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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 (VAMAS) interlaboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage, or sample preparation resulted in a variability in thickness of 53%. The calculation method chosen by XPS participants contributed a variability of 67%. However, variability of 12% was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors since this contributed a variability of 33%. The results from the LEIS participants were more consistent, with variability of less than 10% in thickness, and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films, and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.
Recent advances in vacuum sciences and applications are reviewed. Novel optical interferometer cavity devices enable pressure measurements with ppm accuracy. The innovative dynamic vacuum standard allows for pressure measurements with temporal resolution of 2 ms. Vacuum issues in the construction of huge ultra-high vacuum devices worldwide are reviewed. Recent advances in surface science and thin films include new phenomena observed in electron transport near solid surfaces as well as novel results on the properties of carbon nanomaterials. Precise techniques for surface and thin-film characterization have been applied in the conservation technology of cultural heritage objects and recent advances in the characterization of biointerfaces are presented. The combination of various vacuum and atmospheric-pressure techniques enables an insight into the complex phenomena of protein and other biomolecule conformations on solid surfaces. Studying these phenomena at solid–liquid interfaces is regarded as the main issue in the development of alternative techniques for drug delivery, tissue engineering and thus the development of innovative techniques for curing cancer and cardiovascular diseases. A review on recent advances in plasma medicine is presented as well as novel hypotheses on cell apoptosis upon treatment with gaseous plasma. Finally, recent advances in plasma nanoscience are illustrated with several examples and a roadmap for future activities is presented.
Under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a key comparison, CCQM K55.a, was coordinated by the Bureau International des Poids et Mesures (BIPM) in 2009/2010. Eleven national measurement institutes and the BIPM participated. Participants were required to assign the mass fraction of estradiol present as the main component in the comparison sample (CCQM-K55.a) which consisted of a bulk estradiol hemihydrate material obtained from a commercial supplier that had been extensively but not exhaustively dried prior to sub-division into the units supplied for the comparison.
Estradiol was selected to be representative of the performance of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molar mass range 300500 Da] and low polarity (pKOW < -2) for which related structure impurities can be quantified by capillary gas phase chromatography (GC) or by high performance liquid chromatography (LC).
The majority of participants used a mass balance approach to determine the estradiol content. The key comparison reference value (KCRV) for estradiol in CCQM-K55.a was assigned by combination of KCRVs assigned by consensus from participant results for each orthogonal impurity class. This allowed participants to demonstrate the efficacy (or otherwise) of their implementation of the mass balance approach and to demonstrate that their assigned value for the main component agreed with the KCRV through use of internally consistent contributing methods.
The KCRV for the estradiol content of the material was 984.3 mg/g with a combined standard uncertainty of 0.42 mg/g. The individual participant results showed that a relative expanded uncertainty for the purity assignment of 0.2% is a reasonable estimate of the best achievable result by an individual laboratory for a material of this complexity available in this amount at this level of purity. The relative expanded uncertainties reported by laboratories having results consistent with the KCRV ranged from 0.2% to 0.8%.
The review of results that were biased from the KCRV showed that two major analytical challenges are posed by the material: the measurement of its water content and controlling for related substance artefact formation during the analysis process. The results displaying a positive bias relative to the KCRV (overestimation of estradiol content) were due to underestimation of the water content of the material, while those with a negative bias (underestimation of estradiol) overestimated the total related substance impurities through a failure to detect and control for artefact formation arising from in situ oxidative dimerization of estradiol in neutral solution prior to analysis. There was however good agreement between all participants in the identification and the quantification of the individual related structure impurities actually present in the sample.
The comparison also demonstrated the utility of high-field 1H NMR for both quantitative and qualitative analysis of high purity compounds. It is noted that all the participants who used qNMR as a major or contributing technique and included it as part of, combined it or confirmed it with a conventional 'mass balance' data estimate, obtained results consistent with the KCRV.
Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential Protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms.
A global transition towards more sustainable, affordable and reliable energy systems is being stimulated by the Paris Agreement and the United Nation's 2030 Agenda for Sustainable Development. This poses a challenge for the corrosion industry, as building climate‐resilient energy systems and infrastructures brings with it a long‐term direction, so as a result the long‐term behaviour of structural materials (mainly metals and alloys) becomes a major prospect. With this in mind “Corrosion Challenges Towards a Sustainable Society” presents a series of cases showing the importance of corrosion protection of metals and alloys in the development of energy production to further understand the science of corrosion, and bring the need for research and the consequences of corrosion into public and political focus. This includes emphasis on the limitation of greenhouse gas emissions, on the lifetime of infrastructures, implants, cultural heritage artefacts, and a variety of other topics.
Une transition mondiale vers des systèmes énergétiques plus durables, abordables et fiables a été initiée par l’accord de Paris et l’Agenda 2030 des Nations unies pour un développement durable. Il s’agit là d’un défi industriel majeur car les systèmes et infrastructures énergétiques résilients au changement climatique exigent de se positionner pour le long terme. Se pencher sur le comportement dans la durée des matériaux structurels - principalement des métaux et des alliages - s’impose alors comme une nécessité. Dans cette optique, « La corrosion : un défi pour une société durable »présente une série de cas montrant l’importance de la tenue à la corrosion et de la protection anticorrosion des métaux et des alliages pour le développement de systèmes durables, économiques et fiables de production d’énergie.
Hydrothermal carbonization (HTC) can be used for converting the biomass into a carbon-rich material, whose application as a fuel requires higher heating value, whereas soil amendment needs stable carbon. This work was focused on the characterization of hydrochars derived from microcrystalline cellulose. The chars were investigated using elemental analysis, Brunauer–Emmett–Teller technique, nuclear magnetic resonance spectroscopy, Raman, Fourier transform infrared, and electron spin resonance spectroscopy. Severity in temperature between 230 and 270 °C with reaction times between 2 and 10 h only affect the carbon content moderately. The results show that aromatization of HTC chars correlates well with temperature, which was further supported by the increase of organic radicals with decreasing g values at higher temperatures. Based on these results, the energetic use of chars favors mild HTC (T < 230 °C and t ≤ 6 h), while the soil amendement favors serve conditions (T ≥ 230 °C, and t > 6 h).
This paper discloses two high-sensitivity probes for Eddy Current Nondestructive Test (NDT) of buried and surface defects. These probes incorporate eight and 32 magnetoresistive sensors, respectively, which are optimized for high sensitivity and spatial resolution. The signal processing and interfacing are carried out by a full-custom application-specific integrated circuit (ASIC). The ASIC signal chain performs with a thermal input-referred noise of 30 nV/√Hz at 1 kHz, with 66 mW of power consumption, in a die with 3.7 × 3.4 mm 2 . NDT results are presented, showing that there is an increase in spatial resolution of surface defects when contrasted to prior art, enabling the probes to resolve defects with diameters of 0.44 mm, pitches of 0.6 mm, and minimum edge distance as low as 0.16 mm. The results also show that the probe for buried defects is a good all-round tool for detection of defects under cladding and multiple-plate flat junctions.
Experimental N K-edge NEXAFS data of surface immobilized azide, 1,2,3-triazole and terpyridyl groups are interpreted with the help of DFT spectrum simulations. Assignments of π* resonances in experimental N K-edge NEXAFS spectra to nitrogen atoms within these functional groups have been made. The azide was immobilized on gold as the head group of a thiol SAM, 1,2,3-triazole was formed on this SAM by click reaction and terpyridyl groups were introduced as substituents of the acetylene used for the click reaction. For azide-terminated molecules, DFT spectrum simulations are found to be useful to find measurement conditions delivering experimental N K-edge NEXAFS data with negligible X-ray damage. The 1,2,3-triazole group is found to be rather stable under X-ray irradiation.