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Structural and chemical characterization of nanomaterials provides important information for understanding their functional properties. Nanomaterials with characteristic structure sizes in the nanometer range can be characterized by scanning transmission electron microscopy (STEM). In conventional STEM, two-dimensional (2D) projection images of the samples are acquired, information about the third dimension is lost. This drawback can be overcome by STEM tomography, where the three-dimensional (3D) structure is reconstructed from a series of projection images acquired using various projection directions. However, 3D measurements are expensive with respect to acquisition and evaluation time. Furthermore, the method is hardly applicable to beam-sensitive materials, i.e. samples that degrade under the electron beam. For this reason, it is desirable to know whether sufficient information on structural and chemical information can be extracted from 2D-projection measurements. In the present work, a comparison between 3D-reconstruction and 2D-projection characterization of structure and mixing in nanoparticle hetero-aggregates is provided. To this end, convolutional neural networks are trained in 2D and 3D to extract particle positions and material types from the simulated or experimental measurement. Results are used to evaluate structure, particle size distributions, hetero-aggregate compositions and mixing of particles quantitatively and to find an answer to the question, whether an expensive 3D characterization is required for this material system for future characterizations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The host-microbiome axis has been implicated in promoting anti-inflammatory immune responses. Yet, the underlying molecular mechanisms of commensal-mediated IL-10 production by regulatory B cells (Bregs) are not fully elucidated. Here, we demonstrate that bacterial CpG motifs trigger the signaling downstream of TLR9 promoting IκB NS -mediated expression of Blimp-1, a transcription regulator of IL-10. Surprisingly, this effect was counteracted by the NF-κB transcription factor c-Rel. A functional screen for intestinal bacterial species identified the commensal Clostridium sporogenes, secreting high amounts of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs), as an amplifier of IL-10 production by promoting sustained mTOR signaling in B cells. Consequently, enhanced Breg functionality was achieved by combining CpG with the SCFA butyrate or the BCFA isovalerate thereby synergizing TLR- and mTOR-mediated pathways. Collectively, Bregs required two bacterial signals (butyrate and CpG) to elicit their full suppressive capacity and ameliorate T cell-mediated intestinal inflammation. Our study has dissected the molecular pathways induced by bacterial factors, which might contribute not only to better understanding of host-microbiome interactions, but also to exploration of new strategies for improvement of anti-inflammatory cellular therapy., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Atomic electric fields in a thin GaN sample are measured with the centre-of-mass approach in 4D-scanning transmission electron microscopy (4D-STEM) using a 12-segmented STEM detector in a Spectra 300 microscope. The electric fields, charge density and potential are compared to simulations and an experimental measurement using a pixelated 4D-STEM detector. The segmented detector benefits from a high recording speed, which enables measurements at low radiation doses. However, there is measurement uncertainty due to the limited number of segments analysed in this study., (© 2024 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.)

If quantitative scanning transmission electron microscopy is used for very precise thickness measurements with atomic resolution, it is commonly referred to as »atom counting«. Due to scattering and the finite probe extent the signal recorded in one atomic column is dependent not only on its own height but also on the height of its neighbours. Especially for thicker specimens this crosstalk effect can have significant impact on the measured intensity. If it is not appropriately accounted for in the evaluation, it can result in a deterioration of accuracy that impedes the possibility of actual atom counting. However, as the number of possible neighbour configurations can be excessively large, a comprehensive consideration of all in the evaluation reference is neigh impossible. This work proposes a method that allows for the a-posteriori reduction of crosstalk during the evaluation by algebraic means. Based on a parametric model, which is described in detail in the article, the crosstalk is expressed by an invertible matrix. Applying the inverted matrix to the measurement yields crosstalk corrected intensity values with very little computational effort. These can subsequently be evaluated by direct comparison to simple reference data. The working principle of the method is presented on the example of crystalline gold. The crosstalk parametrisation is found by fitting a model to sets of specifically created multislice simulations. The parameters are given for both aberration corrected and uncorrected STEM. Subsequently the abilities and potential of the technique are assessed in simulative studies on multiple model systems including gold nanoparticles. Overall a significant and robust improvement of the attainable precision can be demonstrated making the proposed method a promising tool for reference-based atom counting., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The immunoproteasome is a central protease complex required for optimal antigen presentation. Immunoproteasome activity is also associated with facilitating the degradation of misfolded and oxidized proteins, which prevents cellular stress. While extensively studied during diseases with increasing evidence suggesting a role for the immunoproteasome during pathological conditions including neurodegenerative diseases, this enzyme complex is believed to be mainly not expressed in the healthy brain. In this study, we show an age-dependent increase in polyubiquitination in the brains of wild-type mice, accompanied by an induction of immunoproteasomes, which was most prominent in neurons and microglia. In contrast, mice completely lacking immunoproteasomes (triple-knockout mice), displayed a strong increase in polyubiquitinated proteins already in the young brain and developed spontaneous epileptic seizures, beginning at the age of 6 months. Injections of kainic acid led to high epilepsy-related mortality of aged triple-knockout mice, confirming increased pathological hyperexcitability states. Notably, the expression of the immunoproteasome was reduced in the brains of patients suffering from epilepsy. In addition, the aged triple-knockout mice showed increased anxiety, tau hyperphosphorylation and degeneration of Purkinje cell population with the resulting ataxic symptoms and locomotion alterations. Collectively, our study suggests a critical role for the immunoproteasome in the maintenance of a healthy brain during ageing., Competing Interests: The authors report no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain.)

Gut microbiota-derived metabolites play a pivotal role in the maintenance of intestinal immune homeostasis. Here, we demonstrate that the human commensal Clostridium sporogenes possesses a specific metabolic fingerprint, consisting predominantly of the tryptophan catabolite indole-3-propionic acid (IPA), the branched-chain acids (BCFAs) isobutyrate and isovalerate and the short-chain fatty acids (SCFAs) acetate and propionate. Mono-colonization of germ-free mice with C. sporogenes (CS mice) affected colonic mucosal immune cell phenotypes, including up-regulation of Il22 gene expression, and increased abundance of transcriptionally active colonic tuft cells and Foxp3 + regulatory T cells (Tregs). In DSS-induced colitis, conventional mice suffered severe inflammation accompanied by loss of colonic crypts. These symptoms were absent in CS mice. In conventional, but not CS mice, bulk RNAseq analysis of the colon revealed an increase in inflammatory and Th17-related gene signatures. C. sporogenes -derived IPA reduced IL-17A protein expression by suppressing mTOR activity and by altering ribosome-related pathways in Th17 cells. Additionally, BCFAs and SCFAs generated by C. sporogenes enhanced the activity of Tregs and increased the production of IL-22, which led to protection from colitis. Collectively, we identified C. sporogenes as a therapeutically relevant probiotic bacterium that might be employed in patients with inflammatory bowel disease (IBD).

Acinetobacter baumannii is an antibiotic-resistant, Gram-negative pathogen that causes a multitude of nosocomial infections. However, pathogenicity mechanisms and the host cell response during infection remain unclear. In this study, we determined virulence traits of A. baumannii clinical isolates belonging to the most widely disseminated international clonal lineage, international cluster 2 (IC2), in vitro and in vivo . Complexome profiling of primary human endothelial cells with A. baumannii revealed that mitochondria, and in particular complexes of the electron transport chain, are important host cell targets. Infection with highly virulent A. baumannii remodelled assembly of mitochondrial protein complexes and led to metabolic adaptation. These were characterized by reduced mitochondrial respiration and glycolysis in contrast to those observed in infection with low-pathogenicity A. baumannii. Perturbation of oxidative phosphorylation, destabilization of mitochondrial ribosomes, and interference with mitochondrial metabolic pathways were identified as important pathogenicity mechanisms. Understanding the interaction of human host cells with the current global A. baumannii clone is the basis to identify novel therapeutic targets. IMPORTANCE Virulence traits of Acinetobacter baumannii isolates of the worldwide most prevalent international clonal lineage, IC2, remain largely unknown. In our study, multidrug-resistant IC2 clinical isolates differed substantially in their virulence potential despite their close genetic relatedness. Our data suggest that, at least for some isolates, mitochondria are important target organelles during infection of primary human endothelial cells. Complexes of the respiratory chain were extensively remodelled after infection with a highly virulent A. baumannii strain, leading to metabolic adaptation characterized by severely reduced respiration and glycolysis. Perturbations of both mitochondrial morphology and mitoribosomes were identified as important pathogenicity mechanisms. Our data might help to further decipher the molecular mechanisms of A. baumannii and host mitochondrial interaction during infection., Competing Interests: The authors declare no conflict of interest.

The ISTEM mode for TEM has been demonstrated to have several advantages in regard to resolution and precision. While previous works primarily focussed on the advantages due to the reduced spatial coherence, the actual image contrast, i.e. how bright or dark certain atom columns are imaged, has mostly been of secondary concern. The present work sets out to achieve the contrast of annular bright field STEM in ISTEM, producing the high contrast of light elements, for which this method is popular. It is shown from theoretical considerations that using an annular condenser aperture this aim can be realised. The optimal size of this aperture is found by simulative studies. It is then manufactured from platinum foil and installed in an image-aberration corrected microscope. ABF-like ISTEM images of strontium titanate in [100] projection are acquired. The pure oxygen columns are clearly resolved with significant contrast. The image pattern is indeed identical to what is achieved by ABF STEM. A close look at the image formation also shows that the dose needed for a given signal-to-noise ratio is at least a quarter smaller for ABF-like ISTEM compared to ABF STEM, assuming detectors of similar detective quantum efficiency., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Increased lactate levels in the tissue microenvironment are a well-known feature of chronic inflammation. However, the role of lactate in regulating T cell function remains controversial. Here, we demonstrate that extracellular lactate predominantly induces deregulation of the Th17-specific gene expression program by modulating the metabolic and epigenetic status of Th17 cells. Following lactate treatment, Th17 cells significantly reduced their IL-17A production and upregulated Foxp3 expression through ROS-driven IL-2 secretion. Moreover, we observed increased levels of genome-wide histone H3K18 lactylation, a recently described marker for active chromatin in macrophages, in lactate-treated Th17 cells. In addition, we show that high lactate concentrations suppress Th17 pathogenicity during intestinal inflammation in mice. These results indicate that lactate is capable of reprogramming pro-inflammatory T cell phenotypes into regulatory T cells., (© 2022 The Authors.)

In this paper we perform angular resolved annular-dark field (ADF) scanning-transmission electron microscopy (STEM) to study the scattered intensity in an InGaN layer buried in GaN as a function of the scattering angle. We achieved angular resolution with a motorized iris aperture in front of the ADF detector. Using this setup, we investigated how the intensities measured in various angular ranges agree with multislice simulations in the frozen-lattice approximation. We observed a strong influence of relaxation induced surface-strain fields on the ADF intensity, measured its angular characteristics and compared the result with simulations. To assess the agreement of the measured intensity with simulations, we evaluated the specimen thickness in GaN and the indium concentration in InGaN for each angular interval by comparing the measured intensities with simulations. The thickness was strongly overestimated for scattering angles below 40mrad and also the evaluated indium concentration varies with the considered angular range. Using simulations, we investigated which angular ranges show a high sensitivity to variations of the thickness and which intervals strongly depend on the indium concentration. By combining two angular intervals, the indium concentration and the specimen thickness were determined simultaneously, which has potential advantages over the usual quantification method. It is shown that inelastic scattering, surface contamination and mistilt can have an influence on the measured intensity, especially at lower scattering angles below 30-50mrad, which might explain the observed difference between the frozen lattice simulation and the experiment., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The measurement of electric fields in scanning transmission electron microscopy (STEM) is a highly investigated field of research. The constant improvement of spatial resolution in STEM and the development of new hardware for the fast acquisition of diffraction patterns even paved the way for the measurement of atomic electric fields. Although the basic principle that an electric field leads to a tilt of the focussed electron probe that can be detected as a shift of the diffraction pattern in the back focal plane of the objective lens seems quite simple, many challenges arose in the measurement of fields in a quantitative way. In the present study we investigate whether a shift of the diffraction pattern that occurs at an interface between two materials can be related to the electric field which is caused by the difference of the mean inner potentials of the two materials. To this end, experiments and simulations are compared. It is demonstrated that the difference in mean inner potential has an influence on the observed effect, but a quantitative interpretation is difficult. The influence of image recording effects such as shot noise and the modulation transfer function are investigated as well as further effects such as e.g. sample tilt. In addition, the influence of the observed effect on a strain measurement is shown., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The participation of proteasomes in vital cellular and metabolic processes that are involved in tumor growth has made this protease complex an attractive target for cancer treatment. In contrast to ubiquitously available constitutive proteasome, the increased enzymatic activity of immunoproteasome is associated with tumor-infiltrating immune cells, such as antigen-presenting cells and T lymphocytes. In various tumors, an effective anti-tumor immunity is provided through generation of tumor-associated antigens by proteasomes, contributing crucially to cancer eradication by T lymphocytes. The knowledge regarding the role of immunoproteasomes in the communication between tumor cells and infiltrating immune cells is limited. Novel data suggest that the involvement of immunoproteasomes in tumorigenesis is more complex than previously thought. In the intestine, in which diverse signals from commensal bacteria and food can contribute to the onset of chronic inflammation and inflammation-driven cancer, immunoproteasomes exert tumorigenic properties by modulating the expression of pro-inflammatory factors. In contrast, in melanoma and non-small cell lung cancer, the immunoproteasome acts against cancer development by promoting an effective anti-tumor immunity. In this review, we highlight the potential of immunoproteasomes to either contribute to inflammatory signaling and tumor development, or to support anti-cancer immunity. Further, we discuss novel therapeutic options for cancer treatments that are associated with modulating the activity of immunoproteasomes in the tumor microenvironment., (© 2022. The Author(s).)

4D-scanning transmission electron microscopy (4D-STEM) can be used to measure electric fields such as atomic fields or polarization-induced electric fields in crystal heterostructures. The paper focuses on effects occurring in 4D-STEM at interfaces, where two model systems are used: an AlN/GaN nanowire superlattice as well as a GaN/vacuum interface. Two different methods are applied: First, we employ the centre-of mass (COM) technique which uses the average momentum transfer evaluated from the intensity distribution in the diffraction pattern. Second, we measure the shift of the undiffracted disc (disc-detection method) in nano-beam electron diffraction (NBED). Both methods are applied to experimental and simulated 4D-STEM data sets. We find for both techniques distinct variations in the momentum transfer at interfaces between materials: In both model systems, peaks occur at the interfaces and we investigate possible sources and routes of interpretation. In case of the AlN/GaN superlattice, the COM and disc-detection methods are used to measure internal polarization-induced electric fields and we observed a reduction of the measured fields with increasing specimen thickness., (Copyright © 2021 Elsevier B.V. All rights reserved.)

In this paper we study the effect of lens aberrations (spherical aberration and astigmatism), beam tilt, contamination and shot noise on the accuracy and precision of position determination in imaging scanning transmission electron microscopy (ISTEM) on the example of BaTiO 3 . ISTEM images are simulated as a function of sample thickness and defocus starting from a nearly perfect microscope setting. A defocus range was identified, in which atom column positions were reliably visible and could be decently measured. By averaging over this defocus and thickness range a figure of merit was defined and used to study the influence of above mentioned disturbing effects as a function of their strength. It turned out that column positions might become inaccurate, but distances are measured accurately. These were used to obtain recommendations for the experimental setup to measure the atomic arrangement that induces ferroelectric switching of BaTiO 3 ., (Copyright © 2021 Elsevier B.V. All rights reserved.)

OXA-48-like carbapenemases are among the most frequent carbapenemases in Gram-negative Enterobacterales worldwide with the highest prevalence in the Middle East, North Africa and Europe. Here, we investigated the so far uncharacterized carbapenemase OXA-484 from a clinical E. coli isolate belonging to the high-risk clone ST410 regarding antibiotic resistance pattern, horizontal gene transfer (HGT) and genetic support. OXA-484 differs by the amino acid substitution 214G compared to the most closely related variants OXA-181 (214R) and OXA-232 (214S). The bla OXA - 484 was carried on a self-transmissible 51.5 kb IncX3 plasmid (pOXA-484) showing high sequence similarity with plasmids harboring bla OXA - 181 . Intraspecies and intergenus HGT of pOXA-484 to different recipients occurred at low frequencies of 1.4 × 10 -7 to 2.1 × 10 -6 . OXA-484 increased MICs of temocillin and carbapenems similar to OXA-232 and OXA-244, but lower compared with OXA-48 and OXA-181. Hence, OXA-484 combines properties of OXA-181-like plasmid support and transferability as well as β-lactamase activity of OXA-232., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Sommer, Gerbracht, Krause, Wild, Tietgen, Riedel-Christ, Sattler, Hamprecht, Kempf and Göttig.)

Modern quantitative TEM methods such as the ζ-factor technique require precise knowledge of the electron beam current. To this end, a macroscopic Faraday cup was designed and constructed. It can replace the viewing screen in the projection chamber of a TEM and guarantees highly accurate measurement of the electron beam with precision only limited by the used amperemeter. The easy to install, affordable device is shown to be highly apt for precision measurement of currents >5pA. The Faraday cup results are used for an assessment and a comparison of various other beam current measurement methods. It is found that the built-in screen amperemeter of the used TEM is quite inaccurate and that measurements using the screen in general tend to underestimate the current. If present, the drift tube of a spectrometer can also be used as a Faraday cup, but certain described peculiarities have to be taken into account. Direct ultrafast electron detection cameras allow precise measurement at very small currents. For the electron counting technique, which exploits single electron detection capabilities of STEM detectors, a systematic current underestimation was observed and investigated. This results in a reformulated routine for the method and with these improvements it is demonstrated to be capable of accurate high-precision measurements for currents <5pA., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The angle-resolved electron scattering is investigated in scanning-transmission electron microscopy (STEM) using a motorised iris aperture placed above a conventional annular detector. The electron intensity scattered into various angle ranges is compared with simulations that were carried out in the frozen-lattice approximation. As figure of merit for the agreement of experiment and simulation we evaluate the specimen thickness which is compared with the thickness obtained from position-averaged convergent beam electron diffraction (PACBED). We find deviations whose strengths depend on the angular range of the detected electrons. As possible sources of error we investigate, for example, the influences of amorphous surface layers, inelastic scattering (plasmon excitation), phonon-correlation within the frozen-lattice approach, and distortions in the diffraction plane of the microscope. The evaluation is performed for four experimental thicknesses and two angle-resolved STEM series under different camera lengths. The results clearly show that especially for scattering angles below 50 mrad, it is mandatory that the simulations take scattering effects into account which are usually neglected for simulating high-angle scattering. Most influences predominantly affect the low-angle range, but also high scattering angles can be affected (e.g. by amorphous surface covering)., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Strain analysis by nano-beam electron diffraction allows for measurements of strain with nanometre resolution in a large field of view. This is done by evaluating distances between diffraction discs in diffraction patterns acquired while a focussed electron beam is scanned across the sample in a transmission electron microscope. The bottleneck of this method is a precise determination of diffraction disc positions, which suffers from the inner structure of the discs caused by dynamical diffraction. Electron beam precession is a tool that solves this problem but it is not commonly available in every microscope. Without precession significant progress has been reported recently by using patterned condenser apertures. The pattern of the aperture is reproduced in patterns of the diffraction discs allowing for a more precise position determination. In this report the accuracy of measured strain profiles using patterned apertures is investigated by evaluation of realistic simulations. This is done especially at interfaces between regions with different lattice plane spacing. It is found by evaluation of the simulations that measured strain profiles are more blurred and hence the accuracy at the interface is worse the more patterns are imprinted to the condenser aperture. An explanation of this effect is given and as a proof of principle a solution to this problem is provided applying geometric phase analysis ptychography., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Scanning transmission electron microscopy (STEM) allows to gain quantitative information on the atomic-scale structure and composition of materials, satisfying one of todays major needs in the development of novel nanoscale devices. The aim of this study is to quantify the impact of inelastic, i.e. plasmon excitations (PE), on the angular dependence of STEM intensities and answer the question whether these excitations are responsible for a drastic mismatch between experiments and contemporary image simulations observed at scattering angles below [Formula: see text] 40 mrad. For the two materials silicon and platinum, the angular dependencies of elastic and inelastic scattering are investigated. We utilize energy filtering in two complementary microscopes, which are representative for the systems used for quantitative STEM, to form position-averaged diffraction patterns as well as atomically resolved 4D STEM data sets for different energy ranges. The resulting five-dimensional data are used to elucidate the distinct features in real and momentum space for different energy losses. We find different angular distributions for the elastic and inelastic scattering, resulting in an increased low-angle intensity ([Formula: see text] 10-40 mrad). The ratio of inelastic/elastic scattering increases with rising sample thickness, while the general shape of the angular dependency is maintained. Moreover, the ratio increases with the distance to an atomic column in the low-angle regime. Since PE are usually neglected in image simulations, consequently the experimental intensity is underestimated at these angles, which especially affects bright field or low-angle annular dark field imaging. The high-angle regime, however, is unaffected. In addition, we find negligible impact of inelastic scattering on first-moment imaging in momentum-resolved STEM, which is important for STEM techniques to measure internal electric fields in functional nanostructures. To resolve the discrepancies between experiment and simulation, we present an adopted simulation scheme including PE. This study highlights the necessity to take into account PE to achieve quantitative agreement between simulation and experiment. Besides solving the fundamental question of missing physics in established simulations, this finally allows for the quantitative evaluation of low-angle scattering, which contains valuable information about the material investigated.

OXA-48 is the most common carbapenemase in Enterobacterales in Germany and one of the most frequent carbapenemases worldwide. Several reports have associated bla OXA - 48 with a virulent host phenotype. To challenge this hypothesis, 35 OXA-48-producing clinical isolates of Escherichia coli ( n = 15) and Klebsiella pneumoniae ( n = 20) were studied in vitro , in vivo employing the Galleria mellonella infection model and by whole-genome sequencing. Clinical isolates belonged to 7 different sequence types (STs) in E. coli and 12 different STs in K. pneumoniae . In 26/35 isolates bla OXA- 48 was located on a 63 kb IncL plasmid. Horizontal gene transfer (HGT) to E. coli J53 was high in isolates with the 63 kb IncL plasmid (transconjugation frequency: ∼10 3 /donor) but low in isolates with non-IncL plasmids (<10 -6 /donor). Several clinical isolates were both highly cytotoxic against human cells and virulent in vivo . However, 63 kb IncL transconjugants generated from these highly virulent isolates were not more cytotoxic or virulent when compared to the recipient strain. Additionally, no genes associated with virulence were detected by in silico analysis of OXA-48 plasmids. The 63 kb plasmid was highly stable and did not impair growth or fitness in E. coli J53. In conclusion, OXA-48 clinical isolates in Germany are diverse but typically harbor the same 63 kb IncL plasmid which has been reported worldwide. We demonstrate that this 63 kb IncL plasmid has a low fitness burden, high plasmid stability and can be transferred by highly efficient HGT which is likely the cause of the rapid dissemination of OXA-48 rather than the expansion of a single clone or gain of virulence., (Copyright © 2019 Hamprecht, Sommer, Willmann, Brender, Stelzer, Krause, Tsvetkov, Wild, Riedel-Christ, Kutschenreuter, Imirzalioglu, Gonzaga, Nübel and Göttig.)

This study addresses the comparison of scanning transmission electron microscopy (STEM) measurements of momentum transfers using the first moment approach and the established method that uses segmented annular detectors. Using an ultrafast pixelated detector to acquire four-dimensional, momentum-resolved STEM signals, both the first moment calculation and the calculation of the differential phase contrast (DPC) signals are done for the same experimental data. In particular, we investigate the ability to correct the segment-based signal to yield a suitable approximation of the first moment for cases beyond the weak phase object approximation. It is found that the measurement of momentum transfers using segmented detectors can approach the first moment measurement as close as 0.13 h/nm in terms of a root mean square (rms) difference in 10 nm thick SrTiO 3 for a detector with 16 segments. This amounts to 35% of the rms of the momentum transfers. In addition, we present a statistical analysis of the precision of first moment STEM as a function of dose. For typical experimental settings with recent hardware such as a Medipix3 Merlin camera attached to a probe-corrected STEM, we find that the precision of the measurement of momentum transfers stagnates above certain doses. This means that other instabilities such as specimen drift or scan noise have to be taken into account seriously for measurements that target, e.g., the detection of bonding effects in the charge density., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Images acquired in transmission electron microscopes can be distorted for various reasons such as e.g. aberrations of the lenses of the imaging system or inaccuracies of the image recording system. This results in inaccuracies of measures obtained from the distorted images. Here we report on measurement and correction of elliptical distortions of diffraction patterns. The effect of this correction on the measurement of crystal lattice strain is investigated. We show that the effect of the distortions is smaller than the precision of the measurement in cases where the strain is obtained from shifts of diffracted discs with respect to their positions in images acquired in an unstrained reference area of the sample. This can be explained by the fact that diffraction patterns acquired in the strain free reference area of the sample are distorted in the same manner as the diffraction patterns acquired in the strained region of interest. In contrast, for samples without a strain free reference region such as nanoparticles or nanoporous structures, where we evaluate ratios of lattice plane distances along different directions, the distortions are usually not negligible. Furthermore, two techniques for the detection of diffraction disc positions are compared showing that for samples in which the crystal orientation changes over the investigated area it is more precise to detect the positions of many diffraction discs simultaneously instead of detecting each disc position independently., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Strain analyses from experimental series of nano-beam electron diffraction (NBED) patterns in scanning transmission electron microscopy are performed for different specimen tilts. Simulations of NBED series are presented for which strain analysis gives results that are in accordance with experiment. This consequently allows to study the relation between measured strain and actual underlying strain. A two-tilt method which can be seen as lowest-order electron beam precession is suggested and experimentally implemented. Strain determination from NBED series with increasing beam convergence is performed in combination with the experimental realization of a probe-forming aperture with a cross inside. It is shown that using standard evaluation techniques, the influence of beam convergence on spatial resolution is lower than the influence of sharp rings around the diffraction disc which occur at interfaces and which are caused by the tails of the intensity distribution of the electron probe., (Copyright © 2018 Elsevier B.V. All rights reserved.)

For simulation of transmission electron microscopic images and diffraction patterns, the accurate inclusion of thermal diffuse scattering by phonons is important. In the frozen phonon multislice algorithm, this is possible, if thermal displacements according to the realistic, quantum mechanical distribution can be generated. For pure crystals, quantum mechanical calculations based on DFT yield those displacements. But for alloys one is usually restricted to the Einstein approximation, where correlations between atoms are neglected. In this article, molecular dynamics simulations are discussed and used as an alternative method for displacement calculation. Employing an empirical Stillinger-Weber type potential, classical motion is used as an approximation for the quantum mechanical dynamics. Thereby, correlations and possible static atomic displacements are inherently included. An appropriate potential is devised for AlGaN by fitting to force constant matrices determined from DFT and elastic constants of AlN and GaN. A comparison shows that the empiric potential reproduces phonon dispersions and displacement expectations from DFT references. The validity for alloys is successfully demonstrated by comparison to DFT calculations in special quasirandom structures. Subsequently, molecular dynamics were used in multislice simulations of both conventional and scanning TEM images. The resulting images are in very good agreement with DFT based calculations, while a slight yet significant deviation from Einstein approximation results can be seen, which can be attributed to the neglect of correlations in the latter. The presented potential hence proves to be a useful tool for accurate TEM simulations of AlGaN alloys., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Ultrathin bimetallic nanowires are of importance and interest for applications in electronic devices such as sensors and heterogeneous catalysts. In this work, we have designed a new, highly reproducible and generalized wet chemical method to synthesize uniform and monodispersed Au-based alloy (AuCu, AuPd, and AuPt) nanowires with tunable composition using microwave-assisted reduction at the liquid-liquid interface. These ultrathin alloy nanowires are below 4 nm in diameter and about 2 μm long. Detailed microstructural characterization shows that the wires have an face centred cubic (FCC) crystal structure, and they have low-energy twin-boundary and stacking-fault defects along the growth direction. The wires exhibit remarkable thermal and mechanical stability that is critical for important applications. The alloy wires exhibit excellent electrocatalytic activity for methanol oxidation in an alkaline medium.

The chemical composition of four Si 1-x Ge x layers grown on silicon was determined from quantitative scanning transmission electron microscopy (STEM). The chemical analysis was performed by a comparison of the high-angle annular dark field (HAADF) intensity with multislice simulations. It could be shown that amorphous surface layers originating from the preparation process by focused-ion beam (FIB) at 30 kV have a strong influence on the quantification: the local specimen thickness is overestimated by approximately a factor of two, and the germanium concentration is substantially underestimated. By means of simulations, the effect of amorphous surface layers on the HAADF intensity of crystalline silicon and germanium is investigated. Based on these simulations, a method is developed to analyze the experimental HAADF-STEM images by taking the influence of the amorphous layers into account which is done by a reduction of the intensities by multiplication with a constant factor. This suggested modified HAADF analysis gives germanium concentrations which are in agreement with the nominal values. The same TEM lamella was treated with low-voltage ion milling which removed the amorphous surface layers completely. The results from subsequent quantitative HAADF analyses are in agreement with the nominal concentrations which validates the applicability of the used frozen-lattice based multislice simulations to describe the HAADF scattering of Si 1-x Ge x in STEM., (Copyright © 2017 Elsevier B.V. All rights reserved.)

In this work, we analyse the microstructure and local chemical composition of green-emitting In x Ga 1- x N/GaN quantum well (QW) heterostructures in correlation with their emission properties. Two samples of high structural quality grown by metalorganic vapour phase epitaxy (MOVPE) with a nominal composition of x = 0.15 and 0.18 indium are discussed. The local indium composition is quantitatively evaluated by comparing scanning transmission electron microscopy (STEM) images to simulations and the local indium concentration is extracted from intensity measurements. The calculations point out that the measured indium fluctuations may be correlated to the large width and intensity decrease of the PL emission peak., (© 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.)

A relatively simple yet accurate analytical model for the image formation in the imaging scanning TEM (ISTEM) imaging mode, which implements partial spatial incoherence using a combination of scanning illumination and conventional imaging, is presented. Based on an object function approximation the ISTEM intensity can be divided into a constant, a linear and a nonlinear term. Under certain conditions, which are discussed, the formation of both linear and nonlinear terms can be expressed by convolutions with point spread functions. A closer inspection of these allows an insight into the advantages of ISTEM compared to conventional TEM (CTEM). The findings of the proposed model are confirmed by comparison to multislice simulations. A close investigation of the linear coherent contrast transfer function allows the derivation of optimal imaging conditions to reach a maximum resolution for a given signal-to-noise ratio. The robustness of ISTEM towards temporal incoherence is finally demonstrated and discussed within the model., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Nano-beam electron diffraction (NBED) is a method which can be applied to measure lattice strain and polarisation fields in strained layer heterostructures and transistors. To investigate precision, accuracy and spatial resolution of such measurements in dependence of properties of the specimen as well as electron optical parameters, simulations of NBED patterns are required which allow to predict the result of common disc-detection algorithms. In this paper we demonstrate by focusing on the detection of the central disc in crystalline silicon that such simulations require to take several experimental characteristics into account in order to obtain results which are comparable to those from experimental NBED patterns. These experimental characteristics are the background intensity, the presence of Poisson noise caused by electron statistics and blurring caused by inelastic scattering and by the transfer quality of the microscope camera. By means of these optimized simulations, different effects of specimen properties on disc detection - such as strain, surface morphology and compositional changes on the nanometer scale - are investigated and discussed in the context of misinterpretation in experimental NBED evaluations. It is shown that changes in surface morphology and chemical composition lead to measured shifts of the central disc in the NBED pattern of tens to hundreds of µrad. These shifts are of the same order of magnitude or even larger than shifts that could be caused by an electric polarisation field in the range of MV/cm., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Nowadays, aberration corrected transmission electron microscopy (TEM) is a popular method to characterise nanomaterials at the atomic scale. Here, atomically resolved images of nanomaterials are acquired, where the contrast depends on the illumination, imaging and detector conditions of the microscope. Visualization of light elements is possible when using low angle annular dark field (LAADF) STEM, annular bright field (ABF) STEM, integrated differential phase contrast (iDPC) STEM, negative spherical aberration imaging (NCSI) and imaging STEM (ISTEM). In this work, images of a NdGaO 3 -La 0.67 Sr 0.33 MnO 3 (NGO-LSMO) interface are quantitatively evaluated by using statistical parameter estimation theory. For imaging light elements, all techniques are providing reliable results, while the techniques based on interference contrast, NCSI and ISTEM, are less robust in terms of accuracy for extracting heavy column locations. In term of precision, sample drift and scan distortions mainly limits the STEM based techniques as compared to NCSI. Post processing techniques can, however, partially compensate for this. In order to provide an outlook to the future, simulated images of NGO, in which the unavoidable presence of Poisson noise is taken into account, are used to determine the ultimate precision. In this future counting noise limited scenario, NCSI and ISTEM imaging will provide more precise values as compared to the other techniques, which can be related to the mechanisms behind the image recording., (Copyright © 2017 Elsevier B.V. All rights reserved.)

In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined., (Copyright © 2016 Elsevier B.V. All rights reserved.)

This paper addresses a novel approach to atomic resolution elemental mapping, demonstrating a method that produces elemental maps with a similar resolution to the established method of electron energy-loss spectroscopy in scanning transmission electron microscopy. Dubbed energy-filtered imaging scanning transmission electron microscopy (EFISTEM) this mode of imaging is, by the quantum mechanical principle of reciprocity, equivalent to tilting the probe in energy-filtered transmission electron microscopy (EFTEM) through a cone and incoherently averaging the results. In this paper we present a proof-of-principle EFISTEM experimental study on strontium titanate. The present approach, made possible by chromatic aberration correction, has the advantage that it provides elemental maps which are immune to spatial incoherence in the electron source, coherent aberrations in the probe-forming lens and probe jitter. The veracity of the experiment is supported by quantum mechanical image simulations, which provide an insight into the image-forming process. Elemental maps obtained in EFTEM suffer from the effect known as preservation of elastic contrast, which, for example, can lead to a given atomic species appearing to be in atomic columns where it is not to be found. EFISTEM very substantially reduces the preservation of elastic contrast and yields images which show stability of contrast with changing thickness. The experimental application is demonstrated in a proof-of-principle study on strontium titanate., (Copyright © 2017 Elsevier B.V. All rights reserved.)

This study sheds light on the prerequisites, possibilities, limitations and interpretation of high-resolution differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). We draw particular attention to the well-established DPC technique based on segmented annular detectors and its relation to recent developments based on pixelated detectors. These employ the expectation value of the momentum transfer as a reliable measure of the angular deflection of the STEM beam induced by an electric field in the specimen. The influence of scattering and propagation of electrons within the specimen is initially discussed separately and then treated in terms of a two-state channeling theory. A detailed simulation study of GaN is presented as a function of specimen thickness and bonding. It is found that bonding effects are rather detectable implicitly, e.g., by characteristics of the momentum flux in areas between the atoms than by directly mapping electric fields and charge densities. For strontium titanate, experimental charge densities are compared with simulations and discussed with respect to experimental artifacts such as scan noise. Finally, we consider practical issues such as figures of merit for spatial and momentum resolution, minimum electron dose, and the mapping of larger-scale, built-in electric fields by virtue of data averaged over a crystal unit cell. We find that the latter is possible for crystals with an inversion center. Concerning the optimal detector design, this study indicates that a sampling of 5mrad per pixel is sufficient in typical applications, corresponding to approximately 10×10 available pixels., (Copyright © 2016 Elsevier B.V. All rights reserved.)

A concise derivation of the principle of reciprocity applied to realistic transmission electron microscopy setups is presented making use of the multislice formalism. The equivalence of images acquired in conventional and scanning mode is thereby rigorously shown. The conditions for the applicability of the found reciprocity relations is discussed. Furthermore the positions of apertures in relation to the corresponding lenses are considered, a subject which scarcely has been addressed in previous publications., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Recently, imaging scanning transmission electron microscopy (ISTEM) has been proposed as a promising new technique combining the advantages of conventional TEM (CTEM) and STEM (Rosenauer et al., 2014 [1]). The ability to visualize light and heavy elements together makes it a particularly interesting new, spatially incoherent imaging mode. Here, we evaluate this technique in term of precision with which atomic column locations can be measured. By using statistical parameter estimation theory, we will show that these locations can be accurately measured with a precision in the picometer range. Furthermore, a quantitative comparison is made with HAADF STEM imaging to investigate the advantages of ISTEM., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Solid-state properties such as strain or chemical composition often leave characteristic fingerprints in the angular dependence of electron scattering. Scanning transmission electron microscopy (STEM) is dedicated to probe scattered intensity with atomic resolution, but it drastically lacks angular resolution. Here we report both a setup to exploit the explicit angular dependence of scattered intensity and applications of angle-resolved STEM to semiconductor nanostructures. Our method is applied to measure nitrogen content and specimen thickness in a GaN x As 1-x layer independently at atomic resolution by evaluating two dedicated angular intervals. We demonstrate contrast formation due to strain and composition in a Si- based metal-oxide semiconductor field effect transistor (MOSFET) with Ge x Si 1-x stressors as a function of the angles used for imaging. To shed light on the validity of current theoretical approaches this data is compared with theory, namely the Rutherford approach and contemporary multislice simulations. Inconsistency is found for the Rutherford model in the whole angular range of 16-255 mrad. Contrary, the multislice simulations are applicable for angles larger than 35 mrad whereas a significant mismatch is observed at lower angles. This limitation of established simulations is discussed particularly on the basis of inelastic scattering.

Nitride-based three-dimensional core-shell nanorods (NRs) are promising candidates for the achievement of highly efficient optoelectronic devices. For a detailed understanding of the complex core-shell layer structure of InGaN/GaN NRs, a systematic determination and correlation of the structural, compositional, and optical properties on a nanometer-scale is essential. In particular, the combination of low-temperature cathodoluminescence (CL) spectroscopy directly performed in a scanning transmission electron microscope (STEM), and quantitative high-angle annular dark field imaging enables a comprehensive study of the nanoscopic attributes of the individual shell layers. The investigated InGaN/GaN core-shell NRs, which were grown by metal-organic vapor-phase epitaxy using selective-area growth exhibit an exceptionally low density of extended defects. Using highly spatially resolved CL mapping of single NRs performed in cross-section, we give a direct insight into the optical properties of the individual core-shell layers. Most interesting, we observe a red shift of the InGaN single quantum well from 410 to 471 nm along the nonpolar side wall. Quantitative STEM analysis of the active region reveals an increasing thickness of the single quantum well (SQW) from 6 to 13 nm, accompanied by a slight increase of the indium concentration along the nonpolar side wall from 11% to 13%. Both effects, the increased quantum-well thickness and the higher indium incorporation, are responsible for the observed energetic shift of the InGaN SQW luminescence. Furthermore, compositional mappings of the InGaN quantum well reveal the formation of locally indium rich regions with several nanometers in size, leading to potential fluctuations in the InGaN SQW energy landscape. This is directly evidenced by nanometer-scale resolved CL mappings that show strong localization effects of the excitonic SQW emission.

Several instrumental imperfections of transmission electron microscopes are characterized and their effects on the results of quantitative scanning electron microscopy (STEM) are investigated and quantified using simulations. Methods to either avoid influences of these imperfections during acquisition or to include them in reference calculations are proposed. Particularly, distortions inflicted on the diffraction pattern by an image-aberration corrector can cause severe errors of more than 20% if not accounted for. A procedure for their measurement is proposed here. Furthermore, afterglow phenomena and nonlinear behavior of the detector itself can lead to incorrect normalization of measured intensities. Single electrons accidentally impinging on the detector are another source of error but can also be exploited for threshold-less calibration of STEM images to absolute dose, incident beam current determination and measurement of the detector sensitivity., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The determination of atom positions from atomically resolved transmission electron micrographs is fundamental for the analysis of crystal defects and strain. In recent years annular bright-field (ABF) imaging has become a popular imaging technique owing to its ability to map both light and heavy elements. Contrast formation in ABF is partially governed by the phase of the electron wave, which renders the technique more sensitive to the tilt of the electron beam with respect to the crystal zone axis than high-angle annular dark-field imaging. Here we show this sensitivity experimentally and use image simulations to quantify this effect. This is essential for error estimation in future quantitative ABF studies., (Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)

Measurement of lattice strain is important to characterize semiconductor nanostructures. As strain has large influence on the electronic band structure, methods for the measurement of strain with high precision, accuracy and spatial resolution in a large field of view are mandatory. In this paper we present a theoretical study of precision and accuracy of measurement of strain by convergent nano-beam electron diffraction. It is found that the accuracy of the evaluation suffers from halos in the diffraction pattern caused by a variation of strain within the area covered by the focussed electron beam. This effect, which is expected to be strong at sharp interfaces between materials with different lattice plane distances, will be discussed for convergent-beam electron diffraction patterns using a conventional probe and for patterns formed by a precessing electron beam. Furthermore, we discuss approaches to optimize the accuracy of strain measured at interfaces. The study is based on the evaluation of diffraction patterns simulated for different realistic structures that have been investigated experimentally in former publications. These simulations account for thermal diffuse scattering using the frozen-lattice approach and the modulation-transfer function of the image-recording system. The influence of Poisson noise is also investigated., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The electronic properties of quaternary AlInGaN devices significantly depend on the homogeneity of the alloy. The identification of compositional fluctuations or verification of random-alloy distribution is hence of grave importance. Here, a comprehensive multiprobe study of composition and compositional homogeneity is presented, investigating AlInGaN layers with indium concentrations ranging from 0 to 17at% and aluminium concentrations between 0 and 39 at% employing high-angle annular dark field scanning electron microscopy (HAADF STEM), energy dispersive X-ray spectroscopy (EDX) and atom probe tomography (APT). EDX mappings reveal distributions of local concentrations which are in good agreement with random alloy atomic distributions. This was hence investigated with HAADF STEM by comparison with theoretical random alloy expectations using statistical tests. To validate the performance of these tests, HAADF STEM image simulations were carried out for the case of a random-alloy distribution of atoms and for the case of In-rich clusters with nanometer dimensions. The investigated samples, which were grown by metal-organic vapor phase epitaxy (MOVPE), were thereby found to be homogeneous on this nanometer scale. Analysis of reconstructions obtained from APT measurements yielded matching results. Though HAADF STEM only allows for the reduction of possible combinations of indium and aluminium concentrations to the proximity of isolines in the two-dimensional composition space. The observed ranges of composition are in good agreement with the EDX and APT results within the respective precisions., (Copyright © 2015 Elsevier B.V. All rights reserved.)

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms.

In an earlier publication Rosenauer et al. introduced a method for determination of composition in AlGaN/GaN heterostructures from high-angle annular dark field (HAADF) images. Static atomic displacements (SADs) were neglected during simulation of reference data because of the similar covalent radii of Al and Ga. However, SADs have been shown (Grillo et al.) to influence the intensity in HAADF images and therefore could be the reason for an observed slight discrepancy between measured and nominal concentrations. In the present study parameters of the Stillinger-Weber potential were varied in order to fit computed elastic constants, lattice parameters and bonding energies to experimental ones. A reference data set of HAADF images was simulated, in which the new parameterization was used to account for SADs. Two reference samples containing AlGaN layers with different Al concentrations were investigated and Al concentrations in the layers determined based on the new data set. We found that these concentrations were in good agreement with nominal concentrations as well as concentrations determined using alternative techniques such as strain state analysis and energy dispersive X-ray spectroscopy.

There are mainly two complementary imaging modes in transmission electron microscopy (TEM): Conventional TEM (CTEM) and scanning TEM (STEM). In the CTEM mode the specimen is illuminated with a plane electron wave, and the direct image formed by the objective lens is recorded in the image plane. STEM is based on scanning the specimen surface with a focused electron beam and collecting scattered electrons with an extended disk or ring-shaped detector. Here we show that combination of CTEM imaging with STEM illumination generally allows extending the point resolution of CTEM imaging beyond the diffraction limit. This new imaging mode improves imaging characteristics, is more robust against chromatic aberration, exhibits direct structural imaging with superior precision, visualizes light elements with excellent contrast, and even allows us to overcome the conventional information limit of a microscope.

The Stobbs factor problem, a major difference of absolute contrast between experimental and simulated high resolution transmission electron microscopy images has been reported frequently. In this respect, some modifications to the multislice simulation techniques were proposed to improve the correspondence to the experiment. The influence of different suggestions on the simulated contrast is investigated by numerical simulations. The agreement between experiment and simulations is then checked by comparison with high-resolution micrographs of crystalline gold. The experimental data is therefore compared to simulated intensities computed for the thickness and orientation of the specimen measured by refinements of diffraction patterns. The agreement of both intensity and contrast is investigated and the remaining contrast discrepancy is determined. The results show a good agreement for a small objective aperture, while for a larger aperture a difference of contrast by a factor of 1.2 can still be observed. Without any aperture, the deviation between experiment and simulations is largest., (© 2013 Elsevier B.V. All rights reserved.)