European Synchrotron Radiation Facility

We combined targeted chemistry and computational design to create a crystal structure for porous chromium terephthalate, MIL-101, with very large pore sizes and surface area. Its zeotype cubic structure has a giant cell volume (approximately 702,000 cubic angstroms), a hierarchy of extra-large pore sizes (approximately 30 to 34 angstroms), and a Langmuir surface area for N2 of approximately 5900 +/- 300 square meters per gram. Beside the usual properties of porous compounds, this solid has potential as a nanomold for monodisperse nanomaterials, as illustrated here by the incorporation of Keggin polyanions within the cages.

Abstract Detector systems introduce distortions into acquired data. To obtain accurate angle and intensity information, it is necessary to calibrate, and apply corrections. Intensity non-linearity, spatial distortion, and non-uniformity of intensity response, are the primary considerations. It is better to account for the distortions within scientific analysis software, but often it is more practical to correct the distortions to produce ‘idealised’ data. Calibration methods and software have been developed for single crystal diffraction experiments, using both approaches. For powder diffraction experiments the additional task of converting a two-dimensional image to a one-dimensional spectrum is used to allow Rietveld analysis. This task may be combined with distortion correction to produce intensity information and error estimates. High-pressure experiments can introduce additional complications and place new demands on software. Flexibility is needed to be able to integrate different angular regions separately, and to produce profiles as a function of angle of azimuth. Methods to cope with awkward data are described, and examples of the techniques applied to data from high pressure experiments are presented.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

A new magneto-optical sum rule is derived for circular magnetic dichroism in the x-ray region (CMXD). The integral of the CMXD signal over a given edge allows one to determine the ground-state expectation value of the orbital angular momentum. Applications are discussed to transition-metal and rare-earth magnetic systems.

Sum rules are derived for the circular dichroic response of a core line (CMXD). They relate the intensity of the CMXD signal to the ground-state expectation value of the magnetic field operators (orbital, spin, and magnetic dipole) of the valence electrons. The results obtained are discussed and tested for transition metals and rare earths.

We analyze the global structure of the worldwide air transportation network, a critical infrastructure with an enormous impact on local, national, and international economies. We find that the worldwide air transportation network is a scale-free small-world network. In contrast to the prediction of scale-free network models, however, we find that the most connected cities are not necessarily the most central, resulting in anomalous values of the centrality. We demonstrate that these anomalies arise because of the multicommunity structure of the network. We identify the communities in the air transportation network and show that the community structure cannot be explained solely based on geographical constraints and that geopolitical considerations have to be taken into account. We identify each city's global role based on its pattern of intercommunity and intracommunity connections, which enables us to obtain scale-specific representations of the network.

Abstract Recent developments in methods and instrumentation have contributed to major advances in our understanding of the fine structure of amylose and amylopectin. The structure of the starch granule slowly unravels with new insight into key structural features. Following a brief presentation of the structural features common to all starches, the most recent findings for the structure of amylose and amylopectin are reported. The organization of different types of chains in amylopectin is discussed with a critical review of the ‘cluster’ model leading to the presentation of alternative models. The locations of molecular components in the starch granule are described according to a progress structural order. The description of the crystalline components is followed by a presentation of their supramolecular arrangements. The crystalline components comprise platelet nanocrystals which have already been identified and characterized, and other less well characterized ‘blocklet components’. The location and state of amylose within the granule is also presented. This comprehensive review aims at distinguishing between those structural features that have received widespread acceptance and those that are still under debate, with the ambition of being educational and to provide stimulation for further fundamental investigation into the starch granule as a macromolecular assembly.

The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

Using a high-efficiency grating interferometer for hard X rays (10-30 keV) and a phase-stepping technique, separate radiographs of the phase and absorption profiles of bulk samples can be obtained from a single set of measurements. Tomographic reconstruction yields quantitative three-dimensional maps of the X-ray refractive index, with a spatial resolution down to a few microns. The method is mechanically robust, requires little spatial coherence and monochromaticity, and can be scaled up to large fields of view, with a detector of correspondingly moderate spatial resolution. These are important prerequisites for use with laboratory X-ray sources.

NiFe and CoFe (MFe) layered double hydroxides (LDHs) are among the most active electrocatalysts for the alkaline oxygen evolution reaction (OER). Herein, we combine electrochemical measurements, operando X-ray scattering and absorption spectroscopy, and density functional theory (DFT) calculations to elucidate the catalytically active phase, reaction center and the OER mechanism. We provide the first direct atomic-scale evidence that, under applied anodic potentials, MFe LDHs oxidize from as-prepared α-phases to activated γ-phases. The OER-active γ-phases are characterized by about 8% contraction of the lattice spacing and switching of the intercalated ions. DFT calculations reveal that the OER proceeds via a Mars van Krevelen mechanism. The flexible electronic structure of the surface Fe sites, and their synergy with nearest-neighbor M sites through formation of O-bridged Fe-M reaction centers, stabilize OER intermediates that are unfavorable on pure M-M centers and single Fe sites, fundamentally accounting for the high catalytic activity of MFe LDHs.

The concept that superconductivity competes with other orders in cuprate superconductors has become increasingly apparent, but obtaining direct evidence with bulk-sensitive probes is challenging. We have used resonant soft x-ray scattering to identify two-dimensional charge fluctuations with an incommensurate periodicity of ~3.2 lattice units in the copper-oxide planes of the superconductors (Y,Nd)Ba(2)Cu(3)O(6+)(x), with hole concentrations of 0.09 to 0.13 per planar Cu ion. The intensity and correlation length of the fluctuation signal increase strongly upon cooling down to the superconducting transition temperature (T(c)); further cooling below T(c) abruptly reverses the divergence of the charge correlations. In combination with earlier observations of a large gap in the spin excitation spectrum, these data indicate an incipient charge density wave instability that competes with superconductivity.

High-resolution Fe K-edge XANES spectra of a series of crystalline Fe2+- and Fe3+-bearing model compounds were measured in an effort to correlate characteristics of the pre-edge feature with oxidation state and local coordination environment of Fe atoms. The model compounds comprise 30 natural minerals and synthetic compounds, with Fe coordination environments ranging from 4 to 12 O atoms for Fe2+, including 5-coordinated trigonal bipyramidal Fe2+, and from 4 to 6 O atoms for Fe3+. Most pre-edge spectra show two components (due to crystal-field splitting) that are located just above the Fermi level.

An unusually large expansion upon solvent adsorption occurs without apparent bond breaking in the network of a series of isoreticular chromium(III) or iron(III) diarboxylates labeled MIL-88A to D [dicarbox = fumarate (88A); terephthalate (1,4-BDC) (88B); 2,6-naphthalenedicarboxylate (2,6-NDC) (88C); and 4-4'-biphenyldicarboxylate (4-4'-BPDC) (88D)]. This reversible "breathing" motion was analyzed in terms of cell dimensions (extent of breathing), movements within the framework (mechanism of transformation), and the interactions between the guests and the skeleton. In situ techniques show that these flexible solids are highly selective absorbents and that this selectivity is strongly dependent on the nature of the organic linker.

The isotropic magnetic moment of a free atom is shown to develop giant magnetic anisotropy energy due to symmetry reduction at an atomically ordered surface. Single cobalt atoms deposited onto platinum (111) are found to have a magnetic anisotropy energy of 9 millielectron volts per atom arising from the combination of unquenched orbital moments (1.1 Bohr magnetons) and strong spin-orbit coupling induced by the platinum substrate. By assembling cobalt nanoparticles containing up to 40 atoms, the magnetic anisotropy energy is further shown to be dependent on single-atom coordination changes. These results confirm theoretical predictions and are of fundamental value to understanding how magnetic anisotropy develops in finite-sized magnetic particles.

Because the refractive index for hard x rays is slightly different from unity, the optical phase of a beam is affected by transmission through an object. Phase images can be obtained with extreme instrumental simplicity by simple propagation provided the beam is coherent. But, unlike absorption, the phase is not simply related to image brightness. A holographic reconstruction procedure combining images taken at different distances from the specimen was developed. It results in quantitative phase mapping and, through association with three-dimensional reconstruction, in holotomography, the complete three-dimensional mapping of the density in a sample. This tool in the characterization of materials at the micrometer scale is uniquely suited to samples with low absorption contrast and radiation-sensitive systems.

pyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

Compression versus pressure at ambient temperature has been measured for tantalum, gold, and platinum to $94\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$ and for aluminum, copper, and tungsten to $153\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$, in a diamond anvil cell. Standard synchrotron x-ray diffraction accuracy in the volume determination could be achieved to the maximum pressure. The current data set is used to recalibrate the static pressure scale based on the ruby luminescence, confirming recent suggestions of an underestimation of pressure. Using an updated pressure calibration, the consistency between ultrasonic, dynamic, and static measurements of the equations of state is improved for these six equations of state. This consistency allows us to test the predictive power of density functional theory, with different approximations, for equation-of-state calculations. For example, the generalized gradient approximation leads to very accurate results, except for gold, the heaviest element.

Phase-contrast x-ray imaging (PCI) is an innovative method that is sensitive to the refraction of the x-rays in matter. PCI is particularly adapted to visualize weakly absorbing details like those often encountered in biology and medicine. In past years, PCI has become one of the most used imaging methods in laboratory and preclinical studies: its unique characteristics allow high contrast 3D visualization of thick and complex samples even at high spatial resolution. Applications have covered a wide range of pathologies and organs, and are more and more often performed in vivo. Several techniques are now available to exploit and visualize the phase-contrast: propagation- and analyzer-based, crystal and grating interferometry and non-interferometric methods like the coded aperture. In this review, covering the last five years, we will give an overview of the main theoretical and experimental developments and of the important steps performed towards the clinical implementation of PCI.

Two different types of amorphous carbon films were deposited on Si substrates, with film hardness of 22 GPa and 40 GPa, by pulsed laser evaporation of graphite targets. The x-ray photoemission spectra (XPS) of the C 1s core level in these films shown two components at 284.3\ifmmode\pm\else\textpm\fi{}0.1 eV and 285.2\ifmmode\pm\else\textpm\fi{}0.1 eV, which were identified with the ${\mathit{sp}}^{2}$ and ${\mathit{sp}}^{3}$ hybrids forms of carbon. The ${\mathit{sp}}^{3}$/${\mathit{sp}}^{2}$ concentration ratio deduced from the area of the components had a value of 2/5 for the harder amorphous carbon film and 1/4 for the softer. Upon annealing the harder film at different temperatures, the ${\mathit{sp}}^{3}$/${\mathit{sp}}^{2}$ ratio remained nearly constant up to about 900 K and then decreased until reaching a value of zero above 1100 K. The C 1s core level shifted 0.3\ifmmode\pm\else\textpm\fi{}0.1 eV toward lower binding energy in the films for annealing temperatures above 900 K. This shift was correlated with an increase in the asymmetry of the C 1s XPS spectra and of the density of states at the Fermi level, as observed by ultraviolet photoemission spectroscopy. There was no detectable \ensuremath{\pi} plasmon in the harder films below 900 K, despite the presence of ${\mathit{sp}}^{2}$ atoms and \ensuremath{\pi} bonds at those temperatures. \textcopyright{} 1996 The American Physical Society.