ted The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era By journals.iucr.org Published On :: 2024-10-03 The availability of highly accurate protein structure predictions from AlphaFold2 (AF2) and similar tools has hugely expanded the applicability of molecular replacement (MR) for crystal structure solution. Many structures can be solved routinely using raw models, structures processed to remove unreliable parts or models split into distinct structural units. There is therefore an open question around how many and which cases still require experimental phasing methods such as single-wavelength anomalous diffraction (SAD). Here, this question is addressed using a large set of PDB depositions that were solved by SAD. A large majority (87%) could be solved using unedited or minimally edited AF2 predictions. A further 18 (4%) yield straightforwardly to MR after splitting of the AF2 prediction using Slice'N'Dice, although different splitting methods succeeded on slightly different sets of cases. It is also found that further unique targets can be solved by alternative modelling approaches such as ESMFold (four cases), alternative MR approaches such as ARCIMBOLDO and AMPLE (two cases each), and multimeric model building with AlphaFold-Multimer or UniFold (three cases). Ultimately, only 12 cases, or 3% of the SAD-phased set, did not yield to any form of MR tested here, offering valuable hints as to the number and the characteristics of cases where experimental phasing remains essential for macromolecular structure solution. Full Article text
ted C-SPAM: an open-source time-resolved specimen vitrification device with light-activated molecules By journals.iucr.org Published On :: 2023-12-14 Molecular structures can be determined in vitro and in situ with cryo-electron microscopy (cryo-EM). Specimen preparation is a major obstacle in cryo-EM. Typical sample preparation is orders of magnitude slower than biological processes. Time-resolved cryo-EM (TR-cryo-EM) can capture short-lived states. Here, Cryo-EM sample preparation with light-activated molecules (C-SPAM) is presented, an open-source, photochemistry-coupled device for TR-cryo-EM that enables millisecond resolution and tunable timescales across broad biological applications. Full Article text
ted Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure By journals.iucr.org Published On :: 2024-04-11 An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer's patients' brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ4–8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis. This enables these peptides to perform redox cycles in a manner that might produce toxicity in human brains. Fluorescence XAS measurements were corrected for systematic errors including defective-pixel data, monochromator glitches and dispersion of pixel spectra. Experimental uncertainties at each data point were measured explicitly from the point-wise variance of corrected pixel measurements. The copper-binding environments of Aβ4–8/12/16 were precisely determined by fitting XAS measurements with propagated experimental uncertainties, advanced analysis and hypothesis testing, providing a mechanism to pursue many similarly complex questions in bioscience. The low-temperature XAS measurements here determine that CuII is bound to the first amino acids in the high-affinity amino-terminal copper and nickel (ATCUN) binding motif with an oxygen in a tetragonal pyramid geometry in the Aβ4–8/12/16 peptides. Room-temperature XAS electrochemical-cell measurements observe metal reduction in the Aβ4–16 peptide. Robust investigations of XAS provide structural details of CuII binding with a very different bis-His motif and a water oxygen in a quasi-tetrahedral geometry. Oxidized XAS measurements of Aβ4–12/16 imply that both CuII and CuIII are accommodated in an ATCUN-like binding site. Hypotheses for these CuI, CuII and CuIII geometries were proven and disproven using the novel data and statistical analysis including F tests. Structural parameters were determined with an accuracy some tenfold better than literature claims of past work. A new protocol was also developed using EXAFS data analysis for monitoring radiation damage. This gives a template for advanced analysis of complex biosystems. Full Article text
ted RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures By journals.iucr.org Published On :: 2024-04-10 The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations. Full Article text
ted Chaperone-mediated MHC-I peptide exchange in antigen presentation By journals.iucr.org Published On :: 2024-04-24 This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation. Full Article text
ted Scanning WAXS microscopy of regenerated cellulose fibers at mesoscopic resolution By journals.iucr.org Published On :: 2024-06-11 In this work, regenerated cellulose textile fibers, Ioncell-F, dry-wet spun with different draw ratios, have been investigated by scanning wide-angle X-ray scattering (WAXS) using a mesoscopic X-ray beam. The fibers were found to be homogeneous on the 500 nm length scale. Analysis of the azimuthal angular dependence of a crystalline Bragg spot intensity revealed a radial dependence of the degree of orientation of crystallites that was found to increase with the distance from the center of the fiber. We attribute this to radial velocity gradients during the extrusion of the spin dope and the early stage of drawing. On the other hand, the fiber crystallinity was found to be essentially homogeneous over the fiber cross section. Full Article text
ted A predicted model-aided reconstruction algorithm for X-ray free-electron laser single-particle imaging By journals.iucr.org Published On :: 2024-06-21 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. Full Article text
ted Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography By journals.iucr.org Published On :: 2024-07-22 Light–oxygen–voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process. Full Article text
ted A predicted model-aided one-step classification–multireconstruction algorithm for X-ray free-electron laser single-particle imaging By journals.iucr.org Published On :: 2024-08-28 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. Full Article text
ted Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography By journals.iucr.org Published On :: 2024-10-29 OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates. Full Article text
ted Unity gives strength: combining Bertaut's and Belov's concepts and the formalism of aperiodic crystals to solve magnetic structures of unprecedented complexity By journals.iucr.org Published On :: 2024-10-29 Full Article text
ted Three-dimensional electron diffraction on clinkers: the belite α'H incommensurate modulated structure By journals.iucr.org Published On :: 2024-03-06 Traditional X-ray methods are extensively applied to commercial cement samples in order to determine their physical and chemical properties. Powder patterns are routinely used to quantify the composition of these phase mixtures, but structure determination becomes difficult because of reflection overlapping caused by the high number of different crystal structures. The fast-growing 3D electron diffraction technique and its related automated acquisition protocols arise as a potentially very interesting tool for the cement industry, since they enable the fast and systematic acquisition of diffraction data from individual particles. In this context, electron diffraction has been used in the investigation of the different crystalline phases present in various commercial clinkers for cement. Automated data collection procedures and subsequent data processing have enabled the structural characterization of the different crystal structures from which the α'H polymorph of Ca2SiO4 (belite) exhibited satellite reflections. Its average crystal structure has been known since 1971 and satellite reflections have been reported previously, yet the modulation was never fully described by means of the superspace formalism. Here, the incommensurately modulated structure is solved and refined using harmonic and crenel functions in the superspace group Pnma(α00)0ss, showing the potential of 3D electron diffraction for systematic crystallographic characterizations of cement. A full description of the different belite polymorphs is provided considering this modulated structure. Full Article text
ted Importance of powder diffraction raw data archival in a curated database for materials science applications By journals.iucr.org Published On :: 2024-08-26 In recent years, there is a significant interest from the crystallographic and materials science communities to have access to raw diffraction data. The effort in archiving raw data for access by the user community is spearheaded by the International Union of Crystallography (IUCr) Committee on Data. In materials science, where powder diffraction is extensively used, the challenge in archiving raw data is different to that from single crystal data, owing to the very nature of the contributions involved. Powder diffraction (X-ray or neutron) data consist of contributions from the material under study as well as instrument specific parameters. Having raw powder diffraction data can be essential in cases of analysing materials with poor crystallinity, disorder, micro structure (size/strain) etc. Here, the initiative and progress made by the International Centre for Diffraction Data (ICDDR) in archiving powder X-ray diffraction raw data in the Powder Diffraction FileTM (PDFR) database is outlined. The upcoming 2025 release of the PDF-5+ database will have more than 20 800 raw powder diffraction patterns that are available for reference. Full Article text
ted A short note on the use of irreducible representations for tilted octahedra in perovskites By journals.iucr.org Published On :: 2024-08-08 It is pointed out that many authors are unaware that the particular choice of unit-cell origin determines the irreducible representations to which octahedral tilts in perovskites belong. Furthermore, a recommendation is made that the preferred option is with the origin at the B-cation site rather than that of the A site. Full Article text
ted Crystal structure of S-n-octyl 3-(1-phenylethylidene)dithiocarbazate and of its bis-chelated nickel(II) complex By journals.iucr.org Published On :: 2023-11-14 The nitrogen–sulfur Schiff base proligand S-n-octyl 3-(1-phenylethylidene)dithiocarbazate, C17H26N2S2 (HL), was prepared by reaction of S-octyl dithiocarbamate with acetophenone. Treatment of HL with nickel acetate yielded the complex bis[S-n-octyl 3-(1-phenylethylidene)dithiocarbazato]nickel(II), [Ni(C17H25N2S2)2] (NiL2), which was shown to adopt a tetrahedrally distorted cis-square-planar coordination geometry, with the NiSN planes of the two ligands forming a dihedral angle of 21.66 (6)°. Changes in the geometry of the L ligand upon chelation of Ni2+ are described, involving a ca 180° rotation around the N(azomethine)—C(thiolate) bond. Full Article text
ted Synthesis and crystal structures of two related Co and Mn complexes: a celebration of collaboration between the universities of Dakar and Southampton By journals.iucr.org Published On :: 2023-11-16 We report the synthesis and structures of two transition-metal complexes involving 2-(2-hydroxyphenyl)benzimidazole (2hpbi – a ligand of interest for its photoluminescent applications), with cobalt, namely, bis[μ-2-(1H-1,3-benzodiazol-2-yl)phenolato]bis[ethanol(thiocyanato)cobalt(II)], [Co2(C13H9N2O)2(NCS)2(C2H6O)2], (1), and manganese, namely, bis[μ-2-(1H-1,3-benzodiazol-2-yl)phenolato]bis{[2-(1H-1,3-benzodiazol-2-yl)phenolato](thiocyanato)manganese(III)} dihydrate, [Mn2(C13H9N2O)4(NCS)2]·2H2O, (2). These structures are two recent examples of a fruitful collaboration between researchers at the Laboratoire de Chimie de Coordination Organique/Organic Coordination Chemistry Laboratory (LCCO), University of Dakar, Senegal and the National Crystallography Service (NCS), School of Chemistry, University Southampton, UK. This productive partnership was forged through meeting at Pan-African Conferences on Crystallography and quickly grew as the plans for the AfCA (African Crystallographic Association) developed. This article therefore also showcases this productive partnership, in celebration of the IUCr's 75 year anniversary and the recent inclusion of AfCA as a Regional Associate of the IUCr. Full Article text
ted An unexpected tautomer: synthesis and crystal structure of N-[6-amino-4-(methylsulfanyl)-1,2-dihydro-1,3,5-triazin-2-ylidene]benzenesulfonamide By journals.iucr.org Published On :: 2024-01-09 The title compound, C10H11N5O2S2, consists of an unexpected tautomer with a protonated nitrogen atom in the triazine ring and a formal exocyclic double bond C=N to the sulfonamide moiety. The ring angles at the unsubstituted nitrogen atoms are narrow, at 115.57 (12) and 115.19 (12)°, respectively, whereas the angle at the carbon atom between these N atoms is very wide, 127.97 (13)°. The interplanar angle between the two rings is 79.56 (5)°. The molecules are linked by three classical hydrogen bonds, forming a ribbon structure. There are also unusual linkages involving three short contacts (< 3 Å) from a sulfonamide oxygen atom to the C—NH—C part of a triazine ring. Full Article text
ted Crystal structures of sulfonamide protected bicyclic guanidines: (S)-8-{[(tert-butyldimethylsilyl)oxy]methyl}-1-[(2,2,4,6,7-pentamethyl-2,3-dihydrobenzofuran-5-yl)sulfonyl]-1,3,4,6,7,8-hexa By journals.iucr.org Published On :: 2024-02-20 Two compounds, (S)-8-{[(tert-butyldimethylsilyl)oxy]methyl}-1-[(2,2,4,6,7-pentamethyl-2,3-dihydrobenzofuran-5-yl)sulfonyl]-1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-1-ium trifluoromethanesulfonate, C27H46N3O4SSi+·CF3O3S−, (1) and (S)-8-(iodomethyl)-1-tosyl-1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-1-ium iodide, C15H21IN3O2S+·I−, (2), have been synthesized and characterized. They are bicyclic guanidinium salts and were synthesized from N-(tert-butoxycarbonyl)-l-methionine (Boc-l-Met-OH). The guanidine is protected by a 2,2,4,6,7-pentamethyldihydrobenzofuran-5-sulfonyl (Pbf, 1) or a tosyl (2) group. In the crystals of both compounds, the guanidinium group is almost planar and the N–H forms an intramolecular hydrogen bond in a six-membered ring to the oxygen atom of the sulfonamide protecting group. Full Article text
ted The unanticipated oxidation of a tertiary amine in a tetracyclic glyoxal-cyclam condensate yielding zinc(II) coordinated to a sterically hindered amine oxide By journals.iucr.org Published On :: 2024-03-06 The complex, trichlorido(1,4,11-triaza-8-azoniatetracyclo[6.6.2.04,16.011,15]hexadecane 1-oxide-κO)zinc(II) monohydrate, [ZnCl3(C12H23N4O)]·H2O, (I), has monoclinic symmetry (space group P21/n) at 120 K. The zinc(II) center adopts a slightly distorted tetrahedral coordination geometry and is coordinated by three chlorine atoms and the oxygen atom of the oxidized tertiary amine of the tetracycle. The amine nitrogen atom, inside the ligand cleft, is protonated and forms a hydrogen bond to the oxygen of the amine oxide. Additional hydrogen-bonding interactions involve the protonated amine, the water solvate oxygen atom, and one of the chloro ligands. Full Article text
ted Synthesis and structural characterization of a hydrated sodium–caesium tetracosatungstate(VI), Na5Cs19[W24O84]·21H2O By journals.iucr.org Published On :: 2024-05-31 Crystal formation of pentasodium nonadecacesium tetracosatungstate(VI) heneikosahydrate, Na5Cs19[W24O84]·21H2O, was successfully achieved by the conversion of [H2W12O42]10− through the addition of excess Cs+. The crystal structure comprising the toroidal isopolyoxidometalate is presented, as well as its Raman spectrum. Na5Cs19(H2O)21W24O84 crystallizes in the rhombohedral space group Roverline{3} with an obverse centering. The title compound represents the addition of a new member to the isopolytungstate family with mixed alkali counter-ions and contains rarely observed five-coordinate tungsten(VI) atoms in the [W24O84]24− anion (site symmetry C3i) arising from the conversion mediated by Cs+ counter-ions. Full Article text
ted The crystal structures and Hirshfeld surface analysis of three new bromo-substituted 3-methyl-1-(phenylsulfonyl)-1H-indole derivatives By journals.iucr.org Published On :: 2024-05-31 Three new 1H-indole derivatives, namely, 2-(bromomethyl)-3-methyl-1-(phenylsulfonyl)-1H-indole, C16H14BrNO2S, (I), 2-[(E)-2-(2-bromo-5-methoxyphenyl)ethenyl]-3-methyl-1-(phenylsulfonyl)-1H-indole, C24H20BrNO3S, (II), and 2-[(E)-2-(2-bromophenyl)ethenyl]-3-methyl-1-(phenylsulfonyl)-1H-indole, C23H18BrNO2S, (III), exhibit nearly orthogonal orientations of their indole ring systems and sulfonyl-bound phenyl rings. Such conformations are favourable for intermolecular bonding involving sets of slipped π–π interactions between the indole systems and mutual C—H⋯π hydrogen bonds, with the generation of two-dimensional monoperiodic patterns. The latter are found in all three structures, in the form of supramolecular columns with every pair of successive molecules related by inversion. The crystal packing of the compounds is additionally stabilized by weaker slipped π–π interactions between the outer phenyl rings (in II and III) and by weak C—H⋯O, C—H⋯Br and C—H⋯π hydrogen bonds. The structural significance of the different kinds of interactions agree with the results of a Hirshfeld surface analysis and the calculated interaction energies. In particular, the largest interaction energies (up to −60.8 kJ mol−1) are associated with pairing of antiparallel indole systems, while the energetics of weak hydrogen bonds and phenyl π–π interactions are comparable and account for 13–34 kJ mol−1. Full Article text
ted Syntheses and crystal structures of the five- and sixfold coordinated complexes diisoselenocyanatotris(2-methylpyridine N-oxide)cobalt(II) and diisoselenocyanatotetrakis(2-methylpyridine N- By journals.iucr.org Published On :: 2024-06-07 The reaction of CoBr2, KNCSe and 2-methylpyridine N-oxide (C6H7NO) in ethanol leads to the formation of crystals of [Co(NCSe)2(C6H7NO)3] (1) and [Co(NCSe)2(C6H7NO)4] (2) from the same reaction mixture. The asymmetric unit of 1 is built up of one CoII cation, two NCSe− isoselenocyanate anions and three 2-methylpyridine N-oxide coligands, with all atoms located on general positions. The asymmetric unit of 2 consists of two cobalt cations, four isoselenocanate anions and eight 2-methylpyridine N-oxide coligands in general positions, because two crystallographically independent complexes are present. In compound 1, the CoII cations are fivefold coordinated to two terminally N-bonded anionic ligands and three 2-methylpyridine N-oxide coligands within a slightly distorted trigonal–bipyramidal coordination, forming discrete complexes with the O atoms occupying the equatorial sites. In compound 2, each of the two complexes is coordinated to two terminally N-bonded isoselenocyanate anions and four 2-methylpyridine N-oxide coligands within a slightly distorted cis-CoN2O4 octahedral coordination geometry. In the crystal structures of 1 and 2, the complexes are linked by weak C—H⋯Se and C—H⋯O contacts. Powder X-ray diffraction reveals that neither of the two compounds were obtained as a pure crystalline phase. Full Article text
ted Crystal structures of four gold(I) complexes [AuL2]+[AuX2]− and a by-product (L·LH+)[AuBr2]− (L = substituted pyridine, X = Cl or Br) By journals.iucr.org Published On :: 2024-06-18 Bis(2-methylpyridine)gold(I) dibromidoaurate(I), [Au(C6H7N)2][AuBr2], (1), crystallizes in space group C2/c with Z = 4. Both gold atoms lie on twofold axes and are connected by an aurophilic contact. A second aurophilic contact leads to infinite chains of alternating cations and anions parallel to the b axis, and the residues are further connected by a short H⋯Au contact and a borderline Br⋯Br contact. Bis(3-methylpyridine)gold(I) dibromidoaurate(I), [Au(C6H7N)2][AuBr2], (2), crystallizes in space group C2/m with Z = 2. Both gold atoms lie on special positions with symmetry 2/m and are connected by an aurophilic contact; all other atoms except for one methyl hydrogen lie in mirror planes. The extended structure is closely analogous to that of 1, although the structures are formally not isotypic. Bis(3,5-dimethylpyridine)gold(I) dichloridoaurate(I), [Au(C7H9N)2][AuCl2], (3) crystallizes in space group Poverline{1} with Z = 2. The cation lies on a general position, and there are two independent anions in which the gold atoms lie on inversion centres. The cation and one anion associate via three short H⋯Cl contacts to form a ribbon structure parallel to the b axis; aurophilic contacts link adjacent ribbons. Bis(3,5-dimethylpyridine)gold(I) dibromidoaurate(I), [Au(C7H9N)2][AuBr2], (4) is isotypic to 3. Attempts to make similar compounds involving 2-bromopyridine led instead to 2-bromopyridinium dibromidoaurate(I)–2-bromopyridine (1/1), (C5H5BrN)[AuBr2]·C5H4BrN, (5), which crystallizes in space group Poverline{1} with Z = 2; all atoms lie on general positions. The 2-bromopyridinium cation is linked to the 2-bromopyridine molecule by an N—H⋯N hydrogen bond. Two formula units aggregate to form inversion-symmetric dimers involving Br⋯Br, Au⋯Br and H⋯Br contacts. Full Article text
ted Crystal structures of seven gold(III) complexes of the form LAuX3 (L = substituted pyridine, X = Cl or Br) By journals.iucr.org Published On :: 2024-07-31 The structures of seven gold(III) halide derivatives of general formula LAuX3 (L = methylpyridines or dimethylpyridines, X = Cl or Br) are presented: trichlorido(2-methylpyridine)gold(III), [AuCl3(C6H7N)], 1 (as two polymorphs 1a and 1b); tribromido(2-methylpyridine)gold(III), [AuBr3(C6H7N)], 2; tribromido(3-methylpyridine)gold(III), [AuBr3(C6H7N)], 3; tribromido(2,4-dimethylpyridine)gold(III), [AuBr3(C7H9N)], 4; trichlorido(3,5-dimethylpyridine)gold(III), [AuCl3(C7H9N)], 5; tribromido(3,5-dimethylpyridine)gold(III), [AuBr3(C7H9N)], 6, and trichlorido(2,6-dimethylpyridine)gold(III), [AuCl3(C7H9N)], 7. Additionally, the structure of 8, the 1:1 adduct of 2 and 6, [AuBr3(C6H7N)]·[AuBr3(C7H9N)], is included. All the structures crystallize solvent-free, and all have Z' = 1 except for 5 and 7, which display crystallographic twofold rotation symmetry, and 4, which has Z' = 2. 1a and 2 are isotypic. The coordination geometry at the gold(III) atoms is, as expected, square-planar. Four of the crystals (1a, 1b, 2 and 8) were non-merohedral twins, and these structures were refined using the ‘HKLF 5’ method. The largest interplanar angles between the pyridine ring and the coordination plane are observed for those structures with a 2-methyl substituent of the pyridine ring. The Au—N bonds are consistently longer trans to Br (average 2.059 Å) than trans to Cl (average 2.036 Å). In the crystal packing, a frequent feature is the offset-stacked and approximately rectangular dimeric moiety (Au—X)2, with antiparallel Au—X bonds linked by Au⋯X contacts at the vacant positions axial to the coordination plane. The dimers are connected by further secondary interactions (Au⋯X or X⋯X contacts, `weak' C—H⋯X hydrogen bonds) to form chain, double chain (`ladder') or layer structures, and in several cases linked again in the third dimension. Only 1b and 7 contain no offset dimers; these structures instead involve C—H⋯Cl hydrogen bonds combined with Cl⋯Cl contacts (1b) or Cl⋯π contacts (7). The packing patterns of seven further complexes LAuX3 involving simple pyridines (taken from the Cambridge Structural Database) are compared with those of 1–8. Full Article text
ted Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ6O)potassium-μ-oxalato-triphenylstannate(IV), the first reported 18-crown-6-stabilized potassium salt of triphenyloxalatostannate By journals.iucr.org Published On :: 2024-08-13 The title complex, (1,4,7,10,13,16-hexaoxacyclooctadecane-1κ6O)(μ-oxalato-1κ2O1,O2:2κ2O1',O2')triphenyl-2κ3C-potassium(I)tin(IV), [KSn(C6H5)3(C2O4)(C12H24O6)] or K[18-Crown-6][(C6H5)3SnO4C2], was synthesized. The complex consists of a potassium cation coordinated to the six oxygen atoms of a crown ether molecule and the two oxygen atoms of the oxalatotriphenylstannate anion. It crystallizes in the monoclinic crystal system within the space group P21. The tin atom is coordinated by one chelating oxalate ligand and three phenyl groups, forming a cis-trigonal–bipyramidal geometry around the tin atom. The cations and anions form ion pairs, linked through carbonyl coordination to the potassium atoms. The crystal structure features C—H⋯O hydrogen bonds between the oxygen atoms of the oxalate group and the hydrogen atoms of the phenyl groups, resulting in an infinite chain structure extending along a-axis direction. The primary inter-chain interactions are van der Waals forces. Full Article text
ted Structural multiplicity in a solvated hydrate of the antiretroviral protease inhibitor Lopinavir By journals.iucr.org Published On :: 2024-10-24 Lopinavir is a potent protease inhibitor that is used as a first-line pharmaceutical drug for the treatment of HIV. The multi-component solvated Lopinavir crystal, systematic name (2S)-N-[(2S,4S,5S)-5-[2-(2,6-dimethylphenoxy)acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide–ethane-1,2-diol–water (8/3/7) 8C37H48N4O5·3C2H6O2·7H2O, was prepared using evaporative methods. The crystalline material obtained from this experimental synthesis was characterized and elucidated by single-crystal X-ray diffraction (SC-XRD). The crystal structure is unusual in that the unit cell contains 18 molecules. The stoichiometric ratio of this crystal is eight Lopinavir molecules [8(C37H48N4O5)], three ethane-1,2-diol molecules [3(C2H6O2)] and seven water molecules [7(H2O)]. The crystal packing features both bi- and trifurcated hydrogen bonds between atoms. Full Article text
ted Reducing heat load density with asymmetric and inclined double-crystal monochromators: principles and requirements revisited By journals.iucr.org Published On :: The major principles and requirements of asymmetric and inclined double-crystal monochromators are re-examined and presented to guide their design and development for significantly reducing heat load density and gradient on the monochromators of fourth-generation synchrotron light sources and X-ray free-electron lasers. Full Article text
ted Form factor of helical structures and twisted fibres By journals.iucr.org Published On :: 2023-11-07 A general formalism is presented for the isotropically averaged single-chain scattering function (form factor) of single, double, triple and higher-order helices, as well as twisted fibres consisting of concentric layers of strands. Form factors for double and triple helices with differently sized grooves have also been derived. The formulas include the longitudinal and transverse interference over the pitch and radius of the helices, respectively. The results may be useful for the analysis of small-angle scattering data of (bio)macromolecules or molecular assemblies exhibiting a helical arrangement. Full Article text
ted Van Vleck analysis of angularly distorted octahedra using VanVleckCalculator By journals.iucr.org Published On :: 2024-02-01 Van Vleck modes describe all possible displacements of octahedrally coordinated ligands about a core atom. They are a useful analytical tool for analysing the distortion of octahedra, particularly for first-order Jahn–Teller distortions, but determination of the Van Vleck modes of an octahedron is complicated by the presence of angular distortion of the octahedron. This problem is most commonly resolved by calculating the bond distortion modes (Q2, Q3) along the bond axes of the octahedron, disregarding the angular distortion and losing information on the octahedral shear modes (Q4, Q5 and Q6) in the process. In this paper, the validity of assuming bond lengths to be orthogonal in order to calculate the Van Vleck modes is discussed, and a method is described for calculating Van Vleck modes without disregarding the angular distortion. A Python package for doing this, VanVleckCalculator, is introduced and some examples of its use are given. Finally, it is shown that octahedral shear and angular distortion are often, but not always, correlated, and a parameter η is proposed as the shear fraction. It is demonstrated that η can be used to predict whether the values will be correlated when varying a tuning parameter such as temperature or pressure. Full Article text
ted Convolutional neural network approach for the automated identification of in cellulo crystals By journals.iucr.org Published On :: 2024-02-23 In cellulo crystallization is a rare event in nature. Recent advances that have made use of heterologous overexpression can promote the intracellular formation of protein crystals, but new tools are required to detect and characterize these targets in the complex cell environment. The present work makes use of Mask R-CNN, a convolutional neural network (CNN)-based instance segmentation method, for the identification of either single or multi-shaped crystals growing in living insect cells, using conventional bright field images. The algorithm can be rapidly adapted to recognize different targets, with the aim of extracting relevant information to support a semi-automated screening pipeline, in order to aid the development of the intracellular protein crystallization approach. Full Article text
ted Design and fabrication of 3D-printed in situ crystallization plates for probing microcrystals in an external electric field By journals.iucr.org Published On :: 2024-04-15 X-ray crystallography is an established tool to probe the structure of macromolecules with atomic resolution. Compared with alternative techniques such as single-particle cryo-electron microscopy and micro-electron diffraction, X-ray crystallography is uniquely suited to room-temperature studies and for obtaining a detailed picture of macromolecules subjected to an external electric field (EEF). The impact of an EEF on proteins has been extensively explored through single-crystal X-ray crystallography, which works well with larger high-quality protein crystals. This article introduces a novel design for a 3D-printed in situ crystallization plate that serves a dual purpose: fostering crystal growth and allowing the concurrent examination of the effects of an EEF on crystals of varying sizes. The plate's compatibility with established X-ray crystallography techniques is evaluated. Full Article text
ted Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III By journals.iucr.org Published On :: 2024-07-04 Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc. Full Article text
ted Patching-based deep-learning model for the inpainting of Bragg coherent diffraction patterns affected by detector gaps By journals.iucr.org Published On :: 2024-06-18 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. Full Article text
ted A simple protocol for determining the zone axis direction from selected-area electron diffraction spot patterns of cubic materials By journals.iucr.org Published On :: 2024-06-18 Using the well known Rn ratio method, a protocol has been elaborated for determining the lattice direction for the 15 most common cubic zone axis spot patterns. The method makes use of the lengths of the three shortest reciprocal-lattice vectors in each pattern and the angles between them. No prior pattern calibration is required for the method to work, as the Rn ratio method is based entirely on geometric relationships. In the first step the pattern is assigned to one of three possible pattern types according to the angles that are measured between the three reciprocal-lattice vectors. The lattice direction [uvw] and possible Bravais type(s) and Laue indices of the corresponding reflections can then be determined by using lookup tables. In addition to determining the lattice direction, this simple geometric analysis allows one to distinguish between the P, I and F Bravais lattices for spot patterns aligned along [013], [112], [114] and [233]. Moreover, the F lattice can always be uniquely identified from the [011] and [123] patterns. Full Article text
ted Ptychographic phase retrieval via a deep-learning-assisted iterative algorithm By journals.iucr.org Published On :: 2024-08-19 Ptychography is a powerful computational imaging technique with microscopic imaging capability and adaptability to various specimens. To obtain an imaging result, it requires a phase-retrieval algorithm whose performance directly determines the imaging quality. Recently, deep neural network (DNN)-based phase retrieval has been proposed to improve the imaging quality from the ordinary model-based iterative algorithms. However, the DNN-based methods have some limitations because of the sensitivity to changes in experimental conditions and the difficulty of collecting enough measured specimen images for training the DNN. To overcome these limitations, a ptychographic phase-retrieval algorithm that combines model-based and DNN-based approaches is proposed. This method exploits a DNN-based denoiser to assist an iterative algorithm like ePIE in finding better reconstruction images. This combination of DNN and iterative algorithms allows the measurement model to be explicitly incorporated into the DNN-based approach, improving its robustness to changes in experimental conditions. Furthermore, to circumvent the difficulty of collecting the training data, it is proposed that the DNN-based denoiser be trained without using actual measured specimen images but using a formula-driven supervised approach that systemically generates synthetic images. In experiments using simulation based on a hard X-ray ptychographic measurement system, the imaging capability of the proposed method was evaluated by comparing it with ePIE and rPIE. These results demonstrated that the proposed method was able to reconstruct higher-spatial-resolution images with half the number of iterations required by ePIE and rPIE, even for data with low illumination intensity. Also, the proposed method was shown to be robust to its hyperparameters. In addition, the proposed method was applied to ptychographic datasets of a Simens star chart and ink toner particles measured at SPring-8 BL24XU, which confirmed that it can successfully reconstruct images from measurement scans with a lower overlap ratio of the illumination regions than is required by ePIE and rPIE. Full Article text
ted Towards dynamically configured databases for CIFs: the new modulated structures open database at the Bilbao Crystallographic Server By journals.iucr.org Published On :: 2024-09-17 This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via JSmol. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework. Full Article text
ted SUBGROUPS: a computer tool at the Bilbao Crystallographic Server for the study of pseudo-symmetric or distorted structures By journals.iucr.org Published On :: 2024-10-01 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. Full Article text
ted Deconstructing 3D growth rates from transmission microscopy images of facetted crystals as captured in situ within supersaturated aqueous solutions By journals.iucr.org Published On :: 2024-09-25 Here, a morphologically based approach is used for the in situ characterization of 3D growth rates of facetted crystals from the solution phase. Crystal images of single crystals of the β-form of l-glutamic acid are captured in situ during their growth at a relative supersaturation of 1.05 using transmission optical microscopy. The crystal growth rates estimated for both the {101} capping and {021} prismatic faces through image processing are consistent with those determined using reflection light mode [Jiang, Ma, Hazlehurst, Ilett, Jackson, Hogg & Roberts (2024). Cryst. Growth Des. 24, 3277–3288]. The growth rate in the {010} face is, for the first time, estimated from the shadow widths of the {021} prismatic faces and found to be typically about half that of the {021} prismatic faces. Analysis of the 3D shape during growth reveals that the initial needle-like crystal morphology develops during the growth process to become more tabular, associated with the Zingg factor evolving from 2.9 to 1.7 (>1). The change in relative solution supersaturation during the growth process is estimated from calculations of the crystal volume, offering an alternative approach to determine this dynamically from visual observations. Full Article text
ted Development of hard X-ray photoelectron spectroscopy in liquid cells using optimized microfabricated silicon nitride membranes By journals.iucr.org Published On :: 2024-10-15 We present first hard X-ray photoelectron spectroscopy (HAXPES) results of aqueous salt solutions and dispersions of gold nanoparticles in liquid cells equipped with specially designed microfabricated thin silicon nitride membranes, with thickness in the 15–25 nm range, mounted in a high-vacuum-compatible environment. The experiments have been performed at the HAXPES endstation of the GALAXIES beamline at the SOLEIL synchrotron radiation facility. The low-stress membranes are fabricated from 100 mm silicon wafers using standard lithography techniques. Platinum alignment marks are added to the chips hosting the membranes to facilitate the positioning of the X-ray beam on the membrane by detecting the corresponding photoemission lines. Two types of liquid cells have been used, a static one built on an Omicron-type sample holder with the liquid confined in the cell container, and a circulating liquid cell, in which the liquid can flow in order to mitigate the effects due to beam damage. We demonstrate that the membranes are mechanically robust and able to withstand 1 bar pressure difference between the liquid inside the cell and vacuum, and the intense synchrotron radiation beam during data acquisition. This opens up new opportunities for spectroscopic studies of liquids. Full Article text
ted Foreword to the special virtual issue dedicated to the proceedings of the PhotonMEADOW2023 Joint Workshop By journals.iucr.org Published On :: 2024-10-11 Full Article text
ted Keyshia Cole arrested on suspicion of battery By www.scpr.org Published On :: Fri, 19 Sep 2014 17:34:44 -0700 Keyshia Cole performs during the 4th annual BET Honors at the Warner Theatre on Jan. 15, 2011 in Washington, DC.; Credit: Kris Connor/Getty Images Police say Grammy-nominated R&B singer Keyshia Cole has been arrested on suspicion of battery after an altercation early Friday morning in Los Angeles. Los Angeles police officer Nuria Vanegas says Cole was arrested around 5 a.m. after someone initiated a private person's arrest. The 32-year-old was booked on suspicion of battery and released from custody Friday afternoon. Police did not release any further details about the incident. An email message sent to Cole's publicist was not immediately returned. Cole's second album, 2007's "Just Like You," produced the songs "Let It Go," ''I Remember" and "Heaven Sent." Full Article
ted Periodic graphs with coincident edges: folding-ladder and related graphs By journals.iucr.org Published On :: We explore a special class of periodic graphs, ladder graphs, whose edges can coincide when embedded vertices are moved. Many of these exhibit additional non-crystallographic graph symmetries. Full Article text
ted Redheffer and Mertens, Accelerated By blogs.mathworks.com Published On :: Mon, 30 Sep 2024 14:28:40 +0000 Shortly after I published the second post about the Mertens conjecture, a reader's comment suggested a new approach to computing Redheffer determinants and the Mertens function. It is now possible to compute a half-million values of the Mertens function in about five hours.... read more >> Full Article Fun History Primes Uncategorized
ted He Inherited A Devastating Disease. A CRISPR Gene-Editing Breakthrough Stopped It By www.scpr.org Published On :: Sat, 26 Jun 2021 10:20:08 -0700 Patrick Doherty volunteered for a new medical intervention of gene-editor infusions for the treatment of genetically-based diseases.; Credit: /Patrick Doherty Rob Stein | NPRPatrick Doherty had always been very active. He trekked the Himalayas and hiked trails in Spain. But about a year and a half ago, he noticed pins and needles in his fingers and toes. His feet got cold. And then he started getting out of breath any time he walked his dog up the hills of County Donegal in Ireland where he lives. "I noticed on some of the larger hill climbs I was getting a bit breathless," says Doherty, 65. "So I realized something was wrong." Doherty found out he had a rare, but devastating inherited disease — known as transthyretin amyloidosis — that had killed his father. A misshapen protein was building up in his body, destroying important tissues, such as nerves in his hands and feet and his heart. Doherty had watched others get crippled and die difficult deaths from amyloidosis. "It's terrible prognosis," Doherty says. "This is a condition that deteriorates very rapidly. It's just dreadful." So Doherty was thrilled when he found out that doctors were testing a new way to try to treat amyloidosis. The approach used a revolutionary gene-editing technique called CRISPR, which allows scientists to make very precise changes in DNA. "I thought: Fantastic. I jumped at the opportunity," Doherty says. On Saturday, researchers reported the first data indicating that the experimental treatment worked, causing levels of the destructive protein to plummet in Doherty's body and the bodies of five other patients treated with the approach. "I feel fantastic," Doherty says. "It's just phenomenal." The advance is being hailed not just for amyloidosis patients but also as a proof-of-concept that CRISPR could be used to treat many other, much more common diseases. It's a new way of using the innovative technology. "This is a major milestone for patients," says Jennifer Doudna of the University of California, Berkeley, who shared a Nobel Prize for her work helping develop CRISPR. "While these are early data, they show us that we can overcome one of the biggest challenges with applying CRISPR clinically so far, which is being able to deliver it systemically and get it to the right place," Doudna says. CRISPR has already been shown to help patients suffering from the devastating blood disorders sickle cell disease and beta thalassemia. And doctors are trying to use it to treat cancer and to restore vision to people blinded by a rare genetic disorder. But those experiments involve taking cells out of the body, editing them in the lab, and infusing them back in or injecting CRISPR directly into cells that need fixing. The study Doherty volunteered for is the first in which doctors are simply infusing the gene-editor directly into patients and letting it find its own way to the right gene in the right cells. In this case, it's cells in the liver making the destructive protein. "This is the first example in which CRISPR-Cas9 is injected directly into the bloodstream — in other words systemic administration — where we use it as a way to reach a tissue that's far away from the site of injection and very specifically use it to edit disease-causing genes," says John Leonard, the CEO of Intellia Therapeutics, which is sponsoring the study. Doctors infused billions of microscopic structures known as nanoparticles carrying genetic instructions for the CRISPR gene-editor into four patients in London and two in New Zealand. The nanoparticles were absorbed by their livers, where they unleashed armies of CRISPR gene-editors. The CRISPR editor honed in on the target gene in the liver and sliced it, disabling production of the destructive protein. Within weeks, the levels of protein causing the disease plummeted. Researchers reported at the Peripheral Nerve Society Annual Meeting and in a paper published in The New England Journal of Medicine. "It really is exciting," says Dr. Julian Gillmore, who is leading the study at the University College London, Royal Free Hospital. "This has the potential to completely revolutionize the outcome for these patients who have lived with this disease in their family for many generations. It's decimated some families that I've been looking after. So this is amazing," Gillmore says. The patients will have to be followed longer, and more patients will have to be treated, to make sure the treatment's safe, and determine how much it's helping, Gillmore stresses. But the approach could help those struck by amyloidosis that isn't inherited, which is a far more common version of the disease, he says. Moreover, the promising results potentially open the door for using the same approach to treatment of many other, more common diseases for which taking cells out of the body or directly injecting CRISPR isn't realistic, including heart disease, muscular dystrophy and brain diseases such as Alzheimer's. "This is really opening a new era as we think about gene-editing where we can begin to think about accessing all kinds of different tissue in the body via systemic administration," Leonard says. Other scientists who are not involved in the research agree. "This is a wonderful day for the future of gene-editing as a medicine," agree Fyodor Urnov, a professor of genetics at the University of California, Berkeley. "We as a species are watching this remarkable new show called: our gene-edited future." Doherty says he started feeling better within weeks of the treatment and has continued to improve in the weeks since then. "I definitely feel better," he told NPR. "I'm speaking to you from upstairs in our house. I climbed stairs to get up here. I would have been feeling breathless. I'm thrilled." 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. Full Article
ted Hospitals Have Started Posting Their Prices Online. Here's What They Reveal By www.scpr.org Published On :: Fri, 02 Jul 2021 04:00:23 -0700 Many hospitals around the country, including Medstar Washington Hospital in Washington DC., have started sharing their prices online in compliance with a recent federal rule.; Credit: DANIEL SLIM/AFP via Getty Images Julie Appleby | NPRA colonoscopy might cost you or your insurer a few hundred dollars — or several thousand, depending on which hospital or insurer you use. Long hidden, such price variations are supposed to be available in stark black and white under a Trump administration price transparency rule that took effect at the start of this year. It requires hospitals to post a range of actual prices — everything from the rates they offer cash-paying customers to costs negotiated with insurers. Many have complied. But some hospitals bury the data deep on their websites or have not included all the categories of prices required, according to industry analysts. A sizable minority of hospitals have not disclosed the information at all. While imperfect and potentially of limited use right now to the average consumer, the disclosures that are available illustrate the huge differences in prices — nationally, regionally and within the same hospital. But they're challenging for consumers and employers to use, giving a boost to a cottage industry that analyzes the data. While it's still an unanswered question whether price transparency will lead to overall lower prices, KHN took a dive into the initial trove of data to see what it reveals. Here are five takeaways from the newly public data and tips for how you might be able to use it to your benefit 1) As expected, prices are all over the map The idea behind the requirement to release prices is that the transparency may prompt consumers to shop around, weighing cost and quality. Perhaps they could save a few hundred dollars by getting their surgery or imaging test across town instead of at the nearby clinic or hospital. Under the Trump-era rule, hospitals must post what they accept from all insurers for thousands of line items, including each drug, procedure or treatment they provide. In addition, hospitals must present this in a format easily readable by computers and include a consumer-friendly separate listing of 300 "shoppable" services, bundling the full price a hospital accepts for a given treatment, such as having a baby or getting a hip replacement. The negotiated rates now being posted publicly often show an individual hospital accepting a wide range of prices for the same service, depending on the insurer, often based on how much negotiating power each has in a market. In some cases, the cash-only price is less than what insurers pay. And prices may vary widely within the same city or region. In Virginia, for example, the average price of a diagnostic colonoscopy is $2,763, but the range across the state is from $208 to $10,563, according to a database aggregated by San Diego-based Turquoise Health, one of the new firms looking to market the data to businesses, while offering some information free of charge to patients. 2) Patients can look up the information, but it's incomplete Patients can try to find the price information themselves by searching hospital websites, but even locating the correct tab on a hospital's website is tricky. Typically, consumers don't comparison-shop, preferring to choose convenience or the provider their doctor recommends. A recent Peterson-KFF Health System Tracker brief, for instance, found that 85% of adults said they had not researched online the price of a hospital treatment. And hospitals say the transparency push alone won't help consumers much, because each patient's situation is different and may vary from the average— and individual deductibles and insurance plans complicate matters. But if you do want to try, here's one tip: "You can Google the hospital name and the words 'price transparency' and see where that takes you," says Caitlin Sheetz, director and head of analytics at the consulting firm ADVI Health in the Washington, D.C., metro area. Typing in "MedStar Health hospital transparency," for example, likely points to the MedStar Washington Hospital Center's "price transparency disclosure" page, with a link to its full list of prices, as well as its separate list of 300 shoppable services. By clicking on the list of shoppable services, consumers can download an Excel file. Searching it for "colonoscopy" pulls up several variations of the procedure, along with prices for different insurers, such as Aetna and Cigna, but a "not available" designation for the cash-only price. The file explains that MedStar does not have a standard cash price but makes determinations case by case. Performing the same Google search for the nearby Inova health system results in less useful information. Inova's website links to a long list of thousands of charges, which are not the discounts negotiated by insurers, and the list is not easily searchable. The website advises those who are not Inova patients or who would like to create their own estimate to log into the hospitals' "My Chart" system, but a search on that for "colonoscopy" failed to produce any data. 3) Third-party firms are trying to make searching prices simpler – and cash in Because of the difficulty of navigating these websites — or locating the negotiated prices once there — some consumers may turn to sites like Turquoise. Another such firm is Health Cost Labs, which will have pricing information for 2,300 hospitals in its database when it goes live July 1. Doing a similar search for "colonoscopy" on Turquoise shows the prices at MedStar by insurer, but the process is still complicated. First, a consumer must select the "health system" button from the website's menu of options, click on "surgical procedures," then click again on "digestive" to get to it. There is no similar information for Inova because the hospital has not yet made its data accessible in a computer-friendly format, said Chris Severn, CEO of Turquoise. Inova spokesperson Tracy Connell said in a written statement that the health system will create personalized estimates for patients and is "currently working to post information on negotiated prices and discounts on services." Firms like Turquoise and Health Cost Labs aim to sell the data gathered from hospitals nationally to insurers, employers and others. In turn, those groups may use it in negotiations with hospitals over future prices. While that may drive down prices in areas with a lot of competition, it might do the opposite where there are few hospitals to choose from, or in situations where a hospital raises its prices to match competitors. 4) Consumers could use this data to negotiate, especially if they're paying cash For consumers who go the distance and can find price data from their hospitals, it may prove helpful in certain situations: Patients who are paying cash or who have unmet deductibles may want to compare prices among hospitals to see if driving farther could save them money. Uninsured patients could ask the hospital for the cash price or attempt to negotiate for the lowest amount the facility accepts from insurers. Insured patients who get a bill for out-of-network care may find the information helpful because it could empower them to negotiate a discount off the hospitals' gross charges for that care. While there's no guarantee of success, "if you are uninsured or out of network, you could point to some of those prices and say, 'That's what I want,'" says Barak Richman, a contract law expert and professor of law at Duke University School of Law. But the data may not help insured patients who notice their prices are higher than those negotiated by other insurers. In those cases, legal experts say the insured patients are unlikely to get a bill changed because they have a contract with that insurer, which has negotiated the price with their contracted hospitals. "Legally, a contract is a contract," says Mark Hall, a health law professor at Wake Forest University. Richman agrees. "You can't say, 'Well, you charged that person less,'" he notes, but neither can they say they'll charge you more. Getting the data, however, relies on the hospital having posted it. 5) Hospitals still aren't really on board When it comes to compliance, "we're seeing the range of the spectrum," says Jeffrey Leibach, a partner at the consulting firm Guidehouse, which found earlier this year that about 60% of 1,000 hospitals surveyed had posted at least some data, but 30% had reported nothing at all. Many in the hospital industry have long fought transparency efforts, even filing a lawsuit seeking to block the new rule. The suit was dismissed by a federal judge last year. They argue the rule is unclear and overly burdensome. Additionally, hospitals haven't wanted their prices exposed, knowing that competitors might then adjust theirs, or health plans could demand lower rates. Conversely, lower-cost hospitals might decide to raise prices to match competitors. The rule stems from requirements in the Affordable Care Act. The Obama administration required hospitals to post their chargemaster rates, which are less useful because they are generally inflated, hospital-set amounts that are almost never what is actually paid. Insurers and hospitals are also bracing for next year when even more data is set to come online. Insurers will be required to post negotiated prices for medical care across a broader range of facilities, including clinics and doctors' offices. In May, the Centers for Medicare & Medicaid Services sent letters to some of the hospitals that have not complied, giving them 90 days to do so or potentially face penalties, including a $300-a-day fine. "A lot of members say until hospitals are fully compliant, our ability to use the data is limited," says Shawn Gremminger, director of health policy at the Purchaser Business Group on Health, a coalition of large employers. His group and others have called for increasing the penalty for noncomplying hospitals from $300 a day to $300 a bed per day, so "the fine would be bigger as the hospital gets bigger," Gremminger says. "That's the kind of thing they take seriously." Already, though, employers or insurers are eyeing the hospital data as leverage in negotiations, says Severn, Turquoise's CEO. Conversely, some employers may use it to fire their insurers if the rates they're paying are substantially more than those agreed to by other carriers. "It will piss off anyone who is overpaying for health care, which happens for various reasons," he says. KHN (Kaiser Health News) is a national newsroom that produces in-depth journalism about health issues. Together with Policy Analysis and Polling, KHN is one of the three major operating programs at KFF (Kaiser Family Foundation). Copyright 2021 Kaiser Health News. To see more, visit Kaiser Health News. This content is from Southern California Public Radio. 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ted New Report Finds Major US Metro Areas, Greater Los Angeles Among Them, Are More Segregated Now Than 30 Years Ago By www.scpr.org Published On :: Wed, 30 Jun 2021 09:31:22 -0700 People rest while riding a Los Angeles Metro Rail train amid the coronavirus pandemic on April 1, 2020 in Los Angeles, California.; Credit: Mario Tama/Getty Images AirTalkDespite the racial reckoning going on in America right now, and despite the fact that attitudes towards race, inclusion and representation are different now than they were 30 years ago, new research from UC Berkeley shows that a large majority of American metro areas are more segregated now than they were in 1990. The new report from Berkeley’s Institute covers a number of topic areas, but among the key findings were from the national segregation report component of the project, which found Los Angeles to be the sixth-most segregated metro area with more than 200,000 people. Today on AirTalk, we’ll talk with the lead researcher on the new report and a local historian to talk about how we see the findings of the report play out in Southern California. Guests: Stephen Menendian, assistant director and director of research at the Othering & Belonging Institute at UC Berkeley, which works to identify and eliminate the barriers to an inclusive, just, and sustainable society in order to create transformative change; he tweets @SMenendian Eric Avila, professor of history, urban planning, and Chicano/a studies at UCLA This content is from Southern California Public Radio. View the original story at SCPR.org. Full Article
ted COVID-19 AMA: LA County’s New COVID-19 Cases Have Doubled, Vaccinated People Who Got Infected Carry Less Virus, CDC Researchers Say And More By www.scpr.org Published On :: Thu, 01 Jul 2021 09:19:33 -0700 Facemasks remain worn as firefighter paramedic Jorge Miranda, holding syringe, speaks with Eduardo Vasquez, who has lived homeless on the streets of Los Angeles since 1992, before administering the one-shot Johnson and Johnson' Janssen Covid-19 vaccine as part of outreach to the homeless by members of the Los Angeles Fire Department's Covid Outreach unit on June 14, 2021 in Los Angeles.; Credit: FREDERIC J. BROWN/AFP via Getty Images James Chow | AirTalkIn our continuing series looking at the latest medical research and news on COVID-19, Larry Mantle speaks with UCSF’s Dr. Peter Chin-Hong. Topics today include: Two weeks after reopening, LA County’s new COVID-19 cases have doubled CDC: Infected vaccinated people carry less COVID-19 virus Delta variant is now detected in all 50 states J&J: “At present, there is no evidence to suggest need for a booster dose to be administered” Novavax claims vaccine’s overall efficacy is 89.7% Another respiratory virus is spreading in the U.S. Curevac’s final trial show shot is far less effective than other vaccines Can we now live with the coronavirus? Israel scrambles to curb rising COVID-19 infection rates Is it time to rethink “one-size-fits-all” approach for masking? Guest: Peter Chin-Hong, M.D., infectious disease specialist and professor of medicine at the UCSF Medical Center; he tweets @PCH_SF This content is from Southern California Public Radio. View the original story at SCPR.org. Full Article
ted Updated USGS Publication, "Eruptions of Hawaiian Volcanoes—Past, Present, and Future" By www.usgs.gov Published On :: Thu, 31 Oct 2024 15:36:52 EDT In this third edition of "Eruptions of Hawaiian Volcanoes—Past, Present, and Future," we include information about Kīlauea’s 2018 eruption in the lower East Rift Zone—the largest and most destructive in at least 200 years—and associated summit-collapse events, the eruptions at Kīlauea’s summit since 2018, and the 2022 eruption of Mauna Loa, which occurred after 38 years of quiescence. Full Article
ted USGS Releases New Topographic Maps for Puerto Rico and the U.S. Virgin Islands - Updated Maps for Essential Needs By www.usgs.gov Published On :: Thu, 31 Oct 2024 16:53:06 EDT 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. Full Article
ted Is This Halted Stock Still a Strong Buy Once It Re-Opens? By www.streetwisereports.com Published On :: Tue, 05 Nov 2024 00:00:00 PST Michael Ballanger of GGM Advisory Inc. shares his thoughts on the silver market and shares one copper stock he believes is a Strong Speculative Buy even though the stock is currently halted. Full Article