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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.
The concept of direct mass-spectrometric analysis, especially exploited by ambient desorption/ionization (ADI) methods, provides numerous means for convenient sample analysis. While many simple and versatile ionization sources have been developed, challenges lay in achieving efficient sample introduction. In previous work, a sample introduction method employing direct current corona discharge (CD) coupled to a surface acoustic wave nebulization (SAWN) device enhanced sampling performance for both polar and nonpolar analytes by up to 4 orders of magnitude. In fact, the SAWN-CD method generated a multiply charged peptide ion signal comparable to that of conventional ESI. Unfortunately, the high cost of the SAWN devices themselves limits their accessibility. Herein, we report on an analogous implementation of CD with an inexpensive ultrasonic nebulizer (USN) on the basis of a commercial room humidifier demonstrating equivalent exemplary performance. We subsequently compare the two methods of SAWN-CD and USN-CD in a screening application of milk for the detection of two antibiotic drugs, ciprofloxacin and ampicillin. Finally, we further investigate the relative softness of these CD-coupled acoustic nebulization methods in comparison to that of ESI using a survival yield study of the thermometer ion nitrobenzylpyridinium.
In this work, which is part of a larger research program, a framework called “virtual data fusion“ was developed to provide an automated and consistent crack detection method that allows for the cross-comparison of results from large quantities of X-ray Computed Tomography (CT) data. A partial implementation of this method in a custom program was developed for use in research focused on crack quantification in Alkali-Silica Reaction (ASR)-sensitive concrete aggregates. During the CT image processing, a series of image analyses tailored for detecting specific, individual crack-like characteristics were completed. The results of these analyses were then “fused” in order to identify crack-like objects within the images with much higher accuracy than that yielded by any individual image analysis procedure. The results of this strategy demonstrated the success of the program in effectively identifying crack-like structures and quantifying characteristics, such as surface area and volume. The results demonstrated that the source of aggregate has a very significant impact on the amount of internal cracking, even when the mineralogical characteristics remain very similar. River gravels, for instance, were found to contain significantly higher levels of internal cracking than quarried stone aggregates of the same mineralogical type.
Implant-associated infections present severe and difficult-to-treat complications after surgery, related to implant biofilm colonization. Systemic administration of antibiotics cannot reach sufficient concentrations at the infected site and may be toxic. Here we describe how mussel-inspired dendritic material coated on a titanium surface can locally activate a prodrug of daptomycin (pro-dapto) to treat methicillin-resistant Staphylococcus aureus. The mechanism of the prodrug activation is based on bio-orthogonal click chemistry between a tetrazine (Tz) and trans-cyclooctene (TCO). The former is attached to the dendritic polymer, while the later converts daptomycin into a prodrug. Characterization of the material's properties revealed that it is hydrophobic, non-toxic, and stable for a prolonged period of time. We envision that the titanium coated dendritic material will be able to improve the treatment of implant-associated infections by concentrating systemically administered antibiotic prodrugs, thus converting them into active localized medicines.
Metal-Assisted and Solvent-Mediated Synthesis of Two-Dimensional Triazine Structures on Gram Scale
(2020)
Covalent triazine frameworks are an emerging material class that have shown promising performance for a range of applications. In this work, we report on a metal-assisted and solvent-mediated reaction between calcium carbide and cyanuric chloride, as cheap and commercially available precursors, to synthesize two-dimensional triazine structures (2DTSs). The reaction between the solvent, dimethylformamide, and cyanuric chloride was promoted by calcium carbide and resulted in dimethylamino-s-triazine intermediates, which in turn undergo nucleophilic substitutions. This reaction was directed into two dimensions by calcium ions derived from calcium carbide and induced the formation of 2DTSs. The role of calcium ions to direct the two-dimensionality of the final structure was simulated using DFT and further proven by synthesizing molecular intermediates. The water content of the reaction medium was found to be a crucial factor that affected the structure of the products dramatically. While 2DTSs were obtained under anhydrous conditions, a mixture of graphitic material/2DTSs or only graphitic material (GM) was obtained in aqueous solutions. Due to the straightforward and gram-scale synthesis of 2DTSs, as well as their photothermal and photodynamic properties, they are promising materials for a wide range of future applications, including bacteria and virus incapacitation.
The oxides, hydroxides, and oxo-hydroxides of iron belong to the most abundant materials on earth. They also feature a wide range of practical applications. In many environments, they can undergo facile phase transformations and crystallization processes.
Water appears to play a critical role in many of these processes. Despite numerous attempts, the role of water has not been fully revealed yet. We present a new approach to study the influence of water in the crystallization and phase transformations of iron oxides.
The approach employs model-type iron oxide films that comprise a defined homogeneous nanostructure. The films are exposed to air containing different amounts of water reaching up to pressures of 10 bar. Ex situ analysis via scanning electron microscopy, Transmission electron microscopy, selected area electron diffraction, and X-ray diffraction is combined with operando near-ambient pressure X-ray photoelectron spectroscopy to follow water-induced changes in hematite nd ferrihydrite. Water proves to be critical for the nucleation of ematite domains in ferrihydrite, the resulting crystallite orientation, and the underlying crystallization mechanism.
For the first time, dielectric and calorimetric investigations of an homologous series of Janus polynorbornenes with rigid main backbones and flexible -Si(OR)3 side groups, of differing length alkyl chains (R = Propyl, Butyl, Hexyl, Octyl, Decyl) is reported. Generally, this class of polymers has some potential for applications in the field of gas separation membranes. Two dielectrically active processes are observed at low temperatures, denoted as β- and α- relaxation. The former can be assigned to localized fluctuations, whilst the latter is related to the glassy dynamics of the flexible -Si(OR)3 side groups, creating a nanophase separation in both the alkyl chain rich and backbone rich domains. This is confirmed through temperature modulated DSC measurements and X-ray scattering experiments. The glass transition temperatures of the backbone rich domains, which are beyond or near to their degradation temperatures in terms of conventional DSC, are determined for the first time using Fast Scanning Calorimetry employing both fast heating and cooling rates. This is complimented with scattering experiments that show how the size of the alkyl chain rich domains increases with chain length. Alongside these results, a significant conductivity contribution was observed for all poly(tricyclononenes) with -Si(OR)3 side groups, which is interpreted in terms of a percolation model.
L-lactide was polymerized in bulk at 120, 140, 160 and 180°C with neat tin(II) 2-ethylhexanoate (SnOct2) as catalyst. At 180°C the Lac/Cat ratio was varied from 25/1 up to 8 000/1 and at 160°C from 25/1 up to 6 000/1. The vast majority of the resulting polylactides consist of cycles in combination with a small fraction of linear chains having one octanoate and one COOH end group. The linear chains almost vanished at high Lac/Cat ratios, as evidenced by MALDI-TOF mass spectrometry and measurements of intrinsic viscosities and dn/dc values. At Lac/Cat ratios <1000/1 the number average molar masses (Mn) are far higher than expected for stoichiometic initiation, and above 400/1 the molar masses vary relatively little with the Lac/Cat ratio. At 180° slight discoloration even at short times and degradation of the molar masses were observed, but at 160°C or below colorless products with weight average molar masses (Mw) up to 310 000 g mol-1 were obtained. The formation of high molar mass cyclic polylactides is explained by a ROPPOC (Ring-Opening Polymerizatiom with simultaneous Polycondensation) mechanism with intermediate formation of linear chains having one Sn-O-CH end group and one mixed anhydride end group. Additional experiments with tin(II)acetate as catalyst confirm this interpretation. These findings together with the detection of several transesterification mechanisms confirm previous critique of the Jacobson-Stockmayer theory.
Thanks to its good strength/mass ratio, a glass fibre reinforced plastic (GFRP) composite is a common material widely used in aviation, power production, automotive and other industries. In its turn, active infrared (IR) nondestructive testing (NDT) is a common inspection technique for detecting and characterizing structural defects in GFRP. Materials to be tested are typically subjected to optical heating which is supposed to occur on the material surface. However, GFRP composite is semitransparent for optical radiation of both visual and IR spectral bands. Correspondingly, the inspection process represents a certain combination of both optical and thermal phenomena. Therefore, the known characterization algorithms based on pure heat diffusion cannot be applied to semi-transparent materials. In this study, the phenomenon of GFRP semi-transparency has been investigated numerically and experimentally in application to thermal NDT. Both Xenon flash tubes and a laser have been used for thermal stimulation of opaque and semi-transparent test objects. It has been shown that the Penetration of optical heating radiation into composite reduces detectability of shallower defects, and the signal-to-noise ratio can be enhanced by applying the technique of thermographic signal reconstruction (TSR). In the inspection of the semi-transparent GFRP composite, the most efficient has been the laser heating followed by the TSR data processing. The perspectives of defect characterization of semi-transparent materials by using laser heating are discussed. A neural network has been used as a candidate tool for evaluating defect depth in composite materials, but its training should be performed in identical with testing conditions.
Inelastic incoherent neutron time-of flight scattering was employed to measure the low frequency density of states for a series of addition polynorbornenes with bulky side groups. The rigid main chain in combination with the bulky side groups give rise to a microporosity of these polymers in the solid state. The microporosity characterized by the BET surfaces area varies systematically in the considered series. Such materials have some possible application as active separation layer in gas separation membranes.
All investigated materials show excess contributions to the Debye type density of states characteristic for glasses known as Boson peak. The maximum position of the Boson peak shifts to lower frequency values with increasing microporosity. Data for PIM-1 and Matrimid included for comparison are in good agreement to this dependency. This result supports the sound wave interpretation of the Boson peak.
The composition of concrete determines its resistance to various degradation mechanisms such as ingress of ions, carbonation or reinforcement corrosion. Knowledge of the composition of the hardened concrete is therefore helpful to assess the remaining service life of an existing structure or evaluate the damage observed during inspections. For example, for most existing concrete structures the type of cement originally used is not known and must therefore be determined afterwards. This paper presents a preliminary study on the application of laser-induced breakdown spectroscopy (LIBS) to identify the type of cement. For this purpose, ten different types of cement were investigated. For every type, three cement paste prisms were produced: (i) prisms dried, ground and pressed into tablets, (ii) prisms dried and (iii) prisms untreated. LIBS measurements were performed with a diode-pumped low energy laser (1064 nm, 3 mJ, 1.5 ns, 100 Hz) in combination with two compact spectrometers which cover the UV and NIR spectral range. A reduced subset of spectral features was used to build a classification model based on linear discriminant analysis. The results show that the classification of homogenized pressed cement powder samples provides a high accuracy, however, factors such as a different sample matrix and moisture content can affect the accuracy of the classification. The study demonstrates that LIBS is a promising tool to identify the type of cement.