Factors limiting quantitative phase retrieval in atomic-resolution differential phase contrast scanning transmission electron microscopy using a segmented detector.

Quantitative differential phase contrast imaging of materials in atomic-resolution scanning transmission electron microscopy using segmented detectors is limited by various factors, including coherent and incoherent aberrations, detector positioning and uniformity, and scan-distortion. By comparing experimental case studies of monolayer and few-layer graphene with image simulations, we explore which parameters require the most precise characterisation for reliable and quantitative interpretation of the reconstructed phases. Coherent and incoherent lens aberrations are found to have the most significant impact. For images over a large field of view, the impact of noise and non-periodic boundary conditions are appreciable, but in this case study have less of an impact than artefacts introduced by beam deflections coupling to beam scanning (imperfect tilt-shift purity).

Improving the depth resolution of STEM-ADF sectioning by 3D deconvolution.

Although the possibility of locating single atom in three dimensions using the scanning transmission electron microscope (STEM) has been discussed with the advent of aberration correction technology, it is still a big challenge. In this report we have developed deconvolution routines based on maximum entropy method (MEM) and Richardson-Lucy algorithm (RLA), which are applicable to the STEM-annular dark-field (ADF) though-focus images to improve the depth resolution. The new three-dimensional (3D) deconvolution routines require a limited defocus-range of STEM-ADF images that covers a whole sample and some vacuum regions. Since the STEM-ADF probe is infinitely elongated along the optical axis, a 3D convolution is performed with a two-dimensional (2D) convolution over xy-plane using the 2D fast Fourier transform in reciprocal space, and a one-dimensional convolution along the z-direction in real space. Using our new deconvolution routines, we have processed simulated focal series of STEM-ADF images for single Ce dopants embedded in wurtzite-type AlN. Applying the MEM, the Ce peaks are clearly localized along the depth, and the peak width is reduced down to almost one half. We also applied the new deconvolution routines to experimental focal series of STEM-ADF images of a monolayer graphene. The RLA gives smooth and high-P/B ratio scattering distribution, and the graphene layer can be easily detected. Using our deconvolution algorithms, we can determine the depth locations of the heavy dopants and the graphene layer within the precision of 0.1 and 0.2 nm, respectively. Thus, the deconvolution must be extremely useful for the optical sectioning with 3D STEM-ADF images.

Suppressing dynamical diffraction artefacts in differential phase contrast scanning transmission electron microscopy of long-range electromagnetic fields via precession.

It is well known that dynamical diffraction varies with changes in sample thickness and local crystal orientation (due to sample bending). In differential phase contrast scanning transmission electron microscopy (DPC-STEM), this can produce contrast comparable to that arising from the long-range electromagnetic fields probed by this technique. Through simulation we explore the scale of these dynamical diffraction artefacts and introduce a metric for the magnitude of their contribution to the contrast. We show that precession over an angular range of a few milliradian can suppress this contribution to the contrast by one-to-two orders of magnitude. Our exploration centres around a case study of GaAs near the [011] zone-axis orientation using a probe-forming aperture semiangle on the order of 0.1 mrad at 300 keV, but the trends found and methodology used are expected to apply more generally.

Atomic resolution electron microscopy in a magnetic field free environment.

Atomic-resolution electron microscopes utilize high-power magnetic lenses to produce magnified images of the atomic details of matter. Doing so involves placing samples inside the magnetic objective lens, where magnetic fields of up to a few tesla are always exerted. This can largely alter, or even destroy, the magnetic and physical structures of interest. Here, we describe a newly developed magnetic objective lens system that realizes a magnetic field free environment at the sample position. Combined with a higher-order aberration corrector, we achieve direct, atom-resolved imaging with sub-Å spatial resolution with a residual magnetic field of less than 0.2 mT at the sample position. This capability enables direct atom-resolved imaging of magnetic materials such as silicon steels. Removing the need to subject samples to high magnetic field environments enables a new stage in atomic resolution electron microscopy that realizes direct, atomic-level observation of samples without unwanted high magnetic field effects.

Large angle illumination enabling accurate structure reconstruction from thick samples in scanning transmission electron microscopy.

Most reconstructions of the electrostatic potential of a specimen at atomic resolution assume a thin and weakly scattering sample, restricting accurate quantification to specimens only tens of Ångströms thick. We demonstrate that using large-angle-illumination scanning transmission electron microscopy (STEM)-a probe forming aperture with convergence angle larger than about 50 mrad-allows us to better meet the weak phase object approximation and thereby accurately reconstruct the electrostatic potential in samples thicker than the order of 100 Å.

On the quantitativeness of grain boundary chemistry using STEM EDS: A ZrO2 Σ9 model grain boundary case study.

Atomic-resolution energy dispersive X-ray spectroscopy (EDS) in scanning transmission electron microscopy (STEM) has recently been shown to be a powerful approach to investigate local chemistry of nanoscale structures quantitatively. While most of the studies have been focused on the quantification of the chemical composition in bulk crystals, few were discussed on interfaces. In this study, we theoretically explored the applicability of STEM EDS for the quantification of local chemistry in grain boundaries (GBs), where the electron channeling can be dramatically changed compared with the bulk due to non-periodic atomic arrangement. We find that: (1) line scan analysis across the GBs or mapping analysis, which have been widely used for interface analysis, sometimes leads to misinterpretation of true interface chemistry. (2) Tilting the specimen, which is effective to reduce the effects of scattering, is not always useful for the quantification of GBs. (3) EDS analysis covering the whole GB structure unit, such as using a box scan, can provide true chemical information. Our study provides useful insights into characterization of interface chemistry using STEM EDS.

Development of immune and microbial environments is independently regulated in the mammary gland.

Breastfeeding is important for mammals, providing immunological and microbiological advantages to neonates, together with the nutritional supply from the mother. However, the mechanisms of this functional diversity in the mammary gland remain poorly characterized. Here, we show that, similar to the gastrointestinal tract, the mammary gland develops immune and microbial environments consisting of immunoglobulin A (IgA) and the microflora, respectively, both of which are important for protecting neonates and the mother from infectious diseases. The IgA production and microflora development are coordinated in the gastrointestinal tract but seem to be independently regulated in the mammary gland. In particular, the chemokine (C-C motif) ligand 28 and poly-Ig receptor, crucial molecules for the IgA production in milk, were expressed normally in germ-free lactating mice but were almost undetectable in postweaning mothers, regardless of the microflora presence. Our findings offer insights into potentially improving the quality of breastfeeding, using both immunological and microbiological approaches.

Measuring nanometre-scale electric fields in scanning transmission electron microscopy using segmented detectors.

Electric field mapping using segmented detectors in the scanning transmission electron microscope has recently been achieved at the nanometre scale. However, converting these results to quantitative field measurements involves assumptions whose validity is unclear for thick specimens. We consider three approaches to quantitative reconstruction of the projected electric potential using segmented detectors: a segmented detector approximation to differential phase contrast and two variants on ptychographical reconstruction. Limitations to these approaches are also studied, particularly errors arising from detector segment size, inelastic scattering, and non-periodic boundary conditions. A simple calibration experiment is described which corrects the differential phase contrast reconstruction to give reliable quantitative results despite the finite detector segment size and the effects of plasmon scattering in thick specimens. A plasmon scattering correction to the segmented detector ptychography approaches is also given. Avoiding the imposition of periodic boundary conditions on the reconstructed projected electric potential leads to more realistic reconstructions.

Flagellar filament structural protein induces Sjögren's syndrome-like sialadenitis in mice.

OBJECTIVE: Sjögren's syndrome (SS) is a systemic autoimmune disease that primarily affects lacrimal and salivary glands. We previously reported that FliC derived from Escherichia coli could induce autoimmune pancreatitis-like lesions. From these results, we speculated that FliC could also induce SS-like exocrinopathy. In this study, we investigated the effects of chronic exposure to FliC on lacrimal and salivary glands and the possibility that it might lead to an autoimmune response. METHODS: C57BL/6 mice were repeatedly injected with FliC and histological changes, serum levels of cytokine/chemokines and autoantibodies were evaluated at different time points after the final injection. The presence of sialadenitis was diagnosed by histological methods. RESULTS: In FliC-treated groups, 57% of subjects developed inflammatory cell infiltrates around ducts in mandibular salivary glands, but not lacrimal glands. In addition, serum levels of total IgG, IgG1, and IgG2a were significantly higher in FliC-treated groups. Intriguingly, serum anti-SSA/Ro levels were also significantly higher in FliC-treated groups. Cytokine analysis revealed that serum levels of IL-1ß, IL-12p70, IL-13, IFN-γ, IL-15, and IL-23 seemed to be higher in FliC-treated mice. CONCLUSIONS: Our data suggest that FliC-treated mice develop an SS-like phenotype. Our model may elucidate the relationship between commensal bacteria and SS.

A new method to detect and correct sample tilt in scanning transmission electron microscopy bright-field imaging.

Important properties of functional materials, such as ferroelectric shifts and octahedral distortions, are associated with displacements of the positions of lighter atoms in the unit cell. Annular bright-field scanning transmission electron microscopy is a good experimental method for investigating such phenomena due to its ability to image light and heavy atoms simultaneously. To map atomic positions at the required accuracy precise angular alignment of the sample with the microscope optical axis is necessary, since misalignment (tilt) of the specimen contributes to errors in position measurements of lighter elements in annular bright-field imaging. In this paper it is shown that it is possible to detect tilt with the aid of images recorded using a central bright-field detector placed within the inner radius of the annular bright-field detector. For a probe focus near the middle of the specimen the central bright-field image becomes especially sensitive to tilt and we demonstrate experimentally that misalignment can be detected with a precision of less than a milliradian, as we also confirm in simulation. Coma in the probe, an aberration that can be misidentified as tilt of the specimen, is also investigated and it is shown how the effects of coma and tilt can be differentiated. The effects of tilt may be offset to a large extent by shifting the diffraction plane detector an amount equivalent to the specimen tilt and we provide an experimental proof of principle of this using a segmented detector system.

Low magnification differential phase contrast imaging of electric fields in crystals with fine electron probes.

To correlate atomistic structure with longer range electric field distribution within materials, it is necessary to use atomically fine electron probes and specimens in on-axis orientation. However, electric field mapping via low magnification differential phase contrast imaging under these conditions raises challenges: electron scattering tends to reduce the beam deflection due to the electric field strength from what simple models predict, and other effects, most notably crystal mistilt, can lead to asymmetric intensity redistribution in the diffraction pattern which is difficult to distinguish from that produced by long range electric fields. Using electron scattering simulations, we explore the effects of such factors on the reliable interpretation and measurement of electric field distributions. In addition to these limitations of principle, some limitations of practice when seeking to perform such measurements using segmented detector systems are also discussed.

Effect of Lipopolysaccharide on the Progression of Non-Alcoholic Fatty Liver Disease in High Caloric Diet-Fed Mice.

The incidence of non-alcoholic steatohepatitis (NASH) is increasing. Because gut microbiota have been highlighted as one of the key factors in the pathogenesis of metabolic syndrome, we investigated the involvement of the bacterial component in the progression of non-alcoholic fatty liver (NAFL) to NASH. C57BL/6 mice were fed with maintenance food (MF, groups A and B) or a high caloric diet (HCD, groups C and D) for 1 month. Mice were then divided into four groups: Groups A and C were inoculated with PBS, while groups B and D were inoculated with lipopolysaccharide (LPS) plus complete Freund's adjuvant (CFA). The inoculations were performed a total of 3 times over 3 months. At 6 months, while hepatic steatosis was observed in groups C and D, cellular infiltration and fibrosis were less evident in group C than in group D. Inflammatory cytokines were upregulated in groups B and D. 16S rRNA pyrosequencing of whole colon homogenates containing faeces showed that certain bacterial groups, such as Bacteroidaceae, Peptostreptococcaceae and Erysipelotrichaceae, were increased in groups C and D. Although loading of bacterial components (LPS) resulted in hepatic inflammation in both MF- and HCD-fed mice, HCD feeding was more crucial in the progression of NAFL during the triggering phase.

Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons.

Differential phase contrast images in scanning transmission electron microscopy can be directly and quantitatively related to the gradient of the projected specimen potential provided that (a) the specimen can be treated as a phase object and (b) full 2D diffraction patterns as a function of probe position can be obtained. Both are challenging to achieve in atomic resolution imaging. The former is fundamentally limited by probe spreading and dynamical electron scattering, and we explore its validity domain in the context of atomic resolution differential phase contrast imaging. The latter, for which proof-of-principle experimental data sets exist, is not yet routine. We explore the extent to which more established segmented detector geometries can instead be used to reconstruct a quantitatively good approximation to the projected specimen potential.

On the quantitativeness of EDS STEM.

Chemical mapping using energy dispersive X-ray spectroscopy (EDS) in scanning transmission electron microscopy (STEM) has recently shown to be a powerful technique in analyzing the elemental identity and location of atomic columns in materials at atomic resolution. However, most applications of EDS STEM have been used only to qualitatively map whether elements are present at specific sites. Obtaining calibrated EDS STEM maps so that they are on an absolute scale is a difficult task and even if one achieves this, extracting quantitative information about the specimen - such as the number or density of atoms under the probe - adds yet another layer of complexity to the analysis due to the multiple elastic and inelastic scattering of the electron probe. Quantitative information may be obtained by comparing calibrated EDS STEM with theoretical simulations, but in this case a model of the structure must be assumed a priori. Here we first theoretically explore how exactly elastic and thermal scattering of the probe confounds the quantitative information one is able to extract about the specimen from an EDS STEM map. We then show using simulation how tilting the specimen (or incident probe) can reduce the effects of scattering and how it can provide quantitative information about the specimen. We then discuss drawbacks of this method - such as the loss of atomic resolution along the tilt direction - but follow this with a possible remedy: precession averaged EDS STEM mapping.

Cancer cell death induced by novel small molecules degrading the TACC3 protein via the ubiquitin-proteasome pathway.

The selective degradation of target proteins with small molecules is a novel approach to the treatment of various diseases, including cancer. We have developed a protein knockdown system with a series of hybrid small compounds that induce the selective degradation of target proteins via the ubiquitin-proteasome pathway. In this study, we designed and synthesized novel small molecules called SNIPER(TACC3)s, which target the spindle regulatory protein transforming acidic coiled-coil-3 (TACC3). SNIPER(TACC3)s induce poly-ubiquitylation and proteasomal degradation of TACC3 and reduce the TACC3 protein level in cells. Mechanistic analysis indicated that the ubiquitin ligase APC/C(CDH1) mediates the SNIPER(TACC3)-induced degradation of TACC3. Intriguingly, SNIPER(TACC3) selectively induced cell death in cancer cells expressing a larger amount of TACC3 protein than normal cells. These results suggest that protein knockdown of TACC3 by SNIPER(TACC3) is a potential strategy for treating cancers overexpressing the TACC3 protein.

Observations of crack propagation along a Zr-doped alumina grain boundary.

Structural ceramics are typically used in polycrystalline form. It is well known that polycrystalline ceramics often show the intergranular fracture. To improve their mechanical properties, transition metals can be used as dopants into a bulk material, which tend to segregate into the grain boundaries[1]. However, the effect of dopant segregation on grain boundary fracture is still uncertain. In order to investigate the fracture behavior of a dopant-segregated grain boundary, we observed the crack propagation of a Zr-doped alumina grain boundary by in situ nanoindentation in a transmission electron microscope (TEM), and characterized the fracture surface by scanning TEM (STEM).An alumina bicrystal with a Zr-doped Σ13 grain boundary was fabricated by diffusion bonding at 1500(o)C for 10 hours in air, where a face of one crystal was coated by Zr metal in advance to the bonding (Fig. 1a). A TEM sample was prepared from the bicrystal by mechanical grinding and Ar ion milling. For in situ indentation, the sample had a free edge perpendicular to the grain boundary (Fig. 1b). The indentation experiment was performed by using a double-tilt indentation holder (Nanofactory) and JEM-2010 (200kV, JEOL). The fracture surface was further observed by high angle annular dark field (HAADF) STEM (ARM-200F, 200kV, JEOL).jmicro;63/suppl_1/i20-a/DFU064F1F1DFU064F1Fig. 1.(a) Schematic illustrations of bicrystal fabrication by diffusion bonding and (b) Bright field TEM image showing the geometric arrangement of the in situ nanoindentation experiment In the in situ TEM nanoindentation experiment, at first a crack was introduced in bulk close to the grain boundary and propagated with the amount of indentation. After the crack reached the grain boundary, it preferentially propagated along the grain boundary. To identify the crack pass at the atomic level, the STEM analysis was performed. We found that three-atomic-layer Zr was formed in the unbroken region of the grain boundary, whereas one to three Zr layers remained on the fracture surface. This indicates that the crack propagated within the segregation region of Zr in the grain boundary. In the presentation, we will discuss the crack propagation behavior and the atomic structure of the fracture surfaces in detail.

Enhanced light element imaging in atomic resolution scanning transmission electron microscopy.

We show that an imaging mode based on taking the difference between signals recorded from the bright field (forward scattering region) in atomic resolution scanning transmission electron microscopy provides an enhancement of the detectability of light elements over existing techniques. In some instances this is an enhancement of the visibility of the light element columns relative to heavy element columns. In all cases explored it is an enhancement in the signal-to-noise ratio of the image at the light column site. The image formation mechanisms are explained and the technique is compared with earlier approaches. Experimental data, supported by simulation, are presented for imaging the oxygen columns in LaAlO3. Case studies looking at imaging hydrogen columns in YH2 and lithium columns in Al3Li are also explored through simulation, particularly with respect to the dependence on defocus, probe-forming aperture angle and detector collection aperture angles.

Simultaneous optical mapping system of endocardial and epicardial excitation.

The cardiac excitation propagation during arrhythmia shows a three-dimensional complex excitation behavior. Numerous optical measurements of the propagation and action potentials of the cardiac muscles have been made to elucidate the detailed arrhythmia phenomenon. The conventional optical measurement system mainly observes the action potential signal of the epicardium, and the endocardial signal measurement without incising the heart is difficult. In addition, an incised heart no longer exhibits the natural excitation behavior. Therefore, we constructed a simultaneous measurement system that integrates the conventional epicardial measurement system and the endocardial measurement system by using an endoscope for an intact heart. Then, we proposed a line-laser registration method that can match correspondence between the epicardial and endocardial images for a short period. We demonstrated that this registration method has a sub-millimeter accuracy. Subsequently, we succeeded in simultaneous optical measurement of the excitation propagation of the epicardium and endocardium of the right heart wall by using an isolated rabbit heart.

A randomised, placebo-controlled, double-blind study of aprepitant in nondrinking women younger than 70 years receiving moderately emetogenic chemotherapy.

BACKGROUND: We evaluated the efficacy of aprepitant plus granisetron and an increased dose of dexamethasone in selected patients undergoing moderately emetogenic chemotherapy (MEC). METHODS: Nondrinking women <70 years undergoing MEC were randomly assigned to aprepitant (day 1, 125 mg; days 2 and 3, 80 mg) or placebo. Dexamethasone on days 1-3 was 12, 4, and 4 mg with aprepitant and 20, 8, and 8 mg with placebo. The primary end point was complete response (CR; no emesis or rescue therapy) during 120 h of the first cycle. Logistic regression analysis was performed to identify predictors of overall CR. RESULTS: Of the 94 patients enrolled, 91 were assessable. Most received carboplatin-based chemotherapy. In the aprepitant (n=45) and placebo (n=46) groups, the overall, acute (day 1), and delayed (days 2-5) CR rates were 62% and 52%, 98% and 96%, and 62% and 52%, respectively. Although not statistically significant, the overall CR rate was 10% higher in the aprepitant group. Both regimens were well tolerated. On multivariate analysis, advanced ovarian cancer (OR, 0.26 (0.10-0.72)) was independently associated with a lower CR. CONCLUSION: Even with an increased dose of dexamethasone, aprepitant seemed more effective than placebo in these selected patients undergoing MEC; however, delayed phase management remains a significant problem.