base A qualitative focus group study on legal experts’ views regarding euthanasia requests based on an advance euthanasia directive By ifp.nyu.edu Published On :: Mon, 04 Nov 2024 14:59:48 +0000 The Dutch Euthanasia law permits euthanasia in patients with advanced dementia lacking decisional capacity based on advance euthanasia directives. Nevertheless, physicians encounter difficulties assessing the … Read the full article › The post A qualitative focus group study on legal experts’ views regarding euthanasia requests based on an advance euthanasia directive was curated by information for practice. Full Article Open Access Journal Articles
base Home-based Exercise for SMI By ifp.nyu.edu Published On :: Fri, 18 Oct 2024 23:29:12 +0000 The post Home-based Exercise for SMI was curated by information for practice. Full Article Clinical Trials
base Testing a Nature-based Social Intevention on Loneliness: the RECETAS-PRG Trial By ifp.nyu.edu Published On :: Tue, 29 Oct 2024 01:20:15 +0000 The post Testing a Nature-based Social Intevention on Loneliness: the RECETAS-PRG Trial was curated by information for practice. Full Article Clinical Trials
base Effectiveness of School-based Substance Abuse Prevention Programme Among Adolescents By ifp.nyu.edu Published On :: Thu, 31 Oct 2024 01:14:58 +0000 The post Effectiveness of School-based Substance Abuse Prevention Programme Among Adolescents was curated by information for practice. Full Article Clinical Trials
base State-dependent Interoception, Value-based Decision-making, and Introspection By ifp.nyu.edu Published On :: Sat, 02 Nov 2024 02:43:45 +0000 The post State-dependent Interoception, Value-based Decision-making, and Introspection was curated by information for practice. Full Article Clinical Trials
base Evidence-based group therapy for eating disorders. By ifp.nyu.edu Published On :: Mon, 04 Nov 2024 15:37:42 +0000 Group Dynamics: Theory, Research, and Practice, Vol 28(3), Sep 2024, 163-177; doi:10.1037/gdn0000221 Objective: The goal was to identify evidence-based group psychotherapy for adults with anorexia nervosa (AN), bulimia nervosa (BN), and binge-eating disorder (BED). Method: We reviewed randomized controlled trials of group psychotherapy for clinical samples of adults diagnosed with AN, BN, and BED published […] The post Evidence-based group therapy for eating disorders. was curated by information for practice. Full Article Journal Article Abstracts
base Conspiracy Theories: Groups, Ideology, and Status as Three Distinct Bases for Expressions in Society By ifp.nyu.edu Published On :: Mon, 04 Nov 2024 20:58:49 +0000 Current Directions in Psychological Science, Ahead of Print. Conspiracy theories have been treated mostly as a homogeneous phenomenon in empirical research. However, to fully understand their causes and consequences, a multifaceted approach to conspiracy theories would be useful. Here, we propose an organizational framework with three facets (groups, ideology, and status) to conceptualize conspiracy theories. […] The post Conspiracy Theories: Groups, Ideology, and Status as Three Distinct Bases for Expressions in Society was curated by information for practice. Full Article Journal Article Abstracts
base Embracing hybridity: the affordances of arts-based research for the professional doctorate in education By ifp.nyu.edu Published On :: Tue, 05 Nov 2024 00:29:22 +0000 Volume 29, Issue 7, October 2024. Read the full article › The post Embracing hybridity: the affordances of arts-based research for the professional doctorate in education was curated by information for practice. Full Article Journal Article Abstracts
base Buses of the All American Girls Professional Baseball League (8/20/2010) By calendar.rsvpa.com Published On :: Fri, 20 Aug 2010 04:00:00 GMT Start Date: 8/20/2010End Date: 8/20/2010All American Girls Professional Baseball League and Their Buses will be a new display for August, 2010 along with an encore presentation of the Buses of the Negro Leagues Baseball Teams which was originally displayed in February of this year at the Antique Automobile Club of America (AACA) Museum. The Museum of Bus Transportation which displays 12 vintage buses on the lower level of the Antique Automobile Club of America (AACA) Museum has arranged this special exhibit for the month of August. Full Article 08/20/2010
base Buses of the All American Girls Professional Baseball League (8/19/2010) By calendar.rsvpa.com Published On :: Thu, 19 Aug 2010 04:00:00 GMT Start Date: 8/19/2010End Date: 8/19/2010All American Girls Professional Baseball League and Their Buses will be a new display for August, 2010 along with an encore presentation of the Buses of the Negro Leagues Baseball Teams which was originally displayed in February of this year at the Antique Automobile Club of America (AACA) Museum. The Museum of Bus Transportation which displays 12 vintage buses on the lower level of the Antique Automobile Club of America (AACA) Museum has arranged this special exhibit for the month of August. Full Article 08/19/2010
base China-Brazil peace plan for Ukraine based on their national inte By english.pravda.ru Published On :: Fri, 27 Sep 2024 20:20:00 +0300 The Russian leadership verbally approves and supports the China-Brazil peace plan for Ukraine. In reality, it is just diplomacy so as not to offend the "allies". China and Brazil peace plan for Ukraine The plan to establish peace in Ukraine called "Common Understandings Between China and Brazil on Political Settlement of the Ukraine Crisis" will be presented on September 27 in New York with the participation of delegations from 20 countries of the Global South, including Colombia, Egypt, Indonesia, Mexico, Saudi Arabia, South Africa, and the UAE. Representatives of European countries and the United States were not invited to the meeting. Full Article World
base Designated Doctor Case-Based Webinar Series: Module 6 - Non – Musculoskeletal Traumatic Brain Injury By www.tdi.texas.gov Published On :: Wed, 16 Apr 2025 17:00:00 GMT Designated Doctor Case-Based Webinar Series: Module 6 - Non – Musculoskeletal Traumatic Brain Injury Full Article
base Designated Doctor Case-Based Webinar Series: Module 5 - Non – Musculoskeletal MMI and IR By www.tdi.texas.gov Published On :: Mon, 14 Apr 2025 17:00:00 GMT Designated Doctor Case-Based Webinar Series: Module 5 - Non – Musculoskeletal MMI and IR Full Article
base Designated Doctor Case-Based Webinar Series: Module 4 - Lower Extremity MMI and IR By www.tdi.texas.gov Published On :: Wed, 09 Apr 2025 17:00:00 GMT Designated Doctor Case-Based Webinar Series: Module 4 - Lower Extremity MMI and IR Full Article
base Designated Doctor Case-Based Webinar Series: Module 3 - Upper Extremity MMI and IR By www.tdi.texas.gov Published On :: Mon, 07 Apr 2025 17:00:00 GMT Designated Doctor Case-Based Webinar Series: Module 3 - Upper Extremity MMI and IR Full Article
base Designated Doctor Case-Based Webinar Series: Module 2 - Spine MMI and IR and Extent of Injury (EOI) By www.tdi.texas.gov Published On :: Wed, 02 Apr 2025 17:00:00 GMT Designated Doctor Case-Based Webinar Series: Module 2 - Spine MMI and IR and Extent of Injury (EOI) Full Article
base Designated Doctor Case-Based Webinar Series: Module 1 - Maximum Medical Improvement By www.tdi.texas.gov Published On :: Mon, 31 Mar 2025 17:00:00 GMT Designated Doctor Case-Based Webinar Series: Module 1 - Maximum Medical Improvement Full Article
base Young-Earth Creationist Helium Diffusion "Dates": Fallacies Based on Bad Assumptions and Questionable Data By www.talkorigins.org Published On :: Updated July 25, 2006: Young-Earth creationists consider the helium diffusion studies of D. Russell Humphreys and others to be one of their greatest achievements in arguing for a 6,000 year old Earth. A geologist shows that these studies are extensively flawed and include: serious miscalculations in their data, sampling the wrong rock type, failing to eliminate possible contamination, using equations that are based on invalid assumptions and relying on questionable data. Appendices C and D have been added in response to Dr. Humphreys' most recent statements in his January 2006 "Trueorigins" essay. Full Article
base Couchbase Capella advancements fuel development of adaptive applications By www.retailtechnologyreview.com Published On :: Couchbase, Inc., the cloud database platform company, has launched Capella Columnar on AWS, which helps organisations streamline the development of adaptive applications by enabling real-time data analysis alongside operational workloads within a single database platform. Full Article Data Capture Retail Supply Chain
base Precision Retail launches rewards-based survey plugin to capture consent-based consumer data By www.retailtechnologyreview.com Published On :: The Golden Quarter of retail is approaching. Perfect time for retailers to gather mounds of consumer data. But how to do so compliantly? Two Toronto-based marketing specialists have an answer: Precision Retail, a new venture offering what they believe to be the world's first and only rewards-based post-purchase survey plugin to capture 0PD. Full Article Data Capture Retail Supply Chain
base New AI-Based Natural Language Feature Makes Complex Searches in Dimensions Faster and Easier By www.newswise.com Published On :: Thu, 07 Nov 2024 09:00:19 EST Digital Science's flagship product Dimensions has launched a beta of a new AI-based Natural Language to Query search technology. Full Article
base 10 Most Dangerous Cities in the World, Based on Homicide Rate By people.howstuffworks.com Published On :: Tue, 05 Nov 2024 10:15:03 -0500 The most dangerous cities in the world are a major concern for residents, visitors, law enforcement and policymakers. While crime exists everywhere, some cities statistically experience consistently high crime levels. We turned to Statista, a global data and business intelligence platform, to find the hard numbers on the murder rate per capita in cities worldwide. Full Article
base BGS updates national CO2 storage database - Agg-Net By news.google.com Published On :: Tue, 30 Jan 2024 08:00:00 GMT BGS updates national CO2 storage database Agg-Net Full Article
base Update released for BGS open-source database software, ETL Helper - British Geological Survey By news.google.com Published On :: Tue, 09 Jul 2024 07:00:00 GMT Update released for BGS open-source database software, ETL Helper British Geological Survey Full Article
base Review of honeycomb-based Kitaev materials with zigzag magnetic ordering By journals.iucr.org Published On :: Full Article text
base Modulating phase segregation during spin-casting of fullerene-based polymer solar-cell thin films upon minor addition of a high-boiling co-solvent By journals.iucr.org Published On :: Combined 100 ms resolved grazing-incidence small/wide-angle X-ray scattering and optical interferometry reveal that the additive diiodooctane can significantly double the solvent evaporation rate, thereby effectively suppressing the rapid spinodal decomposition process in the early stage of spin-coasting, favouring slow phase segregation kinetics with nucleation and growth. Full Article text
base Correlation of refractive index based and THz streaking arrival time tools for a hard X-ray free-electron laser By journals.iucr.org Published On :: 2024-01-22 To fully exploit ultra-short X-ray pulse durations routinely available at X-ray free-electron lasers to follow out-of-equilibrium dynamics, inherent arrival time fluctuations of the X-ray pulse with an external perturbing laser pulse need to be measured. In this work, two methods of arrival time measurement were compared to measure the arrival time jitter of hard X-ray pulses. The methods were photoelectron streaking by a THz field and a transient refractive index change of a semiconductor. The methods were validated by shot-to-shot correction of a pump–probe transient reflectivity measurement. An ultimate shot-to-shot full width at half-maximum error between the devices of 19.2 ± 0.1 fs was measured. Full Article text
base Finback: a web-based data collection system at SSRF biological macromolecular crystallography beamlines By journals.iucr.org Published On :: 2024-01-19 An integrated computer software system for macromolecular crystallography (MX) data collection at the BL02U1 and BL10U2 beamlines of the Shanghai Synchrotron Radiation Facility is described. The system, Finback, implements a set of features designed for the automated MX beamlines, and is marked with a user-friendly web-based graphical user interface (GUI) for interactive data collection. The Finback client GUI can run on modern browsers and has been developed using several modern web technologies including WebSocket, WebGL, WebWorker and WebAssembly. Finback supports multiple concurrent sessions, so on-site and remote users can access the beamline simultaneously. Finback also cooperates with the deployed experimental data and information management system, the relevant experimental parameters and results are automatically deposited to a database. Full Article text
base A differentiable simulation package for performing inference of synchrotron-radiation-based diagnostics By journals.iucr.org Published On :: 2024-02-16 The direction of particle accelerator development is ever-increasing beam quality, currents and repetition rates. This poses a challenge to traditional diagnostics that directly intercept the beam due to the mutual destruction of both the beam and the diagnostic. An alternative approach is to infer beam parameters non-invasively from the synchrotron radiation emitted in bending magnets. However, inferring the beam distribution from a measured radiation pattern is a complex and computationally expensive task. To address this challenge we present SYRIPY (SYnchrotron Radiation In PYthon), a software package intended as a tool for performing inference of synchrotron-radiation-based diagnostics. SYRIPY has been developed using PyTorch, which makes it both differentiable and able to leverage the high performance of GPUs, two vital characteristics for performing statistical inference. The package consists of three modules: a particle tracker, Lienard–Wiechert solver and Fourier optics propagator, allowing start-to-end simulation of synchrotron radiation detection to be carried out. SYRIPY has been benchmarked against SRW, the prevalent numerical package in the field, showing good agreement and up to a 50× speed improvement. Finally, we have demonstrated how SYRIPY can be used to perform Bayesian inference of beam parameters using stochastic variational inference. Full Article text
base A distributed data processing scheme based on Hadoop for synchrotron radiation experiments By journals.iucr.org Published On :: 2024-04-24 With the development of synchrotron radiation sources and high-frame-rate detectors, the amount of experimental data collected at synchrotron radiation beamlines has increased exponentially. As a result, data processing for synchrotron radiation experiments has entered the era of big data. It is becoming increasingly important for beamlines to have the capability to process large-scale data in parallel to keep up with the rapid growth of data. Currently, there is no set of data processing solutions based on the big data technology framework for beamlines. Apache Hadoop is a widely used distributed system architecture for solving the problem of massive data storage and computation. This paper presents a set of distributed data processing schemes for beamlines with experimental data using Hadoop. The Hadoop Distributed File System is utilized as the distributed file storage system, and Hadoop YARN serves as the resource scheduler for the distributed computing cluster. A distributed data processing pipeline that can carry out massively parallel computation is designed and developed using Hadoop Spark. The entire data processing platform adopts a distributed microservice architecture, which makes the system easy to expand, reduces module coupling and improves reliability. Full Article text
base X-ray optics for the cavity-based X-ray free-electron laser By journals.iucr.org Published On :: 2024-06-21 A cavity-based X-ray free-electron laser (CBXFEL) is a possible future direction in the development of fully coherent X-ray sources. CBXFELs consist of a low-emittance electron source, a magnet system with several undulators and chicanes, and an X-ray cavity. The X-ray cavity stores and circulates X-ray pulses for repeated FEL interactions with electron pulses until the FEL reaches saturation. CBXFEL cavities require low-loss wavefront-preserving optical components: near-100%-reflectivity X-ray diamond Bragg-reflecting crystals, outcoupling devices such as thin diamond membranes or X-ray gratings, and aberration-free focusing elements. In the framework of the collaborative CBXFEL research and development project of Argonne National Laboratory, SLAC National Accelerator Laboratory and SPring-8, we report here the design, manufacturing and characterization of X-ray optical components for the CBXFEL cavity, which include high-reflectivity diamond crystal mirrors, a diamond drumhead crystal with thin membranes, beryllium refractive lenses and channel-cut Si monochromators. All the designed optical components have been fully characterized at the Advanced Photon Source to demonstrate their suitability for the CBXFEL cavity application. Full Article text
base X-ray scattering based scanning tomography for imaging and structural characterization of cellulose in plants By journals.iucr.org Published On :: 2024-06-25 X-ray and neutron scattering have long been used for structural characterization of cellulose in plants. Due to averaging over the illuminated sample volume, these measurements traditionally overlooked the compositional and morphological heterogeneity within the sample. Here, a scanning tomographic imaging method is described, using contrast derived from the X-ray scattering intensity, for virtually sectioning the sample to reveal its internal structure at a resolution of a few micrometres. This method provides a means for retrieving the local scattering signal that corresponds to any voxel within the virtual section, enabling characterization of the local structure using traditional data-analysis methods. This is accomplished through tomographic reconstruction of the spatial distribution of a handful of mathematical components identified by non-negative matrix factorization from the large dataset of X-ray scattering intensity. Joint analysis of multiple datasets, to find similarity between voxels by clustering of the decomposed data, could help elucidate systematic differences between samples, such as those expected from genetic modifications, chemical treatments or fungal decay. The spatial distribution of the microfibril angle can also be analyzed, based on the tomographically reconstructed scattering intensity as a function of the azimuthal angle. Full Article text
base StreamSAXS: a Python-based workflow platform for processing streaming SAXS/WAXS data By journals.iucr.org Published On :: 2024-07-15 StreamSAXS is a Python-based small- and wide-angle X-ray scattering (SAXS/WAXS) data analysis workflow platform with graphical user interface (GUI). It aims to provide an interactive and user-friendly tool for analysis of both batch data files and real-time data streams. Users can easily create customizable workflows through the GUI to meet their specific needs. One characteristic of StreamSAXS is its plug-in framework, which enables developers to extend the built-in workflow tasks. Another feature is the support for both already acquired and real-time data sources, allowing StreamSAXS to function as an offline analysis platform or be integrated into large-scale acquisition systems for end-to-end data management. This paper presents the core design of StreamSAXS and provides user cases demonstrating its utilization for SAXS/WAXS data analysis in offline and online scenarios. Full Article text
base TEMPUS, a Timepix4-based system for the event-based detection of X-rays By journals.iucr.org Published On :: 2024-07-23 TEMPUS is a new detector system being developed for photon science. It is based on the Timepix4 chip and, thus, it can be operated in two distinct modes: a photon-counting mode, which allows for conventional full-frame readout at rates up to 40 kfps; and an event-driven time-stamping mode, which allows excellent time resolution in the nanosecond regime in measurements with moderate X-ray flux. In this paper, the initial prototype, a single-chip device, is introduced, and the readout system described. Moreover, and in order to evaluate its capabilities, some tests were performed at PETRA III and ESRF for which results are also presented. Full Article text
base Spexwavepy: an open-source Python package for X-ray wavefront sensing using speckle-based techniques By journals.iucr.org Published On :: 2024-07-30 In situ wavefront sensing plays a critical role in the delivery of high-quality beams for X-ray experiments. X-ray speckle-based techniques stand out among other in situ techniques for their easy experimental setup and various data acquisition modes. Although X-ray speckle-based techniques have been under development for more than a decade, there are still no user-friendly software packages for new researchers to begin with. Here, we present an open-source Python package, spexwavepy, for X-ray wavefront sensing using speckle-based techniques. This Python package covers a variety of X-ray speckle-based techniques, provides plenty of examples with real experimental data and offers detailed online documentation for users. We hope it can help new researchers learn and apply the speckle-based techniques for X-ray wavefront sensing to synchrotron radiation and X-ray free-electron laser beamlines. Full Article text
base RefXAS: an open access database of X-ray absorption spectra By journals.iucr.org Published On :: 2024-08-27 Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs. Full Article text
base Redetermination of germacrone type II based on single-crystal X-ray data By journals.iucr.org Published On :: 2024-04-26 The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C15H22O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022). Powder Diffr. 37, 98–104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the intermolecular interactions of germacrone type II. Full Article text
base Synthesis, crystal structure and in-silico evaluation of arylsulfonamide Schiff bases for potential activity against colon cancer By journals.iucr.org Published On :: 2024-03-28 This report presents a comprehensive investigation into the synthesis and characterization of Schiff base compounds derived from benzenesulfonamide. The synthesis process, involved the reaction between N-cycloamino-2-sulfanilamide and various substituted o-salicylaldehydes, resulted in a set of compounds that were subjected to rigorous characterization using advanced spectral techniques, including 1H NMR, 13C NMR and FT–IR spectroscopy, and single-crystal X-ray diffraction. Furthermore, an in-depth assessment of the synthesized compounds was conducted through Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) analysis, in conjunction with docking studies, to elucidate their pharmacokinetic profiles and potential. Impressively, the ADMET analysis showcased encouraging drug-likeness properties of the newly synthesized Schiff bases. These computational findings were substantiated by molecular properties derived from density functional theory (DFT) calculations using the B3LYP/6-31G* method within the Jaguar Module of Schrödinger 2023-2 from Maestro (Schrodinger LLC, New York, USA). The exploration of frontier molecular orbitals (HOMO and LUMO) enabled the computation of global reactivity descriptors (GRDs), encompassing charge separation (Egap) and global softness (S). Notably, within this analysis, one Schiff base, namely, 4-bromo-2-{N-[2-(pyrrolidine-1-sulfonyl)phenyl]carboximidoyl}phenol, 20, emerged with the smallest charge separation (ΔEgap = 3.5780 eV), signifying heightened potential for biological properties. Conversely, 4-bromo-2-{N-[2-(piperidine-1-sulfonyl)phenyl]carboximidoyl}phenol, 17, exhibited the largest charge separation (ΔEgap = 4.9242 eV), implying a relatively lower propensity for biological activity. Moreover, the synthesized Schiff bases displayed remarkeable inhibition of tankyrase poly(ADP-ribose) polymerase enzymes, integral in colon cancer, surpassing the efficacy of a standard drug used for the same purpose. Additionally, their bioavailability scores aligned closely with established medications such as trifluridine and 5-fluorouracil. The exploration of molecular electrostatic potential through colour mapping delved into the electronic behaviour and reactivity tendencies intrinsic to this diverse range of molecules. Full Article text
base Concerning the structures of Lewis base adducts of titanium(IV) hexafluoroisopropoxide By journals.iucr.org Published On :: 2024-08-13 The reaction of titanium(IV) chloride with sodium hexafluoroisopropoxide, carried out in hexafluoroisopropanol, produces titanium(IV) hexafluoroisopropoxide, which is a liquid at room temperature. Recrystallization from coordinating solvents, such as acetonitrile or tetrahydrofuran, results in the formation of bis-solvate complexes. These compounds are of interest as possible Ziegler–Natta polymerization catalysts. The acetonitrile complex had been structurally characterized previously and adopts a distorted octahedral structure in which the nitrile ligands adopt a cis configuration, with nitrogen lone pairs coordinated to the metal. The low-melting tetrahydrofuran complex has not provided crystals suitable for single-crystal X-ray analysis. However, the structure of chloridotris(hexafluoroisopropoxido-κO)bis(tetrahydrofuran-κO)titanium(IV), [Ti(C3HF6O)3Cl(C4H8O)2], has been obtained and adopts a distorted octahedral coordination geometry, with a facial arrangement of the alkoxide ligands and adjacent tetrahydrofuran ligands, coordinated by way of metal–oxygen polar coordinate interactions. Full Article text
base A web-based dashboard for RELION metadata visualization By journals.iucr.org Published On :: 2024-01-24 Cryo-electron microscopy (cryo-EM) has witnessed radical progress in the past decade, driven by developments in hardware and software. While current software packages include processing pipelines that simplify the image-processing workflow, they do not prioritize the in-depth analysis of crucial metadata, limiting troubleshooting for challenging data sets. The widely used RELION software package lacks a graphical native representation of the underlying metadata. Here, two web-based tools are introduced: relion_live.py, which offers real-time feedback on data collection, aiding swift decision-making during data acquisition, and relion_analyse.py, a graphical interface to represent RELION projects by plotting essential metadata including interactive data filtration and analysis. A useful script for estimating ice thickness and data quality during movie pre-processing is also presented. These tools empower researchers to analyse data efficiently and allow informed decisions during data collection and processing. Full Article text
base Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket By journals.iucr.org Published On :: 2024-01-30 To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography. Full Article text
base A service-based approach to cryoEM facility processing pipelines at eBIC By journals.iucr.org Published On :: 2024-02-20 Electron cryo-microscopy image-processing workflows are typically composed of elements that may, broadly speaking, be categorized as high-throughput workloads which transition to high-performance workloads as preprocessed data are aggregated. The high-throughput elements are of particular importance in the context of live processing, where an optimal response is highly coupled to the temporal profile of the data collection. In other words, each movie should be processed as quickly as possible at the earliest opportunity. The high level of disconnected parallelization in the high-throughput problem directly allows a completely scalable solution across a distributed computer system, with the only technical obstacle being an efficient and reliable implementation. The cloud computing frameworks primarily developed for the deployment of high-availability web applications provide an environment with a number of appealing features for such high-throughput processing tasks. Here, an implementation of an early-stage processing pipeline for electron cryotomography experiments using a service-based architecture deployed on a Kubernetes cluster is discussed in order to demonstrate the benefits of this approach and how it may be extended to scenarios of considerably increased complexity. Full Article text
base A database overview of metal-coordination distances in metalloproteins By journals.iucr.org Published On :: 2024-04-29 Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals. Full Article text
base Likelihood-based interactive local docking into cryo-EM maps in ChimeraX By journals.iucr.org Published On :: 2024-07-26 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. Full Article text
base Dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval based on deep learning By journals.iucr.org Published On :: 2024-01-01 Speckle-tracking X-ray imaging is an attractive candidate for dynamic X-ray imaging owing to its flexible setup and simultaneous yields of phase, transmission and scattering images. However, traditional speckle-tracking imaging methods suffer from phase distortion at locations with abrupt changes in density, which is always the case for real samples, limiting the applications of the speckle-tracking X-ray imaging method. In this paper, we report a deep-learning based method which can achieve dynamic X-ray speckle-tracking imaging with high-accuracy phase retrieval. The calibration results of a phantom show that the profile of the retrieved phase is highly consistent with the theoretical one. Experiments of polyurethane foaming demonstrated that the proposed method revealed the evolution of the complicated microstructure of the bubbles accurately. The proposed method is a promising solution for dynamic X-ray imaging with high-accuracy phase retrieval, and has extensive applications in metrology and quantitative analysis of dynamics in material science, physics, chemistry and biomedicine. Full Article text
base The interoperability of crystallographic data and databases By journals.iucr.org Published On :: 2024-01-01 Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors. Driven by the success within these domains, the IUCr has worked closely with CODATA (the Committee on Data of the International Science Council) to help develop the latter's commitment to cross-domain integration of discipline-specific data. The IUCr has, in particular, emphasized the need for standards relating to data quality and completeness as an adjunct to the FAIR data landscape. This can ensure definitive reusable data, which in turn can aid interoperability across domains. A microsymposium at the IUCr 2023 Congress provided an up-to-date survey of data interoperability within and outside of crystallography, expounded using a broad range of examples. Full Article text
base Chromic soft crystals based on luminescent platinum(II) complexes By journals.iucr.org Published On :: 2024-06-11 Platinum(II) complexes of square-planar geometry are interesting from a crystal engineering viewpoint because they exhibit strong luminescence based on the self-assembly of molecular units. The luminescence color changes in response to gentle stimuli, such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively generate the chromic luminescence phenomenon of Pt(II) complexes. In this topical review, strategies for fabricating chromic luminescent Pt(II) complexes are described from a crystal design perspective, focusing on the structural regulation of Pt(II) complexes that exhibit assembly-induced luminescence via metal–metal interactions and structural control of anionic Pt(II) complexes using cations. The research progress on the evolution of various chromic luminescence properties of Pt(II) complexes, including the studies conducted by our group, are presented here along with the latest research outcomes, and an overview of the frontiers and future potential of this research field is provided. Full Article text
base Supramolecular architectures in multicomponent crystals of imidazole-based drugs and trithiocyanuric acid By journals.iucr.org Published On :: 2024-07-01 The structures of three multicomponent crystals formed with imidazole-based drugs, namely metronidazole, ketoconazole and miconazole, in conjunction with trithiocyanuric acid are characterized. Each of the obtained adducts represents a different category of crystalline molecular forms: a cocrystal, a salt and a cocrystal of salt. The structural analysis revealed that in all cases, the N—H⋯N hydrogen bond is responsible for the formation of acid–base pairs, regardless of whether proton transfer occurs or not, and these molecular pairs are combined to form unique supramolecular motifs by centrosymmetric N—H⋯S interactions between acid molecules. The complex intermolecular forces acting in characteristic patterns are discussed from the geometric and energetic perspectives, involving Hirshfeld surface analysis, pairwise energy estimation, and natural bond orbital calculations. Full Article text
base 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
base K0.72Na1.71Ca5.79Si6O19 – the first oligosilicate based on [Si6O19]-hexamers and its stability compared to cyclosilicates By journals.iucr.org Published On :: 2024-08-30 Synthesis experiments were conducted in the quaternary system K2O–Na2O–CaO–SiO2, resulting in the formation of a previously unknown compound with the composition K0.72Na1.71Ca5.79Si6O19. Single crystals of sufficient size and quality were recovered from a starting mixture with a K2O:Na2O:CaO:SiO2 molar ratio of 1.5:0.5:2:3. The mixture was confined in a closed platinum tube and slowly cooled from 1150°C at a rate of 0.1°C min−1 to 700°C before being finally quenched in air. The structure has tetragonal symmetry and belongs to space group P4122 (No. 91), with a = 7.3659 (2), c = 32.2318 (18) Å, V = 1748.78 (12) Å3, and Z = 4. The silicate anion consists of highly puckered, unbranched six-membered oligomers with the composition [Si6O19] and point group symmetry 2 (C2). Although several thousands of natural and synthetic oxosilicates have been structurally characterized, this compound is the first representative of a catena-hexasilicate anion, to the best of our knowledge. Structural investigations were completed using Raman spectroscopy. The spectroscopic data was interpreted and the bands were assigned to certain vibrational species with the support of density functional theory at the HSEsol level of theory. To determine the stability properties of the novel oligosilicate compared to those of the chemically and structurally similar cyclosilicate combeite, we calculated the electronegativity of the respective structures using the electronegativity equalization method. The results showed that the molecular electronegativity of the cyclosilicate was significantly higher than that of the oligostructure due to the different connectivities of the oxygen atoms within the molecular units. Full Article text