Calcite crystal orientation patterns in the bilayers of laminated shells of benthic rotaliid foraminifera.

Shells of calcifying foraminifera play a major role in marine biogeochemical cycles; fossil shells form important archives for paleoenvironment reconstruction. Despite their importance in many Earth science disciplines, there is still little consensus on foraminiferal shell mineralization. Geochemical, biochemical, and physiological studies showed that foraminiferal shell formation might take place through various and diverse mineralization mechanisms. In this study, we contribute to benthic foraminiferal shell calcification through deciphering crystallite organization within the shells. We base our conclusions on results gained from electron backscattered diffraction (EBSD) measurements and describe microstructure/texture characteristics within the laminated shell walls of the benthic, symbiontic foraminifera: Ammonia tepida, Amphistegina lobifera, Amphistegina lessonii. We highlight crystallite assembly patterns obtained on differently oriented cuts and discuss crystallite sizes, morphologies, interlinkages, orientations, and co-orientation strengths. We show that: (i) crystals within benthic foraminiferal shells are mesocrystals, (ii) have dendritic-fractal morphologies and (iii) interdigitate strongly. Based on crystal size, we (iv) differentiate between the two layers that comprise the shells and demonstrate that (v) crystals in the septa have different assemblies relative to those in the shell walls. We highlight that (vi) at junctions of different shell elements the axis of crystal orientation jumps abruptly such that their assembly in EBSD maps has a bimodal distribution. We prove (vii) extensive twin-formation within foraminiferal calcite; we demonstrate (viii) the presence of two twin modes: 60°/[001] and 77°/~[6 -6 1] and visualize their distributions within the shells. In a broader perspective, we draw conclusions on processes that lead to the observed microstructure/texture patterns.

Micro-CT screening of old shell collections helps to understand the distribution of viviparity in the highly diversified clausiliid clade of land snails.

Current zoological research may benefit in many ways from the study of old collections of shells. These collections may provide materials for the verification of broad zoogeographical and ecological hypotheses on the reproduction of molluscs, as they include records from many areas where sampling is currently impossible or very difficult due to political circumstances. In the present paper we present data on viviparous and embryo-retention reproductive modes in clausiliid land snails (subfamily Phaedusinae) acquired from specimens collected since the nineteenth century in the Pontic, Hyrcanian, and East and Southeast Asian regions. X-ray imaging (micro-CT) enabled relatively quick screening of more than 1,000 individuals classified within 141 taxa, among which we discovered 205 shells containing embryos or eggs. Gravid individuals were found to belong to 55 species, representing, for some of these species, the first indication of brooding reproductive strategy.

Three-dimensional structural evolution of the cuttlefish Sepia officinalis shell from embryo to adult stages.

The cuttlefish shell is an internal structure with a composition and general organization unique among molluscs. Its formation and the structure-function relation are explored during Sepia officinalis development, using computerized axial tomography scanning (CAT-scan) three-dimensional analyses coupled to physical measurements and modelling. In addition to the evolution of the overall form, modifications of the internal structure were identified from the last third embryonic stages to adult. Most of these changes can be correlated to life cycle stages and environmental constraints. Protected by the capsule during embryonic life, the first internal chambers are sustained by isolated pillars formed from the dorsal to the ventral septum. After hatching, the formation of pillars appears to be a progressive process from isolated points to interconnected pillars forming a wall-delineated labyrinthine structure. We analysed the interpillar space, the connectivity and the tortuosity of the labyrinth. The labyrinthine pillar network is complete just prior to the wintering migration, probably to sustain the need to adapt to high pressure and to allow buoyancy regulation. At that time, the connectivity in the pillar network is compensated by an increase in tortuosity, most probably to reduce liquid diffusion in the shell. Altogether these results suggest adjustment of internal calcified structure development to both external forces and physiological needs.

Compressive deformation and failure of trabecular structures in a turtle shell.

Turtle shells comprising of cortical and trabecular bones exhibit intriguing mechanical properties. In this work, compression tests were performed using specimens made from the carapace of Kinixys erosa turtle. A combination of imaging techniques and mechanical testing were employed to examine the responses of hierarchical microstructures of turtle shell under compression. Finite element models produced from microCT-scanned microstructures and analytical foam structure models were then used to elucidate local responses of trabecular bones deformed under compression. The results reveal the contributions from micro-strut bending and stress concentrations to the fractural mechanisms of trabecular bone structures. The porous structures of turtle shells could be an excellent prototype for the bioinspired design of deformation-resistant structures. STATEMENT OF SIGNIFICANCE: In this study, a combination of analytical, computational models and experiments is used to study the underlying mechanisms that contribute to the compressive deformation of a Kinixys erosa turtle shell between the nano-, micro- and macro-scales. The proposed work shows that the turtle shell structures can be analyzed as sandwich structures that have the capacity to concentrate deformation and stresses within the trabecular bones, which enables significant energy absorption during compressive deformation. Then, the trends in the deformation characteristics and the strengths of the trabecular bone segments are well predicted by the four-strut model, which captures the effects of variations in strut length, thickness and orientation that are related to microstructural uncertainties of the turtle shells. The above results also suggest that the model may be used to guide the bioinspired design of sandwich porous structures that mimic the properties of the cortical and trabecular bone segments of turtle shells under a range of loading conditions.

High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms.

Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e., poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e., structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, the random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies-tessellated cartilage from a stingray, the dermal endoskeleton of a starfish, and the prismatic layer of a bivalve mollusc shell-we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized, and analyzed.

Novel insights into the morphology of Plesiochelys bigleri from the early Kimmeridgian of Northwestern Switzerland.

Plesiochelyidae were relatively large coastal marine turtles, which inhabited the epicontinental seas of Western Europe during the Late Jurassic. Their fossil record can be tracked in Germany, Switzerland, the United Kingdom, France, Spain and Portugal. The Jura Mountains, in northwestern Switzerland, have been the main source for the study of this group, mostly thanks to the rich and famous historical locality of Solothurn. In the last two decades, numerous plesiochelyid remains have been collected from Kimmeridgian deposits (Lower Virgula Marls and Banné Marls) in the area of Porrentruy (Canton of Jura, Switzerland). This material was revealed by construction works of the A16 Transjurane highway between 2000 and 2011, and led to the recent description of the new species Plesiochelys bigleri. In the years 2014 and 2016, new fragmentary turtle material was collected from the Banné Marls (Reuchenette Formation, lower Kimmeridgian) near the village of Glovelier, Canton of Jura, Switzerland. The new material consists of a complete shell, additional shell elements, a few bones from the appendicular and vertebral skeleton, and a fragmentary basicranium. This material can be confidently assigned to the species P. bigleri. It supports the presence of this species in the Banné Marls, slightly extends its spatial distribution and confirms the differences with the closely related species P. etalloni. The new material reveals that the split between the cerebral and palatine branches of the internal carotid artery occurs in a vertical plane in P. bigleri. This condition could not be observed in the type material due to poor preservation. This new character clearly distinguishes P. bigleri from P. etalloni and seems to be unique among thalassochelydians.

EEG-Based Control for Upper and Lower Limb Exoskeletons and Prostheses: A Systematic Review.

Electroencephalography (EEG) signals have great impact on the development of assistive rehabilitation devices. These signals are used as a popular tool to investigate the functions and the behavior of the human motion in recent research. The study of EEG-based control of assistive devices is still in early stages. Although the EEG-based control of assistive devices has attracted a considerable level of attention over the last few years, few studies have been carried out to systematically review these studies, as a means of offering researchers and experts a comprehensive summary of the present, state-of-the-art EEG-based control techniques used for assistive technology. Therefore, this research has three main goals. The first aim is to systematically gather, summarize, evaluate and synthesize information regarding the accuracy and the value of previous research published in the literature between 2011 and 2018. The second goal is to extensively report on the holistic, experimental outcomes of this domain in relation to current research. It is systematically performed to provide a wealthy image and grounded evidence of the current state of research covering EEG-based control for assistive rehabilitation devices to all the experts and scientists. The third goal is to recognize the gap of knowledge that demands further investigation and to recommend directions for future research in this area.

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation.

Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales. Understanding the role of templates in biomineral nucleation, and their importance in skeletal geochemistry requires an integrated, multiscale approach, which can place atom-scale observations of organic-mineral interfaces within a broader structural and geochemical context. Here we map the chemistry of an embedded organic template structure within a carbonate skeleton of the foraminifera Orbulina universa using both atom probe tomography (APT), a 3D chemical imaging technique with Ångström-level spatial resolution, and time-of-flight secondary ionization mass spectrometry (ToF-SIMS), a 2D chemical imaging technique with submicron resolution. We quantitatively link these observations, revealing that the organic template in O. universa is uniquely enriched in both Na and Mg, and contributes to intraskeletal chemical heterogeneity. Our APT analyses reveal the cation composition of the organic surface, offering evidence to suggest that cations other than Ca2+, previously considered passive spectator ions in biomineral templating, may be important in defining the energetics of carbonate nucleation on organic templates.

The Evolution and Development of Cephalopod Chambers and Their Shape.

The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth.

The armored carapace of the boxfish.

The boxfish (Lactoria cornuta) has a carapace consisting of dermal scutes with a highly mineralized surface plate and a compliant collagen base. This carapace must provide effective protection against predators as it comes at the high cost of reduced mobility and speed. The mineralized hydroxyapatite plates, predominantly hexagonal in shape, are reinforced with raised struts that extend from the center toward the edges of each scute. Below the mineralized plates are non-mineralized collagen fibers arranged in through-the-thickness layers of ladder-like formations. At the interfaces between scutes, the mineralized plates form suture-like teeth structures below which the collagen fibers bridge the gap between neighboring scutes. These sutures are unlike most others as they have no bridging Sharpey's fibers and appear to add little mechanical strength to the overall carapace. It is proposed that the sutured interface either allows for accommodation of the changing pressures of the boxfish's ocean habitat or growth, which occurs without molting or shedding. In both tension and punch testing the mineralized sutures remain relatively intact while most failures occur within the collagen fibers, allowing for the individual scutes to maintain their integrity. This complex structure allows for elevated strength of the carapace through an increase in the stressed area when attacked by predators in both penetrating and crushing modes.

Microstructure and micromechanics of the heart urchin test from X-ray tomography.

The microstructure of many echinoid species has long fascinated scientists because of its high porosity and outstanding mechanical properties. We have used X-ray microtomography to examine the test of Echinocardium cordatum (heart urchin), a burrowing cousin of the more commonly known sea urchins. Three dimensional imaging demonstrates that the bulk of the test is composed of only two distinct, highly porous, fenestrated regions (stereom), in which the thickness of the struts is constant. Different degrees of porosity are achieved by varying the spacing of the struts. Drawing an analogy to vertebrate trabecular bone, where for example, human bone has a connectivity density of ≈1/mm(3), we measure up to 150,000 strut connections per mm(3). Simulations of mechanical loading using finite element calculations indicate that the test performs at very close to the optimum expected for foams, highlighting the functional link between structure and mechanical properties.

Hierarchical structural design for fracture resistance in the shell of the pteropod Clio pyramidata.

The thecosomes are a group of planktonic pteropods with thin, 1 mm-sized aragonitic shells, which are known to possess a unique helical microstructure consisting of interlocking nanofibres. Here we investigate the detailed hierarchical structural and mechanical design of the pteropod Clio pyramidata. We quantify and elucidate the macroscopic distribution of the helical structure over the entire shell (~1 mm), the structural characteristics of the helical assembly (~10-100 µm), the anisotropic cross-sectional geometry of the fibrous building blocks (~0.5-10 µm) and the heterogeneous distribution of intracrystalline organic inclusions within individual fibres (<0.5 µm). A global fibre-like crystallographic texture is observed with local in-plane rotations. Microindentation and electron microscopy studies reveal that the helical organization of the fibrous building blocks effectively constrains mechanical damages through tortuous crack propagation. Uniaxial micropillar compression and cross-sectional transmission electron microscopy directly reveal that the interlocking fibrous building blocks further retard crack propagation at the nanometre scale.

Origin of the unique ventilatory apparatus of turtles.

The turtle body plan differs markedly from that of other vertebrates and serves as a model system for studying structural and developmental evolution. Incorporation of the ribs into the turtle shell negates the costal movements that effect lung ventilation in other air-breathing amniotes. Instead, turtles have a unique abdominal-muscle-based ventilatory apparatus whose evolutionary origins have remained mysterious. Here we show through broadly comparative anatomical and histological analyses that an early member of the turtle stem lineage has several turtle-specific ventilation characters: rigid ribcage, inferred loss of intercostal muscles and osteological correlates of the primary expiratory muscle. Our results suggest that the ventilation mechanism of turtles evolved through a division of labour between the ribs and muscles of the trunk in which the abdominal muscles took on the primary ventilatory function, whereas the broadened ribs became the primary means of stabilizing the trunk. These changes occurred approximately 50 million years before the evolution of the fully ossified shell.

Self-similar mesostructure evolution of the growing mollusc shell reminiscent of thermodynamically driven grain growth.

Significant progress has been made in understanding the interaction between mineral precursors and organic components leading to material formation and structuring in biomineralizing systems. The mesostructure of biological materials, such as the outer calcitic shell of molluscs, is characterized by many parameters and the question arises as to what extent they all are, or need to be, controlled biologically. Here, we analyse the three-dimensional structure of the calcite-based prismatic layer of Pinna nobilis, the giant Mediterranean fan mussel, using high-resolution synchrotron-based microtomography. We show that the evolution of the layer is statistically self-similar and, remarkably, its morphology and mesostructure can be fully predicted using classical materials science theories for normal grain growth. These findings are a fundamental step in understanding the constraints that dictate the shape of these biogenic minerals and shed light on how biological organisms make use of thermodynamics to generate complex morphologies.

[Radiographic images of the shells]. / Obrazy radiograficzne muszli.

Authors present the X-ray radiography as a method useful for the visualization internal structure of the shells for the conchiology and malacology.

Creation of a voxel phantom of the ICRP reference crab.

The International Commission on Radiological Protection (ICRP) has modeled twelve reference animal and plant (RAP) species using simple geometric shapes in Monte-Carlo (MCNP) based simulations. The focus has now shifted to creating voxel phantoms of each RAP in order to estimate doses to biota with a higher degree of confidence. This paper describes the creation of a voxel model of a Dungeness crab from CT images with shell, gills, gonads, hepatopancreas, and heart identified and segmented. Absorbed fractions were tabulated for each organ as a source and target at twelve photon and nine electron energies: 0.01, 0.015, 0.02, 0.03, 0.05, 0.1, 0.2, 0.5, 1.0, 1.5, 2.0, and 4.0 MeV for photons and 0.1, 0.2, 0.4, 0.5, 0.7, 1.0, 1.5, 2.0 and 4.0 MeV for electrons. AFs whose error exceeded 5% are marked with an underline in the data tables; AFs whose error was higher than 10% were excluded, and are shown in the tabulated data as a dashed line. A representative sample of the data is shown in Figs. 3-8; the entire data set is available as an electronic appendix. The results are consistent with previous small organism studies (Kinase, 2008; Stabin et al., 2006), and suggest that AF values are highly dependent on source organ location and mass.

Embedded soft-tissue image mechanism of a small animal shell with synchrotron-based micro-CT.

Synchrotron-based micro-CT was utilized to image the embedded biological soft-tissue of a small animal shell. Micro-CT images of the biological soft-tissue were acquired using 20, 25, and 27 keV synchrotron X-rays with contrast agents, such as water, physiological saline and iodine. Visualized the complex features of the animal at the above energies with water, physiological saline and iodine. The choice of the optimum energy was chosen based on the contrast mechanisms to know more about soft-matter and the associated internal complex biological features of the small animal shell. This way, the images at 27 keV (optimum energy) was reasonably acceptable for better visualization of the interior micro-architecture, such as soft-anatomy, physiology and internal organs of the animal with better visibility. The introduction of water, physiological, or iodine as contrast agents is shown to enhance minute image features in synchrotron-based tomographic imaging.