Variation in enamel and dentine mineral concentration and density in primate molars.

OBJECTIVE: Variation in enamel and dentine mineral concentration and total effective density can be reliably collected using Micro-CT scans. Both variables are suggested to reflect mechanical properties such as hardness and elastic modulus in dental tissues, meaning Micro-CT methods allow relative composition and mechanical properties to be collected non-destructively. DESIGN: 16 lower molars from 16 Catarrhine primates were Micro-CT scanned alongside hydroxyapatite phantoms using standardized settings and methods to calculate mineral concentration and total effective density. Mineral concentration, total effective density and thickness of dentine and enamel were calculated for four cusps, representing each 'corner' of the tooth and four lateral crown positions (i.e., mesial, buccal, lingual and distal). RESULTS: The results show mean mineral concentration and total effective density values were higher in areas of thicker enamel, while the opposite was observed for dentine. Buccal positions had significantly higher mineral concentration and total effective density values than lingual areas. Cuspal positions had higher mean values than lateral enamel, for both dentine (mineral concentration cuspal: 1.26 g/cm3; lateral: 1.20 g/cm3) and enamel (mineral concentration cuspal: 2.31 g/cm3; lateral: 2.25 g/cm3). Mesial enamel had significantly lower values than other locations. CONCLUSIONS: These common patterns across Catarrhine taxa may be linked to functional adaptations related to optimization of mastication and tooth protection. Variation in mineral concentration and total effective density may also be associated with wear and fracture patterns, and can be used as baseline information to investigate the effect of diet, pathological changes and aging on teeth through time.

3D-localisation of cochlear implant electrode contacts in relation to anatomical structures from in vivo cone-beam computed tomography.

Positioning of the cochlear implant (CI) electrode in relation to the anatomical structures is a key factor for the hearing outcome and the preservation of residual hearing after cochlear implantation. Determining the exact electrode's location is therefore expected to play an important role in optimisation of the electrode design, the surgical techniques and the post-operative device fitting. The aim of this study is the development and validation of a robust and efficient computerised algorithm for three-dimensional (3D) localisation of the CI-electrode contacts with respect to the relevant cochlear structures, such as the basilar membrane and the modiolus, from modern clinical in vivo cone-beam computed tomography (CBCT). In the presented algorithm, the pre- and post-implantation CBCT are spatially aligned. To localise the anatomical structures, a cochlear microanatomical template derived from lab-based X-ray computed microtomography (µCT) measurements is warped to match the patient-specific cochlear shape acquired from pre-implantation CBCT. The electrode-contact locations, determined from the post-operative CBCT, are superimposed onto the cochlear fine-structure of the microanatomical template to localise the array. The accuracy of this method was validated in a temporal bone study by comparing the distance of the electrode contacts from the modiolar wall, as derived by the algorithm from CBCTs, with the distance determined from synchrotron-radiation (SR) µCT on the same specimens. Due to the achievable spatial resolution, good tissue contrast and limited presence of metallic artifacts, the SRµCT technique is considered to be a golden standard in the proposed approach. In contrast to other approaches, this validation method allowed for the evaluation of the final electrode-to-modiolus distance (EMD) error, and covers the error in co-alignment of the images, in the determination of the electrode contact location and in the localisation of the cochlear structures. The absolute mean error on the EMD parameter was determined at 0.11 mm (max = 0.29 mm, SD = 0.07 mm) across five samples, slightly lower than the voxel size of the CBCT-scans. In a retrospective study, the algorithm was applied to identify scalar translocations of the electrode from clinical in vivo CBCT datasets of 23 CI-recipients, which showed perfect (100%) agreement with the blinded opinion of two experienced neuroradiologists.

Growth of Neanderthal infants from Krapina (120-130 ka), Croatia.

Modern humans have a slow and extended period of childhood growth, but to what extent this ontogenetic pathway was present in Neanderthals is debated. Dental development, linked to the duration of somatic growth across modern primates, is the main source for information about growth and development in a variety of fossil primates, including humans. Studies of Neanderthal permanent teeth report a pace of development either similar to recent humans or relatively accelerated. Neanderthal milk teeth, which form and emerge before permanent teeth, provide an opportunity to determine which pattern was present at birth. Here we present a comparative study of the prenatal and early postnatal growth of five milk teeth from three Neanderthals (120 000-130 000 years ago) using virtual histology. Results reveal regions of their milk teeth formed quickly before birth and over a relatively short period of time after birth. Tooth emergence commenced towards the earliest end of the eruption schedules displayed by extant human children. Advanced dental development is consistent with expectations for Neanderthal infant feeding.

Novel strategies for the characterization of cancellous bone morphology: Virtual isolation and analysis.

OBJECTIVES: The advent of micro-computed tomography (µCT) made cancellous bone more accessible than ever before. Nevertheless, the characterization of cancellous bone is made difficult by its inherent complexity and the difficulties in defining homology across datasets. Here we propose novel virtual methodological approaches to overcome those issues and complement existing methods. MATERIALS AND METHODS: We present a protocol for the isolation of the whole cancellous region within a µCT scanned bone. This method overcomes the subsampling issues and allows studying cancellous bone as a single unit. We test the protocol on a set of primate bones. In addition, we describe a set of morphological indices calculated on the topological skeleton of the cancellous bone: node density, node connectivity, trabecular angle, trabecular tortuosity, and fractal dimension. The usage of the indices is shown on a small comparative sample of primate femoral heads. RESULTS: The isolation protocol proves reliable in isolating cancellous structures from several different bones, regardless of their shape. The indices seem to detect some functional differences, although further testing on comparative samples is needed to clarify their potential for the study of cancellous architecture. CONCLUSIONS: The approaches presented overcome some of the difficulties of trabecular bone studies. The methods presented here represent an alternative or supporting method to the existing tools available to address the biomechanics of cancellous bone.

Contamination inside CT gantry in the SARS-CoV-2 era.

We investigated whether the internal gantry components of our computed tomography (CT) scanner contain severe acute respiratory syndrome 2 (SARS-CoV-2) ribonucleic acid (RNA), bacterial or fungal agents. From 1 to 27 March 2020, we performed 180 examinations of patients with confirmed SARS-CoV-2 infection using a dedicated CT scanner. On 27 March 2020, this CT gantry was opened and sampled in each of the following components: (a) gantry case; (b) inward airflow filter; (c) gantry motor; (d) x-ray tube; (e) outflow fan; (f) fan grid; (g) detectors; and (h) x-ray tube filter. To detect SARS-CoV-2 RNA, samples were analysed using reverse transcriptase-polymerase chain reaction (RT-PCR). To detect bacterial or fungal agents, samples have been collected using "replicate organism detection and counting" contact plates of 24 cm2, containing tryptic soy agar, and subsequently cultured. RT-PCR detected SARS-CoV-2 RNA in the inward airflow filter sample. RT-PCR of remaining gantry samples did not reveal the presence of SARS-CoV-2 RNA. Neither bacterial nor fungal agents grew in the agar-based growth medium after the incubation period. Our data showed that SARS-Cov-2 RNA can be found inside the CT gantry only in the inward airflow filter. All remaining CT gantry components were devoid of SARS-CoV-2 RNA.

Locomotion, posture, and the foramen magnum in primates: Reliability of indices and insights into hominin bipedalism.

The position (FMP) and orientation (FMO) of the foramen magnum have been used as proxies for locomotion and posture in extant and extinct primates. Several indices have been designed to quantify FMP and FMO but their application has led to conflicting results. Here, we test six widely used indices and two approaches (univariate and multivariate) for their capability to discriminate between postural and locomotor types in extant primates and fossil hominins. We then look at the locomotion of australopithecines and Homo on the base of these new findings. The following measurements are used: the opisthocranion-prosthion (OP-PR) and the opisthocranion-glabella (OP-GL) indices, the basion-biporion (BA-BP) and basion-bicarotid chords, the foramen magnum angle (FMA), and the basion-sphenoccipital ratio. After exploring the indices variability using principal component analysis, pairwise comparisons are performed to test for the association between each index and the locomotor and postural habits. Cranial size and phylogeny are taken into account. Our analysis indicates that none of the indices or approaches provides complete discrimination across locomotor and postural categories, although some differences are highlighted. FMA and BA-BP distinguish respectively obligate and facultative bipeds from all other groups. For what concerns posture, orthogrades and pronogrades differ with respects to OP-PR, OP-GL, and FMA. Although the multivariate approach seems to have some discrimination power, the results are most likely driven by facial and neurocranial variability embedded in some of the indices. These results demonstrate that indices relying on the anteroposterior positioning of the foramen may not be appropriate proxies for locomotion among primates. The assumptions about locomotor and postural habits in fossil hominins based on foramen magnum indices should be revised in light of these new findings.

Evaluation of novel coronavirus disease (COVID-19) using quantitative lung CT and clinical data: prediction of short-term outcome.

BACKGROUND: Computed tomography (CT) enables quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, helping in outcome prediction. METHODS: From 1 to 22 March 2020, patients with pneumonia symptoms, positive lung CT scan, and confirmed SARS-CoV-2 on reverse transcription-polymerase chain reaction (RT-PCR) were consecutively enrolled. Clinical data was collected. Outcome was defined as favourable or adverse (i.e., need for mechanical ventilation or death) and registered over a period of 10 days following CT. Volume of disease (VoD) on CT was calculated semi-automatically. Multiple linear regression was used to predict VoD by clinical/laboratory data. To predict outcome, important features were selected using a priori analysis and subsequently used to train 4 different models. RESULTS: A total of 106 consecutive patients were enrolled (median age 63.5 years, range 26-95 years; 41/106 women, 38.7%). Median duration of symptoms and C-reactive protein (CRP) was 5 days (range 1-30) and 4.94 mg/L (range 0.1-28.3), respectively. Median VoD was 249.5 cm3 (range 9.9-1505) and was predicted by lymphocyte percentage (p = 0.008) and CRP (p < 0.001). Important variables for outcome prediction included CRP (area under the curve [AUC] 0.77), VoD (AUC 0.75), age (AUC 0.72), lymphocyte percentage (AUC 0.70), coronary calcification (AUC 0.68), and presence of comorbidities (AUC 0.66). Support vector machine had the best performance in outcome prediction, yielding an AUC of 0.92. CONCLUSIONS: Measuring the VoD using a simple CT post-processing tool estimates SARS-CoV-2 burden. CT and clinical data together enable accurate prediction of short-term clinical outcome.

Endomaker, a new algorithm for fully automatic extraction of cranial endocasts and the calculation of their volumes.

OBJECTIVES: Reproducing cranial endocasts is a major goal of researchers interested in vertebrate brain evolution. We present a new R software, named endomaker, which allows the automatic extraction of endocasts from skull meshes along with the calculation of its volume. MATERIALS AND METHODS: We applied endomaker on non-primate and primate skulls including the Australopithecus africanus specimen Sts-5. RESULTS: We proved endomaker is faster, more feature-rich and possibly more accurate than competing software. DISCUSSION: Endomaker is the only available program endowed with the possibility to process an entire mesh directory straight away, promising to expand the scope and phylogenetic breadth of comparative studies of brain evolution.

Three-Dimensional Visualisation of Skeletal Cavities.

Bones contain spaces within them. The extraction and the analysis of those cavities are crucial in the study of bone tissue function and can inform about pathologies or past traumatic events. The use of medical imaging techniques allows a non-invasive visualisation of skeletal cavities opening a new frontier in medical inspection and diagnosis. Here, we report the application of a new mesh-based approach for the isolation of skeletal cavities of different size and geometrical structure. We apply a mesh-based approach to extract (i) the main virtual cavities inside the human skull, (ii) a complete human endocast, (iii) the inner vasculature of the malleus bone and (iv) the medullary of a human femur. The detailed description of the mesh-based isolation method and its pioneristic application to four different case-studies show the potential of this approach in medical visualisation.

A New Tool for Digital Alignment in Virtual Anthropology.

The study of the fossil record is fundamental to understand the evolution of traits. Because fossil remains are often fragmented and/or deformed by taphonomic processes, a preliminary realignment of their constituent parts is often necessary to properly interpret their shapes. In virtual anthropology, these procedures are carried out using digital models of the remains. We present a new semi-automatic alignment R software, Digital Tool for Alignment (DTA), which uses the shape information contained in a reference sample to find the best alignment solution for the disarticulated regions. We tested DTA on three different case-studies: (1) a sample of 14 primate species including both male and female individuals, (2) a simulated, disarticulated skull of Homo sapiens, and (3) a real disarticulated human fossil specimen, Amud 1 (Homo neanderthalensis). In the first case study, we simulated disarticulation directly on digital models of the primate skulls and tested alignment quality as a function of phylogenetic proximity, sex, and body size. In the second, we compared DTA to manual alignments conducted for the same digital models. Finally, we performed DTA on a real-world case study. We found that phylogenetic proximity provides is the most important factor for alignment efficiency. However, sex and allometric effects might also be important and should therefore be taken into account at selecting reference models for alignments. DTA performs at least as well as manual alignments. Yet, as compared to manual procedures, it is faster, requires no prior anatomical knowledge and expertise and allows indefinite manipulation of the fossil items. Anat Rec, 302:1104-1115, 2019. © 2019 Wiley Periodicals, Inc.

The functional significance of dental and mandibular reduction in Homo: A catarrhine perspective.

The reduction in dental size and mandibular robusticity is regarded as a major trend in human evolution, traditionally considered the result of the peculiar extra-oral food processing skills of Homo. The use of stone tools and fire would have allowed our ancestors to chew softer food in smaller bite size, thus relaxing the selective pressures to keep a large dentition and a robust lower jaw. This perspective assumes that differences in dental size and mandibular robusticity in hominins represent functional dissimilarities. This study uses a catarrhine comparative approach to test this fundamental assumption of the hypotheses on dental and mandibular reduction in Homo. A sample of extant catarrhines and fossil hominins was used to test for correlations between dental size, mandibular robusticity, and dietary proxies, the latter include diet quality, diet heterogeneity, feeding time, and microwear variables. The effects of phylogeny and body size were considered. Findings support the association between technological developments in Homo and reduction in incisor size and mandibular corpus robusticity, though not for premolar, molar size, and symphyseal robusticity. These results challenge the functional interpretation of postcanine reduction and symphyseal changes in the genus Homo.

Neuromandibular integration in humans and chimpanzees: Implications for dental and mandibular reduction in Homo.

OBJECTIVES: Although the evolution of the hominin masticatory apparatus has been linked to diet and food processing, the physical connection between neurocranium and lower jaw suggests a role of encephalization in the trend of dental and mandibular reduction. Here, the hypothesis that tooth size and mandibular robusticity are influenced by morphological changes in the neurocranium was tested. MATERIALS AND METHODS: Three-dimensional landmarks, alveolar lengths, and mandibular robusticity data were recorded on a sample of chimpanzee and human skulls. The morphological integration between the neurocranium and the lower jaw was analyzed by means of Singular Warps Analysis. Redundancy Analysis was performed to understand if the pattern of neuromandibular integration affects tooth size and mandibular robusticity. RESULTS: There is significant morphological covariation between neurocranium and lower jaw in both chimpanzees and humans. In humans, changes in the temporal fossa seem to produce alterations of the relative orientation of jaw parts, while the influence of similar neurocranial changes in chimpanzees are more localized. In both species, postcanine alveolar lengths and mandibular robusticity are associated with shape changes of the temporal fossa. CONCLUSIONS: The results of this study support the hypothesis that the neurocranium is able to affect the evolution and development of the lower jaw, although most likely through functional integration of mandible, teeth, and muscles within the masticatory apparatus. This study highlights the relative influence of structural constraints and adaptive factors in the evolution of the human skull.

Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.

OBJECTIVES: We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. MATERIALS AND METHODS: We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. RESULTS: The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. DISCUSSION: Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists.

Surface smoothing, decimation, and their effects on 3D biological specimens.

OBJECTIVE: Smoothing and decimation filters are commonly used to restore the realistic appearance of virtual biological specimens, but they can cause a loss of topological information of unknown extent. In this study, we analyzed the effect of smoothing and decimation on a 3D mesh to highlight the consequences of an inappropriate use of these filters. MATERIALS AND METHODS: Topological noise was simulated on four anatomical regions of the virtual reconstruction of an orangutan cranium. Sequential levels of smoothing and decimation were applied, and their effects were analyzed on the overall topology of the 3D mesh and on linear and volumetric measurements. RESULTS: Different smoothing algorithms affected mesh topology and measurements differently, although the influence on the latter was generally low. Decimation always produced detrimental effects on both topology and measurements. The application of smoothing and decimation, both separate and combined, is capable of recovering topological information. CONCLUSION: Based on the results, objective guidelines are provided to minimize information loss when using smoothing and decimation on 3D meshes.

The evolution of cranial base and face in Cercopithecoidea and Hominoidea: Modularity and morphological integration.

The evolutionary relationship between the base and face of the cranium is a major topic of interest in primatology. Such areas of the skull possibly respond to different selective pressures. Yet, they are often said to be tightly integrated. In this paper, we analyzed shape variability in the cranial base and the facial complex in Cercopithecoidea and Hominoidea. We used a landmark-based approach to single out the effects of size (evolutionary allometry), morphological integration, modularity, and phylogeny (under Brownian motion) on skull shape variability. Our results demonstrate that the cranial base and the facial complex exhibit different responses to different factors, which produces a little degree of morphological integration between them. Facial shape variation appears primarily influenced by body size and sexual dimorphism, whereas the cranial base is mostly influenced by functional factors. The different adaptations affecting the two modules suggest they are best studied as separate and independent units, and that-at least when dealing with Catarrhines-caution must be posed with the notion of strong cranial integration that is commonly invoked for the evolution of their skull shape.