178 research outputs found
3D sub-nanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films
Determining the 3-dimensional crystallography of a material with
sub-nanometre resolution is essential to understanding strain effects in
epitaxial thin films. A new scanning transmission electron microscopy imaging
technique is demonstrated that visualises the presence and strength of atomic
movements leading to a period doubling of the unit cell along the beam
direction, using the intensity in an extra Laue zone ring in the back focal
plane recorded using a pixelated detector method. This method is used together
with conventional atomic resolution imaging in the plane perpendicular to the
beam direction to gain information about the 3D crystal structure in an
epitaxial thin film of LaFeO3 sandwiched between a substrate of (111) SrTiO3
and a top layer of La0.7Sr0.3MnO3. It is found that a hitherto unreported
structure of LaFeO3 is formed under the unusual combination of compressive
strain and (111) growth, which is triclinic with a periodicity doubling from
primitive perovskite along one of the three directions lying in the
growth plane. This results from a combination of La-site modulation along the
beam direction, and modulation of oxygen positions resulting from octahedral
tilting. This transition to the period-doubled cell is suppressed near both the
substrate and near the La0.7Sr0.3MnO3 top layer due to the clamping of the
octahedral tilting by the absence of tilting in the substrate and due to an
incompatible tilt pattern being present in the La0.7Sr0.3MnO3 layer. This work
shows a rapid and easy way of scanning for such transitions in thin films or
other systems where disorder-order transitions or domain structures may be
present and does not require the use of atomic resolution imaging, and could be
done on any scanning TEM instrument equipped with a suitable camera.Comment: Minor fixes, especially in reference
Assessing electron beam sensitivity for SrTiO3 and La0.7Sr0.3MnO3 using electron energy loss spectroscopy
Thresholds for beam damage have been assessed for La0.7Sr0.3MnO3 and SrTiO3 as a function of electron probe current and exposure time at 80 and 200 kV acceleration voltage. The materials were exposed to an intense electron probe by aberration corrected scanning transmission electron microscopy (STEM) with simultaneous acquisition of electron energy loss spectroscopy (EELS) data. Electron beam damage was identified by changes of the core loss fine structure after quantification by a refined and improved model based approach. At 200 kV acceleration voltage, damage in SrTiO3 was identified by changes both in the EEL fine structure and by contrast changes in the STEM images. However, the changes in the STEM image contrast as introduced by minor damage can be difficult to detect under several common experimental conditions. No damage was observed in SrTiO3 at 80 kV acceleration voltage, independent of probe current and exposure time. In La0.7Sr0.3MnO3, beam damage was observed at both 80 and 200 kV acceleration voltages. This damage was observed by large changes in the EEL fine structure, but not by any detectable changes in the STEM images. The typical method to validate if damage has been introduced during acquisitions is to compare STEM images prior to and after spectroscopy. Quantifications in this work show that this method possibly can result in misinterpretation of beam damage as changes of material properties
Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images
Geometric phase analysis (GPA), a fast and simple Fourier space method for strain analysis, can give useful information on accumulated strain and defect propagation in multiple layers of semiconductors, including quantum dot materials. In this work, GPA has been applied to high resolution Z-contrast scanning transmission electron microscopy (STEM) images. Strain maps determined from different g vectors of these images are compared to each other, in order to analyze and assess the GPA technique in terms of accuracy. The SmartAlign tool has been used to improve the STEM image quality getting more reliable results. Strain maps from template matching as a real space approach are compared with strain maps from GPA, and it is discussed that a real space analysis is a better approach than GPA for aberration corrected STEM images
Liftout of high-quality thin sections of a perovskite oxide thin film using a xenon plasma focused ion beam microscope
It is shown that a xenon plasma focused ion beam (FIB) microscope is an excellent tool for high-quality preparation of functional oxide thin films for atomic resolution electron microscopy. Samples may be prepared rapidly, at least as fast as those prepared using conventional gallium FIB. Moreover, the surface quality after 2 kV final polishing with the Xe beam is exceptional with only about 3 nm of amorphized surface present. The sample quality was of a suitably high quality to allow atomic resolution high-angle annular dark field imaging and integrated differential phase contrast without any further preparation, and the resulting images were good enough for quantitative evaluation of atomic positions to reveal the oxygen octahedral tilt pattern. This suggests that such xenon plasma FIB instruments may find widespread application in transmission electron microscope and scanning transmission electron microscope specimen preparation
Increased pulmonary Wnt (wingless/integrated)-signaling in patients with sarcoidosis
SummaryBackgroundSarcoidosis is an inflammatory multisystemic granulomatous disease of unknown aetiology commonly affecting the lungs, and pulmonary fibrosis often develops in chronic sarcoidosis. It has been suggested that Wnt (Wingless/integrated)-signaling has a role in inflammatory and fibrotic processes in the lungs, but its role in sarcoidosis has not been investigated. We hypothesised that Wnts secreted from T cells or other inflammatory cells have a role in the pathogenesis of sarcoidosis.MethodsBrush biopsies and bronchoalveolar lavage (BAL) were obtained through bronchoscopy from healthy controls (n = 18) and patients with sarcoidosis (n = 48). Semi-quantitative RT-PCR, electrophoretic mobility shift assay (EMSA) and immunocytochemistry were performed to analyse Wnt expression and activation of the Wnt-signal transducer β-catenin.ResultsAltered expression of Wnt5A, Wnt7A and Wnt7B mRNA in BAL cells was observed, as well as an increased activation of β-catenin, measured by EMSA and confirmed with immunocytochemistry, in resident lung cells from patients with sarcoidosis. More pronounced changes in Wnt expression were seen with advancing disease stage. Thus, by three independent methods, we have found evidence of increased pulmonary Wnt-activation in sarcoidosis.ConclusionsIn the lungs of patients with sarcoidosis there is a previously unappreciated increased Wnt-signal activation that could contribute to the inflammatory processes
Fast pixelated detectors in scanning transmission electron microscopy. Part II: post acquisition data processing, visualisation, and structural characterisation
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 visualisation 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 visualisation of such
datasets. Throughout, we provide examples of the analysis methodologies
presented, utilising data from a 256×256 pixel Medipix3 hybrid DED
detector, with a particular focus on the STEM characterisation 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 nanoscale lattice parameter mapping with a fractional precision
≤6×10−4 (0.06%)
Flow cytometry for enrichment and titration in massively parallel DNA sequencing
Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols
Self-reported symptom severity, general health, and impairment in post-acute phases of COVID-19: retrospective cohort study of Swedish public employees
This study aimed to examine current symptom severity and general health in a sample of primarily non-hospitalized persons with polymerase chain reaction (PCR) confirmed COVID-19 in comparison to PCR negative controls. During the first quarter of 2021, we conducted an online survey among public employees in West Sweden, with a valid COVID-19 test result. The survey assessed past-month severity of 28 symptoms and signs, self-rated health, the WHO Disability Assessment Schedule (WHODAS) 2.0 and illness severity at the time of test. We linked participants’ responses to their SARS-CoV-2 PCR tests results. We compared COVID-19 positive and negative participants using univariable and multivariable regression analyses. Out of 56,221 invited, 14,222 (25.3%) responded, with a response rate of 50% among SARS-CoV-2 positive individuals. Analysis included 10,194 participants (86.4% women, mean age 45\ua0years) who tested positive 4–12\ua0weeks (N = 1425; subacute) and > 12\ua0weeks (N = 1584; postcovid) prior to the survey, and 7185 PCR negative participants who did not believe that they had had COVID-19. Symptoms were highly prevalent in all groups, with worst symptoms in subacute phase participants, followed by postcovid phase and PCR negative participants. The most specific symptom for COVID-19 was loss of smell or taste. Both WHODAS 2.0 score and self-rated health were worst in subacute participants, and modestly worse in postcovid participants than in negative controls. Female gender, older age and acute illness severity had larger effects on self-rated health and WHODAS 2.0 score in PCR positive participants than in PCR negative. Studies with longer follow-up are needed to determine the long-term improvement after COVID-19
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