TY - CONF A1 - Holstein, Tanja A1 - Kistner, Franziska A1 - Martens, L. A1 - Muth, Thilo T1 - PepGM: A graphical model for taxonomic profiling of viral proteomes N2 - 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. T2 - European bioinformatics community winter school 2022 CY - Lisbon, Portugal DA - 21.03.2022 KW - Bioinformatics KW - Virus protoemics KW - Taxonomic analysis KW - Graphical models PY - 2022 AN - OPUS4-56753 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CHAP A1 - Gornushkin, Igor ED - Galbács, G. T1 - Calibration-Free Quantitative Analysis N2 - Calibration-free methods in laser-induced breakdown spectroscopy, CF LIBS, serve as an alternative to calibration-based LIBS techniques. Their major advantage is the ability for fast chemical analysis in situations where matrix-matched standards are not readily available (as, e.g., in the analysis of biological materials and remote analysis) or amount of samples are limited. Their main applications are in the industry, geology, biology, archeology, and even space exploration. This chapter overviews the principle of operation and performance of CF LIBS techniques. KW - Laser induced plasma KW - Calibration-free LIBS PY - 2022 SN - 978-3-031-14501-8 DO - https://doi.org/10.1007/978-3-031-14502-5 SP - 67 EP - 100 PB - Springer Nature Switzerland AG AN - OPUS4-56651 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Nowatzky, Yannek A1 - Benner, Philipp A1 - Reinert, K. A1 - Muth, Thilo T1 - Mistle: Metaproteomic index and spectral library search engine N2 - Introduction: With the introduction of accurate deep learning predictors, spectral matching applications might experience a renaissance in tandem mass spectrometry (MS/MS) driven proteomics. Deep learning models, e.g., Prosit, predict complete MS/MS spectra from peptide sequences and give the unprecedented ability to accurately predict mass spectra that may arise from any given proteome. However, the amount of spectral data is enormous when querying large search spaces, e.g., metaproteomes composed of many different species. Current spectral library search software, such as SpectraST, is not equipped to meet run time and memory constraints imposed by such large MS/MS databases, covering several millions of peptide spectrum predictions. Methods: Inspired by the fragment index data structure that had been introduced with MSFragger, we implement an efficient peak matching algorithm for computing spectral similarity between query and library spectra. Mistle (Metaproteomic index and spectral library search engine) uses index partitioning and SIMD (Single instruction, multiple data) intrinsics, which greatly improves speed and memory efficiency for searching large spectral libraries. Mistle is written in C++20 and highly parallelized. Results: We demonstrate the efficiency of Mistle on two predicted spectral libraries for the lab-assembled microbial communities 9MM and SIHUMIx. Compared to the spectral library search engine SpectraST, Mistle shows a >10-fold runtime improvement and is also faster than msSLASH, which uses locality-sensitive hashing. Although Mistle is slower than MSFragger, Mistle‘s memory footprint is an order of magnitude smaller. Furthermore, we find evidence that the spectral matching approach to predicted libraries identifies peptides with higher precision. Mistle detects peptides not found by database search via MSFragger and in turn uncovers unnoticed false discoveries among their matches. Conclusion: In this study, we show that predicted spectral libraries can enhance peptide identification for metaproteomics. Mistle provides the means to efficiently search large-scale spectral libraries, highlighted for the microbiota 9MM and SIHUMIx. T2 - HUPO2022 CY - Cancun, Mexico DA - 04.12.2022 KW - Proteomics KW - Mass spectrometry KW - Algorithms KW - Metaproteomics PY - 2022 AN - OPUS4-56695 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Ermilova, Elena A1 - Beck, Uwe A1 - Hertwig, Andreas T1 - Modell based ellipsometry standards for different application cases and their application for real non-ideal systems N2 - Ellipsometry enables the investigation of material properties over a broad spectral range. As a fast and non-destructive method, it is widely used in industry for quality assurance. Despite the wide application of ellipsometry and its high industrial relevance there are some material-specific standards and there have been no generally accepted standards dealing with model validation and measurement uncertainties. The first German standard DIN50989-1: 2018 Ellipsometry – Part1: Principles (currently international standard ISO 23131: 2021) marks the beginning of a 6-part standard series for ellipsometry, which was developed under consideration of GUM. T2 - International Conference on Spectroscopic Ellipsometry (ICSE-9) CY - Beijing, China DA - 22.05.2022 KW - Spectroscopic and imaging ellipsometry KW - Standards KW - Uncertainties PY - 2022 AN - OPUS4-56698 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Ermilova, Elena A1 - Weise, Matthias A1 - Hertwig, Andreas T1 - Hybrid optical measurement technique for detection of defects in epitaxially grown 4H-SiC layers N2 - Recent developments in power electronics require the use of new wide bandgap compound semiconductors. Silicon carbide (SiC) is one of the most promising materials for power electronics due to its outstanding properties and commercial availability. Some types of defects in the SiC substrates or homoepitaxial SiC layers can affect the performance of electronic devices in a serious manner or make its operation even impossible. Optical methods such as imaging ellipsometry (IE) and white light interference microscopy (WLIM) were applied for fast and non-contact investigation of defects in the epitaxially grown 12 µm 4H-SiC layers on 4H- SiC substrates. T2 - EOS Annual Meeting (EOSAM 2022) CY - Porto, Portugal DA - 12.09.2022 KW - Imaging ellipsometry KW - White light interference microscopy KW - Epitaxially grown 4H-SiC layers KW - Wide bandgap compound semiconductors PY - 2022 AN - OPUS4-56705 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Memmolo, V. A1 - Lugovtsova, Yevgeniya A1 - Olino, M. A1 - Prager, Jens ED - Kundu, T. ED - Reis, H. ED - Ihn, J.-B. T1 - Application of Temperature Compensation Strategies for Ultrasonic Guided Waves to Distributed Sensor Networks N2 - Temperature compensation strategies play a key role in the implementation of guided wave based structural health monitoring approaches. The varying temperature influences the performance of the inspection system inducing false alarms or missed detection, with a consequent reduction of reliability. This paper quantitatively assesses two temperature compensation methods, namely the optimal baseline selection (OBS) and the baseline signal stretch (BSS), with the aim to extend their use to the case of distributed sensor networks (DSN). The effect of temperature separation between baseline time-traces in OBS and BSS are investigated considering multiple couples of sensors employed in the DSN. A decision strategy that uses frequent value warning to define the optimal baseline or stretching parameter is found to be effective analyzing data from two several experiments, which use different frequency analysis with either predominantly A0 mode or S0 mode data or both. The focus is given on the fact that different paths are available in a sensor network and several possible combinations of results are available. Nonetheless, introducing a frequent value warning it is possible to increase the efficiency of the OBS and BSS approach making use of fewer signal processing algorithms. In addition, the effectiveness of those approach is quantified using damage indicators as metric, which confirms that the performance of OBS and BSS quantitatively agree with predictions and also demonstrate that the use of compensation strategies improve detectability of damage with a higher reliability of the system. T2 - 2022 49th Annual Review of Progress in Quantitative Nondestructive Evaluation (QNDE 2022) CY - San Diego, CA, USA DA - 25.07.2022 KW - Ultrasound KW - Elastic waves KW - Structural Health Monitoring KW - Environmental Effects KW - Damage Detection PY - 2022 SN - 978-0-7918-8659-5 DO - https://doi.org/10.1115/QNDE2022-98534 SP - 1 PB - The American Society of Mechanical Engineers (ASME) CY - 2 Park Avenue, New York, NY 10016, USA AN - OPUS4-57074 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Stein, L. A1 - Wang, Cui A1 - Förster, C. A1 - Resch-Genger, Ute A1 - Heinze, K. T1 - Bulky ligands protect molecular ruby from oxygen quenching N2 - Chromium(III) complexes can show phosphorescence from the spin-flip excited doublet states 2E/2T1 in the near-infrared with high photoluminescence quantum yields and extremely long lifetimes in the absence of dioxygen. The prototype molecular ruby, [Cr(ddpd)2]3+ (ddpd = N,N’-dimethyl-N,N’-dipyridine-2-ylpyridine-2,6-diamine), has a photoluminescence quantum yield and a luminescence lifetime of 13.7% and 1.1 ms in deaerated acetonitrile, respectively. However, its luminescence is strongly quenched by 3O2 via an efficient Dexter-type energy transfer process. To enable luminescence applications of molecular rubies in solution under aerobic conditions, we explored the potential of sterically demanding ddpd ligands to shield the chromium(III) center from O2 using steady state and time-resolved photoluminescence spectroscopy. The structures of the novel complexes with sterically demanding ligands were investigated by single crystal X-ray diffraction and quantum chemically by density functional theory calculations. The O2 sensitivity of the photoluminescence was derived from absolutely measured photoluminescence quantum yields and excited state lifetimes under inert and aerobic conditions and by Stern–Volmer analyses of these data. Optimal sterically shielded chromium(III) complexes revealed photoluminescence quantum yields of up to 5.1% and excited state lifetimes of 518 μs in air-saturated acetonitrile, underlining the large potential of this ligand design approach to broaden the applicability of highly emissive chromium(III) complexes. KW - Fluorescence KW - Synthesis KW - Production KW - Optical spectroscopy KW - Ligand KW - Photophysics KW - Cr(III) KW - Mechanism KW - NIR KW - Sensor KW - Oxygen PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-570807 DO - https://doi.org/10.1039/d2dt02950b VL - 51 IS - 46 SP - 17664 EP - 17670 PB - The Royal Society of Chemistry CY - Berlin AN - OPUS4-57080 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Piechotta, Christian A1 - Steinhäuser, Lorin A1 - Lardy-Fontan, S. A1 - Lalere, B. A1 - Le Diouron, V. A1 - Heath, E. A1 - Ana Kovačič, A. A1 - Potalivo, M. A1 - de Zorzi, P. A1 - Centioli, D. A1 - Naykki, T. A1 - Viidanoja, J. A1 - Gökcen, T. A1 - Budzinski, H. A1 - Le Menach, K. A1 - Selih, V. T1 - EDC-WFD: A project to deliver reliable measurements for better monitoring survey and risks assessments. N2 - Monitoring programs should generate high-quality data on the concentrations of substances and other pollutants in the aquatic environment to enable reliable risk assessment. Furthermore, the need for comparability over space and time is critical for analysis of trends and evaluation of restoration of natural environment. Additionally, research work and exercises at the European level have highlighted that reliable measurements of estrogenic substances at the PNEC level are still challenging to achieve. The project EDC-WFD Metrology for monitoring endocrine disrupting compounds under the EU Water Framework Directive aims to develop traceable analytical methods for determining endocrine disrupting compounds and their effects, with a specific focus on three estrogens of the first watch list (17-beta-estradiol (17βE2), 17-alpha-ethinylestradiol (EE2), and estrone (E1)). Estrogens 17-alpha-estradiol (17E2) and estriol (E3) will be included to demonstrate the reliability of the developed methods and to support the requirements of Directive 2013/39/EC, Directive 2009/90/EC and Commission Implementation Decision (EU) 2018/840, hence improving the comparability and compatibility of measurement results within Europe. During the EDC-WFD project four selected effect-based methods (EBM) will be deeply investigated in order to improve their rationale use and their support in water quality assessment. In particular, the EBM sensitivity, specificity and accuracy on reference materials with single or mixture solutions of the five substances at a concentration of EQS values will be explored. This contribution will present the objectives and methods applied within the EDC-WFD project. T2 - EuChemS CY - Lisbon, Portugal DA - 29.08.2022 KW - WFD KW - Estrogens KW - Whole water samples KW - EQS PY - 2022 AN - OPUS4-57096 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Piechotta, Christian A1 - Kovačič, A. A1 - Steinhäuser, Lorin A1 - Heath, E. A1 - Lardy-Fontan, S. T1 - A method for monitoring estrogens in whole surface waters by GC-MS/MS N2 - Natural and synthetic estrogens are key endocrine-disrupting chemicals. Despite occurring at ultra-trace levels (below ng L-1), it is believed that they are contributing to an increase in feminized fish and other endocrine disruptive effects, and hence, their inclusion in the Watch list was not unexpected. One of the main sources ofestrogens to surface waters is wastewater effluent. Once in surface waters, they can partition into different compartments, i.e., water and suspended particulate matter. For this reason, there is an urgent need for a methodology to monitor estrogen levels below the environmental quality standards (EQS) set by the Water Framework Directive requirements. In this study, a precise and accurate gas chromatography-mass spectrometry method (GC-MS/MS) for the analysis of estrone (E1), 17β-estradiol (17β-E2), 17α-estradiol (17α- E2), 17-alpha-ethinylestradiol (EE2), and estriol (E3) in whole water samples with ng L-1 limit of quantification (LOQ) was developed and validated in accordance with CEN/TS 16800:2020 guidelines. T2 - IMSC 2022 CY - Maastricht, Netherlands DA - 27.08.2022 KW - EDC KW - WFD KW - GC-MS PY - 2022 AN - OPUS4-57097 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Lozano, Daniel A1 - Bulling, Jannis A1 - Prager, Jens T1 - Quadtree decomposition as a meshing strategy for guided waves simulations using the scaled boundary finite element method N2 - Structural health monitoring techniques associate strongly with damage detection and characterization. Ultrasonic guided waves (UGW), for such scope, arise as one of the most promising methods for many reasons i.e. UGW are able to travel long distances and they have high sensitivity to damage. In this context, the necessity to model realistic wave-defect interaction occurs to be critical. Realistic damage scenarios can be modeled through the usage of image-based quadtree meshes. Images, such as the outcome from X-ray scans, C-scans, etc., can be converted into meshes for further integration in a computational domain. Quadtree meshes are created by converting the intensity of the pixels to quadrilateral cells. Homogeneous regions inside one image result in one quad, whereas fine features such as discontinuities can be described with smaller quads. This contribution proposes an efficient methodology to model wave defect interaction, using as a framework the scaled boundary finite element method (SBFEM) and quadtree meshes. Problems as non-conforming regions in the mesh due to the space tree decomposition can be easily avoided using SBFEM’s polygonal elements. Moreover, the semi-analytical nature of the SBFEM allows the modeling of arbitrarily long prismatic/undamaged regions of the waveguides without an increase in the computational burden. T2 - DAGA 2022 CY - Stuttgart, Germany DA - 21.03.2022 KW - Wave defect interaction KW - Scaled Boundary Finite Element Method KW - Quadtree meshes KW - Image-based models KW - Transient analysis PY - 2022 SP - 887 EP - 890 CY - Stuttgart AN - OPUS4-57153 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -