bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical and numerical investigation of the interaction between phase‐shaped electron probes and plasmonic modes
Authors: Martins Hugo Lourenço , Guzzinati Giulio , Verbeeck Jo , Kociak Mathieu 
Published: December 2016

Optical vortices ‐ i.e. electromagnetic fields with phase singularity ‐ are well known objects and have been used for a decade in a wide range of applications in e.g. optics or astrophysics. Recently, it has been demonstrated that such vortices can be created in an electron microscope by tailoring the phase of the beam [1] and these so‐called electron‐vortex‐beams have already proven their efficiency detecting magnetic state in a material or to probe chirality in a crystal [2].
Simultaneously, EEL spectroscopy in the low‐loss region has attracted a tremendous interest due to its efficiency in resolving plasmonic resonance at the nanometer scale [3] and the underlying formalism is now firmly established [4]. However, because of the invariance of the electron probe along the propagation axis, low‐loss EELS remained unable to detect plasmonic optical activity. However, electron‐vortex‐beams constitute a perfect candidate to overcome this limitation and measure the dichroic behavior of plasmons in an electron microscope ‐ as recently pointed out through simulations by Asenjo‐Garcia and García de Abajo [5].
In the present work, we developed a semiclassical formalism describing the interaction between an electron probe with an arbitrary phase profile and a plasmonic mode. Following [6], we used a quasi‐static and classical description of the plasmon resonances while the electron probe is described in a fully quantum way. We showed that the equation ruling this interaction takes the elegant form of a transition matrix ‐ between two electron states mediated by the eigenpotentials of the plasmon modes. Starting from this formalism, we built an analytical model describing the interaction between point charges and a vortex beam, which gave us a good insight into the physics of plasmonic dichroism. Important experimental inputs, such as convergence and collection angles, were considered. We also implemented a Matlab script within MNPBEM [7] in order to compute our equation and investigate the dichroic behavior of arbitrary plasmonic nano‐structures (see Figure 1).
In the conference, we will present the theoretical formalism and a wide variety of numerical studies of interactions between different nano‐structures (e.g. helix, rod) and phase shaped electron probes (e.g. vortex beams, HG‐like beams…), with a special emphasis on the experimental feasibility of the proposed geometries.
OKA
‐induced tau hyperphosphorylation decrease
BDNF
protein levels in primary cortical neuron cultures
Authors: Atasoy İrem L. , Yilmazer Selma , Dursun Erdİnç , Armağan Derya Metİn , Öztürk Melek , Gezen‐ak Duygu 
Published: December 2016

Intracellular aggregation of abnormally phosphorylated tau in neurofibrillary tangles (NFTs) is a major neuropathological hallmark of Tauopathies such as Alzheimer's disease. Tau phosphorylation is controlled by the homeostasis of glycogen synthase kinase‐3β (GSK‐3β) and protein phosphatase‐2A (PP2A). Okadaic acid (OKA) is a potent inhibitor of PP2A, leading to abnormal tau phosphorylation. Brain‐derived neurotrophic factor (BDNF) is a member of the neurotrophin family and is selectively downregulated in AD brain. In this study, we investigated the effects of tau phosphorylation on secreted and cellular BDNF levels in primary cortical neurons. Primary cortical neurons were prepared from embryonic day 16 (E16) Sprague‐Dawley rat embryos. After 7 days in vitro, neurons were treated with 25 nM OKA for inducing tau hyperphosphorylation. Tau phosphorylation was assessed by Western blot using antibody against phospho‐Thr231 and non‐phosphorylated tau protein was detected with the Tau‐1 antibody. Levels of BDNF secreted to the culture medium were determined by ELISA at the 4th, 8th and 24th hours of treatment. Cellular localization and the protein expression of BNDF were determined by immunofluorescent labeling and fluorescent intensity measurements.
Our results show that after 8 hours of OKA treatment, tau phosphorylation at Thr231 increased, whereas Tau‐1 signal decreased (p<0.0001) Compared with the control groups, BDNF levels in the OKA treated group were significantly lower after 4 and 24 hours of treatment (p<0.0001) but were not significantly different at 8 hours of treatment (p>0.05). While prominent BDNF immunoreactivity was seen in cytoplasm and neurites of the neurons in control groups, BDNF immunoreactivity significantly decreased in the OKA treated group (p<0.0001) and this attenuation was significant especially at neurites.
Our results suggested that decreased BDNF protein levels might depend on the defects in axonal transport as a result of disrupted microtubule structure caused by tau hyperphosphorylation.
Identifying and Mapping the Polytypes and Orientation Relationships in
ZnO / CdSe
Core Shell Nanowire Arrays
Authors: Rapenne Laetitia , Consonni Vincent , Renou Gilles , Roussel Hervé , Gerard Lionel , Rauch Edgar 
Published: December 2016

Core shell ZnO nanowire (NWs) heterostructures have emerged, over the past decade, as a potential building block for a large variety of nanoscale optoelectronic devices, including self‐powered UV photodetectors, dye‐sensitized solar cells (DSSCs), and extremely thin absorber (ETA) solar cells. These heterostructures benefit from a high absorption over the UV and visible parts of the electromagnetic spectrum through sophisticated optical processes (
i.e
., optically guided and radiated modes). In this work, we focused on ZnO / CdSe core shell NW heterostructures. The ZnO NWs are typically grown by chemical bath deposition on top of a ZnO seed layer deposited by sol‐gel process and strongly oriented along the polar c‐axis, but with no in‐plane orientation. Then, the growth of the CdSe shell was performed by molecular beam epitaxy.

CdSe is known to crystallize into the two following polytypes: cubic zinc blende (ZB) and hexagonal wurtzite (WZ). Identifying the different polytypes of CdSe by standard characterization techniques, such as x‐ray diffraction (XRD) and selected area electron diffraction (SAED) using transmission electron microscopy (TEM), as well as Raman scattering, is complicated in the present case. Both the ZB and WZ crystalline phases have very similar properties: most of the diffraction peaks and phonon modes of the ZB crystalline phase are located very closely to those of the WZ crystalline phase; similarly, the bang gap energy of both crystalline phases is almost identical. In addition to the identification of the different polytypes and potential epitaxial relationships, the spatial information on the local scale through mapping is of great interest, but requires the use and development of advanced TEM‐based experiments.
In order to address these issues, the morphology and structural properties of ZnO / CdSe core shell NW heterostructures are thoroughly investigated by field‐emission gun scanning electron microscopy (FEG‐SEM), XRD, Raman spectroscopy, TEM‐HRTEM (Figure 1) and ASTAR (Automated crystal phase and orientation mapping in TEM). We show the strong interest in ASTAR for identifying and mapping the different polytypes of the CdSe shell , but also for revealing the occurrence of orientation relationships with the ZnO NWs, as shown in figure 2.
The Determining Role of Solution Chemistry in Radiation‐Induced Nanoparticles Synthesis in the
STEM
Authors: Abellan Patricia , Arslan Ilke , Hasan Naila Al , Browning Nigel D. , Evans James E. , Grate Jay W. , Karim Ayman M. , Lucas Ivan T. , Moser Trevor H. , Parent Lucas R. , Park Chiwoo , Woehl Taylor J. 
Published: December 2016

In the last decades, radiolytic synthesis routes have exploited the chemical effects of the absorption of high‐energy radiation on precursor solutions, to form nanostructures by reproducing a selective reducing/oxidizing environment. Radiation chemical synthesis provides a powerful means to form nuclei which are homogeneously distributed in the whole volume and where the growth rate can be easily controlled.[1] The latter has recently been achieved using liquid cell electron microscopy, with examples of formation kinetics of particles in polar (water)[2] and non‐polar (toluene)[3] solvents following a linear relation with applied dose rate. Fine control of particles size with conventional radiation sources typically requires increasing the production of radicals (thus applying “high doses”). On the contrary, the challenge in the scanning transmission electron microscope (STEM), where incident doses are inherently higher by orders of magnitude, is to reduce drastically such production. To illustrate this, we recently proposed the use of non‐polar systems (toluene), which are not typically used for radiolytic synthesis outside the STEM, as a solvent that produces much lower amount of radiolytic ionic species upon electron irradiation, as compared to water or other polar solvents such as alcohols (Figure 1 shows an example of
Thus far, most experiments in the liquid cell involved the use of water as a solvent, which explains the large amount of work dedicated to understanding the effects of the electron beam in aqueous conditions. Radiation chemical yields in water are large due to the relatively low bond energies in water molecules, meaning highly reactive oxidizing and reducing radicals and species are created in about an equal amount.[4] Reproducing net reducing conditions for nanoparticle growth can be achieved with the addition of substances that convert primary radicals into free reducing radicals (using OH · scavengers, for instance). The use of organic solvents in the liquid cell allows for tuning the polarity of the medium, giving access to a broader range of synthesis conditions but producing more complex radiolytic products. Here I will discuss, revisiting a number of examples from the literature and presenting our most recent work, general methods for finding more suitable synthesis environments for controlled nanoparticles formation in the liquid cell. Much of the presentation will focus on the solvent radiolysis which is what predominantly dictates the species and yields involved in the chemical processes leading to nanostructure synthesis.[4]
3‐D
EM
exploration of the hepatic microarchitecture ‐ lessons learned for large‐volume in situ serial sectioning
Authors: Shami Gerald , Cheng Delfine , Huynh Minh , Vreuls Celien , Wisse Eddie , Braet Filip 
Published: December 2016

To‐date serial block‐face scanning electron microscopy (SBF‐SEM) dominates as the premier technique for generating three‐dimensional (3‐D) data of resin‐embedded biological samples at an unprecedented resolution and depth volume. Given the relative infancy of the technique, limited literature is currently available regarding the applicability of SBF‐SEM for the ultrastructural investigation of tissues that are inherently low in contrast, including hepatic tissue. Such tissues, relative to neural tissue which has been extensively investigated by means of SBF‐SEM require dedicated SBF‐SEM specimen preparation protocols combined with optimised imaging conditions in order to collect large‐volume 3‐D image data, at appropriate resolution which is devoid of imaging artefacts that are inherent to SEM investigations of uncoated samples.
Therefore, in this study, we provide a comprehensive and rigorous appraisal of different tissue preparation protocols for the large‐volume exploration of hepatic architecture at an unparalleled XY and Z resolution. In so doing, we qualitatively and quantitatively validate the use of a novel and time‐saving SBF‐SEM tissue preparation protocol, which involves the concomitant application of heavy metal fixatives, stains and mordanting agents for the subsequent imaging of contrast‐rich SBF‐SEM data, 3‐D reconstruction and modelling of the hepatic architecture. We further extrapolate large‐volume morphometric data relating to key tissue features of the murine liver, including hepatocytes, the hepatic sinusoids and bile canaliculi network (Fig. 1).
Furthermore, we combine our validated SBF‐SEM specimen preparation protocol with a correlative light and electron microscopy approach, to combine the respective advantages of confocal scanning laser microscopy and SBF‐SEM in order to selectively picture particular subcellular hepatic details in a novel manner. We propose that this correlated multidimensional light and electron imaging approach will allow the study of different liver diseases under relevant experimental tissue models.
Combined multidimensional microscopy as a histopathology imaging tool for the holistic evaluation of the hepatic microvascular and associated tissue cells
Authors: Shami Gerald , Cheng Delfine , Braet Filip 
Published: December 2016

Background
Histological variations in the microanatomical organisation of the functional liver units or hepatic lobules adversely affect general body function. Typically, assessment of liver pathology is based on the examination of paraffin‐embedded histological slides counterstained with dyes using bright‐field light microscopy (BFLM). In some instances, further clinical electron microscopy is recommended to assess the extent of ultrastructural damage to the microvasculature, to determine the nature of hepatic inclusions, or to stage fibrosis, hepatitis, and malignancy in more detail.

Methods
Unfortunately, the above histopathology practice lacks the ability to cross‐correlate observations on the same tissue sample and within a large tissue volume. With the recent advent of smart tissue preparation methodologies and three‐dimensional (3‐D) imaging practices, this can be circumvented in a relatively swift manner, allowing the same tissue to be examined across different microscopy platforms. Herein, we outline the combined application of X‐ray micro‐computed tomography (Micro‐CT), BFLM and 3‐D backscattered electron microscopy (BSEM) on liver tissue as an alternative good practice multimodal imaging approach.

Results
A workflow is presented facilitating the collection of combined structure‐function 3‐D data (i.e., X, Y & Z) on liver architecture from the micron down to the nanometre scale using the same tissue preparation protocol. We illustrated the strength of this combined microscopy methodology to characterise various aspects of the hepatic vasculature, ranging from such large vessels as branches of the hepatic portal vein and hepatic artery, down to the smallest sinusoidal capillaries. Moreover, we were able to further characterise the subcellular features of a range of hepatic sinusoidal cells including, liver sinusoidal endothelial cells, liver‐associated natural liver cells and Kupffer cells. Above all, we demonstrate the capabilities of this specimen manipulation and microscopy workflow to generate quality microscopic detail and subsequently extract relevant quantitative 3‐D information.

Conclusions
This contribution illustrates the capability that advanced histology imaging can bring to the gastroenterologist and/or pathologist in the fine structure‐function assessment of the liver unit, its associated microvasculature, and the individual make‐up of parenchymal and non‐parenchymal tissue cells. This good practice further allows the instant generation of combined quantitative data about size, shape and volume changes of key microanatomical structures across multiple length scales.
TEMcompression of nano‐particles in environmental mode and with atomic resolution observations
Authors: Epicier Thierry , Joly‐Pottuz Lucile , Jenei Istvan , Stauffer Douglas , Dassenoy Fabrice , Masenelli‐Varlot Karine 
Published: December 2016

Characterization of nanomaterials or materials at the nanoscale has drastically increased during the last decades. This increase can be explained by (i) the necessity to obtain materials with nanometer‐size grains, for instance nanocomposites, and by (ii) the use of nanoparticles in different fields, for instance lubrication applications. A challenge lies in thein situmicrostructural characterization of such materials as it can give access to valuable pieces of information regarding the microstructural changes induced by their use.The availability of dedicated TEM (Transmission Electron Microscopy) holders equipped with force and displacement sensors is of a very high interest to test,in situ,the size‐dependent mechanical properties of nanometer‐sized objects [1,2]. On crystalline nano‐objects, Molecular Dynamics simulations have shown that dislocations nucleate at the surface [3,4]. Therefore, the surface state is of utmost importance in determining the nucleation stresses and types of dislocations. For materials which undergo surface reconstruction or changes in the surface chemistry under vacuum, it is necessary to perform experiments in a controlled environment (i.e. under gas pressure) which reproduces the real one.Recently a Hysitron PI 95 Picoindenter has been installed on a Cs‐corrected FEI TITAN ETEM (Environmental TEM) microscope. It opens the possibility of performingin situcompression under gas pressure, with high resolution imaging. We will presentin situtests of cubic CeO2, a multifunctional oxide widely used in catalysis. Nanocubes are compressed along either under vacuum or under air pressure. Introducing oxygen inside the chamber limits or avoids the reduction of CeO2nanocubes induced more or less rapidly by the electron beam. A comparison of slopes of load‐displacement curves obtained under vacuum at different electron doses and under air pressure (see Figure 1) strongly suggests that ceria reduced as Ce2O3under the effect of an intense electron flux has a smaller Young modulus than unreduced or 'oxidized' ceria. Atomic resolution observations performed during the compression tests reveal the formation of dislocations and stacking faults (see Figure 2). Simulations are planned to further understand the deformation mechanisms as a function of the oxidation state (native, unreduced or oxidized states), as well as their reversibility [5].
Efficient and quantitative phase imaging in two‐ and three‐dimensions using electron ptychography in
STEM
Authors: Nellist Peter , Yang Hao , Jones Lewys , Martinez Gerardo , Rutte Reida , Davis Benjamin , Pennycook Timothy , Simson Martin , Huth Martin , Soltau Heike , Strueder Lothar , Sagawa Ryusuke , Kondo Yukihito , Humphry Martin 
Published: December 2016

Historically, the scanning transmission electron microscope (STEM) has not been widely used for phase contrast imaging because the small bright‐field detector required makes use of only a small fraction of the incident electrons and is therefore inefficient with respect to dose. This limitation has hindered the efficient imaging of light elements in STEM. Alternative modes also have limitations. For example, annular dark‐field (ADF) imaging of graphene only makes use of a few percent of the incident electrons, and annular bright‐field imaging (ABF) requires lens aberrations to form an effective phase plate to get contrast from weakly scattering objects.
Electron ptychography in the STEM was first demonstrated more than 20 years ago in the context of improving image resolution [1]. At that time, the image field of view was restricted by the limitations of the camera technology and data handling technology. Here we make use of the pnCCD (S)TEM camera, a direct electron pixelated detector from PNDetector, mounted on the JEOL ARM200‐CF aberration corrected microscope. The detector has a grid of 264x264 pixels and operates at a speed of 1000 frames‐per‐second (fps). The detector can achieve a speed of up to 20,000 fps through binning/windowing. ADF images can be recorded simultaneously, as shown by the schematic in Fig. 1.
The resulting 4D data set is formed of a series of coherent convergent beam diffraction patterns recorded as a function of illuminating probe position. Here we explore how the bright‐field and dark‐field regions of scattering can be used to enhance the capabilities of STEM. We compare a range of methods that can be used to form the phase image from this data set, including single side‐band [2,3], Wigner distribution deconvolution [4] (used to produce Fig. 2) and ePIE [5]. Phase imaging using ptychography has a relatively simple transfer function [3] and also provides an inherent filter of image noise without reducing the signal strength to form high quality phase images (Fig. 2). Furthermore, the four‐dimensional data set is highly redundant and it is possible to detect and correct for residual aberrations in the image.
The ability to deconvolve lens aberrations can further be used to extract three‐dimensional information from a single STEM image acquisition scan. This is achieved by reconstructing the phase image at a specific depth in the sample, which can be performed even though the microscope may not have been focused at that depth (Fig. 3). Finally, we explore the potential for using information outside the bright‐field disc to enhance STEM imaging.
Chemical arrangement and surface effects in
CoAu
nanoparticles
Authors: Tournus Florent , Loiselet Ophelliam , Sato Kazuhisa , March Katia , Stephan Odile 
Published: December 2016

Nanoparticles associating a noble metal and a ferromagnetic metal are appealing from a magneto‐plasmonics point of view, in addition to the problematics of magnetic anisotropy tailoring (interface anisotropy, phase transformation) and of nanoalloy original geometries. Because Co and Au are immiscible in the bulk phase, and since fcc cobalt and gold have highly different cell parameters, chemically separated structures (core‐shell type) are expected for nanoparticles.
We have studied CoAu cluster assemblies, with a diameter between 3 and 10 nm, prepared by low energy cluster beam deposition (LECBD) where nanoparticles are formed in out‐of‐equilibrium conditions by laser vaporization, then deposited on a substrate under ultrahigh vacuum conditions and protected by a capping layer (amorphous carbon, to avoid oxidation). The nanoparticles' structure and chemical arrangement (see figures) have been investigated by HRTEM, STEM‐HAADF and STEM‐EELS before and after annealing (2h around 500°C). A mapping of the low energy electronic excitations has also been performed by STEM‐EELS, which is a challenge on such small nano‐objects.
As prepared particles are found to be inhomogeneous (as deduced from EELS measurements), with interatomic distances always corresponding to pure gold, and they appear to be surrounded by a shell of lighter HAADF intensity which rapidly transforms upon electron beam exposure in STEM. After annealing, a phase separation is observed and CoAu nanoparticles adopt a core‐shell structure where, as observed by HRTEM (with a clearly visible difference of inter‐plane distances between Co and Au regions), STEM‐HAADF and STEM‐EELS, an off‐centered cobalt core is surrounded by a gold shell (see figure). For both as‐prepared and annealed nanoparticles, the Co is not oxidized thanks to the efficient protection of the thin carbon layer. Using low‐loss STEM‐EELS mapping, we are able to observe some surface contributions, which may reflect collective electronic resonances (surface plasmons), with significant differences between as‐prepared and annealed CoAu nanoparticles (in particular, an intense peak is detected on the gold‐rich regions, around 6 eV).
These results shed light on the atomic‐scale behavior of the Co‐Au nanoalloy, here in an amorphous carbon matrix, which will be compared to other dielectric matrices, and will help us to understand the original magnetic properties of these hybrid nanoparticles.