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The interaction between water molecules and surfaces in porous carbon‐based materials plays a significant role in various fields including but not limited to catalysis, gas sorption, or electrochemical energy storage and conversion. The incorporation of nitrogen enhances the hydrophilicity of typically rather nonpolar carbon‐based materials but the molecular understanding of water chemical configuration in such porous materials remains incomplete. Water adsorption on nitrogen‐containing nanoporous carbon surfaces is governed by a subtle balance between water–water and water–surface hydrogen bonding interactions, which together determine the water structures formed and their stability. In this work, in situ Scanning Transmission X‐ray microscopy performed on individual nanoporous carbon particles under a humid atmosphere is used to elucidate the interactions between nitrogen‐containing carbon surfaces and water molecules. The hydrogen bonding of water is found to be nonuniform within the particles and to depend on the nanopore size and the chemical bonding of nitrogen atoms. The nature of the nitrogen sites interacting with water is further characterized by resonance inelastic X‐ray Scattering and near ambient pressure X‐ray Photoelectron Spectroscopy. This study provides new perspectives on water interaction when confined in nanoporous nitrogen‐rich carbons. [ABSTRACT FROM AUTHOR]

X-ray spectromicroscopy is extensively utilized for nondestructive mapping of chemical states in materials. However, understanding and analyzing the geometric and topological aspects of such data pose challenges due to their representation in 4D space, encompassing (x, y, z) coordinates along with the energy (E) axis and often extending to 5D space with the inclusion of time (t) or reaction degree. In this study, we addressed this challenge by developing a new approach and introducing a device named `4D-XASView', specifically designed for visualizing X-ray absorption fine structures (XAFS) data in 4D (comprising 3D space and energy), through a multi-projection system, within the virtual reality (VR) environment. As a test case for the new system, X-ray spectromicroscopy measurements were conducted on a specimen prepared from serpentinized harzburgite sourced from the upper mantle section of the Oman ophiolite. Our 4D-XASView facilitates the visualization and analysis of the geometric and topological aspects of the data using VR goggles, enabling detailed exploration of microstructures via rotation and zooming functionalities. This capability allows us to extract XAFS spectral data by selecting specific positions and regions, thereby aiding in the identification of `trigger sites' (magnetite in serpentine), which are characteristic locations within materials that substantially influence the macroscopic propagation of reactions. Our methodology establishes a new platform for analyzing 4D or 5D XAFS data that has applicability potential in various other multidimensional datasets, including microstructures coupled with spectroscopy and diffraction data.

The typical output of a STXM (Scanning Transmission X-ray (spectro)Microscopy) measurement is a data cube consisting of a set of images (measurements of X-ray transmission at a grid of pixels) taken at a sequence of incident energies. As with any experimental measurement, this raw data must be reduced to some standard form and interpreted. In this paper, I review the basics of how to go from raw data to information about the sample. I will discuss the fundamentals of X-ray spectromicroscopy, data reduction, descriptive and model-based analysis, and available software, with examples taken from the literature.

Implementation of extreme ultraviolet (EUV) lithography in high-volume semiconductor manufacturing requires a reliable and scalable EUV resist platform. A mechanistic understanding of the pros and cons of different EUV resist materials is critically important. However, most material characterization methods with nanometer resolution use an x-ray photon or electron beam as the probe, which often cause damage to the photoresist film during measurement. Here, we illustrated the use of non-destructive infrared nanospectroscopy [or nano-Fourier-Transform infrared spectroscopy (nano-FTIR)] to obtain spatially resolved composition information in patterned photoresist films. Clear evidence of exposure-induced chemical modification was observed at a spatial resolution down to 40 nm, well below the diffraction limit of infrared light. With improvements, such a nano-FTIR technique with nanoscale spatial resolution, chemical sensitivity, and minimal radiation damage can be a promising candidate for the fundamental study of material properties relevant to EUV lithography.

The functions of soils are intimately linked to their three‐dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 µm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi‐isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting‐edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates. [ABSTRACT FROM AUTHOR]

Solid-state batteries (SSB), characterized by solid-state electrolytes—in particular inorganic ones (ISSE)—are an ideal option for the safe implementation of metallic Li anodes. Even though SSBs with ISSEs have been extensively investigated over the last two decades, they still exhibit a series of technological drawbacks. In fact, mechano-chemical issues, mainly the stability of the electrolyte/anode interface, hinder their widespread application. The present investigation focusses on a thin-film LMO (Lithium-Manganese-Oxide)/LAGP (LiAlGe Phosphate)/Copper, anodeless Lithium-metal battery and explores the morphochemical evolution of the electrode/electrolyte interfaces with synchrotron-based Scanning Photoelectron Microscopy (SPEM) of intact pristine and cycled cells. Chemical images were acquired with submicrometer resolution, to highlight the coupled geometrical and chemical-state changes caused by electrochemical ageing. Geometrical changes of the electrolyte/cathode interface were induced by periodic volume changes, causing de-cohesion of the solid-solid contact, but no chemical-state changes accompany the cathodic damaging mode. Instead, shape changes of the electrolyte/anode region pinpoint the correlation between mechanical damaging with the decomposition of the LAGP ISSE, due to the reduction of Ge, triggered by the contact with elemental Li. The micro-spectroscopic approach adopted in this study enabled the assessment of the highly localized nature of the cathodic and anodic degradation modes in SSB devices and to single out the chemical and mechanical contributions. [ABSTRACT FROM AUTHOR]

Reef-building corals and their aragonite (CaCO3) skeletons support entire reef ecosystems, yet their formation mechanism is poorly understood. Here we used synchrotron spectromicroscopy to observe the nanoscale mineralogy of fresh, forming skeletons from six species spanning all reef-forming coral morphologies: Branching, encrusting, massive, and table. In all species, hydrated and anhydrous amorphous calcium carbonate nanoparticles were precursors for skeletal growth, as previously observed in a single species. The amorphous precursors here were observed in tissue, between tissue and skeleton, and at growth fronts of the skeleton, within a low-density nano- or microporous layer varying in thickness from 7 to 20 µm. Brunauer-Emmett-Teller measurements, however, indicated that the mature skeletons at the microscale were space-filling, comparable to single crystals of geologic aragonite. Nanoparticles alone can never fill space completely, thus ion-by-ion filling must be invoked to fill interstitial pores. Such ion-by-ion diffusion and attachment may occur from the supersaturated calcifying fluid known to exist in corals, or from a dense liquid precursor, observed in synthetic systems but never in biogenic ones. Concomitant particle attachment and ion-by-ion filling was previously observed in synthetic calcite rhombohedra, but never in aragonite pseudohexagonal prisms, synthetic or biogenic, as observed here. Models for biomineral growth, isotope incorporation, and coral skeletons' resilience to ocean warming and acidification must take into account the dual formation mechanism, including particle attachment and ion-by-ion space filling.

Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. In spectro-ptychography, a sample is rastered through a focused X-ray beam with varying photon energy so that a series of phaseless diffraction data are recorded. Each chemical component in the material under investigation has a characteristic absorption and phase contrast as a function of photon energy. Using a dictionary formed by the set of contrast functions of each energy for each chemical component, it is possible to obtain the chemical composition of the material from high-resolution multi-spectral images. This paper presents SPA (spectroscopic ptychography with alternating direction method of multipliers), a novel algorithm to iteratively solve the spectroscopic blind ptychography problem. First, a nonlinear spectro-ptychography model based on Poisson maximum likelihood is designed, and then the proposed method is constructed on the basis of fast iterative splitting operators. SPA can be used to retrieve spectral contrast when considering either a known or an incomplete (partially known) dictionary of reference spectra. By coupling the redundancy across different spectral measurements, the proposed algorithm can achieve higher reconstruction quality when compared with standard state-of-the-art two-step methods. It is demonstrated how SPA can recover accurate chemical maps from Poisson-noised measurements, and its enhanced robustness when reconstructing reduced-redundancy ptychography data using large scanning step sizes is shown.

Mounting evidence of recent spectromicroscopic insights have revealed that the distribution of mineral‐associated organic matter (OM) at the microscale and nanoscale is organized heterogeneously in patchy and piled‐up arrangements of varying thickness. Spectromicroscopic approaches could show local deterministic features of distinct OM and mineral composition that influence the heterogeneous lateral OM distribution. OM–OM interactions shape vertical and three‐dimensional OM structures with potentially multilayered composition. Conceptualizing mineral‐associated OM as patchy‐distributed and piled‐up has critical implications for our understanding of soil ecosystem functions as it defines their functional properties in compartmentalized regions at the microscale and nanoscale. The concentrated storage of OM associated to only a minor part of mineral surfaces implies that carbon sequestration may be decoupled from a direct limitation by the amount of fine mineral particles while sustaining mineral surface functionality in other parts. At the microscale and nanoscale, differences in altered surface properties, compartmentalized microhabitats, and biotic architectures shape a conceptual understanding where OM storage and other soil functions are driven by spatially resolved interactions. This novel conceptual framework warrants experimental approaches to incorporate the patchy and piled‐up arrangement of OM and upscale potential effects of its heterogeneous arrangement to systematically understand the effectiveness of soil functions. [ABSTRACT FROM AUTHOR]

Solid-state batteries (SSB), characterized by solid-state electrolytes—in particular inorganic ones (ISSE)—are an ideal option for the safe implementation of metallic Li anodes. Even though SSBs with ISSEs have been extensively investigated over the last two decades, they still exhibit a series of technological drawbacks. In fact, mechano-chemical issues, mainly the stability of the electrolyte/anode interface, hinder their widespread application. The present investigation focusses on a thin-film LMO (Lithium-Manganese-Oxide)/LAGP (LiAlGe Phosphate)/Copper, anodeless Lithium-metal battery and explores the morphochemical evolution of the electrode/electrolyte interfaces with synchrotron-based Scanning Photoelectron Microscopy (SPEM) of intact pristine and cycled cells. Chemical images were acquired with submicrometer resolution, to highlight the coupled geometrical and chemical-state changes caused by electrochemical ageing. Geometrical changes of the electrolyte/cathode interface were induced by periodic volume changes, causing de-cohesion of the solid-solid contact, but no chemical-state changes accompany the cathodic damaging mode. Instead, shape changes of the electrolyte/anode region pinpoint the correlation between mechanical damaging with the decomposition of the LAGP ISSE, due to the reduction of Ge, triggered by the contact with elemental Li. The micro-spectroscopic approach adopted in this study enabled the assessment of the highly localized nature of the cathodic and anodic degradation modes in SSB devices and to single out the chemical and mechanical contributions.

Resistive switching in metal oxides is believed to be caused by a temperature and electric field driven redistribution of oxygen vacancies within a nanometer sized conductive filament. Accordingly, gaining detailed information about the chemical composition of conductive filaments is of key importance for a comprehensive understanding of the switching process. In this work, spectromicroscopy is used to probe the electronic structure of conductive filaments in Ta2O5‐based memristive devices. It is found that resistive switching leads to the formation of a conductive filament with an oxygen vacancy concentration of ≈20%. Spectroscopic insights provide detailed information about the chemical state of the tantalum cations and show that the filament is not composed of a metallic Ta0 phase. As an extreme case, devices after an irreversible dielectric breakdown are investigated. These devices feature larger conductive channels with higher oxygen vacancy concentrations. Using the experimental data as input for finite element simulations, the role of thermodiffusion for the formation process of conductive filaments is revealed. It is demonstrated that thermodiffusion is not the dominating effect for the filament formation here but might play a role in accelerating the forming process, as well as in the stabilization of the filament. [ABSTRACT FROM AUTHOR]

The understanding and control of early hydration of tricalcium silicate (C₃S) is of great importance to cement science and concrete technology. However, traditional characterization methods are incapable of providing morphological and spectroscopic information about in situ hydration at the nanoscale. Using soft X-ray spectromicroscopy, we report the changes in morphology and molecular structure of C₃S at an early stage of hydration. In situ C₃S hydration in a wet cell, beginning with induction (~1 h) and acceleration (~4 h) periods of up to ~8 h, was studied and compared with ex situ measurements in the deceleration period after 15 h of curing. Analysis of the near-edge X-ray absorption fine structure showed that the Ca binding energy and energy splitting of C₃S changed rapidly in the early age of hydration and exhibited values similar to calcium silicate hydrate (C-S-H). The formation of C-S-H nanoseeds in the C₃S solution and the development of a fibrillar C-S-H morphology on the C₃S surface were visualized. Following this, silicate polymerization accompanied by C-S-H precipitation produced chemical shifts in the peaks of the main Si K edge and in multiple scattering. However, the silicate polymerization process did not significantly affect the Ca binding energy of C-S-H.

Oxygen migration in tantalum oxide, a promising next-generation storage material, is studied using in operando X-ray absorption spectromicroscopy. This approach allows a physical description of the evolution of conduction channel and eventual device failure. The observed ring-like patterns of oxygen concentration are modeled using thermophoretic forces and Fick diffusion, establishing the critical role of temperature-driven oxygen migration.

Drug nanocarriers (NCs) with sizes usually below 200 nm are gaining increasing interest in the treatment of severe diseases such as cancer and infections. Characterization methods to investigate the morphology and physicochemical properties of multifunctional NCs are key in their optimization and in the study of their in vitro and in vivo fate. Whereas a variety of methods has been developed to characterize "bulk" NCs in suspension, the scope of this review is to describe the different approaches for the NC characterization on an individual basis, for which fewer techniques are available. The accent is put on methods devoid of labelling, which could lead to artefacts. For each characterization method, the principles and approaches to analyze the data are presented in an accessible manner. Aspects related to sample preparation to avoid artefacts are indicated, and emphasis is put on examples of applications. NC characterization on an individual basis allows gaining invaluable information in terms of quality control, on: i) NC localization and fate in biological samples; ii) NC morphology and crystallinity; iii) distribution of the NC components (drugs, shells), and iv) quantification of NCs' chemical composition. The individual characterization approaches are expected to gain increasing interest in the near future. [ABSTRACT FROM AUTHOR]

Dopants and alloying elements are commonly introduced in amorphous carbon (a-C) materials to tailor their mechanical and tribological properties. While most published studies have focused on doping and alloying a-C coatings with metals or metalloids, doping a-C films with rare-earth elements has only recently been explored. Notably, our understanding of the shear-induced structural changes occurring in rare-earth-element-containing a-C films is still elusive, even in the absence of any liquid lubricants. Here, the friction response of Eu- and Gd-containing a-C films with low hydrogen content deposited by HiPIMS on silicon was evaluated in open air and at room temperature. The load-dependent friction measurements indicated that the introduction of Gd ((2.3 ± 0.1) at.%) and Eu ((2.4 ± 0.1) at.%) into the a-C matrix results in a significant reduction of the shear strength of the sliding interfaces ((41 ± 2) MPa for a-C, (16 ± 1) MPa for a-C:Gd 2.3 at.% , and (11 ± 2) MPa for a-C:Eu 2.4 at.% ). NEXAFS spectromicroscopy experiments provided evidence that no stress-assisted sp 3 -to-sp 2 rehybridization of carbon atoms was induced by the sliding process in the near-surface region of undoped a-C, while the amount of sp 2 -bonded carbon progressively increased in a-C:Gd 2.3 at.% and a-C:Eu 2.4 at.% upon increasing the applied normal load in tribological tests. The formation of an sp 2 -bonded carbon-rich surface layer in a-C:Gd 2.3 at.% and a-C:Eu 2.4 at.% films was not only proposed to be the origin for the reduced duration of the running-in period in tribological test, but was also postulated to induce shear localization within the sp 2 -carbon-rich layer and transfer film formation on the countersurface, thus decreasing the interfacial shear strength. These findings open the path for the use of Gd- and Eu-containing a-C even under critical conditions for nearly hydrogen-free a-C films (i.e., humid air).

The novel approach was proposed for detailed high-resolution studies of morphology and physico-chemical properties concomitantly at one measurement spot of E. coli bacterial cells culture immobilized onto silicon wafer surface in UHV conditions applying PhotoEmission Electron Microscopy under Hg lamp irradiation. For the E. coli characterization scanning electron microscopy (electron beam) and X-ray photoelectron spectroscopy (X-ray tube radiation) were applied prior to PhotoEmission Electron Microscopy measurements. In spite of irradiation doses collected for the cell arrays we were successful in detection of high-resolution images even of single E. coli bacterium by PhotoEmission Electron Microscopy technique followed by detailed high-resolution morphology studies by scanning electron microscopy. These results revealed widespread stability of the E. coli membranes shape after the significant number of applied characterization techniques.

Sea urchin larvae have an endoskeleton consisting of two calcitic spicules. The primary mesenchyme cells (PMCs) are the cells that are responsible for spicule formation. PMCs endocytose sea water from the larval internal body cavity into a network of vacuoles and vesicles, where calcium ions are concentrated until they precipitate in the form of amorphous calcium carbonate (ACC). The mineral is subsequently transferred to the syncytium, where the spicule forms. Using cryo-soft X-ray microscopy we imaged intracellular calcium-containing particles in the PMCs and acquired Ca-L2,3 X-ray absorption near-edge spectra of these Ca-rich particles. Using the prepeak/main peak (L2′/ L2) intensity ratio, which reflects the atomic order in the first Ca coordination shell, we determined the state of the calcium ions in each particle. The concentration of Ca in each of the particles was also determined by the integrated area in the main Ca absorption peak. We observed about 700 Ca-rich particles with order parameters, L2′/ L2, ranging from solution to hydrated and anhydrous ACC, and with concentrations ranging between 1 and 15 M. We conclude that in each cell the calcium ions exist in a continuum of states. This implies that most, but not all, water is expelled from the particles. This cellular process of calcium concentration may represent a widespread pathway in mineralizing organisms. [ABSTRACT FROM AUTHOR]

Reef-building corals and their aragonite (CaCO3) skeletons support entire reef ecosystems, yet their formation mechanism is poorly understood. Here we used synchrotron spectromicroscopy to observe the nanoscale mineralogy of fresh, forming skeletons from six species spanning all reef-forming coral morphologies: Branching, encrusting, massive, and table. In all species, hydrated and anhydrous amorphous calcium carbonate nanoparticles were precursors for skeletal growth, as previously observed in a single species. The amorphous precursors here were observed in tissue, between tissue and skeleton, and at growth fronts of the skeleton, within a low-density nano- or microporous layer varying in thickness from 7 to 20 µm. Brunauer-Emmett-Teller measurements, however, indicated that the mature skeletons at the microscale were space-filling, comparable to single crystals of geologic aragonite. Nanoparticles alone can never fill space completely, thus ion-by-ion filling must be invoked to fill interstitial pores. Such ionby- ion diffusion and attachment may occur from the supersaturated calcifying fluid known to exist in corals, or from a dense liquid precursor, observed in synthetic systems but never in biogenic ones. Concomitant particle attachment and ion-by-ion filling was previously observed in synthetic calcite rhombohedra, but never in aragonite pseudohexagonal prisms, synthetic or biogenic, as observed here. Models for biomineral growth, isotope incorporation, and coral skeletons' resilience to ocean warming and acidification must take into account the dual formation mechanism, including particle attachment and ion-by-ion space filling. [ABSTRACT FROM AUTHOR]

Complex metal hydrides provide high‐density hydrogen storage, which is essential for vehicular applications. However, the practical application of these materials is limited by thermodynamic and kinetic barriers present during the dehydrogenation and rehydrogenation processes as new phases form inside parent phases. An improved understanding of the mixed‐phase mesostructures and their interfaces will assist in improving cyclability. In this work, the phase evolution during hydrogenation of lithium nitride and dehydrogenation of lithium amide with lithium hydride is probed with scanning transmission X‐ray microscopy at the nitrogen K edge. With this technique, core–shell structures are observed in particles of both partially hydrogenated Li3N and partially dehydrogenated LiNH2 + 2LiH. To generate these structures, the rate‐limiting step must shift from internal hydrogen diffusion during hydrogenation to the formation of hydrogen gas at the surface during desorption. [ABSTRACT FROM AUTHOR]

Spatial resolution tests were performed on beamline 1.4.4 at the Advanced Light Source in Berkeley, CA, USA, a third-generation synchrotron light source. This beamline couples the high-brightness synchrotron source to a Thermo-Electron Continumum XL infrared microscope. Two types of resolution tests were performed in both the mid-IR and near-IR. The results are compared with a diffraction-limited spot size theory. At shorter near-IR wavelengths the experimental results begin to deviate from diffraction-limited so a combined diffraction-limit and electron-beam-source-size model is employed. This description shows how the physical electron beam size of the synchrotron source begins to dominate the focused spot size at higher energies. The transition from diffraction-limited to electron-beam-size-limited performance is a function of storage-ring parameters and the optical demagnification within the beamline and microscope optics. The discussion includes how different facilities, beamlines and microscopes will affect the achievable spatial resolution. As synchrotron light sources and other next-generation accelerators such as energy-recovery LINACs and free-electron lasers achieve smaller beam emittances, beta-functions and/or energy spreads, diffraction-limited performance can continue to higher-energy beams, perhaps ultimately into the extreme ultraviolet.

At the Advanced Light Source at Lawrence Berkeley National Laboratory, we are investigating how to increase both the speed and resolution of synchrotron infrared imaging. Synchrotron infrared beamlines have diffraction-limited spot sizes and high signal to noise, however spectral images must be obtained one point at a time and the spatial resolution is limited by the effects of diffraction. One technique to assist in speeding up spectral image acquisition is described here and uses compressive imaging algorithms. Compressive imaging can potentially attain resolutions higher than allowed by diffraction and/or can acquire spectral images without having to measure every spatial point individually thus increasing the speed of such maps. Here we present and discuss initial tests of compressive imaging techniques performed with ALS Beamline 1.4.3?s Nic-Plan infrared microscope, Beamline 1.4.4 Continuum XL IR microscope, and also with a stand-alone Nicolet Nexus 470 FTIR spectrometer.

Detailed spatial resolution tests were performed on beamline 1.4.4 at the Advanced Light Source synchrotron facility in Berkeley, CA. The high-brightness synchrotron source is coupled at this beamline to a Thermo-Electron Continumum XL infrared microscope. Two types of resolution tests in both the mid-IR (using a KBr beamsplitter and an MCT-A* detector) and in the near-IR (using a CaF2 beamsplitter and an InGaAS detector) were performed and compared to a simple diffraction-limited spot size model. At the shorter wavelengths in the near-IR the experimental results begin to deviate from only diffraction-limited. The entire data set is fit using a combined diffraction-limit and demagnified electron beam source size model. This description experimentally verifies how the physical electron beam size of the synchrotron source demagnified to the sample stage on the endstation begins to dominate the focussed spot size and therefore spatial resolution at higher energies. We discuss how different facilities, beamlines, and microscopes will affect the achievable spatial resolution.

PB1-F2 is a non-structural protein of influenza A viruses (IAV) that modulates viral pathogenesis in a host-specific manner. In mammals, this protein has been shown to increase IAV virulence by delaying the early immune response and, eventually, exacerbating lung inflammation at the late stage of infection. PB1-F2 is a small protein, but displays very high sequence polymorphism and sequence length disparity depending on viral strain. These features result in strong variations in the cellular activity of PB1-F2. Studies have also reported that the effect of PB1-F2 is cell-type dependent. It has notably been shown that PB1-F2 can promote apoptosis in immune cells, but not in epithelial cells. This phenomenon appears to be partly related to the higher order structure of the protein, given that the presence of PB1-F2 β-aggregated structures in infected immune cells correlates with cell death induction. In this work, we evaluated, by synchrotron Fourier transform infrared spectromicroscopy, the impact of the transient expression of PB1-F2 on the biochemical composition of the human epithelial cell line HEK293T. Two PB1-F2 variants that are closely related to each other but derived from a strain with high [A/BrevigMission/1/1918 (H1N1)] or a low [A/WSN/1933 (H1N1)] virulence were studied here. Infrared spectra analysis revealed no specific enrichment of β-aggregated structures in PB1-F2-expressing cells. Nevertheless, this analysis suggested that there is a higher content of β-sheet secondary structures in the PB1-F2 from A/WSN/1933 than that from A/BrevigMission/1/1918. Our data also showed no change in membrane composition in the presence of PB1-F2, implying that PB1-F2 does not promote apoptosis in HEK293T cells. Finally, we found that the PB1-F2 from A/WSN/1933 interferes with adenosine triphosphate production, suggesting that this PB1-F2 variant may disturb the mitochondrial activity.

Preserved labile tissues (e.g., skin, muscle) in the fossil record of terrestrial vertebrates are increasingly becoming recognized as an important source of biological and taphonomic information. Here, we combine a variety of synchrotron radiation techniques with scanning electron and optical microscopy to elucidate the structure of 72 million-year-old squamous (scaly) skin from a hadrosaurid dinosaur from the Late Cretaceous of Alberta, Canada. Scanning electron and optical microscopy independently reveal that the three-dimensionally preserved scales are associated with a band of carbon-rich layers up to a total thickness of ∼75 microns, which is topographically and morphologically congruent with the stratum corneum in modern reptiles. Compositionally, this band deviates from that of the surrounding sedimentary matrix; Fourier-transform infrared spectroscopy and soft X-ray spectromicroscopy analyses indicate that carbon appears predominantly as carbonyl in the skin. The regions corresponding to the integumentary layers are distinctively enriched in iron compared to the sedimentary matrix and appear with kaolinite-rich laminae. These hosting carbonyl-rich layers are apparently composed of subcircular bodies resembling preserved cell structures. Each of these structures is encapsulated by calcite/vaterite, with iron predominantly concentrated at its center. The presence of iron, calcite/vaterite and kaolinite may, independently or collectively, have played important roles in the preservation of the layered structures. [ABSTRACT FROM AUTHOR]

This paper describes day-one beamlines of the Iranian Light Source Facility and design concept of powder diffraction and spectromicroscopy beamlines as the most priorities of each synchrotron that cover the research requirements in the fields of physics, chemistry, nano-science, etc. For powder diffraction beamline energy range is 6-30 keV, resolution: 10-4, flux: 1012(ph/s/0.1%B.W.) and spot size at sample is 0.1×0.1-1×10 mm2. For spectromicroscopy beamline energy range is 90-2500 eV, flux: 3×1015(ph/s/0.1%B.W.@96eV), resolving power of 1820 at 1000 eV and spot size at sample is 4×2-27×74 µm2

We have developed an open‐source, Python‐based software platform called ScopeFoundry for performing complex, multidimensional microscopy experiments that integrate diverse types of experimental hardware. ScopeFoundry streamlines experiment development by providing a modular environment where hardware controls and measurement schemes can be arranged and customized. Important software tasks such as data management and user interface generation are automated. Using this platform, we have implemented scanning Auger spectromicroscopy on a modified commercial surface analysis system. Spectromicroscopy produces multidimensional datasets with complete spectra at each image pixel, allowing for detailed analysis of material phases where Auger peaks may change in shape and position. Analysis of the surface phases of an advanced electron emission dispenser cathode is presented as an example. We describe the general ScopeFoundry platform, its application to Auger spectromicroscopy, and ways it can be applied to advance surface analysis and microscopy. [ABSTRACT FROM AUTHOR]

Abstract Principal component analysis (PCA) has become a standard tool in spectromicroscopy and hyperspectral imaging to handle large spectral data sets and to decompose raw data into relevant and residual information. In particular in studies of complex compounds, PCA can be used to disentangle chemical information and thereby deepen the understanding of chemical and physical material properties. Surprisingly, in photoemission electron spectromicroscopy (PEEM), PCA is rarely used. This paper serves to demonstrate how powerful PCA can be to detect hidden chemical information in PEEM data. We demonstrate the capability of PCA in PEEM spectromicroscopy for the case of a thin film of a complex quaternary oxide, Pr 0.5 Ba 0.5 CoO 3-δ (PBCO) which is a main contender catalyst material for electrocatalytic water splitting. Upon annealing in air, PBCO decomposes into different phases at the surface. Two of them become obvious from the raw PEEM images, but one is revealed only after PCA. Highlights • Principal component analysis as a tool to reveal hidden information in XAS PEEM • Detection of unknown domains in complex oxides [ABSTRACT FROM AUTHOR]

By using spatially resolved photoelectron spectromicroscopy, we have investigated the formation of Cu(I) oxide phases when a bulk Cu foil is exposed to a near ambient pressure of molecular oxygen. The experiment was performed by using a novel cell for in operando measurements capable to overcome the so called ‘pressure gap’. We have found that the oxidation of Cu proceeds through the formation of Cu(I) oxide domains in the micron and submicron range size, the evolution of which affects the overall morphology of the Cu surface as well. Chemical and morphological changes have been simultaneously detected. It was, surprisingly, found that during the oxidation process in many areas domains having +1 valence state do not spread on the metallic regions which homogenously oxidize; no chemical oxidizing wave was detected by the available lateral resolution and time frame. [ABSTRACT FROM AUTHOR]

The rheology of modern Portland cement (PC) concrete critically depends on the correct dosage of gypsum (calcium sulfate hydrate) to control the hydration of the most reactive phase - tricalcium aluminate (C 3 A). The underlying physio-chemical mechanism, however, remains unsolved mainly due to the lack of high-spatial-resolved and chemistry-sensitive characterization of the C 3 A dissolution frontier. Here, we fill this gap by integrating synchrotron-radiation based crystallographic, photon-energy-dependent spectroscopic and high-resolution morphological studies of the C 3 A hydration product layer. We propose that ettringite (6CaO·Al 2 O 3 ·SO 3 ·32H 2 O) is the only hydration product after the initial reaction period and before complete gypsum dissolution. We quantify the 2D and 3D morphology of the ettringite network, e.g. the packing density of ettringite at various surface locations and the surface dissolution heterogeneity. Our results show no trace of a rate-controlling diffusion barrier. We expect our work to have significant impact on modeling the kinetics and morphological evolution of PC hydration. [ABSTRACT FROM AUTHOR]

A scanning transmission X‐ray microscope is operational at the 10A beamline at the Pohang Light Source. The 10A beamline provides soft X‐rays in the photon energy range 100–2000 eV using an elliptically polarized undulator. The practically usable photon energy range of the scanning transmission X‐ray microscopy (STXM) setup is from ∼150 to ∼1600 eV. With a zone plate of 25 nm outermost zone width, the diffraction‐limited space resolution, ∼30 nm, is achieved in the photon energy range up to ∼850 eV. In transmission mode for thin samples, STXM provides the element, chemical state and magnetic moment specific distributions, based on absorption spectroscopy. A soft X‐ray fluorescence measurement setup has been implemented in order to provide the elemental distribution of thicker samples as well as chemical state information with a space resolution of ∼50 nm. A ptychography setup has been implemented in order to improve the space resolution down to 10 nm. Hardware setups and application activities of the STXM are presented. [ABSTRACT FROM AUTHOR]

A new fast X‐ray absorption spectroscopy scanning method was recently implemented at the Hard X‐ray Microprobe endstation P06, PETRA III, DESY, utilizing a Maia detector. Spectromicroscopy maps were acquired with spectra for X‐ray absorption near‐edge structure (XANES) acquisition in the sub‐second regime. The method combines XANES measurements with raster‐scanning of the sample through the focused beam. The order of the scanning sequence of the axes, one beam energy axis and two (or more) spatial axes, is a variable experimental parameter and, depending on it, the dwell at each location can be either single and continuous (if the energy axis is the inner loop) or in shorter discontinuous intervals (if a spatial axis is innermost). The combination of improved spatial and temporal resolution may be necessary for rapidly changing samples, e.g. for following in operando chemical reactions or samples highly susceptible to beam damage where the rapid collection of single XANES spectra avoids issues with the emergence of chemical changes developing from latent damage. This paper compares data sets collected on a specially designed test pattern and a geological thin‐section scanning the energy as inner, middle and outer axis in the sequence. The XANES data of all three scanning schemes is found to show excellent agreement down to the single‐pixel level. [ABSTRACT FROM AUTHOR]

Calcium plays an important role in the physiology of bacterial cells and as a free soluble form inside the cells, it is tightly regulated at a low concentration. However, much higher amounts of stored calcium exist within cells and can be remobilized at diverse occasions. As a consequence, there has been a variety of techniques developed to quantitatively map the different forms of Ca in cells. Here we show how scanning transmission x-ray microscopy (STXM), a synchrotron-based microscopy technique, conducted in the soft x-ray range at the Ca L 2,3 edges (340–360 eV) offers an original and informative quantitative view of different Ca reservoirs in bacterial cells at a spatial resolution better than 100 nm. To illustrate this, we analyzed mutants of the cyanobacterium Synechococcus elongatus PCC 7942, overexpressing different versions of a gene called ccyA from two phylogenetically distant cyanobacteria: Gloeomargarita lithophora and Synechococcus sp. PCC 6312. This gene is diagnostic of the capability of some cyanobacteria to form intracellular amorphous calcium carbonate (iACC) but its function remains unknown. Here we show that the overexpression of the ccyA gene in the iACC non-forming cyanobacterium S. elongatus PCC 7942 results in an increased Ca content, especially in some Ca-rich cells. Moreover, we show that STXM can discriminate four different reservoirs of Ca in cyanobacteria and provides quantitative assessment of their relative importance. • STXM is powerful to quantitatively map Ca in bacteria at high spatial resolution. • Four different reservoirs of Ca are discriminated in cyanobacteria. • Mutants overexpressing the ccyA gene have a higher Ca content. [ABSTRACT FROM AUTHOR]

Transition metals have essential roles in brain structure and function, and are associated with pathological processes in neurodegenerative disorders classed as proteinopathies. Synchrotron X-ray techniques, coupled with ultrahigh-resolution mass spectrometry, have been applied to study iron and copper interactions with amyloid β (1−42) or α-synuclein. Ex vivo tissue and in vitro systems were investigated, showing the capability to identify metal oxidation states, probe local chemical environments, and localize metal-peptide binding sites. Synchrotron experiments showed that the chemical reduction of ferric (Fe3+) iron and cupric (Cu2+) copper can occur in vitro after incubating each metal in the presence of Aβ for one week, and to a lesser extent for ferric iron incubated with α-syn. Nanoscale chemical speciation mapping of Aβ-Fe complexes revealed a spatial heterogeneity in chemical reduction of iron within individual aggregates. Mass spectrometry allowed the determination of the highest-affinity binding region in all four metal-biomolecule complexes. Iron and copper were coordinated by the same N-terminal region of Aβ, likely through histidine residues. Fe3+ bound to a C-terminal region of α-syn, rich in aspartic and glutamic acid residues, and Cu2+ to the N-terminal region of α-syn. Elucidating the biochemistry of these metal-biomolecule complexes and identifying drivers of chemical reduction processes for which there is evidence ex-vivo, are critical to the advanced understanding of disease aetiology.

Suspended graphene flakes are exposed simultaneously to fluorine and sulfur ions produced by the μ-wave plasma discharge of the SF 6 precursor gas. The microscopic and spectroscopic analyses, performed by Raman spectroscopy, scanning electron microscopy and photoelectron spectromicroscopy, show the homogeneity in functionalization yield over the graphene flakes with F and S atoms covalently bonded to the carbon lattice. This promising surface shows potential for several applications ranging from biomolecule immobilization to lithium battery and hydrogen storage devices. The present co-doping process is an optimal strategy to engineer the graphene surface with a concurrent hydrophobic character, thanks to the fluorine atoms, and a high affinity with metal nanoparticles due to the presence of sulfur atoms. [ABSTRACT FROM AUTHOR]

Suspended graphene is exposed to different fluorine-containing species produced by a plasma source fed with CF precursor gas. We investigate the fluorination process by selecting two different kinetic energies for the ions striking the graphene surface. The chemical-bonding environment is discussed, and the control of the graphene-fluorination homogeneity is investigated at the individual graphene sheets. The modifications of the electronic and structural properties are examined by scanning photoelectron microscopy, micro-Raman analysis, and scanning electron microscopy. The results are compared with those obtained for supported graphene on copper. Suspended graphene provides a quasi-ideal model for investigating the intrinsic properties of irradiated carbon nano-systems while avoiding damage due to backscattered atoms and recoil due to a supporting substrate. [ABSTRACT FROM AUTHOR]