Algorithm for spin symmetry operation search.

A spin space group provides a suitable way of fully exploiting the symmetry of a spin arrangement with a negligible spin-orbit coupling. There has been a growing interest in applying spin symmetry analysis with the spin space group in the field of magnetism. However, there is no established algorithm to search for spin symmetry operations of the spin space group. This paper presents an exhaustive algorithm for determining the spin symmetry operations of commensurate spin arrangements. The present algorithm searches for spin symmetry operations from the symmetry operations of a corresponding nonmagnetic crystal structure and determines their spin-rotation parts by solving a Procrustes problem. An implementation is distributed under a permissive free software license in spinspg Version 0.1.1, available at https://github.com/spglib/spinspg.

Algorithms for magnetic symmetry operation search and identification of magnetic space group from magnetic crystal structure.

A crystal symmetry search is crucial for computational crystallography and materials science. Although algorithms and implementations for the crystal symmetry search have been developed, their extension to magnetic space groups (MSGs) remains limited. In this paper, algorithms for determining magnetic symmetry operations of magnetic crystal structures, identifying magnetic space-group types of given MSGs, searching for transformations to a Belov-Neronova-Smirnova (BNS) setting, and symmetrizing the magnetic crystal structures using the MSGs are presented. The determination of magnetic symmetry operations is numerically stable and is implemented with minimal modifications from the existing crystal symmetry search. Magnetic space-group types and transformations to the BNS setting are identified by a two-step approach combining space-group-type identification and the use of affine normalizers. Point coordinates and magnetic moments of the magnetic crystal structures are symmetrized by projection operators for the MSGs. An implementation is distributed with a permissive free software license in spglib v2.0.2: https://github.com/spglib/spglib.

High Prevalence of Dysplastic Development of Sacral Vertebral Arches in Pediatric Enuresis.

PURPOSE: This is the first report to compare 3-dimensional computed tomography (3D-CT) images between pediatric patients with enuresis and children without lower urinary tract symptoms who underwent pelvic CT for other reasons. METHODS: Forty-seven children (33 boys and 14 girls) with primary enuresis underwent 3D-CT of sacrococcygeal bones. The control group consisted of 138 children (78 boys and 60 girls) who underwent pelvic CT for other reasons. First, we determined the presence or absence of unfused sacral arches at the L4-S3 levels in both cohorts. Subsequently, we compared the fusion of sacral arches in age- and sex-matched children from these 2 groups. RESULTS: Dysplastic sacral arches, characterized by lack of fusion at 1 or more levels of the S1-3 arches, were observed in nearly all patients in the enuresis group. In the control group (n=138), 54 of 79 children over 10 years old (68%) exhibited fused sacral arches at 3 S1-3 levels. All 11 control children under 4 years old displayed at least 2 unfused sacral arches at the S1-3 levels. In a comparative study of age- and sex-matched patients with enuresis and control children aged 5 to 13 years (n=32 for each group, with 21 boys and 11 girls; mean age, 8.0±2.2 years [range, 5-13 years]), only 1 patient (3%) in the enuresis group exhibited fusion of all S1-3 arches. In contrast, 20 of 32 control group participants (63%) had 3 fused sacral arches (P<0.0001). CONCLUSION: Sacral vertebral arches typically fuse by the age of 10 years. However, in this study, children with enuresis exhibited a significantly elevated prevalence of unfused sacral arches, suggesting that dysplastic development of sacral vertebral arches may play a pathological role in enuresis.

Implementation strategies in phonopy and phono3py.

Scientific simulation codes are public property sustained by the community. Modern technology allows anyone to join scientific software projects, from anywhere, remotely via the internet. The phonopy and phono3py codes are widely used open-source phonon calculation codes. This review describes a collection of computational methods and techniques implemented in these codes and shows their implementation strategies as a whole, aiming to be useful for the community. Some of the techniques presented here are not limited to phonon calculations and may therefore be useful in other areas of condensed matter physics.

LO-mode phonon of KCl and NaCl at 300 K by inelastic x-ray scattering measurements and first principles calculations.

Longitudinal-optical (LO) mode phonon branches of KCl and NaCl were measured using inelastic x-ray scattering (IXS) at 300 K and calculated by the first-principles phonon calculation with the stochastic self-consistent harmonic approximation. Spectral shapes of the IXS measurements and calculated spectral functions agreed well. We analyzed the calculated spectral functions that provide higher resolutions of the spectra than the IXS measurements. Due to strong anharmonicity, the spectral functions of these phonon branches have several peaks and the LO modes along Γ-L paths are disconnected.

Investigation of Superconductivity in Ce-Doped (La,Pr)OBiS2 Single Crystals.

Single crystals of Ce-doped (La,Pr)OBiS2 superconductors, the multinary rare-earth elements substituted ROBiS2, were successfully grown. The grown crystals typically had a size of 1-2 mm and a plate-like shape with a well-developed c-plane. The c-axis lattice constants of the obtained (La,Ce,Pr)OBiS2 single crystals were approximately 13.6-13.7 Å, and the superconducting transition temperature was 1.23-2.18 K. Valence fluctuations of Ce and Pr were detected through X-ray absorption spectroscopy analysis. In contrast to (Ce,Pr)OBiS2 and (La,Ce)OBiS2, the superconducting transition temperature of (La,Ce,Pr)OBiS2 increased with the increasing concentrations of the tetravalent state at the R-site.

Oxide-ion diffusion in brownmillerite-type Ca2AlMnO5+δ from first-principles calculations.

Oxide-ion diffusion pathways in brownmillerite oxides Ca2AlMnO5 and Ca2AlMnO5.5 are systematically investigated using first-principles calculations. These structures reversibly transform into each other by oxidation and reduction. We examine oxide-ion migration in Ca2AlMnO5 and Ca2AlMnO5.5 using the nudged elastic band method. In the reduced structure (Ca2AlMnO5), oxide-ion migration through a vacancy channel is found to have the lowest migration energy barrier, at 0.58 eV. The migration energy barrier of the second-lowest energy path, perpendicular to the vacancy channel, is found to be 0.98 eV. In the oxidized structure (Ca2AlMnO5.5), oxide-ion migration within AlO6 layers has migration energy barriers of 0.55 eV and 0.56 eV in the [100] and [001] directions, respectively. Oxide-ion migration perpendicular to the AlO6 layer has a migration energy barrier of 1.33 eV, suggesting that oxide-ion diffusion in the [010] direction is difficult even at elevated temperature. These results indicate that diffusion in the reduced phase is predominantly one-dimensional whereas it is two-dimensional in the oxidized phase.

Radiation dose for 320-row dose-modulated dynamic coronary CT angiography.

OBJECTIVES: The area detector 320-row CT scanner, which can cover the whole heart in one rotation, can aid in reducing radiation exposure during electrocardiography (ECG)-gated coronary CT angiography (CCTA). Recently, researchers have proposed dose-modulated dynamic CCTA with a 320-row scanner for the detection of functional myocardial ischemia. In the present study, we compared and validated the radiation dose of this method with that of the standard CCTA method and the latest diagnostic reference levels (DRLs). MATERIALS AND METHODS: The study included a total of 164 consecutive patients with suspected or known coronary artery disease (CAD) who underwent CCTA with a 320-row scanner. The patients were randomly divided into dynamic and standard CCTA groups, and the CT dose index (CTDIvol) and dose length product (DLP) calculated by the CT system were compared between the two protocols and with the latest DRL. RESULTS: Standard and dynamic CCTA scans were performed in 77 and 87 patients, respectively. CTDIvol was significantly higher for standard CCTA than for dynamic CCTA (41 ± 35 mGy vs. 22 ± 7 mGy, p = 0.0014). DLP was also significantly higher for standard CCTA than for dynamic CCTA (864 ± 702 mGy × cm vs. 434 ± 106 mGy × cm, p < .0001). For standard scans, CTDIvol and DLP exceeded the 2020 DRL in Japan in 16% (12/77) and 17% (13/77) of cases, respectively. In contrast, rates for the dynamic scan were only 1% (1/87) for CTDIvol and 0% (0/87) for DLP. CONCLUSION: The dose of radiation exposure during dynamic CCTA with a 320-row scanner does not exceed that of standard CCTA and is sufficient to meet the latest DRL. Thus, our results suggest that the method is safe from the perspective of radiation exposure.

Combination of recommender system and single-particle diagnosis for accelerated discovery of novel nitrides.

Discovery of new compounds from wide chemical space is attractive for materials researchers. However, theoretical prediction and validation experiments have not been systematically integrated. Here, we demonstrate that a new combined approach is powerful in significantly accelerating the discovery rate of new compounds, which should be useful for exploration of a wide chemical space in general. A recommender system for chemically relevant composition is constructed by machine learning of Inorganic Crystal Structure Database using chemical compositional descriptors. Synthesis and identification experiments are made at the chemical compositions with high recommendation scores by the single-particle diagnosis method. Two new compounds, La4Si3AlN9 and La26Si41N80O, and two new variants (isomorphic substitutions) of known compounds, La7Si6N15 and La4Si5N10O, are successfully discovered. Finally, density functional theory calculations are conducted for La4Si3AlN9 to confirm the energetic and dynamical stability and to reveal its atomic arrangement.

Acute Megakaryoblastic Leukemia Harboring a Subclone Expressing BCR-ABL1 Fusion Gene Product.

Acute myeloid leukemia (AML) with BCR-ABL1, also termed Philadelphia chromosome-positive AML (Ph+ AML), is a rare leukemia subtype classified by the World Health Organization in 2016. The characteristics of Ph+ AML have not been fully identified yet. We herein report a patient with Ph+ AML who phenotypically exhibited megakaryoblastic characteristics, FAB:M7 and harbored a subclone expressing BCR-ABL1 gene fusion products. This case suggests that BCR-ABL1 was acquired as a subclone due to a secondary event that might have occurred late during leukemia evolution. Our findings may aid in deciphering the mechanism underlying Ph+ AML development in future studies.

Protonic Conduction in the BaNdInO4 Structure Achieved by Acceptor Doping.

The potential of calcium-doped layered perovskite compounds, BaNd1-x Ca x InO4-x/2 (where x is the excess Ca content), as protonic conductors was experimentally investigated. The acceptor-doped ceramics exhibit improved total conductivities that were 1-2 orders of magnitude higher than those of the pristine material, BaNdInO4. The highest total conductivity of 2.6 × 10-3 S cm-1 was obtained in the BaNd0.8Ca0.2InO3.90 sample at a temperature of 750 °C in air. Electrochemical impedance spectroscopy measurements of the x = 0.1 and x = 0.2 substituted samples showed higher total conductivity under humid environments than those measured in a dry environment over a large temperature range (250-750 °C). At 500 °C, the total conductivity of the 20% substituted sample in humid air (∼3% H2O) was 1.3 × 10-4 S cm-1. The incorporation of water vapor decreased the activation energies of the bulk conductivity of the BaNd0.8Ca0.2InO3.90 sample from 0.755(2) to 0.678(2) eV in air. The saturated BaNd0.8Ca0.2InO3.90 sample contained 2.2 mol % protonic defects, which caused an expansion in the lattice according to the high-temperature X-ray diffraction data. Combining the studies of the impedance behavior with four-probe DC conductivity measurements obtained in humid air, which showed a decrease in the resistance of the x = 0.2 sample, we conclude that experimental evidence indicates that BaNd1-x Ca x InO4-x/2 is a fast proton conductor.

A solution-free crystal-mounting platform for native SAD.

The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.

Enumeration of nonequivalent substitutional structures using advanced data structure of binary decision diagram.

A derivative structure is a nonequivalent substitutional atomic configuration derived from a given primitive cell. The enumeration of derivative structures plays an essential role in searching for the ground states in multicomponent systems. However, it is computationally difficult to enumerate derivative structures if the number of derivative structures of a target system becomes huge. In this study, we introduce a novel compact data structure of the zero-suppressed binary decision diagram (ZDD) for enumerating derivative structures much more efficiently. We show its simple applications to the enumeration of structures derived from the face-centered cubic and hexagonal close-packed lattices in binary, ternary, and quaternary systems. The present ZDD-based procedure should contribute to computational approaches based on derivative structures in physics and materials science.

Growth and Characterization of ROBiS2 High-Entropy Superconducting Single Crystals.

A series of high-entropy superconductors, ROBiS2 (R = La + Ce + Pr + Nd + Sm), have been successfully grown in the form of single crystals using CsCl flux. The obtained single crystals have a platelike shape with a size of 0.5-2.0 mm and a thickness of 70-450 µm, and they are cleavable along the c-plane. The c-axis lattice constants of the obtained ROBiS2 single crystals have similar values of 13.47-13.57 Å. The Ce in the obtained ROBiS2 single crystals was in a mixed-valence state, comprising both Ce3+ and Ce4+. On the other hand, Pr and Sm showed only the trivalent state. The superconducting transition temperatures of ROBiS2 single crystals were approximately 2-4 K. The superconducting transition temperature and superconducting anisotropies of R-site mixed high-entropy samples increased with a decrease in the mean ionic radius of the R-site. Moreover, a deviation in the tendency to exhibit superconducting properties was observed based on the difference in the R-site mixed entropy. R-site mixed entropy in ROBiS2 superconductors may affect their superconducting properties.

Flux Growth and Superconducting Properties of (Ce,Pr)OBiS2 Single Crystals.

Ce1-x Pr x OBiS2 (0. 1 ≤ x ≤ 0.9) single crystals were grown using a CsCl flux method. Their structural and physical properties were examined by X-ray diffraction, X-ray absorption, transmission electron microscopy, and electrical resistivity. All of the Ce1-x Pr x OBiS2 single crystals with 0.1 ≤ x ≤ 0.9 exhibited tetragonal phase. With increasing Pr content, the a-axis and c-axis lattice parameters decreased and increased, respectively. Transmission electron microscope analysis of Ce0.1Pr0.9OBiS2 (x = 0.9) single crystal showed no stacking faults. Atomic-resolution energy dispersive X-ray spectrometry mapping revealed that Bi, Ce/Pr, O, and S occupied different crystallographic sites, while Ce and Pr randomly occupied the same sites. X-ray absorption spectra showed that an increase of the Pr ratio increased the ratio of Ce4+/Ce3+. All of the Ce1-x Pr x OBiS2 crystals showed superconducting transition, with a maximum transition temperature of ~4 K at x = 0.9.

Improved visualization of diffusion-prepared MR neurography (SHINKEI) in the lumbosacral plexus combining high-intensity reduction (HIRE) technique.

PURPOSE: This study attempted to improve visualization of the pelvic nervous system using the high-intensity reduction (HIRE)-nerve-SHeath signal increased with INKed rest-tissue RARE Imaging (SHINKEI) technique that involves subtracting signals of 3D heavily T2W images from SHINKEI images. We identified the optimum TE value for 3D heavily T2W images and assessed the usefulness of the HIRE-SHINKEI technique. MATERIALS AND METHODS: Coronal lumbosacral plexus images were acquired from six healthy volunteers at 3 T. We optimized the TE of the 3D heavily T2-weighted (T2W) images in HIRE-SHINKEI and compared HIRE-SHINKEI images with conventional SHINKEI images with respect to nerve depiction, and vein, bladder, and cerebrospinal fluid (CSF) signal suppression using a 5-point scale. RESULTS: In 3D heavily T2W images optimized by HIRE-SHINKEI technique, the signal corresponding to nerves became significantly lower at TE = 400 ms (p < 0.0005), while that of veins occurred at TE = 400 ms and 600 ms (p < 0.05). The suppression of bladder signals was significant at TE = 400, 600, and 800 ms (p < 0.05); however, there was no difference in signal inhibition from CSF at all TEs tested. Based on these results, an optimal TE of 600 ms was identified for 3D heavily T2W images; these images corresponded to the minimal loss of nerve signal and simultaneous maximum subtraction of signals from the bladder, vein, and CSF with dissimilar T2 values. Compared with SHINKEI images, the optimized HIRE-SHINKEI images selectively delineated nerves in greater detail, and along with significant signal suppression of the bladder (p < 0.0001) and veins (p < 0.05). CONCLUSION: HIRE-SHINKEI can be used to better visualize the lumbosacral plexus with higher signal suppression of other pelvic structures. Such detailed Magnetic resonance neurography and selective depiction of nerves are useful for the diagnosis of peripheral nerve disorders.

Bulk superconductivity in a four-layer-type Bi-based compound La2O2Bi3Ag0.6Sn0.4S5.7Se0.3.

Recently, we reported the observation of superconductivity at ~0.5 K in a La2O2M4S6-type (M: metal) layered compound La2O2Bi3AgS6, which is a layered system related to the BiS2-based superconductor system but possesses a thicker Bi3AgS6-type conducting layer. In this study, we have developed the La2O2Bi3AgS6-type materials by element substitutions to increase the transition temperature (Tc) and to induce bulk nature of superconductivity. A resistivity anomaly observed at 180 K in La2O2Bi3AgS6 was systematically suppressed by Sn substitution for the Ag site. By the Sn substitution, Tc increased, and the shielding volume fraction estimated from magnetization measurements also increased. The highest Tc (=2.3 K) and the highest shielding volume fraction (~20%) was observed for La2O2Bi3Ag0.6Sn0.4S6. The superconducting properties were further improved by Se substitutions for the S site. By the combinational substitutions of Sn and Se, bulk-superconducting phase of La2O2Bi3Ag0.6Sn0.4S5.7Se0.3 with a Tc of 3.0 K (Tconset = 3.6 K) was obtained.

Artifact-robust diffusion-weighted whole-body imaging with background suppression at 3 T using improved turbo spin-echo diffusion-weighted imaging.

OBJECTIVE:: To compare single-shot turbo spin-echo (TSE) diffusion-weighted whole-body imaging with background suppression (DWIBS) and echo-planar imaging (EPI) DWIBS to determine the feasibility of direct-coronal TSE-DWIBS. METHODS:: All measurements were performed using a 3.0 T MRI scanner. In the phantom study, we compared the contrast ratios (CRs) of tumor-mimicking phantom (tumor) to muscle-mimicking phantom (muscle) and water to muscle and the signal-to-noise ratio (SNR) between TSE-DWIBS and EPI-DWIBS. In the volunteer study, 10 healthy volunteers were whole-body scanned with direct-coronal TSE-DWIBS, direct-coronal EPI-DWIBS (corEPI-DWIBS), and transverse EPI-DWIBS (traEPI-DWIBS). Two radiologists assessed the image distortion, uniformity of fat suppression, overall artifacts, and overall image quality in maximum intensity projection (MIP) images from each DWIBS image using a 5-point scale. RESULTS:: In the phantom study, the CR of tumor to muscle was found to be lower for TSE-DWIBS (10.57 ± 0.45) than for EPI-DWIBS (15.38 ± 0.27), and the CR of water to muscle was higher for TSE-DWIBS (9.61 ± 0.66) than for EPI-DWIBS (2.52 ± 0.60). The volunteer study revealed good inter observer agreement between TSE-DWIBS and EPI-DWIBS with respect to image distortion, uniformity of fat suppression, overall artifacts, and overall image quality, with weighted Cohen's κ coefficients of 0.91, 0.74, 0.87, and 0.72, respectively. Qualitative analysis scores for image distortion, uniformity of fat suppression, overall artifacts, and overall image quality were significantly higher for TSE-DWIBS than for corEPI-DWIBS or traEPI-DWIBS (p < 0.05). CONCLUSION:: Direct-coronal TSE-DWIBS is robust against magnetic field inhomogeneity. High-quality images without distortion or fat suppression inhomogeneity were obtained. ADVANCES IN KNOWLEDGE:: Many studies on DWIBS have been previously reported; however, these studies used EPI read-out. To the best of our knowledge, no studies using TSE read-out have been reported. In this study, we examined the feasibility of TSE-DWIBS with lesser artifacts than EPI-DWIBS.

Compositional descriptor-based recommender system for the materials discovery.

Structures and properties of many inorganic compounds have been collected historically. However, it only covers a very small portion of possible inorganic crystals, which implies the presence of numerous currently unknown compounds. A powerful machine-learning strategy is mandatory to discover new inorganic compounds from all chemical combinations. Herein we propose a descriptor-based recommender-system approach to estimate the relevance of chemical compositions where crystals can be formed [i.e., chemically relevant compositions (CRCs)]. In addition to data-driven compositional similarity used in the literature, the use of compositional descriptors as a prior knowledge is helpful for the discovery of new compounds. We validate our recommender systems in two ways. First, one database is used to construct a model, while another is used for the validation. Second, we estimate the phase stability for compounds at expected CRCs using density functional theory calculations.