TY - JOUR A1 - Sajulga, R. A1 - Easterly, C. A1 - Riffle, M. A1 - Mesuere, B. A1 - Muth, Thilo A1 - Mehta, S. A1 - Kumar, P. A1 - Johnson, J. A1 - Gruening, B. A1 - Schiebenhoefer, H. A1 - Kolmeder, C. A1 - Fuchs, S. A1 - Nunn, B. A1 - Rudney, J. A1 - Griffin, T. A1 - Jagtap, P. T1 - Survey of metaproteomics software tools for functional microbiome analysis JF - PLoS ONE N2 - To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform. KW - Bioinformatics KW - Metaproteomics KW - Mass spectrometry PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-516358 DO - https://doi.org/10.1371/journal.pone.0241503 SP - e0241503 AN - OPUS4-51635 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Was, G.S. A1 - Bahn, C.-B. A1 - Busby, J. A1 - Cui, B. A1 - Farkas, D. A1 - Gussev, M. A1 - Rigen He, M. A1 - Hesterberg, J. A1 - Jiao, Z. A1 - Johnson, D. A1 - Kuang, W. A1 - McMurtrey, M. A1 - Robertson, I. A1 - Sinjlawi, A. A1 - Song, M. A1 - Stephenson, K. A1 - Sun, K. A1 - Swaminathan, Srinivasan A1 - Wang, M. A1 - West, E. T1 - How irradiation promotes intergranular stress corrosion crack initiation JF - Progress in Material Science N2 - Irradiation assisted stress corrosion cracking (IASCC) is a form of intergranular stress corrosion cracking that occurs in irradiated austenitic alloys. It requires an irradiated microstructure along with high temperature water and stress. The process is ubiquitous in that it occurs in a wide range of austenitic alloys and water chemistries, but only when the alloy is irradiated. Despite evidence of this degradation mode that dates back to the 1960s, the mechanism by which it occurs has remained elusive. Here, using high resolution electron backscattering detection to analyze local stress-strain states, high resolution transmission electron microscopy to identify grain boundary phases at crack tips, and decoupling the roles of stress and grain boundary oxidation, we are able to unfold the complexities of the phenomenon to reveal the mechanism by which IASCC occurs. The significance of the findings impacts the mechanical integrity of core components of both current and advanced nuclear reactor designs worldwide. KW - Irradiation KW - Stress corrosion cracking KW - Grain boundaries KW - Oxidation KW - Austenitic alloys PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-595748 DO - https://doi.org/10.1016/j.pmatsci.2024.101255 SN - 0079-6425 VL - 143 SP - 1 EP - 15 PB - Elsevier AN - OPUS4-59574 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Motzkus, C. A1 - Macé, T. A1 - Gaie-Levrel, F. A1 - Ducourtieux, S. A1 - Delvallee, A. A1 - Dirscherl, K. A1 - Hodoroaba, Vasile-Dan A1 - Popov, I. A1 - Kuselman, I. A1 - Popov, O. A1 - Takahata, K. A1 - Ehara, K. A1 - Ausset, P. A1 - Maillé, M. A1 - Michielsen, N. A1 - Bondiguel, S. A1 - Gensdarmes, F. A1 - Morawska, L. A1 - Johnson, G.R. A1 - Faghihi, E.M. A1 - Kim, C.S. A1 - Kim, Y.H. A1 - Chu, M.C. A1 - Guardado, J.A. A1 - Salas, A. A1 - Capannelli, G. A1 - Costa, C. A1 - Bostrom, T. A1 - Jämting, A.K. A1 - Lawn, M.A. A1 - Adlem, L. A1 - Vaslin-Reimann, S. T1 - Size characterization of airborne SiO2 nanoparticles with on-line and off-line measurement techniques: an interlaboratory comparison study JF - Journal of nanoparticle research N2 - Results of an interlaboratory comparison on size characterization of SiO2 airborne nanoparticles using on-line and off-line measurement techniques are discussed. This study was performed in the framework of Technical Working Area (TWA) 34—'Properties of Nanoparticle Populations' of the Versailles Project on Advanced Materials and Standards (VAMAS) in the project no. 3 'Techniques for characterizing size distribution of airborne nanoparticles'. Two types of nano-aerosols, consisting of (1) one population of nanoparticles with a mean diameter between 30.3 and 39.0 nm and (2) two populations of non-agglomerated nanoparticles with mean diameters between, respectively, 36.2–46.6 nm and 80.2–89.8 nm, were generated for characterization measurements. Scanning mobility particle size spectrometers (SMPS) were used for on-line measurements of size distributions of the produced nano-aerosols. Transmission electron microscopy, scanning electron microscopy, and atomic force microscopy were used as off-line measurement techniques for nanoparticles characterization. Samples were deposited on appropriate supports such as grids, filters, and mica plates by electrostatic precipitation and a filtration technique using SMPS controlled generation upstream. The results of the main size distribution parameters (mean and mode diameters), obtained from several laboratories, were compared based on metrological approaches including metrological traceability, calibration, and evaluation of the measurement uncertainty. Internationally harmonized measurement procedures for airborne SiO2 nanoparticles characterization are proposed. KW - Scanning and transmission electron microscopies KW - Atomic force microscopy KW - Scanning mobility particle size spectrometers KW - Metrological traceability KW - SiO2 nano-aerosol size distribution KW - Interlaboratory comparison PY - 2013 DO - https://doi.org/10.1007/s11051-013-1919-4 SN - 1388-0764 SN - 1572-896X VL - 15 IS - 1919 SP - 1 EP - 36 PB - Kluwer CY - Dordrecht AN - OPUS4-29318 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -