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Lena Park Drops New EP "Stay With Me"

Singer Lena Park released her new EP "Stay With Me."The album was dropped at six p.m. Thursday, according to the singer's management Bonboo Entertainment."Stay With Me" is Park's first album...

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Twice's Music Video Tops 500 Million Views

The music video for girl group TWICE's 2015 song "Like Ooh-Ahh" has surpassed 500 million views on YouTube. The group's management JYP Entertainment said the video broke the 500 million mark...

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3 Essential Steps for Mobile Privacy With Startpage

In today's digital age, safeguarding your mobile privacy is vital. Here are three easy steps, powered by Startpage, to keep your digital life secure.




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Top 6 Privacy and Security Apps to Safeguard Your Digital Life

In a world where digital privacy is increasingly important, finding the right tools to protect your data is essential. With mobile phones becoming central to our lives, it's crucial to choose apps that prioritize privacy.




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What Does the Ace of Cups Reversed Mean in Your Tarot Reading?

Is Ace of Cups Reversed" reveals insights into blocked emotions and self-reflection in tarot readings, offering guidance on relationships and personal growth.




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KOSPI Slips 0.14% on Friday

[Economy] :
The benchmark Korea Composite Stock Price Index shed three-point-48 points, or zero-point-14 percent, on Friday to close at two-thousand-561-point-15. The tech-heavy KOSDAQ gained nine-point-86 points, or one-point-34 percent, to close at 743-point-38.

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KOSPI Slips below 2,500 Threshold for First Time since Black Monday in August

[Economy] :
South Korea’s benchmark Korea Composite Stock Price Index(KOSPI) slipped below the two-thousand-500 threshold on Tuesday for the first time since August’s “Black Monday.” The KOSPI dipped 49-point-09 points, or one-point-94 percent, on Tuesday to close at two-thousand-482-point-57. In the ...

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BGS maps portal - British Geological Survey

BGS maps portal  British Geological Survey









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The structure of a pectin-active family 1 polysaccharide lyase from the marine bacterium Pseudoalteromonas fuliginea

Pseudoalteromonas fuliginea sp. PS47 is a recently identified marine bacterium that has extensive enzymatic machinery to metabolize polysaccharides, including a locus that targets pectin-like substrates. This locus contains a gene (locus tag EU509_03255) that encodes a pectin-degrading lyase, called PfPL1, that belongs to polysaccharide lyase family 1 (PL1). The 2.2 Å resolution X-ray crystal structure of PfPL1 reveals the compact parallel β-helix fold of the PL1 family. The back side of the core parallel β-helix opposite to the active site is a meandering set of five α-helices joined by lengthy loops. A comparison of the active site with those of other PL1 enzymes suggests a catalytic mechanism that is independent of metal ions, such as Ca2+, but that substrate recognition may require metal ions. Overall, this work provides the first structural insight into a pectinase of marine origin and the first structure of a PL1 enzyme in subfamily 2.




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Symmetry groups of the Batak basketweave patterns

The symmetry groups of the weave patterns of the baskets, trays and mats of the Batak, an indigenous community in the Philippines, are discussed in this paper. The two-way twofold weaving technique is used by the Batak, and this study points to a total of 15 layer groups found in the Batak weaves out of the 80 layer groups known in crystallography.




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Similarity score for screening phase-retrieved maps in X-ray diffraction imaging – characterization in reciprocal space

X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed.




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Combination of XEOL, TR-XEOL and HB-T interferometer at the TPS 23A X-ray nanoprobe for exploring quantum materials

In this study, a combination of X-ray excited optical luminescence (XEOL), time-resolved XEOL (TR-XEOL) and the Hanbury-Brown and Twiss (HB-T) interferometer at the Taiwan Photon Source (TPS) 23A X-ray nanoprobe beamline for exploring quantum materials is demonstrated. On the basis of the excellent spatial resolution rendered using a nano-focused beam, emission distributions of artificial micro-diamonds can be obtained by XEOL maps, and featured emission peaks of a selected local area can be obtained by XEOL spectra. The hybrid bunch mode of the TPS not only provides a sufficiently high peak power density for experiments at each beamline but also permits high-quality temporal domain (∼200 ns) measurements for investigating luminescence dynamics. From TR-XEOL measurements, the decay lifetime of micro-diamonds is determined to be approximately 16 ns. Furthermore, the XEOL spectra of artificial micro-diamonds can be investigated by the HB-T interferometer to identify properties of single-photon sources. The unprecedented strategy of combining XEOL, TR-XEOL and the HB-T interferometer at the X-ray nanoprobe beamline will open new avenues with significant characterization abilities for unraveling the emission mechanisms of single-photon sources for quantum materials.




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A new modular framework for high-level application development at HEPS

As a representative of the fourth-generation light sources, the High Energy Photon Source (HEPS) in Beijing, China, utilizes a multi-bend achromat lattice to obtain an approximately 100 times emittance reduction compared with third-generation light sources. New technologies bring new challenges to operate the storage ring. In order to meet the beam commissioning requirements of HEPS, a new framework for the development of high-level applications (HLAs) has been created. The key part of the new framework is a dual-layer physical module to facilitate the seamless fusion of physical simulation models with the real machine, allowing for fast switching between different simulation models to accommodate the various simulation scenarios. As a framework designed for development of physical applications, all variables are based on physical quantities. This allows physicists to analytically assess measurement parameters and optimize machine parameters in a more intuitive manner. To enhance both extensibility and adaptability, a modular design strategy is utilized, partitioning the entire framework into discrete modules in alignment with the requirements of HLA development. This strategy not only facilitates the independent development of each module but also minimizes inter-module coupling, thereby simplifying the maintenance and expansion of the entire framework. To simplify the development complexity, the design of the new framework is implemented using Python and is called Python-based Accelerator Physics Application Set (Pyapas). Taking advantage of Python's flexibility and robust library support, we are able to develop and iterate quickly, while also allowing for seamless integration with other scientific computing applications. HLAs for both the HEPS linac and booster have been successfully developed. During the beam commissioning process at the linac, Pyapas's ease of use and reliability have significantly reduced the time required for the beam commissioning operators. As a development framework for HLA designed for the new-generation light sources, Pyapas has the versatility to be employed with HEPS, as well as with other comparable light sources, due to its adaptability.




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VerSoX B07-B: a high-throughput XPS and ambient pressure NEXAFS beamline at Diamond Light Source

The beamline optics and endstations at branch B of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source are described. B07-B provides medium-flux X-rays in the range 45–2200 eV from a bending magnet source, giving access to local electronic structure for atoms of all elements from Li to Y. It has an endstation for high-throughput X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) measurements under ultrahigh-vacuum (UHV) conditions. B07-B has a second endstation dedicated to NEXAFS at pressures from UHV to ambient pressure (1 atm). The combination of these endstations permits studies of a wide range of interfaces and materials. The beamline and endstation designs are discussed in detail, as well as their performance and the commissioning process.




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Soft X-ray wavefront sensing at an ellipsoidal mirror shell

A reliable `in situ' method for wavefront sensing in the soft X-ray domain is reported, developed for the characterization of rotationally symmetric optical elements, like an ellipsoidal mirror shell. In a laboratory setup, the mirror sample is irradiated by an electron-excited (4.4 keV), micrometre-sized (∼2 µm) fluorescence source (carbon Kα, 277 eV). Substantially, the three-dimensional intensity distribution I(r) is recorded by a CCD camera (2048 × 512 pixels of 13.5 µm) at two positions along the optical axis, symmetrically displaced by ±21–25% from the focus. The transport-of-intensity equation is interpreted in a geometrical sense from plane to plane and implemented as a ray tracing code, to retrieve the phase Φ(r) from the radial intensity gradient on a sub-pixel scale. For reasons of statistical reliability, five intra-/extra-focal CCD image pairs are evaluated and averaged to an annular two-dimensional map of the wavefront error {cal W}. In units of the test wavelength (C Kα), an r.m.s. value sigma_{cal{W}} = ±10.9λ0 and a peak-to-valley amplitude of ±31.3λ0 are obtained. By means of the wavefront, the focus is first reconstructed with a result for its diameter of 38.4 µm, close to the direct experimental observation of 39.4 µm (FWHM). Secondly, figure and slope errors of the ellipsoid are characterized with an average of ±1.14 µm and ±8.8 arcsec (r.m.s.), respectively, the latter in reasonable agreement with the measured focal intensity distribution. The findings enable, amongst others, the precise alignment of axisymmetric X-ray mirrors or the design of a wavefront corrector for high-resolution X-ray science.




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The HEPS synchrotron unleashes new medical frontiers




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GIWAXS experimental methods at the NFPS-BL17B beamline at Shanghai Synchrotron Radiation Facility

The BL17B beamline at the Shanghai Synchrotron Radiation Facility was first designed as a versatile high-throughput protein crystallography beamline and one of five beamlines affiliated to the National Facility for Protein Science in Shanghai. It was officially opened to users in July 2015. As a bending magnet beamline, BL17B has the advantages of high photon flux, brightness, energy resolution and continuous adjustable energy between 5 and 23 keV. The experimental station excels in crystal screening and structure determination, providing cost-effective routine experimental services to numerous users. Given the interdisciplinary and green energy research demands, BL17B beamline has undergone optimization, expanded its range of experimental methods and enhanced sample environments for a more user-friendly testing mode. These methods include single-crystal X-ray diffraction, powder crystal X-ray diffraction, wide-angle X-ray scattering, grazing-incidence wide-angle X-ray scattering (GIWAXS), and fully scattered atom pair distribution function analysis, covering structure detection from crystalline to amorphous states. This paper primarily presents the performance of the BL17B beamline and the application of the GIWAXS methodology at the beamline in the field of perovskite materials.




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Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction

Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methyl­prop­yl)-1-oxa-4,7,10-tri­aza­cyclo­tridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclo­depsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclo­dep­si­peptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enanti­omorphs of beauveriolide I.




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Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii

Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.




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Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection

The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.




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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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A snapshot love story: what serial crystallography has done and will do for us

Serial crystallography, born from groundbreaking experiments at the Linac Coherent Light Source in 2009, has evolved into a pivotal technique in structural biology. Initially pioneered at X-ray free-electron laser facilities, it has now expanded to synchrotron-radiation facilities globally, with dedicated experimental stations enhancing its accessibility. This review gives an overview of current developments in serial crystallography, emphasizing recent results in time-resolved crystallography, and discussing challenges and shortcomings.




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Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.




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Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser

Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. However, despite extensive processing of large image sets collected in cryo-EM experiments to amplify the signal-to-noise ratio, the reconstructed 3D protein-density maps are often limited in quality due to residual noise, which in turn affects the accuracy of the macromolecular representation. Here, crefDenoiser is introduced, a denoising neural network model designed to enhance the signal in 3D cryo-EM maps produced with standard processing pipelines. The crefDenoiser model is trained without the need for `clean' ground-truth target maps. Instead, a custom dataset is employed, composed of real noisy protein half-maps sourced from the Electron Microscopy Data Bank repository. Competing with the current state-of-the-art, crefDenoiser is designed to optimize for the theoretical noise-free map during self-supervised training. We demonstrate that our model successfully amplifies the signal across a wide variety of protein maps, outperforming a classic map denoiser and following a network-based sharpening model. Without biasing the map, the proposed denoising method leads to improved visibility of protein structural features, including protein domains, secondary structure elements and modest high-resolution feature restoration.




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Magnetic space groups versus representation analysis in the investigation of magnetic structures: the happy end of a strained relationship

In recent decades, sustained theoretical and software developments have clearly established that representation analysis and magnetic symmetry groups are complementary concepts that should be used together in the investigation and description of magnetic structures. Historically, they were considered alternative approaches, but currently, magnetic space groups and magnetic superspace groups can be routinely used together with representation analysis, aided by state-of-the-art software tools. After exploring the historical antagonism between these two approaches, we emphasize the significant advancements made in understanding and formally describing magnetic structures by embracing their combined use.




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Determining magnetic structures in GSAS-II using the Bilbao Crystallographic Server tool k-SUBGROUPSMAG

The embedded call to a special version of the web-based Bilbao Crystallographic Server tool k-SUBGROUPSMAG from within GSAS-II to form a list of all possible commensurate magnetic subgroups of a parent magnetic grey group is described. It facilitates the selection and refinement of the best commensurate magnetic structure model by having all the analysis tools including Rietveld refinement in one place as part of GSAS-II. It also provides the chosen magnetic space group as one of the 1421 possible standard Belov–Neronova–Smirnova forms or equivalent non-standard versions.




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Structural characterization and comparative analysis of polymorphic forms of psilocin (4-hy­droxy-N,N-di­methyl­tryptamine)

The title compound, C12H16N2O, is a hy­droxy-substituted mono­amine alkaloid, and the primary metabolite of the naturally occurring psychedelic compound psilocybin. Crystalline forms of psilocin are known, but their characterization by single-crystal structure analysis is limited. Herein, two anhydrous polymorphic forms (I and II) of psilocin are described. The crystal structure of polymorphic Form I, in space group P21/c, was first reported in 1974. Along with the redeterm­ination to modern standards and unambiguous location of the acidic H atom and variable-temperature single-crystal unit-cell determinations for Form I, the Form II polymorph of the title compound, which crystallizes in the monoclinic space group P21/n, is described for the first time. The psilocin mol­ecules are present in both forms in their phenol–amine tautomeric forms (not resolved in the 1974 report). The mol­ecules in Forms I and II, however, feature different conformations of their N,N-dimethyl ethyl­ene substituent, with the N—C—C—C link in Form I being trans and in Form II being gauche, allowing the latter to bend back to the hydroxyl group of the same mol­ecule, leading to the formation of a strong intra­molecular O—H⋯N hydrogen bond between the hydroxyl moiety and ethyl­amino-nitro­gen group. In the extended structure of Form II, the mol­ecules form one-dimensional strands through N—H⋯O hydrogen bonds from the indole group to the oxygen atom of the hydroxyl moiety of an adjacent mol­ecule. Form II exhibits whole-mol­ecule disorder due to a pseudo-mirror operation, with an occupancy ratio of 0.689 (5):0.311 (5) for the two components. In contrast, Form I does not feature intra­molecular hydrogen bonds but forms a layered structure through inter­molecular N—H⋯O and O—H⋯N hydrogen bonds.




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Crystal structures of four thio­glycosides involving carbamimido­thio­ate groups

The compounds 2',3',4',6'-tetra-O-acetyl-β-d-gluco­pyranosyl N'-cyano-N-phenyl­carbamimido­thio­ate (C22H25N3O9S, 5a), 2',3',4',6'-tetra-O-acetyl-β-d-galacto­pyranosyl N'-cyano-N-phenyl­carbamimido­thio­ate, (C22H25N3O9S, 5b), 2',3',4',6'-tetra-O-acetyl-β-d-galacto­pyranosyl N'-cyano-N-methyl­carbamimido­thio­ate (C17H23N3O9S, 5c), and 2',3',4',6'-tetra-O-acetyl-β-d-galacto­pyranosyl N'-cyano-N-p-tolyl­carbamimido­thio­ate (C23H27N3O9S, 5d) all crystallize in P212121 with Z = 4. For all four structures, the configuration across the central (formal) C=N(CN) double bond of the carbamimido­thio­ate group is Z. The torsion angles C5—O1—C1—S (standard sugar numbering) are all close to 180°, confirming the β position of the substituent. Compound 5b involves an intra­molecular hydrogen bond N—H⋯O1; in 5c this contact is the weaker branch of a three-centre inter­action, whereas in 5a and 5d the H⋯O distances are much longer and do not represent significant inter­actions. The C—N bond lengths at the central carbon atom of the carbamimido­thio­ate group are almost equal. All C—O—C=O torsion angles of the acetyl groups correspond to a synperiplanar geometry, but otherwise all four mol­ecules display a high degree of conformational flexibility, with many widely differing torsion angles for equivalent groups. In the crystal packing, 5a, 5c and 5d form layer structures involving the classical hydrogen bond N—H⋯Ncyano and a variety of ‘weak’ hydrogen bonds C—H⋯O or C—H⋯S. The packing of 5b is almost featureless and involves a large number of borderline ‘weak’ hydrogen bonds. In an appendix, a potted history of wavelength preferences for structure determination is presented and it is recommended that, even for small organic crystals in non-centrosymmetric space groups, the use of Mo radiation should be considered.




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X-ray diffraction from dislocation half-loops in epitaxial films

X-ray diffraction from dislocation half-loops consisting of a misfit segment with two threading arms extending from it to the surface is calculated by the Monte Carlo method. The diffraction profiles and reciprocal space maps are controlled by the ratio of the total lengths of the misfit and the threading segments of the half-loops. A continuous transformation from the diffraction characteristic of misfit dislocations to that of threading dislocations with increasing thickness of epitaxial film is studied. Diffraction from dislocations with edge- and screw-type threading arms is considered and the contributions of the two types of dislocations are compared.




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Subperiodic groups, line groups and their applications

Understanding the symmetries described by subperiodic groups – frieze, rod and layer groups – has been instrumental in predicting various properties (band structures, optical absorption, Raman spectra, diffraction patterns, topological properties etc.) of `low-dimensional' crystals. This knowledge is crucial in the tailored design of materials for specific applications across electronics, photonics and materials engineering. However, there are materials that have the property of being periodic only in one direction and whose symmetry cannot be described by the subperiodic rod groups. Describing the symmetry of these materials necessitates the application of line group theory. This paper gives an overview of subperiodic groups while briefly introducing line groups in order to acquaint the crystallographic community with these symmetries and direct them to pertinent literature. Since line groups are generally not sub­periodic, they have thus far remained outside the realm of symmetries traditionally considered in crystallography, although there are numerous `one-dimensional' crystals (i.e. monoperiodic structures) possessing line group symmetry.




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MatchMaps: non-isomorphous difference maps for X-ray crystallography

Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands and time. A popular method for detecting structural differences between crystallographic data sets is the isomorphous difference map. These maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even modest changes in unit-cell properties can render isomorphous difference maps useless. This is unnecessary. Described here is a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. This procedure is implemented in an open-source Python package, MatchMaps, that can be run in any software environment supporting PHENIX [Liebschner et al. (2019). Acta Cryst. D75, 861–877] and CCP4 [Agirre et al. (2023). Acta Cryst. D79, 449–461]. Worked examples show that MatchMaps `rescues' observed difference electron-density maps for poorly isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit or across altogether different crystal forms.




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Patching-based deep-learning model for the inpainting of Bragg coherent diffraction patterns affected by detector gaps

A deep-learning algorithm is proposed for the inpainting of Bragg coherent diffraction imaging (BCDI) patterns affected by detector gaps. These regions of missing intensity can compromise the accuracy of reconstruction algorithms, inducing artefacts in the final result. It is thus desirable to restore the intensity in these regions in order to ensure more reliable reconstructions. The key aspect of the method lies in the choice of training the neural network with cropped sections of diffraction data and subsequently patching the predictions generated by the model along the gap, thus completing the full diffraction peak. This approach enables access to a greater amount of experimental data for training and offers the ability to average overlapping sections during patching. As a result, it produces robust and dependable predictions for experimental data arrays of any size. It is shown that the method is able to remove gap-induced artefacts on the reconstructed objects for both simulated and experimental data, which becomes essential in the case of high-resolution BCDI experiments.




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SUBGROUPS: a computer tool at the Bilbao Crystallographic Server for the study of pseudo-symmetric or distorted structures

SUBGROUPS is a free online program at the Bilbao Crystallographic Server (https://www.cryst.ehu.es/). It permits the exploration of all possible symmetries resulting from the distortion of a higher-symmetry parent structure, provided that the relation between the lattices of the distorted and parent structures is known. The program calculates all the subgroups of the parent space group which comply with this relation. The required minimal input is the space-group information of the parent structure and the relation of the unit cell of the distorted or pseudo-symmetric structure with that of the parent structure. Alternatively, the wavevector(s) observed in the diffraction data characterizing the distortion can be introduced. Additional conditions can be added, including filters related to space-group representations. The program provides very detailed information on all the subgroups, including group–subgroup hierarchy graphs. If a Crystallographic Information Framework (CIF) file of the parent high-symmetry structure is uploaded, the program generates CIF files of the parent structure described under each of the chosen lower symmetries. These CIF files may then be used as starting points for the refinement of the distorted structure under these possible symmetries. They can also be used for density functional theory calculations or for any other type of analysis. The power and efficiency of the program are illustrated with a few examples.




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High-transmission spectrometer for rapid resonant inelastic soft X-ray scattering (rRIXS) maps

The design and first results of a high-transmission soft X-ray spectrometer operated at the X-SPEC double-undulator beamline of the KIT Light Source are presented. As a unique feature, particular emphasis was placed on optimizing the spectrometer transmission by maximizing the solid angle and the efficiencies of spectrometer gratings and detector. A CMOS detector, optimized for soft X-rays, allows for quantum efficiencies of 90% or above over the full energy range of the spectrometer, while simultaneously offering short readout times. Combining an optimized control system at the X-SPEC beamline with continuous energy scans (as opposed to step scans), the high transmission of the spectrometer, and the fast readout of the CMOS camera, enable the collection of entire rapid resonant inelastic soft X-ray scattering maps in less than 1 min. Series of spectra at a fixed energy can be taken with a frequency of up to 5 Hz. Furthermore, the use of higher-order reflections allows a very wide energy range (45 to 2000 eV) to be covered with only two blazed gratings, while keeping the efficiency high and the resolving power E/ΔE above 1500 and 3000 with low- and high-energy gratings, respectively.




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Boxo and Nium launch white-label remittance platform for apps

Boxo has partnered with global payments infrastructure firm



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To Keep Your Brain Young, Take Some Tips From Our Earliest Ancestors

Reconstructions from the Daynès Studio in Paris depict a male Neanderthal (right) face to face with a human, Homo sapiens.; Credit: /Science Source

Bret Stetka | NPR

It's something that many of us reckon with: the sense that we're not quite as sharp as we once were.

I recently turned 42. Having lost my grandfather to Alzheimer's, and with my mom suffering from a similar neurodegenerative disease, I'm very aware of what pathologies might lurk beneath my cranium.

In the absence of a cure for Alzheimer's and other forms of dementia, the most important interventions for upholding brain function are preventivethose that help maintain our most marvelous, mysterious organ.

Based on the science, I take fish oil and broil salmon. I exercise. I try to challenge my cortex to the unfamiliar.

As I wrote my recent book, A History of the Human Brain, which recounts the evolutionary tale of how our brain got here, I began to realize that so many of the same influences that shaped our brain evolution in the first place reflect the very measures we use to preserve our cognitive function today.

Being social, and highly communicative. Exploring creative pursuits. Eating a varied, omnivorous diet low in processed foods. Being physically active.

These traits and behaviors help retrace our past, and, I believe, were instrumental in why we remain on the planet today.

And they all were, at least in part, enabled by our brain.

Social smart alecks finish first

The human saga is riddled with extinctions.

By "human," I don't just mean Homo sapiens, the species we belong to, but any member of the genus Homo. We've gotten used to being the only human species on Earth, but in our not so distant past — probably a few hundred thousand years ago – there were at least nine of us running around.

There was Homo habilis, or the "handy man." And Homo erectus, the first "pitcher." The Denisovans roamed Asia, while the more well-known Neanderthals spread throughout Europe.

But with the exception of Homo sapiens, they're all gone. And there's a good chance it was our fault.

Humans were never the fastest lot on the African plains, and far from the strongest. Cheetahs, leopards and lions held those distinctions. In our lineage, natural selection instead favored wits and wiliness.

Plenty of us became cat food, but those with a slight cognitive edge — especially Homo sapiens — lived on. In our ilk, smarts overcame strength and speed in enabling survival.

Ecology, climate, location and just sheer luck would've played important roles in who persisted or perished as well, as they do for most living beings. But the evolutionary pressure for more complex mental abilities would lead to a massive expansion in our brain's size and neurocircuitry that is surely the paramount reason we dominate the planet like no other species ever has.

Much of this "success," if you can call it that, was due to our social lives.

Primates are communal creatures. Our close monkey and ape cousins are incredibly interactive, grooming each other for hours a day to maintain bonds and relationships. Throw in a few hoots and hollers and you have a pretty complex community of communicating simians.

An active social life is now a known preserver of brain function.

Research shows that social isolation worsens cognitive decline (not to mention mental health, as many of us experienced this past year). Larger social networks and regular social activities are associated with mental preservation and slowed dementia progression.

Entwined in this new social life was an evolutionary pressure that favored innovation. Our eventual ability to generate completely novel thoughts and ideas, and to share those ideas, came to define our genus.

As we hunted and foraged together, and honed stones into hand axes, there was a collective creativity at work that gave us better weapons and tools that enabled more effective food sourcing, and, later, butchering and fire. Effectively sharing these innovations with our peers allowed information to spread faster than ever before - a seed for the larger communities and civilizations to come.

Challenging ourselves to new pursuits and mastering new skills can not only impress peers and ingratiate us to our group, but literally help preserve our brain. New hobbies. New conversations. Learning the banjo. Even playing certain video games and simply driving a new route home from work each day, as neuroscientist David Eagleman does, can keep our function high.

Whether it's honing ancient stone or taking up Sudoku, any pursuit novel and mentally challenging may help keep the neural circuits firing.

We really are what we eat

All the while, as we hunted and crafted in new and communal ways, we had to eat. And we did so with an uniquely adventurous palette.

Homo sapiens is among the most omnivorous species on the planet. Within reason we eat just about anything. Whether it's leaves, meat, fungus, or fruit, we don't discriminate. At some point, one of us even thought it might be a good idea to try the glistening, grey blobs that are oysters - and shellfish are, it turns out, among the healthiest foods for our brain.

The varied human diet is an integral part of our story. As was the near constant physicality required to source it.

On multiple occasions over the past 1 to 2 million years climate changes dried out the African landscape, forcing our ancestors out of the lush forest onto the dangerous, wide-open grasslands. As evolution pressured us to create and commune to help us survive, a diverse diet also supported our eventual global takeover.

Our arboreal past left us forever craving the dangling fruits of the forest, a supreme source of high-calorie sugars that ensured survival. Back then we didn't live long enough to suffer from Type 2 diabetes: if you encountered sweets, you ate them. And today we're stuck with a taste for cookies and candy that, given our longer lifespans, can take its toll on the body and brain.

But humans were just as amenable to dining on the bulbs, rhizomes and tubers of the savanna, especially once fire came along. We eventually became adept scavengers of meat and marrow, the spoils left behind by the big cats, who preferred more nutritive organ meat.

As our whittling improved we developed spears, and learned to trap and hunt the beasts of the plains ourselves. There is also evidence that we learned to access shellfish beds along the African coast and incorporate brain-healthy seafood into our diet.

Studying the health effects of the modern diet is tricky. Dietary studies are notoriously dubious, and often involve countless lifestyle variables that are hard to untangle.

Take blueberries. Multiple studies have linked their consumption with improved brain health. But, presumably, the berry-prone among us are also more likely to eat healthy all around, exercise, and make it to level 5 on their meditation app.

Which is why so many researchers, nutritionists, and nutritional psychiatrists now focus on dietary patterns, like those akin to Mediterranean culinary customs, rather than specific ingredients. Adhering to a Mediterranean diet is linked with preserved cognition; and multiple randomized-controlled trials suggest doing so can lower depression risk.

A similar diversity in our ancestral diet helped early humans endure an ever-shifting climate and times of scarcity. We evolved to subsist and thrive on a wide range of foods, in part because our clever brains allowed us access to them. In turn, a similarly-varied diet (minus submitting to our innate sugar craving of course) is among the best strategies to maintain brain health.

All of our hunting, and foraging, and running away from predators would have required intense physical exertion. This was certainly not unique to humans, but we can't ignore the fact that regular exercise is another effective means of preserving brain health.

Being active improves performance on mental tasks, and may help us better form memories. Long before the Peletons sold out, our brains relied on both mental and physical activity.

But overwhelmingly the evidence points to embracing a collection of lifestyle factors to keep our brain healthy, none of which existed in a Darwinian vacuum.

Finding food was as social an endeavor as it was mental and physical. Our creative brains harnessed information; gossiping, innovating, and cooking our spoils around the campfire.

Researchers are beginning to piece together the complex pathology behind the inevitable decline of the human brain, and despite a parade of failed clinical trials in dementia, there should be promising treatments ahead.

Until then, in thinking about preserving the conscious experience of our world and relationships — and living our longest, happiest lives — look to our past.

Bret Stetka is a writer based in New York and an editorial director at Medscape. His work has appeared in Wired, Scientific American, and on The Atlantic.com. His new book, A History of the Human Brain, is out from Timber/Workman Press. He's also on Twitter: @BretStetka.

Copyright 2021 NPR. To see more, visit https://www.npr.org.

This content is from Southern California Public Radio. View the original story at SCPR.org.




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Hot Vax Summer? How Sex And Relationships In America Are Changing With Vaccines Widely Available

In this photo taken on February 10, 2020 a 'love kit' is seen on the bed in a room at the Dragonfly hotel in Mumbai.; Credit: PUNIT PARANJPE/AFP via Getty Images

AirTalk

A new survey shows that in the era of widespread vaccine availability, American couples are more satisfied in their relationships -- and some are even getting more experimental than they have been.

Led by Indiana University Kinsey Institute researcher Justin Lehmiller in collaboration with the website Lovehoney, which describes itself as “global sexual happiness experts,” the report looked at responses from 2,000 U.S. adults age 18-45, including an oversample of 200 who identified as LGBTQ, and among the major findings of the survey were that more than half (51 percent) of respondents said their sexual interests had changed during the pandemic, and many of those said they’d started trying things they hadn’t before. It also found that 44 percent of people surveyed said they were communicating better with their partner, and among singles surveyed 52 percent say they’re less interested in casual sex and more than a third of them said they weren’t interested in having sex on the first date.

Today on AirTalk, we’ll talk with Professor Lehmiller about the survey, its findings and how the pandemic impacted Americans’ views on relationships and sex.

Guest: 

Justin Lehmiller, social psychologist and research fellow at Indiana University’s Kinsey Institute who conducted the “Summer of Love” survey; author of “Tell Me What You Want: The Science of Sexual Desire and How It Can Help You Improve Your Sex Life” (Hachette Go, July 2020); host of the “Sex and Psychology” podcast; he tweets @JustinLehmiller

This content is from Southern California Public Radio. View the original story at SCPR.org.




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Could California Be The Next State To Legalize Psychedelics?

Don't fear the 'shrooms.; Credit: /iStockphoto.com

AirTalk

California on Tuesday moved another step closer to decriminalizing psychedelics — amid a debate over whether their prohibition is an outdated remnant of the War on Drugs — after the author removed a substance (ketamine) from the bill that opponents said can be used as a date-rape drug.

The bill would allow those 21 and older to possess for personal use and “social sharing” psilocybin, the hallucinogenic component of so-called magic mushrooms. It also covers psilocybin, dimethyltryptamine (DMT), ibogaine, mescaline excluding peyote, lysergic acid diethylamide (LSD) and 3,4-methylenedioxymethamphetamine (MDMA, often called ecstasy).

The bill bars sharing with those under age 21 or possessing the substances on school grounds. It would remove the state’s ban on cultivating or transferring mushroom spores or other material containing psilocybin or psilocybin.

Even if California makes the bill law, the drugs would still be illegal under federal law.

With files from the Associated Press.

Guests:

Scott Wiener, author of SB 519; California State Senator representing Senate District 11, which includes all of the city and county of San Francisco, Broadmoor, Colma, Daly City, and part of South San Francisco; he tweets @Scott_Wiener

John Lovell, legislative director of the California Narcotics Officers Association

This content is from Southern California Public Radio. View the original story at SCPR.org.




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USGS Releases New Topographic Maps for Puerto Rico and the U.S. Virgin Islands - Updated Maps for Essential Needs

The USGS is pleased to announce the release of new US Topo maps for Puerto Rico and the U.S. Virgin Islands. These updated topographic maps offer valuable, current geographic information for residents, visitors, and professionals, providing essential resources for communities in these areas.




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FORT Economist James Meldrum and the Wildfire Research Team win the 2024 CO-LABS Governor’s Awards for High Impact Research: Pathfinding Partnerships Award

The Pathfinding Partnerships Award from CO-LABS recognizes impactful, collaborative research projects organized by four or more research entities, including federal labs, in Colorado. This year, the Wildfire Research (WiRē) team received this award for their support of evidence-based community wildfire education to help communities live with wildfire. 




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Biden Will Visit The Surfside Condominium Collapse This Week

President Biden plans to visit the Champlain Towers condo collapse later this week.; Credit: Lynne Sladky/AP

Brian Naylor | NPR

Updated June 29, 2021 at 12:44 PM ET

The White House says President Biden and first lady Jill Biden will travel to Florida Thursday to view first hand the partial collapse of the Champlain Towers condominium.

Asked by reporters if he planned to visit Surfside, Biden said, "Yes I hope so, as soon as we can. Maybe as early as Thursday." The White House issued a formal announcement of the trip shortly afterward.

The official death toll in the collapse has risen to 11, with some 150 people unaccounted for.

The Biden administration has responded to the disaster, dispatching FEMA administrator Deanne Criswell to the scene earlier this week.

"[The agency] has deployed an Incident Management Assistance Team, as well as building science experts, structural engineers and geotechnical experts to support search-and-rescue operations, and a mobile command center," White House press secretary Jen Psaki said Monday.

Psaki said the U.S. Army Corps of Engineers is also providing technical assistance for debris removal. Two FEMA-supported search-and-rescue teams are also involved in the response to the collapse.

Florida Gov. Ron DeSantis has praised FEMA and the Biden administration for "stepping up to the plate" in providing assistance in the search and recovery effort. Miami-Dade Mayor Daniella Levine Cava said Biden's upcoming trip would be "an important reminder that our county, our state and our nation are giving everything we have to search for the victims of this tragedy and support the families in this incredibly devastating time."

Here's what we know about what led to the collapse. Follow more coverage on the aftermath here.

Florida Division of Emergency Management is urging people with information about loved ones who are either unaccounted for or known to be safe to call 305-614-1819.

Copyright 2021 NPR. To see more, visit https://www.npr.org.

This content is from Southern California Public Radio. View the original story at SCPR.org.




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Progressives Are Hoping That Justice Stephen Breyer Steps Down At The End Of The Term

Progressive activists are watching the end of the Supreme Court session for a possible retirement announcement from Stephen Breyer, the court's oldest current justice. Breyer will turn 83 in August.; Credit: Erin Schaff/The New York Times via AP/Pool

Susan Davis | NPR

For Erwin Chemerinsky, this is a familiar feeling: Seven years ago, the dean of the University of California Berkeley School of Law publicly called for Justice Ruth Bader Ginsburg to retire from the Supreme Court because he reasoned too much was at stake in the 2016 elections.

Ginsburg didn't listen then, but he's hoping Justice Stephen Breyer will listen now — but Breyer has given no indication whether he plans to stay or go.

"If he wants someone with his values and views to take his place, now is the time to step down," Chemerinsky told NPR.

Progressive activists are hoping that Breyer, who will turn 83 in August, will announce he is retiring Thursday, the same day the Supreme Court delivers its final two opinions of the term. But a justice can decide to retire at any time — though both Anthony Kennedy and Sandra Day O'Connor announced their respective retirements at the end of the court's session.

Chemerinsky is part of a growing rank of progressives who are breaking with the polite, political norms of the past when it comes to questioning service on the Supreme Court. Ginsburg's death last year and the subsequent appointment of Amy Coney Barrett to deliver a conservative supermajority on the court had a lot to do with that.

"I think a lot of people who thought that silence was the best approach in 2013 came to regret that in the aftermath of [Ginsburg's] untimely passing last year," said Brian Fallon, executive director of Demand Justice. "I think it would be foolish of us to repeat this same mistake and to greet the current situation passively and not do everything we can to signal to Justice Breyer, that now is the time for him to step down"

Since Democrats took control of the Senate in January, Demand Justice has organized public demonstrations, billboard and ad campaigns, and assembled a list of scholars and activists to join their public pressure campaign for Breyer to retire.

The risk, as Fallon sees it, is twofold. The first is the perils of a 50-50 Senate.

"The Democrats are one heartbeat away from having control switch in the Senate," he said. "There's a lot of octogenarian senators, many of whom have Republican governors that might get to appoint a successor to them if the worst happened."

The second is the 2022 midterms when control of the Senate will be in play.

"If [Senate Minority Leader] Mitch McConnell reassumes the Senate majority leader post, at worst, he might block any Biden pick, and at best, Biden is going to have to calibrate who he selects in order to get them through a Republican-held Senate."

Both Chemerinsky and Fallon concede the public campaign is not without some risk.

"I've certainly heard from some that this might make him less likely to retire, perhaps to dig in his heels," Chemerinsky said.

The campaign has also not caught fire on Capitol Hill, where only a small handful of progressive senators have — tactfully — suggested they'd like to see Breyer retire of his own accord.

Sen. Jeff Merkley, D-Ore., told CNN this month he did not support any Senate-led pressure campaigns on the court, but he added: "My secret heart is that some members, particularly the 82-year-old Stephen Breyer, will maybe have that thought on his own, that he should not let his seat be subject to a potential theft."

Senate Judiciary Chairman Dick Durbin, D-Ill., also distanced himself from the public retirement push, telling NPR: "I'm not on that campaign to put pressure on Justice Breyer. He's done an exceptional job. He alone can make the decision about his future. And I trust him to make the right one."

Absent any change in the status quo, Democrats will control the Senate at least until 2023. If the court's session ends without a retirement announcement, Fallon said he expects the calls for Breyer's retirement will grow louder. It's all part of what he said is a new, more aggressive position on the Supreme Court from the left.

"In some way, we are trying to make a point that progressives for too long, have taken a hands-off approach to the court," he said. "And they've been sort of foolish for doing so because the other side doesn't operate that way."

Copyright 2021 NPR. To see more, visit https://www.npr.org.

This content is from Southern California Public Radio. View the original story at SCPR.org.