a rhombohedral phase (R) and further to martensite (M) variants. The pseudo-elasticity that goes accompanies the phase transformation induces spatial inhomogeneity. To unravel the spatial distribution of the phases, <i>in situ</i> X-ray diffraction analyses are performed while the sample is under tensile load. However, the diffraction spectra of the R phase, as well as the extent of potential martensite detwinning, are not known. A novel algorithm, based on a proper orthogonal decomposition and incorporating inequality constraints, is proposed in order to map out the different phases and simultaneously yield the missing diffraction spectral information. An experimental case study illustrates the methodology.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 3","pages":"750-763"},"PeriodicalIF":6.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9645106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Martin Roelsgaard, Magnus Kløve, Rasmus Christensen, Andreas D Bertelsen, Nils L N Broge, Innokenty Kantor, Daniel Risskov Sørensen, Ann-Christin Dippel, Soham Banerjee, Martin V Zimmermann, Philipp Glaevecke, Olof Gutowski, Mads Ry Vogel Jørgensen, Bo Brummerstedt Iversen
{"title":"A reactor for time-resolved X-ray studies of nucleation and growth during solvothermal synthesis.","authors":"Martin Roelsgaard, Magnus Kløve, Rasmus Christensen, Andreas D Bertelsen, Nils L N Broge, Innokenty Kantor, Daniel Risskov Sørensen, Ann-Christin Dippel, Soham Banerjee, Martin V Zimmermann, Philipp Glaevecke, Olof Gutowski, Mads Ry Vogel Jørgensen, Bo Brummerstedt Iversen","doi":"10.1107/S1600576723002339","DOIUrl":"https://doi.org/10.1107/S1600576723002339","url":null,"abstract":"<p><p>Understanding the nucleation and growth mechanisms of nanocrystals under hydro- and solvothermal conditions is key to tailoring functional nanomaterials. High-energy and high-flux synchrotron radiation is ideal for characterization by powder X-ray diffraction and X-ray total scattering in real time. Different versions of batch-type cell reactors have been employed in this work, exploiting the robustness of polyimide-coated fused quartz tubes with an inner diameter of 0.7 mm, as they can withstand pressures up to 250 bar and temperatures up to 723 K for several hours. Reported here are recent developments of the <i>in situ</i> setups available for general users on the P21.1 beamline at PETRA III and the DanMAX beamline at MAX IV to study nucleation and growth phenomena in solvothermal synthesis. It is shown that data suitable for both reciprocal-space Rietveld refinement and direct-space pair distribution function refinement can be obtained on a timescale of 4 ms.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 3","pages":"581-588"},"PeriodicalIF":6.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9589926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Vakili, Huijong Han, C. Schmidt, A. Wrona, M. Kloos, I. de Diego, K. Dörner, T. Geng, Chan Kim, F. Koua, D. Melo, M. Rappas, A. Round, E. Round, M. Sikorski, J. Valerio, T. Zhou, K. Lorenzen, J. Schulz
{"title":"Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography","authors":"M. Vakili, Huijong Han, C. Schmidt, A. Wrona, M. Kloos, I. de Diego, K. Dörner, T. Geng, Chan Kim, F. Koua, D. Melo, M. Rappas, A. Round, E. Round, M. Sikorski, J. Valerio, T. Zhou, K. Lorenzen, J. Schulz","doi":"10.1101/2022.11.23.517685","DOIUrl":"https://doi.org/10.1101/2022.11.23.517685","url":null,"abstract":"Time-resolved crystallography enabled the visualization of protein molecular motion during reaction. While light is commonly used to initiate reactions in time-resolved crystallography, only a small number of proteins can in fact be activated by light. However, many biological reactions can be triggered by the interaction of proteins with ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D printed microchannels in conjunction with a micronozzle to study the dynamics of samples in viscous media that can be triggered by diffusive mixing. The device design allows for mixing of ligands and protein crystals in a time window of 2 to 20 seconds. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within the lipidic cubic phase, can be mixed efficiently. The potential use of this approach for time-resolved membrane protein crystallography to support in the development of new drugs is also discussed. Synopsis 3D printed mixing-HVE devices address time-resolved membrane protein crystallography challenges via compact dual-flow LCP injection.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 1","pages":"1038 - 1045"},"PeriodicalIF":6.1,"publicationDate":"2023-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49486907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nicholas Burns, Aly Rahemtulla, Scott Annett, Beatriz Moreno, Stefan Kycia
{"title":"An inclined detector geometry for improved X-ray total scattering measurements.","authors":"Nicholas Burns, Aly Rahemtulla, Scott Annett, Beatriz Moreno, Stefan Kycia","doi":"10.1107/S1600576723001747","DOIUrl":"https://doi.org/10.1107/S1600576723001747","url":null,"abstract":"<p><p>X-ray total scattering measurements are implemented using a digital flat-panel area detector in an inclined geometry and compared with the traditional geometry. The traditional geometry is defined here by the incident X-ray beam impinging on and normal to the center-most pixel of a detector. The inclined geometry is defined here by a detector at a pitch angle α, set to 15° in this case, bisected by the vertical scattering plane. The detector is positioned such that the incident X-ray beam strikes the pixels along the bottom edge and 90° scattered X-rays impinge on the pixels along the top edge. The geometric attributes of the inclined geometry translate into multiple benefits, such as an extension of the measurable scattering range to 90°, a 47% increase in the accessible magnitudes of the reciprocal-space vector <i>Q</i> and a leveling of the dynamic range in the measured total scattering pattern. As a result, a sixfold improvement in signal-to-noise ratios is observed at higher scattering angles, enabling up to a 36-fold reduction in acquisition time. Additionally, the extent of applied modification functions is reduced, decreasing the magnitude of termination ripples and improving the real-space resolution of the pair distribution function <i>G</i>(<i>r</i>). Taken all together, these factors indicate that the inclined geometry produces higher quality data than the traditional geometry, usable for simultaneous Rietveld refinement and total scattering studies.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 2","pages":"510-518"},"PeriodicalIF":6.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9641101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Modelling the structural disorder in trigonal-prismatic coordinated transition metal dichalcogenides.","authors":"Federica Ursi, Simone Virga, Candida Pipitone, Alessandra Sanson, Alessandro Longo, Francesco Giannici, Antonino Martorana","doi":"10.1107/S1600576723001589","DOIUrl":"https://doi.org/10.1107/S1600576723001589","url":null,"abstract":"<p><p>Trigonal-prismatic coordinated transition metal dichalcogenides (TMDCs) are formed from stacked (chalcogen)-(transition metal)-(chalcogen) triple layers, where the chemical bond is covalent within the triple layers and van der Waals (vdW) forces are effective between the layers. Bonding is at the origin of the great interest in these compounds, which are used as 2D materials in applications such as catalysis, electronics, photoelectronics, sensors, batteries and thermoelectricity. This paper addresses the issue of modelling the structural disorder in multilayer TMDCs. The structural model takes into account stacking faults, correlated displacement of atoms and average crystallite size/shape, and is assessed by simulation of the X-ray diffraction pattern and fitting to the experimental data relative to a powdered sample of MoS<sub>2</sub> exfoliated and restacked via lithiation. From fitting, an average crystallite size of about 50 Å, nearly spherical crystallites and a definite probability of deviation from the fully eclipsed atomic arrangement present in the ordered structure are determined. The increased interlayer distance and correlated intralayer and interlayer atomic displacement are attributed to the presence of lithium intercalated in the vdW gap between triple layers (Li/Mo molar ratio of about 0.06). The model holds for the whole class of trigonal-prismatic coordinated TMDCs, and is suitably flexible to take into account different preparation routes.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"56 Pt 2","pages":"502-509"},"PeriodicalIF":6.1,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9271762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}