Abstract: It is important to understand the effect of the interfaces between the oxide electrode layers and the ferroelectric layer on the polarization response for optimizing the device performance of all-oxide ferroelectric devices. Herein, the effects of the oxide La0.07Ba0.93SnO3 (LBSO) as an electrode material in an PbZr0.52Ti0.48O3 (PZT) ferroelectric capacitor are compared with those of the more commonly used SrRuO3 (SRO) electrode. SRO (top)/PZT/SRO (bottom), SRO/PZT/LBSO, and SRO/PZT/2 nm SRO/LBSO devices are fabricated. Only marginal differences in crystalline properties, determined by X-ray diffraction and scanning transmission electron microscopy, are found. High-quality polarization loops are obtained, but with a much larger coercive field for the SRO/PZT/LBSO device. In contrast to the SRO/PZT/SRO device, the polarization decreases strongly with increasing field cycling. This fatigue problem can be remedied by inserting a 2 nm SRO layer between PZT and LBSO. It is argued that strongly increased charge injection into the PZT occurs at the bottom interface, because of the low PZT/LBSO interfacial barrier and the much lower carrier density in LBSO, as compared with that in SRO, causing a low dielectric constant, depleted layer in LBSO. The charge injection creates a trapped space charge in the PZT, causing the difference in fatigue behavior.

Abstract: Fast pixelated detectors incorporating direct electron detection (DED) technology are increasingly being regarded as universal detectors for scanning transmission electron microscopy (STEM), capable of imaging under multiple modes of operation. However, several issues remain around the post-acquisition processing and visualization of the often very large multidimensional STEM datasets produced by them. We discuss these issues and present open source software libraries to enable efficient processing and visualization of such datasets. Throughout, we provide examples of the analysis methodologies presented, utilizing data from a 256 x 256 pixel Medipix3 hybrid DED detector, with a particular focus on the STEM characterization of the structural properties of materials. These include the techniques of virtual detector imaging; higher-order Laue zone analysis; nanobeam electron diffraction; and scanning precession electron diffraction. In the latter, we demonstrate a nanoscale lattice parameter mapping with a fractional precision <= 6 x 10(-4) (0.06%).

Abstract: Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge about the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.

Abstract: A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image.

Abstract: In this study, we explore the possibility to use deep learning for the reconstruction of phase images from 4D scanning transmission electron microscopy (4D-STEM) data. The process can be divided into two main steps. First, the complex electron wave function is recovered for a convergent beam electron diffraction pattern (CBED) using a convolutional neural network (CNN). Subsequently, a corresponding patch of the phase object is recovered using the phase object approximation. Repeating this for each scan position in a 4D-STEM dataset and combining the patches by complex summation yields the full-phase object. Each patch is recovered from a kernel of 3x3 adjacent CBEDs only, which eliminates common, large memory requirements and enables live processing during an experiment. The machine learning pipeline, data generation, and the reconstruction algorithm are presented. We demonstrate that the CNN can retrieve phase information beyond the aperture angle, enabling super-resolution imaging. The image contrast formation is evaluated showing a dependence on the thickness and atomic column type. Columns containing light and heavy elements can be imaged simultaneously and are distinguishable. The combination of super-resolution, good noise robustness, and intuitive image contrast characteristics makes the approach unique among live imaging methods in 4D-STEM.

Abstract: Previous reports on Poisson-Nernst-Planck (PNP) simulations of solid-state nanopores have focused on steady state behaviour under simplified boundary conditions. These are Neumann boundary conditions for the voltage at the pore walls, and in some cases also Donnan equilibrium boundary conditions for concentrations and voltages at both entrances of the nanopore. In this paper, we report time-dependent and steady state PNP simulations under less restrictive boundary conditions, including Neumann boundary conditions applied throughout the membrane relatively far away from the nanopore. We simulated ion currents through cylindrical and conical nanopores with several surface charge configurations, studying the spatial and temporal dependence of the currents contributed by each ion species. This revealed that, due to slow co-diffusion of oppositely charged ions, steady state is generally not reached in simulations or in practice. Furthermore, it is shown that ion concentration polarization is responsible for the observed limiting conductances and ion current rectification in nanopores with asymmetric surface charges or shapes. Hence, after more than a decade of collective research attempting to understand the nature of ion current rectification in solid-state nanopores, a relatively intuitive model is retrieved. Moreover, we measured and simulated current-voltage characteristics of rectifying silicon nitride nanopores presenting overlimiting conductances. The similarity between measurement and simulation shows that overlimiting conductances can result from the increased conductance of the electric double-layer at the membrane surface at the depletion side due to voltage-induced polarization charges.

Abstract: The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.

Abstract: Background
During normal pregnancy, placental oxidative stress (OS) is present during all three trimesters and is necessary to obtain normal cell function. However, if OS reaches a certain level, pregnancy complications might arise. In preeclampsia (PE), a dangerous pregnancy specific hypertensive disorder, OS induced in the ischemic placenta causes a systemic inflammatory response and activates maternal endothelial cells. In this study, we aimed to quantify superoxide concentrations (as a measure of systemic OS) using electron paramagnetic resonance (EPR) and correlate them to markers of systemic inflammation, iron status and vascular function.
Methods
Fifty-nine women with a healthy pregnancy (HP), 10 non-pregnant controls (NP) and 28 PE patients (32±3.3weeks) were included. During HP, blood samples for superoxide, neutrophil to lymphocyte ratio (NLR), mean platelet volume (MPV) and iron status were taken at 10, 25 and 39 weeks. Vascular measurements for arterial stiffness (carotid-femoral pulse wave velocity (CF-PWV), augmentation index (AIx), augmentation Pressure (AP)) and microvascular endothelial function (reactive hyperemia index (RHI)) were performed at 35 weeks. In PE, all measurements were performed at diagnosis. CMH (1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine) was used as spin probe for EPR, since the formed CM radical
corresponds to the amount of superoxide.
Results
Superoxide concentration remains stable during pregnancy (p = 0.92), but is significantly higher compared to the NP controls (p<0.0001). At 25 weeks, there is a significant positive correlation between superoxide and ferritin concentration. (p = 0.04) In PE, superoxide, systemic inflammation and iron status are much higher compared to HP (all p<0.001). During HP, superoxide concentrations correlate significantly with arterial stiffness (all p<0.04), while in PE superoxide is significantly correlated to microvascular endothelial function (p = 0.03).
Conclusions
During HP there is an increased but stable oxidative environment, which is correlated to ferritin concentration. If superoxide levels increase, there is an augmentation in arterial stiffness. In PE pregnancies, systemic inflammation and superoxide concentrations are higher and result in a deterioration of endothelial function. Together, these findings support the hypothesis that vascular function is directly linked to the amount of OS and that measurement of OS in combination with vascular function tests might be used in the prediction of PE.

Abstract: Globins occur in all kingdoms of life where they fulfill a wide variety of functions. In the past they used to be primarily characterized as oxygen transport/storage proteins, but since the discovery of new members of the globin family like neuroglobin and cytoglobin, more diverse and complex functions have been assigned to this heterogeneous family. Here we propose a function for a membrane-bound globin of C. elegans, GLB-26. This globin was predicted to be myristoylated at its N-terminus, a post-translational modification only recently described in the globin family. In vivo, this globin is found in the membrane of the head mesodermal cell and in the tail stomato-intestinal and anal depressor muscle cells. Since GLB-26 is almost directly oxidized when exposed to oxygen, we postulate a possible function as electron transfer protein. Phenotypical studies show that GLB-26 takes part in regulating the length of the defecation cycle in C. elegans under oxidative stress conditions.

Abstract: Energy-autonomous sewage treatment can be achieved if nitrogen (N) removal does not rely on organic carbon (∼chemical oxygen demand, COD), so that a maximum of the COD can be redirected to energy recovery. Shortcut N removal technologies such as partial nitritation/anammox and nitritation/denitritation are therefore essential, enabling carbon- and energy-lean nitrogen removal. In this study, a novel three-reactor pilot design was tested and consisted of a denitrification, an intermittent aeration, and an anammox tank. A vibrating sieve was added for differential sludge retention time (SRT) control. The 13 m3 pilot was operated on pre-treated sewage (A-stage effluent) at 12–24 °C. Selective suppression of unwanted nitrite-oxidizing bacteria over aerobic ammonium-oxidizing bacteria was achieved with strict floccular SRT management combined with innovative aeration control, resulting in a minimal nitrate production ratio of 17 ± 10%. Additionally, anoxic ammonium-oxidizing bacteria (AnAOB) activity could be maintained in the reactor for at least 150 days because of long granular SRT management and the anammox tank. Consequently, the COD/N removal ratio of 2.3 ± 0.7 demonstrated shortcut N removal almost three times lower than the currently applied nitrification/denitrification technology. The effluent total N concentrations of 17 ± 3 mg TN per L (at 21 ± 1 °C) and 17 ± 6 mg TN per L (at 15 ± 1 °C) were however too high for application at the sewage treatment plant Nieuwveer (Breda, The Netherlands). Corresponding N removal efficiencies were 52 ± 12% and 37 ± 21%, respectively. Further development should focus on redirecting more nitrite to AnAOB in the B-stage, exploring effluent-polishing options, or cycling nitrate for increased A-stage denitrification.

Abstract: The microstructural and compositional evolution during initial annealing of a superconducting (Bi,Pb)(2)Sr2Ca2Cu3O10+delta/Ag tape is studied using quantitative transmission electron microscopy. Special attention is devoted to the occurrence of Pb-rich liquids, which are crucial for the Bi2Sr2CaCu2O8+delta to (Bi,Pb)(2)Sr2Ca2Cu3O10+delta transformation. Ca and/or Pb-rich (Bi,Pb)(2)Sr2CaCu2O8+delta grains dissolve into a liquid, which reacts with Ca-rich phases to increase the liquid's Ca-content. This leads to (Bi,Pb)(2)Sr2Ca2Cu3O10+delta formation. Apparently, a Ca/Sr ratio of around I is sufficient to keep (Bi,Pb)(2)Sr2Ca2Cu3O10+delta nucleation going. It is confirmed that Ag particles are transported from the Ag-sheath into the oxide core by the liquid and not by mechanical treatment of the tape.

Abstract: The field of discrete tomography focuses on the reconstruction of samples that consist of only a few different materials. Ideally, a three-dimensional (3D) reconstruction of such a sample should contain only one grey level for each of the compositions in the sample. By exploiting this property in the reconstruction algorithm, either the quality of the reconstruction can be improved significantly, or the number of required projection images can be reduced. The discrete reconstruction typically contains fewer artifacts and does not have to be segmented, as it already contains one grey level for each composition. Recently, a new algorithm, called discrete algebraic reconstruction technique (DART), has been proposed that can be used effectively on experimental electron tomography datasets. In this paper, we propose discrete tomography as a general reconstruction method for electron tomography in materials science. We describe the basic principles of DART and show that it can be applied successfully to three different types of samples, consisting of embedded ErSi2 nanocrystals, a carbon nanotube grown from a catalyst particle and a single gold nanoparticle, respectively.

Abstract: Accurate segmentation of nanoparticles within various matrix materials is a difficult problem in electron tomography. Due to artifacts related to image series acquisition and reconstruction, global thresholding of reconstructions computed by established algorithms, such as weighted backprojection or SIRT, may result in unreliable and subjective segmentations. In this paper, we introduce the Partially Discrete Algebraic Reconstruction Technique (PDART) for computing accurate segmentations of dense nanoparticles of constant composition. The particles are segmented directly by the reconstruction algorithm, while the surrounding regions are reconstructed using continuously varying gray levels. As no properties are assumed for the other compositions of the sample, the technique can be applied to any sample where dense nanoparticles must be segmented, regardless of the surrounding compositions. For both experimental and simulated data, it is shown that PDART yields significantly more accurate segmentations than those obtained by optimal global thresholding of the SIRT reconstruction.

Abstract: In this work, the simultaneous iterative reconstruction technique (SIRT), the total variation minimization (TVM) reconstruction technique and the discrete algebraic reconstruction technique (DART) for electron tomography are compared and the advantages and disadvantages are discussed. Furthermore, we describe how the result of a three dimensional (3D) reconstruction based on TVM can provide objective information that is needed as the input for a DART reconstruction. This approach results in a tomographic reconstruction of which the segmentation is carried out in an objective manner.