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Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging

In X-ray diffraction imaging (XDI), electron density maps of a targeted particle are reconstructed computationally from the diffraction pattern alone using phase-retrieval (PR) algorithms. However, the PR calculations sometimes fail to yield realistic electron density maps that approximate the structure of the particle. This occurs due to the absence of structure amplitudes at and near the zero-scattering angle and the presence of Poisson noise in weak diffraction patterns. Consequently, the PR calculation becomes a bottleneck for XDI structure analyses. Here, a protocol to efficiently yield realistic maps is proposed. The protocol is based on the empirical observation that realistic maps tend to yield low similarity scores, as suggested in our prior study [Sekiguchi et al. (2017), J. Synchrotron Rad. 24, 1024–1038]. Among independently and concurrently executed PR calculations, the protocol modifies all maps using the electron-density maps exhibiting low similarity scores. This approach, along with a new protocol for estimating particle shape, improved the probability of obtaining realistic maps for diffraction patterns from various aggregates of colloidal gold particles, as compared with PR calculations performed without the protocol. Consequently, the protocol has the potential to reduce computational costs in PR calculations and enable efficient XDI structure analysis of non-crystalline particles using synchrotron X-rays and X-ray free-electron laser pulses.




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PINK: a tender X-ray beamline for X-ray emission spectroscopy

A high-flux beamline optimized for non-resonant X-ray emission spectroscopy (XES) in the tender X-ray energy range has been constructed at the BESSY II synchrotron source. The beamline utilizes a cryogenically cooled undulator that provides X-rays over the energy range 2.1 keV to 9.5 keV. This energy range provides access to XES [and in the future X-ray absorption spectroscopy (XAS)] studies of transition metals ranging from Ti to Cu (Kα, Kβ lines) and Zr to Ag (Lα, Lβ), as well as light elements including P, S, Cl, K and Ca (Kα, Kβ). The beamline can be operated in two modes. In PINK mode, a multilayer monochromator (E/ΔE ≃ 30–80) provides a high photon flux (1014 photons s−1 at 6 keV and 300 mA ring current), allowing non-resonant XES measurements of dilute substances. This mode is currently available for general user operation. X-ray absorption near-edge structure and resonant XAS techniques will be available after the second stage of the PINK commissioning, when a high monochromatic mode (E/ΔE ≃ 10000–40000) will be facilitated by a double-crystal monochromator. At present, the beamline incorporates two von Hamos spectrometers, enabling time-resolved XES experiments with time scales down to 0.1 s and the possibility of two-color XES experiments. This paper describes the optical scheme of the PINK beamline and the endstation. The design of the two von Hamos dispersive spectrometers and sample environment are discussed here in detail. To illustrate, XES spectra of phosphorus complexes, KCl, TiO2 and Co3O4 measured using the PINK setup are presented.




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Linking solid-state phenomena via energy differences in `archetype crystal structures'

Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305–318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder – and disappearing disorder – occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an R·T energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-Z' structures can also be analysed energetically and understood via archetypes: high-Z' structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds R·T, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.




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Three-dimensional electron diffraction on clinkers: the belite α'H incommensurate modulated structure

Traditional X-ray methods are extensively applied to commercial cement samples in order to determine their physical and chemical properties. Powder patterns are routinely used to quantify the composition of these phase mixtures, but structure determination becomes difficult because of reflection overlapping caused by the high number of different crystal structures. The fast-growing 3D electron diffraction technique and its related automated acquisition protocols arise as a potentially very interesting tool for the cement industry, since they enable the fast and systematic acquisition of diffraction data from individual particles. In this context, electron diffraction has been used in the investigation of the different crystalline phases present in various commercial clinkers for cement. Automated data collection procedures and subsequent data processing have enabled the structural characterization of the different crystal structures from which the α'H polymorph of Ca2SiO4 (belite) exhibited satellite reflections. Its average crystal structure has been known since 1971 and satellite reflections have been reported previously, yet the modulation was never fully described by means of the superspace formalism. Here, the incommensurately modulated structure is solved and refined using harmonic and crenel functions in the superspace group Pnma(α00)0ss, showing the potential of 3D electron diffraction for systematic crystallographic characterizations of cement. A full description of the different belite polymorphs is provided considering this modulated structure.




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The use of ethanol as contrast enhancer in Synchrotron X-ray phase-contrast imaging leads to heterogeneous myocardial tissue shrinkage: a case report

In this work, we showed that the use of ethanol to increase image contrast when imaging cardiac tissue with synchrotron X-ray phase-contrast imaging (X-PCI) leads to heterogeneous tissue shrinkage, which has an impact on the 3D organization of the myocardium.




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Link between b.c.c.–f.c.c. orientation relationship and austenite morphology in CF8M stainless steel

Slow-cooled CF8M duplex stainless steel is used for critical parts of the primary coolant pipes of nuclear reactors. This steel can endure severe service conditions, but it tends to become more brittle upon very long-term aging (tens of years). Therefore, it is essential to understand its specific microstructure and temporal evolution. As revealed by electron backscatter diffraction (EBSD) analyses, the microstructure consists of millimetre-scale ferritic grains within which austenite lath packets have grown with preferred crystallographic orientations concerning the parent ferritic phase far from the ferrite grain boundaries. In these lath packets where the austenite phase is nucleated, the lath morphology and crystal orientation accommodate the two ferrite orientations. Globally, the Pitsch orientation relationship appears to display the best agreement with the experimental data compared with other classical relationships. The austenite lath packets are parallel plate-shaped laths, characterized by their normal n. A novel methodology is introduced to elucidate the expected relationship between n and the crystallographic orientation given the coarse interfaces, even though n is only partly known from the observation surface, in contrast to the 3D crystal orientations measured by EBSD. The distribution of retrieved normals n is shown to be concentrated over a set of discrete orientations. Assuming that the ferrite and austenite obey the Pitsch orientation relationship, the determined lath normals are close to an invariant direction of the parent phase given by the same orientation relationship.




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Back From The Brink

This summer, USGS Western Fisheries Research Center and collaborating scientists were delighted to find that the abundance of wild born juvenile fall Chinook salmon migrating out of the Snake River has increased by almost 2 orders of magnitude within the last 30 years. 




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Report Links Disease to Herbicides - Calls for New Studies of Exposed Vietnam Veterans

Evidence exists linking three cancers and two other health problems with chemicals used in herbicides in the Vietnam War, a committee of the Institute of Medicine (IOM) has concluded.




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Radon in Drinking Water Constitutes Small Health Risk

Radon in household water supplies increases peoples overall exposure to the gas, but waterborne radon poses few risks to human health, says a new report by a committee of the National Research Council.




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Allowable Levels of Copper in Drinking Water Should Not Be Increased Until Studies Are Done

The federal government should not increase the maximum level of copper allowed in drinking water, because higher levels could lead to liver poisoning in infants and children with certain genetic disorders.




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SIDS Not Linked to Number and Variety of Childhood Vaccines

The evidence does not support a causal link between sudden infant death syndrome (SIDS) and either the diphtheria, tetanus, and whole-cell pertussis (DTwP) vaccine or exposure to multiple childhood vaccines, says a new report from the Institute of Medicine of the National Academies.




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Opening Statement by Richard J. Bonnie on Reducing Underage Drinking - A Collective Responsibility

Good morning. I am Richard Bonnie, chair of the Committee on Developing a Strategy to Reduce and Prevent Underage Drinking.




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Indoor Mold, Building Dampness Linked to Respiratory Problems and Require Better Prevention - Evidence Does Not Support Links to Wider Array of Illnesses

Scientific evidence links mold and other factors related to damp conditions in homes and buildings to asthma symptoms in some people with the chronic disorder, as well as to coughing, wheezing, and upper respiratory tract symptoms in otherwise healthy people, says a new report from the Institute of Medicine of the National Academies.




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EPA Standard for Fluoride in Drinking Water Is Not Protective - Tooth Enamel Loss, Bone Fractures of Concern at High Levels

The U.S. Environmental Protection Agencys standard for the maximum amount of fluoride allowed in drinking water -- 4 milligrams of fluoride per liter of water -- does not protect against adverse health effects.




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Studies Suggest a Possible Link Between Military Service and ALS

A limited body of evidence suggests an association between military service and later development of amyotrophic lateral sclerosis (ALS), a rare but fatal neurodegenerative disorder, says a new report from the Institute of Medicine.




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Link Between Ozone Air Pollution and Premature Death Confirmed

Short-term exposure to current levels of ozone in many areas is likely to contribute to premature deaths, says a new National Research Council report, which adds that the evidence is strong enough that the U.S. Environmental Protection Agency should include ozone-related mortality in health-benefit analyses related to future ozone standards.




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Scientific Evidence Of Health Problems From Past Contamination Of Drinking Water At Camp Lejeune Is Limited And Unlikely To Be Resolved With Further Study

Evidence exists that people who lived or worked at Camp Lejeune Marine Base in North Carolina between the 1950s and 1985 were exposed to the industrial solvents tricholorethylene (TCE) or perchloroethylene (PCE) in their water supply, but strong scientific evidence is not available to determine whether health problems among those exposed are due to the contaminants, says a new report from the National Research Council.




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Daniel Kahnemans Thinking, Fast and Slow Wins Best Book Award From Academies - Milwaukee Journal Sentinel, Slate Magazine, and WGBH/NOVA Also Take Top Prizes in Awards 10th Year

Recipients of the 10th annual Communication Awards were announced today by the National Academy of Sciences, National Academy of Engineering, and Institute of Medicine.




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Report Finds Immigrants Come to Resemble Native-Born Americans Over Time, But Integration Not Always Linked to Greater Well-Being for Immigrants

As immigrants and their descendants become integrated into U.S. society, many aspects of their lives improve, including measurable outcomes such as educational attainment, occupational distribution, income, and language ability, but their well-being declines in the areas of health, crime, and family patterns, says a new report from the National Academies of Sciences, Engineering, and Medicine.




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New Report Finds Gulf War Illness Continues to Be Major Health Effect Linked to Persian Gulf War Military Service

Although more than $500 million in federally funded research on Persian Gulf War veterans between 1994 and 2014 has produced many findings, there has been little substantial progress in the overall understanding of the health effects, particularly Gulf War illness, resulting from military service in the war, says a new report from the Institute of Medicine (IOM) of the National Academies of Sciences, Engineering, and Medicine.




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Latest and Final Biennial Review of Health Problems That May Be Linked to Agent Orange Exposure During Vietnam War

The latest and final in a series of congressionally mandated biennial reviews of the evidence of health problems that may be linked to exposure to Agent Orange and other herbicides used during the Vietnam War changed the categorization of health outcomes for bladder cancer, hypothyroidism, and spina bifida and clarified the breadth of the previous finding for Parkinson’s disease.




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Determining Whether There Is a Link Between Antimalarial Drugs and Persistent Health Effects Requires More Rigorous Studies

Although the immediate side effects of antimalarial drugs are widely recognized, few studies were designed specifically to examine health problems that might occur or persist months or years after people stopped taking them.




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Augmenting Our Thinking through the Nexus of Engineering, Science, Technology, and Art

The world faces enormous challenges of unprecedented complexity—problems that intertwine in a dizzyingly interconnected, interdependent, and changing landscape. Few of them—especially those dealing with energy, environment, and social structures—admit clean solutions with clear endpoints.




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Researchers Need to Rethink and Justify How and Why Race, Ethnicity, and Ancestry Labels Are Used in Genetics and Genomics Research, Says New Report

Race, ethnicity, and ancestry labels are often used in genomics and genetics research to describe human genetic differences, which is misleading and inaccurate. Researchers and scientists who utilize genetic and genomic data should rethink and justify how and why they use these descriptors in their work.




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LinkedIn cuts over 700 jobs, exits China app as demand wavers

LinkedIn, which has 20,000 employees, has grown revenue each quarter during the last year, but it joins other major technology companies including its parent in laying off workers amid a weakening global economic outlook.




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Twitter to take on LinkedIn with job posting feature

In order to take on the professional social networking platform LinkedIn, Twitter appears to be working on a job posting feature that will allow verified organisations to post job listings on their profiles




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LinkedIn working on an AI ‘coach’

LinkedIn, owned by Microsoft, is reportedly testing an AI-based tool called LinkedIn Coach to assist users in finding jobs through coaching on developing skills and networking. LinkedIn spokesperson Amanda Purvis said that the company is “always exploring” new ways to upgrade the user experience of the platform. LinkedIn already has AI embedded in its system.




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Rethinking the risk : Video

The Art of Connecting is Rethinking the Risk. Be clear on where you stand with BT Security.




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Rethinking the risk - Video

The Art of Connecting is Rethinking the Risk. Be clear on where you stand with BT Security




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Linking RNA structure and function

Several years ago, biologists discovered a new type of genetic material known as long noncoding RNA. This RNA does not code for proteins and is copied from sections of the genome once believed to be "junk DNA."

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  • Biology & Nature

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Study links altered brain chemistry, behavioral impairments in fish exposed to elevated CO2

Study Links Altered Brain Chemistry, Behavioral Impairments in Fish Exposed to Elevated CO2 Research team studied damselfish behavior and physiology under ocean acidification conditions predicted for year 2300

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  • Biology & Nature

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119: Thinking, Fast and Slow

Grey has an issue with four hundred thousand files, Myke is preparing the balloons, and they both read 'Thinking, Fast and Slow'.




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Eddie edible ink printer releases accessory for doughnuts, confections printing

NSF/GMP-Certified Edible Ink Printer prints graphics onto cookies, white chocolate, macarons, and now doughnuts and taller food items with Platform Kit Accessory.




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Thinking logically: the latest in warehousing and logistics technology

Snack and bakery companies rely on a wide range of logistics and warehousing technology in their operations. 




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The Drinks Bakery to showcase Drinks Biscuits range at Summer Fancy Food Show

The Drinks Bakery creates savory shortbread "Drinks Biscuits" that are flavor-profiled to match drinks from around the world such as craft beer, fine wines, whisky, bourbon, and gin.




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Thinking outside of the pizza box

To pizza and flatbread manufacturers, the secret to a great product goes way beyond the sauce. So what are the trends?




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Sprinkles, Miyoko’s Creamery partner on vegan cupcake

The limited-time bakery treat is made with Miyoko’s Cinnamon Brown Sugar Oat Milk Butter.




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Hostess partners with Dude Dad on mystery Twinkies

The bakery brand and Instagram influencer collaborated on the secret flavor.




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Fun Friday: HI-CHEW and Menchie's collab, Oprah's Favorite Things pound cake, Pinkbox monthly doughnut

This week's Fun Friday includes a Menchie's and HI-CHEW partnership, Oprah's Favorite Things pound cake, Pinkbox Doughnuts' treat of the month, a Haribo and Adidas sneaker collab, and IT'SUGAR's "Chews-Your-Mix" candy experience.




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Study: No link between refined grain foods, heart disease

Despite processed grains’ reputation for causing heart-related health woes, research indicates otherwise.




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think! debuts Minis Protein Snack Bars

The new think! Minis offer a conveniently sized snack option at 100 calories and 6 grams of protein per bar, in dessert-inspired flavors.




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Forward Thinking About Baking Equipment Design

This past year has been an exciting one for the baking industry, especially in terms of the progress made on revising the ANSI/ASB Z50.2 Bakery Equipment Sanitation Standard (formerly known as the “BISSC Standard”). Representatives from across the baking industry, including bakers, bakery engineers, bakery equipment manufacturers and academics have come together to give their input on updating this standard.




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Tool Tips: Toilet and sink water removal

The customer says there is water at the base of the toilet after flushing, which means you get to replace the wax seal. 




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American Fire Sprinkler Association announces Patriot Chapter

The Yankee chapter will now be known as the Patriot chapter in the New England area.




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Using PEX in residential fire sprinkler systems

PEX can be a viable alternative to more traditional materials for fire sprinklers.




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NFSA fights for sprinkler ordinance

Former Philadelphia Fire Commissioner Derrick Sawyer leads charge for residential fire safety.




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Victaulic acquires Globe Fire Sprinkler

Effective July 8, 2019, Victaulic has purchased Globe Fire Sprinkler. Combined, these two respected companies will have the resources and capabilities to bring exciting new solutions to the fire protection industry around the world, Victaulic notes.




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The requirements and challenges of residential fire sprinkler systems and water meters

Now that many jurisdictions across the country are mandating fire sprinkler systems in new-home construction, de-signers need to be aware of the requirements and challenges these systems can face in relation to water meters.




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New trends in corrosion and freeze protection for resilient fire sprinkler systems

How can engineers and contractors design wet fire sprinkler systems equipped to prevent corrosion and dry systems equipped to prevent freezing? That has long been a question central to code requirements and new product development.