Capillarity and active cell movement at mesendoderm translocation in the Xenopus gastrula.

During Xenopus gastrulation, leading edge mesendoderm (LEM) advances animally as a wedge-shaped cell mass over the vegetally moving blastocoel roof (BCR). We show that close contact across the BCR-LEM interface correlates with attenuated net advance of the LEM, which is pulled forward by tip cells while the remaining LEM frequently separates from the BCR. Nevertheless, lamellipodia persist on the detached LEM surface. They attach to adjacent LEM cells and depend on PDGF-A, cell-surface fibronectin and cadherin. We argue that active cell motility on the LEM surface prevents adverse capillary effects in the liquid LEM tissue as it moves by being pulled. It counters tissue surface-tension effects with oriented cell movement and bulges the LEM surface out to keep it close to the curved BCR without attaching to it. Proximity to the BCR is necessary, in turn, for the maintenance and orientation of lamellipodia that permit mass cell movement with minimal substratum contact. Together with a similar process in epithelial invagination, vertical telescoping, the cell movement at the LEM surface defines a novel type of cell rearrangement: vertical shearing.

Phase retrieval in propagation-based X-ray imaging beyond the limits of transport of intensity and contrast transfer function approaches.

We derive a phase retrieval formula for propagation-based phase contrast X-ray imaging that does not require weakly attenuating objects or short propagation distances. It is directly applicable to both single- and multiple-distance scenarios. We show the validity conditions and study the error of the underlying mutual intensity approximation, which uses the common assumptions of weak phase shift variations and phase-attenuation duality. The approximation generalizes those behind the transport of intensity (TIE) and contrast transfer function (CTF) models, and it approaches them when their respective additional assumptions are satisfied. When they are not, it clearly outperforms them, which we show both theoretically and practically on synthetic and measured data.

Bending and reverse bending during the fabrication of novel GaAs/(In,Ga)As/GaAs core-shell nanowires monitored byin situx-ray diffraction.

We report on the fabrication of a novel design of GaAs/(In,Ga)As/GaAs radial nanowire heterostructures on a Si 111 substrate, where, for the first time, the growth of inhomogeneous shells on a lattice mismatched core results in straight nanowires instead of bent. Nanowire bending caused by axial tensile strain induced by the (In,Ga)As shell on the GaAs core is reversed by axial compressive strain caused by the GaAs outer shell on the (In,Ga)As shell. Progressive nanowire bending and reverse bending in addition to the axial strain evolution during the two processes are accessed byin situby x-ray diffraction. The diameter of the core, thicknesses of the shells, as well as the indium concentration and distribution within the (In,Ga)As quantum well are revealed by 2D energy dispersive x-ray spectroscopy using a transmission electron microscope. Shell(s) growth on one side of the core without substrate rotation results in planar-like radial heterostructures in the form of free standing straight nanowires.

Shot noise reduction in radiographic and tomographic multi-channel imaging with self-supervised deep learning.

Shot noise is a critical issue in radiographic and tomographic imaging, especially when additional constraints lead to a significant reduction of the signal-to-noise ratio. This paper presents a method for improving the quality of noisy multi-channel imaging datasets, such as data from time or energy-resolved imaging, by exploiting structural similarities between channels. To achieve that, we broaden the application domain of the Noise2Noise self-supervised denoising approach. The method draws pairs of samples from a data distribution with identical signals but uncorrelated noise. It is applicable to multi-channel datasets if adjacent channels provide images with similar enough information but independent noise. We demonstrate the applicability and performance of the method via three case studies, namely spectroscopic X-ray tomography, energy-dispersive neutron tomography, and in vivo X-ray cine-radiography.

Effect of Underlayer Quality on Microstructure, Stoichiometry, and Magnetic Properties of Hexaferrite BaFe12O19 Grown on YSZ(111) by Pulsed Laser Deposition.

We have studied the effect of platinum underlayer for two deposited thicknesses on the microstructure, crystalline quality, morphology, chemical composition, and magnetic properties as well as magnetic domain formation of BaFe12O19 (BaM) grown on YSZ(111) by pulsed laser deposition (PLD). We found that PLD platinum deposited with a thickness of 25 nm cannot withstand the dewetting phenomenon occurring during the subsequent BaM layer growth. A smooth and continuous Pt underlayer that possesses a sharp interface and omits the intermixing between the BaM and substrate was successfully achieved for a deposited Pt film thickness of 75 nm. Independent of the thickness of the deposited Pt layer, the c-axis orientation as well as coercivity Hc and the anisotropy HA fields were significantly improved due to a remarkable improvement of lattice mismatch in comparison with the BaM layer grown without a Pt underlayer on YSZ(111). By applying high-resolution X-ray diffraction, scanning and transmission electron microscopy (SEM/TEM), and atomically resolved scanning TEM imaging combined with energy-dispersive X-ray spectroscopy, as well as atomic and magnetic force microscopy, a comprehensive investigation of both structure and chemical composition of the deposited BaM films and their interfacial regions was performed. This study aimed to correlate the enhancement of the overall magnetic properties and of the local spin magnetic domain orientation with the modification of BaM microstructure and chemical composition at the nanometer scale due to the Pt underlayer. Finally, we attempted to understand the mechanisms that control the magnetic properties of these BaM films in order to be able to tailor them.

Evolution of flexible biting in hyperdiverse parasitoid wasps.

One key event in insect evolution was the development of mandibles with two joints, which allowed powerful biting but restricted their movement to a single degree of freedom. These mandibles define the Dicondylia, which constitute over 99% of all extant insect species. It was common doctrine that the dicondylic articulation of chewing mandibles remained unaltered for more than 400 million years. We report highly modified mandibles overcoming the restrictions of a single degree of freedom and hypothesize their major role in insect diversification. These mandibles are defining features of parasitoid chalcid wasps, one of the most species-rich lineages of insects. The shift from powerful chewing to precise cutting likely facilitated adaptations to parasitize hosts hidden in hard substrates, which pose challenges to the emerging wasps. We reveal a crucial step in insect evolution and highlight the importance of comprehensive studies even of putatively well-known systems.

Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography.

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.

Altered Elemental Distribution in Male Rat Brain Tissue as a Predictor of Glioblastoma Multiforme Growth-Studies Using SR-XRF Microscopy.

Glioblastoma multiforme (GBM) is a particularly malignant primary brain tumor. Despite enormous advances in the surgical treatment of cancer, radio- and chemotherapy, the average survival of patients suffering from this cancer does not usually exceed several months. For obvious ethical reasons, the search and testing of the new drugs and therapies of GBM cannot be carried out on humans, and for this purpose, animal models of the disease are most often used. However, to assess the efficacy and safety of the therapy basing on these models, a deep knowledge of the pathological changes associated with tumor development in the animal brain is necessary. Therefore, as part of our study, the synchrotron radiation-based X-ray fluorescence microscopy was applied for multi-elemental micro-imaging of the rat brain in which glioblastoma develops. Elemental changes occurring in animals after the implantation of two human glioma cell lines as well as the cells taken directly from a patient suffering from GBM were compared. Both the extent and intensity of elemental changes strongly correlated with the regions of glioma growth. The obtained results showed that the observation of elemental anomalies accompanying tumor development within an animal's brain might facilitate our understanding of the pathogenesis and progress of GBM and also determine potential biomarkers of its extension. The tumors appearing in a rat's brain were characterized by an increased accumulation of Fe and Se, whilst the tissue directly surrounding the tumor presented a higher accumulation of Cu. Furthermore, the results of the study allow us to consider Se as a potential elemental marker of GBM progression.

Juvenile ecology drives adult morphology in two insect orders.

Most animals undergo ecological niche shifts between distinct life phases, but such shifts can result in adaptive conflicts of phenotypic traits. Metamorphosis can reduce these conflicts by breaking up trait correlations, allowing each life phase to independently adapt to its ecological niche. This process is called adaptive decoupling. It is, however, yet unknown to what extent adaptive decoupling is realized on a macroevolutionary scale in hemimetabolous insects and if the degree of adaptive decoupling is correlated with the strength of ontogenetic niche shifts. It is also unclear whether the degree of adaptive decoupling is correlated with phenotypic disparity. Here, we quantify nymphal and adult trait correlations in 219 species across the whole phylogeny of earwigs and stoneflies to test whether juvenile and adult traits are decoupled from each other. We demonstrate that adult head morphology is largely driven by nymphal ecology, and that adult head shape disparity has increased with stronger ontogenetic niche shifts in some stonefly lineages. Our findings implicate that the hemimetabolan metamorphosis in earwigs and stoneflies does not allow for high degrees of adaptive decoupling, and that high phenotypic disparity can even be realized when the evolution of distinct life phases is coupled.

Drought-Induced Xylem Embolism Limits the Recovery of Leaf Gas Exchange in Scots Pine.

Climate change increases the occurrence of prolonged drought periods with large implications for forest functioning. Scots pine (Pinus sylvestris) is one of the most abundant conifers worldwide, and evidence is rising that its resilience to severe drought is limited. However, we know little about its ability to recover from drought-induced embolism. To analyze postdrought hydraulic recovery, we investigated stress and recovery dynamics of leaf gas exchange, nonstructural carbohydrates, and hydraulic properties in 2.5-year-old Scots pine seedlings. We quantified the degree of xylem embolism by combining in vivo x-ray microtomography with intrusive techniques including measurements of hydraulic conductivity and dye staining during drought progression and short-term (2 d) and long-term (4 weeks) recovery. Seedlings were grown under controlled conditions, and irrigation was withheld until stomata closed and xylem water potential declined to -3.2 MPa on average, causing a 46% loss of stem hydraulic conductivity. Following drought release, we found a gradual recovery of leaf gas exchange to 50% to 60% of control values. This partial recovery indicates hydraulic limitations due to drought-induced damage. Whereas xylem water potential recovered close to control values within 2 d, both x-ray microtomography and intrusive measurements revealed no recovery of stem hydraulic conductivity. Moreover, we did not find indications for nonstructural carbohydrate reserves limiting hydraulic recovery. Our findings demonstrate that Scots pine is able to survive severe drought and to partially recover, although we assume that xylem development during the next growing season might compensate for some of the hydraulic impairment. Such drought-induced legacy effects are important when considering vegetation responses to extreme events.

Time-Resolved Morphology and Kinetic Studies of Pulsed Laser Deposition-Grown Pt Layers on Sapphire at Different Growth Temperatures by in Situ Grazing Incidence Small-Angle X-ray Scattering.

Optimizing and monitoring the growth conditions of Pt films, often used as bottom electrodes in multiferroic material systems, represents a highly relevant issue that is of importance for controlling the crystalline quality and performance of ferroelectric oxides such as, e.g. LuFeO3. We performed a time-resolved monitoring of the growth and morphology of Pt films during pulsed laser deposition (PLD) in dependence on the grown film effective thickness and on the growth temperature Tg using in situ grazing incidence small-angle X-ray scattering (GISAXS). Through real-time analysis and modeling of GISAXS patterns, we could fully characterize the influence of Tg on the morphology and on the growth kinetics of the Pt layers. Consequently, critical and characteristic effective thicknesses for the transitions nucleation phase (I)/coalescence phase (II) and coalescence phase (II)/coarsening phase (III) could be determined. In combination with complementary microscopic imaging and chemical mapping via combined SEM/EDXS, we demonstrate the occurrence of a morphological progression in the Pt PLD-grown Pt films, changing from grains at room temperature to a 3D-island morphology at 300 °C, further to a hole-free structure at 500 °C, and finally to a channel structure for 700 and 900 °C. The film topography, as characterized by atomic force microscopy (AFM), favors the PLD growth of Pt layers at temperatures beyond 700 °C where the film is homogeneous, continuous, and hole-free with a flat and smooth surface. The double dependency of the percolation transition on the film effective thickness and on the growth temperature has been established by measuring the electrical conductivity.

Lattice Dynamics and Structural Phase Transitions in Eu2O3.

Using the density functional theory, we study the structural and lattice dynamical properties of europium sesquioxide (Eu2O3) in the cubic, trigonal, and monoclinic phases. The obtained lattice parameters and energies of the Raman modes show a good agreement with the available experimental data. The Eu-partial phonon density of states calculated for the cubic structure is compared with the nuclear inelastic scattering data obtained from a 20 nm thick Eu2O3 film deposited on a YSZ substrate. A small shift of the experimental spectrum to higher energies results from a compressive strain induced by the substrate. On the basis of lattice and phonon properties, we analyze the mechanisms of structural transitions between different phases of Eu2O3.

In situx-ray analysis of misfit strain and curvature of bent polytypic GaAs-InxGa1-xAs core-shell nanowires.

Misfit strain in core-shell nanowires can be elastically released by nanowire bending in case of asymmetric shell growth around the nanowire core. In this work, we investigate the bending of GaAs nanowires during the asymmetric overgrowth by an InxGa1-xAs shell caused by avoiding substrate rotation. We observe that the nanowire bending direction depends on the nature of the substrate's oxide layer, demonstrated by Si substrates covered by native and thermal oxide layers. Further, we follow the bending evolution by time-resolvedin situx-ray diffraction measurements during the deposition of the asymmetric shell. The XRD measurements give insight into the temporal development of the strain as well as the bending evolution in the core-shell nanowire.

Cranial shape evolution of extant and fossil crocodile newts and its relation to reproduction and ecology.

The diversity of the vertebrate cranial shape of phylogenetically related taxa allows conclusions on ecology and life history. As pleurodeline newts (the genera Echinotriton, Pleurodeles and Tylototriton) have polymorphic reproductive modes, they are highly suitable for following cranial shape evolution in relation to reproduction and environment. We investigated interspecific differences externally and differences in the cranial shape of pleurodeline newts via two-dimensional geometric morphometrics. Our analyses also included the closely related but extinct genus Chelotriton to better follow the evolutionary history of cranial shape. Pleurodeles was morphologically distinct in relation to other phylogenetically basal salamanders. The subgenera within Tylototriton (Tylototriton and Yaotriton) were well separated in morphospace, whereas Echinotriton resembled the subgenus Yaotriton more than Tylototriton. Oviposition site choice correlated with phylogeny and morphology. Only the mating mode, with a random distribution along the phylogenetic tree, separated crocodile newts into two morphologically distinct groups. Extinct Chelotriton likely represented several species and were morphologically and ecologically more similar to Echinotriton and Yaotriton than to Tylototriton subgenera. Our data also provide the first comprehensive morphological support for the molecular phylogeny of pleurodeline newts.

Impact of the Shadowing Effect on the Crystal Structure of Patterned Self-Catalyzed GaAs Nanowires.

The growth of regular arrays of uniform III-V semiconductor nanowires is a crucial step on the route toward their application-relevant large-scale integration onto the Si platform. To this end, not only does optimal vertical yield, length, and diameter uniformity have to be engineered, but also, control over the nanowire crystal structure has to be achieved. Depending on the particular application, nanowire arrays with varying area density are required for optimal device efficiency. However, the nanowire area density substantially influences the nanowire growth and presents an additional challenge for nanowire device engineering. We report on the simultaneous in situ X-ray investigation of regular GaAs nanowire arrays with different area density during self-catalyzed vapor-liquid-solid growth on Si by molecular-beam epitaxy. Our results give novel insight into selective-area growth and demonstrate that shadowing of the Ga flux, occurring in dense nanowire arrays, has a crucial impact on the evolution of nanowire crystal structure. We observe that the onset of Ga flux shadowing, dependent on array pitch and nanowire length, is accompanied by an increase of the wurtzite formation rate. Our results moreover reveal the paramount role of the secondary reflected Ga flux for VLS NW growth (specifically, that flux that is reflected directly into the liquid Ga droplet).

Identification, visualization and clonal analysis of intestinal stem cells in fish.

Recently, a stochastic model of symmetrical stem cell division followed by neutral drift has been proposed for intestinal stem cells (ISCs), which has been suggested to represent the predominant mode of stem cell progression in mammals. In contrast, stem cells in the retina of teleost fish show an asymmetric division mode. To address whether the mode of stem cell division follows phylogenetic or ontogenetic routes, we analysed the entire gastrointestinal tract of the teleost medaka (Oryzias latipes). X-ray microcomputed tomography shows a correlation of 3D topography with the functional domains. Analysis of ISCs in proliferation assays and via genetically encoded lineage tracing highlights a stem cell niche in the furrow between the long intestinal folds that is functionally equivalent to mammalian intestinal crypts. Stem cells in this compartment are characterized by the expression of homologs of mammalian ISC markers - sox9, axin2 and lgr5 - emphasizing the evolutionary conservation of the Wnt pathway components in the stem cell niche of the intestine. The stochastic, sparse initial labelling of ISCs ultimately resulted in extended labelled or unlabelled domains originating from single stem cells in the furrow niche, contributing to both homeostasis and growth. Thus, different modes of stem cell division co-evolved within one organism, and in the absence of physical isolation in crypts, ISCs contribute to homeostatic growth.

Revealing misfit dislocations in InAs x P1-x -InP core-shell nanowires by x-ray diffraction.

InAs x P1-x nanowires are promising building blocks for future optoelectronic devices and nanoelectronics. Their structure may vary from nanowire to nanowire, which may influence their average optoelectronic properties. Therefore, it is highly important for their applications to know the average properties of an ensemble of the nanowires. Structural properties of the InAs x P1-x -InP core-shell nanowires were investigated using the coplanar x-ray diffraction performed at a synchrotron facility. Studies of series of symmetric and asymmetric x-ray Bragg reflections allowed us to determine the 26% ± 3% of As chemical composition in the InAs x P1-x core, core-shell relaxation, and the average tilt of the nanowires with respect to the substrate normal. Based on the x-ray diffraction, scanning, and transmission electron microscopy measurements, a model of the core-shell relaxation was proposed. Partial relaxation of the core was attributed to misfit dislocations formed at the core-shell interface and their linear density was estimated to be 3.3 ± 0.3 × 104 cm-1.

X-ray phase-contrast in vivo microtomography probes new aspects of Xenopus gastrulation.

An ambitious goal in biology is to understand the behaviour of cells during development by imaging-in vivo and with subcellular resolution-changes of the embryonic structure. Important morphogenetic movements occur throughout embryogenesis, but in particular during gastrulation when a series of dramatic, coordinated cell movements drives the reorganization of a simple ball or sheet of cells into a complex multi-layered organism. In Xenopus laevis, the South African clawed frog and also in zebrafish, cell and tissue movements have been studied in explants, in fixed embryos, in vivo using fluorescence microscopy or microscopic magnetic resonance imaging. None of these methods allows cell behaviours to be observed with micrometre-scale resolution throughout the optically opaque, living embryo over developmental time. Here we use non-invasive in vivo, time-lapse X-ray microtomography, based on single-distance phase contrast and combined with motion analysis, to examine the course of embryonic development. We demonstrate that this powerful four-dimensional imaging technique provides high-resolution views of gastrulation processes in wild-type X. laevis embryos, including vegetal endoderm rotation, archenteron formation, changes in the volumes of cavities within the porous interstitial tissue between archenteron and blastocoel, migration/confrontation of mesendoderm and closure of the blastopore. Differential flow analysis separates collective from relative cell motion to assign propulsion mechanisms. Moreover, digitally determined volume balances confirm that early archenteron inflation occurs through the uptake of external water. A transient ectodermal ridge, formed in association with the confrontation of ventral and head mesendoderm on the blastocoel roof, is identified. When combined with perturbation experiments to investigate molecular and biomechanical underpinnings of morphogenesis, our technique should help to advance our understanding of the fundamentals of development.

Radial Growth of Self-Catalyzed GaAs Nanowires and the Evolution of the Liquid Ga-Droplet Studied by Time-Resolved in Situ X-ray Diffraction.

We report on a growth study of self-catalyzed GaAs nanowires based on time-resolved in situ X-ray structure characterization during molecular-beam-epitaxy in combination with ex situ scanning-electron-microscopy. We reveal the evolution of nanowire radius and polytypism and distinguish radial growth processes responsible for tapering and side-wall growth. We interpret our results using a model for diameter self-stabilization processes during growth of self-catalyzed GaAs nanowires including the shape of the liquid Ga-droplet and its evolution during growth.

syris: a flexible and efficient framework for X-ray imaging experiments simulation.

An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.