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A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated, quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist’s experiments, while more than half have even failed to reproduce their own experiments1. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique2,3. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g., DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE4), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common Standards and guidelines for quality assessment and reproducibility5.
In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative6 was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models7,8, and tools9,10, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research.
This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of Stakeholders including, researchers, imaging scientists11, bioimage analysts, bioimage informatics developers, corporate partners, Funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREPLiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC.
To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using
these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration.
The lead authors failed to name two collaborators as co-authors. The authors listed should include:
Miss Claudia L. Compean-Gonzalez (ORCID:
0000-0002-2367-8450) and Dr. Giacomo Ceccone (ORCID:
0000-0003-4637-0771).
These co-authors participated in VAMAS project A27, provided data that were analyzed and presented in this publication (and supporting information), and reviewed the manuscript before submission.
Although the concept of structural water that is bound inside hydrophobic pockets and helps to stabilize protein structures is well established, water has rarely found a similar role in supramolecular polymers. Water is often used as a solvent for supramolecular polymerization, however without taking the role of a comonomer for the supramolecular polymer structure. We report a low–molecular weight monomer whose supramolecular polymerization is triggered by the incorporation of water. The presence of water molecules as comonomers is essential to the polymerization process. The supramolecular polymeric material exhibits strong adhesion to surfaces, such as glass and paper. It can be used as a water-activated glue, which can be released at higher temperatures and reused many times without losing its performance.
Understanding the void defect formation mechanism and simultaneous predicting the tool service life in friction stir welding are critical for optimizing the welding parameters. However, the void defect formation mechanism in friction stir welding is not yet elucidated. In this study, a novel integrated thermal-fluid-structure coupling model of the friction stir welding process was proposed for simultaneous prediction of the weld formation and tool service life. A new non-uniform distribution model of the tool-workpiece contact pressure was proposed to describe the interaction between the tool and the workpiece. The void defect formation mechanism was quantitatively studied using the proposed integrated thermal-fluid-structure coupling model. The results show that the plastic material flows in the horizontal direction and can completely fill the cavity behind the tool for the welding condition of forming a sound weld. While the tool-workpiece contact interfacial frictional shear stress in the rear of the tool is decreased significantly which leads to a severe decrease in the plastic material flow velocity. Therefore, after bypassing the tool from the retreating side, the plastic material at the bottom of the weld stagnates, and void defect forms in the middle and lower part of the weld at the advancing side. The difference between the maximum and the minimum tool-workpiece contact pressure could serve as a numerical criterion to predict void defects. A sound joint is formed when the difference is lower than the critical value of 15 MPa, while a void defect is formed in the weld if it is higher than this critical value. The maximum equivalent stress acting on the tool is located at the pin root with severe stress concentration at a high welding speed. The front of the tool is subjected to tensile stress while its rear is subjected to compressive stress, therefore the tool is apt to fracture at its root under an inappropriate welding condition. The average normal stress of the tool varies periodically with its period consistent with the rotation period of the tool. The service life of the tool is decreased with the increase in welding speed and the decrease in rotation speed. The model is validated by experimental results.
The melting behaviour of metal–organic frameworks (MOFs) has aroused significant research interest in the areas of materials science, condensed matter physics and chemical engineering. This work first introduces a novel method to fabricate a bimetallic MOF glass, through meltquenching of the cobalt-based zeolitic imidazolate Framework (ZIF) [ZIF-62(Co)] with an adsorbed ferric coordination complex. The high-temperature chemically reactive ZIF-62-(Co) liquid facilitates the formation of coordinative bonds between Fe and imidazolate ligands, incorporating Fe nodes into the framework after quenching. The resultant Co–Fe bimetallic MOF glass therefore shows a significantly enhanced oxygen evolution reaction performance. The novel bimetallic MOF glass, when combined with the facile and scalable mechanochemical synthesis technique for both discrete powders and surface coatings on flexible substrates, enables significant opportunities for catalytic device Assembly
The effect of structural constriction on molecular mobility is investigated by broadband dielectric spectroscopy (BDS) within three types of molecular arrangements: monomers, oligomers and self-assembled monolayers (SAMs). While disordered monomers exhibit a variety of cooperative and local relaxation processes, the constrained nanodomains of oligomers and highly ordered structure of monolayers exhibit much hindered local molecular fluctuations. Particularly, in SAMs, motions of the silane headgroups are totally prevented whereas the polar endgroups forming the monolayer canopy show only one cooperative relaxation process. This latter molecular fluctuation is, for the first time, observed independently from other overlapping dielectric signals. Numerous electrostatic interactions among those dipolar endgroups are responsible for the strong cooperativity and heterogeneity of the canopy relaxation process. Our data analyses also revealed that the bulkiness of dipolar endgroups can disrupt the organization of the monolayer canopy thus increasing their ability to fluctuate as temperature is increased.
Impact of organic phosphates on the structure and composition of short-range ordered iron nanophases
(2024)
Organic phosphates (OP) are important nutrient components for living cells in natural environments, where they readily interact with ubiquitous iron phases such as hydrous ferric oxide, ferrihydrite (FHY). FHY partakes in many key bio(geo)chemical reactions including iron-mediated carbon storage in soils, or iron-storage in living organisms. However, it is still unknown how OP affects the formation, structure and properties of FHY. Here, we document how β-glycerophosphate (GP), a model OP ligand, affects the structure and properties of GP–FHY nanoparticles synthesized by coprecipitation at variable nominal molar P/Fe ratios (0.01 to 0.5). All GP–FHY precipitates were characterized by a maximum solid P/Fe ratio of 0.22, irrespective of the nominal P/Fe ratio. With increasing nominal P/Fe ratio, the specific surface area of the GP–FHY precipitates decreased sharply from 290 to 3 m2 g−1, accompanied by the collapse of their pore structure. The Fe–P local bonding environment gradually transitioned from a bidentate binuclear geometry at low P/Fe ratios to monodentate mononuclear geometry at high P/Fe ratios. This transition was accompanied by a decrease in coordination number of edge-sharing Fe polyhedra, and the loss of the corner-sharing Fe polyhedra. We show that Fe(III) polymerization is impeded by GP, and that the GP–FHY structure is highly dependent on the P/Fe ratio. We discuss the role that natural OP-bearing Fe(III) nanophases have in biogeochemical reactions between Fe–P and C species in aquatic systems.
An assessment of the elastic-plastic buckling limit state for multi-strake wind turbine support towers poses a particular challenge for the modern finite element analyst, who must competently navigate numerous modelling choices related to the tug-of-war between meshing and computational cost, the use of solvers that are robust to highly nonlinear behaviour, the potential for multiple near-simultaneously critical failure locations, the complex issue of imperfection sensitivity and finally the interpretation of the data into a safe and economic design.
This paper reports on an international ‘round-robin’ exercise conducted in 2022 aiming to take stock of the computational shell buckling expertise around the world which attracted 29 submissions. Participants were asked to perform analyses of increasing complexity on a standardised benchmark of an 8-MW multi-strake steel wind turbine support tower segment, from a linear elastic stress analysis to a linear bifurcation analysis to a geometrically and materially nonlinear buckling analysis with imperfections. The results are a showcase of the significant shell buckling expertise now available in both industry and academia.
This paper is the first of a pair. The second paper presents a detailed reference solution to the benchmark, including an illustration of the Eurocode-compliant calibration of two important imperfection forms.
Matrix‐assisted ionization (MAI) mass spectrometry does not require voltages, a laser beam, or added heat to initiate ionization, but it is strongly dependent on the choice of matrix and the vacuum conditions. High charge state distributions of nonvolatile analyte ions produced by MAI suggest that the ionization mechanism may be similar to that of electrospray ionization (ESI), but different from matrix‐assisted laser desorption/ionization (MALDI). While significant information is available for MAI using mass spectrometers operating at atmospheric and intermediate pressure, little is known about the mechanism at high vacuum.
Eleven MAI matrices were studied on a high‐vacuum time‐of‐flight (TOF) mass spectrometer using a 266 nm pulsed laser beam under otherwise typical MALDI conditions. Detailed comparisons with the commonly used MALDI matrices and theoretical prediction were made for 3‐nitrobenzonitrile (3‐NBN), which is the only MAI matrix that works well in high vacuum when irradiated with a laser.
Screening of MAI matrices with good absorption at 266 nm but with various degrees of volatility and laser energies suggests that volatility and absorption at the laser wavelength may be necessary, but not sufficient, criteria to explain the formation of multiply charged analyte ions. 3‐NBN produces intact, highly charged ions of nonvolatile analytes in high‐vacuum TOF with the use of a laser, demonstrating that ESI‐like ions can be produced in high vacuum. Theoretical calculations and mass spectra suggest that thermally induced proton transfer, which is the major ionization mechanism in MALDI, is not important with the 3‐NBN matrix at 266 nm laser wavelength. 3‐NBN:analyte crystal morphology is, however, important in ion generation in high vacuum.
The 3‐NBN MAI matrix produces intact, highly charged ions of nonvolatile compounds in high‐vacuum TOF mass spectrometers with the aid of ablation and/or heating by laser irradiation, and shows a different ionization mechanism from that of typical MALDI matrices.