Euclidean distance matrix analysis: a coordinate-free approach for comparing biological shapes using landmark data

Automatic extraction of facial median sagittal plane for patients with asymmetry based on the EDMA alignment algorithm

BACKGROUND

We aimed to establish a novel method for automatically constructing three-dimensional (3D) median sagittal plane (MSP) for mandibular deviation patients, which can increase the efficiency of aesthetic evaluating treatment progress. We developed a Euclidean weighted Procrustes analysis (EWPA) algorithm for extracting 3D facial MSP based on the Euclidean distance matrix analysis, automatically assigning weight to facial anatomical landmarks.

METHODS

Forty patients with mandibular deviation were recruited, and the Procrustes analysis (PA) algorithm based on the original mirror alignment and EWPA algorithm developed in this study were used to construct the MSP of each facial model of the patient as experimental groups 1 and 2, respectively. The expert-defined regional iterative closest point algorithm was used to construct the MSP as the reference group. The angle errors of the two experimental groups were compared to those of the reference group to evaluate their clinical suitability.

RESULTS

The angle errors of the MSP constructed by the two EWPA and PA algorithms for the 40 patients were 1.39 ± 0.85°, 1.39 ± 0.78°, and 1.91 ± 0.80°, respectively. The two EWPA algorithms performed best in patients with moderate facial asymmetry, and in patients with severe facial asymmetry, the angle error was below 2°, which was a significant improvement over the PA algorithm.

CONCLUSIONS

The clinical application of the EWPA algorithm based on 3D facial morphological analysis for constructing a 3D facial MSP for patients with mandibular deviated facial asymmetry deformity showed a significant improvement over the conventional PA algorithm and achieved the effect of a dental clinical expert-level diagnostic strategy.

Comparative evaluation of arch form among the Nepalese population: A morphological study

Aims

The study aims to identify sexual dimorphic features in the arch patterns based on tooth arrangement patterns and the maxillary and mandibular arches using Euclidean Distance Matrix Analysis (EDMA).

Settings and Design

A total of 96 Nepalese subjects, aged 18 to 25 were assessed using casts and photographs.

Materials and Methods

Thirteen landmarks representing the most facial portions of the proximal contact areas on the maxillary and mandibular casts were digitised. Seventy-eight possible, Euclidean distances between the 13 landmarks were calculated using the Analysis ToolPak of Microsoft Excel®. The male-to-female ratios of the corresponding distances were computed and ratios were compared to evaluate the arch form for variation in the genders, among the Nepalese population.

Statistical Analysis Used

Microsoft Excel Analysis ToolPak and SPSS 20.0 (IBM Chicago) were used to perform EDMA and an independent t-test to compare the significant differences between the two genders.

Results

The maxillary arch's largest ratio (1.008179001) was discovered near the location of the right and left lateral incisors, indicating that the anterior region may have experienced the greatest change. The posterior-molar region is where the smallest ratio was discovered, suggesting less variation. At the intercanine region, female arches were wider than male ones; however, at the interpremolar and intermolar sections, they were similar in width. Females' maxillary arches were discovered to be bigger antero-posteriorly than those of males. The highest ratio (1.014336113) in the mandibular arch was discovered at the intermolar area, suggesting that males had a larger mandibular posterior arch morphology. At the intercanine area, the breadth of the arch form was greater in males and nearly the same in females at the interpremolar and intermolar regions. Female mandibular arch forms were also discovered to be longer than those of males from the anterior to the posterior.

Conclusions

The male and female arches in the Nepalese population were inferred to be different in size and shape. With references to the landmarks demonstrating such a shift, the EDMA established objectively the presence of square arch forms in Nepali males and tapering arch forms in Nepalese females.

A murine model of hnRNPH2-related neurodevelopmental disorder reveals a mechanism for genetic compensation by Hnrnph1

Mutations in HNRNPH2 cause an X-linked neurodevelopmental disorder with features that include developmental delay, motor function deficits, and seizures. More than 90% of patients with hnRNPH2 have a missense mutation within or adjacent to the nuclear localization signal (NLS) of hnRNPH2. Here, we report that hnRNPH2 NLS mutations caused reduced interaction with the nuclear transport receptor Kapβ2 and resulted in modest cytoplasmic accumulation of hnRNPH2. We generated 2 knockin mouse models with human-equivalent mutations in Hnrnph2 as well as Hnrnph2-KO mice. Knockin mice recapitulated clinical features of the human disorder, including reduced survival in male mice, impaired motor and cognitive functions, and increased susceptibility to audiogenic seizures. In contrast, 2 independent lines of Hnrnph2-KO mice showed no detectable phenotypes. Notably, KO mice had upregulated expression of Hnrnph1, a paralog of Hnrnph2, whereas knockin mice failed to upregulate Hnrnph1. Thus, genetic compensation by Hnrnph1 may counteract the loss of hnRNPH2. These findings suggest that HNRNPH2-related disorder may be driven by a toxic gain of function or a complex loss of HNRNPH2 function with impaired compensation by HNRNPH1. The knockin mice described here are an important resource for preclinical studies to assess the therapeutic benefit of gene replacement or knockdown of mutant hnRNPH2.

Triplication of the interferon receptor locus contributes to hallmarks of Down syndrome in a mouse model

Down syndrome (DS), the genetic condition caused by trisomy 21, is characterized by variable cognitive impairment, immune dysregulation, dysmorphogenesis and increased prevalence of diverse co-occurring conditions. The mechanisms by which trisomy 21 causes these effects remain largely unknown. We demonstrate that triplication of the interferon receptor (IFNR) gene cluster on chromosome 21 is necessary for multiple phenotypes in a mouse model of DS. Whole-blood transcriptome analysis demonstrated that IFNR overexpression associates with chronic interferon hyperactivity and inflammation in people with DS. To define the contribution of this locus to DS phenotypes, we used genome editing to correct its copy number in a mouse model of DS, which normalized antiviral responses, prevented heart malformations, ameliorated developmental delays, improved cognition and attenuated craniofacial anomalies. Triplication of the Ifnr locus modulates hallmarks of DS in mice, suggesting that trisomy 21 elicits an interferonopathy potentially amenable to therapeutic intervention.

Population-specific facial traits and diagnosis accuracy of genetic and rare diseases in an admixed Colombian population

Up to 40% of rare disorders (RD) present facial dysmorphologies, and visual assessment is commonly used for clinical diagnosis. Quantitative approaches are more objective, but mostly rely on European descent populations, disregarding diverse population ancestry. Here, we assessed the facial phenotypes of Down (DS), Morquio (MS), Noonan (NS) and Neurofibromatosis type 1 (NF1) syndromes in a Latino-American population, recording the coordinates of 18 landmarks in 2D images from 79 controls and 51 patients. We quantified facial differences using Euclidean Distance Matrix Analysis, and assessed the diagnostic accuracy of Face2Gene, an automatic deep-learning algorithm. Individuals diagnosed with DS and MS presented severe phenotypes, with 58.2% and 65.4% of significantly different facial traits. The phenotype was milder in NS (47.7%) and non-significant in NF1 (11.4%). Each syndrome presented a characteristic dysmorphology pattern, supporting the diagnostic potential of facial biomarkers. However, population-specific traits were detected in the Colombian population. Diagnostic accuracy was 100% in DS, moderate in NS (66.7%) but lower in comparison to a European population (100%), and below 10% in MS and NF1. Moreover, admixed individuals showed lower facial gestalt similarities. Our results underscore that incorporating populations with Amerindian, African and European ancestry is crucial to improve diagnostic methods of rare disorders.

Morphometric analysis of the size-adjusted linear dimensions of the skull landmarks revealed craniofacial dysmorphology in Mid1-cKO mice

BACKGROUND

The early craniofacial development is a highly coordinated process involving neural crest cell migration, proliferation, epithelial apoptosis, and epithelial-mesenchymal transition (EMT). Both genetic defects and environmental factors can affect these processes and result in orofacial clefts. Mutations in MID1 gene cause X-linked Opitz Syndrome (OS), which is a congenital malformation characterized by craniofacial defects including cleft lip/palate (CLP). Previous studies demonstrated impaired neurological structure and function in Mid1 knockout mice, while no CLP was observed. However, given the highly variable severities of the facial manifestations observed in OS patients within the same family carrying identical genetic defects, subtle craniofacial malformations in Mid1 knockout mice could be overlooked in these studies. Therefore, we propose that a detailed morphometric analysis should be necessary to reveal mild craniofacial dysmorphologies that reflect the similar developmental defects seen in OS patients.

RESULTS

In this research, morphometric study of the P0 male Mid1-cKO mice were performed using Procrustes superimposition as well as EMDA analysis of the size-adjusted three-dimensional coordinates of 105 skull landmarks, which were collected on the bone surface reconstructed using microcomputed tomographic images. Our results revealed the craniofacial deformation such as the increased dimension of the frontal and nasal bone in Mid1-cKO mice, in line with the most prominent facial features such as hypertelorism, prominent forehead, broad and/or high nasal bridge seen in OS patients.

CONCLUSION

 While been extensively used in evolutionary biology and anthropology in the last decades, geometric morphometric analysis was much less used in developmental biology. Given the high interspecies variances in facial anatomy, the work presented in this research suggested the advantages of morphometric analysis in characterizing animal models of craniofacial developmental defects to reveal phenotypic variations and the underlining pathogenesis.

Flexible conservatism in the skull modularity of convergently evolved myrmecophagous placental mammals

Background

The skull of placental mammals constitutes one of the best studied systems for phenotypic modularity. Several studies have found strong evidence for the conserved presence of two- and six-module architectures, while the strength of trait correlations (integration) has been associated with major developmental processes such as somatic growth, muscle-bone interactions, and tooth eruption. Among placentals, ant- and termite-eating (myrmecophagy) represents an exemplar case of dietary convergence, accompanied by the selection of several cranial morphofunctional traits such as rostrum elongation, tooth loss, and mastication loss. Despite such drastic functional modifications, the covariance patterns of the skull of convergently evolved myrmecophagous placentals are yet to be studied in order to assess the potential consequences of this dietary shift on cranial modularity.

Results

Here, we performed a landmark-based morphometric analysis of cranial covariance patterns in 13 species of myrmecophagous placentals. Our analyses reveal that most myrmecophagous species present skulls divided into six to seven modules (depending on the confirmatory method used), with architectures similar to those of non-myrmecophagous placentals (therian six modules). Within-module integration is also similar to what was previously described for other placentals, suggesting that most covariance-generating processes are conserved across the clade. Nevertheless, we show that extreme rostrum elongation and tooth loss in myrmecophagid anteaters have resulted in a shift in intermodule correlations in the proximal region of the rostrum. Namely, the naso-frontal and maxillo-palatine regions are strongly correlated with the oro-nasal module, suggesting an integrated rostrum conserved from pre-natal developmental processes. In contrast, the similarly toothless pangolins show a weaker correlation between the anterior rostral modules, resembling the pattern of toothed placentals.

Conclusions

These results reveal that despite some integration shifts related to extreme functional and morphological features of myrmecophagous skulls, cranial modular architectures have conserved the typical mammalian scheme.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02030-9.

Morphological integration of the hominoid postcranium

Previous research has suggested that magnitudes of integration may be distinct in the postcranium of hominoids when compared to other primate species. To test this hypothesis, we estimated and compared magnitudes of integration of eight postcranial bones from three-dimensional surface scans for 57 Hylobates lar, 58 Gorilla gorilla, 60 Pan troglodytes, 60 Homo sapiens, 60 Chlorocebus pygerythrus, and 60 Macaca fascicularis. We tested the hypotheses that 1) magnitudes of integration would be distinct in the postcranium of hominoids compared to cercopithecoids, with the explicit prediction that magnitudes of integration would be lower in hominoids than in cercopithecoids, and 2) girdle elements (scapula, os coxa) would have lower magnitudes of integration across all taxa. Integration was quantified using the integration coefficient of variation from interlandmark distances reflecting anatomical and developmental modules defined according to a priori criteria. A resampling protocol was employed to generate distributions of integration values that were then compared statistically using Mann-Whitney U tests with Bonferroni adjustment. Support for hypothesis 1 was mixed: with the exception of Gorilla, hominoid taxa were less integrated than the cercopithecoids for all anatomical modules. However, Homo, Gorilla, and, to a lesser extent, Pan showed higher integration than Hylobates and the cercopithecoids for homologous limb elements, with magnitudes of integration for both modules being lowest for Hylobates. These results generally support the hypothesis of distinct patterns of magnitudes of integration in the hominoid postcranium. The high integration of Gorilla may be explained by the effects of overall body size. The results supported the predictions of the second hypothesis. Regardless of taxon, the os coxa and scapula were generally the least integrated skeletal elements, while the femur and radius were the most integrated. The lower integration of the girdle elements suggests that the geometric complexities of particular elements may significantly influence study outcomes.

Thirty years of geometric morphometrics: Achievements, challenges, and the ongoing quest for biological meaningfulness

The foundations of geometric morphometrics were worked out about 30 years ago and have continually been refined and extended. What has remained as a central thrust and source of debate in the morphometrics community is the shared goal of meaningful biological inference through a tight connection between biological theory, measurement, multivariate biostatistics, and geometry. Here we review the building blocks of modern geometric morphometrics: the representation of organismal geometry by landmarks and semilandmarks, the computation of shape or form variables via superimposition, the visualization of statistical results as actual shapes or forms, the decomposition of shape variation into symmetric and asymmetric components and into different spatial scales, the interpretation of various geometries in shape or form space, and models of the association between shape or form and other variables, such as environmental, genetic, or behavioral data. We focus on recent developments and current methodological challenges, especially those arising from the increasing number of landmarks and semilandmarks, and emphasize the importance of thorough exploratory multivariate analyses rather than single scalar summary statistics. We outline promising directions for further research and for the evaluation of new developments, such as "landmark-free" approaches. To illustrate these methods, we analyze three-dimensional human face shape based on data from the Avon Longitudinal Study of Parents and Children (ALSPAC).

Investigation of age-related facial variation among Angelman syndrome patients

Angelman syndrome (AS) is one of the common genetic disorders that could emerge either from a 15q11-q13 deletion or paternal uniparental disomy (UPD) or imprinting or UBE3A mutations. AS comes with various behavioral and phenotypic variability, but the acquisition of subjects for experiment and automating the landmarking process to characterize facial morphology for Angelman syndrome variation investigation are common challenges. By automatically detecting and annotating subject faces, we collected 83 landmarks and 10 anthropometric linear distances were measured from 17 selected anatomical landmarks to account for shape variability. Statistical analyses were performed on the extracted data to investigate facial variation in each age group. There is a correspondence in the results achieved by relative warp (RW) of the principal component (PC) and the thin-plate spline (TPS) interpolation. The group is highly discriminated and the pattern of shape variability is higher in children than other groups when judged by the anthropometric measurement and principal component.

Assessments of bilateral asymmetry with application in human skull analysis

As a common feature, bilateral symmetry of biological forms is ubiquitous, but in fact rarely exact. In a setting of analytic geometry, bilateral symmetry is defined with respect to a point, line or plane, and the well-known notions of fluctuating asymmetry, directional asymmetry and antisymmetry are recast. A meticulous scheme for asymmetry assessments is proposed and explicit solutions to them are derived. An investigation into observational errors of points representing the geometric structure of an object offers a baseline reference for asymmetry assessment of the object. The proposed assessments are applicable to individual, part or all point pairs at both individual and collective levels. The exact relationship between the developed treatments and the widely used Procrustes method in asymmetry assessment is examined. An application of the proposed assessments to a large collection of human skull data in the form of 3D landmark coordinates finds: (a) asymmetry of most skulls is not fluctuating, but directional if measured about a plane fitted to shared landmarks or side landmarks for balancing; (b) asymmetry becomes completely fluctuating if one side of a skull could be slightly rotated and translated with respect to the other side; (c) female skulls are more asymmetric than male skulls. The methodology developed in this study is rigorous and transparent, and lays an analytical base for investigation of structural symmetries and asymmetries in a wide range of biological and medical applications.

Sexual dimorphism in the size and shape of the non-obstetric pelvis across anthropoids

OBJECTIVES

The presence of sexual dimorphism in the birth canals of anthropoid primates is well documented, and birth canal dimorphism tends to be especially robust among species that give birth to relatively large neonates. However, it is less clear whether birth canal dimorphism is accompanied by dimorphism in parts of the pelvis not directly under selection for birth, particularly including bi-iliac breadth, biactetabular breadth, lengths of the ischium and ilium, and 3D shape. This study investigates the patterns of dimorphism among anthropoid primates in those parts of the pelvis which do not directly contribute to the bony birth canal, here termed the non-obstetric pelvis.

METHODS

3D landmark data were collected on the bony pelves of 899 anthropoid primates. Specifically, landmark data were collected on parts of the pelvis not thought to be directly involved in selection for parturition, including portions of the posterior and superior ilium, acetabulum, and lateral ischium. Principal components analysis and Euclidean distance matrix analysis were used to ascertain sexual dimorphism in pelvic sizes and shapes within each species.

RESULTS

Results show that dimorphism in non-obstetric pelvic size and shape exists across anthropoids, just as is seen in the birth canal. However, the magnitude of dimorphism in non-obstetric pelvic shape tends to be greater among anthropoid species that give birth to relatively large neonates compared with those birthing smaller neonates relative to maternal pelvic size.

CONCLUSIONS

Though all anthropoids included in the study show some degree of sexual dimorphism in non-obstetric pelvic size and/or shape, species which give birth to large neonates relative to maternal pelvic size have the highest levels of dimorphism in pelvic shape. Moreover, the magnitude of dimorphism in certain parts of the non-obstetric pelvis mirrors patterns seen in the birth canal. The results of this study are promising for ascertaining pelvic dimorphism and relative neonate size in fossil primates, particularly in fragmentary remains which do not preserve a complete bony birth canal.

Rapidly Decoding Image Categories From MEG Data Using a Multivariate Short-Time FC Pattern Analysis Approach

Recent advances in the development of multivariate analysis methods have led to the application of multivariate pattern analysis (MVPA) to investigate the interactions between brain regions using graph theory (functional connectivity, FC) and decode visual categories from functional magnetic resonance imaging (fMRI) data from a continuous multicategory paradigm. To estimate stable FC patterns from fMRI data, previous studies required long periods in the order of several minutes, in comparison to the human brain that categories visual stimuli within hundreds of milliseconds. Constructing short-time dynamic FC patterns in the order of milliseconds and decoding visual categories is a relatively novel concept. In this study, we developed a multivariate decoding algorithm based on FC patterns and applied it to magnetoencephalography (MEG) data. MEG data were recorded from participants presented with image stimuli in four categories (faces, scenes, animals and tools). MEG data from 17 participants demonstrate that short-time dynamic FC patterns yield brain activity patterns that can be used to decode visual categories with high accuracy. Our results show that FC patterns change over the time window, and FC patterns extracted in the time window of 0∼200 ms after the stimulus onset were most stable. Further, the categorizing accuracy peaked (the mean binary accuracy is above 78.6% at individual level) in the FC patterns estimated within the 0∼200 ms interval. These findings elucidate the underlying connectivity information during visual category processing on a relatively smaller time scale and demonstrate that the contribution of FC patterns to categorization fluctuates over time.

Multimodal Imagery in Forensic Incident Scene Documentation

Various imaging modalities are evaluated for use in forensic incident (crime or accident) scene documentation. Particular attention is paid to the precision vs. cost tradeoff, accomplished by judiciously combining various 3D scans and photogrammetric reconstructions from 2D photographs. Assumptions are proposed for two complementary software systems: an event scene pilot assisting the on-site staff in their work securing evidence and facilitating their communication with stationary support staff, and an evidence keeper, managing the voluminous and varied database of accumulated imagery, textual notes and physical evidence inventory.

[A method for constructing three-dimensional face symmetry reference plane based on weighted shape analysis algorithm]

OBJECTIVE

To establish a novel method based on three-dimensional (3D) shape analysis and weighted Procrustes analysis (WPA) algorithm to construct a 3D facial symmetry reference plane (SRP), automatically assigning weight to facial anatomical landmarks. The WPA algorithm suitability for commonly observed clinical cases of mandibular deviation were analysed and evaluated.

METHODS

Thirty patients with mandibular deviation were recruited for this study. The 3D facial SRPs were extracted independently based on original-mirror alignment method. Thirty-two anatomical landmarks were selected from the overall region by three times to obtain the mean coordinate. The SRP of experimental groups 1 and 2 were using the standard Procrustes analysis (PA) algorithm and WPA algorithm, respectively. A reference plane defined by experts based on regional iterative closest point (ICP) algorithm, served as the ground truth. Three experts manually selecting facial regions with good symmetry for original model, and common region was included in the study. The angle error values between the SRP of WPA algorithm in the experimental group 1 and the truth plane were evaluated in this study, and the SRP of PA algorithm of experimental group 2 was calculated in the same way. Statistics and measurement analysis were used to comprehensively evaluate the clinical suitability of the WPA algorithm to calculate the SRP. A paired t-test analysis (two-tailed) was conducted to compare the angles.

RESULTS

The average angle error between the SRP of WPA algorithm and the ground truth was 1.53°±0.84°, which was smaller than that between the SRP of PA and the ground truth (2.06°±0.86°). There were significant differences in the angle errors among the groups (P < 0.05). For the patients with severe mandibular deviation that the distance between pogonion and facial midline greater than 12 mm, the average angle error of the WPA algorithm was 0.86° smaller than that of the PA algorithm.

CONCLUSION

The WPA algorithm, based on weighted shape analysis, can provide a more adaptable SRP than the standard PA algorithm when applied to mandibular deviation patients and preliminarily simulate the diagnosis strategies of clinical experts.

Effects of Reduced Connexin43 Function on Mandibular Morphology and Osteogenesis in Mutant Mouse Models of Oculodentodigital Dysplasia

Mutations in the gene encoding the gap-junctional protein connexin43 (Cx43) are the cause of the human disease oculodentodigital dysplasia (ODDD). The mandible is often affected in this disease, with clinical reports describing both mandibular overgrowth and conversely, retrognathia. These seemingly opposing observations underscore our relative lack of understanding of how ODDD affects mandibular morphology. Using two mutant mouse models that mimic the ODDD phenotype (I130T/+ and G60S/+), we sought to uncover how altered Cx43 function may affect mandibular development. Specifically, mandibles of newborn mice were imaged using micro-CT, to enable statistical comparisons of shape. Tissue-level comparisons of key regions of the mandible were conducted using histomorphology, and we quantified the mRNA expression of several cartilage and bone cell differentiation markers. Both G60S/+ and I130T/+ mutant mice had altered mandibular morphology compared to their wildtype counterparts, and the morphological effects were similarly localized for both mutants. Specifically, the biggest phenotypic differences in mutant mice were focused in regions exposed to mechanical forces, such as alveolar bone, muscular attachment sites, and articular surfaces. Histological analyses revealed differences in ossification of the intramembranous bone of the mandibles of both mutant mice compared to their wildtype littermates. However, chondrocyte organization within the secondary cartilages of the mandible was unaffected in the mutant mice. Overall, our results suggest that the morphological differences seen in G60S/+ and I130T/+ mouse mandibles are due to delayed ossification and suggest that mechanical forces may exacerbate the effects of ODDD on the skeleton.

Morphometric approach to 3D soft-tissue craniofacial analysis and classification of ethnicity, sex, and age

Background

The application of three-dimensional scan models offers a useful resource for studying craniofacial variation. The complex mathematical analysis for facial point acquisition in three-dimensional models has made many craniofacial assessments laborious.

Method

This study investigates three-dimensional (3D) soft-tissue craniofacial variation, with relation to ethnicity, sex and age variables in British and Irish white Europeans. This utilizes a geometric morphometric approach on a subsampled dataset comprising 292 scans, taken from a Liverpool-York Head Model database. Shape variation and analysis of each variable are tested using 20 anchor anatomical landmarks and 480 sliding semi-landmarks.

Results

Significant ethnicity, sex, and age differences are observed for measurement covering major aspects of the craniofacial shape. The ethnicity shows subtle significant differences compared to sex and age; even though it presents the lowest classification accuracy. The magnitude of dimorphism in sex is revealed in the facial, nasal and crania measurement. Significant shape differences are also seen at each age group, with some distinct dimorphic features present in the age groups.

Conclusions

The patterns of shape variation show that white British individuals have a more rounded head shape, whereas white Irish individuals have a narrower head shape. White British persons also demonstrate higher classification accuracy. Regarding sex patterns, males are relatively larger than females, especially in the mouth and nasal regions. Females presented with higher classification accuracy than males. The differences in the chin, mouth, nose, crania, and forehead emerge from different growth rates between the groups. Classification accuracy is best for children and senior adult age groups.

Multiscale connected chain topological modelling for microcalcification classification

Computer-aided diagnosis (CAD) systems can be employed to help classify mammographic microcalcification clusters. In this paper, a novel method for the classification of the microcalcification clusters based on topology/connectivity has been introduced. The proposed method is distinct from existing techniques which concentrate on morphology and texture of microcalcifications and surrounding tissue. The proposed approach used multiscale morphological relationship of connectivity between microcalcifications where connected chains between nearest microcalcifications were generated at each scale. Subsequently, graph connectivity features at each scale were extracted to estimate the topological connectivity structure of microcalcification clusters for benign versus malignant classification. The proposed approach was evaluated using publicly available digitized datasets: MIAS and DDSM, in addition to the digital OPTIMAM dataset. The classification of features using KNN obtained a classification accuracy of 86.47±1.30%, 90.0±0.00%, 82.5±2.63%, 76.75±0.66% for the DDSM, MIAS-manual, MIAS-auto and OPTIMAM datasets respectively. The study showed that topological/connectivity modelling using a multiscale approach was appropriate for microcalcification cluster analysis and classification; topological connectivity and distribution can be linked to clinical understanding of microcalcification spatial distribution.

Whole-exome sequencing identified four loci influencing craniofacial morphology in northern Han Chinese

Facial shape differences are one of the most significant phenotypes in humans. It is affected largely by skull shape. However, research into the genetic basis of the craniofacial morphology has rarely been reported. The present study aimed to identify genetic variants influencing craniofacial morphology in northern Han Chinese through whole-exome sequencing (WES). Phenotypic data of the volunteers’ faces and skulls were obtained through three-dimensional CT scan of the skull. A total of 48 phenotypes (35 facial and 13 cranial phenotypes) were used for the bioinformatics analysis. Four genetic loci were identified affecting the craniofacial shapes. The four candidate genes are RGPD3, IGSF3, SLC28A3, and USP40. Four single-nucleotide polymorphism (SNP) site mutations in RGPD3, IGSF3, and USP40 were significantly associated with the skull shape (p < 1×10⁻⁶), and three SNP site mutations in RGPD3, IGSF3, and SLC28A3 were significantly associated with the facial shape (p < 1×10⁻⁶). The rs62152530 site mutation in the RGPD3 gene may be closely associated with the nasal length, ear length, and alar width. The rs647711 site mutation in the IGSF3 gene may be closely associated with the nasal length, mandibular width, and width between the mental foramina. The rs10868138 site mutation in the SLC28A3 gene may be associated with the nasal length, alar width, width between tragus, and width between the mental foramina. The rs1048603 and rs838543 site mutations in the USP40 gene may be closely associated with the pyriform aperture width. Our findings provide useful genetic information for the determination of face morphology.

Gait Evaluation Using Procrustes and Euclidean Distance Matrix Analysis

Objective assessment of gait is important in the treatment and rehabilitation of patients with different diseases. In this paper, we propose a gait evaluation system using the Procrustes and Euclidean distance matrix analysis. We design and develop an android app to collect real time synchronous accelerometer and gyroscope data from two inertial measurement unit sensors through Bluetooth connectivity. The data is collected from 12 young (ten for modeling and two for validation) and 20 older subjects. We analyze the data collected from real world for stride, step, stance, and swing gait features. We validate our method with the measurements of gait features. The generalized Procrustes analysis is used to estimate a standard normal mean gait shape (NMGS) for ten young subjects. Each gait feature of both young and older subjects is then converted to find the best match with the NMGS using the ordinary Procrustes analysis. The shape distance between the NMGS and each gait shape is estimated using Riemannian shape distance, Riemannian size-and-shape distance, Procrustes size-and-shape distance, and root-mean-square deviation. A t-test is performed to provide statistical evidence of gait shape differences between young and older gaits. A mean form, which is considered as a standard normal mean gait form (NMGF), and inter-feature distances are estimated from the set of ten young subjects. The form difference is estimated between the NMGF and individual gaits of young and older. The degree of abnormality is then estimated for individual features and the result is plotted to visualize the feature in a gait. Experimental results demonstrate the performance of the proposed method.

Adaptive Data Boosting Technique for Robust Personalized Speech Emotion in Emotionally-Imbalanced Small-Sample Environments

Personalized emotion recognition provides an individual training model for each target user in order to mitigate the accuracy problem when using general training models collected from multiple users. Existing personalized speech emotion recognition research has a cold-start problem that requires a large amount of emotionally-balanced data samples from the target user when creating the personalized training model. Such research is difficult to apply in real environments due to the difficulty of collecting numerous target user speech data with emotionally-balanced label samples. Therefore, we propose the Robust Personalized Emotion Recognition Framework with the Adaptive Data Boosting Algorithm to solve the cold-start problem. The proposed framework incrementally provides a customized training model for the target user by reinforcing the dataset by combining the acquired target user speech with speech from other users, followed by applying SMOTE (Synthetic Minority Over-sampling Technique)-based data augmentation. The proposed method proved to be adaptive across a small number of target user datasets and emotionally-imbalanced data environments through iterative experiments using the IEMOCAP (Interactive Emotional Dyadic Motion Capture) database.

Longitudinal Craniofacial Growth Patterns in Patients with Orofacial Clefts: Geometric Morphometrics

Objective

To demonstrate craniofacial developmental patterns in repaired cleft lip and cleft palate (CLP).

Design

Retrospective, longitudinal.

Setting

Center for Craniofacial Disorders, San Juan, Puerto Rico.

Sample

Males aged 9 to 17 years: 13 noncleft (NC) Class I occlusion (NCC1); 13 NC Class III malocclusion (NCC3); 12 CLP Class I occlusion (CLPC1); and 15 CLP Class III malocclusion (CLPC3).

Main Outcome Measures

Form changes (ages 10, 13, and 16 years), using finite-element scaling analysis.

Results

NCC1, 10 to 13 interval: 30% size increase in upper midface (p < .05), mental region (p < .01), mandibular body (p < .05); 13 to 16 interval: 10% to 35% size increase in bimaxillary region and ramus (p < .01). NCC3, 10 to 13 interval: 10% to 40% size increase in posterior cranial base, upper midface, and mandible (p < .05); 13 to 16 interval: 10% to 30% size increase in bimaxillary region (p < .01), especially ramus. CLPC1, 10 to 13 interval: 10% to 15% size increase in posterior cranial base (p < .01), midface (p < .05), and mandibular ramus (p < .05); 13 to 16 interval: 8% to 20% size increase in upper midface (p < .01), lower midface (p < .05), and mandible (p < .05). CLPC3, 10 to 13 interval: no significant changes; 13 to 16 interval: upper midface and cranial base show nonsignificant size decreases, but ramus showed size increase.

Conclusions

Noncleft and CLP Class 1 occlusion groups show similar craniofacial growth patterns. Noncleft Class III groups show excessive cranial and mandibular growth. Class III malocclusion in CLP patients is associated with clinically deficient craniomaxillary growth. Growth guidance may be indicated in children with CLP with unfavorable craniofacial growth patterns.

The Influence of trisomy 21 on facial form and variability

Triplication of chromosome 21 (trisomy 21) results in Down syndrome (DS), the most common live-born human aneuploidy. Individuals with DS have a unique facial appearance that can include form changes and altered variability. Using 3D photogrammatic images, 3D coordinate locations of 20 anatomical landmarks, and Euclidean Distance Matrix Analysis methods, we quantitatively test the hypothesis that children with DS (n = 55) exhibit facial form and variance differences relative to two different age-matched (4-12 years) control samples of euploid individuals: biological siblings of individuals with DS (n = 55) and euploid individuals without a sibling with DS (n = 55). Approximately 36% of measurements differ significantly between DS and DS-sibling samples, whereas 46% differ significantly between DS and unrelated control samples. Nearly 14% of measurements differ significantly in variance between DS and DS sibling samples, while 18% of measurements differ significantly in variance between DS and unrelated euploid control samples. Of those measures that showed a significant difference in variance, all were relatively increased in the sample of DS individuals. These results indicate that faces of children with DS are quantitatively more similar to their siblings than to unrelated euploid individuals and exhibit consistent, but slightly increased variation with most individuals falling within the range of normal variation established by euploid samples. These observations provide indirect evidence of the strength of the genetic underpinnings of the resemblance between relatives and the resistance of craniofacial development to genetic perturbations caused by trisomy 21, while underscoring the complexity of the genotype-phenotype map.

Methods for Studying Morphological Integration and Modularity

Morphological integration and modularity are closely related concepts about how different traits of an organism are correlated. Integration is the overall pattern of intercorrelation; modularity is the partitioning of integration into evolutionarily or developmentally independent blocks of traits. Modularity and integration are usually studied using quantitative phenotypic data, which can be obtained either from extant or fossil organisms. Many methods are now available to study integration and modularity, all of which involve the analysis of patterns found in trait correlation or covariance matrices. We review matrix correlation, random skewers, fluctuating asymmetry, cluster analysis, Euclidean distance matrix analysis (EDMA), graphical modelling, two-block partial least squares, RV coefficients, and theoretical matrix modelling and discuss their similarities and differences. We also review different coefficients that are used to measure correlations. We apply all the methods to cranial landmark data from and ontogenetic series of Japanese macaques,Macaca fuscatato illustrate the methods and their individual strengths and weaknesses. We conclude that the exploratory approaches (cluster analyses of various sorts) were less informative and less consistent with one another than were the results of model testing or comparative approaches. Nevertheless, we found that competing models of modularity and integration are often similar enough that they are not statistically distinguishable; we expect, therefore, that several models will often be significantly correlated with observed data.

Precuneus proportions and cortical folding: A morphometric evaluation on a racially diverse human sample

Recent analyses have suggested that the size and proportions of the precuneus are remarkably variable among adult humans, representing a major source of geometrical difference in midsagittal brain morphology. The same area also represents the main midsagittal brain difference between humans and chimpanzees, being more expanded in our species. Enlargement of the upper parietal surface is a specific feature of Homo sapiens, when compared with other fossil hominids, suggesting the involvement of these cortical areas in recent modern human evolution. Here, we provide a survey on midsagittal brain morphology by investigating whether precuneus size represents the largest component of variance within a larger and racially diverse sample of 265 adult humans. Additionally, we investigate the relationship between precuneus shape variation and folding patterns. Precuneus proportions are confirmed to be a major source of human brain variation even when racial variability is considered. Larger precuneus size is associated with additional precuneal gyri, generally in its anterior district. Spatial variation is most pronounced in the dorsal areas, with no apparent differences between hemispheres, between sexes, or among different racial groups. These dorsal areas integrate somatic and visual information together with the lateral elements of the parietal cortex, representing a crucial node for self-centered mental imagery. The histological basis and functional significance of this intra-specific variation in the upper precuneus remains to be evaluated.

Influence of prenatal EGCG treatment and Dyrk1a dosage reduction on craniofacial features associated with Down syndrome

Trisomy 21 (Ts21) affects craniofacial precursors in individuals with Down syndrome (DS). The resultant craniofacial features in all individuals with Ts21 may significantly affect breathing, eating and speaking. Using mouse models of DS, we have traced the origin of DS-associated craniofacial abnormalities to deficiencies in neural crest cell (NCC) craniofacial precursors early in development. Hypothetically, three copies of Dyrk1a (dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A), a trisomic gene found in most humans with DS and mouse models of DS, may significantly affect craniofacial structure. We hypothesized that we could improve DS-related craniofacial abnormalities in mouse models using a Dyrk1a inhibitor or by normalizing Dyrk1a gene dosage. In vitro and in vivo treatment with Epigallocatechin-3-gallate (EGCG), a Dyrk1a inhibitor, modulated trisomic NCC deficiencies at embryonic time points. Furthermore, prenatal EGCG treatment normalized some craniofacial phenotypes, including cranial vault in adult Ts65Dn mice. Normalization of Dyrk1a copy number in an otherwise trisomic Ts65Dn mice normalized many dimensions of the cranial vault, but did not correct all craniofacial anatomy. These data underscore the complexity of the gene–phenotype relationship in trisomy and suggest that changes in Dyrk1a expression play an important role in morphogenesis and growth of the cranial vault. These results suggest that a temporally specific prenatal therapy may be an effective way to ameliorate some craniofacial anatomical changes associated with DS.

Fit Testing as a Helmet Development Tool

Fit testing is needed during the development process to reduce cost and optimize the performance quality. This paper describes methods for fit testing, as part of the helmet development process, which utilize new surface scanning and innovative fit assessment technologies. Results from some recent fit tests which employed these methods will be presented. While the methods described will be those applicable to helmets, many aspects will be appropriate to other equipment and clothing items as well. The payoff for using such methods are more capable and less bulky items, a better fit for a wider range of personnel with fewer sizes, and reduced development and logistics costs.

Modularity: genes, development and evolution

Modularity has emerged as a central concept for evolutionary biology, providing the field with a theory of organismal structure and variation. This theory has reframed long standing questions and serves as a unified conceptual framework for genetics, developmental biology and multivariate evolution. Research programs in systems biology and quantitative genetics are bridging the gap between these fields. While this synthesis is ongoing, some major themes have emerged and empirical evidence for modularity has become abundant. In this review, we look at modularity from an historical perspective, highlighting its meaning at different levels of biological organization and the different methods that can be used to detect it. We then explore the relationship between quantitative genetic approaches to modularity and developmental genetic studies. We conclude by investigating the dynamic relationship between modularity and the adaptive landscape and how this potentially shapes evolution and can help bridge the gap between micro- and macroevolution.

Size, shape, and form: concepts of allometry in geometric morphometrics

Allometry refers to the size-related changes of morphological traits and remains an essential concept for the study of evolution and development. This review is the first systematic comparison of allometric methods in the context of geometric morphometrics that considers the structure of morphological spaces and their implications for characterizing allometry and performing size correction. The distinction of two main schools of thought is useful for understanding the differences and relationships between alternative methods for studying allometry. The Gould-Mosimann school defines allometry as the covariation of shape with size. This concept of allometry is implemented in geometric morphometrics through the multivariate regression of shape variables on a measure of size. In the Huxley-Jolicoeur school, allometry is the covariation among morphological features that all contain size information. In this framework, allometric trajectories are characterized by the first principal component, which is a line of best fit to the data points. In geometric morphometrics, this concept is implemented in analyses using either Procrustes form space or conformation space (the latter also known as size-and-shape space). Whereas these spaces differ substantially in their global structure, there are also close connections in their localized geometry. For the model of small isotropic variation of landmark positions, they are equivalent up to scaling. The methods differ in their emphasis and thus provide investigators with flexible tools to address specific questions concerning evolution and development, but all frameworks are logically compatible with each other and therefore unlikely to yield contradictory results.

Size, shape, and form: concepts of allometry in geometric morphometrics

Allometry refers to the size-related changes of morphological traits and remains an essential concept for the study of evolution and development. This review is the first systematic comparison of allometric methods in the context of geometric morphometrics that considers the structure of morphological spaces and their implications for characterizing allometry and performing size correction. The distinction of two main schools of thought is useful for understanding the differences and relationships between alternative methods for studying allometry. The Gould–Mosimann school defines allometry as the covariation of shape with size. This concept of allometry is implemented in geometric morphometrics through the multivariate regression of shape variables on a measure of size. In the Huxley–Jolicoeur school, allometry is the covariation among morphological features that all contain size information. In this framework, allometric trajectories are characterized by the first principal component, which is a line of best fit to the data points. In geometric morphometrics, this concept is implemented in analyses using either Procrustes form space or conformation space (the latter also known as size-and-shape space). Whereas these spaces differ substantially in their global structure, there are also close connections in their localized geometry. For the model of small isotropic variation of landmark positions, they are equivalent up to scaling. The methods differ in their emphasis and thus provide investigators with flexible tools to address specific questions concerning evolution and development, but all frameworks are logically compatible with each other and therefore unlikely to yield contradictory results.

Global deletion of Panx3 produces multiple phenotypic effects in mouse humeri and femora

Pannexins form single-membrane channels that allow passage of small molecules between the intracellular and extracellular compartments. Of the three pannexin family members, Pannexin3 (Panx3) is the least studied but is highly expressed in skeletal tissues and is thought to play a role in the regulation of chondrocyte and osteoblast proliferation and differentiation. The purpose of our study is to closely examine the in vivo effects of Panx3 ablation on long bone morphology using micro-computed tomography. Using Panx3 knockout (KO) and wildtype (WT) adult mice, we measured and compared aspects of phenotypic shape, bone mineral density (BMD), cross-sectional geometric properties of right femora and humeri, and lean mass. We found that KO mice have absolutely and relatively shorter diaphyseal shafts compared with WT mice, and relatively larger areas of muscle attachment sites. No differences in BMD or lean mass were found between WT and KO mice. Interestingly, KO mice had more robust femora and humeri compared with WT mice when assessed in cross-section at the midshaft. Our results clearly show that Panx3 ablation produces phenotypic effects in mouse femora and humeri, and support the premise that Panx3 has a role in regulating long bone growth and development.

Genetics of murine craniofacial morphology: diallel analysis of the eight founders of the Collaborative Cross

Using eight inbred founder strains of the mouse Collaborative Cross (CC) project and their reciprocal F1 hybrids, we quantified variation in craniofacial morphology across mouse strains, explored genetic contributions to craniofacial variation that distinguish the founder strains, and tested whether specific or summary measures of craniofacial shape display stronger additive genetic contributions. This study thus provides critical information about phenotypic diversity among CC founder strains and about the genetic contributions to this phenotypic diversity, which is relevant to understanding the basis of variation in standard laboratory strains and natural populations. Craniofacial shape was quantified as a series of size-adjusted linear dimensions (RDs) and by principal components (PC) analysis of morphological landmarks captured from computed tomography images from 62 of the 64 reciprocal crosses of the CC founder strains. We first identified aspects of skull morphology that vary between these phenotypically 'normal' founder strains and that are defining characteristics of these strains. We estimated the contributions of additive and various non-additive genetic factors to phenotypic variation using diallel analyses of a subset of these strongly differing RDs and the first eight PCs of skull shape variation. We find little difference in the genetic contributions to RD measures and PC scores, suggesting fundamental similarities in the magnitude of genetic contributions to both specific and summary measures of craniofacial phenotypes. Our results indicate that there are stronger additive genetic effects associated with defining phenotypic characteristics of specific founder strains, suggesting these distinguishing measures are good candidates for use in genotype-phenotype association studies of CC mice. Our results add significantly to understanding of genotype-phenotype associations in the skull, which serve as a foundation for modeling the origins of medically and evolutionarily relevant variation.

Performance of single and multi-atlas based automated landmarking methods compared to expert annotations in volumetric microCT datasets of mouse mandibles

BACKGROUND

Here we present an application of advanced registration and atlas building framework DRAMMS to the automated annotation of mouse mandibles through a series of tests using single and multi-atlas segmentation paradigms and compare the outcomes to the current gold standard, manual annotation.

RESULTS

Our results showed multi-atlas annotation procedure yields landmark precisions within the human observer error range. The mean shape estimates from gold standard and multi-atlas annotation procedure were statistically indistinguishable for both Euclidean Distance Matrix Analysis (mean form matrix) and Generalized Procrustes Analysis (Goodall F-test). Further research needs to be done to validate the consistency of variance-covariance matrix estimates from both methods with larger sample sizes.

CONCLUSION

Multi-atlas annotation procedure shows promise as a framework to facilitate truly high-throughput phenomic analyses by channeling investigators efforts to annotate only a small portion of their datasets.

Morphometrics, 3D Imaging, and Craniofacial Development

Recent studies have shown how volumetric imaging and morphometrics can add significantly to our understanding of morphogenesis, the developmental basis for variation, and the etiology of structural birth defects. On the other hand, the complex questions and diverse imaging data in developmental biology present morphometrics with more complex challenges than applications in virtually any other field. Meeting these challenges is necessary in order to understand the mechanistic basis for variation in complex morphologies. This chapter reviews the methods and theory that enable the application of modern landmark-based morphometrics to developmental biology and craniofacial development, in particular. We discuss the theoretical foundations of morphometrics as applied to development and review the basic approaches to the quantification of morphology. Focusing on geometric morphometrics, we discuss the principal statistical methods for quantifying and comparing morphological variation and covariation structure within and among groups. Finally, we discuss the future directions for morphometrics in developmental biology that will be required for approaches that enable quantitative integration across the genotype-phenotype map.

Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.

Selective pressures in the human bony pelvis: Decoupling sexual dimorphism in the anterior and posterior spaces

OBJECTIVES

Sexual dimorphism in the human bony pelvis is commonly assumed to be related to the intensity of obstetrical selective pressures. With intense obstetrical selective pressures, there should be greater shape dimorphism; with minimal obstetrical selective pressures, there should be reduced shape dimorphism. This pattern is seen in the nondimorphic anterior spaces and highly dimorphic posterior spaces. Decoupling sexual dimorphism in these spaces may in turn be related to the differential influence of other selective pressures, such as biomechanical ones.

MATERIALS AND METHODS

The relationship between sexual dimorphism and selective pressures in the human pelvis was examined using five skeletal samples (total female n = 101; male n = 103). Pelvic shape was quantified by collecting landmark coordinate data on articulated pelves. Euclidean distance matrix analysis was used to extract the distances that defined the anterior and posterior pelvic spaces. Sex and body mass were used as proxies for obstetrical and biomechanical selective pressures, respectively.

RESULTS

MANCOVA analyses demonstrate significant effects of sex and body mass on distances in both the anterior and the posterior spaces. A comparison of the relative contribution of shape variance attributed to each of these factors suggests that the posterior space is more influenced by sex, and obstetrics by proxy, whereas the anterior space is more influenced by body mass, and biomechanics by proxy.

CONCLUSIONS

Although the overall shape of the pelvis has been influenced by obstetrical and biomechanical selective pressures, there is a differential response within the pelvis to these factors. These results provide new insight into the ongoing debate on the obstetrical dilemma hypothesis.

Morphometric analysis of brain shape in children with nonsyndromic cleft lip and/or palate

The purpose of this study was to test for differences in brain shape among children with cleft palate only (n = 22), children with cleft lip and palate (n = 35), and controls (n = 39) using Euclidean distance matrix analysis. Sixteen percent of interlandmark distances differed between children with cleft palate only and controls, 10% differed between children with cleft lip and palate and controls, and 10% differed between children with cleft palate only and children with cleft lip and palate. Major differences in brain shape associated with cleft lip and/or palate included posterior expansion of the occipital lobe, reorientation of the cerebellum, heightened callosal midbody, and posterior displacement of the caudate nucleus and thalamus. Differences in brain shape unique to cleft palate only and to cleft lip and palate were also identified. These results expand upon previous volumetric studies on brain morphology in individuals with cleft lip and/or palate and provide additional evidence that the primary defect in cleft lip and/or palate results in both facial and brain dysmorphology.