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Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Der Frequenzbereich der Terahertzwellen liegt im elektromagnetischen Spektrum zwischen den Mikrowellen und dem infraroten Licht – also etwa im Bereich von 0,1 bis 10 Terahertz (THz). Der VDI-Statusreport „Terahertzsysteme und Anwendungen“ stellt die unterschiedlichen Konzepte für Terahertzsysteme vor und zeigt Anwendungsbeispiele, bei denen die Terahertztechnik erfolgreich eingesetzt wird. Umfangreiche Literaturangaben ermöglichen eine intensivere Beschäftigung mit allen Themen des VDI-Statusreports.
The OECD Working Party on Manufactured Nanomaterials (WPMN) has actively worked towards understanding possible safety issues for manufactured nanomaterials and has contributed significantly to resolving these by developing Test Guidelines, Guidance Documents, Test Reports and other publications with the aim of a safe use of manufactured nanomaterials. To address the specific needs of manufactured nanomaterials, the OECD Test Guideline No. 110 “Particle Size Distribution/Fibre Length and Diameter Distributions” was identified as one of the test guidelines (TGs) to require an update. The current TG 110 (adopted in 1981) is only valid for particles and fibres with sizes above 250 nm. The WPMN prioritised to either update TG 110 to be applicable also to particles at the nanoscale or draft a new nanomaterial specific (TG).
Eventually, it was decided to develop a new TG that covers the size range from 1 nm to 1000 nm, intended for particle size and particle size distribution measurements of nanomaterials. Paragraph 11 provides further justification on the need for such measurements for nanomaterials. This TG overlaps with TG 110 in the size range from 250 nm to 1000 nm. When measuring particulate or fibrous materials, the appropriate TG should be selected depending on the size range of particles tested. In line with TG 110, the new TG for nanomaterials includes separate parts for particles and fibres.
For the part of this TG which addresses particles, several methods applicable to nanomaterials were reviewed and included to take into account developments since 1981 when the TG 110 was adopted. This TG includes the following methods: Atomic Force Microscopy (AFM), Centrifugal Liquid Sedimentation (CLS)/Analytical Ultracentrifugation (AUC), Dynamic Light Scattering (DLS), Differential Mobility Analysis System (DMAS), (Nano)Particle Tracking Analysis (PTA/NTA), Small Angle X-Ray Scattering (SAXS), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM). The method Single Particle Inductively Coupled Plasma Mass Spectrometry (sp-ICP-MS) could not be sufficiently validated within the interlaboratory comparison (ILC) carried out for the different methods in this TG (see also paragraph 6 for further details on the ILC). Applicability of sp-ICP-MS is strongly limited to nanomaterials with high mass values in combination with a sufficiently high particle size. However, the general method ICP-MS is widely used and the sp-mode for the size measurement of specific nanomaterials was successfully performed in ILCs elsewhere. The method is therefore included in the Appendix Part C of this TG, which further details the limitations of sp-ICP-MS.
For measuring the diameter and length of fibres, analysing images captured with electron microscopy is currently the only method available. This TG includes Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM).
To test the validity of this TG, an ILC was performed. Test materials were chosen to reflect a broad range of nanomaterial classes, e.g. metals, metal oxides, polymers and carbon materials. Where possible, well-characterised test materials were used.
Additionally, the test materials were chosen to reflect a broad range of sizes representing the size range 1 nm to 1000 nm. Specifically for fibres, a broad range of aspect ratios was included (length/diameter of 3 to > 50). Some of the test materials used are commercially available and further references are given in the validation report of the ILC. Sample preparation for physical chemical characterisation is critical for all listed methods. Due to the differences between individual nanomaterials and due to the wide range of individual material properties it is impossible to have a generic protocol to obtain the best possible sample preparation for every nanomaterial. Therefore, a generic protocol on sample preparation is not part of this TG. Information on sample preparation is given in the paragraphs 25-29, 33, 34 and 39 for particles and in paragraphs 159) for fibres. Further information on sample preparation of nanomaterials for physical chemical characterisation can be found in the OECD Guidance on Sample Preparation and Dosimetry for the Safety Testing of Manufactured Nanomaterials and elsewhere.
In this research project, a new OECD Test Guideline (TG) for the determination of “Particle Size and Particle Size Distributions of Nanomaterials” was developed as the existing OECD TG 110 is considered to be outdated in terms of applicable size range (not covering sizes <200 nm) and methods. By its scope with an applicable size range from 1 to 1000 nm the new Test Guideline (TG PSD) covers the whole nanoscale. The TG PSD is applicable for particulate and fibrous nanomaterials. The prescribed, pairwise measurement of fibre diameter and length in the TG PSD allows for the first time to differen-tiate fibres with regard to their size-dependent hazard properties. Measurement instructions for each included method were validated within two separated interlaboratory comparisons, as a distinction between near spherical particles and fibres when applying the methods has to be made.
Besides information on content and structure of the TG PSD, this final report outlines essential steps, considerations and organisational aspects during the development of the TG. Insights into the selec-tion, preparation and prevalidation of test materials used in the interlaboratory comparison are given. Finally, main results of the interlaboratory comparisons and their impacts on the TG PSD are pre-sented.
Final Draft of the OECD Test Guideline for Particle Size and Particle Size Distribution of Nanomaterials.
The OECD Working Party on Manufactured Nanomaterials (WPMN) has actively worked towards understanding possible safety issues for manufactured nanomaterials and has contributed significantly to resolving these by developing Test Guidelines, Guidance Documents, Test Reports and other publications with the aim of a safe use of manufactured nanomaterials. The OECD website (www.oecd.org/science/nanosafety) and the referenced publications contain more background information.
Among others, the OECD Test Guideline “Particle Size Distribution/Fibre Length and Diameter Distributions” (TG 110, adopted in 1981) was identified to require an update to address the specific needs of manufactured nanomaterials as the TG 110 is currently only valid for particles and fibres with sizes above 250 nm. The WPMN prioritised to either update TG 110 to be applicable also to particles at the nanoscale or draft a new nanomaterial specific Test Guideline (TG). Eventually, it was decided to develop a new TG for particle size and particle size distribution measurements of nanomaterials covering the size range from 1 nm to 1000 nm for further justification. This TG overlaps with TG 110 in the size range from 250 nm to 1000 nm. When measuring particulate or fibrous materials, the appropriate TG should be selected depending on the size range of particles tested. In line with TG 110, the new TG for nanomaterials includes separate parts for particles and fibres. For the part of this TG which addresses particles, several methods applicable to nanomaterials were reviewed and included to take into account developments since 1981 when the TG110 was adopted. This TG includes the following methods: Atomic Force Microscopy (AFM), Centrifugal Liquid Sedimentation (CLS)/Analytical Ultracentrifugation (AUC), Dynamic Light Scattering (DLS), Differential Mobility Analysis System (DMAS), (Nano)Particle Tracking Analysis (PTA/NTA), Small Angle X-Ray Scattering (SAXS), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM).
For measuring the diameter and length of fibres, analysing images captured with electron microscopy is currently the only method available. This TG includes Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM).
To test the validity of this TG, an ILC was performed. Test materials were chosen to reflect a broad 68 range of nanomaterial classes, e.g. metals, metal oxides, polymers and carbon materials. Where possible, well-characterised test materials were used. Additionally, the test materials were chosen, so that they reflect a broad range of sizes representing the size range 1 nm to 1000 nm and finally,
for fibres only, aspect ratios from length/diameter of 3 to > 50.
The steel industry is an important engine for sustainable growth, added value, and high-quality employment within the European Union. It is committed to reducing its CO2 emissions due to production by up to 50% by 2030 compared to 1990′s level by developing and upscaling the technologies required to contribute to European initiatives, such as the Circular Economy Action Plan (CEAP) and the European Green Deal (EGD). The Clean Steel Partnership (CSP, a public–private partnership), which is led by the European Steel Association (EUROFER) and the European Steel Technology Platform (ESTEP), defined technological CO2 mitigation pathways comprising carbon direct avoidance (CDA), smart carbon usage SCU), and a circular economy (CE). CE ap-proaches ensure competitiveness through increased resource efficiency and sustainability and consist of different issues, such as the valorization of steelmaking residues (dusts, slags, sludge) for internal recycling in the steelmaking process, enhanced steel recycling (scrap use), the use of secondary carbon carriers from non-steel sectors as a reducing agent and energy source in the steelmaking process chain, and CE business models (supply chain analyses). The current paper gives an overview of different technological CE approaches as obtained in a dedicated workshop called “Resi4Future—Residue valorization in iron and steel industry: sustainable solutions for a cleaner and more competitive future Europe” that was organized by ESTEP to focus on future challenges toward the final goal of industrial deployment.
Die nicht ionisierende elektromagnetische Strahlung im Bereich von Terahertz-Frequenzen ermöglicht berührungslose und zerstörungsfreie Mess- und Prüftechnik in zahlreichen Bereichen. Nach ersten Anwendungen in der Astronomie und der Atmosphärenforschung wurden in letzter Zeit Anwendungsfelder in der Sicherheitstechnik, der Medizintechnik, der Nachrichtentechnik und der zerstörungsfreien Prozess- und Qualitätskontrolle erschlossen. Dielektrische Materialien wie Kunststoffe und Keramiken können von Terahertz-Wellen durchdrungen werden. Das ermöglicht Untersuchungen des Objektinneren ohne spezielle Schutzmaßnahmen, wie sie z.B. beim Röntgen notwendig sind. Die Richtlinie erleichtert die Verständigung zwischen Nutzern, Herstellern und dem Vertrieb von Terahertz-Systemen. In der Richtlinie werden bekannte Einsatzgebiete sowie die eingesetzten Verfahren und Funktionsprinzipien aufgeführt, um den Leser bei der Auswahlentscheidung zu unterstützen. Nach einer kurzen Einführung in die physikalischen Grundlagen und Hinweisen zur elektromagnetischen Verträglichkeit, zum Strahlenschutz und zur regulierten Frequenzvergabe werden die verschiedenen Geräteklassen von Terahertz-Systemen ausführlich vorgestellt. Die Richtlinie gibt Hinweise zur messtechnischen Charakterisierung von Terahertz-Wellen. Einsatzgebiete von Terahertz-Systemen, wie die zerstörungsfreie Prüfung, die Dicken- und Abstandsmessung, die Tomografie und die chemische Analytik, werden mit ihren spezifischen Eigenschaften im Detail beschrieben. Umfangreiche Literaturverweise vereinfachen eine vertiefte Beschäftigung mit den Themen der Richtlinie. Eine tabellarische Übersicht mit einer Zusammenfassung, welche Terahertz-Systeme für welche Anwendungsfelder eingesetzt werden können, vervollständigt die Richtlinie.
Diese Richtlinie definiert Kenngrößen und Messverfahren, um Terahertzsysteme für die Zeitbereichsspektroskopie (TDS)zu spezifizieren. So können Hersteller ihre Systeme übereinstimmend beschreiben und Anwender einfach Systeme vergleichen. Systeme für die Terahertz-Zeitbereichsspektroskopie sind aktive Systeme und nutzen verschiedene Techniken sowohl zur Erzeugung als auch zur zeitaufgelösten Messung von breitbandigen Terahertzimpulsen. Die dazugehörigen Terahertzspektren und -Phasen werden nach einer zeitlichen Abtastung über eine Fourier-Transformation berechnet. In dieser Richtlinie wird ein Überblick über die Funktionsweisen von Zeitbereichsspektrometern gegeben, die eingesetzten Messverfahren näher erläutert sowie die benötigten Begriffe und Kenngrößen definiert. Die Richtlinie konzentriert sich dabei auf Systeme, die auf sogenannten Abtastmessverfahren (Sampling-Messverfahren) basieren.
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability.
Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
Development of theranostic concepts that include inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) imaging can be hindered by the lack of a direct comparison to more standardly used methods for in vitro and in vivo evaluation; e.g. fluorescence or nuclear medicine. In this study a bimodal (or rather, hybrid) tracer that contains both a fluorescent dye and a chelate was used to evaluate the existence of a direct link between mass spectrometry (MS) and in vitro and in vivo molecular imaging findings using fluorescence and radioisotopes. At the same time, the hybrid label was used to determine whether the use of a single isotope label would allow for MS-based diagnostics.