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Patient Zero: The Triangle

When you're fighting off a cold or flu, it's easy to imagine the battle is being waged solely inside the confines of your body. 

But in order to spread, pathogens rely on nearly every aspect of our shared societies. Food and drink, social customs, our proximity to animals, urban design, income inequality: The science of epidemiology connects them all. 

Patient Zero investigates the spaces where people and pathogens collide. It is a story about Lyme disease, but it is also a story about uncertainty, and what to do in the face of it. 




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Glen Campbell's "Wichita Lineman" reached number one 50 years ago

Glen Campbell's "Wichita Lineman" reached number one on the Billboard Country chart 50 years ago today. Jimmy Webb, who wrote the song, told Songfacts that the inspiration was an image he witnessed while driving one day.




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How Prince worked his magic on the Bangles' 'Manic Monday'

In the 1980s, Prince wrote one of the Bangles' biggest hits, 'Manic Monday.' Now, The Prince Estate has released the demo version of the track as part of the artist's posthumous album, Originals.




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Lauren Daigle’s anthem 'Then I Will' brings Bonhoeffer’s faith, sacrifice to life in new film (exclusive)

Grammy Award-winning artist Lauren Daigle has written and recorded a powerful end-title track for the new film “Bonhoeffer: Pastor. Spy. Assassin” declaring obedience to God’s calling, even in the face of death. 




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Ohio State Basketball Struggles To Survive; Story Of A Star That Never Was

This week on After The Score the guys talk about the slim chance Ohio State basketball has at making the NCAA Tournament, and how the hopes may be all but over before they even get off the air.




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Out of the data jungle: More interoperability for resilient supply chains

By Philipp Pfister, Chief Customer Experience Officer at Transporeon (a Trimble company)

There’s no denying that the transport sector is a prominent cog across most global industries. As the saying goes, “There is no production without procurement logistics, and no trade without delivery traffic.”




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JCS: N. Korea Likely Fired ICBM at High Angle

[Inter-Korea] :
South Korea’s Joint Chiefs of Staff(JCS) suspects that North Korea fired an intercontinental ballistic missile(ICBM) toward the East Sea on Thursday morning.  The JCS said it detected the launch from the Pyongyang area around 7:10 a.m., adding the missile was fired at a steep angle and flew about ...

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Rosé and Bruno Mars' 'APT.' Reaches No. 2 on UK Official Singles Chart

[Culture] :
BLACKPINK member Rosé's latest collab with American pop star Bruno Mars, "APT.," has reached number two on the United Kingdom's Official Singles Chart, the highest ranking on the chart by a female K-pop artist. After debuting at number four on October 25, "APT." jumped two spots to number two in the ...

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Stray Kids to release new single featuring Charlie Puth

Stray Kids is set to release a new digital single featuring global pop star Charlie Puth.The new single “Lose My Breath” will drop on May 10. Charlie Puth is a familiar name in the K-pop industry and...

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Astro's Jinjin drops new single in remembrance of Moonbin

Jinjin of Astro has dropped a single in remembrance of bandmate Moonbin who passed away one year ago.The digital single “Fly”, which features Moonbin’s voice, was co-written by the two members of...

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Sunmi to release new single next month

Sunmi is set to drop a new single in June. The new single has been written by the singer herself, and she recently finished shooting the music video in Croatia.The upcoming single comes around eight months after...

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Jennie to Relase New Single


Jennie, a member of K-pop girl group Blackpink, will be releasing a new single this week. Titled, “Mantra,” the new release will drop Oct. 11. The highly anticipated comeback comes...

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Google Easter Eggs: Sweet Treats Hidden in Plain Sight

Google is home to a ton of super fun hidden Easter eggs you can check out right from your browser. Go ahead, try a couple. You won't be disappointed.





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Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning

Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data.




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The single-atom R1: a new optimization method to solve crystal structures

A crystal structure with N atoms in its unit cell can be solved starting from a model with atoms 1 to j − 1 being located. To locate the next atom j, the method uses a modified definition of the traditional R1 factor where its dependencies on the locations of atoms j + 1 to N are removed. This modified R1 is called the single-atom R1 (sR1), because the locations of atoms 1 to j − 1 in sR1 are the known parameters, and only the location of atom j is unknown. Finding the correct position of atom j translates thus into the optimization of the sR1 function, with respect to its fractional coordinates, xj, yj, zj. Using experimental data, it has been verified that an sR1 has a hole near each missing atom. Further, it has been verified that an algorithm based on sR1, hereby called the sR1 method, can solve crystal structures (with up to 156 non-hydrogen atoms in the unit cell). The strategy to carry out this calculation has also been optimized. The main feature of the sR1 method is that, starting from a single arbitrarily positioned atom, the structure is gradually revealed. With the user's help to delete poorly determined parts of the structure, the sR1 method can build the model to a high final quality. Thus, sR1 is a viable and useful tool for solving crystal structures.




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The smearing function for a multi-slit very small angle neutron scattering instrument

This study validates the feasibility of applying a smearing method for the multi-slit very small angle neutron scattering instrument (MS-VSANS) at the China Spallation Neutron Source. Through analysis limited to a vertical range of 8 mm, the study demonstrates consistency between the predicted smearing function and experimental data, marking a significant milestone in utilizing real data from such instruments.




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Grazing-incidence small-angle neutron scattering at high pressure (HP-GISANS): a soft matter feasibility study on grafted brush films

We present a demonstration of high-pressure grazing-incidence small-angle neutron scattering for soft matter thin films. The results suggest changes in water reorganization at different pressures.




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Improving the reliability of small- and wide-angle X-ray scattering measurements of anisotropic precipitates in metallic alloys using sample rotation

Rotations of small- and wide-angle X-ray scattering samples during acquisition are shown to give a drastic improvement in the reliability of the characterization of anisotropic precipitates in metallic alloys.




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Small-angle scattering and dark-field imaging for validation of a new neutron far-field interferometer

A neutron far-field interferometer is under development at NIST with the aim of enabling a multi-scale measurement combining the best of small-angle neutron scattering (SANS) and neutron imaging and tomography. We use the close relationship between SANS, ultra-SANS, spin-echo SANS and dark-field imaging and measurements of monodisperse spheres as a validation metric, highlighting the strengths and weaknesses of each of these neutron techniques.




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Grazing-incidence small-angle neutron scattering at high pressure (HP-GISANS): a soft matter feasibility study on grafted brush films

Grazing-incidence small-angle neutron scattering (GISANS) under pressure (HP-GISANS) at the solid (Si)–liquid (D2O) interface is demonstrated for the pressure-induced lateral morphological characterization of the nanostructure in thin (<100 nm) soft matter films. We demonstrate feasibility by investigating a hydrophobic {poly[(2,2,3,3,4,4,5,5-octafluoro)pentyl methacrylate]} (POFPMA)–hydrophilic {poly[2-(dimethylamino)ethyl methacrylate]} (PDMAEMA) brush mixture of strong incompatibility between the homopolymers, anchored on Si, at T = 45°C for two pressures, P = 1 bar and P = 800 bar. Our GISANS results reveal nanostructural rearrangements with increasing P, underlining P-induced effects in tethered polymer brush layers swollen with bulk solvent.




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Small-angle scattering and dark-field imaging for validation of a new neutron far-field interferometer

The continued advancement of complex materials often requires a deeper understanding of the structure–function relationship across many length scales, which quickly becomes an arduous task when multiple measurements are required to characterize hierarchical and inherently heterogeneous materials. Therefore, there are benefits in the simultaneous characterization of multiple length scales. At the National Institute of Standards and Technology, a new neutron far-field interferometer is under development that aims to enable a multi-scale measurement combining the best of small-angle neutron scattering (SANS) and neutron imaging and tomography. Spatially resolved structural information on the same length scales as SANS (0.001–1 µm) and ultra-small-angle neutron scattering (USANS, 0.1–10 µm) will be collected via dark-field imaging simultaneously with regular attenuation radiography (>10 µm). The dark field is analogous to the polarization loss measured in spin-echo SANS (SESANS) and is related to isotropic SANS through a Hankel transform. Therefore, we use this close relationship and analyze results from SANS, USANS, SESANS and dark-field imaging of monodisperse spheres as a validation metric for the interferometry measurements. The results also highlight the strengths and weaknesses of these neutron techniques for both steady-state and pulsed neutron sources. Finally, we present an example of the value added by the spatial resolution enabled by dark-field imaging in the study of more complex heterogeneous materials. This information would otherwise be lost in other small-angle scattering measurements averaged over the sample.




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Improving the reliability of small- and wide-angle X-ray scattering measurements of anisotropic precipitates in metallic alloys using sample rotation

Nanometric precipitates in metallic alloys often have highly anisotropic shapes. Given the large grain size and non-random texture typical of these alloys, performing small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on such samples for determining their characteristics (typically size and volume fraction) results in highly anisotropic and irreproducible data. Rotations of flat samples during SAXS/WAXS acquisitions are presented here as a solution to these anisotropy issues. Two aluminium alloys containing anisotropic precipitates are used as examples to validate the approach with a −45°/45° angular range. Clear improvements can be seen on the SAXS I(q) fitting and the consistency between the different SAXS/WAXS measurements. This methodology results in more reliable measurements of the precipitate's characteristics, and thus allows for time- and space-resolved measurements with higher accuracy.




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The smearing function for a multi-slit very small angle neutron scattering instrument

Besides traditional pinhole geometry, the multi-slit very small angle neutron scattering instrument (MS-VSANS) at the China Spallation Neutron Source also utilizes a multi-slit collimation system to focus neutrons. Using the special focusing structures, the minimum scattering vector magnitude (q) can reach 0.00028 Å−1. The special structures also lead to a significantly different smearing function. By comparing the results of theoretical calculations with experimental data, we have validated the feasibility of a smearing method based on a mature theory for slit smearing. We use the weight-averaged intensity of neutron wavelength as a representative to evaluate the effect from a broad wavelength distribution, concentrating on the effect from the geometry of the multi-slit structures and the detector. The consistency of the theoretical calculation of the smearing function with experimental VSANS scattering profiles for a series of polystyrene standards of different diameters proves the feasibility of the smearing method. This marks the inaugural use of real experimental data from an instrument employing a multi-slit collimation system.




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Influence of device configuration and noise on a machine learning predictor for the selection of nanoparticle small-angle X-ray scattering models

Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202–212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.




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Angle-resolved X-ray emission spectroscopy facility realized by an innovative spectrometer rotation mechanism at SPring-8 BL07LSU

The X-ray emission spectrometer at SPring-8 BL07LSU has recently been upgraded with advanced modifications that enable the rotation of the spectrometer with respect to the scattering angle. This major upgrade allows the scattering angle to be flexibly changed within the range of 45–135°, which considerably simplifies the measurement of angle-resolved X-ray emission spectroscopy. To accomplish the rotation system, a sophisticated sample chamber and a highly precise spectrometer rotation mechanism have been developed. The sample chamber has a specially designed combination of three rotary stages that can smoothly move the connection flange along the wide scattering angle without breaking the vacuum. In addition, the spectrometer is rotated by sliding on a flat metal surface, ensuring exceptionally high accuracy in rotation and eliminating the need for any further adjustments during rotation. A control system that integrates the sample chamber and rotation mechanism to automate the measurement of angle-resolved X-ray emission spectroscopy has also been developed. This automation substantially streamlines the process of measuring angle-resolved spectra, making it far easier than ever before. Furthermore, the upgraded X-ray emission spectrometer can now also be utilized in diffraction experiments, providing even greater versatility to our research capabilities.




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Developing an in situ LED irradiation system for small-angle X-ray scattering at B21, Diamond Light Source

Beamline B21 at the Diamond Light Source synchrotron in the UK is a small-angle X-ray scattering (SAXS) beamline that specializes in high-throughput measurements via automated sample delivery systems. A system has been developed whereby a sample can be illuminated by a focused beam of light coincident with the X-ray beam. The system is compatible with the highly automated sample delivery system at the beamline and allows a beamline user to select a light source from a broad range of wavelengths across the UV and visible spectrum and to control the timing and duration of the light pulse with respect to the X-ray exposure of the SAXS measurement. The intensity of the light source has been characterized across the wavelength range enabling experiments where a quantitative measure of dose is important. Finally, the utility of the system is demonstrated via measurement of several light-responsive samples.




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Mango wiggler as a novel insertion device providing a large and symmetrical imaging field of view

A novel insertion device is introduced, designated as the Mango wiggler, designed for synchrotron radiation (SR) imaging that provides a large field of view. This innovative device is constructed from two orthogonal planar wigglers with a small difference in their period lengths, eliciting the phase difference of the magnetic fields to incrementally transitions from 0 to π/2. Such a configuration enlarges the vertical divergence of the light source, as with the horizontal divergence. The appellation `Mango wiggler' derives from the distinctive mango-shaped contour of its radiation field. A comprehensive suite of theoretical analyses and simulations has been executed to elucidate the radiation properties of the Mango wiggler, employing SPECTRA and Mathematica as calculation tools. In conjunction with the ongoing construction of the High Energy Photon Source in Beijing a practical Mango wiggler device has been fabricated for utilization in SR imaging applications. Theoretical analyses were applied to this particular Mango wiggler to yield several theoretical conclusions, and several simulations were performed according to the measured magnetic field results.




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Revealing the structure of the active sites for the electrocatalytic CO2 reduction to CO over Co single atom catalysts using operando XANES and machine learning

Transition-metal nitro­gen-doped carbons (TM-N-C) are emerging as a highly promising catalyst class for several important electrocatalytic processes, including the electrocatalytic CO2 reduction reaction (CO2RR). The unique local environment around the singly dispersed metal site in TM-N-C catalysts is likely to be responsible for their catalytic properties, which differ significantly from those of bulk or nanostructured catalysts. However, the identification of the actual working structure of the main active units in TM-N-C remains a challenging task due to the fluctional, dynamic nature of these catalysts, and scarcity of experimental techniques that could probe the structure of these materials under realistic working conditions. This issue is addressed in this work and the local atomistic and electronic structure of the metal site in a Co–N–C catalyst for CO2RR is investigated by employing time-resolved operando X-ray absorption spectroscopy (XAS) combined with advanced data analysis techniques. This multi-step approach, based on principal component analysis, spectral decomposition and supervised machine learning methods, allows the contributions of several co-existing species in the working Co–N–C catalysts to be decoupled, and their XAS spectra deciphered, paving the way for understanding the CO2RR mechanisms in the Co–N–C catalysts, and further optimization of this class of electrocatalytic systems.




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Study on the UV FEL single-shot damage threshold of an Au thin film

The damage threshold of an Au-coated flat mirror, one of the reflective optics installed on the FEL-2 beamline of the Dalian Coherent Light Source, China, upon far-UV free-electron laser irradiation is evaluated. The surface of the coating is characterized by profilometer and optical microscope. A theoretical approach of the phenomenon is also presented, by application of conventional single-pulse damage threshold calculations, a one-dimensional thermal diffusion model, as well as finite-element analysis with ANSYS.




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Investigating the missing-wedge problem in small-angle X-ray scattering tensor tomography across real and reciprocal space

Small-angle-scattering tensor tomography is a technique for studying anisotropic nanostructures of millimetre-sized samples in a volume-resolved manner. It requires the acquisition of data through repeated tomographic rotations about an axis which is subjected to a series of tilts. The tilt that can be achieved with a typical setup is geometrically constrained, which leads to limits in the set of directions from which the different parts of the reciprocal space map can be probed. Here, we characterize the impact of this limitation on reconstructions in terms of the missing wedge problem of tomography, by treating the problem of tensor tomography as the reconstruction of a three-dimensional field of functions on the unit sphere, represented by a grid of Gaussian radial basis functions. We then devise an acquisition scheme to obtain complete data by remounting the sample, which we apply to a sample of human trabecular bone. Performing tensor tomographic reconstructions of limited data sets as well as the complete data set, we further investigate and validate the missing wedge problem by investigating reconstruction errors due to data incompleteness across both real and reciprocal space. Finally, we carry out an analysis of orientations and derived scalar quantities, to quantify the impact of this missing wedge problem on a typical tensor tomographic analysis. We conclude that the effects of data incompleteness are consistent with the predicted impact of the missing wedge problem, and that the impact on tensor tomographic analysis is appreciable but limited, especially if precautions are taken. In particular, there is only limited impact on the means and relative anisotropies of the reconstructed reciprocal space maps.




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Comparing single-shot damage thresholds of boron carbide and silicon at the European XFEL

Xray free-electron lasers (XFELs) enable experiments that would have been impractical or impossible at conventional X-ray laser facilities. Indeed, more XFEL facilities are being built and planned, with their aim to deliver larger pulse energies and higher peak brilliance. While seeking to increase the pulse power, it is quintessential to consider the maximum pulse fluence that a grazing-incidence FEL mirror can withstand. To address this issue, several studies were conducted on grazing-incidence damage by soft X-ray FEL pulses at the European XFEL facility. Boron carbide (B4C) coatings on polished silicon substrate were investigated using 1 keV photon energy, similar to the X-ray mirrors currently installed at the soft X-ray beamlines (SASE3). The purpose of this study is to compare the damage threshold of B4C and Si to determine the advantages, tolerance and limits of using B4C coatings.




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A new dual-thickness semi-transparent beamstop for small-angle X-ray scattering

An innovative dual-thickness semi-transparent beamstop designed to enhance the performance of small-angle X-ray scattering (SAXS) experiments is introduced. This design integrates two absorbers of differing thicknesses side by side into a single attenuator, known as a beamstop. Instead of completely stopping the direct beam, it attenuates it, allowing the SAXS detector to measure the transmitted beam through the sample. This approach achieves true synchronization in measuring both scattered and transmitted signals and effectively eliminates higher-order harmonic contributions when determining the transmission light intensity through the sample. This facilitates and optimizes signal detection and background subtraction. This contribution details the theoretical basis and practical implementation of this solution at the SAXS station on the 1W2A beamline at the Beijing Synchrotron Radiation Facility. It also anticipates its application at other SAXS stations, including that at the forthcoming High Energy Photon Source, providing an effective solution for high-precision SAXS experiments.




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Redetermination of germacrone type II based on single-crystal X-ray data

The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C15H22O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022). Powder Diffr. 37, 98–104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the inter­molecular inter­actions of germacrone type II.




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Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody

Phenuiviridae nucleoprotein is the main structural and functional component of the viral cycle, protecting the viral RNA and mediating the essential replication/transcription processes. The nucleoprotein (N) binds the RNA using its globular core and polymerizes through the N-terminus, which is presented as a highly flexible arm, as demonstrated in this article. The nucleoprotein exists in an `open' or a `closed' conformation. In the case of the closed conformation the flexible N-terminal arm folds over the RNA-binding cleft, preventing RNA adsorption. In the open conformation the arm is extended in such a way that both RNA adsorption and N polymerization are possible. In this article, single-crystal X-ray diffraction and small-angle X-ray scattering were used to study the N protein of Toscana virus complexed with a single-chain camelid antibody (VHH) and it is shown that in the presence of the antibody the nucleoprotein is unable to achieve a functional assembly to form a ribonucleoprotein complex.




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Validation of electron-microscopy maps using solution small-angle X-ray scattering

The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear resonance methods, but during the last decade, cryogenic transmission electron microscopy (cryo-TEM) has become an equally important tool. As the blotting and flash-freezing of the samples can induce conformational changes, external validation tools are required to ensure that the vitrified samples are representative of the solution. Although many validation tools have already been developed, most of them rely on fully resolved atomic models, which prevents early screening of the cryo-TEM maps. Here, a novel and automated method for performing such a validation utilizing small-angle X-ray scattering measurements, publicly available through the new software package AUSAXS, is introduced and implemented. The method has been tested on both simulated and experimental data, where it was shown to work remarkably well as a validation tool. The method provides a dummy atomic model derived from the EM map which best represents the solution structure.




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Structure determination using high-order spatial correlations in single-particle X-ray scattering

Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns. Here, a method is proposed to determine the 3D structure of a sample by analyzing the double, triple and quadruple spatial correlations in diffraction patterns. This ab initio method can reconstruct the basic shape of an irregular unsymmetric 3D sample without requiring any prior knowledge of the sample. The impact of background and noise on correlations is investigated and corrected to ensure the success of reconstruction under simulated experimental conditions. Additionally, the feasibility of using the correlation-based approach to process incomplete partial diffraction patterns is demonstrated. The proposed method is a variable addition to existing algorithms for 3D reconstruction and will further promote the development and adoption of XFEL single-particle imaging techniques.




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Refining short-range order parameters from the three-dimensional diffuse scattering in single-crystal electron diffraction data

Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0.012 (7) Å for the refinement on diffuse scattering in single-crystal X-ray diffraction data and 0.03 (2) Å for the refinement on the diffuse scattering in single-crystal electron diffraction data. As electron diffraction requires much smaller crystals than X-ray diffraction, this opens up the possibility of refining short-range order parameters in many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.




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The prediction of single-molecule magnet properties via deep learning

This paper uses deep learning to present a proof-of-concept for data-driven chemistry in single-molecule magnets (SMMs). Previous discussions within SMM research have proposed links between molecular structures (crystal structures) and single-molecule magnetic properties; however, these have only interpreted the results. Therefore, this study introduces a data-driven approach to predict the properties of SMM structures using deep learning. The deep-learning model learns the structural features of the SMM molecules by extracting the single-molecule magnetic properties from the 3D coordinates presented in this paper. The model accurately determined whether a molecule was a single-molecule magnet, with an accuracy rate of approximately 70% in predicting the SMM properties. The deep-learning model found SMMs from 20 000 metal complexes extracted from the Cambridge Structural Database. Using deep-learning models for predicting SMM properties and guiding the design of novel molecules is promising.




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A predicted model-aided reconstruction algorithm for X-ray free-electron laser single-particle imaging

Ultra-intense, ultra-fast X-ray free-electron lasers (XFELs) enable the imaging of single protein molecules under ambient temperature and pressure. A crucial aspect of structure reconstruction involves determining the relative orientations of each diffraction pattern and recovering the missing phase information. In this paper, we introduce a predicted model-aided algorithm for orientation determination and phase retrieval, which has been tested on various simulated datasets and has shown significant improvements in the success rate, accuracy and efficiency of XFEL data reconstruction.




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A modified phase-retrieval algorithm to facilitate automatic de novo macromolecular structure determination in single-wavelength anomalous diffraction

The success of experimental phasing in macromolecular crystallography relies primarily on the accurate locations of heavy atoms bound to the target crystal. To improve the process of substructure determination, a modified phase-retrieval algorithm built on the framework of the relaxed alternating averaged reflection (RAAR) algorithm has been developed. Importantly, the proposed algorithm features a combination of the π-half phase perturbation for weak reflections and enforces the direct-method-based tangent formula for strong reflections in reciprocal space. The proposed algorithm is extensively demonstrated on a total of 100 single-wavelength anomalous diffraction (SAD) experimental datasets, comprising both protein and nucleic acid structures of different qualities. Compared with the standard RAAR algorithm, the modified phase-retrieval algorithm exhibits significantly improved effectiveness and accuracy in SAD substructure determination, highlighting the importance of additional constraints for algorithmic performance. Furthermore, the proposed algorithm can be performed without human intervention under most conditions owing to the self-adaptive property of the input parameters, thus making it convenient to be integrated into the structural determination pipeline. In conjunction with the IPCAS software suite, we demonstrated experimentally that automatic de novo structure determination is possible on the basis of our proposed algorithm.




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Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data

Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile.




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Bridging length scales in hard materials with ultra-small angle X-ray scattering – a critical review

Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for in situ characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments.




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A predicted model-aided one-step classification–multireconstruction algorithm for X-ray free-electron laser single-particle imaging

Ultrafast, high-intensity X-ray free-electron lasers can perform diffraction imaging of single protein molecules. Various algorithms have been developed to determine the orientation of each single-particle diffraction pattern and reconstruct the 3D diffraction intensity. Most of these algorithms rely on the premise that all diffraction patterns originate from identical protein molecules. However, in actual experiments, diffraction patterns from multiple different molecules may be collected simultaneously. Here, we propose a predicted model-aided one-step classification–multireconstruction algorithm that can handle mixed diffraction patterns from various molecules. The algorithm uses predicted structures of different protein molecules as templates to classify diffraction patterns based on correlation coefficients and determines orientations using a correlation maximization method. Tests on simulated data demonstrated high accuracy and efficiency in classification and reconstruction.




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Crystal structures of two new high-pressure oxynitrides with composition SnGe4N4O4, from single-crystal electron diffraction

SnGe4N4O4 was synthesized at high pressure (16 and 20 GPa) and high temperature (1200 and 1500°C) in a large-volume press. Powder X-ray diffraction experiments using synchrotron radiation indicate that the derived samples are mixtures of known and unknown phases. However, the powder X-ray diffraction patterns are not sufficient for structural characterization. Transmission electron microscopy studies reveal crystals of several hundreds of nanometres in size with different chemical composition. Among them, crystals of a previously unknown phase with stoichiometry SnGe4N4O4 were detected and investigated using automated diffraction tomography (ADT), a three-dimensional electron diffraction method. Via ADT, the crystal structure could be determined from single nanocrystals in space group P63mc, exhibiting a nolanite-type structure. This was confirmed by density functional theory calculations and atomic resolution scanning transmission electron microscopy images. In one of the syntheses runs a rhombohedral 6R polytype of SnGe4N4O4 could be found together with the nolanite-type SnGe4N4O4. The structure of this polymorph was solved as well using ADT.




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Hard X-ray single-shot spectrometer of PAL-XFEL

A hard X-ray single-shot spectrometer comprising thin, bent Si crystals has been developed for the Pohang Accelerator Laboratory X-ray Free-Electron Laser (XFEL), for detailed analysis of ultrafast 4.5–17 keV XFEL pulses with a high spectral resolution. This instrument facilitates shot-to-shot spectral structure monitoring and optimization of the operating conditions of the XFEL owing to its ability to provide comprehensive data on the spectral properties and fluctuations of self-amplified spontaneous emission, monochromatic and seeded XFEL modes.




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Enhancing the Efficiency of a Wavelength-Dispersive Spectrometer based upon a Slit-less Design Using a Single-Bounce Monocapillary

A slit-less wavelength-dispersive spectrometer design using a single-bounce monocapillary that aligns the sample on the Rowland circle, enhancing photon throughput and maintaining resolution. The compact design supports flexibility and reconfiguration in facilities without complex beamline infrastructure, significantly improving detection efficiency.




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Texture measurements on quartz single crystals to validate coordinate systems for neutron time-of-flight texture analysis

In crystallographic texture analysis, ensuring that sample directions are preserved from experiment to the resulting orientation distribution is crucial to obtain physical meaning from diffraction data. This work details a procedure to ensure instrument and sample coordinates are consistent when analyzing diffraction data with a Rietveld refinement using the texture analysis software MAUD. A quartz crystal is measured on the HIPPO diffractometer at Los Alamos National Laboratory for this purpose. The methods described here can be applied to any diffraction instrument measuring orientation distributions in polycrystalline materials.




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BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and Dmax finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.