war Highly competitive landscape for new POS software projects By www.retailtechnologyreview.com Published On :: Mon, 13 Nov 800 17:02:45 -0001 Competition between vendors to provide POS software remains fierce, with more than 125 suppliers working with major retail and hospitality chains, according to Global POS Software 2023, the latest study from strategic research and consulting firm RBR Data Services, a division of Datos Insights. Full Article EPoS Systems Data Capture Critical Issues
war Integrating Advanced Software Solutions in Retail for Enhanced Customer Experience By www.retailtechnologyreview.com Published On :: By Jeremy Landau, freelance writer.Retail's dynamic environment is seeing a real shift, driven by the integration of advanced software solutions. This goes beyond a mere technological upgrade – it's about completely transforming the customer experience. Full Article EPoS Systems Internet Retailing Retail Supply Chain
war Hot war between Iran and Israel postponed, but for how long? By english.pravda.ru Published On :: Mon, 15 Apr 2024 17:33:00 +0300 The conflict between Iran and Israel did not reach a heated stage this timeб but the parties tested their level of readiness for full-fledged war. Russia could benefit from the conflict in the Middle East, but not in the long term. The market reacted weakly to Iran's attack on Israel on Sunday, April 14. Gold and oil prices showed almost no reaction. The price of gold rose by 0.8 percent to $2,379 per troy ounce, according to trading data on Monday, April 15. At the same time, Brent is trading steadily at $90.4 per barrel, WTI — at $85.6. The conflict appears to have been frozen for a short time unless Israel responds to Iran within a week. The situation is expected to aggravate, but not now — the parties have tested their combat readiness, but preferred not to go full throttle yet. Full Article Incidents
war USA gradually switches Ukraine to terrorist war against Russia By english.pravda.ru Published On :: Fri, 26 Apr 2024 20:24:00 +0300 US Congress will provide $61 billion in military aid to Ukraine. Will Joseph Biden decide to transfer long-range missiles to Kyiv? Does Washington prepare for a terrorist war against Russia? Pravda.Ru asked these and other questions to Alexander Dudchak, candidate of economic sciences, leading researcher at the Institute of CIS Countries. The US Congress approved $61 billion in aid to Ukraine, but this money will be distributed between Ukraine, the American military-industrial complex and allies in Europe for arms procurement. What do you think of the bill? The decision did not come as a surprise. Of course, the bulk of the amount will be spent to support the US defence industry. The Americans say that they need long-term contracts to support the defence industry, and Washington is getting them by supporting Kyiv and the hostilities in Ukraine. A lion's share of those billions will be spent to support the US defence industry in the first place. In addition, they will allocate money for the National Nuclear Safety Committee and the Ministry of Health. Full Article Incidents
war The Retail Technology Show announces the shortlist for its 2024 Innovation Awards By www.retailtechnologyreview.com Published On :: The Retail Technology Show (RTS), the leading industry event that connects retail’s changemakers and leading tech providers, has announced the shortlist of its 2024 Innovation Awards, which champion progressive, best-in-class technologies and solutions. Full Article Exhibitions and Events Retail Supply Chain
war SnapFulfil lands yet another distinguished supply chain and logistics award By www.retailtechnologyreview.com Published On :: The Top Supply Chain Projects 2024 (formerly known as SDCE 100) profiles innovative application success projects designed to automate, optimise, streamline and improve the supply chain. Full Article Retail Supply Chain Exhibitions and Events
war Zyler wins ‘Best Use of Augmented or Virtual Reality’ in The Retail Systems Awards By www.retailtechnologyreview.com Published On :: Anthropics Technology has announced that its AI-powered fashion virtual try-on, Zyler, has won an award by Retail Systems. Full Article Exhibitions and Events Internet Retailing
war CIRRO Fulfillment wins Best New Member Award at UKWA Awards for Excellence 2024 By www.retailtechnologyreview.com Published On :: CIRRO Fulfillment, the e-commerce fulfilment service provider, has been honoured with the Best New Member Award by the UK Warehousing Association (UKWA). Full Article Internet Retailing Exhibitions and Events
war Women in Green Business Awards: The top 20 women accelerating the UK’s net zero transition revealed ahead of Net Zero Festival 2024 By www.retailtechnologyreview.com Published On :: Tue, 13 Nov 2440 17:28:41 +0000 We Mean Business Coalition’s chief executive officer Maria Mendiluce, Zapmap’s co-founder and chief operating officer Melanie Shufflebotham, and co-leader of the Green Party England and Wales Carla Denyer are among those to have been awarded an inaugural Women in Green Business Award celebrating their work driving the UK's net zero transition. Full Article Retail Supply Chain Exhibitions and Events
war Awards, Honors, and Favorable Notices for The Talk.Origins Archive By www.talkorigins.org Published On :: Updated October 9, 2006: Honors won by the TalkOrigins Archive. Full Article
war How retail can reap the rewards of RAIN RFID By www.retailtechnologyreview.com Published On :: By Aileen Ryan, President, RAIN Alliance.As costs spiral across the retail sector, maintaining profitability is a growing challenge. Organisations are increasingly seeking practical, affordable solutions that enable them to drive operational efficiencies and reduce overhead costs. Full Article RFID Data Capture Critical Issues
war 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
war How often can you eat eggs: Chinese dietitian warns By english.pravda.ru Published On :: Tue, 18 Apr 2023 02:58:00 +0300 According to the dietitian Li Yuanjuan, moderate consumption of eggs per week can contribute to a healthy diet. However, he warns about the possible danger of the product as it can increase cholesterol levels in the blood. The dietitian emphasizes that the key to a healthy diet is the correct amount of egg consumption - from three to six per week, no more than one egg per day. In his interview with the Chinese portal Sina, Li Yuanjuan notes that eggs are the main food for those who adhere to a healthy lifestyle, as they contain high-quality protein that is well absorbed by the body. According to the specialist, the proper consumption of eggs in combination with a varied and balanced diet, as well as regular physical exercise, can help reduce the risk of various diseases and elevated cholesterol levels in the blood. Therefore, adhering to the recommended amount of egg consumption per week is an important aspect of a healthy lifestyle. Full Article Health
war Hackensack University Medical Center to Hold Annual Diabetes Awareness Month Event By www.newswise.com Published On :: Tue, 12 Nov 2024 12:45:40 EST Full Article
war When There's No One Else to Blame: The Impact of Coworkers' Perceived Competence and Warmth on the Relations between Ostracism, Shame, and Ingratiation By www.newswise.com Published On :: Wed, 13 Nov 2024 06:25:19 EST Full Article
war Four Approaches to New Venture Creation: Taking Stock and Moving Forward By www.newswise.com Published On :: Fri, 08 Nov 2024 08:45:33 EST Full Article
war Turning a Blind Eye to Team Members' Unethical Behavior: The Role of Reward Systems By www.newswise.com Published On :: Fri, 08 Nov 2024 09:15:26 EST Full Article
war Annual 'Turn Toward Busan' Ceremony Held to Honor UN Troops during Korean War By world.kbs.co.kr Published On :: Mon, 11 Nov 2024 15:40:08 +0900 [Domestic] : An annual commemorative ceremony honoring the sacrifices of United Nations Forces during the Korean War was held on Monday at the UN Memorial Cemetery in the southeastern port city of Busan. This year's "Turn Toward Busan" event began with a burial of an unknown soldier of the UN Forces, whose remains were ...[more...] Full Article Domestic
war World Asked to ‘Turn toward Busan’ to Remember UN Korean War Veterans By world.kbs.co.kr Published On :: Mon, 11 Nov 2024 17:23:38 +0900 [Domestic] : Anchor: On Monday at 11 a.m., the world was asked to “Turn toward Busan,” where Korean War veterans gathered at the United Nations Memorial Cemetery of Korea to honor the fallen soldiers who fought under the UN flag. The annual event in South Korea’s southern port city drew some 800 people, including ...[more...] Full Article Domestic
war Pretrial Detention Warrants Sought for Power Broker and Former PPP Lawmaker By world.kbs.co.kr Published On :: Mon, 11 Nov 2024 17:55:23 +0900 [Domestic] : The prosecution has sought a pretrial detention warrant for Myung Tae-kyun, a self-proclaimed political consultant, and former ruling People Power Party(PPP) lawmaker Kim Young-sun, as part of its probe into a 2022 political funding case. The Changwon District Court said it received such a request from ...[more...] Full Article Domestic
war Police Seek Arrest Warrants for 6 Anti-Yoon Protesters By world.kbs.co.kr Published On :: Mon, 11 Nov 2024 18:51:53 +0900 [Domestic] : Police have requested arrest warrants for six members of the Korean Confederation of Trade Unions(KCTU) who took part in a large protest in downtown Seoul on Saturday urging President Yoon Suk Yeol to step down. The police said Monday that they detained eleven people on Saturday and asked the Central ...[more...] Full Article Domestic
war Ex-Nat'l Security Advisor Warns US Isolationism Could Intensify under 2nd Trump Term By world.kbs.co.kr Published On :: Sat, 09 Nov 2024 15:11:46 +0900 [Politics] : John Bolton, former national security advisor under the first Donald Trump administration, warned that U.S. isolationism is expected to further intensify as Trump returns to office for a second term. In an interview with Japanese daily Yomiuri Shimbun a day before the election on Monday and published on ...[more...] Full Article Politics
war JCS Warns N. Korea Will Face Corresponding Steps if It Infiltrates Drones By world.kbs.co.kr Published On :: Mon, 28 Oct 2024 17:41:20 +0900 [Inter-Korea] : The Joint Chiefs of Staff(JCS) has warned that North Korea will face corresponding countermeasures if it infiltrates drones into South Korean territory. JCS spokesperson Lee Sung-joon unveiled such a stance to reporters on Monday when asked to comment on Kim Yo-jong, the sister of North Korean leader Kim ...[more...] Full Article Inter-Korea
war NIS: Some N. Korean Troops May Be on Front Lines of Russia-Ukraine War By world.kbs.co.kr Published On :: Tue, 29 Oct 2024 14:33:34 +0900 [Inter-Korea] : South Korea’s intelligence agency believes some of the North Korean troops deployed to Russia in support of its military offensive in Ukraine may have been transported to the front lines, including high-ranking generals. According to senior members of the rival political parties on the parliamentary ...[more...] Full Article Inter-Korea
war Heavy Rain Warning and Watch in place For Most Parts of Nation By world.kbs.co.kr Published On :: Fri, 20 Sep 2024 17:44:26 +0900 [Science] : A heavy rain warning has been issued for the five border islands in the Yellow Sea and a heavy rain watch for the Seoul metro area, Gangwon Province and parts of the Jeolla and Gyeongsang provinces. With heavy rain set to pound most parts of the nation through Sunday, the interior and safety ministry on ...[more...] Full Article Science
war Streamline Your Business Operations with Cutting-edge Routing Software By auto.howstuffworks.com Published On :: Tue, 20 Feb 2024 18:33:02 -0500 Efficient route planning is crucial for businesses to stay competitive and meet customer demands. Thankfully, there are several free routing software options available that can help streamline your business operations. Whether you're a small business owner or a logistics manager, these tools can be invaluable in optimizing your routes and maximizing productivity. Full Article
war Pianist Lim Yun-chan Wins Gramophone Award By world.kbs.co.kr Published On :: Thu, 03 Oct 2024 11:28:19 +0900 [Culture] : Pianist Lim Yun-chan has won the prestigious Gramophone Classical Music Award in the piano category. Lim received the award for his album, "Chopin: Etudes" during a ceremony on Wednesday in London, becoming the first South Korean to win the award in the piano category. Lim also won the special award of ...[more...] Full Article Culture
war Korean Pianist Lim Yunchan Wins Gramophone Classical Music Award By world.kbs.co.kr Published On :: Thu, 03 Oct 2024 14:20:12 +0900 [Culture] : Anchor: South Korean Pianist Lim Yunchan has won the Gramophone Classical Music Award in the piano category. This marks the first time that a Korean pianist has received the prestigious prize, often called the Oscars of the classical music world. Kim Bum-soo has more. Report: [Sound bite: Lim ...[more...] Full Article Culture
war Korean American Writer Kim Ju-hea Wins Russia's Yasnaya Polyana Literary Award By world.kbs.co.kr Published On :: Fri, 11 Oct 2024 15:33:06 +0900 [Culture] : Korean American writer Kim Ju-hea was named the winner of the 2024 Yasnaya Polyana Literary Award in the foreign fiction category for her debut novel, "Beasts of a Little Land." Kim and Kirill Batygin, who translated the book into Russian, were awarded Russia's largest annual prize in literature at Moscow's ...[more...] Full Article Culture
war BGS receives award at the World Landslide Forum 2023 - British Geological Survey By news.google.com Published On :: Thu, 30 Nov 2023 11:06:19 GMT BGS receives award at the World Landslide Forum 2023 British Geological Survey Full Article
war 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
war Funding awarded for study on hydrogen storage potential in the East Midlands - British Geological Survey By news.google.com Published On :: Mon, 19 Aug 2024 07:00:00 GMT Funding awarded for study on hydrogen storage potential in the East Midlands British Geological Survey Full Article
war AnACor2.0: a GPU-accelerated open-source software package for analytical absorption corrections in X-ray crystallography By journals.iucr.org Published On :: AnACor2.0 significantly accelerates the calculation of analytical absorption corrections in long-wavelength crystallography, achieving up to 175× speed improvements. This enhancement is achieved through innovative sampling techniques, bisection and gridding methods, and optimized CUDA implementations, ensuring efficient and accurate results. Full Article text
war Towards expansion of the MATTS data bank with heavier elements: the influence of the wavefunction basis set on the multipole model derived from the wavefunction By journals.iucr.org Published On :: This study examines the quality of charge density obtained by fitting the multipole model to wavefunctions in different basis sets. The complex analysis reveals that changing the basis set quality from double- to triple-zeta can notably improve the charge density related properties of a multipole model. Full Article text
war TOMOMAN: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing By journals.iucr.org Published On :: Here we describe TOMOMAN (TOMOgram MANager), an extensible open-sourced software package for handling cryo-electron tomography data preprocessing. TOMOMAN streamlines interoperability between a wide range of external packages and provides tools for project sharing and archival. Full Article text
war AnACor2.0: a GPU-accelerated open-source software package for analytical absorption corrections in X-ray crystallography By journals.iucr.org Published On :: 2024-11-04 Analytical absorption corrections are employed in scaling diffraction data for highly absorbing samples, such as those used in long-wavelength crystallography, where empirical corrections pose a challenge. AnACor2.0 is an accelerated software package developed to calculate analytical absorption corrections. It accomplishes this by ray-tracing the paths of diffracted X-rays through a voxelized 3D model of the sample. Due to the computationally intensive nature of ray-tracing, the calculation of analytical absorption corrections for a given sample can be time consuming. Three experimental datasets (insulin at λ = 3.10 Å, thermolysin at λ = 3.53 Å and thaumatin at λ = 4.13 Å) were processed to investigate the effectiveness of the accelerated methods in AnACor2.0. These methods demonstrated a maximum reduction in execution time of up to 175× compared with previous methods. As a result, the absorption factor calculation for the insulin dataset can now be completed in less than 10 s. These acceleration methods combine sampling, which evaluates subsets of crystal voxels, with modifications to standard ray-tracing. The bisection method is used to find path lengths, reducing the complexity from O(n) to O(log2 n). The gridding method involves calculating a regular grid of diffraction paths and using interpolation to find an absorption correction for a specific reflection. Additionally, optimized and specifically designed CUDA implementations for NVIDIA GPUs are utilized to enhance performance. Evaluation of these methods using simulated and real datasets demonstrates that systematic sampling of the 3D model provides consistently accurate results with minimal variance across different sampling ratios. The mean difference of absorption factors from the full calculation (without sampling) is at most 2%. Additionally, the anomalous peak heights of sulfur atoms in the Fourier map show a mean difference of only 1% compared with the full calculation. This research refines and accelerates the process of analytical absorption corrections, introducing innovative sampling and computational techniques that significantly enhance efficiency while maintaining accurate results. Full Article text
war DOMAS: a data management software framework for advanced light sources By journals.iucr.org Published On :: 2024-02-01 In recent years, China's advanced light sources have entered a period of rapid construction and development. As modern X-ray detectors and data acquisition technologies advance, these facilities are expected to generate massive volumes of data annually, presenting significant challenges in data management and utilization. These challenges encompass data storage, metadata handling, data transfer and user data access. In response, the Data Organization Management Access Software (DOMAS) has been designed as a framework to address these issues. DOMAS encapsulates four fundamental modules of data management software, including metadata catalogue, metadata acquisition, data transfer and data service. For light source facilities, building a data management system only requires parameter configuration and minimal code development within DOMAS. This paper firstly discusses the development of advanced light sources in China and the associated demands and challenges in data management, prompting a reconsideration of data management software framework design. It then outlines the architecture of the framework, detailing its components and functions. Lastly, it highlights the application progress and effectiveness of DOMAS when deployed for the High Energy Photon Source (HEPS) and Beijing Synchrotron Radiation Facility (BSRF). Full Article text
war ProSPyX: software for post-processing images of X-ray ptychography with spectral capabilities By journals.iucr.org Published On :: 2024-02-09 X-ray ptychography is a coherent diffraction imaging technique based on acquiring multiple diffraction patterns obtained through the illumination of the sample at different partially overlapping probe positions. The diffraction patterns collected are used to retrieve the complex transmittivity function of the sample and the probe using a phase retrieval algorithm. Absorption or phase contrast images of the sample as well as the real and imaginary parts of the probe function can be obtained. Furthermore, X-ray ptychography can also provide spectral information of the sample from absorption or phase shift images by capturing multiple ptychographic projections at varying energies around the resonant energy of the element of interest. However, post-processing of the images is required to extract the spectra. To facilitate this, ProSPyX, a Python package that offers the analysis tools and a graphical user interface required to process spectral ptychography datasets, is presented. Using the PyQt5 Python open-source module for development and design, the software facilitates extraction of absorption and phase spectral information from spectral ptychographic datasets. It also saves the spectra in file formats compatible with other X-ray absorption spectroscopy data analysis software tools, streamlining integration into existing spectroscopic data analysis pipelines. To illustrate its capabilities, ProSPyX was applied to process the spectral ptychography dataset recently acquired on a nickel wire at the SWING beamline of the SOLEIL synchrotron. Full Article text
war Optimization of synchrotron radiation parameters using swarm intelligence and evolutionary algorithms By journals.iucr.org Published On :: 2024-02-22 Alignment of each optical element at a synchrotron beamline takes days, even weeks, for each experiment costing valuable beam time. Evolutionary algorithms (EAs), efficient heuristic search methods based on Darwinian evolution, can be utilized for multi-objective optimization problems in different application areas. In this study, the flux and spot size of a synchrotron beam are optimized for two different experimental setups including optical elements such as lenses and mirrors. Calculations were carried out with the X-ray Tracer beamline simulator using swarm intelligence (SI) algorithms and for comparison the same setups were optimized with EAs. The EAs and SI algorithms used in this study for two different experimental setups are the Genetic Algorithm (GA), Non-dominated Sorting Genetic Algorithm II (NSGA-II), Particle Swarm Optimization (PSO) and Artificial Bee Colony (ABC). While one of the algorithms optimizes the lens position, the other focuses on optimizing the focal distances of Kirkpatrick–Baez mirrors. First, mono-objective evolutionary algorithms were used and the spot size or flux values checked separately. After comparison of mono-objective algorithms, the multi-objective evolutionary algorithm NSGA-II was run for both objectives – minimum spot size and maximum flux. Every algorithm configuration was run several times for Monte Carlo simulations since these processes generate random solutions and the simulator also produces solutions that are stochastic. The results show that the PSO algorithm gives the best values over all setups. Full Article text
war PEPICO analysis of catalytic reactor effluents towards quantitative isomer discrimination: DME conversion over a ZSM-5 zeolite By journals.iucr.org Published On :: 2024-06-25 The methanol-to-hydrocarbons (MTH) process involves the conversion of methanol, a C1 feedstock that can be produced from green sources, into hydrocarbons using shape-selective microporous acidic catalysts – zeolite and zeotypes. This reaction yields a complex mixture of species, some of which are highly reactive and/or present in several isomeric forms, posing significant challenges for effluent analysis. Conventional gas-phase chromatography (GC) is typically employed for the analysis of reaction products in laboratory flow reactors. However, GC is not suitable for the detection of highly reactive intermediates such as ketene or formaldehyde and is not suitable for kinetic studies under well defined low pressure conditions. Photoelectron–photoion coincidence (PEPICO) spectroscopy has emerged as a powerful analytical tool for unraveling complex compositions of catalytic effluents, but its availability is limited to a handful of facilities worldwide. Herein, PEPICO analysis of catalytic reactor effluents has been implemented at the FinEstBeAMS beamline of MAX IV Laboratory. The conversion of dimethyl ether (DME) on a zeolite catalyst (ZSM-5-MFI27) is used as a prototypical model reaction producing a wide distribution of hydrocarbon products. Since in zeolites methanol is quickly equilibrated with DME, this reaction can be used to probe vast sub-networks of the full MTH process, while eliminating or at least slowing down methanol-induced secondary reactions and catalyst deactivation. Quantitative discrimination of xylene isomers in the effluent stream is achieved by deconvoluting the coincidence photoelectron spectra. Full Article text
war MuscleX: data analysis software for fiber diffraction patterns from muscle By journals.iucr.org Published On :: 2024-07-30 MuscleX is an integrated, open-source computer software suite for data reduction of X-ray fiber diffraction patterns from striated muscle and other fibrous systems. It is written in Python and runs on Linux, Microsoft Windows or macOS. Most modules can be run either from a graphical user interface or in a `headless mode' from the command line, suitable for incorporation into beamline control systems. Here, we provide an overview of the general structure of the MuscleX software package and describe the specific features of the individual modules as well as examples of applications. Full Article text
war A distributed software system for integrating data-intensive imaging methods in a hard X-ray nanoprobe beamline at the SSRF By journals.iucr.org Published On :: 2024-08-22 The development of hard X-ray nanoprobe techniques has given rise to a number of experimental methods, like nano-XAS, nano-XRD, nano-XRF, ptychography and tomography. Each method has its own unique data processing algorithms. With the increase in data acquisition rate, the large amount of generated data is now a big challenge to these algorithms. In this work, an intuitive, user-friendly software system is introduced to integrate and manage these algorithms; by taking advantage of the loosely coupled, component-based design approach of the system, the data processing speed of the imaging algorithm is enhanced through optimization of the parallelism efficiency. This study provides meaningful solutions to tackle complexity challenges faced in synchrotron data processing. Full Article text
war Applying 3D ED/MicroED workflows toward the next frontiers By journals.iucr.org Published On :: 2024-05-07 We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation. Full Article text
war A small step towards an important goal: fragment screen of the c-di-AMP-synthesizing enzyme CdaA By journals.iucr.org Published On :: 2024-04-29 CdaA is the most widespread diadenylate cyclase in many bacterial species, including several multidrug-resistant human pathogens. The enzymatic product of CdaA, cyclic di-AMP, is a secondary messenger that is essential for the viability of many bacteria. Its absence in humans makes CdaA a very promising and attractive target for the development of new antibiotics. Here, the structural results are presented of a crystallographic fragment screen against CdaA from Listeria monocytogenes, a saprophytic Gram-positive bacterium and an opportunistic food-borne pathogen that can cause listeriosis in humans and animals. Two of the eight fragment molecules reported here were localized in the highly conserved ATP-binding site. These fragments could serve as potential starting points for the development of antibiotics against several CdaA-dependent bacterial species. Full Article text
war Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection By journals.iucr.org Published On :: 2024-06-04 The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields. Full Article text
war Cocrystals of a coumarin derivative: an efficient approach towards anti-leishmanial cocrystals against MIL-resistant Leishmania tropica By journals.iucr.org Published On :: 2024-03-01 Leishmaniasis is a neglected parasitic tropical disease with numerous clinical manifestations. One of the causative agents of cutaneous leishmaniasis (CL) is Leishmania tropica (L. tropica) known for causing ulcerative lesions on the skin. The adverse effects of the recommended available drugs, such as amphotericin B and pentavalent antimonial, and the emergence of drug resistance in parasites, mean the search for new safe and effective anti-leishmanial agents is crucial. Miltefosine (MIL) was the first recommended oral medication, but its use is now limited because of the rapid emergence of resistance. Pharmaceutical cocrystallization is an effective method to improve the physicochemical and biological properties of active pharmaceutical ingredients (APIs). Herein, we describe the cocrystallization of coumarin-3-carboxylic acid (CU, 1a; 2-oxobenzopyrane-3-carboxylic acid, C10H6O4) with five coformers [2-amino-3-bromopyridine (1b), 2-amino-5-(trifluoromethyl)-pyridine (1c), 2-amino-6-methylpyridine (1d), p-aminobenzoic acid (1e) and amitrole (1f)] in a 1:1 stoichiometric ratio via the neat grinding method. The cocrystals 2–6 obtained were characterized via single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermogravimetric analysis, as well as Fourier transform infrared spectroscopy. Non-covalent interactions, such as van der Waals, hydrogen bonding, C—H⋯π and π⋯π interactions contribute significantly towards the packing of a crystal structure and alter the physicochemical and biological activity of CU. In this research, newly synthesized cocrystals were evaluated for their anti-leishmanial activity against the MIL-resistant L. tropica and cytotoxicity against the 3T3 (normal fibroblast) cell line. Among the non-cytotoxic cocrystals synthesized (2–6), CU:1b (2, IC50 = 61.83 ± 0.59 µM), CU:1c (3, 125.7 ± 1.15 µM) and CU:1d (4, 48.71 ± 0.75 µM) appeared to be potent anti-leishmanial agents and showed several-fold more anti-leishmanial potential than the tested standard drug (MIL, IC50 = 169.55 ± 0.078 µM). The results indicate that cocrystals 2–4 are promising anti-leishmanial agents which require further exploration. Full Article text
war Toward a quantitative description of solvation structure: a framework for differential solution scattering measurements By journals.iucr.org Published On :: 2024-05-01 Appreciating that the role of the solute–solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems in situ in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime—where sub-ångström spatial resolution is achieved—remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography. Full Article text
war A step towards 6D WAXD tensor tomography By journals.iucr.org Published On :: 2024-05-09 X-ray scattering/diffraction tensor tomography techniques are promising methods to acquire the 3D texture information of heterogeneous biological tissues at micrometre resolution. However, the methods suffer from a long overall acquisition time due to multi-dimensional scanning across real and reciprocal space. Here, a new approach is introduced to obtain 3D reciprocal information of each illuminated scanning volume using mathematic modeling, which is equivalent to a physical scanning procedure for collecting the full reciprocal information required for voxel reconstruction. The virtual reciprocal scanning scheme was validated by a simulated 6D wide-angle X-ray diffraction tomography experiment. The theoretical validation of the method represents an important technological advancement for 6D diffraction tensor tomography and a crucial step towards pervasive applications in the characterization of heterogeneous materials. Full Article text
war Quantum refinement in real and reciprocal space using the Phenix and ORCA software By journals.iucr.org Published On :: 2024-09-30 X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software Phenix and the freely available quantum mechanical software ORCA. Through application to manganese superoxide dismutase and V- and Fe-nitrogenase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals. Full Article text
war Crystal structure of Staudtienic acid, a diterpenoid from Staudtia kamerunensis Warb. (Myristicaceae) By journals.iucr.org Published On :: 2024-07-19 This title compound, C20H26O2, was isolated from the benzene fraction of the stem bark of Staudtia kamerunensis Warb. (Myristicaceae) using column chromatography techniques over silica gel. The compound was fully characterized by single-crystal X-ray diffraction, one and two-dimensional NMR spectroscopy, IR and MS spectrometry. The compound has two fused cyclohexane rings attached to a benzene ring, with a carboxylic acid on C-4. This cyclohexene ring has a chair conformation while the other adopts a half-chair conformation. The benzene ring is substituted with a propenyl moiety. The structure is characterized by intermolecular O—H⋯O hydrogen bonds, two C—H⋯O intramolecular hydrogen bonds and two C—H⋯π interactions. The molecular structure confirms previous studies carried out by spectroscopic techniques. Full Article text