A well-preserved 'placoderm' (stem-group Gnathostomata) upper jaw from the Early Devonian of Mongolia clarifies jaw evolution.

The origin of jaws and teeth remains contentious in vertebrate evolution. 'Placoderms' (Silurian-Devonian armoured jawed fishes) are central to debates on the origins of these anatomical structures. 'Acanthothoracids' are generally considered the most primitive 'placoderms'. However, they are so far known mainly from disarticulated skeletal elements that are typically incomplete. The structure of the jaws-particularly the jaw hinge-is poorly known, leaving open questions about their jaw function and comparison with other placoderms and modern gnathostomes. Here we describe a near-complete 'acanthothoracid' upper jaw, allowing us to reconstruct the likely orientation and angle of the bite and compare its morphology with that of other known 'placoderm' groups. We clarify that the bite position is located on the upper jaw cartilage rather than on the dermal cheek and thus show that there is a highly conserved bite morphology among most groups of 'placoderms', regardless of their overall cranial geometry. Incorporation of the dermal skeleton appears to provide a sound biomechanical basis for jaw origins. It appears that 'acanthothoracid' dentitions were fundamentally similar in location to that of arthrodire 'placoderms', rather than resembling bony fishes. Irrespective of current phylogenetic uncertainty, the new data here resolve the likely general condition for 'placoderms' as a whole, and as such, ancestral morphology of known jawed vertebrates.

Quantification of Interdependent Dynamics during Laser Additive Manufacturing Using X-Ray Imaging Informed Multi-Physics and Multiphase Simulation.

Laser powder bed fusion (LPBF) can produce high-value metallic components for many industries; however, its adoption for safety-critical applications is hampered by the presence of imperfections. The interdependency between imperfections and processing parameters remains unclear. Here, the evolution of porosity and humps during LPBF using X-ray and electron imaging, and a high-fidelity multiphase process simulation, is quantified. The pore and keyhole formation mechanisms are driven by the mixing of high temperatures and high metal vapor concentrations in the keyhole is revealed. The irregular pores are formed via keyhole collapse, pore coalescence, and then pore entrapment by the solidification front. The mixing of the fast-moving vapor plume and molten pool induces a Kelvin-Helmholtz instability at the melt track surface, forming humps. X-ray imaging and a high-fidelity model are used to quantify the pore evolution kinetics, pore size distribution, waviness, surface roughness, and melt volume under single layer conditions. This work provides insights on key criteria that govern the formation of imperfections in LPBF and suggest ways to improve process reliability.

Dendritic crystallization in hydrous basaltic magmas controls magma mobility within the Earth's crust.

The majority of basaltic magmas stall in the Earth's crust as a result of the rheological evolution caused by crystallization during transport. However, the relationships between crystallinity, rheology and eruptibility remain uncertain because it is difficult to observe dynamic magma crystallization in real time. Here, we present in-situ 4D data for crystal growth kinetics and the textural evolution of pyroxene during crystallization of trachybasaltic magmas in high-temperature experiments under water-saturated conditions at crustal pressures. We observe dendritic growth of pyroxene on initially euhedral cores, and a surprisingly rapid increase in crystal fraction and aspect ratio at undercooling ≥30 °C. Rapid dendritic crystallization favours a rheological transition from Newtonian to non-Newtonian behaviour within minutes. We use a numerical model to quantify the impact of rapid dendritic crystallization on basaltic dike propagation, and demonstrate its dramatic effect on magma mobility and eruptibility. Our results provide insights into the processes that control whether intrusions lead to eruption or not.

On Acquisition Parameters and Processing Techniques for Interparticle Contact Detection in Granular Packings Using Synchrotron Computed Tomography.

X-ray computed tomography (XCT) is regularly employed in geomechanics to non-destructively measure the solid and pore fractions of soil and rock from reconstructed 3D images. With the increasing availability of high-resolution XCT imaging systems, researchers now seek to measure microfabric parameters such as the number and area of interparticle contacts, which can then be used to inform soil behaviour modelling techniques. However, recent research has evidenced that conventional image processing methods consistently overestimate the number and area of interparticle contacts, mainly due to acquisition-driven image artefacts. The present study seeks to address this issue by systematically assessing the role of XCT acquisition parameters in the accurate detection of interparticle contacts. To this end, synchrotron XCT has been applied to a hexagonal close-packed arrangement of glass pellets with and without a prescribed separation between lattice layers. Different values for the number of projections, exposure time, and rotation range have been evaluated. Conventional global grey value thresholding and novel U-Net segmentation methods have been assessed, followed by local refinements at the presumptive contacts, as per recently proposed contact detection routines. The effect of the different acquisition set-ups and segmentation techniques on contact detection performance is presented and discussed, and optimised workflows are proposed.

Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography.

Parallel-beam tomography systems at synchrotron facilities have limited field of view (FOV) determined by the available beam size and detector system coverage. Scanning the full size of samples bigger than the FOV requires various data acquisition schemes such as grid scan, 360-degree scan with offset center-of-rotation (COR), helical scan, or combinations of these schemes. Though straightforward to implement, these scanning techniques have not often been used due to the lack of software and methods to process such types of data in an easy and automated fashion. The ease of use and automation is critical at synchrotron facilities where using visual inspection in data processing steps such as image stitching, COR determination, or helical data conversion is impractical due to the large size of datasets. Here, we provide methods and their implementations in a Python package, named Algotom, for not only processing such data types but also with the highest quality possible. The efficiency and ease of use of these tools can help to extend applications of parallel-beam tomography systems.

Preliminary paleohistological observations of the StW 573 ('Little Foot') skull.

Numerous aspects of early hominin biology remain debated or simply unknown. However, recent developments in high-resolution imaging techniques have opened new avenues in the field of paleoanthropology. More specifically, X-ray synchrotron-based analytical imaging techniques have the potential to provide crucial details on the ontogeny, physiology, biomechanics, and biological identity of fossil specimens. Here we present preliminary results of our X-ray synchrotron-based investigation of the skull of the 3.67-million-year-old Australopithecus specimen StW 573 ('Little Foot') at the I12 beamline of the Diamond Light Source (United Kingdom). Besides showing fine details of the enamel (i.e., hypoplasias) and cementum (i.e., incremental lines), as well as of the cranial bone microarchitecture (e.g., diploic channels), our synchrotron-based investigation reveals for the first time the 3D spatial organization of the Haversian systems in the mandibular symphysis of an early hominin.

Physics of animal health: on the mechano-biology of hoof growth and form.

Global inequalities in economic access and agriculture productivity imply that a large number of developing countries rely on working equids for transport/agriculture/mining. Therefore, the understanding of hoof conditions/shape variations affecting equids' ability to work is still a persistent concern. To bridge this gap, using a multi-scale interdisciplinary approach, we provide a bio-physical model predicting the shape of equids' hooves as a function of physical and biological parameters. In particular, we show (i) where the hoof growth stress originates from, (ii) why the hoof growth rate is one order of magnitude higher than the proliferation rate of epithelial cells and (iii) how the soft-to-hard transformation of the epithelium is possible allowing the hoof to fulfil its function as a weight-bearing element. Finally (iv), we demonstrate that the reason for hoof misshaping is linked to the asymmetrical design of equids' feet (shorter quarters/long toe) together with the inability of the biological growth stress to compensate for such an asymmetry. Consequently, the hoof can adopt a dorsal curvature and become 'dished' overtime, which is a function of the animal's mass and the hoof growth rate. This approach allows us to discuss the potential occurrence of this multifaceted pathology in equids.

High-energy, high-resolution, fly-scan X-ray phase tomography.

High energy X-ray phase contrast tomography is tremendously beneficial to the study of thick and dense materials with poor attenuation contrast. Recently, the X-ray speckle-based imaging technique has attracted widespread interest because multimodal contrast images can now be retrieved simultaneously using an inexpensive wavefront modulator and a less stringent experimental setup. However, it is time-consuming to perform high resolution phase tomography with the conventional step-scan mode because the accumulated time overhead severely limits the speed of data acquisition for each projection. Although phase information can be extracted from a single speckle image, the spatial resolution is deteriorated due to the use of a large correlation window to track the speckle displacement. Here we report a fast data acquisition strategy utilising a fly-scan mode for near field X-ray speckle-based phase tomography. Compared to the existing step-scan scheme, the data acquisition time can be significantly reduced by more than one order of magnitude without compromising spatial resolution. Furthermore, we have extended the proposed speckle-based fly-scan phase tomography into the previously challenging high X-ray energy region (120 keV). This development opens up opportunities for a wide range of applications where exposure time and radiation dose are critical.

Revealing internal flow behaviour in arc welding and additive manufacturing of metals.

Internal flow behaviour during melt-pool-based metal manufacturing remains unclear and hinders progression to process optimisation. In this contribution, we present direct time-resolved imaging of melt pool flow dynamics from a high-energy synchrotron radiation experiment. We track internal flow streams during arc welding of steel and measure instantaneous flow velocities ranging from 0.1 m s-1 to 0.5 m s-1. When the temperature-dependent surface tension coefficient is negative, bulk turbulence is the main flow mechanism and the critical velocity for surface turbulence is below the limits identified in previous theoretical studies. When the alloy exhibits a positive temperature-dependent surface tension coefficient, surface turbulence occurs and derisory oxides can be entrapped within the subsequent solid as result of higher flow velocities. The widely used arc welding and the emerging arc additive manufacturing routes can be optimised by controlling internal melt flow through adjusting surface active elements.

Superior techniques for eliminating ring artifacts in X-ray micro-tomography.

Synchrotron-based X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. In sinograms the artifacts appear as straight lines or stripe artifacts. These artifacts are caused by the irregular response of a detecting system giving rise to a variety of observed types of stripes: full stripes, partial stripes, fluctuating stripes, and unresponsive stripes. The use of pre-processing techniques such as distortion correction or phase retrieval blurs and enlarges these stripes. It is impossible for a single approach to remove all types of stripe artifacts. Here, we propose three techniques for tackling all of them. The proposed techniques are easy to implement; do not generate extra stripe artifacts and void-center artifacts; and give superior quality on challenging data sets and in comparison with other techniques. Implementations in Python and a challenging data set are available for download.

X-ray phase-contrast imaging with engineered porous materials over 50†keV.

X-ray phase-contrast imaging can substantially enhance image contrast for weakly absorbing samples. The fabrication of dedicated optics remains a major barrier, especially in high-energy regions (i.e. over 50 keV). Here, the authors perform X-ray phase-contrast imaging by using engineered porous materials as random absorption masks, which provides an alternative solution to extend X-ray phase-contrast imaging into previously challenging higher energy regions. The authors have measured various samples to demonstrate the feasibility of the proposed engineering materials. This technique could potentially be useful for studying samples across a wide range of applications and disciplines.

In situ X-ray imaging of defect and molten pool dynamics in laser additive manufacturing.

The laser-matter interaction and solidification phenomena associated with laser additive manufacturing (LAM) remain unclear, slowing its process development and optimisation. Here, through in situ and operando high-speed synchrotron X-ray imaging, we reveal the underlying physical phenomena during the deposition of the first and second layer melt tracks. We show that the laser-induced gas/vapour jet promotes the formation of melt tracks and denuded zones via spattering (at a velocity of 1 m s-1). We also uncover mechanisms of pore migration by Marangoni-driven flow (recirculating at a velocity of 0.4 m s-1), pore dissolution and dispersion by laser re-melting. We develop a mechanism map for predicting the evolution of melt features, changes in melt track morphology from a continuous hemi-cylindrical track to disconnected beads with decreasing linear energy density and improved molten pool wetting with increasing laser power. Our results clarify aspects of the physics behind LAM, which are critical for its development.

A three-dimensional placoderm (stem-group gnathostome) pharyngeal skeleton and its implications for primitive gnathostome pharyngeal architecture.

The pharyngeal skeleton is a key vertebrate anatomical system in debates on the origin of jaws and gnathostome (jawed vertebrate) feeding. Furthermore, it offers considerable potential as a source of phylogenetic data. Well-preserved examples of pharyngeal skeletons from stem-group gnathostomes remain poorly known. Here, we describe an articulated, nearly complete pharyngeal skeleton in an Early Devonian placoderm fish, Paraplesiobatis heinrichsi Broili, from Hunsrück Slate of Germany. Using synchrotron light tomography, we resolve and reconstruct the three-dimensional gill arch architecture of Paraplesiobatis and compare it with other gnathostomes. The preserved pharyngeal skeleton comprises elements of the hyoid arch (probable ceratohyal) and a series of branchial arches. Limited resolution in the tomography scan causes some uncertainty in interpreting the exact number of arches preserved. However, at least four branchial arches are present. The final and penultimate arches are connected as in osteichthyans. A single median basihyal is present as in chondrichthyans. No dorsal (epibranchial or pharyngobranchial) elements are observed. The structure of the pharyngeal skeleton of Paraplesiobatis agrees well with Pseudopetalichthys from the same deposit, allowing an alternative interpretation of the latter taxon. The phylogenetic significance of Paraplesiobatis is considered. A median basihyal is likely an ancestral gnathostome character, probably with some connection to both the hyoid and the first branchial arch pair. Unpaired basibranchial bones may be independently derived in chondrichthyans and osteichthyans.

A novel molten-salt electrochemical cell for investigating the reduction of uranium dioxide to uranium metal by lithium using in situ synchrotron radiation.

A novel electrochemical cell has been designed and built to allow for in situ energy-dispersive X-ray diffraction measurements to be made during reduction of UO2 to U metal in LiCl-KCl at 500°C. The electrochemical cell contains a recessed well at the bottom of the cell into which the working electrode sits, reducing the beam path for the X-rays through the molten-salt and maximizing the signal-to-noise ratio from the sample. Lithium metal was electrodeposited onto the UO2 working electrode by exposing the working electrode to more negative potentials than the Li deposition potential of the LiCl-KCl eutectic electrolyte. The Li metal acts as a reducing agent for the chemical reduction of UO2 to U, which appears to proceed to completion. All phases were fitted using Le Bail refinement. The cell is expected to be widely applicable to many studies involving molten-salt systems.

Long-term effects of bisphosphonate therapy: perforations, microcracks and mechanical properties.

Osteoporosis is characterised by trabecular bone loss resulting from increased osteoclast activation and unbalanced coupling between resorption and formation, which induces a thinning of trabeculae and trabecular perforations. Bisphosphonates are the frontline therapy for osteoporosis, which act by reducing bone remodelling, and are thought to prevent perforations and maintain microstructure. However, bisphosphonates may oversuppress remodelling resulting in accumulation of microcracks. This paper aims to investigate the effect of bisphosphonate treatment on microstructure and mechanical strength. Assessment of microdamage within the trabecular bone core was performed using synchrotron X-ray micro-CT linked to image analysis software. Bone from bisphosphonate-treated fracture patients exhibited fewer perforations but more numerous and larger microcracks than both fracture and non-fracture controls. Furthermore, bisphosphonate-treated bone demonstrated reduced tensile strength and Young's Modulus. These findings suggest that bisphosphonate therapy is effective at reducing perforations but may also cause microcrack accumulation, leading to a loss of microstructural integrity and consequently, reduced mechanical strength.

Almost a spider: a 305-million-year-old fossil arachnid and spider origins.

Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasierigen. et sp. nov. from the Late Carboniferous (Stephanian,ca 305-299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography reconstruction. The latter is a first for siderite-hosted fossils and has allowed us to investigate fine anatomical details. Although distinctly spider-like in habitus, this remarkable fossil lacks a key diagnostic character of Araneae: spinnerets on the underside of the opisthosoma. It also lacks a flagelliform telson found in the recently recognized, spider-related, Devonian-Permian Uraraneida. Cladistic analysis resolves our new fossil as sister group to the spiders: the spider stem-group comprises the uraraneids and I. brasieri While we are unable to demonstrate the presence of spigots in this fossil, the recovered phylogeny suggests the earliest character to evolve on the spider stem-group is the secretion of silk. This would have been followed by the loss of a flagelliform telson, and then the ability to spin silk using spinnerets. This last innovation defines the true spiders, significantly post-dates the origins of silk, and may be a key to the group's success. The Montceau-les-Mines locality has previously yielded a mesothele spider (with spinnerets). Evidently, Late Palaeozoic spiders lived alongside Palaeozoic arachnid grades which approached the spider condition, but did not express the full suite of crown-group autapomorphies.

Phase-Contrast Micro-Computed Tomography Measurements of the Intraocular Pressure-Induced Deformation of the Porcine Lamina Cribrosa.

The lamina cribrosa (LC) is a complex mesh-like tissue in the posterior eye. Its biomechanical environment is thought to play a major role in glaucoma, the second most common cause of blindness. Due to its small size and relative inaccessibility, high-resolution measurements of LC deformation, important in characterizing LC biomechanics, are challenging. Here we present a novel noninvasive imaging method, which enables measurement of the three-dimensional deformation of the LC caused by acute elevation of intraocular pressure (IOP). Posterior segments of porcine eyes were imaged using synchrotron radiation phase contrast micro-computed tomography (PC µCT) at IOPs between 6 and 37 mmHg. The complex trabecular architecture of the LC was reconstructed with an isotropic spatial resolution of 3.2 µm. Scans acquired at different IOPs were analyzed with digital volume correlation (DVC) to compute full-field deformation within the LC. IOP elevation caused substantial tensile, shearing and compressive devformation within the LC, with maximum tensile strains at 30 mmHg averaging 5.5%, and compressive strains reaching 20%. We conclude that PC µCT provides a novel high-resolution method for imaging the LC, and when combined with DVC, allows for full-field 3D measurement of ex vivo LC biomechanics at high spatial resolution.

Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography.

Distortion correction or camera calibration for an imaging system which is highly configurable and requires frequent disassembly for maintenance or replacement of parts needs a speedy method for recalibration. Here we present direct techniques for calculating distortion parameters of a non-linear model based on the correct determination of the center of distortion. These techniques are fast, very easy to implement, and accurate at sub-pixel level. The implementation at the X-ray tomography system of the I12 beamline, Diamond Light Source, which strictly requires sub-pixel accuracy, shows excellent performance in the calibration image and in the reconstructed images.

Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in Human Huntington's Disease Neural Stem Cells.

We utilized induced pluripotent stem cells (iPSCs) derived from Huntington's disease (HD) patients as a human model of HD and determined that the disease phenotypes only manifest in the differentiated neural stem cell (NSC) stage, not in iPSCs. To understand the molecular basis for the CAG repeat expansion-dependent disease phenotypes in NSCs, we performed transcriptomic analysis of HD iPSCs and HD NSCs compared to isogenic controls. Differential gene expression and pathway analysis pointed to transforming growth factor ß (TGF-ß) and netrin-1 as the top dysregulated pathways. Using data-driven gene coexpression network analysis, we identified seven distinct coexpression modules and focused on two that were correlated with changes in gene expression due to the CAG expansion. Our HD NSC model revealed the dysregulation of genes involved in neuronal development and the formation of the dorsal striatum. The striatal and neuronal networks disrupted could be modulated to correct HD phenotypes and provide therapeutic targets.

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source.

Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an 'orthogonal' fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and 'facility-independent': it can run on standard cluster infrastructure at any institution.