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This survey will discuss current and emerging isothermal and rapid polymerase chain reaction (PCR) based nucleic acid amplification methods for patient near diagnostics. To assess the clinical need of rapid diagnostics for infectious diseases based on nucleic acid tests (NATs) we performed and analysed a questionnaire among laboratories participating in corresponding INSTAND ring trials for external quality assurance. The questions concerning new amplification technologies like isothermal nucleic acid amplification, potentially suited to significantly decrease turnaround times, were complemented by questions to evaluate the present status of NATs. Besides end-users, companies were also addressed by sending out a manufacturer specific questionnaire. Analysis of the answers from 48 laboratories in 14 European countries revealed that a much shorter turnaround time is requested for selected pathogens compared to about 2 h or longer when applying temperature cycling amplification, i.e. PCR. In this context, most frequently mentioned were MRSA, norovirus, influenza A and B viruses, cytomegalovirus (CMV) as well as hepatitis B virus (HBV) and hepatitis C virus (HCV). At present, 8% of the laboratories having participated in this survey apply isothermal amplification of nucleic acid to identify infectious pathogens.
Recently, C K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of graphite (HOPG) surfaces have been measured for the pristine material, and for HOPG treated with either bromine or krypton plasmas (Lippitz et al., Surf. Sci., 2013, 611, L1). Changes of the NEXAFS spectra characteristic for physical (krypton) and/or chemical/physical modifications of the surface (bromine) upon plasma treatment were observed. Their molecular origin, however, remained elusive. In this work we study by density functional theory, the effects of selected point and line defects as well as chemical modifications on NEXAFS carbon K-edge spectra of single graphene layers. For Br-treated surfaces, also Br 3d X-ray Photoelectron Spectra (XPS) are simulated by a cluster approach, to identify possible chemical modifications. We observe that some of the defects related to plasma treatment lead to characteristic changes of NEXAFS spectra, similar to those in experiment. Theory provides possible microscopic origins for these changes.
Recent advances in vacuum sciences and applications are reviewed. Novel optical interferometer cavity devices enable pressure measurements with ppm accuracy. The innovative dynamic vacuum standard allows for pressure measurements with temporal resolution of 2 ms. Vacuum issues in the construction of huge ultra-high vacuum devices worldwide are reviewed. Recent advances in surface science and thin films include new phenomena observed in electron transport near solid surfaces as well as novel results on the properties of carbon nanomaterials. Precise techniques for surface and thin-film characterization have been applied in the conservation technology of cultural heritage objects and recent advances in the characterization of biointerfaces are presented. The combination of various vacuum and atmospheric-pressure techniques enables an insight into the complex phenomena of protein and other biomolecule conformations on solid surfaces. Studying these phenomena at solid–liquid interfaces is regarded as the main issue in the development of alternative techniques for drug delivery, tissue engineering and thus the development of innovative techniques for curing cancer and cardiovascular diseases. A review on recent advances in plasma medicine is presented as well as novel hypotheses on cell apoptosis upon treatment with gaseous plasma. Finally, recent advances in plasma nanoscience are illustrated with several examples and a roadmap for future activities is presented.
In order to investigate molecular recognition on surfaces, an azide-functionalized monolayer was deposited on gold. The monolayer was characterized by X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) experiments and the decomposition of the azide upon irradiation with X-ray beams was investigated. Subsequently, various alkyne-functionalized host and guest molecules were attached to the azide by 1,3-dipolar cycloaddition. These modified surfaces and their host–guest chemistry were analysed by XPS and angle-resolved NEXAFS. The reversibility of guest binding was shown for one example as a proof of principle.
The combination of complementary characterization techniques such as SEM (Scanning Electron Microscopy), T-SEM (Scanning Electron Microscopy in Transmission Mode), EDX (Energy Dispersive X-ray Spectroscopy) and SAM (Scanning Auger Microscopy) has been proven to be a powerful and relatively quick characterization strategy for comprehensive morphological and chemical characterization of individual silica and titania nanoparticles. The selected real life test materials, silica and titania, are listed in the OECD guidance manual as representative examples because they are often used as commercial nanomaterials. Imaging by high resolution SEM and in the transmission mode by T-SEM allows almost simultaneous surface and in-depth inspection of the same particle using the same instrument. EDX and SAM enable the chemical characterization of bulk and surface of individual nanoparticles. The core–shell properties of silica based materials are addressed as well. Titania nominally coated by silane purchased from an industrial source has been found to be inhomogeneous in terms of chemical composition.
Solgel prepared ternary FeF3–MgF2 materials have become promising heterogeneous catalysts due to their porosity and surface Lewis/Brønsted acidity (bi-acidity). Despite the good catalytic performance, nanoscopic characterisations of this type of material are still missing and the key factors controlling the surface properties have not yet been identified, impeding both a better understanding and further development of ternary fluoride catalysts. In this study, we characterised the interaction between the bi-acidic component (FeF3) and the matrix (MgF2) on the nano-scale. For the first time, the formation pathway of FeF3–MgF2 was profiled and the template effect of MgF2 during the synthesis process was discovered. Based on these new insights two novel materials, FeF3–CaF2 and FeF3–SrF2, were established, revealing that with decreasing the atomic numbers (from Sr to Mg), the ternary fluorides exhibited increasing surface acidity and surface area but decreasing pore size. These systematic changes gave rise to a panel of catalysts with tuneable surface and bulk properties either by changing the matrix alkaline earth metal fluoride or by adjusting their ratios to Fe or both. The template effect of the alkaline earth metal fluoride matrix was identified as the most probable key factor determining the surface properties and further influencing the catalytic performance in ternary fluoride based catalysts, and paves the way to targeted design of next-generation catalysts with tunable properties.
In Near Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy X-Ray photons are used to excite tightly bound core electrons to low-lying unoccupied orbitals of the system. This technique offers insight into the electronic structure of the system as well as useful structural information. In this work, we apply NEXAFS to two kinds of imidazolium based ionic liquids ([CnC₁im]⁺[NTf₂]⁻ and [C₄C₁im]⁺[I]⁻). A combination of measurements and quantum chemical calculations of C K and N K NEXAFS resonances is presented. The simulations, based on the transition potential density functional theory method (TP-DFT), reproduce all characteristic features observed by the experiment. Furthermore, a detailed assignment of resonance features to excitation centers (carbon or nitrogen atoms) leads to a consistent interpretation of the spectra.
A novel photoswitchable rotaxane was synthesised and its switching behaviour in solution was analysed with NMR and UV-Vis. A monolayer of rotaxanes was deposited on glass surfaces and the on-surface photoswitching was investigated. Angle-resolved NEXAFS spectra revealed a preferential orientation that reversibly changes upon switching.
In this work, fullerene has been functionalized with cyanuric Chloride at room temperature by a nitrene mediated [2 + 1] cycloaddition reaction. The adduct after functionalization is inherently in the form of azafulleroid and shows broad UV absorption in the wavelength range of 200–800 nm, as well as photothermal conversion and fluorescence with a high quantum yield.
Materials and chemical producers require detailed knowledge of surface chemistry for research into new products. One way to understand a surface without damaging it is to bombard it with an electron beam, causing its atoms to emit characteristic X-rays enabling identification. The measurement of these must be precise as many elements emissions are close in energy – traceable reference materials will ensure instruments using this technique are stable and accurate.
IND15 JRP SurfChem: Traceable quantitative surface chemical analysis for industrial applications
(2016)
The SurfChem project has made a significant contribution to traceable quantitative surface chemical analysis for industrial applications by delivering new certified reference materials and test samples for specific technical applications. Regular performance tests of instruments, metrological methodology for the detection of (bio)organic surface species, ambient and non-destructive surface chemical analysis for in-line process control and new in situ characterisation techniques of catalytically active surfaces have been achieved.
Real Time Imaging of Deuterium in a Duplex Stainless Steel Microstructure by Time-of-Flight SIMS
(2016)
For more than one century, hydrogen assisted degradation of metallic microstructures has been identified as origin for severe technical component failures but the mechanisms behind have not yet been completely understood so far. Any in-situ observation of hydrogen transport phenomena in microstructures will provide more details for further elucidation of these degradation mechanisms. A novel experiment is presented which is designed to elucidate the permeation behaviour of deuterium in a microstructure of duplex stainless steel (DSS). A hydrogen permeation cell within a TOF-SIMS instrument enables electrochemical charging with deuterium through the inner surface of the cell made from DSS. The outer surface of the DSS permeation cell exposed to the vacuum has been imaged by TOF-SIMS vs. increasing time of charging with subsequent chemometric treatment of image data. This in-situ experiment showed evidently that deuterium is permeating much faster through the ferrite phase than through the austenite phase. Moreover, a direct proof for deuterium enrichment at the austenite-ferrite interface has been found.
The sonication process is commonly used for de-agglomerating and dispersing nanomaterials in aqueous based media, necessary to improve homogeneity and stability of the suspension. In this study, a systematic step-wise approach is carried out to identify optimal sonication conditions in order to achieve a stable dispersion. This approach has been adopted and shown to be suitable for several nanomaterials (cerium oxide, zinc oxide, and carbon nanotubes) dispersed in deionized (DI) water. However, with any change in either the nanomaterial type or dispersing medium, there needs to be optimization of the basic protocol by adjusting various factors such as sonication time, power, and sonicator type as well as temperature rise during the process. The approach records the dispersion process in detail. This is necessary to identify the time Points as well as other above-mentioned conditions during the sonication process in which there may be undesirable changes, such as damage to the particle surface thus affecting surface properties. Our goal is to offer a harmonized approach that can control the Quality of the final, produced dispersion. Such a guideline is instrumental in ensuring dispersion quality repeatability in the nanoscience community, particularly in the field of nanotoxicology.
Magnetic iron oxide nanoparticle clusters (mnpc) coated with organic stabilizers were investigated using scanning transmission x-ray microscopy (STXM). Simultaneous surface and bulk sensitive Fe L3 edge absorption spectra, obtained using a photomultiplier tube and a channeltron, were used to detect subtle changes in the oxidation state in the surface and bulk of Iron Oxide mnpc.
The effectiveness of this mode of STXM operation is demonstrated for These nanoparticle clusters.
Water and aqueous reagents are essential in any biological process or system. But apart from a few special low vapor-pressure cases, liquids have not been accessible to any technique requiring UHV conditions. EnviroESCA opens up this exciting field of applications.
In this paper first results from water based samples are presented as a proof of concept to demonstrate the special capabilities of EnviroESCA analyzing liquid samples. The following solutions were investigated under near ambient pressure conditions: i.) water, ii.) brine, iii.) an oil in water dispersion, iv.) aqueous iron(II) sulfate heptahydrate, and v.) a suspension of nano silver particles in water.
A controlled, reproducible, gram-scale method is reported for the covalent functionalization of graphene Sheets by a one-pot nitrene [2+1] cycloaddition reaction under mild conditions. The reaction between commercially available 2,4,6-trichloro-1,3,5-triazine and sodium azide with thermally reduced graphene oxide (TRGO) results in defined dichlorotriazine-functionalized sheets. The different reactivities of the chlorine substituents on the functionalized graphene allow stepwise post-modification by manipulating the temperature.
This new method provides unique access to defined bifunctional 2D nanomaterials, as exemplified by chiral surfaces and multifunctional hybrid architectures.
Magnetic iron oxide nanoparticle clusters (mnpc) coated with organic stabilizers were investigated using scanning transmission x-ray microscopy (STXM). Simultaneous surface and bulk sensitive Fe L₃ edge absorption spectra, obtained using a photomultiplier tube and a channeltron, were used to detect subtle changes in the oxidation state in the surface and bulk of Iron Oxide mnpc. The effectiveness of this mode of STXM operation is demonstrated for these nanoparticle clusters.
Surface characterisation of Escherichia coli under various conditions by near-ambient pressure XPS
(2018)
Bacteria are inherently in a hydrated state and therefore not compatible to ultra-high vacuum techniques such as XPS without prior sample preparation involving freeze drying or fast freezing.
This has changed with the development of near-ambient pressure (NAP)-XPS, which makes it possible to characterise the bacterial surface with minimal sample preparation. This paper presents NAP-XPS measurements of Escherichia coli under various NAP conditions: at 11 mbar in a humid environment, at 2 mbar after drying in the chamber, pre-dried at 4 mbar, and at 1 mbar after overnight pumping at 10^−4 mbar. The high-resolution spectra of carbon, nitrogen, and oxygen are presented and found to be in general agreement with XPS measurements from freeze-dried and fast-frozen bacteria. However, it was found that the amount of carbon components associated with polysaccharides increases relative to aliphatic carbon during drying and increases further after overnight pumping. This implies that drying has an impact on the bacterial surface.
A scanning transmission X‐ray microscopy (STXM)‐based methodology is introduced for determining the dimensions (shell thickness, core and total diameter) of core‐shell nanoparticles, which exhibit a strong X‐ray absorption contrast and a well‐defined interface between core and shell material. A low radiation dosage during data acquisition and, therefore, less X‐ray beam‐induced damage of the sample is achieved by recording STXM images only at 2 predetermined energies of maximum Absorption contrast, instead of recording a stack of images across the whole absorption edge.
A model core‐shell nanoparticle, polytetrafluoroethylene (PTFE) cores with polystyrene (PS) shell, is used for demonstration. Near‐edge X‐ray absorption fine structure spectroscopy confirms the significant difference in X‐ray absorption behavior between PTFE and PS. Additionally, because of the insolubility of styrene in PTFE a well‐defined interface between particle core and shell is expected. To validate the STXM results, both the naked PTFE cores as well as the complete core‐shell nanoparticles are examined by scanning electron microscopy (SEM). The introduced STXM‐based methodology yields particle dimensions in agreement with the SEM results and provides additional information such as the position of the particle core, which cannot be extracted from a SEM micrograph.
Core–shell nanoparticles (CSNPs) have become indispensable in various industrial applications. However, their real internal structure usually deviates from an ideal core–shell structure. To control how the particles perform with regard to their specific applications, characterization techniques are required that can distinguish an ideal from a nonideal morphology. In this work, we investigated poly(tetrafluoroethylene)–poly(methyl methacrylate) (PTFE–PMMA) and poly(tetrafluoroethylene)–polystyrene (PTFE–PS) polymer CSNPs with a constant core diameter (45 nm) but varying shell thicknesses (4–50 nm). As confirmed by transmission scanning electron microscopy (T-SEM), the shell completely covers the core for the PTFE–PMMA nanoparticles, while the encapsulation of the core by the shell material is incomplete for the PTFE–PS nanoparticles. X-ray photoelectron spectroscopy (XPS) was applied to determine the shell thickness of the nanoparticles. The software SESSA v2.0 was used to analyze the intensities of the elastic peaks, and the QUASES software package was employed to evaluate the shape of the inelastic background in the XPS survey spectra. For the first time, nanoparticle shell thicknesses are presented, which are exclusively based on the analysis of the XPS inelastic background. Furthermore, principal component analysis (PCA)-assisted time-of-flight secondary-ion mass spectrometry (ToF-SIMS) of the PTFE–PS nanoparticle sample set revealed a systematic variation among the samples and, thus, confirmed the incomplete encapsulation of the core by the shell material. As opposed to that, no variation is observed in the PCA score plots of the PTFE–PMMA nanoparticle sample set. Consequently, the complete coverage of the core by the shell material is proved by ToF-SIMS with a certainty that cannot be achieved by XPS and T-SEM.