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MuscleX: data analysis software for fiber diffraction patterns from muscle

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.




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Demonstration of full polarization control of soft X-ray pulses with Apple X undulators at SwissFEL using recoil ion momentum spectroscopy

The ability to freely control the polarization of X-rays enables measurement techniques relying on circular or linear dichroism, which have become indispensable tools for characterizing the properties of chiral molecules or magnetic structures. Therefore, the demand for polarization control in X-ray free-electron lasers is increasing to enable polarization-sensitive dynamical studies on ultrafast time scales. The soft X-ray branch Athos of SwissFEL was designed with the aim of providing freely adjustable and arbitrary polarization by building its undulator solely from modules of the novel Apple X type. In this paper, the magnetic model of the linear inclined and circular Apple X polarization schemes are studied. The polarization is characterized by measuring the angular electron emission distributions of helium for various polarizations using cold target recoil ion momentum spectroscopy. The generation of fully linear polarized light of arbitrary angle, as well as elliptical polarizations of varying degree, are demonstrated.




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Development of a flat jet delivery system for soft X-ray spectroscopy at MAX IV

One of the most challenging aspects of X-ray research is the delivery of liquid sample flows into the soft X-ray beam. Currently, cylindrical microjets are the most commonly used sample injection systems for soft X-ray liquid spectroscopy. However, they suffer from several drawbacks, such as complicated geometry due to their curved surface. In this study, we propose a novel 3D-printed nozzle design by introducing microscopic flat sheet jets that provide micrometre-thick liquid sheets with high stability, intending to make this technology more widely available to users. Our research is a collaboration between the EuXFEL and MAX IV research facilities. This collaboration aims to develop and refine a 3D-printed flat sheet nozzle design and a versatile jetting platform that is compatible with multiple endstations and measurement techniques. Our flat sheet jet platform improves the stability of the jet and increases its surface area, enabling more precise scanning and differential measurements in X-ray absorption, scattering, and imaging applications. Here, we demonstrate the performance of this new arrangement for a flat sheet jet setup with X-ray photoelectron spectroscopy, photoelectron angular distribution, and soft X-ray absorption spectroscopy experiments performed at the photoemission end­station of the FlexPES beamline at MAX IV Laboratory in Lund, Sweden.




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The soft X-ray spectromicroscopy beamline BL08U1A upgrade at SSRF

Beamline BL08U1A is a soft X-ray spectromicroscopy beamline at Shanghai Synchrotron Radiation Facility (SSRF) that exhibits the capabilities of high spatial resolution (30 nm) and high energy resolving power (over 104). As a first-generation beamline of SSRF, owing to its continuous operation over the last ten years, an urgent upgrade of the equipment including the monochromator was deemed necessary. The upgrade work included the overall construction of the monochromator and replacement of the mirrors upstream and downstream of the monochromator. Based on its original skeleton, two elliptically cylinder mirrors were designed to focus the beam horizontally, which can increase the flux density by about three times on the exit slits. Meanwhile, the application of variable-line-space gratings in the monochromator demonstrates the dual functions of dispersing and focusing on the exit slits which can decrease abberations dramatically. After the upgrade of the main components of the beamline, the energy range is 180–2000 eV, the energy resolving power reaches 16333 @ 244 eV and 12730 @ 401 eV, and the photon flux measured in the experimental station is over 2.45 × 109 photons s−1 (E/ΔE = 6440 @ 244 eV).




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A distributed software system for integrating data-intensive imaging methods in a hard X-ray nanoprobe beamline at the SSRF

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.




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

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




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Chromic soft crystals based on luminescent platinum(II) complexes

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.




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Quantum refinement in real and reciprocal space using the Phenix and ORCA software

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.




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ProLEED Studio: software for modeling low-energy electron diffraction patterns

Low-energy electron diffraction patterns contain precise information about the structure of the surface studied. However, retrieving the real space lattice periodicity from complex diffraction patterns is challenging, especially when the modeled patterns originate from superlattices with large unit cells composed of several symmetry-equivalent domains without a simple relation to the substrate. This work presents ProLEED Studio software, built to provide simple, intuitive and precise modeling of low-energy electron diffraction patterns. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results.




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X-Ray Calc 3: improved software for simulation and inverse problem solving for X-ray reflectivity

This work introduces X-Ray Calc (XRC), an open-source software package designed to simulate X-ray reflectivity (XRR) and address the inverse problem of reconstructing film structures on the basis of measured XRR curves. XRC features a user-friendly graphical interface that facilitates interactive simulation and reconstruction. The software employs a recursive approach based on the Fresnel equations to calculate XRR and incorporates specialized tools for modeling periodic multilayer structures. This article presents the latest version of the X-Ray Calc software (XRC3), with notable improvements. These enhancements encompass an automatic fitting capability for XRR curves utilizing a modified flight particle swarm optimization algorithm. A novel cost function was also developed specifically for fitting XRR curves of periodic structures. Furthermore, the overall user experience has been enhanced by developing a new single-window interface.




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

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




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Technique uses magnets, light to control and reconfigure soft robots

Full Text:

National Science Foundation (NSF)-funded researchers from North Carolina State and Elon universities have developed a technique that allows them to remotely control the movement of soft robots, lock them into position for as long as needed and later reconfigure the robots into new shapes. The technique relies on light and magnetic fields. "By engineering the properties of the material, we can control the soft robot's movement remotely; we can get it to hold a given shape; we can then return the robot to its original shape or further modify its movement; and we can do this repeatedly. All of those things are valuable, in terms of this technology's utility in biomedical or aerospace applications," says Joe Tracy, a professor of materials science and engineering at NC State and corresponding author of a paper on the work. In experimental testing, the researchers demonstrated that the soft robots could be used to form "grabbers" for lifting and transporting objects. The soft robots could also be used as cantilevers or folded into "flowers" with petals that bend in different directions. "We are not limited to binary configurations, such as a grabber being either open or closed," says Jessica Liu, first author of the paper and a Ph.D. student at NC State. "We can control the light to ensure that a robot will hold its shape at any point."

Image credit: Jessica A.C. Liu




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Sonata Software adds new functionality to its enterprise mobility product Halosys

Sonata Software announced that its Unified Enterprise Mobility Platform, Halosys, has been enhanced with additional features that boost optimization and usability




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Oracle adds generative AI to its human resources software

Many business users have approached generative AI technology more cautiously because it can make up untrue facts and be tricked into saying unsettling things. Oracle's human resources software is used by big businesses for hiring new employees and providing performance evaluations, among other things. Oracle will put a button on many of the fields in the software that will automatically generate draft text for things like job listings or performance goals.




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Beyond the blue screen of death: Why software updates matter

The widespread IT outages triggered by a faulty CrowdStrike update have put software updates in the spotlight. Here’s why you shouldn’t dread them.




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Data analytics firm Palantir jumps as AI boom powers robust software adoption

The company is among the biggest stock market winners of the generative AI boom, with its shares more than doubling in value this year.




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Should new tech rules apply to Microsoft's Bing, Apple's iMessage, EU asks

The European Commission in September opened investigations to assess whether Microsoft's Bing, Edge and Microsoft Advertising as well as Apple's iMessage should be subject to the Digital Markets Act (DMA).




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Data center firm ESDS Software to hire 300 AI/ML engineers in India

ESDS said its client base includes the Software Technology Parks of India (STPI), SIDBI Bank, Union Bank of India, State Bank of India Capital, and over 400 cooperative banks, as well as, the Embassy Group, Vadilal, and Unibic.




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Nvidia and SoftBank pilot world's first AI and 5G telecom network

"Every other telco will have to follow this new wave," SoftBank Group CEO Masayoshi Son said at an AI event where he was speaking alongside Nvidia CEO Jensen Huang.




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Users can now mark messages as important or urgent in Microsoft Teams

Navigate to the "Mark as important" button which is present beneath the compose box and select either the "Important" or "Urgent" option depending on the level of attention the message requires.




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Oppo aims to make GenAI accessible to 50 mn users in 2024, collaborates with Google, Microsoft

Oppo aims to make generative artificial intelligence accessible to 50 million users by 2024 through collaborations with Google and Microsoft, joining other handset makers like Samsung and Xiaomi in leveraging AI for sales growth.




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Apple announces software tools for developers to create apps for Vision Pro

Apple has announced that starting today, its global community of developers will be able to create spatial computing apps for Vision Pro.




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Microsoft says new computing service for chemicals can slash R&D time

The new offering uses a combination of existing quantum computers, artificial intelligence and conventional high-performance computing systems.




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Microsoft announces AI-powered shopping tools in Bing, Edge

The new tools help users to harness the power of AI "to make it easier to discover, research, and complete your purchase, all in one place with information you need from expert sources," the tech giant said in a blogpost on Thursday.




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Microsoft announces AI-powered shopping tools in Bing, Edge

The new tools help users to harness the power of AI "to make it easier to discover, research, and complete your purchase, all in one place with information you need from expert sources," the tech giant said in a blogpost on Thursday.




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Generative AI biggest weapon and tool for cybersecurity: Microsoft's Brad Smith

Addressing cybersecurity attack concerns raised by generative AI, Smith said that there will be an increasing number of organisations and governments that will use the technology to develop cybersecurity threats.




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CERT-In finds multiple bugs in Microsoft Edge, advises users to update

"Multiple vulnerabilities have been reported in Microsoft Edge (chromium-based) which could allow the remote attacker to cause a denial of service condition, remote code execution, sensitive information disclosure and security restriction bypass on the targeted system," said the CERT-In advisory.




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Microsoft offers cloud customers AMD alternative to Nvidia AI processors

Microsoft's clusters of Advanced Micro Devices' flagship MI300X AI chips will be sold through its Azure cloud computing service. AMD, which expects $4 billion in AI chip revenue this year, has said the chips are powerful enough to train and run large AI models.




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Microsoft to lay off hundreds at Azure cloud unit

Microsoft is cutting hundreds of jobs at its Azure cloud unit, impacting teams like Azure for Operators and Mission Engineering, as reported by Business Insider.




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Microsoft & CISPE reach settlement on cloud licensing dispute, raising industry eyebrows

The deal reportedly totals around 20 million euros but excludes major players like Amazon Web Services (AWS) and Google Cloud Platform. This has drawn criticism from both the companies.




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The $7.5 billion GitHub deal that Microsoft CEO 'sealed' in 20 minutes

Microsoft's CEO Satya Nadella, since 2014, embraced cloud computing and doubled its market share. He quickly approved the $7.5 billion GitHub acquisition at a Suncadia Resort retreat in the Cascade Mountains. GitHub supports global developer collaboration with Microsoft's cloud infrastructure, establishing Microsoft’s No. 2 role behind Amazon in cloud computing, as reported by New York Times.




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Key Technology Introduces Key Discovery suite of software solutions

Key Technology has introduced Key Discovery, a suite of software solutions that is able to collect, analyze, and share data while sorting product.




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Festo to introduce artificial intelligence software platform at IBIE 2022

Festo to introduce AI-based software for machine uptime, soft-robotic grippers, and economical electric motion at IBIE 2022.




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Emerson launches analytics software to automate utilities

Technology replaces error-prone manual record keeping and monitors energy and utilities parameters, improving efficiency and productivity.




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Cybake bakery software integrates with REKKI restaurant app

The partnership seeks to simplify and streamline restaurant orders of breads and other bakery goods.




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Companies search for new and improved warehouse software

Companies often use warehouse management system (WMS) software to track traffic in and out of the warehouse. These systems are often a component of a larger enterprise resource planning (ERP) system.




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Advanced warehouse software solution for snack and bakery operations

Warehouse management software (WMS) and other software and technology solutions for snack and bakery operations.




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Food safety software in the snack and bakery industry: Changes and updates

Every facility needs a food safety plan, and that includes food safety software related to traceability. This software will come in handy whenever a company needs to trace a certain ingredient or product, due to recalls or other reasons.




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Warehouse software challenges for snack and bakery companies

Warehouse software is important for snack and bakery companies, in order to keep track of the comings and goings of products inside their warehouses.




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Traceability software for snack and bakery companies

Traceability is an important facet of warehouses, especially for snack and bakery companies.




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Bellarise organic softener and ESL system

Bakery ingredient manufacturer Pak Group, through its North American brand, Bellarise, has introduced Bellarise BellaSOFT Organic 1500 Plus.




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ERP software solutions for snack and bakery companies

Enterprise resource planning (ERP) software for snack and bakery companies to improve safety, production, and efficiency.




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J&J Snack Foods introduces Brauhaus soft pretzel line

The Bavarian-style sourdough pretzels are intended to deliver authentic European flavor and texture.




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FRITSCH soft dough sheeter

FRITSCH recently released its new Soft Dough Sheeter (SDS).




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SUPERPRETZEL Filled Soft Pretzel Bites

Nationally recognized SUPERPRETZEL  Soft Pretzel brand is expanding its snack offerings, as it was announced that J&J Snack Foods Corp. is introducing SUPERPRETZEL Filled Soft Pretzel Bites.




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Baker Perkins Series3 rotary moulder for soft dough biscuits and sandwich cookies

Baker Perkins’ new Series3 rotary moulder for soft dough biscuits and sandwich cookies sets new standards in hygiene, operation and maintenance, while retaining all the important high performance characteristics of the previous machine.




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Kind Snacks introduces Kind Kids soft-baked bars

The gluten- and peanut-free formulation is designed to be school-friendly.




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Software solutions bring the connected warehouse to life

A warehouse management system (WMS) centers on software that supports day-to-day operations. WMS programs enable centralized management of a wide range of tasks, including tracking inventory levels and stock locations, order fulfillment, and shipping and receiving.




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Thiele SYMACH Palletizers, integrated with Allen-Bradley control software

Thiele Technologies has announced that it soon will integrate Allen-Bradley control software on SYMACH Palletizers.




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Aaron Salow: Data drives plumbing software trends in 2022

Not too long ago, the plumbing industry relied strictly on analog processes. Every job was manual, from installation and repair to dispatch, invoicing and accounting. In 2022, the plumbing profession now runs on advanced technologies that range from thermal-imaging leak detection to smart water heaters and trenchless pipe repair.