bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement of
3D
atom probe tomography reconstruction integrating transmission electron microscopy information
Authors: Mouton Isabelle , Estivill‐Stroud Robert , Grenier Adeline , Gregoire Magalie , Juhel Marc , Barnes Jean Paul 
Published: December 2016

We propose to improve atom probe tomography (APT) reconstruction methods to increase the reliability and the accuracy of the resulting 3D volumes. Currently, 3D reconstructions are done iteratively atom by atom, to convert the ion sequence (
#N
) and the detected position (

X
D

,

Y
D

) into atomic coordinates (
x,y,z
). To obtain a more realistic reconstruction, a better estimation of the main reconstruction parameters (e.g. image compression factor, detection efficiency, evolution of the tip radius) is required [1].

Some techniques have already been developed in order to estimate the reconstruction parameters. Those calibrations are based on voltage curve, tip image, field ion microscopy or desorption images. Most of these techniques have been shown to give accurate results on homogenous or metallic materials (in this case, the crystallographic pole or atomic planes can easily be observed) [2]. Unfortunately, these techniques are poorly suited for semiconductor materials, since the projection laws and the physics of field evaporation affect the reconstruction parameters, especially in the case of multiphase materials where evaporation fields are different from one phase to another.
In this study, we aim to correlate the information obtained by transmission electron microscopy (TEM) with atom probe tomography to improve the current reconstruction model. We focused on high‐K multilayer materials where the evaporation field is very different between each layer. As we can see on figure 1, the original sample contains flat and chemically well‐defined interfaces, whereas those interfaces are strongly distorted (figure2.a) when a classic reconstruction algorithm (with cone angle consideration) is used. This distortion comes from the assumption that two atoms arriving one after the other on the detector were close to one another in the tip, which is not the case in wide field of view APT.
In our model, the reconstruction is performed by dealing separately with different (and previously defined) areas of the detector surface. The ions are labeled independently in every sub‐detector, allowing different reconstruction parameters for each subdetector and therefore a better match of the theoretical thickness of every layer. The new reconstruction (figure 2.b) shows homogenous atom density, flat interfaces and more accurate layer thicknesses, making the chemical quantification more reliable. This study could be extended to 3D objects, where the microstructural features observed in TEM could be used to constrain the resulting APT volume.
This work has been funded by the French ANR Recherche Technologique de Base (RTB) programme. The experiments were performed on the Nanocharacterisation platform (PFNC) at MINATEC.
Three‐dimensional visualization of Tick‐borne encephalitis virus‐cell interactions
Authors: Bily Tomas , Palus Martin , Vancova Marie , Ruzek Daniel , Nebesarova Jana 
Published: December 2016

Tick‐borne encephalitis virus (TBEV) is the etiological agent of Tick‐borne encephalitis, a serious neurological human infection. The endemic region is Europe and Asia with more than 10,000 clinical cases every year. We used electron tomography (ET) technique for visualization of neural cells infected with TBEV prepared by high‐pressure freezing followed by freeze substitution and embedded into epoxy resin [1, 2]. Images of three dimensional volume of the section enables better to understand alterations of neural cells caused by TBEV than 2D Transmission electron microscopy (TEM) projection images, where the visibility of structures depends crucially on section thickness. Here, we showed how to 3D visualization influenced an interpretation of obtained TEM results. Next, we discuss our experience with settings of optimal imaging conditions, appropriate resolution given by Crowther criterion [3], elongation factor [4] and necessity of using of the single or dual tomography. ET was done like a single/dual axis using JEOL 2100F equipped with high tilt stage and Gatan camera Orius SC 1000 controlled with Serial EM software. Tomograms were aligned and reconstructed using IMOD software package. 3D models were generated by manually masking of the area of interest by means of IMOD or Amira.
Our results depicted mainly changes in organisation of rough endoplasmic reticulum (RER) induced by TBEV and a formation of virus‐induced sub‐compartments of RER called smooth membrane structures including a presence of pores. We found that cisterns of RER are often arranged into two tightly apposed cisterns. Depending on the type of host cells, used TBEV strains and length of infection, we described proliferation of RER with harboured sites of replication (3 days post infection) which are reorganised during the extensive infection stress (12 days post infection) into whorls with central part having features of an autophagosome [2]. In primary neurons infected by TBE strain Neudoerfl, virus‐induced tubule‐like structures (18 – 22 nm in diameter) were frequently observed inside of reorganised RER. Most of these structures were connected to the TBEV and run either in parallel lines or in different directions. In several cases, these tubule‐like structures were surrounded with other tubules of 43.8 ± 4.3 nm (N = 7) in diameter [2]. Finally, we imaged vacuoles containing individual virions with nucleocapsids associated with host microtubules [2].
Characterization of Branched Carbon Nanostructures
Authors: Malik Sharali , Nemoto Yoshihiro , Hongxuan Guo , Katsuhiko Ariga , Hill Jonathan 
Published: December 2016

Branched carbon nanostructures such as branched‐Multi‐Walled Carbon Nanotubes (b‐MWCNTs, Fig. 1) are exotic types of carbon nanostructures whose technological potential have not yet been fully explored. Although MWCNTs have been used to improve the properties of composite materials, there are currently still two main problems remaining to be solved before MWCNT/composite materials can realize their full potential:‐
(1) adequate dispersion of the nanotube‐reinforcement material, and
(2) strong enough interfacial bonding between the nanotube‐reinforcement elements and the composite matrix.
These problems can be addressed by utilizing branched‐carbon nanostructures as it is known (from theory and simulation experiments) that branched fibres greatly enhance interfacial bonding e.g. the ancient process of adding straw to mud to make stronger bricks. It is well known that, in the case of carbon nanotube networks, junction resistance is the dominant limiting factor and so, a network of branched‐carbon nanostructures would significantly reduce this network resistance. . Therefore, in addition to potential improvements in composite applications, the electrical properties of networks made of branched‐carbon nanostructures could have major benefits to the existing commercial application of CNT/CNF reinforced composites in Conductive Static Dissipation (ESD) as well as potential use in Supercapacitors, Solar Cells and Li‐Ion batteries.
Structural Mechanism of Assembly and Maturation of the
HBs
Antigen
Authors: Deliot Aurelie , Nicolai Marie‐Claire , Buosi Vanessa , Thion Laurent , Sepulcri Patricia , Nemecek Daniel 
Published: December 2016

Hepatitis B surface antigen (HBsAg) is overexpressed in great excess during hepatitis B (HBV) infection in the form of noninfectious (DNA‐free) subviral particles. These particles greatly outnumber mature virus particles (virions) and presumably function as decoys for the immune system to facilitate infection by the DNA‐containing virions. These properties are exploited in the current HBV vaccine, in which recombinant HBsAg is used as a potent antigen capable to induce a strong immune response and long‐term immunological memory. Several studies have implicated that HBsAg consist of a lipid bilayer with embedded HBs subunits [1‐3]. The particles appear as pleomorphic spheres with an average diameter of ~23 nm and an empty internal cavity. Particles produced for the vaccine contain monomeric HBs subunits that subsequently cross‐link via formation of disulfide bridges within the HBsAg particles.
We employed cryo‐electron tomography to image individual HBsAg particles in their native environment at different times of maturation. Reconstructed 3D tomograms showed different kinds of HBsAg particles that could be classified into three groups: (i) small spherical particles of ~16 nm in diameter, (ii) spherical particles of ~25 nm in diameter with an internal cavity and (iii) elongated oval particles with an internal cavity of ~20 nm diameter and 25‐30 nm length. The electron‐dense shell of HBsAg particles is about 5 nm thick and likely represents the lipid bilayer. The shell contains short protrusions with higher density (Figure 1) that are spaced 5‐6 nm apart and likely represent lipid‐embedded HBs subunits.
Parallel measurements of proton NMR spectra indicated significant structural changes in protein backbone and aliphatic side chains of lipids during HBsAg particles maturation. Those variations support a decreased flexibility and suggested more rigid structure of the lipid bilayer during HBsAg maturation [4].
We analyzed size distribution of HBsAg particles and densities corresponding to HBs subunits within the particles to assess the molecular architecture of particles during maturation. The results provide insights into how structural changes in the lipid bilayer and cross‐linking of HBs subunits affect the molecular architecture of HBsAg particles that is directly related to immunogenicity of the HBV vaccine.
This research has been funded by and performed at Sanofi Pasteur.
Characterization of multicomponent
Al
alloys by
TEM
,
HAADF‐STEM
,
EELS
and
DFT
Authors: Mørtsell Eva , Andersen Sigmund , Marioara Calin , Røyset Jostein , Friis Jesper , Holmestad Randi 
Published: December 2016

Light, environmentally friendly and recyclable materials are of increasing importance, such as in the automotive industry where the age‐hardenable Al‐Mg‐Si alloys are of high interest. By understanding better how microstructure responds to changed processing or composition, costs can be cut and macroscopic properties tailored for particular applications. For example, by reducing the solute amount a softer material will allow higher extrusion speeds, however, on the expense of material strength. Recently, it was shown how adding back a lower at% of ‘exotic’ elements like Li, Cu, Ag and Ge compensates such strength loss [1]. Age hardening is ascribed to dislocation resisting strain‐fields set up in the aluminium during nucleation and growth of the metastable, nanoscale, semi‐coherent precipitate needles in the three <100> Al directions [2]. The replacement elements change precipitate structure and growth conditions.

Precipitate statistics based on transmission electron microscopy (TEM) can elucidate how material strength is related to precipitate number densities, sizes and volume fractions; see example a bright field TEM micrograph in Fig. 1 (a) used for this purpose. The elemental contrast in probe Cs corrected high angle annular dark field scanning TEM (HAADF‐STEM) greatly assists structural characterization of individual precipitate cross sections [3], enabling identification of precipitate type and the composition of individual atomic columns. See example of a
β’’
precipitate in Fig. 1 (b).

Because elements with similar atomic number (Z) express very small intensity differences, electron energy loss spectroscopy (EELS) elemental mapping has been applied to aid resolution. It became clear that EELS in combination with HAADF‐STEM can resolve the hexagonal network of Si columns [4] well, see Fig. 2. It was also found that a significant proportion of the other atomic columns were mixed.
A pressing matter in material design is enhanced control with precipitate characteristics which vary strongly with alloy composition and processing. Density functional theory (DFT) simulations have a great potential for broadening the understanding concerning precipitate nucleation, growth and final microstructure, and how they are connected. Here we have investigated binding between solute atoms and to vacancies, along with volume misfits (see Fig. 4) in the Al lattice, in a venture to relate these parameters to precipitation.
An approach towards solving
3D
information by combining quantitative
ADF STEM
and
EDX
Authors: MacArthur Katherine , Ozkaya Dogan , Lozano‐Perez Sergio , Nellist Peter 
Published: December 2016

Annular dark‐field scanning transmission electron microscopy (ADF STEM) is an invaluable tool for materials characterisation, providing atomic scale information of materials structure and defects. ADF STEM in particular produces images where the intensity contains both composition and thickness information. In fact, through careful quantification of the intensity itself it becomes possible to extract quantitative information and even atom counting. Typically this is either done through comparison with careful standards, comparison with simulations or via statistical methods. For single element nanoparticles it becomes possible to estimate their 3D structure from atom counting and then applying an energy minimisation [1].
Silicon drift detectors (SDDs) have opened up a new era in energy dispersive x‐ray (EDX) microanalysis at the nanometre and even sub‐nanometre scales. The improved detector design allows for larger devices and therefore increased solid angles for x‐ray collection. This provides a significant improvement in x‐ray count rates such that atomic resolution maps and x‐ray tomography are both now possible. In addition, aberration correction in the STEM allows the use of larger probe‐forming apertures to produce increased beam currents in much smaller probes. The combined result provides huge improvements in x‐ray counts from small volumes leading to the potential for improved quantitative analysis at the nanometre scale and below.
In the same way that the scattering cross section, σ, can be calculated from ADF image intensity [2] and for ionisation edges in EELS [3], it is possible to calculate an EDX partial cross section using an approach that demonstrates similarities with the ζ‐factor method [4]. This quantification method was applied to PtCo alloy nanoparticles that have been acid‐leached to provide platinum enrichment (or rather cobalt depletion) at the particle surface. It is possible to quantify the levels of cobalt depletion in the first few atomic layers of the particle, showing that the leaching produces a localised surface depletion that can only be determined by this high resolution EDX quantification [5], [6].
Both of these methods of quantification can be used to yield a range of information about the structure of our material when used individual. Here we look at the potential information which can be achieved through combining the information from each technique. In particular we look at extracting 3D information of bimetallic fuel cell catalysts.
Denoising and compensation of the missing wedge in cryo electron tomography
Authors: Moebel Emmanuel , Kervrann Charles 
Published: December 2016

In this study, we have addressed two important issues in cryo electron tomography images: the low signal‐to‐noise ratio and the presence of a missing wedge (MW) of information in the spectral domain. Indeed, according to the Fourier slice theorem, limited angle tomography results into an incomplete sampling of the Fourier domain. Therefore, the Fourier domain is separated into two regions: the known spectrum (KS) and the unknown spectrum, the latter having the shape of a missing wedge (see Figure). The proposed method tackles both issues jointly, by iteratively applying a denoising algorithm in order to fill up the MW, and proceeds as follows:

Excitation step: Add noise into the MW

Denoising step: Apply a patch‐based denoising algorithm

Repeat steps 1 and 2, by keeping KS constant through the iterations

The excitation step is used to randomly initialize the coefficients of the MW, whereas the denoising step acts as a spatial regularization. The employed denoising algorithm, which exploits the self‐similarity of the image, filters out coefficient values which are dissimilar to KS, thereby keeping similar ones. By iterating these steps, we are able to diffuse the information contained in KS into the MW.
An application example on experimental data can be seen on the Figure, which shows the data in both spectral and spatial domain. The data contains a spherical gold particle, deformed by MW induced artifacts: elongation of the object, side‐ and ray‐artifacts. From the residue image it can be seen that noise and MW artifacts have been reduced, while preserving the details of the image. Experiments are being performed to verify if particle detection and alignment are enhanced by using the method as a pre‐processing step.
Plasma cleaning effect on the stability of theEpon resin sections
Authors: Skoupý Radim , Krzyzanek Vladislav , Nebesarova Jana 
Published: December 2016

Low voltage TEM and STEM (transmission and scanning transmission electron microscope) can be regarded as the method of choice for many structural studies of very thin biological samples like ultrathin sections, viruses etc. [1]. Unfortunately, the specimen contamination increases with electron flux and therefore a specimen cleanliness is an important factor in obtaining of valuable data especially in STEM [2]. An important parameter for imaging of those samples is a sensitivity of the sample to degradation by electron beam. The mass loss indicates a degree of the radiation damage. We investigated the mass loss of embedding medium (Epon resin of middle hardness) in combination of different thickness of the sections (60 nm and 150 nm) with using or not‐using of plasma cleaning which is often used to removing of contamination from the sample.The repeated imaging was performed by SEM Magellan 400L (FEI) at the acceleration voltage of 30 kV and the lowest possible probe current of 1.6 pA in the bright field (BF) using the commercial STEM3 detector (FEI). An electron dose for each scan was about 60 e‐/nm2. The measurement was performed at the eighth day after their preparation by the ultramicrotome Leica Ultracut UCT. Some slices were cleaned by Plasma Cleaner (FEI) installed at the Magellan SEM for 20 seconds just before imaging, so they did not leave high vacuum. For each experiment, three different places on each sample were imaged for downgrading space dependency of the measurement. The mass loss was obtained from the normalized BF signals using the Monte Carlo simulation of electron scattering MONCA [3] using the methodology of mass measurements by STEM [4]. All data processing was programmed in MATLAB (Mathworks).As seen on Fig. 1a, the normalized BF signal (showing the fraction of scattered electron to the BF detector) has similar shape in both thicknesses of the slices without plasma cleaning; the curves are shifted only by the different thickness. However, slices treated with the plasma cleaner show higher sensitivity to incident electron beam with rapidly increasing BF signal; Fig. 1b) shows the remaining mass. At the total irradiation dose of 3000 e‐/nm2there still remains 89% of initial mass for the 150 nm slice and 70% for the 60 nm slice, respectively. However, the slices cleaned by plasma cleaning are much more sensitive to the electron beam, with remaining 55% for the 150 nm slice and local destruction for the 60 nm slice. We observed higher sensitivity of cleaned Epon thin sections under incident electron beam. This limits the usable dose for imaging by the low voltage STEM (for 30 kV) because cleaned sections are more susceptible to burn‐out than non‐cleaned ones.
Large area orientation mapping on nanoscale materials using
SEM
Authors: Palasse Laurie , Goran Daniel 
Published: December 2016

The increasing interest in nanostructured materials has raised the need for high spatial resolution orientation mapping and large‐scale quantitative characterisation of such microstructures. Because Electron Back Scatter Diffraction (EBSD) does not achieve such high spatial resolution on bulk samples, these kind of studies are often done using a Transmission Electron Microscope (TEM). However, TEM‐based orientation mapping techniques suffer from small field of view. As a result, Transmission Kikuchi Diffraction (TKD) in Scanning Electron Microscope (SEM) was developed as a technique capable of delivering the same type of results as EBSD but with a spatial resolution improved by up to one order of magnitude [1,2]. TKD analysis is conducted on an electron transparent sample using the same hardware and software as for EBSD system. But when using conventional EBSD geometry, the transmitted patterns (TKP) are captured by a vertical phosphor screen with a considerable loss of signal and with strong distortions induced by gnomonic projection. Also, with standard TKD detector configuration, most of the transmitted signal does not reach the phosphor screen and results in lower quality patterns which can have negative effect in the measurement quality.
The limitations of such non‐optimal sample‐detector geometry can be overcome by an on‐axis detection system. With a horizontal phosphor screen placed underneath the sample, the transmitted signal is captured where it is the strongest and TKPs will have minimal distortions. Using low probe currents, the spatial resolution can be increased and the beam‐induced specimen drift reduced as compared to standard TKD detector configuration [3]. The improved stability and high spatial resolution allow the user to conduct large‐area TKD orientation mapping.
Using a partially recrystallized ultrafine stainless steel sample, we will demonstrate that statistical data can be obtained for the quantitative characterisation of nanostructured materials in the SEM (figure 1).
Modulation of
DAMP
‐mediated
NET
formation by p33
Authors: Neumann Ariane , Papareddy Praveen , Herwald Heiko 
Published: December 2016

The formation of neutrophil extracellular traps (NETs) is often associated to entrapment and growth inhibition of several pathogens. However, an excessive NET formation or impaired degradation of the DNA fibres can result in the development of autoimmune diseases, such as SLE or psoriasis. Also NET‐associated molecules, like host defence peptide LL‐37 and cationic histones can have harmful effects. Thus, the host organism needs to rely on precautions to circumvent such deleterious effects.
Our group recently published that p33, a multi‐ligand protein present on several cells types, is able to inhibit the cytolytic activity of LL‐37 on endothelial cells. Additionally, it was found that the application of p33 prevents histone‐mediated platelet aggregation as well as lethal haemolysis in mice treated with histones.

In order to investigate whether p33 plays a role in the formation of NETs, first NETosis was analysed microscopically and biochemically. p33 administration abolished the PMA‐mediated release of DNA fibres and additionally reduced the PMA‐triggered production of ROS. Moreover, both cationic LL‐37 and histones significantly triggered the formation of NETs as well as the release of MPO. However, the simultaneous addition of p33 in a 1:2 ratio decreased the amount of released MPO and the protein‐triggered NETosis. Utilising DNA‐intercalating dye PicoGreen, the effect of p33 on the stabilisation of DNA, backbone of the NET structures, was investigated. Due to their cationic properties, histones as well as LL‐37 bind and protect DNA against bacterial nuclease MN. Interestingly, additional application of p33 diminished the protection of DNA mediated by both LL‐37 and Histones against
S. aureus
nuclease. Taking together, we hypothesise that p33 plays a role in modulating NET induction and NET stabilisation.