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Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.
Although metaproteomics, the study of the collective proteome of microbial communities, has become increasingly powerful and popular over the past few years, the field has lagged behind on the availability of user-friendly, end-to-end pipelines for data analysis. We therefore describe the Connection from two commonly used metaproteomics data processing tools in the field, MetaProteomeAnalyzer and PeptideShaker, to Unipept for downstream analysis.
Through these connections, direct end-to-end pipelines are built from database searching to taxonomic and functional annotation.
The Industrial Internet of Things (IIoT) poses multiple challenges to traditional standardization, due to the complexity, dynamics, and accelerating speed of technological progress. The need for a timely availability of standards calls for new approaches and tools to enhance standardization processes for smart manufacturing. Industry and standards development organizations worldwide are seeking new solutions. Testbeds have been acknowledged in innovation policy as a powerful tool for knowledge transfer and the further development of emerging technologies. Lately, they have also attracted increasing attention from the standardization perspective as a promising tool for a more agile standards development process. Proponents of such testbeds expect them to support standardization by providing validated solutions and accelerating the processes to meet the growing demands for faster standardization without any detriment to quality. In an explorative, qualitative approach this article is the first to investigate the operation and impact of testbeds in standardization processes based on a multiple case study on testbeds implemented worldwide in the context of the IIoT.
In the light of digitalization and recent EU policy initiatives, information is an important asset that organizations of all sizes and from all sectors should secure. However, in order to provide common requirements for the implementation of an information security management system, the internationally well-accepted ISO/IEC 27001 standard has not shown the expected growth rate since its publication more than a decade ago.In this article, we apply web mining to explore the adoption of ISO/IEC 27001 through a series of 2664 out of more than 900 000 German firms from the Mannheim Enterprise Panel dataset that refers to this standard on their websites. As a result, we present a “landscape” of ISO/IEC 27001 in Germany, which shows that firms not only seek certifications themselves but often refer on their websites to partners who are certified instead. Consequently, we estimate a probit model and find that larger and more innovative firms are more likely to be certified to ISO/IEC 27001 and that almost half of all certified firms belong to the information and communications technology (ICT) service sector. Based on our findings, we derive implications for policymakers and management and critically assess the suitability of web mining to explore the adoption of management system standards.
Popioły pochodzące z instalacji do spalania komunalnych osadów ściekowych, znajdującej się na terytorium Polski, poddano procesom termochemicznego przekształcania, dzięki czemu otrzymano produkty nawozowe spełniające kryteria dopuszczające je do obrotu jako nawozy mineralne. Ponadto dokonano analizy możliwości wykorzystania popiołów na cele nawozowe zgodnie z obecnie przyjętymi dokumentami strategicznymi i planistycznymi dotyczącymi gospodarki odpadami na poziomie krajowym i europejskim.
A new metallosilicate based on yttrium was synthesized and characterized by XRD, FT-IR, 29Si MAS-NMR, and 89Y MAS-NMR. The mixed framework of the material was confirmed by the detection of distinct chemical shift groups using 29Si MAS-NMR (at -82 to -87 ppm, -91 to -94 ppm, -96 to -102 ppm, and -105 to -108 ppm), as well as four distinct chemical shifts in the 89Y MAS-NMR spectrum (at -89, -142, -160, and -220 ppm). Adsorption and kinetic analyses indicated the potential of the new material for the removal of lead and cadmium from aqueous media. The adsorption results for lead indicated that dynamic equilibrium was reached after five hours, with total lead removal of around 94 %, while for cadmium it was reached in the first hour, with total Cadmium removal of around 74 %. The adsorptions of lead and cadmium were modeled using pseudo-first order (PFO) and pseudo-second order (PSO) kinetic models. Although both models provided high R2 values (0.9903 and 0.9980, respectively), the PSO model presented a much lower χ2 red value (4.41×10−4), compared to the PFO model (2.12×10−3), which indicated that the rate-limiting step was probably due to the chemisorption of lead from the solution onto the yttrium-based metallosilicate.
Understanding the correlation between the morphological and functional properties of particulate materials is crucial across all fields of physical and natural sciences. This manuscript reports on the investigation of the effect of polyethylene glycol (PEG) employed as a capping Agent in the synthesis of SrTiO3 crystals. The crucial influence of PEG on both the shape and size of the strontium titanate particles is revealed, highlighting the effect on the photocurrents measured under
UV–Vis irradiation.
We present an approach towards the in situ solid state NMR monitoring of mechanochemical reactions in a ball mill. A miniaturized vibration ball mill is integrated into the measuring coil of a home-built solid state NMR probe, allowing for static solid state NMR measurements during the mechanochemical reaction within the vessel. The setup allows to quantitatively follow the product evolution of a prototypical mechanochemical reaction, the formation of zinc phenylphosphonate from zinc acetate and phenylphosphonic acid. MAS NMR investigations on the final reaction mixture confirmed a reaction yield of 89% in a typical example. Thus, NMR spectroscopy may in the future provide complementary information about reaction mechanisms of mechanochemical reactions and team up with other analytical methods which have been employed to follow reactions in situ, such as Raman spectroscopy or X-ray diffraction.
Lanthanides (Ln) are critical raw materials, however, their mining and purification have a considerable negative environmental impact and sustainable recycling and separation strategies for these elements are needed. In this study, the precipitation and solubility behavior of Ln complexes with pyrroloquinoline quinone (PQQ), the cofactor of recently discovered lanthanide (Ln) dependent methanol dehydrogenase (MDH) enzymes, is presented. In this context, the molecular structure of a biorelevant europium PQQ complex was for the first time elucidated outside a protein environment. The complex crystallizes as an inversion symmetric dimer, Eu2PQQ2, with binding of Eu in the biologically relevant pocket of PQQ. LnPQQ and Ln1Ln2PQQ complexes were characterized by using inductively coupled plasma mass spectrometry (ICP‐MS), infrared (IR) spectroscopy, 151Eu‐Mössbauer spectroscopy, X‐ray total scattering, and extended X‐ray absorption fine structure (EXAFS). It is shown that a natural enzymatic cofactor is capable to achieve separation by precipitation of the notoriously similar, and thus difficult to separate, lanthanides to some extent.
Tire and road wear particles (TRWPs) are heteroagglomerates of tire rubber and other particles deposited on the road surface and one of the main contributors to non-exhaust emissions of automobile traffic. In this study, samples from road environments were analyzed for their TRWP contents and concentra- tions of eight organic tire constituents. TRWP concentrations were determined by quantifying Zn in the density fraction < 1.9 g/cm ³and by thermal extraction desorption-gas chromatography-mass spectrometry (TED-GC/MS) and the concentrations ranged from 3.7 to 480 mg TRWP/g. Strong and statistically signif- icant correlations with TRWPs were found for 2-hydroxybenzothiazole and 2-aminobenzothiazole, indi- cating that these substances may be suitable markers of TRWPs. The mass distribution of TRWPs in road dust suggests that the main mass fraction formed on roads consists of coarse particles ( > 100 μm). Data for a sedimentation basin indicate that the fine fraction ( < 50 μm) is preferentially transported by road runoffinto receiving waters. The size distribution and density data of TRWP gathered by three different quantitation approaches also suggest that aging of TRWPs leads to changes in their particle density. An improved understanding of the dynamics of TRWP properties is essential to assess the distribution and dissipation of this contaminant of emerging concern in the environment.