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Metaproteomics, the study of the collective proteome within a microbial ecosystem, has substantially grown over the past few years. This growth comes from the increased awareness that it can powerfully supplement metagenomics and metatranscriptomics analyses. Although metaproteomics is more challenging than single-species proteomics, its added value has already been demonstrated in various biosystems, such as gut microbiomes or biogas plants. Because of the many challenges, a variety of metaproteomics workflows have been developed, yet it remains unclear what the impact of the choice of workflow is on the obtained results. Therefore, we set out to compare several well-established workflows in the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. In this benchmarking study, we evaluated the influence of different workflows on sample preparation, mass spectrometry acquisition, and bioinformatic analysis on two samples: a simplified, lab-assembled human intestinal sample and a complex human fecal sample. We find that the same overall biological meaning can be inferred from the metaproteome data, regardless of the chosen workflow. Indeed, taxonomic and functional annotations were very similar across all sample-specific data sets. Moreover, this outcome was consistent regardless of whether protein groups or peptides, or differences at the spectrum or peptide level were used to infer these annotations. Where differences were observed, those originated primarily from different wet-lab methods rather than from different bioinformatic pipelines. The CAMPI study thus provides a solid foundation for benchmarking metaproteomics workflows, and will therefore be a key reference for future method improvement. [doi:10.25345/C5SX64D9M] [dataset license: CC0 1.0 Universal (CC0 1.0)]
Akustische Bestimmung der Werkstoffparameter faserverstärkter Kunststoffe mittels geführter Wellen
(2021)
Akustische Verfahren eignen sich hervorragend zur Bestimmung der Werkstoffeigenschaften. Die Verfügbarkeit derartiger Verfahren ist vor allem für Kunststoffe wichtig, da deren Eigenschaften stark abhängig vom jeweiligen Herstellungsprozess und vom Alterungszustand sind. Exakte und vollständige Werte sind daher in Datenbanken oder von Herstellern nur begrenzt zu finden. Insbesondere die Entwicklung von Methoden zur Charakterisierung faserverstärkter Kunststoffe (FKV) ist nach wie vor Gegenstand der Forschung. Hier müssen anisotropiebedingt mehrere Kennwerte bestimmt werden. Da FKV zumeist als dünnwandige Bauteile zum Einsatz kommen, können die Werkstoffparameter aus den Dispersionseigenschaften der Lamb-Wellen, die sich in diesen Strukturen ausbreiten, abgeleitet werden. Dazu ist eine räumliche Abtastung des sich ausbreitenden Schallfelds erforderlich.
In der vorliegenden Untersuchung wird dieser Ansatz für die relativ neue Werkstoffklasse der faserverstärkten Thermoplaste angewendet. Diese zeichnet ein ausgeprägtes Dämpfungsverhalten und eine Anisotropie der Materialparameter aus. Dazu wurde das Schallfeld im Ultraschallbereich mit einem Laser-Doppler-Vibrometers vermessen. Rechnerisch bestimmte Dispersionskurven wurden dann an die gemessenen Werte angepasst, womit die richtungsabhängigen Materialparameter bestimmt werden konnten.
Im Vortrag wird das Messverfahren vorgestellt und auf spezielle Probleme, die sich z.B. aus dem Dämpfungsverhalten des Werkstoffs ergeben, eingegangen. Ausgewählte gemessene Werte werden mit den Ergebnissen von Referenzverfahren verglichen.
Akustische Verfahren eignen sich hervorragend zur Bestimmung der Werkstoffeigenschaften. Die Verfügbarkeit derartiger Verfahren ist vor allem für Kunststoffe wichtig, da deren Eigenschaften stark abhängig vom jeweiligen Herstellungsprozess und vom Alterungszustand sind. Exakte und vollständige Werte sind daher in Datenbanken oder von Herstellern nur begrenzt zu finden. Insbesondere die Entwicklung von Methoden zur Charakterisierung faserverstärkter Kunststoffe (FKV) ist nach wie vor Gegenstand der Forschung. Hier müssen anisotropiebedingt mehrere Kennwerte bestimmt werden. Da FKV zumeist als dünnwandige Bauteile zum Einsatz kommen, können die Werkstoffparameter aus den Dispersionseigenschaften der Lamb-Wellen, die sich in diesen Strukturen ausbreiten, abgeleitet werden. Dazu ist eine räumliche Abtastung des sich ausbreitenden Schallfelds erforderlich.
In der vorliegenden Untersuchung wird dieser Ansatz für die relativ neue Werkstoffklasse der faserverstärkten Thermoplaste angewendet. Diese zeichnet ein ausgeprägtes Dämpfungsverhalten und eine Anisotropie der Materialparameter aus. Dazu wurde das Schallfeld im Ultraschallbereich mit einem Laser-Doppler-Vibrometers vermessen. Rechnerisch bestimmte Dispersionskurven wurden dann an die gemessenen Werte angepasst, womit die richtungsabhängigen Materialparameter bestimmt werden konnten.
Im Vortrag wird das Messverfahren vorgestellt und auf spezielle Probleme, die sich z.B. aus dem Dämpfungsverhalten des Werkstoffs ergeben, eingegangen. Ausgewählte gemessene Werte werden mit den Ergebnissen von Referenzverfahren verglichen.
This study shows remarkably different features between the oxidation of secondary and primary C₃-C₅ alcohols. The oxidation of primary alcohols is controlled by the oxidative removal of blocking adsorbates, such as CO, formed after the dissociative adsorption of alcohol molecules. Conversely, secondary alcohols do not undergo dissociative adsorption and therefore their oxidation is purely controlled by the energetics of the elementary reaction steps. In this respect, a different role of ruthenium is revealed for the electrooxidation of primary and secondary alcohols on bimetallic platinum-ruthenium catalysts. Ruthenium enhances the oxidation of primary alcohols via the established bifunctional mechanism, in which the adsorption of (hydr)oxide species that are necessary to remove the blocking adsorbates is favored. In contrast, the oxidation of secondary alcohols is enhanced by the Ru-assisted stabilization of an O-bound intermediate that is involved in the potential-limiting step. This alternative pathway enables the oxidation of secondary alcohols close to the equilibrium potential.
In mass spectrometry based proteomics, protein homology leads to
many shared peptides within and between species. This complicates
taxonomic inference. inference. We introduce PepGM, a graphical model for taxonomic profiling of viral proteomes and metaproteomic datasets.
Using the graphical model, our approach computes statistically sound
scores for taxa based on peptide scores from a previous database
search, eliminating the need for commonly used heuristics.
Understanding on how a machine learning model interprets data is a crucial step to verify its reliability and avoid overfitting. While the focus of the scientific community is nowadays orientated towards deep learning approaches, which are considered as black box approaches, this work presents a toolbox that is based on complementary methods of feature extraction and selection, where the classification decisions of the model are transparent and can be physically interpreted. On the example of guided wave benchmark data from the open guided waves platform, where delamination defects were simulated at multiple positions on a carbon fiber reinforced plastic plate under varying temperature conditions, the authors could identify suitable frequencies for further investigations and experiments. Furthermore, the authors presented a realistic validation scenario which ensures that the machine learning model learns global damage characteristics rather than position specific characteristics.
Applying data-driven AI systems makes it possible to extract patterns from given data, generate predictions and helps making decisions. Material research and testing holds a plethora of AI-based applications, for example, for the automatized search and synthesis of new materials, the detection of materials defects, or the prediction of process and materials parameters (inverse problems). However, AI algorithms can often only be as good as the training data from which the corresponding models are learned. Therefore, it is also indispensable to develop measures for the standardization and quality assurance of such data.
For this purpose, we develop and implement methods from transferring data from various sources into a homogeneous data repository with uniform data descriptions. Through the standardization and corresponding machine-readable interfaces, research data can be made usable and reusable for further data analyses. In addition to the technical implementation of integrative platforms, it is crucial that quality-assured research data management is recognized and implemented as an integral part of daily scientific work. Finally, we provide a vision of how the Federal Institute for Materials Research and Testing can benefit from data-driven AI systems. We discuss early applications and take a peek at future research.
Metaproteomics has substantially grown over the past years and supplements other omics approaches by bringing valuable functional information, enabling genotype- phenotype linkages and connections to metabolic outputs. Currently, a wide variety of metaproteomic workflows is available, yet their impact on the results remains to be thoroughly assessed.
Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry acquisition, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.
Although bioinformatic pipelines contributed to variability in peptide identification, wet-lab workflows were the most important source of differences between analyses. Overall, these peptide-level differences largely disappeared at the protein group level. Differences were observed between peptide- and protein-centric approaches for the predicted community composition but similar functional profiles were found across workflows.
The CAMPI findings demonstrate the robustness of current metaproteomics research and provide a perspective for future benchmarking studies.
Due to the ageing of the infrastructure facilities, a reliable assessment of the condition of concrete structures is of great interest to plan timely and appropriate measures. In concrete structures, pittingcorrosion of the reinforcement is the predominant deterioration mechanism affecting serviceability and eventually structural performance. Determination of quantitative chloride ingress is not only necessary to obtain valuable information on the current condition of a structure, but the data obtained can also be used to predict future developments and the associated risks. An overview of the progress and the possibilities of the application of laser-induced breakdown spectroscopy for concrete analysis in daily civil engineering practice is given. High-resolution 2D measurements of drill cores to determine the penetration of harmful species into concrete is presented. Furthermore, the application of a mobile LIBS system in a parking garage is shown. The system consists of a diode-pumped low-energy laser (3 mJ, 1.5 ns, 100 Hz) and a compact NIR spectrometer. A scanner allows two-dimensional element mapping. Progress towards the establishment of LIBS in a leaflet for the analysis of chlorine ingress into concrete in civil engineering is presented.
Time resolved in situ monitoring of mechanochemical transformations by X-ray spectroscopy (XAS)
(2021)
Mechanochemical reactions promise a new direction for environmentally benign preparation of materials, and has been dubbed by IUPAC as one of the 10 chemical innovations that will change our world. Despite this significant promise, very little is known about the mechanisms that drive mechanochemical transformations, posing significant barriers to realizing their full potential. To this end, there is growing need to follow mechanochemical reactions in situ and in real time. We here describe advances in the development and application of XAS methods to monitor material synthesis in real time under mechanochemical conditions. We demonstrate the generality of our approaches by describing mechanochemical syntheses of materials by both vibratory ball milling and by Resonant Acoustic Mixing (RAM), where a time resolution of 1 second is for a whole XAS spectrum was achieved. Moreover, we describe how spectroscopic methods can be coupled to diffraction-based approaches, thereby providing new dimensions in understanding mechanochemical synthesis.
Time resolved in situ monitoring of mechanochemical transformations by X-ray spectroscopy (XAS)
(2021)
Mechanochemical reactions promise a new direction for environmentally benign preparation of materials, and has been dubbed by IUPAC as one of the 10 chemical innovations that will change our world. Despite this significant promise, very little is known about the mechanisms that drive mechanochemical transformations, posing significant barriers to realizing their full potential. To this end, there is growing need to follow mechanochemical reactions in situ and in real time. We here describe advances in the development and application of XAS methods to monitor material synthesis in real time under mechanochemical conditions. We demonstrate the generality of our approaches by describing mechanochemical syntheses of materials by both vibratory ball milling and by Resonant Acoustic Mixing (RAM), where a time resolution of 1 second is for a whole XAS spectrum was achieved. Moreover, we describe how spectroscopic methods can be coupled to diffraction-based approaches, thereby providing new dimensions in understanding mechanochemical synthesis.
Im Europäischen EMPIR-Projekt „NanoXSpot“ (Measurement of the focal spot size of Xray tubes with spot sizes down to 100 nm) werden neue Messmethoden für Brennflecke von Röntgenröhren entwickelt. Teil des Projektes ist die Entwicklung eines zur Lochkameramethode äquivalenten Messverfahrens für kleine Brennflecke. ASTM E 1165-20, Annex A, beschreibt die Bestimmung von Brennfleckgrößen aus Kantenprofilen von Lochaufnahmen für Röntgenröhren mit Brennflecken > 50 μm. Es wurde bereits vorgeschlagen über die Analyse der richtungsabhängigen Kantenunschärfe einer Lochblende und anschließender CT-Rekonstruktion die Intensitätsverteilung des Brennflecks äquivalent zur Lochkameraaufnahme zu berechnen. Die Lochkameramethode, wie in EN 12543-2 und ASTM E 1165-20 beschrieben, ist im unteren Größenbereich für Mikrofokusröhren nicht geeignet, da Pinholes < 10 μm schwer zu fertigen sind und lange Belichtungszeiten erwartet werden. Mit Hilfe exakt gefertigter Lochblenden sowie strukturierter Targets mit
konvergierenden Strukturen wird der Bereich mit der Single-Shot-CT-Methode auf die Messung von Mikrofokusröhren, alternativ zur Vermessung von Kanten oder Strichgruppenkörpern, erweitert. Die rekonstruierten Brennfleckformen werden mit Kantenund Lochkameraaufnahmen quantitativ verglichen, um die Messgenauigkeit zu bewerten.
Außerdem werden CNR und Messzeit bestimmt, um die Wirtschaftlichkeit der Verfahren zu bewerten.
Der Weg zur digitalen Brücke ist eingeschlagen. Im Bereich der Planung, Bauüberwachung und -ausführung wird aktuell das Building Information Modelling (BIM) eingeführt. Ist eine Brücke in der Baulast von Bund und Ländern errichtet, wird ihr Zustand im Zuge von wiederkehrenden Bauwerksprüfungen nach DIN 1076 lückenlos überwacht. Abgespeichert werden die Informationen der Überwachung in einer Datenbank (ASB-ING Teilsystem Bauwerksdaten). Aus dieser Datenbank können anschließend relevante Informationen in ein objektspezifisches Bauwerksbuch überführt werden. In dieser Datenbank werden im Vorfeld definierte Daten abgespeichert. Reine Messdaten oder aber auch die verwendeten ingenieurtechnisch-physikalischen Modelle verbleiben in der Regel bei den beauftragen Dienstleistern. Zusammengefasst existieren verschiedene parallele Insellösungen der Informationsablage. Gegenstand verschiedener Forschungsanstrengungen ist es nun Lösungen zu finden, die einen ganzheitlichen Ansatz für den Informationsfluss von der Errichtung über den Betrieb bis hin zum Abbruch eines Bauwerkes sicherstellen. Im Rahmen einer prototypischen Entwicklung wird auf Grundlage, des für die Industrie 4.0 entwickelten open source Software Framework Eclipse BaSyx, ein möglicher Lösungsansatz – die Verwaltungsschale BBox (Bridge Box) - präsentiert. Dieser Lösungsansatz stellt das physikalisch-ingenieurtechnische Modell zur Zustandsbewertung der Brücke gedanklich in den Mittelpunkt. Unter der Voraussetzung einer durchgängigen Digitalisierung der gesamten Prozessschritte innerhalb der Lebensdauer der Brücke, kann jeder Planungs- und Fertigungsschritt, die Instandhaltung einschließlich des Rückbaus erfasst werden. Das Besondere hierbei ist, dass auch die Grundlagen der Bewertung, wie Messdaten, mit abgespeichert werden. Die Modellstruktur der Verwaltungsschale erlaubt hierbei eine bedarfsgerechte Granularität hinsichtlich der Messdaten auf allen virtuellen Ebenen, um das physikalisch-ingenieurtechnisch Modell mit Daten zu versorgen. Die gewählte Form der Datenablage bildet den Grundstein für zukünftige KI-Auswertungen z.B. mit den Methoden des Maschinellen Lernens (ML). Der Zugriff auf die dafür jeweils benötigten Daten wird durch die Ablage der Daten einschließlich Metadaten und den Einsatz einer Standard S3 Schnittstelle stark vereinfacht. Der Beitrag stellt die Entwicklung und die Systemarchitektur der BBox am Beispiel von 2 Projekten dar.
Raman spectroscopy is a well established tool for the analysis of vibration spectra, which then allow for the determination of individual substances in a chemical sample, or for their phase transitions. In the time-resolved-Raman-sprectroscopy the vibration spectra of a chemical sample are recorded sequentially over a time interval, such that conclusions for intermediate products (transients) can be drawn within a chemical process. The observed data-matrix M from a Raman spectroscopy can be regarded as a matrix product of two unknown matrices W and H, where the first is representing the contribution of the spectra and the latter represents the chemical spectra. One approach for obtaining W and H is the non-negative matrix factorization. We propose a novel approach, which does not need the commonly used separability assumption. The performance of this approach is shown on a real world chemical example.
Engineered nanomaterials (NM) with their unique size-dependent properties are of increasing relevance for current and future developments in various fields such as medical and pharmaceutical industry, computing and electronics or food and consumer products. The performance and safety of NM are determined by the sum of their intrinsic physicochemical properties. Especially, the particle surface chemistry, which is largely controlled by the chemical nature and density of functional groups and ligands, is an important key driver for the performance, stability, and processibility of NM, as well as their interaction with the environment. Thus, methods for functional group quantification can foster the sustainable development of functional and safe(r) NM.
Aiming at the development of simple, versatile and multimodal tools for the quantification of common bioanalytically relevant functional groups, we designed a catch-and-release assay based on cleavable probes that enable the quantification of the cleaved-off reporters in the supernatant after particle separation. Thus, the approach circumvents interferences resulting from particle light scattering and sample-inherent absorption or emission. To study the potential of the assay, commercially available and in-house synthesized aminated and carboxylated polymer and silica nanoparticles of different functional group densities were tested.
Our cleavable probe strategy can be easily adapted to other analytical techniques requiring different reporters, or to different types of linkers that can be cleaved thermally, photochemically, or by variation of pH, utilizing well-established chemistry. In addition, it can contribute to the development of multi-method characterization strategies to provide a more detailed picture of the intrinsic physicochemical property - performance/safety relationships and thus can support the design of tailored nanomaterials with better controlled properties.
Mass Spectrometry (MS) and Nuclear Magnetic Resonance Spectroscopy (NMR) are critical components of every industrial chemical process as they provide information on the concentrations of individual compounds and by-products. These processes are carried out manually and by a specialist, which takes a substantial amount of time and prevents their utilization for real-time closed-loop process control. This paper presents recent advances from two projects that use Artificial Neural Networks (ANNs) to address the challenges of automation and performance-efficient realizations of MS and NMR. In the first part, a complete toolchain has been developed to develop simulated spectra and train ANNs to identify compounds in MS. In the second part, a limited number of experimental NMR spectra have been augmented by simulated spectra to train an ANN with better prediction performance and speed than state-of-theart analysis. These results suggest that, in the context of the digital transformation of the process industry, we are now on the threshold of a possible strongly simplified use of MS and MRS and the accompanying data evaluation by machine-supported procedures, and can utilize both methods much wider for reaction and process monitoring or quality control.
Mit der Bezeichnung Hinterglasmalerei wird allgemein der Begriff der Glasmalerei assoziiert. Auch wenn in beiden Fällen Glas das Trägermaterial ist, bezeichnet Hinterglasmalerei jedoch eine völlig andere Technik. Während bei der Glasmalerei die Farben auf den Bildträger eingebrannt werden, handelt es sich bei der Hinterglasmalerei um eine Kaltmalerei. Selbsttrocknende Farben werden auf die Rückseite der Glastafel aufgetragen, zuweilen wird die Malweise durch aufwendige Veredelungstechniken ergänzt. Mehr und mehr rückt diese Technik, die materialtechnologisch zwischen Tafelmalerei und Glasmalerei zu verorten ist, in den Blickwinkel einer interessierten Öffentlichkeit, wie dies eine zunehmende Anzahl verschiedener Ausstellungen zur Hinterglasmalerei belegen. Die vorliegende Publikation beschäftigt sich in erster Linie mit kunsttechnologischen und materialanalytischen Aspekten der Hinterglasmalerei und ermöglicht tiefe Einblicke in die künstlerische Arbeitsweise und in die Verwendung unterschiedlichster Materialien.
Under the auspices of the Protein Analysis Working Group (PAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a pilot study, CCQM-P216, was coordinated by the Chinese National Institute of Metrology (NIM), National Research Council of Canada (NRC) and the Bureau International des Poids et Mesures (BIPM). Eleven Metrology Institutes or Designated Institutes and the BIPM participated in the first phase of the pilot study (Part 1). The purpose of this pilot study was to develop measurement capabilities for larger proteins using a recombinant humanized IgG monoclonal antibody against Spike glycoprotein of SARS-CoV-2 (Anti-S IgG mAb) in solution. The first phase of the study was designed to employ established methods that had been previously studies by the CCQM Protein Analysis Working Group, involving the digestion of protein down to the peptide or amino acid level. The global coronavirus pandemic has also led to increased focus on antibody quantitation methods. IgG are among the immunoglobulins produced by the immune system to provide protection against SARS-CoV-2. Anti-SARS-CoV-2 IgG can therefore be detected in samples from affected patients. Antibody tests can show whether a person has been exposed to the SARS-CoV-2, and whether or not they potentially show lasting immunity to the disease. With the constant spread of the virus and the high pressure of re-opening economies, antibody testing plays a critical role in the fight against COVID-19 by helping healthcare professionals to identify individuals who have developed an immune response, either via vaccination or exposure to the virus. Many countries have launched large-scale antibody testing for COVID-19. The development of measurement standards for the antibody detection of SARS-CoV-2 is critically important to deal with the challenges of the COVID-19 pandemic. In this study, the SARS-CoV-2 monoclonal antibody is being used as a model system to build capacity in methods that can be used in antibody quantification. Amino acid reference values with corresponding expanded uncertainty of 36.10 ± 1.55 mg/kg, 38.75 ± 1.45 mg/kg, 18.46 ± 0.78 mg/kg, 16.20 ± 0.67 mg/kg and 30.61 ± 1.30 mg/kg have been established for leucine, valine, phenylalanine, isoleucine and proline, respectively. Agreement between nearly all laboratories was achieved for the amino acid analysis within 2 to 2.5 %, with one participant achieving markedly higher results due to a technical issue found in their procedure; this result was thus excluded from the reference value calculations. The relatively good agreement within a laboratory between different amino acids was not dissimilar to previous results for peptides or small proteins, indicating that factors such as hydrolysis conditions and calibration procedures could be the largest sources of variability. Peptide reference values with corresponding expanded uncertainty of 4.99 ± 0.28 mg/kg and 6.83 ± 0.65 mg/kg have been established for ALPAPIEK and GPSVFPLAPSSK, respectively. Not surprisingly due to prior knowledge from previous studies on peptide quantitation, agreement between laboratories for the peptide-based analysis was slightly poorer at 3 to 5 %, with one laboratory's result excluded for the peptide GPSVFPLAPSSK. Again, this level of agreement was not significantly poorer than that achieved in previous studies with smaller or less complex proteins. To reach the main text of this paper, click on Final Report.
This paper describes a new ultrasonic measuring device called “W-Box”. It was developed based on the requirements of the DFG Forschergruppe (research unit) CoDA for a portable device for monitoring of concrete specimens, models and actual structures using embedded ultrasonic transducers as well as temperature and humidity sensors. The W-Box can send ultrasonic pulses with a variable frequency of 50–100 kHz to one selectable transducer and records signals from up to 75 multiplexed channels with a sample rate of 1 MHz and a resolution of 14 bits. In addition, it measures temperature and humidity with high accuracy, adjustable amplification, restarts automatically after a power failure and can be fully controlled remotely. The measured data are automatically stored locally on-site data quality checks and transferred to remote servers. The comparison of the W-Box with a laboratory setup using commercial devices proves that it is equally reliable and precise, at much lower cost. The W-Box also shows that their measurement capacities, with the used embedded ultrasonic transducers, can reach above 6 m in concrete.