bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of propagation‐based phase contrast tomography and full‐field optical coherence tomography on bone tissue
Authors: Di Tommaso Sylvaine , Rositi Hugo , Langer Max , Frindel Carole , Olivier Cécile , Peyrin Françoise , Rousseau David 
Published: December 2016

The current huge development of new 3D microscopic techniques (synchrotron microtomography, optical coherence tomography, light sheet microscopy, …) opens a large variety of new perspectives for life sciences. The contrasts of these new microscopies are mostly well understood on samples of known material content such as those used in physics or instrumentation studies. The situation is different when it comes to the interpretation of the contrasts observed with complex heterogeneous media found in biology. Therefore determining which 3D microscopy technique is suited for which biological question is a topic of current interest (see [1,2] for instance in our group).
In this communication, we propose a comparison of the contrast observed with full‐field optical coherence tomography (OCT) and propagation‐based phase contrast tomography (PCT) on bone tissue at similar spatial resolution. A first comparison of OCT with standard absorption microtomography was given in [3] for bones and we extend this comparison to PCT which is known to provide enhanced contrast on bones at multiple scales [4]. The contrast of both these techniques are a priori interesting to be compared since they both rely on discontinuities of refraction index. This produces phase shift in PCT which operates in the X‐ray domain with a monochromatic beam (generated by a synchrotron) while this generates direct intensity reflexion with OCT which only resorts to white light in the visible domain.
As visible in Figure 1, we specifically focussed our attention on the contrast observed in both techniques around the same bone structural unit, a so‐called osteon, at a microscopic scale with images of same spatial resolution (voxel size 3.5µm). It happens that the osteons are visible in PCT while they are not perceptible with conventional absorption micro computed tomography. Also, concentric lamellae, corresponding to the so‐called Harvers system, appear clearly visible in OCT while they are not perceptible with PCT at this spatial resolution. The contrast between the osteon and the surrounding bone tissue, is found in terms of homogeneous regions in PCT. However, this less spatially resolved contrast in PCT is constant throughout the sample while it is spatially variable in OCT where a continuous degradation of the contrast is observed along the direction Z of the propagation of light. We found, as given in Figure 2, that a certain spatial average of some 30 µm along Z was able to improve optimally the contrast across the concentric lamellae when inspected at the surface (up to 500 µm depth) of the sample with OCT. This contributes to establish quantitatively the complementarity of OCT and PCT for the characterization of bones at the microscopic scale.
Unusually high iron enrichment in hard dental tissues of coypu
Authors: Srot Vesna , Salzberger Ute , Bussmann Birgit , Deuschle Julia , Watanabe Masashi , Pokorny Bostjan , Turinek Ida Jelenko , Mark Alison F. , van Aken Peter A. 
Published: December 2016

Living organisms possess a unique capability to form complex bio‐minerals with very diverse compositions and structures. Organic matrix and crystalline constituents are closely linked together in unique material constructions that are formed under conditions of moderate temperature, pressure and pH value. Many of these bio‐minerals show excellent physical and mechanical properties [1, 2] that cannot be reproduced in the laboratory.
Rodents have long opposing pairs of continuously growing incisors that are worn down by gnawing. The front surface of the incisors is enamel consisting of 96 wt% of inorganic material; the inner part is softer dentine that forms the bulk of the teeth [3]. The surfaces of incisors of different rodent species show a characteristic orange‐brown color and are identified with the presence of iron [4].

In our study, the microstructure and the chemical composition of continuously growing incisors from the coypu (
Myocastor coypus
Molina) were investigated in detail using energy‐dispersive X‐ray spectroscopy (EDX) and electron energy‐loss spectroscopy (EELS) combined with scanning transmission electron microscopy (STEM) imaging at high spatial as well as high energy resolution. VG HB501UX, Zeiss SESAM and Jeol ARM200F microscopes were used and the resulting data were combined with knowledge obtained from mechanical testing experiments.

A layer with variable thickness, which has not been observed before, was detected on the outer surface of the incisors as marked on the optical micrograph image (Fig. 1). An annular dark field (ADF)‐STEM image of a cross‐sectional view showing the interface between the Fe‐rich surface layer (Fe‐SL) and Fe‐rich enamel (Fe‐E) is shown in Figure 2a. Analytical investigations of this surface layer showed much higher amounts of iron compared to the concentration values reported in the literature up to now. Within the iron‐rich surface layer we surprisingly detected multiple iron containing varieties where iron is present in predominantly the 3+ valence state, as revealed by studies of electronic structure. O‐K fine structural features suggest the presence of different intermixing levels of Fe phosphate and Fe oxide/hydroxide (Fig. 2b).
The present discoveries will greatly enhance the understanding of the function of the incorporation of iron at the nanoscale level and its effect on the microstructural properties.
Cell surface properties of probiotic Escherichia coli strains
Authors: Pepoyan Astghik , Balayan Marine , Manvelyan Anahit , Isajanyan Marianna , Tsaturyan Vardan , Hovnanyan Margarita , Hovnanyan Karlen 
Published: December 2016

Background.Beneficial effects of probiotic Nissle 1917 on the host health have been shown in a range of investigations(1). During our previous studies the positive effects ofE. coli 2‐1on human and animals organism have also been described(2), and the liquid‐crystal state of cell walls from theE. colicells was shown by the x‐ray diffraction method under the small and large angles (Fig. 1).Taking into account that solid‐liquid interfaces could have a considerable effect on host bacterial physiology(3) we aimed to investigate the cell surface hydrophobicities of probiotic strainsE. coli M‐17andE. coli 2‐1strains.Methods. The probiotic strainsE. coli 2‐1from the probiotic formulation ASAP (Armenia) andE. coli M‐17from the probiotic formulation Colibacteron (Armenia) were used during these investigations. The twenty‐four gut commensalE. colistrains from the four healthy volunteers were used as controls. The cell surface hydrophobicities of theE. colistrains were determined by a MATH test according to Koss and coauthors(4 ), and the crystallization levels of cell walls (35 % water suspensions) from these strains were assessed semi‐quantitatively at 25'C with polarizing microscopy MIN‐8 with Bertrán's prism and increase x 300. The determination of the sizes of structural units carried out by a standard way with the help an eyepiece ‐ a micrometer; the +150W halogen lamp was a light source.Results. Comparative MATH test experiments show that both investigated probiotic strains' cells surfaces are more hydrophobic than the bacterial surfaces of strains from the normal gut microbiota. At the same time, the low crystallization levels of cell wall proteins for probioticE. colistrains were described. Most probably, the comparative hydrophobic structure of bacterial membranes from probiotic strains regulates “probiotic‐characteristics” ofE. coli M‐17andE. coli 2‐1strains.
3D‐
TEM
microstructure analyses of anisotropic and isotropic aerogels of
TiO2
nanoparticles
Authors: Gramm Fabian , Tervoort Elena , Sologubenko Alla , Minas Clara , Rechberger Felix , Bouville Florian , Studart Andre , Niederberger Markus 
Published: December 2016

Aerogels are fascinating materials with low density and high surface area with great application potential in battery materials, fuel‐ and solar cells and many more.(1‐3) These porous structures are conventionally prepared by sol‐gel chemistry and subsequent supercritical drying.(4) In the case of TiO
2
nanoparticles, the ability of the crystalline nanoparticles to undergo oriented attachment is fundamentally important for the self‐assembly into three‐dimensional interconnected networks. Such structures (Fig.1) are prepared by destabilizing highly concentrated dispersions of well‐defined TiO
2
nanocrystals. The gelation results in a percolating network of ultrafine structures which is preserved by supercritical drying. This processing technique allows for the preparation of crystalline, isotropic and translucent aerogels with broad pore size distributions and disordered pore arrangements (Fig.1).(5)

The aim of our study is to produce structures from destabilized dispersions and subsequent unidirectional freeze‐drying. Compared to the aerogel route, this process results in a different macro‐ and microstructure consisting of about 3 µm large units of compacted aerogel structures. Here, the pores are of a more ordered nature due to the freeze drying procedure.
In this work, aerogels prepared by supercritical drying and structures made via freeze‐drying were analyzed microstructurally. Using TEM tomography, we study the morphology of the 3D networks of the nanocrystals within both structures. Critical performance parameters like pore size, connectivity and tortuosity of those structures are analyzed.
New design of Möllenstedt electrostatic biprism setup for off‐axis electron holography
Authors: Cours Robin , Marcelot Cécile , Houdellier Florent 
Published: December 2016

Many different forms of electron holography have been explored or imagined. The off‐axis configuration that uses a post‐specimen electrostatic Möllenstedt biprism (BP) is the most widespread. It can be easily set up in a modern transmission electron microscope (TEM) thanks to the general introduction of field emission guns. The
In situ
Interferometry Transmission Electron Microscope (I2TEM), is a microscope designed to easily performed electron holography experiment [1,2,3]. The microscope is equipped with a 300kV cold field emission source, one biprism (BP) installed before the three condenser lenses, and three biprisms placed between the intermediate lenses.

Regarding the high numbers of biprisms used in this microscope, their quality, their stability, and their easy servicing are one of the major concerns to maintain the performance of the machine. A wire surrounded with a ground anode basically constitutes commercial biprisms. The wire is, in most of case, produced by coating ultrasmall quartz fibers with noble metals. The resulting biprisms, although they are quite small by most fabrication standards (approximately 700 nm in diameter), can have various mechanical, electrical, structural … properties. Furthermore, their preparation methods are, in general, not very reproducible.
We have developed a new method to produce biprism in a more reproducible way, maintaining the best mechanical and electrical performance of the wire. Regarding the H‐bar shape of these new wires, due to the FIB preparation, the electric field that appears between the wire and the ground electrode, could be strongly affected by the system geometry. Finite element models using Comsol Multiphysics [4], have been used to better understand this effect which can, combining with the biprism holder shape, strongly influence the final hologram performance. We have then proposed a new biprism holder, which overcome all these drawbacks, and test these news holders, with new FIB prepared wires inside the I2TEM microscope.
Model calculations for low‐lossEELspectra of2Dmultilayer systems
Authors: Mohn Michael , Hambach Ralf , Wachsmuth Philipp , Kaiser Ute 
Published: December 2016

Collective electronic excitations (plasmons) in single‐layer and few‐layer graphene have been studied extensively in the past few years. In particular, the dispersion and nature of the π plasmon peak in free‐standing single‐layer graphene was investigated by means of momentum‐resolved electron energy‐loss spectroscopy (MREELS) [1‐3]. Besides, it was also studied how the transition from mono‐ to multilayer graphene changes the shape of EEL spectra. Within a layered electron‐gas (LEG) model, this transition can be modeled very precisely [4,5].For other 2D materials such as transition metal dichalcogenides (TMDs), however, this approach may be highly inaccurate. We therefore evaluate more precise model calculations for multilayer systems. Our calculations are based on time‐dependent DFT calculations for the individual monolayers. The plane‐wave pseudopotential DFT code abinit [6] is used to simulate the ground state within local density approximation (LDA). The linear response is then calculated within random‐phase approximation (RPA) using the dp‐code [7]. Compared to the LEG model where the monolayers are assumed to be perfectly 2‐dimensional and homogeneous, we preserve the layers' microscopic structure in our calculations.We demonstrate that only by taking the finite thickness of the constituent monolayers into account, the spectra of multilayer MoS2can be modeled correctly (see the figure). Our calculations can be also applied to arbitrary van‐der‐Waals heterostructures. Our results are directly compared to MREEL spectra recorded with a Zeiss Libra 200 based TEM prototype (“SALVE I”, [8,2]) equipped with a monochromator and an Ω type in‐column energy filter. This allows for the verification of our calculations over a large range of energy losses (0‐40 eV) and different momentum transfers within the Brillouin zone. [9]
Local Information Powers Heterogeneous Catalysis Research:TEMInvestigation of Industrial Relevant Cu/ZnO/Al2O3 Catalysts for Methanol Synthesis
Authors: Lunkenbein Thomas , Frei Elias , Schumann Julia , Behrens Malte , Willinger Marc Georg , Schlögl Robert 
Published: December 2016

In a simplified picture a heterogeneous catalyst can be described as a high energy material, which is composed of two important parts: bulk and surface. The bulk is defined by a certain crystal and electronic structure as well as defect concentration, and reflects the real structure of the catalyst. It is responsible for the formation and stabilization of the active surface. Although physical and chemical information on the real and surface structure can be obtained by integral methods, important local fluctuations from the ideal structure, which are essential for the catalytic performance, in the catalyst composition may be overlooked.1This highlights the significance of transmission electron microscopy (TEM) as the tool for the local description of the nano‐ and/or mesoscale of heterogeneous catalysts.Here, we focus on a transmission electron microscopic (TEM) description of the local nano‐ and mesoscale of industrial relevant Cu/ZnO/Al2O3catalyst for methanol synthesis. Methanol, one of the most important industrial chemicals, is produced from syngas (CO, CO2, H2) at high pressure (50‐80 bar) and elevated temperature (240‐280 °C) and is considered as a prospective key‐compound for chemical energy and hydrogen storage. The working mechanisms of this industrial methanol catalyst have been investigated extensively.2However, its actual active phase is still debated controversially. On the one hand, the catalytic odyssey may be caused by material, pressure and time gaps, which often do not mirror industrial relevant conditions. On the other hand, the diversity of results indicates the difficulty of investigating and understanding this complex catalyst system, in particular due to the lack of visual local information.Our local observations tackle a detailed description of the mesostructure of the catalyst, the real structure of Cu nanoparticles and the formation of a special polymorph of layered ZnO on top of the Cu nanoparticles after reductive activation on industrial relevant ternary Cu/ZnO/Al2O3catalyst.1bIn addition, we will highlight the temperature, gas and time dependent evolution of this metastable layered ZnO polymorph from minutes to months (Figure 1).3In conclusion, the results demonstrate the power of local TEM investigation in heterogeneous catalysis research. In combination with complementary integral data, they allow a detailed understanding of the system, which would be otherwise hard to obtain. The findings illustrate that methanol synthesis can be considered as an interface mediated process between Cu and ZnO.
Energy dispersive x‐ray analysis of platinum‐nickel nanoparticles embedded in hollow graphitic spheres used as fuel‐cell catalysts
Authors: Swertz Ann‐Christin , Mezzavilla Stefano , Pfänder Norbert , Schüth Ferdi , Lehmann Christian W. 
Published: December 2016

Introduction

Proton Exchange Membrane Fuel Cells (PEM‐FCs) are known as potential energy conversion devices in transportation systems. For the efficiency of these fuel cells a highly efficient and stable catalyst is needed. Platinum‐Nickel bimetallic nanoparticles embedded in hollow graphitic spheres (HGS) have been proven as highly active catalyst for the oxygen‐reduction reaction which plays a key role in the efficiency of PEM‐FCs.
1

These catalysts are synthesized via the confined‐space alloying approach. The synthesis of PtNi@HGS starts with the impregnation of HGS with the metal precursors. After high temperature annealing treatments metallic nanoparticles with a small size (3.5 nm) and a narrow particle size distribution encapsulated in the pores of the HGS can be obtained.
2

Methods
In this study the PtNi@HGS synthesized via confined‐space alloying were analyzed using different electron microscopy methods like HAADF‐STEM, EDX line scan and elemental mapping. Especially the electrochemically degraded samples were of great interest questioning the distribution of the two metals in the metallic nanoparticles.

To confirm the experimental results and to explain the structure of the nanoparticles after degradation theoretical EDX line scan profiles were calculated using Monte‐Carlo‐simulations
3
.

Results
In HR‐STEM images the structure of this catalyst system can be seen clearly: The crystalline metallic nanoparticles are encapsulated in pores of the hollow graphitic spheres (fig. 1). The EDX elemental mapping shows that the metal nanoparticles contain Pt and Ni. EDX line scans with a high spatial resolution clearly evidence a 0.5‐1 nm thick Pt‐rich outer shell and Pt‐Ni core after electrochemical degradation of the catalyst.
To confirm the experimental results and to explain the structure of the nanoparticles theoretical EDX line scan profiles were calculated using Monte‐Carlo simulations. Simulated line scans of PtNi@Pt particles (0.5 nm shell and 3 nm core) show profiles similar to the experimental data as shown in figure 2. This excellent agreement supports the formation of core shell particles during the electrochemical degradation of the catalyst.
Synchrotron Infrared Microspectroscopy, an innovative approach to investigate tissue chemical changes in mouse model of Pompe of disease (glycogenosis type
II
) and to assess efficiency in gene therapy
Authors: Dubreil Laurence , Hordeaux Juliette , Deniaud Johan , Lagalice Lydie , Bey Karim , Sandt Christophe , Jamme Frederic , Colle Marie‐Anne 
Published: December 2016

Pompe disease is an autosomal recessive disorder caused by the deficiency of the lysosomal enzyme acid alpha‐glucosidase (GAA). The disease is characterized by lysosomal glycogen storage in heart and muscles, and manifests as a fatal cardiomyopathy in infantile form. Cardiac correction by enzyme replacement therapy (ERT) has recently prolonged the lifespan of these patients, revealing a new natural history. The emergent neurologic phenotype and the poor correction of skeletal muscles in survivors are currently partly attributed to central nervous system (CNS) glycogen storage, uncorrected by ERT. A gene therapy strategy using AAV vectors delivered to cerebrospinal fluid has been set up to restore GAA activity into the CNS. We demonstrate the use of Infrared Micro spectroscopy with synchrotron light as an innovative tool to map glycogen at the subcellular level in motor neurons and cardiac fibers. Principal Component Analysis (PCA) of infrared spectral data from motor neurons and cardiac fibers show that both treated and wild‐type animals are merged in the same cluster whereas infrared spectra obtained from untreated Pompe mice are characterized by increase of the bands assigned to the carbohydrates of glycogen.
This new analytical approach that allows an highly sensitive and resolutive direct probing of tissue glycogen is required to explore early biochemical change at a subcellular level and therefore to assess therapeutic efficiency for Pompe disease.
Controlled production and growth of hexagonal gold nanostructures during self‐assembly on a Ge(001) surface
Authors: Gauquelin Nicolas , Jany Benedykt , Nikiel Marek , Wilhammar Tom , van Den Bos Karel , van Aert Sandra , Szajna Konrad , Verbeeck Johann , Van Tendeloo Gustaff , Krok Franziszek 
Published: December 2016

Self‐organized gold nanostructures on Ge(001) surfaces are currently of special interest due to their applications for mono‐molecular electronic devices and the growth of Ge nanowires. The understanding of electrical as well as physical properties of the system is of great importance and is strongly linked to its atomic structure.
Here, we report on studies concerning post‐annealing induced nanostructure formation after room temperature deposition of a thin film of Au on Ge(001) in Ultra High Vaccuum (UHV). Deposition of 6 monolayers of Au by Molecular Beam Epitaxy (MBE) resulted in the formation of a continuous Au overlayer which was confirmed to be crystalline by Reflection High Energy Electron Diffraction (RHEED). Just after deposition, the samples were post‐annealed in UHV to temperatures ranging from 473 K to 773 K with different cooling rates. The self‐organized structures, in the form of Au nanoislands, were characterized by HR‐SEM and HR‐STEM methods as well as EBSD. It has been found that a preferential island orientation exists along the crystallographic direction of the substrate surface as can be seen in Fig. 1(a),(b). For an annealing temperature close to the eutectic temperature of the Au/Ge system (640 K), a change in size and shape of the Au nanoislands is observed as well as the occurence of the hexagonal phase of gold, indicating eutectic melting of the system as can be seen in Fig. 1. Au(011) orientation of the Au islands with respect to the Ge surface was revealed, independent of the annealing temperature Fig. 1(c),(d). TEM measurements of Au/Ge(001) sample cross sections revealed that the nanoislands created upon annealing at T640 K part of the islands are buried beneath the substrate surface (Fig. 1g), which confirms eutectic AuGe melting. The chemical composition of the Au/Ge interface was uncovered using quantitative atomically resolved HAADF‐STEM and indicates the absence of alloying (Fig. 1f and 1h). The crystallographic structure of the Au islands and the presence of hexagonal gold as well as the Au/Ge interface were studied by quantitative atomically resolved HAADF‐STEM allowing the determination of the structure.
N.G. and J.V. acknowledge funding from the European Research Council under the 7th Framework Program (FP7), ERC Starting Grant 278510 VORTEX. F.K. acknowledges funding from the Polish National Science Center, grant no. DEC‐2012/07/B/ST5/00906. All authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative (Reference No. 312483‐ESTEEM2).