Africa's oldest dinosaurs reveal early suppression of dinosaur distribution.

The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated across Triassic Pangaea1-11. By the Late Triassic (Carnian stage, ~235 million years ago), cosmopolitan 'disaster faunas' (refs. 12-14) had given way to highly endemic assemblages12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging-there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are proposed to have controlled distribution15-18. During this time of high endemism, dinosaurs began to disperse and thus offer an opportunity to test the timing and drivers of this biogeographic pattern. Increased sampling can test this prediction: if dinosaurs initially dispersed under palaeolatitudinal-driven endemism, then an assemblage similar to those of South America4,19-21 and India19,22-including the earliest dinosaurs-should be present in Carnian deposits in south-central Africa. Here we report a new Carnian assemblage from Zimbabwe that includes Africa's oldest definitive dinosaurs, including a nearly complete skeleton of the sauropodomorph Mbiresaurus raathi gen. et sp. nov. This assemblage resembles other dinosaur-bearing Carnian assemblages, suggesting that a similar vertebrate fauna ranged high-latitude austral Pangaea. The distribution of the first dinosaurs is correlated with palaeolatitude-linked climatic barriers, and dinosaurian dispersal to the rest of the supercontinent was delayed until these barriers relaxed, suggesting that climatic controls influenced the initial composition of the terrestrial faunas that persist to this day.

Enigmatic dinosaur precursors bridge the gap to the origin of Pterosauria.

Pterosaurs were the first vertebrates to evolve powered flight1 and comprised one of the main evolutionary radiations in terrestrial ecosystems of the Mesozoic era (approximately 252-66 million years ago), but their origin has remained an unresolved enigma in palaeontology since the nineteenth century2-4. These flying reptiles have been hypothesized to be the close relatives of a wide variety of reptilian clades, including dinosaur relatives2-8, and there is still a major morphological gap between those forms and the oldest, unambiguous pterosaurs from the Upper Triassic series. Here, using recent discoveries of well-preserved cranial remains, microcomputed tomography scans of fragile skull bones (jaws, skull roofs and braincases) and reliably associated postcrania, we demonstrate that lagerpetids-a group of cursorial, non-volant dinosaur precursors-are the sister group of pterosaurs, sharing numerous synapomorphies across the entire skeleton. This finding substantially shortens the temporal and morphological gap between the oldest pterosaurs and their closest relatives and simultaneously strengthens the evidence that pterosaurs belong to the avian line of archosaurs. Neuroanatomical features related to the enhanced sensory abilities of pterosaurs9 are already present in lagerpetids, which indicates that these features evolved before flight. Our evidence illuminates the first steps of the assembly of the pterosaur body plan, whose conquest of aerial space represents a remarkable morphofunctional innovation in vertebrate evolution.

Deep Gauss-Newton for phase retrieval.

We propose the deep Gauss-Newton (DGN) algorithm. The DGN allows one to take into account the knowledge of the forward model in a deep neural network by unrolling a Gauss-Newton optimization method. No regularization or step size needs to be chosen; they are learned through convolutional neural networks. The proposed algorithm does not require an initial reconstruction and is able to retrieve simultaneously the phase and absorption from a single-distance diffraction pattern. The DGN method was applied to both simulated and experimental data and permitted large improvements of the reconstruction error and of the resolution compared with a state-of-the-art iterative method and another neural-network-based reconstruction algorithm.

Evaluation of imaging setups for quantitative phase contrast nanoCT of mineralized biomaterials.

X-ray nano-tomography with phase contrast (nanoCT) using synchrotron radiation is a powerful tool to non-destructively investigate 3D material properties at the nanoscale. In large bone lesions, such as severe bone fractures, bone cancer or other diseases, bone grafts substituting the lost bone might be necessary. Such grafts can be of biological origin or be composed of a synthetic bone substitute. The long-term functioning of artificial bone substitutes depends on many factors. Synchrotron nanoCT imaging has great potential to contribute to further the understanding of integration of implants into bone tissue by imaging the spatial interaction between bone tissue and implant, and by accessing the interface between implant material and bone tissue. With this aim, a methodology for evaluating the image quality is presented for in-line phase contrast nanoCT images of bone scaffold samples. A PMMA-embedded tricalcium phosphate scaffold was used with both a closed and an open porosity structure and bone ingrowths as a representative system of three known materials. Parameters such as spatial resolution and signal-to-noise ratio were extracted and used to explore and quantitatively compare the effects of implementation choices in the imaging setup, such as camera technology and imaging energy, on the resulting image quality. Increasing the X-ray energy from 17.5 keV to 29.6 keV leads to a notable improvement in image quality regardless of the camera technology used, with the two tested camera setups performing at a comparable level when the recorded intensity was kept constant.

Dose-efficient multimodal microscopy of human tissue at a hard X-ray nanoprobe beamline.

X-ray fluorescence microscopy performed at nanofocusing synchrotron beamlines produces quantitative elemental distribution maps at unprecedented resolution (down to a few tens of nanometres), at the expense of relatively long measuring times and high absorbed doses. In this work, a method was implemented in which fast low-dose in-line holography was used to produce quantitative electron density maps at the mesoscale prior to nanoscale X-ray fluorescence acquisition. These maps ensure more efficient fluorescence scans and the reduction of the total absorbed dose, often relevant for radiation-sensitive (e.g. biological) samples. This multimodal microscopy approach was demonstrated on human sural nerve tissue. The two imaging modes provide complementary information at a comparable resolution, ultimately limited by the focal spot size. The experimental setup presented allows the user to swap between them in a flexible and reproducible fashion, as well as to easily adapt the scanning parameters during an experiment to fine-tune resolution and field of view.

X-ray in-line holography and holotomography at the NanoMAX beamline.

Coherent X-ray imaging techniques, such as in-line holography, exploit the high brilliance provided by diffraction-limited storage rings to perform imaging sensitive to the electron density through contrast due to the phase shift, rather than conventional attenuation contrast. Thus, coherent X-ray imaging techniques enable high-sensitivity and low-dose imaging, especially for low-atomic-number (Z) chemical elements and materials with similar attenuation contrast. Here, the first implementation of in-line holography at the NanoMAX beamline is presented, which benefits from the exceptional focusing capabilities and the high brilliance provided by MAX IV, the first operational diffraction-limited storage ring up to approximately 300 eV. It is demonstrated that in-line holography at NanoMAX can provide 2D diffraction-limited images, where the achievable resolution is only limited by the 70 nm focal spot at 13 keV X-ray energy. Also, the 3D capabilities of this instrument are demonstrated by performing holotomography on a chalk sample at a mesoscale resolution of around 155 nm. It is foreseen that in-line holography will broaden the spectra of capabilities of MAX IV by providing fast 2D and 3D electron density images from mesoscale down to nanoscale resolution.

Acclimation to wind loads and/or contact stimuli? A biomechanical study of peltate leaves of Pilea peperomioides.

Plants are exposed to various environmental stresses. Leaves immediately respond to mechano-stimulation, such as wind and touch, by bending and twisting or acclimate over a longer time period by thigmomorphogenetic changes of mechanical and geometrical properties. We selected the peltate leaves of Pilea peperomioides for a comparative analysis of mechano-induced effects on morphology, anatomy, and biomechanics of petiole and transition zone. The plants were cultivated for 6 weeks in a phytochamber divided into four treatment groups: control (no stimulus), touch stimulus (brushing every 30 s), wind stimulus (constant air flow of 4.6 m s-1), and a combination of touch and wind stimuli. Comparing the four treatment groups, neither the petiole nor the transition zone showed significant thigmomorphogenetic acclimations. However, comparing the petiole and the transition zone, the elastic modulus (E), the torsional modulus (G), the E/G ratio, and the axial rigidity (EA) differed significantly, whereas no significant difference was found for the torsional rigidity (GK). The twist-to-bend ratios (EI/GK) of all petioles ranged between 4.33 and 5.99, and of all transition zones between 0.67 and 0.78. Based on the twist-to-bend ratios, we hypothesize that bending loads are accommodated by the petiole, while torsional loads are shared between the transition zone and petiole.

Nonlinear primal-dual algorithm for the phase and absorption retrieval from a single phase contrast image.

We propose a nonlinear primal-dual algorithm for the retrieval of phase shift and absorption from a single x ray in-line phase contrast, or Fresnel diffraction, image. The algorithm permits us to regularize phase and absorption separately. We demonstrate that taking into account the nonlinearity in the reconstruction improves reconstruction compared with linear methods. We also demonstrate that choosing different regularizers for absorption and phase can improve the reconstructions. The use of the total variation and its generalization in a primal-dual approach allows us to exploit the sparsity of the investigated sample. On both simulated and real datasets, the proposed nonlinear primal-dual hybrid gradient (NL-PDHG) method yields reconstructions with considerably fewer artifacts and improved the normalized mean squared error compared with its linearized version.

Mixed scale dense convolutional networks for x-ray phase contrast imaging.

X-ray in-line phase contrast imaging relies on the measurement of Fresnel diffraction intensity patterns due to the phase shift and the attenuation induced by the object. The recovery of phase and attenuation from one or several diffraction patterns is a nonlinear ill-posed inverse problem. In this work, we propose supervised learning approaches using mixed scale dense (MS-D) convolutional neural networks to simultaneously retrieve the phase and the attenuation from x-ray phase contrast images. This network architecture uses dilated convolutions to capture features at different image scales and densely connects all feature maps. The long range information in images becomes quickly available, and greater receptive field size can be obtained without losing resolution. This network architecture seems to account for the effect of the Fresnel operator very efficiently. We train the networks using simulated data of objects consisting of either homogeneous components, characterized by a fixed ratio of the induced refractive phase shifts and attenuation, or heterogeneous components, consisting of various materials. We also train the networks in the image domain by applying a simple initial reconstruction using the adjoint of the Fréchet derivative. We compare the results obtained with the MS-D network to reconstructions using U-Net, another popular network architecture, as well as to reconstructions using the contrast transfer function method, a direct phase and attenuation retrieval method based on linearization of the direct problem. The networks are evaluated using simulated noisy data as well as images acquired at NanoMAX (MAX IV, Lund, Sweden). In all cases, large improvements of the reconstruction errors are obtained on simulated data compared to the linearized method. Moreover, on experimental data, the networks improve the reconstruction quantitatively, improving the low-frequency behavior and the resolution.

PyPhase - a Python package for X-ray phase imaging.

X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).

3D skull modelling and description of a new baurusuchid (Crocodyliformes, Mesoeucrocodylia) from the Late Cretaceous (Bauru Basin) of Brazil.

Baurusuchidae is one of the most diverse groups of South American notosuchians, unambiguously recorded in Late Cretaceous deposits of Brazil and Argentina. The group is characterized by a reduced tooth formula, a lateromedially compressed rostrum, and a verticalized quadrate, representing one of the top predators of their faunas. Historically, skull morphology is the most employed tool to investigate the relationships of baurusuchids, as most of the species have been primarily based on cranial remains. The present study describes a new baurusuchid species from the Bauru Basin of Brazil, based on the first tridimensional digital reconstruction of individualized skull bones for Notosuchia, and discusses its phylogenetic position within the group. The new species differs from all the other known baurusuchids by a depression on the posterior portion of the nasal bearing a crest, an infraorbital crest of the jugal that extends until the anterior margin of the lacrimal, the dorsal surface of the frontal lacking a longitudinal crest or depression, and the lateral convexity of the squamosal prongs participating in the occipital wall. The new taxon is consistently positioned as sister to the remaining baurusuchines, with Aplestosuchus sordidus and Stratiotosuchus maxhechti, as successive sister-taxa to a monophyletic Baurusuchus (Ba. albertoi, Ba. Salgadoensis, and Ba. pachecoi). Our updated phylogenetic analysis helps to differentiate the two major Baurusuchidae lineages, Baurusuchinae and Pissarrachampsinae. Yet, the new species shares morphological features with both groups, suggesting the occurrence of "Zones of Variability" in the radiation of Baurusuchidae.

Towards Monte Carlo simulation of X-ray phase contrast using GATE.

We describe the first developments towards a Monte Carlo X-ray phase contrast imaging simulator for the medical imaging and radiotherapy simulation software GATE. Phase contrast imaging is an imaging modality taking advantage of the phase shift of X-rays. This modality produces images with a higher sensitivity than conventional, attenuation based imaging. As the first developments towards Monte Carlo phase contrast simulation, we implemented a Monte Carlo process for the refraction and total reflection of X-rays, as well as an analytical wave optics approach for generating Fresnel diffraction patterns. The implementation is validated against data acquired using a laboratory X-ray tomography system. The overall agreement between the simulations and the data is encouraging, which motivates further development of Monte Carlo based simulation of X-ray phase contrast imaging. These developments have been released in GATE version 8.2.

The Protective Role of Bark and Bark Fibers of the Giant Sequoia (Sequoiadendron giganteum) during High-Energy Impacts.

The influences of (1) a high fiber content, (2) the arrangement of fibers in fiber groups, and (3) a layered hierarchical composition of the bark of the giant sequoia (Sequoiadendron giganteum) on its energy dissipation capability are analyzed and discussed regarding the relevance for an application in bioinspired components in civil engineering. The giant sequoia is native to the Sierra Nevada (USA), a region with regular rockfalls. It is thus regularly exposed to high-energy impacts, with its bark playing a major protective role, as can be seen in the wild and has been proven in laboratory experiments. The authors quantify the fundamental biomechanical properties of the bark at various length scales, taking into account its hierarchical setup ranging from the integral level (whole bark) down to single bark fibers. Microtensile tests on single fibers and fiber pairs give insights into the properties of single fibers as well as the benefits of the strong longitudinal interconnection between single fibers arranged in pairs. Going beyond the level of single fibers or fiber pairs, towards the integral level, quasistatic compression tests and dynamic impact tests are performed on samples comprising the whole bark (inner and outer bark). These tests elucidate the deformation behavior under quasistatic compression and dynamic impact relevant for the high energy dissipation and impact-damping behavior of the bark. The remarkable energy dissipation capability of the bark at the abovementioned hierarchical levels are linked to the layered and fibrous structure of the bark structurally analyzed by thin sections and SEM and µCT scans.

3D micro structural analysis of human cortical bone in paired femoral diaphysis, femoral neck and radial diaphysis.

Human bone is known to adapt to its mechanical environment in a living body. Both its architecture and microstructure may differ between weight-bearing and non-weight-bearing bones. The aim of the current study was to analyze in three dimensions, the morphology of the multi-scale porosities on human cortical bone at different locations. Eight paired femoral diaphyses, femoral necks, and radial diaphyses were imaged using Synchrotron Radiation µCT with a 0.7 µm isotropic voxel size. The spatial resolution facilitates the investigation of the multiscale porosities of cortical bone, from the osteonal canals system down to the osteocyte lacunar system. Our results showed significant differences in the microstructural properties, regarding both osteonal canals and osteocytes lacunae, between the different anatomical locations. The radius presents significantly lower osteonal canal volume fraction and smaller osteonal canals than the femoral diaphysis or neck. Osteocytes lacunae observed in the radius are significantly different in shape than in the femur, and lacunar density is higher in the femoral neck. These results show that the radius, a non-weight-bearing bone, is significantly different in terms of its microstructure from a weight-bearing bone such as the femur. This implies that the cortical bone properties evaluated on the femoral diaphysis, the main location studied within the literature, cannot be generalized to other anatomical locations.

Evaluation of phase retrieval approaches in magnified X-ray phase nano computerized tomography applied to bone tissue.

X-ray phase contrast imaging offers higher sensitivity compared to conventional X-ray attenuation imaging and can be simply implemented by propagation when using a partially coherent synchrotron beam. We address the phase retrieval in in-line phase nano-CT using multiple propagation distances. We derive a method which extends Paganin's single distance method and compare it to the contrast transfer function (CTF) approach in the case of a homogeneous object. The methods are applied to phase nano-CT data acquired at the voxel size of 30 nm (ID16A, ESRF, Grenoble, France). Our results show a gain in image quality in terms of the signal-to-noise ratio and spatial resolution when using four distances instead of one. The extended Paganin's method followed by an iterative refinement step provides the best reconstructions while the homogeneous CTF method delivers quasi comparable results for our data, even without refinement step.

An exceptionally preserved association of complete dinosaur skeletons reveals the oldest long-necked sauropodomorphs.

The rise of sauropodomorphs is still poorly understood due to the scarcity of well-preserved fossils in early Norian rocks. Here, we present an association of complete and exceptionally well-preserved dinosaur skeletons that helps fill that gap. They represent a new species, which is recovered as a member of a clade solely composed of Gondwanan Triassic taxa. The new species allows the definition of a set of anatomical changes that shaped sauropodomorph evolution along a period from 233 to 225 Ma, as recorded in the well dated Late Triassic beds of Brazil. In that time span, apart from achieving a more herbivorous diet, sauropodomorph dinosaurs increased their size in a ratio of 230% and their typical long neck was also established, becoming proportionally twice longer than those of basal taxa. Indeed, the new dinosaur is the oldest-known sauropodomorph with such an elongated neck, suggesting that the ability to feed on high vegetation was a key trait achieved along the early Norian. Finally, the clustered preservation mode of the skeletons represents the oldest evidence of gregarious behaviour among sauropodomorphs.

Review of the fossil matamata turtles: earliest well-dated record and hypotheses on the origin of their present geographical distribution.

The matamata (Chelus fimbriatus) is a highly aquatic chelid turtle known exclusively from northern South America. Due to its extremely modified morphology, it is well circumscribed among living taxa, but that is not the case of the two extinct species ascribed to the taxon, Chelus colombianus and Chelus lewisi. These were originally described for the Miocene of Colombia and Venezuela, respectively, and are known mostly from post-cranial material. Few traits have been considered diagnostic for these fossil taxa, and their shared geographic and temporal distributions raise doubts about their distinctiveness. Here, we describe new turtle remains from the early Miocene Castillo Formation, at Cerro la Cruz, northwestern Venezuela, assigning them to C. colombianus. We also review the taxonomy and diagnostic features of the fossil species of Chelus, comparing them with the variation recognized within C. fimbriatus. All alleged differences between the fossil Chelus species were found in our sample of the extant species, and may represent intraspecific variation of a single fossil species. Further, we reviewed the fossil record of Chelus spp. and proposed a paleobiogeographic hypothesis to explain its present geographic range.

Distribution of mesoscale elastic properties and mass density in the human femoral shaft.

Cortical bone properties are determined by tissue composition and structure at several hierarchical length scales. In this study, the spatial distribution of micro- and mesoscale elastic properties within a human femoral shaft has been investigated. Microscale tissue degree of mineralization (DMB), cortical vascular porosity Ct.Po and the average transverse isotropic stiffness tensor C(Micro) of cylindrical-shaped samples (diameter: 4.4 mm, N = 56) were obtained from cortical regions between 20 and 85% of the total femur length and around the periphery (anterior, medial, posterior and lateral quadrants) by means of synchrotron radiation µCT (SRµCT) and 50-MHz scanning acoustic microscopy (SAM). Within each cylinder, the volumetric bone mineral density (vBMD) and the mesoscale stiffness tensor C(Meso) were derived using a numerical homogenization approach. Moreover, microelastic maps of the axial elastic coefficient c33 measured by SAM at distinct cross-sectional locations along the femur were used to construct a 3-D multiscale elastic model of the femoral shaft. Variations of vBMD (6.1%) were much lower than the variations of mesoscale elastic coefficients (11.1-21.3%). The variation of DMB was only a minor predictor for variations of the mesoscale elastic properties (0.05 ≤ R(2) ≤ 0.34). Instead, variations of the mesoscale elastic properties could be explained by variations of cortical porosity and microscale elastic properties. These data were suitable inputs for numerical evaluations and may help to unravel the relations between structure and composition on the elastic function in cortical bone.

Accessing osteocyte lacunar geometrical properties in human jaw bone on the submicron length scale using synchrotron radiation µCT.

The architectural properties of the osteocyte cell network provide a valuable basis for understanding the mechanisms of bone remodelling, mineral homeostasis, ageing and pathologies. Recent advances in synchrotron microtomography enable unprecedented three-dimensional imaging of both the bone lacunar network and the extracellular matrix. Here, we investigate the three-dimensional morphological properties of osteocyte lacunae in human healthy and bisphosphonate-related osteonecrotic jaw bone based on synchrotron X-ray computed tomography images, with a spatial isotropic voxel size of 300 nm. Bisphosphonate-related osteonecrosis of the jaw is a relatively new disease with increasing incidence, which remains poorly understood. A step forward in elucidating this malady is to assess whether, and how, the morphology of the osteocyte lacunar network is modified in the affected jaw tissue. We evaluate thousands of cell lacunae from five specimens of which three originate from patients diagnosed with bisphosphonate-associated osteonecrosis. In this exploratory study, we report three-dimensional quantitative results on lacunar volumes (296-502 µm(3)), shape (approximated by an ellipsoidal shape with principal axes a > b > c, such that a = 2.2b and a = 4c) and spatial distribution (i.e., 50% of the mineralized matrix volume is located within 12 µm to the closest lacunar boundary) at submicron resolution on such specimens. We observe that the average lacunar volumes of the bisphosphonate-related osteonecrotic jaw specimens were within the range of volumes found in the two specimens originating from healthy donors and conclude that lacunar volumes are not the key element in the course of bisphosphonate-related osteonecrotic jaw. In three out of five specimens we observe lacunar volume sizes in segmented osteons to be significantly different compared to lacunar volumes in the adjacent tissue regions. Furthermore, we quantify the number of lacunae containing small dense objects (on average 9%). In contrast to lacunar morphology we report the lacunar density (16,000-50,000 per mm(3)) to be different in jaw bone tissue compared to what has been reported in femoral sites.